Hepatitis C virus NS4B carboxy terminal domain is a membrane binding domain

<p>Abstract</p> <p>Background</p> <p>Hepatitis C virus (HCV) induces membrane rearrangements during replication. All HCV proteins are associated to membranes, pointing out the importance of membranes for HCV. Non structural protein 4B (NS4B) has been reported to induce cellular membrane alterations like the membranous web. Four transmembrane segments in the middle of the protein anchor NS4B to membranes. An amphipatic helix at the amino-terminus attaches to membranes as well. The carboxy-terminal domain (CTD) of NS4B is highly conserved in Hepaciviruses, though its function remains unknown.</p> <p>Results</p> <p>A cytosolic localization is predicted for the NS4B-CTD. However, using membrane floatation assays and immunofluorescence, we now show targeting of the NS4B-CTD to membranes. Furthermore, a profile-profile search, with an HCV NS4B-CTD multiple sequence alignment, indicates sequence similarity to the membrane binding domain of prokaryotic D-lactate dehydrogenase (d-LDH). The crystal structure of E. coli d-LDH suggests that the region similar to NS4B-CTD is located in the membrane binding domain (MBD) of d-LDH, implying analogy in membrane association. Targeting of d-LDH to membranes occurs via electrostatic interactions of positive residues on the outside of the protein with negative head groups of lipids. To verify that anchorage of d-LDH MBD and NS4B-CTD is analogous, NS4B-CTD mutants were designed to disrupt these electrostatic interactions. Membrane association was confirmed by swopping the membrane contacting helix of d-LDH with the corresponding domain of the 4B-CTD. Furthermore, the functionality of these residues was tested in the HCV replicon system.</p> <p>Conclusion</p> <p>Together these data show that NS4B-CTD is associated to membranes, similar to the prokaryotic d-LDH MBD, and is important for replication.</p

Quantification of Cre-mediated recombination by a novel strategy reveals a stable extra-chromosomal deletion-circle in mice

<p>Abstract</p> <p>Background</p> <p>Inducible conditional knockout animals are widely used to get insight in the function of genes and the pathogenesis of human diseases. These models frequently rely on Cre-mediated recombination of sequences flanked by Lox-P sites. To understand the consequences of gene disruption, it is essential to know the efficiency of the recombination process.</p> <p>Results</p> <p>Here, we describe a modification of the multiplex ligation-dependent probe amplification (MLPA), called extension-MLPA (eMLPA), which enables quantification of relatively small differences in DNA that are a consequence of Cre-mediated recombination. eMLPA, here applied on an inducible <it>Pkd1 </it>conditional deletion mouse model, simultaneously measures both the reduction of the floxed allele and the increase of the deletion allele in a single reaction thereby minimizing any type of experimental variation. Interestingly, with this method we were also able to observe the presence of the excised DNA fragment. This extra-chromosomal deletion-circle was detectable up to 5 months after activation of Cre.</p> <p>Conclusion</p> <p>eMLPA is a novel strategy which easily can be applied to measure the Cre-mediated recombination efficiency in each experimental case with high accuracy. In addition the fate of the deletion-circle can be followed simultaneously.</p

Better knowledge on vitamin D and calcium in older people is associated with a higher serum vitamin D level and a higher daily dietary calcium intake

Abstract: Objective: The objective of the present study was to examine knowledge on vitamin D and calcium in a cohort of older adults and to test the association between health knowledge, vitamin D status and dietary calcium intake. Methods: The participants of this cross-sectional survey consisted of 426 individuals (≥65 years), living in residential homes. Participants were tested for their knowledge on vitamin D and calcium using a standardized questionnaire. Serum 25-hydroxyvitamin D3 (25(OH)D3) levels and dietary calcium intake were measured. Results: The mean serum 25(OH)D3 level was 39.1 (±21.4) nmol/l and the mean daily dietary calcium intake was 826 (±242) mg/day. Of the participants, only 3

Selective decontamination of the digestive tract: all questions answered?

Although many studies have shown beneficial effects of SDD on the incidence of respiratory tract infections, SDD did not become routine practice because mortality reduction was not demonstrated in individual trials, beneficial effects on duration of ventilation, ICU stay or hospital stay were not demonstrated, cost-efficacy had not been demonstrated, and selection of antibiotic resistance was considered a serious side-effect. A recent study has now shown improved patient survival and lower prevalence of antibiotic resistance in patients receiving SDD. Why could this study show mortality reduction, where all others studies had failed before? And do the microbiological data unequivocally prove protective effects of SDD on emergence of antibiotic resistance? Interestingly, the reported mortality reductions exceeds even the most optimistic predictions from previous meta-analyses, but a clear explanation is not yet evident. The data on antibiotic resistance, however, are rather superficial and do not allow to interpret the underlying epidemiological dynamics. Therefore, the recent findings are provocative and shed new light on the SDD issue, warranting studies confirming its beneficial effects but also addressing several important aspects related to study design

Genetic Covariance Structure of Reading, Intelligence and Memory in Children

This study investigates the genetic relationship among reading performance, IQ, verbal and visuospatial working memory (WM) and short-term memory (STM) in a sample of 112, 9-year-old twin pairs and their older siblings. The relationship between reading performance and the other traits was explained by a common genetic factor for reading performance, IQ, WM and STM and a genetic factor that only influenced reading performance and verbal memory. Genetic variation explained 83% of the variation in reading performance; most of this genetic variance was explained by variation in IQ and memory performance. We hypothesize, based on these results, that children with reading problems possibly can be divided into three groups: (1) children low in IQ and with reading problems; (2) children with average IQ but a STM deficit and with reading problems; (3) children with low IQ and STM deficits; this group may experience more reading problems than the other two

Decoding expectation and surprise in dementia: the paradigm of music

Making predictions about the world and responding appropriately to unexpected events are essential functions of the healthy brain. In neurodegenerative disorders, such as frontotemporal dementia and Alzheimer's disease, impaired processing of 'surprise' may underpin a diverse array of symptoms, particularly abnormalities of social and emotional behaviour, but is challenging to characterize. Here, we addressed this issue using a novel paradigm: music. We studied 62 patients (24 female; aged 53-88) representing major syndromes of frontotemporal dementia (behavioural variant, semantic variant primary progressive aphasia, non-fluent-agrammatic variant primary progressive aphasia) and typical amnestic Alzheimer's disease, in relation to 33 healthy controls (18 female; aged 54-78). Participants heard famous melodies containing no deviants or one of three types of deviant note-acoustic (white-noise burst), syntactic (key-violating pitch change) or semantic (key-preserving pitch change). Using a regression model that took elementary perceptual, executive and musical competence into account, we assessed accuracy detecting melodic deviants and simultaneously recorded pupillary responses and related these to deviant surprise value (information-content) and carrier melody predictability (entropy), calculated using an unsupervised machine learning model of music. Neuroanatomical associations of deviant detection accuracy and coupling of detection to deviant surprise value were assessed using voxel-based morphometry of patients' brain MRI. Whereas Alzheimer's disease was associated with normal deviant detection accuracy, behavioural and semantic variant frontotemporal dementia syndromes were associated with strikingly similar profiles of impaired syntactic and semantic deviant detection accuracy and impaired behavioural and autonomic sensitivity to deviant information-content (all P < 0.05). On the other hand, non-fluent-agrammatic primary progressive aphasia was associated with generalized impairment of deviant discriminability (P < 0.05) due to excessive false-alarms, despite retained behavioural and autonomic sensitivity to deviant information-content and melody predictability. Across the patient cohort, grey matter correlates of acoustic deviant detection accuracy were identified in precuneus, mid and mesial temporal regions; correlates of syntactic deviant detection accuracy and information-content processing, in inferior frontal and anterior temporal cortices, putamen and nucleus accumbens; and a common correlate of musical salience coding in supplementary motor area (all P < 0.05, corrected for multiple comparisons in pre-specified regions of interest). Our findings suggest that major dementias have distinct profiles of sensory 'surprise' processing, as instantiated in music. Music may be a useful and informative paradigm for probing the predictive decoding of complex sensory environments in neurodegenerative proteinopathies, with implications for understanding and measuring the core pathophysiology of these diseases

A LOFAR DETECTION of the LOW-MASS YOUNG STAR T TAU at 149 MHz

© 2017 Published by Elsevier B.V. Radio observations of young stellar objects (YSOs) enable the study of ionized plasma outflows from young protostars via their free-free radiation. Previous studies of the low-mass young system T Tau have used radio observations to model the spectrum and estimate important physical properties of the associated ionized plasma (local electron density, ionized gas content, and emission measure). However, without an indication of the low-frequency turnover in the free-free spectrum, these properties remain difficult to constrain. This paper presents the detection of T Tau at 149 MHz with the Low Frequency Array (LOFAR)-the first time a YSO has been observed at such low frequencies. The recovered total flux indicates that the free-free spectrum may be turning over near 149 MHz. The spectral energy distribution is fitted and yields improved constraints on local electron density ((7.2 ± 2.1) × 103 cm-3), ionized gas mass ( ± × -1.0 1.8 10-6Ṁ), and emission measure ((1.67 ± 0.14) × 105 pc cm-6)

Gaia Data Release 2: processing of the photometric data

CONTEXT. The second Gaia data release is based on 22 months of mission data with an average of 0.9 billion individual CCD observations per day. A data volume of this size and granularity requires a robust and reliable but still flexible system to achieve the demanding accuracy and precision constraints that Gaia is capable of delivering. AIMS. We aim to describe the input data, the treatment of blue photometer/red photometer (BP/RP) low–resolution spectra required to produce the integrated GBP and GRP fluxes, the process used to establish the internal Gaia photometric system, and finally, the generation of the mean source photometry from the calibrated epoch data for Gaia DR2. METHODS. The internal Gaia photometric system was initialised using an iterative process that is solely based on Gaia data. A set of calibrations was derived for the entire Gaia DR2 baseline and then used to produce the final mean source photometry. The photometric catalogue contains 2.5 billion sources comprised of three different grades depending on the availability of colour information and the procedure used to calibrate them: 1.5 billion gold, 144 million silver, and 0.9 billion bronze. These figures reflect the results of the photometric processing; the content of the data release will be different due to the validation and data quality filters applied during the catalogue preparation. The photometric processing pipeline, PhotPipe, implements all the processing and calibration workflows in terms of Map/Reduce jobs based on the Hadoop platform. This is the first example of a processing system for a large astrophysical survey project to make use of these technologies. RESULTS. The improvements in the generation of the integrated G–band fluxes, in the attitude modelling, in the cross–matching, and and in the identification of spurious detections led to a much cleaner input stream for the photometric processing. This, combined with the improvements in the definition of the internal photometric system and calibration flow, produced high-quality photometry. Hadoop proved to be an excellent platform choice for the implementation of PhotPipe in terms of overall performance, scalability, downtime, and manpower required for operations and maintenance