title: SpeciesRax: A tool for maximum likelihood species tree inference from gene family trees under duplication, transfer, and loss.

abstract: Species tree inference from gene family trees is becoming increasingly popular because it can account for discordance between the species tree and the corresponding gene family trees. In particular, methods that can account for multiple-copy gene families exhibit potential to leverage paralogy as informative signal. At present, there does not exist any widely adopted inference method for this purpose. Here, we present SpeciesRax, the first maximum likelihood method that can infer a rooted species tree from a set of gene family trees and can account for gene duplication, loss, and transfer events. By explicitly modelling events by which gene trees can depart from the species tree, SpeciesRax leverages the phylogenetic rooting signal in gene trees. SpeciesRax infers species tree branch lengths in units of expected substitutions per site and branch support values via paralogy-aware quartets extracted from the gene family trees. Using both empirical and simulated datasets we show that SpeciesRax is at least as accurate as the best competing methods while being one order of magnitude faster on large datasets at the same time. We used SpeciesRax to infer a biologically plausible rooted phylogeny of the vertebrates comprising 188 species from 31612 gene families in one hour using 40 cores. SpeciesRax is available under GNU GPL at https://github.com/BenoitMorel/GeneRax and on BioConda.

category: molecular biology


title: An 18S V4 rDNA metabarcoding dataset of protist diversity in the Atlantic inflow to the Arctic Ocean, through the year and down to 1000 m depth.

abstract: Arctic marine protist communities have been understudied due to challenging sampling conditions, in particular during winter and in deep waters. The aim of this study was to improve our knowledge on Arctic protist diversity through the year, both in the epipelagic (< 200 m depth) and mesopelagic zones (200-1000 m depth). Sampling campaigns were performed in 2014, during five different months, to capture the various phases of the Arctic primary production: January (winter), March (pre-bloom), May (spring bloom), August (post-bloom) and November (early winter). The cruises were undertaken west and north of the Svalbard archipelago, where warmer Atlantic waters from the West Spitsbergen Current meets cold Arctic waters from the Arctic Ocean. From each cruise, station, and depth, 50 L of sea water were collected and the plankton was size-fractionated by serial filtration into four size fractions between 0.45-200 {micro}m, representing the picoplankton, nanoplankton and microplankton. In addition vertical net hauls were taken from 50 m depth to the surface at selected stations. From the plankton samples DNA was extracted, the V4 region of the 18S rRNA-gene was amplified by PCR with universal eukaryote primers and the amplicons were sequenced by Illumina high-throughput sequencing. Sequences were clustered into Amplicon Sequence Variants (ASVs), representing protist genotypes, with the dada2 pipeline. Taxonomic classification was made against the curated Protist Ribosomal Reference database (PR2). Altogether 6,536 protist ASVs were obtained (including 54 fungal ASVs). Both ASV richness and taxonomic composition were strongly dependent on size-fraction, season, and depth. ASV richness was generally higher in the smaller fractions, and higher in winter and the mesopelagic samples than in samples from the well-lit epipelagic zone during summer. During spring and summer, the phytoplankton groups diatoms, chlorophytes and haptophytes dominated in the epipelagic zone. Parasitic and heterotrophic groups such as Syndiniales and certain dinoflagel-lates dominated in the mesopelagic zone all year, as well as in the epipelagic zone during the winter. The dataset is available at https://doi.org/10.17882/79823, (Egge et al., 2014).

category: ecology


title: Deciphering Brassica plant defence responses to cabbage white butterfly egg-associated molecular patterns

abstract: Brassica plants activate a strong hypersensitive response (HR)-like necrosis underneath eggs of cabbage white butterflies, but their molecular response to eggs is poorly understood. Here, we developed a method to generate egg wash to identify potential insect egg-associated molecular patterns (EAMPs) inducing HR-like necrosis. We found that egg wash, containing compounds from Pieris eggs, induced a similar response as eggs. We show that wash of hatched eggs, of egg glue, and of accessory reproductive glands (ARG) that produce this glue, also induced HR-like necrosis, whereas removal of the glue from eggs resulted in a reduced response. Eggs of Pieris butterflies induced callose deposition, production of reactive oxygen species and cell death in B. nigra and B. rapa leaf tissue, also in plants that did not express HR-like necrosis. Finally, only washes from Pieris eggs induced defence genes and ethylene production, whereas egg wash of a generalist moth did not. Our results indicate that EAMPs are in the egg glue and that the response in B. nigra is specific to Pieris species. Our study expands knowledge on the Brassica-Pieris-egg interaction, and paves the way for identification of EAMPs in Pieris egg glue and corresponding receptor in Brassica spp.

category: plant biology


title: Staphylococcus aureus α-toxin induces acid sphingomyelinase release from a human endothelial cell line

abstract: Staphylococcus aureus (S. aureus) is well known to express a plethora of toxins of which the pore-forming hemolysin A (-toxin) is the best-studied cytolysin. Pore-forming toxins (PFT) permeabilize host membranes during infection thereby causing concentration-dependent effects in host cell membranes ranging from disordered ion fluxes to cytolysis. Host cells possess defense mechanisms against PFT attack, resulting in endocytosis of the breached membrane area and delivery of repair vesicles to the insulted plasma membrane as well as a concurrent release of membrane repair enzymes. Since PFTs from several pathogens have been shown to recruit membrane repair components, we here investigated whether staphylococcal -toxin is able to induce these mechanisms in endothelial cells. We show that S. aureus -toxin induced increase in cytosolic Ca2+ in endothelial cells, which was accompanied by p38 MAPK phosphorylation. Toxin challenge led to increased endocytosis of an extracellular fluid phase marker as well as increased externalization of LAMP1-positive membranes suggesting that peripheral lysosomes are recruited to the insulted plasma membrane. We further observed that thereby the lysosomal protein acid sphingomyelinase (ASM) was released into the cell culture medium. Thus, our results show that staphylococcal -toxin triggers mechanisms in endothelial cells, which have been implicated in membrane repair after damage of other cell types by different toxins.

category: microbiology


title: COVID-19 and the abrupt shift to remote learning: Impact on grades and perceived learning for undergraduate biology students

abstract: Institutions across the world transitioned abruptly to remote learning in 2020 due to the COVID-19 pandemic. This rapid transition to remote learning has generally been predicted to negatively affect students, particularly those marginalized due to their race, socioeconomic class, or gender identity. In this study, we examined the impact of this transition in the Spring 2020 semester on the grades of students enrolled in the in-person biology program at a large university in Southwestern United States as compared to the grades earned by students in the fully online biology program at the same institution. We also surveyed in-person instructors to understand changes in assessment practices as a result of the transition to remote learning during the pandemic. Finally, we surveyed students in the in-person program to learn about their perceptions of the impacts of this transition. We found that both online and in-person students received a similar small increase in grades in Spring 2020 compared to Spring 2018 and 2019. We also found no evidence of disproportionately negative impacts on grades received by students marginalized due to their race, socioeconomic class, or gender in either modality. Focusing on in-person courses, we documented that instructors made changes to their courses when they transitioned to remote learning, which may have offset some of the potential negative impacts on course grades. However, despite receiving higher grades, in-person students reported negative impacts on their learning, interactions with peers and instructors, feeling part of the campus community, and career preparation. Women reported a more negative impact on their learning and career preparation compared to men. This work provides insights into students perceptions of how they were disadvantaged as a result of the transition to remote instruction and illuminates potential actions that instructors can take to create more inclusive education moving forward.

category: scientific communication and education


title: Description and comparison of PIMS-TS innate cell signature and immunophenotype with a cohort of healthy children, severe viral and bacterial infections and Kawasaki Disease.

abstract: A new clinical syndrome associated to SARS-CoV-2 has been described in children. It has been named as Pediatric Inflammatory Multisystem Syndrome Temporally Associated with SARS-CoV-2 (PIMS-TS). This new disease is a main cause of hospital and pediatric intensive care unit (PICU). In this work we describe the innate cell signature and immunophenotype of children admitted to PICU because of PIMS-TS. Also, we compare it with healthy controls and children admitted to PICU because bacterial infection, viral infection and Kawasaki disease. We made a prospective-retrospective observational study in a tertiary pediatric hospital. Children admitted to PICU because of PIMS-TS from March 2020 to September 2020 were consecutively included. They were compare with previous cohorts from our center. A total of 247 children were included: 183 healthy controls, 25 viral infections, 20 bacterial infections, 6 Kawasaki disease and 13 PIMS-TS. PIMT-TS showed the lowest percentage of lymphocytes and monocytes with higher relative numbers of CD4+ (p =0,000). At the same time, we describe a differential expression of CD64, CD11a and CD11b. Monocytes and neutrophils in PIMS-TS showed higher levels of CD64 expression compared to all groups (p = 0,000). Also, proteins involved in leukocyte tissue migration, like CD11a and CD11b were highly expressed compare to other severe viral or bacterial infections (p = 0,000). In PIMS-TS this increased CD11a expression could be a sign of the activation and trafficking of these leukocytes. These findings are congruent with an inflammatory process and the trend of these cells to leave the bloodstream. In conclusion, we compare for the first time the innate cellular response of children with PIMS-TS with other severe forms of viral or bacterial infection and Kawasaki disease. Our findings define a differential cell innate signature. These data should be further studied and may facilitate the diagnosis and management of these patients.

category: immunology


title: Combining experiments and in silico modeling to infer the role of adhesion and proliferation on the collective dynamics of cells

abstract: The collective dynamics of cells on surfaces and interfaces poses technological and theoretical challenges in the study of morphogenesis, tissue engineering, and cancer. Different mechanisms are at play, including, cell-cell adhesion, cell motility, and proliferation. However, the relative importance of each one is elusive. Here, experiments with a culture of glioblastoma multiforme cells on a substrate are combined with in silico modeling to infer the rate of each mechanism. By parametrizing these rates, the time-dependence of the spatial correlation observed experimentally is reproduced. The obtained results suggest a reduction in cell-cell adhesion with the density of cells. The reason for such reduction and possible implications for the collective dynamics of cancer cells are discussed.

category: cell biology


title: Correlative Organelle Microscopy: fluorescence guided volume electron microscopy of intracellular processes

abstract:
Intracellular processes depend on a strict spatial and temporal organization of proteins and organelles. Directly linking molecular to nanoscale ultrastructural information is therefore crucial to understand cellular physiology. Volume or 3-dimensional (3D) correlative light and electron microscopy (volume-CLEM) holds unique potential to explore cellular physiology at high-resolution ultrastructural detail across cell volumes. Application of volume-CLEM is however hampered by limitations in throughput and 3D correlation efficiency. Addressing these limitations, we here describe a novel pipeline for volume-CLEM that provides high-precision (<100nm) registration between 3D fluorescence microscopy (FM) and 3D electron microscopy (EM) data sets with significantly increased throughput. Using multi-modal fiducial nanoparticles that remain fluorescent in epoxy resins and a 3D confocal fluorescence microscope integrated in a Focused Ion Beam Scanning Electron Microscope (FIB.SEM), our approach uses FM to target extremely small volumes of even single organelles for imaging in volume-EM, and obviates the need for post correlation of big 3D datasets. We extend our targeted volume-CLEM approach to include live-cell imaging, adding information on the motility of intracellular membranes selected for volume-CLEM. We demonstrate the power of our approach by targeted imaging of rare and transient contact sites between endoplasmic reticulum (ER) and lysosomes within hours rather than days. Our data suggest that extensive ER-lysosome and mitochondria-lysosome interactions restrict lysosome motility, highlighting the unique capabilities of our integrated CLEM pipeline for linking molecular dynamic data to high-resolution ultrastructural detail in 3D.

SignificanceWe have developed a correlative imaging pipeline to (i) correlate 3D-FM to volume-EM data with high precision, directly bridging the FM and EM resolutions (ii) achieve high-throughput volume-CLEM by targeted EM imaging of a single organelle sized region-of-interest, pre-identified by FM (iii) link live-cell fluorescence imaging of cultured mammalian cells to high-throughput volume-CLEM (iv) quantitatively study structure-function relations at subcellular scale (v) link rare (e.g. membrane contact sites) and transient (e.g. organelle interactions) cellular events to 3D ultrastructure.

The targeted volume-CLEM pipeline provides a unique prospect for multi-modal correlative intracellular analysis combining dynamic interaction (live-cell imaging), functional state (live-cell imaging), molecular localization (FM), and 3D-ultrastructure (FIB.SEM) at nanometer scale.


title: Fluorescence lifetime imaging of pH along the secretory pathway

abstract: Many cellular processes are dependent on correct pH levels, and this is especially important for the secretory pathway. Defects in pH homeostasis in distinct organelles cause a wide range of diseases, including disorders of glycosylation and lysosomal storage diseases. Ratiometric imaging of the pH-sensitive mutant of green fluorescent protein (GFP), pHLuorin, has allowed for targeted pH measurements in various organelles, but the required sequential image acquisition is intrinsically slow and therefore the temporal resolution is unsuitable to follow the rapid transit of cargo between organelles. We therefore applied fluorescence lifetime imaging microscopy (FLIM) to measure intraorganellar pH with just a single excitation wavelength. We first validated this method by confirming the pH in multiple compartments along the secretory pathway and compared the pH values obtained by the FLIM-based measurements with those obtained by conventional ratiometric imaging. Then, we analyzed the dynamic pH changes within cells treated with Bafilomycin A1, to block the vesicular ATPase, and Brefeldin A, to block ER-Golgi trafficking. Finally, we followed the pH changes of newly-synthesized molecules of the inflammatory cytokine tumor necrosis factor (TNF)- while they were in transit from the endoplasmic reticulum via the Golgi to the plasma membrane. The toolbox we present here can be applied to measure intracellular pH with high spatial and temporal resolution, and can be used to assess organellar pH in disease models.


title: Stepwise maturation of the peptidyl transferase region of human mitoribosomes

abstract: Mitochondrial ribosomes are specialized for the synthesis of membrane proteins responsible for oxidative phosphorylation. Mammalian mitoribosomes diverged considerably from the ancestral bacterial ribosomes and feature dramatically reduced ribosomal RNAs. Structural basis of the mammalian mitochondrial ribosome assembly is currently not understood. Here we present eight distinct assembly intermediates of the human large mitoribosomal subunit involving 7 assembly factors. We discover that NSUN4-MTERF4 dimer plays a critical role in the process by stabilizing the 16S rRNA in a conformation that exposes the functionally important regions of rRNA for modification by MRM2 methyltransferase and quality control interactions with a conserved mitochondrial GTPase MTG2 that contacts the sarcin ricin loop and the immature active site. The successive action of these factors leads to the formation of the peptidyl transferase active site of the mitoribosome and the folding of the surrounding rRNA regions responsible for interactions with tRNAs and the small ribosomal subunit.

category: biochemistry


title: Evolutionary trade-offs at the Arabidopsis WRR4A resistance locus underpin alternate Albugo candida recognition specificities

abstract:
The oomycete Albugo candida causes white rust of Brassicaceae, including vegetable and oilseed crops, and wild relatives such as Arabidopsis thaliana. Novel White Rust Resistance (WRR)-genes from Arabidopsis enable new insights into plant/parasite co-evolution. WRR4A from Arabidopsis accession Col-0 provides resistance to many but not all white rust races, and encodes a nucleotide-binding (NB), leucine-rich repeat (LRR) (NLR) immune receptor protein. Col-0 WRR4A resistance is broken by a Col-0-virulent isolate of A. candida race 4 (AcEx1). We identified an allele of WRR4A in Arabidopsis accession Oy-0 and other accessions that confers full resistance to AcEx1. WRR4AOy-0 carries a C-terminal extension required for recognition of AcEx1, but reduces recognition of several effectors recognized by the WRR4ACol-0 allele. WRR4AOy-0 confers full resistance to AcEx1 when expressed as a transgene in the oilseed crop Camelina sativa.

SignificanceA C-terminal extension in an allele of the Arabidopsis resistance-protein WRR4A changes effector recognition specificity, enabling the WRR4AOy-0 allele to confer immunity to Albugo candida races that overcome the WRR4ACol-0 allele. This resistance can be transferred to the oil-producing crop Camelina sativa.

Graphical abstract

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title: A cryo-ET study of microtubules in axons

abstract: The microtubule cytoskeleton in axons plays key roles in intracellular transport and in defining cell shape. Despite many years of study of microtubules, many questions regarding their native architecture remain unanswered. Here, we performed cryo-electron tomography of mouse dorsal root ganglion (DRG) and Drosophila melanogaster (Dm) neurons and examined their microtubule ultrastructure in situ. We found that the microtubule minus and plus ends in DRG axons are structurally similar and frequently contact nearby components. The microtubules in DRG axons maintained a 13 protofilament (pf) architecture, even close to lattice break sites. In contrast, microtubules in Dm neurons had 12 or 13 pfs and we detected sites of pf number transition. The microtubule lumen in DRG axons is filled with globular microtubule inner proteins (MIPs). Our data suggest these have a defined structure, which is surprising given they are thought to contain the disordered protein MAP6. In summary, we reveal novel morphological and structural features of microtubules in their native environment.


title: Atg39 links and deforms the outer and inner nuclear membranes in selective autophagy of the nucleus

abstract: In selective autophagy of the nucleus (hereafter nucleophagy), nucleus-derived double membrane vesicles (NDVs) are formed, sequestered within autophagosomes, and delivered to lysosomes or vacuoles for degradation. In Saccharomyces cerevisiae, the nuclear envelope (NE) protein Atg39 acts as a nucleophagy receptor, which interacts with Atg8 to target NDVs to forming autophagosomal membranes. In this study, we revealed that Atg39 is anchored to the outer nuclear membrane (ONM) via its transmembrane domain and also associated with the inner nuclear membrane (INM) via membrane-binding amphipathic helices (APHs) in its perinuclear space region, thereby linking these membranes. We also revealed that overaccumulation of Atg39 causes the NE to protrude towards the cytoplasm, and the tips of the protrusions are pinched off to generate NDVs. The APHs of Atg39 are crucial for Atg39 assembly in the NE and subsequent NE protrusion. These findings suggest that the nucleophagy receptor Atg39 plays pivotal roles in NE deformation during the generation of NDVs to be degraded by nucleophagy.


title: A cryo-ET survey of intracellular compartments within mammalian axons

abstract: The neuronal axon contains many intracellular compartments which travel between the cell body and axon tip. The nature of these cargos and the complex axonal environment through which they traverse is unclear. Here, we describe the internal components of mammalian sensory axons using cryo-electron tomography. We show that axonal endoplasmic reticulum has thin, beaded appearance and is tethered to microtubules at multiple sites. The tethers are elongated, [~] 7 nm long proteins which cluster in small groups. We survey the different membrane-bound cargos in axons, quantify their abundance and describe novel internal features including granules and broken membranes. We observe connecting density between membranes and microtubules which may correspond to motor proteins. In addition to membrane-bound organelles, we detect numerous proteinaceous compartments, including vaults and previously undescribed virus-like capsid particles. The abundance of these compartments suggests they undergo trafficking in axons. Our observations outline the physical characteristics of axonal cargo and provide a platform for identification of their constituents.


title: Conserved and context-dependent roles for Pdgfrb signaling during zebrafish vascular mural cell development

abstract:
Platelet derived growth factor beta and its receptor, Pdgfrb, play essential roles in the development of vascular mural cells, including pericytes and vascular smooth muscle. To determine if this role was conserved in zebrafish, we analyzed pdgfb and pdgfrb mutant lines. Similar to mouse, pdgfb and pdgfrb mutant zebrafish lack brain pericytes and exhibit anatomically selective loss of vascular smooth muscle coverage. Despite these defects, pdgfrb mutant zebrafish did not otherwise exhibit circulatory defects at larval stages. However, beginning at juvenile stages, we observed severe cranial hemorrhage and vessel dilation associated with loss of pericytes and vascular smooth muscle cells in pdgfrb mutants. Similar to mouse, pdgfrb mutant zebrafish also displayed structural defects in the glomerulus, but normal development of hepatic stellate cells. We also noted defective mural cell investment on coronary vessels with concomitant defects in their development. Together, our studies support a conserved requirement for Pdgfrb signaling in mural cells. In addition, these mutants provide an important model for definitive investigation of mural cells during early embryonic stages without confounding secondary effects from circulatory defects.

Summary statementGenetic analysis in zebrafish demonstrates the conserved role of Pdgfb/Pdgfrb signaling in pericyte and vascular smooth muscle cell formation during vascular development in vertebrates.

category: developmental biology


title: EHMT2 Controls Transcriptional Noise and the Developmental Switch after Gastrulation in the Mouse Embryo

abstract: Embryos that carry zygotic or parental mutations in Ehmt2, the gene encoding the main euchromatic histone H3K9 methyltransferase, EHMT2, exhibit variable developmental delay. We asked the question whether the delayed embryo is different transcriptionally from the normally developing embryo when they reach the same developmental stage. We collected embryos carrying a series of genetic deficiencies in the Ehmt2 gene and performed total RNA sequencing of somite stage-matched individual embryos. We applied novel four-way comparisons to detect differences between normal versus deficient embryos, and between 12-somite and 6-somite embryos. Importantly, we also identified developmental changes in transcription that only occur during the development of the normal embryo. We found that at the 6-somite stage, gastrulation-specific genes were not precisely turned off in the Ehmt2-/- embryos, and genes involved in organ growth, connective tissue development, striated muscle development, muscle differentiation, and cartilage development were not precisely switched on in the Ehmt2-/- embryos. Zygotic EHMT2 reduced transcriptional variation of developmental switch genes and at some repeat elements at the six-somite stage embryos. Maternal EHMT2-mutant embryos also displayed great transcriptional variation consistent with their variable survival, but transcription was normal in developmentally delayed parental haploinsufficient embryos, consistent with their good prospects. Global profiling of transposable elements in the embryo revealed that specific repeat classes responded to EHMT2. DNA methylation was specifically targeted by EHMT2 to LTR repeats, mostly ERVKs. Long noncoding transcripts initiated from those misregulated  driver repeats in Ehmt2-/- embryos, and extended to several hundred kilobases, encompassing a multitude of additional, similarly misexpressed  passenger repeats. These findings establish EHMT2 as an important regulator of the transition between gastrulation programs and organ specification programs and of variability.


title: Catch me if you can: Least myelinated white matter develops fastest during early infancy

abstract: Development of myelin, a fatty sheath that insulates nerve fibers, is critical for brain function. Myelination during infancy has been studied with histology, but postmortem data cannot evaluate the longitudinal trajectory of white matter development. Here, we obtained longitudinal diffusion MRI and quantitative MRI measures of R1 in 0, 3 and 6 months-old human infants, and (ii) developed an automated method to identify white matter bundles and quantify their properties in each infants brain. We find that R1 increases from newborns to 6-months-olds in all bundles. R1 development is nonuniform: there is faster development in white matter that is less mature in newborns, and along inferior-to-superior as well as anterior-to-posterior spatial gradients. As R1 is linearly related to myelin fraction in white matter bundles, these findings open new avenues to elucidate typical and atypical white matter myelination in early infancy, which has important implications for early identification of neurodevelopmental disorders.

category: neuroscience


title: White matter myelination during early infancy is explained by spatial gradients and myelin content at birth


title: Complex Computation from Developmental Priors

abstract: Artificial Intelligence (AI) research has provided key insights into the mechanics of learning complex tasks. However, AI models have long overlooked innateness: how strong pressures for survival lead to the encoding of complex behaviors in the nascent wiring of a brain. Although innate neural solutions have inspired AI approaches from layered architectures to ConvNets, the underlying neuroevolutionary search for novel heuristics has not been successfully systematized. In this manuscript, we examine how neurodevelopmental principles can inform the discovery of computational heuristics. We begin by considering the weight matrix of a neural network to be emergent from well-studied rules of neuronal compatibility. Rather than updating the networks weights directly, we improve task fitness by updating the neurons wiring rules, thereby mirroring evolutionary selection on brain development. We find that the resulting framework can not only achieve high performance on standard machine learning tasks, but does so with a fraction of the full networks parameters. When we condition neuronal identity on biologically-plausible spatial constraints, we discover representations that resemble visual filters and are capable of learning transfer. In summary, by introducing realistic developmental considerations into machine learning frameworks, we not only capture the emergence of innate behaviors, but also define a discovery process for structures that promote complex computations.


title: Tbx1, a 22q11.2-encoded gene, is a link between alterations in fimbria myelination and cognitive speed in mice

abstract:
Copy number variants (CNVs) have provided a reliable entry point to identify structural correlates of atypical cognitive development. Hemizygous deletion of human chromosome 22q11.2 is associated with impaired cognitive function; however, the mechanisms by which numerous genes encoded in this CNV contribute to cognitive deficits via diverse structural alterations in the brain remain unclear. This study aimed to determine the cellular basis of the link between alterations in brain structure and cognitive functions in a mouse model. The heterozygosity of Tbx1, a 22q11.2 gene, altered the composition of myelinated axons in the fimbria, reduced oligodendrocyte production capacity, and slowed the acquisition of spatial memory and cognitive flexibility. Our findings provide a cellular basis for specific cognitive dysfunctions that occur in patients with loss-of-function TBX1 variants and 22q11.2 hemizygous deletion.

TeaserA risk gene for autism alters myelin composition in the hippocampal connection and slows cognitive speed.


title: The 3D-atlas builder: a dynamic and expandable 3D-tool for monitoring the changes in the neuronal differentiation domain during hindbrain morphogenesis

abstract: Reconstruction of prototypic three-dimensional (3D) atlases at the scale of whole tissues or organs requires specific methods to be developed. We have established a digital 3D-atlas maker (DAMAKER) and built a digital 3D-temporal atlas to monitor the changes in the growth of the tissue and neuronal differentiation domain in the zebrafish hindbrain. DAMAKER integrates spatial and temporal data from cell populations, neuronal differentiation and brain morphogenesis, through in vivo imaging techniques paired with image analyses and segmentation tools. First, we generated a 3D-reference from several imaged hindbrains and segmented them using a trainable tool; these were aligned using rigid registration, revealing distribution of neuronal differentiation growth patterns along the axes. Second, we quantified the dynamic growth of the neuronal differentiation domain vs. the progenitor domain, and by in vivo neuronal birthdating experiments we generated a digital 3D-temporal map of the neuronal growth in the whole hindbrain, revealing the spatiotemporal dynamics of neuronal differentiation upon morphogenesis. Last, we applied it to glutamatergic and GABAergic neurons, as proof-of-concept that the digital 3D-temporal map could be used as a proxy to infer neuronal birthdate. As this protocol uses open-access tools and algorithms, it can be shared for standardized, accessible, tissue-wide cell population atlas construction.


title: The Digital 3D-Atlas MAKER (DAMAKER): a dynamic and expandable digital 3D-tool for monitoring the temporal changes in tissue growth during hindbrain morphogenesis


title: Identification of neural progenitor cells and their progeny reveals long distance migration in the developing octopus brain

abstract: Cephalopods have evolved nervous systems that parallel the complexity of mammalian brains in terms of neuronal numbers and richness in behavioral output. How the cephalopod brain develops has only been described at the morphological level, and it remains unclear where the progenitor cells are located and what molecular factors drive neurogenesis. Using histological techniques, we located dividing cells, neural progenitors and postmitotic neurons in Octopus vulgaris embryos. Our results indicate that progenitors are located outside the central brain cords in the lateral lips adjacent to the eyes, suggesting that newly formed neurons migrate into the cords. Lineage tracing experiments then showed that progenitors, depending on their location in the lateral lips, generate neurons for the different lobes. The finding that octopus newborn neurons migrate over long distances is reminiscent of vertebrate neurogenesis and suggests it might be a fundamental strategy for large brain development.


title: Oxytocin receptor activation does not mediate associative fear deficits in a Williams Syndrome model

abstract: Williams Syndrome is caused by a deletion of 26-28 genes on chromosome 7q11.23. Patients with this disorder have distinct behavioral phenotypes including learning deficits, anxiety, increased phobias, and hypersociability. Some studies also suggest elevated blood oxytocin and altered oxytocin receptor expression, and this oxytocin dysregulation is hypothesized to be involved in the underlying mechanisms driving a subset of these phenotypes. A  Complete Deletion mouse, modeling the hemizygous critical region deletion in Williams Syndrome, recapitulates many of the phenotypes present in humans. These Complete Deletion mice also exhibited impaired fear responses in the conditioned fear task. Here, we address whether oxytocin dysregulation is responsible for this impaired associative fear memory response. We show direct delivery of an oxytocin receptor antagonist to the central nervous system did not rescue the attenuated contextual or cued fear memory responses in Complete Deletion mice. Thus, increased oxytocin signaling is not acutely responsible for this phenotype. We also evaluated oxytocin receptor and serotonin transporter availability in regions related to fear learning, memory, and sociability using autoradiography in wild type and Complete Deletion mice. While we identified trends in lowered oxytocin receptor expression in the lateral septal nucleus, and trends towards lowered serotonin transporter availability in the striatum and orbitofrontal cortex, we found no significant differences after correction. Together, these data suggest the fear conditioning anomalies in the Williams Syndrome mouse model are independent of any alterations in the oxytocinergic system caused by deletion of the Williams locus.

category: animal behavior and cognition


title: Revisiting the role of Toxoplasma gondii ERK7 in the maintenance and stability of the apical complex

abstract:
Toxoplasma gondii ERK7 is known to contribute to the integrity of the apical complex and to be involved only in the final step of the conoid biogenesis. In the absence of ERK7, mature parasites lose their conoid complex and are unable to glide, invade or egress from host cells. In contrast to a previous report, we show here that depletion of ERK7 phenocopies the depletion of the apical cap proteins AC9 or AC10. The absence of ERK7 leads to the loss of the apical polar ring, the disorganization of the basket of subpellicular microtubules and an impairment in micronemes secretion. Ultra-expansion microscopy (U-ExM) coupled to NHS-Ester staining on intracellular parasites offers an unprecedented level of resolution and highlights the disorganization of the rhoptries as well as the dilated plasma membrane at the apical pole in the absence of ERK7. Comparative proteomics analysis of wild-type and ERK7 or AC9 depleted parasites led to the disappearance of known, predicted, as well as putative novel components of the apical complex. In contrast, the absence of ERK7 led to an accumulation of microneme proteins, resulting from the defect in exocytosis of the organelles.

ImportanceThe conoid is an enigmatic, dynamic organelle positioned at the apical tip of the coccidian subgroup of the Apicomplexa, close to the apical polar ring (APR) from which the subpellicular microtubules (SPTMs) emerge and at the site of microneme and rhoptry secretory organelles exocytosis. In Toxoplasma gondii, the conoid protrudes concomitantly to microneme secretion, during egress, motility and invasion. The conditional depletion of the apical cap structural protein AC9 or AC10 leads to a disorganization of SPTMs as well as the loss of APR and conoid that result in microneme secretion defect and block in motility, invasion and egress. We show here that depletion of the kinase ERK7 phenocopies completely AC9 and AC10 mutants. Moreover, the combination of ultrastructure expansion microscopy with an NHS ester staining revealed that ERK7 depleted parasites exhibit a dilated apical plasma membrane and a mis-positioning of the rhoptry organelles.


title: KinaFrag explores the kinase-ligand fragment interaction space for selective kinase inhibitor discovery

abstract:
Protein kinases play a crucial role in many cellular signaling processes, making them one of the most important families of drug targets. But selectivity put a barrier at the design of kinase inhibitors. Fragment-based drug design strategies have been successfully applied to develop novel selective kinase inhibitors. However, the complicate kinase-fragment interaction and fragment-to-lead process pose challenges to fragment-based kinase discovery. Here, we developed a web source KinaFrag to investigate kinase-fragment interaction space and perform fragment-to-lead optimization. KinaFrag contained 31464 fragments from reported kinase inhibitors, which involved 3244 crystal fragment structures and 7783 crystal kinase-fragment complexes. These crystal fragments were classified by their binding cleft and subpockets, and their 3D structure and interactions were displayed in KinaFrag. In addition, the structural information, physicochemical information, similarity information, and substructure relationship information were contained in KinaFrag. Moreover, a computational fragment growing strategy obviously developed by our group was implemented in the KinaFrag. We test this fragment growing strategy using our fragment libraries, and obtained a lead compound of c-Met with ~1000-fold in vitro activity improvement compared with the hit compound. We hope KinaFrag could become a powerful tool for the fragment-based kinase inhibitor design. KinaFrag is freely available at http://chemyang.ccnu.edu.cn/ccb/database/KinaFrag/.

Biographical noteZhi-Zheng Wang is a PhD student at College of Chemistry, Central China Normal University (CCNU), and the direction of his thesis is computational molecular simulation.

Xing-Xing Shi is PhD student at College of Chemistry, of CCNU, and the direction of her thesis is computational molecular simulation.

Fan Wang is a lecturer at College of Chemistry of CCNU. He received the PhD degree in Computational Chemistry from University of Amiens, France.

Ge-Fei Hao is Professor in Bioinformatics in College of Chemistry of CCNU. He received his PhD in Pesticide Science from CCNU.

Guang-Fu Yang is Professor in Chemical Biology. He is the group leader and has been the Dean at College of Chemistry of CCNU. He received the PhD degree in Pesticide Science from Nankai University, Tianjin, China.

category: bioinformatics


title: Biasing RNA coarse-grained folding simulations with Small--Angle X--ray Scattering (SAXS) data

abstract: RNA molecules can easily adopt alternative structures in response to different environmental conditions. As a result, a molecules energy landscape is rough and can exhibits a multitude of deep basins. In the absence of a high-resolution structure, Small Angle X-ray Scattering data (SAXS) can narrow down the conformational space available to the molecule and be used in conjunction with physical modeling to obtain high-resolution putative structures to be further tested by experiments. Because of the low-resolution of this data, it is natural to implement the integration of SAXS data into simulations using a coarse-grained representation of the molecule, allowing for much wider searches and faster evaluation of SAXS theoretical intensity curves than with atomistic models. We present here the theoretical framework and the implementation of a simulation approach based on our coarse-grained model HiRE-RNA combined with SAXS evaluations "on-the-fly" leading the simulation toward conformations agreeing with the scattering data, starting from partially folded structures as the ones that can easily be obtained from secondary structures predictions based tools. We show on three benchmark systems how our approach can successfully achieve high-resolution structures with remarkable similarity with the native structure recovering not only the overall shape, as imposed by SAXS data, but also the details of initially missing base pairs.

category: biophysics


title: Attentional dynamics of efficient codes

abstract: Top-down attention is hypothesized to dynamically allocate limited neural resources to task-relevant computations. According to this view, sensory neurons are driven not only by stimuli but also by feedback signals from higher brain areas that adapt the sensory code to the goals of the organism and its belief about the state of the environment. Here we formalize this view by optimizing a model of population coding in the visual cortex for maximally accurate perceptual inference at minimal activity cost. The resulting optimality predictions reproduce measured properties of attentional modulation in the visual system and generate novel hypotheses about the functional role of top-down feedback, response variability, and noise correlations. Our results suggest that a range of seemingly disparate attentional phenomena can be derived from a general theory combining probabilistic inference with efficient coding in a dynamic environment.


title: Fifty generations of amitosis: tracing asymmetric allele segregation in polyploid cells with single-cell DNA sequencing

abstract: Amitosis is a widespread form of unbalanced nuclear division whose biomedical and evolutionary significance remain unclear. Traditionally, insights into the genetics of amitosis are acquired by assessing the rate of phenotypic assortment. The phenotypic diversification of heterozygous clones during successive cell divisions reveals the random segregation of alleles to daughter nuclei. Though powerful, this experimental approach relies on the availability of phenotypic markers. Here, we present an approach that overcomes the requirement for phenotypic assortment. Leveraging Paramecium tetraurelia, a unicellular eukaryote with nuclear dimorphism and a highly polyploid somatic nucleus, we use single-cell whole-genome sequencing to track the assortment of developmentally acquired somatic DNA variants. Accounting for genome representation biases, we measure the effect of amitosis on allele segregation across the first [~]50 amitotic divisions post self-fertilization and compare our empirical findings with theoretical predictions estimated via mathematical modeling. In line with our simulations, we show that amitosis in P. tetraurelia produces measurable but modest levels of somatic assortment. In forgoing the requirement for phenotypic assortment and employing developmental, environmentally induced somatic variation as molecular markers, our work provides a new powerful approach to investigate the consequences of amitosis in polyploid cells.

category: genomics


title: Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis

abstract: Arbuscular mycorrhizal (AM) fungi form mutualistic relationships with most land plant species and have long been considered as ancient asexuals. Long-term clonal evolution would be remarkable for a eukaryotic lineage and suggests the importance of alternative mechanisms to promote genetic variability facilitating adaptation. Here, we assessed the potential of transposable elements (TEs) for generating genomic diversity. The dynamic expression of TEs during Rhizophagus irregularis spore development suggests ongoing TE activity. We find Mutator-like elements located near genes belonging to highly expanded gene families. Characterising the epigenomic status of R. irregularis provides evidence of DNA methylation and small RNA production occurring at TE loci. Our results support a potential role for TEs in shaping the genome, and roles for DNA methylation and small RNA-mediated silencing in regulating TEs. A well-controlled balance between TE activity and repression may therefore contribute to genome evolution in AM fungi.


title: Mass recalibration for desorption electrospray ionization mass spectrometry imaging using endogenous reference ions.

abstract:
1BackgroundMass spectrometry imaging (MSI) data often consist of tens of thousands of mass spectra collected from a sample surface. During the time necessary to perform a single acquisition, it is likely that uncontrollable factors alter the validity of the initial mass calibration of the instrument, resulting in mass errors of magnitude significantly larger than their expected values. This phenomenon has a two-fold detrimental effect: a) it reduces the ability to interpret the results based on the observed signals, b) it can affect the quality of the observed signal spatial distributions.

ResultsWe present a post-acquisition computational method capable of reducing the observed mass drift by up to 60 ppm in biological samples, exploiting the presence of typical molecules with a known mass-to-charge ratio. The procedure, tested on time-of-flight (TOF) and Orbitrap mass spectrometry analyzers interfaced to a desorption electrospray ionization (DESI) source, improves the molecular annotation quality and the spatial distributions of the detected ions.

ConclusionThe presented method represents a robust and accurate tool for performing post-acquisition mass recalibration of DESI-MSI datasets and can help to increase the reliability of the molecular assignment and the data quality.


title: Identification of candidate genes for self-compatibility in perennial ryegrass (Lolium perenne L.)

abstract:
Self-incompatibility (SI) is a genetic mechanism preventing self-pollination in approximately 40% of plant species. Two multiallelic loci, called S and Z, control the gametophytic SI system of the grass family (Poaceae), which contains all major forage grasses. Loci independent from S and Z have been reported to disrupt SI and lead to self-compatibility (SC). A locus causing SC in perennial ryegrass (Lolium perenne L.) was previously mapped on linkage group (LG) 5 in a F2 population segregating for SC. Using a subset of the same population (n=68), we first performed low-resolution quantitative trait locus (QTL) mapping to exclude the presence of additional, previously undetected contributors to SC. The previously reported QTL on LG 5 explained 38.4% of the phenotypic variation, and no significant contribution from other genomic regions was found. This was verified by the presence of significantly distorted markers in the region overlapping with the QTL. Second, we fine mapped the QTL to 0.26 cM using additional 2,056 plants and 23 novel sequence-based markers. Using an Italian ryegrass (Lolium multiflorum Lam.) genome assembly as reference, the markers flanking SC were estimated to span a ~3 Mb region encoding for 57 predicted genes. Among these, seven genes were proposed as relevant candidate genes based on their annotation and function described in previous studies. Our work is a step forward to identify SC genes in forage grasses and provides diagnostic markers for marker-assisted introgression of SC into elite germplasm.

Key messageA previously reported QTL conferring self-compatibility to perennial ryegrass was fine mapped to a 0.26 cM locus, corresponding to an estimated ~ 3 Mb physical region containing 57 predicted protein-encoding genes.


title: Shared and unique properties of place cells in anterior cingulate cortex and hippocampus

abstract: In the brain, spatial information is represented by neurons that fire when an animal is at specific locations, including place cells in hippocampus and grid cells in entorhinal cortex. But how this information is processed in downstream brain regions still remains elusive. Using chronic Ca2+ imaging, we examined the activity of neurons in anterior cingulate cortex (ACC), a brain region implicated in memory consolidation, and found neurons that fire in a manner consistent with the properties of place cells. While the ACC place cells showed stability, location and context specificity similar to the hippocampal counterparts, they also have unique properties. Unlike hippocampal place cells that immediately formed upon exposure to a novel environment, ACC place cells increased over days. Also, ACC place cells tend to have additional place fields whereas typical hippocampal place cells have only one. Hippocampal activity is required for the formation of ACC place cells, but once they are established, hippocampal inactivation did not have any impact on ACC place cell firing. We thus identified features of ACC place cells that carry spatial information in a unique fashion.


title: Lysophophatidyl-choline 16:0 mediates persistent joint pain through Acid-Sensing Ion Channel 3: preclinical and clinical evidences

abstract: Rheumatic diseases are often associated to debilitating chronic joint pain, which remains difficult to treat and requires new therapeutic strategies. Here, we describe increased content of lysophosphatidyl-choline (LPC) 16:0 in the knee synovial fluids of two independent cohorts of patients with painful joint diseases. If LPC16:0 levels correlated with pain in patients with osteoarthritis (OA), they do not appear to be the hallmark of a particular joint disease. We found that intra-articular injections of LPC16:0 in mouse produce chronic pain and anxiety-like behaviors in both males and females with no apparent inflammation, peripheral nerve sprouting and damage, nor bone alterations. LPC16:0-induced persistent pain state is dependent on peripheral Acid-Sensing Ion Channel 3 (ASIC3), ultimately leading to central sensitization. LPC16:0 and ASIC3 thus appear as key players of chronic joint pain with potential implications in OA and possibly across others rheumatic diseases.


title: Lysophosphatidyl-choline 16:0 mediates persistent joint pain through Acid-Sensing Ion Channel 3: preclinical and clinical evidences


title: PD-1 expression on NK cells can be related to cytokine stimulation and tissue residency

abstract: Although PD-1 was shown to be a hallmark of T cells exhaustion, controversial studies have been reported on the role of PD-1 on NK cells. Here, we found by flow cytometry and single cell RNA sequencing analysis that PD-1 can be expressed on MHC class I-deficient tumor-infiltrating NK cells in vivo. We also demonstrate distinct alterations in the phenotype of PD-1-deficient NK cells which in part could be attributed to a decrease in tumor-infiltrating NK cells in PD-1-deficient mice. NK cells from PD-1-deficient mice exhibited a more mature phenotype which might reduce their capacity to migrate and kill in vivo. Finally, our results demonstrate that PD-L1 molecules in membranes of PD-1-deficient NK cells migrate faster than in NK cells from wildtype mice, suggesting that PD-1 and PD-L1 form cis interactions with each other on NK cells.


title: Innate immune signaling in trophoblast and decidua organoids defines differential antiviral defenses at the maternal-fetal interface

abstract: Infections at the maternal-fetal interface can directly harm the fetus and induce complications that adversely impact pregnancy outcomes. Innate immune signaling by both fetal-derived placental trophoblasts and the maternal decidua must provide antimicrobial defenses at this critical interface without compromising its integrity. Here, we developed matched trophoblast and decidua organoids from human placentas to define the relative contributions of these cells to antiviral defenses at the maternal-fetal interface. We demonstrate that trophoblast and decidua organoids basally secrete distinct immunomodulatory factors, including the constitutive release of the antiviral type III interferon IFN- {lambda}2 from trophoblast organoids, and differentially respond to viral infections through the induction of organoid-specific factors. Lastly, we define the differential susceptibility of trophoblast and decidua organoids to human cytomegalovirus (HCMV) and the transcriptional and immunological responses of these organoids to HCMV infection. Our findings establish matched trophoblast and decidua organoids as ex vivo models to study vertically transmitted infections and highlight differences in innate immune signaling by fetal-derived trophoblasts and the maternal decidua.


title: Single-cell analysis of the human pancreas in type 2 diabetes using multi-spectral imaging mass cytometry

abstract: Type 2 diabetes mellitus (T2D) is a chronic age-related disorder characterized by hyperglycemia due to the failure of pancreatic beta cells to compensate for increased insulin demand, typically associated with peripheral insulin resistance. However, despite decades of research, the pathogenic mechanisms underlying T2D remain poorly defined. Imaging mass cytometry (IMC) enables multiplexed assessment of the abundance and subcellular localization of multiple proteins on the same tissue section. Herein, we utilized IMC with a panel of 34 antibodies to quantify key markers of pancreatic exocrine, islet, and immune cells as well as stromal components. We employed this panel to analyze over 2.1 million cells from 16 pancreata obtained from donors with T2D and 13 pancreata from age similar non-diabetic controls. In the T2D pancreata, we observed significant alterations in islet architecture, endocrine cell composition, and surprisingly immune cell constituents. Thus, both HLA-DR positive CD8 T cells and macrophages were enriched intra-islet in the T2D pancreas. These efforts demonstrate the utility of IMC to investigate complex events at the cellular level in order to provide new insights into the pathophysiology of T2D.


title: Fast ontogenetic growth drives steep evolutionary scaling of metabolic rate

abstract: Metabolic rate (MR) changes with body mass (BM) as MR = aBMb, where a is a normalisation constant (log-log intercept) and b the scaling exponent (log-log slope). This scaling relationship is fundamental to biology and widely applied, yet a century of research has provided little consensus on why and how steeply metabolic rate scales with body mass. I here show that ontogenetic (within-individual) b can be strongly and positively related to growth rates of juvenile fish when food availability is naturally restricted, with fast growing individuals having steep and near-isometric metabolic scaling (b {approx} 1). I suggest that the steep evolutionary (among-species) scaling also found for fishes (b also approaching 1) is a by-product of natural selection for these fast growing individuals early in ontogeny, and that a weaker relationship between metabolic scaling and growth later in life causes variation in b at lower taxonomic levels (within orders or species). I support these ideas by showing that b within fish orders is linked to natural mortality rates of fish larvae.


title: Interactions, information and emergence: Exploring task allocation in ant colonies using network analysis

abstract:
In animal societies, individuals may take on different roles to fulfil their own needs and the needs of their groups. Ant colonies display high levels of organisational complexity, with ants fulfilling different roles at different timescales (what is known as task allocation). Factors affecting task allocation can be at the individual level (e.g., physiology), or at the group level (e.g., the network of interactions). We focus on group level processes by exploring the relationship between interaction networks, task allocation and task switching using a previously published dataset (Mersch et al., 2013) tracking the behaviour of six Camponotus fellah colonies over 41 days. In our new analyses, our goal was to better explain the noisy process of task switching beyond simple age polyethism. First, we investigated the architecture of interaction networks using node (individual) level network measures and their relation to the individuals task - foraging, cleaning or nursing - and whether or not the ant switched tasks. We then explored how noisy information propagation was among ants, as a function of the colony composition (how many ants carried out which tasks), through the information-theoretic metric of Effective Information. Our results show that interaction history was tied to task allocation: ants who switched to a task are more likely to have interacted with other ants carrying out that task. The degree to which interactions related to task allocation, as well as the noise in those interactions, depended on which groups of ants were interacting. Overall, we showed that colony cohesion was stable even as ant-level network measures varied more for ants when they switched functional groups; thus, ant colonies maintained a high level of information flow as determined by network analysis, and ant functional groups played different roles in maintaining colony cohesion through varied information flows.

HighlightsO_LIWe analysed the interaction networks of six Camponotus fellah colonies
C_LIO_LIWe tested how centrality and information flow were tied to task switching
C_LIO_LINode-level network metrics and the information theoretic measure of Effective Information explained differences among functional groups
C_LIO_LIInteractions were correlated with task switching, but the strength of the correlation differed across functional groups
C_LI


title: Interactions and information: Exploring task allocation in ant colonies using network analysis


title: Don't Stress, It's Under Control: Neural Correlates of Stressor Controllability in Humans

abstract: Animal research has repeatedly shown that experience of control over an aversive event can protect against the negative consequences of later uncontrollable stress. Neurobiologically, this effect is assumed to correspond to persistent changes in the pathway linking the ventromedial prefrontal cortex (vmPFC) and the dorsal raphe nucleus. However, it remains unclear to what extent these findings translate to humans. During functional magnetic resonance imaging, we subjected participants to controllable and uncontrollable aversive but non-painful electric stimuli, as well as to a control condition without aversive stimulation. In each trial, a symbol signalled whether participants could terminate the stressor through correct performance in a button-matching task or whether the stressor would be randomly terminated, i.e., uncontrollable. Along with neural responses, we assessed participants accuracy, reaction times, and heart rate. To relate neural activations and subjective experience, we asked participants to rate perceived control, helplessness, and stress. Results were largely in line with our hypotheses. The vmPFC was generally deactivated by stress, but this effect was attenuated when participants could terminate the stressor compared to when their responses had no effect. Furthermore, activation in stress-responsive regions, including the bilateral insula, was reduced during controllable trials. Under uncontrollable stress, greater vmPFC recruitment was linked to reduced feelings of helplessness. An investigation of condition-dependent differences in vmPFC connectivity yielded no significant results. Our findings further corroborate animal research and emphasise the role of the vmPFC in controllability-dependent regulation of stress responses. Based on the results, we discuss future directions in the context of resilience research and mental health promotion.


title: Astrocytes are implicated in BDNF-mediated enhancement of hippocampal long-term potentiation

abstract: It is known that astrocytes, by the Ca2+-dependent release of gliotransmitters, which then act in pre- and post-synaptic receptors, modulate neuronal transmission and plasticity. Thus, hippocampal {theta}-burst long-term potentiation (LTP), which is a form of synaptic plasticity, can be modulated by astrocytes, since these cells release gliotransmitters that are crucial for the maintenance of LTP. Therefore, in this study, we hypothesized that the facilitatory action of BDNF upon LTP would involve astrocytes. To address that possibility, fEPSP recordings were performed in CA3-CA1 area of hippocampal slices from three different experimental models: Wistar rats where astrocytic metabolism was selectively reduced by a gliotoxin, the DL-fluoricitric acid (FC), IP3R2-/- mice, which lack IP3R2-mediated Ca2+-signaling in astrocytes and dn-SNARE transgenic mice, in which the SNARE-dependent release of gliotransmittersis impaired. For the three models we observed that the astrocytic impairment abolished the excitatory BDNF effect upon hippocampal LTP, only while inducing LTP with a mild {theta}-burst stimulation paradigm. The present data shows for the first time that astrocytes play an active role in the facilitatory action of BDNF upon LTP, depending on stimulation paradigm.


title: Human brain organoids assemble functionally integrated bilateral optic vesicles

abstract: During embryogenesis, optic vesicles develop from the diencephalon via a complex process of organogenesis. Using iPSC-derived human brain organoids, we attempted to simplify the complexities and demonstrate the formation of forebrain-associated bilateral optic vesicles, cellular diversity, and functionality. Around day thirty, brain organoids could assemble optic vesicles, which progressively develop as visible structures within sixty days. These optic vesicle-containing brain organoids (OVB-Organoids) constitute a developing optic vesicles cellular components, including the primitive cornea and lens-like cells, developing photoreceptors, retinal pigment epithelia, axon-like projections, and electrically active neuronal networks. Besides, OVB-Organoids also display synapsin-1, CTIP-positive, myelinated cortical neurons, and microglia. Interestingly, various light intensities could trigger photoreceptor activity of OVB-Organoids, and light sensitivities could be reset after a transient photo bleach blinding. Thus, brain organoids have the intrinsic ability to self-organize forebrain-associated primitive sensory structures in a topographically restricted manner and can allow conducting interorgan interaction studies within a single organoid.


title: Modeling pulsed evolution and time-independent variation improves the confidence level of ancestral and hidden state predictions in continuous traits

abstract: Ancestral state reconstruction is a fundamental tool for studying trait evolution. It is also very useful for predicting the unknown trait values (hidden states) of extant species. A well-known problem in ancestral and hidden state predictions is that the uncertainty associated with predictions can be so large that predictions themselves are of little use. Therefore, for meaningful interpretation of predicted traits and hypothesis testing, it is prudent to accurately assess the uncertainty of the predictions. Commonly used Brownian motion (BM) model fails to capture the complexity of tempo and mode of trait evolution in nature, making predictions under the BM model vulnerable to lack-of-fit errors from model misspecification. Using simulations and empirical data (bacterial genomic traits and vertebrate body size), we show that the presence of pulsed evolution and time-independent variation significantly undermines the confidence level of continuous traits predicted under the BM model. The residual Z-scores are neither homoscedastic nor normally distributed. Consequently, the 95% confidence intervals of predicted traits are so unreliable that the actual coverage probability ranges from 29% (strongly permissive) to 100% (strongly conservative). To remedy the model misspecification problem, we develop RasperGade that accounts for both pulsed evolution and time-independent variation. When applied to simulated and empirical data, RasperGade outperforms commonly used tools such as ape. It restores the normality and homoscedasticity of the Z-score distributions. Accordingly, RasperGade greatly improves the reliability of confidence intervals of predictions and reduces the deviation of their actual coverage probabilities from the 95% expectation by as much as 99%.

category: evolutionary biology


title: Decomposing virulence to understand bacterial clearance in persistent infections

abstract:
Hosts are not always successful at controlling and eliminating a pathogen and the factors causing variation in pathogen clearance are not well understood. To address this problem, we used Drosophila melanogaster to investigate how infections with different bacterial pathogens affects virulence, clearance and persistence. In this context we developed novel hypotheses that focus on how variation in clearance should be related to variation in different components of virulence, where virulence is the infection-related reduction in host fitness. To achieve this, virulence was decomposed into exploitation, i.e., how well bacteria can replicate inside the host, and per parasite pathogenicity (PPP), i.e., the amount of damage per parasite inflicted on the host. We used four bacterial species: Enterobacter cloacae, Providencia burhodogranariea, Lactococcus lactis and Pseudomonas entomophila. The injection doses spanned four orders of magnitude, and survival was followed to estimate virulence. Bacterial load was quantified in live flies during the acute (1-4 days) and chronic (7-35 days) phases of infection, and we tested infection status of flies that had died up to ten weeks post infection. We show that sustained persistent infection and clearance are both possible outcomes for bacterial species across a range of virulence. Bacteria of all species could persist inside the host for at least 75 days, and injection dose partly predicted within-species variation in clearance. Our decomposition of virulence showed that species differences in bacterial virulence could be explained by a combination of variation in both exploitation and PPP. In addition, we found that that higher exploitation leads to lower bacterial clearance, whereas we could not detect any effect of PPP on clearance. The differing effects of exploitation and PPP imply that there can be different means by which variation in virulence is related to clearance, which could critically affect pathogen transmission and the evolution of pathogen virulence.

Author summaryFollowing an infection, hosts are not always able to quickly clear the pathogen, and they instead either die or survive with a persistent infection. Such variation is ecologically and evolutionarily important, because it can affect infection prevalence and transmission, and also virulence evolution. But what causes variation in infection outcomes? Here we contribute towards answering this question by investigating infection dynamics in flies infected with one of four bacterial species. We first establish that the bacterial species differ in virulence, i.e., the host death rate after infection. We find that variation in virulence arises because the bacteria differ in the two components of virulence: bacterial growth inside the host (exploitation), and the amount of damage caused per bacterium (per parasite pathogenicity).

Furthermore, as early-phase exploitation increases, bacterial clearance later in the infection decreases. This finding can be explained by increasing exploitation leading to increasing clearance costs for the host. Taken together we demonstrate that variation in infection outcomes can be partly explained by how virulence, and its components, relate to the rate of pathogen clearance. We propose that the decomposition of virulence is valuable for understanding variation in infection outcomes - potentially also beyond the interrelation between virulence and clearance.


title: lassosum2: an updated version complementing LDpred2

abstract: Publicly available genome-wide association studies (GWAS) summary statistics exhibit uneven quality, which can impact the validity of follow-up analyses. First, we present an overview of possible misspecifications that come with GWAS summary statistics. Then, in both simulations and real data analyses, we show that additional information such as imputation INFO scores, allele frequencies, and per-variant sample sizes in GWAS summary statistics can be used to detect possible issues and correct for misspecifications in the GWAS summary statistics. One important motivation for us is to improve the predictive performance of polygenic scores built from these summary statistics. Unfortunately, due to the lack of reporting standards for GWAS summary statistics, this additional information is not systematically reported. We also show that using well-matched LD references can improve model fit and translate into more accurate prediction. Finally, we discuss how to make polygenic score methods such as lassosum and LDpred2 more robust to these misspecifications to improve their predictive power.

category: genetics


title: Identifying and correcting multiple sources of misspecification in GWAS summary statistics for polygenic scores


title: Identifying and correcting for misspecifications in GWAS summary statistics and polygenic scores


title: Context-dependent transcriptional regulation of microglial proliferation

abstract: Microglia proliferation occurs during brain development and brain lesions, but how this is coordinated at the transcriptional level is not well understood. Here, we investigated transcriptional mechanisms underlying proliferation of mouse microglia during postnatal development and in adults in models of induced microglial depletion-repopulation and brain demyelination. While each proliferative subset displayed globally a distinct signature of gene expression, they also co-expressed a subgroup of 1,370 genes at higher levels than quiescent microglia. Furthermore, expression of these may be coordinated by one of two modes of regulation. A first mode augments expression of genes already expressed in quiescent microglia and is subject to regulation by Klf/Sp, Nfy, and Ets transcription factors. Alternatively, a second mode enables de novo transcription of cell cycle genes and requires additional regulatory input from Lin54 and E2f factors. Overall, proliferating microglia integrate regulation of cell cycle gene expression with their broader, context-dependent, transcriptional landscape.


title: NRF1 Association with AUTS2-Polycomb Mediates Specific Gene Activation in the Brain

abstract: The heterogeneous complexes comprising the family of Polycomb Repressive Complex 1 (PRC1) are instrumental to establishing facultative heterochromatin that is repressive to transcription. Yet, two PRC1 species, PRC1.3 and PRC1.5, are known to comprise novel components, AUTS2, P300, and CK2 that convert this repressive function to that of transcription activation. Here, we report that patients harboring mutations in the HX repeat domain of AUTS2 exhibit defects in AUTS2 and P300 interaction as well as a developmental disorder reflective of Rubinstein-Taybi syndrome, which is mostly associated with a heterozygous pathogenic variant in CREBBP/EP300. As well, the absence of AUTS2 gives rise to a mis-regulation of a subset of developmental genes and curtails motor neuron differentiation from embryonic stem cells in the context of a well-defined system. Moreover, the transcription factor, Nuclear Respiratory Factor 1 (NRF1) exhibits a novel and integral role in this aspect of the neurodevelopmental process, being required for PRC1.3 recruitment to chromatin.


title: ID-Seg: An Accurate and Reliable Infant Deep learning Segmentation Framework for Limbic Structures

abstract: Early postnatal period brain magnetic resonance imaging (MRI) is becoming an important approach to measure the impact of prenatal exposures on neurodevelopment and to investigate early biomarkers for risk. Among brain structures, Limbic structures are particular of interest in psychiatric disorder-related research. However, despite the promise of infant neuroimaging and the success of initial infant MRI studies, assessing limbic regions structure and function remains a significant challenge due to low inter-regional intensity contrast and high curvature (e.g., hippocampus). In addition, the agreement between existing automatic techniques and manual segmentation remains either untested or insufficient, particularly for the amygdala and hippocampus. In this work, we developed an accurate (based on three segmentation evaluation metrics), reliable and efficient infant deep learning segmentation framework (ID-Seg) to address the aforementioned challenges. Specifically, we leveraged a large dataset of 473 infant MRI scans to train ID-Seg and rigorously evaluated ID-Segs performance on internal and external datasets with manual segmentations. Compared with a state-of-the-art segmentation pipeline, we demonstrated that ID-Seg significantly improved the segmentation accuracy of limbic structures (hippocampus and amygdala) in newborn infants. Moreover, in a medium-size dataset, we found that ID-Seg-derived morphometric measures yield strong brain-behavior associations. As such, our ID-Seg may improve our capacity and efficiency to measure MRI-based brain features relevant to neuropsychological development and ultimately advance the success of quantitative analyses on large-scale datasets.

category: bioengineering


title: Mechanically Activated Extracellular Vesicle Functionalised Melt Electrowritten Materials for Bone Regeneration: A Mechano-Biomimetic Scaffold

abstract: 1Mechanobiological cues arising directly via tissue/scaffold mechanics or indirectly via mechanically activated cell secretomes represent potent stimuli that mediate cell behaviour and tissue adaptation. Exploiting these cues in regeneration strategies holds great promise for tissue repair. In this study, we harness indirect biophysical cues originating from osteocytes in a combination with direct biophysical cues from Melt ElectroWritten (MEW) scaffolds to form a single engineered construct with the aim of synergistically enhancing osteogenesis. The secretome of mechanically activated osteocytes was collected within conditioned media (CM) and extracellular vesicles (EV) were subsequently isolated. Building on MEW micro-fibrous scaffolds with controlled microarchitecture and mineral nanotopography optimised for bone repair, a protocol was developed to functionalise these materials with CM or EVs. Human MSC proliferation was enhanced in both CM and EV functionalised scaffolds. EV functionalised scaffolds were further found to significantly enhance MSC osteogenesis, with enhanced alkaline phosphatase expression, collagen production, and mineralisation compared to control scaffolds. Furthermore, enhanced formation of mineralised nodules was identified in EV functionalised materials. Combining direct biophysical cues provided by the fibrous architecture/mineral nanotopography with the indirect cues provided by EVs, these constructs hold great promise to enhance the repair of damaged bone in a physiologically relevant manner.


title: An interpretable meta-clustering framework for single-cell RNA-Seq data integration and evaluation

abstract: Single-cell RNA sequencing (scRNA-Seq) datasets that are produced from clinical samples are often confounded by batch effects and inter-patient variability. Existing batch effect removal methods typically require strong assumptions on the composition of cell populations being near identical across patients. Here we present a novel meta-clustering workflow, CIDER, based on inter-group similarity measures. We demonstrate that CIDER outperforms other scRNA-Seq clustering methods and integration approaches in both simulated and real datasets. Moreover, we show that CIDER can be used to assess the biological correctness of integration in real datasets, while it does not require the existence of prior cellular annotations.


title: Sexual maturation in Atlantic salmon male parr may be triggered both in early spring and late summer under standard farming conditions

abstract: Male Atlantic salmon (Salmo salar) display different sexual strategies, maturing either as parr during the freshwater phase (as sneaky spawners), or as post smolts following one or several years at sea. First sexual maturation (puberty) occurs at different times depending on environmental and genetic factors. To improve our knowledge on the timing (age and season) of first sexual maturation in Atlantic salmon male parr, we investigated pubertal activation in second generation farmed salmon from the Norwegian river Figgjo, reared under natural conditions of photoperiod and water temperature. Histological analysis, in combination with morphometric measurements, plasma androgen levels and pituitary gonadotropin gene expression analysis revealed that, as previously reported, some male parr initiated early sexual maturation in spring at one year of age. Interestingly, some male parr were observed to initiate sexual maturation already in autumn, six months after hatching (under-yearlings), much earlier than reported in previous studies. One-year old maturing males showed a low induction in gonadotropin levels, while under-yearling maturing males displayed a significant increase in fshb transcripts as compared to immature fish. Plasma testosterone, detectable also in immature males, increased constantly during testes development, while 11-ketotestosterone, undetectable in immature and early maturing males, increased during more advanced stages of maturation. A mild feminization of the testes (ovotestes) was detected in a subset of samples. This study brings new knowledge on the little investigated field of sexually maturing under-yearlings in Atlantic salmon. This is also the first study comparing the physiology of under-yearling vs one-year old maturing male parr, thus bringing new insights to the remarkable plasticity of Atlantic salmon puberty.

category: physiology


title: Type 2 innate immunity regulates hair follicle homeostasis to control Demodex pathosymbionts

abstract:
Allergic skin diseases are common, but basal roles for type 2 immunity in cutaneous homeostasis are incompletely understood. Here, we show that skin group 2 innate lymphoid cells (ILC2s) are the predominant resident cells that secretes IL-13, which attenuates epithelial cell proliferation during anagen throughout the hair follicle (HF), including in HF stem cells. Although HF are normal in the absence of type 2 immunity, colonization with the commensal mite, Demodex musculi, results in epithelial proliferation and aberrant hair follicle morphology accompanied by loss of stable commensalism with massive infestation and expansion of inflammatory ILC2s and other immune cells. Topical anti-parasitic agents, but not broad-spectrum antibiotics, reversed the phenotype. Commensal Demodex colonization of mammalian hair follicles is ubiquitous, including in humans, revealing an unanticipated role for ILC2s and type 2 immunity for skin homeostasis in the normal environment.

One Sentence SummaryDynamic regulation of skin physiology by Type 2 innate immunity regulates healthy commensalism by parasitic Demodex mites.


title: Dietary cardenolides enhance growth and change the direction of the fecundity-longevity trade-off in milkweed bugs (Heteroptera: Lygaeinae)

abstract:
O_LISequestration, i.e., the accumulation of plant toxins into body tissues for defence, is primarily observed in specialised insects. Sequestration was frequently predicted to incur a physiological cost mediated by increased exposure to plant toxins and may require resistance traits different from those of non-sequestering insects. Alternatively, sequestering species could experience a cost in the absence of toxins due to selection on physiological homeostasis under permanent exposure of sequestered toxins in body tissues.
C_LIO_LIMilkweed bugs (Heteroptera: Lygaeinae) sequester high amounts of plant-derived cardenolides. Although being potent inhibitors of the ubiquitous animal enzyme Na+/K+-ATPase, milkweed bugs can tolerate cardenolides by means of resistant Na+/K+-ATPases. Both adaptations, resistance and sequestration, are ancestral traits shared by most species of the Lygaeinae.
C_LIO_LIUsing four milkweed bug species and the related European firebug (Pyrrhocoris apterus) showing different combinations of the traits  cardenolide resistance and  cardenolide sequestration, we set out to test how the two traits affect larval growth upon exposure to dietary cardenolides in an artificial diet system. While cardenolides impaired the growth of P. apterus nymphs neither possessing a resistant Na+/K+-ATPase nor sequestering cardenolides, growth was not affected in the non-sequestering milkweed bug Arocatus longiceps, which possesses a resistant Na+/K+-ATPase. Remarkably, cardenolides increased growth in the sequestering dietary specialists Caenocoris nerii and Oncopeltus fasciatus but not in the sequestering dietary generalist Spilostethus pandurus, which all possess a resistant Na+/K+-ATPase.
C_LIO_LIWe then assessed the effect of dietary cardenolides on additional life history parameters, including developmental speed, the longevity of adults, and reproductive success in O. fasciatus. Remarkably, nymphs under cardenolide exposure developed substantially faster and lived longer as adults. However, fecundity of adults was reduced when maintained on cardenolide-containing diet for their entire life-time but not when adults were transferred to non-toxic sunflower seeds.
C_LIO_LIWe speculate that the resistant Na+/K+-ATPase of milkweed bugs is selected for working optimally in a  toxic environment, i.e. when sequestered cardenolides are stored in the body tissues. Contrary to the assumption that toxins sequestered for defence produce a physiological burden, our data suggest that they can even increase fitness in specialised insects.
C_LI

category: ecology


title: Conjugative plasmid transfer is limited by prophages but can be overcome by high conjugation rates

abstract: Antibiotic resistance spread via plasmids is a serious threat to successfully fight infections and makes understanding plasmid transfer in nature crucial to prevent the rise of antibiotic resistance. Studies addressing the dynamics of plasmid conjugation have yet neglected one omnipresent factor: prophages (viruses integrated into bacterial genomes), whose activation can kill host and surrounding bacterial cells. To investigate the impact of prophages on conjugation, we combined experiments and mathematical modelling. Using E. coli, prophage{lambda} and the multidrug-resistant plasmid RP4 we find that prophages can substantially limit the spread of conjugative plasmids. This inhibitory effect was strongly dependent on environmental conditions and bacterial genetic background. Our empirically parameterized model reproduced experimental dynamics of cells acquiring either the prophage or the plasmid well but could only reproduce the number of cells acquiring both elements by assuming complex interactions between conjugative plasmids and prophages in sequential infections. Varying phage and plasmid infection parameters over empirically realistic ranges revealed that plasmids can overcome the negative impact of prophages through high conjugation rates. Overall, the presence of prophages introduces an additional death rate for plasmid carriers, the magnitude of which is determined in non-trivial ways by the environment, the phage and the plasmid.


title: A T-cell independent universal cellular therapy strategy through antigen depletion

abstract: CD19-targeting chimeric antigen receptor (CAR) T-cell therapeutics is a revolutionary, novel and successful treatment for B-cell malignancies. However, while CD19-CAR-T therapy can obtain high rates of complete responses in these patients, a significant fraction of patients may experience CD19-negative relapse. Moreover, the dependency on T-cell mediated cytotoxicity restricts CAR-T therapy as a patient-specific individualized therapy with severe side effects such as cytokine-release syndrome (CRS). Whether CAR-T therapy can be substituted by a non-T-cell based universal cellular therapy is largely unknown. Surprisingly, we have demonstrated here that T-lymphocytic cells, as well as non-lymphocytic cells, can cause CD19 internalization and subsequent depletion when they are armed with a CD19-recognizing moiety. This CD19 antigen depletion can efficiently induce T-cell independent apoptosis in target cancer cells whose survival is dependent upon CD19 expression, suggesting that CD19 antigen depletion constitutes a crucial tumor destroying mechanism for CD19-CAR-T, especially for its long-term efficacy. We therefore proposed a universal strategy for CRS-free cellular therapeutics, utilizing artificial antigen-recognizing cells (AARC), which can be manufactured universally and standardly as "off-the-shelf" mesenchymal stromal cells (MSCs) or other types of non-autologous cell expressing anergic CARs. Our results not only uncovered an unrecognized mechanism for CAR-T cytotoxicity and antigen loss, but also shed new insight into a shift in cellular therapeutics from unique patient-specific autologous therapeutics, to universal and standardized allogeneic treatment.

category: cancer biology


title: Reproducible Coactivation Patterns of Functional Brain Networks Reveal the Aberrant Dynamic State Transition in Schizophrenia

abstract:
It is well documented that massive dynamic information is contained in the resting-state fMRI. Recent studies have identified recurring states dominated by similar coactivation patterns (CAP) and revealed their temporal dynamics. However, the reproducibility and generalizability of the CAP analysis is unclear. To address this question, the effects of methodological pipelines on CAP are comprehensively evaluated in this study, including preprocessing, network construction, cluster number and three independent cohorts. The CAP state dynamics are characterized by fraction of time, persistence, counts, and transition probability. Results demonstrate six reliable CAP states and their dynamic characteristics are also reproducible. The state transition probability is found to be positively associated with the spatial similarity. Furthermore, the aberrant CAP in schizophrenia has been investigated by using the reproducible method on three cohorts. Schizophrenia patients spend less time in CAP states that involve the fronto-parietal network, but more time in CAP states that involve the default mode and salience network. The aberrant dynamic characteristics of CAP are correlated with the symptom severity. These results reveal the reproducibility and generalizability of the CAP analysis, which can provide novel insights into the neuropathological mechanism associated with aberrant brain network dynamics of schizophrenia.

HighlightsO_LIThree coactivation patterns (CAPs) pairs with opposite coactivation profiles were identified, and the between-state transition probability was positively correlated with their spatial similarity.
C_LIO_LIGood spatial and temporal reproducibility and generalizability of CAPs were achieved under varied analytic methods and independent cohorts.
C_LIO_LISchizophrenia patients showed altered temporal dynamics not only within the triple-network but also other primary and higher-order networks.
C_LI


title: The C. elegans PTCHD homolog PTR-4 is required for proper organization of the pre-cuticular apical extracellular matrix

abstract: The Patched-related (PTR) superfamily of transmembrane proteins can transport lipids or other hydrophobic molecules across cell membranes. While the hedgehog receptor Patched has been intensively studied, much less is known about the biological roles of other PTR or Patched domain (PTCHD) family members. C. elegans has a large number of PTR/PTCHD proteins, despite lacking a canonical hedgehog pathway. Here, we show that PTR-4 promotes the assembly of the pre-cuticle apical extracellular matrix (aECM), a transient and molecularly distinct aECM that precedes and patterns the later collagenous cuticle or exoskeleton. ptr-4 mutants share many phenotypes with pre-cuticle mutants, including defects in eggshell dissolution, tube shaping, alae (cuticle ridge) structure, and cuticle barrier function. PTR-4 localizes to the apical side of a subset of outward-facing epithelia, in a cyclical manner that peaks when pre-cuticle matrix is present. Finally, PTR-4 acts in a cell non-autonomous manner to properly localize the secreted ZP domain protein LET-653 to the pre-cuticle aECM. We propose that PTR-4 exports lipids or other hydrophobic components of the pre-cuticle aECM.


title: Epigenetic models predict age and aging in plains zebras and other equids

abstract: Five of the seven extant wild species of the genus Equus are species of significant conservation concern. Effective conservation and management of such threatened wildlife populations depends on the ability to estimate demographic trends and population viability and therefore requires accurate assessment of age structure. However, reliably aging wildlife is challenging as many methods are highly invasive, inaccurate, or both. Epigenetic aging models, which estimate individual age with high accuracy based on genomic methylation patterns, are promising developments in this regard. Importantly, epigenetic aging models developed for one species can potentially predict age with high accuracy in sister taxa. Using blood and biopsy samples from known age plains zebras (Equus quagga), we developed epigenetic clocks (ECs) to predict chronological age, and epigenetic pacemaker (EPM) models to predict biological age. We tested the ability of our blood-based EC to predict ages of Grevys zebras, Somali asses and domestic horses, from blood samples. Because our samples came from a population with a complex pedigree, we also leveraged information from a previous sequencing effort to measure the association between levels of inbreeding (F and ROH) and the age acceleration as measured by DNA methylation. The resulting models describe the trajectory of epigenetic aging in plains zebras and accurately predict the ages of plains zebras and other equids. We found moderate support for a slight acceleration of aging with increased inbreeding.


title: Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome

abstract: Pseudogenes are gene copies presumed to mainly be functionless relics of evolution due to acquired deleterious mutations or transcriptional silencing. When transcribed, pseudogenes may encode proteins or enact RNA-intrinsic regulatory mechanisms. However, the extent, characteristics and functional relevance of the human pseudogene transcriptome are unclear. Short-read sequencing platforms have limited power to resolve and accurately quantify pseudogene transcripts owing to the high sequence similarity of pseudogenes and their parent genes. Using deep full-length PacBio cDNA sequencing of normal human tissues and cancer cell lines, we identify here hundreds of novel transcribed pseudogenes. Pseudogene transcripts are expressed in tissue-specific patterns, exhibit complex splicing patterns and contribute to the coding sequences of known genes. We survey pseudogene transcripts encoding intact open reading frames (ORFs), representing potential unannotated protein-coding genes, and demonstrate their efficient translation in cultured cells. To assess the impact of noncoding pseudogenes on the cellular transcriptome, we delete the nucleus-enriched pseudogene PDCL3P4 transcript from HAP1 cells and observe hundreds of perturbed genes. This study highlights pseudogenes as a complex and dynamic component of the transcriptional landscape underpinning human biology and disease.


title: In vitro teratogenicity testing using a 3D, embryo-like gastruloid system

abstract: Pharmaceuticals that are intended for use in patients of childbearing potential need to be tested for teratogenicity before marketing. Several pharmaceutical companies use animal-free in vitro models which allow a more rapid selection of lead compounds and contribute to 3Rs principles ( replace, reduce and refine) by streamlining the selection of promising compounds that are submitted to further regulatory studies in animals. Currently available in vitro models typically rely on adherent monolayer cultures or disorganized 3D structures, both of which lack the spatiotemporal and morphological context of the developing embryo. A newly developed 3D  gastruloid model has the potential to achieve a more reliable prediction of teratogenicity by providing a robust recapitulation of gastrulation-like events alongside morphological coordination at relatively high-throughput. In this first proof-of-concept study, we used both mouse and human gastruloids to examine a panel of seven reference compounds, with associated in vivo data and known teratogenic risk, to quantitatively assess in vitro teratogenicity. We observed several gross morphological effects, including significantly reduced elongation or decreased size of the gastruloids, upon exposure to several of the reference compounds. We also observed aberrant gene expression using fluorescent reporters, including SOX2, BRA, and SOX17, suggestive of multi-lineage differentiation defects and disrupted axial patterning. Finally, we saw that gastruloids recapitulated some of the known in vivo species-specific susceptibilities between their mouse and human counterparts. We therefore suggest that gastruloids represent a powerful tool for teratogenicity assessment by enabling relevant physiological recapitulation of early embryonic development, demonstrating their use as a novel in vitro teratogenic model system.

category: pharmacology and toxicology


title: Coupling brain cerebrovascular oscillations and CSF flow during wakefulness: An fMRI study

abstract: Cerebrospinal fluid (CSF) plays an important role in the clearance of metabolic waste products from the brain, yet the driving forces of CSF movement are not fully understood. It is commonly believed that CSF movement is facilitated by blood vessel wall movements (i.e., hemodynamic oscillations) in the brain. A coherent pattern of low frequency hemodynamic oscillations and CSF movement was recently found during non-rapid eye movement (NREM) sleep via functional MRI. However, questions remain regarding 1) the explanation of coupling between hemodynamic oscillations and CSF movement from fMRI signals; 2) the existence of the coupling during wakefulness; 3) the direction of CSF movement. In this resting state fMRI study, we proposed a mechanical model to explain the coupling between hemodynamics and CSF movement through the lens of fMRI. We found that the observed delays between hemodynamics and CSF movement match those predicted by the model. Moreover, by conducting separate fMRI scans of the brain and neck, we confirmed the low frequency CSF movement at the fourth ventricle is bidirectional. Our finding also demonstrates that CSF movement is facilitated by hemodynamic oscillations mainly in the low frequency range, even when the individual is awake.


title: Coupling between cerebrovascular oscillations and CSF flow fluctuation during wakefulness: An fMRI study


title: Dynamical processing of orientation precision in the primary visual cortex

abstract: In our daily visual environment, the primary visual cortex (V1) detects oriented features from a large variety of orientation distributions. The precision of these distributions is fluctuating from one part of the visual scenery to another, and it remains unclear how V1 can account for this range of input configurations in order to achieve robust orientation recognition performances. To answer this question, we used natural-like stimuli and characterised the responses of V1 neurons to quantified variations of orientation precision. Generally, decrements of orientation precision correlated with decreased single neuron tuning, but thirty percent of the recorded neurons remained robustly tuned to imprecise inputs. The existence of these resilient neurons, which could be explained by a model of recurrent cortical inhibition, allows to encode both the orientation and its precision, improving the robustness of the overall population response in V1. Altogether, our results support the notion that the processing of orientation involves precision-specific neurons and slow recurrent dynamics, which possibly constitutes an experimental signature of predictive processes occurring in V1.