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Free Virtual Physical Symposium

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Despite its introduction almost three decades ago, the ability to couple the measurement of nonlinear phenomena with the spatial resolution of a microscope objective has continued to rapidly evolve through both the application of more sophisticated techniques and the study of more complex systems. Progress in the field of nonlinear microscopy has afforded deep penetration in biological tissues, additional modalities for chemical contrast, and dynamics on ultrafast timescales. Challenges remain, however, in extracting new information from increasingly congested samples with minimal perturbation. Innovations in instrumentation, the development of new image analysis methodologies, and novel applications of existing techniques promise new insight into intrinsically heterogeneous samples. 

Tessa Calhoun, Associate Professor with the Department of Chemistry, has been co-organizing a symposium for the virtual ACS conference August 17-20, 2020. There will be live Zoom presentations that are free for anyone to participate in. Registration information can be found here. 

This symposium will gather scientists from the fields of chemistry, physics, engineering and biology into a collaborative environment where ideas of technology innovations and sample applications can be shared and discussed. Progress, existing challenges, impact will be emphasized.

While this symposium originated as part of the ACS Fall 2020 Virtual Conference, participation in these Zoom sessions is not limited to those registered for the conference. 

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Scientists Catch a Glimpse of Elusive Cell Membrane Nanodomains

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A collaborative team including University of Tennessee researchers has captured the first direct images of tiny cell membrane domains known as lipid rafts. The images were published in a research article in this week’s edition of Proceedings of the National Academy of Sciences of the USA.

First hypothesized over thirty years ago, rafts are specialized microenvironments found within cell membranes, the sheets of lipid and protein that both surround a cell and delineate its internal compartments. They are thought to play a crucial role in the way cells transport materials and communicate with each other. Some viruses, including influenza and HIV, have even co-opted rafts in their life cycle.

At nearly a thousand times smaller than the width of a human hair, rafts are impossible to detect with conventional microscopy. “Although their existence is well supported by biochemical evidence, the lack of direct visual observations of rafts has led to some healthy skepticism” said Fred Heberle, an assistant professor in the Chemistry Department at UT and lead author of the study.

The researchers used a powerful technique called cryogenic electron microscopy (cryoEM) to take the first pictures of the tiny structures. “An ordinary light microscope can’t resolve objects smaller than a few tenths of a micrometer, but cryoEM can visualize structures as small as a tenth of a nanometer” said Heberle. “It’s revolutionizing the field of structural biology, but to date has mostly been used to look at protein structure. We decided to zoom in on membranes and see if we could visualize rafts.”

The study grew out of a collaboration between Heberle and two research groups at the University of Texas Health Science Center at Houston led by cell biologist Ilya Levental and neurobiologist M. Neal Waxham. “We have a common interest in membrane structure but different ways of approaching it,” said Heberle. “My lab studies synthetic membranes, while Ilya and Neal specialize in more complicated biological membranes. We also have combined expertise in small-angle scattering, molecular simulations, and electron microscopy. Ultimately, we needed all of those tools to convince ourselves that we were really seeing rafts.”

The researchers first imaged model biomimetic membranes to show that cryoEM can resolve sub-nanometer differences in their thickness, a feature known to distinguish rafts from the surrounding membrane. They then used simulations to predict how rafts would appear in a cryoEM image and to fine-tune their analysis, before finally capturing images of raft domains in both biomimetic and biological membrane preparations. A team at the University of Washington led by Sarah Keller and graduate student Caitlin Cornell independently made a similar discovery using a variation of cryoEM called cryo-electron tomography, and the two articles were published together.

While the new images should settle some long-standing questions, many aspects of raft formation and structure remain poorly understood. At a basic level, rafts are a consequence of the immiscibility of different lipids found in cell membranes, much like a mixture of olive oil and vinegar will separate in a bottle of salad dressing. “Cell membranes are fluid mixtures of lipids and proteins, and some of the different types of lipids don’t mix well and can separate to form a raft,” Heberle said.

One problem that has confounded researchers is why rafts remain small rather than coalescing into larger structures, but Heberle says that the ability to finally visualize the domains may eventually provide answers. “A better understanding of rafts will not only give insights into the normal functioning of our own cells, but may also lead to improved therapies for viral infections.”

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Hazari Online

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Dr. Al Hazari Magic ShowAl Hazari, retired UT professor, has been conducting experiments on Zoom to teach and inspire chemistry enthusiasts.

“I have always enjoyed teaching and sharing something of myself and my knowledge with anyone ages 2 to 102,” Hazari said. “What we’re really after are science-literate citizens. Everyone should know about science, be comfortable with science, and never stop being curious and inquisitive about the wonders of science.”

This summer, Hazari has utilized the Zoom platform to teach Forensic Chemistry Camp for middle school students, ORAU workshops, the Harriman Public Library Chemistry Magic Show, and local WBIR presentations. 

Hazari WBIR 1

Hazari WBIR 2

Hazari WBIR 3

Larese Named ACS Fellow

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John Larese, professor in the Department of Chemistry, has been named an 2020 ACS Fellow.

The primary purpose of the ACS Fellows Program is to recognize and honor members of the American Chemical Society for their outstanding achievements in and contributions to the science and the profession and for their equally exemplary service to the Society.

“I have truly benefited by my service to ACS and LSAC and by all of the great individuals who have contributed to my scientific endeavors and career,” Larese said. “I’m especially proud of my effort in leading the science/design/funding case for the VISION Spectrometer at the SNS and the training of future scientists in the use of neutrons and novel materials. Clearly without the support and patience of my wife Maryann and children such pursuits are impossible.”

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Vogiatzis Lab Published in Nature Communications

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Machine learning applications for chemical problems have been rapidly increasing. Their popularity is justified since they have led to the discovery of new molecules and materials with enhanced properties, new reactions, or have contributed to the reduction of computational effort needed of complex calculations and simulations.

The Vogiatzis Lab seeks to address how a computational algorithm can efficiently “read” and “learn” patterns from molecular structures in their research “Representation of molecular structures with persistent homology for machine learning applications in chemistry” recently published in Nature Communications.

In this collaborative work between Jacob Townsend, John Hymel and Konstantinos Vogiatzis (Chemistry, University of Tennessee) and Cassie Micucci and Vasileios Maroulas (Mathematics, University of Tennessee), the group is presenting a novel molecular representation method based on persistent homology, an applied branch of topology, which encodes the atomistic structure of molecules.

A molecule is mapped into a persistence diagram, a two-dimensional point summary, which demystifies the connected components and the empty space that exist in a molecule based on the atom types and the distances among them. A persistence diagram is further vectorized to a persistence image (PI), a weighted representation of the diagram, which captures the chemically driven uncertainty. The PI in that sense is a “molecular fingerprint”, and when used with machine learning, offers an efficient and reliable approach to screen large molecular databases when compared to other popular molecular representation schemes.

The efficiency arises from the low computation effort needed to compare a large number of fingerprints, and the similar-size representations that are generated, independently of the molecular sizes.

The group demonstrates the applicability of the PI method by screening a large molecular database (GDB-9) with 133,885 organic molecules. Their target was to identify novel molecular units that selectively interact with CO2 and can be used as building blocks of materials, such as polymeric membranes.

They began their study by computing with density functional theory (DFT) the CO2 interaction energies of 100 organic molecules. “Since the initial, limited 100 data points were not capturing the diversity of the GDB-9 database, we applied a technique called active learning in order to incrementally obtain data which helped us efficiently screen the 133,885 molecules,” Vogiatzis said. “We found out that the combination of PIs with active learning performed well with data (interaction energies) from only 220 molecules in order to identify new molecules with stronger CO2 binding.”

Their data-driven methodology was able to identify molecular patterns previously unknown to us that increase the CO2 affinity of organic molecules.

 

Two Journal Covers from the Sokolov Group

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The Sokolov Group’s primary focus of research on dynamics of soft materials, including dynamics of biological macromolecules, and nano-composite materials.

Their recent publication “Correlation between the temperature evolution of the interfacial region and the growing dynamic cooperativity length scale” was featured on cover of The Journal of Chemical Physics. They presented an analyses that revealed a clear correlation between the temperature dependence of the characteristic relaxation time, ln(τα(T)/τ0), and the interfacial layer thickness, Lint(T), in nanocomposite materials.

The group also published their work “Perspectives for Polymer Electrolytes: A View from Fundamentals of Ionic Conductivity” which was on the cover of Macromolecules. This research analyzes fundamental mechanisms controlling ionic conductivity and suggests design of novel polymer electrolytes with enhanced conductivity.

Zhao Group Published in Nature Communications

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The Zhao Group is a polymer chemistry research group, focusing on responsive, functional soft and hybrid materials.

The group recently published their work “Breaking translational symmetry via polymer chain overcrowding in molecular bottlebrush crystallization” in Nature Communication.

The research focuses on  the fundamental laws in crystallization is translational symmetry. This piece reports on the spontaneous formation of spherical hollow crystals with broken translational symmetry in crystalline molecular bottlebrush (mBB) polymers. This study unravels a new principle of spontaneous translational symmetry breaking, providing a general route towards designing versatile nanostructures.

First Publication from Bailey Lab

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The Bailey Lab just published their first review article “Site directed mutagenesis as a precision tool to enable synthetic biology with engineered modular polyketide synthases” in Synthetic and Systems Biotechnology. 

This article is an overview on a way to target genetic changes to change as little as one amino acid to change the function of polyketide synthases.  

“Polyketides have a correspondence between their sequence and the structure of the small molecules they create, which are often important pharmaceuticals,” said Assistant Professor Constance Bailey. “Finding ways to subtly alter the structure of the metabolite that forms is a way to enable the discovery of new important drugs.”

The group reviews examples of targeted point mutagenesis to one or a few residues harbored within the PKS that alter domain specificity or selectivity, affect protein stability and interdomain communication, and promote more complex catalytic reactivity.

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Calhoun Lab Publishes Online Detection Method for Microfluidics

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The Calhoun Lab published their article “Total Internal Reflection Transient Absorption Microscopy: An Online Detection Method for Microfluidics” in The Journal of Physical Chemistry A. Brandon Colon, a graduate student in the Calhoun Lab, is the primary author of this work.

Microreactors have garnered widespread attention for their tunability and precise control of synthetic parameters to efficiently produce target species. Despite associated advances, a lack of on-line detection and optimization methods has stalled the progression of microfluidic reactors.

“Here we employ and characterize a total internal reflection transient absorption microscopy (TIRTAM) instrument to image excited state dynamics on a continuous flow device,” Colon said. “The experiments presented demonstrate the capability to discriminate between different chromophores as well as in differentiating the effects of local chemical environments that a chromophore experiences.”

This work presents the first such on-line transient absorption measurements and provides a new direction for the advancement and optimization of chemical reactions in microfluidic devices. 

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