bluuebunny/crossref_metadata_2025 huggingface dataset:
Human Genes Escaping X-inactivation Revealed by Single Cell Expression Data
Authors: Katsir Kerem Wainer , Linial Michal
Published: December 2018

Background

In mammals, sex chromosomes pose an inherent imbalance of gene expression between sexes. In each female somatic cell, random inactivation of one of the X-chromosomes restores this balance. While most genes from the inactivated X-chromosome are silenced, 15-25% are known to escape X-inactivation (termed escapees). The expression levels of these genes are attributed to sex-dependent phenotypic variability.

Results

We used single-cell RNA-Seq to detect escapees in somatic cells. As only one X-chromosome is inactivated in each cell, the origin of expression from the active or inactive chromosome can be determined from the variation of sequenced RNAs. We analyzed primary, healthy fibroblasts (n=104), and clonal lymphoblasts with sequenced parental genomes (n=25) by measuring the degree of allelic-specific expression (ASE) from heterozygous sites. We identified 24 and 49 candidate escapees, at varying degree of confidence, from the fibroblast and lymphoblast transcriptomes, respectively. We critically test the validity of escapee annotations by comparing our findings with a large collection of independent studies. We find that most genes (66%) from the unified set were previously reported as escapees. Furthermore, out of the overlooked escapees, 11 are long noncoding RNA (lncRNAs).

Conclusions

X-chromosome inactivation and escaping from it are robust, permanent phenomena that are best studies at a single-cell resolution. The cumulative information from individual cells increases the potential of identifying escapees. Moreover, despite the use of a limited number of cells, clonal cells (i.e., same X-chromosomes are coordinately inhibited) with genomic phasing are valuable for detecting escapees at high confidence. Generalizing the method to uncharacterized genomic loci resulted in lncRNAs escapees which account for 20% of the listed candidates. By confirming genes as escapees and propose others as candidates from two different cell types, we contribute to the cumulative knowledge and reliability of human escapees.
Spectral memory: Illumination-evoked plasticity
Authors: Adeyefa-Olasupo Ifedayo-Emmanuel
Published: December 2018

Here human trichromats were presented with two types of scenes – geometric and real-world scenes –tinted with a shade of colour in order to destabilize the perceived illumination, and chromaticity of the retinal image of each scene. Each trichromat was instructed to adjust the chromaticity of the object embedded within each scene until its surface appeared devoid of any hue in the DKL colour space which spans two chromatic opponent axes – the S–(L+M) and L– M axis – and a luminance axis – the L+M axis. The following observations were made : (i) across scenes, adjustments were dispersed along the S–(L+M) axis, along which daylight is known to vary; (ii) across trichromats, for the geometric scenes, adjustments were biased towards the S pole of the S–(L+M) axis for one group (group 1), and towards the (L+M) pole for the other group (group 2); (iii) for the real-world scenes, adjustments for both groups systematically converged towards the (L+M) pole. These results suggest that when the core set of priors upon which the human visual system typically relies become ill-equipped, the human visual system is able to recruit one of the two illumination priors – PriorS or PriorL+M – in combination with the representation it has formed over time about the spectral composition of the illuminant associated with scenes the trichromatic observer is currently being exposed to within its ecological niche, as it attempts to stabilize the chromaticity of the retinal image of real-world scenes.
Gamblers: an Antibiotic-induced Evolvable Cell Subpopulation Differentiated by Reactive-oxygen-induced General Stress Response
Authors: Pribis John P , García-Villada Libertad , Zhai Yin , Lewin-Epstein Ohad , Wang Anthony , Liu Jingjing , Xia Jun , Mei Qian , Fitzgerald Devon M. , Bos Julia , Austin Robert , Herman Christophe , Bates David , Hadany Lilach , Hastings P.J. , Rosenberg Susan M
Published: December 2018

Antibiotics can induce mutations that cause antibiotic resistance. Yet, despite their importance, mechanisms of antibiotic-promoted mutagenesis remain elusive. We report that the fluoroquinolone antibiotic ciprofloxacin (cipro) induces mutations that cause drug resistance by triggering differentiation of a mutant-generating cell subpopulation, using reactive oxygen species (ROS) to signal the sigma-S (σS) general-stress response. Cipro-generated DNA breaks activate the SOS DNA-damage response and error-prone DNA polymerases in all cells. However, mutagenesis is restricted to a cell subpopulation in which electron transfer and SOS induce ROS, which activate the σSresponse, allowing mutagenesis during DNA-break repair. When sorted, this small σS-response-“on” subpopulation produces most antibiotic cross-resistant mutants. An FDA-approved drug prevents σSinduction specifically inhibiting antibiotic-promoted mutagenesis. Furthermore, SOS-inhibited cell division, causing multi-chromosome cells, is required for mutagenesis. The data support a model in which within-cell chromosome cooperation together with development of a “gambler” cell subpopulation promote resistance evolution without risking most cells.
Focal adhesion-generated cues in extracellular matrix regulate cell migration by local induction of clathrin-coated plaques
Authors: Bucher Delia , Mukenhirn Markus , Sochacki Kem A. , Saharuka Veronika , Huck Christian , Zambarda Chiara , Taraska Justin W. , Cavalcanti-Adam Elisabetta Ada , Boulant Steeve
Published: December 2018

Clathrin is a unique scaffold protein, which forms polyhedral lattices with flat and curved morphology. The function of curved clathrin-coated pits in forming endocytic structures is well studied. On the contrary, the role of large flat clathrin arrays, called clathrin-coated plaques, remains ambiguous. Previous studies suggested an involvement of plaques in cell adhesion. However, the molecular origin leading to their formation and their precise functions remain to be determined. Here, we study the origin and function of clathrin-coated plaques during cell migration. We revealed that plaque formation is intimately linked to extracellular matrix (ECM) modification by focal adhesions (FAs). We show that in migrating cells, FAs digest the ECM creating extracellular topographical cues that dictate the future location of clathrin-coated plaques. We identify Eps15 and Eps15R as key regulators for the formation of clathrin-coated plaques at locally remodelled ECM sites. Using a genetic silencing approach to abrogate plaque formation and 3D-micropatterns to spatially control the location of clathrin-coated plaques, we could directly correlate cell migration directionality with the formation of clathrin-coated plaques and their ability to recognize extracellular topographical cues. We here define the molecular mechanism regulating the functional interplay between FAs and plaques and propose that clathrin-coated plaques act as regulators of cell migration promoting contact guidance-mediated collective migration in a cell-to-cell contact independent manner.
A genome-wide haploid genetic screen for essential factors in vaccinia virus infection identifies TMED10 as regulator of macropinocytosis
Authors: Luteijn Rutger David , van Diemen Ferdy R , Blomen Vincent A , Boer Ingrid GJ , Manikam Sadasivam Saravanan , van Kuppevelt Toin , Drexler Ingo , Brummelkamp Thijn R , Lebbink Robert Jan , Wiertz Emmanuel JHJ
Published: December 2018

Vaccinia virus is a promising viral vaccine and gene delivery candidate, and has historically been used as a model to study poxvirus-host cell interactions. We employed a genome-wide insertional mutagenesis approach in human haploid cells to identify host factors crucial for vaccinia virus infection. A library of mutagenized HAP1 cells was exposed to Modified Vaccinia Virus Ankara (MVA). Deep-sequencing analysis of virus-resistant cells identified host factors involved in heparan sulfate synthesis, Golgi organization, and vesicular protein trafficking. We validated EXT1, TM9SF2 and TMED10 TMP21/p23/p24δ) as important host factors for vaccinia virus infection. The critical role of EXT1 in heparan sulfate synthesis and vaccinia virus infection was confirmed. TM9SF2 was validated as a player mediating heparan sulfate expression, explaining its contribution to vaccinia virus infection. In addition, TMED10 was found to be crucial for virus-induced plasma membrane blebbing and phosphatidylserine-induced macropinocytosis, suggesting that TMED10 regulates actin cytoskeleton remodelling necessary for virus infection.
The telomeric Cdc13-Stn1-Ten1 complex regulates RNA polymerase II transcription
Authors: Calvo Olga , Grandin Nathalie , Jordán-Pla Antonio , Miñambres Esperanza , González-Polo Noelia , Pérez-Ortín José E. , Charbonneau Michel
Published: December 2018

Specialized telomeric proteins have an essential role in maintaining genome stability through chromosome end protection and telomere length regulation. In the yeastSaccharomyces cerevisiae, the evolutionary conserved CST complex, composed of the Cdc13, Stn1 and Ten1 proteins, largely contributes to these functions. Here, we report the existence of genetic interactions betweenTEN1and several genes coding for transcription regulators. Molecular assays confirmed this novel function of Ten1 and further established that it regulates the occupancies of RNA polymerase II and the Spt5 elongation factor within transcribed genes. Since Ten1, but also Cdc13 and Stn1, were found to physically associate with Spt5, we propose that Spt5 represents the target of CST in transcription regulation. Moreover, CST physically associates with Hmo1, previously shown to mediate the architecture of S phase-transcribed genes. The fact that, genome-wide, the promoters of genes down-regulated in theten1-31mutant are prefentially bound by Hmo1, leads us to propose a potential role for CST in synchronizing transcription with replication fork progression following head-on collisions.
Integrative haplotype estimation with sub-linear complexity
Authors: Delaneau Olivier , Zagury Jean-Francois , Robinson Matthew R , Marchini Jonathan , Dermitzakis Emmanouil
Published: December 2018

The number of human genomes being genotyped or sequenced increases exponentially and efficient haplotype estimation methods able to handle this amount of data are now required. Here, we present a new method, SHAPEIT4, which substantially improves upon other methods to process large genotype and high coverage sequencing datasets. It notably exhibits sub-linear scaling with sample size, provides highly accurate haplotypes and allows integrating external phasing information such as large reference panels of haplotypes, collections of pre-phased variants and long sequencing reads. We provide SHAPET4 in an open source format on https://odelaneau.github.io/shapeit4/ and demonstrate its performance in terms of accuracy and running times on two gold standard datasets: the UK Biobank data and the Genome In A Bottle.
Murine astrotactins 1 and 2 have similar membrane topology and mature via endoproteolytic cleavage catalyzed by signal peptidase
Authors: Lara Patricia , Tellgren-Roth Åsa , Behesti Hourinaz , Horn Zachi , Schiller Nina , Enquist Karl , Cammenberg Malin , Liljenström Amanda , Hatten Mary E , Von Heijne Gunnar , Nilsson IngMarie
Published: December 2018

Astrotactins 1 (Astn1) and Astn2 are membrane proteins that function in glial-guided migration, receptor trafficking and synaptic plasticity in the brain, as well as in planar polarity pathways in skin. Here, we used glycosylation mapping and protease-protection approaches to map the topologies of mouse Astn1 and Astn2 in rough microsomal membranes (RMs), and found that Astn2 has a cleaved N-terminal signal peptide (SP), an N-terminal domain located in the lumen of the RMs (topologically equivalent to the extracellular surface in cells), two transmembrane helices (TMHs), and a large C-terminal lumenal domain. We also found that Astn1 has the same topology as Astn2, but we did not observe any evidence of SP cleavage in Astn1. Both Astn1 and Astn2 mature through endoproteolytic cleavage in the second TMH; importantly, we identified the endoprotease responsible for the maturation of Astn1 and Astn2 as the endoplasmic reticulum signal peptidase. Differences in the degree of Astn1 and Astn2 maturation possibly contribute to the higher levels of the C-terminal domain of Astn1 detected on neuronal membranes of the central nervous system. These differences may also explain the distinct cellular functions of Astn1 and Astn2, such as in membrane adhesion, receptor trafficking, and planar polarity signaling.
Resistance to diet induced obesity in the apolipoprotein E deficient mouse is associated with an attenuated transcriptional response in visceral fat
Authors: Fitzgibbons Timothy P. , Kelly Mark , Kim Jason K. , Czech Michael P.
Published: December 2018

The apolipoprotein E knockout (EKO) mouse is a well-established model of atherosclerosis. Macrophages in the arterial intima of EKO mice serve a protective role, scavenging oxidatively modified LDL in order to protect cells from toxic free cholesterol. Recent studies have highlighted a similar role for macrophage foam cells in restraining the increased rates of lipolysis in adipose tissue of obese and fasting mice. Interestingly, EKO adipocytes have been shown to have increased rates of lipolysisin vitro. Therefore, the aim of this study was to examine how apoE deficiency might alter the transcriptional response of visceral adipose tissue (VAT) to high fat diet (HFD). EKO mice fed HFD for 24 weeks gained less fat mass and were more insulin sensitive than their wild type (WT) littermates. Metabolic cages showed that HFD EKO mice had increased post-prandial oxygen consumption and increased serum β-hydroxybutyrate. DNA microarrays revealed that EKO VAT was comparatively insensitive to HFD in terms of alterations in gene expression, with only 0.1% of probe sets differentially expressed. In contrast, the VAT of WT mice had a 30 fold more extensive alteration in gene expression (3% of probes sets), characterized predominantly by increased expression of immune cell specific genes. In addition, analysis ofa prioridetermined gene sets revealed broad down-regulation of PPARγ target and fatty acid catabolism genes in WT VAT, and increased expression of lipid storage and cholesterol synthesis genes. In comparison, expression of PPARγ target genes was not down-regulated in EKO VAT and expression of fatty acid oxidation genes was increased. In summary, we report three novel findings with regards to metabolism in the EKO mouse: 1) increased post-prandial oxygen consumption, 2) increased serum β hydroxybutyrate concentrations and 3) a dramatically less robust transcriptional response to HFD in EKO VAT. These findings suggest that limiting adipocyte exposure to dietary fatty acids may be an attractive therapy for diet induced obesity, provided that compensatory mechanisms that prevent hyperlipidemia can be activated.
Phylogenetic measures of indel rate variation among the HIV-1 group M subtypes
Authors: Palmer John , Poon Art
Published: December 2018

The transmission and pathogenesis of human immunodeficiency virus type 1 (HIV-1) is disproportionately influenced by evolution in the five variable regions of the virus surface envelope glycoprotein (gp120). Insertions and deletions (indels) are a significant source of evolutionary change in these regions. However, the influx of indels relative to nucleotide substitutions has not yet been quantified through a comparative analysis of HIV-1 sequence data. Here we develop and report results from a phylogenetic method to estimate indel rates for the gp120 variable regions across five major subtypes and two circulating recombinant forms (CRFs) of HIV-1 group M. We processed over 26,000 published HIV-1 gp120 sequences, from which we extracted 6,605 sequences for phylogenetic analysis. In brief, our method employs maximum likelihood to reconstruct phylogenies scaled in time and fits a Poisson model to the observed distribution of indels between closely related pairs of sequences in the tree (cherries). The rate estimates ranged from 3.0e-5 to 1.5e-3 indels/nt/year and varied significantly among variable regions and subtypes. Indel rates were significantly lower in the region encoding variable loop V3, and also lower for HIV-1 subtype B relative to other subtypes. We also found that variable loops V1, V2 and V4 tended to accumulate significantly longer indels. Further, we observed that the nucleotide composition of indel sequences was significantly distinct from that of the flanking sequence in HIV-1 gp120. Indels affected potential N-linked glycosylation sites substantially more often in V1 and V2 than expected by chance, which is consistent with positive selection on glycosylation patterns within these regions of gp120. These results represent the first comprehensive measures of indel rates in HIV-1 gp120 across multiple subtypes and CRFs, and identifies novel and unexpected patterns for further research in the molecular evolution of HIV-1.
cis-Regulatory Chromatin Contacts in Neural Cells Reveal Contributions of Genetic Variants to Complex Neurological Disorders
Authors: Song Michael , Yang Xiaoyu , Ren Xingjie , Maliskova Lenka , Li Bingkun , Jones Ian , Wang Chao , Jacob Fadi , Wu Kenneth , Traglia Michela , Tam Tsz Wai , Jamieson Kirsty , Lu Si-Yao , Ming Guo-Li , Yao Jun , Weiss Lauren A. , Dixon Jesse , Judge Luke M. , Conklin Bruce R , Song Hongjun , Gan Li , Shen Yin
Published: December 2018

Mutations in gene regulatory elements have been associated with a wide range of complex neurological disorders. However, due to their inherent cell type-specificity and difficulties in characterizing their regulatory targets, our ability to identify causal genetic variants has remained limited. To address these constraints, we perform integrative analysis of chromatin interactions using promoter capture Hi-C (pcHi-C), open chromatin regions using ATAC-seq, and transcriptomes using RNA-seq in four functionally distinct neural cell types: iPSC-induced excitatory neurons and lower motor neurons, iPSC-derived hippocampal dentate gyrus (DG)-like neurons, and primary astrocytes. We identify hundreds of thousands of long-rangecisinteractions between promoters and distal promoter-interacting regions (PIRs), enabling us to link regulatory elements to their target genes and reveal putative pathways that are dysregulated in disease. We validate several novel PIRs using CRISPR techniques in human excitatory neurons, demonstrating thatCDK5RAP3, STRAP, andDRD2are transcriptionally regulated by physically linked enhancers. Finally, we show that physical chromatin interactions mediate genetic interactions in autism spectrum disorder (ASD). Our study illustrates how characterizing the 3D epigenome elucidates novel regulatory relationships in the central nervous system (CNS), shedding light on previously unknown functions for noncoding variants in complex neurological disorders.
SeQuiLa-cov: A fast and scalable library for depth of coverage calculations
Authors: Wiewiorka Marek , Szmurlo Agnieszka , Kusmirek Wiktor , Gambin Tomasz
Published: December 2018

Background: Depth of coverage calculation is an important and computationally intensive preprocessing step in a variety of next generation sequencing pipelines, including the analyses of RNA-seq data, detection of copy number variants, or quality control procedures.
Results: Building upon big data technologies, we have developed SeQuiLa-cov, an extension to the recently released SeQuiLa platform, which provides efficient depth of coverage calculations, reaching more than 100x speedup over the state-of-the-art tools. Performance and scalability of our solution allows for exome and genome-wide calculations running locally or on a cluster while hiding the complexity of the distributed computing with Structured Query Language Application Programming Interface.
Conclusions: SeQuiLa-cov provides significant performance gain in depth of coverage calculations streamlining the widely used bioinformatic processing pipelines.
Estrogen promotes pro-resolving microglial behaviour and phagocytic cell clearance through the actions of annexin A1
Authors: Loiola Rodrigo Azevedo , Wickstead Edward S. , Solito Egle , McArthur Simon
Published: December 2018

Local production of estrogen rapidly follows brain tissue injury, but the role this hormone plays in regulating the response to neural damage or in the modulation of mediators regulating inflammation is in many ways unclear. Using the murine BV2 microglia model as well as primary microglia from wild-type and annexin A1 (AnxA1) null mice, we have identified two related mechanisms whereby estradiol can modulate microglial behaviour in a receptor specific fashion. Firstly, estradiol, via estrogen receptor β (ERβ), enhanced the phagocytic clearance of apoptotic cells, acting through increased production and release of the protein AnxA1. Secondly, stimulation of either ERβ or the G protein coupled estrogen receptor GPER promoted the adoption of an anti-inflammatory/proresolving phenotype, an action similarly mediated through AnxA1. Together, these data suggest the hypothesis that locally produced estrogen acts through AnxA1 to exert powerful pro-resolving actions, controlling and limiting brain inflammation and ultimately protecting this highly vulnerable organ. Given the high degree of receptor selectivity in evoking these responses, we suggest that the use of selective estrogen receptor ligands may hold therapeutic promise in the treatment of neuroinflammation, avoiding unwanted generalised effects.
Mapping the bacterial ecology on the phyllosphere of grass hay and the potential hazards of soaking fodder for horse gut health
Authors: Moore-Colyer Meriel , Longland Annette , Harris Pat , Crosthwaite Susan
Published: December 2018

Globally hay is the preferred forage for stabled horses. Variable nutritional and hygienic quality stimulates pre-feeding soaking to reduce dust and nutrients to reduce respiratory and metabolic disorders in horses. However, this practice has potential negative impacts on horse health. The objectives of this study were to map the bacterial profile of different hays and determine how soaking alters this with the aim of recommending best practice when feeding fodder to stabled horses. Two meadow and one Perennial Ryegrass hays were soaked for 0, 1.5, 9 or 16 hours. Post treatment, hays were analysed for water-soluble carbohydrate (WSC) and total aerobic bacteria (TVC), with differences determined using ANOVA and least significant difference. Bacteria were identified via genomic DNA extraction (V3 and V4 variable region of the 16S rRNA gene) and 16S library preparation according to the Illumina protocol. Differences in phyla and family operational taxonomic units within hay types were identified via paired t-tests on the DESeq2 normalised data and false discovery rates accounted for using Padj (P<0.05). Mean WSC losses g/kg DM (+/- SE) increased with soaking time being 30 (10.7), 72 (43.7), 80 (38.8) for 1.5, 9 and 16 hours soak respectively. No relationship existed between WSC leaching and bacteria content or profile. Grass type influenced bacterial profiles. Soaking altered the epiphytic bacterial profile across all hays and 9 hours soaking increased richness and Shannon diversity indices. Clustering of bacteria was seen between meadow hays which differed from perennial rye grass and this difference increased post soaking. The normal industry practice of soaking hay for 9 hours pre-feeding cannot be recommended as it increases total bacteria content with noted increases of some potential pathogens. The alterations in bacteria profile and hygienic quality may explain why changing fodder or pre-feeding treatments can frequently precipitate colic in horses.
Differential trafficking of albumin and IgG facilitated by the neonatal Fc receptor in podocytes in vitro and in vivo.
Authors: Dylewski James , Dobrinskikh Evgenia , Lewis Linda , Tonsawan Pantipa , Jat Parmjit , Blaine Judith
Published: December 2018

Proteinuria is strongly associated with kidney disease progression but the mechanisms underlying podocyte handling of serum proteins such as albumin and IgG remain to be elucidated. We have previously shown that albumin and IgG are transcytosed by podocytes in vitro. In other epithelial cells, the neonatal Fc receptor (FcRn) is required to salvage albumin and IgG from the degradative pathway thereby allowing these proteins to be transcytosed or recycled. Here we directly examine the role of FcRn in albumin and IgG trafficking in podocytes by studying handling of these proteins in FcRn knockout (KO) podocytes in vitro and in a podocyte-specific FcRn knockout mice in vivo. In vitro, we find that knockout of FcRn leads to IgG accumulation in podocytes but does not alter albumin trafficking. Similarly, in vivo, podocyte-specific knockout of FcRn does not result in albumin accumulation in podocytes in vivo as measured by mean albumin fluorescence intensity whereas these mice demonstrate significant intraglomerular accumulation of IgG over time. In addition we find that podocyte-specific FcRn KO mice demonstrate mesangial expansion as they age and activation of mesangial cells as demonstrated by increased expression of ?-smooth muscle actin. Taken together, these results suggest that trafficking pathways for albumin and IgG differ in podocytes and that sustained disruption of trafficking of plasma proteins alters glomerular structure.
Monocyte Infection Dynamics Shape HIV-1 Phyloanatomy in the Peripheral Blood
Authors: Rife Magalis Brittany , Strickland Samantha L. , Shank Stephen D , Autissier Patrick , Schuetz Alexandra , Sithinamsuwam Pasiri , Lerdlum Sukalaya , Fletcher James L.K. , de Souza Mark , Ananworanich Jintanat , Valcour Victor , Williams Kenneth C , Kosakovsky Pond Sergei L , Ratto Kim Silvia , Salemi Marco ,   SEARCH007
Published: December 2018

Human immunodeficiency virus (HIV) RNA and DNA have been isolated from patient monocytes, an immune cell population that is quite different in several aspects from the canonical T-cell viral target. Because monocytes are migratory and resilient to both natural and synthetic antiviral defenses, knowledge of the contribution of monocyte infection to ongoing viral evolution and spread \textit{in vivo} is of significant interest for drug development and treatment strategies. Using single viral genome sequencing from different peripheral blood compartments and phyloanatomic statistical inference, we demonstrate that productively infected monocytes follow an evolutionary trajectory that is distinct from peripheral T cells during multiple stages of disease progression. Gene flow and selection analysis reveal plasticity in the source of monocyte infection and in the region of the HIV envelope glycoprotein that experiences selection pressure across individuals. The findings, thus, point to a potential reservoir showing a range of infection and transmission dynamics, for which the current universal, T cell-targeted treatment strategies would be inadequate.
Mucosal CD8+ T cell responses induced by an MCMV based vaccine vector confer protection against influenza challenge
Authors: Zheng Xiaoyan , Oduro Jennifer Dora , Boehme Julia Désirée , Borkner Lisa , Ebensen Thomas , Heise Ulrike , Gereke Marcus , Pils Marina , Krmpotic Astrid , Guzmán Carlos , Bruder Dunja , Čičin-Šain Luka
Published: December 2018

Cytomegalovirus (CMV) is a ubiquitous β-herpesvirus that establishes life-long latent infection in a high percentage of the population worldwide. CMV induces the strongest and most durable CD8+ T cell response known in human clinical medicine. Due to its unique properties, the virus represents a promising candidate vaccine vector for the induction of persistent cellular immunity. To take advantage of this, we constructed a recombinant murine CMV (MCMV) expressing an MHC-I restricted epitope from influenza A virus (IAV) H1N1 within the immediate early 2 (ie2) gene. Only mice that were immunized intranasally (i.n.) were capable of controlling IAV infection, despite the greater potency of the intraperitoneally (i.p.) vaccination in inducing a systemic IAV-specific CD8+ T cell response. The protective capacity of the i.n. immunization was associated with its ability to induce IAV-specific tissue-resident memory CD8+ T (CD8TRM) cells in the lungs. Our data demonstrate that the protective effect exerted by the i.n. immunization was critically mediated by antigen-specific CD8+ T cells. CD8TRM cells promoted the induction of IFNγ and chemokines that facilitate the recruitment of antigen-specific CD8+ T cells to the lungs. Overall, our results showed that locally applied MCMV vectors could induce mucosal immunity at sites of entry, providing superior immune protection against respiratory infections.
Snf2 controls pulcherriminic acid biosynthesis and connects pigmentation and antifungal activity of the yeastMetschnikowia pulcherrima
Authors: Gore-Lloyd Deborah , Sumann Inés , Brachmann Alexander O. , Schneeberger Kerstin , Ortiz-Merino Raúl A. , Moreno-Beltrán Mauro , Schläfli Michael , Kirner Pascal , Kron Amanda Santos , Wolfe Kenneth H. , Piel Jörn , Ahrens Christian H. , Henk Daniel , Freimoser Florian M.
Published: December 2018

Metschnikowia pulcherrimasynthesizes the red pigment pulcherrimin, from cyclodileucine (cyclo(Leu-Leu)) as a precursor, and exhibits strong antifungal activity against notorious plant pathogenic fungi such asBotrytisandGibberella(i.e.,Fusarium). This yeast therefore has great potential for biocontrol applications against fungal diseases; particularly in the phyllosphere where this species is frequently found. To elucidate the molecular basis of the antifungal activity ofM. pulcherrima, we compared a wildtype strain with a spontaneously occurring, pigmentless, weakly antagonistic mutant derivative. Whole genome sequencing of the wildtype and mutant strains identified a point mutation that creates a premature stop codon in the transcriptional regulatorSNF2in the mutant strain. Complementation of thesnf2mutant strain with the wildtypeSNF2gene restored pigmentation and recovered the strong antifungal activity ofM. pulcherrimaagainst plant pathogensin vitroand on cherries. Ultra-performance liquid chromatography-high resolution heated electrospray ionization mass spectrometry (UPLC HR HESI-MS) proved the presence and structure of the pulcherrimin precursors cyclo(Leu-Leu) and pulcherriminic acid and also identified new compounds that likely represented an additional precursor and degradation products of pulcherriminic acid and/or pulcherrimin. All of these compounds were identified in the wildtype and complemented strain, but were undetectable in the pigmentlesssnf2mutant strain. These results thus identifySNF2as a regulator of antifungal activity and pulcherriminic acid biosynthesis inM. pulcherrimaand provide a starting point for deciphering the molecular functions underlying the antagonistic activity of this yeast.

Significance statement

Metschnikowia pulcherrimais a strongly antifungal yeast and a most promising species for the control of notorious plant diseases. This multidisciplinary study on theM. pulcherrimamode of action compared a wildtype isolate with a pigmentless mutant exhibiting reduced antifungal activity. The transcriptional regulator Snf2 was identified as a “biocontrol regulator” controlling antifungal activity ofM. pulcherrimaviaPULgene transcription, cyclodipeptide synthesis and additional, yet uncharacterized mechanisms. The identification of cyclo(Leu-Leu), pulcherriminic acid, as well as novel precursor and degradation products of pulcherrimin, opens up new avenues for research on the metabolism and functions of pulcherrimin. Overall, this works establishesM. pulcherrimaas a genetically tractable model and will benefit the development of biocontrol solutions for important plant diseases.
Neural dynamics of accumulating and updating linguistic knowledge structures
Authors: Berkers Ruud M.W.J. , van der Linden Marieke , Neville David A. , van Kesteren Marlieke T.R. , Morris Richard G.M. , Murre Jaap M.J. , Fernandez Guillen
Published: December 2018

Knowledge is acquired by generalization and integration across learning experiences, which can then be applied to future instances. This study provides novel insights into how linguistic associative knowledge is acquired by systematically tracking schematic knowledge formation while participants were learning an abstract artificial language organized by higher-order associative regularity. During learning, we found activity in the left inferior frontal gyrus in response to knowledge updating during feedback presentation, as well as in response to available accumulated knowledge during retrieval. A complementary signal was found in the caudate nucleus, where activity correlated with the availability of recently acquired knowledge during retrieval, suggesting it initially supports the retrieval of knowledge. Furthermore, we find that activity in a set of regions, including the medial prefrontal cortex and hippocampus, scaled with accumulated knowledge during feedback presentation, which might be indicative of increased generalization of features of the hierarchical knowledge structure. Together, these results provide a mechanistic insight into how linguistic associative knowledge is acquired by generalization across repeated learning experiences.
Disease and introgression explain the long-lasting contact zone of Modern Humans and Neanderthals and its eventual destabilization
Authors: Greenbaum Gili , Getz Wayne M. , Rosenberg Noah A. , Feldman Marcus W. , Hovers Erella , Kolodny Oren
Published: December 2018

Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to modern humans’ spread into the rest of Eurasia and their replacement of the Neanderthals. That the inter-species boundary remained geographically localized for so long is a puzzle, particularly in light of the rapidity of its subsequent movement. We propose that disease dynamics can explain the localization and persistence of the inter-species boundary; in this view, each species carried pathogens to which it was largely immune and tolerant, but that could spread to the other, vulnerable, species, inducing a significant disease burden. Epidemics and endemic diseases along the interspecies boundary would have mitigated against bands of one species migrating into regions dominated by the other species. Together with decreased population densities and limited inter-group interactions due to disease burden, this mechanism could have resulted in a fixed and narrow contact-zone. We further propose, and support with results from dynamical systems models, that genetic introgression, including transmission of alleles related to the immune system, would have gradually allowed the two species to overcome this barrier to pervasive inter-species interaction, leading to the eventual release of the inter-species boundary from its geographic localization. Asymmetries between the two species in the initial size of their associated “pathogen package” could have created feedback loops that influenced the rates at which immunity to and tolerance of the novel pathogens were acquired. These asymmetries could have allowed modern humans to overcome the disease burden earlier than Neanderthals, giving them a significant advantage in their subsequent spread into Eurasia, particularly upon interaction with Neanderthal populations that had previously been far from the original contact zone in the Levant.
mtDNA eQTLs and the m1A 16S rRNA modification explain mtDNA tissue-specific gene expression pattern in humans
Authors: Cohen Tal , Mordechai Chen , Eran Alal , Mishmar Dan
Published: December 2018

Expression quantitative trait loci (eQTLs) are instrumental in genome-wide identification of regulatory elements, yet were overlooked in the mitochondrial DNA (mtDNA). By analyzing 5079 RNA-seq samples from 23 tissues we identified association of ancient mtDNA SNPs (haplogroups T2, L2, J2 and V) and recurrent SNPs (mtDNA positions 263, 750, 1438 and 10398) with tissue-dependent mtDNA gene-expression. Since the recurrent SNPs independently occurred in different mtDNA genetic backgrounds, they constitute the best candidates to be causal eQTLs. Secondly, the discovery of mtDNA eQTLs in both coding and non-coding mtDNA regions, propose the identification of novel mtDNA regulatory elements. Third, we identified association between low m1A 947 MT-RNR2 (16S) rRNA modification levels and altered mtDNA gene-expression in twelve tissues. Such association disappeared in skin which was exposed to sun, as compared to sun-unexposed skin from the same individuals, thus supporting the impact of UV on mtDNA gene expression. Taken together, our findings reveal that both mtDNA SNPs and mt-rRNA modification affect mtDNA gene expression in a tissue-dependent manner.
Detecting modifications in proteomics experiments with Param-Medic
Authors: May Damon , Tamura Kaipo , Noble William
Published: December 2018

Searching tandem mass spectra against a peptide database requires accurate knowledge of various experimental parameters, including machine settings and details of the sample preparation protocol. In some cases, such as in re-analysis of public data sets, this experimental metadata may be missing or inac- curate. We describe a method for automatically inferring the presence of various types of modifications, including stable-isotope and isobaric labeling, tandem mass tags, and phosphorylation, directly from a given set of mass spectra. We demonstrate the sensitivity and specificity of the proposed approach, and we provide open source Python and C++ implementations in a new version of the software tool Param-Medic.
Hormone-control regions mediate steroid receptor–dependent genome organization
Authors: Le Dily François , Vidal Enrique , Cuartero Yasmina , Quilez Javier , Nacht A. Silvina , Vicent Guillermo P. , Carbonell-Caballero José , Sharma Priyanka , Villanueva-Cañas José Luis , Ferrari Roberto , De Llobet Lara Isabel , Verde Gaetano , Wright Roni H.G. , Beato Miguel
Published: December 2018

In breast cancer cells, some topologically associating domains (TADs) behave as hormonal gene regulation units, within which gene transcription is coordinately regulated in response to steroid hormones. Here we further describe that responsive TADs contain 20- to 100-kb-long clusters of intermingled estrogen receptor (ESR1) and progesterone receptor (PGR) binding sites, hereafter called hormone-control regions (HCRs). In T47D cells, we identified more than 200 HCRs, which are frequently bound by unliganded ESR1 and PGR. These HCRs establish steady long-distance inter-TAD interactions between them and organize characteristic looping structures with promoters in their TADs even in the absence of hormones in ESR1+-PGR+ cells. This organization is dependent on the expression of the receptors and is further dynamically modulated in response to steroid hormones. HCRs function as platforms that integrate different signals, resulting in some cases in opposite transcriptional responses to estrogens or progestins. Altogether, these results suggest that steroid hormone receptors act not only as hormone-regulated sequence-specific transcription factors but also as local and global genome organizers.
4-Methyl-1H-1,5-benzodiazepin-2(3H)-one
Authors: Dioukhane Khadim , Aouine Younas , Faraj Hassane , Alami Anouar , Essassi El Mokhtar , Zouihri Hafid
Published: December 2018

In the title compound, C10H10N2O, the seven-membered heterocycle displays a half-chair conformation. In the crystal, N—H...O and C—H...O hydrogen bonds link the molecules into chains propagating along the a-axis direction.
When life gives you lemons make lemonade: cross-sectional age and gender differences in optimism
Authors: Bharti Teena , Rangnekar Santosh
Published: December 2018

Purpose

The purpose of this paper is to test the cognitive construct of optimism (positive future outcome expectancies) and the age-gender differences in Indian sample.

Design/methodology/approach

The sample consists of 363 older, middle-aged and younger male and female employees. The study adopted a cross-sectional survey based research design.

Findings

Results revealed that middle-aged employees have high levels of optimism as compared to the old age and younger employees. Further, the males reflected high optimism levels in comparison to female employees in middle and old aged adult employees, whereas females have higher optimism level in younger age in Indian select organisations.

Research limitations/implications

The study suggests that the continuous changes in the lifespan lead to changes in one’s attitude and hence results in behavioural changes. The research indicates that optimism should be cultivated in the individuals by providing training and development to promote the competence and skill-building events which would help in enhancing the productivity resulting in better understanding of the scenario at workplace.

Originality/value

The work supplements the existing literature on positive attitude or outcome expectancies by adding to the lifespan development theory.
Designing a pragmatic model for strategic purchasing of health services in health insurance companies
Authors: Rezapour Aziz , Hakimzadeh Seyyed Mostafa , Panahi Sirous , Teymourzadeh Ehsan , Bahadori Mohammadkarim , Bastani Peivand , Tahernezhad Ali
Published: December 2018

Purpose

The purpose of this paper is to identify the most important factors for strategic purchasing of health services in the health sector by the Iran Health Insurance Company and to provide an applicable model for other similar organizations in developing countries.

Design/methodology/approach

The present qualitative study was conducted in 2017 to identify the factors affecting the implementation of strategic purchasing of health services in the health sector by the Iran Health Insurance Company and to provide an indigenous and practical model through two phases: semi-structured interview followed by a Delphi process.

Findings

According to the findings of this study, Ministry of Welfare, Labor and Social Security plays a central role in the strategic purchasing. In addition, this was also approved by the representatives of citizens in communities concerning professional associations, insurance agencies and representative of the Council of Ministers. Model development explored 9 themes and 54 sub-themes.

Research limitations/implications

Based on the model, most attention has been paid to consumer role and inter-sector leadership of the company with other relevant organizations and systems including other insurance organizations and the welfare ministry. More importantly, the health insurance company should be able to communicate with providers and to choose the best providers, receiving price information through competition in the most appropriate mechanism. Guided by this model, it can strategically buy the best and the most effective services for its insured population.

Social implications

It might help developing societies to promote their health systems based on targeting the health budgeting and financial constraints so that it is prioritized according to the strategic purchasing criteria and consequently, economic evaluation.

Originality/value

The linchpins of the present study are as follow: first, the pragmatic model presented in the paper could help developing health systems to overcome the impediment in the implementation progress of strategic purchasing. Second, the model satisfies the need of enough knowledge to apply strategic purchasing in the health system. Third, the indigents have long been given special protection and consideration in the model that has continued to capture the attention of every policy-maker, in particular, developing countries, the portion of which is significant. Fourth, based on this model, attention has been paid to consumer role and inter-sector leadership of organization with other relevant organizations and systems. Fifth, this model could be correspondent for every insurance company in countries with similar developing conditions.
The role of national rural health mission in reducing infant mortality rate in India
Authors: Pandey Ashutosh , Mohan Arvind
Published: December 2018

Purpose

The purpose of this paper is to assess the role of National Rural Health Mission (NRHM) in reducing Infant Mortality in India. The study will help the government in deciding its future course of action regarding the infant mortality rate (IMR) reduction in India.

Design/methodology/approach

This paper adopts the interrupted time series analysis (ITSA) approach with a control group to study the role of NRHM in reducing the IMR in India. The authors examined infant mortality in rural areas of India for the level and trend change before and after the implementation of NRHM. The authors then applied a suitable ARMA model to estimate the coefficients of the regression model. From the estimated results, the study predicts the counterfactuals for both the rural IMR and urban IMR and plots the results.

Findings

The study found the evidence supporting the hypotheses that the NRHM has led to a reduction in the difference between urban IMR and rural IMR. The research shows that the rural IMR declined at steeper rates in the post-NRHM period (2005–2015).

Originality/value

None of the existing studies analyses the impact of a social scheme like NRHM on the reduction of IMR in India by applying the ITSA. The study is unique as it estimates the counterfactuals and plots the results which show the impact of NRHM on reducing IMR.
How do children make sense of food well-being? Food for thought for responsible retailers
Authors: Hémar-Nicolas Valérie , Ezan Pascale
Published: December 2018

Purpose

The purpose of this paper is to provide a better understanding of what well-being means to children in the food context and to formulate recommendations about the way food retailers may take actions to promote children’s food well-being (FWB).

Design/methodology/approach

A qualitative study based on a child-centric perspective is conducted with 25 French children aged 6–11 years. The data collection and analysis use both verbal and graphic data methods including focus groups and drawings in order to help children express their feelings and thoughts.

Findings

The findings put forward that according to children, the concept of FWB relies on five dimensions: sensory taste, health, commensality, empowerment and altruistic behaviours. Their discourses suggest that food practices contributes to objective, hedonic, eudaemonic and social well-being on the short and long term.

Practical implications

Based on children’s intrinsic needs for pleasure and empowerment, our recommendations highlight how food retailers might rethink their own-label offering, retail environment and communication to take into account young consumers’ FWB.

Originality/value

Drawing upon the concept of FWB and positive psychology, the authors do not only examine children’s food representations through a nutritional lens, but enlarge the scope to show how physical, emotional, psychological and social factors, involved in food context, contribute to different aspects of well-being.