School Malaise findings 1 - pests

As announced on Friday I will use some posts this week to showcase the results from the School Malaise Trap Program. We have provided the schools with a list of the top 10 most interesting discoveries which I will share with the blog readers. Today we will start with the ones that represent potential threats to agriculture and forest.

Onion fly (Delia antiqua)

The Onion Fly was the most abundant species collected in the School Malaise Trap Program (6%) in fact, it was found in 79 of the 81 traps! Furthermore, it was found earlier in spring than previously recorded. This fly is found in the temperate regions of North America, Europe, and Asia.

Onion flies are grey and look much like house flies, except their legs are longer and their abdomen is narrower. Adults lay their eggs in the soil near onion bulbs of any member of the genus Allium which contains Onions, Garlic, Leek, Chives. The larvae are 8-10 mm long, white, and feed almost exclusively upon those plants. Damage due to the larvae feeding on young seedlings often results in plant death. Onion flies have three generations per year in Ontario so there is great potential for widespread damage to Allium crops. So far it was assumed that the first generation peeks early to mid June. According to the results at all the schools we are looking rather at early May. Given the fact that the flies need just a little over a week to hatch, mate and lay eggs any week earlier than expected might make a big difference for commercial farming.

Pear thrips (Taeniothrips inconsequens)

Pear thrips are an invasive species from Europe. They arrived in California the early 1900’s and are now be found throughout most of the USA and increasingly often in Canada. They are tiny, measuring only 1.2 to 1.7 mm long, with brown - black colouration, two pairs of wings, and rasping mouthparts. They use these mouthparts to cut open leaves and buds of hardwood trees so they can feed on plant fluids. The collection of pear thrips by the School Malaise Trap Program marks the first time they have been DNA barcoded from a Canadian location. They were found in 53 out 81 traps.

This is a very interesting discovery, and could signal a threat to Canadian forests especially because these animals are not restricted to pear trees as the name might suggest. Actually they are known to feed on a variety of maple species as well. In the late 1980’s pear thrips were responsible for damage to 1.3 million acres of Pennsylvanian forest. In North America, only female pear thrips have been found; they reproduce by parthenogenesis, producing eggs that do not require fertilization by a male.

DNA Barcoding for Undergrads

a guest post by Ralph Imondi

A statewide alliance of California colleges will enlist the participation of undergraduate students in building the global DNA barcode library

Ventura-based Coastal Marine Biolabs (CMB) recently partnered with California State University Channel Islands (CSUCI; Camarillo, CA) and the North Valley Biotechnology Center of American River College (NVBC; Sacramento, CA) to assemble a consortium of 10 California colleges that will adopt DNA barcoding as an embedded research component of undergraduate biology courses. 

This new effort represents an undergraduate extension of the NSF-funded Barcoding Life’sMatrix program – a research education project that engages a national network of high schools in building the DNA Barcode reference library.  Although the project was originally established by CMB as a discovery science-based model to enhance teaching and learning in high school settings, it has attracted widespread interest from college faculty who seek new opportunities to bridge research and undergraduate science education through student participation in iBOL. The assembly and submission of validated reference barcode records by undergraduates will be aided by BOLD-SDP, the customized student interface to the Barcode of Life Data Systems that was formally launched in spring 2013. 

Beginning in fall 2013, faculty from Mira Costa College (San Diego), Orange Coast College (Costa Mesa), Mt. San Jacinto College (Menifee), Fullerton College (Fullerton), Los Angeles Valley College (Valley Glen), Southwest College of Los Angeles (Los Angeles), Oxnard College (Oxnard), Ventura College (Ventura), Santa Barbara CityCollege (Santa Barbara), and Ohlone College (Fremont) will integrate the barcoding project into various upper- and lower-level biology courses.  

This pilot effort is supported by the U.S. Department of Education, and by a CA state grant. 


grant details: [Achieving a Collaborative College Education through STEM Opportunities (Project ACCESO), Title V, Hispanic-Serving Institutions STEM Grant] to CSUCI, and [California Community Colleges Economic and Workforce Development: Applied Biotechnologies (12-317-038)] to NVBC. 

 

Zoo Action Project

Meet the Biotech club from Donald A. Wilson Secondary School in Whitby and learn about their DNA Barcoding Action Project, created to help teach other students & visitors to the Toronto Zoo about the many uses of DNA Barcoding! These videos were developed as part of the DNA Barcoding at the Zoo Action Project by Let's Talk Science.

Let’s Talk Science is a Canadian organization that delivers science learning programs and services that aim to turn children and youth on to science and keep them engaged in learning.

Their approach to science education engages children from the early years through high school with fun, exciting hands-on/minds-on activities that improve their understanding of physical and life science, mathematics and technology. 

High School Students test beef products

guest post by Ralph Imondi

 

Mini Food Authentication Study Conducted by California High School Students Finds No Evidence of Horsemeat DNA in Beef Products

In the wake of the recent European horsemeat scandal, high school seniors working at Ventura-based Coastal Marine Biolabs (CMB) took a brief diversion from building the BOLD reference library to examine the contents of beef products sold at local supermarket chains, health food stores, membership warehouse clubs, fast-food restaurants, and a foreign company better known for its ready-to-assemble urban furniture than for its food markets and restaurants.  A team of 4 students collected a total of 32 food products that included ground beef, shaved steak, cooked and uncooked beef patties, and meatballs. Upon returning to the CMB lab, they then applied DNA Barcoding to detect the presence of horsemeat in each product.  In stark contrast to the results obtained from DNA-based testing of European meat products, the students found no evidence of horsemeat in any of the samples examined with DNA barcoding.  Instead, their testing detected only domestic cow (Bos taurus) DNA in 29 products labeled as 100% beef, and a combination of both domestic cow and pig (Sus scrofa) DNA in 2 products labeled as containing both beef and pork.   

 

FoothillTechnology High School seniors Jongseung Baek, Eric Moll, Emily Park, and Amanda Torres conducted the 5-day food authentication study as an extracurricular science project.  Earlier in the semester, these same students and their classmates assembled a series of BOLD-compliant reference DNA Barcode records for groundfish species collected during the third leg of a NOAA-sponsored trawl survey, which was conducted in summer 2012 around Alaska’s Aleutian Islands.  Both student-led efforts were carried-out in connection with the NSF-funded Barcoding Life’s Matrix program hosted by CMB.

According to Emily Park, one of the team members involved in the projects, “participating in the DNA barcoding initiative, both in the classroom and at Coastal MarineBiolabs, allowed me to do research that has influence outside of  just a local, school context. Not only did I use science for class work, I could contribute to an international database tied to biodiversity conservation and even consumer fraud. It's cool to know that the concepts you learn in DNA barcoding have direct applications in real-life, and that even high school students can take part in that direct application.”

BOLD Student Data Portal

For regular readers of this blog it is not news. The BOLD team has released a Student Data Portal designed to open the world's leading DNA Barcoding database and workbench to the classrooms. Today they also released a nice video to promote the new interface. You should have a look as it is really very well done:

School Malaise Trap Program Week 1

Week one has come to a close. Here some impressions from the school visits we had:

The BIObus is coming

Line up for a peek into the field vehicle

Bugs!

The entomologist's workplace

How an aspirator works - and yes, we don't suck the bugs into our mouth.

An introduction to DNA Barcoding for Grade 6 students

More bugs!

eBOL Launch

This is our week of educational activities. On Tuesday we started with our School Malaise Program

The BIOBus at King George Public School in Guelph

and we've visited three elementary schools so far. Only 57 more to go! Check out Twitter or Facebook for more info and pictures like the one on the right.

Today is the day for the next big news:

Together with our friends from Coastal Marine Biolabs in Ventura, CA and the crew from Spongelab we (BIO and BOLD) launched eBOL a new community tool developed for educators who want to use DNA Barcoding as a classroom tool. Here the official press release:

Developed in partnership with educators, bioinformaticians, researchers, and science media experts, the eBOL Community Web Portal integrates new digital resources to bridge the biodiversity knowledge gap and advance DNA barcoding as an interdisciplinary teaching and learning tool.

"DNA barcoding has stimulated a great deal of interest and excitement from high school science teachers and university instructors who struggle to bring authentic research experiences into their science labs," said Linda Santschi , Scientific Co-Director of the California-based Coastal Marine Biolabs.  The ability of DNA barcoding to bind different life science disciplines within a single scientific workflow is extremely attractive to educators who are frustrated with prescriptive and outmoded lab experiences. "Through eBOL, we have a unique opportunity to not only heighten student awareness of this powerful new technology and how it works, but to develop it as a model to innovate life science education." 

At the center of this open-access resource is a customized student interface to the world-class Barcode of Life Data Systems (BOLD), an enterprise-scale informatics platform that forms the framework for DNA Barcoding technology.  "For the first time since the launch of the landmark International Barcode of Life (iBOL) project, students around the world have a direct link to the biodiversity genomics community," said Sujeevan Ratnasingham, the Director of Informatics at the Biodiversity Institute of Ontario (BIO).  Through the BOLD Student Data Portal (BOLD-SDP), students can utilize a centralized suite of sophisticated informatics tools that enable them to manage, analyze, and share various forms of barcode data with each other and the global iBOL community.  

In addition to BOLD-SDP, the eBOL website provides a gateway to new mobile computing technology for collecting barcode data in the field, and an extensive and indefinitely expandable library of high quality digital learning assets maintained by Spongelab, an award-winning science media and communications group based in Toronto. According to Dirk Steinke , the Director of Education and Outreach at BIO, the establishment of the eBOL website equips educators with the information and tools needed to seamlessly bridge DNA barcoding and education in classrooms worldwide. It also encourages the formation of a diverse and broadly inclusive community committed to revitalizing life science education.  "We envision a future where students working in school and university labs around the world can make lasting contributions to iBOL and meaningfully explore the value of DNA barcoding for addressing a variety of important real-world problems." 

School Malaise Trap Program

We are currently in the last phase to prepare for a new education and outreach project:

Next Tuesday we will start to visit 60 schools in Southern Ontario and team up with grade 6 and grade 12 students to explore the insect diversity in their schoolyards through DNA Barcoding.

Each school will get a visit by our BIObus, an RV converted into a field laboratory, with a team that will introduce students to some methods of fieldwork. We will provide insights into biodiversity research and present DNA Barcoding. Teacher will be supplied with a comprehensive lesson plan designed to fit the respective curricula. 

But that's not all. Each class will put up a so-called Malaise trap to collect insects in the schoolyard over a two-week period in April. 

A malaise trap is a trap for flying insects, particularly flies, wasps, and true bugs. It is usually placed in a natural flyway where it can easily collect hundreds of insects in a week thereby providing a very detailed understanding of local biodiversity. Invented by the Swedish entomologist René Malaise, it resembles a black and white tent with a mesh panel along its central axis. When insects encounter the panel, most will naturally go up towards the white coloured roof in an attempt to pass the obstacle. The insects are directed to the top of the trap where they are caught in a collection bottle. 

Here is how to build up one (our detailed instruction video for the classes):

Once the two weeks are over all samples will be analyzed at our facility and each class will receive a detailed report on species found but also comparisons between all 60 locations.

I'll be on the bus for a couple of (not all) trips over the next 6 weeks. I am sure there will be plenty to blog about. In any event a great opportunity to bring our research into the classrooms and allow the kids to participate in ongoing research.

 

figshare

Recently I have started using figshare to share some figures I've created a while back and that perhaps otherwise would have never seen the light of day. I am certainly not the only one having stuff in the drawer because we never got to finish a manuscript or get to a few more experiments. Another phenomenon playing into this is also widespread and has been named the file drawer effect. Many studies in a given area of research may have been conducted but never reported, because we all have the tendency to not publish negative or inconclusive results. 

There is an open source solution to this available and it doesn't cost you anything aside from a couple of minutes to upload your data. figshare allows researchers to publish research outputs in an easily citable, sharable and discoverable manner. All file formats can be published, including videos and datasets. There is no peer review process, and researchers are actually encouraged to publish null results, avoiding the file drawer effect. figshare uses creative commons licensing and provides you with a DOI and a QR code for every file you've uploaded. Categories and tagging support easy access as well

I have just started using it and I really like this way of sharing results openly. Not only is it a home for all the used (of course the ones published should be up as well) and unused figures but also a great resource when it comes to preparing lectures, courses, and talks. There are some great resources for teachers out there but not as many for university educators.

And most importantly it is real open access. In case you haven't heard of figshare, please check it out and start sharing.

Barcoding Life's Matrix

A comprehensive review conducted by the US National Academies' National Research Council suggests that most high school laboratory experiences fail to conform to established guidelines for effective science instruction. These guidelines advocate designing laboratory experiences such that they produce clear and discernible outcomes, merge science content with learning about the process of science, and integrate hands-on activities into a sequence of traditional didactic course instruction.

So much from the introduction of a community paper that has just been published in PLoS Biology. I remember my own high school times where laboratory experiments had been conducted over and over again for decades. I also remember my disappointment as this had nothing to do with 'real' science. Everything was designed in a way that it could be easily done and the outcome was predictable. There wasn't any surprise element or even a remote sense of discovery. Unfortunately this was also the case in the first two years at university. This is one of the reasons why I am particularly interested in new approaches to scientific education both in schools and universities.

The community paper mentioned above is one of those new approaches and I think it is a very successful one. It describes a project that brought together scientists and educators from the Coastal Marine Biolabs in Ventura, California, the Biodiversity Institute of Ontario, and the New York Hall of Science, New York. Barcoding Life's Matrix includes two main strategies for student engagement: a residential research experience for high school students (grades 11/12), and professional development workshops for high school science teachers.

The students go through an intensive, seven-day residential research experience hosted at Coastal Marine Biolabs biosciences laboratory in Ventura Harbor where they work alongside scientists conducting interrelated field, laboratory, and bioinformatics activities. The results are DNA Barcode reference data that are submitted  to BOLD and GenBank. So, next time you query the BOLD database with a sequence of an unknown marine sample it might match one of the records contributed by these young investigators.

BOLD-SDP's customized five consoles

In order to provide a student-friendly online environment the BOLD team designed the BOLD Student Data Portal (BOLD-SDP). BOLD-SDP is a classroom-focused interface to the BOLD database. It provides both instructors and students with the tools necessary to make contributions to the DNA Barcode library.  It also gives students the opportunity to integrate and analyze specimen and sequence data while providing instructors with tools to monitor student progress and evaluate their work. Students can explore BOLD, but they are also able to add their own data it.

High school science teachers are offered a professional development program which provides in-depth pedagogical and procedural training, multimedia instructional materials, and research equipment needed to engage students in the generation and submission of high-quality barcode data within their own school laboratories. I wish my teachers had enrolled to this course.

The Barcoding Life's Matrix project represents a striking new example of how discovery-based science can be effectively translated into secondary educational settings to address science education reform agendas, overcome extremely difficult challenges associated with molecular life science teaching and learning, and engage large numbers of students in the creation of a valuable public and scientific resource (an aspect of the project that students regard as particularly exciting and transformative).

Thumbs up! A very good read with a commendable strategy. There have been a lot of great projects that engage high school students in DNA Barcoding research but this paper represents a step forward as it formalizes the approach. I am sure it will set a precedent.

Eco-Immersion

Imagine a course where students learn about a country’s delicate ecosystem by exploring the various geographical zones, their inhabitants and the challenges they face. The key to creating an authentic experience rather than providing typical student “destination” travel is meeting with local guides, many of whom are naturalists possessing an intimate knowledge of the ecology and culture of a country or region. Students get acquainted with these so called visionary collaborators, providing them with an opportunity to be inspired by their work. In Costa Rica student groups have the chance to work with the renowned ecologist Dan Janzen and his team, whose conservation field the Area de Conservacion de Guanacaste (ACG) includes more than 325,000 species. Ultimate goal is to generate a DNA Barcode for each one.

The two former teachers Crawford Hill and Eddie Rodriguez are running Chill Expeditions a company that offers teenage students an adrenal rush on their trips, such as whitewater rafting, climbing active volcano peaks and zip-lining hundreds of feet above a rain forest to take in a “monkey’s-eye” view of the jungle canopy. But they are quick to point out the emphasis is just as much an in-your-face cerebral experience as described above. They call this unique experience eco-immersion. To further deepen their interaction with the local communities, the students take part in service projects when available. Hill said, for instance, that about two dozen student groups from all over America recently participated in building a school in Costa Rica over a period of a year. Students have also helped local indigenous people to build and install clean-burning stoves, which use less wood and produce less smoke, replacing those that have caused respiratory illness in their villages. Other projects have included planting organic gardens, laying sidewalks and using recycled materials to build walls.

A great hands-on experience on how ecology impacts a country and its people and a wonderful way to introduce teenagers to an entirely different world.

Why should high school students do DNA Barcoding?

Because it's fun!

You probably have figured out already that I am particular fond of the idea to involve citizens in actual science projects. Especially high school students could benefit from this quite a bit. Here just one example. 

The video is 2 years old but fun to watch anytime.

In case you have a high school teenager at home looking for a science fair project - why not suggesting DNA Barcoding  as a topic?

Barcoding in Schools

Mader, Biology, 11th Edition, 2013

It started in 2008 with a freelance science project of two high school students. Kate Stoeckle and Louisa Strauss checked samples of seafood using DNA Barcoding to see whether the fish New Yorkers buy is what they think they are getting. They found that one-fourth of the fish samples with identifiable DNA were mislabeled and created a big hype in the press - the term "Sushigate" went around the world and found its way in a High School textbook .

This was the start to a couple of projects that involve high school students in DNA Barcoding projects. I think it is a great idea to bring the method into the classrooms and provide students with a hands-on experience in biodiversity science. 

Most high school students are accustomed to learning science in a very different way than it is actually practiced in real-world scientific research settings. As a consequence, students develop an unrealistic perception of science that overlooks many of its most valuable and exciting elements, leaving them disengaged and uninspired.

This excerpt from the website of the Coastal Marine Biolabs in Ventura, California illustrates the reasons for a shift in High School Science education. Their mission is research based science education and DNA Barcoding fits in this concept extremely well as it is hands-on from the field collection all the way to the work in the laboratory. Students can participate in all stages of the process and at the end stands a tangible result -  a barcode as valuable as all the other ones in the databases of the 'real' scientists.The very successful program "Barcoding the Kelp forest" runs already for a few years.

The winners of the Urban Barcode Project

High School students in New York City recently participated in the Urban Barcode Project, a science competition in which student research teams used DNA Barcoding to explore biodiversity in their city. The projects ranged from studies on the ant diversity in the South Bronx to surveys of the fungal biodiversity in Central Park. The winning team used DNA Barcodes to identify the content of Gingko products. 

No matter what example one looks at, the question - can High School students do DNA Barcoding -  is easy to answer: Of course they can! Actually they should as it is a great way to learn the basics of modern genetic methods and develop an appreciation for the biodiversity around us.