CLIC: a pogram on cultivating true leadership

12 May 2012. A Program on cultivating true leadership skills helped participants became more effective team members. Solving jigsaw puzzles using leaders’ portraits, putting leader related situations into drawings, stepping oneself into a leader’s shoe and playing games involving teamworking and leadership values were among the activities enjoyed by the participants of the CLIC program (Contemporary Leadership in Community)

Benchmarking tomographic acquisition schemes for high-resolution structural biology

Cryo electron tomography with subsequent subtomogram averaging is a powerful technique to structurally analyze macromolecular complexes in their native context. Although close to atomic resolution in principle can be obtained, it is not clear how individual experimental parameters contribute to the attainable resolution. Here, we have used immature HIV-1 lattice as a benchmarking sample to optimize the attainable resolution for subtomogram averaging. We systematically tested various experimental parameters such as the order of projections, different angular increments and the use of the Volta phase plate. We find that although any of the prominently used acquisition schemes is sufficient to obtain subnanometer resolution, dose-symmetric acquisition provides considerably better outcome. We discuss our findings in order to provide guidance for data acquisition. Our data is publicly available and might be used to further develop processing routines

Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit.

Post-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been implicated in the stabilization of RNA structure and regulation of ribosome biogenesis and protein synthesis. In some instances, rRNA modifications can confer antibiotic resistance. High-resolution ribosome structures are thus necessary for precise determination of modified nucleotides' positions, a task that has previously been accomplished by X-ray crystallography. Here, we present a cryo-electron microscopy (cryo-EM) structure of the Escherichia coli 50S subunit at an average resolution of 2.2 Å as an additional approach for mapping modification sites. Our structure confirms known modifications present in 23S rRNA and additionally allows for localization of Mg2+ ions and their coordinated water molecules. Using our cryo-EM structure as a testbed, we developed a program for assessment of cryo-EM map quality. This program can be easily used on any RNA-containing cryo-EM structure, and an associated Coot plugin allows for visualization of validated modifications, making it highly accessible

Unsupervised cryo-EM data clustering through adaptively constrained K-means algorithm

In single-particle cryo-electron microscopy (cryo-EM), K-means clustering algorithm is widely used in unsupervised 2D classification of projection images of biological macromolecules. 3D ab initio reconstruction requires accurate unsupervised classification in order to separate molecular projections of distinct orientations. Due to background noise in single-particle images and uncertainty of molecular orientations, traditional K-means clustering algorithm may classify images into wrong classes and produce classes with a large variation in membership. Overcoming these limitations requires further development on clustering algorithms for cryo-EM data analysis. We propose a novel unsupervised data clustering method building upon the traditional K-means algorithm. By introducing an adaptive constraint term in the objective function, our algorithm not only avoids a large variation in class sizes but also produces more accurate data clustering. Applications of this approach to both simulated and experimental cryo-EM data demonstrate that our algorithm is a significantly improved alterative to the traditional K-means algorithm in single-particle cryo-EM analysis.Comment: 35 pages, 14 figure

Estimation under group actions: recovering orbits from invariants

Motivated by geometric problems in signal processing, computer vision, and structural biology, we study a class of orbit recovery problems where we observe very noisy copies of an unknown signal, each acted upon by a random element of some group (such as Z/p or SO(3)). The goal is to recover the orbit of the signal under the group action in the high-noise regime. This generalizes problems of interest such as multi-reference alignment (MRA) and the reconstruction problem in cryo-electron microscopy (cryo-EM). We obtain matching lower and upper bounds on the sample complexity of these problems in high generality, showing that the statistical difficulty is intricately determined by the invariant theory of the underlying symmetry group. In particular, we determine that for cryo-EM with noise variance $\sigma^2$ and uniform viewing directions, the number of samples required scales as $\sigma^6$. We match this bound with a novel algorithm for ab initio reconstruction in cryo-EM, based on invariant features of degree at most 3. We further discuss how to recover multiple molecular structures from heterogeneous cryo-EM samples.Comment: 54 pages. This version contains a number of new result