bluuebunny/crossref_metadata_2025 huggingface dataset:
TASOR is a pseudo-PARP that directs HUSH complex assembly and epigenetic transposon control
Authors: Douse Christopher H. , Tchasovnikarova Iva A. , Timms Richard T. , Protasio Anna V. , Seczynska Marta , Prigozhin Daniil M. , Albecka Anna , Wagstaff Jane , Williamson James C. , Freund Stefan M.V. , Lehner Paul J. , Modis Yorgo
Published: March 2020

The Human Silencing Hub (HUSH) complex epigenetically represses retroviruses, transposons and genes in vertebrates. HUSH therefore maintains genome integrity and is central in the interplay between intrinsic immunity, transposable elements and transcriptional regulation. Comprising three subunits – TASOR, MPP8 and Periphilin – HUSH regulates SETDB1-dependent deposition of the transcriptionally repressive epigenetic mark H3K9me3 and recruits MORC2 to modify local chromatin structure. However the mechanistic roles of each HUSH subunit remain undetermined. Here we show that TASOR lies at the heart of HUSH, providing a platform for assembling the other subunits. Targeted epigenomic profiling supports the model that TASOR binds and regulates H3K9me3 specifically over LINE-1 repeats and other repetitive exons in transcribed genes. We find TASOR associates with several components of the nuclear RNA processing machinery and its modular domain architecture bears striking similarities to that of Chp1, the central component of the yeast RNA-induced transcriptional silencing (RITS) complex. Together these observations suggest that an RNA intermediate may be important for HUSH activity. We identify the TASOR domains necessary for HUSH assembly and transgene repression. Structural and genomic analyses reveal that TASOR contains a poly-ADP ribose polymerase (PARP) domain dispensable for assembly and chromatin localization, but critical for epigenetic regulation of target elements. This domain contains a degenerated and obstructed active site and has hence lost catalytic activity. Together our data demonstrate that TASOR is a pseudo-PARP critical for HUSH complex assembly and H3K9me3 deposition over its genomic targets.
Detailed analysis of public RNAseq data and long non-coding RNA: a proposed enhancement to mesenchymal stem cell characterisation
Authors: Riquier Sebastien , Mathieu Marc , Boureux Anthony , Ruffle Florence , Lemaitre Jean-Marc , Djouad Farida , Gilbert Nicolas , Commes Therese
Published: March 2020

The development of RNA sequencing (RNAseq) and corresponding emergence of public datasets have created new avenues of transcriptional marker search. The long non-coding RNAs (lncRNAs) constitute an emerging class of transcripts with a potential for high tissue specificity and function. Using a dedicated bioinformatics pipeline, we propose to construct a cell-specific catalogue of unannotated lncRNAs and to identify the strongest cell markers. This pipeline usesab initiotranscript identification, pseudoalignment and new methodologies such as a specific k-mer approach for naive quantification of expression in numerous RNAseq data.

For an application model, we focused on Mesenchymal Stem Cells (MSCs), a type of adult multipotent stem-cells of diverse tissue origins. Frequently used in clinics, these cells lack extensive characterisation. Our pipeline was able to highlight different lncRNAs with high specificity for MSCs.In silicomethodologies for functional prediction demonstrated that each candidate represents one specific state of MSCs biology. Together, these results suggest an approach that can be employed to harness lncRNA as cell marker, showing different candidates as potential actors in MSCs biology, while suggesting promising directions for future experimental investigations.
Unlocking the genomic taxonomy of theProchlorococcuscollective
Authors: Tschoeke Diogo , Vidal Livia , Campeão Mariana , Salazar Vinícius W. , Swings Jean , Thompson Fabiano , Thompson Cristiane
Published: March 2020

Prochlorococcusis the most abundant photosynthetic prokaryote on our planet. The extensive ecological literature on theProchlorococcuscollective (PC) is based on the assumption that it comprises one single genus comprising the speciesProchlorococcus marinus, containing itself a collective of ecotypes. Ecologists adopt the distributed genome hypothesis of an open pan-genome to explain the observed genomic diversity and evolution patterns of the ecotypes within PC. Novel genomic data for the PC prompted us to revisit this group, applying the current methods used in genomic taxonomy. As a result, we were able to distinguish the five genera:Prochlorococcus, Eurycolium, Prolificoccus, ThaumococcusandRiococcus. The novel genera have distinct genomic and ecological attributes.
Histone modifications during the life cycle of the brown algaEctocarpus
Authors: Bourdareau Simon , Tirichine Leila , Lombard Bérangère , Loew Damarys , Scornet Delphine , Wu Yue , Coelho Susana M. , Cock J. Mark
Published: March 2020

Background

Brown algae evolved complex multicellularity independently of the animal and land plant lineages and are the third most developmentally complex phylogenetic group on the planet. An understanding of developmental processes in this group is expected to provide important insights into the evolutionary events necessary for the emergence of complex multicellularity. Here we have focused on mechanisms of epigenetic regulation involving post-translational modifications (PTMs) of histone proteins.

Results

A total of 47 histone PTMs were identified, including a novel mark H2AZR38me1, butEctocarpuslacks both H3K27me3 and the major polycomb complexes. ChIP-seq identified PTMs associated with transcription start sites (TSSs) and gene bodies of active genes, and with transposons. H3K79me2 exhibited an unusual pattern, often marking large genomic regions spanning several genes. TSSs of closely spaced divergently transcribed gene pairs shared a common nucleosome depleted region and exhibited shared histone PTM peaks. Overall, patterns of histone PTMs were stable through the life cycle. Analysis of histone PTMs at generation-biased genes identified a correlation between the presence of specific chromatin marks and the level of gene expression.

Conclusions

The overview of histone PTMs in the brown algae presented here will provide a foundation for future studies aimed at understanding the role of chromatin modifications in the regulation of brown algal genomes.
Studying the dynamics of the gut microbiota using metabolically stable isotopic labeling and metaproteomics
Authors: Smyth Patrick , Zhang Xu , Ning Zhibin , Mayne Janice , Moore Jasmine I , Walker Krystal , Lavallée-Adam Mathieu , Figeys Daniel
Published: March 2020

Background

The gut microbiome and its metabolic processes are dynamic systems. Surprisingly, our understanding of gut microbiome dynamics is limited. Here we report a metaproteomic workflow that involves protein stable isotope probing (protein-SIP) and identification and quantification of partially labeled peptides. We also developed a package, which we call MetaProfiler, that corrects for false identifications and performs phylogenetic and time series analysis for the study of gut microbiome functional dynamics.

Results

From the stool sample of five mice that were fed with15N hydrolysate fromRalstonia eutropha, we identified 15,297 non-redundant unlabeled peptides of which 10,839 of their heavy counterparts were quantified. These peptides revealed incorporation profiles over time that were different between and within taxa, as well as between and within clusters of orthologous groups (COGs).

Conclusions

Our study helps unravel the complex dynamics of protein synthesis and bacterial dynamics in the mouse microbiome.

Availability

MetaProfiler and the bioinformatic pipeline are available athttps://github.com/psmyth94/MetaProfiler.git.
Who reviews for predatory journals? A study on reviewer characteristics
Authors: Severin Anna , Strinzel Michaela , Egger Matthias , Domingo Marc , Barros Tiago
Published: March 2020

Background

While the characteristics of scholars who publish in predatory journals are relatively well-understood, nothing is known about the scholars who review for these journals. We aimed to answer the following questions: Can we observe patterns of reviewer characteristics for scholars who review for predatory journals and for legitimate journals? Second, how are reviews for potentially predatory journals distributed globally?

Methods

We matched random samples of 1,000 predatory journals and 1,000 legitimate journals of the Cabells Scholarly Analytics’ journal lists with the Publons database of review reports, using the Jaro-Winkler string metric. For reviewers of matched reviews, we descriptively analysed meta-data on reviewing and publishing behaviour.

Results

We matched 183,743 unique Publons reviews that were claimed by 19,598 reviewers. 6,077 reviews were conducted for 1160 unique predatory journals (3.31% of all reviews). 177,666 were claimed for 6,403 legitimate journals (96.69% of all reviews). The vast majority of scholars either never or only occasionally submitted reviews for predatory journals to Publons (89.96% and 7.55% of all reviewers, respectively). Smaller numbers of scholars claimed reviews predominantly or exclusively for predatory journals (0.26% and 0.35% of all reviewers, respectively). The two latter groups of scholars are of younger academic age and have fewer publications and fewer reviews than the first two groups of scholars.Developing regions feature larger shares of reviews for predatory reviews than developed regions.

Conclusion

The characteristics of scholars who review for potentially predatory journals resemble those of authors who publish their work in these outlets. In order to combat potentially predatory journals, stakeholders will need to adopt a holistic approach that takes into account the entire research workflow.
Visualizing protein-protein interactions in plants by rapamycin-dependent delocalization
Authors: Winkler Joanna , Mylle Evelien , De Meyer Andreas , Pavie Benjamin , Merchie Julie , Grones Peter , Van Damme Daniël
Published: March 2020

Identifying protein-protein interactions (PPI) is crucial for understanding biological processes. Many PPI tools are available, yet only some function within the context of a plant cell. Narrowing down even further, only a few tools allow complex multi-protein interactions to be visualized. Here, we present a conditionalin vivoPPI tool for plant research that meets these criteria. Knocksideways in plants (KSP) is based on the ability of rapamycin to alter the localization of a bait protein and its interactors via the heterodimerization of FKBP and FRB domains. KSP is inherently free from many limitations of other PPI systems. Thisin vivotool does not require spatial proximity of the bait and prey fluorophores and it is compatible with a broad range of fluorophores. KSP is also a conditional tool and therefore the visualization of the proteins in the absence of rapamycin acts as an internal control. We used KSP to confirm previously identified interactions inNicotiana benthamianaleaf epidermal cells. Furthermore, the scripts that we generated allow the interactions to be quantified at high throughput. Finally, we demonstrate that KSP can easily be used to visualize complex multi-protein interactions. KSP is therefore a versatile tool with unique characteristics and applications that complements other plant PPI methods.
BonVision – an open-source software to create and control visual environments
Authors: Lopes Gonçalo , Farrell Karolina , Horrocks Edward A. B. , Lee Chi-Yu , Morimoto Mai M. , Muzzu Tomaso , Papanikolaou Amalia , Rodrigues Fabio R. , Wheatcroft Thomas , Zucca Stefano , Solomon Samuel G. , Saleem Aman B.
Published: March 2020

Real-time rendering of closed-loop visual environments is necessary for next-generation understanding of brain function and behaviour, but is prohibitively difficult for non-experts to implement and is limited to few laboratories worldwide. We developed BonVision as an easy-to-use open-source software for the display of virtual or augmented reality, as well as standard visual stimuli. As the architecture is based on the open-source Bonsai graphical programming language, BonVision benefits from native integration with experimental hardware. BonVision therefore enables easy implementation of closed-loop experiments, including real-time interaction with deep neural networks and communication with behavioural and physiological measurement and manipulation devices.
Communication through coherence by means of cross-frequency coupling
Authors: González Joaquín , Cavelli Matias , Mondino Alejandra , Rubido Nicolás , Tort Adriano BL , Torterolo Pablo
Published: March 2020

The theory of communication through coherence (CTC) posits the synchronization of brain oscillations as a key mechanism for information sharing and perceptual binding. In a parallel literature, hippocampal theta activity (4 – 10 Hz) has been shown to modulate the appearance of neocortical fast gamma oscillations (100 – 150 Hz), a phenomenon known as cross-frequency coupling (CFC). Even though CFC has also been previously associated with information routing, it remains to be determined whether it directly relates to CTC. In particular, for the theta-fast gamma example at hand, a critical question is to know if the phase of the theta cycle influences gamma synchronization across the neocortex. To answer this question, we designed a new screening method for detecting the modulation of the cross-regional high-frequency synchronization by the phase of slower oscillations. Upon applying the method, we found that the long-distance synchronization of neocortical fast gamma during REM sleep depends on the instantaneous phase of the theta rhythm. These results show that CFC is likely to aid long-range information transfer by facilitating the cross-regional synchronization of faster rhythms, thus consistent with classical CTC views.
A Data-driven Surrogate Model for Work Computation of a Periodically Forced Half-Sarcomere
Authors: Rudy Samuel H. , Williams C. David , Kutz J. Nathan , Daniel Thomas L.
Published: March 2020

Muscle force generation follows from molecular scale interactions that drive macroscopic behaviors and macroscopic processes that influence those at the molecular scale. A particuarly challenging issue is that models at the molecular level of organization are often quite difficult to apply to larger spatial scales. This is particularly true of moleuclar models driven by Monte-Carlo simulations. This challenge of multiscale dynamics requires methods to extract reduced order behaviors from detailed high-dimensional simulations. In this work we present a novel deterministic simulation method yielding accurate predictions of force-length behaviors of contracting muscle sarcomeres undergoing periodic length changes (work loops). The model maintains interpretability by tracking macroscopic state variables throughout the simulation while using data-driven representations of dynamics. Parameters of the data-driven dynamics are learned from trajectories from Monte-Carlo simulations of a half-sarcomere. Our method significantly reduces computational cost by tracking the state of the sarcomere in a course grained set of variables while maintaining accurate prediction of macroscopic level observables and time series for course grained variables. This allows for rapid sampling of the model’s output and builds towards the ability to scale to multiple-sarcomere simulations.

Author Summary

We develop a data-driven surrogate model for the dynamics of the half-sarcomere. This model achieves the same behavior with respect to force traces as more sophisticated Monte Carlo models at a substantially lower computational cost. The model is built by finding a course grained description of the full state space of the Monte Carlo simulation and learning dynamical models on the course grained space. Data-driven representations of the dynamics in the course grained space are trained using data from the full model. Data-driven models for forcing are also learned, and the result fed back into the dynamics. In doing so, the model seeks to replicate the effects of filament compliance on macro scale dynamics without explicitly tracking micro scale features. We withhold some input parameter regimes and demonstrate accurate reconstruction of course grained state and force traces using the data-driven model and given only knowledge of the initial condition and input. This work allows for faster computation of the forcing behavior of the half-sarcomere, as well as consistent representations of the course grained state variables. It is therefore promising as a step towards multi-sarcomere or even tissue scale models of skeletal muscle.
D-Retro Inverso (DRI) Amylin and the Stability of Amylin Fibrils
Authors: Pandey Preeti , Nguyen Natalie , Hansmann Ulrich H.E.
Published: March 2020

Motivated by the role that amylin aggregates pay in type-II diabetes, we compare the stability of regular amylin fibrils with the stability of fibrils where L-amino acid chains are replaced by D-Retro Inverso (DRI) amylin,i.e., peptides where the sequence of amino acids is reversed, and at the same time the L-amino acids are replaced by their mirror images. Our molecular dynamics simulations show that despite leading to only marginal difference in fibril structure and stability, aggregating DRI-amylin peptides have different pattern of contacts and hydrogen bonding. Because of these differences does DRI-amylin, when interacting with regular (L) amylin, alter the elongation process and lowers the stability of hybrid amylin fibrils. Our results suggest not only a potential use of DRI-amylin as inhibitor of amylin fibril-formation, but points also to the possibility of using insertion of DRI-proteins in L-assemblies as a way to probe the role of certain kinds of hydrogen bonds in supra-molecular assemblies or aggregates.
A simple, scalable approach to building a cross-platform transcriptome atlas
Authors: Angel Paul W , Rajab Nadia , Deng Yidi , Pacheco Chris M , Chen Tyrone , Lê Cao Kim-Anh , Choi Jarny , Wells Christine A
Published: March 2020

Gene expression atlases have transformed our understanding of the development, composition and function of human tissues. New technologies promise improved cellular or molecular resolution, and have led to the identification of new cell types, or better defined cell states. But as new technologies emerge, information derived on old platforms becomes obsolete. We demonstrate that it is possible to combine a large number of different profiling experiments summarised from dozens of laboratories and representing hundreds of donors, to create an integrated molecular map of human tissue. As an example, we combine 850 samples from 38 platforms to build an integrated atlas of human blood cells. We achieve robust and unbiased cell type clustering using a variance partitioning method, selecting genes with low platform bias relative to biological variation. Other than an initial rescaling, no other transformation to the primary data is applied through batch correction or renormalisation. Additional data, including single-cell datasets, can be projected for comparison, classification and annotation. The resulting atlas provides a multi-scaled approach to visualise and analyse the relationships between sets of genes and blood cell lineages, including the maturation and activation of leukocytes in vivo and in vitro.

In allowing for data integration across hundreds of studies, we address a key reproduciblity challenge which is faced by any new technology. This allows us to draw on the deep phenotypes and functional annotations that accompany traditional profiling methods, and provide important context to the high cellular resolution of single cell profiling. Here, we have implemented the blood atlas in the open access Stemformatics.org platform, drawing on its extensive collection of curated transcriptome data. The method is simple, scalable and amenable for rapid deployment in other biological systems or computational workflows.

Graphical abstract

Recursive approach to generating a multi-scaled atlas. Top panel: The method integrates data from all cell types in the Stemformatics database, and shows clear division of samples into global categories of stromal, pluripotent or blood (inset) cell types. Bottom panel: Integration of only the blood cell subsets provides a blood atlas. Projection of external samples (green) onto the blood atlas. Samples are coloured by curated annotations derived from the original studies, and can be viewed atStemformatics.org
ZNF423 orthologs are highly constrained in vertebrates but show domain-level plasticity across invertebrate lineages
Authors: Hamilton Bruce A.
Published: March 2020

ZNF423encodes 30 C2H2 zinc fingers that bind DNA and a variety of lineage- and signal-dependent transcription factors.ZNF423genetic variants are proposed to cause neurodevelopmental and ciliopathy-related disorders in humans. Mouse models show midline brain defects, including cerebellar vermis hypoplasia, and defects in adipogenesis. Here I show strong protein sequence constraint among 165 vertebrate orthologs. In contrast, orthologs from invertebrate lineages, spanning larger time intervals, show substantial differences in zinc finger number, arrangement, and identity. A terminal zinc finger cluster common among other lineages was independently lost in vertebrates and insects. Surprisingly, a moderately-constrained non-C2H2 sequence with potential to form a C4-class zinc finger is a previously-unrecognized conserved feature of nearly all identified homologs. These results highlight evolutionary dynamics of a likely signal integration node across species with distinct developmental strategies and body plans. Functions of the newly identified C4-like sequence and lineage-specific fingers remain to be studied.
Mechanisms of γ-Secretase Activation and Substrate Processing
Authors: Bhattarai Apurba , Devkota Sujan , Bhattarai Sanjay , Wolfe Michael S. , Miao Yinglong
Published: March 2020

Amyloid β-peptide, the principal component of characteristic cerebral plaques of Alzheimer’s disease (AD), is produced through intramembrane proteolysis of the amyloid precursor protein (APP) by γ-secretase. Despite the importance in pathogenesis of AD, the mechanisms of intramembrane proteolysis and substrate processing by γ-secretase remain poorly understood. Here, complementary all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method and biochemical experiments were combined to investigate substrate processing of wildtype and mutant APP by γ-secretase. The GaMD simulations captured spontaneous activation of γ-secretase, with hydrogen bonded catalytic aspartates and water poised for proteolysis of APP at the ε cleavage site. Furthermore, GaMD simulations revealed that familial AD mutations I45F and T48P enhanced the initial ε cleavage between residues Leu49-Val50, while M51F mutation shifted the ε cleavage site to the amide bond between Thr48-Leu49. Detailed analysis of the GaMD simulations allowed us to identify distinct low-energy conformational states of γ-secretase, different secondary structures of the wildtype and mutant APP substrate, and important active-site sub-pockets for catalytic function of the enzyme. The simulation findings were highly consistent with experimental analyses of APP proteolytic products using mass spectrometry and western blotting. Taken together, the GaMD simulations and biochemical experiments have enabled us to elucidate the mechanisms of γ-secretase activation and substrate processing, which should facilitate rational computer-aided drug design targeting this functionally important enzyme.
Noise-correlation is Modulated by Reward Expectation in the Primary Motor Cortex Bilaterally During Manual and Observational Tasks in Primates
Authors: Moore Brittany , Khang Sheng , Francis Joseph Thachil
Published: March 2020

Reward modulation is represented in the motor cortex (M1) and could be used to implement more accurate decoding models to improve brain computer interfaces (BCIs) (Zhao et al. 2018). Analyzing trial-to-trial noise-correlations between neural units in the presence of rewarding (R) and non-rewarding (NR) stimuli adds to our understanding of cortical network dynamics. We utilized Pearson’s correlation coefficient to measure shared variability between simultaneously recorded units (32 – 112) and found significantly higher noise-correlation and positive correlation between the populations’ signal- and noise-correlation during NR trials as compared to R trials. This pattern is evident in data from two non-human primates (NHPs) during single-target center out reaching tasks, both manual and action observation versions. We conducted mean matched noise-correlation analysis in order to decouple known interactions between event triggered firing rate changes and neural correlations. Isolated reward discriminatory units demonstrated stronger correlational changes than units unresponsive to reward firing rate modulation, however the qualitative response was similar, indicating correlational changes within the network as a whole can serve as another information channel to be exploited by BCIs that track the underlying cortical state, such as reward expectation, or attentional modulation. Reward expectation and attention in return can be utilized with reinforcement learning towards autonomous BCI updating.
Investigating the effect of glycaemic traits on the risk of psychiatric illness using Mendelian randomisation
Authors: Adams Danielle M. , Reay William R. , Geaghan Michael P. , Cairns Murray J.
Published: March 2020

Data from observational studies have suggested an involvement of abnormal glycaemic regulation in the pathophysiology of psychiatric illness. This may be an attractive target for clinical intervention as glycaemia can be modulated by both lifestyle factors and pharmacological agents. However, observational studies are inherently confounded, and therefore causal relationships cannot be reliably established. We employed genetic variants rigorously associated with three glycaemic traits (fasting glucose, fasting insulin, and glycated haemoglobin) as instrumental variables in a two-sample Mendelian randomisation analysis to investigate the causal effect of these measures on the risk for eight psychiatric disorders. A significant protective effect of a unit increase in fasting insulin levels was observed for anorexia nervosa after the application of multiple testing correction (OR = 0.48 [95% CI: 0.33-0.71] – inverse-variance weighted estimate. The relationship between fasting insulin and anorexia nervosa was supported by a suite of sensitivity analyses, with no statistical evidence of instrument heterogeneity or horizontal pleiotropy. Further investigation is required to explore the relationship between insulin levels and anorexia.
Genome-centric portrait of the microbes’ cellulolytic competency
Authors: Wang Yubo , Li Liguan , Xia Yu , Ju Feng , Zhang Tong
Published: March 2020

Neither the abundance of the exo/endoglucase GH modules nor the taxonomy affiliation is informative enough in inferring whether a genome is of a potential cellulolytic microbe or not. By interpreting the complete genomes of 2642 microbe strains whose phenotypes have been well documented, we are trying to reveal a more reliable genotype and phenotype correlation on the specific function niche of cellulose hydrolysis. By incorporating into the annotation approach an automatic recognition of the potential synergy machineries, a more reliable prediction on the corresponding microbes’ cellulolytic competency could be achieved. The potential cellulose hydrolyzing microbes could be categorized into 5 groups according to the varying synergy machineries among the carbohydrate active modules/genes annotated. Results of the meta-analysis on the 2642 genomes revealed that some cellulosome gene clusters were in lack of the surface layer homology module (SLH) and microbe strains annotated with such cellulosome gene clusters were not certainly cellulolytic. Hypothesized in this study was that cellulosome-independent genes harboring both the SLH module and the cellulose-binding carbohydrate binding module (CBM) were likely an alternative gene apparatus initiating the formation of the cellulose-enzyme-microbe (CEM) complexes; and their role is important especially for the cellulolytic anaerobes without cellulosome gene clusters.

Importance

In the genome-centric prediction on the corresponding microbes’ cellulolytic activity, recognition of the synergy machineries that include but are not limited to the cellulosome gene clusters is equally important as the annotation of the individual carbohydrate active modules or genes. This is the first time that a pipeline was developed for an automatic recognition of the synergy among the carbohydrate active units annotated. With promising resolution and reliability, this pipeline should be a good add to the bioinformatic tools for the genome-centric interpretations on the specific function niche of cellulose hydrolysis.
Tilorone: A Broad-Spectrum Antiviral For Emerging Viruses
Authors: Ekins Sean , Madrid Peter B.
Published: March 2020

Tilorone is a 50-year-old synthetic small-molecule compound with antiviral activity that is proposed to induce interferon after oral administration. This drug is used as a broad-spectrum antiviral in several countries of the Russian Federation. We have recently described activityin vitroandin vivoagainst the Ebola Virus. After a broad screening of additional viruses, we now describein vitroactivity against Chikungunya virus (CHIK) and Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV).
OncoGEMINI: Software for Investigating Tumor Variants From Multiple Biopsies With Integrated Cancer Annotations
Authors: Nicholas Thomas J. , Cormier Michael J. , Huang Xiaomeng , Qiao Yi , Marth Gabor T. , Quinlan Aaron R.
Published: March 2020

DNA sequencing has unveiled extensive tumor heterogeneity in several different cancer types, with many exhibiting diverse subclonal populations. Identifying and tracing mutations throughout the expansion and progression of a tumor represents a significant challenge. Furthermore, prioritizing the subset of such mutations most likely to contribute to tumor evolution or that could serve as potential therapeutic targets represents an ongoing problem. Here we describe OncoGEMINI, a new tool designed for exploring the complex patterns and trajectory of somatic and inherited variation observed in heterogeneous tumors biopsied over the course of treatment. This is accomplished by creating a searchable database of variants that includes tumor sampling timepoints and allows for filtering methods that reflect specific changes in variant allele frequencies over time. Additionally, by incorporating existing annotations and resources that facilitate the interpretation of cancer mutations (e.g., CIViC, DGIdb), OncoGEMINI enables rapid searches for, and potential identification of, mutations that may be driving subclonal evolution.
Transcriptional repression of Myc underlies AGO1’s tumour suppressor function
Authors: Zaytseva Olga , Mitchell Naomi C. , Guo Linna , Marshall Owen J. , Parsons Linda M. , Hannan Ross D. , Levens David L. , Quinn Leonie M.
Published: March 2020

Here we report novel tumour suppressor activity for theDrosophilaArgonaute family RNA binding protein AGO1, a component of the miRNA-dependent RNA-induced silencing complex (RISC). The mechanism for growth inhibition does not, however, involve canonical roles as part of the RISC; rather AGO1 controls cell and tissue growth by functioning as a direct transcriptional repressor of the master regulator of growth, Myc. AGO1 depletion in wing imaginal discs drives a significant increase in ribosome biogenesis, nucleolar expansion, and cell growth in a manner dependent on Myc abundance. Moreover, increasedMycpromoter activity and elevatedMycmRNA in AGO1 depleted animals requires RNA Pol II transcription. Further support for transcriptional AGO1 functions is provided by physical interaction with the RNA Pol II transcriptional machinery (chromatin remodelling factors and Mediator Complex), punctate nuclear localisation in euchromatic regions and overlap with Polycomb Group transcriptional silencing loci. Moreover, significant AGO1 enrichment is observed on theMycpromoter and AGO1 interacts with theMyctranscriptional activator Psi. Together our data show AGO1 functions outside of the RISC to repressMyctranscription and inhibit developmental cell and tissue growth.
Molecular basis of ubiquitination catalyzed by the bacterial transglutaminase MavC
Authors: Guan Hongxin , Fu Jiaqi , Yu Ting , Wang Zhao-Xi , Gan Ninghai , Huang Yini , Perčulija Vanja , Li Yu , Luo Zhao-Qing , Ouyang Songying
Published: March 2020

TheLegionella pneumophilaeffector MavC is a transglutaminase that carries out atypical ubiquitination of the ubiquitin (Ub) E2 conjugation enzyme UBE2N by catalyzing the formation of an isopeptide bond between Gln40 of Ub and Lys92 (or to a less extent, Lys94) of UBE2N, which results in inhibition of UBE2N signaling in the NF-κB pathway. In the absence of UBE2N, MavC deamidates Ub at Gln40 or catalyzes self-ubiquitination. However, the mechanisms underlying these enzymatic activities of MavC are not fully understood at molecular level. In this study, we obtained the structure of the MavC-UBE2N-Ub ternary complex that represents a snapshot of covalent cross-linking of UBE2N and Ub catalyzed by MavC. The structure reveals the unique way by which the cross-linked catalytic product UBE2N-Ub binds mainly to the Insertion and the Tail domains of MavC prior to its release. Based on our structural, biochemical and mutational analyses, we proposed the catalytic mechanism for both the deamidase and the transglutaminase activities of MavC. Finally, by comparing the structures of MavC and MvcA, the homologous protein that reverses MavC-induced UBE2N ubiquitination, we identified several key regions of the two proteins responsible for their opposite enzymatic activity. Our results provide insights into the mechanisms for substrate recognition and ubiquitination mediated by MavC as well as explanations for the opposite activity of MavC and MvcA.
Biophysical forces rewire cell metabolism to guide microtubule-dependent cell mechanics
Authors: Torrino Stephanie , Audebert Stephane , Belhadj Ilyes , Lacoux Caroline , Pisano Sabrina , Abélanet Sophie , Brau Frederic , Chan Stephen Y. , Mari Bernard , Oldham William M , Bertero Thomas
Published: March 2020

Mechanical signals regulate cell shape and influence cell metabolism and behavior. Cells withstand external forces by adjusting the stiffness of its cytoskeleton. Microtubules (MTs) act as compression-bearing elements in response to mechanical cues. Therefore, MT dynamics affect cell mechanics. Yet, how mechanical loads control MT dynamics to adjust cell mechanics to its locally constrained environment has remained unclear. Here, we show that mechanical forces rewire glutamine metabolism to promote MT glutamylation and force cell mechanics, thereby modulating mechanodependent cell functions. Pharmacologic inhibition of glutamine metabolism decreased MT glutamylation and affected their mechanical stabilization. Similarly, depletion of the tubulin glutamylase TTLL4 or overexpression of tubulin mutants lacking glutamylation site(s) increased MT dynamics, cell compliance and contractility, and thereby impacted cell spreading, proliferation and migration. Together our results indicate that mechanical cues sustain cell mechanics through glutaminolysis-dependent MT glutamylation, linking cell metabolism to MT dynamics and cell mechanics. Furthermore, our results decipher part of the enigmatic tubulin code that coordinates the fine tunable properties of MT mechanics, allowing cells to adjust the stiffness of their cytoskeleton to the mechanical loads of their environment.
Less is more: Light sampling via throttled visual phototransduction robustly synchronizes theDrosophilacircadian clock in the absence of Cryptochrome
Authors: Ogueta Maite , Hardie Roger C , Stanewsky Ralf
Published: March 2020

The daily changes of light and dark exemplify a prominent cue for the synchronization of internal circadian clocks to external time. The match between external and internal time is crucial for the fitness of organisms and desynchronization has been linked to numerous physical and mental health problems in humans. Organisms therefore developed complex and not fully understood mechanisms to synchronize their circadian clock to light. In mammals and inDrosophilaboth the visual system and dedicated non-image forming photoreceptors contribute to light resetting of the circadian clock. In the fruit fly, light-dependent degradation of the clock protein TIMELESS (TIM) by the blue light photoreceptor Cryptochrome is considered the main mechanism for clock synchronization, although the visual system also contributes. In order to understand the nature of the visual system contribution, we generated a genetic variant exhibiting extremely slow phototransduction kinetics, yet normal sensitivity. We show that in this variant the visual system is able to contribute its full share to circadian clock entrainment, both with regard to behavioral and molecular synchronization to light:dark cycles. This function depends on an alternative Phospholipase C-ß enzyme, encoded byPLC21C, presumably playing a dedicated role in clock resetting by light. We show that this pathway requires the ubiquitin ligase CULLIN-3, presumably mediating CRY-independent degradation of TIM during light:dark cycles. Our results suggest that visual system contribution to circadian clock entrainment operates on a drastically slower time scale compared with fast, visual and image forming phototransduction. Our findings are therefore consistent with the general idea that the visual system samples light over prolonged periods of time (hours) in order to reliably synchronize their internal clocks with the external time.
Peripheral tolerance checkpoints imposed by ubiquitous antigen expression limit antigen-specific B-cell responses under strongly immunogenic conditions
Authors: Brooks Jeremy F. , Murphy Peter R. , Barber James E.M. , Wells James W. , Steptoe Raymond J.
Published: March 2020

A series of layered peripheral checkpoints maintain self-reactive B cells in an unresponsive state. Autoantibody production occurs when these checkpoints are breached, however, when and how this occurs is largely unknown. In particular, how self-reactive B cells are restrained during bystander inflammation in otherwise healthy individuals is poorly understood. A weakness has been the unavailability of methods capable of dissecting physiologically-relevant B-cell responses, without the use of an engineered B-cell receptor. Resolving this will provide insights that decipher how this process goes awry during autoimmunity or could be exploited for therapy. Here we use a strong adjuvant to provide bystander innate and adaptive signals that promote B-cell responsiveness, in conjunction with newly developed B cell detection tools to study in detail the ways that peripheral tolerance mechanisms limit the expansion and function of self-reactive B cells activated under these conditions. We show that although autoreactive B cells are recruited into the germinal centre, their development does not proceed, possibly through rapid counter-selection. Consequently, differentiation of plasma cells is blunted, and autoantibody responses are transient and devoid of affinity maturation. We propose this approach and these tools can be more widely applied to track antigen-specific B cell responses to more disease relevant antigens, without the need for BCR transgenic mice, in settings where tolerance pathways are compromised or have been genetically manipulated to drive stronger insights into the biology underlying B cell-mediated autoimmunity.
Fact retrieval or compacted procedures in arithmetic – a neurophysiological investigation of two hypotheses
Authors: Grabner Roland H. , Brunner Clemens , Lorenz Valerie , Vogel Stephan E. , De Smedt Bert
Published: March 2020

There is broad consensus that adults solve single-digit multiplication problems almost exclusively by fact retrieval (i.e., retrieval of the solution from an arithmetic fact network). In contrast, there has been a long-standing debate on the cognitive processes involved in solving single-digit addition problems. This debate has evolved around two theoretical accounts. Thefact-retrieval accountpostulates that these are solved through fact retrieval, just like multiplications, whereas thecompacted-procedure accountproposes that solving very small additions (i.e., problems with operands between 1 and 4) involves highly automatized and unconscious compacted procedures. In the present electroencephalography (EEG) study, we put these two accounts to the test by comparing neurophysiological correlates of solving very small additions and multiplications. A sample of 40 adults worked on an arithmetic production task involving all (non-tie) single-digit additions and multiplications. Afterwards, participants completed trial-by-trial strategy self-reports. In our EEG analyses, we focused on induced activity (event-related synchronization/desynchronization, ERS/ERD) in three frequency bands (theta, lower alpha, upper alpha). Across all frequency bands, we found higher evidential strength for similar rather than different neurophysiological processes accompanying the solution of very small addition and multiplication problems. This was also true whenn+ 1 andn× 1 problems were excluded from the analyses. In two additional analyses, we showed that ERS/ERD can differentiate between self-reported problem-solving strategies (retrieval vs. procedure) and even betweenn+ 1 andn+mproblems in very small additions, demonstrating its high sensitivity to cognitive processes in arithmetic. The present findings clearly support the fact-retrieval account, suggesting that both very small additions and multiplications are solved through fact retrieval.

HIGHLIGHTS

Neurophysiological test of fact retrieval and compacted procedures account

Induced EEG data are sensitive to cognitive processes in arithmetic problem solving

Both very small additions and multiplications are solved through fact retrieval
The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression
Authors: Petitprez Florent , Lévy Sacha , Sun Cheng-Ming , Meylan Maxime , Linhard Christophe , Becht Etienne , Elarouci Nabila , Roumenina Lubka T. , Ayadi Mira , Sautès-Fridman Catherine , Fridman Wolf H. , de Reyniès Aurélien
Published: March 2020

Quantifying tissue-infiltrating immune and stromal cells provides clinically relevant information for various diseases, notably cancer. While numerous methods allow to quantify immune or stromal cells in human tissue samples based on transcriptomic data, very few are available for mouse studies. Here, we introduce murine Microenvironment Cell Population counter (mMCP-counter), a method based on highly specific transcriptomic markers that allow to accurately quantify 12 immune and 4 stromal murine cell populations. We validated mMCP-counter with flow cytometry data. We also showed that mMCP-counter outperforms existing methods. We showed in mouse models of mesothelioma and kidney cancer that mMCP-counter quantification scores are predictive of response to immune checkpoint blockade Finally, we illustrated mMCP-counter’s potential to analyze immune impacts of Alzheimer’s disease. mMCP-counter is available as an R package from GitHub:https://github.com/cit-bioinfo/mMCP-counter.
DE NOVOSEQUENCING AND ANALYSIS OF THERANA CHENSINENSISTRANSCRIPTOME TO DISCOVER PUTATIVE GENES ASSOCIATED WITH POLYUNSATURATED FATTY ACIDS
Authors: Sun Jingmeng , Wang Zhuoming , Zhang Weiyu
Published: March 2020

Rana chensinensis(R. chensinensis) is an important wild animal found in China, and a precious animal in Chinese herbal medicine.R. chensinensisis rich in polyunsaturated fatty acids (PUFAS). However, information regarding the genes ofR. chensinensisrelated to the synthesis of PUFAs is limited. To identify these genes, we performed Illumina sequencing ofR. chensinensisRNA from the skin and Oviductus Ranae. The Illumina Hiseq 2000 platform was used for sequencing, and the I-Sanger cloud platform was used for transcriptomede novosequencing and information analysis to generate a database. Through the database generated by the transcriptome and the pathway map, we found the pathway for the biosynthesis ofR. chensinensisPUFAs. The Pearson coefficient method was used to analyze the correlation of gene expression levels between samples, and the similarity of gene expression in different tissues and the characteristics in their respective tissues were found. Twelve differentially expressed genes of PUFA in skin and Oviductus Ranae were screened by gene differential expression analysis. The 12 unigenes expression levels of qRT-PCR were used to verify the results of gene expression levels consistent with transcriptome analysis. Based on the sequencing, key genes involved in biosynthesis of unsaturated fatty acids were isolated, which established a biotechnological platform for further research onR. chensinensis.
In silico Design of novel Multi-epitope recombinant Vaccine based on Coronavirus surface glycoprotein
Authors: Behbahani Mandana
Published: March 2020

It is of special significance to find a safe and effective vaccine against coronavirus disease 2019 (COVID-19) that can induce T cell and B cell -mediated immune responses. There is currently no vaccine to prevent COVID-19. In this project, a novel multi-epitope vaccine for COVID-19 virus based on surface glycoprotein was designed through application of bioinformatics methods. At the first, seventeen potent linear B-cell and T-cell binding epitopes from surface glycoprotein were predicted in silico, then the epitopes were joined together via different linkers. The ability of the selected epitopes to induce interferon-gamma was evaluate using IFNepitope web server. One final vaccine was constructed which composed of 398 amino acids and attached to 50S ribosomal protein L7/L12 as adjuvant. Physicochemical properties, as well as antigenicity in the proposed vaccines, were checked for defining the vaccine stability and its ability to induce cell-mediated immune responses. Three-dimensional structure of the mentioned vaccine was subjected to the molecular docking studies with MHC-I and MHC-II molecules. The results proposed that the multi-epitope vaccine with 50S ribosomal protein L7/L12 was a stable construct with high aliphatic content and high antigenicity.