Blog

Apr 09
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Tim Cernak

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Tim Cernak, PhD, is Assistant Professor of Medicinal Chemistry with secondary appointments in Chemistry and the Chemical Biology Program at the University of Michigan, Ann Arbor.

The functional and biological properties of a small molecule are encoded within its structure so synthetic strategies that access diverse structures are paramount to the invention of novel functional molecules such as biological probes, materials or pharmaceuticals. The Cernak Lab studies the interface of chemical synthesis and computer science to understand the relationship of structure, properties and reactions. We aim to use algorithms, robotics and big data to invent new chemical reactions, synthetic routes to natural products, and small molecule probes to answer questions in basic biology. Researchers in the group learn high-throughput chemical and biochemical experimentation, basic coding, and modern synthetic techniques. By studying the relationship of chemical synthesis to functional properties, we pursue the opportunity to positively impact human health.

Mar 08
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Nils G. Walter

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Nils G. Walter, PhD, is the Francis S. Collins Collegiate Professor of Chemistry, Biophysics and Biological Chemistry, College of Literature, Science, and the Arts and Professor of Biological Chemistry, Medical School, at the University of Michigan, Ann Arbor.

Nature and Nanotechnology likewise employ nanoscale machines that self-assemble into structures of complex architecture and functionality.  Fluorescence microscopy offers a non-invasive tool to probe and ultimately dissect and control these nanoassemblies in real-time.  In particular, single molecule fluorescence resonance energy transfer (smFRET) allows us to measure distances at the 2-8 nm scale, whereas complementary super-resolution localization techniques based on Gaussian fitting of imaged point spread functions (PSFs) measure distances in the 10 nm and longer range.  In terms of Big Data Analysis, we have developed a method for the intracellular single molecule, high-resolution localization and counting (iSHiRLoC) of microRNAs (miRNAs), a large group of gene silencers with profound roles in our body, from stem cell development to cancer.  Microinjected, singly-fluorophore labeled, functional miRNAs are tracked at super-resolution within individual diffusing particles.  Observed mobility and mRNA dependent assembly changes suggest the existence of two kinetically distinct assembly processes.  We are currently feeding these data into a single molecule systems biology pipeline to bring into focus the unifying molecular mechanism of such a ubiquitous gene regulatory pathway.  In addition, we are using cluster analysis of smFRET time traces to show that large RNA processing machines such as single spliceosomes – responsible for the accurate removal of all intervening sequences (introns) in pre-messenger RNAs – are working as biased Brownian ratchet machines.  On the opposite end of the application spectrum, we utilize smFRET and super-resolution fluorescence microscopy to monitor enhanced enzyme cascades and nanorobots engineered to self-assemble and function on DNA origami.

Artistic depiction of the SiMREPS platform we are building for the direct single molecule counting of miRNA biomarkers in crude biofluids (Johnson-Buck, A. et al. Kinetic fingerprinting to identify and count single nucleic acids. Nat Biotechnol 33, 730-732 (2015)).

Artistic depiction of the SiMREPS platform we are building for the direct single molecule counting of miRNA biomarkers in crude biofluids (Johnson-Buck, A. et al. Kinetic fingerprinting to identify and count single nucleic acids. Nat Biotechnol 33, 730-732 (2015)).

Mar 08
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Paul Zimmerman

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Paul Zimmerman, PhD, is Assistant Professor of Chemistry, College of Literature, Science, and the Arts, at the University of Michigan, Ann Arbor.

The Zimmerman research group is a pioneer in computational chemical reaction discovery, and has developed algorithms which map out complex multi-component, multi-elementary step reaction mechanisms without reliance on prior chemical knowledge. These methods, being low computational cost compared to other quantum chemical techniques, provide a large amount of detailed and accurate chemical information to be processed and exploited. These data present an opportunity for application of statistical methods, specifically from machine learning, to determine the key chemical features that enable chemical reactions to occur. Machine learning not only provides a detailed analysis of how chemical processes work, but also provides a rapid, predictive method to determine the rate and selectivity of novel chemical reaction sequences. Ongoing work in the Zimmerman group is taking advantage of tools such as the Kernel Ridge and logistic regressions, k-nearest neighbors, and genetic algorithms to transform chemical reaction data into predictive tools applicable to many types of chemistry.

Successful k-NN organization of reaction data involving nearly 700 unique chemical reactions.

Successful k-NN organization of reaction data involving nearly 700 unique chemical reactions.