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chemistry

Alysia Kohlbrand, Former UK Chemistry ChemCat President, Presses on to Graduate School in Chemistry during the Pandemic

Alysia Kohlbrand graduated from the University of Kentucky in 2019 with double majors in Chemistry and Neuroscience.

This interview is part of a series conducted by the department called, "UK Chemistry Alumni: Where Are They Now." This interview was coordinated by Dr. Arthur Cammers.

Exit Seminar - Investigation of Multidrug Efflux Pump Acrab-Tolc in E.Coli: Assembly and Degradation of the Complex and the Dynamics of ACRB

Abstract: The Resistant Nodulation Division (RND) super family member, tripartite AcrA-AcrB-TolC efflux pump is a major contributor in conferring multidrug-resistance in Escherichia coli. The structure of the pump complex, drug translocation by functional rotation mechanism has been widely studied through crosslinking studies, crystallography, and Cryo-EM efforts. Furthermore, the ClpXP system has been identified as important in degrading ssrA tagged AcrB. Despite all this data, the dynamics of assembly process of the pump and AcrB during functional rotation in the process of drug efflux, the proteases in degrading AcrB remains poorly understood. The focus of my thesis is understanding pump assembly process, dynamics of AcrB in functional rotation mechanism, and identifying the proteases that degrade ssrA tagged AcrB. First, I used disulfide bond crosslinking, minimum inhibitory concentration (MIC) and EtBr efflux assay in studying the importance of the relative flexibility at the inter-subunit interface by introducing 6 inter-subunit disulfide bonds into the periplasmic domain of AcrB using site directed mutagenesis. Based on MIC the double Cys mutants tested led to equal or higher susceptibility to AcrB substrates compared to their corresponding single mutants. EtBr accumulation assays was conducted utilizing DTT as the reducing agent. In two cases, the activities of the double Cys-mutants were partially restored by DTT reduction, confirming the importance of relative movement in the respective location for function. In the second project, I tested the effect of over-expressing functionally defective pump components in wild type E. coli cells to probe the pump assembly process. Incorporation of defective component is expected to reduce the efflux efficiency of the complex and leading to the so called “dominant negative” effect. We examined two groups of mutants defective in different aspects and found that none of them demonstrated the expected dominant negative effect, even at concentrations many folds higher than their genomic counterpart. Based on the data the assembly of the AcrAB-TolC complex appears to have a proof-read mechanism that effectively eliminated the formation of futile pump complex. Moreover, I utilized a novel tool- transposons library creation in studying the possible other proteases contribute to degradation of the AcrB-ssrA. The next generation sequencing identified already known ClpXP gene and MIC and western blot analysis confirmed the results. These, findings provide new insights to the dynamics of the AcrAB-TolC efflux pump in E. coli.  Key words: multidrug efflux pump, AcrB, assembly, disulfide, conformational changes, ssrA.

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Exit Seminar - Plasmon Mediated Single Molecule Fluorescence Enhancement in "Zero Mode Waveguides" (ZMWs)

Abstract:: Plasmonic nanostructures have been extensively studied for their potential application in numerous fields such as nanophotonics, biosensors, and bioimaging. One of the key properties of nanostructures that can be manipulated for practical applications is their capabilities to modulate the optical and photophysical properties of fluorophores residing nearby. Surface plasmons (SP), which can be defined as the collective oscillation of the delocalized electrons, are the fundamental characteristic of nanostructures that are primarily responsible for altering those properties. Elucidating fluorophores at the single-molecule level has received significant attention since more specific information can be extracted from single molecule-based studies, which otherwise, could be obscured in ensemble studies. However, single-molecule studies are inherently challenging because the signal from a single molecule is usually deem, which makes it difficult to detect. The situation is even worse in the case of a crowded environment due to higher background noise, such as cellular autofluorescences in the case of cell-based studies. Thus, one of the possible ways out of this single-molecule detection problem is to couple the fluorophore with a plasmonic nanostructure which can potentially enhance the fluorescence intensity of the single fluorophore leading to the improvement in signal to noise ratio. Throughout the projects presented here, I studied the fluorescence characteristics of single fluorophore molecules coupled in a plasmonic nano-aperture which is termed as Zero Mode Waveguides (ZMWs). I utilized single fluorophores of different origins, such as organic dyes and quantum dots (QDs), in ZMWs of different metallic compositions. By probing ZMWs made from the mixture of Aluminum and gold, with a range of ATTO dyes emitting across the visible wavelength, we found that the surface plasmon resonance of ZMWs is tunable by optimizing the metal ratio. Apart from the ATTO dyes, I investigated the photoluminescence (PL) behavior of single QDs in ZMWs and observed a significant enhancement in PL intensity and a substantial improvement in the blinking characteristics of the QDs, which are beneficial for the utility of QDs as a bio-imaging agent or a single-photon source. Single QDs in ZMWs exhibited a significant enhancement in biexciton quantum yield, which is crucial for their potential application in lasing where materials with a high optical gain are desired. I also examined the fluorescence properties of the single fluorophores in gold ZMWs in the presence of a gold nanoparticle (AuNP) and observed a more significant enhancement in fluorescence intensity in the gap between AuZMW and AuNP compared to the case of only AuZMW or only AuNP. The experimental design and the resulting findings throughout the three projects presented here should be a valuable resource for the future development of plasmon-mediated single-molecule studies.

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Understanding the role of charge on particle transport within semidilute and concentrated biopolymer solutions and tau protein condensates.

Abstract: Biological polymer networks such as mucus, extracellular matrix, nuclear pore complex, and bacterial biofilms, play a critical role in governing the transport of nutrients, biomolecules and particles within cells and tissues. The interactions between particle and polymer chains are responsible for effective selective filtering of particles within these macromolecular networks. This selective filtering is not dictated by steric alone but must use additional interactions such electrostatics, hydrophobic and hydrodynamic effects to control particle transport within biogels. Depending on chemical composition and desired function, biogels use selective filtering to allow some particles to permeate while preventing others from penetrating the biogel. The mechanisms underlying selective filtering are still not well understood yet have important ramifications for a variety of biomedical applications. Controlling these non-steric interactions are critical to understanding molecular transport in vivo as well as for engineering optimized gel-penetrating therapeutics. Fluorescence correlation spectroscopy (FCS) is an ideal tool to study particle transport properties within uncharged and charged polymer solutions. In this dissertation, our research focuses primarily on the role of electrostatics on the particle diffusion behavior within polymer solutions in the semi-dilute and concentrated regimes.

Using a series of charged dye molecules, with similar size and core chemistry but varying net molecular charge, we systematically investigated their diffusion behavior in polymer solutions and networks made up of polysaccharide and proteins. Specifically, we studied in Chapter 3 the probe diffusion in semidilute and concentrated dextran solutions. The hindered diffusion observed in attractive gels is dependent on the probe net charge and shows a dependence on the solution ionic strength. Using a biotinylated probe, we also show evidence of an additional non-electrostatic interaction between the biotin molecule and the dextran polymer chains. In contrast, comparisons to a highly charged, water soluble polyvinylamine (PVAm) semidilute solution shows that all probes, regardless of charge, were highly hindered and a weaker dependence on solution ionic strength was observed. In Chapter 4, we characterized the transport properties of our probe molecules within pure and mixed charge solutions of amino(+)-dextran and carboxymethyl(-)-dextran. We show that these mixed charge polymer solutions still have the potential to be efficient filters for interacting particles even with comparably few attractive interaction sites. By chemical modification of the amino dextran, we also compare these results to those obtained in polyampholytic solutions. Lastly, we investigate the transport properties of both probes and a much larger bovine serum albumin (BSA) protein molecule within liquid-liquid phase separated (LLPS) tau protein in chapter 5. Tau is an intrinsically disordered protein with both positive and negatively charged amino acids. We show that despite having a high local protein concentration, tau droplets are relatively low density and comparable to semi-dilute polymer solutions. Both probe molecules and BSA are observed by FCS to be recruited within the liquid droplet resulting in ~10x fold increase in particle concentration inside the tau droplet compared to outside. Probe transport within the phase separated tau is sensitive to probe net charge and solution ionic strength. Lastly, we show that BSA transport inside the tau droplet can be fairly well described by using Stokes-Einstein adjusted for the experimentally determined microviscosity within the tau droplet.

 

Keywords: diffusion, biological gels, fluorescence correlation spectroscopy, electrostatic, interaction filtering.

 

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Chemistry Graduation Celebration

The Department of Chemistry hosts a Graduation Celebration and Awards Ceremony to recognize the outstanding acheivements of our students on an annual basis. This year's event will be streamed via Facebook. Please join us by clicking here!

We are delighted to recognize the following graduates of our PhD, Masters, and Undergraduate programs:

Doctor of Philosophy
Thilini Abeywansha
Qianxiang Ai
Harsha Attanayake
Alex Boehm
Xu Fu
Robby Pace
Alexandra Riddle
Josiah Roberts
Melonie Thomas
Md Aslam Uddin
Namal Wanninayake
Master of Science
Dallas Bell
Heather Everson
Nathaniel George
Thilini Malsha Suduwella
Taylor Varner
Bachelor of Arts
Mary Ball
Matthew Burton
Brandon Cooke
Noah Franklin
Sarah Hodges
Emma Johnson
Danine Lindley
Michael Martin
Maggie McGoldrick
Claire Scott
Lauren Seeger
Sydney Sheldon
Nicholas Strobl
Hanna Suarez*
Phillip Woolery
* Denotes Chemistry Department Honors
Bachelor of Science
Elizabeth Ashley
Jessica Bennion
Bailey Chandler
Courtney Clifford
Gabrielle Evers
Matthew Farmer
Camryn Kennemore
Turner Lee
Alexsandr Lukyanchuk*
Lexius Lynch
Cameron McNeill
Richard Murt
Taylor Nelson
Danielle Peterson
William Sanders
Amanda Shaw
Dakota Smith
James Spagnola
Alyssa Vance
Tyler Vogel*
Madison Webb*
* Denotes Chemistry Department Honors

Undergraduate Scholarships (Fall 2021-Spring 2022)
Thomas B. Nantz Scholarship Linda Omali
Paul G. Sears Chemistry Scholarship Anna Fatta
Paul G. Sears Chemistry Scholarship Andrew Smith
Robert M. Boyer Memorial Scholarship Alexandria Sims
David W. and Eloise C. Young Scholarship Angelina Kue
David W. and Eloise C. Young Scholarship Ashley Bates
Robert Singleton Hart 1907 Scholarship Darcy Adreon
Paul L. Corio Scholarship Jessica Ray
Dr. Hume and Ellen Towle Bedford Scholarship Samantha Hillman
ACS-Hach Land Grant Scholarship Randall Sampson
Fellowships
Stephen H. Cook Memorial Fellowship (Summer 2021) Amanda Medina
Murrill Graduate Fellowship (Fall 2020) Rebekah Duke
Murrill Graduate Fellowship (Fall 2020) Mary Wheeler
Murrill Graduate Fellowship (Spring 2021) Moses Ogbaje

 

Graduate Awards (Fall 2020-Spring 2021)
100% Plus Setareh Saryazdi
Outstanding Graduate Research Mohamed Nishya Raseek
Outstanding Graduate Research Raphael Ryan
Outstanding TA Shashika Bandara
Outstanding TA Manisha De Alwis Goonatilleke
Outstanding General Chemistry TA Kathryn Pitton
Outstanding General Chemistry TA Md Abu Monsur Dinar
Undergradute Awards (Fall 2020-Spring 2021)
General Chemistry Excellence Award (Fall 2020 - CHE105) Abby Roetker
General Chemistry Excellence Award (Fall 2020 - CHE107) Jason Wang
General Chemistry Excellence Award (Spring 2021 - CHE105) Brysen Honeycutt
General Chemistry Excellence Award (Spring 2021 - CHE107) Abby Roetker
Freshman Chemistry Award Sophia Li
Hammond Leadership Award Hunter Mulloy
Willard R. Meredith Memorial Award Matthew Farmer
Nancy J. Stafford Award Bailey Chandler
Hammond Undergraduate Service Award Darcy Adreon
Hammond Undergraduate Service Award Mirindi Kabangu
100% Plus Sam Chasen

 

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Reaction Profiling in Unlimited Detail: Applications of Online HPLC

Abstract: Process analytical technology (PAT) plays an essential role in understanding and optimization chemical manufacturing routes by furnishing data-dense reaction profiles. However, each PAT tool presents certain limitations with respect to chemical component resolution, reaction compatibility or useful operational domain. High-pressure liquid chromatography (HPLC) represents one of the most versatile analytical tools available for providing detailed reaction progress analysis. Yet this technology introduces a new set of challenges relating to sample acquisition and preparation, especially when trying to utilize HPLC as a real time analytical technology.

Our lab has developed a comprehensive set of automated tools, which allow nearly any chemical process to be visualized in real time by HPLC. This includes reactions performed under inert atmosphere, systems with heterogenous reagents, and complex competition reactions with many components. The combination of excellent resolving power of UHPLC, coupled to the high dynamic range of standard UV/Vis and MSD detectors has allowed this tool to be broadly deployed. This has allowed complex reactions to be visualized in exceptional details with unprecedented ease. This presentation will discuss several case studies to demonstrate the flexibility and fidelity of this new online HPLC technology. Examples will include studying reaction mechanisms, measuring crystallization processes and deployment as an in-process control for reaction automation.

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Supramolecular Influences on Luminescence: From Coordination Complexes to Porous Solids

Abstract:

Imparting supramolecular interactions on transition metal systems such as Iridium complexes (with various N^C ligands), can have a profound impact on their luminescence properties. These types of complexes are under intensive investigation due to their excellent performance when used as emitters in phosphorescent organic light emitting diodes (PhOLEDs).1 The ideal interactions for holding supramolecular systems together are hydrogen bonds, as they combine relatively strong intermolecular attractions with excellent reversibility. In using DNA base-pair-like interactions in super strong hydrogen bonding arrays to drive assembly,2 we can influence chromaticity efficiently.3,4 Beyond molecular systems, we can also apply these principles in extended solid-state systems whose porosities are such that small molecule uptake can influence the inherent physical (and photophysical) properties of the host materials.5 In this lecture, a broad view of our research program will be presented, spanning molecular systems to solid-state materials, and how we can make use of inherent luminescence properties for chromaticity modulation, small molecule sensing, and diagnostics.6,7

References:

  1. A.F. Henwood, E. Zysman-Colman, Chem. Commun. 2017, 53, 807.
  2. B.A. Blight, C.A. Hunter, D.A. Leigh, H. McNab, P.I.T. Thomson, Nature Chemistry, 2011, 3, 246.
  3. B. Balónová, D.  Rota Martir, E.R. Clark, H.J. Shepherd, E. Zysman-Colman, B.A. Blight, Inorganic Chemistry, 2018, 57, 8581.
  4. B. Balónová, H.J.  Shepherd, C.J. Serpell, B.A. Blight, Supramolecular Chemistry, 2019, DOI: 10.1080/10610278.2019.1649674
  5. R.J. Marshall, Y. Kalinovskyy; S.L. Griffin, C. Wilson, B.A. Blight, R.S. Forgan, J. Am. Chem. Soc.2017139, 6253.
  6. S.J. Thomas, B. Balónová, J. Cinatl M.N. Wass, C.J. Serpell, B.A. Blight, M. Michaelis, ChemMedChem202015(4), 349.
  7. C.S. Jennings, J.S. Rossman, B.A. Hourihan, R.J. Marshall, R.S. Forgan, B.A. Blight, Soft Matter, 2021, In Press. DOI: 10.1039/D0SM02188A

 

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