Judy Kotler, PhD

About

Dr. Judy Kotler currently holds Adjunct Chemistry Faculty positions at both St. Elizabeth University and Union College of Union County, NJ where she teaches Biochemistry I (with lab), Organic Chemistry I (with lab), and General Chemistry II. She holds a PhD in Biochemistry & Biophysics from Brandeis University, Masters in Chemistry from Brown University, and BS in Biochemistry from Cornell University.

Judy is seeking a full-time faculty position in Chemistry, Biochemistry, or a related subject where she can commit to helping students learn the fundamental knowledge and critical thinking skills necessary for a successful academic and professional career. Her passion for teaching students is fully displayed while employing active learning techniques, explaining complex scientific concepts in simple steps, and applying topics to real world situations. Judy succeeds in teaching due to her genuine enthusiasm in the material and drive to help students learn and succeed in science.

Lastly, Judy has a breadth of experiences working in industry to complement her teaching acumen including drug discovery, immunoassays, food science, and biofuels, enabling her to provide a range of real-world examples in lectures and when advising students with career aspirations. Her teaching experiences, extensive scientific training, excellent scientific communication skills, and passion for helping students learn make her successful in teaching Chemistry, Biochemistry, and Organic Chemistry.

Scientific Experience

Ingredion Incorporated

Bridgewater Township, NJ

Associate Scientist

09/2021 – 06/2024

Protein analytical leader for Applied Research and New Product Development projects via collaboration with Process, Research, Regulatory, Applications, and Sensory teams
Innovation Project Manager: Lead Applied Research projects with matrixed-team environment for novel protein modifications for function in specific food applications
Directly manage and advise 4 members of protein characterization team, conduct laboratory training, and develop protein/enzyme structure analytical methods

Brandeis University

Biochemistry and Biophsyics Department

Waltham, MA

PhD candidate

08/2015 – 09/2021

Independently researched novel electrostatic mechanism of ATP-dependent Hsp70 BiP binding client oligomers
Designed protein and peptide constructs, protein expression protocols in bacteria culture, purification, and chemical-modification methods for insoluble, oligomerizing, and intrinsically-disordered proteins
Discovered 3 chaperone binding sites on one client protein: Created and developed method for fluorescent protein-protein binding assays; conducted enzyme kinetics and binding of client at different salt and pH conditions; Characterized ATP-dependent enzyme activity (Michaelis-Menten); Studied conformation change and enzyme kinetics with FRET
Characterized protein structure, stability, and oligomerization state with CD, absorbance, SEC, DLS, light-scattering, and fluorescence methods

Joule Unlimited Technologies

Bedford, MA

Senior Research Associate

06/2014 – 07/2015

Developed novel enzyme assay to quantify alkane products of metabolically engineered cyanobacteria in small-scale cell culture
Improved enzyme product yield through directed evolution of protein engineering; novel enzyme mutations tested in small and large-scale cell culture experiments
Met deadlines to gather data on alkane-producing enzyme for purpose of commercial fuel production
Collected and analyzed data; documented novel findings; presented at company meetings

Xtal Biostructures, Inc. (Contract-Research Organization)

Natick, MA

Protein Biochemist and Crystallographer

01/2013 – 05/2014

Designed and conducted protein expression in bacterial and insect cell culture, protein purification, protein quantification, protein biophysical binding studies, and protein-drug crystallography for clients
Met customer needs and project deadlines. Communicated data and updates, wrote reports, conducted meetings, and visited customers on-site
Multi-tasked different clients’ projects simultaneously and adjusted priorities. Kept on cost and time.
Trained, managed, and actively mentored other scientists on team. Served as Lab Safety Officer.

Laboratory of Dr. Wolfgang Peti, Chemistry Department, Brown University

Providence, RI

Chemistry Graduate Research Assistant

08/2010 – 12/2012

Investigated modulation of Protein Phosphatase 1 by regulatory protein CReP
Conducted protein solubility expression experiments by varying protein construct length, using solubility- enhancing protein tags, and optimizing microbial cell growth temperature and IPTG concentration
Cloned, co-expressed, and purified novel PP1-CReP complex. Conducted stability experiments by varying salt, pH, and temperature, completed enzyme kinetic assays, and setup x-ray crystallography experiments.

Agrivida, Inc.

Medford, MA

Protein Biochemist

07/2009 – 08/2010

Optimized thermophilic enzyme cocktail to digest holocelluose prepared from corn stover for the production of fuel in metabolically engineered corn
Designed and improved native thermophilic enzyme expression in bacteria and yeast and purification
Optimized assay to test enzyme digestion conditions (enzyme concentrations, pH, temperature, time) to improve sugar yields. Quantified enzyme activity and digestion products by developing absorbance and HPLC assays.

Cornell University

Ithaca, NY

Research Assistant

06/2007 – 08/2007

Under Dr. Olena Vatamaniuk: Purified by reverse-phase chromatography and investigated proteins involved in heavy metal chelatin, phytochelatins, in Arabidopsis thaliana and optimized liquid nutrient solutions and strategies for culturing Arabidopsis hydroponically.
https://blogs.cornell.edu/ovatamaniuk/

Cornell University

Ithaca, NY

Research Assistant

08/2006 – 12/2006

Under Dr. Keith Perry: Transferred plant tissue cultures into test tubes for studies with cucumber mosaic virus in tobacco plants. Conducted general potato and plant maintenance of seeding, transplanting, and watering in greenhouse.
http://www.plantpath.cornell.edu/labs/perry/index.html

Siemens Healthcare

Flanders, NJ

Chemistry Laboratory Technican (Intern)

Summer/Winter 05/2005 – 01/2007

Performed monthly and weekly QC chemistry assays, maintenance, and troubleshooting on four automated blood chemistry analysis instrument lines using chemistry binding kit assays, programming instrument software, and spectrophotometer. Tested and documented new chemistry protocols.

Publications

Kotler, J.L M., Street, T. O. (2023) Mechanisms of Protein Quality Control in the Endoplasmic Reticulum by a Coordinated Hsp40-Hsp70-Hsp90 System. Annual Review of Biophysics, 52.
Deans, EE*, Kotler, J.L.M.*, et al. (2021). Electrostatics drive the molecular chaperone BiP to preferentially bind oligomerized states of a client protein. J Mol Biol, 434 (13). DOI: 10.1016/j.jmb.2022.167638
Jin, Y., Kotler, J. L. M., et al. (2021). The ER chaperones BiP and Grp94 regulate the formation of insulin-like growth factor 2 (IGF2) oligomers. J Mol Biol, 433 (13). DOI: 10.1016/j.jmb.2021.166963
Modi, G., Kotler, J.L.M., et al. (2021). The enzymatic activity of inosine 5’-monophosphate dehydrogenase may not be a vulnerable target for Staphylococcus aureus infections. ACS Infectious Diseases, 7 (11). DOI: 10.1021/acsinfecdis.1c00342
Huang, B., Kotler, J.L.M., et al. (2020) The endoplasmic reticulum chaperone BiP is a closure-accelerating cochaperone of Grp94. PNAS, 119 (5). DOI: 10.1073/pnas.2118793119
Sun M., Kotler J.L.M., et al. (2019). The endoplasmic reticulum (ER) chaperones BiP and Grp94 selectively associate when BiP is in the ADP conformation. J Biol Chem, 294 (16), 6387-6396. DOI: 10.1074/jbc.RA118.007050
Gray, B. N., Bougri, O., Carlson, A. R., Meissner, J., et al. (2011) Global and grain-specific accumulation of glycoside hydrolase family 10 xylanases in transgenic maize (Zea mays). Plant Biotechnol J, 9 (9), 1100-1108. DOI: 10.1111/j.1467-7652.2011.00632.x

Corporate Trainings, Presentations, and Posters

Corporate Training Courses, "Protein Chemistry" Ingredion’s Plant-based Proteins Applications-Specific Masterclasses, 3 remote sessions, May 2023.
Industry Course Presentation, "What’s happening during food processing with protein denaturation and aggregation," Bridge2Food’s Plant-Based Proteins & Foods Course Americas, November 2022.
Corporate Training Course, "Protein Structure and Protein Denaturation" Ingredion’s Plant-based Proteins Masterclass, September 2022.
Scientific Presentation, "Plant-based protein structure-function analysis from the bottom up," American Chemical Society Middle Atlantic Regional Meeting, July 2022.
Scientific Poster, "BiP’s high affinity for ProIGF2 oligomers is driven by electrostatics," Brandeis University Biochemistry & Biophysics Retreat, April 2021.
Scientific Presentation, "How does BiP help fold proIGF2?," Brandeis University Biochemistry & Biophysics Retreat, September 2019.
Scientific Poster, "How do the ER chaperones BiP and Grp94 help fold insulin-like growth factors?," The Protein Society 32nd Annual Symposium, July 2018.
Scientific Poster, "Mechanism of BiP interaction with Grp94 and substrates modulated by nucleotide identity," Brandeis University Biochemistry & Biophysics Retreat, October 2017.
Scientific Poster, "Optimized enzyme cocktails for the digestion of corn stover," American Chemical Society National Meeting, March 2010.

Skills & Expertise

Protein Chemistry and Characterization	Purity: SDS- and Native PAGE, Liquid-separation chromatography (HPLC) Analysis: thermal analysis (TSA), absorbance, fluorescence, enzyme kinetics Stability and unfolding: pH, temperature, urea, salt, detergent, osmolytes Interactions: Other proteins, substrates, and drugs Structure: X-ray crystallography, Circular dichroism, SAXS, DLS, light scattering, FT-IR Maleimide chemistry to fluorescently label proteins and peptides
Small Molecule	FT-IR LC-MS GC-MS NMR spectra
Microbiology and Molecular Biology	Bacterial and yeast cell culture Optimization of microbial growth conditions Designing plasmids and protein constructs PCR Transformation Restriction enzyme digest Ligation Gibson Cloning Agarose gel electrophoresis Primer design Codon optimization Mutagenesis Directed evolution DNA plasmid purification and quantification
Protein Expression	Bacterial, yeast, and insect cell protein expression (1-6 L) Protein expression optimization (temperature, induction, in-vivo refolding, chaperone-assisted) Protein co-expression
Protein Purification	Cell lysis (sonication, high-pressure homogenization, and chemical) Purification design and optimization by FPLC (Akta, GE) and on bench (gravity) Purification of native and affinity-tagged proteins via affinity column, ion-exchange, reverse-phase, and size-exclusion chromatography from soluble lysate and insoluble inclusion bodies, refolding denatured proteins
Protein Characterization	Protein purity (SDS- and Native PAGE) Concentration Absorbance Tryptophan fluorescence FRET Fluorescence polarization Protein-protein and protein-drug interaction studies Thermal shift assay, enzyme kinetics and data analysis X-ray crystallography (setting up trays, drug soak, seeding, collecting data at synchrotron, solving structure) Stability and unfolding experiments with pH, temperature, and urea Secondary structure (CD) SAXS, Oligomerization properties by HPLC analytical SEC
Communication	Presentations of data and journal articles Mentoring and Training scientists Teaching in classroom Writing reports (internal and external to clients) Documenting experiments and protocols (lab notebook and internal) Manuscript composition Collaborative team player
Bioinformatics	Sequence alignment (NCBI, Clustal) Protein parameters (Uniprot) Structure prediction and homology models
Computer	Microsoft Word Microsoft Excel Microsoft PowerPoint Kaleidograph Chimera Pymol ImageJ Solving X-ray crystallography structure software (Coot, CCP4, RefMac)
Other Lab	Good Laboratory Practice (GLP) Lab notebook Equipment and lab maintenance Lab Safety Officer