By Editorial Team May 20th, 2015 at 9:25 am | Comment
By Editorial Team May 14th, 2015 at 6:00 am | Comment
This is a guest post by Michael Bear Citizen Science Project Director at Ocean Sanctuaries. In this post, he describes a citizen science led effort to catalog marine life living in and around the HMCS Yukon. In 2000, the Yukon was transformed into an artificial reef as part of San Diego’s marine conservation effort.
In 2000, the City of San Diego in collaboration with the San Diego Oceans Foundation (SDOF), purchased, cleaned and sank a 366 foot-long Canadian warship called the HMCS Yukon to create an artificial reef, a task at which has been spectacularly successful. Sitting at the bottom of the San Diego coast, the Yukon attracts dozens of local marine life species and is becoming a revenue-generating attraction for tourist divers from around the world.
When this project started, both the SDOF and the local scientific community were curious to understand the effects of an artificial reef on local fish populations and surrounding marine life. A joint study was undertaken by SDOF and Dr. Ed Parnell of Scripps Institution of Oceanography and released in 2004.¹ Crucial to the study was data gathered by local citizen science divers to generate a baseline of marine life species on the ship.
This year, Ocean Sanctuaries, San Diego’s first citizen science oriented, ocean non-profit is conducting a follow up study to the pioneering work of Dr. Parnell and colleagues. Established in 2014, Ocean Sanctuaries encourages and supports citizen science projects which empower local divers to gather marine data under scientific mentorship and forward our understanding of the oceans. Ocean Sanctuaries currently has three active citizen science projects. ‘Sharks of California’ and the ‘Sevengill Shark ID Project’ are both shark related. The third project is the follow-up study on the Yukon called the Yukon Marine Life Survey.
The data gathered in this project will be mainly photographic. Local divers will photograph specific areas of the ship in quadrats and with transect lines and the data will to be compared with the same areas examined in the 2004 study.
The project plans to use a web-based application for wildlife data management called ‘Wildbook’ for cataloging observations made in the Yukon Marine Life Survey. ‘Wildbook’ was originally designed to identify whale sharks, but will be modified as a multi-species database for use with the Yukon Marine Life Survey.²
Referring to the original Yukon Marine Life Survey of 2004¹, Barbara Lloyd, Founder of Ocean Sanctuaries says, “The Yukon Artificial Reef Monitoring Project (ARMP) was a short-term baseline study of fish transects and photo quadrats. The ARMP project has been gathering data for about a decade now. We at Ocean Sanctuaries strongly believe that a follow up study to the original baseline study can provide the research and fishing communities with valuable marine life data. In addition, unlike the original study, we intend to use photographs to ensure verifiable encounter data. We aim to create a large base of citizen scientists to take the photos and enter the data. This crowd-sourced data will allow us to collaborate between citizens and researchers.”
The current Yukon Marine Life Survey will span at least five years. Once completed, the data will inform scientists of changes to the marine life on the ship enabling California coastal managers to evaluate the impact of artificial reefs on local marine species. Take a video tour of the Yukon and learn more about the project at SciStarter.
1. Ecological Assessment of the HMCS Yukon Artificial Reef
off San Diego, CA, Dr. Ed Parnell, 2004:
2. Wildbook: A Web-based Application for Wildlife Data Management
By Carolyn Graybeal May 9th, 2015 at 9:53 am | Comment
From shoveling the third heavy snowfall of winter to spotting the first crocus of spring, each day without fail we experience our environment. Meaning each of us is a potential wealth of information about our local environment. Information that if gathered could inform climate scientists about the local effects and potential indicators of climate change. This is the premise of iSeeChange, a crowdsourced journal of community submitted local weather and environment observations.
The variability of weather and environmental conditions is an inherent challenge in climate science. Is the current drought in California a result of climate change or just an extreme version of the state’s periodic droughts? Was the devastation of Hurricane Sandy a fluke event or foreshadowing of a future trend?
To address this variability, climate scientists collect and average data across large spans of time and space. But managing data this way poses its own issues. “Climate science has a difficult time drilling down and being relevant to everyday people making every day decisions,” says Julia Kumari Drapkin creator of iSeeChange. “We designed iSeeChange to bridge the gap between the big data that the scientists collect and the local experiences of individuals and communities. The project allows people to reach their hands up and meet the big data half way overcoming this problem of scale.”
Since its creation in 2012, iSeeChange has grown from a local weather almanac in Colorado to a nationwide environmental reporting network. Anyone can become a member and submit observations on the website. Viewers can sort through the data by date or season, refining their search through metrics such as humidity, precipitation or cloud cover. Ideally members submit data on a weekly basis but in reality participation can range from a single backyard photo to religiously gathered measurements. One iSeeChange member uploaded observations made in a journal kept by a Dust Bowl era fruit farmer, noted Julia.
But beyond a data repository, the purpose of the project is to encourage conversation between scientists, journalists and individuals. “We want people to be curious, ask questions about what they see and experience. Then scientists and journalists in our network try to answer those questions,” says Drapkin. “The posts help scientists and journalist as well. Member submissions call attention to interesting or unusual events, which get picked up by journalists, transforming a few individual’s observations into a larger story.”
And these stories will become informative climate data for the future. Already researchers are expressing interest in the data. The project’s growth and collaborations with scientific partners at NASA, UC Berkeley and Yale is setting the stage for a larger impact. Due out in summer, iSeeChange co-developed an app with NASA that will ping community members to send in local observations whenever satellites are overhead. “The app will allow for real time comparisons between what the satellite sees and what is happening on a local level,” explains Drapkin. “We will learn what the impacts are and why it matters. We will be able to take the quantitative data and match it to the qualitative data and see how they compare over time.”
Ultimately iSeeChange is about empowering individuals and communities to document and investigate their environment. “People are experts of their own backyards. The granular changes they observe add up to bigger picture changes,” says Drapkin. “Already, these community observations have given scientists and journalist new insights and heads up on environmental trends.”
If you collect data about your local environment, want to share an interesting change you have notice or have a question you, visit iSeeChange and become part of a large scale effort to document your environment. To learn more about iSeeChange view their trailer.
By Editorial Team May 7th, 2015 at 6:20 am | Comment 1
By Arvind Suresh (Editor) April 29th, 2015 at 8:30 am | Comments (7)
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
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
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.
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.”