---

MIP Undergraduate Students that received their B.S. Degrees on December 19...

Blair Cabradilla
Devin Cramer
Kelsie Furutani
Peter Garza
Laurel Haskall Dove
Katrina Hernandez
Stella Kratzer
Jacquelyn Kruger
Erin Mikkelsen
Dania Smith
Amanda Watkins

MIP Graduate Students that received their M.S. Degrees on December 18...

Monali Bera
Tamara Hess

MIP Graduate Students that received their Ph.D. Degrees on December 18...

Stephen Deus
Marcela Henao-Tamayo
Carolina Mehaffy
Rama Sakamuri
Anna Winters

As part of a Department-wide Training Grant initiative, we’re pleased to announce that MIP has recently been awarded a USDA National Food and Agriculture Institute Training Grant as part of the National Needs Graduate Fellowships Program. The $156,000 award establishes the “Animal Biosecurity Pathology Training Program” here in MIP. The award will support the PhD training of two students for three years. Congratulations to Jeff Wilusz (PI) and Sandy Quackenbush (Co-PI) on this award. Taking a break from debating Health Care Legislation, Senator Udall’s office even called to congratulate us!

Congratulations to Jerome Lee on being awarded a one year pre-doctoral fellowship from the American Heart Association for his project entitled, "Post-Transcriptional Control by CUGBP1 in the Heart". Jerome is a PhD student in the Wilusz² Lab

Several MIP Undergraduate students attended the Fall meeting of the Rocky Mountain Chapter of the American Society for Microbiology held on Saturday, November 21st at the UCD Anschutz Medical Campus in Aurora. Pictured below are our students posing with the fruits of their labor.

Jackie Kruger, Justine Maselli, and mentor Alan Godwin

Holly Hamilton

MIP Veterinary Residents, Chuck Halsey, Laura Brandt, and Matt Feirer, recently traveled to Monterey, California to participate in the Annual ACVP Meeting. Chuck and Laura both won the ACVP/AAVLD Travel Awards for the conference.  Chuck’s presentation was entitled, "Feline Intestinal Sclerosing Mast Cell Tumor: 50 Cases (1997-2008)".  Laura’s award-winning poster was entitled, "The identification and localization of renal proteins in the dog and cat kidney using immunohistochemistry".

Comparative Genomic and Phylogeographic Analysis of Mycobacterium leprae

Marc Minot, John S. Spencer, Patrick J. Brennan, Stewart T. Cole (and 27 others)

Nature Genetics (December 2009) 41: 1282-1289

Sequencing strains of the organism that causes leprosy (M. leprae) on the surface might seem to be pretty repetitive, boring work. After all, the four strains now sequenced to date are 99.995% identical and only ~3 percent of the proteins even show a single amino acid change. So why in the world would we choose a paper that reports the sequence of M. leprae strains from Brazil, Thailand and the good old US of A as our coveted ‘Paper of the Month®’?

Well in many regards this particular paper should be worthy of its own episode on CSI or Cold Case. The storyline of this scientific article involves tracking killers and looking for evidence in graveyards. Here’s the scoop this potential Emmy-winning screenplay: The limited genetic variation of M. leprae can actually be exploited to identify unique classes of DNA called ‘SNPs’ that John, Pat et al used to divided the leprosy bacillus up into 4 major SNP families (each of which can be divided into 3-4 additional subtypes for you connoisseurs out there). These classes can then be used in Sherlock Holmes-fashion to track and reconstruct the origin of M. leprae and the global spread of the organisms throughout human history. The leprosy bacteria (SNP 2) appears to have originated in East Africa. It mutated a very little bit (SNP3) when it moved west into the Middle East and Europe. Interestingly, it arrived in Asia by two routes – SNP1 took a southern track from Africa and SNP4 arrived from the European SNP3 M. leprae strain along the ‘Silk Road’ trade route. In a curious case of tit-for-tat, this was the same route that Yersina pestis took to get to Europe for China to start the devastating Black Plague in the Middle Ages. Finally, based on this SNP analysis, the leprosy bacillus very likely came to the Americas via European trade and settlement. To test their model, the research group did a little ‘Paleomicrobiology’ – going to gravesights and isolating/characterizing SNPs from 13 ancient M. leprae isolates from corpses who succumbed to the disease. All in all, one of the coolest applications of Solexa and conventional sequence analysis we’re aware of to date.

By the way if you had #3,268,071 in the ‘Guess the number of basepairs in the BR4923 Brazilian isolate of M. leprae’ Contest, you win!

MIP Publications Late November - Early December 2009

• Attoui H, Mendez-Lopez MR, Rao S, Hurtado-Alendes A, Lizaraso-Caparo F, Jaafar FM, Samuel AR, Belhouchet M, Pritchard LI, Melville L, Weir RP, Hyatt AD, Davis SS, Lunt R, Calisher CH, Tesh RB, Fujita R, Mertens PP.  Peruvian horse sickness virus and Yunnan orbivirus, isolated from vertebrates and mosquitoes in Peru and Australia.  Virology. 2009 Nov 25;394(2):298-310.
• Ballweber LR.  Taenia crassiceps subcutaneous cysticercosis in an adult dog.  Vet Rec. 2009 Dec 5;165(23):693-4.
• Barker CM, Bolling BG, Moore CG, Eisen L.  Relationship between distance from major larval habitats and abundance of adult mosquitoes in semiarid plains landscapes in Colorado.  J Med Entomol. 2009 Nov;46(6):1290-8
• Bevins SN, Tracey JA, Franklin SP, Schmit VL, Macmillan ML, Gage KL, Schriefer ME, Logan KA, Sweanor LL, Alldredge MW, Krumm C, Boyce WM, Vickers W, Riley SP, Lyren LM, Boydston EE, Fisher RN, Roelke ME, Salman M, Crooks KR, Vandewoude S.  Wild felids as hosts for human plague, Western United States.  Emerg Infect Dis. 2009 Dec;15(12):2021-4.
• Bolling BG, Barker CM, Moore CG, Pape WJ, Eisen L.  Seasonal patterns for entomological measures of risk for exposure to Culex vectors and West Nile virus in relation to human disease cases in northeastern Colorado.  J Med Entomol. 2009 Nov;46(6):1519-31.
• Brennan PJ.  IDEAL: in the footsteps of IMMLEP and THELEP.  Lepr Rev. 2009 Sep;80(3):236-45.
• Eisen L, Beaty BJ, Morrison AC, Scott TW.  ProactiveVector control strategies and improved monitoring and evaluation practices for dengue prevention.  J Med Entomol. 2009 Nov;46(6):1245-55.
• Fontes AN, Sakamuri RM, Baptista IM, Ura S, Moraes MO, Martínez AN, Sarno EN, Brennan PJ, Vissa VD, Suffys PN  Genetic diversity of mycobacterium leprae isolates from Brazilian leprosy patients.  Lepr Rev. 2009 Sep;80(3):302-15.
• Huang CY, Butrapet S, Moss KJ, Childers T, Erb SM, Calvert AE, Silengo SJ, Kinney RM, Blair CD, Roehrig JT.  The dengue virus type 2 envelope protein fusion peptide is essential for membrane fusion.  Virology. 2010 Jan 20;396(2):305-15.
• Issur M, Geiss BJ, Bougie I, Picard-Jean F, Despins S, Mayette J, Hobdey SE, Bisaillon M.
  The flavivirus NS5 protein is a true RNA guanylyltransferase that catalyzes a two-step reaction to form the RNA cap structure.  RNA. 2009 Dec;15(12):2340-50. 
• McCoy AM, Hackett ES, Callan RJ, Powers BE.  Alimentary-associated carcinomas in five Vietnamese potbellied pigs.  J Am Vet Med Assoc. 2009 Dec 1;235(11):1336-41.
• Monot M, Honoré N, Garnier T, Zidane N, Sherafi D, Paniz-Mondolfi A, Matsuoka M, Taylor GM, Donoghue HD, Bouwman A, Mays S, Watson C, Lockwood D, Khamispour A, Dowlati Y, Jianping S, Rea TH, Vera-Cabrera L, Stefani MM, Banu S, Macdonald M, Sapkota BR, Spencer JS, Thomas J, Harshman K, Singh P, Busso P, Gattiker A, Rougemont J, Brennan PJ, Cole ST.  Comparative genomic and phylogeographic analysis of Mycobacterium leprae.  Nat Genet. 2009 Dec;41(12):1282-9.
• Penilla RP, Ranson H, Padilla N, Morgan JC, Steen K, Pignatelli P, Rodríguez AD, Hemingway J, Brogdon WG, Black WC 4th, Benedict MQ.  Towards a genetic map for Anopheles albimanus: identification of microsatellite markers and a preliminary linkage map for chromosome 2.  Am J Trop Med Hyg. 2009 Dec;81(6):1007-12.
• Rosenbaum MD, VandeWoude S, Johnson TE.  Effects of cage-change frequency and bedding volume on mice and their microenvironment.  J Am Assoc Lab Anim Sci. 2009 Nov;48(6):763-73.
• Sakamuri RM, Harrison J, Gelber R, Saunderson P, Brennan PJ, Balagon M, Vissa V.  A continuation: study and characterisation of Mycobacterium leprae short tandem repeat genotypes and transmission of leprosy in Cebu, Philippines.  Lepr Rev. 2009 Sep;80(3):272-9.
• Sharpe SA, Eschelbach E, Basaraba RJ, Gleeson F, Hall GA, McIntyre A, Williams A, Kraft SL, Clark S, Gooch K, Hatch G, Orme IM, Marsh PD, Dennis MJ.  Determination of lesion volume by MRI and stereology in a macaque model of tuberculosis.  Tuberculosis (Edinb). 2009 Nov;89(6):405-16.
• Srisungnam S, Rudeeaneksin J, Lukebua A, Wattanapokayakit S, Pasadorn S, Mahotarn K, Ajincholapan, Sakamuri RM, Kimura M, Brennan PJ, Phetsuksiri B, Vissa V.  Molecular epidemiology of leprosy based on VNTR typing in Thailand.  Lepr Rev. 2009 Sep;80(3):280-9.
• Williams A, Hall Y, Orme IM.  Evaluation of new vaccines for tuberculosis in the guinea pig model.  Tuberculosis (Edinb). 2009 Nov;89(6):389-97.

This year MIP planned on ‘adopting’ three needy families for the holidays through the Salvation Army's "Angels Among Us" program. Because of your overwhelming generosity, we had to add a fourth family this year! Overall we collected gifts for 10 kids from the four families + ~ $225 in Walmart cards. Your contributions REALLY made a difference for these families during these troubled economic times. A big thanks to Carol Wilusz for coordinating these efforts.

Tired of the ups and downs associated with basic research? We’ll you’re not alone. Due to a pressing need for vital maintenance (rather than as some suspect a clever plot by MIP’s Stayin’ Alive coordinator Barb Andre to increase the overall level of exercise in the MIP Department), the Micro Building’s sole elevator will be out of commission from December 16 through January 6th. Pictured above are several MIPer’s enjoying one of the last rides of the decade in the old clunker.

ATTENTION MICRO MAJORS

Fellowship awards to support your research for a 10 week period this summer in an MIP laboratory – as well as for your travel to present your data at the 2011 National Meeting of the American Society fro Microbiology are available from the 2010 ASM Undergraduate Research Fellowship Program. Applications are due February 1st. For more info check out the ASM Undergraduate Research Fellowship Website.

Spring Faculty Seminars

MIP is kicking off the decade with an exciting array of internal and external speakers in our Friday morning seminar program. Check it out at the Faculty Seminar Webpage.

Many MIP'ers participated in Holiday/End-of-Year celebrations; whether a group get-to-gether at a local watering hole or a more formal organized event. The MRL held their yearly potluck which this year included a cooking contest for best appetizer, main dish, and desert! The AIDL held a potluck with quite an impressive assortment of good cooking! The department administrative staff participated in a potluck that included a white elephant gift exchange--check out some of the fine gifts staff went home with!

Best wishes from the MIP News Staff for a Happy Holiday and a Fantastic 2010!

In case you think this doesn't apply to you, think again. The Sexual Harassment Training is mandatory for all employees including students, and must be completed by January 15, 2010.

The link to the training is http://oeod.colostate.edu/. Please be sure to print the certificate of completion, sign and forward to Bev Meyer by the deadline.

Wedding at the end of a rainbow...

Congratulations to Mary Sanders and John Poor on their marriage on October 3 at North Hero Island, Lake Champlain, Vermont!

MIP700 – Topics
Dr. Torsten Eckstein will lead this course for Spring 2010. The title will be "lipidomics". Basic chemistry will be covered but the course will focus on the involvement of lipids in pathogenicity and virulence. Contact Torsten with any questions.

AGRI680a2 - Integrated Systems Biology Seminar
Class Time: Wednesday 3:00PM-3:50PM Microbiology B120
Coordinator: Jessica Prenni
Summary: Through lectures as part of the Integrated Systems Biology Seminar Series, students will be exposed to broader perspectives in systems biology, specifically the application of genomics, proteomics, metabolomics, and bioinformatics, and will learn how they can integrate these tools and approaches into their own research.

BSPM/MIP576 - Practical Bioinformatics
Class time: Monday, Wednesday 10:00AM-10:50AM Plant Science E5
(lectures/seminars) Friday 02:00PM-02:50PM Shepardson 218 (practice) Instructor: Andrey Ptitsyn
Summary: This course will be geared towards development of practical skills and recipes for solving common problems in biomedical research using computational techniques and available bioinformatics software.

STAT 580 - Design and Data Analysis for Bioinformatics
Class Times: Tuesdays and Thursdays 9:30-10:45am
Prerequisite: STAT511 or STAT540 or permission of the instructor
Instructor: Ann Hess
Summary: Statistical methods for bioinformatics including design and analysis for gene expression and proteomics studies. Students will learn to program in R. Full course outline can be found at Ann Hess’ website

BSPM580 - Understanding Genomes
Spring 2010, T/TR 9-10:15 AM
Plant Sciences Room E008
Instructor: Stephen Chisholm
Email: Chisholm@colostate.edu
Summary: A graduate-level introduction to how bioinformatics and genome science allow scientists to address biological questions at a genome level and the proper use of web-based genome resources. The aim of the course if to teach students how to analyze genomic data and incorporated it into their individual research programs.

The College Research Council (CRC) 2010 Call for Proposals information is now available on the web at the College Faculty Resources Webpage. The deadline for proposal submission is 5:00pm on Monday, March 22, 2010.

The 11th Annual CVMBS Research Day Symposium will be held on Saturday, January 23, 2010 at the Hilton, Fort Collins.

“May all your troubles last as long as your New Year's resolutions! ”

MIP Grad student Katie Poole-Smith revising her dissertation during one of the frequent power outages in San Juan, PR.

• Intrepid MIP grad student Katie Poole-Smith recording the domestic human landing rate for Aedes aegypti.
• Photographic proof of the proverbial light at the end of the tunnel of PhD research.
• Well looky here - an MIP student who's ‘in the dark’.....
• "...and I thought I had it rough trying to work at my desk in the shower stall at AIDL"
• Submit your own

Questions for MIPuzzle #49
MIPuzzle #49 Answers

As we close out this up and down year, let’s take a moment to remember the good old days when the elevator in the Micro Bldg was working as well as some of the Department’s highlights from 2009:

1. MIP researchers published an impressive 148 papers in 2009 by our unofficial count.  Department publications were up slightly in the Fall (45), reflecting either the faculty taking advantage of summer break to write up their labs’ data or delays in publication due to the troublesome ‘3rd reviewer’ from the YouTube video that’s been making the rounds throughout academia.
2. MIP launched 80 graduates out into the real world this year (8 PhD, 7 MS and 65 BS) along with 4 individuals who completed their Pathology residencies.  If you’re keeping score, that’s 84 more people than were launched from South Fort Collins in a balloon on that infamous afternoon of October 15th.
3. The Department continued its impressive performance in the research grant-apalooza, bringing in almost $34 million dollars in extramural funding in 2009 from 177 individual awards according to the CSU VPR website.  This includes 12 ARRA grants – a ‘stimulating’ 46% of the total Recovery Act grants obtained by the university.
4. MIP faculty received a number of impressive awards in 2009, most notably being Dr. Ian Orme’s long overdue recognition as a University Distinguished Professor.  In case your curious, MIP is now only one short of being able to field a team in the UDP intramural basketball league.
5. MIP students also took home significant bling in 2009 for their research at local, regional and national meetings.  This includes awards won by 11 graduate students, 6 undergrads and even a high school student (3rd place at the International Science Fair).  Frankly of all of the department’s accomplishments, these awards are by far the most satisfying to report.  You guys and gals ROCK!
6. A decade of effort by Barb Powers and company finally paid off in 2009 as the brand spanking new Diagnostic Medicine Center opened in 2009 and was christened on September 11th.  Perhaps not quite as exciting (unless of course you’re cruising the foothills looking for a place to rest your Subaru), we also christened a new parking lot west of AIDL. 
7. Five hard working MIP faculty were promoted and/or received tenure in 2009.  In addition, we were able to stabilize the positions of two well-deserving special appointment faculty by switching them to tenure-track status.  Given the challenging financial times, we sure hope that these trends in our faculty roster will continue.
8. The MIP Dept also proved that it wasn’t just a hard working, nose-to-the-microscope 24/7 kinda group.  From 75 MIPers singing, “take me out to the ballgame” to the overflowing plates at our Thanksgiving Potluck, we repeatedly showed in 2009 that we know how to have a good time.  The Department also once again displayed its heart and generosity through its ‘Adopt-A-Family’ holiday tradition. 
9. In 2009 we said goodbye (and good luck) to four members of our Admin staff (Wendy, Claire, Kathy and Tansi), Densovirologist-extraordinaire Jon Carlson (although lucky for us he seems to be spending his retirement on the 4th floor of Micro….) and (sniff) our good old department copiers and printers. 
10. Last but not least, while 428 magazines folded in 2009, the MIPnews celebrated its 5th anniversary in August 2009! 

Take a walk down memory lane by looking at the photos in our Decade in Pictures montage.

As the ‘00’s come to a close, it seems fitting to leave you with MIPnews’

Top Ten MIP Predictions for the next decade

• Career Development Opportunities

  NIH has recently re-issued the RFA for the following career-oriented grant programs:

  • PA-10-063, NIH Pathway to Independence Award (Parent K99/R00)
  • PA-10-062, Mentored Quantitative Research Development Award (Parent K25)
  • PA-10-061,Midcareer Investigator Award in Patient-Oriented Research (Parent K24)
  • PA-10-059, Mentored Clinical Scientist Research Career Development Award (Parent K08)
  • PA-10-057, Independent Scientist Award (Parent K02)
  • PA-10-056, Mentored Research Scientist Development Award (Parent K01)

  Also note that for all Career Development awards, NIH has recently mandated that trainees have at least eight hours of formal instruction at least once during each career stage, at least every four years. Thus you will need to include a plan on how you will address this in your application.

• An uptick in NIAID R01 paylines

  A little good news from Bethesda: R01 paylines at NIAID have been recently raised to the 8 percentile (12th percentile for new investigators)

• Additional Bioinformatics Resources from NIAID

  As you snuggle up with your egg nog by the fireplace this holiday season, you may want to check out the following resources:

  • Bioinformatics Resource Centers
  • Influenza Research Database
  • Immune Epitope Database and Analysis Resource
  • ImmPort -- Immunology Database and Analysis Portal
  • Systems Immunology

Carol Wilusz , "Post-Transcriptional Control by CUGBPI in the Heart ", American Heart Association.

Jeffrey Wilusz , "Animal Biosecurity Pathology Training Grant ", USDA-Food & Nutrition Services.

Mon	Tue	Wed	Thur	Fri
	1 Grad Seminar	2 Microscopy Seminar	3	4
7	8 Grad Seminar	9 Microscopy Seminar	10	11
14 F W	15 I E	16 N E	17 A K	18 LS
21	22	23 Univ Holiday Offices Closed	24 Univ Holiday Offices Closed	25 Univ Holiday Offices Closed
28	29	30	31

Mon	Tue	Wed	Thur	Fri
				1 Univ Offices Closed
4	5	6	7	8
11	12	13	14	15
18 Univ Offices Closed	19 Classes Begin	20	21	22
25	26	27	28	29

Do you have NEWS or PICTURES you would like to share?

Send In your ideas or newsworthy items. Contributions make the Newsletter better!