title: Inter-individual deep image reconstruction

abstract:
The sensory cortex is characterized by general organizational principles such as topography and hierarchy. However, measured brain activity given identical input exhibits substantially different patterns across individuals. Though anatomical and functional alignment methods have been proposed in functional magnetic resonance imaging (fMRI) studies, it remains unclear whether and how hierarchical and fine-grained representations can be converted between individuals while preserving the encoded perceptual content. In this study, we evaluated machine learning models called neural code converters that predict a target subjects brain activity pattern from a source subject given the same stimulus by decoding hierarchical visual features and reconstructing perceived images. The training data consisted of fMRI data obtained with identical sets of natural images presented to pairs of individuals. The converters were trained using the voxels on the visual cortex that covers from V1 through the ventral object areas without explicit labels of the visual areas. We decoded the converted brain activity patterns into the hierarchical visual features of a deep neural network using decoders pre-trained on the target brain and then reconstructed images via the decoded features. Without explicit information about the visual cortical hierarchy, the converters automatically learned the correspondence between visual areas of the same levels. Deep neural network feature decoding at each layer showed higher decoding accuracies from corresponding levels of visual areas, indicating that hierarchical representations were preserved after conversion. The visual images were reconstructed with recognizable silhouettes of objects even when relatively small numbers of data were used for converter training. The conversion also allowed pooling data across multiple individuals for decoder training, leading to a slight improvement over the decoders trained on a single individual. These results demonstrate that the conversion learns hierarchical correspondence and preserves the fine-grained representations of visual features, enabling visual image reconstruction using decoders trained on other individuals.

HighlightsO_LIThe neural code converter converts the brain activity patterns across individuals with moderate conversion accuracy and learns reasonable visual area correspondences at the same level between individuals.
C_LIO_LIThe converted brain activity patterns can be decoded into hierarchical DNN features to reconstruct visual images, even though the converter is trained with a small number of data.
C_LIO_LIThe information of hierarchical and fine-scale visual features that enable visual image reconstruction are preserved after conversion.
C_LI


title: An in vivo pig model for testing novel PET radioligands targeting cerebral protein aggregates

abstract:
Positron emission tomography (PET) has become an essential clinical tool for diagnosing neurodegenerative diseases with abnormal accumulation of proteins like amyloid-{beta} or tau. Despite many attempts, it has not been possible to develop an appropriate radioligand for imaging aggregated -synuclein in the brain for diagnosing, e.g., Parkinsons Disease. Access to a large animal model with -synuclein pathology would critically enable a more translationally appropriate evaluation of novel radioligands.

We here establish a pig model with cerebral injections of -synuclein preformed fibrils or brain homogenate from postmortem human brain tissue from individuals with Alzheimers disease (AD) or dementia with Lewy body (DLB) into the pigs brain, using minimally invasive surgery and validated against saline injections. In the absence of a suitable -synuclein radioligand, we validated the model with the unselective amyloid-{beta} tracer [11C]PIB, which has a high affinity for {beta}-sheet structures in aggregates. Gadolinium-enhanced MRI confirmed that the blood-brain barrier was intact. A few hours post-injection, pigs were PET scanned with [11C]PIB. Quantification was done with Logan invasive graphical analysis and simplified reference tissue model 2 using the occipital cortex as a reference region. After the scan, we retrieved the brains to confirm successful injection using autoradiography and immunohistochemistry.

We found four times higher [11C]PIB uptake in AD-homogenate-injected regions and two times higher uptake in regions injected with -synuclein-preformed-fibrils compared to saline. The [11C]PIB uptake was the same in non-injected (occipital cortex, cerebellum) and injected (DLB-homogenate, saline) regions. With its large brains and ability to undergo repeated PET scans as well as neurosurgical procedures, the pig provides a robust, cost-effective, and good translational model for assessment of novel radioligands including, but not limited to, proteinopathies.

category: neuroscience


title: Neuronal cell-type and circuit basis for visual predictive processing

abstract:
Bayesian Brain theory suggests brain utilises predictive processing framework to interpret the noisy world1-11. Predictive processing is essential to perception, action, cognition and psychiatric disease12, but underlying neural circuit mechanisms remain undelineated. Here we show the neuronal cell-type and circuit basis for visual predictive processing in awake, head-fixed mice during self-initiated running. Preceding running, vasoactive intestinal peptide (VIP)-expressing inhibitory interneurons (INs) in primary visual cortex (V1) are robustly activated in absence of structured visual stimuli. This pre-running activation is mediated via distal top-down projections from frontal, parietal and retrosplenial areas known for motion planning, but not local excitatory inputs associated with the bottom-up pathway. Somatostatin (SST) INs show pre-running suppression and post-running activation, indicating a VIP-SST motif. Differential VIP-SST peri-running dynamics anisotropically suppress neighbouring pyramidal (Pyr) neurons, preadapting Pyr neurons to the incoming running. Our data delineate key neuron types and circuit elements of predictive processing brain employs in action and perception.

One Sentence SummaryVIP-SST-Pyr microcircuit in visual predictive processing during voluntary running


title: Region-specific alterations of perineuronal net expression in postmortem autism brain tissue

abstract: Genetic variance in ASD is often associated with mechanisms that broadly fall into the category of neuroplasticity. Parvalbumin positive neurons and their surrounding perineuronal nets (PNNs) are important factors in critical period plasticity and have both been implicated in ASD. PNNs are found in high density within output structures of the cerebellum and basal ganglia, two regions that are densely connected to many other brain areas and have the potential to participate in the diverse array of symptoms present in an ASD diagnosis. The dentate nucleus and globus pallidus were therefore assessed for differences in PNN expression in human postmortem ASD brain tissue. While Purkinje cell loss is a consistent neuropathological finding in ASD, in this cohort, the Purkinje cell targets within the dentate nucleus did not show differences in number of cells with or without a PNN. However, the density of parvalbumin positive neurons with a PNN were significantly reduced in the globus pallidus internus and externus of ASD cases, which was not dependent on seizure status. It is unclear whether these alterations manifest during development or are a consequence of activity-dependent mechanisms that lead to altered network dynamics later in life.


title: Epithelial MHC class II directs microbiota-specific intestinal immune homeostasis

abstract: Dysregulated immune responses to resident microbes promote pathologic inflammation, however, the mechanisms instructing commensal-specific T cells remain poorly understood. Here, we find that non-hematopoietic intestinal epithelial cells (IECs) represent the primary cells expressing major histocompatibility complex (MHC) II at the intestinal host-microbiota interface. Interestingly, epithelial MHCII and commensal-specific CD4+ T cells were concurrently induced by post-natal microbiota colonization, provoking the hypothesis that epithelial MHCII regulates local commensal-specific CD4+ T cells. While MHCII on classical antigen presenting cells directs expansion of antigen-specific CD4+ T cells, loss of IEC-intrinsic MHCII surprisingly led to elevated commensal-specific CD4+ T cells in the intestine. Further, epithelial MHCII expression actively limited accumulation of antigen-specific CD4+ T cells in adult mice. Expansion of commensal-specific Th17 cells was restricted by epithelial MHCII, and remarkably mice lacking epithelial MHCII were highly susceptible to microbiota-triggered inflammation. Collectively, these data indicate that impaired epithelial MHCII-T cell regulation within mucosal tissues alters microbiota-specific immunity and predisposes to chronic inflammation.

category: immunology


title: Capsaicin potently blocks Salmonella typhimurium invasion of Vero cells

abstract: As at 2021, the center for disease control (CDC) reported that Salmonella causes 1.2 million illness in the United States each year, with a mortality rate approaching 500 deaths per annum. Infants, the elderly, and persons with compromised immunity are the population with higher risk of mortality from this infection. At present there is no commercially available, safe and efficacious vaccine for the control and management of Salmonella typhimurium (S. typhimurium). More so, S. typhimurium has been shown to develop resistance against most antibiotics used for treatment of the infection. Capsaicin, a bioactive compound from Capsicum chinense (C. chinenses) is undoubtedly one of the most widely used spice in the world. This heat producing compound is not only been used as food additive but have been demonstrated to possess unique properties that have pharmacological, physiological, and antimicrobial applications. In this work, the antimicrobial property of pure capsaicin or capsaicin extract against S. typhimurium is tested to determine the compounds effectiveness in S. typhimurium inhibition. Capsaicin extract showed potent inhibition of S. typhimurium growth at concentrations as low as 100 ng/ml, whereas pure capsaicin comparatively showed poorer inhibition of the bacteria. Furthermore, both capsaicin extract and pure capsaicin potently blocked S. typhimurium invasion of an animal cell line in vitro. Taken together, this work revealed that capsaicin might work synergistically with dihydrocapsaicin or the other capsaicinoids to inhibit S. typhimurium growth, whereas individually, capsaicin or dihydrocapsaicin could potently block the bacteria entry and invasion of Vero cells.

category: microbiology


title: Dealing with the promise of metabarcoding in mega-event biomonitoring: EXPO2015 unedited data

abstract:
As human activities on our planet persist, causing widespread and irreversible environmental degradation, the need to biomonitor ecosystems has never been more pressing. These circumstances have required a renewal in monitoring techniques, encouraged by necessity to develop more rapid and accurate tools which will support timely observations of ecosystem structure and function. The World Exposition (from now  EXPO2015) hosted in Milan from May to October 2015 was a global event that could be categorized as a mega-event, which can be defined as an acute environmental stressor, possibly generating biodiversity alteration and disturbance.

During the six months of EXPO2015, exhibitors from more than 135 countries and 22 million visitors insisted on a 1.1 million square meters area. Faced with such a massive event, we explore the potential of DNA metabarcoding using three molecular markers to improve the understanding of anthropogenic impacts in the area, both considering air and water monitoring. Furthermore, we explore the effectiveness of the taxonomy assignment phase considering different taxonomic levels of analysis and the use of data mining approaches to predict sample origin. Unless the degree of taxa identification still remains open, our results showed that DNA metabarcoding is a powerful genomic-based tool to monitor biodiversity at the microscale, allowing us to capture exact fingerprints of specific event sites and to explore in a comprehensive manner the eukaryotic community alteration. With this work, we aim to disentangle and overcome the crucial issues related to the generalization of DNA metabarcoding in order to support future applications.

category: molecular biology


title: Release of HIV-1 particles from the viral compartment in macrophages requires an associated cytoskeleton and is driven by mechanical constraints

abstract: A defining feature of HIV-1 replication in macrophages is that viral assembly occurs at the limiting membrane of a compartment often named VCC (virus-containing compartments) that is connected to the extracellular medium. The newly formed viral progeny pinches of the membrane and accumulates in the lumen of the VCC. While HIV budding has been extensively studied, very little is known about how viral particles present in the lumen of VCC are released in the extracellular medium. Here we show that the actin dynamics are critical for this process by combining ultrastructural analyses, time-lapse microscopy and perturbations of the actin cytoskeleton. We found that jasplakinolide, which stabilizes actin fibres, inhibited viral release from HIV-1-infected macrophages. Furthermore, in jasplakinolide-treated macrophages, VCC became scattered and no longer co-localized with the integrin CD18, nor the phosphorylated form of the focal adhesion kinase PYK2. Inhibition of PYK2 activity in infected macrophages promoted intracellular retention of viral particles in VCC that were no longer connected to the plasma membrane. Finally, we stimulated the rapid release of viral particles from the VCC by subjecting infected macrophages to frustrated phagocytosis. As macrophages spread on IgG-coated glass surfaces, VCC rapidly migrated to the basal membrane and released their viral content in the extracellular medium, which required their association with CD18 and the actin cytoskeleton. These results highlight that VCC trafficking and virus release are intimately linked to the reorganization of the macrophage actin cytoskeleton in response to external physical cues, suggesting that it might be regulated in tissues by the mechanical stress to which these cells are exposed.

category: cell biology


title: Applying biostimulants boosts forage productivity without affecting soil biotic and abiotic parameters on a Central Coast California rangeland

abstract: There is increasing interest in using biostimulant products, such as microbial inoculants and humic substances, to help manage rangelands regeneratively. Understanding how plant and soil communities on rangelands respond to these products is therefore important. In this study, we examined the combined effects of a commercial inoculant and humic product that are currently on the market, and asked whether they influenced rangeland forage productivity and quality, soil microbial biomass and community composition, and abiotic soil parameters in Central Coastal California. We found that forage productivity and some metrics of forage quality responded positively to the foliar application of a commercial microbial inoculant and humic product, but that these benefits were not mirrored by changes belowground in the microbial community or abiotic parameters. Depending on the goals of using the products, this could be seen as a winning scenario and suggests microbial inoculants and humic products could warrant attention as a potential tool for regenerative stewardship of rangelands. While our study derives from one ranch and therefore requires confirmation of its ubiquity prior to broadscale adoption, our results provide new insights into the usefulness of this approach for managing rangeland productivity in Californias Central Coast.

category: ecology


title: Temporal variation of patch connectivity determines biodiversity recovery from recurrent disturbances

abstract: Understanding the capacity of ecological systems to withstand and recover from disturbances is a major challenge for ecological research in the context of environmental change. Disturbances have multi-scale effects: they can cause species extinctions locally and alter connectivity between habitat patches at the metacommunity level. Yet, our understanding of how disturbances influence landscape connectivity remains limited. To fill this gap, we develop a novel connectivity index that integrates the temporal variation of patch connectivity induced by disturbances, which can be applied to any spatially-structured habitat. We then combine this index with a metacommunity model to specifically investigate biodiversity recovery from drying events in river network metacommunities. We demonstrate that patch connectivity explains variations of species richness between groups of organisms with contrasting dispersal modes and captures the effect of drying intensity (i.e., fraction of patches that dry-up) and drying location on community recovery. As a general rule, loss of patch connectivity decreases community recovery, regardless of patch location in the river network, dispersal mode, or drying intensity. Local communities of flying organisms maintained higher patch connectivity in drying river networks compared to organisms with strictly aquatic dispersal, which explained the higher recovery capacity of this group from drying events. The general relationship between patch connectivity and community recovery we found can be applied to any spatial network subject to temporal variation of connectivity, thus providing a powerful tool for biodiversity management in dynamic landscapes.


title: Local climate and vernalization requirements explain the latitudinal patterns of flowering initiation in the crop wild relative Linum bienne

abstract:
Background and AimsDays to flowering initiation in species with large geographic distribution often correlate with latitude. Latitude reflects climatic gradients, but it is unclear if large-scale differentiation in flowering results from adaptation to local climate, and whether adaptation to local climate could constrain shifts in distribution and colonization of new environments.

MethodsIn its Western range in Europe, L. bienne populations were surveyed to describe latitudinal patterns of flowering initiation and determine its correlation with the local climate of populations. This was measured under standardized greenhouse conditions, with a vernalization experiment to learn if chilling advances flowering, and with a reciprocal transplant experiment at three sites along the latitudinal gradient, recording flowering at the central site and plant survival in all sites. Also, genetic differentiation of populations along the latitudinal range was studied using microsatellite markers.

Key ResultsFlowering initiation varied with latitude, with southern populations flowering earlier than northern populations. Latitude also predicted population response to vernalization, with chilling inducing a greater advance of flowering initiation in northern than southern populations. In general, plant survival in the reciprocal transplant experiment decreased with the geographic distance of populations to the experimental site and, at the central site, flowering initiation varied with latitude of origin. However, across experiments, the local climate of populations better predicted the differentiation in flowering initiation and vernalization response than latitude of origin. Finally, the microsatellite data revealed genetic differentiation of populations forming two groups that agree with a Mediterranean and Atlantic lineage.

ConclusionsThe consistent result across experiments of a latitudinal cline in flowering initiation and in the vernalization response suggests that flowering is under genetic regulation and yet dependent on particular environmental and climatic cues at local scale. However, the genetic differentiation suggests that past population history might influenced the flowering initiation patterns detected.


title: Role of vegetation characteristics on the distribution of three hornbill species in and around Pakke Tiger Reserve, Arunachal Pradesh, India

abstract: The relationship between various vegetation characteristics and the relative abundance of three hornbill species [Great Pied Hornbill (Buceros bicornis), Wreathed Hornbill (Rhyticeros undulatus) and Oriental Pied Hornbill (Anthracoceros albirostris)] was studied in and around Pakke Tiger Reserve, Arunachal Pradesh. We walked transects (n=11; 22 walks) in three study sites to detect hornbills. Vegetation sampling was done using circular plots (n=33; 10 m radius) at every 400m interval along each transect. Encounter rate (1.5{+/-} 0.188/km) of Great Pied Hornbill (Buceros bicornis) was highest in the protected and undisturbed forest area where food and roosting tree density were also high (114/ha). Oriental Pied Hornbill was common in both the sites within Pakke Tiger reserve near riverine forests (0.75{+/-}0.25/km) and also in the dense undisturbed forest (0.875{+/-}0.226/km). Multivariate analysis revealed that tree density, presence of fruiting trees (utilized by hornbills), canopy cover, and tree diversity in a particular area are the major factors responsible for the assemblage of more than one species of hornbills. The study shows that protection of the forest patches to keep the diversity and density of the tree species intact is crucial for the survival and distribution of the hornbills in the landscape.


title: A simple island biodiversity model is robust to trait dependence in diversification and colonization rates

abstract: The application of state-dependent speciation and extinction (SSE) models to phylogenetic trees has revealed an important role for traits in diversification. However, this role remains comparatively unexplored on islands, which can include multiple independent clades resulting from different colonization events. Here, we perform a robustness study to identify how trait-dependence in rates of island colonization, extinction and speciation (CES rates) affects the estimation accuracy of a phylogenetic model that assumes no rate variation between trait states. We extend the DAISIE (Dynamic Assembly of Islands through Speciation, Immigration and Extinction) simulation model to include state-dependent rates, and evaluate the robustness of the DAISIE inference model using simulated data. Our results show that when the CES rate differences between trait states are moderate, DAISIE shows negligible error for a variety of island diversity metrics. However, for large differences in speciation rates, we find large errors when reconstructing clade size variation and non-endemic species diversity through time. We conclude that for many biologically realistic scenarios with trait-dependent speciation and colonization, island diversity dynamics can be accurately estimated without the need to explicitly model trait dynamics. Nonetheless, our new simulation model may provide a useful tool for studying patterns of trait variation.

category: evolutionary biology


title: Investigating neurotrophin genetics and hippocampal volume

abstract: As individuals get older, the structural integrity of brain regions becomes progressively diminished. Neurotrophic function might aid in preventing such losses through increased synaptogenesis and neurogenesis, particularly in the hippocampus, a brain structure relevant for cognitive function. However, the carriage of certain genetic alleles for genes involved in neurotrophic function might restrain the effectiveness of neurotrophin signalling, hindering neuroprotection. Yet, research on the contribution of single nucleotide polymorphisms (SNPs) within genes coding for neurotrophins and their receptors to hippocampal volumes is scarce, with the exception of rs6265 within the brain-derived neurotrophic factor gene. Therefore, the aim of this study was to identify SNPs within genes involved neurotrophic function that are associated with hippocampal volume in a sample of 23,776 cognitively normal older adults from the UK Biobank. We found that, in individuals older than 50, homozygote carriage of the major alleles rs4839435-A within nerve growth factor gene and rs56405676-T within the neurotrophic receptor tyrosine kinase 2 gene, were associated with increase hippocampal volumes, compared to carriage of 1 or 2 copies of the minor alleles. However, only rs56405676-T was significantly associated with greater hippocampal volumes in individuals older than 60. Hence this study might serve to identify populations at higher risk of hippocampal attrition and cognitive decline.

category: genetics


title: Cell-based screen identifies human type I interferon-stimulated regulators of Toxoplasma gondii Infection

abstract: Macrophages activated with interferons (IFNs) respond with transcriptional changes that enhance clearance of intracellular pathogens such as Toxoplasma, a ubiquitous apicomplexan parasite that infects more than a billion people worldwide. Although IFNs generally inhibit Toxoplasma, the parasite can also induce components of the host IFN signalling pathway to enhance survival in host cells. Compared to the type II IFN gamma (IFN{gamma}), the role of type I IFNs in macrophage response to Toxoplasma is relatively not well characterized. Here, using fluorescent Toxoplasma and a CRISPR/Cas9 knockout library that only targets interferon-stimulated genes (ISGs), we adapted a loss-of-function flow cytometry-based approach to systematically identify type I ISGs that control Toxoplasma growth in THP-1 cells, a human macrophage cell line. The system enabled the rapid screening of more than 1900 ISGs for type I (IFN)-induced inhibitors and enhancers of Toxoplasma growth in THP-1 cells. We identified 26 genes that are associated with Toxoplasma growth arrest out of which we confirmed MAX, SNX5, F2RL2, and SSB, as potent IFN-induced inhibitors of Toxoplasma in THP1 cells. These findings provide a genetic and experimental roadmap to elucidate type I IFN-induced cell-autonomous responses to Toxoplasma.

category: genomics


title: Whole genome sequencing of hematologically stained cells catapulted from Cell smears

abstract: Analyzing archived peripheral blood smears is a potential route towards gaining cell morphology and genome information of blood cell types from various diseases. Yet, acquiring whole genome information from morphologically targeted cells was difficult, especially for rare cell types. The main causes for such difficulty were the inevitable usage of cell stains leading to whole genome amplification inhibition, and insufficient cell isolation performance of previously introduced laser microdissection (LMD) techniques. Here, we introduce a new laser-based cell isolation technique and a whole genome amplification (WGA) protocol optimized for whole genome analysis from minute input of hematologically stained cells. We were able to perform whole genome copy number profiling and SNP analysis from as little as 5 cells.


title: High Speed Visual Insect Swarm Tracker (Hi-VISTA) used to identify the effects of confinement on individual insect flight

abstract: Individual insects flying in crowded assemblies perform complex aerial maneuvers by sensing and feeding back neighbor measurements to small changes in their wing motions. To understand the individual feedback rules that permit these fast, adaptive behaviors in group flight, a high-speed tracking system is needed capable of tracking both body motions and more subtle wing motion changes for multiple insects in simultaneous flight. This capability extends tracking beyond the previous focus on individual insects to multiple insects. This paper presents Hi-VISTA, which provides a capability to track wing and body motions of multiple insects using high speed cameras (9000 fps). Processing steps consist of automatic background identification, data association, hull reconstruction, segmentation, and feature measurement. To improve the biological relevance of laboratory experiments and develop a platform for interaction studies, this paper applies the Hi-VISTA measurement system to Apis mellifera foragers habituated to transit flights through a transparent tunnel. Binary statistical analysis (Welchs t-test, Cohens d effect size) of 95 flight trajectories is presented, quantifying the differences between flights in an unobstructed tunnel and in a confined tunnel volume. The results indicate that body pitch angle, heading rate, flapping frequency, and vertical speed (heave) are all affected by confinement, and other flight variables show minor or statistically insignificant changes. These results form a baseline as swarm tracking and analysis begins to isolate the effects of neighbors from environment.

category: animal behavior and cognition


title: Cooperative phagocytosis underlies macrophage immunotherapy of solid tumours and initiates a broad anti-tumour IgG response

abstract: Macrophages are abundant in solid tumours and typically associate with poor prognosis, but macrophage clusters in tumour nests have also been reported as beneficial even though dispersed macrophages would have more contacts with cancer cells. Here, by maximizing both phagocytic activity and macrophage numbers, we discover cooperative phagocytosis by low entropy clusters in rapidly growing engineered immuno-tumouroids. The results fit the calculus of proliferation-versus-engulfment, and rheological measurements and molecular perturbations provide a basis for understanding phagocytic disruption of a tumours cohesive forces in soft cellular phases. The perturbations underscore the utility of suppressing a macrophage checkpoint in combination with an otherwise ineffective tumour-opsonizing monoclonal antibody, and the approach translates in vivo to tumour elimination that durably protects mice from re-challenge and metastasis. Adoptive transfer of engineered macrophages increases the fraction of mice that eliminate tumours and potentially overcomes checkpoint blockade challenges in solid tumours like insufficient permeation of blocking antibodies and on-target, off-tumour binding. Finally, anti-cancer IgG induced in vivo are tumour-specific but multi-epitope and contribute to a phagocytic feedback that drives macrophage clustering in vitro. Given that solid tumours remain challenging for immunotherapies, durable anti-tumour responses here illustrate unexpected advantages in maximizing net phagocytic activity.

category: bioengineering


title: SpotLink enables sensitive and precise identification of site non-specific cross-links at the proteome scale

abstract: We developed SpotLink software for identifying site non-specific cross-links at the proteome scale. Contributed by the dual pointer dynamic pruning (DPDP) algorithm and the quality control of cross-linking sites, SpotLink identified more than 3000 cross-links from human proteome database with rich site information in a few days. We demonstrated that SpotLink outperformed other approaches in terms of sensitivity and precision on a simulated dataset and a protein complexes dataset with known structures. Additionally, we discovered some valuable protein-protein interaction (PPI) information contained in the protein complexes dataset and HeLa dataset, indicating the unique identification advantages of site non-specific cross-linking. The excellent performance of SpotLink will increase the usage of site non-specific cross-linking in the near future. SpotLink is publicly available on GitHub [https://github.com/DICP1810/SpotLink].

category: bioinformatics


title: Counting fluorescently labeled proteins in tissues in the spinning disk microscope using single-molecule calibrations

abstract: Quantification of molecular numbers and concentrations in living cells is critical for testing models of complex biological phenomena. Counting molecules in cells requires estimation of the fluorescence intensity of single molecules, which is generally limited to imaging near cell surfaces, in isolated cells, or where motions are diffusive. To circumvent this difficulty, we have devised a calibration technique for spinning-disk confocal (SDC) microscopy, commonly used for imaging in tissues, that uses single-step bleaching kinetics to estimate the single-fluorophore intensity. To cross-check our calibrations, we compared the brightness of fluorophores in the SDC microscope to those in the total-internal-reflection (TIRF) and epifluorescence microscopes. We applied this calibration method to quantify the number of EB1-eGFP proteins in the comets of growing microtubule ends and to measure the cytoplasmic concentration of EB1-eGFP in sensory neurons in fly larvae. These measurements allowed us to estimate the dissociation constant of EB1-eGFP from the microtubules as wells as the GTP-tubulin cap size. Our results show the unexplored potential of single-molecule imaging using spinning disk confocal microscopy and provide a straight-forward method to count the absolute number of fluorophores in tissues which can be applied to a wide range of biological systems and imaging techniques.

category: biophysics


title: Phase tracking algorithms detect both real and imaginary components of outer hair cell nonlinear membrane capacitance that exhibits dielectric loss.

abstract: Outer hair cell (OHC) nonlinear membrane capacitance (NLC) represents voltage-dependent sensor charge movements within prestin (SLC26a5) that drive OHC electromotility. Dielectric loss, a shift in charge movement phase from purely "capacitive" to "resistive", is likely indicative of prestins interaction with the viscous lipid bilayer and has been suggested to correspond to prestin power output. The frequency response of NLC in OHC membrane patches has been measured with phase tracking and complex capacitance methodologies. While the latter approach can directly determine the presence of dielectric loss by assessing charge movement both in and out of phase with driving voltage, the former has been suggested to fail in this regard. Here we show that standard phase tracking in the presence of dielectric loss does indeed register this loss. Such estimates of NLC correspond to the absolute magnitude of complex NLC, indicating that total charge movement regardless of phase is assessed, thereby validating past and present measures of NLC frequency response that limits its effectiveness at high frequencies. This observation has important implications for understanding prestins role in cochlear amplification.


title: P2RX7 inhibition reduces breast cancer induced osteolytic lesions - implications for bone metastasis

abstract: Breast cancer metastasis to bone is a major contributor to morbidity and mortality in patients and remains an unmet clinical need. Purinergic signalling via the P2X7 receptor (P2RX7) in the primary tumour microenvironment is associated with progression of several cancers. It has also now become evident that intra-tumoural hypoxia facilitates cancer metastasis and reduces patient survival. In this study, we present data suggesting that hypoxia regulates the expression of P2RX7 in the primary tumour microenvironment; and importantly, inhibition with a selective antagonist (10mg/kg A740003) increased cancer cell death via apoptosis in a E0771/C57BL-6J syngeneic murine model. Furthermore, micro-computed tomography demonstrated reduced number of osteolytic lesions and lesion area following P2RX7 inhibition in absence of overt metastases by decreasing osteoclast numbers. We also demonstrate that activation of P2RX7 plays a role in the secretion of extracellular vesicles (EVs) from breast cancer cells. Mass-spectrometric analyses showed a distinct protein signature for EVs derived from hypoxic compared with normoxic cancer cells which elicit specific responses in bone cells that are associated with pre-metastatic niche formation. Thus, inhibiting P2RX7 provides a novel opportunity to preferentially target the hypoxic breast cancer cells preventing tumour progression and subsequent metastasis to bone

category: cancer biology


title: Simultaneous overexpression of multiple herbicide-metabolizing genes for broad-spectrum resistance in an agricultural weed Echinochloa phyllopogon

abstract: The use of herbicides in agricultural fields has driven the evolution of weeds for resistance, causing a grave threat to the current agriculture. One big mystery of weed resistance involves multiple-herbicide resistance (MHR) concomitant to enhanced herbicide metabolism. Previous research unveiled that the overexpression of catalytically promiscuous cytochrome P450s underlies the metabolism-based cross-resistance in multiple species. However, the concept of activation of promiscuous enzymes does not fully accommodate the resistance to diverse herbicides in MHR Echinochloa phyllopogon although the genetic inheritance of MHR was suggested as under a single gene control. Here, we show that the high-level resistance to diclofop-methyl in E. phyllopogon is caused by the simultaneous overexpression of CYP81A12/21, the previously identified promiscuous P450s, and a novel P450 CYP709C69. We found that the MHR line rapidly produced two distinct hydroxylated-diclofop-acid, only one of which was the major metabolite produced by CYP81As. RNA-seq followed by real-time PCR in the crossed progeny of MHR and sensitive lines identified several P450 genes whose overexpressions were associated with MHR. Gene functional characterization revealed that only CYP709C69 conferred diclofop-methyl resistance in rice calli and produced another hydroxylated-diclofop-acid in yeast, reinforcing the relatively low activity of CYP81As to diclofop-methyl. Plants transformed with CYP709C69 had unchanged sensitivity to 46 herbicides except for clomazone, where transgenic plants became more susceptible. The present findings establish a novel concept that simultaneous overexpression of herbicide-metabolizing genes enhances and broadens the profile of metabolic resistance in weeds.

category: plant biology


title: Concerted expansion and contraction of immune receptor gene repertoires in plant genomes

abstract: Recent reports suggest that cell-surface and intracellular immune receptors function synergistically to activate robust defence against pathogens, but whether or not they co-evolve is unclear. Here we determined the copy numbers of cell-surface and intracellular immune receptors in 208 species. Surprisingly, these receptor gene families contract and/or expand together in plant genomes, suggesting the mutual potentiation of immunity initiated by cell-surface and intracellular receptors is reflected in the concerted co-evolution of the size of their repertoires across plant species.


title: Apoplastic CBM1-interacting proteins bind conserved carbohydrate binding module 1 motifs in fungal hydrolases to counter pathogen invasion

abstract:
When infecting plants, fungal pathogens secrete cell wall degrading enzymes (CWDEs) that break down cellulose and hemicellulose, the primary components of plant cell walls. Some fungal CWDEs contain a unique domain, named the carbohydrate binding module (CBM), that facilitates their access to polysaccharides. However, little is known about how plants counteract pathogen degradation of their cell walls. Here, we show that the rice cysteine-rich repeat secretion protein OsCBMIP binds to and inhibits xylanase MoCel10A of the blast fungus pathogen Magnaporthe oryzae, interfering with its access to the rice cell wall and degradation of rice xylan. We found binding of OsCBMIP to various CBM1-containing enzymes, suggesting it has a general role in inhibiting the catalytic activities of fungal enzymes. OsCBMIP is localized to the apoplast, and its expression is strongly induced in leaves infected with M. oryzae. Remarkably, knockdown of OsCBMIP reduced rice defense against M. oryzae, demonstrating that inhibition of CBM1-containing fungal enzymes by OsCBMIP is crucial for rice defense. We also identified additional CBMIP-related proteins from Arabidopsis thaliana and Setaria italica, indicating that a wide range of plants counteract pathogens through this mechanism.

SummaryPlants have evolved various activity-inhibiting proteins as a defense against fungal cell wall degrading enzymes (CWDEs), but how plants counteract the function of fungal enzymes containing carbohydrate binding modules (CBMs) remains unknown. Here, we demonstrate that OsCBMIP, a member of the cysteine-rich repeat secretion protein family, interacts with fungal CBM1. OsCBMIP binding to CBM1 of a blast fungal xylanase blocks access to cellulose, resulting in the inhibition of xylanase enzymatic activity. Our study provides significant insights into plant countermeasure against CWDEs in the apoplastic space during plant-fungal pathogen interactions. It also reveals a molecular function of the DUF26 domain widely distributed in plant proteins.


title: Low-cost arabinose induced genetic circuit for protein production: Modeling.

abstract:
A low-cost reagent-producing genetic circuit was designed during this work. Its functioning is based on a positive feedback loop induced by a small amount of arabinose, allowing users to obtain reactants in a safe, constant, and controlled manner. The "design only" approach to the project allows us to work in different kinds of computational models, thus, an ODE-based model was thoroughly developed and a cellular automata-based one was experimented with.

Working on the ODE model, equilibrium states and system stability were studied. Circuit properties were also focused on one of which was a high concentration of interest protein produced by low inductor inputs. As a result, a mathematical expression capable of describing the quantity of produced reagent was obtained. In addition, the cellular automata model offers a new perspective, given its differences from the ODE model e.g. this type of model is a stochastic analysis and describes each cell individually instead of describing the whole cellular population.

category: synthetic biology


title: PlasmidMaker: a Versatile, Automated, and High Throughput End-to-End Platform for Plasmid Construction

abstract: Plasmids are used extensively in basic and applied biology. However, design and construction of plasmids, specifically the ones carrying complex genetic information, remains one of the most time-consuming, labor-intensive, and rate-limiting steps in performing sophisticated biological experiments. Here, we report the development of a versatile, robust, automated end-to-end platform named PlasmidMaker that allows error-free construction of plasmids with virtually any sequences in a high-throughput manner. This platform consists of a most versatile DNA assembly method using Pyrococcus furiosus Argonaute (PfAgo)-based artificial restriction enzymes, a user-friendly frontend for plasmid design, and a backend that streamlines the workflow and integration with a robotic system. As a proof of concept, we used this platform to generate 101 plasmids from six different species ranging from 5 to 18 kb in size from up to 11 DNA fragments within 3 days. PlasmidMaker should greatly expand the potential of synthetic biology.


title: An ultra-sensitive and easy-to-use multiplexed single-cell proteomic analysis

abstract: Proteins analysis from an average cell population often overlooks the cellular heterogeneity of expressed effector molecules, and knowledge about the regulations of key biological processes may remain obscure. Therefore, the necessity of single-cell proteomics (SCP) technologies arises. Without microfluidic chip, expensive ultrasonic equipment, or reformed liquid chromatogram (LC) system, we established an Ultra-sensitive and Easy-to-use multiplexed Single-Cell Proteomic workflow (UE-SCP). Specifically, the flexible sorting system ensured outstanding cell activity, high accuracy, remarkable efficiency, and robustness during single-cell isolation. Multiplex isobaric labeling realized the high-throughput analysis in trapped ion mobility spectrometry coupled with quadrupole time-of-flight mass spectrometry (timsTOF MS). Using this pipeline, we achieved single-cell protein quantities to a depth of over 2,000 protein groups in two human cell lines, Hela and HEK-293T. A small batch experiment can identify and quantify more than 3200 protein groups in 32 single cells, while a large batch experiment can identify and quantify about 4000 protein groups in 96 single cells. All the 128 single cells from different cell lines could been unsupervised clustered based on their proteomes. After the integration of data quality control, data cleaning, and data analysis, we are confident that our UE-SCP platform will be easy-to-marketing popularization and will promote biological applications of single-cell proteomics.

category: systems biology


title: Bacterial composition and inferring function profiles in the biofloc system rearing Litopenaeus vannamei postlarvae at a low salinity

abstract: This study aimed to investigate the bacterial composition and inferring function profiles in the biofloc system rearing Litopenaeus vannamei postlarvae (PL) at a low salinity condition. PL (~ stage 15) were stocked in four parallel tanks filled in water with a salinity of 5.0{per thousand} at a density of 4000 individuals per m3 for a 28-days culture experiment, during which glucose was added as carbon source with a C:N of 20:1. At the end of experiment, water was sampled from each tank and pooled to extract microbial DNA for high-throughput sequencing of V3-V4 region of 16S rRNA gene. Results showed that the bacterial community at 28 d was dominated by phyla of Proteobacteria (45.8%), Bacteroidetes (21.1%), Planctomycetes (13.5%), Chlamydiae (10.3%) and Firmicutes (6.8%). A proportion of 81% inferring KEGG functions of this bacterial community associated with metabolism. Among functions relating to nitrogen metabolism, 48.5% were involved in the conversion of ammonia to glutamate, but the proportion of those involved in transformation among ammonia, nitrite and nitrate was 18.0% in total, inferring higher protein-synthesis but lower inorganic nitrogen-transformation capacities of the bacterial community. At the same time (28 d), high levels of total nitrogen (231.3{+/-}6.0 mg L-1) and biofloc (127.0{+/-}63.0 mL L-1), but low concentrations of ammonia (0.04{+/-}0.01 mg L-1), nitrite (0.2{+/-}0.1 mg L-1) and nitrate (12.9{+/-}2.5 mg L-1) were observed. The results supply a novel insight for understanding the function of bacterial community in the biofloc system nursing L. vannamei PL at a low salinity.


title: Efficient simulation of 3D reaction-diffusion in models of neurons and networks

abstract:
Neuronal activity is the result of both the electrophysiology and chemophysiology. A neuron can be well represented for the purposes of electrophysiological simulation as a tree composed of connected cylinders. This representation is also apt for 1D simulations of their chemophysiology, provided the spatial scale is larger than the diameter of the cylinders and there is radial symmetry. Higher dimensional simulation is necessary to accurately capture the dynamics when these criteria are not met, such as with wave curvature, spines, or diffusion near the soma.

We have developed a solution to enable efficient finite volume method simulation of reaction-diffusion kinetics in intracellular 3D regions in neuron and network models and provide an implementation within the NEURON simulator. An accelerated version of the CTNG 3D reconstruction algorithm transforms morphologies suitable for ion-channel based simulations into consistent 3D voxelized regions. Kinetics are then solved using a parallel algorithm based on Douglas-Gunn that handles the irregular 3D geometry of a neuron; these kinetics are coupled to NEURONs 1D mechanisms for ion channels, synapses, etc. The 3D domain may cover the entire cell or selected regions of interest. Simulations with dendritic spines and of the soma reveal details of dynamics that would be missed in a pure 1D simulation. We describe and validate the methods and discuss their performance.

category: neuroscience


title: Cooperative regulation of C1-domain membrane recruitment polarizes atypical Protein Kinase C

abstract: Recruitment of the Par complex protein atypical Protein Kinase C (aPKC) to a specific membrane domain is a key step in the polarization of animal cells. While numerous proteins and phospholipids interact with aPKC, how these interactions cooperate to control its membrane recruitment has been unknown. Here we identify aPKCs C1 domain as a phospholipid interaction module that targets aPKC to the membrane of Drosophila neural stem cells (NSCs). The isolated C1 binds the NSC membrane in an unpolarized manner during interphase and mitosis and is uniquely sufficient among aPKC domains for targeting. Other domains, including the catalytic module and those that bind the upstream regulators Par-6 and Baz, restrict C1s membrane targeting activity spatially and temporally - to the apical NSC membrane during mitosis. Our results suggest that Par complex polarity results from cooperative activation of autoinhibited C1 membrane binding activity.


title: Temporal control of the integrated stress response by a stochastic molecular switch

abstract: Stress granules (SGs) are formed in the cytosol as an acute response to environmental cues and activation of the integrated stress response (ISR), a central signaling pathway controlling protein synthesis. Using chronic virus infection as stress model, we previously uncovered a unique temporal control of the ISR resulting in recurrent phases of SG assembly and disassembly. Here, we elucidate the molecular network generating this fluctuating stress response, by integrating quantitative experiments with mathematical modeling, and find that the ISR operates as a stochastic switch. Key elements controlling this switch are the cooperative activation of the stress-sensing kinase PKR, the ultrasensitive response of SG formation to the phosphorylation of the translation initiation factor eIF2, and negative feedback via GADD34, a stress-induced subunit of protein phosphatase 1. We identify GADD34 mRNA levels as the molecular memory of the ISR that plays a central role in cell adaptation to acute and chronic stress.


title: Potential geographic distribution and ecological niche of the insect order Megaloptera: the case of the neartic-neotropical transition zone

abstract: The dobsonflies (Megaloptera, Corydalidae) are an interesting group of insects, but among the New World dobsonflies, it is not known the effect of the Neartic-Neotropical transition zone on their biogeographic distribution. Here we studied at the species level, the records on the geographic range of the dobsonflies that occurred in and near the transition zone. We presented potential geographic distributions based on ecological niche models for several species of dobsonflies. Results suggested that the geographic range of dobsonflies in the transition zone is associated to mountainous formations and that most species favor warm climates with higher precipitation rates. Climate types tend to be important for species that show narrow geographic ranges, but precipitation tends to be the most important variable to explain species dispersion. Overall, our models support the dispersion of dobsonflies from the Neotropics to North America and explain the two endemic species in Mexico as the result of the formation of the transition zone.


title: Potential geographic distribution and ecological niche of New World dobsonflies (Megaloptera, Corydalidae): the case of the Neartic-Neotropical transition zone


title: Controlling critical mistag-associated false discoveries in metagenetic data

abstract:
O_LIMetagenetic methods are commonplace within ecological and environmental research. One concern with these methods is the phenomenon of critical mistagging, where sequences from one sample are erroneously inferred to have originated from another sample due to errors in the attachment, PCR replication or sequencing of sample-specific dual-index tags. For studies using PCR-based library preparation on large sample sizes, the most cost-effective approach to limiting mistag-associated false detections involves using an unsaturated Latin square dual-indexing design. This allows researchers to estimate mistagging rates during sequencing but the statistical procedures for filtering out detections using this mistag rate have received little attention.
C_LIO_LIWe propose a straightforward method to limit mistag-associated false discoveries during metabarcoding applications. We analyzed two Illumina metabarcoding datasets produced using unsaturated Latin square designs to explore the distribution of mistagged sequences across dual-index combinations on a per taxon basis. We tested these data for conformity to the assumptions that 1) mistagging follows a binomial distribution [i.e., X ~ B(n, p)] where p, the probability of a sequence being mistagged, varies minimally across taxa and 2) mistags are distributed uniformly across dual-index combinations. We provide R functions that estimate the 95th percentile of expected mistags per dual-index combination for each taxon under these assumptions.
C_LIO_LIWe show that mistagging rates were consistent across taxa within the datasets analyzed and that modelling mistagging as a binomial process with uniform distribution across dual-index combinations enabled robust control of mistag-associated false discoveries.
C_LIO_LIWe propose that this method of taxon-specific filtering of detections based on the maximum mistags expected per dual-index combination should be broadly accepted during metagenetic analysis, provided that experimental and control sequence abundances per taxon are strongly correlated. When this assumption is violated, data may be better fit by assuming that the distribution of mistags across combinations follows Poisson characteristics [i.e., X ~ Pois({lambda})], with{lambda} empirically estimated from the abundance distribution of mistags among control samples. We provide a second R function for this case, though we have yet to observe such a dataset. Both functions and demonstrations associated with this work are freely available at https://github.com/RTRichar/ModellingCriticalMistags.
C_LI


title: Prenatal murine skeletogenesis partially recovers from absent skeletal muscle as development progresses

abstract: Skeletal muscle contractions are critical for normal growth and morphogenesis of the skeleton, but it is unclear how the detrimental effects of absent muscle on the bones and joints change over time. Joint size, shape and cavitation, and rudiment length and mineralisation were assessed in multiple rudiments at two developmental stages (Theiler Stage (TS)24 and TS27) in the splotch-delayed "muscleless limb" mouse model and littermate controls. As development progressed, the effects of absent muscle on all parameters except for cavitation become less severe. All major joints in muscleless limbs were qualitatively and quantitatively abnormal in shape at TS24, while, by TS27, most muscleless joint shapes were normal, or nearly normal. In contrast, any joints which were fused at TS24 did not cavitate by TS27. Therefore, recovery in joint shape over development occurred despite absent cavitation. Mineralisation showed the most pronounced changes between TS24 and TS27 in the muscleless limbs. At TS24, all muscleless rudiments studied had less mineralisation than the controls, while at TS27, muscleless limb rudiments had either the same or significantly more mineralisation than controls of the same age. We conclude that the effects of absent muscle on prenatal murine skeletogenesis are most pronounced in early skeletal development and reduce in severity prior to birth. Understanding how mammalian bones and joints continue to develop in an environment without muscle contractions, but with mechanical stimulation due to the movement of the mother, provides important insights into conditions affecting human babies such as developmental dysplasia of the hip and arthrogryposis.

category: developmental biology


title: Intestinal Mucin Is a Chaperone of Multivalent Copper

abstract: Mucus protects the body by many mechanisms, but a role in managing toxic transition metals was not previously known. Here we report that secreted mucins, the major mucus glycoproteins coating the respiratory and intestinal epithelia, are specific copper-binding proteins. Most remarkably, the intestinal mucin, MUC2, has two juxtaposed copper binding sites, one that accommodates Cu2+ and the other Cu1+, which can be formed in situ by reduction with vitamin C. Copper is an essential trace metal because it is a cofactor for a variety of enzymes catalyzing electron transfer reactions, but copper damages macromolecules when unregulated. We observed that MUC2 protects against copper toxicity while permitting nutritional uptake into cells. These findings introduce mucins, produced in massive quantities to guard extensive mucosal surfaces, as extracellular copper chaperones and potentially important players in physiological copper homeostasis.

category: biochemistry


title: The Layer 7 Cortical Interface: A Scalable and Minimally Invasive Brain-Computer Interface Platform

abstract: Progress toward the development of brain-computer interfaces has signaled the potential to restore, replace, or augment lost or impaired neurological function in a variety of disease states. Existing brain-computer interfaces rely on invasive surgical procedures or brain-penetrating electrodes, which limit addressable applications of the technology and the number of eligible patients. Here we describe a novel approach to constructing a neural interface, comprising conformable thin-film electrode arrays and a minimally invasive surgical delivery system that together facilitate communication with large portions of the cortical surface in bidirectional fashion (enabling both recording and stimulation). We demonstrate the safety and feasibility of rapidly delivering reversible implants containing over 2,000 microelectrodes to multiple functional regions in both hemispheres of the Gottingen minipig brain simultaneously, without requiring a craniotomy, at an effective insertion rate faster than 40 ms per channel, without damaging the cortical surface. We further demonstrate the performance of this system for high-density neural recording, focal cortical stimulation, and accurate neural decoding. Such a system promises to accelerate efforts to better decode and encode neural signals, and to expand the patient population that could benefit from neural interface technology.


title: A wMel Wolbachia variant in Aedes aegypti from field-collected Drosophila melanogaster with increased phenotypic stability under heat stress

abstract: Mosquito-borne diseases such as dengue, Zika and chikungunya remain a major cause of morbidity and mortality across tropical regions. Population replacement strategies involving the wMel strain of Wolbachia are being used widely to control mosquito-borne diseases transmitted by Aedes aegypti. However, these strategies may be influenced by environmental temperature because wMel is vulnerable to heat stress. wMel infections in their native host Drosophila melanogaster are genetically diverse, but few transinfections of wMel variants have been generated in Ae. aegypti mosquitoes. Here we successfully transferred a wMel variant (termed wMelM) originating from a field-collected D. melanogaster population from Victoria, Australia into Ae. aegypti. The new wMelM variant (clade I) is genetically distinct from the original wMel transinfection (clade III) generated over ten years ago, and there are no genomic differences between wMelM in its original and transinfected host. We compared wMelM with wMel in its effects on host fitness, temperature tolerance, Wolbachia density, vector competence, cytoplasmic incompatibility and maternal transmission under heat stress in a controlled background. wMelM showed a higher heat tolerance than wMel, with stronger cytoplasmic incompatibility and maternal transmission when eggs were exposed to heat stress, likely due to higher overall densities within the mosquito. Both wMel variants had minimal host fitness costs, complete cytoplasmic incompatibility and maternal transmission, and dengue virus blocking under standard laboratory conditions. Our results highlight phenotypic differences between closely related Wolbachia variants. wMelM shows potential as an alternative strain to wMel in dengue control programs in areas with strong seasonal temperature fluctuations.

category: microbiology


title: Optogenetic Manipulation of Cell Migration with High Spatiotemporal Resolution Using Lattice Lightsheet Microscopy

abstract: Lattice lightsheet microscopy (LLSM) is modified with the aim of manipulating cellular behavior with subcellular resolution through three-dimensional (3D) optogenetic activation. In this study, we report a straightforward implementation of the activation source in LLSM in which the stimulating light can be generated by changing the spatial light modulator (SLM) patterns and the annual masks. As a result, a Bessel beam as a stimulation source is integrated into the LLSM without changing the optical configuration, achieving better spatiotemporal control of photoactivation. We show that the energy power required for optogenetic reactions is lower than 1 nW (or 24 mW/cm2), and membrane ruffling can be activated at different locations within a cell with subcellular resolution. We also demonstrate guided cell migration using optogenetic stimulation for up to 6 h, where 463 imaging volumes are collected, without noticeable damage to cells.

category: cell biology


title: Asymmetric habitat isolation and sexual isolation predicted by the cost of migration and hybridization generate novel signatures of reinforcing selection

abstract: Reinforcement is an evolutionary process whereby increased prezygotic reproductive isolation evolves in response to the cost of hybridization. Despite theory predicting that multiple prezygotic barriers can evolve via reinforcement, most empirical studies examine a single barrier. We test novel predictions for the reinforcement of both habitat isolation and sexual isolation between ecologically divergent lineages under asymmetric migration--the lineage that emigrates more should evolve stronger habitat isolation due to the lower fitness of immigrants in the alternative habitat, while the lineage that receives more immigrants should exhibit stronger sexual isolation due to the lower fitness of hybrids. We found both signatures of reinforcement in two sympatric sister species of gall wasps that are host specific to the southern live oaks, Quercus virginiana and Q. geminata, respectively. Specifically, we observed stronger habitat isolation in the species with higher emigration rates, Belonocnema treatae, and stronger sexual isolation in the species facing more immigrants, B. fossoria. In contrast, comparisons of both species to a third, allopatric, species showed that B. kinseyi exhibited both lower habitat isolation and sexual isolation than the sympatric species, consistent with the classic predictions of reinforcement. Our study provides a rare examination of the interplay of ecology and geography in the evolution of multiple reproductive barriers to gene flow. Given that asymmetric migration between ecologically divergent lineages increasingly appears to be the rule rather than the exception, concomitant asymmetries in the strength of habitat and sexual isolation could be more widespread than currently understood.


title: Connectional architecture of the prefrontal cortex in the marmoset brain

abstract: The primate prefrontal cortex (PFC) has greatly expanded to evolve specialized architecture, but its roles in top-down brain control remain enigmatic. Based on connectomics mapping of the marmoset PFC, we characterized two contrasting features of corticocortical and corticostriatal projections. One is the  focalness of projections, exemplified by multiple columnar axonal terminations in the cortical layers and the other is the  widespreadness of weaker projections, whose patterns consisted of several common motifs representing the framework of PFC connectivity. We clarified the topographic rules of distribution for these features, which should constrain how PFC neurons can coordinate to control the target regions as populations. These features are observed only primitively in rodents and are considered critical in understanding the roles of the PFC in neuropsychiatric disorders.


title: Uncovering a neural circuit controlling adult quiescent neural stem cell activation in the subventricular zone

abstract: The maintenance and differentiation of the adult neural stem cells (NSCs) in the subventricular zone (SVZ) are controlled by cell-intrinsic molecular pathways that interact with extrinsic signaling cues. How neurogenesis in the SVZ is regulated by neural circuit activity remains poorly understood. Here we identified a novel neural circuit that regulates the state of lateral ventricular wall (LV) NSCs. Our results demonstrate that direct glutamatergic inputs from the frontal cortex, as well as local inhibitory interneurons, control the activity of subependymal cholinergic neurons. In vivo optogenetic and chemogenetic stimulation of defined neuronal populations within this circuit were sufficient to control LV NSC proliferation and SVZ neurogenesis. Moreover, acetylcholine (Ach), which activates M1 muscarinic ACh receptors, triggers the activation of quiescent NSCs. These findings shed light on neural activity-dependent regulation of postnatal and adult LV NSCs activation and SVZ neurogenesis.


title: Single-cell analysis of microglial transcriptomic diversity in subarachnoid hemorrhage

abstract:
BackgroundSubarachnoid hemorrhage (SAH) is a severe stroke and the advanced treatment for SAH is still limited. Recent studies have shown that microglia-mediated neuroinflammation plays a critical role in the pathogenesis of SAH. Microglia can transform their states in response to central nervous system injury. However, the transcriptomic features of microglia remained unknown in SAH. Recent developed single-cell RNA sequencing (scRNA-seq) provides a possible way to solve this problem.

MethodsEndovascular perforation (EVP) murine SAH model was established to reproduce experimental SAH. Microglia states are examined with immune staining and quantitate analysis. Post-SAH microglial single-cell suspension were harvest and sequenced using 10X scRNA-seq platform. Then, the detailed single-cell transcriptomic characterization of post-SAH microglia were analyzed with bioinformatics.

ResultsTranscriptional analysis revealed at least ten diverse microglial subgroups, including SAH-associated microglia (SAM), inflammatory-associated microglia (IAM) and proliferation-associated microglia (PAM), which all exhibit distinct marker gene expression patterns. Microglia subsets interaction reveals the functional relationship between elevated signaling pathways and microglial sub-populations in SAH. Receptor-ligand pair analysis revealed that complex inter-cellular interactions exist between the microglia subsets and other cell types, and indicated that microglia are important mediators of neuroinflammation after SAH. Integrated analysis with normal microglia further proved the existence of these microglia subpopulations and different gene markers associated with SAH were clarified.

ConclusionsCollectively, we first report the single-cell transcriptome of post-SAH microglia and found specific biomarkers related to the neuroinflammation in SAH. These results enhanced our understanding of the pathological mechanisms of microglial response to SAH, and may guide future development of SAH monitoring methods and therapeutics.


title: Properties and computational consequences of fast dendritic spikes during natural behavior

abstract: Dendritic membrane potential was recently measured for the first time in drug-free, naturally behaving rats over several days. These showed that neuronal dendrites generate a lot of sodium spikes, up to ten times as many as the somatic spikes. These key experimental findings are reviewed here, along with a discussion of computational models, and computational consequences of such intense spike traffic in dendrites. We overview the experimental techniques that enabled these measurements as well as a variety of models, ranging from conceptual models to detailed biophysical models. The biophysical models suggest that the intense dendritic spiking activity can arise from the biophysical properties of the dendritic voltage-dependent and synaptic ion channels, and delineate some computational consequences of fast dendritic spike activity. One remarkable aspect is that in the model, with fast dendritic spikes, the efficacy of synaptic strength in terms of driving the somatic activity is much less dependent on the position of the synapse in dendrites. This property suggests that fast dendritic spikes is a way to confer to neurons the possibility to grow complex dendritic trees with little computational loss for the distal most synapses, and thus form very complex networks with high density of connections, such as typically in the human brain. Another important consequence is that dendritically localized spikes can allow simultaneous but different computations on different dendritic branches, thereby greatly increasing the computational capacity and complexity of neuronal networks.


title: Expanded ACE2 dependencies of diverse SARS-like coronavirus receptor binding domains

abstract: Viral spillover from animal reservoirs can trigger public health crises and cripple the world economy. Knowing which viruses are primed for zoonotic transmission can focus surveillance efforts and mitigation strategies for future pandemics. Successful engagement of receptor protein orthologs is necessary during cross-species transmission. The clade 1 sarbecoviruses including SARS-CoV and SARS-CoV-2 enter cells via engagement of ACE2, while the receptor for clade 2 and clade 3 remains largely uncharacterized. We developed a mixed cell pseudotyped virus infection assay to determine whether various clade 2 and 3 sarbecovirus spike proteins can enter HEK 293T cells expressing human or Rhinolophus horseshoe bat ACE2 proteins. The receptor binding domains from BtKY72 and Khosta-2 used human ACE2 for entry, while BtKY72 and Khosta-1 exhibited widespread use of diverse rhinolophid ACE2s. A lysine at ACE2 position 31 appeared to be a major determinant of the inability of these RBDs to use a certain ACE2 sequence. The ACE2 protein from R. alcyone engaged all known clade 3 and clade 1 receptor binding domains. We observed little use of Rhinolophus ACE2 orthologs by the clade 2 viruses, supporting the likely use of a separate, unknown receptor. Our results suggest that clade 3 sarbecoviruses from Africa and Europe use Rhinolophus ACE2 for entry, and their spike proteins appear primed to contribute to zoonosis under the right conditions.


title: Effector-mediated subversion of proteasome activator (PA)28αβ enhances lysosomal targeting of Legionella pneumophila within cytokine-activated macrophages

abstract: Legionella pneumophila is a natural pathogen of protozoa that causes Legionnaires Disease pneumonia via replication within macrophages using hundreds of translocated effector proteins. In metazoans, effectors can also enhance pathogen clearance via effector-triggered immunity. The effector LegC4 confers a fitness disadvantage on L. pneumophila uniquely within cytokine-activated macrophages, but the mechanism is unknown. Here, we demonstrate that LegC4 restriction occurs via subversion of proteasome activator (PA)28{beta}, which is induced by cytokines and functions to resolve oxidative stress. LegC4 impaired resolution of oxidative stress and LegC4-mediated restriction was abolished within PA28{beta}-deficient macrophages. Impaired proteasome activity upregulates lysosomal degradation pathways and, indeed, subversion PA28{beta} by LegC4 enhanced lysosomal fusion with the Legionella-containing vacuole. PA28{beta} has been traditionally associated with antigen presentation; however, our data support a new model whereby subversion of PA28{beta} enhances macrophage cell-autonomous immunity against L. pneumophila. This work provides a solid foundation to evaluate induced proteasome regulators as mediators of innate immunity.


title: Single-cell RNA-Seq analysis reveals dual sensing of HIV-1 in blood Axl+ dendritic cells

abstract: Sensing of incoming viruses represents one of the pivotal tasks of dendritic cells (DC). Human primary blood DC encompass various subsets that are diverse in their susceptibility and response to HIV-1. The recent identification of Axl+DC, a new blood DC subset, endowed with unique capacities to bind, replicate, and transmit HIV-1 prompted us to evaluate its anti-viral response. We show that HIV-1 induced two main broad and intense transcriptional programs in different Axl+DC potentially induced by different sensors; a NF-{kappa}B-mediated program that led to DC maturation and efficient antigen-specific CD4+T cell activation, and a program mediated by STAT1/2 that activated type I IFN and an ISG response. These responses were absent from cDC2 exposed to HIV-1 except when viral replication occurred. Finally, Axl+DC actively replicating HIV-1 identified by quantification of viral transcripts exhibited a mixed NF-{kappa}B/ISG innate response. Our results suggest that the route of HIV-1 entry may dictate different innate sensing pathway by DC.

category: immunology


title: Retrieval context determines whether event boundaries impair or enhance temporal order memory

abstract: Meaningful changes in context create "event boundaries", segmenting continuous experience into distinct episodes in memory. A foundational finding in this literature is that event boundaries impair memory for the temporal order of stimuli spanning a boundary compared to equally spaced stimuli within an event. This seems surprising in light of intuitions about memory in everyday life, where the order of within-event experiences (did I have coffee before the first bite of bagel?) often seems more difficult to recall than the order of events per se (did I have breakfast or do the dishes first?). Here, we aimed to resolve this discrepancy by manipulating whether stimuli carried information about their encoding context during retrieval, as they often do in everyday life (e.g., bagel-breakfast). In Experiments 1 and 2, we show that stimuli inherently associated with a unique encoding context produce a "flipped" order memory effect, whereby temporal memory was superior for cross-boundary than within-event item pairs. In Experiments 3 and 4, we added context information at retrieval to a standard laboratory event memory protocol where stimuli were encoded in the presence of arbitrary context cues (colored frames). We found that whether temporal order memory for cross-boundary stimuli was enhanced or impaired relative to within-event items depended on whether the context was present or absent during the memory test. Taken together, we demonstrate that the effect of event boundaries on temporal memory is malleable, and determined by the availability of context information at retrieval.


title: The First High-Quality Genome Assembly and Data Analysis of the Malaysian mahseer (Tor tambroides)

abstract: The Malaysian mahseer (Tor tambroides), one of the most valuable freshwater fish in the world, is mainly targeted for human consumption. The mitogenomic data of this species is available to date, but the genomic information is still lacking. For the first time, we sequenced the whole genome of an adult fish on both Illumina and Nanopore platforms. The hybrid genome assembly had resulted in a sum of 1.5 Gb genomic sequence from the 44,726 contigs found with 44 kb N50 length and BUSCO genome completeness of 84.3%. Four types of SSRs had been detected and identified within the genome with a greater AT abundance than that of GC. Predicted protein sequences had been functionally annotated to public databases, namely GO, KEGG and COG. A maximum likelihood phylogenomic tree containing 53 Actinopterygii species and two outgroups was constructed, providing first insights into the genome-based evolutionary relationship of T. tambroides with other ray-finned fish. These data are crucial in facilitating the study of population genomics, species identification, morphological variations, and evolutionary biology, which are helpful in the conservation of this species.


title: DRP1-mediated mitochondrial fission is essential to maintain cristae morphology and bioenergetics

abstract: Mitochondria and peroxisomes are both dynamic signaling organelles that constantly undergo fission. While mitochondrial fission is known to coordinate cellular metabolism, proliferation, and apoptosis, the physiological relevance of peroxisome dynamics and the implications for cell fate are not fully understood. DRP1 (dynamin-related protein 1) is an essential GTPase that executes both mitochondrial and peroxisomal fission. Patients with de novo heterozygous missense mutations in the gene that encodes DRP1, DNM1L, present with encephalopathy due to defective mitochondrial and peroxisomal fission (EMPF1). EMPF1 is a devastating neurodevelopmental disease with no effective treatment. To interrogate the mechanisms by which DRP1 mutations cause cellular dysfunction, we utilized human-derived fibroblasts from patients with mutations in DRP1 who present with EMPF1. As expected, patient cells display elongated mitochondrial morphology and lack of fission. Patient cells display a lower coupling efficiency of the electron transport chain, increased proton leak, and upregulation of glycolysis. In addition to these metabolic abnormalities, mitochondrial hyperfusion results in aberrant cristae structure and hyperpolarized mitochondrial membrane potential, both of which are tightly linked to the changes in metabolism. Peroxisome structure is also severely elongated in patient cells and results in a potential functional compensation of fatty acid oxidation. Understanding the mechanism by which DRP1 mutations cause these metabolic changes will give insight into the role of mitochondrial dynamics in cristae maintenance and the metabolic capacity of the cell, as well as the disease mechanism underlying EMPF1.


title: Human red blood cells express the RNA sensor TLR7 and bind viral RNA

abstract:
Red blood cells (RBCs) express the nucleic acid-sensing toll-like receptor 9 (TLR9) and bind CpG-containing DNA. However, whether human RBCs express other nucleic acid-sensing TLRs and bind RNA is unknown. Here we show that human RBCs express the RNA sensor, TLR7. TLR7 is present on the red cell membrane and associates with the RBC membrane protein Band 3. RBCs bind synthetic single-stranded RNA and RNA from pathogenic single-stranded RNA viruses. RNA acquisition by RBCs is attenuated by recombinant TLR7 and inhibitory oligonucleotides. Thus, RBCs may represent a previously unrecognized reservoir for RNA, although how RNA-binding by RBCs modulates the immune response has yet to be elucidated. These findings add to the growing list of non-gas exchanging RBC immune functions.

SignificanceRed blood cells interact with pathogens, cytokines, and CpG-containing DNA; however, their immune functions remain largely unexplored. Here, we report that RBCs can bind synthetic or viral RNA and express TLR7. TLR7 interacts with the RBC membrane protein Band 3 and this interaction is increased during acute infection with SARS-CoV-2. Our study suggests that RBCs may have immune functions mediated by viral RNA, and RNA-carrying RBCs can potentially be a reservoir for RNA-based diagnostics.


title: Dynamic evolution of small signaling peptide compensation in plant stem cell control

abstract: Gene duplications are a hallmark of plant genome evolution and a foundation for genetic interactions that shape phenotypic diversity1-5. Compensation is a major form of paralog interaction6-8, but how compensation relationships change as allelic variation accumulates is unknown. Here, we leveraged genomics and genome editing across the Solanaceae family to capture the evolution of compensating paralogs. Mutations in the stem cell regulator CLV3 cause floral organs to overproliferate in many plants9-11. In tomato, this phenotype is partially suppressed by transcriptional upregulation of a closely related paralog12. Tobacco lost this paralog, resulting in no compensation and extreme clv3 phenotypes. Strikingly, the paralogs of petunia and groundcherry nearly completely suppress clv3, indicating a potent ancestral state of compensation. Cross-species transgenic complementation analyses show this potent compensation partially degenerated in tomato due to a single amino acid change in the paralog and cis-regulatory variation that limits its transcriptional upregulation. Our findings show how genetic interactions are remodeled following duplications, and suggest that dynamic paralog evolution is widespread over short time scales and impacts phenotypic variation from natural and engineered mutations.


title: ClusTrast: a short read de novo transcript isoform assembler guided by clustered contigs

abstract:
MotivationTranscriptome assembly from RNA-sequencing data in species without a reliable reference genome has to be performed de novo, but studies have shown that de novo methods often have inadequate reconstruction ability of transcript isoforms. This impedes the study of alternative splicing, in particular for lowly expressed isoforms.

ResultWe present the de novo transcript isoform assembler ClusTrast, which clusters a set of guiding contigs by similarity, aligns short reads to the guiding contigs, and assembles each clustered set of short reads individually. We tested ClusTrast on datasets from six eukaryotic species, and showed that ClusTrast reconstructed more expressed known isoforms than any of the other tested de novo assemblers, at a moderate reduction in precision. An appreciable fraction were reconstructed to at least 95% of their length. We suggest that ClusTrast will be useful for studying alternative splicing in the absence of a reference genome.

Availability and implementationThe code and usage instructions are available at https://github.com/karljohanw/clustrast.

Contactolofem@kth.se

Supplementary informationSupplementary material is available.


title: Vps68 cooperates with ESCRT-III in intraluminal vesicle formation

abstract: The endosomal sorting complex required for transport (ESCRT)-III mediates budding and abscission of intraluminal vesicles (ILVs) into multivesicular endosomes. To further define the role of the ESCRT-III associated protein Mos10/Vps60 in ILV formation, we screened for new interaction partners by SILAC/MS. Here, we focused on the newly identified interaction partner Vps68. Our data suggest that Vps68 cooperates with ESCRT-III in ILV formation. The deletion of VPS68 caused a sorting defect similar to the SNF7 deletion, when the cargo load was high. The composition of ESCRT-III was altered, the level of core components was higher and the level of associated proteins was lower in the deletion strain. This suggests that a shift occurs from an active complex to a disassembly competent complex and that this shift is blocked in the{Delta} vps68 strain. We present evidence that during this shift Snf7 is replaced by Mos10. Vps68 has an unusual membrane topology. Two of its potential membrane helices are amphipathic helices localized to the luminal side of the endosomal membrane. Based on this membrane topology we propose that Vps68 and ESCRT-III cooperate in the abscission step by weakening the luminal and cytosolic leaflets of the bilayer at the abscission site.

category: molecular biology


title: Microtubules restrict F-actin to the immune synapse via GEF-H1 to maintain polarity in lymphocytes

abstract: Immune synapse formation is a key step for lymphocyte activation. In B lymphocytes, the immune synapse controls the production of high-affinity antibodies, thereby defining the efficiency of humoral immune responses. While the key roles played by both the actin and microtubule cytoskeletons in the formation and function of the immune synapse have become increasingly clear, how the different events involved in synapse formation are coordinated in space and time by actin-microtubule interactions is not understood. Using a microfluidic pairing device, we studied with unprecedented resolution the dynamics of the various events leading to immune synapse formation and maintenance. Our results identify two groups of events, local and global dominated by actin and microtubules dynamics, respectively. They further highlight an unexpected role for microtubules and the GEF-H1-RhoA axis in restricting F-actin polymerization at the immune synapse to define the cell polarity axis, allowing the formation and maintenance of a unique competent immune synapse.


title: Evaluation of lamin A/C mechanotransduction under different surface topography in LMNA related muscular dystrophy.

abstract: Most of the single point mutations of the LMNA gene are associated with distinct muscular dystrophies, marked by heterogenous phenotypes but primarily the loss and symmetric weakness of skeletal muscle tissue. The molecular mechanism and phenotype-genotype relationships in these muscular dystrophies are poorly understood. An effort has been here to delineating the adaptation of mechanical inputs into biological response by mutant cells of lamin A associated muscular dystrophy. In this study we implement engineered smooth and pattern surfaces of particular young modulus to mimic muscle physiological range. Using fluorescence and atomic force microscopy we present distinct architecture of the actin filament along with abnormally distorted cell and nuclear shape in mutants, which showed a tendency to deviate from wild type cells. Topographic features of pattern surface antagonizes the binding of the cell with it. Correspondingly, from the analysis of genome wide expression data in wild type and mutant cells, we report differential expression of the gene products of the structural components of cell adhesion as well as LINC (linkers of nucleoskeleton and cytoskeleton) protein complexes. This study also reveals mis expressed downstream signaling processes in mutant cells, which could potentially lead to onset of the disease upon the application of engineered materials to substitute the role of conventional cues in instilling cellular behaviors in muscular dystrophies. Collectively, these data support the notion that lamin A is essential for proper cellular mechanotransduction from extracellular environment to the genome and impairment of the muscle cell differentiation in the pathogenic mechanism for lamin A associated muscular dystrophy.


title: mBeRFP, a versatile fluorescent tool to enhance multichannel live imaging and its applications

abstract: Cell and developmental biology increasingly require live imaging of protein dynamics in cells, tissues or living organisms. Thanks to the discovery and the development of a panel of fluorescent proteins over the last decades, live imaging has become a powerful and commonly used approach. However, multicolor live imaging remains challenging. The generation of long Stokes shift red fluorescent proteins, such as mBeRFP, offers interesting new perspectives to bypass this limitation. Here, we constructed a set of mBeRFP-expressing vectors and provided a detailed characterization of this fluorescent protein for in vivo live imaging and its applications in Drosophila. Briefly, we showed that a single illumination source is sufficient to simultaneously stimulate mBeRFP and GFP. We demonstrated that mBeRFP can be easily combined with classical green and red fluorescent protein without any crosstalk. We also showed that the low photobleaching of mBeRFP is suitable for live imaging, and that this protein can be used for quantitative applications such as FRAP or laser ablation. Finally, we believe that this fluorescent protein, with the set of new possibilities it offers, constitutes an important tool for cell, developmental and mechano biologists in their current research.


title: Distinct roles of core autophagy-related genes (ATGs) in zebrafish definitive hematopoiesis

abstract: Despite the well-described discrepancy between some of the macroautophagy/autophagy-related genes (ATGs) in the regulation of hematopoiesis, the varying essentiality of core ATGs in vertebrate definitive hematopoiesis remains largely unclear. Here, we employed zebrafish (Danio rerio) to compare the function of six core atgs from the core autophagy machineries, which included atg13, beclin1 (becn1), atg9a, atg2a, atg5, and atg3, in vertebrate definitive hematopoiesis via CRISPR-Cas9 ribonucleoprotein targeting. Zebrafish embryos with various atg mutations showed autophagic deficiency throughout the body, including hematopoietic cells. The atgs mutations unsurprisingly caused distinctive hematopoietic abnormalities in zebrafish. Notably, becn1 or atg9a mutation resulted in hematopoietic stem cells (HSCs) expansion during the development of the embryo into a larva, which can be attributed to the proteomic changes in metabolism, HSCs regulators, and apoptosis. Besides, atg3 mutation lowered the leukocytes in developing zebrafish embryos. Intriguingly, a synergistic effect on HSCs expansion was identified in atg13+becn1 and atg9a+atg2a or atg3 double mutations, in which atg13 mutation and atg2a or atg3 mutation exacerbated and mitigated the HSCs expansion in becn1 and atg9a mutations, respectively. In addition, the myeloid cell type-specific effects of various atgs were also determined between neutrophils and macrophages. Of these, a skewed ratio of neutrophils versus macrophages was found in atg13 mutation, while both of them were reduced in atg3 mutation. These findings demonstrated the distinct roles of atgs and their interplays in zebrafish definitive hematopoiesis, thereby suggested that the vertebrate definitive hematopoiesis is regulated in an atgs-dependent manner.


title: Design Maps of TRPM8 as a Thermometer for Cold Detection

abstract: The menthol sensor TRPM8 can be activated by cold and thus serves as a thermometer in a primary afferent sensory neuron for noxious cold detection. However, the underlying design principle is unknown. Here, a hairpin topological structural model and graph theory were prepared to test a role of the cold-dependent hairpin formation in the cold-evoked gating pathway of TRPM8. The results showed that the formation of a large lipid-dependent hairpin initiates a low temperature threshold in favor of TRPM8 activation. Furthermore, two smaller hairpins, which enhance the coupled interactions of the voltage-sensor-like domain with both the pore domain and the TRP domain, can stabilize the cold efficacy and work as a fuse to prevent cold denaturation. The cold-induced hairpin rearrangements along the gating pathway may be necessary for the high cold sensitivity. This hairpin model may provide a structural basis for activation of the thermo-gated TRP channels at low temperature.


title: Heat-Dependent Hairpin Melting Drives TRPV1 Opening

abstract: The capsaicin receptor TRPV1 is a bio-thermometer in a primary afferent sensory neuron for noxious heat detection. However, the underlying molecular mechanism is unclear. Here, a hairpin thermodynamic model, together with graph theory, was to examine a role of temperature-dependent hairpin sizes in controlling the temperature threshold and sensitivity and gating states of TRPV1. The results showed that heat-dependent melting of the largest hairpin initiates a temperature threshold for channel opening while the smaller hairpins stabilize the open state and increase the heat efficacy or sensitivity. Therefore, this model may provide a broad structural basis for the thermo-gated TRP channels.


title: Heat-Dependent Hairpin Melting Drives Thermo-gated TRPV1 Opening


title: Analysis of SARS-CoV-2 Omicron Neutralization Data up to 2021-12-22

abstract: The rapid spread of the Omicron SARS-CoV-2 variant (B.1.1.529) resulted in international efforts to quickly assess its escape from immunity generated by vaccines and previous infections. Numerous laboratories published Omicron neutralization data as preprints and reports. The understandable limitations and variability in such rapid reporting of early results however made it difficult to make definitive statements about the data. Here, we aggregate and analyze Omicron neutralization data from 23 reporting laboratories up to 2021-12-22. There are enough data to identify multiple trends and make two definitive points. First, in twice-vaccinated individuals, titer fold drop of Omicron relative to wild type is more than 19x, likely substantially more given the number of measurements below the limit of detection of the assay. Second, out to one month post third vaccination with an mRNA vaccine, or twice vaccinated after an earlier infection, the titer fold drop to Omicron is substantially less at approximately 7x. This substantially lower fold drop and somewhat higher titers after 3rd vaccination are strong early evidence for the utility of booster vaccination.


title: Reduced Pathogenicity of the SARS-CoV-2 Omicron Variant in Hamsters

abstract: The SARS-CoV-2 Omicron (B.1.1.529) variant has proven highly transmissible and has outcompeted the Delta variant in many regions of the world1. Early reports have also suggested that Omicron may result in less severe clinical disease in humans. Here we show that Omicron is less pathogenic than prior SARS-CoV-2 variants in Syrian golden hamsters. Infection of hamsters with the SARS-CoV-2 WA1/2020, Alpha, Beta, or Delta strains led to 4-10% weight loss by day 4 and 10-17% weight loss by day 6, as expected2,3. In contrast, infection of hamsters with two different Omicron challenge stocks did not result in any detectable weight loss, even at high challenge doses. Omicron infection still led to substantial viral replication in both the upper and lower respiratory tracts and pulmonary pathology, but with a trend towards higher viral loads in nasal turbinates and lower viral loads in lung parenchyma compared with WA1/2020 infection. These data suggest that the SARS-CoV-2 Omicron variant may result in more robust upper respiratory tract infection but less severe lower respiratory tract clinical disease compared with prior SARS-CoV-2 variants.


title: Cystic fibrosis patient-derived bronchial organoids unveil druggable pathways against Mycobacterium abscessus infection.

abstract: Mycobacterium abscessus (Mabs) drives life-shortening mortality in cystic fibrosis (CF) patients, primarily because of its resistance to chemotherapeutic agents. Both our knowledge on and models to investigate the host and bacterial determinants that drive Mabs pathology in CF patients remain rudimentary. Here, we evaluated whether the lung organoid technology from CF patients is appropriate for modelling Mabs infection and whether antioxidant treatment is a candidate therapeutic approach in the context of CF disease. We derived airway organoids (AOs) from lung biopsy of a CF patient and characterized these AO by assessing CF transmembrane conductance regulator (CFTR) function, mucus and reactive oxygen species (ROS) production, lipid peroxidation, and cell death. We microinjected smooth (S-) or rough (R-)Mabs in the lumen of AOs to evaluate its fitness, responses of AOs to infection, and treatment efficacy by colony forming unit assay, qPCR and microscopy. We show that CF patient-derived AOs exhibited low residual CFTR function, enhanced mucus accumulation, and increased oxidative stress, lipid peroxidation, and cell death at basal state. While in AOs, S Mabs formed biofilm, R Mabs formed cord serpentines and displayed a higher virulence. S and R Mabs replicated more efficiently in CF AOs than in AOs derived from healthy lung. Pharmacological activation of antioxidant pathways resulted in better control of Mabs growth. In conclusion, we have established CF patient-derived AOs as a suitable human system to decipher mechanisms of CF-enhanced respiratory infection by Mabs and confirmed antioxidant approaches as a potential host-directed strategy to improve Mabs infection control.


title: Macrocycle-stabilization of its interaction with 14-3-3 increases plasma membrane localization and activity of CFTR

abstract: Impaired activity of the chloride channel CFTR is the cause of cystic fibrosis. 14-3-3 proteins have been shown to stabilize CFTR and increase its biogenesis and activity. Here, we report the identification and mechanism of action of a macrocycle stabilizing the 14-3-3/CFTR complex, a first-in-class molecular glue. This molecule rescues plasma membrane localization and chloride transport of F508del-CFTR and works additively with the CFTR pharmacological chaperone corrector lumacaftor (VX-809).


title: Robust expansion of phylogeny for fast-growing genome sequence data

abstract: Massive sequencing of SARS-CoV-2 genomes has led to a great demand for adding new samples to a reference phylogeny instead of building the tree from scratch. To address such challenge, we proposed an algorithm  TIPars by integrating parsimony analysis with pre-computed ancestral sequences. Compared to four state-of-the-art methods on four benchmark datasets (SARS-CoV-2, Influenza virus, Newcastle disease virus and 16S rRNA genes), TIPars achieved the best performance in most tests. It took only 21 seconds to insert 100 SARS-CoV-2 genomes to a 100k-taxa reference tree using near 1.4 gigabytes of memory. Its efficient and accurate phylogenetic placements and incrementation for phylogenies with highly similar and divergent sequences suggest that it will be useful in a wide range of studies including pathogen molecular epidemiology, microbiome diversity and systematics.