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ChBE Department & Affiliates,

Our third ChBE seminar of the Fall Quarter will be Thursday, October 6th at 9am in the Francis Searle Building, room 1441. Thomas Epps from University of Delaware will present a seminar titled, “Generating Functional Materials from Nanostructured Polymers” detailed information is given below:

Date & Time: Thursday, October 6th 9:00 am – 10:00 am
Location: Searle 1441 (refreshments will be available at 8:45am)

Speaker: Dr. Thomas Epps, University of Delaware
Title: Generating Functional Materials from Nanostructured Polymers

Abstract
The self-assembly of block copolymers (BCP)s can facilitate materials design for many emerging nanotechnologies. In the Epps group, we are focused on understanding and applying the structure/property/function relationships inherent in nanostructured polymers to design, synthesize, and characterize new systems exhibiting molecular-level assembly. A particular interest in our research group is the coupling of thermodynamic and kinetic constraints in self-assembling polymers to develop materials for a variety of potential platforms including lithium battery membranes, green and bio-based materials, mechanical property enhancers, coatings, nanoscale templates, and drug delivery capsules. Three areas of recent progress in the group involve: (1) manipulating inter-block interactions to improve ion transport in block copolymers, (2) fabricating stimuli-responsive copolymers for gene therapy applications, and (3) designing bio-based alternatives, based on lignin, for thermoplastic applications. In the first area, we employ synthetic modifications to the traditional BCP architecture (using chemical tapering between blocks) to control the ordering transitions, glass transitions, and phase behavior in diblock and triblock polymers. Thus, we can create more processable and effective ion-conducting materials for lithium battery membranes. In the second area, we use photo-responsive functionalities, as well as our understanding of solution self-assembly, to create nucleic acid delivery vehicles. These systems show increased cellular uptake, stable packaging, on-demand unpackaging, and controlled/tunable/efficient delivery relative to standard nucleic acid transfection agents. In the third area, we explore the modification of lignin model compounds for use in the controlled synthesis of bio-based materials. One recent task has been the investigation of styrene-alternatives for BCPs with tunable glass transition and degradation temperatures that are suitable for thermoplastic elastomer applications.

Biography
Thomas Epps is the Thomas and Kipp Gutshall Professor of Chemical and Biomolecular Engineering at the University of Delaware (UD) with a joint appointment in Materials Science and Engineering and an affiliated appointment in Biomedical Engineering. He received his B.S. degree in Chemical Engineering from MIT in 1998 and an M.S. degree in Chemical Engineering from MIT in 1999. He completed his graduate research at the University of Minnesota and received a Ph.D. in Chemical Engineering in 2004; he then joined NIST as a National Research Council Postdoctoral Fellow. Prof. Epps joined UD in the summer of 2006.

His research interests include nanostructured assemblies for targeted drug delivery and gene therapy, polymeric materials for bio-separation and ion-conduction membranes, nanostructured soft materials from biobased feedstocks, and polymer films for nanotemplating. At UD, he is a member of the Center for Neutron Science and the Center for Molecular and Engineering Thermodynamics. Prof. Epps has received several honors and awards including: the John H. Dillon Medal from APS (2016); the Owens-Corning Early Career Award from AIChE (2015); named a Kavli Fellow by the National Academy of Sciences (2014); the Sigma Xi Young Investigator Award (2014); the Martin Luther King, Jr. Visiting Professorship at MIT (2012); the Thomas & Kipp Gutshall Professorship at UD (2012); the UD Alison Society, Gerard J. Mangone Young Scholars Award (2011); the DuPont Young Professor Grant Award (2010); the Presidential Early Career Award for Scientists and Engineers (PECASE) (2009); the Air Force Young Investigator Award (2008); the National Organization for the Professional Advancement of Black Chemists and Chemical Engineers (NOBCChE) Lloyd N. Ferguson Young Scientist Award (2007), a National Science Foundation (NSF) CAREER Award (2007), and an NRC Postdoctoral Fellowship (2004) among others. Prof. Epps also is active in the American Chemical Society (ACS Board of Directors Development Advisory Board), American Institute of Chemical Engineers, American Physical Society (Polymers Division), and Sigma Xi. He is on the editorial advisory boards of Polymer Chemistry, Soft Matter, and the Journal of Polymer Science: Polymer Physics.

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ChBE fourth seminar of the Fall Quarter will be held on Thursday, October 13th at 9am in the Francis Searle Building, room 1441. ChBE's very own graduate students are presenting this Thursday, detailed information is given below:

Date & Time: Thursday, October 13th 9:00 am – 10:00 am
Location: Searle 1441 (refreshments will be available at 8:45am)

Speaker: Jessica Perez, PhD candidate, Jewett Lab
Title: Improving Genomically Recoded Escherichia coli for the Production of Proteins Containing Non-Standard Amino Acids

Abstract
The genetic code, responsible for translating mRNA codons into the twenty standard amino acids used in protein synthesis, was once thought to be immutable. However, as we expanded our understanding of molecular biology, more variations in this genetic code were found across many species, allowing for non-standard, chemically diverse amino acids to be incorporated into proteins by the ribosome in vivo. By hijacking these mechanisms, expansion of the genetic code has the potential to transform how we synthesize materials and therapeutics, investigate protein structure, and understand the evolution of the translation system.

A pioneering effort has recently developed an Escherichia coli strain lacking all TAG amber stop codons and release factor 1 which allows for more efficient genetic encoding of an additional non-standard amino. This strain however has not previously been optimized for protein production which is critical for industrial application and wide spread use. Here, I will describe the construction of a series of genomically recoded organisms that are optimized for protein production and have the additional ability to tune protein expression through a T7 RNA polymerase (T7RNAP). We found that reduction of nuclease and protease activity increases wildtype sfGFP production by 260% and sfGFP containing 2TAGs production by 225% and 560% with p-azidophenylalanine and N6-(propargyloxycarbonyl)-L-Lysine (ProCarb), respectively. Additionally, we constructed several strains containing an optimized IPTG inducible T7RNAP cassette which shows a 17-fold improvement in production of sfGFP containing 2TAGs with ProCarb. We envision that our library of strains will provide the community with multiple strain options for expression of proteins containing non-standard amino acids with increased protein yield and cell density which is crucial as the non-standard amino field grows.

Speaker: Gary Wilk, PhD candidate, Braun Lab
Title: Identifying genomic variants that modulate microRNA regulation of gene expression in cancer

Abstract

Cancer is a disease comprising dynamic changes in the genome that broadly affect gene expression and gene regulatory networks. microRNAs (miRNAs) are small RNA molecules in gene regulatory networks which negatively modulate gene expression post-transcriptionally. In mammalian cells miRNA targeting of genes is nonspecific and can be influenced by genetic variation. In recent years, miRNAs have gained widespread interest since aberrant miRNA regulation is associated with many diseases, most notably in cancer. Here we investigate how miRNAs regulate genes in cancer in the context of genetic variation. We mine multiple high-dimensional genomic and expression datasets from The Cancer Genome Atlas (TCGA), a free repository of genomic data across several cancer types, and integrate them into an analysis pipeline. Our pipeline identifies a) entire systems of genes that are dysregulated in tumors by miRNAs and b) genomic variants in those dysregulated systems that appear to influence miRNA regulation of gene expression in tumors. We then corroborate these results using computational biophysics techniques to better understand their physical basis.

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The Department of Chemical and Biological Engineering presents:

12th Annual Richard S.H. Mah Lectures – Featured Speaker: Dr. Arup Chakraborty

Robert T. Haslam Professor of Chemical Engineering, MIT

October 19th, 2016

Pancoe Auditorium, Room 1101
2200 Campus Drive
Arthur and Gladys Pancoe-NSUHS Life Sciences Pavilion
Evanston IL 60208

4:30 PM – Seminar, Rational Design of Vaccines Against Highly Mutable Pathogens: Hitting HIV Where It Hurts with Antibodies

Abstract
Infectious pathogens have plagued humanity since antiquity. Vaccines have successfully combated, and even eradicated, many such pathogens. Indeed, no medical procedure has saved more lives than vaccination. But, today pathogens have evolved that have defied successful vaccination using the paradigms pioneered by Jenner and Pasteur. Many of these infectious agents are highly mutable or present themselves in different guises. HIV is a prominent example. What is required to combat such scourges on the planet is rational, rather than empirical, design of vaccines based on obtaining and harnessing a mechanistic understanding of the pertinent immunology and virology. In these two lectures, I will first discuss the scale of the human toll exacted by HIV infections, and then describe mechanistic studies aimed toward rational design of effective vaccines against such highly mutable pathogens. In this first lecture, the focus will be on computational studies (and complementary experiments) aimed to develop rational vaccination strategies that can induce broadly neutralizing antibodies that neutralize diverse HIV strains.

***5:30 PM – Mah Lecture Reception in the Pancoe NSUHS Cafe

Bio
Arup K. Chakraborty is the Robert T. Haslam Professor of Chemical Engineering, Physics, Chemistry, and Biological Engineering at MIT. He is the founding Director of MIT’s Institute for Medical Engineering and Science. He is also a founding steering committee member of the Ragon Institute of MIT, MGH, and Harvard, and an Associate Member of the Broad Institute of MIT & Harvard. After obtaining his undergraduate degree from the Indian Institute of Technology (Kanpur), PhD in chemical engineering at the University of Delaware, and postdoctoral studies at the University of Minnesota, he joined the faculty at the University of California at Berkeley in December 1988. He rose through the ranks, and ultimately served as the Warren and Katherine Schlinger Distinguished Professor and Chair of Chemical Engineering, Professor of Chemistry, and Professor of Biophysics at Berkeley. He was also Head of Theoretical and Computational Biology at Lawrence Berkeley National Laboratory. In September 2005, Chakraborty moved to MIT. His entire career has been focused on research at the intersection of disciplines. After an early career in engineering of polymers and catalysts, since 2000, Chakraborty’s work has focused on bringing together immunology and statistical physics. Chakraborty's predictive computational/theoretical work has impacted both experimental basic immunology and infectious disease research. He has especially contributed to our understanding of T cell signaling, T cell development and pathogen specificity, the immunological vulnerabilities of HIV and rational vaccine design. Chakraborty’s work has been recognized by numerous honors, including the NIH Director’s Pioneer Award, the E.O. Lawrence Medal for Life Sciences from the US DOE, the Allan P. Colburn and Professional Progress awards from the AIChE, a Dreyfus Teacher-Scholar award, and a National Young investigator award. Chakraborty was elected a member of the National Academy of Sciences and the National Academy of Engineering for different bodies of work. He is a Fellow of the American Academy of Arts & Sciences and the American Association for the Advancement of Science, and serves on the US Defense Science Board. Chakraborty has received four teaching awards at Berkeley and MIT.

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Details TBA