February Research Round-Up

Congratulations to our amazing research teams here in the Department of Chemistry for their publications this month!

Conticello Group

Kreutzberger, M. A., Hughes, S., Conticello, V., & Egelman, E. H. (2019). Structural Studies of the T-and RP4-Pili using Cryo-EMBiophysical Journal116(3), 573a.

Dunham Group

Mehrani, A., Hoffer, E. D., Goralski, T. D., Keiler, K. C., Dunham, C. M., & Stagg, S. (2019). Investigating the Structural Mechanism of the Stalled Bacterial Ribosome Bound to a Drug that Targets Trans-TranslationBiophysical Journal116(3), 573a-574a.

Nguyen, H. A., Hoffer, E. D., & Dunham, C. M. (2019). Importance of tRNA anticodon loop modification and a conserved, noncanonical anticodon stem pairing in tRNAProCGG for decodingJournal of Biological Chemistry, jbc-RA119.

Schureck, M. A., Meisner, J., Hoffer, E. D., Wang, D., Onuoha, N., Ei Cho, S., … & Dunham, C. M. (2019). Structural basis of transcriptional regulation by the HigA antitoxinMolecular microbiology.

Heaven Group

Khvatov, N. A., Zagidullin, M. V., Tolstov, G. I., Medvedkov, I. A., Mebel, A. M., Heaven, M. C., & Azyazov, V. N. (2019). Product Channels of the reactions of O2 (b1Σg+)Chemical Physics.

Hill Group

Hill, C., & Sullivan, K. (2019). U.S. Patent Application No. 16/061,327.

Lian Group

Lian, T., Koper, M. T., Reuter, K., & Subotnik, J. E. (2019). Special Topic on Interfacial Electrochemistry and Photo (electro) catalysis.

Musaev Group

Gair, J., Haines, B. E., Filatov, A. S., Musaev, D. G., & Lewis, J. C. (2019). Di-Palladium Complexes are Active Catalysts for Mono-N-Protected Amino Acid Accelerated Enantioselective CH Functionalization.

Salaita Group

Brockman, J. M., & Salaita, K. (2019). Mechanical Proofreading: A General Mechanism to Enhance the Fidelity of Information Transfer Between Cells Phys. 7: 14. doi: 10.3389/fphy.

Blanchard, A., & Salaita, K. (2019). Autochemophoretic DNA Motors Generate 100+ Piconewton ForcesBiophysical Journal116(3), 292a-293a.

Rao, T. C., Ma, V. P. Y., Urner, T. M., Grandhi, S., Salaita, K., & Mattheyses, A. L. (2019). EGFR Activation Enables Increased Integrin Forces and Organization of Mature Focal AdhesionsBiophysical Journal116(3), 413a.

Quach, M. E., Combs, D., Salaita, K., & Li, R. (2019). Force-Induced Unfolding of a Mechanosensory Domain in Platelet Glycoprotein (Gp) Ib-IX under Solution and Adherent ConditionsBiophysical Journal116(3), 376a.

Weinert Group

Cary, S. P., Boon, E. M., Weinert, E., Winger, J. A., & Marletta, M. A. (2019). U.S. Patent Application No. 10/202,428.

 

November Research Round-Up

Congratulations to our amazing research teams here in the Department of Chemistry for their publications this month!

Bowman Group:

Chen, Q., & Bowman, J. M. (2018). Quantum approaches to vibrational dynamics and spectroscopy: is ease of interpretation sacrificed as rigor increases?Physical Chemistry Chemical Physics.

Yang, B., Zhang, P., Chen, Q., Stancil, P., Bowman, J. M., Naduvalath, B., & Forrey, R. C. (2018). Inelastic Vibrational Dynamics of CS in Collision with H2 Using a Full-dimensional Potential Energy SurfacePhysical Chemistry Chemical Physics.

Dunham Group:

Hong, S., Sunita, S., Maehigashi, T., Hoffer, E. D., Dunkle, J. A., & Dunham, C. M. (2018). Mechanism of tRNA-mediated+ 1 ribosomal frameshiftingProceedings of the National Academy of Sciences115(44), 11226-11231.

Rivera, S., Young, P. G., Hoffer, E. D., Vansuch, G. E., Metzler, C. L., Dunham, C. M., & Weinert, E. E. (2018). Structural Insights into Oxygen-Dependent Signal Transduction within Globin Coupled SensorsInorganic chemistry.

Hoffer, E. D., Maehigashi, T., Fredrick, K., & Dunham, C. M. (2018). Ribosomal ambiguity (ram) mutations promote the open (off) to closed (on) transition and thereby increase miscodingNucleic Acids Research.

Hill Group:

Sullivan, K. P., Wieliczko, M., Kim, M., Yin, Q., Collins-Wildman, D. L., Mehta, A. K., … & Hill, C. L. (2018). Speciation and Dynamics in the [Co4V2W18O68] 10-/Co (II) aq/CoOx Catalytic Water Oxidation SystemACS Catalysis.

Kaledin, A. L., Troya, D., Karwacki, C. J., Balboa, A., Gordon, W. O., Morris, J. R., … & Musaev, D. G. (2018). Key Mechanistic Details of Paraoxon Decomposition by Polyoxometalates: Critical Role of Para-Nitro SubstitutionChemical Physics.

Lian Group:

Clark, M. L., Ge, A., Videla, P. E., Rudshteyn, B., Miller, C. J., Song, J., … & Kubiak, C. P. (2018). CO2 Reduction Catalysts on Gold Electrode Surfaces Influenced by Large Electric FieldsJournal of the American Chemical Society.

Lutz Group:

Williams, E., Jung, S. M., Coffman, J. L., & Lutz, S. (2018). Pore engineering for enhanced mass transport in encapsulin nano-compartmentsACS synthetic biology.

Musaev Group:

Kaledin, A. L., Troya, D., Karwacki, C. J., Balboa, A., Gordon, W. O., Morris, J. R., … & Musaev, D. G. (2018). Key Mechanistic Details of Paraoxon Decomposition by Polyoxometalates: Critical Role of Para-Nitro Substitution. Chemical Physics.

Salaita Group:

Hong, J., Ge, C., Jothikumar, P., Yuan, Z., Liu, B., Bai, K., … & Palin, A. (2018). A TCR mechanotransduction signaling loop induces negative selection in the thymusNature Immunology, 1.

Weinert Group

Rivera, S., Young, P. G., Hoffer, E. D., Vansuch, G. E., Metzler, C. L., Dunham, C. M., & Weinert, E. E. (2018). Structural Insights into Oxygen-Dependent Signal Transduction within Globin Coupled SensorsInorganic chemistry.

Fontaine, B. M., Duggal, Y., & Weinert, E. E. (2018). Exploring the Links Between Nucleotide Signaling and Quorum Sensing Pathways in Regulating Bacterial VirulenceACS infectious diseases.

Wuest Group:

Kontos, R. C., Schallenhammer, S. A., Bentley, B. S., Morrison, K. R., Feliciano, J. A., Tasca, J. A., … & Minbiole, K. P. (2018). An Investigation Into Rigidity‐Activity Relationships in bisQAC Amphiphilic AntisepticsChemMedChem.

Shapiro, J. A., Varga, J. J., Parsonage, D., Walton, W., Redinbo, M. R., Ross, L. J., … & Goldberg, J. B. (2018). Identification of Specific and Non‐specific Inhibitors of Bacillus anthracis Type III Pantothenate Kinase (PanK)ChemMedChem.

Kilgore, M. B., Morrison, K. R., Wuest, W. M., & Chandler, J. D. (2018). Influence of pH on the reactions of heme peroxidase-derived oxidants with R19SFree Radical Biology and Medicine128, S101-S102.

Emory Chemistry Students Celebrate NSF GRFP Awards

Congratulations to Dayna Patterson (Weinert Group) and Kevin Hoang (EC 17′; Davies Group) for being awarded 2018 Graduate Research Fellowships from the National Science Foundation!

Congratulations also to Brendan Deal (Salaita Group) and Michael Hollerbach (Chemistry Graduate Program entering class of 2018) who received Honorable Mentions.

For the 2016 competition, NSF received over 12,000 applications and made 2,000 award offers.

The NSF Graduate Research Fellowship Program recognizes and supports outstanding graduate students in NSF-supported science, technology, engineering, and mathematics disciplines who are pursuing research-based Master’s and doctoral degrees at accredited United States institutions. As the oldest graduate fellowship of its kind, the GRFP has a long history of selecting recipients who achieve high levels of success in their future academic and professional careers.

Meet the Honorees

Dayna Patterson came to Emory from Houston Baptist University where she had the opportunity to engage in undergraduate research with the Welch Foundation and as an NSF REU participant at Baylor University. Her research in  the Weinert Group focuses on understanding how bacteria change their phenotypes in response to environmental signals. In January 2018, Dayna received the Carl Storm Underrepresented Minority Fellowship to attend the Gordon Research Conference on Metals in Biology and share her research. She has also shared her research with the Atlanta community through the Atlanta Science Festival. She is the current treasurer for Pi Alpha Chemical Society and an associate fellow with the NIH-funded Initiative to Maximize Student Development.

Kevin Hoang conducted undergraduate research in the Davies Group at Emory and graduated in 2017 with a B.S. in chemistry. He is now at Yale University in the Herzon Laboratory.

Brendan Deal is a second year Ph.D. candidate in the lab of Dr. Khalid Salaita. He completed his undergraduate studies at Davidson College just outside of Charlotte, North Carolina. Brendan’s research is focused on the development of DNA-nanoparticle conjugates with potential applications in the fields of medicine and biotechnology.

 

Michael Hollerbach will be joining Emory this summer after receiving a B.S. in Biochemistry from the College of Charleston in South Carolina.  He chose Emory after seeing all of the exciting research opportunities and looks forward to participating in upcoming research rotations, starting with a summer rotation in the McDonald Group.  His research interests are in Organic Chemistry with a focus on small molecule synthesis and methodology development.  Currently, he is teaching Honors Chemistry at a local high school and wrapping up his undergraduate research at the College of Charleston. At Emory, he looks forward to the opportunity to share his love of Chemistry as a TA and to participate in outreach in the Atlanta community.

First Person: Discovering the WaterHub at Emory

Analytical chemistry students listen to a tour guide at the WaterHub at Emory.
Analytical chemistry students listen to a tour guide in the front hall of the WaterHub at Emory.

By: Laura Briggs (EC ’19)

I didn’t know that the WaterHub existed until this semester, which is a shame because it’s right in my backyard. From my dorm room at 15 Eagle Row, I can see the greenhouse and the mysterious metal trapdoors embedded in the grassy area near Peavine Creek Drive. But it wasn’t until my analytical chemistry lab trekked across campus, collection bottles and safety goggles in hand, that I learned how awesome the WaterHub really is.

One of the first things you see when you enter the WaterHub is a banana tree, happily flourishing among the greenery in the heat and humidity. Besides providing me with a bit of joy, the tree is working full-time for a greater cause. Its roots are the centerpiece of a hydroponic reactor beneath the greenhouse that harnesses the natural design of plants to provide efficient and stable water treatment.

As our tour guide explained to the class, the WaterHub recycles up to 400,000 gallons of water every day, meeting almost 40% of Emory’s total water needs. Don’t worry, though- our guide reassured us that repurposed sewage is not coming out of the water fountains. Instead, the recycled water heats and cools buildings and helps flush toilets in some of Emory’s dorms.

How does this Cinderella transformation occur? The treatment process begins with a series of moving bed bioreactors to settle out and digest the – um – solid components of sewage. These large tanks contain a floating plastic netting system where bacteria can settle and grow into compact communities called biofilms.

Different kinds of bacteria proliferate in different bioreactors, and the WaterHub puts each of them to work cleaning various components of the wastewater. Oxygen levels control the types of bacteria that flourish. One bioreactor is completely anaerobic, encouraging the growth of bacteria that can “denitrify” the water, reducing dangerous nitrates into harmless nitrogen gas. Other bioreactors have different oxygen conditions, and the microbes that grow there perform other functions.

The next step in the process also relies on nature; a vast network of plant roots dips down into a series of hydroponic reactors, providing maximum surface area for more junk-eating microbes to inhabit. Alongside the plants, there’s also an artificial system of textile webbing to provide additional filtration.

At this point in the treatment system, the water is pretty clear, and almost all contaminants have been removed. Still, the process isn’t over. Water passes through a clarifier and a filter, removing any remaining solids, nutrients, and color from the water. Finally, any straggling biological contaminants are zapped away with a combination of chlorine and ultraviolet (UV) light. Our class sampled this fully-repurposed water to test for various contents (Here is my blog post exploring this process in-depth!)

The WaterHub – once a mystery to me – is a brilliant marriage of sustainability, engineering, chemistry, and biology right on Peavine Creek Drive! Thanks to Dr. Weaver’s analytical chemistry lab course, I can now look out my dorm room window and appreciate the source of the water that heats the building on these cold winter nights – and the beautifully-evolved natural processes that keep it clean.

orange line

Laura BriggsLaura Briggs is a sophomore majoring in chemistry and dance. Laura is a Woodruff Scholar and the Vice President of the Emory Swing Dance Club. She is also a member of the Emory Dance Company and hosts a weekly, science-themed radio show. Laura is a research assistant in the Weinert lab, where she studies really cool bacteria that attack potatoes. Laura plans to pursue either a Ph.D. in biochemistry or a master’s in science writing.

To learn more about the WaterHub, check out this link from Campus Services!

http://www.campserv.emory.edu/fm/energy_utilities/water-hub/

Weinert Group in Nature Communications

Clip from the image RsbR haem pocket model and haem spectra." This image, and the article referenced, are licensed under a Creative Commons Attribution 4.0 International License.
Clip from the image RsbR haem pocket model and haem spectra.” This image, and the article referenced, are licensed under a Creative Commons Attribution 4.0 International License.

The Weinert Group has research featured in the June issue of Nature Communications. The paper, “An O2-sensing stressosome from a Gram-negative bacterium,” is co-authored by Xin Jia, Jian-bo Wang, Shannon Rivera, Duc Duong, and Emily E. Weinert.

Abstract:

Bacteria have evolved numerous pathways to sense and respond to changing environmental conditions, including, within Gram-positive bacteria, the stressosome complex that regulates transcription of general stress response genes. However, the signalling molecules recognized by Gram-positive stressosomes have yet to be identified, hindering our understanding of the signal transduction mechanism within the complex. Furthermore, an analogous pathway has yet to be described in Gram-negative bacteria. Here we characterize a putative stressosome from the Gram-negative bacterium Vibrio brasiliensis. The sensor protein RsbR binds haem and exhibits ligand-dependent control of the stressosome complex activity. Oxygen binding to the haem decreases activity, while ferrous RsbR results in increased activity, suggesting that the V. brasiliensis stressosome may be activated when the bacterium enters anaerobic growth conditions. The findings provide a model system for investigating ligand-dependent signalling within stressosome complexes, as well as insights into potential pathways controlled by oxygen-dependent signalling within Vibrio species.

[Full Article]