Department of Biochemistry & Biophysics and

The Graduate Group in Biochemistry & Molecular Biophysics



Poster Session and Reception:

7:30 – 10:00 P.M. on Thursday, November 17, Evergreen Ballroom

Poster Session 1: 7:30 – 8:45 p.m. (odd-numbered posters)
Poster Session 2: 8:45 – 10:00 p.m. (even-numbered posters)

*Poster Presenter
Names of students eligible for prizes are underlined

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Instructions to Presenters

Poster Judging Criteria

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  1. Szigety, Katherine M.*, Fang Liu-Walsh and Sarah E. Millar. Epigenetic regulation of epidermal barrier function and innate immunity.
  2. Zandarashvili, Levani* and Ben E. Black. Molecular mechanisms of PARP-1 activation and inhibition.
  3. Kerstetter, Nicole E.*, Brian Fuglestad, Trevor M. Penning and A. Joshua Wand. Putting drug discovery in the bag.
  4. Lin Shiao, Enrique*, Morgan A. Sammons and Shelley L. Berger. Role of p53 family members in epithelial lineage establishment and maintenance.
  5. Auman, Dirk *, Christopher P. Bialas*, Lauren E. Jarocha, Kevin Henbest, Tilo M. Zolltisch, Goutham Kodali, P.J. Hore, Christopher C. Moser and P. Leslie Dutton. Engineering an artificial flavoprotein magnetosensor.
  6. Olenick, Mara A.*, Mariko Tokito, Malgorzata Boczkowska, Jean-Baptiste Fournier, Roberto Dominguez and Erika L.F. Holzbaur. Organelle-specific regulation of dynein-driven motility by adaptor proteins.
  7. Babiash, Eric S.* and Gideon Dreyfuss. The minimal snRNP assembly machine.
  8. Dempsey, Elizabeth M.H.* and Andrew Tsourkas. Biodegradable gold-loaded polymeric micelles using pH-responsive dextran.
  9. Schutsky, Emily K.*, Jamie E. DeNizio, Christopher S. Nabel and Rahul M. Kohli. Defining and exploiting APOBEC3A’s cytidine deaminase activity on the extended epigenome.
  10. Wang, Hejia Henry*, Burcin Altun, Kido Nwe and Andrew Tsourkas. The development of proximity-based sortase-mediated ligation.
  11. March, Zachary M.*, Oscar Hernandez, Laura M. Castellano and James Shorter. Defining the molecular basis of substrate selection by Hsp104 homologues.
  12. DeNizio, Jamie E.*, Sajid Marhon, Kyoung Jae Won and Rahul M. Kohli. Role of TET processivity in shaping the extended epigenome.
  13. Caro, José A.*, Jasmine A. Smith, Vignesh Kasinath, Kathleen G. Valentine and A. Joshua Wand. Role of conformational entropy in extremely high affinity protein interactions.
  14. Eskici, Gõzde* and Paul H. Axelsen. AB fibril nucleation in reverse micelle.
  15. Dawicki-McKenna, Jennine M.* , Aiko Iwata-Otsubo, Samantha J. Falk, Lukas Chmatal, Karren Yang, Richard M. Schultz, Michael A. Lampson and Ben E. Black. The number of satellite repeats dictates centromere strength in mammals.
  16. Karch, Kelly R.*, Ben E. Black and Benjamin A. Garcia. Monitoring nucleosome dynamics with hydrogen deuterium exchange coupled to top-down mass spectrometry.
  17. Schulte, Jane* and Mark Goulian. New roles for the phospho-histidine phosphatase SixA.
  18. Gupta, Kushol*. The Johnson Foundation Biophysical and Structural Biology Core Facility: thermodynamic and solution methods.
  19. Doliba, Nicolai M.*, Qin Liu, Changhong Li, Chengyang Liu, Ali Naji and Franz M. Matschinsky. Protection against pancreatic beta-cell glucolipotoxicity by a Casein kinase 2 inhibitor.
  20. Kelow, Simon P.*, Jared Adolf-Bryfogle and Roland L. Dunbrack, Jr. Structural analysis of antibody framework region reveals new insights for antibody variable region binding.
  21. McCracken, Daniel S.*, Kasirajan Ayyanathan, Hongzhuang Peng and Frank J. Rauscher. Transcriptional regulation of the metastatic phenotype by Twist.
  22. Gerace, Morgan* and Ben E. Black. Measuring the affinity of defined DNA sequence for centromeric histone complexes.
  23. Szantai-Kis, D. Miklos*, Yanxin J. Wang, Christopher R. Walters and E. James Petersson. Investigating structural perturbation by thioamides.
  24. Iwanicki, Martin J.*, Joshua A. Mancini, P. Leslie Dutton, Christopher C. Moser, Sergei A. Vinogradov and Bohdana M. Discher. Designing optical voltage-sensing probes using synthetic proteins.
  25. Allu, Praveen Kumar*, Kenji Murakami and Ben E. Black. EM studies of the core centromeric nucleosome complex.
  26. Jordan, Earl J.* and Ravi Radhakrishnan. We can predict the effects of kinase domain mutations using molecular dynamics and machine learning.
  27. Hostetler, Zachary M.*, Itthipol Sungweinwong, Matthew J. Culyba, E. James Petersson and Rahul M. Kohli. The mechanism of RecA*-mediated LexA auto-proteolysis, the key reaction in the pro-mutagenic SOS pathway in bacteria.
  28. Kubiak, Jeffrey M.* and Rahul M. Kohli. A synthetic circuit for inducible, small molecule control of the bacterial SOS pathway.
  29. Kearse, Michael G.*, Ashley Viera-Ortiz* and Jeremy E. Wilusz. Unexpected regulation of
    non-AUG translation initiation.
  30. Bhanu, Natarajan V.*, Simone Sidoli and Benjamin A. Garcia. Turnover profiles of histone post-translational modifications in a myogenic model using SILAC labeling, enzyme networks and trend clustering analysis.
  31. Woody, Michael S.*, John H. Lewis, Michael J. Greenberg, Yale E. Goldman and E. Michael Ostap. MEMLET: An easy-to-use tool for data fitting and model comparison using maximum likelihood estimation.
  32. Fuglestad, Brian*, Nathaniel V. Nucci, Christine Jorge, Connie Lao, Hannah Cai, Patricia Jennings and A. Joshua Wand. Hydration on the surface and in the cavities of interleukin-1β.
  33. Jorge, Christine*, Bryan S. Marques and A. Joshua Wand. Measuring protein hydration with NMR spectroscopy.
  34. Hesketh, Christina D.* and James Shorter. Engineering NBD2 of Hsp104 to potentiate mutations.
  35. Jackrel, Meredith E.* and James Shorter. Potentiated Hsp104 variants to counter protein
  36. Remsberg, Jarrett R.*, Sean M. Armour*, Manashree Damle, Simone Sidoli, Wesley Ho, Benjamin A. Garcia and Mitchell A. Lazar. An HDAC3-PROX1 corepressor module acts on HNF4a to control hepatic triglycerides.
  37. Kotaru, Sravya*, Xuejun Yao, Jack Wee Lim, Kathleen G. Valentine and A. Joshua Wand. How proteins deal with a hot mess: tracking the conformational entropy of RNaseH and IGPS across the temperature induced evolutionary landscape.
  38. Thompson, Matthew G.*, Amir Mor, Ke Zhang, Matthew R. Gazzara, Beatriz M.A. Fontoura and Kristen W. Lynch. Host proteins hnRNP K and NS1-BP cooperatively regulate Influenza A M RNA alternative splicing and a subset of host splicing events.
  39. Chongsheng, He, Simone Sidoli, Robert R. Warneford-Thomson*, Benjamin A. Garcia and Roberto Bonasio. Mapping the RNA-interactions of polycomb complex PRC2 via photocrosslinking and mass spectrometry.
  40. Huang, Chuan* and Jeremy E. Wilusz. Defining the mechanism of circular RNA nuclear export.
  41. Lund, Peder J.*, Sarah Smith, Gary Wu and Benjamin A. Garcia. Influence of the microbiota on intestinal epigenetics through butyrate metabolism.
  42. O’Brien, Evan S.*, Danny Lin and A. Joshua Wand. The role of intrinsic dynamics in the function of sensory rhodopsin II.
  43. Song, Shufei* and F. Bradley Johnson. Regulation of gene expression in senescent cells.
  44. Glover, Starla D.*, Robin Tyburski, Leif Hammarström and Cecilia Tommos. Investigating
    proton-coupled electron transfer in de novo α3X protein systems - the study of formation,
    stabilization, and decay of amino acid radicals in native protein environments.
  45. McKibben, Kristen M.* and Elizabeth Rhoades. N-terminal inserts of tau and tau-tubulin
  46. Marchione, Dylan* and Benjamin A. Garcia. The role of histone H3 lysine 36 dimethylation in
    diffuse intrinsic pontine glioma.
  47. Chuang, Edward*, Mariana Torrente and James Shorter. Characterizing the mechanics of Hsp104A503V hyperactivity.
  48. Guo, Jiannan*, Chao Di, Jung-Min Oh, Christopher Venters, Lili Wan, Michael G. Berg, Ihab
    Younis, Zhenxi Zhang and Gideon Dreyfuss. U1 snRNP telescripting: overarching mRNA regulation and cell phenotype.
  49. Wu, Ranran*, Kevin Janssen and Benjamin A. Garcia. Establishing a novel NanoLC-MS platform for DNA methylation quantification.
  50. Coradin, Mariel*, Simone Sidoli, Mariel Mendoza and Benjamin A. Garcia. Proteolytic processing of histone H2A by the cathepsin L protease.
  51. Cupo, Ryan R.* and James Shorter. The engineered mitochondrial chaperone Hsp78 rescues
    proteotoxicity in S. cerevisiae disease models of neurodegeneration.
  52. Guo, Lin*, Hejia Henry Wang, Nikita Singh and James Shorter. Defining Kapβ2 as a protein
    disaggregase for ALS disease protein: FUS.
  53. Lin, JiaBei* and James Shorter. Developing therapeutic protein disaggregases for Alzheimer’s
  54. Carey, Jeffrey N.*, Manuela Roggiani, Kevin S. Myers, Patricia J. Kiley and Mark Goulian.
    Regulation and physiology of aerobic trimethylamine oxide respiration in Escherichia coli.
  55. Turegun, Bengi* and Roberto Dominguez. Regulatory mechanism of the RSC remodeler complex by Rtt102-Arp7/9.
  56. Wein, Samuel P.* and Benjamin A. Garcia. Improvements to RNA detection by mass spectrometry: steps toward in vivo relevance.
  57. Cravens , Shannen L.*, Kyle W. Harpole, Leland Mayne, Cecilia Tommos, S. Walter Englander and A. Joshua Wand. MAP-ing the folding pathway of p38a.
  58. Damodaren, Nivedita*, Trevor P. van Eeuwen, Rina Fujiwara and Kenji Murakami. Structural basis of transcription regulation in response to cellular stress.
  59. Mack, Korrie L.*, Meredith E. Jackrel, Jamie E. DeNizio and James Shorter. Engineering potentiated Hsp104 variants with enhanced substrate-specificity to counter neurodegeneration.
  60. Ahmed, Ismail A.*, Thomas Troxler and Feng Gai. Where does a protein go in a reverse micelle?
  61. Fernandez Garcia, Meilin*, Gregory Donahue, Naomi Takenaka, Rina Fujiwara and Kenneth S. Zaret. Pioneer factors: mechanistic features underlying nucleosome binding.
  62. Stetz, Matthew A.* and A. Joshua Wand. A general method for accelerating the measurement of protein dynamics without losing quantitative accuracy.
  63. Magin, Robert S.*, Glen Liszczak and Ronen Marmorstein. The molecular basis for histone
    H4- and H2A specific amino terminal acetylation by NatD.
  64. Gozalo, Alejandro, L.* and Maya Capelson. Discerning the link between chromatin and nucleoporins.
  65. Mattes, Emily J.* and Elizabeth Rhoades. The effect of post-translational modifications on
    alpha-synuclein behavior and function.
  66. Dimitrova, Valentina S.*, John Lewis and Zhe Lu. Using visible light to study ligand-induced
    conformational changes in the TrkA/H potassium transport complex.
  67. Rego, Nicolas B.*, Erte Xi, Zhitong Jiang and Amish Patel. Characterizing the hydration of complex molecular surfaces to inform interactions and behavior.
  68. Paolella, Lauren M.*, Cassie M. Tran, Katarzyna Kulej, Cecilia Vitali, James G. Davis, Aisha Wilson, Daniel J. Rader, Benjamin A. Garcia and Joseph A. Baur. Investigating the hypercholesterolemia caused by rapamycin treatment.
  69. Weiner, Amber K.*, Simone Sidoli, Sharon J. Diskin and Benjamin A. Garcia. Gia Pronto: a one-click graph visualization software for proteomics datasets.
  70. Janssen, Kevin*, Ranran Wu and Benjamin A. Garcia. RNA nucleoside modification detection by LC-MS/MS.
  71. Shestov, Alexander A.*, Lili Guo, Seung-Cheol Lee, David S. Nelson, Ian A. Blair, Mariusz A. Wasik and Jerry D. Glickson. 13C metabolomic and fluxomic study of human B-cell lymphoma metabolic network.
  72. Torre, Eduardo A.*, Sydney Shaffer, Benjamin Emert, Junwei Shi, Sara Cherry and Arjun Raj.
    Identification of pathways that influence rare-cell expression variability in resistance to targeted cancer therapies.
  73. Cember, Abigail T.J.*, Shane Plunkett and Sergei A. Vinogradov. Imaging friendly upconverting molecules based on Triplet Triplet Annihilation.
  74. Zelent, Bogumil*, Christopher P. Bialas, R. Chib, I. Gryczynski, Pan Chen, M.G. Corradini,
    R.D. Ludescher, Jane M. Vanderkooi and Franz M. Matschinsky. Structural changes of recombinant human glucokinase caused by its natural substrate D-glucose or by glycerol and other osmolytes studied by tryptophan fluorescence.
  75. Gomes, Edward*, Lin Guo and James Shorter. Poly (ADP-ribose) promotes TDP-43 liquid droplets but reduces TDP-43 aggregation.

Instructions for presenters:

  • Presenters should remain at their posters during the assigned time. If you are graduate student, your poster will be judged then.
  • All poster presenters are asked to submit abstracts by October 26, 2016.
  • Easels, poster boards (40" × 60"), and push pins will be provided on site.
  • Posters can be set up at any time, but should be in place by 4:00 p .m. on Thursday, and remain in place both days of the retreat.
  • Posters should be removed by 1:00 p.m. on Friday. Pushpins should be returned to the registration table. Please make sure that no pushpins are on the floor in your area and do not leave any pushpins on the poster boards. Easels and poster boards can remain in place.
  • The Department of Biochemistry and Biophysics will be awarding prizes for the top posters with a graduate student as the first author.
  • First and second year BMB graduate students will be judging the graduate student posters. Abstracts and judging criteria will be forwarded to the judges before the retreat. The ballots should be returned to the registration table by 10:15 p.m. on Thursday.
  • Poster awards will be announced on Friday afternoon, at the beginning of Session 4.