Bacteriophages to Bioinformatics
"Phage Hunters" exposes students to the research experience
Bacteriophages to Bioinformatics: “Phage Hunters” opens students’ eyes to the research experience
by Sarah L. Hansen
photo Tim Ford
Imagine being the first to discover and name a previously unknown virus. Does that seem like a stretch of the imagination for the average undergraduate? Well, the thrill of scientific discovery is reality for undergraduate biology majors in Dr. Steven Caruso’s BIOL 302L: Molecular and General Genetics Lab. The course is affectionately known as “Phage Hunters” and has been offered each fall at UMBC since 2008.
This unique course gives undergraduates the opportunity to isolate novel bacteriophages, viruses that infect bacterial cells, from local soil samples they collect. Students then examine their phages under the powerful Transmission Electron Microscope in the Keith R. Porter Imaging Facility on campus, and even give them permanent scientific names. Dr. Caruso calls this type of lab course “immersive research.”
The course gives students, most of whom will not pursue research careers, a feel for what goes on at the bench. They experience all the glory of new discoveries – and all the frustration associated with the scientific process. At the end of the course, student David Tatum commented, “One of the main lessons learned throughout this process of discovery was the value of persistence in the face of a perversely uncooperative universe,” (quoted here).
Students in Phage Hunters don’t conduct cookbook experiments with known outcomes. This is real science, folks. 302L teaches students to get creative when things go wrong and persevere in the face of challenging situations. Even if they aren’t going to become career researchers, the experience gives them a taste for what it takes to make scientific progress. Part of Caruso’s goal is to create “educated citizens.” He hopes that the education they get in Phage Hunters may one day influence their decisions at the polling place or how they respond to challenges in other areas of their lives. It’s about much more than a tiny bacteriophage.
And research on the newly-discovered phages doesn’t end when Caruso packs up the lab for winter break. Students determine which phages will be sent off-site for DNA sequencing in the “Phage Olympics” at the end of the fall semester. Then in the spring, students can follow 302L with BIOL 316L: “Phage Hunters” Genome Analysis. This class is co-taught by Caruso and computational biologist Dr. Ivan Erill, Assistant Professor of Biology at UMBC. In 316L students analyze the sequenced phage DNA using sophisticated computer programs with access to huge databases of genetic information. “They also use bioinformatics tools to further investigate the phages – to understand more about individual genes, their relationship to other, previously sequenced phages, etc.,” says Caruso. At the end of the course, the genome and its analysis are archived in GenBank, a massive, publicly available database used by scientists all over the world. The phages themselves are put in deep freeze and archived, as well.
Each spring the class members vote to select one student to present at the annual Howard Hughes Medical Institute Science Symposium in June. In 2011, HHMI disbursed $825 million for scientific research and $80 million for grants for science education. One of those grants belongs to UMBC to support the NEXUS project. HHMI also funded the Phage Hunters program from 2008-2011.
Originally, Phage Hunters was aimed at non-majors and enrolled 15-20 students per year. Caruso says that the lab experience “dramatically changed their view” of how science works. As of Fall 2012, though, the course is exclusively for students majoring in biology, and about 80 students enroll each year. Twenty-four students take the genome analysis course in the spring. HHMI continues to partially fund the courses by covering software and symposium costs.
Caruso himself is a graduate of UMBC’s biology program at the undergraduate and doctoral levels. He worked in Dr. Hal Schreier’s lab as a PhD student and also served as a teaching assistant for the Department of Biological Sciences. Caruso says he enjoyed teaching as a break from research. When he was about to graduate, a lecturer position opened up at UMBC and he was encouraged to apply. He did, and he’s been teaching full-time at UMBC ever since. He admits he misses research, but he believes his calling is in teaching. Caruso is so dedicated to undergraduate education that he’s thought about pursuing science education research in the future.
Always looking for ways to improve his teaching, Caruso is trying to incorporate investigative elements into the more-traditional version of 302L that runs during the spring semester. A potential collaboration with Dr. Hua Lu, Associate Professor of Biology at UMBC whose expertise is in plant molecular biology, is in the works. He welcomes any other ideas.
Caruso comments that “The kids are always amazing in this class. They work their tails off.” He praises the students’ motivation and eagerness to take ownership of their projects – so much so that he’s had to find additional people to supervise the lab space throughout the day. What generates this kind of work ethic in undergraduates, some of whom never even considered doing research before? Maybe it’s the immersive research approach. Maybe it’s Caruso’s and Erill’s teaching. The point is that here at UMBC students are learning to love and appreciate the process of science more than they ever did before. Imagine that.
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Bacteriophages to Bioinformatics: “Phage Hunters” opens students’ eyes to the research experience by Sarah L. Hansen photo Tim Ford Imagine being the first to discover and name a previously...
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Fri, 28 Mar 2014 18:18:10 -0400
Chasing Their Star, on YouTube
The message to aspiring video makers on YouTube is clear, and seductive: Attract an audience, build your brand. But success, let alone stardom and wealth, remains elusive.
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The message to aspiring video makers on YouTube is clear, and seductive: Attract an audience, build your brand. But success, let alone stardom and wealth, remains elusive.
http://www.nytimes.com/2014/02/02/business/chasing-their-star-on-youtube.html?partner=rss&emc=rss
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Strategies: Trying to See Apple From a Different Angle
Wall Street can’t decide whether a giant company can still grow by leaps and bounds — or whether it even needs to.
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Wall Street can’t decide whether a giant company can still grow by leaps and bounds — or whether it even needs to.
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Bits Blog: When Your App Is in the Cloud
The telecommunications services business, worth $1 trillion in annual sales, is starting to feel the effects of cloud computing, one of this era’s most important advances in high tech.
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The telecommunications services business, worth $1 trillion in annual sales, is starting to feel the effects of cloud computing, one of this era’s most important advances in high tech.
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Mon, 03 Feb 2014 15:19:05 -0500
Technophoria: When No One Is Just a Face in the Crowd
Facial recognition technology may soon help stores track their best customers — and that has privacy advocates concerned.
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Facial recognition technology may soon help stores track their best customers — and that has privacy advocates concerned.
http://www.nytimes.com/2014/02/02/technology/when-no-one-is-just-a-face-in-the-crowd.html?partner=rss&emc=rss
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Comics of the week #220
Every week we feature a set of comics created exclusively for WDD.
The content revolves around web design, blogging and funny situations that we encounter in our daily lives as designers.
These great cartoons are created by Jerry King, an award-winning cartoonist who’s one of the most published, prolific and versatile cartoonists in the world today.
So for a few moments, take a break from your daily routine, have a laugh and enjoy these funny cartoons.
Feel free to leave your comments and suggestions below as well as any related stories of your own…
Complaint interaction
Back-end Kardashian
Digital digit
Can you relate to these situations? Please share your funny stories and comments below…
Source
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Every week we feature a set of comics created exclusively for WDD. The content revolves around web design, blogging and funny situations that we encounter in our daily lives as designers....
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Mr. Alaiad becomes a phd candidate
Figure 34: Mr. Alaiad defends his proposal successfully
Congratulations to Ahmad! He has passed his proposal exam and formally
become a PhD candidate. A brief summary of Ahmad's PhD research topic is
as follows:
Healthcare is one of the largest growing burdens for the US economy.
Effective and efficient home healthcare can help control healthcare
costs and improve healthcare quality and increase patient independence.
In the future, it will be almost unimaginable to consider home
healthcare without the emerging home healthcare information technology
including wireless sensor networks and robotics. Despite their potential
for home healthcare, previous research on these technologies has largely
focused on the technical implementation, technology improvement and
clinical applications with very limited discussion of the larger
socio-technical, cognitive, and contextual issues that are arguably
equally important. Ahmad's PhD dissertation aims to bridge this
knowledge gap by building a generic model that explains the adoption
behavior for these emerging technologies in home healthcare.
]]>
Figure 34: Mr. Alaiad defends his proposal successfully Congratulations to Ahmad! He has passed his proposal exam and formally become a PhD candidate. A brief summary of Ahmad's PhD...
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Apply to the UMBC Cyber Scholars Program by 14 February
Computer Engineering, Computer Science, and Information Systems majors with at least a 3.25 GPA and an interest in cybersecurity are encouraged to apply for 2014-15 cohort of the UMBC Cyber Scholars Program.
The Cyber Scholars Program is a merit-based scholarship program for talented undergraduates majoring in computer science, information systems of computer engineering who are interested in pursuing a career within the field of cybersecurity. Cyber Scholars are supported financially and incorporated into a scholarship community, unique courses, mentoring, and the chance to take part in cybersecurity research and internships during in their academic careers.
Apply by 14 February 2014 by submitting a application along with two letters of recommendation and an official college transcript.
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Computer Engineering, Computer Science, and Information Systems majors with at least a 3.25 GPA and an interest in cybersecurity are encouraged to apply for 2014-15 cohort of the UMBC Cyber...
http://www.csee.umbc.edu/2014/01/apply-to-the-umbc-cyber-scholars-program-by-14-february/
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Fri, 31 Jan 2014 23:07:07 -0500
Tech Rides Are Focus of Hostility in Bay Area
Rising resentment against elite technology firms manifests itself in demonstrations at public bus stops in San Francisco, where private shuttle buses ferry engineers to work.
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Rising resentment against elite technology firms manifests itself in demonstrations at public bus stops in San Francisco, where private shuttle buses ferry engineers to work.
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Fri, 31 Jan 2014 22:19:53 -0500
Get Involved with B'More Proud 2014!
Annual LGBTQIA Leadership Summit is held at JHU this March!
From Rebecca Rivera, Programming Co-Chair of B'More Proud 2014:
My name is Rebecca Rivera and I am the current Programming Co-Chair for the B'More Proud LGBTQIA Leadership Summit, which will be held at Johns Hopkins University on March 30th, 2014. The goal of B'More Proud is participation from members of the Baltimore community.
On behalf of the planning committee, I would like to invite UMBC's Freedom Alliance to participate in the day-long B'More Proud LGBTQIA Leadership Summit. Registration is free, and we firmly believe that members of your student group would benefit greatly from the various breakout sessions and the resources fair that we will be holding. There will also be entertainment at the end of the day to allow our attendees to relax after an eventful day.
If you would like to get involved with B'More Proud by volunteering or hosting a breakout session look at the attached file that details information about those opportunities.
]]>
From Rebecca Rivera, Programming Co-Chair of B'More Proud 2014: My name is Rebecca Rivera and I am the current Programming Co-Chair for the B'More Proud LGBTQIA Leadership Summit, which will...
http://www.bmoreproud.org
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