Yubin is employing genetically-encoded libraries to develop synthetic materials that control differentiation of Cancer Stem Cells (CSC) and promote or suppress epithelial-to-mesenchymal transitions (EMT).
Carson is employing genetically-encoded libraries to develop strategies for delivery of drugs to and through the blood-brain barrier.
Nick is developing new technologies and platforms for genetic encoding and presentation of diverse molecular structures on phage. He is applying these technologies to identify ligands for immune lectin DC-SIGN. The ultimate goal of this project is discovery of molecules and constructs that facilitate DC-SIGN-mediated delivery of antigens to dendritic cells, their internalization, processing and subsequent presentation to immune cells.
1. Sattar S., Bennett N.J., Wen, W.X., Guthrie, J.M., Blackwell, L.F., Conway, J.F., Rakonjac, J. (2015) Ff-nano, short functionalized nanorods derived from Ff (f1, fd, or M13) filamentous bacteriophage. Front Microbiol April 20;6(316)
2. Lacbay, C. M., Mancuso, J., Lin, Y. S., Bennett N., Gotte M., Tsantrizos Y. S. (2014). Modular Assembly of Purine-like Bisphosphonates as Inhibitors of HIV-1 Reverse Transcriptase. J Med Chem 57(17): 7435-7449.
3. Bennett N, Götte M. (2012) Utility of the Bacteriophage RB69 Polymerase gp43 as a Surrogate Enzyme for Herpesvirus Orthologs.Viruses. Jan 8;5(1):54-86.
4. Bennett NJ, Gagic D, Sutherland-Smith AJ, Rakonjac J. (2011) Characterization of a dual-function domain that mediates membrane insertion and excision of Ff filamentous bacteriophage. Journal of Molecular Biology. Sep 2;411(5):972-85.
5. Rakonjac J, Bennett NJ, Spagnuolo J, Gagic D, Russel M. (2011) Filamentous bacteriophage: biology, phage display and nanotechnology applications. Current Issues in Molecular Biology. 13(2):51-76.
6. Bennett, N.J. & Rakonjac, J. (2006) Unlocking of the filamentous bacteriophage virion during infection is mediated by the C domain of pIII. Journal of Molecular Biology. 356, 266-273.
I am developing new chemical strategies for the synthesis of genetically-encoded macrocycle and bicycle libraries.
I did my doctoral research in synthetic organic chemistry under the supervision of Prof. Amit Basak in the department of chemistry, Indian Institute of Technology Kharagpur and post-doctoral research in chemical biology (especially on genetic code expansion) with Prof. Abhishek Chatterjee at the Chemistry Department in Boston College, U.S.A.
In my post doctoral research, I have developed a leucyl amino acyl tRNA synthetase (aaRS) which is orthogonal in mammalian cell and which can thereby site specifically introduce a huge range of cysteine based leucyl type unnatural amino acids (UAA) containing a broad range of bio-othogonal handles like terminal azides, alkynes, alkenes, thiols, alcohols, halides, keto functionalities etc. The incorporation of these UAA’s are proved by protein mass spectroscopy, fluorescent labeling followed by mass spectroscopy and in-gel-fluorescence.
My doctoral research was mainly focused on the area of diradical generating systems, especially their mechanisms and application towards natural product synthesis. I have synthesized a series of 1-indole-3-yl carbazoles by using Garratt-Braverman Cyclization as a key step and extended this strategy towards the synthesis of an advanced intermediate en route to the naturally occurring alkaloid pityriazole. I have studied the AChE (Acetylcholineesterase) inhibition with the synthesized indolocarbazoles. I have also worked on the total synthesis of marine alkaloid analogue 7’-desmethylkealiiquinone of kealiiquinone class. Following the methodology I have also made some advancement towards the synthesis of the natural products of kealiinine family. In the initial year of my Ph.D, I got acquainted with the field of asymmetric catalysis comprising 2, 2’-dihydroxy azobenzene templated peptide based ligand design, synthesis and their application in the asymmetric cyclopropanation of a, b-unsaturated carbonyl systems.
Daniel’s research focus involves the development of genetically encoded glycopeptide libraries displayed in M13 phages and the use of these libraries to develop ligands for Galectin-3 protein.
Daniel has obtained his Bsc in Biochemistry from the University of Havana, Cuba in 2008. After completing his undergraduate training, Daniel worked for a Biotech company in Havana, Cuba (Heber-Biotec.Sa) working for to the Clinical Research division on custom biochemical analysis of biological samples from clinical trials of biotech drugs. In the fall 2013 he joined to the Graduate Program of the Department of Chemistry at the University of Alberta, and started to work within Dr. Derda’s group as a graduate student, since September,2013. Daniel has obtained a Visiting Research Scholar Position within Derda lab for the period October,2012 until April, 2013 as he was awarded with one of the Emerging Leaders for Americas Program scholarships, funded by the Canadian Bureau for International Education (CBIE) from Government of Canada.
P Kitov, D F Vinals , S Ng , K F Tjhung , and R Derda “Rapid, Hydrolytically Stable Modification of Aldehyde-terminated Proteins and Phage Libraries”, J. Am. Chem. Soc., 2014, 136, 8149–8152.
Ali is using genetically-encoded glycopeptide libraries to discover glycopeptide antigens for antibodies that recognize the fragments of cell wall of Mycobacterium Tuberculosis (TB) (collaboration with Todd Lowary group). Long-term goal: serological diagnostic of TB.
Publications from Derda Lab:
1. K. F. Tjhung, F. Deiss, J. Tran, Y. Chou, R. Derda*, “Intra-domain phage display (ID-PhD) of peptides and mini-domain proteins censored from canonical pIII phage display“, 2015 Front. Microbiol. 6:340.
2. H. Anany, Y. Chou, S Cucic, S. Evoy, R. Derda, MW Griffiths*, “From Bits and Pieces to Whole Phage to Nanomachines: Pathogen Detection Using Bacteriophage“, Annu. Rev. Food Sci. Tech., 2017, 8.
Vivian is developing strategies for genetic selection of chemical reactions that convert natural peptides to topologically-complex molecules (e.g., macrocycles and bi-cycles).
Jeffrey is employing genetically-encoded chemical libraries to identify early drug leads that inhibit anti-tumor protein Nodal
Yuki is developing new microfluidics and microdroplet-based technology for selection of genetically-encoded libraries, to study nucleation of supercooled water. Yuki is also supervising high school students in project related to heterogeneous and light-directed water nucleation. Yuki’s awards include Silver medal of iGEM2014 Competition, “Circular mRNA – the world’s longest protein”, October 2014, (Boston, USA) and Japan Student Services Organization (JASSO) Student Exchange Support Program Scholarship in September, 2015.
EXCHANGE GRADUATE STUDENT
Bifang is developing computational / bioinformatic tools for mining and sharing next-generation sequencing data emanation from genetically-encoded selection experiments.
Jessica joined Derda Lab in 2012, when she was an 11th grade high-school student. She was working on portable bacteria cultures for detection of antibiotic resistance. In 2014, she won the 1st prize in Alberta in Sanofi BioGenius competition for her work on taxol-resistance of breast cancer cells in paper-based 3D cultures. During summer 2014, she investigated differentiation of breast cancer stem cells using quantitative PCR. She started her undergraduate degree at the University of Alberta in Sep 2014. Jessica is currently supervising high-school students from Harry Ainlay High School, who investigate freezing of super-cooled water.
1. E. Lin, A. Sikhand, J. Wickware, Y. Hao and R Derda* “Peptide Microarray Patterning for Controlling and Monitoring Cell Growth” Acta Biomater., 2016, doi:10.1016/j.actbio.2016.01.028
Fall 2016 to present, Rifah Chowdhury, Preet Lat, Garrett Corkey and Hallie Trono high school students, volunteer in the Derda Lab. They are working on materials that trigger freezing of supercooled water.
Fall 2013 to Spring 2015, Patricia Yan and Amy Li, high school students, volunteer in the Derda Lab. They were involved in the development of the electrochemical detection of bacteria in paper-based culture devices.
Fall 2011 to Summer 2012, four high school students–Ally Wu, Eszter Szepesvari, Pavitra Rajendran, Nicholas Kwan-Wong–were involved in development of portable diagnostic devices for developing countries. They were co-authors on the manuscript in Lab on a Chip:
MF Huacca, A Wu, E Szepesvari, P Rajendran, N Kwan-Wong, A Razgulin, Y Shen, J Kagira, R Campbell, R Derda* “Portable cultures for phage and bacteria made of paper and tape” Lab Chip, 2012, 12, 4269-4278