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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

2017-18

14

14

2016-17

10

10

2015-16

11

11

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

2017-18

5

5

0

2016-17

1

1

0

2015-16

1

1

0

Oral Qualifying Exams

 

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

2017-18

2

1

0

2016-17

2

0

0

2015-16

1

1

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

2019

0

4

2018

0

5

2017

1

5


2017 Ph.D. Student Oral Presentations

Jenna Bouvang, Jamie Burgess, Robert Burgess, Yalemi Morales, Sean Johnson, Nick Dickenson. 
Structural and Biochemical Characterization of Spa47 Provides Mechanistic Insight into Type Three Sectretion System ATPase activation and Shigella Virulence Regulation. Utah Conference on Undergraduate Research in Orem, 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.


2017 Ph.D. Student Poster Presentations

Hannah Demler, Jamie Burgess, Yalemi Morales, Sean Johnson, Nick Dickenson. Characterization of Predicted Interfacial Salt Bridges in Spa47 to Better Understand the Mechanism of Oligomer Based Spa47 Activation. 2017 Hansen Life Sciences Retreat at Utah State University in Logan, Utah.

Jenna Bouvang, Abram Bernard, Nick Dickenson. Development and Characterization of a Highly Soluble Construct of the Shigella Flexneri Translocator Protein IpaC. 2017 Hansen Life Sciences Retreat at Utah State University in Logan, Utah.

Abram Bernard, T Jessop, Prashant Kumar, Nick Dickenson. Deoxycholate – Enhanced Shigella Virulence is Regulated by a R are π - Helix in the Type Three Secretion System Tip Protein IpaD.  2017 Hansen Life Sciences Retreat at Utah State University in Logan, Utah.

Jamie Burgess, Joshua Reid, Nick Dickenson. Exploring Oligomerization States of Spa47, a Shigella Type Three Secretion System (T3SS) ATPase. 2017 Hansen Life Sciences Retreat at Utah State University in Logan, Utah.

Heather Jones, Nick Dickenson. Shigella Spa47 Regulator Proteins Provide a Potential Means of Controlling Type Three Secretion System Activation and Pathogen Virulence. 2017 Hansen Life Sciences Retreat at Utah State University in Logan, Utah.

Publications

 

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

 

Number of publications with one of more PhD students as authors

2019

6

2018

8


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

2017-18

2

2

0

2016-17

3

3

0

2015-16

2

2

0