Ancient DNA Found Hidden Below Sea Floor

In the middle of the South Atlantic, there’s a patch of sea almost devoid of life. There are no birds, few fish, not even much plankton. But researchers report that they’ve found buried treasure under the empty waters: ancient DNA hidden in the muck of the sea floor, which lies 5000 meters below the waves.

The DNA, from tiny, one-celled sea creatures that lived up to 32,500 years ago, is the first to be recovered from the abyssal plains, the deep-sea bottoms that cover huge stretches of Earth. In a separate finding published this week, another research team reports teasing out plankton DNA that’s up to 11,400 years old from the floor of the much shallower Black Sea. The researchers say that the ability to retrieve such old DNA from such large stretches of the planet’s surface could help reveal everything from ancient climate to the evolutionary ecology of the seas.

“We have been able to show that the deep sea is the largest long-time archive of DNA, and a major window to study past biodiversity,” writes Pedro Martinez Arbizu, a deep-sea biologist of the German Centre for Marine Biodiversity Research in Wilhelmshaven and an author of the paper on South Atlantic DNA in an e-mail.

The new studies are “very exciting,” says micropaleontologist Bridget Wade of the University of Leeds in the United Kingdom, who was not connected to the research. Until now, it wasn’t clear “how far back in time you could take these DNA studies. … These records are telling you new information that wasn’t found in the fossil record.”

The South Atlantic team went looking for DNA in plugs of silt and clay coaxed out of the ocean floor hundreds of kilometers off the Brazilian coast. The researchers were after genetic material from two related groups of marine organisms, the foraminifera and the radiolarians. Both are single-celled, and both include many species with beautiful pearly shells that fossilize nicely, making them a favorite target of researchers studying the prehistoric oceans.

The researchers used special pieces of DNA specific to radiolarians and foraminifera to fish out DNA from those groups. Then they sequenced the DNA and compared the results to known foraminifera and radiolarian DNA sequences. Their analysis showed they’d found 169 foraminifera species and 21 radiolarian species, many of which were unknown. What’s more, many of the foraminifera species belonged to groups that don’t form fossils, the researchers report online today in Biology Letters.

The work shows that it’s possible to trace all species, not just those that fossilize, says Jan Pawlowski, a foraminifera specialist and one of the paper’s authors, of the University of Geneva in Switzerland. The results give “us a completely different view … [that] may open new insights into what’s happened in the past,” he says. For example, he says, different species of these wee creatures prefer different water temperatures. So DNA from buried sediments could be used to track the abundance of different species over time, revealing changes in ocean temperature.

The second team looked at DNA buried in the floor of the Black Sea, which was once a giant lake but became connected to the Mediterranean Sea roughly 9000 years ago, though the date is debated. The researchers examined sediments from waters only 980 meters deep, which is much shallower than the abyssal plain. But the oldest Black Sea layers that were analyzed were similar to those at the South Atlantic site: The mud at the sea bottom had scant amounts of organic matter and had been exposed to oxygen, which, in theory, should have made it tough to scrape up any preserved DNA.

It didn’t. New material had buried the older layers, cutting off their oxygen, and more recent Black Sea sediments weren’t exposed to oxygen at all. The result was a rich trove of ancient DNA from as many as 2700 species, including green algae, fungi, and dinoflagellates, a type of one-celled aquatic creature. The diverse collection allowed the scientists to track the fate of different species over time, as their DNA blinked in and out of the sediments.

One type of marine fungus, for example, first appeared in the sediments roughly 9600 years ago—exactly when some forms of freshwater plankton and a freshwater mussel vanish, the team reports this week in the Proceedings of the National Academy of Sciences. That suggests that marine waters started to invade the lake roughly 600 years earlier than thought. The team also found DNA from a form of marine alga in 9300-year-old sediments, though the alga doesn’t show up in the fossil record until 2500 years ago, says molecular paleoecologist Marco Coolen of the Woods Hole Oceanographic Institution in Massachusetts and an author of the Black Sea paper.

Other ancient DNA studies have been discredited after supposedly ancient genetic material turned out to be modern contaminants, but those fears don’t apply to this new research, says micropaleontologist Michal Kucera of the University of Bremen in Germany. He says that both teams took the necessary steps to avoid contamination, and their results don’t look like contaminants. In the Biology Letters results, for instance, DNA from older sediments is more degraded than material from more recent sediment—not what you’d expect if the DNA were a laboratory stowaway.

Kucera and Wade praised both studies as paving the way for the use of ancient marine DNA to illuminate the history of the ocean. Coolen’s finding of marine species invading the Black Sea earlier than had been thought “is not something you could see from looking at fossils or sediment properties,” Kucera says.

Wade says that it may be possible, once researchers can identify the DNA of species that prefer certain environmental conditions, to use deep-water DNA to reveal changes in climate. “Most of the environment on Earth is marine deep ocean,” including the area where Pawlowski’s team found DNA, she says. “So it makes it very exciting that they’re looking in this environment and finding DNA.”

image: Minute fossil sea creatures recovered from sediments containing ancient DNA. credit: Lejzerowicz et al./Biology Letters

(Source: jereblog, via invaderxan)

Normal brain activities cause DNA damage, too

The breaks in DNA strands ‘may be part of normal learning’ that we all experience.

(Source: mothernaturenetwork)

Mystery of ‘junk DNA’ solved

The findings suggest junk DNA really isn’t needed for healthy plants — and that may also hold for other organisms.

(Source: mothernaturenetwork, via mothernaturenetwork)

(Source: music4airports, via applepiesfromscratch)

Juan Enriquez: The Next Species Of Human | TED

Even as mega-banks topple, Juan Enriquez says the big reboot is yet to come. But don’t look for it on your ballot — or in the stock exchange. It’ll come from science labs, and it promises keener bodies and minds. Our kids are going to be … different.

Why You Should Listen To Him:
A broad thinker who studies the intersection of science, business and society, Juan Enriquez has a talent for bridging disciplines to build a coherent look ahead. Enriquez was the founding director of the Harvard Business School Life Sciences Project, and has published widely on topics from the technical (global nucleotide data flow) to the sociological (gene research and national competitiveness), and was a member of Celera Genomics founder Craig Venter’s marine-based team to collect genetic data from the world’s oceans.

Formerly CEO of Mexico City’s Urban Development Corporation and chief of staff for Mexico’s secretary of state, Enriquez played a role in reforming Mexico’s domestic policy and helped negotiate a cease-fire with Zapatista rebels. He is a Managing Director at Excel Medical Ventures, a life sciences venture capital firm, and the chair and CEO of Biotechonomy, a research and investment firm helping to fund new genomics firms. The Untied States of America looks at the forces threatening America’s future as a unified country.

In his TED Book Homo Evolutis (written with Steve Gullens), Enriquez explores the far reaches of human change, and asks: Are we done evolving?

Most of my unpublished writerly output - handwritten manuscripts and letters, lectures and lab notes, university and government documents that I helped prepare - is deposited in the archives of Harvard University and of Cold Spring Harbor Laboratory. In time, it will all become available to the public, mostly through the Internet, for those preternaturally curious about how I have moved through life. Rather than let other commentators have the first crack at those writings, I opted to be the first to employ them extensively to prepare this look at my life before middle age became obvious - my childhood, university years, career as an active scientist and professor, and my first years as director of the Cold Spring Harbor Laboratory.

As this book’s broad features came to cohere, I began to see Avoid Boring People as an object lesson, if not quite an exemplary history of the making of a scientist. It is my advice in the form of recollections of manners I deployed to navigate the worlds of science and academia. The thought that this instructive value might be made explicit in the form of self-help led me to conclude each chapter with a set of “remembered lessons” - rules of conduct that in retrospect figured decisively in turning so many of my childhood dreams into reality. Suffice it to say, this is a book for those on their way up, as well as for those on top who do not want their leadership ears to be an assemblage of opportunities gone astray.

Skipping high school’s last years led to my never learning how to type, and even today I generate left-hand-written version sof the first drafts of all my writings. Without my administrative assistant Maureen Berejka’s ever-increasing skill in handling strings of seemingly indecipherable squiggles, this book could never have come into existence. In preparing successive early drafts of the manuscript, I much benefitted from the able Barnard College chemistry graduate, Kiryn Haslinger, whose expert knowledge of the English language led to many improvements in my word use. New York University psychology graduate Marisa Macari ably provided help in inserting period photographs and documents. Later, Stanford biology major Agnieszka Milczarek invaluably corrected the many errors of fact and spelling spotted by friends to whom I sent preliminary drafts. Finally, I much thank George Andreou of Knopf for masterly editing that has much improved this volume’s clarity and intellectual thrust.

James (Jim) Watson, Author of The Double Helix, Nobel Prize Winner for revealing the structure of DNA, March 26, 2007; Avoid Boring [Other] People: Preface

*I picked this up awhile back and I’ve been anxious to get to it. As I journey through the text, I’m bound to share much more bits with you all. Stay curious*

Scientists Have Engineered The World’s First Glow-In-The Dark Sheep

Nighttime sheep-herders rejoice, for green-glowing sheep are now a thing. Two questions, though. How? And why?

Here’s the how: last year, a team of researchers led by Alejo Menchaca at the Animal Reproduction Institue of Uruguay genetically modified some wooly ruminants to express a peptide commonly known as green fluorescent protein, or “GFP.” GFP glows green when exposed to ultraviolet light, and was originally isolated from the jellyfish Aequorea victoria. Today, it’s used to label molecules of biomedical interest – to determine whether those molecules are being expressed, and in what quantity. In the last twenty years, GFP and its derivatives have become such ubiquitous and invaluable research tools that its discoverers were awarded a Nobel Prize back in 2008.

Menchaca’s sheep – which were born last October and, apart from their corporeal glow, appear to have developed just like an unmodified flock – express the protein in tissues throughout their bodies, causing them to glow under ultraviolet light. Menchaca says that, in this particular instance, the sheep were modified merely as a proof of concept. As in: Look everybody, we can breed a totally healthy sheep that also happens to glow. Isn’t that swell? Well yes, it is. It’s kind of eerie (look into the eyes of the GFP-sheep up top and tell me you aren’t afraid), but also pretty cool. But why make a sheep glow in the first place?

GFP animals are a growing (glowing?) trend in biomedical research. To date, scientists have genetically engineered a wide swath of the animal kindgdom to express GFP, a recent example being this litter of glow-in-the-dark kittens. Because GFP can be engineered to show up only when it’s expressed with another, specific protein, researchers can use glowing animals to study and better understand biological processes that occur on the whole-body scale. In the case of the cats, the green glow is used to help researchers identify, at a glance, the body-wide expression of an antiviral protein that could prove useful in suppressing the spread of HIV.

One of Menchaca’s research interestes is the development of a genetically modified sheep that can produce milk imbued with human growth hormones – milk which could be used to help treat humans suffering from endocrine disorders. It’s not hard to imagine how his team might use GFP to clearly label which sheep have been born with the ability to produce these hormones. This, of course, is just one potential application of the technology, which Menchaca says is still very much in development.

“The technique is complex and demands much work and is one of the limiting factors, so despite the global interest and demand it is still a slow process,” he said in a statement.

“Our focus is generating knowledge and making it public so the scientific community can be informed and help in the long run march to generate tools so humans can live better.”

Photo courtesy Funcación IRAUy/J. Calvelo

taken @ the AMNH, NYC

DNA: Celebrate the unknowns | Philip Ball

On the 60th anniversary of the double helix, we should admit that we don’t fully understand how evolution works at the molecular level, suggests Philip Ball.

This week’s diamond jubilee of the discovery of DNA’s molecular structure rightly celebrates how Francis Crick, James Watson and their collaborators launched the ‘genomic age’ by revealing how hereditary information is encoded in the double helix. Yet the conventional narrative — in which their 1953 Nature paper led inexorably to the Human Genome Project and the dawn of personalized medicine — is as misleading as the popular narrative of gene function itself, in which the DNA sequence is translated into proteins and ultimately into an organism’s observable characteristics, or phenotype.

Sixty years on, the very definition of ‘gene’ is hotly debated. We do not know what most of our DNA does, nor how, or to what extent it governs traits. In other words, we do not fully understand how evolution works at the molecular level.

That sounds to me like an extraordinarily exciting state of affairs, comparable perhaps to the disruptive discovery in cosmology in 1998 that the expansion of the Universe is accelerating rather than decelerating, as astronomers had believed since the late 1920s. Yet, while specialists debate what the latest findings mean, the rhetoric of popular discussions of DNA, genomics and evolution remains largely unchanged, and the public continues to be fed assurances that DNA is as solipsistic a blueprint as ever.

[Read more]

(Source: heythereuniverse, via theolduvaigorge)

Sex with Other Early Species Might Have Been Secret of Homo sapiens Success

Just a few tens of thousands of years ago, Homo sapiens existed next to several close evolutionary cousins, including Neanderthals and Homo floresiensis. But shortly after our human species migrated out of Africa, we were left as the only hominin species on Earth.

What was the secret to our success? Did we out-compete the others for resources? Did we just flat-out kill them? Did we reproduce faster? All of those theories have some merit, but thanks to DNA analysis of ancient human and Neanderthal genomes, a new idea is emerging: We may have interbred our way to the top.

By analyzing how much of our genomes (nuclear and mitochondrial) we share with these other species, it appears that there was significant “genetic mixing”, if you know what I mean. Many of these hybrid gene mixes could have added new tools for our early immune system, leading to tougher, more survivable humans.

We still lack many details in this story, and lots of questions remain. But it’s pretty clear that human evolution does not follow a single line out of Africa. Instead, it’s a web that stretches first across Europe and then into Asia, mixing and branching along the way into the global population that today we see mixing in entirely new ways.

Check out the wonderfully detailed full story by Michael Hammer at Scientific American.

(via jtotheizzoe)

The Evolution of Evolution: Darwin’s Gemmule Theory Revisited

The advances in genetics have been absolutely amazing over the last few decades since the discovery that DNA was the hereditary material. For example, we’ve sequenced the genomes of many, many different organisms, including at this point, hundreds of plant genomes. And so we now can read the genetic code very easily.

In the last decade or couple of decades we’ve realized that there is an epigenetic code, a second code, if you like, that’s layered on top of this DNA sequence and can drastically influence both the normal development of a plant or an animal as well as the inheritance of these traits.

So for example, in the 19th century the famous botanist Jean-Baptiste Lamarck proposed the idea that is now called the Inheritance of Acquired Traits in which he suggested that maybe the experience of an organism in one generation could somehow lead to changes in the progeny that would benefit them in the next generation. He famously thought that the giraffe’s neck had been extended by reaching higher and higher into trees for nutrition.

While we don’t think that Lamarck’s ideas should be interpreted too literally, we’re beginning to find evidence that epigenetics can, in fact, influence the next generation in a way that’s at least partially Lamarckian. So one of the most important discoveries in the last decade has been a phenomenon called RNA Interference where small RNAs can very drastically influence the activity and the importance of genes.

One of the discoveries that my lab was part of was seeing how those small RNAs could actually make more permanent changes in the chromosome that could be inherited from cell to cell. So that actually provides a potential mechanism for Lamarckian Inheritance because the small RNAs can arise from anywhere in the body. They can move around and implant. We know that they move around a lot and potentially could influence the inheritance of chromosomes in the germ line.

It was actually Darwin who first realized this potential. He was a big fan of Lamarck. A lot of people don’t realize that, but in The Variation of Animals and Plants under Domestication he wrote that if Lamarckian Inheritance—the inheritance of acquired traits—was true then there must be some property arising in the body that could enter the germ line and change the germ line for the next generation. And Darwin called these gemmules—which is a wonderful name and we think small RNAs are very good candidates for those gemmules.

via BigThink

laboratoryequipment:

Humans don’t “own” their own genes, the cellular chemicals that define who they are and what diseases they might be at risk for. Through more than 40,000 patents on DNA molecules, companies have essentially claimed the entire human genome for profit, report two researchers who analyzed the patents…

laboratoryequipment:

DNA Tech to Speed Species Discovery

Scientists from CSIRO and the Univ. of Western Australia have teamed up with Kimberley Traditional Owners to test a new molecular technique that has the potential to revolutionize the discovery of new species, particularly those living in remote and poorly studied parts of the world.

Working in the virtually inaccessible rainforest vine thickets of Australia’s National Heritage-listed Kimberley region, the team are using a technique known as “ecogenomics” to survey the area’s insect biodiversity, and rapidly describe what are expected to be hundreds of unique and rare species. The technique involves identifying species based on their DNA and morphology, and is much faster and more cost effective than traditional taxonomic approaches.

Read more: http://www.laboratoryequipment.com/news/2013/03/dna-tech-speed-species-discovery

theolduvaigorge:

Entire Neandertal Genome Decoded

“The Max Planck Institute for Evolutionary Anthropology, in Leipzig, Germany, has completed the genome sequence of a Neandertal and makes the entire sequence available to the scientific community today.

In 2010, Dr. Svante Pääbo and his colleagues presented the first draft version of the Neandertal genome from data collected from three bones found in a cave in Croatia. 

They have now used a toe bone excavated in 2010 in Denisova Cave in southern Siberia to generate a high-quality genome from a single Neandertal individual.

The Leipzig team has used sensitive techniques they have developed over the past two years to sequence every position in the genome about 50 times over, using DNA extracted from 0.038 grams of the toe bone. The analysis of the genome together with partial genome sequences from other Neandertals, and the genome from a small finger bone discovered in the same cave, shows that the individual is closely related to other Neandertals in Europe and western Russia (see Figure). Remarkably, Neandertals and their relatives, Denisovans, were both present in this unique cave in the Altai Mountains on the border between Russia, China, Mongolia and Kazakhstan” (read more).

See also:

• The Neandertal Genome Project

(Source: Max Planck Institute, Department of Evolutionary Genetics)