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March/April 2015

Research on small cellular changes my lead to big cancer solutions

Among cancers, scientists have spent their entire research careers looking for cellular similarities that may lead to a single cure for many cancers -- the rare chance to have a single answer to a multifaceted problem. In 1997, scientists discovered a gene that they believed was the key to cellular immortality. Telomerase Reverse Transcriptase, or TERT, is a catalytic piece of telomerase, and while cellular immortality sounds like a good idea, it is actually how cancerous tumors grow and proliferate in cancer patients.

 

In the late nineties, the unanswered question was whether or not TERT was a cancer-causing gene. Scientists spent the next decade hunting for the mutations that activate it but no one was able to find mutations in TERT. Two years ago, two groups of researchers discovered that TERT didn't have any mutations at all. Instead, the mutations were occurring in the regulatory region that controls the expression of the gene. These mutations showed up in melanoma, and in many cancers found in the brain, liver and bladder.

 

"It was at that point that I realized we had all the tools and expertise in our lab to understand the mechanisms of these mutations. What my lab did with our collaborators at CU's Anschutz Medical Campus was to trace the effect of the mutation from the DNA to the increased RNA levels, to the increased protein levels, to the increased telomerase levels," says BioFrontiers Director Tom Cech, who recently published his team's findings in the journal, Science. "We were able to show this effect in 23 bladder cancer cell lines by comparing those with mutations to those without mutations." Read more

Aaron Clauset wins 2015 NSF CAREER Award
BioFrontiers' Aaron Clauset, Assistant Professor of Computer Science, was recently awarded the National Science Foundation's Faculty Early Career Development (CAREER) Award. He joins six other winners this year at CU-Boulder, all from the College of Engineering and Applied Science.

Aaron earned the award for his work on creating advanced algorithms for automatically extracting and evaluating the hierarchical organization of real-world networks. These networks are present everywhere and are a feature of complex social and biological systems from genetic interaction networks to online social networking.

CAREER Awards are NSF's most prestigious awards for junior faculty. They are given to professors who exemplify the role of teacher-scholars through outstanding research and education. The awards are based on innovative research, and education and community outreach. Winners are chosen by the White House Office of Science and Technology.

Aaron joins 2014 CAREER Award winner, BioFrontiers' Robin Dowell, who is researching the costs and benefits of aneuploidy using a yeast model. Three additional BioFrontiers faculty members are past winners of the award: Stephanie Bryant (2009), Amy Palmer (2010) and Hubert Yin (2010).
Recent papers by our faculty 

The p38beta mitogen-activated protein kinase possesses an intrinsic autophosphorylation activity, generated by a short region composed of the alpha-G helix and MAPK insert. (J Biol Chem) - Natalie Ahn

Development of a Cellularly Degradable PEG Hydrogel to Promote Articular Cartilage Extracellular Matrix Deposition. (Adv Healthc Mater.) - Kristi Anseth

Photoresponsive Elastic Properties of Azobenzene-Containing Poly(ethylene-glycol)-Based Hydrogels. (Biomacromolecules) - Kristi Anseth

Cancer. TERT promoter mutations and telomerase reactivation in urothelial cancer. (Science) - Tom Cech

Contributions of the TEL-patch Amino Acid Cluster on TPP1 to Telomeric DNA Synthesis by Human Telomerase. (J Mol Biol.) - Tom Cech

Toward a Consensus on the Binding Specificity and Promiscuity of PRC2 for RNA. (Mol Cell.) - Tom Cech

Biochemical Properties and Biological Functions of FET Proteins. (Annu Rev Biochem) - Tom Cech and Roy Parker

Engineered calcium-precipitable restriction enzyme. (ACS Synth Biol.) - Robin Dowell

Structure analysis of the major capsid proteins of human polyomaviruses 6 and 7 reveals an obstructed sialic acid binding site. (J Virol.) - Robert Garcea

miR-30 Family microRNAs Regulate Myogenic Differentiation and Provide Negative Feedback on the microRNA Pathway. (PLoS One) - Leslie Leinwand

Dietary phytoestrogens present in soy dramatically increase cardiotoxicity in male mice receiving a chemotherapeutic tyrosine kinase inhibitor. (Mol Cell Endocrinol.) - Leslie Leinwand

Sex-Based Differences in Skeletal Muscle Kinetics and Fiber-Type Composition. (Physiology) - Leslie Leinwand

The python project: a unique model for extending research opportunities to undergraduate students. (CBE Life Sci Educ.) - Leslie Leinwand

Biallelic Mutations in BRCA1 Cause a New Fanconi Anemia Subtype. (Cancer Discov.) - Sara Sawyer

The effect of species representation on the detection of positive selection in primate gene datasets. (Mol Biol Evol) - Sara Sawyer
  Upcoming Events 

BioFrontiers Seminar
Linda Hsieh-Wilson
Calif. Institute of Technology
April 14 - 4:00 pm
JSCBB-Butcher Auditorium
Hosted by Zhongping Tan

BioFrontiers Seminar
David Pellman
Harvard
May 12 - 4:00 pm
JSCBB-Butcher Auditorium
Hosted by Robin Dowell
IQ Biology Blog: Computer Machinery & Mouse Genomes
Daniel Malmer is a second-year graduate student in the IQ Biology program at BioFrontiers. 

I recently attended the 2014 Association for Computing Machinery Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB) with fellow IQ Biology student Joey Azofeifa and our advisor Robin Dowell. 

 

The conference had many interesting talks, ranging from theory-heavy explanations of algorithm improvements to very applied talks on using computational analysis for medical procedures. 

 

Joey presented his work on FStitch, a tool for measuring RNA transcription with GRO-seq data, which is soon to be published in the conference journal. His talk went very well and he fielded many good questions from interested attendees. In addition, Robin was a panelist for the "Women in Bioinformatics Panel" which addressed specific issues women might face in the field of bioinformatics.

 

I presented my poster titled "Inferring Ancestry in Mouse Genomes using a Hidden Markov Model", where I showed my work on determining haplotype block inheritance using single-nucleotide polymorphism data from two selectively bred mouse strains and six of the eight ancestor strains that they were bred from (the other two ancestor strains haven't been sequenced). Read more

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