Automatic post-picking improves particle image detection from Cryo-EM micrographs

Cryo-electron microscopy (cryo-EM) studies using single particle reconstruction is extensively used to reveal structural information of macromolecular complexes. Aiming at the highest achievable resolution, state of the art electron microscopes acquire thousands of high-quality images. Having collected these data, each single particle must be detected and windowed out. Several fully- or semi-automated approaches have been developed for the selection of particle images from digitized micrographs. However they still require laborious manual post processing, which will become the major bottleneck for next generation of electron microscopes. Instead of focusing on improvements in automated particle selection from micrographs, we propose a post-picking step for classifying small windowed images, which are output by common picking software. A supervised strategy for the classification of windowed micrograph images into particles and non-particles reduces the manual workload by orders of magnitude. The method builds on new powerful image features, and the proper training of an ensemble classifier. A few hundred training samples are enough to achieve a human-like classification performance.Comment: 14 pages, 5 figure

Strategic Display and Response to Emotions: Developing Evidence-based Negotiation Expertise in Emotion Management (NEEM)

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/74964/1/j.1750-4716.2008.00020.x.pd

Conformational states of macromolecular assemblies explored by integrative structure calculation

A detailed description of macromolecular assemblies in multiple conformational states can be very valuable for understanding cellular processes. At present, structural determination of most assemblies in different biologically relevant conformations cannot be achieved by a single technique and thus requires an integrative approach that combines information from multiple sources. Different techniques require different computational methods to allow efficient and accurate data processing and analysis. Here, we summarize the latest advances and future challenges in computational methods that help the interpretation of data from two techniques—mass spectrometry and three-dimensional cryo-electron microscopy (with focus on alignment and classification of heterogeneous subtomograms from cryo-electron tomography). We evaluate how new developments in these two broad fields will lead to further integration with atomic structures to broaden our picture of the dynamic behavior of assemblies in their native environment

Toolbox for Non-Intrusive Structural and Functional Analysis of Recombinant VLP Based Vaccines: A Case Study with Hepatitis B Vaccine

Background: Fundamental to vaccine development, manufacturing consistency, and product stability is an understanding of the vaccine structure-activity relationship. With the virus-like particle (VLP) approach for recombinant vaccines gaining popularity, there is growing demand for tools that define their key characteristics. We assessed a suite of non-intrusive VLP epitope structure and function characterization tools by application to the Hepatitis B surface antigen (rHBsAg) VLP-based vaccine. Methodology: The epitope-specific immune reactivity of rHBsAg epitopes to a given monoclonal antibody was monitored by surface plasmon resonance (SPR) and quantitatively analyzed on rHBsAg VLPs in-solution or bound to adjuvant with a competitive enzyme-linked immunosorbent assay (ELISA). The structure of recombinant rHBsAg particles was examined by cryo transmission electron microscopy (cryoTEM) and in-solution atomic force microscopy (AFM). Principal Findings: SPR and competitive ELISA determined relative antigenicity in solution, in real time, with rapid turnaround, and without the need of dissolving the particulate aluminum based adjuvant. These methods demonstrated the nature of the clinically relevant epitopes of HBsAg as being responsive to heat and/or redox treatment. In-solution AFM and cryoTEM determined vaccine particle size distribution, shape, and morphology. Redox-treated rHBsAg enabled 3D reconstruction from CryoTEM images – confirming the previously proposed octahedral structure and the established lipidto-protei

γ-TEMPy: simultaneous fitting of components in 3D-EM maps of their assembly using a genetic algorithm

We have developed a genetic algorithm for building macromolecular complexes using only a 3D-electron microscopy density map and the atomic structures of the relevant components. For efficient sampling the method uses map feature points calculated by vector quantisation. The fitness function combines a mutual information score that quantifies the goodness-of-fit with a penalty score that helps to avoid clashes between components. Testing the method on ten assemblies (containing 3 to 8 protein components) and simulated density maps at 10, 15, and 20 Å resolution resulted in identification of the correct topology in 90%, 70% and 60% of the cases, respectively. We further tested it on four assemblies with experimental maps at 7.2-23.5 Å resolution, showing the ability of the method to identify the correct topology in all cases. We have also demonstrated the importance of the map feature-point quality on assembly fitting in the lack of additional experimental information

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

The Emerging View of Emotion as Social Information

Emotions play an important role in coordinating social life. In the last decade, traditional research on the intrapersonal effects of emotions has been complemented by a growing focus on interpersonal effects. I propose that a primary function of emotion at this interpersonal level is to disambiguate social interaction by providing information about the expresser’s feelings, goals, motives, and intentions. Building on this idea, I introduce the emotions as social information (EASI) model. The model posits that emotional expressions influence observers by eliciting affective reactions in them and/or by triggering inferential processes, depending on the observer’s information processing motivation and ability and on social-contextual factors. I discuss implications of this view for theorizing about the social functions of emotions; the evolution of emotion; the influence of emotional expressivity, emotion recognition, and emotion regulation; and the role of culture