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Undergraduate Research Initiative Welcomes Students With Hearing Loss

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Katelyn Stokan (left) and Hannah Hughes work in a lab on campus

by Amy Beth Miller

About three dozen students who are deaf or hard of hearing (DHH) have conducted research in recent years through the Department of Biochemistry and Cellular and Molecular Biology (BCMB) at the University of Tennessee, Knoxville. 

Professor Gladys Alexandre has been working with DHH students since 2016, and the effort has expanded to other labs.

“We have training and mentoring for all advisors, and this helps promote the Deaf culture in the hearing community and better prepare diverse scientists to host these underrepresented individuals,” said Alexandre, now BCMB department head. “We are helping the campus to become more welcoming to DHH students.”

Recruiting

Alexandre was director of the Program for Excellence and Equity in Research (PEER), which focuses on recruiting and training underrepresented students in science, technology, engineering, and math (STEM) fields. “There are many pools of talents that have not been fully tapped for the benefits of our society, and in my case, research, DHH students represent such an overlooked pool of talents,” she said.

The director of the UT Center on Deafness, David Smith, connected Alexandre with colleagues from the National Technical Institute for the Deaf at the Rochester Institute of Technology (NTID/RIT), where she started recruiting undergraduate students as a pilot. Since then, BCMB Professors Tessa (Burch-Smith) Calhoun, Liz Howell, and Dan Roberts also have hosted students from NTID during the summer.

Data from those experiences helped BCMB receive its first National Science Foundation (NSF) Research Experience for Undergraduates (REU) award in 2019 under Roberts, who is now retired. Professor Elena Shpak received a 2023 NSF REU award to continue BCMB’s efforts through summer 2026. 

Alexandre also has budgeted funding from her own NSF awards to train DHH students in research every summer.

One of the first graduate students Alexandre recruited from NTID/RIT was Amie Fornah Sankoh, whose PhD from BCMB in 2023 made her the first deaf Black woman to earn a STEM doctorate in the United States, according to Chemistry World.

BCMB also recruits DHH students through colleagues at Gallaudet and other universities, plus it is on an NSF REU site that prospective students can consult to find research opportunities.

Rethinking communication

Alexandre did not have previous experience with a person who has hearing loss but said communicating was not as challenging as she anticipated. “It simply needs to slow down and to be as clear as possible,” she said. “We use writing, a few ASL [American Sign Language] signs we know, [PowerPoint] captions, and ASL interpreters to communicate.”

“Being flexible and open-minded goes a long way to effectively communicate with DHH individuals,” she said. “This is also not a heterogenous group: Some students sign, some don’t, some can lip-read, many can’t.”

Each lab’s principal investigator and in-lab mentor—a graduate student or post-doctoral researcher—completes online training through Project Access (For Educators) on understanding hearing loss and improving communication. “We then have a meeting where we discuss expectations and how to set up the projects for success,” Alexandre said. “We specifically discuss what worked and didn’t work so that we can improve every year.”

“We also ask that the lab writes detailed protocols and provide them in advance and then demonstrate them,” she said, noting that advance access is critical for the students who are deaf or hard of hearing to have time to become familiar with the material.

“As long as I am funded, I will continue this effort,” Alexandre said. “It is transformative for all involved, and it definitely enhances communication between the lab members. Taking the time to explain difficult concepts using a variety of approaches is incredibly effective, but it takes a lot more time.”

She noted that clearer nonverbal communication also benefits individuals who are not deaf but may have difficulty hearing. 

BCMB’s efforts to improve diversity and create a welcoming community are receiving recognition. Alexandre received the 2019 American Society for Microbiology William A. Hinton Award for the Advancement of a Diverse Community of Microbiologists and a 2022 NTID Co-op and Career Center Outstanding Employer Partner Award.

Two women pose together for a photo with a painting of Ayres Hall

Cheryl Hodge Retires after 45 Years at UT

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Two women pose together for a photo with a painting of Ayres Hall

by Amy Beth Miller

Cheryl Hodge laughed when she received her first paycheck from the University of Tennessee, Knoxville, in 1979. “The silly thing said that I would be eligible for retirement in the year 2021,” she said, and that date was so far in the future she couldn’t imagine it. 

Hodge stayed even longer, retiring at the end of June as an administrative specialist in the Department of Biochemistry and Cellular and Molecular Biology (BCMB).

She started in the Department of Audiology and Speech Pathology, going on to work in the School of Art and in Human Resources as well.

“It is great that her 45-year career at UT allowed her to connect to people and programs as she served the university,” said Beauvais Lyons, divisional dean for arts and humanities and Chancellor’s Professor of Art. “The School of Art faculty and staff adored Cheryl during the decade she worked with us.”  

‘Everything changes’ 

When Hodge started her career, parking on the UT campus was $5 a quarter and she used a manual typewriter. She recalls with excitement when she received an IBM Selectric typewriter, which allowed her to change fonts.

“Everything changes all the time,” she said of working at the university, and she had shown the flexibility to keep up. Hodge took advantage of training through UT and the International Association of Administrative Professionals, also serving in the leadership of the Knoxville chapter.   

Her first responsibility at UT was secretarial, and then she began working with graduate student records. “I was in charge of making sure they were all getting the classes they needed, and keeping all their records; and that was all on paper in filing cabinets, long before computers,” she explained. 

“I’m still very close friends with quite a few of those kids—they’re not kids,” she said with a laugh, noting they are about five years older than she is.

From there she went to the School of Art, working with hundreds of applications for each of the handful of graduate school positions, another role she loved.

Leaving her mark

While in the School of Art she became a member of a UT Employee Relations Committee (ERC). “I got really involved in the fact that this was a place where employees could voice their concerns, could ask for things they felt the university needed,” she explained.

That led to her next position, as principal secretary in UT Human Resources, working with five ERCs and the retirees’ association. “It got to a point in the mid-90s where practically everyone on campus knew my name,” she said. “I loved my years there.” 

She also left a visible impact, the traffic signal at the intersection of Pat Sumitt Drive and Volunteer Drive. After several accidents at the intersection, Hodge put the proposed signal on every committee meeting agenda for more than six years, and she went to Knoxville City Council meetings to advocate for it. 

Now every time they go to a play at the Clarence Brown Theatre, Hodge points and tells her husband, Roy, “See my light!”

What’s next?

When her position in the HR office was eliminated, Hodge found a new family of coworkers in BCMB. 

“She has a love for working with people and helping people,” said BCMB Business Manager LaShel Stevens. “She has a very caring heart.”

Hodge said while her work has been fulfilling, “in every place I’ve been, it’s the people who have kept me.” 

“Loyalty is important,” Hodge said. “Getting into a spot that means something to you and staying is important.” 

After 45 years as a UT employee, Hodge has a clear definition of what being a Volunteer means to her: “someone with a servant’s heart, someone who wants to see the people around them succeed, who wants to make sure that the folks that they work for and with—and even see around—are getting what they need.”

“It means going above and beyond whatever you’re expected to do, to do what needs to be done,” Hodge said.

She has told people that her plan for retirement is “to sit on a pillow and eat bonbons,” but she won’t laze around long. She and her husband, who retired from the UT treasurer’s office in 2005, plan to volunteer at an animal shelter, travel, and take in the sights of Knoxville.

Cheryl also hopes to return to acting in community theatre productions and hiking Mt. LeConte, if she regains the memory and energy that have been lagging since she had COVID.

While she won’t be working on campus this fall, one tradition will continue. She and Roy plan to be selling candy apples this September at the Tennessee Valley Fair, where they first met.

Photo of a nematode

Jianbin Wang Team Publishes on Chromosome Dynamics in Nematodes

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Photo of a nematode

by Randall Brown

Assistant Professor Jianbin Wang and his lab team in the Department of Biochemistry and Cellular and Molecular Biology focus their studies on the mechanism and function of programmed DNA elimination (PDE).

PDE is a process that violates the paradigm of genome integrity, selectively removing genetic material from the genome. However, hundreds of thousands of diverse species undergo PDE, suggesting that it must have evolutionary benefits.

Wang and colleagues published their most recent findings about PDE in Current Biology this May in an article titled “Chromosome fusion and programmed DNA elimination shape karyotypes of nematodes.” Their findings provide a biological explanation of the different numbers and sizes of chromosomes in various nematodes (roundworms), many of which are parasites of humans and other veterinary animals—enhancing our understanding of genome changes and the potential functions of PDE in these important parasites.

“Maintenance of genomes is essential for the survival and propagation of species,” said Wang. “We found that PDE is an ancient mechanism of genome dynamics—possibly one that was harnessed to sculpt genomes during evolution. PDE may also have been adapted as a way to regulate the expression of genes during reproduction, as many genes and regulatory elements are deleted, permanently silencing them in the somatic cells.”

In the new research, the team looked specifically at nematode karyotypes (a full set of chromosomes) by assembling the full genomes using high throughput sequencing methods and comparing many genomes from diverse nematodes through bioinformatic analysis.

“Chromosome fusion will lead to fewer germline chromosomes,” said Ryan Simmons, a post-doctoral researcher and lead author of the paper for the Wang Lab. “This could benefit the organisms since having fewer numbers of chromosomes may reduce errors generated during meiosis.”

An error such as mis-segregation of the chromosomes can lead to aneuploidy (abnormal number of chromosomes) and other abnormalities, so chromosome fusion can reduce the number of gametes that are not usable. This provides benefits for the overall survival and reproduction of the organism.

In contrast, a benefit of PDE could be to split fused chromosomes in the germline—cells that carry genetic information from one generation to the next—to many smaller chromosomes in the somatic cells.

“Even though these fused chromosomes may be beneficial to meiosis, they may cause problems in gene expression and regulation in the somatic cells and thus need to be removed,” said Simmons. “Thus, nematodes with PDE and chromosome fusions seem to have taken advantage of both the fused germline chromosomes and split somatic chromosomes.”

To learn more about the function of PDE, the Wang Lab looks to create mutant nematodes that do not experience the process.

“Although a nematode that fails to fully stop PDE is yet to be established in the lab, we are working on a free-living nematode model on which we have created several mutants that fail to eliminate some portions of the normally eliminated DNA,” said Wang. His team published about this work in 2022, also in Current Biology. “These mutant worms survived, and their phenotypes are currently being evaluated in the lab.”
Meanwhile, the recently published work by Wang’s team has already been highlighted in a commentary on genome organization by colleagues at the Institute of Human Genetics, CNRS, and University of Montpellier, Montpellier, France.

Mother And Daughter Professors Forge A Big Orange Family Legacy

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by Randall Brown

Not everyone starts forming career goals as a toddler, but not every toddler spends time visiting their mother’s parasitology lab.

“I would say, ‘I’m going to work in my mother’s lab—that will be my plan,’” said Rachel Patton McCord, now an associate professor in UT’s Department of Biochemistry and Cellular and Molecular Biology.

It helped her strong early sense of direction that her mother is Professor Emeritus Sharon Patton, who was the first female faculty member in the UT College of Veterinary Medicine (UTCVM) and taught at UT for 38 years.

“I started as a professor at UT in 2016, the year after she retired, so it’s almost like handing off the baton,” said McCord. “I don’t know if there are any other mother/daughter professor pairs at UT. It’s not something I necessarily expected to be possible in my life.”

McCord earned her PhD in biophysics at Harvard University and did postdoctoral research at the University of Massachusetts Medical School before looking for a permanent faculty position. She hoped to find one not too far from her family in Knoxville but didn’t know she would become a “second-generation professor” at Rocky Top.

“Finding academic jobs is not trivial, and you very well may not have the opportunity to work at the same place as your parents,” she said. “But the job came available here to do exactly what I do. It was the opportunity to be back in the place where I grew up, going into my mother’s office and watching what she did as a professor.”

Patton joined UTCVM in 1977, during its inaugural year of classes (the college is currently celebrating the 50th anniversary of its official founding).

“The first time parasitology was taught, I was there to help teach it,” said Patton. “When the first students arrived, I arrived with them—the building was still being built.”

She arrived at UT from the University of Kentucky (UK) more prepared than the average new faculty hire—she had her own collection of example parasites, inherited from her recently retired faculty mentor at UK.

“I showed up with all these bottles of worms, which of course the vet school didn’t have at that time,” said Patton. “It helped that we had all these things through the years. I would say that by the time I retired, we had one of the best collections anywhere.”

She also brought a personalized teaching style to her classes, engaging students in a call-and-response style of participation to convey important principles, something she likens to “an old-time gospel meeting.” She also developed a special end-of-class message of encouragement over the years.

“I would tell them, ‘That’s all for today. Remember, I love you,’” said Patton. “When I first said that I didn’t really mean it—I was just saying it, you know? But as time goes by, you really do love them.”

Her teaching impacted many students over the years, including incoming UTCVM Dean Paul Plummer, who had classes with Patton and earned his DVM at UT in 2000. The impression she made on McCord was, of course, the deepest.

“I always saw how much she loved her students and could impact their lives,” said McCord. “I learned to teach by imitating my mother: when I’m talking in class, the tone of voice I use. I practiced until it became something I could do.”

Rachel Patton McCord working in a lab

McCord also absorbed knowledge growing up that helps her in her field, even though her specialty is DNA and human genome structure, not parasitology.

“We have a professor just two doors down the hall who is working on parasites, but more related to what I do,” said McCord. “I’m studying DNA structure, he’s studying DNA in parasites, and in collaborating with him I’m suddenly getting to work with things I heard about growing up—all these words are as familiar to me as some people might be with, ‘Oh, my mother’s cooking,’ or ‘my mother’s quilts.’ I’m like, ‘Oh toxoplasmosis, that sounds so familiar.’”

Patton is happy that she helped connect her daughter to the scientific world, and happy to have McCord continue their family’s teaching legacy at UT. 

“It feels great,” said Patton. “She’s really a good, careful researcher, and a good teacher. Of course, I’m her mother, so I think she’s talented in all respects. But after she’d done her postdoc work and came to UT—it was overwhelming. It was just wonderful.”

In addition to sharing their family bond through UT academics, both mother and daughter proudly say their “blood runs orange.” McCord recalls hearing the Pride of the Southland Band practicing their Vol walk while working on a grant proposal in her first fall semester back on campus.

“You could hear ‘Rocky Top’ through the window, and without even thinking, I jumped up and ran outside,” she said. “It was amazing how it made me feel inspired to go write my grant better. Like, I will give my all for Tennessee today!”

Faculty Publications – 2023

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  1. Acharyya D, Cooper J and Prosser RA. Ex vivo comparative investigation of suprachiasmatic nucleus excitotoxic resiliency F1000Research 2023, 11:1242.
  2. Adhikari A, Khanal S, Magar SR, Thapa S, Khati S, Lamichhane R, Marasini K. (2023) Aspergillus Coinfection in a Hydatid Cyst Cavity of Lung in an Immunocompetent Host: A Case Report and Review of Literature Case Reports in Infectious Diseases https://doi.org/10.1155/2023/6975041.
  3. Adhikari A, Shrestha S, Bhattarai P, Khanal S, Lamichhane R, Balayar R, Panta S, Marasini K. (2022) Cleidocranial dysplasia—A case report of incidentally found and lately diagnosed disorder Clinical Case Reports 10 (10), e6440.
  4. Agarwal R and Smith JC. Speed vs accuracy: Effect on ligand pose accuracy of varying box size and exhaustiveness in AutoDock Vina Molecular Informatics 42(3) 2200188 (2023). 
  5. Ancajas CJ, Alam A, Alves DS, Zhou Y, Wadsworth NM, Cassilly CD, Ricks TJ, Carr AJ, Reynolds TB, Barrera BN, Best MD. (2023) Cellular Labeling of Phosphatidylserine Using Clickable Serine Probes. ACS Chemical Biology 18 (2), 377-384.
  6. Azhar BJ, Abbas S, Aman S, Yamburenko MV, Chen W, Müller L, Jewell DA, Dong J, Shakeel SN, Groth G, Binder BM, Grigoryan G, Schaller GE. (2023) Basis for high-affinity ethylene binding by the ethylene receptor ETR1 of Arabidopsis. Proceedings of the National Academy of Sciences, USA. 120: e2215195120.
  7. Bogati B, Wadsworth N, Barrera F, Fozo EM. Improved growth of Escherichia coli in aminoglycoside antibiotics by the zor-orz toxin-antitoxin system. Journal of Bacteriology (2022) JB0040721. doi: 10.1128/JB.00407-21 PMID: 34570627.
  8. Brenya E, Dutta E, Herron B, Walden LH, Roberts DM, and Binder BM. (2023) Ethylene-Mediated Metabolic Priming Increases Photosynthesis and Metabolism to Enhance Plant Growth and Stress Tolerance. PNAS-Nexus doi: 10.1093/pnasnexus/pgad216.
  9. Brueggeman JM, Windham IA, Nebenführ A (2022) Nuclear movement in growing Arabidopsis root hairs involves both actin filaments and microtubules. Journal of Experimental Botany 73: 5388-5399. DOI: 10.1093/jxb/erac207. PMID: 35554524.
  10. Das P, San Martin R, McCord RP. Differential contributions of nuclear lamina association and genome compartmentalization to gene regulation. Nucleus. 2023 Dec;14(1):2197693. doi: 10.1080/19491034.2023.2197693. PubMed PMID: 37017584; PubMed Central PMCID: PMC10078145.
  11. Dockendorff TC, Estrem B, Reed J, Simmons JR, Bahrami Zadegan S, Zagoskin MV, Terta V, Seaberry E, Wang J: The Nematode Oscheius tipulae as A Genetic Model for Programmed DNA Elimination. Current Biology. 2022, 32(23):5083-5098. https://doi.org/10.1016/j.cub.2022.10.043.
  12. Espinoza-Araya, C., Starbird, R., Prasad, E.S., Venkatesan, R., Mulchandani, A., Bruce, B.D, and Villarreal, C.C., (2023) A bacteriorhodopsin-based biohybrid solar cell using carbon-based electrolyte and cathode components. BBA-Bioenergetics, 1864:4, 148985; https://doi.org/10.1016/j.bbabio.2023.148985.
  13. Estrem B, Wang J: Programmed DNA elimination in the parasitic nematode Ascaris. PLoS Pathogens. 2023 Feb; 19(2):e1011087. https://doi.org/10.1371/journal.ppat.1011087.
  14. Ganusova, E.E., Rost, M., Aksenova, A., Abdulhussein, M., Holden, A. and Alexandre, G. 2023. Azospirillum brasilense AerC and Tlp4b Cytoplasmic Chemoreceptors are promiscuous and interact with the two Membrane-Bound Chemotaxis Signaling Clusters mediating chemotaxis responses. J Bacteriol 205(6): e0048422.; doi: 10.1128/jb.00484-22.
  15. Gao, J., Carnahan, J., Alexandre, G. and Trolinger J. 2022. “Digital holographic microscopy for volumetric, three-dimensional characterization of bacterial motility,” Proc. SPIE 12223, Interferometry XXI, 122230E (3 October 2022); https://doi.org/10.1117/12.2633136.
  16. Gray ALH, Norman V, Oluwatoba DS, Prosser RA, Do TD. Potential Protective Function of Aβ42 Monomer on Tauopathies. J Am Soc Mass Spectrom. 2023 Mar 1;34(3):472-483. 
  17. Gross LJ, McCord RP, LoRE S, Ganusov VV, Hong T, Strickland WC, Talmy D, von Arnim A, Wiggins G (2023). Enhancing Quantitative and Data Science Education for Graduate Students in Biomedical Science. PloS One. Apr 27;18(4):e0284982. doi: 10.1371/journal.pone.0284982.
  18. Groves SM, Panchy N, Tyson DR, Harris LA, Quaranta V, Hong T. Involvement of Epithelial-Mesenchymal Transition Genes in Small Cell Lung Cancer Phenotypic Plasticity. Cancers (Basel). 2023 Feb 25;15(5):1477. doi: 10.3390/cancers15051477.
  19. Gurumoorthy V, Shrestha U, … Smith JC, Petridis L, O’Neill H. Disordered domain shifts the conformational ensemble of the folded regulatory domain of the multidomain oncoprotein c-Src. Biomacromolecules. 24, 2, 714–723 (2023).
  20. Lee G, Zeng K, Duffy CM, Sriharasha Y, Yoo S, Park JH. 2023. In vivo characterization of the maturation steps of PDF neuropeptide precursor in the Drosophila circadian pacemaker neurons. Genetics, in press. doi: 10.1093/genetics/iyad118
  21. Li H, McCord RP. Actin up: shifting chromosomes toward repair, but also translocations. Nat Struct Mol Biol. 2023 Jan;30(1):2-4. doi: 10.1038/s41594-022-00906-4. PubMed PMID: 36577921.
  22. Li J, Xie J …. Smith JC, Hong L. Non-ergodicity of a globular protein extending beyond its functional timescale. Chemical Science. 13 (33), 9668-9677 (2022).
  23. Liang, L, Wang Y …. Smith JC ….. O’Neill H, Davison BH, Raguskas AJ. Chemical and Morphological Structure of Transgenic Switchgrass Organosolv Lignin Extracted by Ethanol, Tetrahydrofuran, and -Valerolactone Pretreatments. ACS Sustainable Chemistry and Engineering. 10 (28), 9041-9052 (2022).
  24. Liu J, Willems HME, Sansevere EA, Allert S, Barker KS, Lowes DJ, Dixson AC, Xu Z, Miao J, DeJarnette C, Tournu H, Palmer GE, Richardson JP, Barrera FN, Hube B, Naglik JR, Peters BM. A variant ECE1 allele contributes to reduced pathogenicity of Candida albicans during vulvovaginal candidiasis. PLoS Pathogens (2021) e1009884. doi: 10.1371/journal.ppat.1009884. PMID: 34506615.
  25. Liu S-H,; Xiao S…. Smith JC ….. Loukas P. Identification of Small-Molecule Inhibitors of Fibroblast Growth Factor 23 Signaling via In Silico Hot Spot Prediction and Molecular Docking to α-Klotho Journal of Chemical Information and Modeling. 62 (15), 3627-3637 (2022).
  26. Lokdarshi A and von Arnim AG (2023) A Miniature Sucrose Gradient for Polysome Profiling. Bio-protocol 13: e4622. DOI: 10.21769/BioProtoc.4622.
  27. Lou J, Schuster JA, Barrera FN, Best MD. ATP-Responsive Liposomes via Screening of Lipid Switches Designed to Undergo Conformational Changes upon Binding Phosphorylated Metabolites. J. Amer. Chem. Soc. (2022) ;144(8):3746-3756. PMID: 35171601 DOI: 10.1021/jacs.2c00191.
  28. Luxem K, Sun JJ, Bradley SP, Krishnan K, Pereira TD, Yttri EA, Zimmermann J, Laubach M. “Open-source tools for behavioral video analysis: Setup, Methods and Development”. eLife, 2023.
  29. Mamontov E, Bordalla HN … Smith JC, Sokalov AP. Broadband Wide-Angle VElocity Selector (BWAVES) neutron spectrometer designed for the SNS Second Target Station. EPJ Web of Conferences 272 02003 (2022).
  30. McClintic WT, Scott HL, Moore N, Farahat M, Maxwell M, Schuman CD, Bolmatov D, Barrera FN, Katsaras J, Collier CP. (2023) Heterosynaptic plasticity in biomembrane memristors controlled by pH. MRS bulletin 48 (1), 13-21
  31. Melchionna M.V., Gullett J.M., Bouveret E., Shrestha H.K., Abraham P.E., Hettich R.L., Alexandre G. 2022. Bacterial Homologs of Progestin and AdipoQ Receptors (PAQRs) Affect Membrane Energetics Homeostasis but Not Fluidity. J. Bacteriol. 204(4):e0058321. doi: 10.1128/jb.00583-21.
  32. Miller GM, Ellis A …. Smith JC, Lupu DS. Hypothesis‑Agnostic Network‑Based Analysis of Real‑World Data Suggests Ondansetron is Associated with Lower COVID‑19 Any Cause Mortality. Drugs – RealWorldOutcomes 9 (3), 359-375 (2022).
  33. Mohan M, … Smith JC, Kidder M, Singh S. Accurate Prediction of Carbon Dioxide Capture by Deep Eutectic Solvents using Quantum Chemistry and a Neural Network. Green Chemistry 25(9) 3475 (2023).
  34. Mohan M, Smith MD …. Smith JC. Predictive understanding of the surface tension and velocity of sound in ionic liquids using machine learning. J. Chem. Phys. 158, 214502 (2023).
  35. Mohan M, Smith MD …. Smith JC. Quantum Chemistry-Driven Machine Learning Approach for the Prediction of the Surface Tension and Speed of Sound of Ionic Liquids. ACS Sustainable Chem. Eng. 2023, 11, 20, 7809–7821 
  36. Mongès A, Yaakoub H, Bidon B, Glévarec G, Héricourt F, Carpin S, Chauderon L, Drašarová L, Spichal L, Binder BM, Papon N, Rochange S. (In press) Are histidine kinases of arbuscular mycorrhizal fungi involved in the response to ethylene and cytokinins? Molecular Plant-Microbe Interactions
  37. Mykins M, Layo-Carris D, Dunn L, Skinner DW, Perez S, McBryar A, Shultz TR, Willems A, Lau BYB, Hong T, Krishnan K. “Wild-type MECP2 expression coincides with age-dependent sensory deficits in a female mouse model for Rett syndrome”. Journal of Neuroscience Research, 2023. 
  38. Mykins M, Marrero K, Cataldo G, Aruljothi K, Krishnan K, Brumberg J. “Barrels XXXV: Barrels In-Person”. Somatosensory & Motor Research, 2023. 
  39. Nordick B, Chae-Yeon Park M, Quaranta V, Hong T. Cooperative RNA degradation stabilizes intermediate epithelial-mesenchymal states and supports a phenotypic continuum. iScience. 2022 Sep 27;25(10):105224. doi: 10.1016/j.isci.2022.105224. 
  40. Panchy N, Watanabe K, Takahashi M, Willems A, Hong T. Comparative single-cell transcriptomes of dose and time dependent epithelial-mesenchymal spectrums. NAR Genom. Bioinform. 2022 Sep 21;4(3):lqac072. doi: 10.1093/nargab/lqac072. 
  41. Park HL, Seo DH, Lee HL, Bakshi A, Park C, Chien Y-C, Kieber JJ, Binder BM, Yoon GM (2023) Ethylene-triggered subcellular trafficking of CTR1 enhances the response to ethylene gas. Nature Communications 124: 365. doi: 10.1038/s41467-023-35975-6.
  42.  Rajeshwart T & Smith JC. Structural Patterns in Class 1 Major Histocompatability Complex-restricted Nonamer Peptide Binding to T-cell Receptors. Proteins: Structure, Function and Bioinformatics. 90(9):1645-1654 (2022).
  43. Roger D, Agarwal R, …. Glaser J, Smith JC. SARS-CoV2 Billion-Compound Docking. Nature Scientific Data. 10(1)173 (2023).
  44. Russell CM, Rybak JA, Miao J, Peters BM, Barrera FN. (2022) The Candida albicans virulence factor candidalysin polymerizes in solution to form membrane pores and damage epithelial cells. Elife 11, e75490.
  45. Russell CM, Rybak JA, Miao J, Peters BM, Barrera FN. (2022) Candidalysin: connecting the pore forming mechanism of this virulence factor to its immunostimulatory properties. Journal of Biological Chemistry, 102829.
  46. Rybak JA, Sahoo AR, Kim S, Pyron RJ, Pitts SB, Guleryuz S, Smith AW, Buck M, Barrera FN. (2023) Allosteric inhibition of the epidermal growth factor receptor through disruption of transmembrane interactions. Journal of Biological Chemistry, https://doi.org/10.1016/j.jbc.2023.104914.
  47. San Martin R, Das P, Sanders JT, Hill AM, McCord RP. Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification. Elife. 2022 Dec 29;11. doi: 10.7554/eLife.81290. PubMed PMID: 36579892.
  48. Schaefer KG, Pittman AE, Barrera FN, King GM. “Atomic force microscopy for quantitative understanding of peptide-induced lipid bilayer remodeling”. Methods (2022) 197:20-29. doi: 10.1016/j.ymeth.2020.10.014.
  49. Shelby SA, Castello-Serrano I, Wisser KC, Levental I, Veatch SL. Membrane phase separation drives responsive assembly of receptor signaling domains. Nat Chem Biol. 2023 Jun;19(6):750-758. doi: 10.1038/s41589-023-01268-8. Epub 2023 Mar 30.
  50. Shelby SA, Shaw TR, Veatch SL. Measuring the Co-Localization and Dynamics of Mobile Proteins in Live Cells Undergoing Signaling Responses. Methods Mol Biol. 2023;2654:1-23. doi: 10.1007/978-1-0716-3135-5_1.
  51. Shelby SA, Veatch SL. The Membrane Phase Transition Gives Rise to Responsive Plasma Membrane Structure and Function. Cold Spring Harb Perspect Biol. 2023 Aug 8:a041395. doi: 10.1101/cshperspect.a041395.
  52. Shen S, Parks JM, Smith JC. HCLus: HLA Class I Supertype Classification. BMC Bioinformatics. 24(1) 1-13 (2023).
  53. Shen S, Parks JM, Smith JC. HLA Class I Supertype Classification Based on Structural Similarity. Journal of Immunology. 210(1) 103-114 (2023).
  54. Sobe R.C., Gilbert C., Vo, L. Alexandre G. and Scharf, B. E. 2022. FliL and its paralog MotF have distinct roles in the stator activity of the Sinorhizobium meliloti flagellar motor. Mol Microbiol 118(3):223-243. doi:10.1111/mmi.14964.
  55. Tan L, Scott H, … Smith JC, Davison J, Elkins J, Nickels J. Amphiphilic co-solvents modulate structure of membrane domains. ACS Sustainable Chemistry & Engineering. 11 4 1598-1609 (2023).
  56. Tan L, Smith MD, Scott H …. Smith JC, Davison BH, Nickels JD. Modeling the partitioning of amphiphilic molecules and co-solvents in biomembranes. Journal of Applied Crystallography. 55(6), 1401-1412 (2022).
  57. Taylor MK, Williams EP, …. Smith JC, Jonsson CBB. Dissecting Phenotype from Genotype with Clinical Isolates of SARS-CoV-2 First Wave Variants. Viruses. 15(3) 611(2023).
  58. Veatch SL, Rogers N, Decker A, Shelby SA. The plasma membrane as an adaptable fluid mosaic. Biochim Biophys Acta Biomembr. 2023 Mar;1865(3):184114. doi: 10.1016/j.bbamem.2022.184114. Epub 2022 Dec 26.
  59. Voloshin R.A., Bozieva A.M., Bruce B.D., and Allakhverdiev S.I. (2023) Photosynthetic microbial fuel cells: practical applications of electron transfer chains. Russian Chem. Reviews, 92:5, 5073; https://doi.org/10.57634/RCR5073.
  60. Willems A, Panchy N, Hong T. Using Single-Cell RNA Sequencing and MicroRNA Targeting Data to Improve Colorectal Cancer Survival Prediction. Cells. 2023 Jan 5;12(2):228. doi: 10.3390/cells12020228.
  61. Workman, C.E., Cawthon, C., Brady, N.G., Bruce, B.D., and Long, B., (2022) Degradation of Esterified Styrene-Maleic Acid Copolymers. Biomacromolecules 23, 11, 4749–4755109; https://doi.org/10.1021/acs.biomac.2c00928.
  62. Xu Y, Kramann R, McCord RP, Hayat S. MASI enables fast model-free standardization and integration of single-cell transcriptomics data. Commun Biol. 6, 465 (2023). doi: 10.1038/s42003-023-04820-3. 
  63. Yao T, Zhang J … Binder BM, …. Chen J-G, Muchero W. (In press) eQTL mapping identified PtrXB38 as a key hub gene in adventitious root development in Populus. New Phytologist.
  64. Zharmukhamedov, S.K., Shabanova, M.S., Huseynova, I.M., Karacan, M.S., Karacan, N., Akar, H., Kreslavski, V.D., Alharby, H.F., Bruce, B.D., and Allakhverdiev, S.I. (2023) Probing the influence of novel organometallic copper (II) complexes on spinach PSII photochemistry using OJIP fluorescence transient measurements. Biomolecules 13(7), 1058; https://doi.org/10.3390/biom13071058.
  65. Zhou, Y., Syed, J., Semchonok, D.A., Kyrilis, F.L., Hamdi, F., Kastrittis, P.L., Wright, E., Bruce, B.D., and Reynolds, T.B. (2023) Solubilization, purification and characterization of the hexameric form of phosphatidylserine synthase from Candida albicans. J. Biol. Chem., 299:6,104756; https://doi.org/10.1016/j.jbc.2023.104756.

Updates – 2023

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Faculty Updates

  • Rachel P. McCord received a College of Arts and Sciences Excellence in Research/Creative Achievement Award and a grant from Science Alliance StART (Support for Affiliated Research Teams).
  • Gladys Alexandre and BCMB were given the 2022 NTID (National Technical Institute for the Deaf at Rochester Institute of Technology) Co-op and Career Center Outstanding Partner Award for involvement in mentoring Deaf and hard-of-hearing students.
  • Albrecht von Arnim will assume a part time (33%) appointment to serve the UT-Oak Ridge Innovation Institute to continue as Director of the Genome Science and Technology graduate program. BCMB faculty have been among the more active in training students in the intercollegiate GST program. The GST program took its place as the third sister program in the Bredesen Center next to the programs in Energy Science and Engineering and Data Science and Engineering.
  • Dan Roberts has retired from UT after over 35 years.
  • Keerthi Krishnan was honored with the Undergraduate Research Mentor of the Year Award from Provost’s Office and an award for Outstanding Graduate Research Mentor from the Graduate Student Senate.

Postdoc and Graduate Student Updates

  • Heng Li (McCord Lab) and Boomer Russell (Barrera Lab) were awarded Graduate Advancement Training and Education (GATE) Fellowships from the Science Alliance.
  • Brandon Estrem (Wang Lab) was given a Division of Biology Cokkinias/Fite Award for Outstanding Scholarly Achievement by a graduate student.
  • Hannah Hughes, postdoc in the Alexandre lab, won best poster by a postdoc at the BLAST (Bacterial Locomotion And Signal Transduction) XVII meeting.
  • Debalina Acharyya (Prosser Lab) won first place in the 3-Minute Thesis (3MT) competition.
  • Morgan House (Joshi Lab) won best post at the FASEB ER structure and function meeting.
  • Boomer Russell (Barrera Lab) received the Graduate Student Senates Award for Excellence in Graduate Research.
  • Mike Mykins was awarded a Herbert Freidberg Nachlas Postdoctoral Fellowship. He also was a college nominee for the Jimmy and Ileen Cheek Graduate Student Medal of Excellence.

Undergraduate Updates

  • Congratulation to undergraduates who won Exhibition of Undergraduate Research and Creative Achievement (EURēCA) awards in the Natural Sciences Division: Vincent Terta, Angela Jo, Benjamin Bridges, Alexandra McBryar, Joseph Martin, Shabre Eskridgé, Raegan van Wirt, Sanaz Hossain, Renata Dos Reis Marques, Christiane Alvarez.
  • Trinity Rose Shultz received an Appalachian Students Promoting the Integration of Research in Education (ASPIRE) scholarship to conduct summer research in the Krishnan lab
  • Breanna Ceesay received a Faculty Research Assistant Fellowship (FRAF) to conduct summer research in the Krishnan lab
  • Joseph Martin was awarded an Advanced Undergraduate Research Activity (AURA), to conduct summer research in the Krishnan lab

Alumni Updates

Jordan Roach (class of 2016) received a UT Volunteer 40 under 40 award during the annual reception.

Congratulations to the 2022-2023 MS and PhD Graduates: Yujie Ye, Amie Sankoh, Mike Mykins, Scott Carlew, Mark Edens, Anwesha Dasgupta.

Research News – 2023

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Fran Barrera

Fighting Candida Virulence

Candida albicans is a fungal human pathogen that causes severe disease by infecting epithelial and immune cells. C. albicans secretes candidalysin, a virulence factor that is required for infection. Candidalysin is a peptide that perforates the lipid membrane that coats cells. This damages the integrity of human cells and initiates the infection process. However, the molecular mechanism that candidalysin uses to form pores is not known, in part due to difficulties in probing interfacial membrane processes with high resolution. 

Research in the Barrera lab has started to get around this problem. Boomer Russell, a graduate student in the Barrera laboratory, is first author on a manuscript published in eLife that unravels how candidalysin works. It turns out that candidalysin uses a molecular mechanism that has never been observed. Against all expectations, candidalysin peptides get together in solution with high affinity, forming a polymer. These polymers close to form loops, which then bind to membranes and form a membrane pore. 
This quite unexpected mechanism is reviewed in an article written by Russell and another graduate student in the lab, Jen Rybak in The Journal of Biological Chemistry. Understanding the candidalysin mechanism will allow for the development of drugs that block its role in fungal infection of humans.


Brad Binder

Ethylene Priming to Grow Bigger and More Stress Tolerant Plants

Ethylene is a gaseous plant hormone that affects plant growth and stress responses. Its practical applications in horticulture, such as ripening bananas, are common knowledge. The Binder lab recently made several advances to understand ethylene signaling. In collaboration with long-time collaborator Eric Schaller at Dartmouth College, they published an article in the Proceedings of the National Academy of Sciences that combines computational and experimental approaches to understand the structural basis for the high affinity binding and signal propagation by ethylene receptors. 

A second collaboration with the lab of Gyeong Mee Yoon at Purdue University published in Nature Communications expands our understanding of the spatiotemporal dynamics involved in ethylene signaling components down-stream of the receptors. Most recently, the Binder lab, in collaboration with Dan Roberts, found that transiently treating germinating seeds with ethylene causes a priming effect leading to large increases in both plant growth and stress tolerance which persist throughout the plants’ lifetime. This discovery, published in PNAS-Nexus, is particularly exciting since growth and stress tolerance usually exhibit an inverse relationship. 

Lead author Eric Brenya, a postdoctoral researcher in the Binder lab, highlights the potential of this finding for horticulture and agriculture: “Given the challenges posed by global warming and diminishing arable land, these discoveries are crucial in sustaining the growing human population.”

The Binder lab is now determining the mechanisms for this priming with funding from a recently awarded NSF grant.


Dynamics of G Protein-Coupled Receptors

G protein-coupled receptors (GPCRs) carry out diverse and important functions and are the target of many therapeutic drugs. The Lamichhane lab continues unraveling the dynamics of GPCRs using single-molecule fluorescence microscopy. 

Recently, they made progress to better understand how GPCRs function by characterizing the dynamics of helix 7 of the human A2A adenosine receptor. These findings, published with graduate student Shushu Wei as lead author in Structure, illustrate that there is a critical intermediate conformational state that has been missed in the currently available structures of this receptor. They also showed that the conformational dynamics of these receptors are temporally ordered, which has implications for understanding how agonists and antagonists affect these receptors and could lead to better drug design to target these receptors. They also have made progress in understanding the dynamics of the extracellular domain of the glucagon receptor, which is important in carbohydrate homeostasis. 
Their findings, detailed in Journal of Biological Chemistry, provide information for the development of therapeutics for diabetes and underscores the lab’s commitment to advancing our knowledge of molecular interactions and conformational changes of these important receptors. These studies were made possible because of an R35 Maximizing Investigators’ Research Award from NIH to Lamichhane.


Seedling

Nature’s Artistry: Exploring the Mesmerizing World of Plant Shapes and Forms

From towering trees with sprawling canopies to delicate vines that elegantly entwine, from the intricate geometry of fern fronds to the symmetrically layered petals of a flower, the diversity in plant shapes is truly captivating. 

All above-ground organs of plants originate from the shoot apical meristem (SAM), a group of undifferentiated stem cells located between the cotyledons of an embryo and later at the apex of a plant’s stem. Even though cells are constantly growing and dividing, the size of the SAM remains unchanged throughout development due to a tight balance between cell proliferation and incorporation of cells into forming organs. 

Researchers in the Shpak lab study cell-cell communications in the SAM. Recently, they uncovered that two signaling pathways are necessary to promote the differentiation of organs in the periphery of the SAM. This research, published in Development, shows that when these signaling pathways are nonfunctional, the SAM grows bigger and bigger but never can form stems, leaves, and flowers. The pathways inhibit the expression of a transcription factor that promotes stem cell identity.
More recent research from the Shpak lab published in Plant Physiology indicates that there is a complex interplay between auxin and other signaling pathways to regulate SAM. Currently, members of the lab are studying signaling that promotes the initiation of leaves and regulates the shape of flowers and the formation of ovules. This work will help us to uncover the molecular mechanisms responsible for the kaleidoscope of plant shapes and forms.