bluuebunny/crossref_metadata_2025 huggingface dataset:
Graphene-based biosensors
Authors: Szunerits Sabine , Boukherroub Rabah
Published: April 2018

Reliable data obtained from analysis of DNA, proteins, bacteria and other disease-related molecules or organisms in biological samples have become a fundamental and crucial part of human health diagnostics and therapy. The development of non-invasive tests that are rapid, sensitive, specific and simple would allow patient discomfort to be prevented, delays in diagnosis to be avoided and the status of a disease to be followed up. Bioanalysis is thus a progressive discipline for which the future holds many exciting opportunities. The use of biosensors for the early diagnosis of diseases has become widely accepted as a point-of-care diagnosis with appropriate specificity in a short time. To allow a reliable diagnosis of a disease at an early stage, highly sensitive biosensors are required as the corresponding biomarkers are generally expressed at very low concentrations. In the past 50 years, various biosensors have been researched and developed encompassing a wide range of applications. This contrasts the limited number of commercially available biosensors. When it comes to sensing of biomarkers with the required picomolar (pM) sensitivity for real-time sensing of biological samples, only a handful of sensing systems have been proposed, and these are often rather complex and costly. Lately, graphene-based materials have been considered as superior over other nanomaterials for the development of sensitive biosensors. The advantages of graphene-based sensor interfaces are numerous, including enhanced surface loading of the desired ligand due to the high surface-to-volume ratio, excellent conductivity and a small band gap that is beneficial for sensitive electrical and electrochemical read-outs, as well as tunable optical properties for optical read-outs such as fluorescence and plasmonics. In this paper, we review the advances made in recent years on graphene-based biosensors in the field of medical diagnosis.
New routes to the functionalization patterning and manufacture of graphene-based materials for biomedical applications
Authors: De Sanctis A. , Russo S. , Craciun M. F. , Alexeev A. , Barnes M. D. , Nagareddy V. K. , Wright C. D.
Published: April 2018

Graphene-based materials are being widely explored for a range of biomedical applications, from targeted drug delivery to biosensing, bioimaging and use for antibacterial treatments, to name but a few. In many such applications, it is not graphene itself that is used as the active agent, but one of its chemically functionalized forms. The type of chemical species used for functionalization will play a key role in determining the utility of any graphene-based device in any particular biomedical application, because this determines to a large part its physical, chemical, electrical and optical interactions. However, other factors will also be important in determining the eventual uptake of graphene-based biomedical technologies, in particular the ease and cost of manufacture of proposed device and system designs. In this work, we describe three novel routes for the chemical functionalization of graphene using oxygen, iron chloride and fluorine. We also introduce novel
in situ
methods for controlling and patterning such functionalization on the micro- and nanoscales. Our approaches are readily transferable to large-scale manufacturing, potentially paving the way for the eventual cost-effective production of functionalized graphene-based materials, devices and systems for a range of important biomedical applications.
Using virtual reality to estimate aesthetic values of coral reefs
Authors: Vercelloni Julie , Clifford Sam , Caley M. Julian , Pearse Alan R. , Brown Ross , James Allan , Christensen Bryce , Bednarz Tomasz , Anthony Ken , González-Rivero Manuel , Mengersen Kerrie , Peterson Erin E.
Published: April 2018

Aesthetic value, or beauty, is important to the relationship between humans and natural environments and is, therefore, a fundamental socio-economic attribute of conservation alongside other ecosystem services. However, beauty is difficult to quantify and is not estimated well using traditional approaches to monitoring coral-reef aesthetics. To improve the estimation of ecosystem aesthetic values, we developed and implemented a novel framework used to quantify features of coral-reef aesthetics based on people's perceptions of beauty. Three observer groups with different experience to reef environments (Marine Scientist, Experienced Diver and Citizen) were virtually immersed in Australian's Great Barrier Reef (GBR) using 360° images. Perceptions of beauty and observations were used to assess the importance of eight potential attributes of reef-aesthetic value. Among these, heterogeneity, defined by structural complexity and colour diversity, was positively associated with coral-reef-aesthetic values. There were no group-level differences in the way the observer groups perceived reef aesthetics suggesting that past experiences with coral reefs do not necessarily influence the perception of beauty by the observer. The framework developed here provides a generic tool to help identify indicators of aesthetic value applicable to a wide variety of natural systems. The ability to estimate aesthetic values robustly adds an important dimension to the holistic conservation of the GBR, coral reefs worldwide and other natural ecosystems.
Interact: Automated analysis of protein-ligand interactions by 1D and 2D NMR
Authors: Millard Pierre , Lippens Guy
Published: April 2018

NMR titration experiments contain rich information on the thermodynamic, kinetic and structural aspects of protein-ligand interactions. Automated tools are required to process the large number of signals typically acquired in these experiments and facilitate quantitative interpretations. We present Interact, a Python script accessible within the Bruker BioSpin TopSpin™ software, which allows automated analysis of both 1D and 2D NMR titration experiments. Interact performs peak picking and annotation of the successive spectra and supports quantitative interpretation of changes in chemical shifts and linewidths induced by the ligand (e.g. to estimate dissociation constants) through different fitting procedures. Interact can be applied to all types of 1D and 2D NMR experiments and all nuclei, hence facilitating routine analysis of existing and forthcoming NMR titration data. Interact was implemented in Python and can be used on Windows, Unix and MacOS platforms. The source code is distributed under OpenSource license at http://github.com/MetaSys-LISBP/Interact.
Cluster Tendency Assessment in Neuronal Spike Data
Authors: Mahallati Sara , Bezdek James C. , Popovic Milos R. , Valiante Taufik A.
Published: April 2018

Sorting spikes from extracellular recording into clusters associated with distinct single units (putative neurons) is a fundamental step in analyzing neuronal populations. Such spike sorting is intrinsically unsupervised, as the number of neurons are not known a priori. Therefor, any spike sorting is an unsupervised learning problem that requires either of the two approaches: specification of a fixed value c for the number of clusters to seek, or generation of candidate partitions for several possible values of c, followed by selection of a best candidate based on various post-clustering validation criteria. In this paper, we investigate the first approach and evaluate the utility of several methods for providing lower dimensional visualization of the cluster structure and on subsequent spike clustering. We also introduce a visualization technique called improved visual assessment of cluster tendency (iVAT) to estimate possible cluster structures in data without the need for dimensionality reduction. Experimental results are conducted on two datasets with ground truth labels. In data with a relatively small number of clusters, iVAT is beneficial in estimating the number of clusters to inform the initialization of clustering algorithms. With larger numbers of clusters, iVAT gives a useful estimate of the coarse cluster structure but sometimes fails to indicate the presumptive number of clusters. We show that noise associated with recording extracellular neuronal potentials can disrupt computational clustering schemes, highlighting the benefit of probabilistic clustering models. Our results show that t-Distributed Stochastic Neighbor Embedding (t-SNE) provides representations of the data that yield more accurate visualization of potential cluster structure to inform the clustering stage. Moreover, The clusters obtained using t-SNE features were more reliable than the clusters obtained using the other methods, which indicates that t-SNE can potentially be used for both visualization and to extract features to be used by any clustering algorithm.
Accurate Nonlinear Mapping between MNI Volumetric and FreeSurfer Surface Coordinate Systems
Authors: Wu Jianxiao , Ngo Gia H. , Greve Douglas , Li Jingwei , He Tong , Fischl Bruce , Eickhoff Simon B. , Yeo B.T. Thomas
Published: April 2018

The results of most neuroimaging studies are reported in volumetric (e.g., MNI152) or surface (e.g., fsaverage) coordinate systems. Accurate mappings between volumetric and surface coordinate systems can facilitate many applications, such as projecting fMRI group analyses from MNI152/Colin27 to fsaverage for visualization, or projecting resting-state fMRI parcellations from fsaverage to MNI152/Colin27 for volumetric analysis of new data. However, there has been surprisingly little research on this topic. Here, we evaluated three approaches for mapping data between MNI152/Colin27 and fsaverage coordinate systems by simulating the above applications: projection of group-average data from MNI152/Colin27 to fsaverage and projection of fsaverage parcellations to MNI152/Colin27. Two of the approaches are currently widely used. A third approach (registration fusion) was previously proposed, but not widely adopted. Two implementations of the registration fusion (RF) approach were considered, with one implementation utilizing the Advanced Normalization Tools (ANTs). We found that RF-ANTs performed the best for mapping between fsaverage and MNI152/Colin27, even for new subjects registered to MNI152/Colin27 using a different software tool (FSL FNIRT). This suggests that RF-ANTs would be useful even for researchers not using ANTs. Finally, it is worth emphasizing that the most optimal approach for mapping data to a coordinate system (e.g., fsaverage) is to register individual subjects directly to the coordinate system, rather than via another coordinate system. Only in scenarios where the optimal approach is not possible (e.g., mapping previously published results from MNI152 to fsaverage), should the approaches evaluated in this manuscript be considered. In these scenarios, we recommend RF-ANTs (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion).
ALS-linked SOD1 Mutants Enhance Outgrowth, Branching, and the Formation of Actin-Based Structures in Adult Motor Neurons
Authors: Osking Zachary , Ayers Jacob I. , Hildebrandt Ryan , Skruber Kristen , Brown Hilda , Ryu Daniel , Eukovich Amanda R. , Golde Todd E. , Borchelt David R. , Read Tracy-Ann , Vitriol Eric A.
Published: April 2018

Amyotrophic lateral sclerosis (ALS) is a progressive, fatal neurodegenerative disease characterized by motor neuron cell death. However, not all motor neurons are equally susceptible. Most of what we know about the surviving motor neurons comes from gene expression profiling, less is known about their functional traits. We found that resistant motor neurons cultured from SOD1 ALS mouse models have enhanced axonal outgrowth and dendritic branching. They also have an increase in the number and size of actin-based structures like growth cones and filopodia. These phenotypes occur in cells cultured from presymptomatic mice and mutant SOD1 models that do not develop ALS, but not in embryonic motor neurons. Enhanced outgrowth and upregulation of filopodia can be induced in wild-type adult cells by expressing mutant SOD1. These results demonstrate that mutant SOD1 can enhance the regenerative capability of ALS resistant motor neurons. Capitalizing on this mechanism could lead to new therapeutic strategies.
Natural ITD statistics predict human auditory spatial perception
Authors: Pavão Rodrigo , Sussman Elyse S. , Fischer Brian J. , Peña José L.
Published: April 2018

A neural code adapted to the statistical structure of sensory cues may optimize perception. We investigated whether interaural time difference (ITD) statistics inherent in natural acoustic scenes are parameters determining spatial discriminability. The natural ITD rate of change across azimuth (ITDrc) and ITD variability over time (ITDv) were combined in a Fisher information statistic for assessing the amount of azimuthal information conveyed by this sensory cue. We hypothesized that natural ITD statistics drive the neural code for ITD and thus influence spatial perception. Human spatial discriminability and spatial novelty detection of sounds with invariant statistics correlated with natural ITD statistics. The lack of natural statistics in the stimuli suggests that this correlation results from natural statistics driving the neural code. Additionally, the density distribution of ITD tuning matching natural statistics is consistent with classic models of ITD coding and can explain the ITD tuning distribution observed in the mammalian brainstem.

Impact statement

Human brain has incorporated natural statistics of spatial cues to the neural code supporting perception of sound location.

Major subject area

Neuroscience;

Research organism

Human;
Modelling the influence of the hippocampal memory system on the oculomotor system
Authors: Ryan Jennifer D. , Shen Kelly , Kacollja Arber , Tian Heather , Griffiths John , Bezgin Gleb , McIntosh Anthony R.
Published: April 2018

Visual exploration is related to activity in the hippocampus (HC) and/or extended medial temporal lobe system (MTL), is influenced by stored memories, and is altered in amnesic cases. An extensive set of polysynaptic connections exists both within and between the HC and oculomotor systems such that investigating how HC responses ultimately influence neural activity in the oculomotor system, and the timing by which such neural modulation could occur is not trivial. We leveraged TheVirtualBrain, a software platform for large-scale network simulations, to model the functional dynamics that govern the interactions between the two systems in the macaque cortex. Evoked responses following the stimulation of the MTL and some, but not all, subfields of the HC resulted in observable responses in oculomotor regions, including the frontal eye fields (FEF), within the time of a gaze fixation. Modeled lesions to some MTL regions slowed the dissipation of HC signal to oculomotor regions, whereas HC lesions generally did not affect the rapid MTL activity propagation to oculomotor regions. These findings provide a framework for investigating how information represented by the HC/MTL may influence the oculomotor system during a fixation and predict how HC lesions may affect visual exploration.

Author Summary

No major account of oculomotor (eye movement) guidance considers the influence of the hippocampus (HC) and broader medial temporal lobe (MTL) system, yet it is clear that information is exchanged between the two systems. Prior experience influences current viewing, and cases of amnesia due to compromised HC/MTL function show specific alterations in viewing behaviour. By modeling large-scale network dynamics, we show that stimulation of subregions of the HC, and of the MTL, rapidly results in observable responses in oculomotor control regions, and that HC/MTL lesions alter signal propagation. These findings suggest that information from memory may readily guide visual exploration, and calls for a reconsideration of the neural circuitry involved in oculomotor guidance.
Targeting Human Retinoblastoma Binding Protein 4 (RBBP4) and 7 (RBBP7)
Authors: Abbey Megha , Trush Viacheslav , Gibson Elisa , Vedadi Masoud
Published: April 2018

RBBP4 and RBBP7 (RBBP4/7) are highly homologous nuclear WD40 motif containing proteins widely implicated in various cancers and are valuable drug targets. They interact with multiple proteins within diverse complexes such as NuRD and PRC2, as well as histone H3 and H4 through two distinct binding sites. FOG-1, PHF6 and histone H3 bind to the top of the donut shape seven-bladed β-propeller fold, while SUZ12, MTA1 and histone H4 bind to a pocket on the side of the WD40 repeats. Here, we briefly review these six interactions and present binding assays optimized for medium to high throughput screening. These assays enable screening of RBBP4/7 toward the discovery of novel cancer therapeutics.
Induction of muscle stem cell quiescence by the secreted niche factor Oncostatin M
Authors: Sampath Srinath C. , Sampath Srihari C. , Ho Andrew T.V. , Corbel Stéphane Y. , Millstone Joshua D. , Lamb John , Walker John , Kinzel Bernd , Schmedt Christian , Blau Helen M.
Published: April 2018

The balance between stem cell quiescence and proliferation in skeletal muscle is tightly controlled, but perturbed in a variety of disease states. Despite progress in identifying activators of stem cell proliferation, the niche factor(s) responsible for quiescence induction remain unclear. Here we report an in vivo imaging-based screen which identifies Oncostatin M (OSM), a member of the interleukin-6 family of cytokines, as a potent inducer of muscle stem cell (MuSC, satellite cell) quiescence. OSM is produced by muscle fibers, induces reversible MuSC cell cycle exit, and maintains stem cell regenerative capacity as judged by serial transplantation. Conditional OSM receptor deletion in satellite cells leads to stem cell depletion and impaired regeneration following injury. These results identify Oncostatin M as a secreted niche factor responsible for quiescence induction, and for the first time establish a direct connection between induction of quiescence, stemness, and transplantation potential in solid organ stem cells.
Identification and biochemical characterization of a novel PP2C-like Ser/Thr phosphatase inE. coli
Authors: Rajagopalan Krithika , Dworkin Jonathan
Published: April 2018

In bacteria, signaling phosphorylation is thought to occur primarily on His and Asp residues. However, phosphoproteomic surveys in phylogenetically diverse bacteria over the past decade have identified numerous proteins that are phosphorylated on Ser and/or Thr residues. Consistently, genes encoding Ser/Thr kinases are present in many bacterial genomes such asE. coli,which encodes at least three Ser/Thr kinases. Since Ser/Thr phosphorylation is a stable modification, a dedicated phosphatase is necessary to allow reversible regulation. Ser/Thr phosphatases belonging to several conserved families are found in bacteria. One family of particular interest are Ser/Thr phosphatases which have extensive sequence and structural homology to eukaryotic Ser/Thr PP2C phosphatases. These proteins, called eSTPs (eukaryotic-like Ser/Thr phosphatases), have been identified in a number of bacteria, but not inE. coli.Here, we describe a previously unknown eSTP encoded by anE. coliORF,yegK,and characterize its biochemical properties including its kinetics, substrate specificity and sensitivity to known phosphatase inhibitors. We investigate differences in the activity of this protein in closely relatedE. colistrains. Finally, we demonstrate that this eSTP acts to dephosphorylate a novel Ser/Thr kinase which is encoded in the same operon.

Importance

Regulatory protein phosphorylation is a conserved mechanism of signaling in all biological systems. Recent phosphoproteomic analyses of phylogenetically diverse bacteria including the model Gram-negative bacteriumE. colidemonstrate that many proteins are phosphorylated on serine or threonine residues. In contrast to phosphorylation on histidine or aspartate residues, phosphorylation of serine and threonine residues is stable and requires the action of a partner Ser/Thr phosphatase to remove the modification. Although a number of Ser/Thr kinases have been reported inE. coli, no partner Ser/Thrphosphatases have been identified. Here, we biochemically characterize a novel Ser/Thr phosphatase that acts to dephosphorylate a Ser/Thr kinase that is encoded in the same operon.
Probing compression versus stretch activated recruitment of cortical actin and apical junction proteins using mechanical stimulations of suspended doublets
Authors: Gao Xumei , Acharya Bipul R. , Otto Engl Wilfried Claude , De Mets Richard , Thiery Jean Paul , Yap Alpha S. , Viasnoff Virgile
Published: April 2018

We report an experimental approach to study the mechanosensitivity of cellcell contact upon mechanical stimulation in suspended cell-doublets. The doublet is placed astride an hourglass aperture, and a hydrodynamic force is selectively exerted on only one of the cells. The geometry of the device concentrates the mechanical shear over the junction area. Together with mechanical shear, the system also allows confocal quantitative live imaging of the recruitment of junction proteins (e.g. E-cadherin, ZO-1, Occludin and actin). We observed the time sequence over which proteins were recruited to the stretched region of the contact. The compressed side of the contact showed no response. We demonstrated how this mechanism polarizes the stress-induced recruitment of junctional components within one single junction. Finally, we demonstrated that stabilizing the actin cortex dynamics abolishes the mechanosensitive response of the junction. Our experimental design provides an original approach to study the role of mechanical force at a cell-cell contact with unprecedented control over stress application and quantitative optical analysis.
TFEA.ChIP: A tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets
Authors: Puente-Santamaria Laura , del Peso Luis
Published: April 2018

The identification of transcription factors (TFs) responsible for the co-regulation of specific sets of genes is a common problem in transcriptomics. Herein we describe TFEA.ChIP, a tool to estimate and visualize TF enrichment in gene lists representing transcriptional profiles. To generate the gene sets representing TF targets, we gathered ChIP-Seq experiments from the ENCODE Consortium and GEO datasets and used the correlation between Dnase Hypersensitive Sites across cell lines to generate a database linking TFs with the genes they interact with in each ChIP-Seq experiment. In its current state, TFEA.ChIP covers 327 different transcription factors from 1075 ChIP-Seq experiments, with over 150 cell types being represented. TFEA.ChIP accepts gene sets as well as sorted lists differentially expressed genes to compute enrichment scores for each of the datasets in its internal database using an Fisher’s exact association test or a Gene Set Enrichment Analysis. We validated TFEA.ChIP using a wide variety of gene sets representing signatures of genetic and chemical perturbations as input and found that the relevant TF was correctly identified in 103 of a total of 144 analyzed datasets with a median area under the curve (AUC) of 0.86. In depth analysis of an RNAseq dataset, illustrates that the use of ChIP-Seq data instead of PWM-based provides key biological context to interpret the results of the analysis. To facilitate its integration into transcriptome analysis pipelines and allow easy expansion and customization of the TF-gene database, we implemented TFEA.ChIP as an R package that can be downloaded from Bioconductor: https://www.bioconductor.org/packages/devel/bioc/html/TFEA.ChIP.html and github: https://github.com/LauraPS1/TFEA-drafts In addition, make it available to a wide range of researches, we have also developed a web application that runs the package from the server side and enables easy exploratory analysis through interactive graphs: https://www.iib.uam.es/TFEA.ChIP/
The rodent lateral orbitofrontal cortex represents expected Pavlovian outcome value but not identity
Authors: Panayi Marios C. , Killcross Simon
Published: April 2018

The orbitofrontal cortex (OFC) is critical for updating reward-directed behaviours flexibly when task contingencies are reversed, or when outcomes are devalued. We systematically examined the generality of these findings using lesions of the rodent lateral OFC (LO) in instrumental action-outcome, and Pavlovian cue-outcome, learning using specific satiety and taste aversion methods of outcome devaluation. LO lesions disrupted outcome devaluation in Pavlovian but not instrumental procedures. Furthermore, this effect was only observed when using taste-aversion devaluation. Using a specific Pavlovian-to-Instrumental transfer procedure, we established that LO is not necessary for the representation of specific outcome properties, but rather in using these properties to access the current motivational value of outcomes. The role of LO in outcome devaluation and reversal learning was also dissociable between anterior and posterior subregions. These novel dissociable task- and subregion-specific effects suggest a way to reconcile contradictory findings between rodent and non-human primate OFC research.
TGF-β induced CXCL13 in CD8+ T cells is associated with tertiary lymphoid structures in cancer
Authors: Workel HH , Lubbers JM , Arnold R , Prins T , van der Vlies P , de Lange K , Bosse T , van Gool I , Eggink FA , Wouters MCA , Komdeur FL , Creutzberg CL , Kol A , Plat A , Glaire M , Church DN , Nijman HW , de Bruyn M
Published: April 2018

Coordinated immune responses against human tumors are frequently characterized by tertiary lymphoid structures (TLS) which predict improved prognosis. The development of TLS is dependent on the chemokine CXCL13, reported to be secreted by dendritic cells and follicular helper T cells only. We report the unexpected finding that CXCL13 is also secreted by activated CD8+ T cells following stimulation by transforming growth factor beta (TGF-β). Using single cell RNA sequencing we found that expression ofCXCL13in CD8+ T cells was restricted to the intraepithelial CD103+ population. Accordingly, CD8+ T cells activated in the presence of TGF-β simultaneously upregulated CD103 and secreted CXCL13.CXCL13expression was strongly correlated with neo-antigen burden and cytolytic gene signatures in bulk tumors. In line with this, TLS were abundant in neo-antigen-high, CD103+ T cell-enriched tumors. TGF-β thus appears to play a role in coordinating immune responses against human tumors through CD8-dependent CXCL13-associated formation of TLS.
Determining protein structures using genetics
Authors: Schmiedel Jörn M. , Lehner Ben
Published: April 2018

Determining the three dimensional structures of macromolecules is a major goal of biological research because of the close relationship between structure and function. Structure determination usually relies on physical techniques including x-ray crystallography, NMR spectroscopy and cryo-electron microscopy. Here we present a method that allows the high-resolution three-dimensional structure of a biological macromolecule to be determined only from measurements of the activity of mutant variants of the molecule. This genetic approach to structure determination relies on the quantification of genetic interactions (epistasis) between mutations and the discrimination of direct from indirect interactions. This provides a new experimental strategy for structure determination, with the potential to reveal functional and in vivo structural conformations at low cost and high throughput.
Genetic studies of accelerometer-based sleep measures in 85,670 individuals yield new insights into human sleep behaviour
Authors: Jones Samuel E. , Hees Vincent T. van , Mazzotti Diego R. , Marques-Vidal Pedro , Sabia Séverine , der Spek Ashley van , Dashti Hassan S. , Engmann Jorgen , Kocevska Desana , Tyrrell Jessica , Beaumont Robin N. , Hillsdon Melvyn , Ruth Katherine S. , Tuke Marcus A. , Yaghootkar Hanieh , Sharp Seth , Jie Yingjie , Harrison Jamie W. , Freathy Rachel M. , Murray Anna , Luik Annemarie I. , Amin Najaf , Lane Jacqueline M. , Saxena Richa , Rutter Martin K. , Tiemeier Henning , Kutalik Zoltan , Kumari Meena , Frayling Timothy M. , Weedon Michael N. , Gehrman Philip , Wood Andrew R.
Published: April 2018

Sleep is an essential human function but its regulation is poorly understood. Identifying genetic variants associated with quality, quantity and timing of sleep will provide biological insights into the regulation of sleep and potential links with disease. Using accelerometer data from 85,670 individuals in the UK Biobank, we performed a genome-wide association study of 8 accelerometer-derived sleep traits, 5 of which are not accessible through self-report alone. We identified 47 genetic associations across the sleep traits (P<5×10-8) and replicated our findings in 5,819 individuals from 3 independent studies. These included 26 novel associations for sleep quality and 10 for nocturnal sleep duration. The majority of newly identified variants were associated with a single sleep trait, except for variants previously associated with restless legs syndrome that were associated with multiple sleep traits. Of the new associated and replicated sleep duration loci, we were able to fine-map a missense variant (p.Tyr727Cys) in PDE11A, a dual-specificity 3’,5’-cyclic nucleotide phosphodiesterase expressed in the hippocampus, as the likely causal variant. As a group, sleep quality loci were enriched for serotonin processing genes and all sleep traits were enriched for cerebellar-expressed genes. These findings provide new biological insights into sleep characteristics.
Dynamic causal modelling of fluctuating connectivity in resting-state EEG
Authors: Van de Steen Frederik , Almgren Hannes , Razi Adeel , Friston Karl , Marinazzo Daniele
Published: April 2018

Functional and effective connectivity are known to change systematically over time. These changes might be explained by several factors, including intrinsic fluctuations in activity-dependent neuronal coupling and contextual factors, like experimental condition and time. Furthermore, contextual effects may be subject-specific or conserved over subjects. To characterize fluctuations in effective connectivity, we used dynamic causal modelling (DCM) of cross spectral responses over 1 min of electroencephalogram (EEG) recordings during rest, divided into 1-sec windows. We focused on two intrinsic networks: the default mode and the saliency network. DCM was applied to estimate connectivity in each time-window for both networks. Fluctuations in DCM connectivity parameters were assessed using hierarchical parametric empirical Bayes (PEB). Within-subject, between-window effects were modelled with a second-level linear model with temporal basis functions as regressors. This procedure was conducted for every subject separately. Bayesian model reduction was then used to assess which (combination of) temporal basis functions best explain dynamic connectivity over windows. A third (between-subject) level model was used to infer which dynamic connectivity parameters are conserved over subjects. Our results indicate that connectivity fluctuations in the saliency network comprised both subject-specific components and a common component. For the default mode network, connectivity trajectories only showed a common component. For both networks, connections to higher order regions appear to monotonically increase during the one minute period. These results not only establish the predictive validity of dynamic connectivity estimates – in virtue of detecting systematic changes over subjects – they also suggest a network-specific dissociation in the relative contribution of fluctuations in connectivity that depend upon experimental context. We envisage these procedures could be useful for characterizing brain state transitions that may be explained by their cognitive or neuropathological underpinnings.
Frequencies of circulating Th1-biased T follicular helper cells in acute HIV-1 infection correlate with the development of HIV-specific antibody responses and lower set point viral load
Authors: Baiyegunhi Omolara , Ndlovu Bongiwe , Ogunshola Funsho , Ismail Nasreen , Walker Bruce D. , Ndung’u Thumbi , Ndhlovu Zaza M.
Published: April 2018

Despite decades of focused research, the field has yet to develop a prophylactic vaccine. In the RV144 vaccine trial, non-neutralizing antibody responses were identified as a correlate for prevention of HIV acquisition. However, factors that predict the development of such antibodies are not fully elucidated. We sought to define the contribution of circulating T follicular helper (cTfh) cell subsets to the development of non-neutralizing antibodies in HIV-1 clade C infection. Study participants were recruited from an acute HIV-1 clade C infection cohort. Plasma anti-gp41, -gp120, -p24 and -p17 antibodies were screened using a customized multivariate Luminex assay. Phenotypic and functional characterization of cTfh were performed using HLA class II tetramers and intracellular cytokine staining. In this study, we found that acute HIV-1 clade C infection skewed differentiation of functional cTfh subsets towards increased Tfh1 (p=0.02) and Tfh2 (p<0.0001) subsets, with a concomitant decrease in overall Tfh1-17 (that shares both Tfh1 and Tfh17 properties) (p=0.01) and Tfh17 subsets (p<0.0001) compared to HIV negative subjects. Interestingly, the frequencies of Tfh1 during acute infection (5.0-8.0 weeks post-infection) correlated negatively with set point viral load (p=0.03, r=-60) and were predictive of p24-specific plasma IgG titers at one year of infection (p=0.003, r=0.85). Taken together, our results suggest that circulating the Tfh1 subset plays an important role in the development of anti-HIV antibody responses and contributes to HIV suppression during acute HIV-1 infection. These results have implications for vaccine studies aimed at inducing long lasting anti-HIV antibody responses.

Importance

The HIV epidemic in southern Africa accounts for almost half of the global HIV burden with HIV-1 clade C being the predominant strain. It is therefore important to define immune correlates of clade C HIV control that might have implications for vaccine design in this region. T follicular helper (Tfh) cells are critical for the development of HIV-specific antibody responses and could play a role in viral control. Here we showed that the early induction of circulating Tfh1 cells during acute infection correlated positively with the magnitude of p24-specific IgG and was associated with lower set point viral load. This study highlights a key Tfh cell subset that could limit HIV replication by enhancing antibody generation. This study underscores the importance of circulating Tfh cells in promoting non-neutralizing antibodies during HIV-1 infection.
Early detection of active Human Cytomegalovirus infection after living-donor liver transplantation
Authors: Rizk Mohamed Anies , Agha Salah Abd Elfatah , Zaki Maysaa El Sayed , El-Mashad Noha Badr El-Deen , El-Saadany Mohamed Mahmoud Fahmy
Published: April 2018

Human cytomegalovirus (HCMV) is a member of the beta herpes virinae. It is one of the most important virus in transplantation. It has direct and indirect impact on liver transplant recipient outcome. We aimed to diagnose early active HCMV infection in living donor liver transplant (LDLT) recipients. Also, to correlate the associated clinical and laboratory findings with HCMV infection. Here, we investigate 76 LDLT recipients for early detection of active HCMV infection in a period of 1-6 months after liver transplantation upon their suggested clinical data. These samples were collected in the period from 4/2013 to 12/ 2015 at Gastroenterology center, Mansoura University. They were 68 males and 8 females. HCMV infection diagnosed by ELISA (Ig M, Ig G) and real time PCR. Seventy-four patients were IgG seropositive recipient. Three patients (3.9%) were positive IgM. Ten samples from 76 patients (13.2%) were positive by real-time polymerase chain reaction (PCR). In this study, we concluded that, LDLT recipients are at high risk of HCMV infection (13.2%) and the most suitable method for HCMV detection was PCR.
Implicit but not explicit exposure to threat conditioned stimulus prevents spontaneous recovery of threat potentiated startle responses in humans
Authors: Oyarzún JP , Càmara E , Kouider S , Fuentemilla L , de Diego-Balaguer R
Published: April 2018

It has long been posited that threat learning operates and forms under an affective and a cognitive learning system that are supported by different brain circuits. A primary drawback in exposure-based therapies is the high rate of relapse when higher order inhibitory structures failed to inhibit the emotional responses driven by the defensive circuit. It has been shown that implicit exposure of fearful stimuli leads to a long-lasting reduction of avoidance behavior in patients with phobia through the facilitation of fear processing areas in the absence of subjective fear. Despite the potential benefits of this approach in the treatment of phobias and PTSD, implicit exposure to fearful stimuli is still under-investigated. Here, we used unconscious presentation of threat-conditioned stimuli in healthy humans, using a continuous flash suppression technique. We found that implicit exposure of a conditioned stimulus reduced, on the following day, defensive responses to the conditioned stimulus measured by threat-potentiated startle responses but not by the electrodermal activity. Our results suggest that implicit exposure using CFS might facilitate the modulation of the affective component of fearful memories, representing an important therapeutic target to further advance exposure-based psychotherapies.
Self-organised segregation of bacterial chromosomal origins
Authors: Hofmann Andreas , Mäkelä Jarno , Sherratt David , Heermann Dieter , M. Murray Seán
Published: April 2018

In spite of much effort, many aspects of chromosome organisation and segregation in bacteria remain unclear. Even for Escherichia coli, the most widely studied bacterial model organism, we still do not know the underlying mechanisms. Like many other bacteria, the chromosomal origin of replication in E. coli is dynamically positioned throughout the cell cycle. Initially maintained at mid-cell, where replication occurs, origins are subsequently partitioned to opposite quarter positions. The Structural Maintenance of Chromosomes (SMC) complex, MukBEF, which is required for correct chromosome compaction and organisation, has been implicated in this behaviour but the mode of action is unknown. Here, we build on a recent self-organising model for the positioning of E. coli MukBEF, to propose an explanation for the positioning and partitioning of origins. We propose that a specific association of MukBEF with the origin region, results in a non-trivial feedback between the self-organising MukBEF gradient and the origins, leading to accurate positioning and partitioning as an emergent property. We compare the model to quantitative experimental data of origin dynamics and their colocalisation with MukBEF clusters and find excellent agreement. Overall, the model suggests that MukBEF and origins act together as a self-organising system for chromosome segregation and introduces protein self-organisation as an important consideration for future studies of chromosome dynamics.
Benchmarking Statistical Multiple Sequence Alignment
Authors: Nute Michael , Saleh Ehsan , Warnow Tandy
Published: April 2018

The estimation of multiple sequence alignments of protein sequences is a basic step in many bioinformatics pipelines, including protein structure prediction, protein family identification, and phylogeny estimation. Statistical co-estimation of alignments and trees under stochastic models of sequence evolution has long been considered the most rigorous technique for estimating alignments and trees, but little is known about the accuracy of such methods on biological benchmarks. We report the results of an extensive study evaluating the most popular protein alignment methods as well as the statistical co-estimation method BAli-Phy on 1192 protein data sets from established benchmarks as well as on 120 simulated data sets. Our study (which used more than 230 CPU years for the BAli-Phy analyses alone) shows that BAli-Phy is dramatically more accurate than the other alignment methods on the simulated data sets, but is among the least accurate on the biological benchmarks. There are several potential causes for this discordance, including model misspecification, errors in the reference alignments, and conflicts between structural alignment and evolutionary alignments; future research is needed to understand the most likely explanation for our observations. multiple sequence alignment, BAli-Phy, protein sequences, structural alignment, homology
TheDrosophilaTNF Eiger activates caspase-dependent necrosis when apoptosis is blocked
Authors: Li Mingli , Fan Yun
Published: April 2018

Eiger (Egr), the homolog of the mammalian tumor-necrosis factor (TNF), is the ligand of the c-Jun N-terminal kinase (JNK) stress response signaling pathway inDrosophila. Although expression of Egr frequently leads to apoptosis, it has also been implicated in activation of non-apoptotic cell death. However, it is not yet clear how Egr can induce both apoptosis and non-apoptotic cell death, and if so, how such processes are coordinated. Here, we show that expression of Egr in the developingDrosophilaeye induces apoptosis and non-apoptotic developmental defects, both of which are JNK-dependent. Intriguingly, when apoptotic effector caspases DrICE and Dcp-1 are defective or inhibited, expression of Egr induces necrosis characterized by loss of cell membrane integrity, translucent cytoplasm and aggregation of cellular organelles. Surprisingly, the induction of necrosis depends on the catalytic activity of the initiator caspase Dronc and the input from JNK signaling independently of their roles in apoptosis. Therefore, similar to the mammalian caspase-8, caspases inDrosophilaalso have dual roles in promoting TNF-mediated apoptosis and inhibiting necrosis.
The Amyloid Precursor-like Protein APL-1 Regulates Axon Regeneration
Authors: Zeng Lewie , El Bejjani Rachid , Hammarlund Marc
Published: April 2018

Members of the Amyloid Precursor Protein (APP) family have important functions during neuronal development. However, their physiological functions in the mature nervous system are not fully understood. Here we use theC. elegansGABAergic motor neurons to study the post-developmental function of the APP-like protein APL-1 in vivo. We find thatapl-1has minimum roles in the maintenance of gross neuron morphology and function. However, we show thatapl-1is an inhibitor of axon regeneration, acting on mature neurons to limit regrowth in response to injury. The small GTPase Rab6/RAB-6.2 also inhibits regeneration, and does so in part by maintaining protein levels of APL-1. To inhibit regeneration, APL-1 functions via the E2 domain of its ectodomain; the cytoplasmic tail, transmembrane anchoring, and the E1 domain are not required for this function. Our data defines a novel role for APL-1 in modulating the neuronal response to injury.
Possibilities for improvement of humoral innate immunity in turkeys and hens in conditions of thermal stress by the immunomodulator Immunobeta
Authors: Bozakova N. , Sotirov L. , Denev S. , Koynarski Ts.
Published: April 2018

The experiments for evaluation of the effect of Immunobeta were performed with turkeys and organically reared layer hens. Turkeys received Immunobeta at a dose of 4 g/kg feed during the beginning of lay (cold period), thermoneutral period and hot summer period. In hens, two dietary levels of Immunobeta were tested: 2 g/kg and 4 g/kg. Blood serum and egg lysozyme levels, alternative pathway of complement activation (APCA) and beta-lysins concentrations were determined. It was found out that Immunobeta had a beneficial effect on serum lysozyme, APCA activity and beta-lysins in turkeys and hens. The lysozyme concentration in egg white was statistically significantly higher in eggs produced by birds treated with both doses of the immunomodulator.
On the relationship between high-order linkage disequilibrium and epistasis
Authors: Zan Yanjun , Forsberg Simon K. G. , Carlborg Örjan
Published: April 2018

A plausible explanation for statistical epistasis revealed in genome wide association analyses is the presence of high order linkage disequilibrium (LD) between the genotyped markers tested for interactions and unobserved functional polymorphisms. Based on findings in experimental data, it has been suggested that high order LD might be a common explanation for statistical epistasis inferred between local polymorphisms in the same genomic region. Here, we empirically evaluate how prevalent high order LD is between local, as well as distal, polymorphisms in the genome. This could provide insights into whether we should account for this when interpreting results from genome wide scans for statistical epistasis. An extensive and strong genome wide high order LD was revealed between pairs of markers on the high density 250k SNP-chip and individual markers revealed by whole genome sequencing in the A. thaliana 1001-genomes collection. The high order LD was found to be more prevalent in smaller populations, but present also in samples including several hundred individuals. An empirical example illustrates that high order LD might be an even greater challenge in cases when the genetic architecture is more complex than the common assumption of bi-allelic loci. The example shows how significant statistical epistasis is detected for a pair of markers in high order LD with a complex multi allelic locus. Overall, our study illustrates the importance of considering also other explanations than functional genetic interactions when genome wide statistical epistasis is detected, in particular when the results are obtained in small populations of inbred individuals.
Live-cell imaging of marked chromosome regions reveals dynamics of mitotic chromosome resolution and compaction
Authors: Eykelenboom John K. , Gierliński Marek , Yue Zuojun , Hegarat Nadia , Pollard Hilary , Fukagawa Tatsuo , Hochegger Helfrid , Tanaka Tomoyuki U.
Published: April 2018

When human cells enter mitosis, chromosomes undergo substantial changes in their organisation to resolve sister chromatids and compact chromosomes. Despite the fundamental importance of this phenomenon to genome stability, we still do not fully comprehend the timing and coordination of these events. To address these questions, we need to evaluate the progression of both sister chromatid resolution and chromosome compaction in one assay. We achieved this by analysing changes in configuration of marked chromosome regions over time, with high spatial and temporal resolution. This assay showed that sister chromatid resolution is an iterative process that begins in late G2 phase and completes in prophase. Cohesins and WAPL antagonistically regulate sister chromatid resolution in late G2 and prophase whilst local enrichment of cohesin on chromosomes prevents precocious sister chromatid resolution. Moreover, our assay allowed quantitative evaluation of the timing and efficiency of condensin II and I activities in promoting sister chromatid resolution and chromosome compaction, respectively. Thus, our real-time assay sheds new light on the dynamics of mitotic chromosome resolution and compaction.