Crowdsourcing, for the Birds

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“As soon as the heat maps began to come out, everybody recognized this is a game changer in how we look at animal populations and their movement”

On a warm morning not long ago on the shore of a small prairie lake outside this state capital, Bob Martinka trained his spotting scope on a towering cottonwood tree heavy with blue heron nests. He counted a dozen of the tall, graceful birds and got out his smartphone, not to make a call but to type the number of birds and the species into an app that sent the information to researchers in New York.

Mr. Martinka, a retired state wildlife biologist and an avid bird-watcher, is part of the global ornithological network eBird. Several times a week he heads into the mountains to scan lakes, grasslands, even the local dump, and then reports his sightings to theCornell Lab of Ornithology, a nonprofit organization based at Cornell University.

“I see rare gulls at the dump quite frequently,” Mr. Martinka said, scanning a giant mound of bird-covered trash.

Tens of thousands of birders are now what the lab calls “biological sensors,” turning their sightings into digital data by reporting where, when and how many of which species they see. Mr. Martinka’s sighting of a dozen herons is a tiny bit of information, but such bits, gathered in the millions, provide scientists with a very big picture: perhaps the first crowdsourced, real-time view of bird populations around the world.

Birds are notoriously hard to count. While stationary sensors can measure things like carbon dioxide levels and highway traffic, it takes people to note the type and number of birds in an area. Until the advent of eBird, which began collecting daily global data in 2002, so-called one-day counts were the only method.

While counts like the Audubon Christmas Bird Count and the Breeding Bird Survey bring a lot of people together on one day to make bird observations across the country, and are scientifically valuable, they are different because they don’t provide year-round data.

And eBird’s daily view of bird movements has yielded a vast increase in data — and a revelation for scientists. The most informative product is what scientists call a heat map: a striking image of the bird sightings represented in various shades of orange according to their density, moving through space and time across black maps. Now, more than 300 species have a heat map of their own.

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via Google News and Bing News

Biology’s drive toward engineering

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Biology is on the verge of getting its versions of the lever, wheel and axle, pulley and other basic machines that enable engineers to build almost any mechanical device, a new analysis has concluded.

The viewpoint article on availability of this new toolkit — for engineering biological factories that can produce new biofuels, crops and chemicals, among others — appears in the journal ACS Synthetic Biology.

Kevin Munnelly, CEO of synthetic biology start-up Gen9, explains that people have been using basic genetic engineering for centuries to breed stronger oxen, faster horses and improved food crops. In recent years, however, there have been great leaps forward in the field of “synthetic biology.” Powered in part by advances in genome sequencing, chip-based processing and chemical innovations, that field is developing a solid engineering foundation of biological parts that can be assembled with the same precision and predictability of engineers constructing bridges or engines, and applied at the scale required for industrial manufacturing. Using synthetic biology, innovators across industries are building billion-dollar-plus markets for plants that churn out biofuels, create new textiles or yield crops that will thrive in any environment. They are also tackling data storage. For example, the entire contents of the Library of Congress could fit within a shot-glass of DNA.

In this viewpoint article, Munnelly describes the significant accomplishments that have shaped the synthetic biology landscape, as well as possible future innovations. Synthetic biology is already building its basic toolkit, with a switch and an oscillator, for instance, and scientists have stored 70 billion copies of a book in genetic material the size of a garden pea. On the horizon are drop-in genes, protein signaling pathways and other interchangeable parts for the emerging industrial biotechnology toolkit.

via American Chemical Society
 

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Boosting ‘cellular garbage disposal’ can delay the aging process

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UCLA life scientists have identified a gene previously implicated in Parkinson’s disease that can delay the onset of aging and extend the healthy life span of fruit flies. The research, they say, could have important implications for aging and disease in humans.

The gene, called parkin, serves at least two vital functions: It marks damaged proteins so that cells can discard them before they become toxic, and it is believed to play a key role in the removal of damaged mitochondria from cells.

“Aging is a major risk factor for the development and progression of many neurodegenerative diseases,” said David Walker, an associate professor of integrative biology and physiology at UCLA and senior author of the research. “We think that our findings shed light on the molecular mechanisms that connect these processes.”

In the research, published today in the early online edition of the journal Proceedings of the National Academy of Sciences, Walker and his colleagues show that parkin can modulate the aging process in fruit flies, which typically live less than two months. The researchers increased parkin levels in the cells of the flies and found that this extended their life span by more than 25 percent, compared with a control group that did not receive additional parkin.

“In the control group, the flies are all dead by Day 50,” Walker said. “In the group with parkin overexpressed, almost half of the population is still alive after 50 days. We have manipulated only one of their roughly 15,000 genes, and yet the consequences for the organism are profound.”

“Just by increasing the levels of parkin, they live substantially longer while remaining healthy, active and fertile,” said Anil Rana, a postdoctoral scholar in Walker’s laboratory and lead author of the research. “That is what we want to achieve in aging research — not only to increase their life span but to increase their health span as well.”

Treatments to increase parkin expression may delay the onset and progression of Parkinson’s disease and other age-related diseases, the biologists believe. (If parkin sounds related to Parkinson’s, it is. While the vast majority of people with the disease get it in older age, some who are born with a mutation in the parkin gene develop early-onset, Parkinson’s-like symptoms.)

“Our research may be telling us that parkin could be an important therapeutic target for neurodegenerative diseases and perhaps other diseases of aging,” Walker said. “Instead of studying the diseases of aging one by one — Parkinson’s disease, Alzheimer’s disease, cancer, stroke, cardiovascular disease, diabetes — we believe it may be possible to intervene in the aging process and delay the onset of many of these diseases. We are not there yet, and it can, of course, take many years, but that is our goal.”

‘The garbage men in our cells go on strike’

To function properly, proteins must fold correctly, and they fold in complex ways. As we age, our cells accumulate damaged or misfolded proteins. When proteins fold incorrectly, the cellular machinery can sometimes repair them. When it cannot, parkin enables cells to discard the damaged proteins, said Walker, a member of UCLA’s Molecular Biology Institute.

“If a protein is damaged beyond repair, the cell can recognize that and eliminate the protein before it becomes toxic,” he said. “Think of it like a cellular garbage disposal. Parkin helps to mark damaged proteins for disposal. It’s like parkin places a sticker on the damaged protein that says ‘Degrade Me,’ and then the cell gets rid of this protein. That process seems to decline with age. As we get older, the garbage men in our cells go on strike. Overexpressed parkin seems to tell them to get back to work.”

Rana focused on the effects of increased parkin activity at the cellular and tissue levels. Do flies with increased parkin show fewer damaged proteins at an advanced age? “The remarkable finding is yes, indeed,” Walker said.

Parkin has recently been shown to perform a similarly important function with regard to mitochondria, the tiny power generators in cells that control cell growth and tell cells when to live and die. Mitochandria become less efficient and less active as we age, and the loss of mitochondrial activity has been implicated in Alzheimer’s, Parkinson’s and other neurodegenerative diseases, as well as in the aging process, Walker said.

Parkin appears to degrade the damaged mitochondria, perhaps by marking or changing their outer membrane structure, in effect telling the cell, “This is damaged and potentially toxic. Get rid of it.”

If parkin is good, is more parkin even better?

While the researchers found that increased parkin can extend the life of fruit flies, Rana also discovered that too much parkin can have the opposite effect — it becomes toxic to the flies. When he quadrupled the normal amount of parkin, the fruit flies lived substantially longer, but when he increased the amount by a factor of 30, the flies died sooner.

“If you bombard the cell with too much parkin, it could start eliminating healthy proteins,” Rana said.

In the lower doses, however, the scientists found no adverse effects. Walker believes the fruit fly is a good model for studying aging in humans — who also have the parkin gene — because scientists know all of the fruit fly’s genes and can switch individual genes on and off.

Previous research has shown that fruit flies die sooner when you remove parkin, Walker noted.

Walker and Rana do not know what the optimal amount of parkin would be in humans.

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via University of California – Los Angeles
 

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Synthetic biology research community grows significantly

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Update to synthetic biology map identifies new activity across the globe

The number of private and public entities conducting research in synthetic biology worldwide grew significantly between 2009 and 2013, according to the latest version of an interactive map produced by the Synthetic Biology Project at the Woodrow Wilson International Center for Scholars. The map is available online at http://www.synbioproject.org/map.

Synthetic biology, an area of research focused on the design and construction of new biological parts and devices, or the re-design of existing biological systems, is an emerging field and the focus of labs and companies around the world. The map, which builds on work the project started in 2009, is populated with more than 500 companies, universities, research institutions and other entities working on synthetic biology, showing clusters of activity in California, Massachusetts, Western Europe and East Asia.

“Part of this new activity has been driven by continuing government investments in the science,” said David Rejeski, who directs the Synthetic Biology Project. “Another important factor has been the rapidly declining costs of gene sequencing, which has supported more effective approaches to engineering biological systems.”

The Synthetic Biology Project found that the number of companies conducting synthetic biology research increased three-fold since 2009. A plurality of the companies involved in synthetic biology is focusing on developing bio-based specialty chemicals, fuels and/or medicines.

Since 2009, the industry has also experienced moderate levels of consolidation and failure. Of the 61 companies included on the initial 2009 inventory, six were acquired by other companies, closed their doors or can longer be identified. An additional 11 companies that were tracked between the release of the 2009 inventory and the 2013 update were also acquired, closed or cannot be identified.

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via Woodrow Wilson International Center for Scholars/Science and Technology Innovation Program & EurekAlert
 

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How to get fossil fuels from ice cream and soap

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The advance could lead to more innovative ways of sourcing fuel from natural resources

Writing in PNAS, the researchers have shown that the emerging field of synthetic biology can be used to manipulate hydrocarbon chemicals, found in soaps and shampoos, in cells.

This development, discovered with colleagues at the University of Turku in Finland, could mean fuel for cars or household power supplies could be created from naturally-occurring fatty acids.

The researchers, led by Professor Nick Turner from The University of Manchester, used synthetic biology to hijack the naturally-existing fatty acids and direct those fatty molecules towards the production of ready-to-use fuel and household chemicals.

Hydrocarbon chemicals are everywhere in our daily lives; as fragrance in soap, thickener in shampoo and fuel in the car. Their number of carbons and whether they are acid, aldehyde, alcohol or alkane are important parameters that influence how toxic they are to biological organisms, the potential for fuel and their olfactory perception as aroma compounds.

The breakthrough allows researchers to further explore how to create renewable energy from sustainable sources, and the advance could lead to more innovative ways of sourcing fuel from natural resources.

Synthetic biology is an area of biological research and technology that combines science and engineering for the benefit of society. Significant advances have been made in this field in recent years.

Professor Turner said: “In our laboratories in Manchester we currently work with many different biocatalysts that catalyse a range of chemical reactions – the key is to match up the correct biocatalyst with the specific product you are trying to make.

“Biocatalysts recognise molecules in the way that a lock recognises a key – they have to fit perfectly together to work. Sometime we redesign the lock so that if can accept a slightly different key allowing us to make even more interesting products.

“In this example we need to make sure that the fatty acid starting materials would be a perfect match for the biocatalysts that we discovered and developed in our laboratories.

“As with many leading areas of science today, in order to make major breakthroughs it is necessary for two or more laboratories around the world to come together to solve challenging problems.”

via University of Manchester – EurekaAlert
 

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