BIMS

When Angelo Falcon chose his water source for the first project in BIOL 3410 Microbiology lab, he had little idea that it would bring to light an issue being discussed in Abilene City Hall.  The class was charged with finding various sources of ground water and surface water to test for the numbers and types of bacteria present.  Angelo sampled water from a man-made waterfall downtown, while others in the class tested streams and lakes and ponds and wells in and around Abilene.  Testing included a standard MPN (most probable number) assay, followed by isolation and purification of a Gram negative bacterium, characterization of its colony morphology and staining characteristics, and biochemical testing to provide hints at its identity.  The project culminated in confirming the identifications of isolates using BD-BBL Crystal(R) E/NF panels for rapid identification of enteric and non-fermenting Gram negative rods.  Angelo’s isolate came back as Enterobacter cloacae, and a little snooping revealed this to be a microbe frequently associated with sewage and soil.  A conversation with people associated with the waterfall revealed the water source to be a shallow well tapping into an aquifer found under much of northern Abilene.

And that is things began to add up.  In early September, Abilene’s City Council dealt with the issue of shallow ground water in northern Abilene and its unsanitary condition by issuing a warning to residents with wells into this water source – do not drink the water, do not use the water for irrigating vegetables, do not allow pets or livestock to drink the water.  Angelo can testify to the presence of nasty bacteria in the water.  Add to Angelo’s work confirming evidence from Amanda Carter, a classmate who tested water from her father’s north-side well, and you have every reason to believe City Council made the right decision.

http://www.reporternews.com/news/2011/sep/16/another-msd-vote-looms/?print=1

Its nice when what you are doing in the lab to develop basic skills has a purpose and relevance to society.

This fall at universities around the world, some students will engage in a two-pronged approach to learning the knowledge and skills of microbiology lab technique.  They will learn the conventional way, loop and burner and tubes and plates, and they will expand their opportunity to think like a microbiologist and simulate their lab work using their computers with software developed by Dr. Gary Wilson and his partners at Intuitive Systems, Inc.  The software, VirtualUnknown(TM) Microbiology, is now over a decade old, and this summer marks the end of a two year-long development program to create a new, more versatile version.  Dr. Wilson’s son, Marcus Wilson, has been the Java-developer making it all happen.

The original VU Microbiology was developed with particular goals in mind:  solid microbiology instruction, true-to-life simulation requiring knowledge of aseptic technique, opportunities for students to make mistakes with consequences, detailed reporting in the Virtual Lab Report of all errors in technique and judgment – all in a game-like atmosphere.  Judging by the popularity of the software with allied health programs, it scores on all points.  But the leaps in technology over the past ten years have necessitated parallel improvements in the software.  Whereas the original product was PC-exclusively and largely stand-alone, the new version will be “platform neutral” and Web-based.  Testing on Mac, Linux, and Windows have all gone well, meaning any student with any computer will soon have equal access to this tool.  VirtualUnknown(TM) Microbiology Web Edition (VUWEB) will be “Micro Anywhere!” incarnate.

To make that happen, Dr. Wilson has spent the summer taking care of the content and support components, while Marcus has been polishing the look, feel, and action of the software.  Several tests were replaced with updated versions.  New Help files had to be created that accounted for the current state of computer skills in average students, rather than on the average computer skills of 1998.  A new lab activities manual was written, entitled Micro Digital Media(TM), along with an instructor’s key.  MDM gets right to the nuts and bolts of microbiology and spends its 100 pages helping students learn how lab skills are used in a health setting.  There is even an exercise to help students learn how to make fancy research posters to display their work.

What’s left?  The Help files are text- and graphic-centered,  but will also have extensive videos still in production.  And there’s extensive beta testing to come.  Anticipated product release will be Spring 2012.

Last night I finished a book on the submarine the USS Scorpion and was struck by how busy naval ships are when they return to their home ports.  Rather than the boats sitting idle while the crew gets some R&R, it is a time when systems are tested, problems are fixed, and improvements are made.  With the close of the spring semester and the onset of summer, we find our BIMS program returning from a year “at sea” where the courses and techniques and facilities have been operating to conduct our “mission” – teaching BIMS majors.  Now with the conclusion of the year, we are  back in “home port” doing the same program tests, fixes, and upgrades submariners do before we take our program back out to sea next fall.  We find ourselves taking stock of what worked, what didn’t, and what comes next…

What worked.

• We were pleased with the direction taken in BIMS 1300 Introduction to Scientific Research.  The focus on learning the basics of how science is conducted, how to critically analyze the world around us, and how to apply the skills of science and analysis to better understand  our world was a positive development this year.
• We were pleased with the functionality of the new spaces for teaching and research that came online in November.  The micro lab was used by three different lab/lecture classes without any trainwrecks.  The student project spaces gave us flexible space to support student work outside of regular hours that functioned flawlessly.  Student card access to the labs was appreciated by students and allowed some previously impossible activities (round-the-clock monitoring of growth) to take place.  New equipment in the student research labs and teaching labs gave new approaches for studying lab problems.
• We were pleased with the new Genetics course taught by Dr. Brosius.  As a more balanced mixture of Mendelian, population, and molecular genetics, it gave an exceptional foundation for students ready to delve deeper in Molecular Cell Biology classes next year.
• We were pleased with the transition to a new schedule for offering BIMS courses in the freshman sequence.  Next year, our new sequence will be fully operational.

What didn’t work.

• We found the positioning of some pieces of equipment in our new spaces to be less than ideal.  For instance, a large rack for placement of backpacks and student materials went unused and students continued to put those things on the floor of the lab.  Incubators were crowded together making access by students from two classes meeting simultaneously very difficult.  After “living in the spaces” for a full semester, we will “rearrange some of the furniture” this summer.
• We found less success in Advanced Micro and capstones than was hoped.  We realized halfway through the semester that student ownership of the projects was necessary in order to move them toward self-sufficiency and greater investment in getting results, and so we made adjustments to that effect.  Still, at the end we realized there were other steps we could have taken to improve the experience and the productivity.
• A hiring freeze undermined our efforts to fill the vacant molecular biologist position that has hamstrung us during the year.  We are unable to deliver our complete BIMS program without that person, and so we found ourselves scrambling to substitute courses to allow students to graduate.  The result was for those graduates a fine degree but in some ways lacking of all the breadth and depth BIMS should have.

What’s next?

• BIMS faculty are spending May taking stock of what worked and what didn’t with the intention to refine our efforts to improve our program.  This annual review and planning insures we don’t continue doing the same things in the same ways out of habit or because it is easy.
• Even in the midst of a hiring freeze, we have secured the services of McM alumna Sheena Banks to teach molecular courses for us as an adjunct.  Sheena received her MS in Immunology from UTMB and is working as a Research Associate at the TTUHSC School of Pharmacy.  This should help us bring a major portion of the molecular dimension of the BIMS program back online.
• We will continue to experiment with courses and their delivery next year.  For instance, the BIOL 1301 Unicellular Organisms course and BIMS 1101 Uni Lab will receive a major overhaul next year to help strengthen areas in student learning that our testing of junior and senior BIMS students has revealed.  Also,  the BIMS 4491 Advanced Micro course for the fall will focus on spore ecology and physiology, and will meet in two hour blocks three times weekly.  Students will see how different compositions of growth media influence the size and resistance of Bacillus thuringiensis endospores.  Our expectation is that this work will result in presentation at the spring meeting of the Texas Branch of the American Society for Microbiology and subsequent publication.

All this is to say the BIMS program is not static, is never satisfied.  While for many on campus the summer represents a time of rest, for us it is a very busy time.  We want our program to be the best it can be – battle-ready and tested, improved – when we set sail again next fall to accomplish our mission to give BIMS majors the very best knowledge and skills and experiences possible.