Archive for the ‘Biology’ Category
What happens when you combine professional cheerleaders, microbiologists, and astronauts? The answer is Project MERCCURI and the Microbial Playoffs… in SPAAACE!
SPACE FLORIDA, FL — Today, something amazing is headed toward the ISS—microbial life from earth!This moment is the culmination of a citizen science experiment called Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on the ISS), a collaboration between NASA, UC Davis, SciStarter, and Science Cheerleaders.
Watch the launch LIVE today at 4:58pm ET / 1:58 PT on NASA TV!!
There were two main goals for the project. The first involves a huge competition that will take place on the ISS between 47 different microbes that have been collected by thousands of public participants from the surfaces of various public spaces (mostly sporting venues). The microbial competitors will face off against each other to see who will grow the fastest, and the race will be monitored by astronauts on the ISS, using standard laboratory equipment. Researchers at UC Davis will host an identical race using the same kind of equipment on Earth.
The second goal involves sending 4,000 cell samples to Argonne National Lab to be sequenced by Jack Gilbert. The lab will identify which microbes are present on the surfaces of cell phones and shoes and compare them to other cell phone and shoe samples from around the country. While astronauts do not carry cell phones or wear shoes, they will be swabbing similar surfaces onboard the ISS, like foot holds that they strap their feet into while they are operating the external robotic arms and their wall-mounted communication devices.
You can get to know all of the microbial competitors, who they are, where they’re from, and why they are so cool on the official website. If you want, you can even print your own Microbial Trading Cards. Cell phone and shoe collections will continue through April!
The microbes are sailing into space today aboard Space X’s Dragon spacecraft. SciStarter’s founder, Darlene Cavalier, is on site today at the launch. She notes, “We’re here, in part, as representatives of the thousands of citizen scientists who participated in this important research project to study microbes on Earth and in space!”
— Liz Heinecke (@KitchPantrySci) April 14, 2014
— Phil Plait (@BadAstronomer) April 14, 2014
Thank you to all who made this project possible. It’s pure proof that the sky is the limit for what we can do in science, together.
For more, follow #SpaceMicrobes on Twitter.
Image: Darlene Cavalier
This week on The Pulse and SciStarter’s segment about citizen science, producer Kimberly Haas highlights some spring projects that you can get involved in this season.
Spring is in the air, and so it citizen science! As SciStarter founder Darlene Cavalier told WHYY, ”Springtime is the time for citizen science [...] So you can find, in our project finder, everything from collecting information about precipitation to checking out bird nests and looking for incubating eggs.”
Listen to a teaser of the piece below, then read WHYY’s related blog post to learn more about the variety of projects you can get involved in. You’ll find the full audio there.
Here’s where you can help. If you’re a citizen science researcher, project manager, or participant in the PA, NJ, or DE areas, we want to hear from you! If you have an interesting story to share about a citizen science project or experience, let us know. Send your stories for consideration to Lily@SciStarter.com.
WHYY (90.9 FM in Philly) Friday on-air schedule:
6-9 a.m. – Morning Edition
9-10 a.m. – The Pulse
10 a.m. to 12 p.m. – Radio Times
10 a.m. following Sunday – The Pulse (rebroadcast)
The equinox is upon us. Budding trees and baby birds will soon greet us. As the weather gets warmer, be ready to Spring into action with these five springtime citizen science projects!
Help scientists understand the impacts of global climate change! Report data on the timing of leafing, flowering, and fruiting of plants in your area. To participate, you simply need access to a plant. Get started!
Camel Cricket Census
The Your Wild Life team needs citizen scientists to share observations and photos of camel crickets in your home! Many keen citizen observers have reported a preponderance of camel crickets, and interesting patterns in cricket distribution have emerged! Get started!
Where’s the Elderberry Longhorn Beetle?
This beautiful beetle species lived throughout eastern North America but in recent decades it’s all but disappeared. To help solve this mystery, a Drexel University researcher wants you to be on the lookout for this beauty of a beetle now through June. Get started!
CoCoRaHS:Rain, Hail, Snow Network
When a rain, hail, or snow storm occurs, take measurements of precipitation from your location.Your data will be used by the National Weather Service, meteorologists, the U.S. Department of Agriculture, mosquito control, ranchers and farmers, and more! Get started!
Help scientists understand how environmental change and habitat destruction affect breeding birds. Visit nests once or twice each week and monitor their progression from incubating eggs to fuzzy chicks to fully feathered adults. Get started!
See how WCVE’s Science Matter’s is also jumping for citizen science this spring with FrogWatchUSA!
Want to bring citizen science into the classroom? Check out our Educators Page to learn more about how to integrate projects into your curriculum.
SciStarter and Azavea (with support from Sloan Foundation) spent the last year investigating developments in software, hardware, and data processing capability for citizen science. Here’s what we found.
Calling hackers and developers! SciStarter is organizing pop-up hackathons to develop open APIs and other tools to help citizen scientists. Contact the SciStarter Team if you’d like to join us in Boston, Philly, NYC, or Washington, DC in April! Email firstname.lastname@example.org.
Want your project featured in our newsletter? Contact email@example.com
Citizen scientists can help ID the progression of bacterial infection in plant cells by determining how “clumpy” plant cell images are.
The language on the Clumpy homepage might be considered a challenge for the average citizen scientist: “The model plant-pathogen system comprising the plant Arabidopsis thaliana and the pathogenic bacterium Pseudomonas syringae has been used very effectively to elucidate the nature of the pathogenic interaction.” However, once you get started on this citizen science project, you will soon get a feel for it, and perhaps even enjoy it as I did.
Clumpy is a citizen science project that tests for a bacterial infection in plants. When microbiologists found that organelles in the plant’s photosynthetic cells (i.e. chloroplasts) tended to “clump” together when subjected to bacterial infection, they saw opportunity for a citizen science experiment whereby the public could assist with help in classifying images for ‘clumpiness.’
The Clumpy project came out of observations made by Dr. Littlejohn, a postdoctoral researcher in the Bioscience Department at the University of Exeter; Dr. Murray Grant, a Professor of Plant Molecular Biology; and Dr. John Love, Associate Professor in Plant and Industrial Biotechnology at the University of Exeter. They noticed this unusual phenomenon, which might have important implications for how they understand plant-pathogen interactions. “It was through a conversation with Professor Richard Everson at an Exeter Imaging Network meeting, that the multidisciplinary team got together to set up the online experiment,” said Littlejohn.
The idea to use citizen science to annotate bacterial infections in plants came about in part due to the difficulty in using computational methods alone. Trying to characterize images using abstract notions such as ‘clumpiness’ is an area where humans can easily outperform current computational approaches. In addition, annotation of the images doesn’t require any special expertise, so the problem seemed like an ideal match for citizen science. “We also thought the images themselves were intrinsically interesting, which would help motivate people to provide a wide range of annotations,” said Hugo Hutt, a PhD student in the Department of Physics at the University of Exeter.
Dr. Littlejohn commented, “It would be great to know if it were the plant or the bacterium that initiates the ‘clumping’ of chloroplasts in the leaves. This might help us understand why the chloroplasts clump and which partner in the pathosystem is benefiting from it.” What does this do for society, you might ask? The benefit of a study like this might include fighting diseases in food crops for one.
Verifying the Data
When I first started to use the Clumpy website to classify whether an image was clumpy or not clumpy, I kept second guessing myself, and moved through the selections very deliberately, mulling each one over carefully. They all looked too similar, which got me to thinking about verification of the data. Since all science depends on accurate data, how do they know whether or not answers provided by the average Joe are accurate or not?
Hutt was involved with this aspect of Clumpy—the verification of data:
In 2013 we published an article in Computational Intelligence about this. We tested statistical methods to evaluate the accuracy and reliability of users. For example, to evaluate the accuracy we compared the user annotations with those assigned by an expert. We also measured the degree of consensus among users based on how correlated their annotations were.
The results showed a surprising level of accuracy, which my purely objective test might support—after about 15 attempts I began to recognize ‘clumpiness’ more intuitively, and after just 30 I felt I had it nailed. Hutt and colleagues hope to publish an extended version of the paper this year in a special issue of Soft Computing.
With respect to obtaining a consensus score people were asked to make annotations in one of three paradigms: classification, scoring and ranking. Termed “a web-based citizen science experiment,” Clumpy tasks are evaluated in relation to the accuracy and agreement among the participants using both simulated and real-world data from the experiment. The results show a clear difference in performance between the three tasks, with the ranking task obtaining the highest accuracy and agreement among the participants. That means people like me were capable of producing accurate results when we checked in to Clumpy!
Until now the results have been used to publish more on the computer-collection side, than on the plant biology side, but Littlejohn said, “We are looking to fit this result in with a broader biological study.”
The project has been running since August 2012 and currently houses over 10,000 annotated images. Imagine the cost, time and resources allocated to this process, if citizen scientists had not been involved!
Images: Courtesy of clumpy.ex.ac.uk
Ian Vorster has a MS in Environmental Communications and most recently served as director of communications at the Woods Hole Research Center in Massachusetts. Prior to that he worked in the health communications field. Ian has served as a designer, writer, photographer, editor and project leader in the field of science, and now works freelance in a blend of these roles. You can see more of Ian’s work at www.dragonflyec.com.
Participate in American Gut to find out what bacteria live in your body and help scientists gather data on the diversity of microorganisms that affect our health.
Bacteria usually get a pretty bad rap. Perpetrators of strep throat, food poisoning, hospital infections, the list goes on. But not all bacteria are insidious in their intentions–in fact, many are harmless and even friendly, including the trillions that tag along in and on our bodies on a daily basis. In return for providing these microorganisms with a comfortable and long-lasting residence, they perform a number of chores for us and proactively help maintain our health.
Notably, they extract energy out of the food we eat, aid in the development of our immune system, and fend off intruding pathogens. Bacteria live in multiple areas on the human body, but bacteria in the gut have received the bulk of scientists’ attention so far. And not without good reason–these bugs amount to a whole kilogram in an average individual’s gastrointestinal tract, meaning that on a yearly basis a human adult will excrete their own weight in fecal bacteria. Recent work has shown that bacteria in the gut environment play a causative role in weight gain, obesity, and malnutrition, and that sustained changes in diet can have substantial effects on the composition of these bacterial populations. So not only do the bugs in our gut affect our health and well-being, but our diet and lifestyle modulate what bacteria live there, giving the phrase “you are what you eat” a whole new meaning.
Thus far, most scientific studies on gut-residing bacteria have focused on specific cohorts of carefully selected individuals. As a result, these studies reflect our diversity “to about the same extent that Congress does,” as a team of researchers at the University of Colorado, Boulder puts it. This team, led by microbial ecologists Rob Knight and Jeff Leach, wants to remedy current limitations by obtaining a larger set of bacterial data from a much more diverse population- basically people like you and me, or even literally you and me.
In a citizen science project called American Gut, Knight, Leach, and collaborators offer anyone living in the U.S. the opportunity to submit a biosample (from your skin, mouth, or fecal matter), and for a $99 donation they will process and analyze your sample and give you a detailed description of the microorganisms on your body, in your mouth, or in your gut (depending on the source of your sample). Additionally, the analysis offers you a relative comparison of your bacterial community to the thousands of other people who have participated in the project.
So what’s happening with all the data that’s being collected? American Gut asks participants to take a lifestyle survey and a detailed week-long dietary inventory to accompany their biosample. American Gut researchers and collaborators seek to associate different factors like smoking, veganism, or gluten intolerance to different microbial communities. ”We’re interested in whether we can pick up diet, geographical or seasonal associations. There are also some more specific projects being run through American Gut on inflammatory bowel disease, autism, and several other diseases” said Knight. Overall, scientists studying the human microbiome (or the collective genome of host-associated bacteria) want to know which of these factors make a difference in shaping our microbial populations and what that means for our health. By crowd-sourcing data from all walks of life, American Gut is amassing what’s arguably the largest and most diverse set of information on host-associated communities to start discerning this information. “It will substantially expand our knowledge of the kinds of microbiomes that are out there, will give us a better understanding of what matters and what doesn’t (in terms of factors and controls), and will perhaps allow us to start seeing similarities among different disease states (depending on how many people who are willing to share de-identified medical information sign up).”
Using a citizen science approach offers the benefit of having a large pool of data to work with, but there are some downsides. “The main challenge is cleaning up errors in the data, for example, we don’t really think we have participants who were born in 1060 or in the future (and we don’t know how they managed to bypass the web form validation either),” said Knight. In line with its citizen science goals, Knight and Leach have prioritized making the project open source and open access. The data, in the form of sequences of bacterial DNA (with no personal information), will be publically available for anyone to obtain and analyze. Most academic labs don’t have the funding to generate this type of data, so American Gut enables researchers to independently pursue their own hypotheses about the microbiome and its complex interplay with the environment and human health.
Interested in knowing what bugs are in and on your body? Perhaps you want to know how your bacteria change over time or what bacteria you share with a family member or significant other? Check out different options for your donation to American Gut. Even biosamples from dogs are welcome!
Image: Courtesy of Rob Knight at American Gut
More reading on the microbiome:
Sheetal R. Modi is a postdoctoral fellow at the Wyss Institute for Biologically Inspired Engineering at Harvard University where she studies how bacteria develop and spread antibiotic resistance. She has a PhD in Biomedical Engineering, and when she’s not growing her bacterial cultures (and repeatedly killing them), she enjoys science communication and being outside.