bluuebunny/crossref_metadata_2025 huggingface dataset:
Assembly bias evidence in close galaxy pairs
Authors: Ferreras I , Hopkins A M , Lagos C , Sansom A E , Scott N , Croom S , Brough S
Published: May 2019

The growth channel of massive galaxies involving mergers can be studied via close pairs as putative merger progenitors, where the stellar populations of the satellite galaxies will be eventually incorporated into the massive primaries. We extend our recent analysis of the GAMA-based sample of close pairs presented in Ferreras et al. to the general spectroscopic data set of SDSS galaxies (DR14), for which the high S/N of the data enables a detailed analysis of the differences between satellite galaxies with respect to the mass of the primary galaxy. A sample of approximately 2000 satellites of massive galaxies is carefully selected within a relatively narrow redshift range (0.07<z<0.14). Two main parameters are considered as major drivers of the star formation history of these galaxies, namely: the stellar velocity dispersion of the satellite (σ), as a proxy of ‘local’ drivers, and the ratio between the stellar mass of the satellite and the primary, μ = MSAT/MPRI, meant to serve as an indicator of environment. Consistently with the independent, GAMA-based work, we find that satellites around the most massive primaries appear older, at fixed velocity dispersion, than satellites of lower mass primaries. This trend is more marked in lower mass satellites (σ ∼ 100 km s−1), with SSP-equivalent age differences up to ∼0.5 Gyr, and can be interpreted as a one-halo assembly bias, so that satellites corresponding to smaller values of μ represent older structures, akin to fossil groups.
Many Options, Few Solutions: Over 60 My Snakes Converged on a Few Optimal Venom Formulations
Authors: Barua Agneesh , Mikheyev Alexander S
Published: May 2019

Gene expression changes contribute to complex trait variations in both individuals and populations. However, the evolution of gene expression underlying complex traits over macroevolutionary timescales remains poorly understood. Snake venoms are proteinaceous cocktails where the expression of each toxin can be quantified and mapped to a distinct genomic locus and traced for millions of years. Using a phylogenetic generalized linear mixed model, we analyzed expression data of toxin genes from 52 snake species spanning the 3 venomous snake families and estimated phylogenetic covariance, which acts as a measure of evolutionary constraint. We find that evolution of toxin combinations is not constrained. However, although all combinations are in principle possible, the actual dimensionality of phylomorphic space is low, with envenomation strategies focused around only four major toxin families: metalloproteases, three-finger toxins, serine proteases, and phospholipases A2. Although most extant snakes prioritize either a single or a combination of major toxin families, they are repeatedly recruited and lost. We find that over macroevolutionary timescales, the venom phenotypes were not shaped by phylogenetic constraints, which include important microevolutionary constraints such as epistasis and pleiotropy, but more likely by ecological filtering that permits a small number of optimal solutions. As a result, phenotypic optima were repeatedly attained by distantly related species. These results indicate that venoms evolve by selection on biochemistry of prey envenomation, which permit diversity through parallelism, and impose strong limits, since only a few of the theoretically possible strategies seem to work well and are observed in extant snakes.
IAMBEE: a web-service for the identification of adaptive pathways from parallel evolved clonal populations
Authors: Perez-Romero Camilo Andres , Weytjens Bram , Decap Dries , Swings Toon , Michiels Jan , De Maeyer Dries , Marchal Kathleen
Published: May 2019

IAMBEE is a web server designed for the Identification of Adaptive Mutations in Bacterial Evolution Experiments (IAMBEE). Input data consist of genotype information obtained from independently evolved clonal populations or strains that show the same adapted behavior (phenotype). To distinguish adaptive from passenger mutations, IAMBEE searches for neighborhoods in an organism-specific interaction network that are recurrently mutated in the adapted populations. This search for recurrently mutated network neighborhoods, as proxies for pathways is driven by additional information on the functional impact of the observed genetic changes and their dynamics during adaptive evolution. In addition, the search explicitly accounts for the differences in mutation rate between the independently evolved populations. Using this approach, IAMBEE allows exploiting parallel evolution to identify adaptive pathways. The web-server is freely available at http://bioinformatics.intec.ugent.be/iambee/ with no login requirement.
IEDB-AR: immune epitope database—analysis resource in 2019
Authors: Dhanda Sandeep Kumar , Mahajan Swapnil , Paul Sinu , Yan Zhen , Kim Haeuk , Jespersen Martin Closter , Jurtz Vanessa , Andreatta Massimo , Greenbaum Jason A , Marcatili Paolo , Sette Alessandro , Nielsen Morten , Peters Bjoern
Published: May 2019

The Immune Epitope Database Analysis Resource (IEDB-AR, http://tools.iedb.org/) is a companion website to the IEDB that provides computational tools focused on the prediction and analysis of B and T cell epitopes. All of the tools are freely available through the public website and many are also available through a REST API and/or a downloadable command-line tool. A virtual machine image of the entire site is also freely available for non-commercial use and contains most of the tools on the public site. Here, we describe the tools and functionalities that are available in the IEDB-AR, focusing on the 10 new tools that have been added since the last report in the 2012 NAR webserver edition. In addition, many of the tools that were already hosted on the site in 2012 have received updates to newest versions, including NetMHC, NetMHCpan, BepiPred and DiscoTope. Overall, this IEDB-AR update provides a substantial set of updated and novel features for epitope prediction and analysis.
Histone H4 H75E mutation attenuates global genomic and Rad26-independent transcription-coupled nucleotide excision repair
Authors: Selvam Kathiresan , Rahman Sheikh Arafatur , Li Shisheng
Published: May 2019

Nucleotide excision repair (NER) consists of global genomic NER (GG-NER) and transcription coupled NER (TC-NER) subpathways. In eukaryotic cells, genomic DNA is wrapped around histone octamers (an H3–H4 tetramer and two H2A–H2B dimers) to form nucleosomes, which are well known to profoundly inhibit the access of NER proteins. Through unbiased screening of histone H4 residues in the nucleosomal LRS (loss of ribosomal DNA-silencing) domain, we identified 24 mutations that enhance or decrease UV sensitivity of Saccharomyces cerevisiae cells. The histone H4 H75E mutation, which is largely embedded in the nucleosome and interacts with histone H2B, significantly attenuates GG-NER and Rad26-independent TC-NER but does not affect TC-NER in the presence of Rad26. All the other histone H4 mutations, except for T73F and T73Y that mildly attenuate GG-NER, do not substantially affect GG-NER or TC-NER. The attenuation of GG-NER and Rad26-independent TC-NER by the H4H75E mutation is not due to decreased chromatin accessibility, impaired methylation of histone H3 K79 that is at the center of the LRS domain, or lowered expression of NER proteins. Instead, the attenuation is at least in part due to impaired recruitment of Rad4, the key lesion recognition and verification protein, to chromatin following induction of DNA lesions.
A post-transcriptional respiratome regulon in trypanosomes
Authors: Trenaman Anna , Glover Lucy , Hutchinson Sebastian , Horn David
Published: May 2019

Post-transcriptional regulons coordinate the expression of groups of genes in eukaryotic cells, yet relatively few have been characterized. Parasitic trypanosomatids are particularly good models for studies on such mechanisms because they exhibit almost exclusive polycistronic, and unregulated, transcription. Here, we identify the Trypanosoma brucei ZC3H39/40 RNA-binding proteins as regulators of the respiratome; the mitochondrial electron transport chain (complexes I–IV) and the FoF1-ATP synthase (complex V). A high-throughput RNAi screen initially implicated both ZC3H proteins in variant surface glycoprotein (VSG) gene silencing. This link was confirmed and both proteins were shown to form a cytoplasmic ZC3H39/40 complex. Transcriptome and mRNA-interactome analyses indicated that the impact on VSG silencing was indirect, while the ZC3H39/40 complex specifically bound and stabilized transcripts encoding respiratome-complexes. Quantitative proteomic analyses revealed specific positive control of >20 components from complexes I, II and V. Our findings establish a link between the mitochondrial respiratome and VSG gene silencing in bloodstream form T. brucei. They also reveal a major respiratome regulon controlled by the conserved trypanosomatid ZC3H39/40 RNA-binding proteins.
NMD-Based Gene Regulation—A Strategy for Fitness Enhancement in Plants?
Authors: Ohtani Misato , Wachter Andreas
Published: May 2019

Post-transcriptional RNA quality control is a vital issue for all eukaryotes to secure accurate gene expression, both on a qualitative and quantitative level. Among the different mechanisms, nonsense-mediated mRNA decay (NMD) is an essential surveillance system that triggers degradation of both aberrant and physiological transcripts. By targeting a substantial fraction of all transcripts for degradation, including many alternative splicing variants, NMD has a major impact on shaping transcriptomes. Recent progress on the transcriptome-wide profiling and physiological analyses of NMD-deficient plant mutants revealed crucial roles for NMD in gene regulation and environmental responses. In this review, we will briefly summarize our current knowledge of the recognition and degradation of NMD targets, followed by an account of NMD’s regulation and physiological functions. We will specifically discuss plant-specific aspects of RNA quality control and its functional contribution to the fitness and environmental responses of plants.
Salt-Responsive Genes are Differentially Regulated at the Chromatin Levels Between Seedlings and Roots in Rice
Authors: Zheng Dongyang , Wang Lei , Chen Lifen , Pan Xiucai , Lin Kande , Fang Yuan , Wang Xiu-e , Zhang Wenli
Published: May 2019

The elucidation of epigenetic responses of salt-responsive genes facilitates understanding of the underlying mechanisms that confer salt tolerance in rice. However, it is still largely unknown how epigenetic mechanisms are associated with the expression of salt-responsive genes in rice and other crops. In this study, we reported tissue-specific gene expression and tissue-specific changes in chromatin modifications or signatures between seedlings and roots in response to salt treatment. Our study indicated that among six of individual mark examined (H3K4me3, H3K27me3, H4K12ac, H3K9ac, H3K27ac and H3K36me3), a positive association between salt-related changes in histone marks and the expression of differentially expressed genes (DEGs) was observed only for H3K9ac and H4K12ac in seedlings and H3K36me3 in roots. In contrast, chromatin states (CSs) with combinations of six histone modification marks played crucial roles in the differential expression of salt-responsive genes between seedlings and roots. Most importantly, CS7 containing the bivalent marks H3K4me3 and H3K27me3, with a mutual exclusion of functions with each other, displayed distinct functions in the expression of DEGs in both tissues. Specifically, H3K27me3 in CS7 mainly suppressed the expression of DEGs in roots, while H3K4me3 affected the expression of down- and up-regulated genes, possibly by antagonizing the repressive role of H3K27me3 in seedlings. Our findings indicate distinct impacts of the CSs on the differential expression of salt-responsive genes between seedlings and roots in rice, which provides an important background for understanding chromatin-based epigenetic mechanisms that might confer salt tolerance in plants.
Fc-gamma receptors and S100A8/A9 cause bone erosion during rheumatoid arthritis. Do they act as partners in crime?
Authors: Di Ceglie Irene , Kruisbergen Nik N L , van den Bosch Martijn H J , van Lent Peter L E M
Published: May 2019

Bone erosion is one of the central hallmarks of RA and is caused by excessive differentiation and activation of osteoclasts. Presence of autoantibodies in seropositive arthritis is associated with radiographic disease progression. ICs, formed by autoantibodies and their antigens, activate Fcγ-receptor signalling in immune cells, and as such stimulate inflammation-mediated bone erosion. Interestingly, ICs can also directly activate osteoclasts by binding to FcγRs on their surface. Next to autoantibodies, high levels of alarmins, among which is S100A8/A9, are typical for RA and they can further activate the immune system but also directly promote osteoclast function. Therefore, IC-activated FcγRs and S100A8/A9 might act as partners in crime to stimulate inflammation and osteoclasts differentiation and function, thereby stimulating bone erosion. This review discusses the separate roles of ICs, FcγRs and alarmins in bone erosion and sheds new light on the possible interplay between them, which could fuel bone erosion.
Treatment failure in inflammatory arthritis: time to think about syndemics?
Authors: Nikiphorou Elena , Lempp Heidi , Kohrt Brandon A.
Published: May 2019

Social determinants of health play a crucial role in health and disease. In current times, it has become increasingly known that biological and non-biological factors are potentially linked and help to drive disease. For example, links between various comorbidities, both physical and mental illnesses, are known to be driven by social, environmental and economic determinants. This contributes to worse disease outcomes. This article discusses the concept of syndemics, which although well-described in some conditions, represents a novel concept in the context of rheumatic and musculoskeletal diseases. Written in the form of a viewpoint, the article focuses on a novel theoretical framework for studying inflammatory arthritis, based on a syndemic approach that takes into account the social context, biocultural disease interaction, and socio-economic characteristics of the setting. Syndemics involving inflammatory arthritis may be most likely in a social context involving limited access to health care, lack of physical activity and obesogenic diets, high rates of alcohol consumption, and high exposure to stressful life events.
Statistical Comparison of Trait-Dependent Biogeographical Models Indicates That Podocarpaceae Dispersal Is Influenced by Both Seed Cone Traits and Geographical Distance
Authors: Klaus Kristina V , Matzke Nicholas J
Published: May 2019

The ability of lineages to disperse long distances over evolutionary timescales may be influenced by the gain or loss of traits adapted to enhance local, ecological dispersal. For example, some species in the southern conifer family Podocarpaceae have fleshy cones that encourage bird dispersal, but it is unknown how this trait has influenced the clade’s historical biogeography, or its importance compared with other predictors of dispersal such as the geographic distance between regions. We answer these questions quantitatively by using a dated phylogeny of 197 species of southern conifers (Podocarpaceae and their sister family Araucariaceae) to statistically compare standard, trait-independent biogeography models with new BioGeoBEARS models where an evolving trait can influence dispersal probability, and trait history, biogeographical history, and model parameters are jointly inferred. We validate the method with simulation-inference experiments. Comparing all models, those that include trait-dependent dispersal accrue 87.5% of the corrected Akaike Information Criterion (AICc) model weight. Averaged across all models, lineages with nonfleshy cones had a dispersal probability multiplier of 0.49 compared with lineages with fleshy cones. Distance is included as a predictor of dispersal in all credible models (100% model weight). However, models with changing geography earned only 22.0% of the model weight, and models submerging New Caledonia/New Zealand earned only 0.01%. The importance of traits and distance suggests that long-distance dispersal over macroevolutionary timespans should not be thought of as a highly unpredictable chance event. Instead, long-distance dispersal can be modeled, allowing statistical model comparison to quantify support for different hypotheses.
A Phenome-wide Mendelian Randomisation study on genetically determined serum urate levels in UK Biobank cohort
Authors: Li Xue , Meng Xiangrui , He Yazhou , Spiliopoulou Athina , Timofeeva Maria , Wei Wei-Qi , Gifford Aliya , Yang Tian , Varley Tim , Tzoulaki Ioanna , Joshi Peter , Denny Joshua C. , Mckeigue Paul , Campbell Harry , Theodoratou Evropi
Published: May 2019

Introduction

The role of serum urate level has been extensively investigated in observational studies. However, the extent of any causal effect remains unclear, making it difficult to evaluate its clinical relevance.

Objectives

To explore any causal or pleiotropic association between serum urate level and a broad spectrum of disease outcomes.

Methods

Phenome-wide association study (PheWAS) together with a Bayesian analysis of tree-structured phenotypic models (TreeWAS) was performed to examine disease outcomes related to genetically determined serum urate levels in 339,256 UK Biobank participants. Mendelian Randomisation (MR) analyses were performed to replicate significant findings using various GWAS consortia data. Sensitivity analyses were conducted to examine possible pleiotropic effects on metabolic traits of the genetic variants used as instruments for serum urate.

Results

PheWAS analysis, examining the association with 1,431 disease outcomes, identified a multitude of disease outcomes including gout, hypertension, hypercholesterolemia, and heart diseases (e.g., coronary atherosclerosis, myocardial infarction, and ischaemic heart disease) that were associated (p<3.35e-04) with genetically determined serum urate levels. TreeWAS analysis, examining 10,750 ICD-10 diagnostic terms, identified more sub-phenotypes of cardiovascular and cerebrovascular diseases (e.g., angina pectoris, heart failure, cerebral infarction). MR analysis successfully replicated the association with gout, hypertension, heart diseases and blood lipid levels, but indicated the existence of genetic pleiotropy. Sensitivity analyses support an inference that pleiotropic effects of genetic variants on urate and metabolic traits contribute to the observational associations with cardiovascular diseases.

Conclusions

High serum urate levels are associated with different types of cardiac events. The finding of genetic pleiotropy indicates the existence of common upstream pathological elements influencing both urate and metabolic traits, and this may suggest new opportunities and challenges for developing drugs targeting a more distal mediator that would be beneficial for both the treatment of gout and the prevention of cardiovascular comorbidities.
B-SIDER: Computational Algorithm for the Design of Complementary β-sheet Sequences
Authors: Yu Tae-Geun , Kim Hak-Sung , Choi Yoonjoo
Published: May 2019

The β-sheet is an element of protein secondary structure, and intra-/inter-molecular β-sheet interactions play pivotal roles in biological regulatory processes including scaffolding, transporting, and oligomerization. In nature, a β-sheet formation is tightly regulated because dysregulated β-stacking often leads to severe diseases such as Alzheimer’s, Parkinson’s, systemic amyloidosis, or diabetes. Thus, the identification of intrinsic β-sheet forming propensities can provide valuable insight into protein designs for the development of novel therapeutics. However, structure-based design methods may not be generally applicable to such amyloidogenic peptides mainly owing to high structural plasticity and complexity. Therefore, an alternative design strategy based on complementary sequence information is of significant importance. Herein, we developed a database search method called B-SIDER for the design of complementary β-strands. This method makes use of the structural database information and generates query-specific score matrices. The discriminatory power of the B-SIDER score function was tested on representative amyloidogenic peptide substructures against a sequence-based score matrix (PASTA2.0) and two popularab initioprotein design score functions (Rosetta and FoldX). B-SIDER is able to distinguish wild-type amyloidogenic β-strands as favored interactions in a more consistent manner than other methods. B-SIDER was prospectively applied to the design of complementary β-strands for a splitGFP scaffold. Three variants were identified to have stronger interactions than the original sequence selected through a directed evolution, emitting higher fluorescence intensities. Our results indicate that B-SIDER can be applicable to the design of other β-strands, assisting in the development of therapeutics against disease-related amyloidogenic peptides.
CRISPR adenine and cytosine base editors with reduced RNA off-target activities
Authors: Grünewald Julian , Zhou Ronghao , Iyer Sowmya , Lareau Caleb A. , Garcia Sara P. , Aryee Martin J. , Keith Joung J.
Published: May 2019

CRISPR-guided DNA base editors enable the efficient installation of targeted single-nucleotide changes. Cytosine or adenine base editors (CBEs or ABEs), which are fusions of cytidine or adenosine deaminases to CRISPR-Cas nickases, can efficiently induce DNA C-to-T or A-to-G alterations in DNA, respectively1-4. We recently demonstrated that both the widely used CBE BE3 (harboring a rat APOBEC1 cytidine deaminase) and the optimized ABEmax editor can induce tens of thousands of guide RNA-independent, transcriptome-wide RNA base edits in human cells with high efficiencies5. In addition, we showed the feasibility of creating SElective Curbing of Unwanted RNA Editing (SECURE)-BE3 variants that exhibit substantially reduced unwanted RNA editing activities while retaining robust and more precise on-target DNA editing5. Here we describe structure-guided engineering of SECURE-ABE variants that not only possess reduced off-target RNA editing with comparable on-target DNA activities but are also the smallest Streptococcus pyogenes Cas9 (SpCas9) base editors described to date. In addition, we tested CBEs composed of cytidine deaminases other than APOBEC1 and found that human APOBEC3A (hA3A) cytidine deaminase CBE induces substantial transcriptome-wide RNA base edits with high efficiencies. By contrast, a previously described “enhanced” A3A (eA3A) cytidine deaminase CBE or a human activation-induced cytidine deaminase (hAID) CBE induce substantially reduced or near background levels of RNA edits. In sum, our work describes broadly useful SECURE-ABE and -CBE base editors and reinforces the importance of minimizing RNA editing activities of DNA base editors for research and therapeutic applications.
Emergence and evolution of the ERM proteins and merlin in metazoans
Authors: Shabardina V. , Kashima Y. , Suzuki Y. , Makalowski W.
Published: May 2019

Ezrin, radixin, moesin, and merlin are the cytoskeletal proteins which functions are specific to metazoans. They participate in cell cortex rearrangements, including cell-cell contact formation, and play important role in cancer progression. Here we perform a comprehensive phylogenetic analysis of the proteins spanning 87 species. The results describe a possible mechanism of the protein family origin in the root of Metazoa, paralogs diversification in vertebrates and acquisition of novel functions, including tumor suppression. In addition, a merlin paralog, present in most of vertebrates, but lost in mammals, has been described. We also highlight the set of amino acid variations within the conserved motifs as the candidates for determining physiological differences between the ERM paralogs.
Contact sensitivity in paediatric patients with atopic dermatitis in Laos
Authors: Wootton Catriona I. , Sodaly Mong K. , Billamay Somxay X. , English John S.C. , Mayfong Mayxay
Published: May 2019

Background

Dermatological services in Laos, South East Asia are limited mainly to the capital and patch testing is currently not available, so no data exists regarding the common cutaneous allergens in this population.

Objectives

The aim of this study was to document common allergens in paediatric patients with atopic dermatitis attending the allergy clinic in the capital, Vientiane.

Patients/Materials/Methods

Fifty paediatric patients with atopic dermatitis were patch tested using TRUE Test® panels 1 to 3 (35 allergens). Readings were taken at Days 2 and 4.

Results

Twenty-six positive patch tests were recorded on Day 4 in 15 children (30%). The most common allergens were: gold (18%), nickel (10%), formaldehyde (6%) and p-Phenylenediamine (6%). Other positive allergens were potassium dichromate (2%), cobalt dichloride (2%), Bronopol (2%), paraben mix (2%), fragrance mix 1 (2%) and neomycin (2%). The majority of the patients with positive reactions were female.

Conclusions

This study represents the first documented patch test results in the Lao population. It is hoped that these findings will help clinicians to advise the families of children with atopic dermatitis on common allergens to avoid and inform future work on contact dermatitis in this population.
PIME: a package for discovery of novel differences among microbial communities
Authors: Roesch Luiz Fernando W. , Dobbler Priscila Thiago , Pylro Victor Satler , Kolaczkowski Bryan , Drew Jennifer C. , Triplett Eric W.
Published: May 2019

Massive sequencing of genetic markers, such as the 16S rRNA gene for prokaryotes, allows the comparative analysis of diversity and abundance of whole microbial communities. However, the data used for profiling microbial communities is usually low in signal and high in noise preventing the identification of real differences among treatments. PIME (Prevalence Interval for Microbiome Evaluation) fills this gap by removing those taxa that may be high in relative abundance in just a few samples but have a low prevalence overall. The reliability and robustness of PIME were compare against the existing methods and verified by a number of approaches using 16S rRNA independent datasets. To remove the noise, PIME filters microbial taxa not shared in a per treatment prevalence interval starting at 5% with increments of 5% at each filtering step. For each prevalence interval, hundreds of decision trees are calculated to predict the likelihood of detecting differences in treatments. The best prevalence-filtered dataset is user-selected by choosing the prevalence interval that keeps the majority of the 16S rRNA reads in the dataset and shows the lowest error rate. To obtain the likelihood of introducing bias while building prevalence-filtered datasets, an error detection step based in random permutations is also included. A reanalysis of previews published datasets with PIME uncovered previously missed microbial associations improving the ability to detect important organisms, which may be masked when only relative abundance is considered.
Conditional silencing of H-2Dbclass I molecule expression on dendritic cells modulates the protective and pathogenic kinetics of virus-antigen specific CD8 T cell responses during Theiler’s Virus infection
Authors: Tritz Zachariah P. , Orozco Robin C. , Malo Courtney S. , Yokanovich Lila T , Ayasoufi Katayoun , Fain Cori E. , Khadka Roman H. , Settell Megan L. , Hansen Mike J. , Jin Fang , Johnson Aaron J
Published: May 2019

Theiler’s murine encephalomyelitis virus (TMEV) infection of the central nervous system is rapidly cleared in C57BL/6 mice by an anti-viral CD8 T cell response restricted by the MHC class I molecule, H-2Db. While the CD8 T cell response against neurotropic viruses is well characterized, the identity and function of the antigen presenting cell(s) involved in this process is(are) less well defined. To address this gap in knowledge, we developed a novel C57BL/6 H-2Dbconditional knockout mouse that expresses an H-2Dbtransgene in which the transmembrane domain locus is flanked by LoxP sites. We crossed these H-2DbLoxP mice with MHC class I-deficient mice expressing Cre-recombinase under either the CD11c or LysM promoter in order to silence H-2Dbrestricted antigen presentation predominantly in dendritic cells or macrophages, respectively. Upon challenge with intracranial TMEV infection, we observe that CD11c+ APCs are critical for early priming of CD8 T cells against the immunodominant TMEV peptide VP2121-130 presented in the context of the H-2Dbmolecule. This stands in stark contrast to later time points post TMEV infection where CD11c+ APCs appear dispensable for the activation of antigen-specific T cells; the functionality of these late-arising antiviral CD8 T cells is reflected in the restoration of viral control at later time points. These late-arising CD8 T cells also retain their capacity to induce blood-brain barrier disruption. In contrast, when H-2Dbrestricted antigen presentation was selectively silenced in LysM+ APCs there was no overt impact on the priming of Db:VP2121-130 epitope-specific CD8 T cells, although a modest reduction in immune cell entry into the CNS was observed. This work establishes a model system which enables critical dissection of MHC class I restricted antigen presentation to T cells, revealing cell specific and temporal features involved in the generation of antiviral CD8 T cell responses. Employing this novel system, we established CD11c+ cells as a pivotal driver of acute, but not later-arising, antiviral CD8 T cell responses against the TMEV immunodominant epitope VP2121-130, with functional implications both for T cell-mediated viral control and immunopathology.
Differential impact of self and environmental antigens on the ontogeny and maintenance of CD4+ T cell memory
Authors: Hogan Thea , Nowicka Maria , Cownden Daniel , Pearson Claire , Yates Andrew J. , Seddon Benedict
Published: May 2019

Laboratory mice develop populations of circulating memory CD4+ T cells in the absence of overt infection. We have previously shown that these populations are replenished from naive precursors at high levels throughout life (Gossel et al., 2017). However, the nature, relative importance and timing of the forces generating these cells remain unclear. Here, we tracked the generation of memory CD4+ T cell subsets in mice housed in facilities differing in their ‘dirtiness’. We found evidence for sequential naive to central memory to effector memory development, and confirmed that both memory subsets are heterogeneous in their rates of turnover. We also inferred that early exposure to self and environmental antigens establishes persistent memory populations at levels determined largely, though not exclusively, by the dirtiness of the environment. After the first few weeks of life, however, these populations are continuously supplemented by new memory cells at rates that are independent of environment.
Human cardiac fibrosis-on-a-chip model recapitulates disease hallmarks and can serve as a platform for drug screening
Authors: Mastikhina Olya , Moon Byeong-Ui , Williams Kenneth , Hatkar Rupal , Gustafson Dakota , Sun Xuetao , Koo Margaret , Lam Alan Y.L. , Sun Yu , Fish Jason E. , Young Edmond W.K. , Nunes Sara S.
Published: May 2019

While interstitial fibrosis plays a significant role in heart failure, our understanding of disease progression in humans is limited. To address this limitation, we have engineered a cardiac-fibrosis-on-a-chip model consisting of a microfabricated device with live force measurement capabilities using co-cultured human cardiac fibroblasts and pluripotent stem cell-derived cardiomyocytes. Transforming growth factor-β was used as a trigger for fibrosis. Here, we have reproduced the classic hallmarks of fibrosis-induced heart failure including high collagen deposition, increased tissue stiffness, BNP secretion, and passive tension. Force of contraction was significantly decreased in fibrotic tissues that displayed a transcriptomic signature consistent with human cardiac fibrosis/heart failure. Treatment with an anti-fibrotic drug decreased tissue stiffness and BNP secretion, with corresponding changes in the transcriptomic signature. This model represents an accessible approach to study human heart failure in vitro, and allows for testing anti-fibrotic drugs while facilitating the real-time assessment of cardiomyocyte function.
Functional tunability from a distance: Rheostat positions influence allosteric coupling between two distant binding sites
Authors: Wu Tiffany , Swint-Kruse Liskin , Fenton Aron W.
Published: May 2019

For protein mutagenesis, a common expectation is that important positions will behave like on/off “toggle” switches (i.e., a few substitutions act like wildtype, most abolish function). However, there exists another class of important positions that manifests a wide range of functional outcomes upon substitution: “rheostat” positions. Previously, we evaluated rheostat positions located near the allosteric binding sites for inhibitor alanine (Ala) and activator fructose-1,6-bisphosphate (Fru-1,6-BP) in human liver pyruvate kinase. When substituted with multiple amino acids, many positions demonstrated moderate rheostat effects on allosteric coupling between effector binding and phosphoenolpyruvate (PEP) binding in the active site. Nonetheless, the combined outcomes of all positions sampled the full range of possible allosteric coupling (full tunability). However, that study only evaluated allosteric tunability of “local” positions, i.e., positions were located near the binding sites of the allosteric ligand being assessed. Here, we evaluated tunability of allosteric coupling when mutated sites were distant from the allosterically-coupled binding sites. Positions near the Ala binding site had rheostat outcomes on allosteric coupling between Fru-1,6-BP and PEP binding. In contrast, positions in the Fru-1,6-BP site exhibited modest effects on coupling between Ala and PEP binding. Analyzed in aggregate, both PEP/Ala and PEP/Fru-1,6-BP coupling were again fully tunable by amino acid substitutions at this limited set of distant positions. Furthermore, some positions exhibited rheostatic control over multiple parameters and others exhibited rheostatic effects on one parameter and toggle control over a second. These findings highlight challenges in efforts to both predict/interpret mutational outcomes and engineer functions into proteins.
Systematic discovery of Short Linear Motifs decodes calcineurin phosphatase signaling
Authors: Wigington Callie P. , Roy Jagoree , Damle Nikhil P. , Yadav Vikash K. , Blikstad Cecilia , Resch Eduard , Wong Cassandra J. , Mackay Douglas R. , Wang Jennifer T. , Krystkowiak Izabella , Bradburn Devin , Tsekitsidou Eirini , Hong Su Hyun , Kaderali Malika Amyn , Xu Shou-Ling , Stearns Tim , Gingras Anne-Claude , Ullman Katharine S. , Ivarsson Ylva , Davey Norman E. , Cyert Martha S.
Published: May 2019

Short linear motifs (SLiMs) drive dynamic protein-protein interactions essential for signaling, but sequence degeneracy and low binding affinities make them difficult to identify. We harnessed unbiased systematic approaches for SLiM discovery to elucidate the regulatory network of calcineurin (CN)/PP2B, the Ca2+-activated phosphatase that recognizes LxVP and PxIxIT motifs. In vitro proteome-wide detection of CN-binding peptides, in vivo SLiM-dependent proximity labeling, and in silico modeling of motif determinants uncovered unanticipated CN interactors, including NOTCH1, which we establish as a CN substrate. Unexpectedly, CN shows SLiM-dependent proximity to centrosomal and nuclear pore complex (NPC) proteins – structures where Ca2+ signaling is largely uncharacterized. CN dephosphorylates human and yeast NPC proteins and promotes accumulation of a nuclear transport reporter, suggesting conserved NPC regulation by CN. The CN network assembled here provides a resource to investigate Ca2+ and CN signaling and demonstrates synergy between experimental and computational methods, establishing a blueprint for examining SLiM-based networks.
Physiotherapist confidence level in mobilising stroke patients after decompressive hemicraniectomy: are helmets useful?
Authors: Budhdeo Sanjay , Meek Toby , Cosco Theodore D , Turaga Sanchit , Chari Aswin , Sharma Nikhil
Published: May 2019

Introduction

Decompressive hemicraniectomy is a lifesaving measure in malignant middle cerebral artery infarction; however, this leaves patients with a skull defect. There is variability of helmet use in this patient group across Britain. We aimed to examine whether (1) specialist physiotherapist were more confident mobilising a patient with hemiparesis and skull defect than a non-specialist physiotherapist (2) non-specialist and specialist physiotherapists would be more comfortable mobilising this patient with a helmet as opposed to without a helmet.

Methods

We carried out a cross-sectional online survey of specialist physiotherapists and non-specialist physiotherapists in Britain. Recruitment was through mailing lists. Physiotherapists were asked to rank their confidence level on a 5-point Likert scale of mobilising an example patient with and without a helmet. They were also asked about the number of additional therapists needed to safely mobilise the patient.

Findings

96 physiotherapists completed the survey; 44 were specialists and 52 were non-specialists. Specialist physiotherapists felt more comfortable mobilising patients (mean difference = 0.68, p < 0.001). Non-specialist physiotherapists felt significantly more comfortable mobilising patients with a helmet (mean difference = 0.96, p value < 0.001), as did specialist physiotherapists (mean difference = 0.68, p value < 0.001). There was no difference in confidence level arising from helmet use between the two groups (p = 0.72).

Conclusions

Use of helmets may allow specialist and non-specialist physiotherapists to feel more comfortable when mobilising stroke patients post-decompressive hemicraniectomy. Consideration should be made by hospitals and health systems for the provision of helmets this patient group, to maximise functional gains.
Generating kinetic environments to study dynamic cellular processes in single cells
Authors: Thiemicke Alexander , Jashnsaz Hossein , Li Guoliang , Neuert Gregor
Published: May 2019

Cells of any organism are consistently exposed to changes over time in their environment. The kinetics by which these changes occur are critical for the cellular response and fate decision. It is therefore important to control the temporal changes of extracellular stimuli precisely to understand biological mechanisms in a quantitative manner. Most current cell culture and biochemical studies focus on instant changes in the environment and therefore neglect the importance of kinetic environments. To address these shortcomings, we developed two experimental methodologies to precisely control the environment of single cells. These methodologies are compatible with standard biochemistry, molecular, cell and quantitative biology assays. We demonstrate applicability by obtaining time series and time point measurements in both live and fixed cells. We demonstrate the feasibility of the methodology in yeast and mammalian cell culture in combination with widely used assays such as flow cytometry, time-lapse microscopy and single-molecule RNA Fluorescent in-situ Hybridization. Our experimental methodologies are easy to implement in most laboratory settings and allows the study of kinetic environments in a wide range of assays and different cell culture conditions.
Automated cell boundary and 3D nuclear segmentation of cells in suspension
Authors: Kesler Benjamin , Li Guoliang , Thiemicke Alexander , Venkat Rohit , Neuert Gregor
Published: May 2019

To characterize cell types, cellular functions and intracellular processes, an understanding of the differences between individual cells is required. Although microscopy approaches have made tremendous progress in imaging cells in different contexts, the analysis of these imaging data sets is a long-standing, unsolved problem. The few robust cell segmentation approaches that exist often rely on multiple cellular markers and complex time-consuming image analysis. Recently developed deep learning approaches can address some of these challenges, but they require tremendous amounts of data and well-curated reference data sets for algorithm training. We propose an alternative experimental and computational approach, called CellDissect, in which we first optimize specimen preparation and data acquisition prior to image processing to generate high quality images that are easier to analyze computationally. By focusing on fixed suspension and dissociated adherent cells, CellDissect relies only on widefield images to identify cell boundaries and nuclear staining to automatically segment cells in two dimensions and nuclei in three dimensions. This segmentation can be performed on a desktop computer or a computing cluster for higher throughput. We compare and evaluate the accuracy of different nuclear segmentation approaches against manual expert cell segmentation for different cell lines acquired with different imaging modalities.
FGF signalling plays similar roles in development and regeneration of the skeleton in the brittle starAmphiura filiformis
Authors: Czarkwiani Anna , Dylus David V. , Carballo Luisana , Oliveri Paola
Published: May 2019

Regeneration is an adult developmental process considered to be an epiphenomenon of embryonic development. Although several studies have shown that various embryonic genes are expressed during regeneration, there have been no large-scale, direct and functional comparative studies between the development and regeneration of a specific structure in one animal. Here, we use the brittle starAmphiura filiformisto characterise the role of the FGF signalling pathway during skeletal development and regeneration. In both processes, we find the ligands expressed in ectodermal cells flanking underlying mesodermal cells, and the receptors expressed specifically by these skeletogenic cells. Perturbation of FGF but not VEGF signalling during skeletogenesis completely inhibited skeleton formation in both embryogenesis and regeneration, without affecting other key developmental processes like cell migration or proliferation. Transcriptome-wide differential analysis identified a highly similar cohort of skeletogenic differentiation genes downstream of the FGF signalling pathway, whereas upstream transcription factors involved in the initial specification of the skeletogenic lineage where unaffected. Comparison to the sea urchin indicated that many of the affected genes are associated with differentiation. Moreover, several genes showed no homology to a cohort from other species, leading to the discovery of brittle star specific, downstream skeletogenic genes. In conclusion, our results show that the FGF pathway is crucial for skeletogenesis in the brittle star, as it is in other deuterostomes, and for the first time provide evidence for the re-deployment of a gene regulatory module during both regeneration and development.
Validation study of a diffusion MRI derived vessel density biomarker for detecting viral hepatitis-b induced liver fibrosis
Authors: Xiao Ben-Heng , Huang Hua , Wang Li-Fei , Qiu Shi-Wen , Guo Sheng-Wen , Wáng Yì Xiáng J.
Published: May 2019

Aim

Liver vessel density can be evaluated by an imaging biomarker DDVD (diffusion derived vessel density): DDVD/area(b0b2) = Sb0/ROIarea0 – Sb2/ROIarea2, where Sb0 and Sb2 refer to the liver signal whenbis 0 or 2 (s/mm2); ROIarea0 and ROIarea2 refer to the region-of-interest onb= 0 or 2 images; and Sb2 may be replaced by Sb15 (b=15). This concept was validated in this study.

Materials and Methods

Liver diffusion images were acquired at 1.5T. For a scan-rescan repeatability study of 6 subjects,b-values of 0 and 2 were used. The validation study composed of 26 healthy volunteers and 19 consecutive suspected chronic viral hepatitis-b patients, and diffusion images with 16b-values of 0, 2, 4, 7, 10, 15, 20, 30, 46, 60, 72, 100, 150, 200, 400, 600 were acquired. Four patients did not have liver fibrosis, and the rest were four stage-1, three stage-2, four stage 3, and one stage-4 patients respectively.

Results

Intraclass correlation coefficient for repeatability was 0.994 for DDVD/area(Sb0Sb2), and 0.978 for DDVD/area(Sb0Sb15). In the validation study, DDVD/area(Sb0Sb2) and area(Sb0Sb15) were 14.80±3.06 and 26.58±3.97 for healthy volunteers, 10.51±1.51 and 20.15±2.21 for stage 1-2 fibrosis patients, and 9.42±0.87 and 19.42±1.89 for stage 3-4 fibrosis patients. For 16 patients where IVIM analysis was performed, a combination of DDVD/area, PF, and Dfast achieved the best differentiation for non-fibrotic livers and fibrotic livers. DDVD/area were weakly correlated with PF or Dfast.

Conclusion

Both DDVD/area(Sb0Sb2) and area(Sb0Sb15) are useful imaging biomarker to separate fibrotic and non-fibrotic livers, with fibrotic livers had lower measurements.
Liquid condensation drives telomere clustering during ALT
Authors: Zhang Huaiying , Liu Michel , Dilley Robert , Chenoweth David M. , Greenberg Roger A. , Lampson Michael A.
Published: May 2019

Telomerase-free cancer cells employ a recombination-based alternative lengthening of telomeres (ALT) pathway that depends on ALT-associated promyelocytic leukemia (PML) nuclear bodies (APBs), whose function is unclear. We find that APBs behave as liquid condensates, suggesting two potential mechanisms to promote telomere elongation: condensation to enrich DNA repair factors for telomere synthesis and coalescence to cluster telomeres to provide repair templates. Using chemically-induced dimerization, we show that telomere sumoylation nucleates APB condensation via SUMO-SIM (SUMO interaction motif) interactions and clusters telomeres. The induced APBs lack DNA repair factors, indicating that these factors are clients recruited to the APB scaffold rather than components that drive condensation. Telomere clustering, however, relies only on liquid properties of the condensate, as an alternative condensation chemistry also induces clustering. Our results demonstrate how the material properties and chemical composition of APBs independently contribute to ALT, suggesting a general framework for how liquid condensates promote cellular functions.