title: Compaction of Drosophila histoblasts in a crowded epidermis is driven by buckling of their apical junctions

abstract:
In many proliferating epithelia, cells present a polygonal shape that results from tensile forces of the cytoskeletal cortex and from the packing geometry set by the cell cycle1, 2. In the larval Drosophila epidermis, two cell populations, histoblasts and larval epithelial cells, compete for space as they grow on a limited body surface. They do so in the absence of cell divisions. Here we show that histoblasts, which are initially polygonal, undergo a dramatic morphological transition in the course of larval development. Histoblasts change from a tensed network configuration, with straight cell outlines at the level of adherens junctions, to a highly folded morphology. The apical surface of histoblasts shrinks while their growing adherens junctions fold. Volume increase of growing histoblasts is accommodated basally, compensating for the shrinking apical area. The folded geometry of apical junctions is reminiscent of elastic buckling. In accordance, we show that folding of junctions results from an imbalance between the growth of the junctions and the increasing crowding of the epidermis. The process also correlates with a change in the junctional acto-myosin cortex and possibly mechanical properties.

We propose a model in which crowding of the epidermis imposes a compressive load on the growing junctions which induces their buckling. Buckling effectively compacts histoblasts at their apical plane and may serve to avoid physical harm to these adult epidermis precursors during larval life. Our work also indicates that in growing non-dividing cells, compressive forces, instead of tension, may drive cell morphology.

category: developmental biology


title: Sexual coercion in a natural mandrill population

abstract: Increasing evidence indicates that sexual coercion is widespread. While some coercive strategies are conspicuous, such as forced copulation or sexual harassment, less is known about the ecology and evolution of intimidation, where repeated male aggression promotes future rather than immediate mating success with targeted females. Although known in humans, intimidation was recently reported in chimpanzees (Pan troglodytes) and chacma baboons (Papio ursinus), where males are regularly violent against females. Here, we investigate the nature of male coercive strategies in wild mandrills (Mandrillus sphinx), a primate living in large polygynandrous groups where severe male aggression towards females is rare and females can form coalitions against males. Yet, we found support for all three predictions of the sexual coercion hypothesis, namely that male aggression (1) specifically targets sexually receptive females, (2) inflicts costs to these females, and (3) increases male mating success in the long-term. These results hold true when considering only non-physical threats, or only severe aggression. Finally, we show that high-ranking females are most targeted by males, probably because of their higher reproductive performances, while high-ranking males are most coercive. These results indicate that sexual intimidation is widespread in sexually dimorphic and group-living mammals, and that males and females vary in their propensities to use, and to be exposed to sexual coercion, respectively.

category: ecology


title: False-Positive IRESes from Hoxa9 and other genes resulting from errors in mammalian 5' UTR annotations

abstract: Hyperconserved genomic sequences have great promise for understanding core biological processes. It has been recently proposed that scores of hyperconserved transcript leaders (hTLs) encode Internal Ribosome Entry Sites (IRESes) that drive cap-independent translation in part via interactions with ribosome expansion segments. However, the direct functional significance of such interactions has not yet been definitively demonstrated. We provide evidence that the putative IRESes previously reported in Hoxa gene hTLs are not transcribed. Instead, these regions function independently as transcriptional promoters. In addition, we find the proposed RNA structure of the putative Hoxa9 IRES is not conserved. Instead, sequences previously shown to be essential for putative IRES activity encode a hyperconserved transcription factor binding site (E-box) that contributes to its promoter activity by binding to the transcription factors USF1 and USF2. Similar E-box sequences enhance the promoter activities of other putative Hoxa gene IRESes. Moreover, we provide evidence that the vast majority of hTLs with putative IRES activity overlap transcriptional promoters, enhancers, and 3 splice sites that are most likely responsible for their reported IRES activities. These results argue strongly against recently reported widespread IRES-like activities from hTLs and contradict proposed interactions between ribosomal expansion segment ES9S and putative IRESes. Our work underscores the importance of accurate transcript annotations, controls in bicistronic reporter assays, and the power of synthesizing publicly available data from multiple sources.

category: genomics


title: A pore-forming β-trefoil lectin with specificity for the tumor-related glycosphingolipid Gb3

abstract: Lectins are efficient multivalent glycan receptors, deciphering the glyco-code on cell surfaces. The {beta}-trefoil fold, characterized by three lobe-shaped repeats, is adopted by several classes of lectins, often associated with other domains having enzymatic or toxic activity. Based on the UniLectin3D database classification, the sequence signature of trefoil lobes was defined and used to predict 44714 lectins from 4497 species. Among them, SaroL-1 from the lower eukaryote Salpingoeca rosetta was predicted to contain both {beta}-trefoil and aerolysin-like pore-forming domain. Recombinant SaroL-1 binds to galactose and derivatives, with a stronger affinity for cancer-related -galactosylated epitopes such as glycosphingolipid Gb3 embedded in giant unilamellar vesicles or cell membranes. Crystal structures in complex with Gb3 trisaccharide and GalNAc show similarity with pore-forming toxins. Recognition of the Gal epitope on glycolipids was necessary for hemolysis of rabbit erythrocytes and toxicity on cancer cells through carbohydrate-dependent pore-formation.

category: biochemistry


title: A pair of isoleucyl-tRNA synthetases in Bacilli fulfill complementary roles to enhance fitness and provide antibiotic resistance

abstract: Isoleucyl-tRNA synthetase (IleRS) is an essential enzyme that covalently couples isoleucine to the corresponding tRNA. Bacterial IleRSs group in two clades, ileS1 and ileS2, the latter bringing resistance to the natural antibiotic mupirocin. Generally, bacteria rely on either ileS1 or ileS2 as a standalone housekeeping gene. However, we have found an exception by noticing that Bacillus species with genomic ileS2 consistently also keep ileS1, which appears mandatory in the genus Bacillus. Taking Bacillus megaterium as a model organism, we showed that BmIleRS1 is constitutively expressed, while BmIleRS2 is stress-induced. Both enzymes share the same level of the aminoacylation accuracy. Yet, BmIleRS1 exhibited a two-fold faster aminoacylation turnover (kcat) than BmIleRS2 and permitted a notably faster cell-free translation. At the same time, BmIleRS2 displayed a 104-fold increase in its Ki for mupirocin, arguing that the aminoacylation turnover in IleRS2 could have been traded-off for antibiotic resistance. As expected, a B. megaterium strain deleted for ileS2 was mupirocin-sensitive. We also succeed in the construction of a mupirocin-resistant strain lacking ileS1, a solution not found among Bacilli in nature. However, B. megaterium {Delta}ileS1 displayed a severe fitness loss and was seriously compromised in biofilm formation. Neither of these phenotypes were rescued by BmIleRS2 expressed from the constitutive promotor of ileS1. Thus, BmIleRS1 safeguards B. megaterium fitness, likely by promoting faster translation than BmIleRS2, whereas the later enzyme is maintained to provide antibiotic resistance when needed. Our data are consistent with an emerging picture in which fast-growing organisms predominantly use IleRS1 for competitive survival.


title: Predictions of Skin Permeability Using Molecular Dynamics Simulation from Two-Dimensional Sampling of Spatial and Alchemical Perturbation Reaction Coordinates

abstract: A molecular level understanding of skin permeation may rationalize and streamline product development, and improve quality and control, of transdermal and topical drug delivery systems. It may also facilitate toxicity and safety assessment of cosmetics, skin care products. Here, we present new molecular dynamics simulation approaches that make it possible to efficiently sample the free energy and local diffusion coefficient across the skins barrier structure and predict skin permeability and the effects of chemical penetration enhancers. In particular, we introduce a new approach to use two-dimensional reaction coordinates with so-called Accelerated Weight Histograms, where we combine sampling along spatial coordinates with an alchemical perturbation virtual coordinate. We present predicted properties for twenty permeants, and demonstrate how our approach improves correlation with ex vivo/in vitro skin permeation data. For the compounds included in this study, the ob-tained [Formula] mean square difference was 0.8 cm2 h-2.

category: biophysics


title: Controlling cluster size in 2D phase-separating binary mixtures with specific interactions

abstract: By varying the concentration of molecules in the cytoplasm or on the membrane, cells can induce the formation of condensates and liquid droplets through phase separation. Their thermodynamics, much studied, depends on the mutual interactions between microscopic constituents. Here, we focus on the kinetics and size control of 2D clusters, forming on membranes. Using molecular dynamics of patchy colloids, we model a system of two species of proteins, giving origin to specific heterotypic bonds. We find that concentrations, together with valence and bond strength, control both the size and the growth time rate of the clusters. In particular, if one species is in large excess, it gradually saturates the binding sites of the other species: the system becomes then kinetically arrested and cluster coarsening slows down or stops, thus yielding effective size selection. This phenomenology is observed both in solid and fluid clusters, which feature additional generic homotypic interactions and are reminiscent of the ones observed on biological membranes.


title: Spliceosomic dysregulation unveils NOVA1 as an actionable therapeutic target in pancreatic neuroendocrine tumors

abstract: Dysregulation of the splicing machinery is emerging as a hallmark in cancer due to its association with multiple dysfunctions in tumor cells. Inappropriate function of this machinery can generate tumor-driving splicing variants and trigger oncogenic actions. However, its role in pancreatic neuroendocrine tumors (PanNETs) is poorly defined. In this study we aimed to characterize the expression pattern of a set of splicing machinery components in PanNETs, and their relationship with aggressiveness features. A qPCR-based array was first deployed to determine the expression levels of components of the major (n=13) and minor spliceosome (n=4) and associated splicing factors (n=27), using a microfluidic technology in 20 PanNETs and non-tumoral adjacent samples. Subsequently, in vivo and in vitro models were applied to explore the pathophysiological role of NOVA1. Expression analysis revealed that a substantial proportion of splicing machinery components was altered in tumors. Notably, key splicing factors were overexpressed in PanNETs samples, wherein their levels correlated with clinical and malignancy features. Using in vivo and in vitro assays, we demonstrate that one of those altered factors, NOVA1, is tightly related to cell proliferation, alters pivotal signaling pathways and interferes with responsiveness to drug treatment in PanNETs, suggesting a role for this factor in the aggressiveness of these tumors and its suitability as therapeutic target. Altogether, our results unveil a severe alteration of the splicing machinery in PanNETs and identify the putative relevance of NOVA1 in tumor development/progression, which could provide novel avenues to develop diagnostic biomarkers and therapeutic tools for this pathology.

category: cancer biology


title: NICEgame: A workflow for annotating the knowledge gaps in metabolic reconstructions, using known and hypothetical reactions

abstract: Advances in medicine and biotechnology rely on the further understanding of biological processes. Despite the increasingly available types and amounts of omics data, significant biochemical knowledge gaps remain uncharacterized. Several approaches have been developed during the past years to identify missing metabolic annotations in genome-scale. However, these approaches suggest missing metabolic reactions within a limited set of already characterized metabolic capabilities. In this study, we introduce NICEgame (Network Integrated Computational Explorer for Gap Annotation of Metabolism), a workflow to characterize missing metabolic capabilities in genome-scale metabolic models using the ATLAS of Biochemistry. NICEgame suggests alternative sets of known and hypothetical reactions to resolve gaps in metabolic networks, assesses their thermodynamic feasibility, and suggests candidate genes and proteins to catalyze the introduced reactions. We use gene essentiality data use to identify metabolic gaps in the latest genome-scale model of Escherichia coli, iML1515. We apply our gap-filling approach and further enhance its genome annotation, by suggesting reactions and putative genes to resolve 46 % of the false negative gene essentiality predictions.

category: systems biology


title: Opponent processing in the retinal mosaic of nymphalid butterflies

abstract: The eyes of nymphalid butterflies, investigated with incident illumination, show colourful facet reflection patterns, the eye shine, which is uniform or heterogeneous, dependent on the species. Facet colours suggest that the ommatidia contain different sets of photoreceptors and screening pigments, but how the colours and the cell characteristics are associated has not been clearly established. Here we analyse the retinae of two nymphalids, Apatura ilia, which has a uniform eyeshine, and Charaxes jasius, a species with a heterogeneous eye shine, using single-cell recordings, spectroscopy and optical pupillometry. Apatura has UV, blue and green-sensitive photoreceptors, allocated into three ommatidial types. The UV and blue-sensitive cells are long visual fibres (LVFs), receiving opponent input from the green-sensitive short visual fibres (SVFs). Charaxes has an expanded set of photoreceptors, allocated into three additional, red-reflecting ommatidial types. All red ommatidia contain green-sensitive LVFs, receiving opponent input from red receptors. In both species, the SVFs do not receive any opponent input. The simple retina of Apatura with three ommatidial types and two colour-opponent channels can support trichromatic vision. Charaxes has six ommatidial types and three colour-opponent channels. Its expanded receptor set can support tetrachromatic vision.

category: neuroscience


title: The midpoint of cortical thinning between late childhood and early adulthood differs across individuals and regions: Evidence from longitudinal modelling in a 12-wave sample

abstract: Charting human brain maturation between childhood and adulthood is a fundamental prerequisite for understanding the rapid psychological changes during adolescence. Two barriers have precluded the quantification of maturational trajectories: demands on data and demands on estimation. Using high-temporal resolution neuroimaging data of up to 12-waves in the HUBU cohort (N = 90, aged 7-21 years) we investigate changes in apparent cortical thickness across childhood and adolescence. Fitting a four-parameter logistic nonlinear random effects mixed model, we quantified the characteristic, s-shaped, trajectory of cortical thinning in adolescence. This approach yields biologically meaningful parameters, including the midpoint of cortical thinning (MCT), which corresponds to the age at which the cortex shows most rapid thinning - in our sample occurring, on average, at 15 years of age. These results show that, given suitable data and models, cortical maturation can be quantified with precision for each individual and brain region.


title: CD8 T Cell Memory Inflation is Driven by Latent CMV Infection of Lymphatic Endothelial Cells

abstract:
CMV, a ubiquitous herpesvirus, elicits an extraordinarily large T cell response that is sustained or increases over time, a phenomenon termed  memory inflation. Remarkably, even latent, non-productive infection can drive memory inflation. Despite intense research on this phenomenon, the infected cell type(s) involved are unknown. To identify the responsible cell type(s), we designed a Cre-lox murine CMV (MCMV) system, where a spread-deficient ({Delta}gL) virus expresses recombinant SIINFEKL only in Cre+ host cells. We found that latent infection of endothelial cells (ECs), but not dendritic cells (DCs) or hepatocytes, was sufficient to drive CD8 T cell memory inflation. Infection of Lyve-1-Cre and Prox1-CreERT2 mice revealed that amongst EC subsets, infection of lymphatic ECs was sufficient. Genetic ablation of {beta}2m on lymphatic ECs did not prevent inflation, suggesting another unidentified cell type can also present antigen to CD8 T cells during latency. This novel system definitively shows that antigen presentation by lymphatic ECs drives robust CD8 T cell memory inflation.

SUMMARYActive T cell immunosurveillance during latent CMV infection results in T cell  memory inflation. A novel Cre-lox genetic system for cell-specific antigen expression reveals that lymphatic ECs, but not DCs or hepatocytes, can drive CD8 T cell memory inflation.

category: immunology


title: Pneumolysin promotes host cell necroptosis and bacterial competence during pneumococcal meningitis as shown by whole animal dual RNA-seq

abstract:
Pneumolysin is a major virulence factor of Streptococcus pneumoniae that plays a key role in interaction with the host during invasive disease. How pneumolysin influences these dynamics between host and pathogen interaction during early phase of central nervous system infection in pneumococcal meningitis remains unclear. Using a whole animal in vivo dual RNA-seq approach, we identified pneumolysin-specific transcriptional responses in both S. pneumoniae and zebrafish (Danio rerio) during early pneumococcal meningitis. By functional enrichment analysis we identified host pathways known to be activated by pneumolysin, and discovered the importance of necroptosis for host survival. Inhibition of this pathway using the drugs necrostatin-5 or GSK872 increased host mortality during pneumococcal meningitis. On the pathogens side, we find that pneumolysin-dependent competence activation is crucial for intra-host replication and virulence and that not all bacteria activate competence at the same time. Altogether, this study provides new insights into pneumolysin-specific transcriptional responses and identifies key pathways involved in pneumococcal meningitis.

GRAPHICAL ABSTRACT

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/479878v1_ufig1.gif" ALT="Figure 1">
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C_LIO_LIDiscovery of a functional necroptosis or necroptosis-like pathway in zebrafish
C_LIO_LIHeterogeneity in competence development during infection
C_LIO_LICompetence development is an important virulence determinant
C_LI

category: microbiology


title: Transcriptional response of individual Hawaiian Culex quinquefasciatus mosquitoes to the avian malaria parasite Plasmodium relictum

abstract: Culex quinquefasciatus, the mosquito vector of avian malaria in Hawai{square}i, became established in the islands in the 1820s and the deadly effects of malaria on endemic bird species have been documented for many decades. To evaluate the gene expression response of the mosquito to the parasite, we let the offspring of wild-collected Hawaiian Cx. quinquefasciatus feed on a domestic canary infected with Plasmodium relictum GRW4 freshly isolated from a wild-caught Hawaiian honeycreeper. Control mosquitoes were fed on an uninfected canary. We sequenced the individual transcriptomes of five infected and three uninfected individual mosquitoes at three different stages of the parasite life cycle: 24 h post feeding (hpf) during ookinete invasion; 5 days post feeding (dpf) when oocysts are developing; 10 dpf when sporozoites are released and invade the salivary glands. Differential gene expression analyses showed that during ookinete invasion (24 hpf), genes related to oxidoreductase activity and galactose catabolism had lower expression levels in infected mosquitoes compared to controls. Oocyst development (5 dpf) was associated with reduced expression of a gene with a predicted innate immune function. At 10 dpf, infected mosquitoes had reduced expression levels of a serine protease inhibitor. Overall, the gene expression response of Hawaiian Culex exposed to a Plasmodium infection intensity that occur naturally in Hawaii was low, but more pronounced during ookinete invasion. The low fitness costs often documented in Culex infected with avian Plasmodium likely reflect the relatively small transcriptional changes observed in mosquito genes related to immune response and nutrient metabolism.


title: Sulfide toxicity as key control on anaerobic oxidation of methane in eutrophic coastal sediments

abstract: Coastal zones account for significant global marine methane emissions to the atmosphere. In coastal ecosystems, the tight balance between microbial methane production and oxidation in sediments prevents most methane from escaping to the water column. Anthropogenic activities, causing eutrophication and bottom water deoxygenation, could disrupt this balance in the microbial methane cycle and lead to increased methane release from coastal sediments. Here, we combined microbiological and biogeochemical analyses of sediments from three sites along a bottom water redox gradient (oxic-hypoxic-euxinic) in the eutrophic Stockholm Archipelago to investigate the impact of anthropogenically-induced redox shifts on microbial methane cycling. At both the hypoxic and euxinic site, sediments displayed a stronger depletion of terminal electron acceptors at depth and a shoaling of the sulfate-methane transition zone in comparison to the oxic site. Porewater methane and sulfide concentrations and potential methane production rates were also higher at the hypoxic and euxinic site. Analyses of metagenome-assembled genomes and 16S rRNA gene profiling indicated that methanogens became more abundant at the hypoxic and euxinic site, while anaerobic methane-oxidizing archaea (ANME), present in low coverage at the oxic site, increased at the hypoxic site but virtually disappeared at the euxinic site. A 98% complete genome of an ANME-2b Ca. Methanomarinus archaeon had genes encoding a complete reverse methanogenesis pathway, several multiheme cytochromes, and a sulfite reductase predicted to detoxify sulfite. Based on these results, we infer that sulfide exposure at the euxinic site led to toxicity in ANME, which, despite the abundance of substrates at this site, could no longer thrive. These mechanistic insights imply that the development of euxinia, driven by eutrophication, could disrupt the coastal methane biofilter, leading to increased benthic methane release and potential increased methane emissions from coastal zones to the atmosphere.


title: IL11 stimulates ERK/P90RSK to inhibit LKB1/AMPK and activate mTOR in hepatocytes, the stroma and cancer cells

abstract: Interleukin 11 (IL11) stimulates stromal cell activation but also causes hepatocyte metabolic dysfunction. The mechanisms underlying these seemingly unrelated processes are not known. Here we report that IL11-stimulated ERK/P90RSK activity causes the sequential phosphorylation of LKB1 (STK11) at S325 and S428, leading to its inactivation. This leads to a reduction in AMPK activity whilst concomitantly activating mTOR in human fibroblasts, hepatic stellate cells, hepatocytes and cancer cells. In fibroblasts and hepatic stellate cells, IL11-mediated LKB1/AMPK inhibition causes myofibroblast transformation whereas in hepatocytes it inhibits autophagy and fatty acid oxidation and is toxic. Across cell types, the self-amplifying loop of autocrine IL11 activity was inhibited by AMPK activation with metformin, AICAR or 991. In mice on a western diet with fructose, anti-IL11 therapy or hepatocyte-specific deletion of Il11ra1 rescues LKB1/AMPK activity and reduces NASH. In contrast, restoration of IL11 signalling in hepatocytes of mice with global Il11ra1 deletion inactivates LKB1/AMPK and exacerbates NASH. These data show that LKB1, an important tumour suppressor and master kinase, is not constitutively active and identify the IL11/LKB1/AMPK/mTOR axis as a point of signalling convergence for epithelial homeostasis, fibrogenesis, immunometabolism and cancer.

category: molecular biology


title: Aryl hydrocarbon receptor-dependent and -independent pathways mediate curcumin anti-aging effects

abstract:
The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor whose activity can be modulated by polyphenols such as curcumin. AhR and curcumin have evolutionarily conserved effects on aging. Here, we investigated whether and how the AhR mediates the anti-aging effects of curcumin across species. Using a combination of in vivo, in vitro, and in silico analyses, we demonstrated that curcumin has AhR-dependent or -independent effects in a context-specific manner. We found that in Caenorhabditis elegans, AhR mediates curcumin-induced lifespan extension, most likely through a ligand-independent inhibitory mechanism related to its antioxidant activity. Curcumin also showed AhR-independent anti-aging activities such as protection against aggregation-prone proteins and oxidative stress in C. elegans and promotion of the migratory capacity of human primary endothelial cells. These AhR-independent effects are largely mediated by the Nrf2/SKN-1 pathway.

Graphical Abstract

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title: OzTracs: Optical Osmolality Reporters Engineered from Mechanosensitive Ion Channels

abstract: Interactions between physical forces and membrane proteins underpin many forms of environmental sensation and acclimation. Microbes survive sudden osmotic stresses with the help of mechanically gated ion channels and osmolyte transporters. Plant mechanosensitive ion channels have been shown to function in defense signaling. Here, we engineered genetically encoded osmolality sensors (OzTracs) by fusing green fluorescent protein spectral variants to the mechanosensitive ion channels MscL from E. coli or MSL10 from A. thaliana. When expressed in yeast cells, OzTrac sensors reported osmolality changes as a proportional change in emission ratio of the two fluorescent protein domains. Live-cell imaging revealed accumulation of fluorescent sensors in internal aggregates presumably derived from the endomembrane system. Thus, OzTrac sensors serve as osmolality-dependent reporters through an indirect mechanism, such as effects on molecular crowding or fluorophore solvation.

category: cell biology


title: Mechanism of commitment to a mating partner in  Saccharomyces cerevisiae

abstract: Many cells detect and follow gradients of chemical signals to perform their functions. Yeast cells use gradients of extracellular pheromones to locate mating partners, providing a tractable model to understand how cells decode the spatial information in gradients. To mate, yeast cells must orient polarity toward the mating partner. Polarity sites are mobile, exploring the cell cortex until they reach the proper position, where they stop moving and "commit" to the partner. A simple model to explain commitment posits that a high concentration of pheromone is only detected upon alignment of partner cells polarity sites, and causes polarity site movement to stop. Here we explore how yeast cells respond to partners that make different amounts of pheromone. Commitment was surprisingly robust to varying pheromone levels, ruling out the simple model. We also tested whether adaptive pathways were responsible for the robustness of commitment, but our results show that cells lacking those pathways were still able to accommodate changes in pheromone. To explain this robustness, we suggest that the steep pheromone gradients near each mating partners polarity site trap the polarity site in place. This mechanism has evolutionary implications because it enables sexual selection for cells making more pheromone.


title: Reducing Cholesterol in Resting Macrophage Activates NF-kB through Mitochondria, Resulting in Epigenomic Reprogramming to Dampen Inflammation in Activated Macrophages

abstract: Cholesterol plays an important role in macrophage functions including their immune response1. Recently, NF-kB was shown to reprogram the epigenome in macrophages2. Here, we show that NF-kB pathway is activated in resting macrophages when cholesterol is reduced by statin or methyl-{beta}-cyclodextrin (MCD). Activated NF-kB increases the expression of histone-modifying enzymes, such as demethylase JMJD3. We provide evidence that the epigenome in these macrophages is reprogrammed, likely driven by NF-kB and histone modifications2. We also show that cholesterol reduction in macrophages results in suppression of mitochondria respiration. Specifically, cholesterol levels in the inner membrane of the mitochondria is reduced, which impairs the efficiency of ATP synthase (complex V). Consequently, protons accumulate in the intermembrane space to active NF-kB and JMJD3, thereby modifying the epigenome. When subsequently challenged by the inflammatory stimulus lipopolysaccharide (LPS), cholesterol-reduced macrophages generate responses that are less pro-inflammatory and more homeostatic, which should favour inflammation resolution. Taken together, we describe a mechanism by which the level of mitochondrial cholesterol in resting macrophages regulates the epigenome through NF-kB, thereby preparing macrophage for future immune activation.


title: Trait-based population dynamics shape the contours of fitness landscapes

abstract: Ecological responses to environmental change are driven by population demography1,2, yet trait-based population dynamics are rarely used to project community assemblages3. Fitness landscapes describe how selection influences the evolution of species4,5 and can be extended to multispecies communities along environmental gradients based on the matching of traits to local environmental conditions6. Knowing the contours of fitness landscapes would improve our understanding of how selection shapes ecological communities and would permit predictions of community dynamics in changing environments. However, the shape of fitness landscapes for multispecies communities is unknown because we have lacked a framework for estimating fitness across individuals, phenotypes, and environments. Here we describe a new framework to estimate multispecies fitness landscapes and illustrate model results for trees in temperate forests across a climatic gradient in the eastern United States. Demographic models showed that multivariate phenotypes interact with climate to influence rates of tree growth, survival, and reproduction and generate demographic trade-offs that constrain life history strategies. By integrating trait effects on demographic performance across the life cycle, we estimated the net effect of traits on fitness and reveal the shapes of fitness landscapes driven by temperature. With increasing availability of trait7 and demographic data8,9, our approach can be applied to any ecological system, providing a pathway to generate mechanistic, general predictions of population and community responses to environmental change.


title: No leeway to enhance carbon sequestration and stock capacity via changes to forest management

abstract: Forest management interventions can act as value-based agents to remove CO2 from the atmosphere and slow anthropogenic climate change and thus might play a strategic role in the framework of the EU forestry-based mitigation strategy. To what extent diversified management actions could lead to quantitatively important changes in carbon sequestration potential and stocking capacity at the tree level remains to be thoroughly assessed. To that end, we used a state-of-the-science bio-geochemically based forest growth model to assess effects of multiple alternative forest management scenarios on plant net primary productivity (NPP) and potential carbon woody stocks (pCWS) under differing scenarios of climate change. The experiments indicated that the capacity of trees to assimilate and store atmospheric CO2 in recalcitrant standing woody tissue is already being attained as its optimum under business-as-usual forest management conditions regardless of the different climate change scenarios investigated. Nevertheless, on the long-term and under increasing atmospheric CO2 concentration and warming, managed forests show both higher productivity and a larger pool of stored carbon than unmanaged ones as long as forest thinning and tree harvesting are of moderate intensity.


title: Genomic signatures of hybridization on the neo-X chromosome of Rumex hastatulus

abstract: Natural hybrid zones provide opportunities for studies of the evolution of reproductive isolation in wild populations. Although several recent investigations have found that the formation of neo-sex chromosomes is associated with reproductive isolation, the mechanisms remain unclear in most cases. Here, we assess the contemporary structure of gene flow in the contact zone between largely allopatric cytotypes of the dioecious plant Rumex hastatulus, a species in which there is evidence of sex chromosome turn-over. Males to the west of the Mississippi river, USA, have an X and a single Y chromosome, whereas populations to the east of the river have undergone a chromosomal rearrangement giving rise to a larger X and two Y chromosomes. Using reduced-representation sequencing, we provide evidence that hybrids form readily and survive multiple backcross generations in the field, demonstrating the potential for ongoing gene flow between the cytotypes. At the scale of chromosomes, cline analysis of each chromosome separately captured no signals of difference in cline shape between chromosomes. However, when comparing SNPs, principal component regression revealed a significant increase in the contribution of individual SNPs to inter-cytotype differentiation on the neo-X, but no correlation with recombination rate. Cline analysis revealed that the only SNPs with significantly shallower clines than the genome-average were located on the neo-X. Our data are consistent with a role for the neo-sex chromosome in reproductive isolation between R. hastatulus cytotypes. Our investigation highlights the importance of studying plant hybrid zones in species with sex chromosomes for understanding mechanisms of reproductive isolation and for understanding the role of gene flow in governing the spread of the neo-X chromosomes.

category: evolutionary biology


title: Plant phenotypic plasticity changes pollinator-mediated selection

abstract: Many organisms change their phenotype in response to the environment, a phenomenon called phenotypic plasticity. Yet we hardly understand how such plasticity can affect biotic interactions and the resulting phenotypic selection. Here we use fast cycling Brassica rapa plants in a proof-of-concept experiment in the greenhouse to study the link between plasticity and selection. We detected strong plasticity in morphology, nectar, and floral scent in response to different soil types and aphid herbivory. We found positive selection on nectar and several morphological traits. Bumblebee-mediated selection on a principle component representing plant height, flower number, and flowering time (mPC3) differed depending on soil type and herbivory. For plants growing in richer soil, selection was stronger in the absence of herbivores, whereas for plants growing in poorer soil selection was stronger with herbivory. We showed that bumblebees visited tall plants with many flowers over-proportionally when they were rare (i.e. in plants in poor soil with herbivory), thus causing stronger positive selection on this trait-combination. We suggest that with strong plasticity under most stressful conditions, a shift in pollinator behavior may speed up adaptation to local environmental factors.


title: Meiotic, genomic and evolutionary properties of crossover distribution in Drosophila yakuba

abstract:
The number of crossovers and their location across genomes are highly regulated during meiosis, yet the key components controlling them are fast evolving, hindering our understanding of the mechanistic causes and evolutionary consequences of changes in crossover rates. Drosophila melanogaster has been a model species to study meiosis for more than a century, with an available high-resolution crossover map that is, nonetheless, missing for closely related species, thus preventing evolutionary context. Here, we applied a novel and highly efficient approach to generate whole-genome high-resolution crossover maps in D. yakuba and tackle multiple questions that benefit from being addressed collectively within an appropriate phylogenetic framework, in our case the D. melanogaster species subgroup. The genotyping of more than 1,600 individual meiotic events allowed us to identify several key distinct properties relative to D. melanogaster. We show that together with higher crossover rates than D. melanogaster, D. yakuba has a stronger centromere effect and stronger crossover assurance than any Drosophila species analyzed to date. We also report the presence of an active crossover-associated meiotic drive mechanism for the X chromosome that results in the preferential inclusion in oocytes of chromatids with crossovers. Our evolutionary and genomic analyses suggest that the genome-wide landscape of crossover rates in D. yakuba has been fairly stable and captures a significant signal of the ancestral crossover landscape for the whole D. melanogaster subgroup, even informative for the D. melanogaster lineage. Contemporary crossover rates in D. melanogaster, on the other hand, do not recapitulate ancestral crossovers landscapes. As a result, the temporal stability of crossover landscapes observed in D. yakuba makes this species an ideal system for applying population genetic models of selection and linkage, given that these models assume temporal constancy in linkage effects. Our studies emphasize the importance of generating multiple high-resolution crossover rate maps within a coherent phylogenetic context to broaden our understanding of crossover control during meiosis and to improve studies on the evolutionary consequences of variable crossover rates across genomes and time.

AUTHOR SUMMARYMeiotic recombination is a fundamental cellular process required for the formation of gametes in most eukaryotic organisms. Recombination also plays a fundamental role in evolution, increasing rates of adaptation. Paradoxically for such an essential process, key components evolve fast, and model organisms differ vastly in number of recombination events and distribution across chromosomes. This variation has limited our understanding of how recombination is controlled or why it can vary according to environmental cues. D. melanogaster has been a model species to study meiosis and recombination for more than a century and, in this study, we applied a new and highly efficient whole-genome genotyping scheme to identify recombination properties for a closely species, D. yakuba, thus providing an informative counterpoint and needed phylogenetic context. Our results describe important differences relative to D. melanogaster, including the first description of a mechanism favoring the segregation of recombinant chromatids to the functional egg pole under benign conditions. We argue that such a mechanism may also be active in other species. Moreover, our studies suggest that D. yakuba has maintained its recombination landscape for a longer time than D. melanogaster, indicating that the former species may be more adequate for evolutionary analyses. Combined, we show the importance of tackling the current siloed approach that focuses on model species with a more comprehensive analysis that requires the inclusion of closely related species when studying the causes and consequences of recombination variation.

category: genetics


title: Architecture of the human erythrocyte ankyrin-1 complex

abstract: The stability and shape of the erythrocyte membrane is provided by the ankyrin-1 complex, but how it tethers the spectrin-actin cytoskeleton to the lipid bilayer and the nature of its association with the band 3 anion exchanger and the Rhesus glycoproteins remains unknown. Here we present structures of ankyrin-1 complexes purified from human erythrocytes. We reveal the architecture of a core complex of ankyrin-1, the Rhesus proteins RhAG and RhCE, the band 3 anion exchanger, protein 4.2 and glycophorin A. The distinct T-shaped conformation of membrane-bound ankyrin-1 facilitates recognition of RhCE and unexpectedly, the water channel aquaporin-1. Together, our results uncover the molecular details of ankyrin-1 association with the erythrocyte membrane, and illustrate the mechanism of ankyrin-mediated membrane protein clustering.


title: dbDEMC 3.0: Functional Exploration of Differentially Expressed miRNAs in Cancers of Human and Model Organisms

abstract: microRNAs (miRNAs) are important regulators in gene expression. The deregulation of miRNA expression is widely reported in the transformation from physiological to pathological state of cells. A large amount of differentially expressed miRNAs (DEMs) have been identified in various human cancers by using high-throughput technologies, such as microarray and miRNA-seq. Through mining of published researches with high-throughput experiment information, the database of differentially expressed miRNAs in human cancers (dbDEMC) was constructed with the aim of providing a systematic resource for the storage and query of the DEMs. Here we report an update of the dbDEMC to version 3.0, containing two-fold more data entries than the previous version, now including also data from mouse and rat. The dbDEMC 3.0 contains 3,268 unique DEMs in 40 different cancer types. The current datasets for differential expression analysis have expanded to 9 generalized categories. Moreover, the current release integrates functional annotations of DEMs obtained from experimentally validated targets. The annotations can greatly benefit integrative analysis of DEMs. In summary, dbDEMC 3.0 provides a valuable resource for characterizing molecular functions and regulatory mechanisms of DEMs in human cancers. The dbDEMC 3.0 is freely accessible at https://www.biosino.org/dbDEMC.

category: bioinformatics


title: Longitudinally modeling anti-neoantigen immunity under paradigms of immunodominance

abstract: Neoantigen clonal architecture influences the efficacy of immunotherapy. The longitudinal dynamics of clonal neoantigen immunodominance over a canvas of heterogeneous subclonal neoantigens is critical to response durability, but challenging to characterize clinically and experimentally. We developed a computational model of neoantigen evolution that longitudinally tracks the "presentome" - that is, a cells aggregate neoantigen repertoire and HLA status - of simulated non-small cell lung cancer (NSCLC) prior to and during treatment with checkpoint blockade. Using well-established neoantigen immunogenicity parameters, we first recapitulated the clinically observed presentomes of early-stage NSCLC tumors. After validating simulated neoantigen burden in an independent cohort, we simulated response to PD-1 blockade in silico. In addition to recapitulating known phenomena, such as the correlation of pre-treatment clonal neoantigen burden with response to PD-1 blockade, we found several additional salient features of response, including a profound clonal collapse among completely responding tumors and an insensitivity of response to increased oligoclonality of anti-neoantigen-presenting cell cytotoxicity. Our work can be adapted to longitudinally model the neoantigen architecture of other cancers, modalities of immunotherapy, and preclinical tumor models, ultimately informing cognizant strategies for future therapeutic development.


title: Protein binding and differential distribution of calcitonin in the sub-compartments of blood: An In vitro study

abstract: The pharmacodynamics effects of therapeutically administered calcitonin is observed for extended duration much beyond its reported short half-life. The rationale for this pharmacodynamic-pharmacokinetics mismatch of calcitonin is not known. Hence in this study the hypothesis on sub-compartmentalization of calcitonin in blood to explain the extended pharmacodynamics effects of calcitonin was evaluated in vitro using the sheep blood model. A relatively higher proportion of calcitonin concentration was observed in the WBC compartment. The partition coefficient analysis showed levels of calcitonin to be higher on WBC membrane compared to intracellular. Molecular modelling to assess the binding of calcitonin with protein in plasma and WBC membranes indicated physiologically relevant higher affinity with beta-2-microglobulins in plasma and glycoproteins (CD44), sushi domains (CD25), fibronectins (CD206) and siglecs (CD22) on WBC membrane. The physiologically relevant higher affinity with several proteins on WBC membrane and plasma can be responsible for extended pharmacodynamics effects observed for therapeutically administered calcitonin.

category: pharmacology and toxicology


title: Rhamnan Sulfate Reduces Atherosclerotic Plaque Formation and Vascular Inflammation

abstract:
ObjectiveWhile lipid-lowering drugs have become a mainstay of clinical therapy these treatments only slow the progression of the disease and can have side effects. Thus, new treatment options are needed to supplement the effects of lipid lowering therapy for treating atherosclerosis. We examined the use of an inexpensive and widely available marine polysaccharide rhamnan sulfate as an oral therapeutic for limiting vascular inflammation and atherosclerosis.

Methods and ResultsWe found rhamnan sulfate enhanced the barrier function of endothelial cells, preventing the deposition of LDL and maintaining barrier function even in the presence of glycocalyx-degrading enzymes. Rhamnan sulfate was also found to bind directly to FGF-2, PDGF-BB and NF-{kappa}B subunits with high affinity. In addition, rhamnan sulfate was a potent inhibitor of NF-{kappa}B pathway activation in endothelial cells by TNF-. We treated ApoE-/- mice with a high fat diet for 4 weeks and then an addition 9 weeks of high fat diet with or without rhamnan sulfate. Rhamnan sulfate reduced vascular inflammation and atherosclerosis in both sexes of ApoE-/- mice but had a stronger therapeutic effect in female mice. Oral consumption of rhamnan sulfate induced a significant decrease in cholesterol plasma levels in female mice but not in male mice.

ConclusionsRhamnan sulfate has beneficial effects in reducing inflammation, binding growth factors and NF-{kappa}B, enhancing endothelial barrier function and reducing atherosclerotic plaque formation in ApoE-/- mice.

category: physiology


title: The Voices of Medical Education Science: Describing the Published Landscape

abstract:
IntroductionMedical education has been described as a dynamic and growing field, driven in part by its unique body of scholarship. The voices of authors who publish medical education literature have a powerful impact on the discourses of the community. While there have been numerous studies looking at aspects of this literature, there has been no comprehensive view of recent publications.

MethodThe authors conducted a bibliometric analysis of all articles published in 24 medical education journals published between 2000-2020 to identify article characteristics, with an emphasis on author gender, geographic location, and institutional affiliation. This study replicates and greatly expands on two previous investigations by examining all articles published in these core medical education journals.

ResultsThe journals published 37,263 articles with the majority of articles published in 2020 (n=3,957, 10.7%) and the least in 2000 (n=711, 1.9%) representing a 456.5% increase. The articles were authored by 139,325 authors of which 62,708 were unique. Males were more prevalent across all authorship positions (n=62,828; 55.7%) than females (n=49,975; 44.3%). Authors listed 154 country affiliations with the United States (n=42,236, 40.4%), United Kingdom (n=12,967, 12.4%), and Canada (n=10,481, 10.0%) most represented. Ninety-three countries (60.4%) were low- or middle-income countries accounting for 9,684 (9.3%) author positions. Few articles were written by multinational teams (n=3,765; 16.2%). Authors listed affiliations with 4,372 unique institutions. Across all author positions, 48,189 authors (46.1%) were affiliated with a top 200 institution, as ranked by the Times Higher Education ranking.

DiscussionThere is a relative imbalance of author voices in medical education. If the field values a diversity of perspectives, there is considerable opportunity for improvement.

category: scientific communication and education


title: Subcortical and cortical tracking of communication sound envelopes in challenging listening conditions

abstract: Humans and animals constantly face challenging acoustic environments such as various background noises restricting the detection, discrimination and identification of behaviorally salient sounds. Here, we disentangled the role of temporal envelope tracking on the decrease in neuronal and behavioral discrimination between communication sounds in situations of acoustic degradations. We simulated responses of auditory nerve fibers and recorded neuronal activity in cochlear nucleus, inferior colliculus, thalamus and auditory cortex in anesthetized guinea-pigs. Furthermore, a Go/No-Go sound discrimination task involving two of the guinea-pig whistles was performed on mice in silence and noise. For all conditions, we found that auditory neurons better track the slow amplitude modulations (<20 Hz) of the stimulus envelopes than the faster ones. In addition, the decrease in neuronal and behavioral discrimination performance in noise can be explained by an increased similarity of the vocalization envelopes in the low frequency range (<20 Hz). Together, these results suggest that slow envelope tracking is a general property of auditory neurons, and any difference between the slow envelopes of natural stimuli allows coping with degraded conditions.


title: Active tactile discrimination is coupled with and modulated by the cardiac cycle

abstract: Perception and cognition are modulated by the phase of the cardiac signal in which the stimuli are presented. This has been shown by locking the presentation of stimuli to distinct cardiac phases. However, in everyday life sensory information is not presented in this phase-locked and passive manner, instead we actively sample the world. Whether active sensing is coupled and modulated with the cardiac cycle remains largely unknown. Here we recorded the ECGs of human participants while they actively performed a tactile grating orientation task. Here we show that the duration of subjects touch varied as a function of the cardiac phase in which they initiated it. Touches initiated in the systolic phase of the cardiac cycle were held for longer periods of time than touches initiated in the diastolic phase. This effect was driven by the elongation of their holds to sample the most difficult gratings. Conversely, while touches in the control condition were coupled to the cardiac cycle, their length was not modulated as a function of when in the cycle these were initiated. In line with interoceptive inference accounts, these results are consistent with the hypotheses that we actively adjust our sensory sampling so that we spend more time in the diastole period of the cardiac cycle in which perceptual sensory sensitivity is greatest.


title: Assessing Quantitative MRI Techniques using Multimodal Comparisons

abstract: The study of brain change in neuroscience studies is commonly conducted using macroscopic morphological measures of the brain such as regional volume or cortical thickness, providing little insight into the microscopic mechanisms underlying brain disease. In contrast, quantitative MRI allows the monitoring of microscopic brain change non-invasively in-vivo, and provides normative values for comparisons between tissues, regions, and individuals. To support the development and common use of qMRI for cognitive neuroscience, we analysed a set of qMRI metrics (R1, R2*, Magnetization Transfer saturation, Proton Density saturation, Fractional Anisotropy, Mean Diffusivity) in 101 healthy young adults. Here we provide a comprehensive descriptive analysis of these metrics and their linear relationships to each other in grey and white matter to develop a more complete understanding of the relationship to tissue microstructure. Furthermore, we provide evidence that combinations of metrics may uncover informative microstructural cortical gradients across the brain by showing that dimensionality reduction through PCA provides cortical gradients that were hidden in individual metrics. We discuss these results and their links to microstructural and physiological neuroscience research.


title: Structural basis of human IL-18 sequestration by the decoy receptor IL-18 binding protein (IL-18BP) in inflammation and tumor immunity

abstract:
Human Interleukin-18 (IL-18) is an omnipresent pro-inflammatory cytokine of the IL-1 family with central roles in autoimmune and inflammatory diseases, and serving as a staple biomarker in the evaluation of inflammation in physiology and disease, including the inflammatory phase in COVID-19. The sequestration of IL-18 by its soluble decoy receptor IL-18 Binding Protein (IL-18BP) is critical to the regulation of IL-18 activity. Since an imbalance in expression and circulating levels of IL-18 is associated with disease, structural insights into how IL-18BP outcompetes binding of IL-18 by its cognate cell-surface receptors would be highly desirable. However, the structure of human IL-18BP in complex with IL-18 had remained elusive. Here, we elucidate the sequestration mechanism of human IL-18 mediated by IL-18BP based on the crystal structure of the IL-18:IL-18BP complex. These detailed structural snapshots reveal the interaction landscape leading to the ultra-high affinity of IL-18BP towards IL-18 and identify substantial differences with respect to previously characterized complexes of IL-18 with IL-18BP of viral origin. Furthermore, our structure captured a fortuitous higher-order assembly between IL-18 and IL-18BP coordinated by a disulfide-bond distal to the binding surface connecting IL-18 and IL-18BP molecule from different complexes, resulting in a novel complex with 2:2 stoichiometry. This tetrapartite assembly was found to restrain IL-18 activity more effectively than the canonical 1:1 complex. Collectively, our findings will provide a framework for innovative structure-driven therapeutic strategies and further functional interrogation of IL-18 in physiology and disease.

Significance statementElevated levels of interleukin-18 (IL-18) have long been implicated in numerous inflammatory diseases while also displaying potent anti-tumoral activities. Recent research on COVID-19 has now underscored the role of IL-18 and IL-18 binding protein (IL-18BP), a soluble receptor serving to regulate IL-18 activity, as key players in viral immunity and as promising biomarkers and predictors of disease severity. In this work, we present detailed structural insights into how human IL-18 and IL-18BP interact thereby completing the structural repertoire of IL-18 in complex with its cognate human receptors and viral decoy receptors. Our findings will support structure-based efforts to either disrupt or enhance the interactions of IL-18 with its cognate receptors for therapeutic purposes.


title: The regulatory protein ChuP connects heme and siderophore-mediated iron acquisition systems required for Chromobacterium violaceum virulence

abstract: Chromobacterium violaceum is an environmental Gram-negative beta-proteobacterium that causes systemic infections in humans. C. violaceum uses siderophore-based iron acquisition systems to overcome the host-imposed iron limitation, but its capacity to use other iron sources is unknown. In this work, we characterized ChuPRSTUV as a heme utilization system employed by C. violaceum to explore an important iron reservoir in mammalian hosts, free heme and hemoproteins. We demonstrate that the chuPRSTUV genes comprise a Fur-repressed operon that is expressed under iron limitation. The chu operon potentially encodes a small regulatory protein (ChuP), an outer membrane TonB-dependent receptor (ChuR), a heme degradation enzyme (ChuS), and an inner membrane ABC transporter (ChuTUV). Our nutrition growth experiments using C. violaceum chu deletion mutants revealed that, with the exception of chuS, all genes of the chu operon are required for heme and hemoglobin utilization in C. violaceum. The mutant strains without chuP displayed increased siderophore halos on CAS plate assays. Significantly, we demonstrate that ChuP connects heme and siderophore utilization by acting as a positive regulator of chuR and vbuA, which encode the TonB-dependent receptors for the uptake of heme (ChuR) and the siderophore viobactin (VbuA). Our data favor a model of ChuP as a heme-binding post-transcriptional regulator. Moreover, our virulence data in a mice model of acute infection demonstrate that C. violaceum uses both heme and siderophore for iron acquisition during infection, with a preference for siderophores over the Chu heme utilization system.


title: A conserved biosynthetic gene cluster is regulated by quorum sensing in a shipworm symbiont

abstract:
Bacterial symbionts often provide critical functions for their hosts. For example, wood-boring bivalves called shipworms rely on cellulolytic endosymbionts for wood digestion. However, how the relationship between shipworms and their bacterial symbionts is formed and maintained remains unknown. Quorum sensing (QS) often plays an important role in regulating symbiotic relationships. We identified and characterized a QS system found in Teredinibacter sp. strain 2052S, a gill isolate of the wood-boring shipworm Bactronophorus cf. thoracites. We determined that 2052S produces the signal N-decanoyl-L-homoserine lactone (C10-HSL), and that this signal controls activation of a biosynthetic gene cluster co-located in the symbiont genome that is conserved among all symbiotic Teredinibacter isolates. We subsequently identified extracellular metabolites associated with the QS regulon, including ones linked to the conserved biosynthetic gene cluster, using mass spectrometry-based molecular networking. Our results demonstrate that QS plays an important role in regulating secondary metabolism in this shipworm symbiont. This information provides a step towards deciphering the molecular details of the relationship between these symbionts and their hosts. Furthermore, because shipworm symbionts harbor vast yet underexplored biosynthetic potential, understanding how their secondary metabolism is regulated may aid future drug discovery efforts using these organisms.

IMPORTANCEBacteria play important roles as symbionts in animals ranging from invertebrates to humans. Despite this recognized importance, much is still unknown about the molecular details of how these relationships are formed and maintained. One of the proposed roles of shipworm symbionts is the production of bioactive secondary metabolites due to the immense biosynthetic potential found in shipworm symbiont genomes. Here, we report that a shipworm symbiont uses quorum sensing to coordinate activation of its extracellular secondary metabolism, including the transcriptional activation of a biosynthetic gene cluster that is conserved among many shipworm symbionts. This work is a first step towards linking quorum sensing, secondary metabolism, and symbiosis in wood-boring shipworms.


title: Simultaneous therapeutic targeting of inflammation and virus ameliorates influenza pneumonia and protects from morbidity and mortality

abstract:
Pneumonia is a severe complication caused by inflammation of the lungs following infection with seasonal and pandemic strains of influenza A virus (IAV) that can result in lung pathology, respiratory failure and death. There is currently no treatment available for severe disease and pneumonia caused by IAV. Antivirals are available, but they are far from satisfactory if treatment is not initiated within 48 hours of symptoms onset. Influenza complications and mortality are often associated with high viral load and excessive lung inflammatory cytokine response. Therefore, we simultaneously targeted IAV with the antiviral drug oseltamivir and inflammation with the anti-inflammatory drug etanercept, targeting TNF after the onset of clinical signs to treat IAV pneumonia effectively. The combined treatment effectively reduced lung viral load, lung pathology, morbidity and mortality during respiratory IAV infection in mice, contemporaneous with significant downregulation of the inflammatory cytokines TNF, IL-1{beta}, IL-6, IL-12p40, chemokines CCL2, CCL5 and CXCL10 and dampened STAT3 activation. Consequently, combined therapy with oseltamivir and a STAT3 inhibitor also effectively reduced clinical disease and lung pathology. Combined treatment using either of the anti-inflammatory drugs and oseltamivir dampened an overlapping set of cytokines. Thus, combined therapy targeting a specific cytokine or cytokine signaling pathway plus an antiviral drug provides an effective treatment strategy for ameliorating IAV pneumonia. Effective treatment of IAV pneumonia required multiple doses of etanercept and a high dose of oseltamivir. This approach might apply to the treatment of pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Significance StatementAntivirals against influenza A virus (IAV) are ineffective in treating pneumonia if administered 48 h after onset of disease symptoms. The host inflammatory response and tissue damage caused by IAV are responsible for lung pathology. We reasoned that targeting both virus and inflammation would be more effective in reducing lung pathology and pneumonia, morbidity and mortality. The simultaneous treatment with an anti-inflammatory drug targeting TNF or STAT3, combined with the anti-IAV antiviral drug, oseltamivir, significantly improved clinical disease, reduced lung viral load and pathology, and protected mice from severe pneumonia. The combined treatment suppressed multiple pro-inflammatory cytokines and cytokine signaling pathways. Thus, after the onset of disease symptoms, both virus and inflammation must be targeted to treat IAV pneumonia effectively.


title: The RNA-binding protein landscapes differ between mammalian organs and cultured cells

abstract: System-wide approaches have unveiled an unexpected breadth of the RNA-bound proteomes of cultured cells. Corresponding information regarding RNA-binding proteins (RBPs) of mammalian organs is still missing, largely due to technical challenges. Here, we describe ex vivo eRIC (enhanced RNA interactome capture) to characterize the poly(A)RNA-bound proteomes of three different mouse organs. The resulting organ atlases encompass more than 1300 RBPs active in brain, kidney or liver. Nearly a quarter (291) of these had formerly not been identified in cultured cells, with more than 100 being metabolic enzymes. Remarkably, RBP activity differs between organs independent of RBP abundance, suggesting organ-specific levels of control. Similarly, we identify systematic differences in RNA binding between animal organs and cultured cells. The pervasive RNA binding of enzymes of intermediary metabolism in organs points to tightly knit connections between gene expression and metabolism, and displays a particular enrichment for enzymes that use nucleotide cofactors. We describe a generically applicable refinement of the eRIC technology and provide an instructive resource of RBPs active in intact mammalian organs, including the brain.


title: 24-Nor-ursodeoxycholic acid counteracts TH17/Treg imbalance and ameliorates intestinal inflammation by restricting glutaminolysis in differentiating TH17 cells

abstract:
Objective24-Nor-ursodeoxycholic acid (NorUDCA) is a novel therapeutic bile acid for treating primary sclerosing cholangitis (PSC), an immune-mediated cholestatic liver disease. Since PSC strongly associates with inflammatory bowel diseases (IBD) driven by TH17/Treg imbalance, we aimed to explore NorUDCAs immunomodulatory potential on intestinal TH17/Treg balance.

DesignNorUDCAs impact on TH17/Treg tissue distribution was first assessed in Mdr2-/- mouse model of PSC. We specifically investigated NorUDCAs effect on modulating TH17/Treg balance in a CD4+ T cell driven colitis model induced by adoptive transfer of CD25-CD44lowCD45RBhighCD4+ TNaive cells into Rag2-/- mice, mimicking human IBD. Mechanistic studies were performed using molecular approaches, flow cytometry and metabolic assays in murine TH17 cells in vitro. NorUDCAs signaling effects observed in murine system were further validated in circulating CD4+ T cells from PSC patients with co-existing IBD.

ResultsNorUDCA promoted Treg generation in both liver and intestine in the Mdr2-/- model. In the experimental IBD model, NorUDCA attenuated intestinal immunopathology. Mechanistically, NorUDCA demonstrated strong immunomodulatory efficacy in counteracting TH17/Treg imbalance by restricting glutaminolysis in differentiating TH17 cells, thus suppressed -Ketoglutarate-dependent mTORC1 activation, glycolysis and enhanced FOXP3 expression. NorUDCAs impact on mTORC1 signaling was further confirmed in circulating CD4+ T-cells from PSC patients with IBD.

ConclusionNorUDCA possesses direct immunometabolic modulatory potency to counteract TH17/Treg imbalance and ameliorate excessive TH17 cell driven intestinal immunopathology. These findings extend future clinical applications of NorUDCA for treatment of TH17 cell-mediated disorders along the gut-liver axis and beyond.

Significance of this studyO_ST_ABSWhat is already known on this subject?C_ST_ABSO_LIPSC is an immune-mediated cholestatic liver disease highly associated with IBD where TH17/Treg imbalance drives immunopathogenesis; seeking effective therapeutics covering both liver and intestinal disease in PSC is of high clinical relevance.
C_LIO_LIIndependent of anti-cholestatic effects, NorUDCA has recently been shown to possess direct immunomodulatory properties on CD8+ T cell metabolism, lymphoblastogenesis and clonal expansion through targeting mTORC1 signaling.
C_LIO_LISince mTORC1 serves as critical metabolic checkpoint orchestrating TH17/Treg axis, inhibiting mTORC1 activity represents a potential treatment avenue counteracting TH17/Treg imbalance under intestinal inflammatory conditions.
C_LI

What are the new findings?O_LINorUDCA enriches FOXP3+ Treg population in both liver and intestinal tissue in the cholestatic Mdr2-/- mouse model of PSC.
C_LIO_LINorUDCA exhibits direct immunomodulatory efficacies in suppressing excess TH17 cell-mediated intestinal immunopathology and promotes FOXP3+ Treg generation in an experimental IBD model.
C_LIO_LIMechanistically, NorUDCA counteracts TH17/Treg imbalance by restricting glutaminolysis in differentiating TH17 cells, thus suppresses -Ketoglutarate-dependent mTORC1 activation, glycolysis and enhances FOXP3 expression.
C_LIO_LINorUDCAs impact on mTORC1 signaling was further confirmed in circulating CD4+ T cells from patients with PSC and IBD.
C_LI

How might it impact on clinical practice in the foreseeable future?These findings advance our current understanding of therapeutic potentials of NorUDCA, which might represent a novel therapeutic strategy in the treatment of PSC and concomitant IBD and other TH17-mediated intestinal diseases.


title: The Ndc80 complex is essential for the initial kinetochore-microtubule capture during early mitosis

abstract: Mitotic kinetochores are initially captured by dynamic microtubules via a  search-and-capture mechanism. The microtubule motor, dynein, is critical for kinetochore capture as it has been shown to transport microtubule-attached chromosomes towards the spindle pole during early mitosis. In metaphase, the kinetochore localized, microtubule-binding complex, Ndc80, plays a central role in stabilizing kinetochore-microtubule (kMT) attachments. It is not yet clear, however, if Ndc80, which is recruited to kinetochores very early during mitosis contributes to initial kMT capture. Here, by combining CRISPR/Cas9-mediated knockout and RNAi technology with assays specifically targeted to study kMT capture, we show that mitotic cells lacking Ndc80 exhibit severe defects in this function during prometaphase. Rescue experiments show that Ndc80 mutants deficient in microtubule-binding are unable to execute proper kMT capture. While cells inhibited of dynein alone are predominantly able to make initial kMT attachments, cells co-depleted of Ndc80 and dynein show severe defects in kMT capture. Further, we demonstrate a novel physical interaction between Ndc80 and dynein during prometaphase. Thus, our studies, for the first time, identify a distinct event in the formation of initial kMT attachments, which is directly mediated by Ndc80 followed by a coordinated function with dynein, both of which are required for efficient kMT capture and proper chromosome alignment.


title: Cortical neuronal differentiation is not impaired by elevated levels of α-synuclein in human pluripotent stem cells

abstract: -Synuclein (Syn) is a small, disordered protein that becomes aggregated in Lewy body diseases, such as Parkinsons disease (PD) and dementia with Lewy bodies (DLB). Human induced pluripotent stem cells (hiPSCs) potentially provide a tractable disease model to monitor early molecular changes associated with PD/DLB. We and others have previously derived hiPSC lines from patients with duplication and triplication of the SNCA gene, encoding for Syn. It is now recognised that to perform meaningful disease modelling with these hiPSC lines, it is critical to generate isogenic control cell lines that lack the disease causing mutations. In order to complement the existing and emerging hiPSC models for PD/DLB, we have generated an allelic series of Syn over-expressing hESC lines on the same isogenic background. An unresolved question is whether pluripotent stem cell lines, with elevated levels of Syn, can undergo efficient differentiation into dopaminergic and cortical neurons to model PD and DLB, respectively. We took advantage of our isogenic collection of hESC lines to determine if increased expression of Syn affects neural induction and neuronal differentiation. Clonal hESC lines with significantly different levels of Syn expression proliferated normally and maintained expression of pluripotent markers, such as OCT4. All cell lines efficiently produced PAX6+ neuroectoderm and there was no correlation between Syn expression and neural induction efficiency. Finally, global transcriptomic analysis of cortical differentiation of hESC lines with low or high levels of Syn expression demonstrated robust and similar induction of cortical neuronal expression profiles. Gene expression differences observed were unrelated to neural induction and neuronal differentiation. We conclude that elevated expression of Syn in human pluripotent stem cells does not adversely affect their neuronal differentiation potential and that collections of isogenic cell lines with differing levels of Syn expression are valid and suitable models to investigate synucleinopathies.


title: An isogenic collection of pluripotent stem cell lines with elevated α-synuclein expression


title: Identification of CD317-Positive Pro-inflammatory Immune Stromal Cells in Human Mesenchymal Stromal Cell Preparations

abstract: Mesenchymal stromal cell (MSC) heterogeneity clouds biological understanding and hampers their clinical development. In MSC cultures most commonly used in research and therapy, we have identified an MSC subtype characterised by CD317 expression (CD317pos (29.77{+/-}3.00% of the total MSC population), comprising CD317dim (28.10{+/-}4.60%) and CD317bright (1.67{+/-}0.58%) MSCs) and a constitutive interferon signature linked to human disease. We demonstrate that CD317pos MSCs induced cutaneous tissue damage when applied a skin explant model of inflammation, whereas CD317neg MSCs had no effect. Only CD317neg MSCs were able to suppress proliferative cycles of activated human T cells in vitro, whilst CD317pos MSCs increased polarisation towards pro-inflammatory Th1 cells and CD317neg cell lines did not. Using an in vivo peritonitis model, we found that CD317neg and CD317pos MSCs suppressed leukocyte recruitment but only CD317neg MSCs suppressed macrophage numbers. Using MSC-loaded scaffolds implanted subcutaneously in immunocompromised mice we were able to observe tissue generation and blood vessel formation with CD317neg MSC lines, but not CD317pos MSC lines. Our evidence is consistent with the identification of an immune stromal cell, which is likely to contribute to specific physiological and pathological functions and influence clinical outcome of therapeutic MSCs.


title: Lem2 is essential for cardiac development by maintaining nuclear integrity

abstract:
Nuclear envelope integrity is essential for compartmentalisation of nucleus and cytoplasm. Importantly, mutations in nuclear envelope-encoding genes are the second-highest cause of familial dilated cardiomyopathy. One such nuclear envelope protein that causes cardiomyopathy in humans and affects mouse heart development is Lem2. However, its role in mechanically active tissue such as heart remains poorly understood.

We generated mice in which Lem2 was specifically ablated in cardiomyocytes and carried out detailed physiological, tissue and cellular analyses. Importantly, our data showed that Lem2 was essential for cardiac development, and hearts from Lem2 cKO mice were morphologically and transcriptionally underdeveloped. Lem2 cKO hearts displayed high levels of DNA damage, nuclear rupture, and apoptosis. Crucially, we found that these defects were driven by muscle contraction as they were ameliorated by inhibiting myosin contraction and conversely were exacerbated upon myosin activation.

Our data suggest that Lem2 is critical for integrity at the nascent nuclear envelope in fetal hearts, and protects the nucleus from the mechanical forces of muscle contraction. Taken together, these data provide novel insight into mechanisms underlying striated muscle diseases caused by altered nuclear envelope integrity.


title: Acoel single-cell atlas reveals expression dynamics and heterogeneity of a pluripotent stem cell population

abstract: Pluripotent adult stem cell populations underlie whole-body regeneration in many distantly related animal lineages. These collectively pluripotent populations of cells share some features across species, such as the expression of piwi and other germline-related genes. Studies of how these cells operate during regeneration are needed in diverse systems to determine how underlying cellular and molecular mechanisms of renewal and differentiation compare. Here, we sought to characterize stem cells and their dynamics in the acoel Hofstenia miamia, a highly regenerative marine worm with a piwi-expressing stem cell population called neoblasts. Transcriptome profiling at single cell resolution revealed cell types shared across postembryonic stages, including stem cells and differentiated cell types such as neural, epidermal, muscle, and digestive cells. Reconstruction of single-cell differentiation trajectories followed by functional studies confirmed that neoblasts are the source of differentiated cells and identified transcription factors needed for the formation of major cell types. Next, analysis of single-cell transcriptomes from regenerating worms showed that both differentiated cells and stem cells dynamically alter gene expression in response to amputation. Further analysis of the stem cells recovered subpopulations of neoblasts, each with specific transcriptional profiles suggesting that the majority of neoblasts are specialized to differentiated lineages, reflecting putatively lineage-primed progenitors. Notably, neoblast subsets in Hofstenia were identifiable consistently across postembryonic stages and also displayed differential expression dynamics in response to wounding. Altogether, these data suggest that whole-body regeneration is accomplished by the coordination of cells with distinct and dynamic transcriptomic profiles through time. Furthermore, the data generated here will enable the study of how this coordination is achieved, enhancing our understanding of pluripotent stem cells and their evolution across metazoans.

category: developmental biology


title: High diversity of type I polyketide genes in Bacidia rubella as revealed by the comparative analysis of 23 lichen fungal genomes

abstract: Fungi involved in lichen symbioses produce a large array of different secondary metabolites. The high diversity of those substances has been known for decades and are often considered characteristic for taxonomical delimitation in lichen-forming fungi. Polyketides, the most common secondary metabolites, are synthesized by the Type I Polyketide synthases (TI-PKS) comprised of different enzymatic domains. We present a phylogenetic overview of Type I PKS genes recovered from the de-novo sequenced genome of Bacidia rubella in the context of additional twenty-one fungal genomes from the largest radiation of lichen-forming Ascomycetes (Lecanoromycetes) as well as the lichen-forming Eurotiomycete, Endocarpon pusillum. Using de-novo gene prediction and functional annotation combined with a phylogenetic analysis, we provide insights into the biosynthetic potential and PKS gene diversity of lichen-forming fungi. We discuss genes predicted in the lichen-forming fungal genomes in relation to previously characterized PKS genes from other fungi and bacteria. Our results reveal a high number of biosynthetic gene clusters and their gene domain composition. PKS gene content outnumbers known secondary substances produced by the lichen-forming fungi. We were able to assign putative functions to several of those PKS genes in silico, based on similarity to already characterized genes. In particular, we identified a putative PKS23 gene of Bacidia rubella, producing the common lichen substance atranorin. However, we also found that several lichen-forming fungi still possess homologs of different biosynthetic genes without producing the corresponding substances in detectable amounts. Although many PKSs remain without functional assignments in our analysis, our findings highlight that genes from lichen-forming fungi represent an untapped source of novel polyketide compounds. However, additional experimental approaches are necessary to link biosynthetic genes and secondary metabolites with confidence.


title: Integrated single-cell sequencing reveals principles of epigenetic regulation of human gastrulation and germ cell development in a 3D organoid model

abstract: The emergence of different cell types and the role of the epigenome in regulating transcription is a key yet understudied event during human gastrulation. Investigating these questions remain infeasible due to the lack of availability of embryos at these stages of development. Further, human gastrulation is marked by dynamic changes in cell states that are difficult to isolate at high purity, thereby making it challenging to map how epigenetic reprogramming impacts gene expression and cellular phenotypes. To overcome these limitations, we describe scMAT-seq, a high-throughput one-pot single-cell multiomics technology to simultaneously quantify DNA methylation, DNA accessibility and the transcriptome from the same cell. Applying scMAT-seq to 3D human gastruloids, we characterized the epigenetic landscape of major cell types corresponding to the germ layers and primordial germ cell-like cells (hPGCLC). As the identity of the progenitors that give rise to human PGCLCs remain unclear, we used this system to discover that the progenitors emerge from epiblast cells and show transient characteristics of both amniotic- and mesoderm-like cells, before getting specified towards hPGCLCs. Finally, as cells differentiate along different lineages during gastrulation, we surprisingly find that while changes in DNA accessibility are tightly correlated to both upregulated and downregulated genes, reorganization of gene body DNA methylation is strongly related to only genes that get downregulated, with genes that turn on displaying a lineage trajectory-dependent correlation with DNA methylation. Collectively, these results demonstrate that scMAT-seq is a high-throughput and sensitive approach to elucidate epigenetic regulation of gene expression in complex systems such as human gastrulation that are marked by rapidly transitioning cell states.

category: genomics


title: Fentanyl reinstatement to discriminative cues after conflict in sign- and goal-tracking rats

abstract:
RationaleDiscriminative stimuli (DS) are cues that predict reward availability. DS are resistant to extinction and motivate drug seeking even after long periods of abstinence. Previous studies have demonstrated that sign tracking (ST) and goal tracking (GT) individual differences in Pavlovian approach to food cues predict distinct vulnerabilities to CS and DS reinstatement of cocaine seeking, respectively. Compared to goal-trackers, sign-trackers show heightened CS relapse even after electric barrier induced abstinence. We do not know whether DS relapse persists after electric barrier induced abstinence, or whether tracking-related relapse vulnerabilities generalize to models of opioid relapse.

ObjectivesWe sought to determine if DS-induced reinstatement of fentanyl seeking persists in the presence of reduced adverse consequences after electric barrier-induced abstinence. We also aimed to determine whether tracking differences predict the magnitude of DS-induced reinstatement of fentanyl seeking after electric barrier-induced abstinence.

MethodsFirst we used Pavlovian lever autoshaping (PLA) training to determine sign-, goal- and intermediate tracking groups in male and female Sprague Dawley rats. We then trained rats in a DS model of intermittent fentanyl self-administration, and extinguished drug seeking by imposing an electric barrier of increasing intensity. We then measured the level of DS-induced reinstatement in the presence of a reduced electric barrier intensity.

ResultsWe report that DS produce large increases in fentanyl seeking after electric barrier induced abstinence. Contrary to our expectations, the magnitude of the DS induced reinstatement effect was not related to tracking group.

ConclusionsDiscriminative stimuli powerfully motivate opioid seeking, despite continued aversive consequences. Individual differences in Pavlovian approach do not predict the level of DS reinstatement to fentanyl seeking after conflict induced abstinence.

category: animal behavior and cognition


title: Histone H4K20 Trimethylation is Decreased in Murine Models of Heart Disease

abstract:
Heart disease is the leading cause of death in the developed world, and its comorbidities such as hypertension, diabetes, and heart failure are accompanied by major transcriptomic changes in the heart. During cardiac dysfunction, which leads to heart failure, there are global epigenetic alterations to chromatin that occur concomitantly with morphological changes in the heart in response to acute and chronic stress. These epigenetic alterations include the reversible methylation of lysine residues on histone proteins. Lysine methylation on histone H3K4 and H3K9 were among the first methylated lysine residues identified and have been linked to gene activation and silencing, respectively. However, much less is known regarding other methylated histone residues, including histone H4K20. Trimethylation of histone H4K20 has been shown to repressive gene expression, however this mark has never been examined in the heart. Here we utilized immunoblotting and mass spectrometry to quantify histone H4K20 trimethylation in three models of cardiac dysfunction. Our results show that lysine methylation at this site is regulated in a biphasic manner leading to increased H4K20 trimethylation during acute hypertrophic stress and decreased H4K20 trimethylation during sustained ischemic injury and cardiac dysfunction. In addition, we examined publicly available datasets to analyze enzymes that regulate H4K20 methylation and identified one demethylase (KDM7C) and two methyltransferases (KMT5A and SMYD5) which were all upregulated in heart failure patients. This is the first study to examine histone H4K20 trimethylation in the heart and to determine how this post-translational modification is differentially regulated in multiple models of cardiac disease.

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category: biochemistry


title: Comparison of proton transfer paths to the QA and QB sites of the Rb. sphaeroides photosynthetic reaction centers

abstract: The photosynthetic bacterial reaction centers from purple non-sulfur bacteria use light energy to drive the transfer of electrons from cytochrome c to ubiquinone. Ubiquinone bound in the QA site cycles between quinone, QA, and anionic semiquinone, QA*-, being reduced once and never binding protons. In the QB site, ubiquinone is reduced twice by QA*-, binds two protons and is released into the membrane as the quinol, QH2. The network of hydrogen bonds formed in a molecular dynamics trajectory was drawn to investigate proton transfer pathways from the cytoplasm to each quinone binding site. QA is isolated with no path for protons to enter from the surface. In contrast, there is a complex and tangled network requiring residues and waters that can bring protons to QB. There are three entries from clusters of surface residues centered around HisH126, GluH224, and HisH68. The network is in good agreement with earlier studies, Mutation of key nodes in the network, such as SerL223, were previously shown to slow proton delivery. Mutational studies had also shown that double mutations of residues such as Asp M17 and AspL210 along multiple paths in the network presented here slow the reaction, while single mutations do not. Likewise, mutation of both HisH126 and HisH128, which are at the entry to two paths reduce the rate of proton uptake.

category: biophysics


title: SOCIALITY, COMMUNITIES AND MORPHOLOGICAL FEATURES OF ANTS FROM MID-CRETACEOUS BURMESE AMBER

abstract: We consider morphological diversity of ants from mid-Cretaceous Burmese amber. An eco-ethological hypothesis concerning its origin and features of Mesozoic and Cenozoic ant communities is proposed. It appears that some morphological features of representatives of the stem taxa allow us to speak about the absence of effective communication and, subsequently, group foraging in these ants. Therefore, the diversity of primitive Cretaceous ants, as predators, reflects their food specialization according to types of prey, on condition of their social lifestyle, that results in division of the ecological space among ant species into ecological niches. The occurrence of both effective communication and group foraging (mobilization) in the crown ant taxa, as crucial adaptation, has permitted them to exceed the bounds of niches of specialized predators, since type and size of prey are not strictly correlated to size of an ant and its mandibles; it also has given a chance to maintain large colonies. Due to this, myrmecocomplexes of modern ants are arranged on the principle of colonies dominance rather than the principle of division of ecological niches, like Mesozoic.

category: paleontology


title: Exploring the frame effect

abstract: Probes flashed within a moving frame are dramatically displaced (Ozkan et al, 2021; Wong &Mack, 1981). The effect is much larger than that seen on static or moving probes (induced motion, Duncker, 1929; Wallach et al, 1978). These flashed probes are often perceived with the separation they have in frame coordinates -- a 100% effect. Here we explore this frame effect on flashed tests with several versions of the standard stimulus. We find that the frame effect holds for smoothly or abruptly displacing frames, even when the frame changed shape or orientation between the endpoints of its travel. The path could be non-linear, even circular. The effect was driven by perceived not physical motion. When there were competing overlapping frames, the effect was determined by which frame was attended. There were a number of constraints that limited the effect. A static anchor near the flashes suppressed the effect but an extended static texture did not. If the probes were continuous rather than flashed, the effect was abolished. The observational reports of 30 online participants suggest that the frame effect is robust to many variations in its shape and path and leads to a perception of flashed tests in their locations relative to the frame as if the frame were stationary. Our results highlight the role of frame continuity and of the grouping of the flashes with the frame in generating the frame effect.

category: neuroscience


title: Meningeal neutrophils play a role in modulating CNS output

abstract: It has become increasingly evident that immune cells play a role in modulating brain function. Neutrophils are the most abundant innate immune cell in mammals. Until recently, our understanding of the physiological role of these cells was limited to infection and cancer. Recently, it has emerged that neutrophils play critical roles in modulating tissue health and physiology. There has been evidence that neutrophils populate the rodent meninges. As such, we hypothesized that like other meningeal immune cells, neutrophils play a neuromodulatory role. Using a depletion paradigm, anti-Ly6G antibody injection, we demonstrate that the loss of neutrophils leads to changes in cognitive flexibility and social interactions in mice. Furthermore, the depletion paradigm led to a 50% decrease in the number of neutrophils in the meninges, which in turn led to the proliferation of resident immature neutrophils within the meninges. Finally, our data show that this immature population reenters the cell cycle only in response to specific physiological stimuli (neutrophil depletion, and stress). In conclusion, this study demonstrates that there are resident neutrophils within the meninges and that elucidating their function in the nervous system will deepen our understanding of immune regulation of brain function.


title: Modulating neutrophils leads to changes in CNS output


title: Oligodendrocyte precursor cells engulf synaptic inputs in an experience- and microglia-dependent manner

abstract: Oligodendrocyte precursor cells (OPCs) are a highly proliferative class of non-neuronal progenitors that largely give rise to myelinating oligodendrocytes. Although OPCs persist across the lifespan, their functions beyond oligodendrogenesis remain to be fully characterized. Here, we show that OPCs contribute to neural circuit remodeling by internalizing presynaptic thalamocortical inputs in both the developing and adult mouse visual cortex. Inputs internalized by OPCs localize to lysosomal compartments, consistent with OPC engulfment of synapses occuring through phagocytosis. We further show that engulfment by OPCs is heightened during experience-dependent plasticity, and that this experience-dependent increase in engulfment requires microglia. These data identify a new function for OPCs beyond the generation of oligodendrocytes and reveal that distinct non-neuronal populations collaborate to modulate synaptic connectivity.


title: HiDiver: A Suite of Methods to Merge Magnetic Resonance Histology, Light Sheet Microscopy, and Complete Brain Delineations

abstract: We have developed new imaging and computational workflows to produce accurately aligned multimodal 3D images of the mouse brain that exploit high resolution magnetic resonance histology (MRH) and light sheet microscopy (LSM) with fully rendered 3D reference delineations of brain structures. The suite of methods starts with the acquisition of geometrically accurate (in-skull) brain MRIs using multi-gradient echo (MGRE) and new diffusion tensor imaging (DTI) at an isotropic spatial resolution of 15 m. Whole brain connectomes are generated using over 100 diffusion weighted images acquired with gradients at uniformly spaced angles. Track density images are generated at a super-resolution of 5 m. Brains are dissected from the cranium, cleared with SHIELD, stained by immunohistochemistry, and imaged by LSM at 1.8 m/pixel. LSM channels are registered into the reference MRH space along with the Allen Brain Atlas (ABA) Common Coordinate Framework version 3 (CCFv3). The result is a high-dimensional integrated volume with registration (HiDiver) that has a global alignment accuracy of 10-50 m. HiDiver enables 3D quantitative and global analyses of cells, circuits, connectomes, and CNS regions of interest (ROIs). Throughput is sufficiently high that HiDiver is now being used in comprehensive quantitative studies of the impact of gene variants and aging on rodent brain cytoarchitecture.


title: Evolution of inflammation and immunity in a dengue virus 1 human infection model

abstract: Dengue virus (DENV) infections are significant sources of morbidity and mortality throughout the tropics and subtropics. Over 400 million infections are estimated to occur every year, resulting in nearly 100 million symptomatic infections and over 20,000 deaths. Early immune response kinetics to infection remain unclear, in large part due to the variable incubation period exhibited by the DENVs after introduction into a susceptible host. To fill this knowledge gap, we performed a comprehensive virologic and immunologic analysis of individuals experimentally infected with the under-attenuated DENV-1 strain 45AZ5. This analysis captured both the kinetics and composition of the innate, humoral, and cellular immune responses elicited by experimental DENV-1 infection, as well as virologic and clinical features. Revealed in this analysis was a robust DENV-specific IgA antibody response that manifested between the appearance of DENV-specific IgM and IgG in all challenged individuals, as well as the presence of a non-neutralizing/NS1-specific antibody response that was delayed relative to the appearance of DENV-virion specific humoral immunity. RNAseq analysis also revealed several distinct and temporally-restricted gene modules that allowed for the identification and differentiation of the innate and adaptive immune response to DENV-infection. Our analysis provides a detailed description, in time and space, of the evolving matrix of DENV-elicited human inflammation and immunity and reveals several previously unappreciated immunological aspects of primary DENV-1 infection that can inform countermeasure development and evaluation.

category: immunology


title: Mechanism of RNA Polymerase I selection by transcription factor UAF

abstract: Pre-ribosomal RNA is selectively transcribed by RNA Polymerase (Pol) I in eukaryotes. The yeast transcription factor Upstream Activating Factor (UAF) represses Pol II transcription and mediates Pol I preinitiation complex (PIC) formation during the early stages of transcription initiation at the 35S ribosomal RNA gene. To unravel the DNA recognition and Pol I selection mechanisms of UAF, we determined the structure of UAF bound to native promoter DNA and transcription factor TBP. We found that UAF recognizes DNA using a hexameric histone-like scaffold with markedly different interactions than the nucleosome and the histone-fold-rich TFIID. UAF strategically sequesters TBP from DNA and Pol II/III-specific factors, and positions it for Core Factor binding, supporting Pol I recruitment. Our findings therefore reveal the molecular basis of Pol I selection for ribosome biogenesis. As well, they reveal an unexpected potential within the histone fold as a motif for specific protein-DNA interactions inside the cell.