title: Benchmarking metagenomic classification tools for long-read sequencing data

abstract:
We performed a comprehensive assessment of metagenomics classification tools on long sequenced reads. In addition to well defined mock communities, we prepared various synthetic datasets to simulate real-life scenarios. The results show that off-the-shelf mappers such as Minimap2 or Ram are at least comparable with mapping-based classification tools in most accuracy measures while not being much slower than kmer based tools and requiring equal or less RAM. Majority of tested tools are prone to report organisms not present in datasets and underperform in the case of high presence of hosts genetic material. Furthermore, longer read lengths make classification easier, but due to the difference in read length distributions among species, the usage of only longest reads reduces the accuracy. Finally, evaluation on a mock community shows the importance of careful isolation of genetic material and sequencing preparation.

Availability and implementationPython scripts used to generate all figures and tables in this study, and all supplementary texts and figures are available via the Github repository https://github.com/lbcb-sci/MetagenomicsBenchmark. Datasets, supporting files, analysis results and reports are available via Zenodo repository https://doi.org/10.5281/zenodo.5203182.

category: bioinformatics


title: Environment-driven reprogramming of gamete DNA methylation occurs during maturation and is transmitted intergenerationally in salmon

abstract: An epigenetic basis for transgenerational plasticity is widely theorized, but convincing empirical support is limited by taxa-specific differences in the presence and role of epigenetic mechanisms. In teleost fishes, DNA methylation generally does not undergo extensive reprogramming and has been linked with environmentally-induced intergenerational effects, but solely in the context of early life environmental differences. Using whole genome bisulfite sequencing, we demonstrate that differential methylation of sperm occurs in response to captivity during the maturation of Atlantic Salmon (Salmo salar), a species of major economic and conservation significance. We show that adult captive exposure further induces differential methylation in an F1 generation that is associated with fitness-related phenotypic differences. Genes targeted with differential methylation were consistent with genes differential methylated in other salmonid fishes experiencing early-life hatchery rearing, as well as genes under selection in domesticated species. Our results support a mechanism of transgenerational plasticity mediated by intergenerational inheritance of DNA methylation acquired late in life for salmon. To our knowledge, this is the first-time environmental variation experienced later in life has been directly demonstrated to influence gamete DNA methylation in fish.

category: evolutionary biology


title: How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a micro-endemic Malagasy tree

abstract:
AO_SCPLOWBSTRACTC_SCPLOWUnderstanding landscape changes is central to predicting evolutionary trajectories and defining conservation practices. While human-driven deforestation is intense throughout Madagascar, exception in areas like the Loky-Manambato region (North) raises questions. This region also harbors a rich and endemic flora, whose evolutionary origin remains poorly understood.

We assessed the genetic diversity of an endangered micro-endemic Malagasy olive species (Noronhia spinifolia) to better understand the vegetation dynamic in the Loky-Manambato region and its influence on past evolutionary processes. We characterized 72 individuals sampled across eight forests through nuclear and mitochondrial restriction associated sequencing data (RADseq) and chloroplast microsatellites (cpSSR). Extremely high genetic diversity was revealed in two genomic compartments (chloroplast h = 0.99, and mitochondrial h = 0.85). Combined population and landscape genetics analyses indicate that N. spinifolia diversity is best explained by the current forest cover (R2 = 0.90), highlighting a long-standing habitat mosaic in the region. Our results further suggest a predominant role of forest-dwelling organisms in mediating pollen and seed dispersals.

This sustains a major and long-term role of riparian corridors in maintaining connectivity across those antique mosaic-habitats, calling for the study of organismal interactions that promote gene flow.

category: genomics


title: Host-directed FDA-approved drugs with antiviral activity against SARS-CoV-2 identified by hierarchical in silico/in vitro screening methods

abstract:
The unprecedent situation generated by the COVID-19 global emergency prompted us to actively work to fight against this pandemic by searching for repurposable agents among FDA approved drugs to shed light into immediate opportunities for the treatment of COVID-19 patients.

In the attempt to proceed toward a proper rationalization of the search for new antivirals among approved drugs, we carried out a hierarchical in silico/in vitro protocol which successfully combines virtual and biological screening to speed up the identification of host-directed therapies against COVID-19 in an effective way.

To this end a multi-target virtual screening approach focused on host-based targets related to viral entry followed by the experimental evaluation of the antiviral activity of selected compounds has been carried out. As a result, five different potentially repurposable drugs interfering with viral entry, cepharantine, clofazimine, metergoline, imatinib and efloxate, have been identified.

category: microbiology


title: Patterns and Causes of Signed Linkage Disequilibria in Flies and Plants

abstract: Most empirical studies of linkage disequilibrium (LD) study its magnitude, ignoring its sign. Here, we examine patterns of signed LD in two population genomic datasets, one from Capsella grandiflora and one from Drosophila melanogaster. We consider how processes such as drift, admixture, Hill-Robertson interference, and epistasis may contribute to these patterns. We report that most types of mutations exhibit positive LD, particularly, if they are predicted to be less deleterious. We show with simulations that this pattern arises easily in a model of admixture or distance biased mating, and that genome-wide differences across site types are generally expected due to differences in the strength of purifying selection even in the absence of epistasis. We further explore how signed LD decays on a finer scale, showing that loss of function mutations exhibit particularly positive LD across short distances, a pattern consistent with intragenic antagonistic epistasis. Controlling for genomic distance, signed LD in C. grandiflora decays faster within genes, compared to between genes, likely a by-product of frequent recombination in gene promoters known to occur in plant genomes. Finally, we use information from published biological networks to explore whether there is evidence for negative synergistic epistasis between interacting radical missense mutations. In D. melanogaster networks, we find a modest but significant enrichment of negative LD, consistent with the possibility of intra-network negative synergistic epistasis.


title: Adaptive divergence and the evolution of hybrid trait mismatch in threespine stickleback

abstract: Hybrid fitness can be negatively impacted by trait mismatch, whereby hybrids resemble one parent population for some phenotypic traits and the other parent population for other traits. In this study, we used threespine stickleback fish (Gasterosteus aculeatus L.) to test whether trait mismatch in hybrids increases with the magnitude of phenotypic divergence between parent populations. We measured morphological traits in parents and hybrids in crosses between a marine population representing the ancestral form and twelve freshwater populations that have diverged from this ancestral state to varying degrees according to their environments. We found that trait mismatch was greater in more divergent crosses for both F1 and F2 hybrids. In the F1, the divergence-mismatch relationship was caused by traits having dominance in different directions whereas it was caused by segregating phenotypic variation in the F2. Selection against mismatched traits is an ecological analogue to selection against intrinsic hybrid incompatibilities, and our results imply that extrinsic hybrid incompatibilities accumulate predictably as phenotypic divergence proceeds.


title: Orthogonal targeting of KDM6A/B and HDACs mediates potent therapeutic effects in IDH1-mutant glioma

abstract:
BackgroundIDH1/2-mutant gliomas are primary brain tumors for which curative treatments are lacking. Mutant IDH-dependent 2-hydroxyglutarate (2-HG) accumulation leads to DNA and histone hypermethylation. Based on this distinct phenotype, we interrogated epigenetic dependencies of IDH-mutant glioma that can be targeted therapeutically.

MethodsWe conducted a chemical screen targeting chromatin modifiers in patient derived IDH1-mutant GBM cells. We investigated mechanisms of action of compound hits and their combinations through cell-based functional assays, live-cell imaging, Western blot, CRISPR knockout, RNA-seq and ChIP experiments. The therapeutic concept was validated in vivo using chemical inhibitors GSK-J4 and Belinostat in an orthotopic GBM model.

ResultsWe identified the H3K27me3 demethylase (KDM6) inhibitor GSK-J4 and histone deacetylase inhibitor Belinostat as potent, genotype-selective agents against IDH1-mutant glioma. RNA-sequencing on paired wild-type and IDH1R132H cells revealed inhibition of cholesterol biosynthesis and activation of cellular stress in IDH1R132H cells, which were reversible with a mutant IDH1 inhibitor. GSK-J4 caused further repression of cholesterol biosynthesis pathway genes through H3K27me3 deposition and exacerbated the ATF4-mediated integrated stress response. Belinostat inhibited anti-apoptotic pathways through activation of TGF-{beta} signaling and induced cell cycle arrest. Together, the GSK-J4 and Belinostat combination activated DDIT3/CHOP-dependent apoptosis in IDH1-mutant cells and extended survival in an IDH1-mutant orthotopic model in vivo.

ConclusionsThese results provide a possible therapeutic approach that exploits epigenetic vulnerabilities of IDH-mutant gliomas.

Key points- Combination of GSK-J4 and Belinostat selectively targets IDH1-mutant cells.
- GSK-J4 downregulates cholesterol biosynthesis and activates an ATF4-mediated stress response.
- Belinostat activates the TGF{beta} pathway, induces G2/M arrest and inhibits anti-apoptotic pathways.

Importance of the studyIDH1/2 genes are frequently mutated in low grade glioma and secondary glioblastoma. These tumors exhibit a distinct epigenomic signature with increased DNA and histone methylation; therefore, identifying and exploiting their epigenetic vulnerabilities may lead to effective therapies. We discovered that targeting of KDM6A/6B together with HDACs provides a promising therapeutic approach for IDH1-mutant glioma.

category: cancer biology


title: Ethanolamine phosphate on the second mannose as bridge in GPI anchored proteins: Towards understanding inherited PIGG deficiency

abstract: Glycosylphosphatidylinositols (GPIs) are glycolipids that anchor many proteins (GPI-APs) on the cell surface. The core glycan of GPI precursor has three mannoses, which in mammals, are all modified by ethanolamine-phosphate (EthN-P). It is postulated that EthN-P on the third mannose (EthN-P-Man3) is the bridge between GPI to the protein and the second (EthN-P-Man2) is removed after GPI-protein attachment. However, EthN-P-Man2 may not be always transient, as mutations of PIGG, the enzyme that transfers EthN-P to Man2, result in inherited GPI deficiencies (IGDs), characterized by neuronal dysfunctions. Here, we show EthN-P on Man2 is the preferential bridge in some GPI-APs, among them, the ect-5-nucleotidase and netrin G2. We found that CD59, a GPI-AP, is attached via EthN-P-Man2 both in PIGB-knockout cells, in which GPI lacks Man3 and with a small fraction, in wild type cells. Our findings modify the current view of GPI anchoring and provide mechanistic bases of IGDs caused by PIGG mutations.

category: molecular biology


title: A comparative study of data integration methods, integrating genetic association and functional annotation summary statistics

abstract:
Functional annotations have the potential to increase the power of genome-wide association studies (GWAS) by prioritizing variants according to their biological function. Focusing on variant-specific annotation meta-scores including CADD (Kircher et al., 2014) and Eigen (Ionita-laza et al., 2016), we broadly examined GWAS summary statistics of 1,132 traits from the UK Biobank (Sudlow et al., 2015) using the weighted p-value approach (Genovese et al., 2006) and stratified false discovery control (sFDR) method (Sun et al., 2006). These 1,132 traits were rated by Benjamin Neales lab from the Broad Institute as having medium to high confidence for their heritability estimates.

Averaged across the 1,132 UK Biobank traits, sFDR was more robust to uninformative meta-scores, but the weighted p-value method identified more variants using CADD or Eigen, based on performance measures that included type I error control, recall, precision, and relative efficiency. Our application results were consistent with those from an extensive simulation study using three different designs, including leveraging the real genetic data combined with simulated genomic data and vice versa.

We also considered the recent FINDOR method (Kichaev et al., 2019), which leverages a set of individual 75 functional annotations into GWAS. An earlier application of FINDOR to 27 traits selected from the z7 category (SNP-heritability p-value < 1.27 x 10-12 by Nealelab) detected 13%-20% additional genome-wide significant loci as compared to the standard annotation-free GWAS, which we confirmed. Moreover, across all 438 traits in the z7 category, 46,631 out 59,764 (80%) significant loci discovered are common across the three data-integration methods.

However, across all the 1,132 UK Biobank traits examined, the median [Q1,Q3] of the total numbers of new, genome-wide significant independent loci were 0 [0, 3] by FINDOR, 0 [0, 2] by weighted p-value, and 0 [0, 0] by sFDR. Notably, 162 traits (89%) in the nonsig trait category (SNP-heritability p-value > 0.05, "likely reflecting limited statistical power rather than a true lack of heritability" by Nealelab) had no new discoveries after data-integration by any of the three methods. Our findings suggest that more informative scores or new data integration methods are warranted to further improve the power of GWAS by leveraging the variant functional annotations.

category: genetics


title: Profiling sensory neuron microenvironment after peripheral and central axon injury reveals key pathways for neural repair

abstract: Sensory neurons with cell bodies in dorsal root ganglia (DRG) represent a useful model to study axon regeneration. Whereas regeneration and functional recovery occurs after peripheral nerve injury, spinal cord injury or dorsal root injury is not followed by regenerative outcomes. Regeneration of sensory axons in peripheral nerves is not entirely cell autonomous. Whether the DRG microenvironment influences the different regenerative capacities after injury to peripheral or central axons remains largely unknown. To answer this question, we performed a single cell transcriptional profiling of mouse DRG in response to peripheral (sciatic nerve crush) and central axon injuries (dorsal root crush and spinal cord injury). Each cell type responded differently to the three types of injuries. All injuries increased the proportion of a cell type that shares features of both immune cells and glial cells. A distinct subset of satellite glial cells (SGC) appeared specifically in response to peripheral nerve injury. Activation of the PPAR signaling pathway in SGC, which promotes axon regeneration after peripheral nerve injury, failed to occur after central axon injuries. Treatment with the FDA-approved PPAR agonist fenofibrate increased axon regeneration after dorsal root injury. This study provides a map of the distinct DRG microenvironment responses to peripheral and central injuries at the single cell level and highlights that manipulating non-neuronal cells could lead to avenues to promote functional recovery after CNS injuries or disease.

category: neuroscience


title: Establishment of Multi-stage Intravenous Self-administration in Mice

abstract: A genetically tractable animal model would provide a needed strategy to resolve the biological basis of drug addiction. Intravenous self-administration (IVSA) is the gold standard for modeling cocaine and opioid addiction in animals, but technical limitations have precluded the widespread use of IVSA in mice. Here, we describe the first IVSA paradigms for mice that capture the multi-stage nature of the disease and permit predictive modeling. Mice with long-standing indwelling jugular catheters engaged in cocaine or opioid-associated lever responding that was fixed ratio- and dose-dependent, extinguished by the withholding of drug, and reinstated by the presentation of paired cues. Machine learning revealed that vulnerability to drug seeking and relapse were predicted by a mouses a priori response to novelty, sensitivity to drug-induced locomotion, and drug-taking behavior. Application of this behavioral and analysis approach to genetically-engineered mice will facilitate the identification of the neural circuits driving addiction susceptibility and relapse and focused therapeutic development.


title: Plant provenance affects pollinator network: implications for ecological restoration

abstract:
The selection of plant provenance for ecological restoration is an intensively debated topic. Throughout this debate, arguments mostly focus on plant performance, but little attention is paid to the effects of provenance on other members of the restored ecosystem. On the other hand, in restoration projects that focus specifically on supporting interacting biota, for example flower stripes among fields to support pollinators, the provenance choice is often not considered, partly because the effect of provenance on pollinators is unknown. In this pioneering case study, we tested whether pollinators differentiate between experimental plant communities of different provenances.

We established experimental plant communities with the same species composition but with plants originating from three different provenances. We then recorded plant phenology and observed pollinators and flower visitors interacting with these experimental communities and related the pollinator visitation to the provenance identity.

The provenances of the experimental plant communities had a strong and significant effect on the diversity and abundance of flower-pollinator interactions, with one provenance interacting twice as often as the other two provenances. The effect was driven by the differences in flowering phenology among provenances.

Synthesis and applicationsPlant provenances substantially differ in their interactions with local pollinators. Therefore, the selection of plant provenance should be considered when planning restoration projects for the support of pollinators.

category: ecology


title: CICLOP: A Robust, Faster, and Accurate Computational Framework for Protein Inner Cavity Detection

abstract:
Internal cavities in proteins are of critical functional importance. They can serve as substrate/ligand binding sites, pave path for movement of bio-molecules and even mediate structural conformations occurring between domain interfaces during structural transitions. Yet, there is a paucity of computational tools that can accurately, and reliably characterize the inner cavities of the proteins, a prerequisite for elucidating their functions. We have developed a novel method, CICLOP, that can accurately identify these regions at an atomic resolution. The method is able to accurately detect residues lining the inner cavity, the diameter and volume occupied by the cavity, as well as physicochemical properties of residues lining the cavity such as their hydrophobicity and secondary structure distribution in detail. Additionally, our method also provides an option for computing conservation scores for the residues detected on the inside, allowing for a thorough functional characterization of the cavity.

AvailabilityCICLOP is available at http://ciclop.raylab.iiitd.edu.in/. A compiled Linux executable can be downloaded from https://ciclop.raylab.iiitd.edu.in/standalone/


title: Robotic Search for Optimal Cell Culture in Regenerative Medicine

abstract: Induced differentiation is one of the most experience- and skill-dependent experimental processes in regenerative medicine, and establishing optimal conditions often takes years. We developed a robotic AI system with a batch Bayesian optimization algorithm that autonomously induces the differentiation of induced pluripotent stem cell-derived retinal pigment epithelial (iPSC-RPE) cells. The system performed 216 forty-day cell culture experiments, with a total experimentation time of 8,640 days. From 200 million possible parameter combinations, the system performed cell culture in 143 different conditions in 111 days, resulting in 88% better iPSC-RPE production than that by the pre-optimized culture in terms of pigmented scores. Our work demonstrates that the use of autonomous robotic AI systems drastically accelerates systematic and unbiased exploration of experimental search space, suggesting immense use in medicine and research.

category: systems biology


title: Revisiting the Neural Architecture of Adolescent Decision-Making: Univariate and Multivariate Evidence for System-Based Models

abstract:
Understanding adolescent decision-making is significant for informing basic models of neurodevelopment as well as for the domains of public health and criminal justice. System-based theories posit that adolescent decision-making is guided by activity amongst reward and control processes. While successful at explaining behavior, system-based theories have received inconsistent support at the neural level, perhaps because of methodological limitations. Here, we used two complementary approaches to overcome said limitations and rigorously evaluate system-based models. Using decision-level modeling of fMRI data from a risk-taking task in a sample of 2000+ decisions across 51 human adolescents (25 females, mean age = 15.00 years), we find support for system-based theories of decision-making. Neural activity in lateral prefrontal cortex and a multivariate pattern of cognitive control both predicted a reduced likelihood of risk-taking, whereas increased activity in the nucleus accumbens predicted a greater likelihood of risk-taking. Interactions between decision-level brain activity and age were not observed. These results garner support for system-based accounts of adolescent decision-making behavior.

Significance StatementAdolescent decision-making behavior is of great import for basic science, and carries equally consequential implications for public health and criminal justice. While dominant psychological theories seeking to explain adolescent decision-making have found empirical support, their neuroscientific implementations have received inconsistent support. This may be partly due to statistical approaches employed by prior neuroimaging studies of system-based theories. We used brain modeling--an approach that predicts behavior from brain activity--of univariate and multivariate neural activity metrics to better understand how neural components of psychological systems guide decision behavior in adolescents. We found broad support for system-based theories such that neural systems involved in cognitive control predicted a reduced likelihood to make risky decisions, whereas value-based systems predicted greater risk-taking propensity.


title: FrustratometeR: an R-package to compute Local frustration in protein structures, point mutants and MD simulations

abstract:
Once folded, natural protein molecules have few energetic conflicts within their polypeptide chains. Many protein structures do however contain regions where energetic conflicts remain after folding, i. e. they have highly frustrated regions. These regions, kept in place over evolutionary and physiological timescales, are related to several functional aspects of natural proteins such as protein-protein interactions, small ligand recognition, catalytic sites and allostery. Here we present FrustratometeR, an R package that easily computes local energetic frustration on a personal computer or a cluster. This package facilitates large scale analysis of local frustration, point mutants and molecular dynamics (MD) trajectories, allowing straightforward integration of local frustration analysis into pipelines for protein structural analysis.

Contactgonzalo.parra@embl.de

Availability and implementationhttps://github.com/proteinphysiologylab/frustratometeR


title: Predicting the impact of sequence motifs on gene regulation using single-cell data

abstract:
BackgroundBinding of transcription factors (TFs) at proximal promoters and distal enhancers is central to gene regulation. Yet, identification of TF binding sites, also known as regulatory motifs, and quantification of their impact on gene expression remains challenging.

ResultsHere we infer putative regulatory motifs along with their cell type-specific importance using a convolutional neural network trained on single-cell data. Comparison of the importance score to expression levels across cells allows us to identify the TFs most likely to be binding at a given motif. Using multiple mouse tissues we obtain a model with cell type resolution which explains 29% of the variance in gene expression. Finally, by applying scover to distal enhancers identified using scATAC-seq from the mouse cerebral cortex we characterize changes in distal regulatory motifs during development.

ConclusionsIt is possible to identify regulatory motifs as well as their importance from single-cell data using a neural network model where all of the parameters and outputs are easily interpretable to the user.


title: A Non-Genetic, Cell Cycle Dependent Mechanism of Platinum Resistance in Lung Adenocarcinoma

abstract: We previously used a pulse-based in vitro assay to unveil targetable signalling pathways associated with innate cisplatin resistance in lung adenocarcinoma (Hastings et al., 2020). Here we advanced this model system and identified a non- genetic mechanism of resistance that drives recovery and regrowth in a subset of cells. Using RNAseq and a suite of biosensors to track single cell fates both in vitro and in vivo, we identified that early S phase cells have a greater ability to maintain proliferative capacity, which correlated with reduced DNA damage over multiple generations. In contrast, cells in G1, late S or those treated with PARP/RAD51 inhibitors, maintained higher levels of DNA damage and underwent prolonged S/G2 phase arrest and senescence. Combined with our previous work, these data indicate that there is a non-genetic mechanism of resistance in lung adenocarcinoma that is dependent on the cell cycle stage at the time of cisplatin exposure.

category: cell biology


title: An initial 'snapshot' of sensory information biases the likelihood and speed of subsequent changes of mind

abstract:
We often need to rapidly change our mind about perceptual decisions in order to account for new information and correct mistakes. One fundamental, unresolved question is whether information processed prior to a decision being made ( pre-decisional information) has any influence on the likelihood and speed with which that decision is reversed. We investigated this using a luminance discrimination task in which participants indicated which of two flickering greyscale squares was brightest. Following an initial decision, the stimuli briefly remained on screen, and participants could change their response. Using psychophysical reverse correlation, we examined how moment-to-moment fluctuations in stimulus luminance affected participants decisions. This revealed that the strength of even the very earliest (pre-decisional) evidence was associated with the likelihood and speed of later changes of mind. To account for this effect, we propose an extended diffusion model in which an initial  snapshot of sensory information biases ongoing evidence accumulation.

Author SummaryTo avoid harm in an ever-changing world we need to be able to rapidly change our minds about our decisions. For example, imagine being unable to overrule a decision to run across a street when you realise a speeding car is approaching. In this study, we examined the information processing dynamics which underlie perceptual judgements and changes of mind. By reverse correlating participants decisions with the moment-to-moment sensory evidence they received, we show that the very earliest information, processed prior to an initial decision being made, can have a lasting influence over the speed and likelihood of subsequent changes of mind. To account for this, we develop a model of perceptual decisions in which initial sensory evidence exerts a lasting bias over later evidence processing. When fit to participants behavioural responses alone, this model predicted their observed information usage patterns. This suggests that an initial  snapshot of sensory information may influence the ongoing dynamics of the perceptual decision process, thus influencing the speed and likelihood of decision reversals.

category: animal behavior and cognition


title: Nonlinear Stability Analysis for Artificial Kidney Multi-compartmental Models

abstract: This paper addresses a new global stability analysis for a specific class of nonlinear multi-compartment models with non-positive flows and whose balances are described by equilibrium sets. We apply the stability analysis to our physiological-based model of extracellular fluid used during dialysis therapy in end-stage kidney disease patients. To gain an in-depth understanding of the risk associated with fluid removal by the artificial kidney during the short time (3-5hrs) of the dialysis therapy, we use the stability results to analyze the solutions behavior of our model under standard ultrafiltration and patient-specific ultrafiltration profiles. Therefore, the standard ultrafiltration profiles do not guarantee optimal outcomes, and we highly recommend incorporating physiological insights into the ultrafiltration profiles to improve outcomes.

category: bioengineering


title: Fast and sensitive taxonomic assignment to metagenomic contigs

abstract:
MMseqs2 taxonomy is a new tool to assign taxonomic labels to metagenomic contigs. It extracts all possible protein fragments from each contig, quickly retains those that can contribute to taxonomic annotation, assigns them with robust labels and determines the contigs taxonomic identity by weighted voting. Its fragment extraction step is suitable for the analysis of all domains of life. MMseqs2 taxonomy is 2-18x faster than state-of-the-art tools and also contains new modules for creating and manipulating taxonomic reference databases as well as reporting and visualizing taxonomic assignments.

AvailabilityMMseqs2 taxonomy is part of the MMseqs2 free open-source software package available for Linux, macOS and Windows at https://mmseqs.com.

Contacteli.levy.karin@gmail.com


title: When less feels stronger: Earliest cortical responses differentially reflect stimulus intensity and neural excitability

abstract: Perception of sensory information is determined by stimulus features (e.g., intensity) and instantaneous neural states (e.g., excitability). Commonly, it is assumed that both are reflected similarly in evoked brain potentials, that is, higher evoked activity leads to a stronger percept of a stimulus. We tested this assumption in a somatosensory discrimination task in humans, simultaneously assessing (i) single-trial excitatory post-synaptic currents inferred from short-latency somatosensory evoked potentials (SEP), (ii) pre-stimulus alpha oscillations (8-13 Hz), and (iii) peripheral nerve measures. Fluctuations of neural excitability shaped the perceived stimulus intensity already during the very first cortical response (at [~]20 ms) yet demonstrating opposite neural signatures as compared to the effect of presented stimulus intensity. We reconcile this discrepancy via a common framework based on modulations of electro-chemical membrane gradients linking neural states and responses, which calls for reconsidering conventional interpretations of brain potential magnitudes in stimulus intensity encoding.


title: Neural excitability and sensory input determine intensity perception with opposing directions in initial cortical responses


title: Overexpressed microrna-129-5p reverses CCl4-Induced hepatic fibrosis by suppressing PEG3 expression and the NF-κB signaling pathway

abstract: The authors have withdrawn their manuscript whilst they perform additional experiments to test some of their conclusions further. This preprint does not represent the final version. Therefore, the authors do not wish this work to be cited as reference for the project.

category: pharmacology and toxicology


title: Whole-brain dynamics of human sensorimotor adaptation

abstract: Humans vary greatly in their motor learning abilities, yet little is known about the neural processes that underlie this variability. We identified distinct profiles of human sensorimotor adaptation that emerged across two days of learning, linking these profiles to the dynamics of whole-brain functional networks early on the first day, when cognitive strategies toward sensorimotor adaptation are believed to be most prominent. During early learning, greater recruitment of a network of higher-order brain regions, involving prefrontal and anterior temporal cortex, was associated with faster learning. At the same time, greater integration of this  cognitive network with a sensorimotor network was associated with slower learning, consistent with the notion that cognitive strategies toward adaptation operate in parallel with implicit learning processes of the sensorimotor system. On the second day, greater recruitment of a network that included the hippocampus was associated with faster re-learning, consistent with the notion that savings involves declarative memory systems. Together, these findings provide novel evidence for the role of higher-order brain systems in driving individual differences in adaptation.


title: Quantifying the relevance of alternative stable states in many-species food webs

abstract: Alternative stable ecosystem states are possible under the same environmental conditions in many models of 2-3 interacting species and an array of feedback loops. However, multi-species food webs might dissipate the feedbacks that create alternative stable states through species-specific traits and feedbacks. To test this potential, we develop a manyspecies model of consumer-resource interactions with two classes of feedbacks: specialized feedbacks where individual resources become unpalatable at high abundance, or aggregate feedbacks where overall resource abundance reduces consumer recruitment. We quantify how trophic interconnectedness and species differences in demography affect the potential for either feedback to produce alternative stable states dominated by consumers or resources. We find that alternative stable states are likely to happen in many-species food webs when aggregate feedbacks or lower species differences increase redundancy in species contributions to persistence of the consumer guild. Conversely, specialized palatability feedbacks with distinctive species roles in consumer guild persistence reduce the potential for alternative states but increase the likelihood that losing vulnerable consumers cascades into a food web collapse at low stress levels, a dynamic absent in few-species models. Altogether, among-species trait variation can limit the set of processes that create alternative stable states and impede consumer recovery from disturbance.


title: Unveiling functions of the visual cortex using task-specific deep neural networks

abstract: The human visual cortex enables visual perception through a cascade of hierarchical computations in cortical regions with distinct functionalities. Here, we introduce an AI-driven approach to discover the functional mapping of the visual cortex. We related human brain responses to scene images measured with functional MRI (fMRI) systematically to a diverse set of deep neural networks (DNNs) optimized to perform different scene perception tasks. We found a structured mapping between DNN tasks and brain regions along the ventral and dorsal visual streams. Low-level visual tasks mapped onto early brain regions, 3-dimensional scene perception tasks mapped onto the dorsal stream, and semantic tasks mapped onto the ventral stream. This mapping was of high fidelity, with more than 60% of the explainable variance in nine key regions being explained. Together, our results provide a novel functional mapping of the human visual cortex and demonstrate the power of the computational approach.


title: Establishment of Culex modestus in Belgium and a glance into the virome of Belgian mosquito species

abstract:
Culex modestus mosquitoes are known transmission vectors of West Nile virus and Usutu virus. Their presence has been reported across several European countries, including only one larva confirmed in Belgium in 2018. Mosquitoes were collected in the city of Leuven and surroundings in the summer of 2019 and 2020. Species identification was performed based on morphological features and partial sequences of the mitochondrial cytochrome oxidase subunit 1 (COI) gene. The 107 mosquitoes collected in 2019 belonged to eight mosquito species: Cx. pipiens (24.3%), Cx. modestus (48.6%), Cx. torrentium (0.9%), Culiseta annulata (0.9%), Culiseta morsitans (0.9%), Ae. sticticus (14.0%), Ae. cinereus (9.3%) and Anopheles plumbeus (0.9%), suggesting the presence of an established Cx. modestus population in Belgium. Collection of Cx. modestus mosquitoes at the same locations in 2020, confirmed the establishment in the region.

Haplotype network analysis of the COI sequences for Cx. modestus showed that the Belgian population is rather diverse, suggesting that it may have been established in Belgium for some time. The Belgian Cx. modestus population was most closely related to populations from the UK and Germany. Characterization of the virome of the collected mosquitoes resulted in the identification of at least 33 eukaryotic viral species. Nine (near-) complete genomes belonging to 6 viral species were identified, all of which were closely related to known viruses.

In conclusion, we here report the presence of Cx. modestus in the surroundings of Leuven, Belgium. As this species is known to be a vector of several arboviruses, the implementation of vector surveillance programs monitoring this species is recommended.

ImportanceCulex modestus is a mosquito species that plays a role as a  bridge vector, being able to transmit pathogens between birds, as well as from birds to mammals, including humans. In Belgium, this mosquito species was considered absent, until the finding of one larva in 2018 and subsequent evidence of a large population in 2019-2020 described here. We collected mosquitoes in the summer of 2019 and 2020 in the city of Leuven and surroundings. The mosquito species was identified by morphological and molecular methods, demonstrating the presence of Cx. modestus in this region. The ability of mosquitoes to transmit pathogens can depend on several factors, one of them being their natural virus composition. Therefore, we identified the mosquito-specific viruses harboured by Belgian mosquitoes. As Cx. modestus is able to transmit viruses such as West Nile virus and Usutu virus, the establishment of this mosquito species may increase the risk of virus transmission in the region. It is thus advisable to implement mosquito surveillance programs monitoring this species.


title: 3D super-resolution fluorescence microscopy maps the variable molecular architecture of the Nuclear Pore Complex

abstract: Nuclear pore complexes (NPCs) are large macromolecular machines that mediate the traffic between the nucleus and the cytoplasm. In vertebrates, each NPC consists of ~1000 proteins, termed nucleoporins, and has a mass of over 100 MDa. While a pseudo-atomic static model of the central scaffold of the NPC has recently been assembled by integrating data from isolated proteins and complexes, many structural components still remain elusive due to the enormous size and flexibility of the NPC. Here, we explored the power of 3D super-resolution microscopy combined with computational classification and averaging to explore the 3D structure of the NPC in single human cells. We show that this approach can build the first integrated 3D structural map containing both central as well as peripheral NPC subunits with molecular specificity and nanoscale resolution. Our unbiased classification of over ten thousand individual NPCs indicates that the nuclear ring and the nuclear basket can adopt different conformations. Our approach opens up the exciting possibility to relate different structural states of the NPC to function in situ.


title: Tackling the phylogenetic conundrum of Hydroidolina (Cnidaria: Medusozoa: Hydrozoa) by assessing competing tree topologies with targeted high-throughput sequencing.

abstract: Higher-level relationships of the Hydrozoan subclass Hydroidolina, which encompasses the vast majority of medusozoan cnidarian species diversity, have been elusive to confidently infer. The most widely adopted phylogenetic framework for Hydriodolina based on ribosomal RNA data received low support for several higher level relationships. To address this issue, we developed a set of RNA baits to target more than a hundred loci from the genomes of a broad taxonomic sample of Hydroidolina for high-throughput sequencing. Using these data, we inferred the relationships of Hydroidolina using maximum likelihood and Bayesian approaches. Both inference methods yielded well-supported phylogenetic hypotheses that largely agree with each other. Using maximum likelihood and Baysian hypothesis testing frameworks, we found that several alternate topological hypotheses proposed previously may be rejected in light of the genomic data generated for this study. Both the maximum likelihood and Bayesian topologies inferred herein consistently score well across testing frameworks, suggesting that their consensus represents the most likely phylogenetic hypothesis of Hydroidolina. This phylogenetic framework places Aplanulata as sister lineage to the remainder of Hydroidolina. This is a strong deviation from previous phylogenetic analyses that placed Capitata or Siphonophorae as sister group to the remainder of Hydroidolina. Considering that Aplanulata represents a lineage comprised of species that for the most part possess a life cycle involving a solitary polyp and free-swimming medusa stage, the phylogenetic hypotheses presented herein have potentially large implications for clarifying the evolution of life cycles, coloniality, and the division of labor in Hydrozoa as taxon sampling for phylogenetic analyses becomes more complete.


title: Profiling Germline Adaptive Immune Receptor Repertoire with gAIRR Suite

abstract: Genetic profiling of germline adaptive immune receptor repertoire (AIRR), including T cell receptor (TR) and immunoglobulin (IG), is imaginably relevant to numerous immune-related conditions, but currently insurmountable due to high genetic complexity. Our gAIRR Suite comprises three modules. gAIRR-seq, a probe capture-based targeted sequencing pipeline, profiles AIRR from individual DNA samples. gAIRR-call and gAIRR-annotate call alleles from gAIRR-seq reads and annotate whole-genome assemblies respectively. We gAIRR-seqed TRV and TRJ of seven Genome in a Bottle (GIAB) DNA samples with 100% accuracy, and discovered novel alleles. We also gAIRR-seqed and gAIRR-called a subject from both the peripheral blood mononuclear cells (PBMC) and oral mucosal cells. The calling results from these two cell types have a high concordance (99% for all known AIRR alleles). We gAIRR-annotated 36 genomes to cumulatively unearth 325 novel TRV alleles and 29 novel TRJ alleles. We could further profile the flanking sequences, including the recombination signal sequence (RSS). We validated two structural variants for HG002. We uncovered substantial conflicts of AIRR genes in references GRCh37 and GRCh38. The gAIRR Suite can potentially benefit future genetic study and clinical applications of various immune-related phenotypes.


title: Human induced pluripotent stem cell-derived vessels as dynamic atherosclerosis model on a chip

abstract: Atherosclerosis is an arterial disease characterized by intravascular plaques. Disease hallmarks are vessel stenosis and hyperplasia, eventually escalating into plaque rupture and acute clinical presentations. Innate immune cells and local variations in hemodynamics are core players in the pathology, but their mutual relationship has never been investigated before due to the lack of modeling systems with adequate degree of complexity. Here, we combined computational fluid dynamics and tissue-engineering to achieve, for the first time in vitro, full atherosclerotic plaque development. Our model incorporates induced pluripotent stem cell-derived populations into small-caliber arteries that are cultured in atheroprone conditions. Using machine-learning-aided immunophenotyping, molecular and nanoprobe-based tensile analyses, we found that immune cells, extracellular matrix components and tensional state were comparable between in vitro and ex vivo human lesions. Our results provide further insights into the relation between hemodynamics and inflammation, introducing a versatile, scalable modeling tool to study atherosclerosis onset and progression.


title: The impact of phenotypic heterogeneity of tumour cells on treatment and relapse dynamics

abstract:
Intratumour heterogeneity is increasingly recognized as a frequent problem for cancer treatment as it allows for the evolution of resistance against treatment. While cancer genotyping becomes more and more established and allows to determine the genetic heterogeneity, less is known about the phenotypic heterogeneity among cancer cells. We investigate how phenotypic differences can impact the efficiency of therapy options that select on this diversity, compared to therapy options that are independent of the phenotype. We employ the ecological concept of trait distributions and characterize the cancer cell population as a collection of subpopulations that differ in their growth rate. We show in a deterministic model that growth rate-dependent treatment types alter the trait distribution of the cell population, resulting in a delayed relapse compared to a growth rate-independent treatment. Whether the cancer cell population goes extinct or relapse occurs is determined by stochastic dynamics, which we investigate using a stochastic model. Again, we find that relapse is delayed for the growth rate-dependent treatment type, albeit an increased relapse probability, suggesting that slowly growing subpopulations are shielded from extinction. Sequential application of growth rate-dependent and growth rate-independent treatment types can largely increase treatment efficiency and delay relapse. Interestingly, even longer intervals between decisions to change the treatment type may achieve close-to-optimal efficiencies and relapse times. Monitoring patients at regular check-ups may thus provide the temporally resolved guidance to tailor treatments to the changing cancer cell trait distribution and allow clinicians to cope with this dynamic heterogeneity.

Author summaryThe individual cells within a cancer cell population are not all equal. The heterogeneity among them can strongly affect disease progression and treatment success. Recent diagnostic advances allow measuring how the characteristics of this heterogeneity change over time. To match these advances, we developed deterministic and stochastic trait-based models that capture important characteristics of the intratumour heterogeneity and allow to evaluate different treatment types that either do or do not interact with this heterogeneity. We focus on growth rate as the decisive characteristic of the intratumour heterogeneity. We find that by shifting the trait distribution of the cancer cell population, the growth rate-dependent treatment delays an eventual relapse compared to the growth rate-independent treatment. As a downside, however, we observe a refuge effect where slower-growing subpopulations are less affected by the growth rate-dependent treatment, which may decrease the likelihood of successful therapy. We find that navigating along this trade-off may be achieved by sequentially combining both treatment types, which agrees qualitatively with current clinical practice. Interestingly, even rather large intervals between treatment changes allow for close-to-optimal treatment results, which again hints towards a practical applicability.


title: Unheeded SARS-CoV-2 protein? Look deep into negative-sense RNA

abstract:
SARS-CoV-2 is a novel positive-sense single-stranded RNA virus from the Coronaviridae family (genus Betacoronavirus), which has been established as causing the COVID-19 pandemic. The genome of SARS-CoV-2 is one of the largest among known RNA viruses, comprising of at least 26 known protein-coding loci. Studies thus far have outlined the coding capacity of the positive-sense strand of the SARS-CoV-2 genome, which can be used directly for protein translation. However, it has been recently shown that transcribed negative-sense viral RNA intermediates that arise during viral genome replication from positive-sense viruses can also code for proteins. No studies have yet explored the potential for negative-sense SARS-CoV-2 RNA intermediates to contain protein coding-loci. Thus, using sequence and structure-based bioinformatics methodologies, we have investigated the presence and validity of putative negative-sense ORFs (nsORFs) in the SARS-CoV-2 genome. Nine nsORFs were discovered to contain strong eukaryotic translation initiation signals and high codon adaptability scores, and several of the nsORFs were predicted to interact with RNA-binding proteins. Evolutionary conservation analyses indicated that some of the nsORFs are deeply conserved among related coronaviruses. Three-dimensional protein modelling revealed the presence of higher order folding among all putative SARS-CoV-2 nsORFs, and subsequent structural mimicry analyses suggest similarity of the nsORFs to DNA/RNA-binding proteins and proteins involved in immune signaling pathways. Altogether, these results suggest the potential existence of still undescribed SARS-CoV-2 proteins, which may play an important role in the viral lifecycle and COVID-19 pathogenesis.

Contactpetr.pecinka@osu.cz; tlb20@cam.ac.uk


title: Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA


title: Ultrafast end-to-end protein structure prediction enables high-throughput exploration of uncharacterised proteins

abstract:
Deep learning-based prediction of protein structure usually begins by constructing a multiple sequence alignment (MSA) containing homologues of the target protein. The most successful approaches combine large feature sets derived from MSAs, and considerable computational effort is spent deriving these input features. We present a method that greatly reduces the amount of preprocessing required for a target MSA, while producing main chain coordinates as a direct output of a deep neural network. The network makes use of just three recurrent networks and a stack of residual convolutional layers, making the predictor very fast to run, and easy to install and use. Our approach constructs a directly learned representation of the sequences in an MSA, starting from a one-hot encoding of the sequences. When supplemented with an approximate precision matrix, the learned representation can be used to produce structural models of comparable or greater accuracy as compared to our original DMPfold method, while requiring less than a second to produce a typical model. This level of accuracy and speed allows very large-scale 3-D modelling of proteins on minimal hardware, and we demonstrate that by producing models for over 1.3 million uncharacterized regions of proteins extracted from the BFD sequence clusters. After constructing an initial set of approximate models, we select a confident subset of over 30,000 models for further refinement and analysis, revealing putative novel protein folds. We also provide updated models for over 5,000 Pfam families studied in the original DMPfold paper.

Significance StatementWe present a deep learning-based predictor of protein tertiary structure that uses only a multiple sequence alignment (MSA) as input. To date, most emphasis has been on the accuracy of such deep learning methods, but here we show that accurate structure prediction is also possible in very short timeframes (a few hundred milliseconds). In our method, the backbone coordinates of the target protein are output directly from the neural network, which makes the predictor extremely fast. As a demonstration, we generated over 1.3 million models of uncharacterised proteins in the BFD, a large sequence database including many metagenomic sequences. Our results showcase the utility of ultrafast and accurate tertiary structure prediction in rapidly exploring the "dark space" of proteins.


title: Linear integration of sensory evidence over space and time underlies face categorization

abstract: Visual object recognition relies on elaborate sensory processes that transform retinal inputs to object representations, but it also requires decision-making processes that read out object representations and function over prolonged time scales. The computational properties of these decision-making processes remain underexplored for object recognition. Here, we study these computations by developing a stochastic multi-feature face categorization task. Using quantitative models and tight control of spatiotemporal visual information, we demonstrate that humans categorize faces through an integration process that first linearly adds the evidence conferred by task-relevant features over space to create aggregated momentary evidence, and then linearly integrates it over time with minimum information loss. Discrimination of stimuli along different category boundaries (e.g., identity or expression of a face) is implemented by adjusting feature weights of spatial integration. This linear but flexible integration process over space and time bridges past studies on simple perceptual decisions to complex object recognition behavior.


title: Diverse molecular mechanisms contribute to differential expression of human duplicated genes

abstract: Emerging evidence links genes within human-specific segmental duplications (HSDs) to traits and diseases unique to our species. Strikingly, despite being nearly identical by sequence (>98.5%), paralogous HSD genes are differentially expressed across human cell and tissue types, though the underlying mechanisms have not been examined. We compared cross-tissue mRNA levels of 75 HSD genes from 30 families between humans and chimpanzees and found expression patterns consistent with pseudo- or neofunctionalization. In general, ancestral paralogs exhibited greatest expression conservation with chimpanzee orthologs, though exceptions suggest certain derived paralogs may retain or supplant ancestral functions. Concordantly, analysis of long-read isoform sequencing datasets from diverse human tissues and cell lines found that about half of derived paralogs exhibited globally lower expression. To understand mechanisms underlying these differences, we leveraged data from human lymphoblastoid cell lines (LCLs) and found no relationship between paralogous expression divergence and post- transcriptional regulation, sequence divergence, or copy number variation. Considering cis-regulation, we reanalyzed ENCODE data and recovered hundreds of previously unidentified candidate CREs in HSDs. We also generated large-insert ChIP-sequencing data for active chromatin features in an LCL to better distinguish paralogous regions. Some duplicated CREs were sufficient to drive differential reporter activity, suggesting they may contribute to divergent cis-regulation of paralogous genes. This work provides evidence that cis-regulatory divergence contributes to novel expression patterns of recent gene duplicates in humans.


title: Investigations into modifications of neuromuscular physiology by axonal transport disruptions in Drosophila SOD1 mutants

abstract: Cu/Zn superoxide dismutase (SOD1) is a cytoplasmic antioxidant enzyme, which, when mutant in humans, is linked to familial cases of the motor neurodegenerative disease amyotrophic lateral sclerosis (ALS). The Drosophila SOD1 gene (Sod) shares a highly conserved sequence with the human homolog, and this study includes examinations of the established hypomorphic n108 allele (Sodn108), alongside a knock-in construct of the G85R allele found in human ALS patients (SodG85R). In addition to previously documented decreased adult lifespan and attenuated motor function, we show that Sod mutant Drosophila can display significant mortality during larval and pupal development. Immunostaining of neuronal membrane at neuromuscular synapses in Sod mutant larvae revealed presynaptic terminals of abnormal morphology, with incompletely segregated and enlarged synaptic boutons along the motor terminal branches, in which vital staining indicated mitochondrial aggregation. We demonstrate strong genetic interactions between SodG85R and the axon transport-linked Pk mutants PkPk and PkSple in larval NMJ morphology and neuromuscular transmission. Intracellular recordings of larval excitatory junction potentials (EJPs) demonstrate enhanced EJP size in the double-mutant of PkPk and SodG85R. To examine synaptic terminal excitability, maintained by Ca2+ channel action and independent of Na+ channel function, we used the NaV blocker TTX, along with the KV1 blocker 4-aminopyridine (4-AP) and the commonly used broad-spectrum K+ channel blocker tetraethylammonium (TEA). We were able to induce prolonged "plateau-like" EJPs, which were further extended in Pk mutants and Pk;Sod double-mutants. These observations were corroborated with focal EJP recording from individual boutons. Altogether, this study highlights alterations in synaptic morphology and function at a developmental stage prior to neurodegeneration and death of Sod mutant organisms, along with a potential role of axonal transport in the maintenance of neuronal health.


title: Dynamic decision policy reconfiguration under outcome uncertainty

abstract: In uncertain or unstable environments, sometimes the best decision is to change your mind. To shed light on this flexibility, we evaluated how the underlying decision policy adapts when the most rewarding action changes. Human participants performed a dynamic two-armed bandit task that manipulated the certainty in relative reward (conflict) and the reliability of action-outcomes (volatility). Continuous estimates of conflict and volatility contributed to shifts in exploratory states by changing both the rate of evidence accumulation (drift rate) and the amount of evidence needed to make a decision (boundary height), respectively. At the trialwise level, following a switch in the optimal choice, the drift rate plummets and the boundary height weakly spikes, leading to a slow exploratory state. We find that the drift rate drives most of this response, with an unreliable contribution of boundary height across experiments. Surprisingly, we find no evidence that pupillary responses associated with decision policy changes. We conclude that humans show a stereotypical shift in their decision policies in response to environmental changes.


title: Jack-of-all-trades paradigm meets long-term data: generalist herbivores are more widespread and locally less abundant

abstract:
Ecological specialization is one of the most interesting and perplexing attributes of biological systems. While certain macroecological patterns, such as an increase in specialization at lower latitudes, have long been subjects of investigation, there is much yet to be learned about inter-specific variation in specialization within diverse communities. High levels of specialization have been documented for some dominant ecological interactions, such as parasitism and herbivory, but much less is known about the relative abundance of specialists and generalists within those broad functional groups. We examine untested assumptions about the positive association between local abundance and dietary specialization using a 17-year dataset of caterpillar-plant interactions in Ecuador. Our long-term data consist of experimental verification of caterpillar-plant associations and include standardized plot-based samples as well as general, regional collections of caterpillars, allowing for investigations across spatial scales and using different indices of abundance for 1,917 morphospecies of Lepidoptera ("caterpillars") from 33 families. We find that more specialized caterpillars are locally more abundant than generalists, consistent with a key component of the "jack of all trades, master of none" hypothesis, which has otherwise received poor to mixed support from previous studies that have mostly involved fewer species and shorter time series. At larger scales, generalists achieve greater prevalence across the landscape, and we find some evidence for geographic variation in the abundance-diet breadth relationship, in particular among elevational bands. Interspecific variation in abundance had a negative relationship with diet breadth, with specialists having more variable abundances across species. The interesting result that more specialized species can be both rare and common highlights the ecological complexity of specialization.

Statement of authorshipCS wrote the first draft of the manuscript. DMS, MLF and LAD contributed substantially to consequent drafts and revisions. LAD, TRW, SV and DMS collected field data. CS, MLF and LAD generated research questions and designed statistical analyses. CS, DMS, LAD and MLF conducted statistical analyses.

Data statementData supporting the results and conclusions can be found on a website caterpillars.org. Statistical analyses supporting the results are available upon request.


title: Characterisation and chemometric evaluation of 17 elements in ten seaweed species from Greenland

abstract: Several Greenland seaweed species have potential as foods or food ingredients, both for local consumption and export. However, knowledge regarding their content of beneficial and deleterious elements on a species specific and geographical basis is lacking. This study investigated the content of 17 elements (As, Ca, Cd, Cr, Cu, Fe, Hg, I, K, Mg, Mn, Na, Ni, P, Pb, Se and Zn) in 77 samples of ten species (Agarum clathratum, Alaria esculenta, Ascophyllum nodosum, Fucus distichus, Fucus vesiculosus, Hedophyllum nigripes, Laminaria solidungula, Palmaria palmata, Saccharina latissima and Saccharina longicruris). Element profiles differed between species but showed similar patterns within the same family. For five species, different thallus parts were investigated separately, and showed different element profiles. A geographic origin comparison of Fucus species indicated regional differences. The seaweeds investigated were especially good sources of macrominerals (K > Na > Ca > Mg) and trace minerals, such as Fe. Iodine contents were high, especially in macroalgae of the family Laminariaceae. None of the samples exceeded the EU maximum levels for Cd, Hg or Pb, but some exceeded the stricter French regulations, especially for Cd and I. In conclusion, these ten species are promising food items.

category: biochemistry


title: Differential Contribution of Dopaminergic Transmission at D1- and D2-like Receptors to Cost/Benefit Evaluation for Motivation in Monkeys

abstract: It has been widely accepted that dopamine (DA) plays a major role in motivation, yet the specific contribution of DA signaling at D1-like receptor (D1R) and D2-like receptor (D2R) to cost-benefit trade-off remains unclear. Here, by combining pharmacological manipulation of DA receptors (DARs) and positron emission tomography imaging, we assessed the relationship between the degree of D1R/D2R blockade and changes in benefit- and cost-based motivation for goal-directed behavior of macaque monkeys. We found that the degree of blockade of either D1R or D2R was associated with a reduction of the positive impact of reward amount and increasing delay-discounting. Workload-discounting was selectively increased by D2R antagonism. In addition, blocking both D1R and D2R had a synergistic effect on delay-discounting but an antagonist effect on workload-discounting. These results provide fundamental in-sight into the distinct mechanisms of DA action in the regulation of the cost and benefit-based motivation, which have important implications for motivational alterations in both neurological and psychiatric disorders.


title: D1- and D2-like Receptors Differentially Mediate the Effects of Dopaminergic Transmission on Cost/Benefit Evaluation and Motivation in Monkeys


title: PP2A-Cdc55 phosphatase coordinates actomyosin ring contraction and septum formation during cytokinesis

abstract: Eukaryotic cells divide and separate all their components after chromosome segregation by a process called cytokinesis to complete cell division. Cytokinesis is highly regulated by recruitment of the components to the division site and through post-translational modifications such as phosphorylations. The budding yeast mitotic kinases Cdc28-Clb2, Cdc5, and Dbf2-Mob1 phosphorylate several cytokinetic proteins contributing to the regulation of cytokinesis. The PP2A-Cdc55 phosphatase regulates mitosis counteracting Cdk1- and Cdc5-dependent phosphorylation. This prompted us to propose that PP2A-Cdc55 could also be counteracting the mitotic kinases during cytokinesis. Here, we demonstrate that primary septum formation and actomyosin ring contraction are impaired in the absence of PP2A-Cdc55. In addition, by in vivo and in vitro assays, we show that PP2A-Cdc55 dephosphorylates the chitin synthase II (Chs2 in budding yeast) a component of the Ingression Progression Complexes (IPCs) involved in cytokinesis. Interestingly, the non-phosphorylable version of Chs2 rescues the asymmetric AMR contraction observed in cdc55{Delta} mutant cells. Therefore, timely dephosphorylation of the Chs2 by PP2A-Cdc55 is crucial for proper actomyosin ring contraction. These findings reveal a new mechanism of cytokinesis regulation by the PP2A-Cdc55 phosphatase and extend our knowledge in the involvement of multiple phosphatases during cytokinesis.


title: Predicting Brain Regions Related to Alzheimer's Disease Based on Global Feature

abstract: Alzheimers disease (AD) is a common neurodegenerative disease in the elderly, early diagnosis and timely treatment are very important to delay the course of the disease. In the past, most of the brain regions related to AD were identified based on the imaging method, which can only identify some atrophic brain regions. In this work, we used mathematical models to find out the potential brain regions related to AD. First, diffusion tensor imaging (DTI) was used to construct the brain structural network. Next, we set a new local feature index 2hop-connectivity to measure the correlation among different areas. The 2hop-connectivity utilizes the higher-order information of the graph structure relative to the traditional graph theory metrics. And for this, we proposed a novel algorithm named 2hopRWR to measure 2hop-connectivity. At last, we proposed a new index GFS (Global Feature Score) based on a global feature by combing 5 local features: degree centrality, betweenness centrality, closeness centrality, the number of maximal cliques, and 2hop-connectivity, to judge which brain regions are likely related to Alzheimers Disease. As a result, all the top ten brain regions in the GFS scoring difference between the AD group and the non-AD group were related to AD by literature verification. Literature validation results comparing GFS with local features showed that GFS outperforms individual local features. Finally, the results of the canonical correlation analysis showed that the GFS was significantly correlated with the scores of the mini-mental state examination (MMSE) scale and the Montreal cognitive assessment (MoCA) scale. So, we believe the GFS can also be used as a new index to assist in diagnosis and objective monitoring of disease progression. Besides, the method proposed in this paper can be used as a differential network analysis method in other areas of network analysis.


title: Translesion DNA synthesis-driven mutagenesis in very early embryogenesis of fast cleaving embryos

abstract: In early embryogenesis of fast cleaving embryos DNA synthesis is short and surveillance mechanisms preserving genome integrity are inefficient implying the possible generation of mutations. We have analyzed mutagenesis in Xenopus laevis and Drosophila melanogaster early embryos. We report the occurrence of a high mutation rate in Xenopus and show that it is dependent upon the translesion DNA synthesis (TLS) master regulator Rad18. Unexpectedly, we observed a homology-directed repair contribution of Rad18 in reducing the mutation load. Genetic invalidation of TLS in the pre-blastoderm Drosophila embryo resulted in reduction of both the hatching rate and Single Nucleotide Variations on specific chromosome regions in adult flies. Altogether, these findings indicate that during very early Xenopus and Drosophila embryos TLS strongly contributes to the high mutation rate. This may constitute a previously unforeseen source of genetic diversity contributing to the polymorphisms of each individual with implications for genome evolution and species adaptation.

category: developmental biology


title: De novo activated transcription of insertd foreign coding sequences is inheritable in the plant genome

abstract: The manner in which inserted foreign coding sequences become transcriptionally activated and fixed in the plant genome is poorly understood. To examine such processes of gene evolution, we performed an artificial evolutionary experiment in Arabidopsis thaliana. As a model of gene-birth events, we introduced a promoterless coding sequence of the firefly luciferase (LUC) gene and established 386 T2-generation transgenic lines. Among them, we determined the individual LUC insertion loci in 76 lines and found that one-third of them were transcribed de novo even in the intergenic or inherently unexpressed regions. In the transcribed lines, transcription-related chromatin marks were detected across the newly activated transcribed regions. These results agreed with our previous findings in A. thaliana cultured cells under a similar experimental scheme. A comparison of the results of the T2-plant and cultured cell experiments revealed that the de novo-activated transcription concomitant with local chromatin remodelling was inheritable. During one-generation inheritance, it seems likely that the transcription activities of the LUC inserts trapped by the endogenous genes/transcripts became stronger, while those of de novo transcription in the intergenic/untranscribed regions became weaker. These findings may offer a clue for the elucidation of the mechanism by which inserted foreign coding sequences become transcriptionally activated and fixed in the plant genome.


title: Plant genome response to incoming coding sequences: stochastic transcriptional activation independent of integration loci

abstract: Horizontal gene transfer can occur between phylogenetically distant organisms, such as prokaryotes and eukaryotes. In these cases, how do the translocated genes acquire transcriptional competency in the alien eukaryotic genome? According to the conventional view, specific loci of the eukaryotic genome are thought to provide transcriptional competency to the incoming coding sequences. To examine this possibility, we randomly introduced the promoterless luciferase (LUC)-coding sequences into the genome of Arabidopsis thaliana cultured cells and performed a genome-wide "transgene location vs. expression" scan. We mapped 4,504 promoterless LUC inserts on the A. thaliana chromosomes, and found that about 30% of them were transcribed. Only a small portion of them were explained by the conventional transcriptional fusions with the annotated genes, and the remainder occurred in a quite different manner; (1) they occurred all over the chromosomal regions, (2) independently of the insertion sites relative to the annotated gene loci, inherent transcribed regions, or heterochromatic regions, and (3) with one magnitude lower transcriptional level than the conventional transcriptional fusions. This type of transcriptional activation occurred at about 30% of the inserts, raising a question as to what this 30% means. We tested two hypotheses: the activation occurred at 30% of the entire chromosomal regions, or stochastically at 30% of each insertion event. Our experimental analysis indicates that the latter model could explain this transcriptional activation, a new type of plant genome response to the incoming coding sequences. We discuss the possible mechanisms and evolutionary roles of this phenomenon in the plant genome.


title: Continuous cis-regulatory changes in an advantageous gene are linked with adaptive radiation in cichlid fishes

abstract: Deciphering why some lineages produce spectacular radiations while others do not provides important insights into biodiversity, but the molecular basis underlying this process remains largely unknown. Here, we identified a lineage-restricted gene, which we named lg. Combined omics analyses showed that lg is under positive selection in the most species-rich lineage of cichlid fishes, the modern haplochromine (MH) lineage, indicating its evolutionary advantage. Using transgenic zebrafish, we functionally showed that a cichlid fish-specific upstream insertion of lg can drive new and strong eGFP expression in tissues noted for adaptation in the MH lineage, but not in other lineages. Furthermore, the deletion of three MH-specific SNPs within this region can reconstitute weak and limited expression patterns similar to those in non-MH lineages. We thus demonstrated that a series of cis-regulatory changes in an advantageous gene are linked with a gain of expression that is related to an astonishingly adaptive radiative lineage.


title: Diagnostic design with machine learning model-based optimization

abstract: Diagnostics, particularly for rapidly evolving viruses, stand to benefit from a principled, measurement-driven design that harnesses machine learning and vast genomic data--yet the capability for such design has not been previously built. Here, we develop and extensively validate an approach to designing viral diagnostics that applies a learned model within a combinatorial optimization framework. Concentrating on CRISPR-based diagnostics, we screen a library of 19,209 diagnostic-target pairs and train a deep neural network that predicts, from RNA sequence alone, diagnostic signal better than contemporary techniques. Our model then makes it possible to design assays that are maximally sensitive over the spectrum of a viruss genomic variation. We introduce ADAPT (https://adapt.guide), a system for fully-automated design, and use ADAPT to design optimal diagnostics for the 1,933 vertebrate-infecting viral species within 2 hours for most species and 24 hours for all but 3. We experimentally show ADAPTs designs are sensitive and specific down to the lineage level, including against viruses that pose challenges involving genomic variation and specificity. ADAPTs designs exhibit significantly higher fluorescence and permit lower limits of detection, across a viruss entire variation, than the outputs of standard design techniques. Our model-based optimization strategy has applications broadly to viral nucleic acid diagnostics and other sequence-based technologies, and, paired with clinical validation, could enable a critically-needed, proactive resource of assays for surveilling and responding to pathogens.


title: Designing viral diagnostics with model-based optimization


title: First demonstration of the FLASH effect with ultrahigh dose-rate high-energy X-rays

abstract: Ultrahigh dose-rate (FLASH) radiotherapy has attracted immense attention because of its tumor control efficiency and healthy tissue protection during preclinical experiments with electrons, kilo-voltage X-rays, and protons. Using high-energy X-rays (HEXs) in FLASH is advantageous owing to its deep penetration, small divergence, and cost-effectiveness. This is the first report on the implementation of HEXs with FLASH (HEX-FLASH) and its corresponding application in vivo. With a high-current and high-energy superconducting linear accelerator, FLASH with a good dose rate and high penetration was achieved. Breast cancers artificially induced in BAL b/c mice were efficiently controlled, and normal tissues surrounding the thorax/abdomen in C57BL/6 mice were protected from radiation with HEX-FLASH. Theoretical analyses of cellular responses following HEX-FLASH irradiation were performed to interpret the experimental results and design further experiments. Thus, this study highlights the generation of HEX-FLASH for the first time and its potential in future clinical applications.


title: Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis

abstract:
Linker histones play a pivotal role in shaping chromatin architecture, notably through their globular H1 (GH1) domain that contacts the nucleosome and linker DNA. Yet, interplays of H1 with chromatin factors along the epigenome landscape are just starting to emerge. Here, we report that Arabidopsis H1 occupies and favors both chromatin compaction and H3K27me3 enrichment on a majority of Polycomb-target protein-coding genes. In contrast, H1 prevents H3K27me3 accumulation on telomeres and pericentromeric interstitial telomeric repeats (ITRs) while orchestrating long-distance interactions regulating the 3D organization of these chromosome regions. Mechanistically, H1 prevents ITRs from being invaded by Telomere Repeat Binding 1 (TRB1), a GH1-containing telomere component with extra-telomeric functions in Polycomb recruitment. Based on these findings, we propose that H1 represses H3K27me3 accumulation on large blocks of telomeric repeats by antagonizing TRB1 association to linker DNA, conferring to linker histones an additional and sequence-specific role in modulating H3K27me3 epigenome homeostasis.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/402172v4_ufig1.gif" ALT="Figure 1">
View larger version (37K):
org.highwire.dtl.DTLVardef@1ecbee5org.highwire.dtl.DTLVardef@1e8ce33org.highwire.dtl.DTLVardef@139859corg.highwire.dtl.DTLVardef@172d4c7_HPS_FORMAT_FIGEXP  M_FIG C_FIG


title: Multielectrode Cortical Stimulation Selectively Induces Unidirectional Wave Propagation

abstract: Cortical stimulation is emerging as an experimental tool in basic research and a promising therapy for a range of neuropsychiatric conditions. As multielectrode arrays enter clinical practice, the possibility of using spatiotemporal patterns of electrical stimulation to induce desired physiological patterns has become theoretically possible, but in practice can only be implemented by trial-and-error because of a lack of predictive models. Experimental evidence increasingly establishes travelling waves as fundamental to cortical information-processing, but we lack understanding how to control wave properties despite rapidly improving technologies. This study uses a hybrid biophysical-anatomical and neural-computational model to predict and understand how a simple pattern of cortical surface stimulation could induce directional traveling waves via asymmetric activation of inhibitory interneurons. It reveals local circuit mechanisms to control spatiotemporal cortical dynamics and predicts interventions that can be developed to treat a broad range of cognitive disorders.


title: The TRPV Channel OSM-9 is Required for Sleep-Dependent Olfactory Memory and is Expressed in Sensory Neurons That Do Not Promote Butanone Attraction

abstract:
Memory, defined as an alteration in behavior that follows as a consequence of experience, can form when a sensory stimulus is encountered at the same time that the animal experiences a negative or positive internal state. How this coincident detection of external and internal stimuli stably alters responses to the external stimulus is still not fully understood, especially in the context of an intact animal. One barrier to understanding how an intact biological circuit changes is knowing what molecular processes are required to establish and maintain the memory. The optically accessible and compact nervous system of C. elegans provides a unique opportunity to examine the molecular and cellular processes that promote memory formation. The C. elegans nematode can remember an odor such as butanone when it is paired with a single negative experience and the transient receptor potential (TRP) OSM-9/TRPV5/TRPV6 channel is known to be required for this memory. The multiple gating mechanisms of TRPV channels give them the potential to be the coincidence detectors required to integrate internal state and external stimuli. Here, we report that this TRPV channel is also required for acquisition and possibly consolidation of sleep-dependent, long-term memory of butanone. Using an endogenous CRISPR-based tag, we find that OSM-9 is expressed in the paired AWA olfactory neurons, the ASH nociceptive neuron pair, the mechanosensory OLQ tetrad, and the paired ADF and ADL sensory neurons. In these cells, OSM-9 protein is concentrated in the sensory endings, dendrites, and cell bodies, but excluded from the neurites in the nerve ring. In the tail, OSM-9 is expressed in the nociceptive phasmid neurons PHA and PHB, possibly PQR as well as PVP. In the midbody, it is possibly expressed in the mechanosensitive PVD neuron. Because OSM-9 is expressed in sensory neurons that do not participate in butanone chemosensory behavior, this indicates that cells extrinsic to the primary sensory circuit may participate in acquiring and consolidating memory.

Author summaryHow organisms learn from their environment and keep these memories for the long term ensures their survival. There is much known about the regions of the brain and the various proteins that are essential for memory, yet the exact molecular mechanisms and dynamics required are not known. We aimed to understand the genetics that underlie memory formation. We tested a gene that encodes a transient potential receptor channel vanilloid channel, which is similar to the channels we have that sense spicy foods and other harmful cues. Our studies have shown that this gene is required specifically to acquire and perhaps consolidate memory. This protein is not expressed in the sensory neurons that respond to odor or in other downstream interneurons in this circuit, but it is expressed and possibly acts in a distinct set of sensory neurons. This indicates that long-term memory involves a wider array of sensory neurons than is required for the primary sensation. These channels are also implicated in neurological disorders where memory is affected, including Alzheimers disease. Thus, understanding how a circuit of sensory neurons memory formation involves a circuit could also help us learn how to treat these disorders.


title: CSF1R-dependent macrophages control postnatal somatic growth and organ maturation.

abstract: Homozygous mutation of the Csf1r locus (Csf1rko) in mice, rats and humans leads to multiple postnatal developmental abnormalities. To enable analysis of the mechanisms underlying the phenotypic impacts of Csf1r mutation, we bred a rat Csf1rko allele to the inbred dark agouti (DA) genetic background and to a Csf1r-mApple reporter transgene. The Csf1rko led to almost complete loss of embryonic macrophages and ablation of most adult tissue macrophage populations. We extended previous analysis of the Csf1rko phenotype to early postnatal development to reveal impacts on musculoskeletal development and proliferation and morphogenesis in multiple organs. Expression profiling of 3-week old wild-type (WT) and Csf1rko livers identified 2760 differentially expressed genes associated with the loss of macrophages, severe hypoplasia, delayed hepatocyte maturation, disrupted lipid metabolism and the IGF1/IGF binding protein system. Older Csf1rko rats developed severe hepatic steatosis. Consistent with the developmental delay in the liver Csf1rko rats had greatly-reduced circulating IGF1. Transfer of WT bone marrow (BM) cells at weaning without conditioning repopulated resident macrophages in all organs, including microglia in the brain and reversed the mutant phenotypes enabling long term survival and fertility. WT BM transfer restored osteoclasts, eliminated osteopetrosis, restored bone marrow cellularity and architecture and reversed granulocytosis and B cell deficiency. Csf1rko rats had an elevated circulating CSF1 concentration which was rapidly reduced to WT levels following BMT. However, CD43hi non-classical monocytes, absent in the Csf1rko, were not rescued and bone marrow progenitors remained unresponsive to CSF1. The results demonstrate that the Csf1rko phenotype is autonomous to BM-derived cells and indicate that BM contains a progenitor of tissue macrophages distinct from hematopoietic stem cells. The model provides a unique system in which to define the pathways of development of resident tissue macrophages and their local and systemic roles in growth and organ maturation.


title: Metabolic depression in sea urchin barrens associated with food deprivation

abstract: The proliferation of sea urchins can decimate macroalgal forests in coastal ecosystems, leading to persistent barren seascapes. While kelp forests are among the most productive ecosystems on the planet, productivity in these urchin barrens is dramatically reduced. Moreover, urchins inhabiting these food-depauperate barrens face starvation and many survive in these barrens for years or decades. Urchins in barrens can persist by eating food subsidies from drift algae, pelagic salps, tubeworms, as well as encrusting and filamentous algae, microbial mats, and slow-growing species resistant to herbivory. Despite both food from endogenous production and exogenous subsidies, many urchins in barrens likely experience prolonged food deprivation. This resource limitation may create a trade-off between reproduction and survival; for example, fecundity of purple sea urchins (Strongylocentrotus purpuratus) is 99.9% lower in barrens. Despite food constraints, red sea urchins (Mesocentrotus franciscanus), the dominant urchin species at our study sites, can live in excess of 100 years and barrens in Haida Gwaii, British Columbia (BC), Canada, have persisted for at least 143 years. While these phenomena are widespread and well documented, the bioenergetic adaptations that allow urchins to persist in these food-depauperate barrens remain poorly understood. To quantify habitat-specific differences in metabolic rates and energy reserves (as measured by gonadal mass), we conducted respirometry on and measured gonadal mass in M. franciscanus at three locations in BC inside and outside of adjacent kelp forest and barrens habitat. Here we demonstrate that M. franciscanus in barrens versus kelp forests have substantially lower energy reserves and, importantly, also exhibit dramatic reductions in size-specific resting metabolic rates (RMR), even after standardizing by metabolically active body mass. On average, gonadal mass was 44.6% lower and RMR scaled to metabolically active body mass was 40% lower in barrens urchins than in kelp forest urchins. Such a shift in metabolic rate may provide a mechanism that facilitates barren state stability over long time scales as M. franciscanus can lower energetic demands while they wait for small pulses of food, scrape by on low-productivity resources, and suppress recruitment of macroalgae for months, years, or decades.


title: An altered balance of integrated and segregated brain activity is a marker of cognitive deficits following sleep deprivation

abstract:
Sleep deprivation (SD) leads to impairments in cognitive function. Here, we tested the hypothesis that cognitive changes in the sleep-deprived brain can be explained by information processing within and between large-scale cortical networks. We acquired functional magnetic resonance imaging (fMRI) scans of 20 healthy volunteers during attention and executive tasks following a regular night of sleep, a night of sleep deprivation, and a recovery nap containing non-rapid eye movement (NREM) sleep. Overall, sleep deprivation was associated with increased cortex-wide functional integration, driven by a rise of integration within cortical networks. The ratio of within vs between network integration in the cortex increased further in the recovery nap, suggesting that prolonged wakefulness drives the cortex toward a state resembling sleep. This balance of integration and segregation in the sleep-deprived state was tightly associated with deficits in cognitive performance. This was a distinct and better marker of cognitive impairment than conventional indicators of homeostatic sleep pressure, as well as the pronounced thalamo-cortical connectivity changes that occurs towards falling asleep. Importantly, restoration of the balance between segregation and integration of cortical activity was also related to performance recovery after the nap, demonstrating a bi-directional effect. These results demonstrate that intra- and inter-individual differences in cortical network integration and segregation during task performance may play a critical role in vulnerability to cognitive impairment in the sleep deprived state.

Significance StatementSleep deprivation has significant negative consequences for cognitive function. Understanding how changes in brain activity underpin changes in cognition is important not only to discover why performance declines following extended periods of wakefulness, but also for answering the fundamental question of why we require regular and recurrent sleep for optimal performance. Finding neural correlates that predict performance following sleep deprivation also has the potential to understand which individuals are particularly vulnerable to sleep deprivation, and what aspects of brain function may protect them from these negative consequences on performance. Finally, understanding how perturbations to regular (well-rested) brain functioning affect cognitive performance, will provide important insight into how underlying principles of information processing in the brain may support cognition generally.


title: Cwl0971, a novel peptidoglycan hydrolase, plays pleiotropic roles in Clostridioides difficile R20291

abstract: Clostridioides difficile is a Gram-positive, spore-forming, toxin-producing anaerobe that can cause nosocomial antibiotic-associated intestinal disease. Although the production of toxin A (TcdA) and toxin B (TcdB) contribute to the main pathogenesis of C. difficile, the mechanism of TcdA and TcdB release from cell remains unclear. In this study, we identified and characterized a new cell wall hydrolase Cwl0971 (CDR20291_0971) from C. difficile R20291, which is involved in bacterial autolysis. The gene 0971 deletion mutant (R20291{Delta}0971) generated with CRISPR-AsCpfI exhibited significantly delayed cell autolysis and increased cell viability compared to R20291, and the purified Cwl0971 exhibited hydrolase activity for Bacillus subtilis cell wall. Meanwhile, 0971 gene deletion impaired TcdA and TcdB release due to the decreased cell autolysis in the stationary / late phase of cell growth. Moreover, sporulation of the mutant strain decreased significantly compared to the wild type strain. In vivo, the defect of Cwl0971 decreased fitness over the parent strain in a mouse infection model. Collectively, Cwl0971 is involved in cell wall lysis and cell viability, which affects toxin release, sporulation, germination, and pathogenicity of R20291, indicating that Cwl0971 could be an attractive target for C. difficile infection therapeutics and prophylactics.


title: Brain transcriptomic changes in Japanese quail reveal roles for neurotensin and urocortin 3 in avian parental care

abstract: For many species, parental care critically affects offspring survival. But what drives animals to display parental behaviours towards young? In mammals, pregnancy-induced physiological transformations seem key in preparing the neural circuits that lead towards attraction (and reduced-aggression) to young. Beyond mammalian maternal behaviour, knowledge of the neural mechanisms that underlie parental care is severely lacking. We took advantage of a domesticated bird species, the Japanese quail, for which parental behaviour towards chicks can be induced through a sensitization procedure, a process that is not effective in all animals. We used the variation in parental responses to study neural transcriptomic changes associated with the sensitization procedure itself and with the outcome of the procedure (i.e., presence of parental behaviours). Out of the brain regions studied, we found that most differences in gene expression were located in the hypothalamus. Two genes identified are of particular interest, as no role in avian parental care was known for those genes. One is neurotensin, previously only demonstrated to be causally associated with maternal care in mammals. The other one is urocortin 3, causally demonstrated to affect young-directed neglect and aggression in mammals. Our work opens new avenues of research into understanding the neural basis of parental care in non-placental species.


title: Central Neural Regulation of Parathyroid Hormone

abstract: Parathyroid hormone (PTH) is one of the most important hormones responsible for bone turnover and calcium homeostasis. In mammals, PTH is secreted through the parathyroid glands, unlike in fishes, which are secreted through central nervous system. Studies indicated that a variety of peripheral nerve regulates serum PTH level, however, the mechanism underlying central neural regulation of PTH in mammals remains largely unknown. With an approach including neural-specific retrograde tracing, PTH-Biotin binding assay, and cFos staining, we identified the subfornical organ (SFO) and the paraventricular nucleus (PVN) as two important brain nuclei that responded to serum PTH and calcium changes. Using chemogenetics, we found that serum PTH was suppressed by stimulation of GABAergic neurons in SFO followed by a decrease in trabecular bone mass. Conversely, stimulation of glutamatergic neurons in SFO promoted serum PTH and bone mass. Moreover, we found that the majority of neurons expressing parathyroid hormone 1 receptor (PTH1R) were GABAergic neurons and the majority of neurons expressing parathyroid hormone 2 receptor (PTH2R) were glutamatergic neurons. The paraventricular nucleus (PVN) is downstream of the SFO, and chemogenetic activation of glutamatergic neurons in PVN induced an increase in serum PTH. In summary, our study demonstrates for the first time that distinct neuronal subtypes in the SFO are responsible for bidirectional regulation of serum PTH and bone metabolism, which is mediated through the PVN and the peripheral nervous system. These findings reveal important central neural nodes and will advance our understanding of the central neural regulation of PTH at the molecular, cellular and circuit level.


title: Bidirectional Control of Parathyroid Hormone and Bone Mass by Subfornical Organ


title: The molecular logic of synaptic wiring at the single cell level

abstract: The correct wiring of neuronal circuits is one of the most complex processes in development, since axons form highly specific connections out of a vast number of possibilities. Circuit structure is genetically determined in vertebrates and invertebrates, but the mechanism guiding each axon to precisely innervate a unique pre-specified target cell is poorly understood. Here, we used single cell genomics, imaging and genetics to show that single-cell specific connections between motoneurons and target muscles are specified through a combinatorial code of immunoglobulin domain proteins. These programs are orchestrated by a homeodomain transcription factor code that specifies cellular identities down to the level of biologically unique cells. Using spatial mapping, we show that this code follows spatial patterns already observed at early embryonic stages, while acting at a much later stage to specify motor circuits. Taken together, our data suggest that a relatively simple homeo-immunoglobulin-code determines neuronal circuit structure.


title: Experimental evaluation of thermodynamic speed limit in living cells via information geometry

abstract:
Chemical reactions are responsible for information processing in living cells, and thermodynamic trade-off relations can explain their accuracy and speed. Its experimental test in living cells had not existed despite its importance because it is hard to justify sample size sufficiency. This paper reports the first experimental test of the thermodynamic trade-off relation, namely the thermodynamic speed limit, in living systems at the single-cell level where the sample size is relatively small. Due to the information-geometric approach, we can demonstrate the thermodynamic speed limit for the extracellular signal-regulated kinase phosphorylation using time-series fluorescence imaging data. Our approach quantifies the intrinsic speed of cell proliferation and can potentially apply other signal transduction pathways to detect their information processing speed.

One-Sentence SummaryExperimental measurement of information thermodynamic speed by fluorescence imaging in living cells

category: biophysics