The mechanisms of calcium homeostasis and signalling in the lens

Excessive Ca2+ can be detrimental to cells and raised levels of Ca2+ in human lenses with cortical cataract have been found to play a major role in the opacification process. Ca2+ homeostasis is therefore, recognised as having fundamental importance in lens pathophysiology. Furthermore, Ca2+ plays a central role as a second messenger in cell signalling and mechanisms have evolved which give cells exquisite control over intracellular Ca2+ ([Ca2+]i) via an array of specialised regulatory and signalling proteins. In this review we discuss these mechanisms as they apply to the lens. Ca2+ levels in human aqueous humour are approximately 1 mM and there is a large, 10,000 fold, inwardly directed gradient across the plasma membrane. In the face of such a large gradient highly efficient mechanisms are needed to maintain low [Ca2+]i. The Na+/Ca2+ exchanger (NCX) and plasma membrane Ca2+-ATPase (PMCA) actively remove Ca2+ from the cells, whereas the sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) sequesters Ca2+ in the endoplasmic reticulum (ER) Ca2+ store. In lens epithelial cells the dominant role is played by the ATPases, whilst in the fibre cells NCX activity appears to be more important. Usually, [Ca2+]i can be increased in a number of ways. Ca2+ influx through the plasma membrane, for example, is mediated by an array of channels with evidence in the lens for the presence of voltage-operated Ca2+ channels (VOCCs), receptor-operated Ca2+ channels (ROCCs) and channels mediating store-operated Ca2+ entry (SOCE). Ca2+ signalling is initiated via activation of G-protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTK) of which the lens expresses a surprisingly diverse array responding to various neurotransmitters, hormones, growth factors, autocoids and proteases. Downstream of plasma membrane receptors are IP3-gated channels (IP3Rs) and ryanodine receptors (RYRs) located in the ER, which when activated cause a rapid increase in [Ca2+]i and these have also been identified in the lens. Through an appreciation of the diversity and complexity of the mechanisms involved in Ca2+ homeostasis in normal lens cells we move closer to an understanding of the mechanisms which mediate pathological Ca2+ overload as occurs in the process of cataract formation

Illuminating Choices for Library Prep: A Comparison of Library Preparation Methods for Whole Genome Sequencing of Cryptococcus neoformans Using Illumina HiSeq.

The industry of next-generation sequencing is constantly evolving, with novel library preparation methods and new sequencing machines being released by the major sequencing technology companies annually. The Illumina TruSeq v2 library preparation method was the most widely used kit and the market leader; however, it has now been discontinued, and in 2013 was replaced by the TruSeq Nano and TruSeq PCR-free methods, leaving a gap in knowledge regarding which is the most appropriate library preparation method to use. Here, we used isolates from the pathogenic fungi Cryptococcus neoformans var. grubii and sequenced them using the existing TruSeq DNA v2 kit (Illumina), along with two new kits: the TruSeq Nano DNA kit (Illumina) and the NEBNext Ultra DNA kit (New England Biolabs) to provide a comparison. Compared to the original TruSeq DNA v2 kit, both newer kits gave equivalent or better sequencing data, with increased coverage. When comparing the two newer kits, we found little difference in cost and workflow, with the NEBNext Ultra both slightly cheaper and faster than the TruSeq Nano. However, the quality of data generated using the TruSeq Nano DNA kit was superior due to higher coverage at regions of low GC content, and more SNPs identified. Researchers should therefore evaluate their resources and the type of application (and hence data quality) being considered when ultimately deciding on which library prep method to use

Therapeutic hypothermia to reduce intracranial pressure after traumatic brain injury: the Eurotherm3235 RCT

Background: Traumatic brain injury (TBI) is a major cause of disability and death in young adults worldwide. It results in around 1 million hospital admissions annually in the European Union (EU), causes a majority of the 50,000 deaths from road traffic accidents and leaves a further ≈10,000 people severely disabled. Objective: The Eurotherm3235 Trial was a pragmatic trial examining the effectiveness of hypothermia (32–35 °C) to reduce raised intracranial pressure (ICP) following severe TBI and reduce morbidity and mortality 6 months after TBI. Design: An international, multicentre, randomised controlled trial. Setting: Specialist neurological critical care units. Participants: We included adult participants following TBI. Eligible patients had ICP monitoring in place with an ICP of > 20 mmHg despite first-line treatments. Participants were randomised to receive standard care with the addition of hypothermia (32–35 °C) or standard care alone. Online randomisation and the use of an electronic case report form (CRF) ensured concealment of random treatment allocation. It was not possible to blind local investigators to allocation as it was obvious which participants were receiving hypothermia. We collected information on how well the participant had recovered 6 months after injury. This information was provided either by the participant themself (if they were able) and/or a person close to them by completing the Glasgow Outcome Scale – Extended (GOSE) questionnaire. Telephone follow-up was carried out by a blinded independent clinician. Interventions: The primary intervention to reduce ICP in the hypothermia group after randomisation was induction of hypothermia. Core temperature was initially reduced to 35 °C and decreased incrementally to a lower limit of 32 °C if necessary to maintain ICP at  20 mmHg, titrated therapeutic hypothermia successfully reduced ICP but led to a higher mortality rate and worse functional outcome. Limitations: Inability to blind treatment allocation as it was obvious which participants were randomised to the hypothermia group; there was biased recording of SAEs in the hypothermia group. We now believe that more adequately powered clinical trials of common therapies used to reduce ICP, such as hypertonic therapy, barbiturates and hyperventilation, are required to assess their potential benefits and risks to patients. Trial registration: Current Controlled Trials ISRCTN34555414. Funding: This project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 22, No. 45. See the NIHR Journals Library website for further project information. The European Society of Intensive Care Medicine supported the pilot phase of this trial

The Intensive Care Global Study on Severe Acute Respiratory Infection (IC-GLOSSARI): a Multicenter, Multinational, 14-Day Inception Cohort Study

PURPOSE: In this prospective, multicenter, 14-day inception cohort study, we investigated the epidemiology, patterns of infections, and outcome in patients admitted to the intensive care unit (ICU) as a result of severe acute respiratory infections (SARIs). METHODS: All patients admitted to one of 206 participating ICUs during two study weeks, one in November 2013 and the other in January 2014, were screened. SARI was defined as possible, probable, or microbiologically confirmed respiratory tract infection with recent onset dyspnea and/or fever. The primary outcome parameter was in-hospital mortality within 60 days of admission to the ICU. RESULTS: Among the 5550 patients admitted during the study periods, 663 (11.9 %) had SARI. On admission to the ICU, Gram-positive and Gram-negative bacteria were found in 29.6 and 26.2 % of SARI patients but rarely atypical bacteria (1.0 %); viruses were present in 7.7 % of patients. Organ failure occurred in 74.7 % of patients in the ICU, mostly respiratory (53.8 %), cardiovascular (44.5 %), and renal (44.6 %). ICU and in-hospital mortality rates in patients with SARI were 20.2 and 27.2 %, respectively. In multivariable analysis, older age, greater severity scores at ICU admission, and hematologic malignancy or liver disease were independently associated with an increased risk of in-hospital death, whereas influenza vaccination prior to ICU admission and adequate antibiotic administration on ICU admission were associated with a lower risk. CONCLUSIONS: Admission to the ICU for SARI is common and associated with high morbidity and mortality rates. We identified several risk factors for in-hospital death that may be useful for risk stratification in these patients

High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses

<p>Abstract</p> <p>Background</p> <p>Microarray experiments are becoming increasingly common in biomedical research, as is their deposition in publicly accessible repositories, such as Gene Expression Omnibus (GEO). As such, there has been a surge in interest to use this microarray data for meta-analytic approaches, whether to increase sample size for a more powerful analysis of a specific disease (e.g. lung cancer) or to re-examine experiments for reasons different than those examined in the initial, publishing study that generated them. For the average biomedical researcher, there are a number of practical barriers to conducting such meta-analyses such as manually aggregating, filtering and formatting the data. Methods to automatically process large repositories of microarray data into a standardized, directly comparable format will enable easier and more reliable access to microarray data to conduct meta-analyses.</p> <p>Methods</p> <p>We present a straightforward, simple but robust against potential outliers method for automatic quality control and pre-processing of tens of thousands of single-channel microarray data files. GEO GDS files are quality checked by comparing parametric distributions and quantile normalized to enable direct comparison of expression level for subsequent meta-analyses.</p> <p>Results</p> <p>13,000 human 1-color experiments were processed to create a single gene expression matrix that subsets can be extracted from to conduct meta-analyses. Interestingly, we found that when conducting a global meta-analysis of gene-gene co-expression patterns across all 13,000 experiments to predict gene function, normalization had minimal improvement over using the raw data.</p> <p>Conclusions</p> <p>Normalization of microarray data appears to be of minimal importance on analyses based on co-expression patterns when the sample size is on the order of thousands microarray datasets. Smaller subsets, however, are more prone to aberrations and artefacts, and effective means of automating normalization procedures not only empowers meta-analytic approaches, but aids in reproducibility by providing a standard way of approaching the problem.</p> <p>Data availability: matrix containing normalized expression of 20,813 genes across 13,000 experiments is available for download at . Source code for GDS files pre-processing is available from the authors upon request.</p

Quasi-Neutral theory of epidemic outbreaks

Some epidemics have been empirically observed to exhibit outbreaks of all possible sizes, i.e., to be scalefree or scale-invariant. Different explanations for this finding have been put forward; among them there is a model for "accidental pathogens" which leads to power-law distributed outbreaks without apparent need of parameter fine tuning. This model has been claimed to be related to self-organized criticality, and its critical properties have been conjectured to be related to directed percolation. Instead, we show that this is a (quasi) neutral model, analogous to those used in Population Genetics and Ecology, with the same critical behavior as the voter-model, i.e. the theory of accidental pathogens is a (quasi)-neutral theory. This analogy allows us to explain all the system phenomenology, including generic scale invariance and the associated scaling exponents, in a parsimonious and simple way.Comment: 13 pages, 6 figures Accepted for publication in PLoS ONE the text have been modified in orden to improve the figure's resolutio