Phage isolation, electron microscopy, DNA sequencing in the first semester, annotation and comparative genomics in the second. And I get to teach the bioinformatics bit: annotation and comparative genomics. Woo-hoo! The great thing about this course, is that unlike most lab courses, the students (and faculty) will be setting up experiments intended not only to teach, but also to discover something new.  Also, the results of the research are meaningful. Genomics data generated by student participants will be used by other researchers to answer medical, ecological, and evolutionary scientific questions

The students isolated, sequenced and annotated two previously unknonwn mycobacteriophages, HINdeR and Phrux. The links are to the Mycobacteriophage Database phagesdb.org where the sequences and associated metadata (where and when HINdeR and Phrux were found and isolated) can be found. The annotations will be there shortly.

I had a great time teaching this course, together with Mitch Balish from my department, who is not only a great teacher, but shares my vice for keeping the students guessing when we are being serious and when we are kidding.  Mitch is the guy with the goatee in the short sleeved shirt; I’m the one in the black sweatshirt. Here’s what the students had to say about the course (original site at Miami University). Mitch starts talking at 2:57, I’m at 4:08, Gary Janssen (who taught the first semester) is at 5:08:

A decade ago a small group of documentary filmmakers set out with a dream to create a film rooted in the music of the streets. Not only has that dream been realized, it has blossomed into a global sensation called Playing For Change, a project including musicians of every level of renown, that has touched the lives of millions of people around the world.

While traveling the world filming and recording musicians, the crew became intimately involved with the music and people of each community they visited. Although many of these communities had limited resources and a modest standard of living, the people in them were full of generosity, warmth, and above all they were connected to each other by a common thread: music.

Out of these discoveries, the Playing For Change Foundation was born and made its mission to ensure that anyone with the desire to receive a music education would have the opportunity to do so. The Playing For Change Foundation is dedicated to the fundamental idea that peace and change are possible through the universal language of music.

Playing for Change’s hallmark is a series of videos of street musicians as well as better-known names from around the world, all performing the same song. Here is their take on the Stones’ Gimme Shelter:

Gimme Shelter | Playing For Change from Playing For Change on Vimeo.

Miami University has  joined the National Genomics Research Initiative (NGRI) offered by HHMI Science Education Alliance (SEA) in their Phage Genomics course. The students go directly into the lab, participating in an authentic research experience. In a full-year academic course they:

• isolate and characterize bacterial viruses from their local soil
• prepare the viral DNA for sequencing
• annotate and compare the sequenced genome

The Department of Microbiology at Miami University is offering this course in the upcoming year: four of our faculty will be teaching it. Phage isolation, electron microscopy, DNA sequencing in the first semester, annotation and comparative genomics in the second. And I get to teach the bioinformatics bit: annotation and comparative genomics. Woo-hoo! The great thing about this course, is that unlike most lab courses, the students (and faculty) will be setting up experiments intended not only to teach, but also to discover something new.  Also, the results of the research are meaningful. Genomics data generated by student participants will be used by other researchers to answer medical, ecological, and evolutionary scientific questions. Bacteriophages (viruses that infect bacteria) affect the biopsphere so profoundly, it is almost impossible to imagine. Their sheer biomass is equal to that of 75 million blue whales, and marine bacteriophages  kill about half of marine microbes every day. Bacteriophages have a huge host range, mind-boggling number of particles in the biosphere (10³⁰) and, above all, the genetic diversity is unmatched by all other life combined. Participating students will see how their data may be used by other researchers in the SEA network — truly collaborative, crowdsourced science. Here are the genomic sequences of SEA-sequenced bacteriophages already in GenBank.

If you are an incoming Miami freshman, and want to jump in and do some real science, it doesn’t get much better than this. Check out our course page, and ask about the Bacteriophage Biology course in your orientation. You may even get your name on a paper like these students from other participating universities.

Pope, W., Jacobs-Sera, D., Russell, D., Peebles, C., Al-Atrache, Z., Alcoser, T., Alexander, L., Alfano, M., Alford, S., Amy, N., Anderson, M., Anderson, A., Ang, A., Ares, M., Barber, A., Barker, L., Barrett, J., Barshop, W., Bauerle, C., Bayles, I., Belfield, K., Best, A., Borjon, A., Bowman, C., Boyer, C., Bradley, K., Bradley, V., Broadway, L., Budwal, K., Busby, K., Campbell, I., Campbell, A., Carey, A., Caruso, S., Chew, R., Cockburn, C., Cohen, L., Corajod, J., Cresawn, S., Davis, K., Deng, L., Denver, D., Dixon, B., Ekram, S., Elgin, S., Engelsen, A., English, B., Erb, M., Estrada, C., Filliger, L., Findley, A., Forbes, L., Forsyth, M., Fox, T., Fritz, M., Garcia, R., George, Z., Georges, A., Gissendanner, C., Goff, S., Goldstein, R., Gordon, K., Green, R., Guerra, S., Guiney-Olsen, K., Guiza, B., Haghighat, L., Hagopian, G., Harmon, C., Harmson, J., Hartzog, G., Harvey, S., He, S., He, K., Healy, K., Higinbotham, E., Hildebrandt, E., Ho, J., Hogan, G., Hohenstein, V., Holz, N., Huang, V., Hufford, E., Hynes, P., Jackson, A., Jansen, E., Jarvik, J., Jasinto, P., Jordan, T., Kasza, T., Katelyn, M., Kelsey, J., Kerrigan, L., Khaw, D., Kim, J., Knutter, J., Ko, C., Larkin, G., Laroche, J., Latif, A., Leuba, K., Leuba, S., Lewis, L., Loesser-Casey, K., Long, C., Lopez, A., Lowery, N., Lu, T., Mac, V., Masters, I., McCloud, J., McDonough, M., Medenbach, A., Menon, A., Miller, R., Morgan, B., Ng, P., Nguyen, E., Nguyen, K., Nguyen, E., Nicholson, K., Parnell, L., Peirce, C., Perz, A., Peterson, L., Pferdehirt, R., Philip, S., Pogliano, K., Pogliano, J., Polley, T., Puopolo, E., Rabinowitz, H., Resiss, M., Rhyan, C., Robinson, Y., Rodriguez, L., Rose, A., Rubin, J., Ruby, J., Saha, M., Sandoz, J., Savitskaya, J., Schipper, D., Schnitzler, C., Schott, A., Segal, J., Shaffer, C., Sheldon, K., Shepard, E., Shepardson, J., Shroff, M., Simmons, J., Simms, E., Simpson, B., Sinclair, K., Sjoholm, R., Slette, I., Spaulding, B., Straub, C., Stukey, J., Sughrue, T., Tang, T., Tatyana, L., Taylor, S., Taylor, B., Temple, L., Thompson, J., Tokarz, M., Trapani, S., Troum, A., Tsay, J., Tubbs, A., Walton, J., Wang, D., Wang, H., Warner, J., Weisser, E., Wendler, S., Weston-Hafer, K., Whelan, H., Williamson, K., Willis, A., Wirtshafter, H., Wong, T., Wu, P., Yang, Y., Yee, B., Zaidins, D., Zhang, B., Zúniga, M., Hendrix, R., & Hatfull, G. (2011). Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution PLoS ONE, 6 (1) DOI: 10.1371/journal.pone.0016329

This year, PhD Challenge step it up:

We are excited to announce that the new 2011 PhD Challenge is now open for submissions. The goal of this year’s challenge is to get either the nickname “DIRTY OLD MAN” or“CRAZY CAT LADY” included in the byline for at least one author in the final version of a peer-reviewed academic paper. As an example, an eligible submission could contain the authors John “Dirty Old Man” Smith and/or Jane “Crazy Cat Lady” Smith. The task for this challenge is quite difficult, but we are confident that the world’s best and brightest minds are eager to overcome adversity.

The official Call for Participation contains all of the details of the contest, including the submission dates and the prizes to be awarded to the winner. The PhD Challenge is open to all current graduate students in four-year universities and institutions. Be sure to also read the eligibility rules to make sure that your submission follows the guidelines of the contest.

I’d love to see you get that one in, grad students (Master’s students are also eligible). For more information go to the PhD Challenge site.

Muahahaha!

It is sad that we need a book with such a title. But thanks for writing it, Prof. Coyne

selected reflects somewhat on the state of evolution by natural selection, at least in the USA, as a cultural controversy rather than as a scientific theory. Of the seven, two books are polemics, and one of those is a creationist polemic.  When the centennial of Einstein’s publication of  Special Relativity was celebrated in universities, museums and schools around the world, there was no “teach the controversy”; there was just “teach”. Unfortunately, this is not yet the case for the theory of evolution by natural selection.

– Celebrate Darwin’s 200th Birthday With a Natural Selection of Books Zelda Roland / Wired