Career Stats
Undergraduate: Oxford College of Emory University, Associate of Arts
University of Georgia, Bachelor of Science in Biochemistry and Molecular Biology, Magna Cum Laude
Graduate: Ph.D. in Chemistry from Emory University, biomolecular division
Lab Home: Salaita group
Contact info: jpetree331[at]gmail.com
University of Georgia, Bachelor of Science in Biochemistry and Molecular Biology, Magna Cum Laude
Graduate: Ph.D. in Chemistry from Emory University, biomolecular division
Lab Home: Salaita group
Contact info: jpetree331[at]gmail.com
CV/resume: click here
Rotation Projects: click here
Current Project: see below and/or email me and I'd love to tell you all about it!
Rotation Projects: click here
Current Project: see below and/or email me and I'd love to tell you all about it!
What do I do? Find out here!
Science blog: My place for research updates, fun facts, lab activities, here.
Rolling Statuses: Daily ramblings about research student life, here.
Grad Questions: What is grad life like? Why do I love the Salaita lab? Click here.
Fun Facts about Salaita Lab: Lab member gallery, with photos and published works, here.
Yuan Chang's Flickr: Lab life in photos, here.
Rolling Statuses: Daily ramblings about research student life, here.
Grad Questions: What is grad life like? Why do I love the Salaita lab? Click here.
Fun Facts about Salaita Lab: Lab member gallery, with photos and published works, here.
Yuan Chang's Flickr: Lab life in photos, here.
Salaita Lab
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Introduction to the major research theme in the Salaita lab - surface chemistry and biophysics - measuring the force that cells pull on their ligands.
Salaita Lab in the NewsEmory News, Nov 2016: Emory's Rolosense wins bronze in Collegiate Inventors Competition
Emory News, Sept 2016: Emory's 'Rolosense' rolling to finals of Collegiate Inventors Competition YouTube, Dec 2015: First rolling DNA motor speeds up 'nano-walkers’ Phys Org, Dec 2015: "Nano-walkers take speedy leap forward with first rolling DNA-based motor," and other news outlets here. Phys Org, Oct 2014: "Molecular beacons shine light on how cells 'crawl'" YouTube, Sept 2014: How Salaita lab got into studying cellular force Phys Org, Nov 2011: "Chemists reveal the force within you" |
Current Project
My research features a different branch of the lab, combining bioengineering, chemistry and molecular biology. The major goal is RNA gene therapy! I'm not supposed to give details about it until I have a paper published, but please, if you want to hear more, contact me! I'm perpetually excited to talk about it with anyone.
Techniques used: protein expression in E.coli, protein isolation via Ni-NTA column, SDS-PAGE, imaging gels on Typhoon fluorescence instrument, UV-vis (Nanodrop), RNA transcription, RT-PCR, column chromatography, gold nanoparticle synthesis, particle functionalization
Techniques used: protein expression in E.coli, protein isolation via Ni-NTA column, SDS-PAGE, imaging gels on Typhoon fluorescence instrument, UV-vis (Nanodrop), RNA transcription, RT-PCR, column chromatography, gold nanoparticle synthesis, particle functionalization
What got me into science and chemistry
I became interested in the sciences through my mom, a nurse. She fanned my curiosity into flame and taught me how to chase down answers to my questions. With her encouragement, I was able to attend the GA State Science and Engineering Fair twice in eighth and tenth grade. Since both her and her sister have type I diabetes and are insulin dependent, we also liked to talk about diabetes research together, coming up with elaborate theories.
My freshman and sophomore years of college were spent at Oxford College, where I was blessed with wonderful chemistry teachers such as Brenda Harmon (organic chem lab), Dr. Lloyd Parker (gen chem) and Dr. Reza Saadein (organic chem), who taught me how to use critical thinking rather than memorization to solve problems. I began to see that if one understands the chemistry biomolecules, one can predict how they will behave. Thus, I became convinced that a strong understanding of chemistry and attention to detail were important for understanding molecular interactions and thinking critically.
My freshman and sophomore years of college were spent at Oxford College, where I was blessed with wonderful chemistry teachers such as Brenda Harmon (organic chem lab), Dr. Lloyd Parker (gen chem) and Dr. Reza Saadein (organic chem), who taught me how to use critical thinking rather than memorization to solve problems. I began to see that if one understands the chemistry biomolecules, one can predict how they will behave. Thus, I became convinced that a strong understanding of chemistry and attention to detail were important for understanding molecular interactions and thinking critically.
Previous research experience
Emory - summer 2009 - Conticello labAfter my sophomore year, I was eager to get lab experience and joined Emory’s SURE (Summer Undergraduate Research) program in Dr. Conticello’s lab. Under Melissa Patterson, a grad student at the time, I worked on a project building a biopolymer that could replace rough materials for use in sutures. To create the polymer, I incorporated the unnatural amino acid L-DOPA into an elastin mimetic polypeptide. We then expressed, isolated and analyzed this peptide with mass spectrometry and were able to obtain rudimentary data.
Through her, I became more confident in working in the lab. She guided me through each of the experiments, and remained as a continual resource for questions. Additionally, she assisted me in going through relevant literature, explaining jargon I did not understand. After the program, I was able to present my work at an undergraduate seminar with other students, was judged by faculty, and received a research award. UGA- Jan 2010 - Dec 2011
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I continued my studies at UGA, pursuing a B.S. in Biochemistry and Molecular Biology. While there, I conducted research for two years in Dr. Kushner’s genetics lab. I chose his lab due to my interest in RNA, as well as a desire to tackle the challenge of RNA extraction. I thought that learning to do this technique, often declared to be one of the most difficult, would prepare me best for graduate school.
Life in the Kushner Lab
Under Dr. Bijoy Mohanty, senior research scientist, I learned how to work independently and balance research with coursework, taking three classes each semester and doing ~40 hours of research a week. I started out learning basic techniques, such as doing lysates and growth curves, moving on to more advanced experiments as I mastered them. Dr. Mohanty would demonstrate each technique once while I took notes. Afterward, he expected me to repeat them without assistance. I kept a lab notebook and attended weekly lab meetings. Later, a post-doc suggested that I write a summary of what I did at the end of each week, so that I would have an easier time keeping track of it. It has been a great help to me already in graduate school.
After the second semester, I acted much like a graduate student, only talking to Dr. Mohanty once a week to discuss my data. At the time, it was a difficult lesson, but a very fruitful one. As a result of his teaching, my transition to graduate school was made far less painful. In the course of my research, I conducted numerous growth curves and lysates, constructed twenty-one E.coli strains, successfully isolated RNA four times, conducted two Northern blots and probed them with [γ-32P]ATP, all while working independently.
Project: Analyzing the maturation pathways of two tRNAs, a layman's guide
The focus of my project was the "maturation of tRNA." What is that? To answer that question, one has to know the Central Dogma. This tenet of biology states that information transfer in a cell flows from DNA to RNA, which is copied from it, and translated into protein. Just as DNA is made up of subunits called nucleotides, proteins are made up of their own subunits, known as amino acids. The work horse that constructs proteins inside a cell is the ribosome. tRNAs are the shuttles that take each amino acid to the ribosome for protein construction.
tRNAs themselves are constructed of single-stranded RNA (see figure above). Their RNA is also copied from the DNA and must be processed before it is ready for use, e.g. bits are edited out of it, its end piece is shorted, to remove unnecessary nucleotides. The enzymes that edit or process tRNAs are known as RNases, of which there are many. I worked on identifying the role of RNase PH, RNase T, RNase D and RNase BN, as well as Poly(A) Polymerase 1 overexpression, on the 3’ end processing of pro and metZ tRNA in E.coli.
In the end, the data suggested that RNase D and RNase BN do not process either tRNApro or tRNAmetZ transcripts. As I finished my degree, I elected to do a thesis, so that I could practice scientific writing. By the time I finished my thesis work, I felt as if I was close to being a graduate student.
Life in the Kushner Lab
Under Dr. Bijoy Mohanty, senior research scientist, I learned how to work independently and balance research with coursework, taking three classes each semester and doing ~40 hours of research a week. I started out learning basic techniques, such as doing lysates and growth curves, moving on to more advanced experiments as I mastered them. Dr. Mohanty would demonstrate each technique once while I took notes. Afterward, he expected me to repeat them without assistance. I kept a lab notebook and attended weekly lab meetings. Later, a post-doc suggested that I write a summary of what I did at the end of each week, so that I would have an easier time keeping track of it. It has been a great help to me already in graduate school.
After the second semester, I acted much like a graduate student, only talking to Dr. Mohanty once a week to discuss my data. At the time, it was a difficult lesson, but a very fruitful one. As a result of his teaching, my transition to graduate school was made far less painful. In the course of my research, I conducted numerous growth curves and lysates, constructed twenty-one E.coli strains, successfully isolated RNA four times, conducted two Northern blots and probed them with [γ-32P]ATP, all while working independently.
Project: Analyzing the maturation pathways of two tRNAs, a layman's guide
The focus of my project was the "maturation of tRNA." What is that? To answer that question, one has to know the Central Dogma. This tenet of biology states that information transfer in a cell flows from DNA to RNA, which is copied from it, and translated into protein. Just as DNA is made up of subunits called nucleotides, proteins are made up of their own subunits, known as amino acids. The work horse that constructs proteins inside a cell is the ribosome. tRNAs are the shuttles that take each amino acid to the ribosome for protein construction.
tRNAs themselves are constructed of single-stranded RNA (see figure above). Their RNA is also copied from the DNA and must be processed before it is ready for use, e.g. bits are edited out of it, its end piece is shorted, to remove unnecessary nucleotides. The enzymes that edit or process tRNAs are known as RNases, of which there are many. I worked on identifying the role of RNase PH, RNase T, RNase D and RNase BN, as well as Poly(A) Polymerase 1 overexpression, on the 3’ end processing of pro and metZ tRNA in E.coli.
In the end, the data suggested that RNase D and RNase BN do not process either tRNApro or tRNAmetZ transcripts. As I finished my degree, I elected to do a thesis, so that I could practice scientific writing. By the time I finished my thesis work, I felt as if I was close to being a graduate student.
Career goals and motivation for seeking PhD
My motivation for seeking a PhD in the chemistry is purely a love for research. I have good days and bad days like anyone else, but one thing never changes - I'm in love with my job. Scientific research is what makes me come alive! There is nothing more exciting to me than pursuing the cutting edge of knowledge. Questioning, reading, studying, writing and thinking about new possibilities has become a way of life, and I believe that research in chemistry allows me to develop these skills to their greatest potential. I hope to use them to benefit as many as possible.
My ultimate goal after graduate school is to be a research scientist. I originally considered professorship, since I enjoy teaching. However, I've learned that this end does not suit me. Professors have a bird's eye view of research, are not in close contact with it, but guide the work of their graduate students. I prefer to dive into the details, get my hands dirty, and do my own projects and bench work. I also have too many professor friends not to be aware of what they deal with, to some extent - a lot of paperwork and red tape. I want to be directly connected to my work with no wall in between, become the expert of it, and perhaps lead a small, specialized team.
The focus of my research will be applying a chemical understanding of biology to disease mechanisms and molecular functions. I learned early that if one understands the chemistry of a molecular, one can predict how it will behave. Thus, a firm foundation in chemistry is essential to critical thinking within the lab. Additionally, I continue to have an interest in RNA largely because it acts as the primary method of conveying biological information. With my habitual thirst for information, the idea that RNA is the focal point for its transfer in biology and that there is so much unknown about it is fascinating to me.
Last updated 6-4-14 (paragraphs) Last updated (top) 1-23-16
My ultimate goal after graduate school is to be a research scientist. I originally considered professorship, since I enjoy teaching. However, I've learned that this end does not suit me. Professors have a bird's eye view of research, are not in close contact with it, but guide the work of their graduate students. I prefer to dive into the details, get my hands dirty, and do my own projects and bench work. I also have too many professor friends not to be aware of what they deal with, to some extent - a lot of paperwork and red tape. I want to be directly connected to my work with no wall in between, become the expert of it, and perhaps lead a small, specialized team.
The focus of my research will be applying a chemical understanding of biology to disease mechanisms and molecular functions. I learned early that if one understands the chemistry of a molecular, one can predict how it will behave. Thus, a firm foundation in chemistry is essential to critical thinking within the lab. Additionally, I continue to have an interest in RNA largely because it acts as the primary method of conveying biological information. With my habitual thirst for information, the idea that RNA is the focal point for its transfer in biology and that there is so much unknown about it is fascinating to me.
Last updated 6-4-14 (paragraphs) Last updated (top) 1-23-16
Pictures from around the Kushner lab, Jan 2010 - Dec 2011
The Kushner lab, as it was when I graduated. I worked there my junior and senior year at UGA, and finished thesis work. Left to right: Mark Stead, Sidney Kushner, Bijoy Mohanty, Valerie Maples, me, Nick Wiese, Katie Bowden and Ankit Agrawal. Doesn't include Marly Richter-Roche, Sarah, Nikkii DuBose, Kristen Mildenhall or Gargi Chaudhuri.
Since this photo, all of the members have graduated. |
Candid Videos Before Group Picture
Grad Students Messing Around - 6 min 14 sec - Mark wonders allowed how he'll manage to insult Katie properly once he moves to NY; Ankit discusses dry ice bombs, leading to a string of pranking. Dr. Kushner Waits for the Dry Ice Bomb to Go Off - 32 sec |
Science NewsSeptember 2016
Won a special interest group student research award at the Biomaterials Day Conference at GA Tech June 2016 First co-author paper is published! See here. "Endonucleolytic cleavages by RNase E generate the mature 3′ termini of the three proline tRNAs in Escherichia coli" August 2015 Became an ARCS Foundation Scholar May 2014 Received honorable mention in the NSF graduate research fellowship December 2012 Was acknowledged in the paper, “Deregulation of poly(A)polymerase I in Escherichia coli inhibits protein synthesis and leads to cell death," in the journal Nucleic Acids Research (in press, December 2012). Can find the paper here. Organic Chemistry, Oxford, Class of 2009 |
Journal ArticlesThe following are links to articles that I've found interesting.
"General Chemistry Gets a Boost," about my former professor Dr. Jack Eichler
Making Sense of DNAzymes
Taking NMR And MRI To The Nanoscale - fascinating!!
Review: Looking into live cells with in-cell NMR spectroscopy
In-cell NMR spectroscopy: mini-review
In-cell NMR can now capture intracellular dynamics at atomic level
In-cell NMR in E. coli to Monitor Maturation Steps of hSOD1
Chemosensitization of cancer cells by siRNA using targeted nanogel delivery
Challenges and Opportunities for Small Molecule Aptamer Development
Evolution and protein packaging of small-molecule RNA aptamers |