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.

 

Looking Back on 2018

Happy New Year! As we enter 2019, a new year of innovation and achievement, let’s take some time to appreciate some of the wonderful things that took place in the Department of Chemistry during 2018.

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.

Graduate Student Spotlight: Shannon Rivera

Sitting in her 6th grade science classroom, as a gallon of milk sat outside warming under the hot Georgia sun, Shannon learned two things. First, she learned about the effects of high temperatures on the properties and states of liquids. And second, she learned that she really, really loved chemistry. She recalls how the hands-on teaching style in her middle school science classroom sparked her enthusiasm for the subject, an enthusiasm which only grew stronger through high school, where she had the chance to serve as a chemistry teacher’s assistant.

Through these experiences, Shannon gained an understanding of how chemistry can shape the world. “Instead of being a giant jumbled puzzle, you could actually figure out the small pieces, start putting it together, and start getting a better picture of what’s really going on,” says Shannon. “Chemistry was definitely challenging, but I loved how these small little pieces would come together and things would click.”

Motivated by her passion for chemistry and encouragement from her teachers, Shannon went on to earn her BS in chemistry from the University of Georgia, where she performed undergraduate research under the guidance of Dr. Ron Orlando. In Dr. Orlando’s lab, Shannon worked on creating a database of N-glycans for different species and designing a method for quantifying different IgG products. During this time, Shannon also had the opportunity to participate in Virginia Commonwealth University’s Summer Research Experience for Undergraduates where she spent 10 weeks in the lab of Dr. Julio Alvarez studying the use of glutathione as a source of green energy for new batteries.

In the fall of 2014, Shannon began her graduate studies in chemistry here at Emory. She joined the Weinert group, studying how the globin-coupled sensor protein family senses oxygen and transmits the binding signal into downstream events. “I work primarily with proteins from infectious bacteria. The idea behind my research is that if we can understand this one part of this very dangerous bug, then maybe we can create a new treatment method,” says Shannon. “I love working with the proteins I do because they are all heme proteins, so they are all red!”

Since joining the lab, Shannon has contributed to five publications, one as the primary author and two as co-first author. Her most recent publication is a book chapter in Advances in Microbial Physiology currently in press. “Shannon’s talent for research science, combined with her incredible drive, make it a true pleasure to work with her,” says Dr. Weinert. “Shannon’s fearlessness when it comes to trying new techniques has yielded results that have opened new insights into sensor globins and changed the way we think about how organisms sense and respond to oxygen.”

In addition to her scientific achievements, Shannon has also received several honors and awards during her time at Emory. She was awarded the Emory Graduate Diversity Fellowship for demonstrating outstanding academic achievement, the Outstanding Analytical Teacher’s Assistant Award for being the highest rated teacher’s assistant of the year, and the Carl Storm Underrepresented Minority Fellowship to attend the Gordon Research Conference.

Shannon is a member of the Pi Alpha Chemical Society (PACS), chemistry’s graduate student social and service organization. With PACS, she has had the chance to participate in outreach events and develop valuable relationships with her peers and coworkers. In addition, Shannon serves as communications chair and member of the Association for Women in Science at Emory (AWIS). With AWIS, she has participated in science demonstrations for young students at local schools and helped run a booth at the Atlanta Science Festival celebrating famous women scientists. Shannon is also on the board for the Chemistry Graduate School Prep Club, an organization designed to help prepare chemistry undergraduates from underrepresented backgrounds for future graduate studies. The prep club works primarily with students at institutions that aren’t currently associated with graduate programs to advise them on furthering their education by providing resources on research opportunities, applications, interviews, preparing for the GRE, and more.

After graduation, Shannon plans to go into industry research, where she is looking forward to leading her own projects.

Student Spotlight: Notes from a Dancing Scientist

Laura Briggs performing their solo, Backtalk. Photo by Lori Teague.

By: Laura Briggs (EC ’19)

Most college students are used to answering the age-old question, “So what are you majoring in?” But people aren’t usually expecting the response, “I’m majoring in chemistry and dance!” Usually, they assume one of two things: 1) I want to dance, but my parents made me take up the chemistry major for job security, or 2) I’m serious about science, and the dance major is “just for fun”. These assumptions are almost always followed by the sarcastic question, “So what are you going to do with that?”

In reality, my parents did not force me to major in chemistry, and I take my dance classes just as seriously as my science classes. And as for the question about my future, I intend to pursue careers in both research science and professional dance. I don’t see why I have to choose between one and the other. At Emory, there are many students who are drawn to both science and the arts, but they struggle with prioritizing their passions and making decisions about what to pursue. My response is that life is much too short to give up something you love, so I have decided not to give up anything I love. My two fields inform each other, forgive each other, and infuse my life with balance, inspiration, and excitement.

You might find it hard to believe, but being a dancer makes me a better scientist. There are many skills that scientists need, but aren’t taught in their undergraduate science classes. Communication skills, interpersonal skills, creative thinking, and versatility are all great qualifications for graduate school, but most science classes reinforce lecture-style learning, independent work, rote memorization, and specificity.

Dance, on the other hand, exercises a completely different part of the brain and a much more widespread skill set. Communication is a vital part of being a dancer, whether you are teaching dance, writing a reflection paper, collaborating with other artists, or just talking about your experience in class. An embodied, experiential discipline built on empathy, dance teaches you to understand other people, be flexible (both physically and mentally), and think outside the box. These skills transfer directly from the studio into the science lab; thanks to my dance major, I am comfortable collaborating, asking for help, communicating my work, and trying new things.

Of course, there are other benefits to having two disparate lives on campus. Dance is a solace from the rigor of academia, too. Nobody will tell you that being a chemistry major is easy, especially when juggling extracurricular responsibilities, lab work, and taking care of my adorable pet lizard Ada Lovelace. But when I step into the studio for dance class every day, I am encouraged to leave everything else at the door and focus on myself, my body, and my artistry. It’s self-indulgent in a healthy and necessary way. After I leave the studio, sweaty and satisfied, I can return to the chemistry building refreshed and ready to study again.

The biggest takeaway from my time as a double-major is that no one should have to compromise one passion for the sake of pursuing another. In fact, having multiple equally-demanding facets to your life can be rich and exciting. So next time someone tells you that they’re majoring in chemistry and dance, or environmental science and religion, or computer science and classics, don’t raise your eyebrows! Instead, celebrate the fact that we go to a school where you can do both, and encourage those students to keep being interesting, pushing boundaries, and seeking connections.


Laura Briggs is a junior double-majoring in Chemistry and Dance & Movement Studies. Laura works in the Weinert lab in the Chemistry Department, trying to understand the chemical mechanisms behind plant pathogens. They are a Woodruff Scholar, the founder of the Emory Women in STEM House, and a nominee for the Goldwater Scholarship. Laura’s hobbies include caring for their pet lizard, Ada Lovelace. After college, Laura wants to pursue a Ph.D in biochemistry with a focus on plant chemistry.


 

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]