Archive for the ‘scistarter’ tag

Hook, Line and Sinker! Marblar’s Super-Biotin Project

By August 19th, 2013 at 4:13 pm | Comment

This is one bait you should take.

Illustration of a potential application of Super-Biotin – to image tumor cells with high specificity

Illustration of a potential application of Super-Biotin – to image tumor cells with high specificity

What possibilities could you think of to use a super strong ‘molecular’ hook? That’s what the inventors of Super-Biotin are asking you. This challenge appears on Marblar, a startup that “crowdsources market applications for emerging and existing technologies” as Mr Daniel Bayley, project organizer and part of the Marblar team describes it.

To understand Super-Biotin, we have to take a few steps back and see how old fashioned biotin works as part of a scientist’s toolkit. Biotin and Streptavidin are two naturally occurring proteins that exhibit an extraordinarily strong affinity for each other. Scientists (including myself!) have been able to use this property of biotin to pick out specific molecules from complex biological mixtures.  Sort of like baiting fish in a lake. Only here you get to pick the fish you want in a lake filled with several thousand kinds.

As an example, to selectively pick out molecule X from a mixture, biotin is first linked to a ‘bait’ such as an antibody that binds selectively to X. The biotin linked bait is now thrown in to the ‘lake’ which in this case happens to be a cocktail of many thousand proteins. Once the bait binds to X, streptavidin is used as the ‘hook’ to pull the entire complex (biotin-antibody-X) out of the solution.

Structure of the ‘Hook’ – ‘Super Biotin’ – ‘Bait’ Complex

Structure of the ‘Hook’ – ‘Super Biotin’ – ‘Bait’ Complex

While this technique works quite well in a laboratory setting, an enzyme called biotinidase found in bodily fluids can chew up the link between biotin and the bait protein (antibody to X in the example above) rendering the extraction process ineffective in a clinical setting. Working around this problem, the inventors of Super-Biotin at the University of Edinburgh invented a biotinidase-resistant linker which also retained the streptavidin specificity.

To find potential ‘problems to this solution’, the inventors along with the technology transfer arm of the university, Edinburgh Research and Innovation Ltd., presented the idea to Marblar which created the Super-Biotin challenge. The challenge webpage has a wealth of information that makes it easy for anyone to get started on it.

To sweeten the deal, Marblar is offering a cash prize of US$1,000 for the winning idea. But that’s not the main goal, Mr Bayley explains. “The cash prize definitely doesn’t hurt. But it is the chance to see your idea become an actual product in the market that is the key. Our users are more interested in realizing the promise of science than the cash prize” he sasys.

Additionally, if you like these sorts of challenges, you can find a lot more to feed your grey cells on Marblar. The aim is to get lots of people thinking about a particular project, encouraging as many ideas as possible. “Just like we did for super-biotin, the technology for each challenge is broken down into an easily digestible form so anyone can understand its capabilities and pitch in with their ideas” says Mr Bayley.

Find out for yourself how this works and start ideating!

Form more on the avidin-biotin interaction and its applications you can view this YouTube video from the Weizmann Institute of Science.


Photos: Marblar Super Biotin Challenge

Arvind Suresh is a graduate student in Cell Biology and Molecular Physiology at the University of Pittsburgh. He holds a Bachelor’s degree in Biotechnology from PSG College of Technology, India. For his thesis, he has been studying the molecular mechanisms behind uterine contraction during pregnancy. He is also an information addict, gobbling up everything he can find on and off the internet. He enjoys reading, teaching, talking and writing science, and following that interest led him to SciStarter. Outside the lab and the classroom, he can be found behind the viewfinder of his camera. www.suresharvind.com

Proceed to the Perseids with NASA’s Meteor Counter

By August 10th, 2013 at 9:31 am | Comment

meteor

The first time I ever saw the Perseids, I was 15 years old.

I snuck out of the house in the middle of the night (without telling my parents, of course) and found the darkest spot at the park nearby. What followed was one of the most awesome sights I had witnessed up until then: hundreds of staggered streaks of light, tearing through an ink-black sky. Part of me knew it was strict science. Another part of me was convinced it was magic. Who knew that a phenomenon that happens every day could resonate so profoundly?

Every day, on average, more than 40 tons of meteoroids strike our planet.  Most are tiny specks of dust that disintegrate harmlessly high up in Earth’s atmosphere, producing a slow drizzle of “shooting stars” in the night sky. Meteors (what they’re called before they enter our atmosphere) are made of cosmic material–silicate rock, iron, and metals–left over from the early formation of our solar system.

Where do the Perseids come from?

As the Earth rotates around the sun this weekend, it will pass through the debris field of the comet Swift-Tuttle, a dirty snowball of remnants that never became planets nor stars. The comet takes about 133.2 years to orbit the sun. As it moves, a tail of gas, ice and dust is left behind it.

Each year, from mid-July to early August, the cosmic debris in this comet’s tail culminate in an evening spectacular called the Perseids.

When and How to View

This year, the meteor shower peaks late Sunday (8/11)  into early Monday (8/12) just before dawn.

Find a dark field away from any light pollution. Look for the constellation Perseus, where the Perseids derive their name. It should be observable in the northeastern sky. During a Perseid meteor shower, you can expect to observe up to 100 meteoroids in an hour.

perseid_map2

What to Bring

What’s nice about the Perseids is you don’t need any special viewing equipment. The naked eye is adequate. Grab a blanket and/or lawn chair, a cup of warm liquid, some snacks, and sit back to wait for the forthcoming light show.

NASA has a Meteor Counter app that iPhone users can download. Viewers of the Perseids can help report how many they see within a particular time frame. The app’s “piano key” interface allows you to tap keys as you view meteoroids. It records critical data for each meteor: time, magnitude, latitude, and longitude, along with optional verbal annotations. Afterward, these data are automatically uploaded to NASA researchers for analysis.

While you’re out there, you might as well turn an otherwise passive (albeit amazing) viewing experience into a participatory one in the name of citizen science.

SciStarter wishes you a happy viewing for this year’s Perseids. If it doesn’t make you feel too cheesy, make a wish when you see your first meteoroid. I know the fifteen year old in me won’t forget to.

If you live in Alabama, you can participate in the Alabama Meteor Tracking Project.


Sources:

Photos: NASA.gov

Lily Bui holds dual (non-science) bachelors’ degrees in International Studies and Spanish from the University of California Irvine. She has worked on Capitol Hill in Washington, D.C.; served in AmeriCorps in Montgomery County, Maryland; worked for a New York Times bestselling ghostwriter; and performed across the U.S. as a touring musician. She currently works in public media at WGBH-TV and the Public Radio Exchange (PRX) in Boston, MA. In her spare time, she thinks of cheesy science puns. Follow @dangerbui. 

 

 

Shark Week: A Feeding Frenzy for Citizen Scientists

By August 5th, 2013 at 1:02 pm | Comment

That’s right–it’s the moment you’ve all been waiting for. It’s Shark Week, and SciStarter has a slew of projects for you to try out. Let’s see if you bite. Whether it’s fascination or fear, the sight of a shark makes our hearts skip a beat. Thanks to these featured citizen science projects, that sight can also contribute to shark conservation!

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Shark Count

Increasing protection for sharks requires information about local populations. Provide data about sharks you see while diving or snorkeling.

Get started!

 

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Sevengill Shark Sightings

The Shark Observation Network invites Southern California divers to report and submit sightings of Sevengill Sharks, a species whose numbers are seemingly on the rise in the waters off San Diego.

Get started!

 

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The Great Eggcase Hunt from Shark Trust

Hunt for empty eggcases that have been washed ashore to help researchers locate potential shark and ray nurseries. This generates important data for researchers and conservationists working with sharks, skates and rays around the world.

Get started!

 

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New England Basking Shark Project

The New England Coastal Wildlife Alliance invites boaters, fishermen, and divers to report and share sightings of basking sharks to help scientists monitor the local population and better understand their migration patterns.

Get started!

 

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ECOCEAN Whale Shark Photo-identification

Upload your own shark photos or identify sharks in existing photos using this visual database of whale sharks!

Get started!

 


Want even more? Subscribe to SciStarter’s newsletter! 

This digest of SciStarter Weekly Featured Projects was curated by Jenna Lang. If you’d like to see your project featured in our digest, e-mail jenna@scistarter.com

More Gills or Eyes? The Purported Increase of Sevengill Shark Populations off the Coast of San Diego

By August 4th, 2013 at 9:44 am | Comment

Shaw2520Sevengill

Emerging technologies have a profound effect on how citizen scientists conduct their work. An underwater creature of ancient lineage helps to tell this modern story of technology’s importance to citizen science. Notorynchus cepedianus, the sevengill shark, of the ancient Hexanchidae family (cow sharks), features seven gill slits and a single dorsal fin, giving a prehistoric visage to this predator. Despite its uncanny appearance, this shark is one that has demonstrated little aggression toward humans, with fewer than five wild attacks accounted for since the 16th century.

In fact, divers have been increasingly encountering these creatures off the coast of San Diego. Harmless as these encounters are, they are spectacular and haunting, as Michael Bear, founder of the Sevengill Shark Tracking Project, would tell you. In the summer of 2009 he experienced the sevengill himself, after hearing rumors of its increased presence in the San Diego coastal area, when a giant seven-foot long (2.1 meters) sevengill glided between him and a dive-buddy. Describing that moment, Bear says that, “it is a humbling experience being in the presence of one of these large, apex predators­­––they have a grace and a majesty about them that is unforgettable.” But are these encounters an indicator of increasing sevengill populations or a product of increased numbers of divers––or perhaps divers with attentive eyes?

For many years few sightings were reported, but more anecdotal reports began to trickle in, and, Bear tells us, the “period that we really began hearing a significant increase in reports was 2009-2010.” Bear wanted to know more (and for good reason). The sevengill is a high-order or apex marine predator and therefore may be important to ecological structure, interactions, and ecosystem management (Williams et al., 2011 and 2012). In 2010 Bear’s project began to take shape.

The Sevengill Shark Tracking Project is a citizen science effort to collect baseline population data on the sevengill. Though it started out small, the project has grown, partnering with the Shark Observation Network. Now a single global database aggregates data on sightings to help determine baseline population information. Though a study of this kind can take many years, Bear’s project already has important insights for citizen science projects, especially in the use of new technologies.

Bear has developed the Sevengill Shark Tracking project’s smartphone app, called “Shark Observers.” It’s available for Android devices and allows divers to log sightings once they’ve surfaced and, presumably, dried off. While this particularly benefits sevengill tracking, the application actually allows users to submit logs for any kind of shark encounter to the Shark Observation Network database. This application can be downloaded through Google Play.

In addition to the app and database cataloguing the date, time, water temperature, and sightings––with separate databases for photographic and video recordings—the project has also started to use pattern recognition technology to identify individual sharks. This is an inexpensive alternative to costly and labor-intensive shark tagging.

With the I3S pattern recognition algorithm, which is also used for mapping star patterns on Whale Sharks, the sevengill project uses collected high definition photos to track individual sharks by their “freckling” pattern. Using the algorithm, Bear is able to identify the unique patterning on individual sevengill sharks. Eight individuals have been identified and tracked using this method, allowing Bear and other researchers to track the return of these sharks each year. What is crucial for this approach, Bear tells us, “is to have high resolution photographs where the freckling pattern is visible.” While crucial, this technological demand is not a significant barrier for most of the diver-citizen scientists, says Bear, since “most divers these days are using hi def cameras anyway.”

Since the motivation for Bear’s project was to determine baseline populations, knowing more about the number of sharks that are present and returning to the area becomes crucial. Tracking individuals helps to sort out the matter of whether the population of sharks or the population of divers (and therefore reported sightings) is increasing. Securing more data is essential to draw reasonable conclusions about these populations and so the Sevengill Shark Sightings project continues to collect sightings, including those with video and photographic data, submitted by divers in the San Diego area. Specifically, Bear’s project is interested in the population data over a 5- to 10-year period, asking whether the population density appears to stay relatively static or if there are notable changes.

In addition to these research interests, science education is built into this citizen science model. Bear hopes to train local divers in identification techniques for the sevengill shark. The Sevengill Shark Sighting project provides an interesting example of how technology can help citizen scientist organize anecdotal data into important scientific datasets.

Ashley Rose Kelly is a Ph.D. candidate in the Communication, Rhetoric, & Digital Media program at North Carolina State University. Ashley studies how emerging technologies may be changing science communication. She also teaches scientific and technical writing courses as well as an introductory course on science, technology, and society. You can find Ashley on Twitter as: @ashleyrkelly
Notes:

(1) Michael Bear is Science Diving Editor for California Diver Magazine and Contributor to Marine Science Today. He lives and works in San Diego, California.

References

Williams, GD, Andrews, KS, Farrer, DA, Bargmann, GG, and Levin, PS. (2011). Occurrence and biological characteristics of broadnose sevengill sharks (Notorynchus cepedianus) in Pacific Northwest coastal estuaries. Environmental Biology of Fishes 91: 379–388. doi: 10.1007/s10641-011-9797-z.

Williams GD, Andrews KS, Katz SL, Moser ML, Tolimieri N, Farrer DA, Levin PS. (2012).
Scale and pattern of broadnose sevengill shark Notorynchus cepedianus movement in
estuarine embayments. Journal of Fish Biology 80(5): 1380–1400. doi:
10.1111/j.1095-8649.2011.03179.x

Photo: Michael Bear; photo credit Kelli Shaw, 2011.