Tag Archives: dna sequencing

Pap tests could one day tell women if they have breast or ovarian cancer

Experts have identified changes in a woman’s cervix that can help detect tumors elsewhere in the body. These tests involve scraping cells from the cervix to detect any abnormalities that could cause cervical cancer. But researchers from Innsbruck University and gynecological cancer research charity The Eve Appeal found the cells from this test can also give clues and alerts for other types of cancers. With development, they state that the method used could one day predict the risk of developing ovarian, breast, womb, and cervical cancers from a straightforward smear pap test.

They developed their system using a process known as DNA methylation — epigenetic modifications to DNA that don’t alter the genetic sequence but do determine whether a gene expresses or stifles its function: in this case, forming or preventing cancer in the body. These modifications leave ‘methylation markers or signatures’ on genomic regions that scientists can read to determine what has occurred within a person’s body throughout their lifetime. Akin to the rings of a tree, this method can provide chronological clues as to what has happened in our biological life.

Researchers created the test, dubbed WID (Women’s Risk Identification), to analyze markers left by cancerous activity in the DNA of cervical cells. By calculating a woman’s WID, they hope to identify those with a high risk of developing ovarian, breast, womb, or cervical cancers: providing an early-warning system for medical teams to increase treatment outcomes.

The team was able to spot these modifications because they matched DNA markers found in diseased cervical, breast, ovarian, and womb biopsy tissue (a highly invasive procedure) to those found in the easier to access cells of the cervix — whose similar biological structures undergo the same hormonal changes as the tissues these cancers flourish in.

Finding cancer through the cervix

The first study examined cervical cell samples collected from 242 women with ovarian cancer and 869 healthy controls. To develop the WID risk scale, the scientists measured 14,000 epigenetic changes to identify ovarian cancer’s unique DNA signature to spot the presence of the disease in epithelial tissue scraped from the cervix.

They then validated the signature in an additional cohort of 47 women who had ovarian cancer and 227 healthy subjects. Results identified 71% of women under 50 and roughly 55% of the volunteers older than 50 who had previously tested positive for the disease — giving the tests an overall specificity of 75%. A test’s specificity is its ability to correctly identify people without the disease.

Professor Martin Widschwendter of the University of Innsbruck and UCL, heading up the research, said the findings suggest their WID index is picking up cancer predisposition, adding that the results were similar to a study on women with cancer of the womb. He is adamant their test cannot predict ovarian, with more studies needed.

A possible screening method for an undetectable cancer 

In the second study, the same team analyzed epigenetic changes in cervical cell samples provided by 329 women with breast cancer against those from the same 869 healthy volunteers in the first study. Using the WID index, they were able to identify women with breast cancer based on a unique epigenetic signature. The group once again confirmed these markers in a smaller consort of 113 breast cancer patients and 225 women without this condition.

The researchers also used the patterns to predict whether patients had breast cancer-but they didn’t say exactly how accurate the tests were. Instead, they stressed that further trials are needed-with the hope that clinicians could use their WID as a regular test for women in the future-specifically for those under fifty years of age who do not have access to screening for this disease.

“This research is incredibly exciting,” said Liz O’Riordan, a breast cancer surgeon who was also diagnosed with this disease. “At the moment, there is no screening test for breast cancer in women under the age of 50. If this test can help pick up women with a high risk of developing breast, ovarian, cervical, and uterine cancer at a younger age, it could be a game-changer.”

The team adds that these findings are also crucial for ovarian cancer, whose symptoms can be as benign as a bloated abdomen. The biggest killer of women out of gynecological-based tumors, this disease is diagnosed late by clinicians in an alarming 3 out of four cases.

But for now, Widschwendter says, the findings suggest that the molecular signatures in cervical cells may detect the predisposition to other women-specific cancers rather than providing a solid prediction of the disease.

Because of the pandemic, women have stopped taking pap tests

A pap smear test detects abnormal cells on the cervix, which is the entrance to the uterus from the vagina. Removing these cells can prevent cervical cancer, which most commonly affects sexually-active women aged between 30 and 45. In most cases, the human papillomavirus causes this cancer after being acquired through unprotected sex or skin-to-skin contact. To summarise, the whole point of these tests is to detect women at risk of developing cancer and encourage them to carry further health check-ups, not to find those displaying cancer symptoms.

Around the world, the number of women taking smear tests has dropped substantially during the pandemic. In England, for instance, one of the countries with the highest testing rates, just 7 out of 10 eligible women got a cervical check-up — and conditions are expected to worsen due to a new policy brought in by the UK government at the start of 2022, which saw all eligible women in Wales have their wait times increased from three to five years in between tests. The government expects to roll out the policy in England this year after the pandemic caused the delay of its initial release. Experts insisted the move was safe, but campaigners hit back at the plans, arguing it would cause preventable deaths by delaying the detection of cancer or pre-cancerous issues.

In a statement to the Guardian, the UK’s Secretary for Patient Safety and Primary Care says it’s “great to see how this new research could help alert women who are at higher risk to help prevent breast, ovarian, womb, and cervical cancer before it starts.” Until this time, cancer screening remained vital and urged all women aged 25 and above to attend their appointments when invited. The secretary did not remark on the new government policy.

An ovarian cancer specialist urged caution in interpreting the data: They show a “moderate association” between the methylation signature and ovarian cancer, said Dr. Rebecca Stone, the Kelly Gynecologic Oncology Service director at Johns Hopkins Hospital. “They are not showing that it’s predictive or diagnostic,” Stone stressed. Clarifying that to see whether the cervical cell signature predicts cancer, a study would have to observe a large group of women over a long period.

Filling the gap in screening options for women

In contrast, Athena Lamnisos, CEO of the Eve Appeal, emphasizes the importance of a new screening tool:

“Creating a new screening tool for the four most prevalent cancers that affect women and people with gynae organs, particularly the ones which are currently most difficult to detect at an early stage, from a single test could be revolutionary.”

The Eve Appeal goes on that women could get separate risk scores for each of the four cancers in the future where medical teams could offer those with high scores more active monitoring, regular mammograms, risk-reducing surgery, or therapeutics.

Ultimately, it’s better to prevent than to treat, and this method could offer women worldwide access to proper screening services that could save lives through the application of early intervention and preventative medicine.

Pueblo Bonito. Credit: Douglas Kennett / Penn State University.

Genetic analysis shows the mysterious Chaco Civilization was a society ruled by women

 Pueblo Bonito. Credit: Douglas Kennett / Penn State University.

Pueblo Bonito. Credit: Douglas Kennett / Penn State University.

Scientists analyzed DNA sampled from human remains discovered deep in a crypt at the Ancestral Puebloan site of Chaco Canyon. The lavishness of the crypt, which was found right at the center of an ancient 650-room estate, suggests the people buried there formed the elite of the Chaco culture, a civilization that dominated the southwestern United States from the mid-9th to early 13th centuries. Surprisingly, however, the DNA analysis suggests the ancient Chaco were ruled by women who formed a matrilineal dynasty.

Chaco Culture is an umbrella term used to describe the network of sites discovered in northwestern New Mexico where outstanding elements of a vast pre-Columbian cultural complex can be found. These sites were a focus for ceremonies, trade, and political activity and they are remarkable for their monumental public and ceremonial buildings and distinctive multi-storey “great houses.”

One such great house called Pueblo Bonito was discovered by archaeologists in 1896 who were stunned by its complexity and hundreds of rooms. In the middle of this massive house lied a crypt which housed the remains of 14 individuals, accompanied by gorgeous artifacts. These include necklaces, bracelets, and other kinds of jewelry made from thousands of turquoise and shell beads, as well as bones. Clearly, these people were from the Chaco upper hierarchy.

“It has been clear for some time that these were venerated individuals, based on the exceptional treatment they received in the afterlife – most Chacoans were buried outside of the settlement and never with such high quantities of exotic goods,” said, Adam Watson from the American Museum of Natural History who is also one of the lead authors of the new study published in Nature Communications.

Researchers from the American Museum of Natural History (AMNH) in New York City, where the Chaco remains have been stored ever since the excavations ended, wanted to know what was the genetic relationship between these individuals.

Some of the turquoise and shell artifacts found in Room 33 of Pueblo Bonito. Credit: Roderick Mickens.

Some of the turquoise and shell artifacts found in Room 33 of Pueblo Bonito. Credit: Roderick Mickens.

One of the initial burials was that of a male in his 40s who died violently following a blow to the head. His is the richest tomb ever found in the American Southwest, adorned with more than 11,000 turquoise beads, many abalone shells, and even a conch shell trumpet which must have come from the Pacific Ocean and the Gulf of California. Above this initial interment, another male was buried. A split plank floor placed above these two graves separated them from another 12 burials. These burials took place over the span of 300 years.

Watson and colleagues analyzed the ancient DNA from nine of these individuals and found they all shared the same mitochondrial genome sequence. Mitochondrial DNA (mtDNA) is inherited only from the mother’s side, so matching mtDNA indicates that not only were all the individuals from the same family, but the inheritance was matrilineal.

Credit: T. Harper; Kennet et al. Nature Communications.

The researchers also sequenced nuclear DNA, inherited from both mother and father, from six of the individuals. This analysis revealed more intimate details. For instance, at least two pairs of individuals were very closely related, possibly a mother-daughter or grandmother-grandson.

“First we thought this could be some kind of contamination problem,” said Douglas J. Kennett, head and professor of anthropology, Penn State, who is one of the authors of the study. “We checked for contamination, but found no evidence for it and David Reich’s laboratory at Harvard Medical School corroborated our results.”

The social and civil construct of the Chacho civilization has always been a matter of debate among scholars. Some claim this was an egalitarian society where no ruler was in charge while others suggested Chaco was a state-level society or kingdom with a clear chain of command. These latest findings seem to add weight to the latter hypothesis. Moreover, Chaco seems to have been a hierarchically organized society ruled by women which is pretty rare seeing how most civilizations in history have been patriarchal.

“For the first time, we’re saying that one kinship group controlled Pueblo Bonito for more than 300 years,” said Steve Plog, the David A. Harrison Professor of Archaeology, University of Virginia, who was responsible for radiocarbon dating the Chaco remains. “This is the best evidence of a social hierarchy in the ancient Southwest.”

While the present work fantastically proves that ancient DNA sequencing can output very valuable archaeological and cultural evidence, some voices have criticized the manner in which it was carried. Speaking to Scientific American, Rebecca Tsosie, a law professor of Native American descent at the University of Arizona, said the team did not act ethically.

“I am dismayed that there was not an effort to engage contemporary tribal leaders prior to undertaking and publishing this study,” she said.

George Perry, an ancient DNA expert at Penn State and author of the new paper, confirms the team did not formally consult with tribal leaders. However, he said he is personally “working diligently to engage with multiple groups in the Southwest” and hopes to receive “blessings” for further investigations. One future project might involve sequencing the DNA of  Chacoan ancestors to see if there’s any relation to the ancient ruling Chaco lineage.

 

 

human genome

Leading scientists will synthesize human genomes from scratch by 2026

Around 130 leading scientists, entrepreneurs and key government officials met behind closed doors at Harvard University a couple of weeks ago. The whole meeting was shrouded in secrecy and speculations ran amok. Now, this ad-hoc convention has made public its most ambitious plan: build and deploy a fully synthetic human genome in human cell lines within 10 years.

human genome

Credit: YouTube

The Human Genome Project Write (HGP-Write), is the next obvious step after the roaring success of the Human Genome Project (HGP-Read) launched in the 1990s. HGP-Read was one of the most serious scientific ventures in history. Instead of focusing outward, like studying the mechanics of the physical universe, HGP-Read ventured inward so that we might understand how genes code the human body.

HGP-read was finally completed in April 2003, thirteen years and $3 billion later from its launch. Today, however, the cost of sequencing a person’s DNA has fallen below the $1,000 threshold. DNA sequencing is now widely used in anything from crop breeding to forensics, to medical research.

While HGP-Read enabled us to read the human genome, HGP-Write ought to lend us the necessary knowledge and tools to write code in the human genome.

“The ability to write the genome, essentially by typing it into a computer, would be revolutionary. If it were possible, it can be used for many applications – from engineering microbes that can produce industrially relevant chemical and biological compounds to generating engineered human cells for therapeutic applications, such as for treating cancer and tissue regeneration,” said Dr. Kris Saha, Assistant Professor of Biomedical Engineering, University of Wisconsin-Madison.

Scientists will work on HGP-Write over a decade-long period, and the Center of Excellence for Engineering Biology — the non-profit that coordinates the whole affair — will seek to raise $100 million this year. The largest genome synthesis project to date is Sc 2.0, which aims to create an entirely synthetic yeast in the next five years.  The size of even the smallest human chromosome is 48 million base pairs which is 22 times the size of the largest yeast chromosome at 2.2 million base pairs.

“Relative to Sc2.0, HGP-write is 200x larger and includes a much higher proportion of difficult-to-synthesize ‘low complexity’ DNA,” said Dr. Samuel Deutsch, Head of DNA Synthesis and Assembly, DOE Joint Genome Institute.

The authors of the announcement claim fabricating synthetic human genomes, or at least regions or parts of it, will provide significant advances in medicine and biology. It could, for instance, lead to the manufacturing of pig organs that are compatible with the human body, hence fit for transplant.

DNA_Sequencing_Cost_per_Genome_Over_Time

A lot of critics have voiced ethical concerns over the project, especially during the first meetings which were shrouded in the utmost secrecy. The lead proponents of HGP-Write said they were required to keep the meetings confidential to avoid unnecessary publicity until the announcement could be made in a peer-reviewed journal. The project was officially announced on Thursday, in the journal Science.

Many are concerned that HGP-Write will open the flood gates to engineering humans. Indeed, this could be theoritically possible, but is not the scope of the project.

“It is very important to make a clear distinction between synthesizing a human genome in somatic cell lines as is proposed, and modifying human germline cells that could be hereditably transmitted, which is not in the scope of this project. Nevertheless, all technology that could be potentially used to modify human genomes needs to proceed in the context of open and transparent dialogue with many societal stakeholders, and under a regulatory framework that governs how such technology can be used in a safe and ethically acceptable manner,” Deutsch said.

“The authors propose that a percentage of all funding raised for this project be dedicated to ethical, legal and social issues. This is not only advisable but also essential. By starting a broad, transparent and inclusive conversation early on, both the scientific community and society in general will be better positioned to address the societal implications of HGP-write as the technology comes of age,” he added.

“The second part of that subtitle is the ethical framework. The project is not as controversial as some observers might be saying. First we already replace segments of human genes in cells growing in culture dishes. This is well regulated and is the very core of the new advances in medical genetics.  Making large and larger pieces of human chromosomes and putting them into host cells in culture dishes will enable more deeper understanding of what all the genes and the non-coding DNA actually does. On the route to the final goal of this new initiative will be a myriad of new therapies for treating medical conditions from genetic diseases to viral infections.  There is no call to make an entire human being just as there is no push for doing that with current studies using human embryos,” Prof John Ward, Professor of Synthetic Biology for Bioprocessing, The Advanced Centre for Biochemical Engineering, UCL, said in a statement.

“The 25 scientists propose that this project would be carried out with public involvement using the framework of Responsible Innovation where common goals of both the public and the science are identified and worked on from the beginning. The debate by scientists at a recent meeting gave rise to this white paper and it’s fascinating to see the speed of progress from that debate only 23 days ago to this carefully formulated proposal.”

Right now, scientists are already able to insert new genes or modify existing ones to breed genetically modified organisms. Genome editing tools, like the famous Crispr, have made genomic engineering even easier. Though counterintuitive, in many instances building a synthethic genome from scratch could be more efficient than modifying existing genomes, besides opening avenues of opportunity unavailable using today’s tech.

If successful HGP-Write will make history, and ought to help science at least as much as HGP-Read. Many ethical challenges have to be addressed first, though. At some point, we might even have to consider pulling the plug.

craig_venter

Transmitting DNA sequence over the web and printing life at a distance. Not a fantasy, just the future

craig_venter

Craig Venter at Synthetic Genomics. (c) Mark Mahaney/Redux /Eyevine

Craig Venter may just be the most arrogant high-profile scientist today, but in his defense the man has a lot to show for. You might not remember the name, but you might remember his hallmark achievement – the creation of the world’s first synthetic life. Now, with the release of his second book, Life at the Speed of LightFrom the Double Helix to the Dawn of Digital Life, Venter takes advantage of the opportunity to reveal one of the most powerful biological application science has had to offer in the past few decades. Venter and his company, Synthetic Genomics Incorporated (SGI), have created a prototype for a device that can remotely receive DNA sequences over the internet  to synthesise proteins, viruses and even living cells.

Antibiotics and other health applications are first at mind for such a device. It could, for example, fill a prescription for insulin, provide flu vaccine during a pandemic or even produce phage viruses targeted to fight antibiotic-resistant bacteria. A while ago I wrote about how two big DNA sequencing companies are battling each other to be the first who gets to put a DNA sequencer on the next Mars rover – Venter’s SGI and Jonathan Rothberg’s Ion Torrent. Studies have shown that DNA can not be preserved for longer than 1 million years, so both space agencies like NASA and private ventures have to embark with the idea that life is already presented on Mars. Even so, IF there actually is life on Mars, a digital version of the DNA-based life form could be made on-site, sent back to earth and then recreated in the lab! All using a combination of the technologies currently being developed at SGI.

Synthetic life

In 2010, Venter grabbed everyone’s attention by announcing what he calls the “world’s first synthetic life”. The first major breakthrough from that line of work came in 2003, when Venter’s team made simple virus Phi X 174 synthetically. In 2008 he synthesised the genome of a bacteria that infects the human urinary tract, Mycoplasma genitalium.

“We’ve now been able to take our synthetic chromosome and transplant it into a recipient cell – a different organism.

As soon as this new software goes into the cell, the cell reads [it] and converts into the species specified in that genetic code,” Venter told the BBC at the time.

The new bacteria replicated over a billion times, producing copies that contained and were controlled by the constructed, synthetic DNA.

“This is the first time any synthetic DNA has been in complete control of a cell,” said Dr Venter.

Notice how Venter mentions the term software. “Life is a DNA software system,” says Venter. All living things are solely reducible to DNA and the cellular apparatus it uses to run on.

A biological teleportation device

Synthetic cell and original cell - 2010. (c) Science Mag

Synthetic cell and original cell – 2010. (c) Science Mag

Building synthetic life: chromosome of an existing bacterial cell is sequenced; then this code was copied and used to chemically construct a new synthetic chromosome, piecing together blocks of DNA; finally, this chromosome is inserted into a bacterial cell which replicated itself. Synthetic bacteria might be used to make new fuels and drugs.

Building synthetic life: chromosome of an existing bacterial cell is sequenced; then this code was copied and used to chemically construct a new synthetic chromosome, piecing together blocks of DNA; finally, this chromosome is inserted into a bacterial cell which replicated itself. Synthetic bacteria might be used to make new fuels and drugs.

Back to 2013 and Venter’s Digital Biological Converter or DBC. The current prototype, supported by DARPA, is intended to be miniaturized and sold by Synthetic Genomics for use in hospitals, workplaces and homes. So far, the device can only produce DNA, and not proteins or living cells yet. Venter believes, however, that even the current prototype is accurate enough for producing DNA precisely enough for it to be used as a vaccine.

“The future will be that if you have a [bacterial] infection you quickly get its genome sequenced – that will take minutes – and in a very short period of time we could design a phage that would attack just that bacteria very specifically,” he says. Because of the way phages attack their bacteria victims, making just the DNA of the one a person needs is enough, says Venter. “The DNA is the drug that kills the bacteria.”

In the future, Venter hopes he can refine the DBC to be able to print living cells, based on his breakthrough 2010 work pertaining to synthetic life. Efforts so far are concentrating on building what Venter calls an  “universal recipient cell”, a sort of blank cell which when combined with synthetic genome would come to life. Ultimately, you can wind up with a biological teleportation device – a machine systematically sequences the DNA from a living sample, digitizes the information, relays it to a remote DBC anywhere in the world which then recreates the original life in a whole new location. Of course, this doesn’t mean you could teleport humans…

 “That is not going to happen any time that we know of … They are two different worlds and two different scales and the science isn’t anywhere remotely supportive of that any more than it is recreating a Neanderthal with a willing woman.” Venter said.

Story via Guardian

Research suggests we use 4 times more DNA than previously believed

Less than 1.5 percent of our DNA is used in a conventional way, that is to encode for proteins – this was the common sense around this issue 10 years ago; recently, previous research has shown that 5-8% of the genome is conserved at the level of DNA sequence, indicating that it is functional, but we don’t really know exactly what it does. However, a new study conducted by Australian geneticisits suggests that much more (possibly up to 30%) is conserved, and actually used at the level of RNA structure.

dna

Credit: © Maridav / Fotolia

At a very basic level, DNA is the blueprint for our bodies – but it must be copied into another instance before it is actualised. The DNA molecule encodes the genetic instructions used in the development and functioning of all known living organisms and many viruses. Through a process called ‘transcription’, DNA is copied into RNA, some of which encodes the proteins that carries out various tasks required by our cells. Just like very small Lego blocks, RNA molecules bind with each other in very specific ways, creating a very complex 3D structure. Dr Martin Smith and Professor John Mattick, from Sydney’s Garvan Institute of Medical Research, have created a very complicated method of predicting these RNA structures.

“Genomes accumulate mutations over time, some of which don’t change the structure of associated RNAs. If the sequence changes during evolution, yet the RNA structure stays the same, then the principles of natural selection suggest that the structure is functional and is required for the organism,” explained Dr Martin Smith.

Using this method, they ultimately concluded that we actively use much more DNA for coding than previously believed.

“Our hypothesis is that structures conserved in RNA are like a common template for regulating gene expression in mammals – and that this could even be extrapolated to vertebrates and less complex organisms.”

“We believe that RNA structures probably operate in a similar way to proteins, which are composed of structural domains that assemble together to give the protein a function.”

“We suspect that many RNA structures recruit specific molecules, such as proteins or other RNAs, helping these recruited elements to bond with each other. That’s the general hypothesis at the moment – that non-coding RNAs serve as scaffolds, tethering various complexes together, especially those that control genome organization and expression during development.”

Medieval skeletons give clues to leprosy origin

Leprosy, or Hansen’s disease (HD), is a chronic infection caused by the bacteria Mycobacterium leprae and Mycobacterium lepromatosis. It was quite a common disease in Europe until the 16th century. Now, researchers have extracted DNA from skeletons that were 1,000 years old, analyzing the disease genetic code and comparing it to that of new strains, which exist today.

The medieval remains were taken from graves in the UK, Denmark and Sweden

The medieval remains were taken from graves in the UK, Denmark and Sweden

The first, rather intriguing discovery was the fact that the medieval Crusades (religiously motivated campaigns conducted between the 11th and 16th centuries by the Christians, mostly against muslims, but also agains pagans, heretics, and others) helped spread leprosy.

In medieval times, a sufferer of leprosy was a pariah – cast away into quarantined colonies. Then as now, there was a social stigma with having the disease, but the disease can be cured if discovered quickly; if not, the lesions can leave the sufferers crippled and/or deformed.

The DNA comparison showed that the disease spread by the crusaders is pretty much the same as the one present in the Middle East now. It is still not clear if the disease originated in Europe and was brought eastwards by the crusaders, of if it originated there, and they brought it on their way back.

“This skeleton can only tell us it was present in Asia around 4,000 years ago, but we do not know where the origin of the disease is,” Prof Krause explained.

Another strain, similar to the medieval one, is found in the Americas. This is definitely not something that originated there, and likely, not something which was brought by the first settlers – but rather something that Europeans brought along when they were colonizing the continents.

“One really surprising finding was that the DNA was so well preserved, better than any ancient DNA I have ever studied,” he said. “This opens up the possibility to study the evolution of the disease in much older remains, to understand how it evolved and adapted to humans.”

There is a strong case that the disease developed in Europe, however. Some 95% of all population has already developed natural immunity to disease, while the people from the middle east are lagging behind. Still, global leprosy remains a threat, with over 225.000 cases registered annually.

“The bacterium is still pathogenic, the same way it was 1,000 years ago, but our social conditions have changed and we have much better medical treatment. But at the same time, it’s still a very prevalent disease,” said Prof Krause.

What’s interesting is that the bubonic plague might have actually played a part in eliminating it – when the pandemic hit, wiping out almost a third of all European popullation, it struck first in people suffering from leprosy.

“It’s been proposed that [bubonic plague (“Black Death”)] killed off a large part of the European population, including those suffering from leprosy. One of the interesting things about this paper is that the medieval and current strains are the same, whereas leprosy disappeared fairly rapidly from Europe. It’s clear that leprosy has created a strong selective pressure on the immune system. The European Caucasian populations have acquired resistance to leprosy, they have certain characteristic mutations in genes that make them less susceptible,” Prof Cole told concluded.

Today, India has the most cases in the world, followed by Brasil.

Via BBC

Hand-held device for extracting DNA. (c) UW/NanoFacture/KNR

New, tiny device can extract clean DNA material within minutes

Hand-held device for extracting DNA. (c) UW/NanoFacture/KNR

Hand-held device for extracting DNA. (c) UW/NanoFacture/KNR

The human genome has been sequenced a mere few years ago, and since then a great deal of advancements have been made in the field. This is extremely important since in the future, personalized medicine needs each individual’s genetic markup such that treatment may get the most effective punch or diseases and afflictions might be avoided altogether.

The DNA sequencing industry is growing rapidly, having turned into a multi-billion dollar industry. Since the turn of the new millennium, however, a lot of companies have seen rapid growth, only to plummet at the hand of counter effective technology.

Collecting and sequencing DNA is still expensive, too expensive for gross use at least. That may soon change. For instance, University of Washington engineers and NanoFacture, a Bellevue, Wash., company, have recently unveiled a small, light-weight device that can allegedly collect viable DNA material for samples in mere minutes, instead of hours – all without risking damaging the DNA itself as is the case with current methods.

“It’s very complex to extract DNA,” said Jae-Hyun Chung, a UW associate professor of mechanical engineering who led the research. “When you think of the current procedure, the equivalent is like collecting human hairs using a construction crane.”

Chung isn’t overreacting at all. Current methods rely on centrifuges and chemical solutions, some of which are toxic, to extract DNA. Micro-filters that strain DNA from the bulk fluid is also commonly used. These methods are slow and expensive, however.

The UW device is comprised of tiny, microscopic probing tips that dip into a fluid sample – saliva, sputum or blood – and apply an electric field within the liquid. The field guides particles towards the surface of the probing tips, however larger ones bounces away while DNA molecules stick. Using this method, it takes only 2-3 minutes to purify and separate DNA. The researchers claim they can scale the technology to analyse 96 samples at a time, which is standard for large-scale handling.

A miniature version, the size and shape of a pen, has also been developed which patients can use to swipe saliva at home and ship them to hospitals where their DNA is readily separated and collected for analysis, without having to leave their homes.

Combined with other recent efforts geared towards cheap sequencing, the technology developed by Chung and colleagues might lend a great hand in the strive to form a huge medical DNA database to battle diseases.

[source University of Washington]

The coelacanth is classed as a sarcopterygian, a term meaning fleshy fins. (c) Chip Clark/Smithsonian National Museum of Natural History, via Associated Press

“Living fossil” fish DNA may help explain how the first animals to walk on land evolved

The coelacanth is classed as a sarcopterygian, a term meaning fleshy fins. (c)  Chip Clark/Smithsonian National Museum of Natural History, via Associated Press

The coelacanth is classed as a sarcopterygian, a term meaning fleshy fins. (c) Chip Clark/Smithsonian National Museum of Natural History, via Associated Press

A matter of great debate and ardent discussion in the field of evolutionary biology today is the transition of complex life from a watery environment to land. So far, there have been numerous speculations put forward in attempt to explain how tetrapods (four-legged land animals) first evolved and washed ashore to start life fresh as land-based animals, however the missing links that mark this transition have eluded scientists.

After sequencing the DNA of a primitive fish that hasn’t evolved much in the past 400 million years and that was thought to have disappeared around the time of the dinosaur extinction, scientists lead by  Chris Amemiya, a biologist at the University of Washington in Seattle, found a gene which when inserted into mice caused them to sprout limbs. The findings might help reveal how fish ultimately swapped their fins for legs and transitioned to walking on land.

[RELATED] First four-legged land animals moved about like seals

The fish in question is called the coelacanth, and was thought to be extinct. However, in 1931 fishermen caught a living specimen, identified later as an African coelacanth, in South African shores. Later, hundreds of specimens were found around the Comoros Islands in the Indian Ocean, as well as off parts of Indonesia. What makes it extremely appealing to researchers is the fact that it has changed very little in the past 400 million years, which is why it’s considered by many as a “living fossil.”

“It really is a cornerstone from which we can view tetrapod evolution,” said study co-author Chris Amemiya, a geneticist at the Benaroya Research Institute in Seattle, Washington.

A captured coelacanth. (c) Simon Maina/Agence France-Presse — Getty Images

A captured coelacanth – notice it’s fleshy fins. (c) Simon Maina/Agence France-Presse — Getty Images

The gene in question is an enhancer that was present in both coelacanths and four-legged creatures, but missing in other fish, which helps in the formation of limbs in animals during the embryonic stage. The gene is not used by the coelacanth itself, since it lies in the “dark matter” side of its genome, responsible for turning genes on or off, but with no protein coding. They then inserted the coelacanth enhancer DNA into mice.

“It lit up right away and made an almost normal limb,” said Neil Shubin, meaning that the coelacanth gene enhancer successfully encouraged the mouse genes to make a limb. Dr. Shubin, a member of the team, is a paleontologist at the University of Chicago.

In addition, the researchers also found a gene related to those that, in animal species, build the placenta. Being a fish, of course the coelacanth doesn’t have a placenta, its blood-filled eggs are very large however, and hatch inside the fish.

The coelacanths aren’t the only primitive fish that might reveal secrets scientists can use to unravel tetrapod evolution. Another fish, the lungfish, is also studied by researchers, however it’s genome has 100 billion DNA units in length, compared to only 2.8 billion both the coelacanth and human genome have. As such, the lungfish’s genome can’t be decoded with present tech.

The findings were reported in an article published in the journal Nature.

Altai dog fossil skull. (c) PLos ONE

DNA evidence suggests modern dog is 33,000 years old

Altai dog fossil skull. (c) PLos ONE

Altai dog fossil skull. (c) PLos ONE

New DNA analysis of an ancient dog tooth sample found in Siberia suggests that the modern dog might be as well as 33,000 years old. If indeed the sample comes from a domesticated dog, then it would push back the origin of today’s house pets more than 18,000 years.

This significant discovery was made after researchers at the Russian Academy of Sciences tested the DNA from the fossilized teeth of an ancient dog, now known as the Altai dog, found in 1975. Though the fossil remains of the dog were discovered decades ago, only recently did it have its DNA analyzed, and what the researchers found is nothing short of a gold-mine.

“Our analyses support the hypothesis that the Altai specimen is more closely related to domestic dogs than to extant wolves,” the researchers said. “This preliminary analysis affirms the conclusion that the Altai specimen is likely an ancient dog with a shallow divergence from ancient wolves.”

The dog’s DNA was compared to that of the DNA of other prehistoric dogs, wolves, and modern dogs, and then mapped out their relatedness based on how different the DNA sequences were. Previously, it was thought modern day dogs split from wolves some 15,000 years ago in the Middle East of East Asia, as suggested by studies.

The analysis showed 99% similarity to dogs, but no exact match to existing dogs or wolves. Naturally, more work needs to be done, and other laboratories need to confirm the Russian scientists’ work before this rather important claim can be settled as true or false. Currently, there is only one dog fossil that is older than the Altai dog – the Goyet dog, dated between 32,000 and 36,000 years old and found in Belgium. DNA analysis hasn’t been possible since it’s too deteriorated for sequencing.

Findings were reported in the journal PLoS One.

Preposterous science: researchers invent scientific journal to publish bigfoot paper

Bigfoot 2008

Myth, wonder, mysticism these are just a few concepts that has entertained and has fascinated the human mind for thousands of years. Be it from boredom of life’s seemingly casual existence or drawn by aspirations of a higher self, many people have been, currently are and will be for a long time seduced by what they can’t explain themselves – though few search a bit farther for answers – or by the outworldly.

Some people have discredited and feel dishearten by science because it “kills the joy of life and mystery”. Now, this couldn’t be more wrong. If anything, science does the opposite and actually springs from the same mechanisms that attract the easily gullible cheap mystery hunters – questions as to why nature, phenomena or even life itself exists. However, where as the mystery hunter is easily satisfied by the seductive power of wonder, those who  sincerely look for truth need to embark on a journey governed by uncertainty – until all things point to the truth.

It’s remarkable how in the 21st century so many people choose to blindly accept without questioning some, let’s say, seductive ideas with no reasonable basis. God forbid you engage in heated conversations with unreasonable people, it won’t get you anywhere. It’s true, skeptics aren’t burned to the stake like in the middle ages – they just lose friends nowadays, and I guess from this perspective, society has evolved, yet it’s still a shame. It’s an even greater shame when self professed scientists settle to make great claims, with little to few evidence. “Extraordinary claims require extraordinary evidence“, Carl Sagan said once, but apparently a group of scientists, with a forensic science background, took little consideration for this aspect.

Back in November, the group boasted that they have finally found evidence that Bigfoot (Sasquatch, Yeti, whatever) truly exists. Not surprisingly, they found a tough time getting their paper published by any journal. So, of course, they proceeded in making their own journal, called DeNovo Journal of Science (I chose not to link to their website, but you can find it if you’re interested).

The journal’s first volume and edition is comprised of only one paper – of course the one discussing Big Foot, and while the website advertises the journal as open-access, apparently those interested in actually reading the paper need to pay $30. Credibility? Well wait until you hear about their conclusions.

Little foot

Dr. Melba S. Ketchum along with colleagues analyzed 111 samples, either collected or received from other parties, allegedly  coming from Big Foot, or Homo sapiens cognatus as the paper’s authors call it, since they believe we’re dealing with a surviving hominid, the result of interbreeding between humans and some sort of ape. Samples include hair, fur, and even blood (the researchers hypothesize that the blood was spilled after a Sasquatch chewed on a pipe. Yeeeeesh!).

The researchers sequenced 20 whole, and 10 partial mitochondrial genomes, as well as 3 whole nuclear genomes. Mitochondrial DNA, or mtDNA, comes from mitochondria and is passed down on maternal lineage across generations. Nuclear DNA (nuDNA) is the genetic information contained in the cell nucleus, and is the equal combination of DNA from parents of an individual.

“Clearly non-human hair (morphologically), washed thoroughly as is accepted procedure in forensic science to remove contaminates by two laboratories with two techniques, yielded human mitochondrial DNA sequence in all 111 samples in the study,” she said. “Thirty samples were taken past the screening to yield human mitochondrial haplotypes with twenty of those being entire mitochondrial genomes 16,500 bases long. Since species identification depends on the mitochondrial DNA in forensics, this clearly placed the samples in the family Homo, ie hominin. Screening by sequencing with universal primers would have also shown contamination if it had been there.”

Typically, in similar identification work procedure requires that all data needs to be run across a DNA database in order to establish if they belong to a known species. This hasn’t been done, however. There are numerous glitches to the paper actually, as Ars Technica which has had access to the paper clearly outlines in one of their articles. It’s enough to say that the paper in question is riddled with all sort of unfounded references, likes pictures of said-Sasquatch footprints, dubious photos and even a video of said-Sasquatch embedded in the paper that actually looks like a moving carpet. Sigh.

 

how a pig is cloned

Cloned animals aren’t identical – we’re still far from the perfect clone

It is generally believed that a cloned animal is identical to its host from where cells were initially harvested, however this may be wrong. Researchers at the  National Veterinary Institute at the Technical University of Denmark have provided evidence that suggests cloned pigs are just as genetically varied as normally bred pigs, supporting the idea that cloning as it is performed today is far from being perfect. The findings are the latest in a number of similar reports from other Universities, calling for attention to the matter and consideration of this fact when carrying research on cloned animals – especially in the field of medicine.

Currently it is believed that cloned animals are more akin to one another compared to normally bred animals, since they are copies of one another just like identical twins are. This means they have fewer genetic variants, allowing scientists to gather results with fewer specimens at hand. Researchers from Denmark however argue that this isn’t true, and that actually  pig clones are often highly varied and also respond differently than non-clones – which goes against the popular belief.

For their study, the researchers looked at how the immune system of cloned and normally bred pigs responded to obesity. Comparisons were made of so-called acute phase proteins in the blood and of the gene expression of immune factors in three types of adipose tissue and in liver tissue.

Why clones aren’t identical

Their findings suggest that cloned animals have an altered immune system compared to normally bred ones. For instance, the amount of acute phase proteins in the blood increases dramatically during inflammation, however for the clones the levels of some markers were upregulated in relation to the levels in the non-cloned group.

Most importantly, though, it was observed that the variation in the expression of these genetic markers was just as great for cloned pigs as in non-cloned pigs. As an analogy, this is as saying that a quintuplets’ innate immune systems are as different as five regular siblings’. This means cloned animals are indeed different.

how a pig is cloned

It was also observed that cloned animals behave differently from non-cloned animals. For instance cloned pigs were more fearful and anxious than naturally bred pigs. They also weigh less and are often found to have a higher metabolism than non-clones.

Part of the explanation lies in the current methods of cloning, which disrupt the sensitive processes that take place during embryonic development. Then there’s epigenetics – heritable changes in gene expression, which are not caused by changes in the underlying DNA sequence. In other words, you can have two pigs with identical DNA sequences however these cloned animals will be far from being identical since they’ll express completely different genes and thus make them look entirely different.

Hence, researchers have yet to crack the code on how we can control genomic imprinting. Until this happens, the perfect clone is still out of reach. Now, this knowledge is highly important to consider, especially since a lot of scientists working with clones apparently aren’t fully aware of this, according to the Danish researchers.

via  Science Nordic

(a–c) Shrinkage of a ∼3.3-nm-diameter nanopore, indicated by circles, and (d–f) enlargement of a ∼6-nm-diameter nanopore in a graphene sheet at 1200 °C.

Cheap DNA sequencing is a step closer with graphene nanopores

Graphene is the strongest material ever discovered by man, and naturally its applications has been extended to a variety of fields – most recently genetics.  University of Texas at Dallas scientists have used advanced manipulation techniques to shrink a sheet of graphene to the point that it’s small enough to read DNA. This successful attempt now opens doors for the possible introduction of graphene based, cheap DNA sequencing devices.

“Sequencing DNA at a very cheap cost would enable scientists and doctors to better predict and diagnose disease, and also tailor a drug to an individual’s genetic code,” said Dr. Moon Kim, UT-Dallas professor of materials science and engineering.

(a–c) Shrinkage of a ∼3.3-nm-diameter nanopore, indicated by circles, and (d–f) enlargement of a ∼6-nm-diameter nanopore in a graphene sheet at 1200 °C.

(a–c) Shrinkage of a ∼3.3-nm-diameter nanopore, indicated by circles, and (d–f) enlargement of a ∼6-nm-diameter nanopore in a graphene sheet at 1200 °C. (c) University of Texas

The first complete human genome sequence was finally presented in 2003 by the international scientific research group known as the Human Genome Project after more than a decade of research and $2.3 billion. Now, various institutions and scientific groups are pushing the current technological limits to reach the $1000 DNA sequencing threshold cost for a person.

With fast and cheap DNA sequencing, physicians could easily prescribe medications keeping in mind your genetic tendencies, as well as avert various serious illnesses before they can evolve by tackling your genetic predispositions.  Graphene might become an essential components in such cheap DNA sequencing devices.

Because it’s so thin, but strong, the researchers saw it as a perfect candidate, and sought ways to control its pore size. The team of researchers manipulated the size of the nanopore by using an electron beam from an advanced electron microscope and in-situ heating up to 1200 degree Celsius temperature.  The nanopore shrinking process can be stopped by blocking the electron beam.

“This is the first time that the size of the graphene nanopore has been controlled, especially shrinking it,” said Kim. “We used high temperature heating and electron beam simultaneously, one technique without the other doesn’t work.”

As graphene pore size control has been proven, the next logical step is to implement it into a working device, something more of a challenge.

“If we could sequence DNA cheaply, the possibilities for disease prevention, diagnosis and treatment would be limitless,” Kim said. “Controlling graphene puts us one step closer to making this happen.”

Findings were published in the journal Carbon.

via KurzweilAI

caribbean-skinks

24 new lizard species discovered in the Caribbean – already faced with extinction

A team of researchers at Penn State University has identified 24 new species of skinks, a subspecies of lizards, native to the Caribbean Islands, turning the region’s fauna from one of the smallest lizard groups in the world to one of the largest. However, half of these new species are considered already extinct or very close to extinction, while the other half is threatened by extinction. The scientists blame the mongoose for Caribbean skink holocaust, a predatory mammal introduced by farmers to control rats in sugarcane fields during the late 19th century.

caribbean-skinks

About 130 new species of reptiles are added each year to the world species count, however this was the first time since the 1800s when more than 20 new species had been added and described in a single paper. In total, the Penn State scientists looked at 39 skink species, of which six were already recognized, nine had already been described and given names but were considered invalid until now, and the rest are absolutely new species. Why did it take so long for these many skink species to be identified by scientists when the region is booming with humans and numerous scientific expeditions? The scientists explain that first of all, because of the dwindling number of surviving specimens, the newly found skink species are elusive and rarely seen, and secondly, the variations between species are very subtle and hard to notice, hence it’s very common to believe a specimen is part of an already well known species, when in fact it might be part of an entirely unidentified species. Some of the new species are six times larger in body size than other species in the new fauna.

“Now, one of the smallest groups of lizards in this region of the world has become one of the largest groups,” Hedges said. “We were completely surprised to find what amounts to a new fauna, with co-occurring species and different ecological types.”

The team of researchers, lead by Blair Hedges, professor of biology at Penn State University, used DNA sequences to identify the new animal species, but most of the taxonomic information, such as counts and shapes of scales, came from examination of the animals themselves either of museum specimens or live ones.

Not your ordinary backyard gecko

It’s believed the Caribbean skinks surfaced in the region some 18 million years ago after  from Africa by floating on mats of vegetation. That may be impressive, however what makes these reptiles truly special is the fact that females  produce a human-like placenta, which is an organ that directly connects the growing offspring to the maternal tissues that provide nutrients.

“While there are other lizards that give live birth, only a fraction of the lizards known as skinks make a placenta and gestate offspring for up to one year,” Hedges said.

This lengthy gestation period also gave their predators a hefty advantage, as gestation females are considerably slower and easier to catch.

“The mongoose is the predator we believe is responsible for many of the species’ close-to-extinction status in the Caribbean,” Hedges said. “Our data show that the mongoose, which was introduced from India in 1872 and spread around the islands over the next three decades, has nearly exterminated this entire reptile fauna, which had gone largely unnoticed by scientists and conservationists until now.”

“By 1900, less than 50 percent of those mongoose islands still had their skinks, and the loss has continued to this day,” Hedges said.

The research team reports on the newly discovered skinks in a 245-page article published today (April 30) in the journal Zootaxa.

source: Penn State Live

MinION portable DNA sequencing device plugged to the USB port of a laptop

USB-powered DNA sequencer puts genetic analysis out of the lab to your laptop

Since the advent of modern DNA sequencing technology, biological research and discoveries has been dramatically accelerated. It’s absolutely instrumental to genetic research nowadays, which among other great achievements, has lead to the sequencing of the human genome. The methods and technologies involved in DNA sequencing are terribly complex, however, and usually require sophisticated research laboratories. What if you could simplify the process?

MinION portable DNA sequencing device plugged to the USB port of a laptop

Oxford Nanopore (ON) had this idea in mind for some time, and recently unveiled an extraordinary product the company has completed developing – a fast, portable, and disposable nucleotide sequencer the gets powered via USB and runs analysis on the same computer it gets plugged in. Extreme costs are promised to be alleviated once this products gets introduced on the market, eliminating the need for highly expensive facility usage for small projects and offering the possibility to perform genetic analysis on the go when needed.

The MinION, as it’s been dubbed by ON researchers, doesn’t need polymerase chain reaction (PCR) or other DNA amplification technique for optimum sensitivity, and can sequence up to 150 million base pairs within its six hour working life. The device accepts samples of  blood, plasma, and serum for an immediate analysis.

MinION’s centerpiece is its nanopore port. A nanopore is basically an organic molecule with a very narrow hole, just a few nanometers in width. This nanopore is embedded inside two molecule thick synthetic polymer membrane, which has a very high electrical resistance, such that the nanopore hole forms a path from one side of the membrane to the other. Through the nanopore hole electrophysiological fluid is inserted, which has its volume divided in half as a result of a specific geometry.

When passing through the variable geometry in the nanopore hole, the electrophysiological fluid is swept by an ionic current which causes a voltage difference. Each molecule, including DNA or RNA, has its own characteristic voltage, and thus using this technique the MinION can detect and identify the sample. Of course, the MinION’s main purpose is that of sequencing DNA, so the device is optimized to differentiate the four nucleobases (adenine, cytosine, guanine, and thymine) which encode genes in DNA. To analyze the DNA, the MiniON uses strand sequencing.

This diagram shows a protein nanopore set in an electrically resistant membrane bilayer.  An ionic current is passed through the nanopore by setting a voltage across this membrane. (c) Oxford Nanopore Technology

This diagram shows a protein nanopore set in an electrically resistant membrane bilayer. An ionic current is passed through the nanopore by setting a voltage across this membrane. (c) Oxford Nanopore Technology

The device’s sensing electronics has  512 nanopores embedded onto its sample chip, resulting in a total strand reading rate of about 7500 bases/second. During its limited 6 hours operation life time, the MinION can read 150 million bases; enough to read small chromosomes or bacteria genome. Check out this excellent video from Oxford Nanopore explain in great detail how the MinION works and how the DNA sequencing process unfolds.

Nanopore DNA sequencing from Oxford Nanopore on Vimeo.

The researchers working on the device have already tested the device successfully, after sequencing the genome of the lambda bacteriophage – 48500 base pairs in length. Clive Brown, the Chief Technology Officer of Oxford Nanopores, has been cited during the product’s announcement at AGBT 2012, that the MinION might be introduced on the market with a $900 price tag!

“The exquisite science behind nanopore sensing has taken nearly two decades to reach this point; a truly disruptive single molecule analysis technique, designed alongside new electronics to be a universal sequencing system.  GridION and MinION are poised to deliver a completely new range of benefits to researchers and clinicians,” said Dr Gordon Sanghera, CEO of Oxford Nanopore.  “Oxford Nanopore is as much an electronics company as a biotechnology company, and the development of a high-throughput electronics platform has been essential for us to design and screen a large number of new candidate nanopores and enzymes. Our toolbox is customer-ready and we will continue to develop improved nanopore devices over many years, including ongoing work in solid state devices.”

press release / via Gizmag

Ozzy Osborne’s genome reveals why he is still alive

The lead singer, rock legend bat beheader has done pretty much anything you can do in this life. He played in front of thousands, ate/drank/smoked/injected pretty much everything that can be, had motorcycle accidents, never ate right, and yet, at the proud age of 61 he’s alive and kicking just as he ever was. Researchers wanted to find out why this is happening (not that anybody would have something against it), analyzed his genome and found some interesting mutations.

Ozzy Osborne joined DNA co-discoverer James Watson and Harvard University professor Henry Louis Gates in having his genome analyzed by Cofactor Genomics, a Saint Louis–based company and Knome, Inc. At first, he said he was a bit skeptical, but after a while thought he actually has something to give to science.

[read this in his voice]”I was curious,” he wrote in his column. “Given the swimming pools of booze I’ve guzzled over the years—not to mention all of the cocaine, morphine, sleeping pills, cough syrup, LSD, Rohypnol…you name it—there’s really no plausible medical reason why I should still be alive. Maybe my DNA could say why.”

It is in fact pretty curious how he managed to survive after such a lifestyle, and researchers were interested in finding out how he metabolized things, and how this was affected by his substance use; they also found some interesting mutations regarding the way the brain processes dopamine. Here are just a few questions Scientific American asked Jorge Conde, co-founder and chief executive as Knome:

[..]

Is Ozzy the first rock star to have his full genome sequenced?

Conde: Yes, as far as I know. I can definitely tell you he’s the first prince of darkness to have his genome sequenced and analyzed.

Can we see in his genome any traces of his legendary rock-and-roll lifestyle—or evidence of his body’s efforts to repair any damage?

Conde: We cannot find the “Ozzy Osbourne” gene. But what we did see, as one of our scientists refers to it, is a lot of interesting smoke—but not any specific fire. We found many variants—novel variants—in genes associated with addiction and metabolism that are interesting but not quite definitive.

So can his genomes tell us anything about his ability to survive so many years of hard partying?

Pearson: I talked with Ozzy, and we looked at the genome with an eye toward the nerves. If you think about what makes Ozzy unusual, it’s that he’s a world-class musician, he has an addictive personality, he has a tremor, he’s dyslexic, he gets up very early in the morning. And many of these can be traced back to the nervous system.

One variant involves a gene that makes CLTCL1, which is a really interesting protein. When a cell takes in things from the outside membrane, it pulls itself in like a basket to pull things in. It does this in all kinds of cells, including nerve cells. He has two copies of an unusual variant that makes a grossly different version of the protein than most people produce. Here’s a gene that’s central to how nerve cells communicate with each other, so it’s curious to us to see a grossly different protein variant. It’s thought provoking.

We didn’t find anything that can explain to you from point A to point B why Ozzy can think up good songs or why he is so addicted to cocaine, but we found some things that would be interesting to follow up on.

Such as?

Pearson: Alcohol dehydrogenase genes. They’re involved in breaking down alcohol when you drink. Ozzy has an unusual variant near one of his alcohol dehydrogenase genes, ADH4, that help regulate how much of the protein gets made. Given his troubles with alcohol in the past, obviously we would like to clarify why his body responds differently than other people’s.

What can we learn from Ozzy’s genome?

Pearson: I think one lesson is understanding music. It’s a pretty interesting thing we do at humans—that some of us can synchronize to a beat, that we like to sing songs. But we don’t understand it well genetically, so one of the open questions is we’ll get a better understanding of what makes a good musician, what kinds of variants help us keep a beat, make a good tune. I think looking ahead, sequencing the genomes of more musicians would be a good idea.

If you could sequence any other celebrity genomes, whose would you choose?

Pearson: Ozzy suggested Keith Richards. Our partners who did the sequencing suggested we sequence Ozzie Smith, the baseball player, as a control. He’s always been a good teetotaler.

Full interview here

Domestic Cat Genome Sequenced

cinnamon


Not a long time ago scientists have sequenced chimpanzee, mouse, rat, dog, and cow DNA. This made it possible for them to understand numerous things including the hundreds of chromosomal rearrangements that have occurred among the different lineages of mammals since they diverged from a diminutive ancestor that roamed the earth among the dinosaurs some 100 million years ago.The cat used for sequencing is a 4-year-old Abyssinian cat named Cinnamon. This genome sequence analysis is bound to lead to some important findings in medicine for cats as they have over 250 naturally occurring hereditary disorders. But the cat serves as a good model for studying human disorders; in fact this is the reason why the National Human Genome Research Institute (NHGRI) initially authorized the cat genome sequencing about three years ago.

Scientists used the data from the DNA sequencing and they identified several hundred thousand genomic variants which give clues about the genetic basis of numerous hereditary conditions. They found other interesting things such as microRNAs, Numts (pronounced “new mights”–nuclear genomic fragments that migrated to cat chromosomes from mitochondria) and they found a link between repetitive elements and some retroviruses which could cause cancer.

The study showed that Cinnamon’s pedigree carries a genetic mutation that causes retinitis pigmentosa, a degenerative eye disease that can lead to blindness and is harmful for humans. Cinnamon is shy and reticent, preferring to sit quietly and watch the other cats play and carouse. This sequencing could help her and other 1 in 3,500 people affected by this condition