Archive for the ‘Chemistry’ Category

Spec-tacular Science: Use Public Lab’s DIY Spectrometer to find out what stuff is made of!

By February 19th, 2014 at 12:01 pm | Comment

PublicLab Spectrometer Project. Images: publiclab.org

Public Lab’s DIY spectrometry kit makes it possible for citizen scientists to do their own spectrometric analysis at home.

Come to your senses! SciStarter has curated a list of citizen science projects for all five senses.

 

Spectrometry. Listen to yourself say it out loud. Admit it. It sounds cool just to say “spectrometry.”(Whoa you just did it again!) As fans of Star Trek or Star Wars will attest to, spectrometers are must-have instruments in the scientific arsenal. I’m happy to let you know, however, that the use of a spectrometer (a.k.a ‘spec’) is not limited to fictional, futuristic worlds. In fact, from discovering new chemical elements to measuring DNA, spectrometry is a technique that’s dipped its toes in almost every field of research.

What’s all the fuss about a spectrometer? 

Before I talk to you about a spectrometer, let me get into a little bit about the properties of light. You might know that objects appear a certain color because they absorb certain wavelengths of light while reflecting others. For example, leaves appear green because they absorb other colors except green. So if you took some leaf extract in a glass tube and passed light through it on one side, the light that comes out of the other side will have lots of green and little of the other colors (because they were absorbed by the leaf extract).

Put on your scientist hat (or a lab coat) and think about that for a moment. You’ll probably say, “Hey! If I can figure out what specific mix of colors a known substance is made of then I can use that to find out what an unknown substance is made of!” And put simply, that’s what a spec does. It’s an instrument that uses light to determine what a substance is made of.

Emission_spectrum-Fe

Spectrum produced by iron

A spec identifies the specific mix of colors that is absorbed by a sample producing what is known as an ‘absorption spectra‘ which is characteristic of that sample. Think of it like a fingerprint for every material. To do this accurately, the spec needs something that can effectively split light into its constituent colors. One option is to use a prism, which you’ve probably seen at some point. Another way is to use a ‘diffraction grating’ which is a surface with many small parallel lines that can also do the same job of splitting light.

DVD as a diffraction grating

DVD as a diffraction grating for a spectrometer

One cool everyday object that acts as a diffraction grating is a CD or DVD. The tiny grooves on the disc act like a grating and split white light giving off the rainbow of colors that you see on its back side. The Public Lab DIY spec uses a DVD as a diffraction grating. The image below describes how a simple DIY spec works. And that’s the Cliffs Notes version. Public Lab’s spectrometer curriculum has lots more detail!

The Public Lab DIY Spectrometer

Our friends over at Public Lab have made it possible for you to do your own spectrometric analysis at home! When it started, the goal of the project was to create a cheap, do-it-yourself spectrometer that anybody could use to analyze materials and contaminants like oil spills and tar residues in urban waterways. In 2012, the team came up with an idea for a spec and crowd-funded it on Kickstarter.  The Kickstarter project was a massive success and now Public Lab is selling the DIY desktop kit for $40 in its online store. However, if you prefer to build it from the materials you have at home, they have a great instruction manual for how to make it yourself.

They have also made a smartphone compatible Foldable Mini Spectrometer ($10 in the store) that you can carry around (and show off!). To be able to actually use the spec, the team at PublicLab built an open source software called Spectral Workbench that runs within your browser to help you record and analyze the data you collect. Whether you buy the kit or build it yourself, the Public Lab community has a wiki style page that is a great information resource.

To make it easier to get started, I’ve put together a plan to get you started with making and using your shiny new instrument:

Getting Started

1. What would you like to do with your spec? Check out this page of spectrometry activities. You can also look up this really cool (and really big!) Kickstarter backers-suggested list of ideas. For fun experiments you can test things like coffee, wine or beer! On a more serious note, you can read about detecting pesticides in fruits. At the end I would suggest you make a list of 2-3 experiments you want to try (if it’s your first time experimenting with a spec, start with an easy one!)

2. Buy the kit or make one yourself. Here’s the list of materials you will need (from the Public Lab website) and here are the instructions.

  • stiff black card paper
  • a clean DVD-R
  • a USB webcam (preferably HD)
  • a Type LB conduit body (basically a light-proof box with a couple holes)
  • double-sided foam tape and a box cutter/x-acto knife

3. Ready with your spec? Now read up about how to use Spectral Workbench, the software that PublicLab has built to help you capture and analyze your data. You can also watch the introductory video. Spectral workbench also has an open source database of spectra for different materials that you can compare yours to.

4. Connect your spec and fire up Spectral Workbench. Make sure to calibrate your spec using a fluorescent light bulb. This will ensure that your readings are accurate and can be compared between samples.

5. Based on your project, find out how you can prepare your samples for testing.

6. Get some science done! Document your research and share it with the PublicLab community (you will need to sign up to post your research notes). Get input from your fellow citizen scientists to answer questions you might have or improve your experiment.

7. (Optional but definitely recommended!) If Scistarter helped you get started, tell us how it worked out. Give us a shout out on Twitter or Facebook! If you haven’t already, sign up to learn about cool projects in the future.

 

Images: PublicLab.org, Wikipedia


Arvind Sureh graduated with his MS in Cell Biology and Molecular Physiology from the University of Pittsburgh. He holds a Bachelor’s degree in Biotechnology from PSG College of Technology, India. 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. Connect with him on Twitter, LinkedIn or at his Website.

Liberty and Science for All: Project MERCCURI press release

By January 31st, 2014 at 8:52 am | Comment

Darlene Cavalier, founder of SciStarter, swabs the Liberty Bell for microbes in Philadelphia.

Darlene Cavalier, founder of SciStarter, swabs the Liberty Bell for microbes in Philadelphia.

Thanks to the Independence National Historical Park for giving me access to the Liberty Bell. I had a lot of fun collecting microbes from this national treasure in my hometown!

Happy to announce that the microbes from the Liberty Bell have been selected to fly on the International Space Station where their growth rates will be analyzed and compared to their counterparts back at the UC Davis lab! We will be announcing each selected microbe over the course of the next two weeks, with Philly first.

This research is part of Project MERCCURI, a citizen science project from UC Davis, Science Cheerleader and SciStarter, to examine the diversity of microbes on Earth and on the International Space Station.

Check out this particular microbe’s very own trading card! Here’s an excerpt:

Where we found it: On the Liberty Bell (Philadelphia, PA)

Why it’s awesome: This is an important industrial organism, used for the production of penicillin, vitamins, various drugs, and numerous enzymes

Fun fact: The species name of this microbe means “big beast” and it is among the largest bacteria ever discovered

In addition to the microbes from the Liberty Bell, six other microbes from Philadelphia were selected by UC Davis researchers to blast into space for research at the International Space Station. Here are links to images and more information about the microbes collected from the following sites in Philadelphia and selected to fly on the International Space Station:

Chemical Heritage Foundation
Philadelphia Phillies
Philadelphia 76ers
The Franklin Institute
The Academy of Natural Sciences (microbes collected by St. Peter’s School students)
St. Joseph’s Preparatory School
WHYY studio

A total of 48 samples were selected from across the country.

Here’s more information about this project:

Davis, CA. (Jan. 30, 2014) — Microbes collected from Philadelphia landmarks will soon blast into orbit for research and a microgravity growth competition on the International Space Station (ISS). This citizen science project, known as Project MERCCURI, investigates how microbes from different places on Earth compare to each other and to those found on the International Space Station.

Led by the Science Cheerleaders (current and former NFL and NBA cheerleaders pursuing science and technology careers), thousands of people across the United States participated in the project. Several Pop Warner cheer teams swabbed practice fields, shoes, and cell phones for microbes. Other people collected microbial samples at NFL, NBA, and MLB stadiums; from schools; from landmarks like the Liberty Bell, Sue the T-Rex, the statue of Ben Franklin in Philadelphia, and the Smithsonian Air and Space Museum; and during events including Yuri’s Nights, a series of gatherings across the country to commemorate the first human in space.

The microbes they gathered were examined by the “microbiology team” in the laboratory of Dr. Jonathan Eisen at the University of California at Davis. The team selected 48 microbes (SEVEN of which are from Philadelphia!), which, with approval from NASA, are to ride the SpaceX Falcon 9 to the Space Station for further research. The rocket is scheduled to launch from the Kennedy Space Center in early March.

The public will be able to follow Project MERCCURI as it continues over the next several months via the web site SpaceMicrobes.org. The site will include updates from the research on the Space Station including results of the “microbial playoffs” growth competition. The site also features free interactive visualization tools, lesson plans for teachers, and even trading cards that include photos and the details of each microbe selected for the project, as well as their importance.

In addition to the research in space, thousands of additional samples collected by the public are being analyzed further at UC Davis and by the lab of Dr. Jack Gilbert at Argonne National Laboratory. The microbes found in these samples are being assayed using DNA sequencing technology, and the resulting data will be made available to the public and also integrated with results of the Earth Microbiome Project. Scientists hope to gain insights into what is living at the ISS, how microbes vary between different places on Earth and in space, and to compare growth of microbes on Earth and in microgravity. Philadelphia 76ers fans will have the opportunity to participate in this part of the research during Science at the Sixers night on 2/18 when the 76ers host the Cleveland Cavaliers.

“We are in the midst of a revolution in our ability to study the hidden world of microbes found throughout the planet,” said Jonathan Eisen, Professor at UC Davis and leader of the microBEnet (microbiology of the built environment network) team doing the microbiology side of Project MERCCURI. “One area of growing interest is in studying the microbes living right around us – in our buildings – on our phones – and elsewhere. The Science Cheerleader group has allowed us to get thousands of people to not only think more about the microbes among us, but to also participate in a microbial diversity research project. And those people have helped us get more samples than we have been able to obtain previously.”

“A lot of people ask us *why* we’re sending microbes into space,” said Dr. David Coil, a microbiologist at UC Davis. “Understanding how microbes behave in microgravity is critically important for planning long-term manned spaceflight but also has the possibility of giving us new insight into how these microbes behave in built environments on Earth.”

“This initiative is not just about significant research,” said Darlene Cavalier, a former 76ers cheerleader and Founder of Science Cheerleader and SciStarter, both based in Philadelphia. “It’s about engaging the public in that research. Microbes that were collected at Georgia Tech are taking a ride on the International Space Station. They’re the subject of research by microbiologists and astronauts. We hope that inspires youngsters as well as adults to become more aware of and involved in science.”

Project MERCCURI is coordinated by Science Cheerleader, SciStarter.com, and UC Davis, in conjunction with the Argonne National Laboratory. The Project is made possible by Space Florida, NanoRacks, and the Alfred P. Sloan Foundation.

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Note to editors: To arrange interviews with the research team at UC Davis, members of the Science Cheerleader or SciStarter teams, or with local groups that participated in collecting the microbes, please email Claire LaBeaux, claire@prclaire.com.

Image: Courtey of Darlene Cavalier

This post originally appeared on the Science Cheerleader blog.

Just Add Water: Why Water Monitoring is Important

By September 18th, 2013 at 12:56 pm | Comment

Today is World Water Monitoring Day! Participate by ordering a test kit and submitting sample data through December of this year. Also, check out the ocean of other water citizen science projects on SciStarter.

IMG-20130918-WA0001_1

Here at SciStarter, we spend a lot of time supporting citizen science, but we also happen to be citizen scientists ourselves. In the spirit of World Water Monitoring Day, I trekked to the Charles River in Boston to grab a water sample. Barring all potential parking and trespassing violations, it was a success! Still, you might wonder, why does this sample matter? Why care about water?

I’m glad you asked. But before I dive deeper (pun intended), here are some facts to consider. An adult human is made of ~60% water. About 70% of Earth is covered by water. We need water for our metabolic processes internally and for our day-to-day tasks externally. Water is there when you shower, brush your teeth, or guzzle down a drink after a run. Water is also essential for the productivity of farms, which, in turn, provide us food. You get the picture: we need water. Likewise, so do other animals and plants, especially those that live in or near aquatic environments.

Consequently, the sample data collected and submitted by millions of people on World Water Monitoring Day not only benefit us human beings. It also helps scientists better understand a multitude of aquatic environments around the globe.

Participating couldn’t be easier. World Water Monitoring Challenge, an education and outreach program, provides kits that you can purchase and use to sample the water in your area. Here are the main concepts behind what you can test and why it’s important to do so.

Turbidity, the measure of relative water clarity. This is important when producing drinking water for human consumption and for many manufacturing uses. Turbid water may be the result of soil erosion, urban runoff, algal blooms, and bottom sediment disturbances caused by boat traffic and bottom-feeding fish. (You can even make your own secchi disk to measure turbidity.)

pHa measurement of the acidic or basic quality of water. Most aquatic animals are adapted to a specific range of pH level and could die, stop reproducing, or move away if the pH of the water varies beyond their range. Low pH levels can also allow toxic compounds to be exposed to aquatic plants and animals. pH can be affected by atmospheric deposition (acid rain), wastewater discharge, drainage from mines, or the type of rock in the surrounding area.

20130918_105910_1

World Water Monitoring Challenge test kit

Dissolved oxygen levels. Natural water with consistently high dissolved oxygen levels is most likely to sustain stable and healthy environments. Changes to aquatic environments can affect the availability of oxygen in the water. High levels of bacteria or large amounts of rotting plants can cause the oxygen saturation to decrease, which affects the ability of plants and animals to survive in and around it.

Water temperatureIf temperatures are outside an organism’s normal range, the organism could become stressed or potentially die. Temperature also affects the rate of photosynthesis in aquatic plants as well as their sensitivity to toxic wastes, parasites, and disease. Furthermore, water temperature can affect the amount of oxygen water can hold (cold water holds more oxygen than warm water).

This project is ideal for anyone who lives near a water source, educators who want ideas to teach students about water chemistry, or citizen scientists hoping to contribute to an increasingly important field of research.

It’s the perfect project to illustrate that when it comes to citizen science, you can dive right in.

References:

How Much Water is There On, In, and Above Earth?” USGS. Web. 9/18/13

Importance of Turbidity.” Environmental Protection Agency. 9/18/13

The Water in You.” USGS. Web. 9/18/13

World Water Monitoring Challenge booklet

World Water Monitoring Day.” Wikipedia. Wikimedia Foundation, Inc. Web. 9/18/13

Images: Lily Bui


Lily Bui is the executive editor of SciStarter. She holds dual 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.

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

From Screensavers to Saving the World Through Citizen Science: World Community Grid

By June 20th, 2012 at 10:10 am | Comment

wcgimage1

Idleness never looked more productive. Here’s a citizen science project that quite literally requires zero energy from you in order to participate!

The World Community Grid is a global project that harnesses energy from idle computers to contribute to scientific research. When your computer goes idle, instead of changing to a screensaver featuring swimming fish, slideshows of your favorite animals, or free-floating geometric designs, your computer can request data for a specific project on the World Community Grid server. The Grid uses technology developed by UC Berkeley (BOINC) in order to collect and pool valuable research data. Each computation provides scientists with critical information that accelerates the pace of research.

Grid computing” technology joins together remote individual computers, creating a large system with massive computational power that surpasses that of many supercomputers. Because the work is split into small pieces, research time is reduced from years to months. Not only is this more time efficient, but it’s also more cost effective.

One of their first projects, Human Proteome Folding, identified the proteins produced by human genes. With this information, scientists discovered how defects in proteins can cause disease, making it easier to find cures. In 2003, with grid computing, in less than three months, scientists identified 44 potential treatments to fight the deadly smallpox disease. Without the grid, the work would have taken more than one year to complete. Current projects include Computing for Sustainable Water, GO Fight Against Malaria, and Discovering Dengue Drugs Together.

Donate your idle computer time to a greater good in scientific research by registering for the World Community Grid and downloading their free and secure software to get started!

From screensavers to saving the world through scientific research. Get started now!

Categories: Chemistry