title: Annelid functional genomics reveal the origins of bilaterian life cycles

abstract: Indirect development with an intermediate larva exists in all major animal lineages1, and thus larvae are central to most scenarios for animal evolution2-12. Yet how larvae evolved remains disputed. Here we show that changes in the timing of trunk formation underpin the diversification of larvae and bilaterian life cycles. Combining chromosome-scale genome sequencing with transcriptomic and epigenomic profiling in the slow-evolving oweniid Owenia fusiformis13, we found that different genes and genomic regulatory elements control the development of its feeding larva and adult stage. First, O. fusiformis embryos develop into an enlarged anterior domain that forms larval tissues and the adult head, as posterior growth and trunk patterning is deferred to pre-metamorphic stages. These traits also occur in the so-called "head larvae" of other bilaterians14,15, with whom O. fusiformis larva shows extensive transcriptomic similarities. Conversely, animals with non-feeding larvae and gradual metamorphoses, such as the annelid Capitella teleta, start trunk differentiation during embryogenesis, like direct developers. Together, our findings suggest that the ancestral temporal decoupling of head and trunk formation, as retained in extant "head larvae", allowed larval evolution in Bilateria, questioning prevailing scenarios that propose either co-option10,11 or innovation12 of gene regulatory programmes to explain larva and adult origins.


title: Local extensional flows promote long-range fiber alignment in 3D collagen hydrogels

abstract: Randomly oriented type I collagen (COL1) fibers in the extracellular matrix (ECM) are reorganized by biophysical forces into aligned domains extending several millimeters and with varying degrees of fiber alignment. These aligned fibers can transmit traction forces, guide tumor cell migration, facilitate angiogenesis, and influence tissue morphogenesis. To create aligned COL1 domains in microfluidic cell culture models, shear flows have been used to align thin COL1 matrices (<50m in height) in a microchannel. However, there has been limited investigation into the role of shear flows in aligning 3D hydrogels (>130m). Here, we show that pure shear flows do not induce fiber alignment in 3D atelo COL1 hydrogels, but the simple addition of local extensional flow promotes alignment that is maintained across several millimeters, with a degree of alignment directly related to the extensional strain rate. We further advance experimental capabilities by addressing the practical challenge of accessing a 3D hydrogel formed within a microchannel by introducing a magnetically coupled modular platform that can be released to expose the microengineered hydrogel. We demonstrate the platforms capability to pattern cells and fabricate multi-layered COL1 matrices using layer-by-layer fabrication and specialized modules. Our approach provides an easy-to-use fabrication method to achieve advanced hydrogel microengineering capabilities that combine fiber alignment with biofabrication capabilities.

category: bioengineering


title: An Oscillatory Shear Index-based Model to Describe Progressive Carotid Artery Stenosis

abstract:
Background and aimsThis study describes and demonstrates the applicability of a novel in silico method for modeling progressive carotid artery stenosis using the oscillatory shear index (OSI) as the basis of stenosis function.

MethodsThree-dimensional reconstructions of 11 carotid arteries were generated using patient-derived magnetic resonance angiography and duplex ultrasound data. Computational fluid dynamic simulations were sequentially performed following computational stenosis assessment, and corresponding changes in OSI were observed and used as measure of morphological stabilization.

ResultsSix carotid models showed progressive stenosis with statistically significant increases in regions of high OSI (OSI > 0.2, p < 0.05) with eventual carotid occlusion in one of the cases. Three models remained free or nearly free of increased OSI, whereas one model showed an overall decrease in high OSI regions (p < 0.05) and another trended in that direction but did not achieve statistical significance (p = 0.145).

ConclusionsTo our knowledge, this is the first computational model describing progressive stenosis in any peripheral artery including the carotid. Taken together, this study provides a novel framework for computational hemodynamic investigations on progressive atherosclerosis in the carotid artery.

category: bioinformatics


title: Equilibrium dynamics of the pre- and post-cleavage regions of SP1 are separately shifted by the HIV-1 maturation inhibitor Bevirimat

abstract: Human immunodeficiency virus type 1 (HIV-1) assembly and maturation proceeds in two distinct steps. During assembly, viral Gag oligomerizes into a hexagonal polyprotein lattice incorporating the capsid protein (CA) and spacer peptide 1 (SP1) domains, that constitute the immature Gag lattice. During maturation, CTD-SP1 hexamers formed in the previous step are cleaved by HIV-1 protease, causing a dramatic rearrangement of the immature virion to its mature, infectious form. The first-generation maturation inhibitor (MI) bevirimat (BVM) is reported to block the final cleavage between CA and SP1, thus blocking HIV maturation. In contrast, the host factor inositol hexakisphosphate (IP6) is a co-factor of Gag assembly and facilitates the formation of a quaternary arrangement of SP1 known as the six helix bundle (6HB). Here, starting from a MAS NMR structure and using atomistic free energy calculations, we establish that binding of BVM and IP6 to the immature lattice lacks any cooperativity or avidity. Furthermore, we rationalize the molecular origin of HIV resistance to BVM by determining the role of BVM on the stability of the 6HB and by revealing that SP1 shows independent dynamics for its pre- and post-cleavage regions. Finally, results from our simulations permit us to propose a novel chemical scaffold for the design of maturation inhibitors based on BVM and IP6.

category: biophysics


title: Extrachromosomal DNA is associated with decreased immune cell infiltration and antigen presentation, represents a potential cancer immune evasion mechanism

abstract: Extrachromosomal DNA (ecDNA) is a type of circular and tumor specific genetic element. EcDNA has been reported to display open chromatin structure, facilitate oncogene amplification and genetic material unequal segregation, and is associated with poor cancer patients prognosis. The ability of immune evasion is a typical feature for cancer progression, however the tumor intrinsic factors that determine immune evasion remain poorly understood. Here we show that the presence of ecDNA is associated with markers of tumor immune evasion, and obtaining ecDNA could be one of the mechanisms employed by tumor cells to escape immune surveillance. Tumors with ecDNA usually have comparable TMB and neoantigen load, however they have lower immune cell infiltration and lower cytotoxic T cell activity. The microenvironment of tumors with ecDNA shows increased immune desert, decreased immune enriched fibrotic types. Both MHC class I and class II antigen presentation genes expression are decreased in tumors with ecDNA, and this could be the underlying mechanism for ecDNA associated immune evasion. This study provides evidence that the presence of ecDNA is an immune escape mechanism for cancer cells.

category: cancer biology


title: Complex genotype-phenotype relationships shape the response to treatment of Down Syndrome Childhood Acute Lymphoblastic Leukaemia

abstract: Extensive genetic and epigenetic variegation has been demonstrated in many malignancies. Importantly, their interplay has the potential to contribute to disease progression and treatment resistance. To shed light on the complex relationships between these different sources of intra-tumour heterogeneity, we explored their relative contributions to the evolutionary dynamics of Acute Lymphoblastic Leukaemia (ALL) in children with Down syndrome, which has particularly poor prognosis. We quantified the tumour propagating potential of genetically distinct sub-clones using serial transplantation assays and SNP-arrays. While most leukaemias were characterized by a single dominant subclone, others were highly heterogeneous. Importantly, we provide clear and direct evidence that genotypes and phenotypes with functional relevance to leukemic progression and treatment resistance can co-segregate within the disease. Hence, individual genetic lesions can be restricted to well-defined cell immunophenotypes, corresponding to different stages of the leukemic differentiation hierarchy and varied proliferation potentials. As a result of this difference in fitness, which can be accurately quantified via competitive transplantation assays, matching diagnostic, post-treatment, and relapse leukaemias can be dominated by different genotypes, including pre-leukemic clones persisting throughout the disease progression and treatment. Intriguingly, plasticity also appears to be a temporally defined property that can segregate with genotype. These results suggest that Down Syndrome ALL should be viewed as a complex matrix of cells exhibiting genetic and epigenetic heterogeneity that foster extensive clonal evolution and competition. Therapeutic intervention reshapes this  ecosystem and may provide the right conditions for the preferential expansion of selected compartments and subsequent relapse.


title: Reconstructing phylogeny of the hornless rhinoceros Aceratheriinae

abstract: This study presents the first phylogenetic analysis focused on the Subfamily Aceratheriinae to date, with 391 characters coded from 43 taxa at the species level. We added 77 newly defined and 33 revised characteristics, including features of the skull, teeth, and postcranial bones. In the present analysis, the tribe Teleoceratini, as well as the tribe Aceratheriini, was reclassified within Aceratheriinae, however, the traditionally established monophyly of each tribe was decomposed. Combined with detailed morphological comparisons, we reconstructed the phylogeny of Aceratheriinae and revised the diagnosis of Aceratheriinae. The reported skull and teeth specimens of Turkanatherium from the late Early Miocene indicate that it is not an acerathere and has been placed as a basal rhinocerotid. The Aceratheriinae has undergone evolutionary adaptation several times during the early stage of evolution, and several genera from the Oligocene to the Early Miocene have been reconstructed as early diverging taxa, such as Molassitherium, Protaceratherium, Plesiaceratherium and Chilotheridium; Aprotodon and Mesaceratherium from the Late Oligocene to the Early Miocene were united as the earliest divergent clade of Aceratheriinae; meanwhile, due to the limited materials, the phylogenies of Floridaceras and Dromoceratherium are unstable in this analysis, and both have been tentatively considered as the early diverging clades of Aceratheriinae. Alicornops was reclassified a member of Teleoceratini. Aceratheriini and Teleoceratini have been redefined as two highly specialized groups. Furthermore, Aceratheriini has been divided into two/three clades based on the difference in the skull outlines and the occlusal patterns of the cheek teeth.

category: paleontology


title: Targeted nanocarriers coopting pulmonary leukocytes for drug delivery to the injured brain

abstract:
Selective drug delivery to injured regions of the brain is an elusive, but biomedically important, goal. It is tempting to co-opt migrating white blood cells (WBC) to carry drugs to the injured brain, using natural WBC tropism. Current approaches to load cargoes to WBC have limited utility, particularly in acute conditions, due to the need for time consuming ex vivo manipulation and loading of cells. Physiological, in vivo loading of WBC may be advantageous in this scenario. Here we devised such a strategy, capitalizing on the unique features of the direct blood exchange between brain and lungs. Mediators emanating from the injured brain directly travel to the pulmonary vasculature via venous flow. In response to these mediators, WBCs, transiently residing in the pulmonary microvascular lumen, disembark and flow with arterial blood to the brain microvasculature, where they adhere and transmigrate to the brain parenchyma via the local chemoattractant gradient. We posited that direct in vivo targeting of cargoes to the pulmonary WBC pool may provide drug transfer to brain via this natural mechanism. To test this, we intravenously injected agents targeted to intercellular adhesion molecule 1 (ICAM) in mice with acute brain inflammation caused by direct injection of tumor necrosis factor alpha (TNF-). We found that: A) At 2 hours, >20% of ICAM/NP accumulated in lungs, predominantly in WBCs; B) At 6 and 22 hours, ICAM/NP pulmonary uptake markedly decreased; C) In contrast, ICAM/NP uptake in brain increased ~5-fold in this time interval, concomitantly with migration of WBCs to the brain. Cranial window fluorescent microscopy confirmed WBC transport of ICAM/NP to the brain in TNF--challenged mice beyond the BBB. Importantly, demonstrating the pharmacologic relevance of this strategy, dexamethasone-loaded ICAM/liposomes abrogated brain edema in this model. In sum, coopting the natural homing of WBC from the lungs via ICAM-targeting to injured brain is an attractive strategy for precise interventions for treatment of acute brain injuries.

VISUAL ABSTRACT O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

category: pharmacology and toxicology


title: Expectation for sweet taste changes peripheral glucose metabolism via basolateral amygdala

abstract:
Anticipatory physiological responses to food were first reported by Ivan Pavlov a century ago but the associated neural mechanism is still ill-defined. Here, we identified two types of neurons in the basolateral amygdala (BLA), which are activated by sweetener (saccharin) or water after sucrose conditioning, representing expected sweet taste and unmet expectation, respectively. Saccharin-induced met-expectation of sweet taste enhances, while H2O-induced unmet-expectation deteriorates, glucose metabolism in peripheral tissues. Deletion of saccharin-responsive neurons in BLA impaired saccharin-induced increase in insulin sensitivity. Deletion of H2O-responsive neurons in BLA improved glucose intolerance by unmet-expectation. Saccharin- and H2O-responsive neurons had different gene expressions. Our data suggest that the gap between the expected incoming sugar and sweet taste is evaluated by distinct BLA neurons to control peripheral glucose metabolism.

One-Sentence SummaryNeurons in the basolateral amygdala control blood glucose levels by comparing anticipated sugar intake and sweet taste

category: physiology


title: Genome-microbiome interplay provides insight into the determinants of the human blood metabolome

abstract: Variation in the blood metabolome is intimately related to human health. Prior work has shown that host genetics and gut microbiome composition, combined, explain sizable, but orthogonal, components of the overall variance in blood metabolomic profiles. However, few details are known about the interplay between genetics and the microbiome in explaining variation on a metabolite-by-metabolite level. Here, we performed analyses of variance for each of the 945 blood metabolites that were robustly detected across a cohort of 2,049 individuals, while controlling for a number of relevant covariates, like sex, age, and genetic ancestry. Over 60% of the detected blood metabolites were significantly associated with either host genetics or the gut microbiome, with more than half of these associations driven solely by the microbiome and around 30% under hybrid genetic-microbiome control. The variances explained by genetics and the microbiome for each metabolite were indeed largely additive, although subtle, but significant, non-additivity was detected. We found that interaction effects, where a metabolitemicrobe association was specific to a particular genetic background, were quite common, albeit with modest effect sizes. The outputs of our integrated genetic-microbiome regression models provide novel biological insights into the processes governing the composition of the blood metabolome. For example, we found that unconjugated secondary bile acids were solely associated with the microbiome, while their conjugated forms were under strong host genetic control. Overall, our results reveal which components of the blood metabolome are under strong genetic control, which are more dependent on gut microbiome composition, and which are dependent upon both. This knowledge will help to guide targeted interventions designed to alter the composition of the blood metabolome.

category: systems biology


title: An unbiased pathway analysis (UPA) designed for multi-omics inference of cell signaling pathways

abstract: New tools for unbiased cell signaling pathway inference from multi-omics data are needed. Here we propose a new unbiased method, the unbiased pathway analysis (UPA), to model and combine omics data into regulatory complexes and pathways. UPA was validated with publicly available omics data and was found accurate in discovering protein-protein interactions, kinase substrate phosphosite relationships, transcription factor target gene relationships, and signaling pathways. Transcription factor, kinase, subcellular location and function prediction algorithms were devised for transcriptome, phosphoproteome and interactome regulatory complexes and pathways, respectively. To apply UPA in a biologically relevant context, interactome, phosphoproteome, transcriptome and proteome data were collected from analyses carried out using melanoma cells to address gamma-secretase cleavage-dependent signaling characteristics of the receptor tyrosine kinase TYRO3. Significant differences were discovered between full-length and gamma-secretase cleaved TYRO3 when signaling modules associated with cell cycle and growth, cell adhesion and motility, cell morphology, or immune responses were compared. The pathways modeled with UPA reflected both the predicted function and direction of the predicted function in validation experiments.


title: Quantitative modeling of pentose phosphate pathway response to oxidative stress reveals a cooperative regulatory strategy

abstract: Living cells use signaling and regulatory mechanisms to adapt to environmental stresses. In the case of oxidative stress due for instance to hydrogen peroxide exposure, the adaptation response relies on co-regulation of enzymes in both glycolysis and pentose phosphate pathways (PPP), so as to support PPP-dependent NADPH and redox homeostasis. To understand the regulatory logic underlying early oxidative stress response, available metabolomics and 13C fluxomics dataset are used to infer a probabilistic ensemble of kinetic models. Model ensemble properties of parameter distributions, transient dynamics, dose-response curves and loss-of-function phenotypes all highlights significant and cooperative effects of allosteric regulations of G6PD, PGI and GAPD in early oxidative response. Indeed, efficient flux rerouting into PPP is shown to require dose-dependent coordination between upregulated G6PD enzyme and increased G6P metabolite, the latter requiring fine-tuned inhibition of upper and lower glycolytic enzymes. This set of allosteric regulation also combines negative and positive feedback loops in a subtle manner prone to generate paradoxical perturbation phenotypes for instance related to 6PGD modulation.


title: AI reveals insights into link between CD33 and cognitive impairment in Alzheimer's Disease

abstract:
Modeling biological mechanisms is a key for disease understanding and drug-target identification. However, formulating quantitative models in the field of Alzheimers Disease is challenged by a lack of detailed knowledge of relevant biochemical processes. Additionally, fitting differential equation systems usually requires time resolved data and the possibility to perform intervention experiments, which is difficult in neurological disorders. This work addresses these challenges by employing the recently published Variational Autoencoder Modular Bayesian Networks (VAMBN) method, which we here trained on combined clinical and patient level gene expression data while incorporating a disease specific knowledge graph. Our approach, called iVAMBN, resulted in a quantitative model that allowed us to simulate a down-expression of the putative drug target CD33, including potential impact on cognitive impairment and brain pathophysiology. Experimental validation demonstrated a high overlap of molecular mechanism predicted to be altered by CD33 perturbation with cell line data. Altogether, our modeling approach may help to select promising drug targets.

Author SummaryFor the last 20 years the field of Alzheimers Disease (AD) is marked by a series of continuous failures to deliver demonstrably effective medications to patients. This is also highlighted by the highly controversial recent approval of Aduhelm (Biogen) by the FDA, which is now investigated internally due to the lack of clear efficacy.

One of the reasons for the continuous failure of trials in AD is the choice of the wrong target mechanism. In essence there is a lack of understanding, how targeting a certain molecule would affect cognitive impairment in human. One way to address this issue is the development of quantitative system level models connecting the molecular level with the phenotype. However, formulating such models in the field of Alzheimers Disease is challenged by a lack of detailed knowledge of relevant biochemical processes and the connection of molecular mechanisms to cognitive impairment. Additionally, fitting of differential equation systems, which are often used in systems biology, requires time resolved data and the possibility to perform intervention experiments, which is difficult in neurological disorders due to the lack of realistic model systems.

Our work addresses these challenges by employing a novel hybrid Artificial Intelligence (AI) approach combining variational autoencoders with Bayesian Networks. Our proposed approach, named Integrative Variational Autoencoder Modular Bayesian Networks (iVAMBN), was trained on combined clinical and patient level gene expression data while incorporating a disease specific knowledge graph. Our method resulted in an interpretable, quantitative model. It showed connections between various biological mechanisms playing a role in AD. Furthermore, iVAMBN directly connected the molecular level to the disease phenotype. Our model allowed us to simulate a down-expression of the putative drug target CD33. Results showed a significantly increased cognition and predicted perturbation of a number of biological mechanisms. We experimentally validated these predictions using gene expression data from a knock-out THP-1 monocyte cell line. This experiment confirmed our model predictions up to a very high extend. To our knowledge we thus developed the first experimentally validated, quantitative, multi-scale model connecting molecular mechanisms with clinical outcomes in the AD field.


title: Single-molecule imaging reveals Tau trapping at nanometer-sized dynamic hot spots near the plasma membrane

abstract: Accumulation of Tau aggregates is a pathological hallmark of Alzheimers disease, but little is known about where these aggregates assemble and how stable these assemblies are. Using quantitative, single-molecule imaging, we show that Tau exhibits spatial and kinetic heterogeneity near the plasma membrane, resulting in the formation of nanometer-sized hot spots smaller than the diffraction limit. The hot spots lasted tens of seconds, much longer than the short dwell time (~40 ms) of Tau on microtubules. Pharmacological and biochemical disruption of Tau/microtubule interactions did not affect hot spot formation, suggesting that these are different from the reported Tau condensation on microtubules. Although cholesterol removal has been shown to reduce Tau pathology, its depletion did not affect Tau hot spot dynamics. Our study identifies an intrinsic dynamic property of Tau near the plasma membrane that may facilitate the formation of assembly sites for Tau to assume its physiological and pathological functions.

category: neuroscience


title: Tau forms dynamic hot spots that are resistant to microtubule perturbations and cholesterol depletion


title: Bidirectional crosstalk between epithelial-mesenchymal plasticity and IFNγ-induced PD-L1 expression promotes tumor progression

abstract:
Epithelial-Mesenchymal Transition (EMT) and immunoevasion through upregulation of Programmed Death-Ligand 1 (PD-L1) are important drivers of cancer progression. While EMT has been proposed to facilitate PD-L1-mediated immunosuppression, the molecular mechanisms of their interaction remain obscure. Here we provide insight into these mechanisms by proposing a mathematical model that describes the crosstalk between EMT and Interferon gamma (IFN{gamma})-induced PD-L1 expression. Our model shows that via interaction with microRNA-200 (miR-200), the multistability of the EMT regulatory circuit is mirrored in the PD-L1 levels, which are further amplified by IFN{gamma} stimulation. This IFN{gamma}-mediated effect is most prominent for cells in a fully mesenchymal state, and less strong for those in an epithelial or partially mesenchymal state. Additionally, bi-directional crosstalk between miR-200 and PD-L1 implies that IFN{gamma} stimulation allows cells to undergo EMT for lower amounts of inducing signal, and that IFN{gamma} presence accelerates EMT and decelerates Mesenchymal-Epithelial Transition (MET). Overall, our model agrees with published findings and provides insight into possible mechanisms behind EMT-mediated immune-evasion; and primary, adaptive, or acquired resistance to immunotherapy. Our model can be used as a starting point to explore additional crosstalk mechanisms, as an improved understanding of these mechanisms is indispensable for developing better diagnostic and therapeutic options for cancer patients.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/478950v1_ufig1.gif" ALT="Figure 1">
View larger version (15K):
org.highwire.dtl.DTLVardef@1e5fde0org.highwire.dtl.DTLVardef@7e929dorg.highwire.dtl.DTLVardef@1cb9f6borg.highwire.dtl.DTLVardef@14f50ad_HPS_FORMAT_FIGEXP  M_FIG C_FIG Schematic overview of the crosstalk between Epithelial-Mesenchymal Transition (EMT) and Interferon gamma (IFN{gamma})-induced Programmed Death-Ligand 1 (PD-L1) expression. IFN{gamma}-induced PD-L1 expression promotes the occurrence of EMT. EMT, also induced by, for example, Transforming Growth Factor Beta (TGF{beta}), increases PD-L1 expression levels, facilitating tumor immunoevasion.


title: Dynamical management of potential threats regulated by dopamine and direct- and indirect-pathway neurons in the tail of the striatum

abstract: Avoiding potential threats before experiencing an actual outcome is critical to prevent a disaster. Here we examined roles of the tail of the striatum (TS) and its dopamine input in threat management. Mice were presented with a potential threat (a moving object) while pursuing rewards. Mice initially failed to obtain rewards, but gradually successfully obtained rewards in later trials. We show that the initial failures depended on dopamine and direct-pathway neurons in TS, and variability in failure rate across trials and individuals was positively correlated with the activity of these neurons. In contrast, indirect-pathway neurons in TS were critical for eventual improvement in reward acquisition, and their activity was positively correlated with successful reward acquisition. These results demonstrate that direct- and indirect-pathway TS neurons promote and suppress threat avoidance, respectively, at different stages, providing a mechanism for overcoming a potential threat while maintaining the threat estimates.


title: Compressive forces stabilise microtubules in living cells

abstract: Cell mechano-sensation and adaptation are supported by the actin network. The microtubule network is not considered to be directly sensitive to mechanical forces acting on a cell. However, recent studies on isolated microtubules in vitro have shown that bending forces have an impact on their structure, composition and lifespan, suggesting that, in a cellular context, microtubules may react to mechanical forces. We tested this hypothesis in living cells by subjecting them to cycles of compressive forces and found that microtubules became distorted, less dynamic and more stable. This mechano-stabilisation depends on CLASP2, which relocates from the end to the deformed shaft of microtubules. These results demonstrate that microtubules in living cells have mechano-responsive properties that allow them to resist and even counteract the forces to which they are subjected.

category: cell biology


title: Rhythmic interactions between the mediodorsal thalamus and prefrontal cortex precede human visual perception

abstract: The thalamus is much more than a simple sensory relay. High-order thalamic nuclei, such as the mediodorsal thalamus, exert a profound influence over animal cognition. However, given the difficulty of directly recording from the thalamus in humans, next-to-nothing is known about thalamic and thalamocortical contributions to human cognition. To address this, we analysed simultaneously-recorded thalamic iEEG and whole-head MEG in six patients (four female, two male; plus MEG recordings from twelve healthy controls) as they completed a visual detection task. We observed that the phase of both ongoing mediodorsal thalamic and prefrontal low-frequency activity was predictive of perceptual performance. Critically however, mediodorsal thalamic activity mediated prefrontal contributions to perceptual performance. These results suggest that it is thalamocortical interactions, rather than cortical activity alone, that is predictive of upcoming perceptual performance and, more generally, highlights the importance of accounting for the thalamus when theorising about cortical contributions to human cognition.


title: Novel cerebello-amygdala connections provide missing link between cerebellum and limbic system

abstract: The cerebellum is emerging as a powerful regulator of cognitive and affective processing and memory in both humans and animals and has been implicated in affective disorders. How the cerebellum supports affective function remains poorly understood. The short-latency (just a few ms) functional connections that were identified between the cerebellum and amygdala -a structure crucial for the processing of emotion and valence-more than 4 decades ago raise the exciting, yet untested, possibility that a cerebellum-amygdala pathway communicates information important for emotion. The major hurdle in rigorously testing this possibility is the lack of knowledge about the anatomy and functional connectivity of this pathway. Our initial anatomical tracing studies in mice excluded the existence of a direct monosynaptic pathway between cerebellum and amygdala. Using transneuronal tracing techniques, we have identified a novel disynaptic pathway that connects the cerebellar output nuclei to the basolateral amygdala. This pathway recruits the understudied intralaminar thalamus as a node. Using ex vivo optophysiology and super-resolution microscopy, we provide the first evidence for the functionality of the pathway, thus offering a missing mechanistic link between the cerebellum and amygdala. This discovery provides a connectivity blueprint between the cerebellum and a key structure of the limbic system. As such, it is the requisite first step toward obtaining new knowledge about cerebellar function in emotion, thus fundamentally advancing understanding of the neurobiology of emotion, which is perturbed in mental and autism spectrum disorders.


title: A transcytotic actin shift polarizes vesicle trajectories and partitions apicobasal epithelial membrane domains

abstract: AbstractIn prevailing epithelial polarity models, membrane-based polarity cues such as the partitioning-defective PARs specify the positions and identities of apicobasal membrane domains. Recent findings suggest, however, that vesicle-associated polarity cues specify membrane polarity by positioning the apical domain, upstream of membrane-based polarity cues. These findings raised the question how vesicles acquire apicobasal directionality independent of polarized target membrane domains. Here, we show that the apical directionality of vesicle trajectories depends on intracellular actin dynamics during the establishment of membrane polarity in the C. elegans intestine. We find that actin, powered by branched-chain actin dynamics, determines the position of apical membrane components, PARs, and itself on expanding membranes. Using photomodulation, we demonstrate that F-actin travels through the cytoplasm and along the cortex towards the future apical domain. Our findings suggest an alternative polarity model where actin-dependent directional trafficking inserts the nascent apical domain into the growing membrane to partition its apicobasal domains.


title: The optimal docking strength for reversibly tethered kinases

abstract: Many kinases use reversible docking interactions to augment the specificity of their catalytic domains. Such docking interactions are often structurally independent of the catalytic domain, which allow for flexible combination of modules in evolution and in bioengineering. The affinity of docking interactions spans several orders of magnitude. This led us to ask how the affinity of the docking interaction affects enzymatic activity, and how to pick the optimal interaction module to complement a given substrate. Here, we develop equations that predict the optimal binding strength of a kinase docking interaction and validate it using numerical simulations and steady-state phosphorylation kinetics for tethered protein kinase A. We show that a kinase-substrate pair has an optimum docking strength that depends on their enzymatic constants, the tether architecture, the substrate concentration and the kinetics of the docking interactions. We show that a reversible tether enhances phosphorylation rates most when: I) The docking strength is intermediate, II) the substrate is non-optimal, III) the substrate concentration is low, IV) the docking interaction has rapid exchange kinetics, and V) the tether optimizes the effective concentration of the intra-molecular reaction. This work serves as a framework for interpreting mutations in kinase docking interactions and as a design guide for engineering enzyme scaffolds.


title: Apremilast prevents blistering in human epidermis by stabilization of keratinocyte adhesion in pemphigus.

abstract:
Pemphigus vulgaris (PV) is a life-threatening blistering skin disease caused by autoantibodies (PV-IgG) destabilizing desmosomal adhesion. Current therapies focus on suppression of autoantibody formation and thus treatments directly stabilizing keratinocyte adhesion would fulfill an unmet medical need. We here demonstrate that apremilast, a phosphodiesterase 4 inhibitor used e.g. in psoriasis, prevents blistering in PV. Apremilast abrogated PV-IgG-induced loss of keratinocyte cohesion in ex-vivo epidermis and in vitro. This was paralleled by inhibition of keratin retraction and desmosome splitting but affected neither desmoglein (Dsg) depletion nor Dsg3 binding properties.

Apremilast induced phosphorylation of plakoglobin at serine 665 - a mechanisms which is known to stabilize cardiomyocyte cohesion. Interestingly, keratinocytes phospho-deficient at this side showed altered organization of Dsg1, Dsg3 and keratin filaments and impaired adhesion, which was not rescued by apremilast. These data identified a new mechanism of desmosome regulation and propose that apremilast is protective in pemphigus by stabilizing keratinocyte cohesion.


title: Metabolic-scale gene activation screens identify SLCO2B1 as a heme transporter that enhances cellular iron availability

abstract: Iron is the most abundant transition metal in cells and essential for a wide range of biochemical processes. While most mammalian cells take up iron through receptor-mediated endocytosis of transferrin, molecular players involved in iron utilization under iron-limiting conditions are incompletely understood. To address this, we performed several parallel metabolism-focused CRISPRa gain of function screens, which revealed metabolic limitations under stress conditions. Screens for iron restriction identified expected members of iron utilization pathways, but also SLCO2B1, a poorly characterized membrane carrier. Expression of SLCO2B1 is sufficient to increase intracellular iron stores, bypass the essentiality of transferrin receptor-mediated iron uptake and enable cell proliferation under iron restriction. Mechanistically, SLCO2B1 mediates heme-analog import in cellular assays. Heme uptake by SLCO2B1 provides sufficient iron for cell proliferation through heme oxygenases. Notably, SLCO2B1 is predominantly expressed in microglia in the brain and primary microglia from Slco2b1-/- mice exhibit a strong defect in heme analog import. Altogether, our work identifies SLCO2B1 as a microglia-enriched plasma membrane heme importer and provides a genetic platform to identify metabolic limitations under stress conditions.


title: A pair of primers facing at the double-strand break site enables to detect NHEJ-mediated indel mutations at a 1-bp resolution

abstract: The introduction of small insertion/deletion (indel) mutations in the coding region of genes by the site-specific nucleases such as Cas9 allows researchers to obtain frameshift null mutants. Technically simple and costly reasonable genotyping methods are awaited to efficiently screen the frameshift null mutant candidates. Here, we developed a simple genotyping method called DST-PCR (Double-strand break Site-Targeted PCR) using "face-to-face" primers where the 3 ends of forward and reverse primers face each other at the position between 3-bp and 4-bp upstream of the PAM sequence, which is generally the Cas9-mediated double-strand break site. Generated amplicons are directly subjected to TBE-High-Resolution PAGE, which contains a high concentration of bis-acrylamide, for mutant clones detection with 1-bp resolution. We demonstrate six examples of CRISPR/Cas9-engineered knockout cells, to screen indels to obtain potential KO cell clones utilizing our approach. This method allowed us to detect 1-bp to 2-bp insertion and 1-bp to 4-bp deletion in one or both alleles of mutant cell clones. In addition, this technique also allowed the identification of heterozygous and homozygous biallelic functional KO candidates. Thus, DST-PCR coupled with TBE-High-Resolution PAGE is a simple method for genotyping of the CRISPR/Cas9-engineered cell lines, which can be performed without special equipment and techniques.


title: FGF8 induces chemokinesis and regulates condensation of mouse nephron progenitor cells

abstract: Kidneys develop via iterative branching of the ureteric epithelial tree and subsequent nephrogenesis at the branch points. Nephrons form in the cap mesenchyme as the metanephric mesenchyme (MM) condenses around the epithelial ureteric buds (UBs). Previous work demonstrated that FGF8 is important for the survival of nephron progenitor cells (NPCs), and early deletion of Fgf8 leads to the cessation of nephron formation, which results in post-natal lethality. We now reveal a novel function of FGF8. By combining transgenic mouse models, quantitative imaging assays, and data-driven computational modelling, we show that FGF8 has a strong chemokinetic effect and that this chemokinetic effect is important for the condensation of NPCs to the UB. The computational model shows that the motility must be lower close to the UB to achieve NPC attachment. We conclude that the FGF8 signalling pathway is crucial for the coordination of NPCs behaviour to the UB. Chemokinetic effects have been described also for other FGFs and may be relevant more generally for the formation of mesenchymal condensations.

category: developmental biology


title: High-throughput cryo-EM structure determination of amyloids

abstract: The formation of amyloid filaments is characteristic of various degenerative diseases. Recent breakthroughs in electron cryo-microscopy (cryo-EM) have led to atomic structure determination of multiple amyloid filaments, both of filaments assembled in vitro from recombinant proteins, and of filaments extracted from diseased tissue. These observations revealed that a single protein may adopt multiple different amyloid folds, and that in vitro assembly does not necessarily lead to the same filaments as those observed in disease. In order to develop relevant model systems for disease, and ultimately to better understand the molecular mechanisms of disease, it will be important to determine which factors determine the formation of distinct amyloid folds. High-throughput cryo-EM, in which structure determination becomes a tool rather than a project in itself, will facilitate the screening of large numbers of in vitro assembly conditions. To this end, we describe a new filament picking algorithm based on the Topaz approach, and we outline image processing strategies in Relion that enable atomic structure determination of amyloids within days.


title: Comparative analysis of cell-cell communication at single-cell resolution

abstract: Inference of cell-cell communication (CCC) from single-cell RNA-sequencing data is a powerful technique to uncover putative axes of multicellular coordination, yet existing methods perform this analysis at the level of the cell type or cluster, discarding single-cell level information. Here we present Scriabin - a flexible and scalable framework for comparative analysis of CCC at single-cell resolution. We leverage multiple published datasets to show that Scriabin recovers expected CCC edges and use spatial transcriptomic data, genetic perturbation screens, and direct experimental manipulation of receptor-ligand interactions to validate that the recovered edges are biologically meaningful. We then apply Scriabin to uncover co-expressed programs of CCC from atlas-scale datasets, validating known communication pathways required for maintaining the intestinal stem cell niche and revealing species-specific communication pathways. Finally, we utilize single-cell communication networks calculated using Scriabin to follow communication pathways that operate between timepoints in longitudinal datasets, highlighting bystander cells as important initiators of inflammatory reactions in acute SARS-CoV-2 infection. Our approach represents a broadly applicable strategy to leverage single-cell resolution data maximally toward uncovering CCC circuitry and rich niche-phenotype relationships in health and disease.


title: A Suite of TMPRSS2 Assays for Screening Drug Repurposing Candidates as Potential Treatments of COVID-19

abstract: SARS-CoV-2 is the causative viral pathogen driving the COVID-19 pandemic that prompted an immediate global response to the development of vaccines and antiviral therapeutics. For antiviral therapeutics, drug repurposing allowed for rapid movement of existing clinical candidates and therapies into human clinical trials to be tested as COVID-19 therapies. One effective antiviral treatment strategy used early in symptom onset is to prevent viral entry. SARS-CoV-2 enters ACE2-expressing cells when the receptor-binding domain of the spike protein on the surface of SARS-CoV-2 binds to ACE2 followed by cleavage at two cut sites on the spike protein. TMPRSS2 has a protease domain capable of cleaving the two cut sites; therefore, a molecule capable of inhibiting the protease activity of TMPRSS2 could be a valuable antiviral therapy. Initially, we used a fluorogenic high-throughput screening assay for the biochemical screening of 6030 compounds in NCATS annotated libraries. Then, we developed an orthogonal biochemical assay that uses mass spectrometry detection of product formation to ensure that hits from the primary screen are not assay artifacts from the fluorescent detection of product formation. Finally, we assessed the hits from the biochemical screening in a cell-based SARS-CoV-2 pseudotyped particle entry assay. Of the six molecules advanced for further studies, two are approved drugs in Japan (camostat and nafamostat), two have entered clinical trials (PCI-27483 and otamixaban), while the other two molecules are peptidomimetic inhibitors of TMPRSS2 taken from the literature that have not advanced into clinical trials (compounds 92 and 114). This work demonstrates a suite of assays for the discovery and development of new inhibitors of TMPRSS2.

category: biochemistry


title: Mutations of Omicron variant at the interface of the receptor domain motif and human angiotensin-converting enzyme-2

abstract: The most recent Omicron variant of SARS-CoV-2 has caused global concern and anxiety. The only thing certain about this strain, with large number of mutations in the spike protein, is that it spreads quickly, seems to evade immune defense and mitigates the benefits of existing vaccines. Based on the ultra-large-scale ab initio computational modeling of the receptor binding motif (RBM) and human angiotensin-converting enzyme-2 (ACE2) interface we provide the details of the effect of Omicron mutations at the fundamental atomic scale level. In-depth analysis anchored in the novel concept of amino acid-amino acid bond pair units (AABPU), indicates that mutations in the Omicron variant are connected with (i) significant changes in the shape and structure of AABPU components, together with (ii) significant increase in the positive partial charge which facilitates the interaction with ACE2. The calculated bond order, based on AABPU, reveals that the Omicron mutations increase the binding strength of RBM to ACE2. Our findings correlate with and are instrumental to explain the current observations and can contribute to the prediction of next potential new variant of concern.


title: Theta band-power shapes amyloid-driven longitudinal EEG changes in pre-clinical Alzheimer's Disease

abstract: Alzheimers Disease (AD) includes progressive symptoms spread along a continuum of pre-clinical (pre-AD) and clinical stages. Pre-AD refers to cognitively healthy individuals with presence of positive pathophysiological biomarkers of AD (i.e., markers of amyloidopathy and tauopathy). Although numerous studies uncovered the neuro-cognitive changes of AD, very little is known on the natural history of brain lesions and modifications of brain networks of pre-AD. To address this issue, we analysed resting-state EEG data of 318 cognitively healthy individuals with subjective memory complains from the INSIGHT-preAD cohort at the time of their first visit (M0) and two-years later (M24). Using 18F-florbetapir PET-scanner, subjects were stratified between amyloid positive (A-; n=230) and amyloid negative (A+; n=88) groups. Differences between A+ and A- individuals were estimated at source level in each band of the EEG power spectrum. At M0, we found an increase of theta-band power in the mid-frontal cortex in A+ compared to A-. No significant association was found between mid-frontal theta power and the individuals cognitive performance. While the very same effect was not replicated at M24, theta-band power increased in A+ relative to A- individuals in the posterior cingulate cortex and the pre-cuneus. Furthermore, alpha band revealed a peculiar decremental trend in posterior brain regions in the A+ relative to the A- group only at M24. These results provide the first source-level longitudinal evidence on the impact of brain amyloidosis on the EEG dynamics of a large-scale, monocentric cohort of pre-AD. Theta-band power increase over the mid-frontal and mid-posterior cortices suggests an hypoactivation of the default-mode network in individuals at-risk of AD and a non-linear longitudinal progression of the AD-spectrum.


title: Phage therapy potentiates second-line antibiotic treatment against pneumonic plague

abstract:
Plague pandemics and outbreaks have killed millions of people during the history of humankind. The disease, caused by Yersinia pestis bacteria, can currently be treated efficiently with antibiotics. However, in the case of multidrug-resistant (MDR) bacteria, alternative treatments are required. Bacteriophage (phage) therapy has shown efficient antibacterial activity in various experimental animal models and in human patients infected with different MDR pathogens. Herein, we evaluated the efficiency of {phi}A1122 and PST phage therapy, alone or in combination with second-line antibiotics, using a well-established mouse model of pneumonic plague. Phage treatment significantly delayed mortality and limited bacterial proliferation in the lungs. However, the treatment did not prevent bacteremia, suggesting that phage efficiency may decrease in circulation. Indeed, in vitro phage proliferation assays indicated that blood has inhibitory effects on lytic activity, which may be the major cause of treatment inefficiency.

Combining phage therapy and second-line ceftriaxone treatment, which are individually insufficient, provided protection that led to survival of all infected animals, presenting a synergistic protective effect that represents a proof of concept for efficient combinatorial therapy in an emergency event of a plague outbreak involving MDR Y. pestis strains.

Author summaryPlague, caused by Yersinia pestis bacteria, can be efficiently treated with antibiotics. However, alternative therapies for the case of natively evolved or maliciously generated antibiotic-resistant Y. pestis must be developed. Due to the global increase in antibiotic resistance, there is renewed interest in examining the effectiveness of bacteriophage-based alternative therapies. Here, using a mouse model of pneumonic plague, we demonstrate that phage treatment significantly delayed mortality. By monitoring bioluminescence of engineered Y. pestis strain and live bacterial counts, we show that phage therapy effectively inhibited bacterial proliferation in the lung but not in blood. In vitro analyses showed decreased phage activity in the presence of blood, which probably explains the low efficacy of phage treatment alone. Because combination therapies will be used in an emergency situation, we tested the efficacy of Y. pestis-lysing phages as adjunctive therapy with a second-line antibiotic, ceftriaxone.

Whereas each individual treatment was insufficient, the combination provided effective protection and rescued all infected animals. These results clearly demonstrated the synergistic effect of combined phage and antibiotic therapy and represent a proof of concept for this alternative therapy against multidrug-resistant Y. pestis strains.

category: microbiology


title: Feedback regulation of RNase E during UV-stress response in the cyanobacterium Synechocystis sp. PCC 6803

abstract: Endoribonucleases govern the maturation and degradation of RNA and are indispensable in the posttranscriptional regulation of gene expression. A key endoribonuclease in many bacteria is RNase E. To ensure an appropriate supply of RNase E, some bacteria, such as E. coli, have evolved tightly functioning feedback regulation of RNase E that is mediated in cis by the rne 5'-untranslated region (5' UTR); however, the mechanisms involved in the control of RNase E in other bacteria largely remain unknown. Cyanobacteria rely on solar light as an energy source for photosynthesis, despite the inherent ultraviolet (UV) irradiation. Here, we investigated the global gene expression response in the cyanobacterium Synechocystis sp. PCC 6803 after exposure to UV light and discovered a unique response of RNase E: a rapidly increasing enzymatic activity, although the stability of the protein was decreased. In parallel, we observed an increased accumulation of full-length rne mRNA that was caused by the stabilization of its 5' UTR and suppression of premature transcriptional termination but not by an increased transcription rate. Mapping of RNA 3' ends and in vitro cleavage assays revealed that RNase E cleaves within a stretch of six consecutive uridine residues within the rne 5' UTR, indicating autoregulation via its own 5' UTR. These observations imply that RNase E in cyanobacteria contributes substantially to reshaping the transcriptome during the UV stress response and that its required activity level is maintained despite enhanced turnover of the protein by posttranscriptional feedback regulation.


title: Enterovirus replication and dissemination are differentially controlled by type I and III interferons in the GI tract

abstract: Enteroviruses are amongst the most common viral infectious agents of humans and cause a broad spectrum of mild-to-severe illness. Enteroviruses are primarily transmitted by the fecal-oral route, but the events associated with their intestinal replication in vivo are poorly defined. Here, we developed a neonatal mouse model of enterovirus infection by the enteral route using echovirus 5 and used this model to define the differential roles of type I and III interferons (IFNs) in enterovirus replication in the intestinal epithelium and subsequent dissemination to secondary tissues. We show that human FcRn, the primary receptor for echoviruses, is essential for intestinal infection by the enteral route and that type I IFNs control dissemination to secondary sites, including the liver. In contrast, type III IFNs limit enterovirus infection in the intestinal epithelium and mice lacking this pathway exhibit persistent epithelial replication. Finally, we show that echovirus infection in the small intestine is cell-type specific and occurs exclusively in enterocytes. These studies define the type-specific roles of IFNs in enterovirus infection of the GI tract and the cellular tropism of echovirus intestinal replication.


title: Inflammatory monocytes promote pyogranuloma formation to counteract Yersinia blockade of host defense

abstract: Granulomas are organized immune cell aggregates that form in response to chronic infection or antigen persistence. Yersinia pseudotuberculosis (Yp) blocks innate inflammatory signaling and phagocytosis, inducing formation of neutrophil-rich pyogranulomas within lymphoid tissues. Here, we uncover that Yp triggers pyogranuloma formation within the murine intestinal mucosa, a site not known to contain such structures. Mice lacking circulating monocytes fail to form defined pyogranulomas, have defects in neutrophil activation, and succumb to Yp infection. Yersinia lacking the virulence factors that block phagocytosis did not induce pyogranulomas, indicating that intestinal pyogranulomas form in response to Yp disruption of phagocytosis. Notably, mutation of a single anti-phagocytic virulence factor, YopH, restored pyogranuloma formation and control of Yp infection in monocyte-deficient mice, demonstrating that monocytes override YopH-dependent blockade of innate immune defense. This work reveals an unappreciated site of Yersinia intestinal invasion, and defines host and pathogen drivers of intestinal granuloma formation.


title: Ruminococcus bromii enables the growth of proximal Bacteroides thetaiotaomicron by releasing glucose during starch degradation

abstract:
Complex carbohydrates shape the gut microbiota and the collective fermentation of resistant starch by gut microbes positively affects human health through enhanced butyrate production. The keystone species Ruminococcus bromii (Rb) is a specialist in degrading resistant starch; its degradation products are used by other bacteria including Bacteroides thetaiotaomicron (Bt). We analyzed the metabolic and spatial relationships between Rb and Bt during potato starch degradation and found that Bt utilizes glucose that is released from Rb upon degradation of resistant potato starch and soluble potato amylopectin. Additionally, we found that Rb produces a halo of glucose around it when grown on solid media containing potato amylopectin and that Bt cells deficient for growth on potato amylopectin ({Delta}sus Bt) can grow within the halo. Furthermore, when these {Delta}sus Bt cells grow within this glucose halo, they have an elongated cell morphology. This long-cell phenotype depends on the glucose concentration in the solid media: longer Bt cells are formed at higher glucose concentrations. Together, our results indicate that starch degradation by Rb cross-feeds other bacteria in the surrounding region by releasing glucose. Our results also elucidate the adaptive morphology of Bt cells under different nutrient and physiological conditions.

Impact StatementDietary intake of complex carbohydrates including resistant starch benefits human health by supporting the growth of keystone species that increase the microbiome diversity via cross-feeding. For instance, Ruminococcus bromii (Rb) is a specialist in degrading resistant starch, and the byproducts of this degradation process are used by bacterial species. In this study, we show that Bacteroides thetaiotaomicron (Bt) cross-feeds on the glucose released during potato starch degradation by Rb. We also show that proximity to Rb cells that are releasing sugars is important for the growth of the cross-fed Bt in solid media. Additionally, we find a longer phenotype for Bt cells grown on solid media in high glucose conditions, indicating that, like other bacteria, human gut bacteria undergo significant nutrient-dependent morphological adaptations.


title: Widespread emergence of OmpK36 loop 3 insertions among multidrug-resistant clones of Klebsiella pneumoniae

abstract:
Mutations in outer membrane porins act in synergy with carbapenemase enzymes to increase carbapenem resistance in the important nosocomial pathogen, Klebsiella pneumoniae (KP). A key example is a di-amino acid insertion, Glycine-Aspartate (GD), in the extracellular loop 3 (L3) region of OmpK36 which constricts the pore and restricts entry of carbapenems into the bacterial cell. Here we combined genomic and experimental approaches to characterise the diversity, spread and impact of different L3 insertion types in OmpK36. We identified L3 insertions in 3588 (24.1%) of 14,888 KP genomes with an intact ompK36 gene from a global collection. GD insertions were most common, with a high concentration in the ST258/512 clone that has spread widely in Europe and the Americas. Aspartate (D) and Threonine-Aspartate (TD) insertions were prevalent in genomes from Asia, due in part to acquisitions by ST16 and ST231 and subsequent clonal expansions. By solving the crystal structures of novel OmpK36 variants, we found that the TD insertion causes a pore constriction of 41%, significantly greater than that achieved by GD (10%) or D (8%), resulting in the highest levels of resistance to selected antibiotics. In a murine pneumonia model, KP mutants harbouring L3 insertions have a competitive disadvantage relative to a strain expressing wild-type OmpK36 in the absence of antibiotics. This explains the reversion of GD and TD insertions observed at low frequency among KP genomes. Finally, we demonstrate that strains expressing L3 insertions remain susceptible to drugs targeting carbapenemase-producing KP, including novel beta lactam-beta lactamase inhibitor combinations. This study provides a contemporary global view of OmpK36-mediated resistance mechanisms in KP, integrating surveillance and experimental data to guide treatment and drug development strategies.

Author summaryRapidly rising rates of antibiotic resistance among Klebsiella pneumoniae (KP) necessitate a comprehensive understanding of the diversity, spread and clinical impact of resistance mutations. In KP, mutations in outer membrane porins play an important role in mediating resistance to carbapenems, a key class of antibiotics. Here we show that resistance mutations in the extracellular loop 3 (L3) region of the OmpK36 porin are found at high prevalence among clinical genomes and we characterise their diversity and impact on resistance and virulence. They include amino acid insertions of Aspartate (D), Glycine-Aspartate (GD) and Threonine-Aspartate (TD), which act by decreasing the pore size and restricting entry of carbapenems into the bacterial cell. We show that these L3 insertions are associated with large clonal expansions of resistant lineages and impose only a low fitness cost. Critically, strains harbouring L3 insertions remain susceptible to novel drugs, including beta lactam-beta lactamase inhibitor combinations. This study highlights the importance of monitoring the emergence and spread of strains with OmpK36 L3 insertions for the control of resistant KP infections and provides crucial data for drug development and treatment strategies.


title: Statistical learning and uncommon soil microbiota explain biogeochemical responses after wildfire

abstract: 1Wildfires are a perennial event globally and the biogeochemical underpinnings of soil responses at relevant spatial and temporal scales are unclear. Soil biogeochemical processes regulate plant growth and nutrient losses that affect water quality, yet the response of soil after variable intensity fire is difficult to explain and predict. To address this issue, we examined two wildfires in Colorado, USA across the first and second post-fire years and leveraged Statistical Learning (SL) to predict and explain biogeochemical responses. We found that SL predicts biogeochemical responses in soil after wildfire with surprising accuracy. Of the 13 biogeochemical analytes analyzed in this study, 9 are best explained with a hybrid microbiome + biogeochemical SL model. Biogeochemical-only models best explain 3 features, and 1 feature is explained equally well with hybrid or biogeochemical-only models. In some cases, microbiome-only SL models are also effective (such as predicting NH4+). Whenever a microbiome component is employed, selected features always involve uncommon soil microbiota (i.e., the  rare biosphere, existing at < 1% relative abundance). Here, we demonstrate that SL paired with DNA sequence and biogeochemical data predict environmental features in post-fire soils, though this approach could likely be applied to any biogeochemical system.


title: Modified E2 glycoprotein of hepatitis C virus enhances pro-inflammatory cytokines and protective immune response in mice

abstract:
Hepatitis C virus (HCV) is characterized by a high number of chronic cases owing to an impairment of innate and adaptive immune responses. CD81 on the cell surface facilitates HCV entry by interacting with the E2 envelope glycoprotein. On the other hand, CD81/E2 binding on immune related cells may also influence host response outcome to HCV infection. Here, we performed site-specific amino acid substitution in the front layer of E2 sequence to reduce CD81 binding and evaluate HCV candidate vaccine potential. The altered sE2 protein (F442NYT), unlike sE2, displayed a significant reduction in CD81 binding, induced pro-inflammatory cytokines, and repressed anti-inflammatory response in primary monocyte-derived macrophages as antigen presenting cells. Further, sE2F442NYT stimulated CD4+T cell proliferation. Immunization of Balb/c mice with an E1/sE2F442NYT RNA-lipid nanoparticle (LNP) displayed improved IgG1 to IgG2a isotype switching, an increase in HCV pseudotype virus neutralizing antibodies, and resistance to challenge infection with a surrogate recombinant vaccinia virus expressing HCV E1-E2-NS2(aa134-966), unlike parental E1/sE2 immunization. Further investigation on modified E2 antigen for selection as antigen may provide helpful information for HCV vaccine development.

One Sentence SummaryReduced HCV E2-CD81 binding and immune response


title: Genome-wide identification of fitness determinants in the Xanthomonas campestris bacterial pathogen during early stages of plant infection

abstract: Plant diseases are an important threat to food production. While major pathogenicity determinants required for disease have been extensively studied, less is known on how pathogens thrive during host colonization especially at early infection stages. Here, we used randomly barcoded-transposon insertion site sequencing (RB-TnSeq) to perform a genome-wide screen and identify key bacterial fitness determinants of the vascular pathogen Xanthomonas campestris pv. campestris (Xcc) during infection of the cauliflower host plant (Brassica oleracea). This high-throughput analysis was conducted in hydathodes, the natural entry site of Xcc, in xylem sap and in synthetic media. Xcc did not face a strong bottleneck during hydathode infection. 183 genes important for fitness were identified in plant-associated environments with functional enrichment in genes involved in metabolism when only few genes known to be involved in virulence were found to be affected. The biological relevance of 13 genes was independently confirmed by phenotyping single mutants. Notably, we show that the XC_3388, a protein with no known function (DUF1631), plays a key role in the adaptation and virulence of Xcc possibly through c-di-GMP-mediated regulation. This study thus revealed yet unsuspected social behaviors adopted by Xcc individuals when confined inside hydathodes at early infection stages.


title: Identification of functional Spo0A residues critical for sporulation in Clostridioides difficile

abstract: Clostridioides difficile is an anaerobic, Gram-positive pathogen that is responsible for C. difficile infection (CDI). To survive in the environment and spread to new hosts, C. difficile must form metabolically-dormant spores. The formation of spores requires activation of the transcription factor Spo0A, which is the master regulator of sporulation in all endospore-forming bacteria. Though the sporulation initiation pathway has been delineated in the Bacilli, including the model spore-former Bacillus subtilis, the direct regulators of Spo0A in C. difficile remain undefined. C. difficile Spo0A shares highly conserved protein interaction regions with the B. subtilis sporulation proteins Spo0F and Spo0A, although many of the interacting factors present in B. subtilis are not encoded in C. difficile. To determine if comparable Spo0A residues are important for C. difficile sporulation initiation, site-directed mutagenesis was performed at conserved receiver domain residues and the effects on sporulation were examined. Mutation of residues important for homodimerization and interaction with both positive and negative regulators of B. subtilis Spo0A and Spo0F impacted C. difficile Spo0A function. The data also demonstrated that mutation of many additional conserved residues altered C. difficile Spo0A activity, even when the corresponding Bacillus interacting proteins are not apparent in the C. difficile genome. Finally, the conserved aspartate residue at position 56 of C. difficile Spo0A was determined to be the phosphorylation site that is necessary for Spo0A activation. The finding that Spo0A interacting motifs maintain functionality suggests that C. difficile Spo0A interacts with yet unidentified proteins that regulate its activity and control spore formation.


title: Detection of SARS-CoV-2 Omicron variant (B.1.1.529) infection of white-tailed deer

abstract:
White-tailed deer (Odocoileus virginianus) are highly susceptible to infection by SARS-CoV-2, with multiple reports of widespread spillover of virus from humans to free-living deer. While the recently emerged SARS-CoV-2 B.1.1.529 Omicron variant of concern (VoC) has been shown to be notably more transmissible amongst humans, its ability to cause infection and spillover to non-human animals remains a challenge of concern. We found that 19 of the 131 (14.5%; 95% CI: 0.10-0.22) white-tailed deer opportunistically sampled on Staten Island, New York, between December 12, 2021, and January 31, 2022, were positive for SARS-CoV-2 specific serum antibodies using a surrogate virus neutralization assay, indicating prior exposure. The results also revealed strong evidence of age-dependence in antibody prevalence. A significantly ({chi}2, p < 0.001) greater proportion of yearling deer possessed neutralizing antibodies as compared with fawns (OR=12.7; 95% CI 4-37.5). Importantly, SARS-CoV-2 nucleic acid was detected in nasal swabs from seven of 68 (10.29%; 95% CI: 0.0-0.20) of the sampled deer, and whole-genome sequencing identified the SARS-CoV-2 Omicron VoC (B.1.1.529) is circulating amongst the white-tailed deer on Staten Island. Phylogenetic analyses revealed the deer Omicron sequences clustered closely with other, recently reported Omicron sequences recovered from infected humans in New York City and elsewhere, consistent with human to deer spillover. Interestingly, one individual deer was positive for viral RNA and had a high level of neutralizing antibodies, suggesting either rapid serological conversion during an ongoing infection or a "breakthrough" infection in a previously exposed animal. Together, our findings show that the SARS-CoV-2 B.1.1.529 Omicron VoC can infect white-tailed deer and highlights an urgent need for comprehensive surveillance of susceptible animal species to identify ecological transmission networks and better assess the potential risks of spillback to humans.

Key FindingsThese studies provide strong evidence of infection of free-living white-tailed deer with the SARS-CoV-2 B.1.1.529 Omicron variant of concern on Staten Island, New York, and highlight an urgent need for investigations on human-to-animal-to-human spillovers/spillbacks as well as on better defining the expanding host-range of SARS-CoV-2 in non-human animals and the environment.


title: Designing a novel monitoring approach for the effects of space travel on astronauts' health

abstract: Space exploration and extraterrestrial civilization have fascinated humankind since the earliest days of human history. However, it was only until last century that humankind finally began taking significant steps towards these goals by sending astronauts into space, landing on the moon, and building the International Space Station. However, space voyage is very challenging and dangerous, and astronauts are under constant space radiation and microgravity. It has been shown that astronauts are at a high risk of developing a broad range of diseases/disorders. Thus, it is critical to develop a rapid and effective assay to monitor astronauts health in space. In this study, gene expression and correlation patterns were analyzed for 10 astronauts (8 male and 2 female) using the publicly available microarray dataset E-GEOD-74708. We identified 218 differentially expressed genes between In-flight and Pre-flight and noticed that space travel decreased genome regulation and gene correlations across the entire genome, as well as individual signaling pathways. Furthermore, we rationally designed a rapid assay of 32 genes which could be used to monitor astronauts health during space travel. Further studies, including microgravity experiments, are warranted to optimize and validate the proposed assay.

category: molecular biology


title: Development of a Ribosome Profiling Protocol to Study Translation in the yeast Kluyveromyces marxianus

abstract:
Kluyveromyces marxianus is an interesting and important yeast because of particular traits like thermotolerance and rapid growth, and applications in food and industrial biotechnology. Knowing how K. marxianus responds and adapts to changing environments is important to achieve a full understanding of the its biology and to develop bioprocesses. For this, a full suite of omics tools to measure and compare global patterns of gene expression and protein synthesis is needed. Whereas transcriptome analysis by RNA-Seq quantifies mRNA abundance, ribosome profiling allows codon-resolution of translation on a genome-wide scale by deep sequencing of ribosome locations on mRNAs and is emerging as a valuable tool to study translation control of gene expression. We report here the development of a ribosome profiling method for K. marxianus and we make the procedure available as a step by step protocol. To aid in the analysis and sharing of ribosome profiling data, we also added the K. marxianus genome as well as transcriptome and ribosome profiling data to the publicly accessible GWIPS-viz and Trips-Viz browsers. Users are able to upload custom ribosome profiling and RNA-Seq data to both browsers, therefore allowing easy analysis and sharing of data. As many studies only focus on the use of RNA-Seq to study K. marxianus in different environments, the availability of ribosome profiling is a powerful addition to the K. marxianus toolbox.

Graphical abstractDevelopment of a Ribosome Profiling protocol to study gene expression in the thermotolerant yeast Kluyveromyces marxianus.

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title: Spatio-temporal monitoring of lake fish spawning activity using environmental DNA metabarcoding

abstract: Determining the timing and location of fish reproductive events is crucial for the implementation of correct management and conservation schemes. Conventional methods used to monitor these events are often unable to assess the spawning activity directly or can be invasive and therefore problematic. This is especially the case when threatened fish populations are the study subject, such as the Arctic charr (Salvelinus alpinus L.) populations in Windermere (Cumbria, UK). Arctic charr populations have been studied in this lake since the 1940s, and the locations and characteristics of spawning grounds have been described in detail using techniques such as hydroacoustics, as well as physical and visual surveys of the lake bottom. Here, in conjunction with established netting surveys, we added an environmental DNA (eDNA) metabarcoding approach to assess the spatial distribution of Arctic charr in the lake throughout the year to test whether this tool could allow us to identify spawning locations and activity. Sampling was carried out between October 2017 and July 2018 at three locations in the lake, covering putative and known spawning sites. eDNA metabarcoding provided accurate spatial and temporal characterisation of Arctic charr spawning events. Peaks of Arctic charr read counts from eDNA metabarcoding were observed during the spawning season and at specific locations of both putative and known spawning sites. Net catches of mature Arctic charr individuals confirmed the association between the Arctic charr spawning activity and the peaks of eDNA metabarcoding read counts. This study demonstrates the ability of eDNA metabarcoding to effectively and efficiently characterize the spatial and temporal nature of fish spawning in lentic systems.


title: Sugar alcohols have the potential as bee-safe feeding stimulants for wasp control

abstract:
Pest insects are often baited with poisoned feeding stimulants, the most common of which are sugars. However, sugars are attractive for most animal species, which makes it difficult to target only a specific pest insect species. Here, we assessed different sugar alcohols for their potential as more species-selective feeding stimulants for pest insects. We tested the attractiveness of the sugar alcohols sorbitol, xylitol and erythritol with a capillary feeder assay in wasps (as potential pest insects, because introduced wasps are a pest in many regions) and bees (as non-target insects). For the common wasp (Vespula vulgaris), sorbitol and xylitol acted as nutritive feeding stimulants, and erythritol acted as a non-nutritive feeding stimulant. For the buff-tailed bumble bee (Bombus terrestris), sorbitol acted as a feeding stimulant, while for the honey bee (Apis mellifera), none of the sugar alcohols acted as feeding stimulant. The species-specific preferences for sugar alcohols suggest their potential as species-selective insect baits. The wasp-specific preference for xylitol suggests its potential as bee-safe alternative to sugar-containing bait for wasp pest control.

GRAPHICAL ABSTRACT O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY We tested the attractiveness of sugar alcohols with a capillary feeder assay in wasps and bees. Species-specific preferences suggests that sugar alcohols have the potential for being used as bee-safe insect baits.

C_FIG_DISPLAY

category: ecology


title: Predictability and transferability of local biodiversity environment relationships

abstract: Biodiversity varies in space and time, and often in response to environmental heterogeneity. Indicators in the form of local biodiversity measures - such as species richness or abundance - are common tools to capture this variation. The rise of readily available remote sensing data has enabled the characterization of environmental heterogeneity in a globally robust and replicable manner. Based on the assumption that differences in biodiversity measures are generally related to differences in environmental heterogeneity, these data have enabled projections and extrapolations of biodiversity in space and time. However so far little work has been done on quantitatively evaluating if and how accurately local biodiversity measures can be predicted. Here I combine estimates of biodiversity measures from local biodiversity surveys with remotely-sensed data on environmental heterogeneity globally. I then determine through a cross-validation framework how accurately local biodiversity measures can be predicted within ("predictability") and across similar ("transferability")biodiversity surveys. I found that prediction errors can be substantial, with error magnitudes varying between different biodiversity measures, taxonomic groups, sampling techniques and types of environmental heterogeneity characterizations. And although errors associated with model predictability were in many cases relatively low, these results question - particular for transferability - our capability to accurately predict and project local biodiversity measures based on environmental heterogeneity. I make the case that future predictions should be evaluated based on their accuracy and inherent uncertainty, and ecological theories be tested against whether we are able to make accurate predictions from local biodiversity data.


title: Imputation of 3D genome structure by genetic-epigenetic interaction modeling in mice

abstract:
Gene expression is known to be affected by interactions between local genetic variation and DNA accessibility, with the latter organized into three-dimensional chromatin structures. Analyses of these interactions has previously been limited, obscuring their regulatory context, and the extent to which they occur throughout the genome. Here we undertake a genome-scale analysis of these interactions in a genetically diverse population to systematically identify global genetic-epigenetic interaction, and reveal constraints imposed by chromatin structure. We establish the extent and structure of genotype-by-epigenotype interaction using embryonic stem cells derived from Diversity Outbred mice. This mouse population segregates millions of variants from eight inbred founders, enabling precision genetic mapping with extensive genotypic and phenotypic diversity. With 176 samples profiled for genotype, gene expression, and open chromatin, we used regression modeling to infer genetic-epigenetic interactions on a genome-wide scale. Our results demonstrate that statistical interactions between genetic variants and chromatin openness are common throughout the genome. We found that these interactions occur within the local area of the affected gene, and that this locality corresponds to topologically associated domains (TADs). The likelihood of interaction was most strongly defined by the 3D domain structure rather than linear DNA sequence. We show that stable 3D genome structure is an effective tool to guide searches for regulatory elements and, conversely, that regulatory elements in genetically diverse populations provide a means to infer 3D genome structure. In stem cells, open chromatin participating in the most significant regression models demonstrated an enrichment for developmental genes and the TAD-forming CTCF binding complex, providing an opportunity for statistical inference of TAD boundaries operating during early development. These findings provide evidence that genetic and epigenetic factors operate within the context of three-dimensional chromatin structure.

Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

category: genetics


title: Olfactory detection and discrimination in domestic dogs (Canis lupus familiaris)

abstract: The extraordinary olfactory capabilities in detection and rescue dogs are well-known. However, the olfactory performance varies by breed and search environment (Jezierski et al., 2014), as well as by the quantity of training (Horowitz et al., 2013). While detection of an olfactory cue inherently demands a judgment regarding the presence or absence of a cue at a given location, olfactory discrimination requires an assessment of quantity, a task demanding more attention and, hence, decreasing reliability as an informational source (Horowitz et al., 2013). This study aims at gaining more clarity on detection and discrimination of olfactory cues in untrained dogs and in a variety of dog breeds. Using a two-alternative forced choice (2AFC) paradigm, we assessed olfactory detection scores by presenting a varied quantity of food reward under one or the other hidden cup, and discrimination scores by presenting two varied quantities of food reward under both hidden cups. We found relatively reliable detection performances across all breeds and limited discrimination abilities, modulated by breed. We discuss our findings in relation to the cognitive demands imposed by the tasks and the cephalic index of the dog breeds.

category: animal behavior and cognition


title: DIP2 is a unique regulator of diacylglycerol lipid homeostasis in eukaryotes

abstract: Chain-length specific subsets of diacylglycerol (DAG) lipids are proposed to regulate differential physiological responses ranging from signal transduction to modulation of the membrane properties. However, the mechanism or molecular players regulating the subsets of DAG species remains unknown. Here, we uncover the role of a conserved eukaryotic protein family, DISCO-interacting protein 2 (DIP2) as a homeostatic regulator of a chemically distinct subset of DAGs using yeast, fly and mouse models. Genetic and chemical screens along with lipidomics analysis in yeast reveal that DIP2 prevents the toxic accumulation of specific DAGs in the logarithmic growth phase, which otherwise leads to endoplasmic reticulum stress. We also show that the fatty acyl-AMP ligase-like domains of DIP2 are essential for the redirection of the flux of DAG subspecies to storage lipid, triacylglycerols. Such modulation of selective DAG abundance by DIP2 is found to be crucial for optimal vacuole-membrane fusion and consequently osmoadaptation in yeast. Thus, the study illuminates an unprecedented DAG metabolism route and provides new insights on how cell fine-tunes DAG subspecies for cellular homeostasis and environmental adaptation.


title: Glycan shield of the ebolavirus envelope glycoprotein GP

abstract: The envelope glycoprotein GP of the ebolaviruses is essential for host cell attachment and entry. It is also the primary target of the protective and neutralizing antibody response in both natural infection and vaccination. GP is heavily glycosylated with up to 17 predicted N-linked sites, numerous O-linked glycans in its disordered mucin-like domain (MLD), and three predicted C-linked mannosylation sites. Glycosylation of GP is important for host cell attachment to cell-surface lectins, as well as GP stability and fusion activity. Moreover, it has been shown to shield GP from neutralizing activity of serum antibodies. Here, we use mass spectrometry-based glycoproteomics to profile the site-specific glycosylation patterns of ebolavirus GP. We detect up to 16 unique O-linked glycosylation sites in the mucin-like domain, as well as two O-linked sites in the head and glycan cap domains of the receptor-binding GP1 subunit. Multiple O-linked glycans are observed at the S/T residues of N-linked glycosylation sequons, suggesting possible crosstalk between the two types of modifications. We also confirmed the presence of C-mannosylation at W288 in the context of trimeric GP. We find heterogenous, complex N-linked glycosylation at the majority of predicted sites as expected. By contrast, the two conserved sites N257 and N563 are enriched in unprocessed high-mannose and hybrid glycans, suggesting a role in host-cell attachment via DC-SIGN/L-SIGN. We discuss our findings in the context of antibody recognition to show how glycans contribute to and restrict neutralization epitopes. This information on how N-, O-, and C-linked glycans together build the heterogeneous glycan shield of GP can guide future immunological studies and functional interpretation of ebolavirus GP-antibody interactions.


title: Lipid network and moiety analyses reveal enzymatic dysregulation and altered mechanisms from lipidomics

abstract:
Lipidomics is of growing importance for clinical and biomedical research due to an increasing number of discovered associations between lipid metabolism and diseases. However, sophisticated computational methods are required for biological interpretation including an understanding of metabolic processes, and their underlying (patho)mechanisms from lipidomics data. This can be achieved by using metabolic networks in combination with graph algorithms. Here, we present a lipid network analysis framework (Lipid Network Explorer, short LINEX) that allows biological interpretation of changes in lipidome composition. We developed an algorithm to generate data-specific lipid species networks from reaction database information. Using these networks, we developed a network enrichment algorithm that infers changes in enzymatic activity from lipidomics data, by leveraging multispecificity of lipid enzymes. Our inference method successfully recovered the MBOAT7 enzyme from knock-out lipidomics data. Additionally, we predict a PLA2 member to be at the center of dysregulation in adipose tissue in obesity. In our work, we showed the potential of lipidomics data to unravel mechanisms of metabolic regulation. Thereby our presented method can make lipidomics more clinically relevant by elucidating potential disease mechanisms.

Synopsis

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/479101v1_ufig1.gif" ALT="Figure 1">
View larger version (30K):
org.highwire.dtl.DTLVardef@b1bfd5org.highwire.dtl.DTLVardef@1a95b28org.highwire.dtl.DTLVardef@19fb162org.highwire.dtl.DTLVardef@136bb9d_HPS_FORMAT_FIGEXP  M_FIG C_FIG The Lipid Network Explorer (LINEX) is a framework to visualize and analyze quantitative lipidomics data. The included algorithms offer new perspectives on the lipidome and can propose potential mechanisms of dysregulation.

O_LIUsing the Reactome and Rhea databases, a comprehensive set of lipid class reactions is included and utilized to map the lipidome on custom data-specific networks.
C_LIO_LIWith a novel network enrichment method, enzymatic dysregulation can be recovered from lipidomics data.
C_LIO_LIWe validate its usability on data with a central lipid enzymatic deficiency.
C_LIO_LILINEX is the first tool capable of such analysis and includes complementary analyses options for structural lipid analysis. It is freely available as a web service (https://exbio.wzw.tum.de/linex).
C_LI


title: Probabilistic Modeling Confirms Delayed, But Non-Deficient Locomotor Development in Low Birth Weight Piglets

abstract: 1In the study of vertebrate locomotion, kinematic measures of gait, dynamic posture, and coordination often change when comparing subjects of different body mass, size, and age. Is it, conversely, possible to infer subject characteristics from the kinematic measures? For this study, piglets (Sus domesticus) were filmed from lateral perspective during their first ten hours of life, an age at which body mass and size have major consequences for survival. We then apply deep learning methods for point digitization (DeepLabCut), calculate joint angle profiles, and apply information-preserving transfromations (Fourier Series and PCA) to retrieve a multivariate kinematic data set. We train a probabilistic model to predict subject characteristics from kinematics. The model infers subject characteristics accurately for strides from piglets of normal birth weight (i.e. the category it was trained on), but surprisingly predicts the body mass and size of low birth weight piglets (which were left out of training, out-of-sample prediction) to be "normal". The discrepancies between prediction and observation confirm that dynamic posture and coordination are unaffected by lower birth weight and lower size, which is evidence that low birth weight does not imply locomotor deficits. However, the age of some (but not all) low birth weight individuals is underestimated, supporting the hypothesis that these piglets can experience a delay in locomotor maturation.

category: zoology


title: HIV-1 cell-to-cell spread overcomes the virus entry block of non-macrophage-tropic strains in macrophages

abstract:
Macrophages (M{Phi}) are increasingly recognized as HIV-1 target cells involved in the pathogenesis and persistence of infection. Paradoxically, in vitro infection assays suggest that virus isolates are mostly T-cell-tropic and rarely M{Phi}-tropic. The latter are assumed to emerge under CD4+ T-cell paucity in tissues such as the brain or at late stage when the CD4 T-cell count declines. However, assays to qualify HIV-1 tropism use cell-free viral particles and may not fully reflect the conditions of in vivo M{Phi} infection through cell-to-cell viral transfer. Here, we investigated the capacity of viruses expressing primary envelope glycoproteins (Envs) with CCR5 and/or CXCR4 usage from different stages of infection, including transmitted/founder Envs, to infect M{Phi} by a cell-free mode and through cell-to-cell transfer from infected CD4+ T cells. The results show that most viruses were unable to enter M{Phi} as cell-free particles, in agreement with the current view that non-M-tropic viruses inefficiently use CD4 and/or CCR5 or CXCR4 entry receptors on M{Phi}. In contrast, all viruses could be effectively cell-to-cell transferred to M{Phi} from infected CD4+ T cells. We further showed that viral transfer proceeded through Env-dependent cell-cell fusion of infected T cells with M{Phi} targets, leading to the formation of productively infected multinucleated giant cells. Compared to cell-free infection, infected T-cell/M{Phi} contacts showed enhanced interactions of R5 M- and non-M-tropic Envs with CD4 and CCR5, resulting in a reduced dependence on receptor expression levels on M{Phi} for viral entry. Altogether, our results show that virus cell-to-cell transfer overcomes the entry block of isolates initially defined as non-macrophage-tropic, indicating that HIV-1 has a more prevalent tropism for M{Phi} than initially suggested. This sheds light into the role of this route of virus cell-to-cell transfer to M{Phi} in CD4+ T cell rich tissues for HIV-1 transmission, dissemination and formation of tissue viral reservoirs.

Author SummaryUnderstanding how HIV-1 hijacks the functions of immune cells to promote viral spreading remains a challenge in the fight against infection. M{Phi} are ubiquitous tissue-resident cells, involved in tissue homeostasis and immunity. In HIV-1 infection, along with CD4+ T lymphocytes, M{Phi} serve as vectors for virus dissemination and as viral reservoirs, impeding HIV-1 eradication. However, the mechanisms of their infection remain incompletely understood. A paradox is that infected M{Phi} are found in a large range of tissues whereas in vitro cellular tropism assays indicate that only a limited number of HIV-1 isolates can enter M{Phi}. We hypothesized that these assays, which evaluate infection using cell-free viruses, might not fully reflect the modes of M{Phi} infection in patients. We report here that virus cell-to-cell transfer through cell-cell fusion with infected CD4+ T cells is a very effective means of infecting M{Phi}, even with virus isolates characterized as non-macrophage tropic in cell-free infection. This intercellular viral transfer is facilitated by enhanced interactions between the HIV-1 envelope glycoproteins and cellular entry receptors. We propose that M{Phi} infection through viral transfer from infected CD4+ T cells impacts different aspects of the pathophysiology of HIV-1 infection, renewing our understanding of the role of M{Phi} in HIV-1 pathogenesis and persistence.


title: The role of the gut microbiota in patients with Kleefstra syndrome

abstract: Kleefstra Syndrome (KS) is a rare monogenetic syndrome, caused by haploinsufficiency of the EHMT1 gene, an important regulator of neurodevelopment. The clinical features of KS include intellectual disability, autistic behavior and gastrointestinal problems. The gut microbiota may constitute a, yet unexplored, mechanism underlying clinical variation, as they are an important modifier of the gut-brain-axis. To test whether variation in the gut microbiota is part of KS, we investigated the gut microbiota composition of 23 individuals with KS (patients) and 40 of their family members. Both alpha and beta diversity of patients were different from their family members. Genus Coprococcus 3 was lower in abundance in patients compared to family members. Moreover, abundance of genus Merdibacter was lower in patients versus family members, but only in the participants reporting intestinal complaints. Within the patient group, behavioral problems explained 7% variance in the beta diversity. Also, within this group, we detected higher levels of Coprococcus 3 and Atopobiaceae - uncultured associated with higher symptoms severity. Our results show significant differences in the gut microbiota composition of patients with KS compared to their family members, suggesting that these differences are part of the KS phenotype.


title: SARS-CoV-2 variant of concern type and biological sex affect efficacy of molnupiravir in dwarf hamster model of severe COVID-19

abstract: Summary ParagraphSARS-CoV-2 variants of concern (VOC) have triggered distinct infection waves in the coronavirus disease 2019 (COVID-19) pandemic, culminating in currently all-time high incidence rates of VOC omicron. Orally available direct-acting antivirals such as molnupiravir promise to improve disease management and limit SARS-CoV-2 spread. However, molnupiravir efficacy against VOC delta was questioned based on clinical trial results and its potency against omicron is unknown. This study evaluates molnupiravir against a panel of relevant VOC in three efficacy models: primary human airway epithelium organoids, the ferret model of upper respiratory disease, and a lethal Roborovski dwarf hamster efficacy model of severe COVID-19-like acute lung injury. All VOC were equally efficiently inhibited by molnupiravir in cultured cells and organoids. Treatment consistently reduced upper respiratory VOC shedding in ferrets and prevented viral transmission. Pathogenicity in the dwarf hamsters was VOC-dependent and highest for gamma, omicron, and delta with fulminant lung histopathology. Oral molnupiravir started 12 hours after infection resulted in complete survival of treated dwarf hamsters independent of challenge VOC. However, reduction in lung virus differed VOC-dependently, ranging from one (delta) to four (gamma) orders of magnitude compared to vehicle-treated animals. Dwarf hamsters infected with VOC omicron showed significant individual variation in response to treatment. Virus load reduction was significant in treated males, but not females. The dwarf hamster model recapitulates mixed efficacy of molnupiravir seen in human trials and alerts that therapeutic benefit of approved antivirals must be continuously reassessed in vivo as new VOC emerge.


title: NGS data reveals the phyllosphere microbiome of wheat plants infected by the fungal pathogen Zymoseptoria tritici

abstract: The fungal pathogen Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB), a major wheat disease in Western Europe. Microorganisms inhabiting wheat leaves might act as beneficial, biocontrol or facilitating agents that could limit or stimulate the development of Z. tritici. Improving our understanding of microbial communities in the wheat phyllosphere would lead to new insights into STB management. This resource announcement provides fungal and bacterial metabarcoding datasets obtained by sampling wheat leaves differing in the presence of symptoms caused by Z. tritici. Tissues were sampled from three wheat commercial varieties on three sampling dates during a cropping season. Weeds around wheat fields were sampled as well. In total, more than 450 leaf samples were collected. The pathogen Z. tritici was quantified using qPCR. We provide the raw metabarcoding datasets, the Amplicon Sequence Variant (ASV) tables obtained after bioinformatic processing, the metadata associated to each sample (sampling date, wheat variety and tissue health condition), a preliminary descriptive analysis of the data, and the code used for bioinformatic and descriptive statistical analysis.


title: Discovery of integrons in Archaea: platforms for cross-domain gene transfer

abstract: Horizontal gene transfer between different domains of life is increasingly being recognised as an important driver of evolution, with the potential to provide the recipient with new gene functionality and assist niche adaptation1-3. However, the molecular mechanisms underlying the integration of exogenous genes from foreign domains are mostly unknown. Integrons are a family of genetic elements that facilitate this process within Bacteria via site-specific DNA recombination4-7. Integrons, however, have not been reported outside Bacteria, and thus their potential role in cross-domain gene transfer has not been investigated. Here we show that integrons are also present among diverse phyla within the domain Archaea. Further, we provide experimental evidence that integron-mediated recombination can facilitate the recruitment of archaeal genes by bacteria. Our findings establish a new mechanism that can facilitate horizontal gene transfer between the two domains of prokaryotes, which has important implications for prokaryotic evolution in both clinical and environmental contexts.