The EMRLab (Molecular Biomedical Sciences) and the Rojas-Pierce lab (Plant and Microbial Biology) have recently received an NSF grant in support of their joint efforts to reveal the molecular rules underlying a critical dynamic function in plants: stoma opening as mediated by regulated vacuole fusion. The 3 year award will support interdisciplinary research and outreach activities and provide research training for highschool, undergraduate, and graduate students. The project also provides for transdisciplinary training of 2 postdocs. Are you interested in joining us? If so, keep reading.
NSF #1918746 Vacuole remodeling in guard cells during stomata movements
Postdoctoral Research Scholar Position in Computational Systems Biology A postdoctoral research scholar position is available immediately in the laboratory of Dr Belinda Akpa at North Carolina State University. The postdoc will work closely with plant cell biologists to develop a multi-scale model bridging intra-cellular protein dynamics with evolution of cell morphology by predicting organelle fusion dynamics. Responsibilities include mentoring undergraduate students and participating in outreach activities.
Applicants must have their PhD in Chemical Engineering, Bioengineering, Mathematical Biology, or a related field. Preference will be given to applicants with a demonstrated facility with cross-disciplinary communication and experience with computational modeling that includes working with varied experimental datasets. Experience with the following is particularly desirable: stochastic modeling, parameter estimation and uncertainty quantification, statistical inference, machine learning, and quantitative image analysis. Evidence of research productivity in the form of publications is important. Must have excellent communication skills and experience working in interdisciplinary teams. The successful candidate should be a productive and highly motivated self-starter. The appointment is on an annual basis and renewable for up to 3 years.
“The University of Tennessee, Knoxville (UT), will host its third 21st Century Cures: Southeast Conference in March 2019 which will focus on applying systems biology to biomedical research.
Guests will hear insights from prestigious scientists, learn about research priorities and funding opportunities from leaders at the National Institutes of Health, and meet potential collaborators from across the Southeast. In addition, the event will include an interactive poster session to allow faculty and students to share their ideas with other attendees.”
Registration is open and abstracts are being accepted for poster presentations.
Things are busy at the EMRLab. A big thank you to all our lab members for their hard work!
Nik recently passed his prelim defense with flying colors. Last week he went on to present this work in a platform session at the Biophysical Society Annual Meeting. Abstract
Lab alumna Manuela Ayee was also at the meeting. She presented her recently highlighted postdoctoral work with Dr Irena Levitan of the UIC College of Medicine. Go Manuela!
In just one semester, David’s contributions to the lab are taking us in new directions. With his co-authorship on a manuscript in Human Biology and a chapter in a book on Humanitarian Forensic Science, David’s Bayesian approaches have taken us into the field of Computational Forensics, with new collaborator Dr Chelsey Ann Juarez. David’s work has also impacted our other modeling efforts involving scarce and qualitative data, with applications in membrane fusion and plant physiology.
Dr Akpa recently highlighted our collaborative work with NCSU Plant Biology colleague Dr Marcela Rojas-Pierce in a keynote presentation at the NC State Genomic Sciences and Biomathematics Symposium. Her talk, entitled “Realizing the potential of ‘tiny data’: a cell biology case study”, described our successes in building quantitative, multi-scale signaling models based on qualitative data describing cell and organelle morphology. This talk highlighted the critical role that modeling can play at very early stages of biological inquiry, helping to precisely frame biological questions and experimental strategies. Drs Akpa and Rojas-Pierce will speak about the nature of their integrative work at this year’s NSF-sponsored Finding Your Inner Modeler workshop (June 12-14), which is now open for registration.
Congrats to Nik for his first lead-author publication! Online Now at Biophysical Journal
Molecular Dynamics Simulations of Kir2.2 Interactions with an Ensemble of Cholesterol Molecules
Nicolas Barbera, Manuela A.A. Ayee, Belinda S. Akpa*, Irena Levitan* (*co-corresponding)
Abstract: Cholesterol is a major regulator of multiple types of ion channels, but the specific mechanisms and the dynamics of its interactions with the channels are not well understood. Kir2 channels were shown to be sensitive to cholesterol through direct interactions with “cholesterol-sensitive” regions on the channel protein. In this work, we used Martini coarse-grained simulations to analyze the long (μs) timescale dynamics of cholesterol with Kir2.2 channels embedded into a model membrane containing POPC phospholipid with 30 mol% cholesterol. This approach allows us to simulate the dynamic, unbiased migration of cholesterol molecules from the lipid membrane environment to the protein surface of Kir2.2 and explore the favorability of cholesterol interactions at both surface sites and recessed pockets of the channel. We found that the cholesterol environment surrounding Kir channels forms a complex milieu of different short- and long-term interactions, with multiple cholesterol molecules concurrently interacting with the channel. Furthermore, utilizing principles from network theory, we identified four discrete cholesterol binding sites within the previously identified cholesterol sensitive region, which exist depending on the conformational state of the channel – open or closed. We also discovered that a 2-fold decrease in the cholesterol level of the membrane, which we found earlier to increase Kir2 activity, results in a site-specific decrease of cholesterol occupancy at these sites in both the open and closed states: cholesterol molecules at the deepest of these discrete sites shows no change in occupancy at different cholesterol levels, while the remaining sites showed a marked decrease in occupancy.
Congratulations to Dr Manuela Ayee for starting her faculty career as Assistant Professor of Chemical Engineering and Chemistry at Dordt College. After completing her PhD with us in Chemical Engineering, Manuela spent 3 years as a postdoc with Dr Irena Levitan at UIC’s College of Medicine. There she expanded on her computational interests in the structure and mechanics of lipid layers and acquired a skillset in complementary experimental methods in cell biology. Several publications later, she is now launching her independent, interdisciplinary research career at Dordt College just as it makes its transition to Dordt University. Congrats, Manuela!
Congrats to Nik for having his abstract accepted for an oral at the 2018 AIChE Annual Meeting. Nik will be presenting on Wednesday October 31st at 9AM in a session on Modeling of Lipid Membranes and Membrane Proteins.
Kir-Cholesterol Interactions: Molecular Simulations Reveal a Dynamic Ensemble of Lipid Ligands and a Composite Binding Domain of Asymmetric Concentration Dependence