Recruiting: Summer 2023 Undergraduate Student – Bioinformatics for Epigenetic Engineering
The Haynes lab at Emory is seeking bright, talented, and motivated undergraduate students from Emory University or Georgia Tech to fill one summer research position with a start date of May or June 2023. This position is a great opportunity to gain hands-on research experience in synthetic biology as it applies to health and medicine. Dr. Haynes has several years of experience mentoring undergraduate research in the classroom, in her research lab (see our publications and posters that include undergraduates), and for the International Genetically Engineered Machines Competition (iGEM).
Undergraduate Researcher, Bioinformatics for Epigenetic Engineering
This opportunity is currently [OPEN]
Type: Volunteer or Course credit
- Processing of raw data from next generation sequencing (NGS) experiments (e.g. RNA-seq, ATAC-seq, ChIP-seq) that involve epigenetically engineered cells
- Downstream gene function and network analyses, with guidance from the PI or other supervisor
- Creation of NGS data figures for posters and publications
- Course: Genomics & Applied Bioinformatics (BIOS 4150); minimum grade of B
- Course: Biological Networks & Genomics (BMED 4477); desired but not required
- Proficiency in basic RNA-seq data processing tools (e.g. Trimmomatic, STAR, DESeq2, etc.)
- Ability to learn advanced NGS software such as BowTie, Picard Tools, MACS, DeepTools, etc.
About the Haynes Lab at Emory: The Haynes lab is part of the joint Emory/ GA Tech W.H. Coulter Department of Biomedical Engineering. We are located in a new state-of-the-art facility in the Health Sciences Research Building. The space is furnished with benches, a dedicated tissue culture room, shared autoclaves and a cold room, and office desks located in a food-friendly area adjacent to the lab. Core facilities for mouse models, next-generation sequencing, flow cytometry, are located on the same campus. A state-of-the-art and microscopy core (including wide-field and confocal) is located in the same building one level below the Haynes lab.
How to Apply: Send a letter of interest as an e-mail with your resume or c.v. as an attachement to kahayne at emory dot edu. In your letter of interest be sure to include your current year, expected graduation year, your major, your GPA, your current or previous (most recent) lab affiliation (if applicable), and explain how you expect the associated Responsibilities (listed above) to support your career development, and summarize how your background fits the Requirements outlined above.
Haynes lab members present research at the 2021 SEED conference
Four members from the Haynes lab presented their latest research at the 2021 Synthetic Biology: Engineering, Evolution & Design (SEED) conference that took place June 16 – 18, 2021 on a virtual platform. SEED 2021 focused on advances in science, technology, applications, and related investments in the field of synthetic biology. Dr. Karmella Haynes served as session chair for “Translating Synthetic Biology into the Clinic” and the “Funder’s Panel.” The four poster presentations from the Haynes lab included:
- Dr. Isioma Enwerem (postdoc), “Time-course expression profiling reveals early and late responders to a synthetic chromatin regulator”
- Harrison Priode (research specialist), “Synthetic epigenetic reader engineering with an all-in-one cell-free expression and protein interaction microarray”
- Paige Steppe (undergraduate researcher), “Using newly-identified epigenetic reader-effector BAHCC1 to engineer a H3K27me3-binding transcriptional activator”
- Dr. Natecia Williams (senior research specialist), “A synthetic chromatin reader-effector activates key silenced tumor suppressor genes in triple negative breast cancer cells”
Paige Steppe receives 2021 NSF GRFP award
Undergraduate researcher Paige Steppe has received a 2021 National Science Foundation Graduate Research Fellows Program (NSF GRFP) award! This highly competitive award recognizes and supports outstanding students in STEM disciplines who are pursuing research-based graduate degrees at US institutions. The five-year fellowship includes three years of financial support including an annual stipend of $34,000 and $12,000 for tuition support. Paige is a college senior in the Chemical and Biomolecular Engineering program at Georgia Tech. She joined the Haynes lab in 2020 to investigate the evolutionary diversity of a chromatin-binding protein motif to inform rational design of synthetic epigenetic regulators in cancer. Congratulations, Paige!
Congratulations to Dr. Brady Laughlin, M.D.
Brady Laughlin, a former undergraduate researcher in the Haynes lab at ASU has earned his M.D. from the University of Arizona College of Medicine this year. Previously at ASU, Brady was an undergraduate Biomedical Engineering major and a Barrett Honors student. He did chromatin engineering research as a FURI Fellow in the Haynes lab and also gained research experience as a TGen Helios Scholar. He is now a resident in radiation oncology at the Mayo Clinic. Congratulations, Dr. Laughlin!
Research – Frontiers – Engineered orthogonal quorum sensing systems for synthetic gene regulation
Engineered orthogonal quorum sensing systems for synthetic gene regulation
Tekel SJ, Smith CL, Lopez B, Mani A, Connot C, Livingstone X, Haynes KA. (2019) Front Bioeng Biotech. 7:80.
PMID: 31058147 | PMCID: PMC6478669
For the past two years, the undergraduate ASU International Genetically Engineered Machines (iGEM) Competition teams have been investigating the use of quorum sensing to build bacteria (E. coli) that can carry out chemical signaling with each other, without signaling to a different group of bacteria. In a continuation of the quorum sensing project from the 2016 team, the 2017 ASU iGEM team built and tested six new quorum sensors (Receivers) in addition to the previous sensor, LuxR. After exposing a total of seven Receivers to HSLs from ten different synthases (Senders), the team identified two sets of signaling pathways that exhibited orthogonal behavior. These results expand the toolbox of characterized components for engineering microbial communities. The plasmid constructs featured in this paper were contributed to public collections for use by the scientific community.
- Pre-print: Engineered orthogonal quorum sensing systems for synthetic gene regulation. bioRxiv. doi: https://doi.org/10.1101/499681
- Arizona_State 2017 iGEM Team Project: “EVR-QST – Engineering Variable Regulators for a Quorum Sensing Toolbox.” http://2017.igem.org/Team:Arizona_State
Luis Sanchez selected for a Mayo Clinic internship
Congratulations to Haynes lab undergraduate researcher Luis Sanchez De La Vegas Covarrubias, who was selected for a position as a Mayo Clinic Special Research Student at Mayo Clinic, Scottsdale in Arizona, starting January 4, 2019. This highly selective program is being organized by the Mayo Clinic College of Medicine and Science (MCCMS).
Christina Smith receives 2018 FURI fellowship for undergrad research
Congratulations to Christina Smith (Undergrad, Biomedical Engineering) who will receive a stipend, materials and supplies, and an opportunity for conference travel support to complete a project in the Haynes lab this summer. Sponsorship is provided by the Fulton Undergraduate Research Initiative (FURI). This will be her second FURI award since joining the Haynes lab.
Research – PLOS ONE – Characterization of Diverse Homoserine Lactone Synthases in Escherichia coli
Characterization of Diverse Homoserine Lactone Synthases in Escherichia coli
Daer R, Barrett CM, Melendez EL, Wu J, Tekel SJ, Xu J, Dennison B, Muller R, Haynes KA. (2018) PLOS ONE. doi:10.1371/journal.pone.0202294
PMID: 30138364 | PMCID: PMC6107141
The Haynes lab focuses on advanced chromosome engineering in human cells, but also provides opportunities for undergraduates to learn synthetic biology using simpler organisms like bacteria (E. coli). In this paper, the 2016 ASU International Genetically Engineered Machines (iGEM) Competition team and their graduate advisors report their work to identify useful, new cell-cell communication components to use in engineered systems. Homoserine lactone (HSL) synthases appear as a wide variety of different forms in the bacterial kingdom, and produce various chemical signals that regulate genes in neighboring bacteria. When these are combined to build synthetic circuits in a common lab strain (E. coli), the signals are sometimes not produced as expected. Therefore, it is important to systematically characterize HSL synthases in context. The team also used experiments to identify the most effective way to neutralize unused HSLs in biological waste. The ten HSL synthases characterized in this paper were contributed to public collections for use by the scientific community.
- Pre-print: Characterization of Diverse Homoserine Lactone Synthases in Escherichia coli. bioRxiv. https://www.biorxiv.org/content/early/2018/03/09/279349
- Arizona_State 2016 iGEM Team Project: “Ringtones -Diverse homoserine lactone systems for cellular communication.” http://2016.igem.org/Team:Arizona_State
Haynes lab undergad researcher Jiaqi Wu receives prestigous Bidstrup Fellowship
Jiaqi Wu, a computer science major who is fascinated with computational biology and bioinformatics, has been awarded a prestigious Bidstrup Undergraduate Fellowship for academic year 2017 – 2018. This award is a testament to the outstanding commitment to academic excellence made by Jiaqi and Dr. Haynes as a faculty-student team. Read the rest of this entry »
Congratulations to the ASU 2017 iGEM Team
The 2017 ASU International Genetically Engineered Machines Competition (iGEM) team brought home a Gold medal and two nominations for competitive prizes. The team presented their project “EVR QST: Engineering Variable Regulators for a Quorum Sensing Toolbox” to a panel of judges (academic, policy, and industry professionals) and an international audience. The 2017 iGEM Giant Jamboree took place in Boston, MA at the Hynes Convention Center on November 9 – 13, 2017. Read the rest of this entry »