Jillian Angeline https://twitter.com/JLAngeline from Accuweather Channel interviewed me about our ASM poster. It was a well-done clip, and I appreciated her thoroughness regarding details.
Here is the direct link (embed does not work)
Interview by Accuweather channel
Reporting from ASM Microbe 2022
First in-person conference in a long time! The American Society of Microbiology yearly meeting (ASM Microbe 2022) took place in Washington DC June 9-12. Our small group (Andrea, Allison, and myself- the 3 As!) headed to the nation’s capital to attend.
It was great to be able to meet people in real life versus through Zoom screens. ASM did a good job trying to control Covid exposure. Besides vaccine/test requirements, masking was required throughout the event. Of course, sometimes the discipline was hard to maintain during reception times and social events, but as far as I know, only a few people reported getting Covid.
I confess we spent a lot of time in the Exhibit Hall, which also housed the poster sessions. It was fun to get updates on instrumentation, explore new tools, and then head to the poster boards and get updates on science.
Andrea’s poster got some extra attention, and it was featured in a ASM press release: https://asm.org/Press-Releases/2022/June/Plastic-Pollution-in-Ocean-May-Harbor-Novel-Antibi
So what is new from the results presented at SCASM?
- Following advice we were given there, we acquired from the CDC a panel of antibiotic resistant strains and started testing our producers. Some of our isolates have activity against antibiotic resistant Citrobacter freundii and Enterococcus faecalis. Due to safety concerns, this process is slower than our usual testing, so we have a few more to test.
- All antibiotic experts say that in order to move ahead with this project we need to figure out the chemistry of the antibiotic activity. So there have been a lot of organic extractions and the setup of a more quantitative activity test using 96-well plates. With it, some challenges of variable activity.
- Just days before the poster presentation we received sequencing data for a couple of our producers. One of them was ID-ed as Cobetia, which is interesting and unique.
The beauty of being surrounded by experts was the great number of advice and suggestions we received. It’s amazing how quickly questions are answered in an-in person setting instead of via interminable email threads. We took lots of notes, and hopefully we’ll be able to address them if/when things slow down a bit.
Stay tuned.
Andrea Price wins 2021 SCASM Student Poster prize!
The Southern California chapter of the American Society of Microbiology (SCASM) holds every year in their Fall conference a Student Collegiate Poster competition. We are ecstatic that our own undergraduate researcher Andrea Price (IG @andreaevolves, Twitter @andreaevolves) won this prestigious and competitive award. In her poster, Andrea presented a panel of antibiotic producing bacteria she and others isolated from the ocean plastic project. The workflow followed that of Tiny EarthTM , with some adaptation for use with marine microbes. The producers were effective against both Gram positive and negative bacteria. PCR sequencing revealed the most bacteria belonged to the genera Vibrio and Phaeobacter. While some Phaeobacter species have been shown to produce antibiotics, the same cannot be said about Vibrios. Being at SCASM provided additional insight about the issues of antibiotic resistance, and we got a good tip about getting antibiotic resistant strains from the CDC for testing.
Congratulations Andrea! She will be presenting her research at the national ASM meeting next June in Washington DC. Lots to test until then!
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Tagged conferences, news, sequencing, vibrio
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We are all movie stars!
The short video above was recorded in November 2020, when we did a typical plastic sample collection and deployment at the Scripps pier . That was the month when we ran the first iteration of the online version of the project, for which we developed a bunch of video material. National University’s video team, Saul Torres and Nelson Fernandez spent hours with us, armed with a drone, a fancy GoPro, even fancier cameras and recording equipment, and the results have been impressive.
The final videos are almost done, and they include a detailed pier video with interviews, and a more detailed lab video documenting the process from piece of plastic to shiny PCR band under UV light. We just finalized our second round of the online version of the field trip experience, and the truth is, we were able to reach this way over 100 students in one month- many more than in one onsite course. And it was clear that the documentary we always show, Into the gyre, together with the videos and pictures of what was happening on the pier and the lab, made an impression. When we had our live Q&A with Jeff, Emelia, several members of Jeff’s lab, and NU instructors and students, students came with questions and ideas about how to prevent and solve plastic pollution in the ocean. These students were not science majors, but they cared about pollution, the ocean, and the environment in general. It was a stimulating discussion, and showed us that when people are engaged there is hope.
And of course, big part of the engagement was thanks to the power of images. Thank you Saul and Nelson for providing invaluable materials for our project!
Posted in SIO visits, STEM education
Tagged online education, video
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The wonders of the microbial world, SEM edition
Every time we collect the plastic from the ocean deployments, we marvel at the thickness of the biofilm attached to it, laugh at the little crabs running around, and just ooh and awe at life using any surface to grow and expand. We can see it, and we can feel it- especially when the cages need to be scrubbed and washed in a sonicated bath before reuse. But there is a special appreciation when we can actually “see it” at the microscopic level thanks to technology, in this case scanning electron microscopy (SEM).
Last time we collected samples back in December we planned for SEM in coordination with The Scripps Research Institute (TSRI) Microscopy Core. It was a chore- EM in general is finicky and samples have to be handled in a way that it preserves morphology. That meant not exposing the samples coming from underwater to air at any time. The logistics of the process were a bit daunting, and were solved by using a big “Ace hardware” bucket full of ocean water to haul the cages from the divers to our processing station. The TSRI people made the fixative using ocean water, and Rachel and I were elbow deep in the water opening cages and cutting the plastic to get them in the fixative. Our prospective research student Andrea Price was there, thankfully! She helped both with organizing the tubes and taking great pictures of the process.
Samples were then dropped off at TSRI and the wait began. The sampling happened just before Christmas so it took a while. But yesterday we finally had our SEM watching session (via zoom, of course). Dr. Kim Vanderpool walked us through the samples and the controls, and we spent a few hours looking for organisms to take pictures of. The one below is from plastic #4 (a typical grocery bag plastic) after 53 days. We called the large things “diatoms,” Emelia said they could be coccolithophores. I claim ignorance in knowledge of algae 🙂 On the other hand it was fun to see all the bacteria in-between and on top, of all kinds of shapes and forms.
This is just one sample- we have pictures of three plastics, both control and samples, at different magnifications. What it shows is something we knew macroscopically- that there is a huge biological richness to the plastisphere even after a relatively short incubation. Most SEM images have come from microplastics that have been in the water for much longer time, allowing the plastic to break down to tiny pieces. We are looking forward the next DNA results, in which we’ll be able to compare colonization by means of a surface only (glass slides) versus by attraction to plastic.
But yesterday was a fun day. One of those that left us with a warm fuzzy inner glow. Scientists need it once in a while!
2020: A challenging but strangely rewarding year
Since we started collecting the CURE data, there was always a recurring issue: getting enough students to answer the surveys and sign up for focus groups. When 2020 started, we had plans for expansion and dissemination, and we we were starting to outline how to broaden the reach of the CURE to other classes.
Woody Allen famously said “If you want to make God laugh, tell him about your plans,” although the original source seems to be the Bible. In any case, right after the February 2020 class attended the field trip, the Covid-19 pandemic exploded and turned the world upside down. And with onsite classes stopped and Scripps pier activities being limited, we were looking at a no activities for the foreseeable future. While in the fall we were able to get back in the lab and start prepping and collecting samples, there was no way to get students back to the pier.
When life gives you lemons, you make lemonade. The pandemic forced us educators to adapt laboratory classes to the online environment. And while we mourn the lack of hands-on experience, possibilities open in other dimensions- the ability to stagger the information overload (in educators’ jargon, scaffolded), the capacity to make the message more organized and appealing, and most importantly, to make the experience accessible for many more students.
So we worked on recording lectures and writing scripts, the National University video team recorded us on the pier and in the lab, and in record time the content was uploaded in time for the November classes: 3 sections of nonmajors and one of majors. All online of course.
This was the overall design for the virtual field trip experience:
- Week 2: Watch the documentary Into the gyre and discuss in the weekly discussion board
- Week 3: Watch recorded lectures re ocean plastic research and our project (these were usually delivered the day of the field trip). Assessed as part of the weekly quiz. Watch footage of the deployment and collection of samples, discuss during synchronous session. At the end of the week, students participated a a live Q&A with researchers to talk about plastic pollution, research, and career options/skills.
- Week 4: Nonmajors observe pictures of plates inoculated with microbes. Majors observed the pictures, and then did Blast searches of DNA sequences provided to identify the colonies.
The results were amazing. The engagement from students was palpable from the beginning. The live Q&A, held on a Saturday morning, was well-attended, and students had a lot of questions and comments. For the first time, we had students signing up to the focus groups. And finally, the survey data arrived.
The heatmap below shows the Likert scores to the survey questions. The questions cover students perception of knowledge of scientific research, laboratory techniques, ocean plastic research, and appreciation of science. There was a significant increase in scores between before and after the field trip for both onsite and online students. As you can see from the dark colors, online students’ “before” scores were lower than those of the onsite counterparts (in fact, statistically significantly lower). However, there is no significant difference in the “after” scores between onsite and online students.
Well, of course we need more data. But these results are very encouraging. Seems like we’ll be able to keep exposing students to the research experience even in an online setting, and this experience seems to be comparable to the onsite one. While as lab scientists we wish for students to be able to actively participate in hands-n activities, this is an alternative that can reach a much higher number of students independently on their geographical location or ability to do field trips.
So yes, we are pleased. The final versions of the videos (edited and with interviews) are in the works, and we are planning for a new set of virtual field trips in February 2021.
Happy New Year!
Posted in SIO visits, STEM education
Tagged covid, online education
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Ben’s microcosm paper is out!
The email came this morning, and although expected, it brought a great sense of satisfaction and joy. CURE Plastics alumnus Ben Stenson’s paper is officially out now, published in the excellent undergraduate research paper Fine Focus: https://openjournals.bsu.edu/finefocus/article/view/3322
Ben was my student in a microbiology class and he was interested in doing research, so he was one of the first undergrads joining the project in 2018. Over a year or so, he became responsible for prepping the plastic material for the sampling (a long and tedious process) and helping out during the field trips. He had many wide-ranging ideas of individual projects, and finally settled on looking at the chemical degradation part. And one day he came up with the microcosm idea. I won’t lie, I was skeptical. Not sure about the logistics and the whole setup, I decided to let Ben run the show. Which he did quite successfully.
There were hiccups along the way, issues that were simple to solve, and others that were more complicated. As a mentor, I was delighted to see the progress from enthusiasm mixed with lack of expertise to a more solid, robust understanding of what scientific research was about. And when it was time to write and analyze, it was great to see how much could be extracted from data, as long as they were recorded and saved.
The review process was fun too. As a first timer experiencing “revise and resubmit,” Ben was dejected while I was elated. For me, it also gave me the opportunity of putting in writing the disciplined steps of addressing a revision, from tackling the low-hanging fruit first to the “be courteous to the reviewers” mantra.
With this publication, we are closing a cycle. Ben is a graduate now, although he expressed he was looking a masters in chemistry. And I told him how we were planning to look more in depth at the degradation part because…(I guess that would be a good topic for another posting). So the story continues. But in the meantime, congrats, Ben!
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We are back in the lab!
After 7 months, we have made it back into the lab! A few weeks ago, our team was able to visit the pier and deploy a new set of samples into the water. We all were outfitted with masks and were able to social distance, both important in these uncertain times. The deployment itself was different, as we usually have a whole college-level biology class observing. We are so excited to finally resume the research we have been waiting to get back to.
Currently, in the lab, we are planning and preparing to analyze our new data set that will be collected at the end of the month. In a way, it feels like starting new, as some of our research was destroyed when laboratories were shut down. This upcoming deployment will include high-density polyethylene, low-density polyethylene, polypropylene, and a new addition will be a glass sample. Can anyone guess why?
The toughest part of being out of the lab for such a long period of time is readjusting to the workflow. Many of us are creatures of habit and returning to a new workspace involves adjusting and making sure everything still works like before. A test run was completed, and we are ready to intake new samples from the next sample collection.
Educational data are in…and they look good
We are in annual report time for the grant. Having a hard deadline to look at accomplishments and shortcomings once per year does wonders for a better understanding of where we are. But this year I was not looking forward it. Last year we had lots of material to show, from developing curriculum to the system of deploying and collecting surveys to new research sprouting up as undergraduate researchers embarked on their projects.
But the pandemic brought a screeching halt to our projects, laboratories were closed making side projects impossible, and we suffered a few setbacks including the thawing of a -80 oC freezer holding samples. Most people doing research has been affected, and there is an understanding that NSF understands it. That did not make the report writing a task I was looking forward to. And yet.
Summer and Fall of 2019 was full of field trips and data collections, and we had one more field trip February 2020, after which everything stopped. With the craziness of moving classes online and all other disruptions, we did not really look closely at the data until recently. And they look really interesting.
Last year, most of our students were non majors. This year, we have enough majors’ data that we could look at them separately.
This graph (from our external evaluator, dr. Steuck’s report) shows the impact the field trip had on our non majors. The gain is much higher for them compared to the majors. This is not completely unexpected- students in the biology major are probably more invested/committed already to science than non majors. But it was still cool to see. If one half day field trip and an extra week of discussions around it could make this change, what could be done with more regular activities and a curriculum incorporating research from the early Gen Ed courses?
So right now we are focusing on three aspects:
- We got started on a new sampling set (blog post coming soon!)
- We are developing a “virtual field trip” alternative (which besides allowing as to keep collecting data will also reach many more students)
- Writing! It is time to really crunch the data (both in education and biology) and get manuscripts out. There must be a silver lining to no travel and lots of computer hours!
Stay tuned 🙂
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Tagged data
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Is Recycling a Myth?
As educators of science in a world of viral headlines and information overload, it is sometimes hard to separate the process of science from scientists and people in the orbit of science. My students especially, who are overwhelmingly working adults with real life experiences and concerns, will often bring bring valuable discussions to class. More than once, during our post-field trip discussions, many of our Navy or former Navy students will show impressive knowledge of handling of plastic debris on ships. Those into surfing are often involved with Surfrider‘s and other community organizations’ cleanup efforts. And parents particularly are often very aware of plastic pollution: they think of the future of their children in a world awash with plastic. They worry not only of the ugliness of plastic debris on the shore or in the water, but also of the minuscule plastic particles that seem to be even in our food supplies.
So when this article came out about the push for recycling plastic as a way to assuage the public’s concern about plastic pollution, knowing it was an effort meant to fail, my heart sank. Not only about my own personal faith that while recycling was not THE solution, but it was still part of the solution. I just thought about how to adjust our future conversations with students when we explain the numbers in the triangles and discuss plastic pollution and possible solutions. At the end of the day, we are part of the problem as scientists- it is much easier to tear open a bag of plastic sterile tubes ready to be used instead of washing and autoclaving glass tubes.
In the recent years there has been a growing awareness of the importance of science communication and outreach. I have gone myself from a reluctant presenter of my research to a facilitate science communication workshops. In those trainings, we stress the importance of personal and emotional connection with the audience. And lately, I realize this also includes recognizing our own mistakes and vulnerabilities in areas of our expertise. As we gear up to resuming our field trip experiences (in a more distanced and virtual setup, stay tuned), we also have to be ready to discuss the issue of plastic pollution in the ocean at a deeper level. As Rachel’s posting showed, things have gotten worse since the Covid-19 pandemic started.
On the other hand, challenges also bring new opportunities. Our forced hiatus from the bench and the pier have brought many new ideas about adapting to the new pandemic normal, and at the same time adapting to confront this new normal with possible new directions in our research.
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