Making Medicines from Soil: Going Behind the Scenes of a Citizen Science Project

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Making Medicines from Soil (Image Credit: C Coker, Cichewicz Lab)

Taking you behind the scenes and into the laboratory of the Citizen Science Soil Collection Program

This is a guest post by Dr Robert H. Cichewicz a professor at the University of Oklahoma and leader of the Citizen Science Soil Collection Program. Dr Cichewicz previously wrote on SciStarter about how you can participate in this project. In this post, he describes what really happens behind the scenes in his laboratory that helps their team discover (with your help!) new compounds from fungi that could prove to be useful in treating diseases. Find germs and microbes intriguing?Check out more microbe themed projects that we’ve picked out for you at SciStarter!

For millennia, our ancestors turned to the Earth as a source of healing agents to address all manner of illness. For example, the Ebers Papyrus (written in the vicinity of Egypt around 1500 BC) provides hundreds of examples of medicinal plants and minerals used to treat many disease conditions including pain, vomiting, and infections. Fast forward to modern times and we see that the research methods used to study diseases have changed dramatically, but the idea that the Earth is the best source of lifesaving drugs has endured. The philosophy that our planet still holds many secrets to modern ailments is substantiated by a large and growing list of drugs that come from nature. Many of these medicines are made by soil-dwelling bacteria and fungi. Microbes have yielded a wide variety of important compounds (for example penicillin, statins, and cyclosporins originally come from fungi) for treating cancer and infections. But finding these beneficial dirt-dwelling microbes and turning them into life-saving medicines is not a simple task. It requires teams of researchers, as well as help from people such as you. A few weeks ago, I wrote a blog post inviting to you to be a part of this process and become a citizen scientist by sending us a soil sample from your backyard. We have had an overwhelming response to our requests, recieving thousands of samples which we are now processing through in the hope of discovering the next amazing secret that nature holds.

You might ask yourself, “What really happens after I send this sample?” or “How long does it actually take for you to discover something from what I send you?”.  In an attempt to answer some of those questions and tell you what happens behind the scenes, I decided to write this post.

Hop on and let me take you on a journey that turns a handful of dirt into a life-saving drug.

Step 1: From your yard to our lab

The journey begins when you request a free Citizen Science Soil Collection Kit from our lab. After you pick a favorite place in your yard, put a small handful of soil in the collection bag, seal it and drop the packet in your mailbox (we’ve already paid the return postage for you!). It takes less than 5 minutes, and did I mention it’s free?

Step 2: Growing fungi from soil

Soil samples spread on a petri dish to grow fungi (Image Credit: C Coker)

Soil samples spread on a petri dish to grow fungi (Image Credit: C Coker, Cichewicz Lab)

Our hardworking team of students and researchers begin the process of isolating fungi from your sample. Most soils are teeming with several kinds of microbes including fungi – a great source of new and useful drug-like molecules. Even if you cannot see them, there are likely thousands in your sample. We spread the soil on the surface of a petri dish that is filled with a gel infused with fungi-food which include things like soil “tea,” blended-up worms, simple sugars, and ground tomatoes – Yum!.

Step 3: Identifying fungal species using DNA sequencing

After growing and isolating the fungi in the soil sample, the next step is to identify new species using genetic sequence information. Hidden in vast landscape of the fungus’ DNA there is a small stretch of genetic material known as the internal transcribed spacer (ITS). This fungal ‘barcode’ helps us distinguish between different species, identify new ones or categorize them into a larger group known as genera. It is estimated that somewhere around 5 million different fungi live on Earth, but only about 2% have been identified. Given these odds, you’ve probably had one or more new kinds of fungi living in your yard all along and never knew it!

Thanks to the fantastic response to our outreach, we’ve received hundreds of samples, which is a good thing. But the sheer volume of samples we are dealing with means that growing and identifying fungi might take microbiologists a year or more to get your sample processed. But we won’t keep you in the dark! We will be setting up a fungus photo album so you can see what fungi were isolated from your sample. Check out our website for updates!

Step 4: Extracting fungal compounds and testing them in different models of disease

Fungi's favorite food? Why Cheerios of course! (Image Credit: C Coker)

Fungi’s favorite food? Why Cheerios of course! (Image Credit: C Coker, Cichewicz Lab)

Ultimately, it comes down to the chemistry that each fungus is making to help us determine if it has something ‘good’ that could help treat a disease. We grow the fungi on their favorite food – Cheerios breakfast cereal. As it turns out, Cheerios is not only a great food for toddlers, children, and adults, but fungi really like them too. We place Cheerios in test tubes along with the fungus and let it grow for several weeks allowing it to consume the cereal. The fungus is then extracted to remove its special compounds (the natural products) and these are stored in a freezer for later tesacting.

One by one, the fungal compounds are tested for biological activity that might prove useful in a therapeutic setting. For example, we add the compounds to cancer cells to see if we can stop them from dividing or give them to pathogenic bacteria to try and stop their growth. The compounds are also entered into a collection that is tested when new disease targets become available. Growing the fungus and extrting the compounds takes about two months but testing, conducted by our biology team can take as little as a few days or up to years to complete.

Step 6:  Purifying the compound and finding its chemical structure

To figure out what the fungi are making, we grow them in large bags containing Cheerios. We then use chemical techniques to purify the desirable natural product away from all the other compounds in the fungal cells. Chemical structure determination then ensues. This step is rather similar to solving a big puzzle where we try and figure out the chemical makeup of the unknown substance. This is a highly variable step that might take weeks and sometimes many months to complete. Solving the structures of unknown compounds is fun, but it takes a lot of patience and the hard work of chemists in our lab.

Testing natural compounds against disease models in the laboratory

Testing natural compounds against disease models in the laboratory (Image Credit: C Coker, Cichewicz Lab)

Step 6: Further testing purified natural product

We study the biological uses of the compounds, as well as share them with our collaborators, many of whom are pharmacologists trained in cancer and infectious disease biology. We work with a network of great scientists from around the country to try and determine the best use for the many new compounds from the fungi. This step can take years to compete, but the good news is that we have many dedicated scientists ready and excited to test the new and amazing compounds from fungi.

It is truly amazing when you consider the lengthy and complex chain of events that unfold once you, a member of our Citizen Scientist Team, takes that first small step of sending in a soil sample. You never know what we may find or where we might find it. Despite all of these uncertainties, there is one thing that is undeniable – without you, we cannot hope to beat diseases like cancer and infections. So do not delay a second longer; request your Citizen Science Soil Collection kit today and join the fight. Or as we like to say, “Get your hands dirty. Make a difference.”

 

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Coop’s Scoop: Speak for the Trees on next #CitSciChat

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B Rosen enjoying The Lorax

B Rosen enjoying The Lorax

In the mid-1800s, when J. Sterling Morton moved to the Nebraska Territory, he soon was homesick for trees. Maybe he missed the sound of leaves rustling in the breeze. Or maybe the pine-fresh scent.  In 1872, as secretary for the Territory, Morton established Arbor Day, and 1 million trees were planted on that first Arbor Day in the Nebraska Territory.

Most fundamentally, trees provide fresh air. Not only do they take in carbon dioxide and release oxygen, they reduce pollutants in the air, improving overall air quality.  The benefits include the shade of full-grown trees (which can lower heating bills). Trees are also habitat (food and shelter) for wildlife, they provide privacy, and place for tire swings and tree houses. Being outside is revitalizing, and being in a landscape with trees and greenery helps people cope with chronic stress.

Great Lawn in Central Park by Ed Yourdon

Great Lawn in Central Park by Ed Yourdon

Because trees provide so many benefits to people, tree-planting events continue, particularly for city trees (avoiding the stinky ones that smell like rotten fish). Cities have programs for residents to help with the care and stewardship of city trees, as with the million tree initiative in New York City. In Philadelphia, residents map planting sites and newly planted trees in PhillyTreeMap, in order to visualize and keep track of the positive impacts of the city’s trees.

Many species of trees face blights of insect pests and diseases. Citizen science efforts monitor tree health.  For example, in OakMapper, participants in California can report suspected cases of Sudden Oak Death (caused by a pathogen).  Seventh and eighth graders in Ohio discovered the emerald ash borer parasitoid in woods adjacent to their school. As millions of ash trees across Europe are killed by a fungus (Chalara fraxinea), citizen scientists participate in a Facebook game (pictured below), Fraxinus, to help align DNA sequences to assess variability in different strains of the pathogen. The results can help researchers understand the genetic code behind the disease.

In recognition of Arbor Day, we’ll discuss citizen science related to trees in the next #CitSciChat. To join the Twitter chat, this Wednesday April 29 at (7:00pm GMT; 2:00pm ET), follow the hashtag #CitSciChat.

Figure 1.

 

 

 

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SciStarter and Citizen Science at Philly Tech Week and the Philadelphia Science Festival!

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met
Wednesday, April 22
9:00am12:00pm 
Excite Center

3401 Market St, Philadelphia, Pennsylvania 19104
In partnership with Drexel University’s Center for Science, Technology & Society and the ExCITe Center, this event will workshop digital projects and their platforms to improve accessibility and empower citizen scientists.SciStarter.com is a Philly start-up with international reach featuring 1,000 citizen science projects in need of help from the public. TheAsthmaFiles.orgis a collaborative ethnographic research project designed to advance understanding and efforts to address environmental public health challenges around the world. Both platforms will benefit from enhanced cyberinfrastructure to make it easier for people to participate in citizen science, track their contributions, connect with others, and more.At this event, representatives from the programs will present an overview and describe their cyber infrastructure challenges.Learn about the projects then weigh in during the hands-on workshop designed to enhance the platforms and improve the experience for participants.
soil
Saturday, April 25
11:00am – 2:00pm
The Schuylkill Center for Environmental Education

8480 Hagys Mill Rd, Philadelphia, Pennsylvania 19128
Meet the SciStarter team and get involved in citizen science to collect microbes from soil for drug discoveries, track air quality, monitor phenology, map tress, build your own ZomBEE trap and more! We’re partnering with Discover Magazine and Astronomy Magazine to bring you more opportunities to get your hands dirty with science!
phillies
Saturday, April 25
6:00pm
SciStarter, Science Cheerleader Discover Magazine and Astronomy Magazine present:
“Be a Citizen’s (Bank) Scientist!”
Get involved in real research projects right in Citizen’s Bank Park at thePhiladelphia Phillies ! Monitor air quality, light pollution, and help inform NASA’s Asteroid Initiative from your stadium seat. Learn about the 1,000 opportunities to become a citizen scientist wherever you are!
fishtown
Sunday, April 26 2pm
Frankford Hall
1210 Frankford Ave, Philadelphia, Pennsylvania 19114
Take pub hopping to a whole new level during the Fishtown Science Crawl! Enjoy great drink specials as you explore your favorite Fishtown spots. Be A Citizen Scientist: Take part in some Citizen Science with SciStarter and explore Leafsnap, an electronic field guide, or if you’re feeling daring learn all about and zombees! FREE to attend, $5.00 wristband for Happy Hour prices at all venues.
psc
Saturday, May 2
10:00am – 4:00pm
Ben Franklin Parkway
Science like you’ve never enjoyed it before! Meet the SciStarter team andScience Cheerleader s. We’re joined forces with Discover Magazine andAstronomy Magazine to bring you tons of opportunities to do citizen science and make a difference in the world. Find microbes in soil that may advance drug discoveries. Learn how to use low cost sensors to track air and water quality. Design your own community research question and more. Pick up a #citizenscience pin or a copy of a magazine. #GetNerdy!
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Monarch Larva Monitoring Project Helps Citizen Scientists Build Connections to Nature

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monarch larvaThis guest post by Eva Lewandowski describes her experiences with citizen scientists from the Monarch Larva Monitoring Project, which was featured in our recent Spring themed newsletter. Check out the rest of the projects on that list here. The Monarch Larva Monitoring Project is also one of more than 800 citizen science projects on SciStarter. Use our project finder to find one that fits your interests!


What do citizen scientists gain when they collect data for a research study? What do they learn, and how does it change them? These are some of the questions that I try to answer in the course of my PhD research. As a graduate student in the University of Minnesota’s Monarch Lab, I have an up-close view of our lab’s citizen science project, the Monarch Larva Monitoring Project (MLMP), which has given me an excellent opportunity to find out how citizen science affects the citizen scientists themselves.  Over the past few years I’ve spent a great deal of time meeting, writing about, and studying our MLMP volunteers. More often than not, what strikes me about these interactions is the volunteers’ familiarity with and connection to their monitoring sites.

At the MLMP, we study how the population of monarch butterflies varies in space and time; given the dramatic decline in monarch numbers over the past decade, it’s more important than ever that we understand the factors impacting the monarch population. Each fall, monarchs west of the Rocky Mountains migrate to the California coast to overwinter, while the monarchs east of the Rocky Mountains travel thousands of miles to Mexico, where they spend the winter.  In the spring, the monarchs in Mexico begin to make their way north throughout the United States and Canada, going through several generations before they reach their northern-most destinations. Once there, they continue to reproduce until it is time for a new generation to fly south the Mexico.

Throughout the breeding season, MLMP volunteers across North America monitor milkweed patches weekly for monarch eggs and larvae. Volunteers choose their own sites, and the only requirement is that it has milkweed; monarch butterflies will only lay their eggs on milkweed, so it must be present if you hope to find monarch eggs or caterpillars. Milkweed isn’t as prevalent as it once was, but it can still be found in gardens, parks, pastures, and roadways, so volunteers don’t usually have trouble finding a patch to observe; those that do can plant their own milkweed. In addition to counting the number of eggs and larvae that they see, volunteers also provide data on the number and types of milkweed and flowering plants at their site.

volunteer monitoringBecause MLMP volunteers monitor the same milkweed patch week after week, and often year after year, they are usually extremely familiar with their site. Most can tell you off the top of their heads what species of milkweed and nectar plants they have, as well as when they come up and when they bloom; many also know which plants are the monarchs’ favorites and which are preferred by other insects. And because monitoring for monarch eggs and larvae involves carefully examining the leaves of milkweed plants, volunteers encounter a lot more than just monarchs on their milkweed plants. From soldier bugs to milkweed beetles to aphids, MLMP volunteers are familiar with a wide variety of insects that make their home on or around milkweed. Many MLMP volunteers can use the field guide Milkweed, Monarchs and More, coauthored by MLMP Director Dr. Karen Oberhauser, to identify and learn about the flora and fauna commonly found in milkweed patches.

The book focuses mainly on plants, insects, and arachnids, but our volunteers also enjoy observing birds, amphibians, and mammals while collecting data. Participants often snap a picture of the interesting animals they see in their plots to contribute to the MLMP Photo Gallery, such as when long-time MLMP volunteer Jan Sharp found herself “eye to eye” with a tree frog perched on her milkweed, or when Diane Rock stumbled across a black bear in her milkweed patch.

Observing and learning about the plants, animals, and overall ecosystem of their monitoring site is one of the best parts about being an MLMP volunteer, but our volunteers also love that they can share that experience with others. Many of our participants monitor with children, usually their own or their grandchildren, which gives them a chance to connect young people to nature. We even have a few second-generation MLMP volunteers, people who started monitoring with their parents and now monitor their own site or have taken over the original site.

MLMP is so much more than just collecting data on monarch abundance. It’s an opportunity to get outside, to learn about a piece of land and everything that lives on it, and to share that connection with others. We’re always in need of more volunteers; if you’re looking for a chance to get outside and connect with nature, while making a meaningful contribution to science and conservation at the same time, join the MLMP!

Photo: Wendy Caldwell (larva), Gail Gilliland (volunteer monitoring)

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Is Climate Change Causing the Seasons to Change? Citizen Scientists in the UK Help Find Out with Nature’s Calendar

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A Seven spot ladybird (Image Credit: Richard Bekker)

A Seven spot ladybird (Image Credit: Richard Bekker)

Interested in more spring themed citizen science projects? Check out the ones the SciStarter team has handpicked for you here! Or use SciStarter’s project finder to find one that piques your curiosity!


In 1998 Tim Sparks, a research biologist at Britain’s Centre for Ecology and Hydrology in Cambridge started a pilot project designed to record the first blush of spring. Sparks saw the importance of continuous phenology records—a record of when plants start to bud and flower, and wanted to revive a phenology network in the UK. Shortly thereafter The Woodland Trust (the UK’s largest woodland conservation charity) joined forces with the Centre for Ecology and Hydrology to promote the scheme to a wider audience, which is how the citizen science project Nature’s Calendar was born.
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Nature’s Notebook: Through the Eyes of a Citizen Scientist

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Bobcat in Chihuahuan Desert, New Mexico. Image Credit: Sharman Apt Russel

Bobcat in Chihuahuan Desert, New Mexico. Image Credit: Sharman Apt Russel

This guest post by Sharman Apt Russel describes a citizen science experience with the the project, Nature’s Notebook featured on our recent Spring themed newsletter. Check out the rest of the projects on that list here. Nature’s Notebook is also one of more than 800 citizen science projects on SciStarter. Use our project finder to find one that fits your interests!

Here in the Chihuahuan Desert of southwestern New Mexico, I am intimate now with three trees in my backyard: a box elder (Acer negundo), a desert willow (Chilopsis linearis), and a honey mesquite (Prosopsis glandulosa). I know when these plants become luminous with the green of new leaves, when they flower, when their flowers turn to fruit, and when their fruit falls. I also have a warm relationship with a male four-winged saltbush (Atriplex canescens), having rubbed his yellow pollen sensuously between my fingers, and with a female four-winged saltbush, admiring her extravagant and seasonal cloak of papery seeds. Perhaps my greatest new friend, however, is a soaptree yucca (Yucca elata), whose single stalk grows up quickly and prominently in late spring, its buds producing a mass of scented creamy-white flowers—like a six-foot-high candle glowing in the dusk.
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Spring is the Season for Citizen Science

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flower

Photo: NPS

Here are six projects in need of your help as you walk the dog, work in your garden, clean the gutters, or do spring cleaning.

And check out these  new citizen science projects just added to the Project Finder on SciStarter.


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Coop’s Scoop: Tweeting about Spring Citizen Science

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citscichat_logoWith the occurrence of the spring equinox, there are many cultural and religious celebrations of life, renewal, bounty, and freedom. Over 300 million people celebrate the Persian festival of Nowruz. In South Asia, there are festivals for Chaitra Sukladi, Ugadi, Gudi Padava, Chetti Chand, Navreh, Sajibu Cheiraoba, and more. Pagans celebrate Ostara. There will be Easter egg hunts and Passover Seders.

In Washington, DC, celebration of the National Cherry Blossom Festival began on March 20 and continues through April 12. Noting, and celebrating, the timing of cherry blossoms in DC is a tradition that originated in Japan. The DC Festival commemorates the friendship between the US and Japan that was symbolized by a gift of 3,000 cherry trees from Tokyo’s mayor in 1912 to our nation’s capital.

Washington_DC_-_Tidal_Basin_-_Cherry_Blossoms_by_Andrew_Bossi

The cherry blossoms in Kyoto, Japan are perhaps the oldest example of a spring tradition that has proven useful to climate change research. For centuries, the exact timing of annual cherry blossom festivals varied depending on the peak flowering of Japanese mountain cherries, which in turn varied depending on the warmth of the weather. Because the festivals were timed to coincide with peak blooms, and the timing of blooms were tied directly to spring temperatures, scientists can now estimate past spring temperatures based on the timing of historic festivals. Good records of the festival dates go back to the 15th and 16th centuries, and some, though less complete, records go back as far as the 11th century.

In addition to old traditions of noting when flowers bloom, there are traditions of noting when birds and insects arrive on their migration, when insects emerge, and a host of other observations about the timing the spring. Instead of festivities and dancing around maypoles, in citizen science projects, the traditions involve following field protocols. Either way, it is time to notice the natural world during a change in season. As more cultural traditions that connect us with nature seem to lost over time, citizen science is filling those gap with scientific hobbies.

Spring citizen science is the theme for the March #CitSciChat, a monthly Twitter chat session co-sponsored by SciStarter and the NC Museum of Natural Sciences. Join us for the March #CitSciChat on Wednesday March 25, 7pm GMT, which is 3pm ET in the US.

Follow our March guest panelists who represent a variety of projects relevant to tracking spring, including the Migratory Dragonfly Partnership (@Dragonfly_MDP), Journal North (@journeynorthorg), Operation Rubythroat (@rubythroat1), the Monarch Larva Monitoring Project (@MLMPCitSci), BudBurst (@PBudBurst), eBird (@Team_ebird), and Snapshot in Time (@OrianneSociety).

We’ll discuss springtime scientific discoveries, education lesson plans, best practices for project design, and what’s on the horizon for citizen science.

Photo credit: Washington DC Tidal Basin Cherry Blossoms by Andrew Bossi

 

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Journey North: Tracking the Stories of Survival with Citizen Science

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A group of Gray Whales Count volunteers count gray whales at Coal Oil Point in Santa Barbara.  (ianvorsterphotography.com)

A group of Gray Whales Count volunteers count gray whales at Coal Oil
Point in Santa Barbara. (ianvorsterphotography.com)

It was a crisp morning following a cold night in Goleta’s Coronado Monarch Butterfly Preserve. As Luke crossed a beam that had been dropped across a swampy area, he looked up at the Eucalyptus grove and sighed quietly. “Where are the butterflies Dad,” he asked me—with one part expectation and one part disappointment.


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Finding our origins: The Genographic Project uses genetics to map the past

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Ancient human migration patterns. Source: National Geographic.

Ancient human migration patterns. Source: National Geographic.

Have you ever tried tracing back your family tree only to get stuck at great great Grandpa Jim? Are you curious about who your ancestors were and where they might have come from? If so, you’ll definitely want to check out National Geographic’s The Genographic Project. Not only will you learn about your lineage but you’ll have the opportunity to contribute to our scientific understanding of the human story.


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