Author Archives: BSA

Dr Charlie Hodgens joins the lab

The EMRLab is very excited to welcome new member Dr Charles Hodgens.  Dr Hodgens is joining the NSF-funded collaboration with our plant biology colleagues in Dr Marcela Rojas-Pierce’s lab at NC State University.  Charlie is a talented, discipline-crossing biologist who will be responsible for the computational aspects of this research effort.  He holds a PhD in Genetics and Molecular Biology with a Certificate in Bioinformatics and Computational Biology from UNC-Chapel Hill. Check out the latest publication from his thesis work in the Kieber Lab: Mutagenomics: A rapid, high-throughput method to identify causative mutations from a genetic screen .  Welcome Charlie!!!

Dr Akpa receives an AIChE highlight!

Belinda Akpa on Computational Systems Physiology

What inspired you to do research in your field?
Working in computational systems physiology gives me an excuse to marry multiple fields of interest in the pursuit of solving tough problems. It is also a chance to work in diverse teams, as the work often relies critically on expertise beyond what typically exists in one research group. It requires effective communication across different disciplinary cultures, and I’ve always been fascinated by cross-cultural communication in science and otherwise. More…

Funded and hiring!

nsf1To apply:

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 any of the following is particularly desirable: parameter estimation and uncertainty quantification, statistical inference, machine learning, and quantitative image analysis. Evidence of research productivity in the form of publications is important. The appointment is on an annual basis and renewable for up to 3 years.


Dr Akpa to speak at the 21st Century Cures: Southeast Conference

21stC curesFrom UTK:
“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.


2019 is off to a great start!

Things are busy at the EMRLab. A big thank you to all our lab members for their hard work!

HeadshotNik 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!

DTFIn 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.

New first author publication for PhD student Nicolas Barbera!

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)

Cover pic for website


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.