Current Methods and Pipelines for Image-Based Quantitation of Nuclear Shape and Nuclear Envelope Abnormalities.

Any given cell type has an associated "normal" nuclear morphology, which is important to maintain proper cellular functioning and safeguard genomic integrity. Deviations from this can be indicative of diseases such as cancer or premature aging syndrome. To accurately assess nuclear abnormalities, it is important to use quantitative measures of nuclear morphology. Here, we give an overview of several nuclear abnormalities, including micronuclei, nuclear envelope invaginations, blebs and ruptures, and review the current methods used for image-based quantification of these abnormalities. We discuss several parameters that can be used to quantify nuclear shape and compare their outputs using example images. In addition, we present new pipelines for quantitative analysis of nuclear blebs and invaginations. Quantitative analyses of nuclear aberrations and shape will be important in a wide range of applications, from assessments of cancer cell anomalies to studies of nucleus deformability under mechanical or other types of stress.FEBS Long-Term Fellowship

HSV-1 glycoprotein endocytosis

Herpes simplex virus-1 (HSV-1) is a large enveloped DNA virus that belongs to the family of Herpesviridae. It has been recently shown that the cytoplasmic membranes that wrap the newly assembled capsids are endocytic compartments derived from the plasma membrane. Here, we show that dynamin-dependent endocytosis plays a major role in this process. Dominant-negative dynamin and clathrin adaptor AP180 significantly decrease virus production. Moreover, inhibitors targeting dynamin and clathrin lead to a decreased transport of glycoproteins to cytoplasmic capsids, confirming that glycoproteins are delivered to assembly sites via endocytosis. We also show that certain combinations of glycoproteins colocalize with each other and with the components of clathrin-dependent and -independent endocytosis pathways. Importantly, we demonstrate that the uptake of neutralizing antibodies that bind to glycoproteins when they become exposed on the cell surface during virus particle assembly leads to the production of non-infectious HSV-1. Our results demonstrate that transport of viral glycoproteins to the plasma membrane prior to endocytosis is the major route by which these proteins are localized to the cytoplasmic virus assembly compartments. This highlights the importance of endocytosis as a major protein-sorting event during HSV-1 envelopment.This work was supported by grants from the Leverhulme Trust (grant RPG‐2012‐793), the Royal Society (University Research Fellowship UF090010), the Engineering and Physical Sciences Research Council, UK (grant EP/H018301/1, EP/L015889/1) and by the Medical Research Council (grant MR/K015850/1)

Critical points for an accurate human genome analysis

Next-generation sequencing is radically changing how DNA diagnostic laboratories operate. What started as a single-gene profession is now developing into gene panel sequencing and whole exome and genome sequencing (WES/WGS) analyses. With further advances in sequencing technology and concomitant price reductions, whole genome sequencing (WGS) will soon become the standard and be routinely offered. Here we focus on the critical steps involved in performing WGS, with a particular emphasis on points where WGS differs from WES, the important variables that should be taken into account, and the quality control measures that can be taken to monitor the process. The points discussed here, combined with recent publications on guidelines for reporting variants, will facilitate the routine implementation of WGS into a diagnostic setting. This article is protected by copyright. All rights reserved.status: publishe

Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants

Plant–microbe interactions in the rhizosphere have important roles in biogeochemical cycling, and maintenance of plant health and productivity, yet remain poorly understood. Using RNA-based metatranscriptomics, the global active microbiomes were analysed in soil and rhizospheres of wheat, oat, pea and an oat mutant (sad1) deficient in production of anti-fungal avenacins. Rhizosphere microbiomes differed from bulk soil and between plant species. Pea (a legume) had a much stronger effect on the rhizosphere than wheat and oat (cereals), resulting in a dramatically different rhizosphere community. The relative abundance of eukaryotes in the oat and pea rhizospheres was more than fivefold higher than in the wheat rhizosphere or bulk soil. Nematodes and bacterivorous protozoa were enriched in all rhizospheres, whereas the pea rhizosphere was highly enriched for fungi. Metabolic capabilities for rhizosphere colonisation were selected, including cellulose degradation (cereals), H2 oxidation (pea) and methylotrophy (all plants). Avenacins had little effect on the prokaryotic community of oat, but the eukaryotic community was strongly altered in the sad1 mutant, suggesting that avenacins have a broader role than protecting from fungal pathogens. Profiling microbial communities with metatranscriptomics allows comparison of relative abundance, from multiple samples, across all domains of life, without polymerase chain reaction bias. This revealed profound differences in the rhizosphere microbiome, particularly at the kingdom level between plants

An Official American Thoracic Society/European Respiratory Society Statement: Key Concepts and Advances in Pulmonary Rehabilitation

Background: Pulmonary rehabilitation is recognized as a core component of the management of individuals with chronic respiratory disease. Since the 2006 American Thoracic Society (ATS)/European Respiratory Society (ERS) Statement on Pulmonary Rehabilitation, there has been considerable growth in our knowledge of its efficacy and scope. Purpose: The purpose of this Statement is to update the 2006 document, including a new definition of pulmonary rehabilitation and highlighting key concepts and major advances in the field. Methods: A multidisciplinary committee of experts representing the ATS Pulmonary Rehabilitation Assembly and the ERS Scientific Group 01.02, “Rehabilitation and Chronic Care,” determined the overall scope of this update through group consensus. Focused literature reviews in key topic areas were conducted by committee members with relevant clinical and scientific expertise. The final content of this Statement was agreed on by all members. Results: An updated definition of pulmonary rehabilitation is proposed. New data are presented on the science and application of pulmonary rehabilitation, including its effectiveness in acutely ill individuals with chronic obstructive pulmonary disease, and in individuals with other chronic respiratory diseases. The important role of pulmonary rehabilitation in chronic disease management is highlighted. In addition, the role of health behavior change in optimizing and maintaining benefits is discussed. Conclusions: The considerable growth in the science and application of pulmonary rehabilitation since 2006 adds further support for its efficacy in a wide range of individuals with chronic respiratory disease Read More: http://www.atsjournals.org/doi/abs/10.1164/rccm.201309-1634S