Jonathan Ly Email & Phone Number

Worked under Dr. Scott Taylor of the Department of Chemistry at the University of Waterloo as an undergraduate researcher for fourth year thesis project.Project consisted of synthesizing analogs of the lipopeptide antibiotic Daptomycin, using solid phase peptide synthesis. Said analogs were then verified with HPLC and mass spectrometry and their biological activity tested using minimum inhibitory concentration assays. Another component of my undergraduate research involved the synthesis of a Fmoc-Agp-OH amino acid building block for solid phase peptide synthesis. Various side chain protecting groups were attempted, although the project was not finished before the end of my time at the Taylor Lab. Relevant techniques used involved various organic synthesis techniques such as flash column chromatography, liquid/liquid extraction, and NMR operation.Thesis results were then presented at a department seminar day to various department professors and students. Results will be used towards eventual publication as well.

Toronto, Ontario, Canada

Research technician in the Gingras lab working under Anne-Claude Gingras. Part of the proteomics team in which I conducted sample prep, tissue culture, instrument operation, and analysis of mass spec data. One of my main projects included the alteration of experimental conditions of the SP3 method for in depth proteomic coverage at low cell counts (>100K cells). Another one of my projects included the optimization of an offline fractionation method for the highest number of hits for HeLa digest. Cell lines cultured included HeLa, and HEK293, as well as familiarity with the flp-ln system. Sample preparation methods conducted included protein digestion methods such as single pot solid phase (SP3) and S-Trap column methods. Other sample prep methods included offline reverse phased fractionation with Agilent 1260 Nanoelute system, and desalting peptide preparations with C18 stage tips. Also became proficient in proximity labelling with biotin (BioID) as well as other various lysis and digestion methods. Operated on various mass spec systems including Bruker timsTOF, Thermo Fisher LUMOS orbitrap, and SCIEX 6600 systems. Also has some familiarity with SCIEX SelexION systems. LC systems used included EvoSEP ONE, Eksigent nanoLC, Bruker Nanoelute as well as observing installation of ThermoFisher Neo Vanquish system. Software operation included Bruker Hystar, SCIEX analyst and peakview, ThermoFisher XCalibur and Qualbrowser, and Chronos software for EvoSep. Also utilized python to aid in the analysis of mass spec data.

Worked as a Research Assistant with the Nanomaterials group of the Faculty of Engineering from the Univeristy of Waterloo. Worked under Dr. Kevin Musselman, as well as assisting the graduate students in the group with various projects. Utilized a FilmSense Ellipsometer to characterize thin films for a machine learning database. Created models on ellipsometer which assessed for refractive index, band gap, and thickness of films of varying compositions. Compiled this data in an easy-to-read manner using Microsoft excel. Coded a program in NI LabVIEW to measure resistance using a four-point probe of thin films, as well as taking a picture of the film with each measurement. This was used in a water vapor transmission rate project with a grad student in the group. Optimized an SOP for thin film removal off glass substrate. Utilized AutoCAD to design custom racks and assessed the efficiency of various solvents and solutions such as NaOH to remove thin films of various compositions.

Waterloo, Ontario, Canada

Worked as a sample prep technician for R&D at LabStat in this role. One of the main projects was to assess the matrix effects of propylene glycol/vegetable glycerin on the ability of ICP-MS detection of metals. Created standards of varying metals and matrix concentrations to achieve this and analyzed resultant data in excel. Worked in a team of 3 co-op students to assist in sample preparation. One task involved creating calibration curves and chemical standards for GC-MS and LC-MS to a high degree of accuracy of pipetting and analytical weighing. Another task was to extract different chemicals from tobacco and e-cigarette juice using various techniques such as liquid-liquid extraction, smoking machines, and solid-phase extraction. Also gained background knowledge in Agilent analytical instruments such as GC-MS, LC-MS, and ICP-MS, such as instrument maintenance, column replacement, and solvent prep.

Ottawa, Ontario, Canada

Worked as a research assistant during my time here under Dr. Yadienka Martinez-Rubi with the Nanocomposites group of the Securities and Disruptive technologies division of the National Research Council of Canada.Main project involved the assessment of Boron Nitride Nanotube (BNNT) quality with Regioregular poly(3-hexylthiophene-2,5-diyl) (P3HT) titration and UV-VIS analysis. Utilized sonication, pipetting, and a Cary5000 model spectrometer. Also familiar with working while equipped in P1000 respirators and handling hazardous chemicals. Synthesized Nanotube/Polymer composites for 3D printing. Attempted to optimize procedure with different nanotube loadings, as well as synthesis and 3D printing conditions. Looked for effects on strength, elastic modulus, and decomposition. Utilized techniques such as 3D printing with PRUSA 3, filament making with a filabot EX2 extruder, and thermogravimetric analysis.Synthesized Nanotube/Polymer bucky papers to assess effects of manufacture conditions on adsorption of nanotube onto the polymer. Changed synthesis conditions such as solvents used, nanotube and polymer loadings, as well as heat pressing. Vacuum filtration, sonication, were some of the techniques used to obtain the data, which was then processed in microsoft excel. Also created large scale buckypaper for the Canadian Space Agency.

Master'S Degree, Mechanical And Mechatronics Engineering - Nanotechnology

Bachelor Of Science - Bs, Biochemistry And Molecular Biology