bluuebunny/crossref_metadata_2025 huggingface dataset:
Relating the past with the present: Information integration and segregation during ongoing narrative processing
Authors: Chang Claire H. C. , Lazaridi Christina , Yeshurun Yaara , Norman Kenneth A. , Hasson Uri
Published: January 2020

This study examined how the brain dynamically updates event representations by integrating new information over multiple minutes while segregating irrelevant input. A professional writer custom-designed a narrative with two independent storylines, interleaving across minute-long segments (ABAB). In the last (C) part, characters from the two storylines meet and their shared history is revealed. Part C is designed to induce the spontaneous recall of past events, upon the recurrence of narrative motifs from A/B, and to shed new light on them. Our fMRI results showed storyline-specific neural patterns, which were reinstated (i.e. became more active) during storyline transitions. This effect increased along the processing timescale hierarchy, peaking in the default mode network. Similarly, the neural reinstatement of motifs was found during part C. Furthermore, participants showing stronger motif reinstatement performed better in integrating A/B and C events, demonstrating the role of memory reactivation in information integration over intervening irrelevant events.
The hippocampal formation as a hierarchical generative model supporting generative replay and continual learning
Authors: Stoianov Ivilin , Maisto Domenico , Pezzulo Giovanni
Published: January 2020

We advance a novel computational theory of the hippocampal formation as a hierarchical generative model that organizes sequential experiences, such as rodent trajectories during spatial navigation, into coherent spatiotemporal contexts. We propose that the hippocampal generative model is endowed with inductive biases to identify individual items of experience (first hierarchical layer), organize them into sequences (second layer) and cluster them into maps (third layer). This theory entails a novel characterization of hippocampal reactivations asgenerative replay: the offline resampling of fictive sequences from the generative model, which supports the continual learning of multiple sequential experiences. We show that the model learns and efficiently retains multiple spatial navigation trajectories, by organizing them into spatial maps. Furthermore, the model reproduces flexible and prospective aspects of hippocampal dynamics that are challenging to explain within existing frameworks. This theory reconciles multiple roles of the hippocampal formation in map-based navigation, episodic memory and imagination.
Benchmarking kinetic models ofEscherichia colimetabolism
Authors: Shepelin Denis , Machado Daniel , Nielsen Lars K. , Herrgård Markus J.
Published: January 2020

Predicting phenotype from genotype is the holy grail of quantitative systems biology. Kinetic models of metabolism are among the most mechanistically detailed tools for phenotype prediction. Kinetic models describe changes in metabolite concentrations as a function of enzyme concentration, reaction rates, and concentrations of metabolic effectors uniquely enabling integration of multiple omics data types in a unifying mechanistic framework. While development of such models forEscherichia colihas been going on for almost twenty years, multiple separate models have been established and systematic independent benchmarking studies have not been performed on the full set of models available. In this study we compared systematically all recently published kinetic models of the central carbon metabolism ofEscherichia coli. We assess the ease of use of the models, their ability to include omics data as input, and the accuracy of prediction of central carbon metabolic flux phenotypes. We conclude that there is no clear winner among the models when considering the resulting tradeoffs in performance and applicability to various scenarios. This study can help to guide further development of kinetic models, and to demonstrate how to apply such models in real-world setting, ultimately enabling the design of efficient cell factories.

Author summary

Kinetic modeling is a promising method to predict cell metabolism. Such models provide mechanistic description of how concentrations of metabolites change in the cell as a function of time, cellular environment and the genotype of the cell. In the past years there have been several kinetic models published for various organisms. We want to assess how reliably models ofEscherichia colimetabolism could predict cellular metabolic state upon genetic or environmental perturbations. We test selected models in the ways that represent common metabolic engineering practices including deletion and overexpression of genes. Our results suggest that all published models have tradeoffs and the model to use should be chosen depending on the specific application. We show in which cases users could expect the best performance from published models. Our benchmarking study should help users to make a better informed choice and also provides systematic training and testing dataset for model developers.
Resolving mechanisms of immune-mediated disease in primary CD4 T cells
Authors: Bourges C , Groff AF , Burren OS , Gerhardinger C , Mattioli K , Hutchinson A , Hu T , Anand T , Epping MW , Wallace C , Smith KGC , Rinn JL , Lee JC
Published: January 2020

Deriving mechanisms of immune-mediated disease from GWAS data remains a formidable challenge, with attempts to identify causal variants being frequently hampered by linkage disequilibrium. To determine whether causal variants could be identified via their functional effects, we adapted a massively-parallel reporter assay for use in primary CD4 T-cells, key effectors of many immune-mediated diseases. Using the results to guide further study, we provide a generalisable framework for resolving disease mechanisms from non-coding associations – illustrated by a locus linked to 6 immune-mediated diseases, where the lead functional variant causally disrupts a super-enhancer within an NF-κB-driven regulatory circuit, triggering unrestrained T-cell activation.
The relationship between longevity and diet is genotype dependent and sensitive to desiccation
Authors: McCracken Andrew W , Buckle Eleanor , Simons Mirre J. P.
Published: January 2020

Dietary restriction (DR) is a key focus in ageing research. Specific conditions and genotypes were recently found to negate lifespan extension by DR, questioning its universal relevance. However, the conceptual framework of dietary reaction norms explains why DR’s effects might not be apparent in some situations. We tested comprehensively the importance of dietary reaction norms by measuring longevity and fecundity on five diets in five genotypes, with and without water supplementation in the fly (N>25,000). We found substantial genetic variation in the reaction norm between diet and lifespan. Environments supplemented with water rescued putative desiccation stress but only at the richest diets. Fecundity declined at these richest diets, but was unaffected by water and is thus most likely caused by nutritional toxicity. Our results demonstrate empirically that any conclusion on the absence of DR is only justified when a range of diets is considered in a reaction norm framework.
DrawAlignR: An interactive tool for across run chromatogram alignment visualization
Authors: Gupta Shubham , Sing Justin , Mahmoodi Arshia , Röst Hannes
Published: January 2020

Multi-run alignment is widely used in proteomics to establish analyte correspondence across runs. Generally alignment algorithms return a cumulative score, which may not be easily interpretable for each peptide. Here we present a novel tool, DrawAlignR, to visualize each chromatographic alignment for DIA/SWATH data. Furthermore, we have developed a novel C++ based implementation of raw chromatogram alignment which is 35 times faster than the previously published algorithm. This not only enables users to plot alignment interactively by DrawAlignR, but also allows other software platforms to use the algorithm. DrawAlignR is an open-source web application using R Shiny that can be hosted using the source-code available athttps://github.com/Roestlab/DrawAlignR.
Variant-specific changes in persistent or resurgent Na+current inSCN8A-EIEE13 iPSC-derived neurons
Authors: Tidball Andrew M. , Lopez-Santiago Luis F. , Yuan Yukun , Glenn Trevor W. , Margolis Joshua L. , Walker J. Clayton , Kilbane Emma G. , Isom Lori L. , Parent Jack M
Published: January 2020

Missense variants in the voltage-gated sodium channel (VGSC) gene,SCN8A, are linked to early-infantile epileptic encephalopathy type 13 (EIEE13). EIEE13 patients exhibit a wide spectrum of intractable seizure types, severe developmental delay, movement disorders, and elevated risk of sudden unexpected death in epilepsy (SUDEP). The mechanisms by whichSCN8Avariants lead to epilepsy are poorly understood, although heterologous expression systems and mouse models have demonstrated altered sodium current (INa) properties. To investigate these mechanisms using a patient-specific model system, we generated induced pluripotent stem cells (iPSCs) from three patients with missense variants inSCN8A: p.R1872>L (P1); p.V1592>L (P2); and p.N1759>S (P3). Using small molecule differentiation into excitatory neurons, iPSC-derived neurons from all three patients displayed altered INa. P1 and P2 had elevated persistent INa, while P3 had increased resurgent INacompared to controls. Further analyses focused on one of the patients with increased persistent INa(P1) and the patient with increased resurgent INa(P3). Excitatory cortical neurons from both patients had prolonged action potential (AP) repolarization and shorter axon initial segment lengths compared to controls, the latter analyzed by immunostaining for ankyrin-G. Using doxycycline-inducible expression of the neuronal transcription factors Neurogenin 1 and 2 to synchronize differentiation of induced excitatory cortical-like neurons (iNeurons), we investigated network activity and response to pharmacotherapies. Both patient neurons and iNeurons displayed similar abnormalities in AP repolarization. Patient iNeurons showed increased burstiness that was sensitive to phenytoin, currently a standard treatment for EIEE patients, or riluzole, an FDA-approved drug used in amyotrophic lateral sclerosis and known to block persistent and resurgent INa, at pharmacologically relevant concentrations. Patch-clamp recordings showed that riluzole suppressed spontaneous firing and increased the AP firing threshold of patient-derived neurons to more depolarized potentials. Our results indicate that patient-specific neurons are useful for modeling EIEE13 and demonstrateSCN8Avariant-specific mechanisms. Moreover, these findings suggest that patient-specific iPSC neuronal disease modeling offers a useful platform for discovering precision epilepsy therapies.
Fast estimation of L1-regularized linear models in the mass-univariate setting
Authors: Mohr Holger , Ruge Hannes
Published: January 2020

In certain modeling approaches, activation analyses of task-based fMRI data can involve a relatively large number of predictors. For example, in the encoding model approach, complex stimuli are represented in a high-dimensional feature space, resulting in design matrices with many predictors. Similarly, single-trial models and finite impulse response models may also encompass a large number of predictors. In settings where only few of those predictors are expected to be informative, a sparse model fit can be obtained via L1-regularization. However, estimating L1-regularized models requires an iterative fitting procedure, which considerably increases computation time compared to estimating unregularized or L2-regularized models, and complicates the application of L1-regularization on whole-brain data and large sample sizes. Here we provide several functions for estimating L1-regularized models that are optimized for the mass-univariate analysis approach. The package includes a parallel implementation of the coordinate descent algorithm for CPU-only systems and two implementations of the alternating direction method of multipliers algorithm requiring a GPU device. While the core algorithms are implemented in C++/CUDA, data input/output and parameter settings can be conveniently handled via Matlab. The CPU-based implementation is highly memory-efficient and provides considerable speed-up compared to the standard implementation not optimized for the mass-univariate approach. Further acceleration can be achieved on systems equipped with a CUDA-enabled GPU. Using the fastest GPU-based implementation, computation time for whole-brain estimates can be reduced from 9 hours to 5 minutes in an exemplary data setting. Overall, the provided package facilitates the use of L1-regularization for fMRI activation analyses and enables an efficient employment of L1-regularization on whole-brain data and large sample sizes.
A bright and high-performance genetically encoded Ca2+indicator based on mNeonGreen fluorescent protein
Authors: Zarowny Landon , Aggarwal Abhi , M.S. Rutten Virginia , Kolb Ilya ,   The GENIE Project, Patel Ronak , Huang Hsin-Yi , Chang Yu-Fen , Phan Tiffany , Kanyo Richard , Ahrens Misha , Allison W. Ted , Podgorski Kaspar , Campbell Robert E.
Published: January 2020

Genetically encodable calcium ion (Ca2+) indicators (GECIs) based on green fluorescent proteins (GFP) are powerful tools for imaging of cell signaling and neural activity in model organisms. Following almost two decades of steady improvements in theAequorea victoriaGFP (avGFP)-based GCaMP series of GECIs, the performance of the most recent generation (i.e., GCaMP7) may have reached its practical limit due to the inherent properties of GFP. In an effort to sustain the steady progression towards ever-improved GECIs, we undertook the development of a new GECI based on the bright monomeric GFP, mNeonGreen (mNG). The resulting indicator, mNG-GECO1, is 60% brighter than GCaMP6sin vitroand provides comparable performance as demonstrated by imaging Ca2+dynamics in cultured cells, primary neurons, andin vivoin larval zebrafish. These results suggest that mNG-GECO1 is a promising next-generation GECI that could inherit the mantle of GCaMP and allow the steady improvement of GECIs to continue for generations to come.
DCyFIR: a high-throughput CRISPR platform for multiplexed G protein-coupled receptor profiling and ligand discovery
Authors: Kapolka NJ , Taghon GJ , Rowe JB , Morgan WM , Enten JF , Isom DG
Published: January 2020

More than 800 G protein-coupled receptors (GPCRs) comprise the largest class of membrane receptors in humans. While there is ample biological understanding and many approved drugs for prototypic GPCRs, most GPCRs still lack well-defined biological ligands and drugs. Here, we report our efforts to tap the potential of understudied GPCRs by developing yeast-based technologies for high-throughput CRISPR engineering and GPCR ligand discovery. We refer to these technologies collectively as Dynamic Cyan induction by Functional Integrated Receptors: DCyFIR. A major advantage of DCyFIR is that GPCRs and other assay components are CRISPR-integrated directly into the yeast genome, making it possible to decode ligand specificity by profiling mixtures of GPCR-barcoded yeast strains in a single tube. To demonstrate the capabilities of DCyFIR, we engineered a yeast strain library of 30 human GPCRs and their 300 possible GPCR-Gα coupling combinations. Profiling of these 300 strains, using parallel (DCyFIRscreen) and multiplex (DCyFIRplex) DCyFIR modes, recapitulated known GPCR agonism with 100% accuracy, and identified unexpected interactions for the receptors ADRA2B, HCAR3, MTNR1A, S1PR1, and S1PR2. To demonstrate DCyFIR scalability, we profiled a library of 320 human metabolites and observed new GPCR-ligand interactions with amino acid, lipid, sugar, and steroid metabolites. Remarkably, many of these findings pertained to understudied “pharmacologically dark” receptors GPR4, GPR65, GPR68, and HCAR3. For example, we found that kynurenic acid activated HCAR3 with a nearly 20-fold lower EC50than GPR35, its known receptor. Taken together, these findings demonstrate the power of DCyFIR for identifying novel ligand interactions with prototypic and understudied GPCRs.

Significance Statement

G protein-coupled receptors (GPCRs) are the largest class of membrane receptors in humans. As such, GPCR signaling is central to human biology and medicine. While more than 30% of approved drugs target roughly 150 GPCRs, most receptors lack well-defined endogenous ligands and are currently not druggable. To address this challenge, we created a GPCR screening platform for ligand and drug discovery. This innovative technology enables the cost-effective profiling of ligands and drug compounds against mixtures of hundreds of GPCR-barcoded cell strains in a single experiment. Because a ligand or drug is tested against a collection of receptors all at once, our novel method accelerates the process of identifying potential GPCR ligands and drugs.
A hierarchical clustering and data fusion approach for disease subtype discovery
Authors: Pfeifer Bastian , Schimek Michael G.
Published: January 2020

Recent advances in multi-omics clustering methods enable a more fine-tuned separation of cancer patients into clinical relevant clusters. These advancements have the potential to provide a deeper understanding of cancer progression and may facilitate the treatment of cancer patients. Here, we present a simple hierarchical clustering and data fusion approach, namedHC-fused, for the detection of disease subtypes. Unlike other methods, the proposed approach naturally reports on the individual contribution of each single-omic to the data fusion process. We perform multi-view simulations withdisjointanddisjunctcluster elements across the views to highlight fundamentally different data integration behaviour of variousstate-of-the-artmethods.HC-fusedcombines the strengths of some recently published methods and shows superior performance on real world cancer data from the TCGA (The Cancer Genome Atlas) database. An R implementation of our method is available on GitHub (pievos101/HC-fused).
neuPrint: Analysis Tools for EM Connectomics
Authors: Clements Jody , Dolafi Tom , Umayam Lowell , Neubarth Nicole L. , Berg Stuart , Scheffer Louis K. , Plaza Stephen M.
Published: January 2020

Due to technological advances in electron microscopy (EM) and deep learning, it is now practical to reconstruct a connectome, a description of neurons and the connections between them, for significant volumes of neural tissue. The limited scope of past reconstructions meant they were primarily used by domain experts, and performance was not a serious problem. But the new reconstructions, of common laboratory creatures such as the fruit flyDrosophila melanogaster, upend these assumptions. These natural neural networks now contain tens of thousands of neurons and tens of millions of connections between them, with yet larger reconstructions pending, and are of interest to a large community of non-specialists. This requires new tools that are easy to use and efficiently handle large data. We introduceneuPrintto address these data analysis challenges. neuPrint is a database and analysis ecosystem that organizes connectome data in a manner conducive to biological discovery. In particular, we propose a data model that allows users to access the connectome at different levels of abstraction primarily through a graph database, neo4j, and its powerfully expressive query languageCypher. neuPrint is compatible with modern connectome reconstruction workflows, providing tools for assessing reconstruction quality, and offering both batch and incremental updates to match modern connectome reconstruction flows. Finally, we introduce a web interface and programmer API that targets a diverse user skill set. We demonstrate the effectiveness and efficiency of neuPrint through example database queries.
Encoding of 3D Head Orienting Movements in Primary Visual Cortex
Authors: Guitchounts Grigori , Masis Javier , Wolff Steffen BE , Cox David
Published: January 2020

Animals actively sample from the sensory world by generating complex patterns of movement that evolve in three dimensions. At least some of these movements have been shown to influence neural codes in sensory areas. For example, in primary visual cortex (V1), locomotion-related neural activity influences sensory gain, encodes running speed, and predicts the direction of visual flow. As most experiments exploring movement-related modulation of V1 have been performed in head-fixed animals, it remains unclear whether or how the naturalistic movements used to interact with sensory stimuli– like head orienting–influence visual processing. Here we show that 3D head orienting movements modulate V1 neuronal activity in a direction-specific manner that also depends on the presence or absence of light. We identify two largely independent populations of movement-direction-tuned neurons that support this modulation, one of which is direction-tuned in the dark and the other in the light. Finally, we demonstrate that V1 gains access to a motor efference copy related to orientation from secondary motor cortex, which has been shown to control head orienting movements. These results suggest a mechanism through which sensory signals generated by purposeful movement can be distinguished from those arising in the outside world, and reveal a pervasive role of 3D movement in shaping sensory cortical dynamics.
Dynamical determinants of different spine movements and gait speeds in rotary and transverse gallops
Authors: Kamimura Tomoya , Aoi Shinya , Higurashi Yasuo , Wada Naomi , Tsuchiya Kazuo , Matsuno Fumitoshi
Published: January 2020

Quadruped gallop is categorized into two types: rotary and transverse. While the rotary gallop involves two types of flight with different spine movements, the transverse gallop involves only one type of flight. The rotary gallop can achieve faster locomotion than the transverse gallop. To clarify these mechanisms from a dynamic viewpoint, we developed a simple model and derived periodic solutions by focusing on cheetahs and horses. The solutions gave a criterion to determine the flight type: while the ground reaction force does not change the direction of the spine movement for the rotary gallop, it changes for the transverse gallop, which was verified with the help of animal data. Furthermore, the criterion provided the mechanism by which the rotary gallop achieves higher-speed than the transverse gallop based on the flight duration. These findings improve our understanding of the mechanisms underlying different gaits that animals use.
Why most transporter mutations that cause antibiotic resistance are to efflux pumps rather than to import transporters
Authors: Mendes Pedro , Girardi Enrico , Superti-Furga Giulio , Kell Douglas B.
Published: January 2020

Genotypic microbial resistance to antibiotics with intracellular targets commonly arises from mutations that increase the activities of transporters (pumps) that cause the efflux of intracellular antibiotics.A prioriit is not obvious why this is so much more common than are mutations that simply inhibit the activity of uptake transporters for the antibiotics. We analyse quantitatively a mathematical model consisting of one generic equilibrative transporter and one generic concentrative uptake transporter (representing any number of each), together with one generic efflux transporter. The initial conditions are designed to give an internal concentration of the antibiotic that is three times the minimum inhibitory concentration (MIC). The effect of varying the activity of each transporter type 100-fold is dramatically asymmetric, in that lowering the activities of individual uptake transporters has comparatively little effect on internal concentrations of the antibiotic. By contrast, increasing the activity of the efflux transporter lowers the internal antibiotic concentration to levels far below the MIC. Essentially, these phenomena occur because inhibiting individual influx transporters allows others to ‘take up the slack’, whereas increasing the activity of the generic efflux transporter cannot easily be compensated. The findings imply strongly that inhibiting efflux transporters is a much better approach for fighting antimicrobial resistance than is stimulating import transporters. This has obvious implications for the development of strategies to combat the development of microbial resistance to antibiotics and possibly also cancer therapeutics in human.
PE5-PPE4-EspG3trimer structure from mycobacterial ESX-3 secretion system gives insight into cognate substrate recognition by ESX systems
Authors: Williamson Zachary A. , Chaton Catherine T. , Ciocca William A. , Korotkova Natalia , Korotkov Konstantin V.
Published: January 2020

Mycobacterium tuberculosis(Mtb) has evolved numerous type VII secretion (ESX) systems to secrete multiple factors important for both growth and virulence across their cell envelope. Three such systems; ESX-1, ESX-3, and ESX-5; have been shown to each secrete a unique set of substrates. A large class of these substrates secreted by these three systems are the PE and PPE families of proteins. Proper secretion of the PE-PPE proteins requires the presence of EspG, with each system encoding its own unique copy. There is no cross-talk between any of the ESX systems and how each EspG is recognizing its subset of PE-PPE proteins is currently unknown. The only current structural characterization of PE-PPE-EspG trimers is from the ESX-5 system. Here we present the crystal structure of the PE5mt-PPE4mt-EspG3mmtrimer, from the ESX-3 system. Our trimer reveals that EspG3mminteracts exclusively with PPE4mtin a similar manner to EspG5, shielding the hydrophobic tip of PPE4mtfrom solvent. The C-terminal helical domain of EspG3mmis dynamic, alternating between an ‘open’ and ‘closed’ form, and this movement is likely functionally relevant in the unloading of PE-PPE heterodimers at the secretion machinery. In contrast to the previously solved ESX-5 trimers, the PE-PPE heterodimer of our ESX-3 trimer is interacting with it’s chaperone at a drastically different angle, and presents different faces of the PPE protein to the chaperone. We conclude that the PPE-EspG interface from each ESX system has a unique shape complementarity that allows each EspG to discriminate amongst non-cognate PE-PPE pairs.
A Whole-Brain Regression Method to Identify Individual and Group Variations in Functional Connectivity
Authors: Zhao Yi , Caffo Brian S. , Wang Bingkai , Li Chiang-shan R. , Luo Xi
Published: January 2020

Resting-state functional connectivity is an important and widely used measure of individual and group differences. These differences are typically attributed to various demographic and/or clinical factors. Yet, extant statistical methods are limited to linking covariates with variations in functional connectivity across subjects, especially at the voxel-wise level of the whole brain. This paper introduces a generalized linear model method that regresses whole-brain functional connectivity on covariates. Our approach builds on two methodological components. We first employ whole-brain group ICA to reduce the dimensionality of functional connectivity matrices, and then search for matrix variations associated with covariates using covariate assisted principal regression, a recently introduced covariance matrix regression method. We demonstrate the efficacy of this approach using a resting-state fMRI dataset of a medium-sized cohort of subjects obtained from the Human Connectome Project. The results show that the approach enjoys improved statistical power in detecting interaction effects of sex and alcohol on whole-brain functional connectivity, and in identifying the brain areas contributing significantly to the covariate-related differences in functional connectivity.
Oxygen supply limits the heat tolerance of locusts during the first instar only
Authors: Youngblood Jacob P. , VandenBrooks John M. , Babarinde Oluwatosin , Donnay Megan E. , Elliott Deanna B. , Fredette-Roman Jacob , Angilletta Michael J.
Published: January 2020

Extreme heat directly limits an organism’s survival and reproduction, but scientists cannot agree on what causes organisms to lose function or die during heating. According to the theory of oxygen- and capacity-limitation of thermal tolerance, heat stress occurs when a warming organism’s demand for oxygen exceeds its supply, triggering a widespread drop in ATP concentration. This model predicts that an organism’s heat tolerance should decrease under hypoxia, yet most terrestrial organisms tolerate the same amount of warming across a wide range of oxygen concentrations. This point is especially true for adult insects, who deliver oxygen through highly efficient respiratory systems. However, oxygen limitation at high temperatures may be more common during immature life stages, which have less developed respiratory systems. To test this hypothesis, we measured the effects of heat and hypoxia on the survival of locusts (Schistocerca cancellata) throughout development. We demonstrate that the heat tolerance of locusts depends on oxygen supply during the first instar but not during later instars. This finding provides further support for the idea that oxygen limitation of thermal tolerance depends on respiratory performance, especially during immature life stages.
Opposing forms of adaptation in mouse visual cortex are controlled by distinct inhibitory microcircuits and gated by locomotion
Authors: Heintz Tristan G. , Hinojosa Antonio J. , Lagnado Leon
Published: January 2020

Cortical processing of sensory signals adjusts to changes in both the external world and the internal state of the animal. We investigated the neural circuitry by which these processes interact in the primary visual cortex of mice. An increase in contrast caused as many pyramidal cells (PCs) to sensitize as depress, reflecting the dynamics of adaptation in different types of interneuron (PV, SST and VIP). Optogenetic manipulations demonstrate that the net effect within PCs reflects the balance of PV inputs, driving depression, and a subset of SST interneurons, driving sensitization. Locomotor behaviour increased the gain of PC responses by disinhibition through both the VIP->SST and SST->PV pathways, thereby maintaining the balance between opposing forms of plasticity. These experiments reveal how inhibitory microcircuits interact to purpose different subsets of PCs for the signalling of increases or decreases in contrast while also allowing for behavioural control of gain across the population.
Threshold illumination for non-invasive imaging of cells and tissues
Authors: Emon M A Bashar , Knoll Samantha , Doha Umnia , Baietto Danielle , Ladehoff Lauren , Sivaguru Mayandi , Saif M Taher A
Published: January 2020

Fluorescent microscopy employs monochromatic light which can affect the cells being observed. We reported earlier that fibroblasts relax their contractile force in response to green light of typical intensity. Here we show that such effects are independent of extracellular matrix and type of cell. In addition, we establish a threshold light that invokes minimal effect on cells. We cultured fibroblasts on soft 2D elastic hydrogels embedded with fluorescent beads to trace substrate deformation. The beads move towards cell center when cells contract, but they move away when cells relax. We use relaxation/contraction ratio, λr, as a measure of cell response to light. The cells were exposed to green (wavelength, λ = 545-580 nm) and red (λ = 635-650 nm) light with a range of intensities. We find red light with intensity less than ~ 57 W/m2 results in λr = 1, i.e., cells maintain force homeostasis. Higher intensities and smaller wavelengths result in widespread force-relaxation in cells with λr > 1. We suggest the use of λ > 650 nm light with low intensity (I ≤ 57 W/m2) for time-lapse imaging of cells and tissues in order to avoid light-induced artifacts in experimental observations.
Dissociable Neural Systems Support the Learning and Transfer of Hierarchical Control Structure
Authors: Eichenbaum Adam , Scimeca Jason M. , D’Esposito Mark
Published: January 2020

Humans can draw insight from previous experiences in order to quickly adapt to novel environments that share a common underlying structure. Here we combine functional imaging and computational modeling to identify the neural systems that support the discovery and transfer of hierarchical task structure. Human subjects completed multiple blocks of a reinforcement learning task that contained a global hierarchical structure governing stimulus-response action mapping. First, behavioral and computational evidence showed that humans successfully discover and transfer the hierarchical rule structure embedded within the task. Next, analysis of fMRI BOLD data revealed activity across a frontal-parietal network that was specifically associated with the discovery of this embedded structure. Finally, activity throughout a cingulo-opercular network and in caudal frontal cortex supported the transfer and implementation of this discovered structure. Together, these results reveal a division of labor in which dissociable neural systems support the learning and transfer of abstract control structures.
Two pectate lyases fromCaldicellulosiruptor besciiwith the same CALG domain had distinct properties on plant biomass degradation
Authors: Hamouda Hamed I. , Ali Nasir , Su Hang , Feng Jie , Lu Ming , Li Fu-Li
Published: January 2020

Pectin deconstruction is the initial step in breaking the recalcitrance of plant biomass by using selected microorganisms that carry pectinolytic enzymes. Pectate lyases that cleave α-1,4-galacturonosidic linkage of pectin are widely used in industries, such as paper making and fruit softening. However, reports on pectate lyases with high thermostability are few. Two pectate lyases (CbPL3 andCbPL9) from a thermophilic bacteriumCaldicellulosiruptor besciiwere investigated. Although these two enzymes belonged to different families of polysaccharide lyase, both were Ca2+-dependent. Similar biochemical properties were shown under optimized conditions 80 °C–85 °C and pH 8–9. However, the degradation products on pectin and polygalacturonic acids (pGA) were different, revealing the distinct mode of action. A concanavalin A-like lectin/glucanase (CALG) domain, located in theN-terminus of twoCbPLs, shares 100% amino acid identity. CALG-truncated mutant ofCbPL9 showed lower activities than the wild-type, whereas theCbPL3 with CALG knock-out portion was reported with enhanced activities, thereby revealing the different roles of CALG in twoCbPLs. I-TASSER predicted that the CALG in twoCbPLs is structurally close to the family 66 carbohydrate binding module (CBM66). Furthermore, substrate-binding assay indicated that the catalytic domains in twoCbPLs had strong affinities on pectate-related substrates, but CALG showed weak interaction with a number of lignocellulosic carbohydrates, except sodium carboxymethyl cellulose and sodium alginate. Finally, scanning electron microscope analysis and total reducing sugar assay showed that the two enzymes could improve the saccharification of switchgrass. The twoCbPLs are impressive sources for degradation of plant biomass.

Importance

Thermophilic proteins could be implemented in diverse industrial applications. We sought to characterize two pectate lyases,CbPL3 andCbPL9, from a thermophilic bacteriumCaldicellulosiruptor bescii. The two enzymes had high optimum temperature, low optimum pH, and good thermostability at evaluated temperature. A family-66 carbohydrate binding module (CBM66) was identified in twoCbPLs with sharing 100% amino acid identity. Deletion of CBM66 obviously decreased the activity ofCbPL9, but increase the activity and thermostability ofCbPL3, suggesting the different roles of CBM66 in two enzymes. Moreover, the degradation products by twoCbPLs were different. These results revealed these enzymes could represent a potential pectate lyase for applications in paper and textile industries.
Most of Staphylococcus aureus and Pseudomonas aeruginosa co-infecting isolates coexist, a condition that may impact clinical outcomes in Cystic Fibrosis patients
Authors: Briaud Paul , Bastien Sylvère , Camus Laura , Boyadjian Marie , Reix Philippe , Mainguy Catherine , Vandenesch François , Doléans-Jordheim Anne , Moreau Karen
Published: January 2020

Staphylococcus aureus (SA) is the major colonizer of the lung of cystic fibrosis (CF) patient during childhood and adolescence. As patient aged, the prevalence of SA decreases and Pseudomonas aeruginosa (PA) becomes the major pathogen infecting adult lungs. Nonetheless, SA remains significant and patients harbouring both SA and PA are frequently found in worldwide cohort. Impact of coinfection remains controversial. Furthermore, co-infecting isolates may compete or coexist. The aim of this study was to analyse if co-infection and coexistence of SA and PA could lead to worse clinical outcomes. The clinical and bacteriological data of 212 Lyon CF patients were collected retrospectively, and patients were ranked into three groups, SA only (n=112), PA only (n=48) or SA plus PA (n=52). In addition, SA and PA isolates from co-infecting patients were tested in vitro to define their interaction profile. Sixty five percent (n=34) of SA/PA pairs coexist. Using univariate and multivariate analysis, we confirm that SA patients have a clinical condition less severe than others, and PA induce a poor outcome independently of the presence of SA. FEV1 is lower in patients infected by competition strain pairs than in those infected by coexisting strain pairs compared to SA mono-infection. Coexistence between SA and PA may be an important step in the natural history of lung bacterial colonization within CF patients.
Assessing Knowledge, Attitudes, and Practices towards Causal Directed Acyclic Graphs: a qualitative research project
Authors: Barnard-Mayers Ruby , Childs Ellen , Corlin Laura , Caniglia Ellen C , Fox Matthew P , Donnelly John P. , Murray Eleanor J
Published: January 2020

Background

Causal graphs provide a key tool for optimizing the validity of causal effect estimates. Although a large literature exists on the mathematical theory underlying the use of causal graphs, less literature exists to aid applied researchers in understanding how best to develop and use causal graphs in their research projects.

Methods

We sought to understand why researchers do or do not regularly use DAGs by surveying practicing epidemiologists and medical researchers on their knowledge, level of interest, attitudes, and practices towards the use of causal graphs in applied epidemiology and health research. We used Twitter and the Society for Epidemiologic Research to disseminate the survey.

Results

Overall, a majority of participants reported being comfortable with using causal graphs and reported using them ‘sometimes’, ‘often’, or ‘always’ in their research. Having received training appeared to improve comprehension of the assumptions displayed in causal graphs. Many of the respondents who did not use causal graphs reported lack of knowledge as a barrier to using DAGs in their research.

Conclusion

Causal graphs are of interest to epidemiologists and medical researchers, but there are several barriers to their uptake. Additional training and clearer guidance are needed. In addition, methodological developments regarding visualization of effect measure modification and interaction on causal graphs is needed.
Dynamic longitudinal behavior in animals exposed to chronic social defeat stress
Authors: Wendelmuth M. , Willam M. , Todorov H. , Radyushkin K. , Gerber S. , Schweiger S.
Published: January 2020

Chronic social defeat (CSD) can lead to impairments in social interaction and other behaviors that are supposed to model features of major depressive disorder (MDD). Not all animals subjected to CSD, however, develop these impairments, and maintained social interaction in some animals is widely used as a model for resilience to stress-induced mental dysfunctions. So far, animals have mainly been studied shortly (24 hours and 7 days) after CSD exposure and longitudinal development of behavioral phenotypes in individual animals has been mostly neglected. We have analyzed social interaction and novel object recognition behavior of stressed mice at different time points after CSD and have found very dynamic courses of behavior of individual animals. Instead of the two groups, resilient or susceptible, that are found at early time points our data suggest four groups with (i, ii) animals behaving resilient or susceptible at early and late time points, respectively (iii) animals that start susceptible and recover with time or (iv) animals that are resilient at early time points but develop vulnerability later on.
Complement C5a impairs phagosomal maturation in the neutrophil through phosphoproteomic remodelling
Authors: Wood Alexander J.T. , Vassallo Arlette M. , Ruchaud-Sparagano Marie-Hélène , Scott Jonathan , Zinnato Carmelo , Gonzalez-Tejedo Carmen , Kishore Kamal , D’Santos Clive S. , Simpson A. John , Menon David K. , Summers Charlotte , Chilvers Edwin R. , Okkenhaug Klaus , Morris Andrew Conway
Published: January 2020

Critical illness is accompanied by the release of large amounts of the anaphylotoxin, C5a. C5a suppresses antimicrobial functions of neutrophils which is associated with adverse outcomes. The signalling pathways that mediate C5a-induced neutrophil dysfunction are incompletely understood. Healthy donor neutrophils exposed to purified C5a demonstrated a prolonged defect (7 hours) in phagocytosis ofStaphylococcus aureus. Phosphoproteomic profiling of 2712 phosphoproteins identified persistent C5a signalling and selective impairment of phagosomal protein phosphorylation on exposure toS. aureus.Notable proteins included early endosomal marker ZFYVE16 and V-ATPase proton channel component ATPV1G1. A novel assay of phagosomal acidification demonstrated C5a-induced impairment of phagosomal acidification which was recapitulated in neutrophils from critically ill patients. Examination of the C5a-impaired protein phosphorylation indicated a role for the phosphatidylinositol 3-kinase VPS34 in phagosomal maturation. Inhibition of VPS34 impaired neutrophil phagosomal acidification and killing ofS. aureus. This study provides a phosphoproteomic assessment of human neutrophil signalling in response toS. aureusand its disruption by C5a, identifying a defect in phagosomal maturation and new mechanisms of immune failure in critical illness.
Accelerated EM Connectome Reconstruction using 3D Visualization and Segmentation Graphs
Authors: Hubbard Philip M. , Berg Stuart , Zhao Ting , Olbris Donald J. , Umayam Lowell , Maitin-Shepard Jeremy , Januszewski Michal , Katz William T. , Neace Erika R. , Plaza Stephen M.
Published: January 2020

Recent advances in automatic image segmentation and synapse prediction in electron microscopy (EM) datasets of the brain enable more efficient reconstruction of neural connectivity. In these datasets, a single neuron can span thousands of images containing complex tree-like arbors with thousands of synapses. While image segmentation algorithms excel within narrow fields of views, the algorithms sometimes struggle to correctly segment large neurons, which require large context given their size and complexity. Conversely, humans are comparatively good at reasoning with large objects. In this paper, we introduce several semi-automated strategies that combine 3D visualization and machine guidance to accelerate connectome reconstruction. In particular, we introduce a strategy to quickly correct a segmentation through merging andcleaving, or splitting a segment along supervoxel boundaries, with both operations driven by affinity scores in the underlying segmentation. We deploy these algorithms as streamlined workflows in a tool calledNeu3and demonstrate superior performance compared to prior work, thus enabling efficient reconstruction of much larger datasets. The insights into proofreading from our work clarify the trade-offs to consider when tuning the parameters of image segmentation algorithms.
Identification of a novel population of peripheral sensory neuron that regulates blood pressure
Authors: Morelli Chiara , Castaldi Laura , Brown Sam J. , Streich Lina L. , Websdale Alexander , Taberner Francisco J. , Cerreti Blanka , Barenghi Alessandro , Blum Kevin M. , Sawitzke Julie , Frank Tessa , Steffens Laura , Doleschall Balint , Serrao Joana , Lechner Stefan G. , Prevedel Robert , Heppenstall Paul A.
Published: January 2020

The vasculature is innervated by a network of peripheral afferents that sense and regulate blood flow. Here, we describe a system of non-peptidergic sensory neurons with cell bodies in the spinal ganglia that regulate vascular tone in the distal arteries. We identify a population of mechanosensitive neurons marked by TrkC and Tyrosine hydroxylase in the dorsal root ganglia that project to blood vessels. Local stimulation of these neurons decreases vessel diameter and blood flow, while systemic activation increases systolic blood pressure and heart rate variability via the sympathetic nervous system. Chemogenetic inactivation or ablation of the neurons provokes variability in local blood flow leading to a reduction in systolic blood pressure, increased heart rate variability and ultimately lethality within 48 hours. Thus, TrkC/Tyrosine hydroxylase positive sensory neurons form part of a sensory feedback mechanism that maintains cardiovascular homeostasis through the autonomic nervous system.
Radula diversification promotes ecomorph divergence in an adaptive radiation of freshwater snails
Authors: Hilgers Leon , Hartmann Stefanie , Pfaender Jobst , Lentge-Maaß Nora , von Rintelen Thomas , Hofreiter Michael
Published: January 2020

Adaptive diversification of complex traits plays a pivotal role for the evolution of organismal diversity. However, the underlying molecular mechanisms remain largely elusive. In the freshwater snail genusTylomelania,adaptive radiations were likely promoted by trophic specialization via diversification of their key foraging organ, the radula. To investigate the molecular basis of radula diversification and its contribution to lineage divergence, we use pooled tissue-specific transcriptomes of two sympatricTylomelania sarasinorumecomorphs. We show that divergence in both gene expression and coding sequences is stronger between radula transcriptomes compared to mantle and foot transcriptomes. These findings support the hypothesis that diversifying selection on the radula is driving speciation inTylomelaniaradiations. We also identify several candidate genes for radula divergence. Putative homologs of some candidates (hh,arx,gbb) also contributed to trophic specialization in cichlids and Darwin’s finches, indicating that some molecular pathways may be especially prone to adaptive diversification.