title: A nuclear pore sub-complex restricts the propagation of Ty retrotransposons by limiting their transcription

abstract:
Beyond their canonical function in nucleocytoplasmic exchanges, nuclear pore complexes (NPCs) regulate the expression of protein-coding genes. Here, we have implemented transcriptomic and molecular methods to specifically address the impact of the NPC on retroelements, which are present in multiple copies in genomes. We report a novel function for the Nup84 complex, a core NPC building block, in specifically restricting the transcription of LTR-retrotransposons in yeast. Nup84 complex-dependent repression impacts both Copia and Gypsy Ty LTR-retrotransposons, all over the S. cerevisiae genome. Mechanistically, the Nup84 complex restricts the transcription of Ty1, the most active yeast retrotransposon, through the tethering of the SUMO-deconjugating enzyme Ulp1 to NPCs. Strikingly, the modest accumulation of Ty1 RNAs caused by Nup84 complex loss-of-function is sufficient to trigger an important increase of Ty1 cDNA levels, resulting in massive Ty1 retrotransposition. Altogether, our studies expand our understanding of the complex interactions between retrotransposons and the NPC, and highlight the importance for the cells to keep retrotransposon under tight transcriptional control.

AUTHOR SUMMARYRetroelements, which replicate by reverse transcription of their RNA into a cDNA that is integrated into the host genetic material, play an important role in the plasticity of eukaryotic genomes. The study of yeast retrotransposons has led to the identification of host factors that limit retroelement mobility, including components of the nuclear pore complex (NPC), most of them still awaiting mechanistic characterization. Here, we investigated the contribution of the Nup84 complex, a core NPC scaffold, to retrotransposon biology in budding yeast. Our findings uncover that the Nup84 complex restricts the transcription of phylogenetically-distinct Ty retroelements. By focusing on Ty1 retrotransposons, we provide evidence that repression by the Nup84 complex depends on the maintenance at the NPC of the SUMO-protease Ulp1, an essential enzyme of the SUMO pathway with multiple targets in the transcription machinery. We finally show that this transcriptional control is critical for genome dynamics, since a small increase in the accumulation of Ty1 RNAs leads to massive retrotransposition. Our data reveal that although relatively abundant, Ty transcripts are limiting for retrotransposition, underscoring the importance of a tight control of their expression. They also characterize a new non-canonical function of NPCs, confirming their connection with genome expression and stability.


title: Sample-wise unsupervised deconvolution of complex tissues

abstract:
MotivationComplex biological tissues are often a heterogeneous mixture of several molecularly distinct cell or tissue subtypes. Both subtype compositions and expressions in individual samples can vary across different biological states or conditions. Computational deconvolution aims to dissect patterns of bulk gene expression data into subtype compositions and subtype-specific expressions. Typically, existing deconvolution methods can only estimate averaged subtype-specific expressions in a population, while detecting differential expressions or co-expression networks in particular subtypes requires unique subtype expression estimates in individual samples. Different from population-level deconvolution, however, individual-level deconvolution is mathematically an underdetermined problem because there are more variables than observations.

ResultsWe report a sample-wise Convex Analysis of Mixtures (swCAM) method that can estimate subtype proportions and subtype-specific expressions in individual samples from bulk tissue transcriptomes. We extend our previous CAM framework to include a new term accounting for between-sample variations and formulate swCAM as a nuclear-norm and{ell} 2,1-norm regularized matrix factorization problem. We determine hyperparameter values using a cross-validation scheme with random entry exclusion and obtain a swCAM solution using an efficient alternating direction method of multipliers. The swCAM is implemented in open-source R scripts. Experimental results on realistic simulation data show that swCAM can accurately estimate subtype-specific expressions in individual samples and successfully extract co-expression networks in particular subtypes that are otherwise unobtainable using bulk expression data. Application of swCAM to bulk-tissue data of 320 samples from bipolar disorder patients and controls identified changes in cell proportions, expression and coexpression modules in patient neurons. Mitochondria related genes showed significant changes suggesting an important role of energy dysregulation in bipolar disorder.

Availability and implementationThe R Scripts of swCAM is freely available at https://github.com/Lululuella/swCAM. A users guide and a vignette are provided.

Contactyuewang@vt.edu

Supplementary informationSupplementary data are available at Bioinformatics online.

category: bioinformatics


title: swCAM: estimation of subtype-specific expressions in individual samples with unsupervised sample-wise deconvolution


title: Comberons from single cell transcriptomics in endothelial cells

abstract:
VEGF inhibitor drugs have been successful, especially in ophthalmology, but not all patients respond to them. Combinations of drugs are likely to be needed for more effective therapies of angiogenesis-related diseases. In this paper we describe naturally occurring combinations of receptors in endothelial cells that might help to understand how cells communicate and to identify targets for drug combinations. We also develop and share a new software tool called DECNEO to identify them.

Single-cell gene expression data are used to identify a set of co-expressed endothelial cell receptors, conserved among species (mice and humans) and enriched, within a network, of connections to up-regulated genes. This set includes several receptors previously shown to play a role in angiogenesis. Multiple statistical tests from large datasets, including an independent validation set, support the reproducibility, evolutionary conservation and role in angiogenesis of these naturally occurring combinations of receptors. We also show tissue-specific combinations and, in the case of choroid endothelial cells, consistency with both well-established and recent experimental findings, presented in a separate paper.

The results and methods presented here advance the understanding of signaling to endothelial cells. The methods are generally applicable to the decoding of intercellular combinations of signals.

category: systems biology


title: Naturally occurring combinations of receptors from single cell transcriptomics in endothelial cells


title: No Evidence for a Single Oscillator Underlying Discrete Visual Percepts

abstract: Theories of perception based on discrete sampling posit that visual consciousness is reconstructed based on snapshot-like perceptual moments, as opposed to being updated continuously. According to a model proposed by Schneider (2018), discrete sampling can explain both the flash-lag and the Frohlich illusion, whereby a lag in the conscious updating of a moving stimulus alters its perceived spatial location in comparison to a stationary stimulus. The alpha-band frequency, which is associated with phasic modulation of stimulus detection and the temporal resolution of perception, has been proposed to reflect the duration of perceptual moments. The goal of this study was to determine whether a single oscillator (e.g., alpha) is underlying the duration of perceptual moments, which would predict that the point of subjective equality (PSE) in the flash-lag and Frohlich illusions are positively correlated across individuals. Although our displays induced robust flash-lag and Frohlich effects, virtually zero correlation was seen between the PSE in the two illusions, indicating that the illusion magnitudes are unrelated across observers. These findings suggest that, if discrete sampling theory is true, these illusory percepts either rely on different oscillatory frequencies or not on oscillations at all. Alternatively, discrete sampling may not be the mechanism underlying these two motion illusions or our methods were ill-suited to test the theory.

category: neuroscience


title: Super-resolution shadow imaging reveals local remodeling of astrocytic microstructures and brain extracellular space after osmotic challenge

abstract:
The extracellular space (ECS) plays a central role for brain physiology, shaping the time course and spread of neurochemicals, ions and nutrients that ensure proper brain homeostasis and neuronal communication. Astrocytes are the most abundant type of glia cell in the brain, whose processes densely infiltrate the brains parenchyma. As astrocytes are highly sensitive to changes in osmotic pressure, they are capable of exerting a potent physiological influence on the ECS.

However, little is known about the spatial distribution and temporal dynamics of the ECS that surrounds astrocytes, owing mostly to a lack of appropriate techniques to visualize the ECS in live brain tissue. Mitigating this technical limitation, we applied the recent SUper-resolution SHadow Imaging technique (SUSHI) to astrocyte-labeled organotypic hippocampal brain slices, which allowed us to concurrently image the complex morphology of astrocytes and the ECS with nanoscale resolution in a live experimental setting.

Focusing on ring-like astrocytic microstructures in the spongiform domain, we found them to enclose sizable pools of interstitial fluid and cellular structures like dendritic spines. Upon an experimental osmotic challenge, these microstructures remodeled and swelled up at the expense of the pools, effectively increasing the physical contact between astrocytic and cellular structures.

Our study reveals novel facets of the dynamic microanatomical relationships between astrocytes, neuropil and the ECS in living brain tissue, which could be of functional relevance for neuronglia communication in a variety of (patho)physiological settings, e.g. LTP induction, epileptic seizures or acute ischemic stroke, where osmotic disturbances are known to occur.


title: Beyond the intraclass correlation: A hierarchical modeling approach to test-retest assessment

abstract: The concept of test-retest reliability indexes the consistency of a measurement across time. High reliability is critical for any scientific study, but specifically for the study of individual differences. Evidence of poor reliability of commonly used behavioral and functional neuroimaging tasks is mounting. Reports on low reliability of task-based fMRI have called into question the adequacy of using even the most common, well-characterized cognitive tasks with robust population-level effects, to measure individual differences. Here, we lay out a hierarchical framework that estimates reliability as a correlation divorced from trial-level variability, and show that reliability estimates tend to be higher compared to the conventional framework that adopts condition-level modeling and ignores across-trial variability. We examine how estimates from the two frameworks diverge and assess how different factors (e.g., trial and subject sample sizes, relative magnitude of cross-trial variability) impact reliability estimates. We also show that, under specific circumstances, the two statistical frameworks converge. Results from the two approaches are approximately equivalent if (a) the trial sample size is sufficiently large, or (b) cross-trial variability is in the same order of magnitude as, or less than, cross-subject variability. As empirical data indicate that cross-trial variability is large in most tasks, this work highlights that a large number of trials (e.g., greater than 100) may be required to achieve precise reliability estimates. We reference the tools TRR and 3dLMEr for the community to apply trial-level models to behavior and neuroimaging data and discuss how to make these new measurements most useful for current studies.


title: Trial and error: a hierarchical modeling approach to test-retest assessment


title: Associations between brain structure and sleep patterns across adolescent development

abstract:
ImportanceStructural brain maturation and sleep are complex processes that exhibit significant changes over adolescence and are linked to healthy physical and mental development. The precise timing and magnitude of these changes influence function throughout the lifespan. However, the relationships between gray matter structure and sleep patterns during adolescence are not fully understood. A detailed characterization of brain-sleep associations during this sensitive period is crucial for understanding factors contributing to optimal neurodevelopmental trajectories in adolescence.

ObjectiveTo investigate whether sleep-gray matter relationships are developmentally-invariant (i.e., stable across age) or developmentally-specific (i.e., only present during discrete time windows) from late childhood through young adulthood.

SettingThe Neuroimaging and Pediatric Sleep Databank was constructed from 8 research studies conducted at the University of Pittsburgh between 2009 and 2020.

ParticipantsThe final sample consisted of 240 participants without current psychiatric diagnoses (9-25 years), and with good quality sleep tracking and structural MRI (sMRI) data.

DesignParticipants completed a sMRI scan and 5-7 days of wrist actigraphy to assess naturalistic sleep. We examined cross-sectional associations between sMRI measures and sleep patterns, as well as the effects of age, sex, and their interaction with sMRI measures on sleep.

Main Outcome(s) and Measure(s)Using Freesurfer software, we extracted cortical thickness and subcortical volumes from T1-weighted MRI. Sleep patterns (duration, timing, continuity, regularity) were estimated from wrist actigraphy.

ResultsShorter sleep duration, later sleep timing, and poorer sleep continuity were associated with a stable pattern of thinner cortex and altered subcortical volumes in diverse brain regions across adolescence. In a discrete subset of regions (e.g., posterior cingulate), thinner cortex was associated with these sleep patterns from late childhood through early-to-mid adolescence, but not in late adolescence and young adulthood.

Conclusions and RelevanceIn childhood and adolescence, developmentally-invariant and developmentally-specific associations exist between sleep patterns and gray matter structure, in a wide array of brain regions linked to many sensory, cognitive, and emotional processes. Sleep intervention during specific developmental periods could potentially promote healthier neurodevelopmental outcomes.

KEY POINTSO_ST_ABSQuestionC_ST_ABSDoes age modulate associations between gray matter structure and actigraphic sleep patterns across adolescent development?

FindingsThis cross-sectional study reports stable associations between regional gray matter structure and shorter duration, later timing, and poorer continuity of sleep from ages 9 to 25 years-old, as well as developmentally-specific associations that are present only from late childhood to early-to-mid adolescence.

MeaningStronger coupling of gray matter and sleep patterns from late childhood to early-to-mid adolescence potentially implicates this discrete developmental window as a period of vulnerability to adverse sleep-brain interactions. Sleep intervention during this developmental stage may support healthier neurodevelopmental trajectories.


title: Cholesteryl Hemiazelate Induces Lysosome Dysfunction and Exocytosis in Macrophages

abstract:
OBJECTIVEA key event in atherogenesis is the formation of lipid-loaded macrophages, lipidotic cells, which exhibit irreversible accumulation of undigested modified low-density lipoproteins in lysosomes. This event culminates with the loss of cell homeostasis, inflammation and cell death. In this study we propose to identify the chemical etiological factors and understanding the molecular and cellular mechanisms responsible for the impairment of lysosome function in macrophages.

APPROACH AND RESULTSUsing shotgun lipidomics we have discovered that a family of oxidized lipids (cholesteryl hemiesters, ChE), end products of oxidation of polyunsaturated cholesteryl esters, occurs at higher concentrations in the plasma of two cohorts of cardiovascular disease patients than in the plasma of a control cohort. Macrophages exposed to the most prevalent ChE, cholesteryl hemiazelate (ChA) exhibit lysosome enlargement, peripheral lysosomal positioning, lysosome dysfunction and lipidosis which are irreversible. The transcriptomic profile of macrophages exposed to ChA indicates that the lysosome pathway is deeply affected and is well correlated with lysosome phenotypic and functional changes. Interestingly, the dysfunctional peripheral lysosomes are more prone to fuse with the plasma membrane, secreting their undigested luminal content into the extracellular milieu with potential consequences to the pathology.

CONCLUSIONWe identify ChA not only as one of the molecules involved in the etiology of irreversible lysosome dysfunction culminating with lipidosis but also as a promoter of exocytosis of the dysfunctional lysosomes. The latter event is a new mechanism that may be important in the pathogenesis of atherosclerosis.

category: cell biology


title: Latitudinal patterns in intertidal ecosystem structure in West Greenland suggest resilience to climate change

abstract: Climate change has ecosystem-wide cascading effects. Little is known, however, about the resilience of Arctic marine ecosystems to environmental change. Here we quantify and compare large-scale patterns in rocky intertidal biomass, coverage and zonation in six regions along a north-south gradient of temperature and ice conditions in West Greenland (60-72{degrees}N). We related the level and variation in assemblage composition, biomass and coverage to latitudinal-scale environmental drivers. Across all latitudes, the intertidal assemblage was dominated by a core of stress-tolerant foundation species that constituted >95% of the biomass. Hence, canopy-forming macroalgae, represented by Fucus distichus subsp. evanescens and F. vesiculosus and, up to 69 {degrees}N, also Ascophyllum nodosum, together with Semibalanus balanoides, occupied >70% of the vertical tidal range in all regions. Thus, a similar functional assemblage composition occurred across regions, and no latitudinal depression was observed. The most conspicuous difference in species composition from south to north was that three common species (the macroalgae Ascophyllum nodosum, the amphipod Gammarus setosus and the gastropod Littorina obtusata) disappeared from the mid-intertidal, although at different latitudes. There were no significant relationships between assemblage metrics and air temperature or sea ice coverage as obtained from weather stations and satellites, respectively. Although the mean biomass decreased >50% from south to north, local biomass in excess of 10 000 g ww m-2 was found even at the northernmost site, demonstrating the patchiness of this habitat and the effect of small-scale variation in environmental characteristics. Hence, using the latitudinal gradient in a space-for-time substitution, our results suggest that while climate modification may lead to an overall increase in the intertidal biomass in north Greenland, it is unlikely to drive dramatic functional changes in ecosystem structure in the near future. Our dataset provides an important baseline for future studies to verify these predictions for Greenlands intertidal zone.

category: ecology


title: Plastid phylogenomics of the Sansevieria clade (Dracaena; Asparagaceae) resolves a rapid evolutionary radiation

abstract: Sansevierias are a diverse group of flowering plants native to Africa, Madagascar, the Arabian Peninsula and the Indian subcontinent, popular outside their native range as low maintenance houseplants. Traditionally recognized as a distinct genus, Sansevieria was recently merged with the larger genus Dracaena based on molecular phylogenetic data. Within the Sansevieria clade, taxonomic uncertainties remain despite numerous attempts to classify the species. We aim to arrive at a robust phylogeny using a plastid phylogenomic approach, and estimate a time-frame of diversification to infer the evolutionary history of the group, including geographical and morphological evolution. Molecular data was obtained using genome skimming for 50 Sansevieria, representing all informal groups previously instated based on morphology, and two Dracaena sensu stricto species. The resulting Maximum Likelihood phylogenetic hypotheses are generally well supported, except for some very short branches along the backbone of the tree. The time-calibrated phylogeny indicates a recent rapid radiation with the main clades emerging in the Pliocene. Two well-supported clades align with previously defined informal groups, i.e., Sansevieria section Dracomima, characterised by the Dracomima-type inflorescence, and the Zeylanica group, native to the Indian subcontinent. Other morphologically defined informal groups are shown to be polyphyletic: a pattern due to convergent evolution of the identifying characters. Cylindrical leaves arose multiple times independently in the evolution of the Sansevieria clade and similarly, the Cephalantha-type inflorescence has originated multiple times from an ancestor with a Sansevieria-type inflorescence. To provide a more accessible tool for species identification and delimitation, genes and spacer regions were screened for variability and phylogenetic informativeness to investigate their potential as chloroplast DNA barcodes. Candidate chloroplast DNA barcodes include the trnH-rpl12, ndhH-rps15, psbE-petL, psbT-psbN, rps18-rpl20 intergenic spacers, the chloroplast gene rps8 and the first intron of ycf3.

category: evolutionary biology


title: Mutagenesis Mapping of RNA Structures within the Foot-and-Mouth Disease Virus Genome Reveals Functional Elements Localised in the Polymerase (3Dpol) Encoding Region.

abstract:
AbstractRNA structure plays a crucial role in the replication of positive sense RNA viruses and can form functional elements within the untranslated regions (UTRs) and the protein coding sequences (or open reading frames (ORFs)). While RNA structures in the UTRs of several picornaviruses have been functionally characterised, the roles of putative RNA structures predicted for the ORF remain largely undefined. Here we have undertaken a bioinformatic analysis of the foot-and-mouth disease virus (FMDV) genome and predicted the existence of 53 evolutionarily conserved RNA structures within the ORF. Forty-five (45) of these structures were located in the regions encoding the non-structural proteins (nsps). To investigate if the structures in the regions encoding the nsps are required for FMDV replication we used a mutagenesis method, CDLR mapping, where sequential coding segments were shuffled to minimise RNA secondary structures while preserving protein coding, native dinucleotide frequencies and codon usage. To examine the impact of these changes on replicative fitness, mutated sequences were inserted into an FMDV sub-genomic replicon. We found that three of the RNA structures, all at the 3 termini of the FMDV ORF, were critical for replicon replication. Contrastingly, disruption of the other 42 conserved RNA structures that lie within the regions encoding the nsps had no effect on replicon replication, suggesting that these structures are not required for initiating translation or replication of viral RNA. Conserved RNA structures that are not essential for virus replication could provide ideal targets for the rational attenuation of a wide range of FMDV strains.

ImportanceSome RNA structures formed by the genomes of RNA viruses are critical for viral replication. Our study shows that of 45 conserved RNA structures located within the regions of the foot-and-mouth disease virus (FMDV) genome that encode the non-structural proteins, only three are essential for replication of an FMDV sub-genomic replicon. Replicons replication is dependent on RNA translation and synthesis; thus, our results suggest that the three RNA structures are critical for either initiation of viral RNA translation and/or viral RNA synthesis. Although further studies are required to identify if the remaining 42 RNA structures have other roles in virus replication, they may provide targets for the rational large-scale attenuation of a wide range of FMDV strains. FMDV causes a highly contagious disease posing a constant threat to global livestock industries. Such weakened FMDV strains could be investigated as live-attenuated vaccines or could enhance biosecurity of conventional inactivated vaccine production.


title: Integration of Protein Interactome Networks with Congenital Heart Disease Variants Reveals Candidate Disease Genes

abstract: Congenital heart disease (CHD) is present in 1% of live births, yet identification of causal mutations remains a challenge despite large-scale genomic sequencing efforts. We hypothesized that genetic determinants for CHDs may lie in protein interactomes of GATA4 and TBX5, two transcription factors that cause CHDs. Defining their interactomes in human cardiac progenitors via affinity purification-mass spectrometry and integrating results with genetic data from the Pediatric Cardiac Genomic Consortium revealed an enrichment of de novo variants among proteins that interact with GATA4 or TBX5. A consolidative score that prioritized interactome members based on variant, gene, and proband features identified likely CHD-causing genes, including the epigenetic reader GLYR1. GLYR1 and GATA4 widely co-occupied cardiac developmental genes, resulting in co-activation, and the GLYR1 missense variant associated with CHD disrupted interaction with GATA4. This integrative proteomic and genetic approach provides a framework for prioritizing and interrogating the contribution of genetic variants in disease.

category: genetics


title: Genome Wide Association Study in the New Haven Lexinome Project Identifies GARRE1 as a Novel Gene for Reading Performance

abstract:
Despite high prevalence and high heritability, few candidate genes have been identified for reading disability. To identify novel genetic variants we performed a genome-wide association study (GWAS) using high-depth whole genome sequencing and predicated on reading performance in 407 subjects enrolled in a longitudinal study of response-to-intervention, called the New Haven Lexinome Project. The primary GWAS identified a single peak of 31 SNPs on chromosome 19 that achieved the threshold for genome-wide significance (rs2599553 P=3.13x10-8) located over an expression quantitative trait locus (eQTL) for GARRE1 (Granule Associated Rac And RHOG Effector 1). Little is known about the function of GARRE1, except that it is highly and developmentally expressed in human cerebellum relative to cortex. Local ancestry regression showed the strongest association for the lead variant in African or Admixed American populations, who have been under-represented in previous genetic studies of reading. We replicated our chromosome 19 results in the Genes, Reading, and Dyslexia (GRaD) cohort and found a moderating effect of age with implications for the consideration of developmental effects in the design of future analyses. Growth curve modeling demonstrated that minor alleles of the lead SNP are related to reading longitudinally from Grade 1 to Grade 5, and that children with at least 1 minor allele of rs2599553 persistently underperformed relative to their peers by 0.33 to 0.5 standard deviations on standardized assessments of non-word decoding and reading fluency.

Significance StatementTo the best of our knowledge, this work represents the only GWAS predicated on longitudinal reading performance data. Starting with initial discovery, we replicate our association in a second cohort, address common causes of type I error, localize the signal to a single gene, implicate a region of the brain most likely to be affected by variation in our candidate, show a gene-by-age effect with implications for study design in this field, and demonstrate that minor alleles of our lead SNP are associated with significant and persistent clinical effects on reading development in children.


title: MYC overexpression leads to increased chromatin interactions at superenhancers and c-Myc binding sites

abstract: The MYC oncogene encodes for the c-Myc protein and is frequently dysregulated across multiple cancer cell types, making it an attractive target for cancer therapy. There have been many difficulties in targeting c-Myc, due to its complex network of regulators and the unstructured nature of its protein. Thus, we are interested in looking at the downstream cancer-specific functions of c-Myc. Overexpression of MYC leads to c-Myc binding at active enhancers, resulting in a global transcriptional amplification of active genes. However, the mechanism underlying this c-Myc enhancer invasion has not been well studied. To that end, we performed ChIP-seq, RNA-seq, 4C-seq and SIQHiC (Spike-in Quantitative Hi-C) on the U2OS osteosarcoma cell line with tetracycline-inducible MYC. MYC overexpression in U2OS cells modulated histone acetylation and increased c-Myc binding at superenhancers. SIQHiC analysis revealed increased global chromatin contact frequency, particularly at chromatin interactions connecting c-Myc binding sites. Our results suggest that c-Myc molecules are recruited to and accumulates within zones of high transcription activity, binding first at stable promoter binding sites at low expression levels, then at superenhancer binding sites when overexpressed. At the same time, the recruitment of c-Myc and other transcription factors may stabilize chromatin interactions to increase chromatin contact frequency. The accumulation of c-Myc at cancer-type specific superenhancers may then drive the expression of interacting oncogenes that each cancer is highly reliant on. By elucidating the chromatin landscape of c-Myc driven cancers, we can potentially target these chromatin interactions for cancer therapy, without affecting physiological c-Myc signaling.

category: genomics


title: Single molecule analysis reveals positive allosteric modulators are required to stabilize the active state of a metabotropic glutamate receptor

abstract: Much hope in drug development comes from the discovery of positive allosteric modulators (PAM) that display target subtype selectivity, and act by increasing agonist potency and efficacy. How such compounds can allosterically influence agonist action remains unclear. Metabotropic glutamate receptors (mGlu) are G protein-coupled receptors that represent promising targets for brain diseases, and for which PAMs acting in the transmembrane domain have been developed. Here, we explore the effect of a PAM on the structural dynamics of mGlu2 in optimized detergent micelles using single molecule FRET at submillisecond timescales. We show that glutamate only partially stabilizes the extracellular domains in the active state. Full activation is only observed in the presence of a PAM or the Gi protein. Our results provide important insights on the role of allosteric modulators in mGlu activation, by stabilizing the active state of a receptor that is otherwise rapidly oscillating between active and inactive states.

category: biophysics


title: Allosteric modulators enhance agonist efficacy by increasing the residence time of a GPCR in the active state


title: Cell motility driven by long-lived spatial memory

abstract: Many living cells actively migrate in their environment to perform key biological functions - from unicellular organisms looking for food to single cells such as fibroblasts, leukocytes or cancer cells that can shape, patrol or invade tissues. Cell migration results from complex intracellular processes that enable cell self-propulsion 1,2, and has been shown to also integrate various chemical or physical extracellular signals 3,4,5. While it is established that cells can modify their environment by depositing biochemical signals or mechanically remodeling the extracellular matrix, the impact of such self-induced environmental perturbations on cell trajectories at various scales remains unexplored. Here, we show that cells remember their path: by confining cells on 1D and 2D micropatterned surfaces, we demonstrate that motile cells leave long-lived physicochemical footprints along their way, which determine their future path. On this basis, we argue that cell trajectories belong to the general class of self-interacting random walks, and show that self-interactions can rule large scale exploration by inducing long-lived ageing, subdiffusion and anomalous first-passage statistics. Altogether, our joint experimental and theoretical approach points to a generic coupling between motile cells and their environment, which endows cells with a spatial memory of their path and can dramatically change their space exploration.


title: Inferring the Neural Basis of Binaural Detection Using Deep Learning

abstract:
Broad organizational features of the auditory pathway have been replicated by artificial neural networks trained on diverse and naturalistic stimuli. It is credible that neural network analogues could also reveal specific neural computations underlying targeted auditory phenomena. This remains to be established. Here, we examined a modified autoencoder (a deep neural network akin to symbolic regression) trained to imitate an auditory behavior rooted in the binaural system. The behavior promoted the use of split-second interaural timing cues to improve the detection of a tone presented in noise. In the optimal network, we observed the emergence of specialized computations with prominent similarities to animal models. Artificial neurons developed a sensitivity to temporal delays that increased deeper into the network and were widely distributed in preference (extending to delays beyond the range permitted by head width), and the ensuing dynamics were consistent with a binaural cross-correlation mechanism. Our results attest to the generality of these solutions for performing signal detection at low frequencies. Moreover, this is a primary demonstration that deep learning methods can be used to infer tangible mechanisms underlying auditory perception.

AUTHOR SUMMARYDo artificial intelligence (AI) systems process sounds in a similar way to the brain? If so, they represent a vital resource with which to investigate sensory systems. Here, we report an AI system that automatically developed auditory computations similar to those described in animal neurophysiology. The network learnt to use subtle discrepancies across its "two ears" to better detect a signal amongst a background noise. In the process, tuning to timing cues and established mechanisms of binaural hearing (relating to the use of both ears) developed internally. The results offer insight into computations occurring in deep brain structures that are difficult to measure with non-invasive techniques. Further, the results endorse informed associations made between AI systems and the auditory brain.


title: Inferring the neural basis of binaural phenomena with a modified autoencoder


title: Corticospinal correlates of hand preference for reaching during whole-body motion

abstract: Behavioral studies have shown that humans account for inertial acceleration in their decisions of hand choice when reaching during body motion. Physiologically, it is unclear at what stage of movement preparation information about body motion is integrated in the process of hand selection. Here, we addressed this question by applying transcranial magnetic stimulation over motor cortex (M1) of human participants who performed a preferential reach task while they were sinusoidally translated on a linear motion platform. If M1 only represents a read-out of the final hand choice, we expect the body motion not to affect the MEP amplitude. If body motion biases the hand selection process prior to target onset, we expect corticospinal excitability to modulate with the phase of the motion, with larger MEP amplitudes for phases that show a bias to using the right hand. Behavioral results replicate our earlier findings of a sinusoidal modulation of hand choice bias with motion phase. MEP amplitudes also show a sinusoidal modulation with motion phase, suggesting that body motion influences corticospinal excitability which may ultimately reflect changes of hand preference. The modulation being present prior to target onset suggests that competition between hands is represented throughout the corticospinal tract. Its phase relationship with the motion profile suggests that other processes after target onset take up time until the hand selection process has been completely resolved, and the reach is initiated. We conclude that the corticospinal correlates of hand preference are modulated by body motion.


title: Novel Dynamics are Represented as a Mixture of Multiple Coordinate Systems

abstract: Skillful and accurate object manipulation requires the objects dynamics to be represented within a motor memory. Despite extensive research, how the motor system represents novel dynamics is still an open question. This representation is normally examined by testing the spatial generalization of the learned forces. However, previous studies have not been able to provide a consistent view of this representation in the motor system, with each study providing evidence favoring an extrinsic coordinate system, an intrinsic coordinate system, an object-based representation, or mixtures of these coordinate systems, but no study could definitively exclude other possibilities. Most previous studies used a skew viscous force field, but these force fields limit the use of channel trials and can therefore prevent us from distinguishing between different coordinate systems. Here we propose a novel method to overcome these disadvantages, by developing a new force field in which a curl force field is scaled by a trigonometric function of movement direction allowing precise assessment of the learned generalization. In a series of four experiments we show that the representation of ambiguous external dynamics is formed by a mixture of extrinsic, intrinsic and object-based coordinate systems with a slightly higher weighting for the object-based representation compared with Cartesian or joint representations. These results highlight the existence of multiple representations in the motor system but more importantly it shows that for certain dynamics the motor system prefers representation using a mixture of representations over single frame based representation.


title: Human induced pluripotent stem cell-derived three-dimensional cardiomyocyte tissues ameliorate the rat ischemic myocardium by remodeling the extracellular matrix and cardiac protein phenotype

abstract: The extracellular matrix (ECM) plays a key role in the viability and survival of implanted human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). We hypothesized that coating of three-dimensional (3D) cardiac tissue-derived hiPSC-CMs with the ECM protein fibronectin (FN) would improve the survival of transplanted cells in the heart and improve heart function in a rat model of ischemic heart failure. To test this hypothesis, we first explored the tolerance of FN-coated hiPSC-CMs to hypoxia in an in vitro study. For in vivo assessments, we constructed 3D-hiPSC cardiac tissues (3D-hiPSC-CTs) using a layer-by-layer technique, and then the cells were implanted in the hearts of a myocardial infarction rat model (3D-hiPSC-CTs, n = 10; sham surgery control group (without implant), n = 10). Heart function and histology were analyzed 4 weeks after transplantation. In the in vitro assessment, cell viability and lactate dehydrogenase assays showed that FN-coated hiPSC-CMs had improved tolerance to hypoxia compared with the control cells. In vivo, the left ventricular ejection fraction of hearts implanted with 3D-hiPSC-CT was significantly better than that of the sham control hearts. Histological analysis showed clear expression of collagen type IV and plasma membrane markers such as desmin and dystrophin in vivo after implantation of 3D-hiPSC-CT, which were not detected in 3D-hiPSC-CMs in vitro. Overall, these results indicated that FN-coated 3D-hiPSC-CT could improve distressed heart function in a rat myocardial infarction model with a well-expressed cytoskeletal or basement membrane matrix. Therefore, FN-coated 3D-hiPSC-CT may serve as a promising replacement for heart transplantation and left ventricular assist devices and has the potential to improve survivability and therapeutic efficacy in cases of ischemic heart disease.


title: Covid19Risk.ai: An open source repository and online calculator of prediction models for early diagnosis and prognosis of Covid-19

abstract:
ObjectiveThe current pandemic has led to a proliferation of predictive models being developed to address various aspects of COVID-19 patient care. We aimed to develop an online platform that would serve as an open source repository for a curated subset of such models, and provide a simple interface for included models to allow for online calculation. This platform would support doctors during decision-making regarding diagnoses, prognoses, and follow-up of COVID-19 patients, expediting the models transition from research to clinical practice.

MethodsIn this proof-of-principle study, we performed a literature search in PubMed and WHO database to find suitable models for implementation on our platform. All selected models were publicly available (peer reviewed publications or open source repository) and had been validated (TRIPOD type 3 or 2b). We created a method for obtaining the regression coefficients if only the nomogram was available in the original publication. All predictive models were transcribed on a practical graphical user interface using PHP 8.0.0, and published online together with supporting documentation and links to the associated articles.

ResultsThe open source website https://covid19risk.ai/ currently incorporates nine models from six different research groups, evaluated on datasets from different countries. The website will continue to be populated with other models related to COVID-19 prediction as these become available. This dynamic platform allows COVID-19 researchers to contact us to have their model curated and included on our website, thereby increasing the reach and real-world impact of their work.

ConclusionWe have successfully demonstrated in this proof-of-principle study that our website provides an inclusive platform for predictive models related to COVID-19. It enables doctors to supplement their judgment with patient-specific predictions from externally-validated models in a user-friendly format. Additionally, this platform supports researchers in showcasing their work, which will increase the visibility and use of their models.


title: Extracellular matrix changes in colorectal carcinoma and correlation with lymph node metastasis

abstract: The process of proliferation and invasion of tumor cells depends on changes in the extracellular matrix (ECM) through the activation of enzymes and alterations in the profile of ECM components. We aimed to investigate the mRNA and protein expression of ECM components such as heparanase (HPSE), heparanase-2 (HPSE2), matrix metalloproteinase-9 (MMP-9), and syndecan-1 (SYND1) in neoplastic and non-neoplastic tissues of patients with colorectal carcinoma (CRC). It is a cross-sectional study in which twenty-four adult patients that had CRC were submitted to resection surgery. We analyzed the expression of HPSE, HPSE2, MMP-9, and SYND1 by quantitative RT-PCR and immunohistochemistry. Differing from most of the studies that compare the mRNA expression between tumor samples and non-neoplastic tissues, we decided to investigate whether variations exist in the expression of the ECM components between the affected tissue and nontumoral tissue collected from the same patient with CRC. We removed both tissue samples immediately after the surgical resection of CRC. The data showed higher mRNA and protein expression of HPSE2 (P = 0.0058), MMP-9 (P = 0.0268), and SYND1 (P = 0.0002) in tumor samples compared to the non-neoplastic tissues, while there was only an increase in the level of HPSE protein in tumor tissues. A greater expression of HPSE2 was observed in patients with lymph node metastasis (P = 0.048), suggesting that such protein can be a marker of lymph node metastasis in CRC.

category: cancer biology


title: EMS-based mutants are useful for enhancing drought tolerance in spring wheat

abstract: Sustainable wheat production in drought prone areas can be achieved by developing resilient wheat varieties. In the present study, chemical mutagenesis was used to induce mutations in a cultivated wheat variety  NN-Gandum-1. In total, 44 mutants were selected based on their high yield potential for exposing to well-watered (W1) and rainfed (W2) conditions for one season. Then 24 mutants were selected, and were exposed to W1 and W2 regimes. On the basis of least relative reduction in physiological parameters under W2 regime, five mutants were selected for conducting exome capturing assays. In total, 184 SNPs were identified in nine genes (ABC transporter type 1, Aspartic peptidase, Cytochrome P450, transmembrane domain, Heavy metal-associated domain, HMA, NAC domain, NAD (P)-binding domain, S-type anion channel, Ubiquitin-conjugating enzyme E2 and UDP-glucuronosyl/UDP-glucosyltransferase). Maximum number of mutations were observed in chr.2D, which contained mutations in three genes i.e. ABC transporter type 1, NAD (P)-binding domain and UDP-glucuronosyl/UDP-glucosyltransferase which may have a role in conferring drought tolerance. The selected mutants were further tested for studying their biochemical responses under both the regimes for two years. The extent of membrane damage was estimated through malondialdehydeand hydrogen per oxidase and tolerance to drought stress was assessed via antioxidant enzymes in leaves. The selected mutants under drought stress increased the accumulation of proline content, total soluble sugars, total free amino acids, while decreased total chlorophyll content, carotenoids and total soluble protein. Finally, the procedure of narrowing down the number of developed mutants from a large mutation population (>4000) is found useful for exploring the complex trait like drought without compromising yield potential. These mutants can further be explored to understand the genetic circuits of drought tolerance in wheat which will pave the way towards improving livelihood of resource poor farming community mostly relying on cereal food.

category: plant biology


title: How to attract and retain health workers in rural areas of a fragile state: findings from a labour market survey in Guinea

abstract:
Most countries face challenges attracting and retaining health staff in remote areas but this is especially acute in fragile and shock-prone contexts, like Guinea, where imbalances in staffing are high and financial and governance arrangements to address rural shortfalls are weak.

The objective of this study was to understand how health staff could be better motivated to work and remain in rural, under-served areas in Guinea. In order to inform the policy dialogue on strengthening human resources for health, we conducted three nationally representative cross-sectional surveys, adapted from tools used in other fragile contexts.

We found that the locational job preferences of health workers in Guinea are particularly influenced by opportunities for training, working conditions, and housing. Most staff are satisfied with their work and with supervision, however, financial aspects and working conditions are considered least satisfactory, and worrying findings include the high proportion of staff favouring emigration, their high tolerance of informal user payments, as well as their limited exposure to rural areas during training.

Based on our findings, we highlight measures which could improve rural recruitment and retention in Guinea and similar settings. These include offering upgrading and specialization in return for rural service; providing greater exposure to rural areas during training; increasing recruitment from rural areas; experimenting with fixed term contracts in rural areas; and improving working conditions in rural posts. The development of incentive packages should be accompanied by action to tackle wider issues, such as reforms to training and staff management.

category: scientific communication and education


title: Essential oil composition of Callistemon citrinus (Curtis) and its protective assessment towards Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae)

abstract: Essential oil (EO) was extracted from Callistemon citrinus leaves by hydro-distillation. The extracted oil was analysed by GC and Mass Spectroscopy. Analysis report showed that the major constituent of the essential oil was eucalyptol (40.44%). The EO of C. citrinus exhibited 100% fumigation toxicity (adult mortality) against adult and 95.8% larvicidal activity against Tribolium castaneum at 160 L/L (12 hrs) and 320 L/L (48 hrs), respectively. The effective concentration of 37.05 L/L (adult) and 144.31 L/L (larva) at 24 and 48 hrs respectively. A 100% repellent activity was observed at 20 l for adult beetles and 93.3% for larvae of T. castaneum at 20 l after 24 h. Exposure to C. citrinus EO significantly reduced beetle fecundity, ovicidal activity, egg hatching, larvae survival, and emergence of adult. The effect of EO on detoxification enzymes of T. castaneum adults was examined. Results indicated that the activity of detoxification enzymes drastically varied when compared with control. This EO had toxicant effects on all stages of the life of T. castaneum. Hence it may be used as fumigant instead of the use of using synthetic chemical fumigants.

category: zoology


title: The chromatin remodelling factor Chd7 protects auditory neurons and sensory hair cells from stress-induced degeneration

abstract: Neurons and sensory cells are particularly vulnerable to oxidative stress due to their high oxygen demand during stimulus perception and transmission1-4. The mechanisms that protect them from stress-induced death and degeneration remain elusive. Here we show that embryonic deletion of the chromodomain helicase DNA-binding protein 7 (CHD7) in auditory neurons or hair cells leads to sensorineural hearing loss due to postnatal degeneration of both cell types. Mechanistically, we demonstrate that CHD7 controls the expression of major stress pathway components. In its absence, hair cells are hypersensitive, dying rapidly after brief exposure to stress inducers, suggesting that sound at the onset of hearing triggers their degeneration. In humans, CHD7 haploinsufficiency causes CHARGE syndrome, a disorder affecting multiple organs including the ear5,6. Our findings suggest that CHD7 mutations cause developmentally silent phenotypes that predispose cells to postnatal degeneration due to a failure of protective mechanisms.

category: developmental biology


title: Glucocorticoid receptor activation induces gene-specific transcriptional memory and universally reversible changes in chromatin accessibility

abstract: Glucocorticoids are stress hormones that elicit cellular responses by binding to the glucocorticoid receptor (GR), a ligand-activated transcription factor. The exposure of cells to this hormone induces wide-spread changes in the chromatin landscape and gene expression. Previous studies have suggested that some of these changes are reversible whereas others persist even when the hormone is no longer around. However, when we examined chromatin accessibility in human airway epithelial cells after hormone washout, we found that the hormone-induced changes were universally reversed after one day. Reversibility of hormone-induced changes are found for GR-occupied opening sites and also for closing sites that typically lack GR occupancy. These closing sites are enriched near repressed genes, suggesting that transcriptional repression by GR does not require nearby GR binding. Mirroring what we say in terms of chromatin accessibility, we found that transcriptional responses to hormone are universally reversable. Moreover, priming of cells by a previous exposure to hormone, in general, did not alter the transcriptional response to a subsequent encounter of the same cue. Interestingly, despite the short-lived nature of hormone-induced changes in the chromatin landscape, we identified a single gene, ZBTB16, that displays transcriptional memory manifesting itself as a more robust transcriptional response upon repeated hormone stimulation. Single-cell analysis revealed that the more robust response is driven by a higher probability of primed cells to activate ZBTB16 and by a subset of cells that express the gene at levels that are higher than the induction levels observed for naive cells. Although our study shows that hormone-induced changes are typically reversable, exposure to hormone can induce gene-specific changes in the response to subsequent exposures which may play a role in habituation to stressors and changes in glucocorticoid sensitivity.


title: Training level reveals a dynamic dialogue between stress and memory systems in birds

abstract: It is now well-accepted that memory is a dynamic process, and that stress and training level may influence which memory system an individual engages when solving a task. In this work, we investigated whether and how chronic stress impacts spatial and cue-based memories according to training level. To that aim, control and chronically stressed Japanese quail were trained in a task that could be solved using spatial and cue-based memory and tested for their memory performances after 5 and 15 training days (initial training and overtraining, respectively) and following an emotional challenge (exposure to an open field). While chronic stress negatively impacted spatial memory in chronically stressed birds after initial training, this impact was lowered after overtraining compared to control quail. Interestingly, the emotional challenge reinstated the differences in performance between the two groups, revealing that chronic stress/overtraining did not eliminate spatial memory. Differences caused by previous stressors can re-emerge depending on the more immediate psychological state of the individual. Contrary to spatial memory, cue-based memory was not impaired in any test occasion, confirming that this form of memory is resistant to chronic stress. Altogether these findings reveal a dynamic dialogue between stress, training, and memory systems in birds.

category: animal behavior and cognition


title: Emergent organization of multiple visuotopic maps without a feature hierarchy

abstract:
The primate visual system is comprised of multiple visual areas. Despite their foundational relevance, there are no normative accounts for why there are multiple areas nor why they have their signature "mirrored map" topography. Here I show that the stereotyped cortical organization of multiple mirrored areas naturally emerges in simulated cortex, in which self-organizing processes are used to map a multi-scale representation of visual space smoothly onto a two-dimensional cortical sheet. Predominant accounts of multiple areas emphasize hierarchical processing, where each area extends and elaborates on the previous areas representation. Here, no explicit hierarchical relationships were required to manifest this multi-areal organization, suggesting that feature hierarchies may be the derived rather than the driving force of this organization. This modeling work thus provides a simple computational explanation for the hallmark features of early visual topography, and the presence of multiple areas, as emergent from a single functional goal -- to smoothly represent the visual field at multiple spatial scales.

One Sentence SummaryThis work presents a formal model of simulated cortex with multiple visual areas, where purely spatial relationships underlie the large-scale motifs of visual cortex.


title: Vangl2, a core component of the WNT/PCP pathway, regulates adult hippocampal neurogenesis and age-related decline in cognitive flexibility

abstract: Decline in episodic memory is one of the hallmarks of aging and represents one of the most important health problems facing western societies. A key structure in episodic memory is the hippocampal formation and the dentate gyrus in particular, as the continuous production of new dentate granule neurons in this brain region was found to play a crucial role in memory and in age-related decline in memory. As such, understanding the molecular processes that regulate the relationship between adult neurogenesis and aging of memory function holds great therapeutic potential. Recently, we found that Vang-gogh like 2 (Vangl2), a core component of the planar cell polarity signaling pathway, is enriched in the dentate gyrus of adult mice. In this context, we sought to evaluate the involvement of this effector of the Wnt/PCP pathway in both adult neurogenesis and memory abilities in adult and middle-aged mice. Using a heterozygous mouse model carrying a dominant negative mutation in Vangl2 gene, we show that alteration in Vangl2 expression decreases the survival of adult-born granule cells and advances the onset of decrease in cognitive flexibility. Inability of mutant mice to erase old irrelevant information to the benefit of new relevant ones highlights a key role of Vangl2 in interference-based forgetting. Taken together, our findings show for the first that Vangl2 activity may constitute an interesting target to prevent age-related decline in hippocampal plasticity and memory.


title: Generation of Pathogenic TPP1 Mutations in Human Stem Cells as a Model for CLN2 Disease

abstract: Neuronal ceroid lipofuscinosis type 2 (CLN2 disease) is an autosomal recessive neurodegenerative disorder generally with onset at 2 to 4 years of age and characterized by seizures, loss of vision, progressive motor and mental decline, and premature death. CLN2 disease is caused by loss-of-function mutations in the tripeptidyl peptidase 1 (TPP1) gene leading to deficiency in TPP1 enzyme activity. Approximately 60% of patients have one of two pathogenic variants (c.509-1G>C or c.622C>T [p.(Arg208*)]). In order to generate a human stem cell model of CLN2 disease, we used CRISPR/Cas9-mediated knock-in technology to introduce these mutations in a homozygous state into H9 human embryonic stem cells. Heterozygous lines of the c.622C>T (p.(Arg208*)) mutation were also generated, which included a heterozygous mutant with a wild-type allele and different compound heterozygous coding mutants resulting from indels on one allele. We describe the methodology that led to the generation of the lines and provide data on the initial validation and characterization of these CLN2 disease models. Notably, both mutant lines (c.509-1G>C and c.622C>T [p.(Arg208*)]) in the homozygous state were shown to have reduced or absent protein, respectively, and deficiency of TPP1 enzyme activity. These models, which we are making available for wide-spread sharing, will be useful for future studies of molecular and cellular mechanisms underlying CLN2 disease and for therapeutic development.


title: Functional plasticity of polarity proteins controls epithelial tissue architecture

abstract: The Drosophila polarity protein Crumbs is essential for the establishment and growth of the apical domain in epithelial cells. The protein Yurt limits the ability of Crumbs to promote apical membrane growth, thereby defining proper apical/lateral membrane ratio that is crucial for forming and maintaining complex epithelial structures such as tubes or acini. Here, we show that Yurt also increases Myosin-dependent cortical tension downstream of Crumbs. Yurt overexpression thus induces apical constriction in epithelial cells. The kinase aPKC phosphorylates Yurt, thereby dislodging the latter from the apical domain and releasing apical tension. In contrast, the kinase Pak1 promotes Yurt dephosphorylation through activation of the phosphatase PP2A. The Pak1- PP2A module thus opposes aPKC function and supports Yurt-induced apical constriction. Hence, the complex interplay between Yurt, aPKC, Pak1 and PP2A contributes to the functional plasticity of Crumbs. Overall, our data increase our understanding of how proteins sustaining epithelial cell polarization and Myosin-dependent cell contractility interact with one another to control epithelial tissue architecture.


title: Pak1 and PP2A antagonize aPKC function to support cortical tension induced by the Crumbs-Yurt complex


title: Different translation dynamics of β- and γ-actin regulates cell migration

abstract: {beta}- and {gamma}-cytoplasmic actins are ubiquitously expressed in every cell type and are nearly identical at the amino acid level but play vastly different roles in vivo. Their essential roles in embryogenesis and cell migration critically depend on the nucleotide sequences of their genes, rather than their amino acid sequence. However it is unclear which gene elements underlie this effect. Here we address the specific role of the coding sequence in {beta}- and {gamma}-cytoplasmic actins intracellular functions, using stable cell lines with exogenously expressed actin isoforms and their "codon-switched" variants. When targeted to the cell periphery using the {beta}-actin 3'UTR, {beta}-actin and {gamma}-actin have differential effects on cell migration. These effects directly depend on the coding sequence. Single molecule measurements of actin isoform translation, combined with fluorescence recovery after photobleaching, demonstrate a pronounced difference in {beta}- and {gamma}-actins translation elongation rates, leading to changes in their dynamics at focal adhesions, impairments in actin bundle formation, and reduced cell anchoring to the substrate during migration. Our results demonstrate that coding sequence-mediated differences in actin translation play a key role in cell migration.


title: Aurora B phosphorylates Bub1 to promote spindle assembly checkpoint signaling

abstract: Accurate chromosome segregation during cell division requires amphitelic chromosome attachment to the spindle apparatus. It is ensured by the combined activity of the Spindle Assembly Checkpoint1 (SAC), a signaling mechanism that delays anaphase onset in response to unattached chromosomes, and an error correction mechanism that eliminates syntelic attachments2. The SAC becomes active when Mps1 kinase sequentially phosphorylates the kinetochore protein Spc105/KNL1 and the signaling proteins that Spc105/KNL1 recruits to facilitate the production of the Mitotic Checkpoint Complex3-8 (MCC). The error correction mechanism is regulated by the Aurora B kinase, but Aurora B also promotes SAC signaling via indirect mechanisms9-12. Here we present evidence that Aurora B kinase activity directly promotes MCC production by working downstream of Mps1 in budding yeast and human cells. Using the ectopic SAC activation (eSAC) system, we find that the conditional dimerization of Aurora B in budding yeast, and an Aurora B recruitment domain in HeLa cells, with either Bub1 or Mad1, but not the phosphodomain of Spc105/KNL1, leads to ectopic MCC production and mitotic arrest13-16. Importantly, Bub1 must recruit both Mad1 and Cdc20 for this ectopic signaling activity. These and other data show that Aurora B cooperates with Bub1 to promote MCC production, but only after Mps1 licenses Bub1 recruitment to the kinetochore. This direct involvement of Aurora B in SAC signaling may maintain SAC signaling even after Mps1 activity in the kinetochore is lowered.


title: Codon composition in human oocytes reveals age-associated defects in mRNA decay

abstract: Oocytes from women of advanced reproductive age have lower developmental potential, yet the underlying mechanisms of this phenomena are incompletely understood. Oocyte maturation is dependent upon translational control of stored maternal mRNA that were synthesized during oocyte growth. We observed that GC content of mRNA was negatively associated with half-life in oocytes from reproductively young women (< 30 years), contrastingly directly with oocytes from reproductively aged women ([≥] 40 years) where mRNA half-lives were positively associated with GC nucleotide content. Additionally, we observed that mRNA half-lives were negatively associated with protein abundance in young oocytes, while GC content was positively associated with protein abundance in aged oocytes. Examination of codon composition during the GV-to-MII transition revealed that codons that facilitate rapid translation promoted mRNA stability and are considered optimal, while codons that slow translation destabilized mRNA, and are considered non-optimal. GC-containing codons were more optimal in reproductive aging, and also correlated positively with protein abundance. This study indicates that reproductive aging coincides with the stabilization of a subset of mRNA that have the potential to be over-translated during oocyte maturation, this is likely to lead to observed decreases in oocyte quality in older women. Because oocyte mRNA decay is translationally linked, this suggests that maternal aging causes defects in translation, which results in reduced translational efficiency and the retention of maternal mRNA that are normally degraded in oocytes from young women. In the case of oocytes, defects in translation can alter the RNA decay pathways and result in incorrect maternal mRNA dosage, which may negatively impact embryonic development.


title: Evidence, evolution and pattern of contractile elements in villous vascular walls and stroma of human placentas of premature infants of different gestational ages. An immuno-morphologic comparative study.

abstract:
The contractile elements of the human placenta villous tree represent a topic of interest and many issues persist still open. Histology of the stroma and muscular wall and their evolution, in relation with the gestational age, remains to be clarified for a deeper understanding of the adaptive potential and pathogenetic mechanisms.

In our study, 56 premature placentas (21-36 wks) were considered, sub-divided into four groups based on age of gestation and compared to 23 at-term placentas (37-40 wks). All cases were tested with anti-smooth muscle actin (SMA) and anti-desmin antibodies to identify the contractile elements in the stroma and in vascular walls of villi.

SMA and desmin staining show evident decreased expressions during the pregnancy (temporal variation) and from proximal to distal part of the villous tree (spatial variation) being higher in the stem villi.

Both pre-term and at-term placentas showed persisting, although variable, positivity for SMA and desmin staining in the stroma and in the vessel walls of the mature intermediate and terminal villi. This represents an unexpected finding and nothing alike has been previously reported in literature.

Both highly premature and term placentas seem to maintain contractile components within each type of villi, represented by both myofibroblasts and mature smooth muscular cells. These components may be present in both villous vascular walls and stroma, albeit with different staining intensity.

This finding allows us to imagine an active function in the regulation of the blood flow, not only in stem and intermediate immature villi but even in smaller villi.


title: Relocation of rDNA repeats for repair is dependent on SUMO-mediated nucleolar release by the Cdc48/p97 segregase

abstract: Ribosomal RNA genes (rDNA) are highly unstable and susceptible to rearrangement due to active transcription and their repetitive nature. Compartmentalization of rDNA in the nucleolus suppresses uncontrolled recombination. However, broken repeats must be released to the nucleoplasm to allow repair by homologous recombination. The process of rDNA relocation is conserved from yeast to humans, but the underlying molecular mechanisms are currently unknown. Here we show that DNA damage induces phosphorylation of the CLIP-cohibin complex, releasing membrane-tethered rDNA from the nucleolus in Saccharomyces cerevisiae. Downstream of phosphorylation, SUMOylation targets CLIP-cohibin for disassembly mediated by the Cdc48/p97 chaperone, which recognizes SUMOylated CLIP-cohibin through its cofactor, Ufd1. Consistent with a conserved mechanism, UFD1L depletion impairs rDNA release in human cells. The dynamic and regulated assembly and disassembly of the rDNA-tethering complex is therefore a key determinant of nucleolar rDNA release and genome integrity.

category: molecular biology


title: A novel skeletal-specific adipogenesis pathway defines key origins and adaptations of bone marrow adipocytes with age and disease

abstract: Bone marrow adipocytes (BMAs) accumulate with age and in diverse disease states. However, their age- and disease-specific origins and adaptations remain unclear, impairing our understanding of their context-specific endocrine functions and relationship with surrounding tissues. In this study, we identified a novel, bone marrow-specific adipogenesis pathway using the AdipoqCre+/DTA+  fat free mouse (FF), a model in which Adipoq-Cre drives diphtheria toxin-induced cell death in all adiponectin-expressing cells. Adiponectin is highly expressed by BMAs, peripheral adipocytes, and a subset of bone marrow stromal progenitor cells with preadipocyte-like characteristics. Consistent with this, FF mice presented with uniform depletion of peripheral white and brown adipose tissues, in addition to loss of BMAs in canonical locations such as the tail vertebrae. However, unexpectedly, a distinctly localized subset of BMAs accumulated with age in FF mice in regions such as the femoral and tibial diaphysis that are generally devoid of bone marrow adipose tissue (BMAT). Ectopic BMAs in FF mice were defined by increased lipid storage and decreased expression of cytokines including hematopoietic support factor Cxcl12 and adipokines adiponectin, resistin, and adipsin. FF BMAs also displayed resistance to lipolytic stimuli including cold stress and {beta}3-adrenergic agonist CL316,243. This was associated with reduced expression of adrenergic receptors and monoacylglycerol lipase. Global ablation of adiponectin-expressing cells regulated bone accrual in an age- and sex-dependent manner. High bone mass was present early in life and this was more pronounced in females. However, with age, both male and female FF mice had decreased cortical thickness and mineral content. In addition, unlike BMAs in healthy mice, expansion of ectopic BMAs in FF mice was inversely correlated with cortical bone volume fraction. Subcutaneous fat transplant and normalization of systemic metabolic parameters was sufficient to prevent ectopic BMA expansion in FF mice but did not prevent the initial onset of the high bone mass phenotype. Altogether, this defines a novel, secondary adipogenesis pathway that relies on recruitment of adiponectin-negative stromal progenitors. This pathway is unique to the bone marrow and is activated with age and in states of metabolic stress, resulting in expansion of BMAs specialized for lipid storage with compromised lipid mobilization and endocrine function within regions traditionally devoted to hematopoiesis. Our findings further distinguish BMAT from peripheral adipose tissues and contribute to our understanding of BMA origins and adaptation with age and disease.


title: Dietary specialisation in a Critically Endangered pipefish revealed by faecal eDNA metabarcoding

abstract: The estuarine pipefish, Syngnathus watermeyeri, is one of the rarest animals in Africa and occurs in only two South African estuaries. The species was declared provisionally extinct in 1994, but was later rediscovered and is currently listed by the IUCN as Critically Endangered. A conservation programme was launched in 2017, with the re-introduction of captive-bred individuals into estuaries where this species was recorded historically was the main aims. Successful captive breeding requires knowledge of the species dietary requirements. In the present study, we used metabarcoding of faecal DNA to identify prey species consumed by wild-captured S. watermeyeri from one of the two surviving populations. We compared the diet of the estuarine pipefish with that of the longsnout pipefish, S. temminckii, in the same estuary, to determine whether these two species compete for the same prey items. Both species occupy similar estuarine habitats, but S. temminckii has a much wider distribution and also occurs in the marine environment. Our results show that even though both pipefish species prey on three major invertebrate classes (Gastropoda, Malacostraca and Maxillopoda), the relative proportions differ. Syngnathus watermeyeri primarily targets Maxillopoda, with a single species of calanoid copepod constituting >95% of the Amplicon Sequence Variants (ASVs) identified from its faecal DNA, whereas the diet of S. temminckii mostly comprises snail and decapod crustacean larvae. Our finding supports the hypothesis that population declines and localised extirpations of S. watermeyeri during previous decades may have been the result of reductions in the abundance of calanoid copepods. Calanoids rely on freshwater pulses to thrive, but such events have become rare in the two estuaries inhabited by S. watermeyeri due to excessive freshwater abstraction for urban and agricultural use.


title: Protist and Fungal Metaxin-Like Proteins: Relationship to Vertebrate Metaxins that Function in Protein Import into Mitochondria

abstract: Metaxin-like proteins are shown to be encoded in the genomes of a wide range of protists and fungi. The metaxin proteins were originally described in humans and mice, and were experimentally demonstrated to have a role in the import of nascent proteins into mitochondria. In this study, metaxin-like proteins of protists and fungi predicted from genome sequences were identified by criteria including their sequence homology with vertebrate metaxin proteins and the existence of distinctive metaxin protein domains. Protists of diverse taxa, including amoebae, protozoa, phytoplankton, downy mildews, water molds, and algae, were found to possess genes for metaxin-like proteins. With fungi, the important taxonomic divisions (phyla) of Ascomycota, Basidiomycota, Chytridiomycota, Mucoromycota, and Zoopagomycota had species with metaxin-like protein genes. The presence of distinctive GST_N_Metaxin, GST_C_Metaxin, and Tom37 domains in the predicted proteins indicates that the protist and fungal proteins are related to the vertebrate metaxins. However, the metaxin-like proteins are not direct homologs of vertebrate metaxins 1, 2, or 3, but have similarity to each of the three. The alignment of the metaxin-like proteins of a variety of protists with vertebrate metaxins 1 and 2 showed about 26% and 19% amino acid identities, respectively, while for fungal metaxin-like proteins, the identities were about 29% and 23%. The different percentages with the two vertebrate metaxins indicates that the metaxin-like proteins are both metaxin 1-like and, to a lesser degree, metaxin 2-like. The secondary structures of protist and fungal metaxin-like proteins both consist of nine -helical segments, the same as for the vertebrate metaxins, with a negligible contribution from {beta}-strand. Phylogenetic analysis demonstrated that the protist and fungal metaxin-like proteins and the vertebrate metaxins form distinct and separate groups, but that the groups are derived from a common ancestral protein sequence.


title: A simple method of suspending implant wear particles for more physiological modelling of cell-particle interactions in vitro

abstract: Arthroplasty implants e.g. hip, knee, spinal disc sustain relatively high compressive loading and friction wear, which lead to the formation of wear particles or debris between articulating surfaces. Despite advances in orthopaedic materials and surface treatments, the production of wear debris from any part of a joint arthroplasty implant is currently unavoidable. Implant wear debris induces host immune responses and inflammation, which causes patient pain and ultimately implant failure through progressive inflammation-mediated osteolysis and implant loosening, where the severity and rate of periprosthetic osteolysis depends on the material and physicochemical characteristics of the wear particles. Evaluating the cytotoxicity of implant wear particles is important for regulatory approved clinical application of arthroplasty implants, as is the study of cell-particle response pathways. However, the particles of polymeric materials commonly used for arthroplasty implants tend to float when placed in culture media, which limits their contact with cell cultures. This study reports a simple means of suspending wear particles in liquid medium using sodium methylcellulose (NaCMC) to provide a more realistic proxy of the interaction between cells and tissues to wear particles in vivo, which are free-floating in synovial fluid within the joint cavity. Low concentrations of NaCMC dissolved in culture medium were found to be effective for suspending polymeric wear particles. Such suspensions may be used as more physiologically-relevant means for testing cellular responses to implant wear debris, as well as studying the combinative effects of shear and wear particle abrasion on cells in a dynamic culture environments such as perfused tissue-on-chip devices.

category: bioengineering


title: LiquidCNA: tracking subclonal evolution from longitudinal liquid biopsies using somatic copy number alterations

abstract: Cell-free DNA (cfDNA) measured via liquid biopsies provides a way for minimally-invasive monitoring of tumour evolutionary dynamics during therapy. Here we present liquidCNA, a method to track subclonal evolution from longitudinally collected cfDNA samples based on somatic copy number alterations (SCNAs). LiquidCNA utilises SCNA profiles derived through cost-effective low-pass whole genome sequencing to automatically and simultaneously genotype and quantify the size of the dominant subclone without requiring prior knowledge of the genetic identity of the emerging clone. We demonstrate the accuracy of liquidCNA in synthetically generated sample sets and in vitro and in silico mixtures of cancer cell lines. Application in vivo in patients with metastatic lung cancer reveals the progressive emergence of a novel tumour sub-population. LiquidCNA is straightforward to use, computationally inexpensive and enables continuous monitoring of subclonal evolution to understand and control therapy-induced resistance.

category: bioinformatics


title: HLA-SPREAD: A comprehensive resource for HLA associated diseases, drug reactions and SNPs across populations

abstract: Extreme complexity in the Human Leukocyte Antigens (HLA) system and its nomenclature makes it difficult to interpret and integrate relevant information for HLA associations with diseases, Adverse Drug Reactions (ADR) and Transplantation. PubMed search displays [~]144,000 studies on HLA reported from multiple diseases in diverse locations. Currently, IPD-IMGT/HLA database houses data on 28,320 HLA alleles. We developed an automated pipeline with a unified graphical user interface HLA-SPREAD that provides a structured information on SNPs, Populations, REsources, ADRs and Diseases information. Information on HLA was extracted from [~]24 million PubMed abstracts extracted using Natural Language Processing (NLP). Python scripts were used to mine and curate information on diseases, filter false positives and categorize to 24 tree hierarchical groups and named Entity Recognition (NER) algorithms followed by semantic analysis to infer HLA association(s). This resource from 112 countries and 32 ethnic groups provides interesting insights on: markers associated with allelic/haplotypic association in autoimmune, cancer, viral and skin diseases, transplantation outcome and ADRs for hypersensitivity. Summary information on clinically relevant biomarkers related to HLA disease associations with mapped susceptible/risk alleles are readily retrievable from HLASPREAD. The resource is available at URL http://hla-spread.igib.res.in/. This resource is first of its kind that can help uncover novel patterns in HLA gene-disease associations.


title: HLA-SPREAD: A Natural Language Processing based resource for curating HLA association from PubMed abstracts


title: Binding and activation of serotonergic G-protein coupled receptors by the multimodal antidepressant vortioxetine.

abstract: G-protein coupled receptors are important pharmacological targets. Despite substantial progress, important questions still remain concerning the details of activation: how can a ligand act as an agonist in one receptor, but as an antagonist in a homologous receptor, and how can agonists activate a receptor despite lacking polar functional groups able to interact with helix 5? Studying vortioxetine, an important multimodal antidepressant drug, may elucidate both questions. Herein, we present a thorough in silico analysis of vortioxetine binding to 5-HT1A, 5-HT1B, and 5-HT7 receptors and compare to available experimental data. We are able to rationalize the differential mode of action of vortioxetine at different receptors, but also, in the case of the 5-HT1A receptor, we observe the initial steps of activation suggesting that interaction with helix 5 does not necessarily require a hydrogen bond as previously suggested. The results extend our current understanding of agonist and antagonist action at GPCRs.


title: Agonistic CD40 antibody therapy induces tertiary lymphoid structures but impairs the response to immune checkpoint blockade in glioma

abstract: Gliomas are brain tumors characterized by immunosuppression. Immunostimulatory agonistic CD40 antibodies (CD40) are in clinical development for solid tumors but are yet to be evaluated for glioma. Here, systemic delivery of CD40 led to cytotoxic T cell dysfunction and impaired the response to immune checkpoint inhibitors in preclinical glioma models. This was associated with an accumulation of suppressive CD11b+ B cells. However, CD40 also induced tertiary lymphoid structures (TLS). In human glioma, TLS correlated with increased T cell infiltration indicating enhanced immune responses. Our work unveils the pleiotropic effects of CD40 therapy in glioma, which is of high clinical relevance.


title: RASSF1C oncogene elicits amoeboid invasion, cancer stemness and invasive EVs via a novel SRC/Rho axis

abstract: Cell plasticity is a crucial hallmark leading to cancer metastasis. Upregulation of Rho/ROCK pathway drives actomyosin contractility, protrusive forces and contributes to the occurrence of highly invasive amoeboid cells in tumors. Cancer stem cells are similarly associated with metastasis, but how these populations arise in tumors is not fully understood. Here we show that the novel oncogene RASSF1C drives mesenchymal to amoeboid transition and stem cell attributes in breast cancer cells. Mechanistically, RASSF1C activates Rho/ROCK via SRC mediated RhoGDI inhibition, resulting in generation of actomyosin contractility. Moreover, we demonstrate that amoeboid cells display the cancer stem cell markers CD133, ALDH1 and the pluripotent marker Nanog; are accompanied by higher invasive potential in vitro and in vivo; and employ extracellular vesicles to transfer the invasive phenotype to target cells and tissue. Importantly, the underlying RASSF1C driven biological processes concur to explain clinical data: namely, methylation of the RASSF1C promoter correlates with better survival in early stage breast cancer patients. Therefore, we propose the use of RASSF1 gene promoter methylation status as a biomarker for patient stratification.


title: Natural variation in Caenorhabditis elegans responses to the anthelmintic emodepside

abstract:
Treatment of parasitic nematode infections depends primarily on the use of anthelmintics. However, this drug arsenal is limited, and resistance against most anthelmintics is widespread. Emodepside is a new anthelmintic drug effective against gastrointestinal and filarial nematodes. Nematodes that are resistant to other anthelmintic drug classes are susceptible to emodepside, indicating that the emodepside mode of action is distinct from previous anthelmintics. The laboratory-adapted Caenorhabditis elegans strain N2 is sensitive to emodepside, and genetic selection and in vitro experiments implicated slo-1, a BK potassium channel gene, in emodepside mode of action. In an effort to understand how natural populations will respond to emodepside, we measured brood sizes and developmental rates of wild C. elegans strains after exposure to the drug and found natural variation across the species. Some of the observed variation in C. elegans emodepside responses correlates with amino acid substitutions in slo-1, but genetic mechanisms other than slo-1 coding variants likely underlie emodepside resistance in wild C. elegans strains. Additionally, the assayed strains have higher offspring production in low concentrations of emodepside (a hormetic effect), which could impact treatment strategies when parasites are underdosed. We find that natural variation affects emodepside sensitivity, supporting the suitability of C. elegans as a model system to study emodepside responses across natural nematode populations.

Graphical abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/425329v2_ufig1.gif" ALT="Figure 1">
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org.highwire.dtl.DTLVardef@1139cf4org.highwire.dtl.DTLVardef@a56a30org.highwire.dtl.DTLVardef@1de8b2forg.highwire.dtl.DTLVardef@183e4a6_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LIEmodepside responses vary across the C. elegans species.
C_LIO_LIWild strains of C. elegans model natural differences in parasite emodepside responses.
C_LIO_LIVariation in the emodepside target slo-1 and other loci correlate with resistance.
C_LIO_LILow doses of emodepside cause a hormetic effect on offspring production.
C_LI

category: pharmacology and toxicology


title: Specific Adaptive Gene Expression of Smooth Muscle Cells Challenged by Organotelluranes.

abstract:
Organotelluranes RT3 and RT4 are thiol reagents that induce mitochondrial transition pore (MTP) opening in a sensitive and insensitive manner to cyclosporin A. Although RT3 and RT4 promote glutathione depletion, paradoxically, they are also an efficient antioxidant for membrane lipids. These compounds antagonistic effects elicited the challenging question of how the gene expression of antioxidant enzymes would respond to treatment with these compounds. The influence of RT3 and RT4 on antioxidant enzyme expression was investigated in cultured aortic smooth muscle cells (ASMC). RT3 and RT4 promoted disruption of ionic calcium homeostasis, mitochondrial transmembrane potential ({Delta}{Psi}), and cell death in a dose-dependent manner. The cell death mechanisms responded qualitatively to the increase of the organotellurane concentration and changed from apoptosis to necrosis. RT3 and RT4 increased the expression of thioredoxin significantly. RT3 also increased the expression of glutaredoxin and glutathione peroxidase, slightly the catalase expression without significant effects on SOD expression. The results are consistent with GSH and protein thiol depletion and discussed based on the cell toxicity mechanism exhibited by these compounds.

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/425411v4_ufig1.gif" ALT="Figure 1">
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org.highwire.dtl.DTLVardef@52bb82org.highwire.dtl.DTLVardef@19476d9org.highwire.dtl.DTLVardef@6aa99org.highwire.dtl.DTLVardef@1aa605e_HPS_FORMAT_FIGEXP  M_FIG C_FIG


title: Cellular feedback to organotelluranes displays modulation of antioxidant proteins gene expression


title: Sugar feeding enhances gut immunity and protects against arboviral infection in the mosquito vector Aedes aegypti

abstract: As mosquito females require a blood meal to reproduce, they can act as vectors of numerous pathogens, such as arboviruses (e.g. Zika, dengue and chikungunya viruses), which constitute a substantial worldwide public health burden. In addition to blood meals, mosquito females can also take sugar meals to get carbohydrates for their energy reserves. It is now recognised that diet is a key regulator of health and disease outcome through interactions with the immune system. However, it has been mostly studied in humans and model organisms. So far, the impact of sugar feeding on mosquito immunity and in turn, how this could affect vector competence for arboviruses has not been analysed. Here, we show that sugar feeding increases and maintains antiviral immunity in the digestive tract of the main arbovirus vector Aedes aegypti. Our data demonstrate that the gut microbiota does not mediate the sugar-induced immunity but partly inhibits it. Importantly, sugar intake prior to an arbovirus-infected blood meal further protects females against infection with arboviruses from different families, highlighting a broad antiviral action of sugar. Sugar feeding blocks arbovirus initial infection and dissemination from the gut, lowers infection prevalence and intensity, thereby decreasing transmission potential of female mosquitoes. Overall, our findings uncover a crucial role of sugar feeding in mosquito antiviral immunity and vector competence for arboviruses. Since Ae. aegypti almost exclusively feed on blood in some natural settings, our findings suggest that this could increase the spread of mosquito-borne arboviral diseases.

category: physiology


title: The AFB1 auxin receptor controls rapid auxin signaling and root growth through membrane depolarization in Arabidopsis thaliana

abstract: The existence of an electric gradient across membranes is essential for a cell operation. In plants, application of the growth regulator auxin (IAA) causes almost instantaneous membrane depolarization in various cell types, making membrane depolarization a hallmark of the rapid non-transcriptional responses to IAA. Auxin triggers rapid root growth inhibition; a process that underlies gravitropic bending. The growth and depolarization responses to auxin show remarkable similarities in dynamics, requirement of auxin influx and the involvement of the TIR1/AFB auxin coreceptors, but whether auxin-induced depolarization participates in root growth inhibition remains unanswered. Here, we established a toolbox to dynamically visualize membrane potential in vivo in Arabidopsis thaliana roots by combining the DISBAC2(3) fluorescent probe with microfluidics and vertical stage microscopy. This way we show that auxin-induced membrane depolarization tightly correlates with rapid root growth inhibition and that the cells of the transition zone/early elongation zone are the most responsive to auxin. Further, we demonstrate that auxin cycling in and out of the cells through AUX1 influx and PIN2 efflux is not essential for membrane depolarization and rapid root growth inhibition but acts as a facilitator of these responses. The rapid membrane depolarization by auxin instead strictly depends on the AFB1 auxin receptor, while the other TIR1/AFB paralogues contribute to this response. The lack of membrane depolarization in the afb1 mutant explains the lack of the immediate root growth inhibition. Finally, we show that AFB1 is required for the rapid depolarization and rapid growth inhibition of cells at the lower side of the gravistimulated root. These results are instrumental in understanding the physiological significance of membrane depolarization for the gravitropic response of the root and clarify the role of AFB1 as the receptor central for rapid auxin responses, adding another piece to the puzzle in understanding the biology of the phytohormone auxin.


title: Aberration correction in STED microscopy to increase imaging depth in living brain tissue

abstract: We demonstrate an approach based on adaptive optics to improve the spatial resolution of STED microscopy inside thick biological tissue by a priori correction of spherical aberrations as a function of imaging depth. We first measured the aberrations in a phantom sample of gold and fluorescent nanoparticles suspended in an agarose gel with a refractive index closely matching living brain tissue. Using a spatial light modulator to apply corrective phase shifts, we imaged neurons in living brain slices and show that the corrections can substantially increase image quality. Specifically, we could measure structures as small as 80 nm at a depth of 90 m inside the biological tissue, and obtain a 60% signal increase after correction.

category: neuroscience


title: Seeing the World Like Never Before: Human stereovision through perfect optics

abstract:
Stereovision is the ability to perceive fine depth variations from small differences in the two eyes images. Using adaptive optics, we show that even minute optical aberrations that are not clinically correctable, and go unnoticed in everyday vision, can affect stereo acuity. Hence, the human binocular system is capable of using unnaturally fine details that are not encountered in everyday vision. More importantly, stereoacuity was still considerably variable even with perfect optics. This variability can be attributed to neural adaptation. Our visual system tries to compensate for these aberrations through neural adaptation that optimizes stereovision when viewing stimuli through ones habitual optics. However, the same adaptation becomes ineffective when the optics are changed, even if improved. Beyond optical imperfections, we show that stereovision is limited by neural adaptation to ones own optics.

Significance statementHumans, and animals with front-facing eyes, view the world from slightly different vantage points. This creates small differences in the left and right images that can be utilized for fine depth perception (stereovision). Retinal images are also subject to imperfections that are often different in the optics of the two eyes. Using advanced optical correction techniques, we show that even the smallest imperfections that escape clinical detection affect stereovision. We also find that neural processes become adapted to a persons own optics. Hence, stereovision is directly impacted by the optics of the eyes, and indirectly via neural adaptation. Since the optics change over the lifespan, our results imply that the adult binocular system is adaptable with possibilities for binocular rehabilitation.


title: A New Sensory Skill Shows Automaticity and Integration Features in Multisensory Interactions

abstract: People can learn new sensory skills that augment their perception, such as human echolocation. However, it is not clear to what extent these can become an integral part of the perceptual repertoire. Can they show automatic use, integrated with the other senses, or do they remain cognitively-demanding, cumbersome, and separate? Here, participants learned to judge distance using an echo-like auditory cue. We show that use of this new skill met three key criteria for automaticity and sensory integration: (1) enhancing the speed of perceptual decisions; (2) processing through a non-verbal route and (3) integration with vision in an efficient, Bayes-like manner. We also show some limits following short training: integration was less-than-optimal, and there was no mandatory fusion of signals. These results demonstrate key ways in which new sensory skills can become automatic and integrated, and suggest that sensory augmentation systems may have benefits beyond current applications for sensory loss.


title: Complete microglia deficiency accelerates prion disease without enhancing CNS prion accumulation

abstract:
Prion diseases are transmissible, neurodegenerative disorders associated with misfolding of the prion protein. Previous studies show that reduction of microglia accelerates CNS prion disease and increases the accumulation of prions in the brain, suggesting that microglia provide neuroprotection by phagocytosing and destroying prions. In Csf1r{Delta}FIRE mice, the deletion of an enhancer within Csf1r specifically blocks microglia development, however, their brains develop normally and show none of the deficits reported in other microglia-deficient models. Csf1r{Delta}FIRE mice were used as a refined model in which to study the impact of microglia-deficiency on CNS prion disease. Although Csf1r{Delta}FIRE mice succumbed to CNS prion disease much earlier than wild-type mice, the accumulation of prions in their brains was reduced. Instead, astrocytes displayed earlier, non-polarized reactive activation with enhanced synaptic pruning and unfolded protein responses. Our data suggest that rather than simply phagocytosing and destroying prions, the microglia instead provide host-protection during CNS prion disease and restrict the harmful activities of reactive astrocytes.

Main pointsCNS prion disease is accelerated in mice completely lacking microglia. The rate of prion accumulation in the brain was unaltered in absence of microglia. Microglia provide host-protection during CNS prion disease independent of prion clearance.