Biology subjects

Amaro, R.

Publications and source records attributed to Amaro, R..

3 recordsLinked to original sources

bioRxiv2019

The Five-Primer Challenge: An inquiry-based laboratory module for synthetic biology

New technologies in DNA synthesis and assembly give genetic engineers complete freedom in genetic design, where virtually any plasmid DNA sequence can be created efficiently and economically. Learning how to design, construct, and test new DNA sequences is a critical skill for researchers in molecular biology and biotechnology. Here we present a student-centered, inquiry-based module in which students learn how to control bacterial gene expression by appplying various DNA assembly techniques. The central activity in this learning module is termed the Five-Primer Challenge. Each student is allowed to order up to five 60-mer oligonucleotide primers to then modify a GFP expression plasmid with the goal of increasing GFP expression as much as possible. This module was developed and implemented at the 2016 Cold Spring Harbor Laboratory Synthetic Biology Course, and was effective at engaging students in critical thinking and in promoting student learning.

scientific communication and education↗

bioRxiv2019

GAMer 2: A System for 3D Mesh Processing of Cellular Electron Micrographs

ObjectiveRecent advances in electron microscopy have, for the first time, enabled imaging of single cells in 3D at a nanometer length scale resolution. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. However, this will require a system for going from EM images to 3D volume meshes which can be used in finite element simulations. MethodsIn this paper, we develop an end-to-end pipeline for this task by adapting and extending computer graphics mesh processing and smoothing algorithms. Our workflow makes use of our recently rewritten mesh processing software, GAMer 2, which implements several mesh conditioning algorithms and serves as a platform to connect different pipeline steps. ResultsWe apply this pipeline to a series of electron micrographs of dendrite morphology explored at three different length scales and show that the resultant meshes are suitable for finite element simulations. ConclusionOur pipeline, which consists of free and open-source community driven tools, is a step towards routine physical simulations of biological processes in realistic geometries. SignificanceWe posit that a new frontier at the intersection of computational technologies and single cell biology is now open. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery.

systems biology↗

bioRxiv2018

Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking

1Docking calculations can be used to accelerate drug discovery by providing predictions of the poses of candidate ligands bound to a targeted protein. However, studies in the literature use varied docking methods, and it is not clear which work best, either in general or for specific protein targets. In addition, a complete docking calculation requires components beyond the docking algorithm itself, such as preparation of the protein and ligand for calculations, and it is difficult to isolate which aspects of a method are most in need of improvement. To address such issues, we have developed the Continuous Evaluation of Ligand Protein Predictions (CELPP), a weekly blinded challenge for automated docking workflows. Participants in CELPP create a workflow to predict protein-ligand binding poses, which is then tasked with predicting 10-100 new (never before released) protein-ligand crystal structures each week. CELPP evaluates the accuracy of each workflows predictions and posts the scores online. CELPP is a new cyberinfrastructure resource to identify the strengths and weaknesses of current approaches, help map docking problems to the algorithms most likely to overcome them, and illuminate areas of unmet need in structure-guided drug design.

biophysics↗