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Biochemistry Ph.D. Outcome Data
students and professors at convocation

Annual Reviews

The following table shows the number of Ph.D. students who participated in annual reviews each during each of the last three academic years.

 

Number of Ph.D. students in program required to complete annual review

Number of Ph.D. students who participated in an annual review

2019-20

 13

 13

2018-19

14

14

2017-18

10

10

Written Candidacy Exams

 

The following table provides information about Ph.D. student success in written candidacy exams during the last three academic years.

 

Number of Ph.D. students who took written candidacy exams

Number of Ph.D. students who passed written candidacy exams

Number of Ph.D. students who left program due to failure to pass written candidacy exams

2019-20

5

5

0

2018-19

5

5

0

2017-18

1

1

0

Oral Qualifying Exams

 

The following table provides information about Ph.D. student success in written candidacy exams during the last three academic years.

 

Number of Ph.D. students who took oral candidacy exams

Number of Ph.D. students who passed oral candidacy exams

Number of Ph.D. students who left program due to failure to pass oral candidacy exams

2019-20

 4

4

0

2018-19

2

1

0

2017-18

2

0

0

 

Oral and Poster Presentations

 

The number of students who took the Seminar Course (CHEM 7800) is provided in the table under Coursework. 

The following table provides information about the number of presentations (oral and poster) given at conferences and professional meetings that included Ph.D. students as authors during the last three years.

 

Number of oral presentations at conferences or research meetings with PhD student authors

Number of poster presentations at conferences or research meetings with PhD student authors

2020

0

 11

2019

0

4

2018

0

5


2020 Ph.D. Student Poster Presentations

Dylan Keiser, Hannah Domgaard, Valerie Crowley, Chase Beisel, Oleg Dmytrenko. Biochemical Characterization of the Newly Discovered Type V CRISPR Associated Endonuclease Cms1. 2020 Hansen Life Sciences Retreat at Utah State University in Logan, Utah.

Hannah N. Taylor, Yi Zhou, Jack P. Bravo, Jurre Steens, Raymond Staals, David Taylor, Ryan Jackson. Cryo-EM structure of a CRISPR-Cas ribonucleoprotein complex. 2020 Hansen Life Sciences Retreat at Utah State University in Logan, Utah.

Joshua M. Denson, Sean Johnson. Biochemical Characterization of Mtr4 Modulation of Trf4 in the TRAMP Complex. 2020 Hansen Life Sciences Retreat at Utah State University in Logan, Utah.

Justin Pinkston, Jihye Jo, Drake Comer, Keith Olsen, Sean Johnson, J. Patrick Loria, Alvan C. Hengge. Dual general acid catalysis in the protein tyrosine phosphatase SsoPTP. 2020 Hansen Life Sciences Retreat at Utah State University in Logan, Utah.

Koleton D. Hardy, Nicholas E. Dickenson. Post-Translational Phosphorylation of Tyrosine-274 Modulates Spa47 ATPase Activity. 2020 Hansen Life Sciences Retreat at Utah State University in Logan, Utah.

Mark Gold. Characterization of Post-translational Modifications on Mtr4. 2020 Hansen Life Sciences Retreat at Utah State University in Logan, Utah.

Matthew K. Yim, Sean J. Johnson. Initial Biochemical Characterization of Mtr4 Homologs in Arabidopsis thaliana and Examination of Conserved Motifs in the Helical Bundle Domain. 2020 Hansen Life Sciences Retreat at Utah State University in Logan, Utah.

Owen Price. Use of Cancer-Associated Mutations to Probe the Role of Dimerization in Protein Arginine Methyltransferase 1 Catalysis. 2020 Hansen Life Sciences Retreat at Utah State University in Logan, Utah.

Ruidan Shen, Sean J. Johnson, Alvan C. Hengge. Mutation of a noncatalytic residue on a dynamic loop unexpectedly alters the pH-rate profiles of PTP1B and YopH. 2020 Hansen Life Sciences Retreat at Utah State University in Logan, Utah.

Samuel A. Barker. Elucidating the Role of the IpaD Pi-Helix in Shigella Virulence. 2020 Hansen Life Sciences Retreat at Utah State University in Logan, Utah.

Spencer Slaugh. Reduction of Nitrate and Nitrite by Nitrogenase. 2020 Hansen Life Sciences Retreat at Utah State University in Logan, Utah.

2019 Ph.D. Student Poster Presentations

Ruidan Shen, Keith Olsen, Alex Tolman, Sean Johnson, J. Patrick Loria, Alvan Hengge. Insights from PTP1B/YopH Chimeras into the Importance of WPD-loop Sequence for Activity and Structure in Protein Tyrosine Phosphatases. 258th National Meeting of the American Chemical Society in San Diego, California.

Heather Case, Dominic Mattock, Bill Miller III, Nick Dickenson. Identifying Small Molecule Inhibitors Against the Shigella Type Three Secretion System ATPase Spa47. 2019 Hansen Life Sciences Retreat at Utah State University in Logan, Utah.

Koleton Hardy, Nick Dickenson. Post-translational Phosphorylation Inhibits Spa47 ATPase Activity and Shigella Virulence. 2019 Hansen Life Sciences Retreat at Utah State University in Logan, Utah.

Samuel Barker, Abram Bernard, Yalemi Morales, Sean Johnson, Nick Dickenson. Structure Function Analyses of the Shigella T3SS Protein IpaD Implicate a Rare Pi-helix Secondary in DOC-enhanced Virulence. 2019 Hansen Life Sciences Retreat at Utah State University in Logan, Utah.


2018 Ph.D. Student Poster Presentations

Heather Case. MxiN Differentially Regulates Monomeric and Oligomeric Species of the Shigella Type Three Secretion System ATPase Spa47. American Society for Biochemistry and Molecular Biology (ASBMB) Meeting.

Hannah Demler, Heather Case, Abram Bernard, Yalemi Morales, Sean Johnson, Nick Dickenson. Characterization of Predicted Interfacial Salt Bridges in Spa47 to Better Understand the Mechanism of Oligomer Based Spa47 Activation. 2018 Hansen Life Sciences Retreat in Logan, Utah.

Jenna Bouvang, Abram Bernard, Nick Dickenson. Development of Stable Protein Constructs Provides Insight into Type Three Secretion System Induced Cell Membrane Disruption. 2018 Hansen Life Sciences Retreat in Logan, Utah.

Heather Case, Nick Dickenson. MxiN Differentially Regulates Monomeric and Oligomeric Species of the Shigella Type Three Secretion System ATPase Spa47. 2018 Hansen Life Sciences Retreat in Logan, Utah.

Koleton Hardy, Nick Dickenson. Post-Translational Modifications of Tyrosine 274 Modulate Spa47 TAPase Activity and Shigella Virulence. 2018 Hansen Life Sciences Retreat in Logan, Utah.

Publications

 

The following table provides information about the number of publications with Ph.D. student authors during 2018, 2019, and 2020.

 

Number of publications with one of more PhD students as authors

2020

 5

2019

6

2018

8


2020 Ph.D. Student Publications

Heather B. Case, Dominic S. Mattock, Bill R. Miller, and Nicholas E. Dickenson (2020) "Novel Noncompetitive Type Three Secretion System ATPase Inhibitors Shut Down Shigella Effector Secretion." Biochemistry 59 (28), 2667-2678

Burgess JL, Case HB, Burgess RA, Dickenson NE (2020) "Dominant negative effects by inactive Spa47 mutants inhibit T3SS function and Shigella virulence." PLoS ONE 15(1): e0228227.

Price, Owen M.; Hevel, Joan M. (2020) "Toward Understanding Molecular Recognition between PRMTs and their Substrates." Current Protein and Peptide Science, Volume 21, Number 7, 2020, pp. 713-724(12).

Joan M. Hevel, Owen M. Price (2020) "Rapid and direct measurement of methyltransferase activity in about 30 min."
Methods, Volume 175, 2020, Pages 3-9.

Yi ZhouJack P.K. BravoHannah N. TaylorJurre SteensRyan N. JacksonRaymond H.J. StaalsDavid W. Taylor (2020) "tructure of a type IV CRISPR-Cas effector complex." bioRxiv 2020.07.31.231399; doi: https://doi.org/10.1101/2020.07.31.231399

2019 Ph.D. Student Publications


Badalyan, A., Yang, Z., Hu, B., Luo, J., Hu, M., Liu, T.L., Seefeldt, L.C. (2019) “An Efficient Viologen-Based Electron Donor to Nitrogenase.” Biochemistry 2019, 58, 46, 4590-4595.

Hevel, J., Price, O.M. (2019) “Rapid and direct measurement of methyltransferase activity in about 30 min.” Methods, 10.1016, 2019.10.002.

Harris, D.F., Lukoyanov, D.A., Kallas, H., Trncik, C., Yang, Z., Compton, P., Kelleher, N., Einsle, O., Dean, D.R., Hoffman, B.M., Seefeldt, L.C. (2019) “Mo-, V-, and Fe-Nitrogenases Use a Universal Eight-Electron Reductive-Elimination Mechanism to Achieve N2 Reduction.” Biochemistry 2019, 58, 3293-3301.

Taylor, H.N., Warner, E.E., Armbrust, M.J., Crowley, V.M., Olsen, K.J., Jackson, R.N. (2019) “Structural basis of Type IV CRISPR RNA biogenesis by a Cas6 encoribonuclease.” RNA Biology, 16:10, 1438-1447.

Demler, H.J., Case, H.B., Morales, Y., Bernard, A.R., Johnson, S.J., Dickenson, N.E. (2019) “Interfacial amino acide support Spa47 oligomerization and shigella type three secretion system activation.” Proteins. 2019; 1-12.

Hu, B., Hu, M., Seefeldt, L., Liu, T.L. (2019) “Electrochemical dinitrogen Reduction to Ammonia by Mo2N: Catalysis or Decomposition?” ACS Energy Lett. 2019, 4, 1053-1054.

2018 Ph.D. Student Publications

Case, H.B., Mattock, D.S., Dickenson, N.E. (2018) Shutting down shigella secretions: characterizing small molecule type three secretion system ATPase inhibitors.” Biochemistry 2018, 57, 50, 6906-6916.

Case, H.B, Dickenson, N.E. (2018) “Kinetic characterization of the shigella type three secretions system ATPase spa47 using ATP.” bio-protocol, 8, 21.

Moise, G., Morales, Y., Beaumont, V., Caradonna, T., Loria, J.P., Johnson, S.J., Hengge, A.C. (2018) “A yoph ptp1b chimera shows the importance of the wpd-loop sequence to the activity, structure, and dynamics of protein tyrosine phosphatases.” Biochemistry 2018, 57, 36, 5315-5326.

Morales, Y., Olsen, K.J., Bulcher, J.M., Johnson, S.J. (2018) “Structure of frequency-interacting RNA helicase from neurospora crassa reveals high flexibility in a domain critical for circadian rhythm and RNA surveillance.” PLoS one, 13(5): e0196642.

Hu, B., Harris, D.F., Dean, D.R., Liu, T.L., Yang, Z., Seefeldt, L.C. (2018) “Electrocatalytic CO2 reduction catalyzed by nitrogenase MoFe and FeFe proteins.” Bioelectrochemistry, 120, April 2018, 104-109.

Case, H.B., Dickenson, N.E. (2018) “MxiN differentially regulates monomeric and oligomeric species of the Shigella type three secretion system ATPase Spa47.” Biochemistry 2018, 57, 15, 2266-2277.

Harris, D.F., Lukoyanov, D.A., Shaw, S., Compton, P., Tokmina-Lukaszweska, M., Bothner, B., Kelleher, N., Dean, D.R., Hoffman, B.M., Seefeldt, L.C. (2018) “Mechanism of N2 reduction catalyzed by Fe-nitrogenase involves reductive elimination of H2.” Biochemistry 2018, 57, 5, 701-710.

Caceres, T.B., Thakur, A., Price, O.M., Ippolito, N., Li, J., Qu, J., Acevedo, O., Hevel, J.M. (2018) “Phe71 in type III trypanosoomal protein rrginine methyltransferase 7 (TbPRMT7) restricts to monomethylation.” Biochemistry 2018, 57, 1349-1359.

Dissertation Defenses

 

The following table provides information about the number of dissertation defenses during the last three academic years.

 

Number of Ph.D. students who undertook a dissertation defense

Number of Ph.D. students who passed the dissertation defense

Number of Ph.D. students who left the program due to failure to pass the dissertation defense

2019-20

 0  0

0

2018-19

2

2

0

2017-18

3

3

0