title: Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model

abstract:
1 -Digital light microscopy provides powerful tools for quantitatively probing the real-time dynamics of subcellular structures. While the power of modern microscopy techniques is undeniable, rigorous record-keeping and quality control are required to ensure that imaging data may be properly interpreted (quality), reproduced (reproducibility), and used to extract reliable information and scientific knowledge which can be shared for further analysis (value). Keeping notes on microscopy experiments and quality control procedures ought to be straightforward, as the microscope is a machine whose components are defined and the performance measurable. Nevertheless, to this date, no universally adopted community-driven specifications exist that delineate the required information about the microscope hardware and acquisition settings (i.e., microscopy "data provenance" metadata) and the minimally accepted calibration metrics (i.e., microscopy quality control metadata) that should be automatically recorded by both commercial microscope manufacturers and customized microscope developers. In the absence of agreed guidelines, it is inherently difficult for scientists to create comprehensive records of imaging experiments and ensure the quality of resulting image data or for manufacturers to incorporate standardized reporting and performance metrics. To add to the confusion, microscopy experiments vary greatly in aim and complexity, ranging from purely descriptive work to complex, quantitative and even sub-resolution studies that require more detailed reporting and quality control measures.

To solve this problem, the 4D Nucleome Initiative (4DN) (1, 2) Imaging Standards Working Group (IWG), working in conjunction with the BioImaging North America (BINA) Quality Control and Data Management Working Group (QC-DM-WG) (3), here propose light Microscopy Metadata specifications that scale with experimental intent and with the complexity of the instrumentation and analytical requirements. They consist of a revision of the Core of the Open Microscopy Environment (OME) Data Model, which forms the basis for the widely adopted Bio-Formats library (4-6), accompanied by a suite of three extensions, each with three tiers, allowing the classification of imaging experiments into levels of increasing imaging and analytical complexity (7, 8). Hence these specifications not only provide an OME-based comprehensive set of metadata elements that should be recorded, but they also specify which subset of the full list should be recorded for a given experimental tier. In order to evaluate the extent of community interest, an extensive outreach effort was conducted to present the proposed metadata specifications to members of several core-facilities and international bioimaging initiatives including the European Light Microscopy Initiative (ELMI), Global BioImaging (GBI), and European Molecular Biology Laboratory (EMBL) - European Bioinformatics Institute (EBI). Consequently, close ties were established between our endeavour and the undertakings of the recently established QUAlity Assessment and REProducibility for Instruments and Images in Light Microscopy global community initiative (9). As a result this flexible 4DN-BINA-OME (NBO namespace) framework (7, 8) represents a turning point towards achieving community-driven Microscopy Metadata standards that will increase data fidelity, improve repeatability and reproducibility, ease future analysis and facilitate the verifiable comparison of different datasets, experimental setups, and assays, and it demonstrates the method for future extensions. Such universally accepted microscopy standards would serve a similar purpose as the Encode guidelines successfully adopted by the genomic community (10, 11). The intention of this proposal is therefore to encourage participation, critiques and contributions from the entire imaging community and all stakeholders, including research and imaging scientists, facility personnel, instrument manufacturers, software developers, standards organizations, scientific publishers, and funders.


title: Pan-cancer survey of tumour mass dormancy and underlying mutational processes

abstract: Tumour mass dormancy is the key intermediate step between immune surveillance and cancer progression, yet due to its transitory nature it has been difficult to capture and characterise. Little is understood of its prevalence across cancer types and of the mutational background that may favour such a state. While this balance is finely tuned internally by the equilibrium between cell proliferation and cell death, the main external factors contributing to tumour mass dormancy are immunological and angiogenic. To understand the genomic and cellular context in which tumour mass dormancy may develop, we comprehensively profiled signals of immune and angiogenic dormancy in 9,631 cancers from the Cancer Genome Atlas and linked them to tumour mutagenesis. We find evidence for immunological and angiogenic dormancy-like signals in 16.5% of bulk sequenced tumours, with a frequency of up to 33% in certain tissues. Mutations in the CASP8 and HRAS oncogenes were positively selected in dormant tumours, suggesting an evolutionary pressure for controlling cell growth/apoptosis signals. By surveying the mutational damage patterns left in the genome by known cancer risk factors, we found that ageing-induced mutations were relatively depleted in these tumours, while patterns of smoking and defective base excision repair were linked with increased tumour mass dormancy. Furthermore, we identified a link between APOBEC mutagenesis and dormancy, which comes in conjunction with immune exhaustion and may partly depend on the expression of the angiogenesis regulator PLG as well as interferon and chemokine signals. Tumour mass dormancy also appeared to be impaired in hypoxic conditions in the majority of cancers. The microenvironment of dormant cancers was enriched in cytotoxic and regulatory T cells, as expected, but also in macrophages and showed a reduction in inflammatory Th17 signals. Finally, tumour mass dormancy was linked with improved patient survival outcomes. Our analysis sheds light onto the complex interplay between dormancy, exhaustion, APOBEC activity and hypoxia, and sets directions for future mechanistic explorations.

category: cancer biology


title: SIX1 is a master regulator of the Rhabdomyosarcoma undifferentiated state

abstract:
Rhabdomyosarcoma (RMS) is a pediatric skeletal muscle sarcoma characterized by the expression of the myogenic-lineage transcription factors (TF) MYOD1 and MYOG. Despite high expression of these TFs, RMS cells fail to terminally differentiate, suggesting the presence of factors that alter their function. Here, we demonstrate that the developmental TF, SIX1, is highly expressed in RMS and is critical to maintain a muscle progenitor-like state. SIX1 loss induces terminal differentiation of RMS cells into myotube-like cells and dramatically impedes tumor growth in vivo. We show that SIX1 maintains the RMS undifferentiated state by controlling enhancer activity and MYOD1 occupancy at loci more permissive to tumor growth over terminal muscle differentiation. Finally, we demonstrate that a gene signature derived from SIX1 loss correlates with differentiation status in RMS and predicts RMS progression in human disease. Our findings demonstrate a master regulatory role for SIX1 in the repression of RMS differentiation via genome-wide alterations in MYOD1-mediated transcription.

HighlightsO_LISIX1 prevents differentiation in RMS while it promotes differentiation during normal development
C_LIO_LIFN-RMS are highly dependent on SIX1 for growth in both zebrafish and mouse xenograft models
C_LIO_LILoss of SIX1 alters the transcriptional landscape of RMS cells, inducing a growth to differentiation switch
C_LIO_LISIX1 knockdown in FN-RMS causes reduced super enhancer-based activity at stem-related genes and enhanced MYOD1 binding to differentiation loci, resulting in the activation of a myogenic differentiation program
C_LIO_LIA gene signature derived from SIX1 loss strongly correlates with myogenic differentiation status and is predictive of advanced RMS.
C_LI


title: SIX1 Reprograms Myogenic Transcription Factors to Maintain the Rhabdomyosarcoma undifferentiated state


title: Hypo-osmotic Stress Induces ATP Release via Volume-regulated Anion Channels in Undifferentiated Mammary Cells

abstract: The high interstitial ATP concentration in the cancer microenvironment is a major source of adenosine, which acts as a strong immune suppressor. However, the source of ATP release has not been elucidated. We measured the ATP release during hypotonic stress using a real-time ATP luminescence imaging system in primary cultured mammary cells and in breast cell lines. In primary cultured cells, ATP was intermittently released with transient-sharp peaks, while in breast cell lines ATP was released with a slowly rising diffuse pattern. The diffuse ATP release pattern was changed to a transient-sharp pattern by cholera toxin treatment and the reverse change was induced by transforming growth factor (TGF) {beta} treatment. DCPIB, an inhibitor of volume-regulated anion channels (VRACs), only suppressed the diffuse pattern. The inflammatory mediator sphingosine-1-phosphate (S1P) induced a diffuse ATP release pattern isovolumetrically. The knockdown of A isoform of leucine-rich repeat-containing protein 8 (LRRC8A), the essential molecular entity of VRACs, using shRNA suppressed the diffuse pattern. These results suggest that abundantly expressed VRACs are a conduit of ATP release in undifferentiated cells, including cancer cells.

category: physiology


title: Dissecting the co-transcriptome landscape of plants and microbiota members

abstract: Interactions between plants and neighboring microbial species are fundamental elements that collectively determine the structure and function of the plant microbiota. However, the molecular basis of such interactions is poorly characterized. Here, we monocolonized Arabidopsis leaves with nine plant- associated bacteria from all major phyla of the plant microbiota and profiled co- transcriptomes of plants and bacteria. We detected both common and distinct co- transcriptome signatures among plant-commensal pairs. In planta responses of commensals were similar to those of a disarmed pathogen characterized by the suppression of genes involved in general metabolism in contrast to a virulent pathogen. We identified genes that are enriched in the genome of plant-associated bacteria and induced in planta, which may be instrumental for bacterial adaptation to the host environment and niche separation. This study provides insights into how plants discriminate among bacterial strains and lays the foundation for in- depth mechanistic dissection of plant-microbiota interactions.

category: plant biology


title: Dual reference method for high precision infrared measurement of leaf surface temperature under field conditions

abstract:
O_LITemperature is a key control over biological activities from the cellular to the ecosystem scales. However, direct, high precision measurements of surface temperature of small objects such as leaves under field conditions with large variations in ambient conditions remain rare. Contact methods such as thermocouples are prone to large errors. The use of non-contact remote sensing methods such as thermal infrared measurements provides an ideal solution, but their accuracy has been low (in the order of ~2 {degrees}C) due to necessity for corrections for material emissivity and fluctuations in background radiation (Lbg).
C_LIO_LIA novel  dual-reference method was developed to increase the accuracy of infrared needle-leaf surface temperature measurements in the field. It accounts for variations in Lbg and corrects for the systematic camera offset using two reference plates.
C_LIO_LIWe accurately captured surface temperature and leaf-to-air temperature differences of needle-leaves in a forest ecosystem with large diurnal and seasonal temperature fluctuations with an uncertainty of {+/-}0.23 and {+/-}0.25 {degrees}C, respectively.
C_LIO_LIRoutine high precision leaf temperature measurements even under harsh field conditions, such as demonstrated here, opens the way for investigating a wide range of leaf-scale processes and its dynamics.
C_LI


title: Scaling between stomatal size and density in forest plants

abstract: The size and density of stomatal pores limit the maximum rate of leaf carbon gain and water loss (gmax) in land plants. The limits of gmax due to anatomy, and its constraint by the negative correlation of stomatal size and density at broad phylogenetic scales, has been unclear and controversial. The prevailing hypothesis posits that adaptation to higher gmax is typically constrained by geometry and/or an economic need to reduce the allocation of epidermal area to stomata (stomatal-area minimization), and this would require the evolution of greater numbers of smaller stomata. Another view, supported by the data, is that across plant diversity, epidermal area allocated to guard cells versus other cells can be optimized without major trade-offs, and higher gmax would typically be achieved with a higher allocation of epidermal area to stomata (stomatal-area increase). We tested these hypotheses by comparing their predictions for the structure of the covariance of stomatal size and density across species, applying macroevolutionary models and phylogenetic regression to data for 2408 species of angiosperms, gymnosperms, and ferns from forests worldwide. The observed stomatal size-density scaling and covariance supported the stomatal-area increase hypothesis for high gmax. A higher gmax involves construction costs and maintenance costs that should be considered in models assessing optimal stomatal conductance for predictions of water use, photosynthesis, and water-use efficiency as influences on crop productivity or in Earth System models.


title: Accuracy and Precision of Social Relationship Indices

abstract: Combining interaction rates of different social behaviours into social relationship indices to represent the structure of dyadic relationships on one underlying dimension is common practice in animal sociality studies. However, the properties of these relationship indices are not well explored - mainly because, for real-world social systems, the  true value of relationships is unobservable. Here, we use simulation studies to estimate the accuracy and precision of three relationship indices: the Dyadic Composite Sociality Index, the Composite Relationship Index, and the Dynamic Dyadic Sociality Index. We simulated one year of social interactions for multiple groups of 25 individuals and 4 interaction types with different properties, and tested the impact of different focal follow regimes, data densities and sampling conditions on the representation of social relationships. Accuracy and precision of social relationship indices were strongly driven by sample size, similar to simple interaction rates. Under the assumption that there was a clear, one-dimensional relationship underlying interactions, and that different interaction types constituting an index were highly correlated, indices indeed increased accuracy over single interaction rates for small sample sizes. Including uninformative constituting behaviours (i.e., those not highly correlated with the underlying relationship dimension) reduced the accuracy of all indices. The precision of each index (i.e., whether multiple simulated focal follow regimes achieve the same dyadic values for the same data) was generally poor and was driven by the precision of the least precise constituting behaviour, making them less precise than some single interaction rates. Our results showed that social relationship indices do not remove the need to have sufficient data for each individual constituting interaction type. Index quality was defined by the least accurate and precise constituting interaction type. Indices might only be useful if all constituting interaction rates are highly correlated and if there are clear indications that one dimension is sufficient to represent social relationships in a group.

category: zoology


title: A closed-loop stimulation approach with real-time estimation of the instantaneous phase of neural oscillations by a Kalman filter

abstract: We propose a novel method to estimate the instantaneous oscillatory phase to implement a real-time system for closed-loop sensory stimulation in electroencephalography (EEG) experiments. The method uses Kalman filter-based prediction to estimate current and future EEG signals. We tested the performance of our method in a real-time situation. We demonstrate that the performance of our method shows higher accuracy in predicting the EEG phase than the conventional autoregressive model-based method. A Kalman filter allows us to easily estimate the instantaneous phase of EEG oscillations based on the automatically estimated autoregressive model implemented in a real-time signal processing machine. The proposed method has a potential for versatile applications targeting the modulation of EEG phase dynamics and the plasticity of brain networks in relation to perceptual or cognitive functions.

category: neuroscience


title: The cortical hubs related to recovery of consciousness

abstract:
Background and ObjectivesThe neural mechanism that enables the recovery of consciousness in patients with unresponsive wakefulness syndrome (UWS) remains unclear. The aim of the current study is to characterize the cortical hub regions related to the recovery of consciousness in patients with UWS.

MethodsVoxel-wise degree centrality analysis was adopted to identify the cortical hubs related to the recovery of consciousness, for which a total of 27 UWS patients were used, including 13 patients who emerged from UWS (UWS-E), and 14 patients who remained in UWS (UWS-R) at least three months after the experiment performance. Furthermore, other recoverable unconscious states including three independent deep sleep datasets (n = 12, 9, 9 respectively) and three independent anesthesia datasets (n = 27, 14, 6 respectively) were adopted as validation groups. Spatial similarity of the hub characteristic with the validation groups between the UWS-E and UWS-R was compared using the dice coefficient. Finally, with the cortical regions persistently shown as hubs across UWS-E and validation states, functional connectivity analysis was further performed to explore the connectivity patterns underlying the recovery of consciousness.

ResultsFour cortical hubs were identified with significantly higher degree centrality for UWS-E than UWS-R, including the anterior precuneus, left inferior parietal lobule, left inferior frontal gyrus, and left middle frontal gyrus, of which the degree centrality value also positively correlated with the patients Glasgow Outcome Scale (GOS) score. Furthermore, the anterior precuneus was found to show significantly higher similarity of hub characteristics as well as functional connectivity pattern between UWS-E and validation groups, compared with UWS-R.

DiscussionThe results suggest that the recovery of consciousness may be relevant to the integrity of cortical hubs, especially the anterior precuneus. The identified cortical hub regions could serve as potential targets for noninvasive stimulation aimed at promoting the patients consciousness recovery.


title: Escitalopram Administration, Neuroplastic Effects and Relearning: A Diffusion Tensor Imaging Study in Healthy Individuals

abstract:
BackgroundNeuroplastic processes are influenced by selective serotonergic reuptake inhibitors, while learning in conjunction with the administration of serotonergic agents alters white matter microstructure in humans. The goal of this double-blind, placebo-controlled imaging study was to investigate the influence of escitalopram on white matter plasticity during (re)learning.

MethodsSeventy-one healthy individuals (age = 25.6{+/-}5.0, 43 females) underwent 3 diffusion magnetic resonance imaging sessions: at baseline, after 3-weeks of associative learning (emotional/non-emotional content) and after relearning shuffled associations for an additional 3 weeks. During the relearning phase, subjects received daily escitalopram 10 mg or placebo orally. Statistical analysis was performed with statistical parametric mapping (SPM) and using sandwich estimator.

ResultsA three-way and two-way rmANOVA was conducted to analyze the effects of escitalopram on AD, FA, MD and RD during the learning and relearning period. We found no significant three-way or two-way interactions for each DTI metrics (pFDR > 0.05), thus neither after 3 nor after 6 weeks we found significant changes in white matter microstructure.

ConclusionWe examined neither an effect of escitalopram nor learning (or relearning) interventions on different DTI metrics. The duration and intensity of study interventions (i.e. administration of escitalopram and learning as the relearning task) might have been chosen insufficiently to induce detectable alterations. Previous studies examining the effects of SSRIs on white matter tracts in humans are underrepresented, but do mainly yield towards non-significant findings. The results implicate that escitalopram does not impact white matter microstructures in healthy subjects.


title: Beyond linear dynamic functional connectivity: a vine copula change point model

abstract: To estimate dynamic functional connectivity for functional magnetic resonance imaging (fMRI) data, two approaches have dominated: sliding window and change point methods. While computationally feasible, the sliding window approach has several limitations. In addition, the existing change point methods assume a Gaussian distribution for and linear dependencies between the fMRI time series. In this work, we introduce a new methodology called Vine Copula Change Point (VCCP) to estimate change points in the functional connectivity network structure between brain regions. It uses vine copulas, various state-of-the-art segmentation methods to identify multiple change points, and a likelihood ratio test or the stationary bootstrap for inference. The vine copulas allow for various forms of dependence between brain regions including tail, symmetric and asymmetric dependence, which has not been explored before in the dynamic analysis of neuroimaging data. We apply VCCP to various simulation data sets and to two fMRI data sets: a reading task and an anxiety inducing experiment. In particular, for the former data set, we illustrate the complexity of textual changes during the reading of Chapter 9 in Harry Potter and the Sorcerers Stone and find that change points across subjects are related to changes in more than one type of textual attributes. Further, the graphs created by the vine copulas indicate the importance of working beyond Gaussianity and linear dependence. Finally, the R package vccp implementing the methodology from the paper is available from CRAN.


title: A large lipoprotein mediates target specificity for T6SS-dependent killing

abstract: Interbacterial competition is prevalent in host-associated microbiota, where it can shape community structure and function, impacting host health in both positive and negative ways. However, the factors that permit bacteria to discriminate among their various neighbors for targeted elimination of competitors remain elusive. We identified a specificity factor in Vibrio species that is used to target specific competitors for elimination. Here, we describe this specificity factor, which is associated with the broadly-distributed type VI secretion system (T6SS), by studying symbiotic Vibrio fischeri, which use the T6SS to compete for colonization sites in their squid host. We demonstrate that a large lipoprotein (TasL) allows V. fischeri cells to restrict T6SS-dependent killing to certain genotypes by selectively integrating competitor cells into aggregates while excluding other cell types. TasL is also required for T6SS-dependent competition within juvenile squid, indicating the adhesion factor is active in the host. Because TasL homologs are found in other host-associated bacterial species, this newly-described specificity factor has the potential to impact microbiome structure within diverse hosts.

category: microbiology


title: Kinetochore-associated Mps1 regulates the strength of kinetochore-microtubule attachments via Ndc80 phosphorylation

abstract: Dividing cells detect and correct erroneous kinetochore-microtubule attachments during mitosis, thereby avoiding chromosome mis-segregation. Most studies of this process have focused on the Aurora B kinase, which phosphorylates microtubule-binding elements specifically at incorrectly attached kinetochores, promoting their release and providing another chance for proper attachments to form. However, growing evidence suggests additional mechanisms, potentially involving Mps1 kinase, that also underlie error correction. Because these mechanisms overlap in vivo, and because both Mps1 and Aurora B function in numerous other vital processes, their contributions to the correction of erroneous kinetochore attachments have been difficult to disentangle. Here we directly examine how Mps1 activity affects kinetochore-microtubule attachments using a reconstitution-based approach that allowed us to separate its effects from Aurora B activity. When endogenous Mps1 that co-purifies with isolated kinetochores is activated in vitro, it weakens their attachments to microtubules via phosphorylation of Ndc80, a major microtubule-binding element of the outer kinetochore. Mps1 phosphorylation of Ndc80 appears to contribute to error correction because phospho-deficient Ndc80 mutants exhibit genetic interactions and segregation defects when combined with mutants in an intrinsic error correction pathway. In addition, Mps1 phosphorylation of Ndc80 is stimulated on kinetochores lacking tension. These data suggest that Mps1 provides an additional mechanism for correcting erroneous kinetochore-microtubule attachments, complementing the well-known activity of Aurora B.

category: cell biology


title: Regulation of Vg1 biogenesis during mesendoderm induction

abstract: The TGF-beta signals Vg1 and Nodal form heterodimers to induce the vertebrate mesendoderm. The Vg1 proprotein is a monomer retained in the endoplasmic reticulum (ER) and is processed and secreted upon heterodimerization with Nodal. Here we investigate the mechanisms underlying Vg1 retention, processing, secretion and signaling in zebrafish. First, using a newly devised Synthetic Processing (SynPro) system, we find that Vg1 can be processed by intra- or extracellular proteases. Second, Vg1 can be processed without Nodal but requires Nodal for secretion and signaling. Third, Vg1-Nodal signaling activity requires Vg1 processing, whereas Nodal can remain unprocessed. Fourth, Vg1 employs exposed cysteines, glycosylated asparagines, and BiP chaperone-binding motifs for monomer retention in the ER. Our results establish SynPro as a new in vivo processing system and define molecular mechanisms and motifs that facilitate the generation of active Vg1-Nodal heterodimers. These observations suggest two strategies for rapid mesendoderm induction: chaperone-binding motifs help store Vg1 as an inactive but ready-to-heterodimerize monomer in the ER, and the flexibility of Vg1 processing location allows efficient generation of active heterodimers both intra- and extracellularly.

category: developmental biology


title: Implications of drift and rapid evolution on negative niche construction

abstract:
O_LIOrganisms throughout their lives constantly modify their surrounding environment; such activities are often termed niche construction. An important property of niche construction is that its consequences can persist for a long period of time and several subsequent generations can be affected. This phenomenon is described as a time lag in niche construction, or ecological inheritance.
C_LIO_LIStudies have suggested that time lag in niche construction can help avoiding the tragedy of the commons. In other words, it can lead to evolution of contribution to a common good, which is associated with positive niche construction, or to the limitation of a common bad, which is associated with negative niche construction.
C_LIO_LIIn this article, we will study the evolutionary consequences of incorporating time lags in a negative niche construction process: waste production. We consider a population that extrudes waste into its environment as it consumes resources to grow and reproduce. Higher consumption rates can lead to higher waste production. Individuals that adopt this selfish strategy are expected to be selected as toxic effects are equally shared among all individuals.
C_LIO_LIWe show that indeed this tragedy of the commons persists in many cases and selfish strategies evolve in general. When evolution is rapid and intragenerational time lag is incorporated, however, selfish strategies are no longer favoured and strategies resulting in less waste production can be selected. Importantly, heavy pollution results in smaller population sizes, so that drift becomes more important than natural selection and limits the evolution of higher waste production.
C_LI

category: evolutionary biology


title: Identity signaling, identity reception and the evolution of social recognition in a Neotropical frog

abstract: Animals recognize familiar individuals to perform a variety of important social behaviors. Social recognition is often mediated by communication between signalers who produce signals that contain identity information and receivers who categorize these signals based on previous experience. We tested two hypotheses about adaptations in signalers and receivers that enable the evolution of social recognition using two species of closely related territorial poison frogs. Male golden rocket frogs (Anomaloglossus beebei) recognize the advertisement calls of conspecific territory neighbors and display a "dear enemy effect" by responding less aggressively to neighbors than strangers, while male Kai rocket frogs (A. kaiei) do not. Our results did not support the identity signaling hypothesis: both species produced advertisement calls that contain similar amounts of identity information. Our results did support the identity reception hypothesis: both species exhibited habituation of aggression to playbacks simulating the arrival of a new neighbor, but only golden rocket frogs showed renewed aggression when they subsequently heard calls from a different male. These results suggest that an ancestral mechanism of plasticity in aggression common among frogs has been modified through natural selection to be specific to calls of individual males in golden rocket frogs, enabling a social recognition system.

category: animal behavior and cognition


title: Production of a Highly Immunogenic Antigen from SARS-CoV-2 by Covalent Coupling of the Receptor Binding Domain of Spike Protein to a Multimeric Carrier

abstract: Since the discovery of SARS-CoV-2, several antigens have been proposed to be part of COVID-19 vaccines. The receptor binding domain (RBD) of Spike protein is one of the promising candidates to develop effective vaccines since it can induce potent neutralizing antibodies. We previously reported the production of RBD in Pichia pastoris and showed it is structurally identical to the protein produced in mammalian HEK-293T cells. In this work we designed an RBD multimer construct with the purpose of increasing RBD immunogenicity. We produced multimeric particles by a transpeptidation reaction between the RBD expressed in P. pastoris and Lumazine Synthase from Brucella abortus (BLS), which is a highly immunogenic and very stable decameric protein of 170 kDa. We vaccinated mice with two doses 30 days apart, and then we measured humoral immune response. When the number of RBD copies coupled to BLS was high (6-7 RBD molecules per BLS decamer, in average), the immune response was significantly better than that elicited by RBD alone or even by RBD-BLS comprising low number of RBD copies (1-2 RBD molecules per BLS decamer). Remarkably, the construct with high number of RBD copies induced high IgG titers with high neutralizing capacity. Furthermore, a superior immune response was observed when Al(OH)3 adjuvant was added to this formulation, exhibiting a higher titer of neutralizing antibodies. Altogether our results suggest that RBD covalent coupled to BLS forming a multimer-particle shows an advantageous architecture to the antigen-presentation to the immune system which enhances immune responses. This new antigen should be considered a potent candidate for a protein-based vaccine.

category: biochemistry


title: Light Attention Predicts Protein Location from the Language of Life

abstract:
SummaryAlthough knowing where a protein functions in a cell is important to characterize biological processes, this information remains unavailable for most known proteins. Machine learning narrows the gap through predictions from expert-designed input features leveraging information from multiple sequence alignments (MSAs) that is resource expensive to generate. Here, we showcased using embeddings from protein language models (pLMs) for competitive localization prediction without MSAs. Our lightweight deep neural network architecture used a softmax weighted aggregation mechanism with linear complexity in sequence length referred to as light attention (LA). The method significantly outperformed the state-of-the-art (SOTA) for ten localization classes by about eight percentage points (Q10). So far, this might be the highest improvement of just embeddings over MSAs. Our new test set highlighted the limits of standard static data sets: while inviting new models, they might not suffice to claim improvements over the SOTA.

AvailabilityOnline predictions are available at http://embed.protein.properties. Predictions for the human proteome are available at https://zenodo.org/record/5047020. Code is provided at https://github.com/HannesStark/protein-localization.

category: bioinformatics


title: Pressure drives rapid burst-like collective migration from 3D cancer aggregates

abstract: Collective migration of cells is a key behaviour observed during morphogenesis, wound healing and cancer cell invasion. Hence, understanding the different aspects of collective migration is at the core of further progress in describing and treating cancer and other pathological defects. The standard dogma in cell migration is that cells exert forces on the environment to move and cell-cell adhesion-based forces provide the coordination for collective migration. Here, we report a new collective migration mechanism that is independent of pulling forces on the extra-cellular matrix (ECM), as it is driven by the pressure difference generated inside model tumours. We observe a striking collective migration phenotype, where a rapid burst-like stream of HeLa cervical cancer cells emerges from the 3D aggregate embedded in matrices with low collagen concentration (0.5 mg ml-1). This invasion-like behaviour is recorded within 8 hours post embedding (hpe), and is characterised by high cell velocity and super-diffusive collective motion. We show that cellular swelling, triggered by the soft matrix, leads to a rise in intrinsic pressure, which eventually drives an invasion-like phenotype of HeLa cancer aggregates. These dynamic observations provide new evidence that pressure-driven effects need to be considered for a complete description of the mechanical forces involved in collective migration and invasion.

category: biophysics


title: Targeting the mitochondrial RNA methyltransferase TRMT61B reveals new therapeutic opportunities in aneuploid cancer cells

abstract: Chromosomal instability (CIN) is an important source of genetic and phenotypic variation that has been extensively reported as a critical cancer related property that improves tumor cell adaptation and survival. CIN and its immediate consequence, aneuploidy, provoke adverse effects on cellular homeostasis that need to be overcome by developing efficient anti-stress mechanisms. Perturbations in these safeguard responses might be detrimental for cancer cells and represent an important tumor specific Achilles heel since CIN and aneuploidy are very rare events in normal cells. On the other hand, epitranscriptomic marks catalyzed by different RNA modifying enzymes have been found to change under several stress insults. Although CIN and aneuploidy are important intracellular stressors, their biological connection with RNA modifications is pending to be determined. In an in silico search for new cancer biomarkers, we have identified TRMT61B, a mitochondrial RNA methyltransferase enzyme, to be associated with high levels of aneuploidy. In the present work, we study the connection of this molecule with cancer and aneuploidy. First, we show increased protein amounts of TRMT61B in tumor cell lines with imbalanced karyotype as well as in different tumor types compared to unaffected control tissues. In addition, we demonstrate that depletion of TRMT61B in melanoma cells reduces cell proliferation either by fostering apoptosis and inhibiting autophagy in high-aneuploid (ANEhigh) cells or by inducing senescence in the case of low-aneuploid (ANElow) cell lines. Further, TRMT61B elimination compromises mitochondrial function and reduces the expression of several mitochondrial encoded proteins that are part of the electron transport chain. Finally, transwell and xenograft experiments revealed a reduced invasive and tumorigenic capacity upon TRMT61B depletion that strengthen the therapeutic value of this aneuploidy-associated biomarker. These results, which connect tumorigenesis, aneuploidy and mitochondrial RNA methylation, bring to the cancer field a new putative strategy to specifically target high aneuploid tumors.


title: The oldest peracarid crustacean reveals a Late Devonian freshwater colonisation by isopod relatives

abstract: Peracarida (e.g., woodlice & side-swimmers) are, together with their sister-group Eucarida (e.g. krill & decapods), the most speciose group of modern crustaceans, suggested to have appeared as early as the Ordovician. While eucarids incursion onto land consists of mainly freshwater and littoral grounds, some peracarids have evolved fully terrestrial ground-crawling ecologies, inhabiting even our gardens in temperate regions (e.g. pillbugs and sowbugs). Their fossil record extends back to the Carboniferous and consists mainly of marine occurrences. Here, we provide a complete re-analysis of a fossil arthropod - Oxyuropoda - reported in 1908 from the Late Devonian floodplains of Ireland, and left with unresolved systematic affinities despite a century of attempts at identification. Known from a single specimen preserved in two-dimensions, we analysed its anatomy using digital microscopy and multispectral macro-imaging to enhance contrast of morphological structures. The new anatomical characters and completeness of Oxyuropoda, together with a phylogenetic analysis with representatives of all major Eumalacostraca groups, indicate that Oxyuropoda is a crown-peracarid, part of a clade including amphipods and isopods. As such, Oxyuropoda is the oldest known Peracarida, and provides evidence that derived peracarids had an incursion into freshwater and terrestrial environments as early as the Famennian, more than 360 million years ago.

category: paleontology


title: Control-theoretic immune tradeoffs explain SARS-CoV-2 virulence and transmission variation

abstract: Dramatic variation in SARS-CoV-2 virulence and transmission between hosts has driven the COVID-19 pandemic. The complexity and dynamics of the immune response present a challenge to understanding variation in SARS-CoV-2 infections. To address this challenge, we apply control theory, a framework used to study complex feedback systems, to establish rigorous mathematical bounds on immune responses. Two mechanisms of SARS-CoV-2 biology are sufficient to create extreme variation between hosts: (1) a sparsely expressed host receptor and (2) potent, but not unique, suppression of interferon. The resulting model unifies disparate and unexplained features of the SARS-CoV-2 pandemic, predicts features of future viruses that threaten to cause pandemics, and identifies potential interventions.

category: systems biology


title: The microRNA miR-18a links proliferation and inflammation during photoreceptor regeneration in the injured zebrafish retina

abstract: In mammals, photoreceptor loss causes permanent blindness, but in zebrafish (Danio rerio), photoreceptor loss reprograms Muller glia to function as stem cells, producing progenitors that regenerate photoreceptors. MicroRNAs (miRNAs) regulate CNS neurogenesis, but the roles of miRNAs in injury-induced neuronal regeneration are largely unknown. In the embryonic zebrafish retina, miR-18a regulates photoreceptor differentiation. The purpose of the current study was to determine, in zebrafish, the function of miR-18a during injury-induced photoreceptor regeneration. RT-qPCR, in-situ hybridization and immunohistochemistry showed that miR-18a expression increases throughout the retina between 1 and 5 days post-injury (dpi). To test miR-18a function during photoreceptor regeneration, we used homozygous miR-18a mutants (miR-18ami5012), and knocked down miR-18a with morpholino oligonucleotides. During photoreceptor regeneration, miR-18ami5012 retinas have fewer mature photoreceptors than WT at 7 and 10 dpi, but there is no difference at 14 dpi, indicating that photoreceptor regeneration is delayed. Labeling dividing cells with 5-bromo-2'-deoxyuridine (BrdU) showed that at 7 and 10 dpi, there are excess dividing progenitors in both mutants and morphants, indicating that miR-18a negatively regulates injury-induced proliferation. Tracing 5-ethynyl-2'-deoxyuridine (EdU) and BrdU-labeled cells showed that in miR-18ami5012 retinas excess progenitors migrate to other retinal layers in addition to the photoreceptor layer. Inflammation is critical for photoreceptor regeneration, and RT-qPCR showed that in miR-18ami5012 retinas, inflammatory gene expression and microglia activation are prolonged. Suppressing inflammation with dexamethasone rescues the miR-18ami5012 phenotype. Together, these data show that in the injured zebrafish retina, disruption of miR-18a alters proliferation, inflammation, the microglia/macrophage response, and the timing of photoreceptor regeneration.


title: Disruption of miR-18a alters proliferation, photoreceptor replacement kinetics, inflammatory signaling and microglia/macrophage numbers during retinal regeneration in zebrafish


title: Neural mechanisms of context-dependent segmentation tested on large-scale recording data

abstract: The brain performs various cognitive functions by learning the spatiotemporal salient features of the environment. This learning likely requires unsupervised segmentation of hierarchically organized spike sequences, but the underlying neural mechanism is only poorly understood. Here, we show that a recurrent gated network of neurons with dendrites can context-dependently solve difficult segmentation tasks. Dendrites in this model learn to predict somatic responses in a self-supervising manner while recurrent connections learn a context-dependent gating of dendro-somatic current flows to minimize a prediction error. These connections select particular information suitable for the given context from input features redundantly learned by the dendrites. The model selectively learned salient segments in complex synthetic sequences. Furthermore, the model was also effective for detecting multiple cell assemblies repeating in large-scale calcium imaging data of more than 6,500 cortical neurons. Our results suggest that recurrent gating and dendrites are crucial for cortical learning of context-dependent segmentation tasks.


title: Functional coupling between target selection and acquisition in the superior colliculus

abstract:
To survive in unpredictable environments, animals must continuously evaluate their surroundings for behavioral targets, such as food and shelter, and direct their movements to acquire those targets. Although the ability to accurately select and acquire spatial targets depends on a shared network of brain regions, how these processes are linked by neural circuits remains unknown. The superior colliculus (SC) mediates the selection of spatial targets and remains active during orienting movements to acquire targets, which suggests the underexamined possibility that common SC circuits underlie both selection and acquisition processes. Here, we test the hypothesis that SC functional circuitry couples target selection and acquisition using a default motor plan generated by selection-related neuronal activity. Single-unit recordings from intermediate and deep layer SC neurons in male mice performing a spatial choice task demonstrated that choice-predictive neurons, including optogenetically identified GABAergic SC neurons whose activity was causally related to target selection, exhibit increased activity during movement to the target. By strategically recording from both rostral and caudal SC neurons, we also revealed an overall caudal-to-rostral shift in activity as targets were acquired. Finally, we used an attractor model to examine how target selection activity in the SC could generate a rostral shift in activity during target acquisition using only intrinsic SC circuitry. Overall, our results suggest a functional coupling between SC circuits that underlie target selection and acquisition, elucidating a key mechanism for goal-directed behavior.

Significance StatementThe ability to quickly select and acquire spatial targets is essential to animal survival. Neural circuits underlying these processes are shared in an interconnected network of brain regions, however it is unclear how circuits link decision-making processes with motor commands to execute choices. Here, we examine single-unit activity in the superior colliculus (SC) as mice select and acquire spatial targets to test the hypothesis that choice-related activity promotes target acquisition by generating a default motor plan for orienting movements. By demonstrating that choice-predictive neurons increase their firing rates during movement and capturing the dynamics of SC activity with an attractor model of intrinsic SC circuitry, our results support a role for SC circuits in coupling target selection and acquisition.


title: Super-resolution microscopy informs on the molecular architecture of alpha-synuclein inclusions in model systems and in the human brain

abstract:
Lewy bodies (LBs) and Lewy neurites are pathological hallmarks of Parkinsons disease and other progressive neurodegenerative disorders known as Lewy body diseases (LBD). These proteinaceous deposits are immunopositive for alpha-synuclein (aSyn) and several other proteins, as neurofilament components. The structural organization and composition of aSyn inclusions is still unclear and needs to be addressed in greater detail, as this may open novel avenues for our understanding of the disease-relevant pathological events.

In this study, we investigated the molecular architecture of aSyn inclusions, both in cell models and in human brain tissue, using state-of-art super resolution X10 Expansion microscopy (ExM). This approach physically expands specimens embedded into a swellable gel, preserving their biological information. Then, the specimen can be analyzed using standard epifluorescence microscopes, thereby obtaining nanoscale information.

The combination of different cell models, mouse and human brain tissue enabled us to distinguish different types aSyn assemblies (e.g. ring shape or tubular structures), and a conserved pattern of aSyn inclusions surrounded/encaged by intermediate filament proteins. Overall, X10 ExM enabled us to gain insight into the architecture and biology of aSyn inclusions and constitutes a powerful tool in the quest to understanding underlying disease mechanisms in synucleinopathies.


title: Early changes in corticomotor excitability underlie proactive inhibitory control of error correction

abstract:
Converging evidence indicates that response inhibition may arise from the interaction of effortful proactive and reflexive reactive mechanisms. However, the distinction between the neural basis sustaining proactive and reactive inhibitory processes is still unclear. To identify reliable neural markers of proactive inhibition, we examined the behavioral and electrophysiological correlates elicited by manipulating the degree of inhibitory control in a task that involved the detection and amendment of errors. Restraining or encouraging the correction of errors did not affect the time course of the behavioral and neural correlates associated to reactive inhibition. We rather found that a bilateral and sustained decrease of corticomotor excitability was required for an effective proactive inhibitory control, whereas selective strategies were associated with defective response suppression. Our results provide behavioral and electrophysiological conclusive evidence of a comprehensive proactive inhibitory mechanism, with a distinctive underlying neural basis, governing the commission and amendment of errors. Together, these findings hint at a decisive role for changes in corticomotor excitability in determining whether an action will be successfully suppressed.

SIGNIFICANCE STATEMENTResponse inhibition is a fundamental brain function that must be flexible enough to incorporate volitional goal-directed demands, along with rapid, automatic and well consolidated behaviors. Previous studies reflect a lack of consensus regarding the neural correlates subserving these two -proactive and reactive- distinct modes of inhibitory control. We combined electrophysiological recordings with behavioral measures within a paradigm of detection and correction of errors under two degrees of inhibitory control to identify genuine neural markers of proactive inhibitory control. We found evidence supporting a sustained and global -not selective- reduction of corticomotor excitability subserving successful proactive inhibition of motor responses. Our findings favor a distinctive mechanism of comprehensive inhibitory control to amend errors under a high degree of response competition.


title: A SARS CoV-2 nucleocapsid vaccine protects against distal viral dissemination

abstract: The SARS CoV-2 pandemic has killed millions of people. This viral infection can also result in substantial morbidity, including respiratory insufficiency and neurological manifestations, such as loss of smell and psychiatric diseases. Most SARS CoV-2 vaccines are based on the spike antigen, and although they have shown extraordinary efficacy at preventing severe lung disease and death, they do not always confer sterilizing immune protection. We performed studies in K18-hACE2 mice to evaluate whether the efficacy of SARS CoV-2 vaccines could be augmented by incorporating nucleocapsid as a vaccine antigen. We vaccinated mice with adenovirus-based vaccines encoding spike antigen alone, nucleocapsid antigen alone, or combined spike and nucleocapsid antigens. Mice were then challenged intranasally with SARS CoV-2, and acute viral loads were quantified at a proximal site of infection (lung) and a distal site of infection (brain). Interestingly, the spike-based vaccine conferred acute protection in the lung, but not in the brain. The spike-based vaccine conferred acute protection in the brain only if combined with the nucleocapsid-based vaccine. These findings suggest that nucleocapsid-specific immunity is important for the distal control of SARS CoV-2, warranting the inclusion of nucleocapsid in next-generation COVID-19 vaccines.

category: immunology


title: A potently neutralizing anti-SARS-CoV-2 antibody inhibits variants of concern by binding a highly conserved epitope

abstract: With the emergence of SARS-CoV-2 variants with increased transmissibility and potential resistance, antibodies and vaccines with broadly inhibitory activity are needed. Here we developed a panel of neutralizing anti-SARS-CoV-2 mAbs that bind the receptor binding domain of the spike protein at distinct epitopes and block virus attachment to cells and its receptor, human angiotensin converting enzyme-2 (hACE2). While several potently neutralizing mAbs protected K18-hACE2 transgenic mice against infection caused by historical SARS-CoV-2 strains, others induced escape variants in vivo and lost activity against emerging strains. We identified one mAb, SARS2-38, that potently neutralizes all SARS-CoV-2 variants of concern tested and protects mice against challenge by multiple SARS-CoV-2 strains. Structural analysis showed that SARS2-38 engages a conserved epitope proximal to the receptor binding motif. Thus, treatment with or induction of inhibitory antibodies that bind conserved spike epitopes may limit the loss of potency of therapies or vaccines against emerging SARS-CoV-2 variants.


title: Analysis of viral RNA-host protein interactomes enables rapid antiviral drug discovery

abstract:
RNA viruses including SARS-CoV-2, Ebola virus (EBOV), and Zika virus (ZIKV) constitute a major threat to global public health and society. The interactions between viral genomes and host proteins are essential in the life cycle of RNA viruses and thus provide targets for drug development. However, viral RNA-host protein interactions have remained poorly characterized. Here we applied ChIRP-MS to profile the interactomes of human proteins and the RNA genomes of SARS-CoV-2, EBOV, and ZIKV in infected cells. Integrated interactome analyses revealed interaction patterns that reflect both common and virus-specific host responses, and enabled rapid drug screening to target the vulnerable host factors. We identified Enasidenib as a SARS-CoV-2 specific antiviral agent, and Trifluoperazine and Cepharanthine as broad spectrum antivirals against all three RNA viruses.

One Sentence SummaryInteractome analyses of host proteins and the SARS-CoV-2, EBOV, and ZIKV RNA genomes unveil viral biology and drug targets.


title: Insertions in SARS-CoV-2 genome caused by template switch and duplications give rise to new variants of potential concern

abstract: The appearance of multiple new SARS-CoV-2 variants during the winter of 2020-2021 is a matter of grave concern. Some of these new variants, such as B.1.617.2, B.1.1.7, and B.1.351, manifest higher infectivity and virulence than the earlier SARS-CoV-2 variants, with potential dramatic effects on the course of the COVID-19 pandemic. So far, analysis of new SARS-CoV-2 variants focused primarily on point nucleotide substitutions and short deletions that are readily identifiable by comparison to consensus genome sequences. In contrast, insertions have largely escaped the attention of researchers although the furin site insert in the spike protein is thought to be a determinant of SARS-CoV-2 virulence and other inserts might have contributed to coronavirus pathogenicity as well. Here, we investigate insertions in SARS-CoV-2 genomes and identify 347 unique inserts of different lengths. We present evidence that these inserts reflect actual virus variance rather than sequencing errors. Two principal mechanisms appear to account for the inserts in the SARS-CoV-2 genomes, polymerase slippage and template switch that might be associated with the synthesis of subgenomic RNAs. We show that inserts in the Spike glycoprotein can affect its antigenic properties and thus merit monitoring. At least, three inserts in the N-terminal domain of the Spike (ins245IME, ins246DSWG, and ins248SSLT) that were first detected in 2021 are predicted to lead to escape from neutralizing antibodies, whereas other inserts might result in escape from T-cell immunity.


title: Insertions in SARS-CoV-2 genome caused by template switch and duplications give rise to new variants that merit monitoring


title: Tetratricopeptide repeat domain 36 protects renal tubular cells from cisplatin-induced apoptosis via maintaining mitochondrial homeostasis

abstract: The apoptosis of proximal tubule epithelial cells (PTECs) is a critical event of acute kidney injury (AKI). Tetratricopeptide repeat domain 36 (TTC36) with three tetratricopeptide repeats is evolutionarily conserved across mammals, which functions as a chaperone for heat shock protein 70. We have revealed that TTC36 is specifically expressed in PTECs in our previous work. There are few studies about the role TTC36 played in AKI. Therefore, in this study, we investigated the function of TTC36 in the apoptosis of HK2 cells, which are derived from the human proximal tubule. Firstly, we observed that TTC36 was obviously down-regulated and was negatively related to the kidney damage degree in a mouse model of acute kidney injury established by ischemia/reperfusion. In addition, TTC36 overexpression protected HK2 cells against cisplatin-induced apoptosis. Moreover, we discovered the mechanism that TTC36 mitigated cisplatin-triggered mitochondrial disorder via sustaining the membrane potential of mitochondria and mitochondrial autophagy-related gene expression. Collectively, these results suggested that TTC36 plays a protective role in the cisplatin-induced apoptosis of renal tubular cells through maintaining the mitochondrial potential and mitochondrial autophagy-related gene expression. These observations highlight the essential role of TTC36 in regulating PTEC apoptosis and imply TTC36/mitochondrial homeostasis axis as a potential target for the therapeutic intervention in AKI.


title: Coronary blood vessels from distinct origins converge to equivalent states during mouse and human development

abstract: Most cell fate trajectories during development follow a diverging, tree-like branching pattern, but the opposite can occur when distinct progenitors contribute to the same cell type. During this convergent differentiation, it is unknown if cells "remember" their origins transcriptionally or whether this influences cell behavior. Most coronary blood vessels of the heart develop from two different progenitor sources--the endocardium (Endo) and sinus venosus (SV)--but whether transcriptional or functional differences related to origin are retained is unknown. We addressed this by combining lineage tracing with single-cell RNA sequencing (scRNAseq) in embryonic and adult mouse hearts. Shortly after coronary development begins, capillary ECs transcriptionally segregated into two states that retained progenitor-specific gene expression. Later in development, when the coronary vasculature is well-established but still remodeling, capillary Ecs again segregated into two populations, but transcriptional differences were primarily related to tissue localization rather than lineage. Specifically, ECs in the heart septum expressed genes indicative of increased local hypoxia and decreased blood flow. Adult capillary ECs were more homogeneous with respect to both lineage and location. In agreement, SV- and Endo-derived ECs in adult hearts displayed similar responses to injury. Finally, scRNAseq of developing human coronary vessels indicated that the human heart followed similar principles. Thus, over the course of development, transcriptional heterogeneity in coronary ECs is first influenced by lineage, then by location, until heterogeneity declines in the homeostatic adult heart. These results highlight the plasticity of ECs during development, and the validity of the mouse as a model for human coronary development.


title: Morph-specific patterns of sex organ positions in species with style length polymorphism

abstract: In style length polymorphism, morph-specific sequence of encountering male and female sex organs within a flower by pollinators can cause differences in the need to avoid self-pollination and encourage inter-morph pollination. We asked if this difference can lead to disparity in stigma-anther separation (herkogamy) between morphs and spatial match between sex organs of complementary morphs (reciprocity). Further, we tested if herkogamy, and hence the level of selfing, is fairly constant among individuals of a population. Additionally, we examined the relationship between herkogamy and reciprocity among individuals of a population to understand functional interactions between these two morphological traits. Using data on sex organ heights for >200 heterostylous species from the literature, we observed that the short-styled morph had higher herkogamy as compared to the long-styled morph indicating a higher need to avoid selfing. Reciprocity did not show a consistent difference between the upper and lower sex organs implying a strong influence of local ecological factors. In most populations, allometric relationships suggested that herkogamy and hence the level of selfing remains constant. Finally, we observed that herkogamy and reciprocity can be related among individuals of a population, sometimes indicating a potential trade-off between avoidance of self-pollination and facilitation of inter-morph pollination.

category: ecology


title: Plant demographic knowledge is biased towards short-term studies of temperate-region herbaceous perennials

abstract:
O_LIPlant population dynamics research has a long history, and data collection rates have increased through time. The inclusion of this information in databases enables researchers to investigate the drivers of demographic patterns globally and study life history evolution.
C_LIO_LIStudies aiming to generalise demographic patterns rely on data being derived from a representative sample of populations. However, the data are likely to be biased, both in terms of the species and ecoregions investigated and in how the original studies were conducted.
C_LIO_LIMatrix population models (MPMs) are a widely-used tool in plant demography, so an assessment of publications that have used MPMs is a convenient way to assess the distribution of plant demographic knowledge. We assessed bias in this knowledge using data from the COMPADRE Plant Matrix Database, which contains MPMs for almost 800 plant species.
C_LIO_LIWe show that tree species and tropical ecoregions are under-represented, while herbaceous perennials and temperate ecoregions are over-represented. In addition, there is a positive association between the number of studies per country and the wealth of the country. Furthermore, we found a strong tendency towards low spatiotemporal replication: More than 50% of the studies were conducted over fewer than 4 years, and only 17% of the studies have replication across >3 sites. This limited spatiotemporal coverage means that the data may not be representative of the environmental conditions experienced by the species.
C_LIO_LISynthesis: The biases and knowledge gaps we identify are a challenge for the progress of theory and limit the usefulness of current data for determining patterns that would be useful for conservation decisions, such as determining general responses to climate change. We urge researchers to close these knowledge gaps with novel data collection.
C_LI


title: Multi-tissue integrative analysis of personal epigenomes

abstract: Evaluating the impact of genetic variants on transcriptional regulation is a central goal in biological science that has been constrained by reliance on a single reference genome. To address this, we constructed phased, diploid genomes for four cadaveric donors (using long-read sequencing) and systematically charted noncoding regulatory elements and transcriptional activity across more than 25 tissues from these donors. Integrative analysis revealed over a million variants with allele-specific activity, coordinated, locus-scale allelic imbalances, and structural variants impacting proximal chromatin structure. We relate the personal genome analysis to the ENCODE encyclopedia, annotating allele- and tissue-specific elements that are strongly enriched for variants impacting expression and disease phenotypes. These experimental and statistical approaches, and the corresponding EN-TEx resource, provide a framework for personalized functional genomics.

category: genomics


title: A chromosome-level genome assembly and annotation of a maize elite breeding line Dan340

abstract:
The maize cultivar Dan340 is an excellent backbone inbred line of Luda Red Cob Group with several desirable characters, such as disease resistance, lodging resistance, high combining ability, wide adaptability and so on. In this study, we constructed a high-quality chromosome-level reference genome for Dan340 by combining PacBio long HiFi sequencing, Illumina short reads and chromosomal conformational capture (Hi-C) sequencing reads. The final assembly of Dan340 genome was 2,348.72 Mb, including 2,738 contigs and 2,315 scaffolds with a N50 of 41.49 Mb and 215.35 Mb, respectively. The percent of high quality Illumina reads mapped to the reference genome was up to 97.48%. The assembly of this genome will not only facilitate our understanding about intraspecific genome diversity in maize, but also provides a novel resource for maize breeding.

Key findingsO_LIThe final assembly of Dan340 genome was 2,348.72 Mb, including 2,738 contigs and 2,315 scaffolds with a N50 of 41.49 Mb and 215.35 Mb, respectively.
C_LIO_LIThe percent of reads mapped to the reference genome was up to 97.48%.
C_LIO_LIThe results showed that 96.84% of the plant single-copy orthologues were complete. Complete single-copy and multi copy genes accounted for 87.36% and 9.48% of the genes, respectively. Taken together, these results indicated that our Dan340 genome assembly presented high quality and coverage.
C_LI


title: A chromosome-level genome assembly of a maize elite breeding line Dan340


title: Social experience alters different types of learning abilities controlled by distinct brain nuclei in Kryptolebias marmoratus

abstract:
Fighting experiences strongly influence aggressive behavior and physiology (winner-loser effects). These effects are conserved from invertebrates to vertebrates, but the underlying mechanisms remain unclear. Recent studies indicate that the brain social decision-making network (SDN) plays a key role in guiding experience-induced behavioral change. Also, while most studies have focused on how winning and losing experiences alter aggression, growing evidence points to these experiences driving multiple behavioral effects, including changes in the ability to learn. In mangrove rivulus fish (Kryptolebias marmoratus), we discovered that single winning experiences significantly improved spatial learning but not risk-avoidance learning, whereas single losing experiences drove the exact opposite to occur. These results provide strong evidence that winning and losing modulate diverse behaviors served by key nodes within the SDN, specifically the dorsolateral pallium (Dl; fish homolog to mammalian hippocampus, which serves spatial learning) and dorsomedial pallium (Dm; fish homolog to mammalian basolateral amygdala, which responds to fear). We therefore quantified whole-proteome expression within the forebrain (where Dm and Dl are located) of adult rivulus with divergent social experiences. We discovered 23 proteins were significantly differentially expressed in the forebrains of winners and losers. Differentially expressed proteins in losers related to modulation of cellular processes, apoptosis and learning while those in winners related to neuronal plasticity, neuroendocrine homeostasis, energy utilization, and learning. These results imply that winner-loser effects might be governed by very different patterns of protein expression, which could explain why winners and losers show such pronounced differences in behavioral performance.

Significance StatementSocial interactions permeate the daily lives of most animals and often result in changes in behavior for all parties. This implies that social experiences reorganize the brain in ways that promote the expression of alternative behaviors, or that help individuals cope with the outcome of such interactions. But how do aggressive interactions sculpt the brain at the molecular level? We used an emerging model organism, Kryptolebias marmoratus, to examine whether experiences modulate learning ability and then probe the potential neural mechanisms underlying these behavioral changes. We discovered that single winning and losing experiences dramatically altered spatial learning and risk-avoidance learning, respectively, indicating that winning and losing experiences have markedly different effects on the brain and cognitive processes.

ClassificationBiological Sciences, Ecology


title: Mechanical phenotyping of acute promyelocytic leukemia reveals unique biomechanical responses in retinoic acid-resistant populations

abstract: While all-trans retinoic acid (ATRA) is an essential therapy in the treatment of acute promyelocytic leukemia (APL), an aggressive subtype of acute myeloid leukemia, nearly 20% of APL patients are resistant to ATRA. As no biomarkers for ATRA resistance yet exist, we investigated whether cell mechanics could be associated with this pathological phenotype. Using mechano-node-pore sensing, a single-cell mechanical phenotyping platform, and patient-derived APL cell lines, NB4 (ATRA-sensitive) and AP-1060 (ATRA-resistant), we discovered that ATRA-resistant APL cells are less mechanically pliable. By investigating how different subcellular components of APL cells contribute to whole-cell mechanical phenotype, we determined that nuclear mechanics strongly influence an APL cells mechanical response. By arresting APL cells in S-phase or M-phase in the cell cycle, we found cell pliability to be inversely related to DNA content. In addition to DNA content affecting cell pliability, we observed that chromatin condensation also affects nuclear mechanics: decondensing chromatin with trichostatin A is especially effective in softening ATRA-resistant APL cells. RNA-Seq allowed us to compare the transcriptomic differences between ATRA-resistant and ATRA-responsive APL cells and highlighted gene expression changes that could be associated with mechanical changes. Overall, we demonstrate the potential of "physical" biomarkers in identifying APL resistance.

category: bioengineering


title: The megakaryocytic transcription factor ARID3A suppresses leukemia pathogenesis

abstract:
Given the plasticity of hematopoietic stem/progenitor cells, multiple routes of differentiation must be blocked during acute myeloid leukemia pathogenesis - the molecular basis of which is incompletely understood. Here we report that post-transcriptional repression of transcription factor ARID3A by miR-125b is a key event in megakaryoblastic leukemia (AMKL) pathogenesis. AMKL is frequently associated with trisomy 21 and GATA1 mutations (GATA1s), and children with Down syndrome are at a high risk of developing this disease. We show that chromosome 21-encoded miR-125b synergizes with Gata1s to drive leukemogenesis in this context. Leveraging forward and reverse genetics, we uncover Arid3a as the main miR-125b target underlying this synergy. We demonstrate that during normal hematopoiesis this transcription factor promotes megakaryocytic differentiation in concert with GATA1 and mediates TGF{beta}-induced apoptosis and cell cycle arrest in complex with SMAD2/3. While Gata1s mutations perturb erythroid differentiation and induce hyperproliferation of megakaryocytic progenitors, intact ARID3A expression assures their megakaryocytic differentiation and growth restriction. Upon knockdown, these tumor suppressive functions are revoked, causing a dual megakaryocytic/erythroid differentiation blockade and subsequently AMKL. Inversely, restoring ARID3A expression relieves the megakaryocytic differentiation arrest in AMKL patient-derived xenografts. This work illustrates how mutations in lineage-determining transcription factors and perturbation of post-transcriptional gene regulation interplay to block multiple routes of hematopoietic differentiation and cause leukemia. Surmounting this differentiation blockade in megakaryoblastic leukemia by restoring the tumor suppressor ARID3A represents a promising strategy for treating this lethal pediatric disease.

Key pointsO_LIRepression of megakaryocytic transcription factor ARID3A by miR-125b synergizes with GATA1s to induce leukemia
C_LIO_LIRestoring ARID3A expression relieves megakaryocytic differentiation arrest in megakaryoblastic leukemia
C_LI

Graphical abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/440795v1_ufig1.gif" ALT="Figure 1">
View larger version (49K):
org.highwire.dtl.DTLVardef@146c2a7org.highwire.dtl.DTLVardef@9599fdorg.highwire.dtl.DTLVardef@1b0d22borg.highwire.dtl.DTLVardef@1b61447_HPS_FORMAT_FIGEXP  M_FIG C_FIG

category: cancer biology


title: The F-box protein AFF1 regulates ARF protein accumulation to regulate auxin response

abstract: Auxin critically regulates nearly every aspect of plant growth and development. Auxin-driven transcriptional responses are mediated through the AUXIN RESPONSE FACTOR (ARF) family of transcription factors. Although ARF protein stability is regulated via the 26S proteasome, molecular mechanisms underlying ARF stability and turnover are unknown. Here, we report the identification and functional characterization of an F-box E3 ubiquitin ligase, which we have named AUXIN RESPONSE FACTOR F-BOX1 (AFF1). AFF1 directly interacts with ARF19 and regulates its accumulation. Mutants defective in AFF1 display ARF19 protein hyperaccumulation, attenuated auxin responsiveness, and developmental defects. Together, our data suggest a new mechanism, namely control of ARF protein stability, in regulating auxin response.

category: plant biology


title: TIC236 gain-of-function mutations unveil the link between plastid division and plastid protein import

abstract: The chloroplast translocons TOC75 and TIC236 are homologs of the bacterial translocation and assembly module (Tam) A and TamB involved in protein export. Here, we unveil a TIC236-allied component, the chloroplast outer membrane protein CRUMPLED LEAF (CRL), absence of which impairs plastid division and induces autoimmune responses in Arabidopsis thaliana. A forward genetic screen aimed at finding crl suppressors revealed multiple TIC236 gain-of-function mutations (TIC236GFs). Despite the low sequence identity between TIC236 and bacterial TamB, each mutated TIC236GF residue is conserved in TamB. Consistently, a tic236- knockdown mutant exhibited multiple lesion phenotypes similar to crl, indicating a shared functionality of CRL and TIC236. Ensuing reverse genetic analyses revealed genetic interaction between CRL and SP1, a RING-type ubiquitin E3 ligase, as well as with the plastid protease FTSH11, which function in TOC and TIC protein turnover, respectively. Loss of either SP1 or FTSH11 rescued crl mutant phenotypes to varying degrees due to increased translocon levels. Consistent with impaired plastid division exhibited by both crl and tic236-knockdown mutants, CRL interacts with the transit peptides of proteins essential in plastid division, and TIC236GF mutant proteins reinforce their import via increased TIC236 stability. Overall, our data shed new light on the links between plastid division, plant stress response and plastid protein import. We have also isolated and characterized the first GF mutants exhibiting increased protein import efficiency, which may inspire chloroplast engineering for agricultural advancement.


title: Abscisic acid modulates auxin-responsive hypocotyl elongation

abstract: Auxin regulates many aspects of plant growth and development in concert with other plant hormones. Auxin interactions with these other phytohormones to regulate distinct processes is not fully understood. Using a forward genetics screen designed to identify seedlings resistant to the suppressive effects of auxin on dark-grown hypocotyl elongation, we identified a mutant defective in ABA ALDEHYDE OXIDASE3 (AAO3), which encodes for the enzyme that carries out the final step in the biosynthesis of the plant hormone abscisic acid (ABA). We found that all examined ABA deficient mutants display resistance to the inhibitory effects of auxin on dark-grown hypocotyl elongation, suggesting that aspects of ABA signaling are downstream of auxin in regulating dark-grown hypocotyl elongation. Conversely, these mutants display wild type responsiveness to auxin in root elongation assays, suggesting that ABA does not act downstream of auxin in regulating elongation of the root. Our RNA-seq analysis suggests that many auxin-repressed genes in the hypocotyl require an intact ABA pathway for full repression. Our results suggest a model in which auxin partially requires intact ABA biosynthesis in order to regulate hypocotyl elongation, but not to regulate primary root elongation, suggesting that the genetic interactions between these two pathways are tissue-dependent.


title: A new paradoxosomatid millipede, Manikidesmus suriensis (Polydesmida: Paradoxosomatidae) from West Bengal, India.

abstract:
A new genus and species of the family Paradoxosomatidae from southern part of West Bengal, India is described. The new genus Manikidesmus gen. n. is diagnosed by combination of following characters: reduced paranota, distinct pleural keel, unpaired sternal lamella on 5th sternite, prefemur with setal brush, setal brush on tibia and tarsus in male, lamina medialis long straight with a curved hook, expanded post femoral lamina with a spine and tibiotarsus with a spine on the distofemoral process.

The genus is distinguished from its Indian congeners by one or more diagnosed characters. In Manikidesmus suriensis, sp. n. tibia and tarsus bear setal brush in male (vs. absent in Oxidus and Chondromorpha), gonopod femur short, flat and without post femoral demarcation (vs. long, thin cylindrical with post femoral demarcation in Polydrepanum and Orthomorpha), tibiotarsus of gonopod long and a spine on the distofemoral process (vs. short and without spine in Anoplodesmus). In Kronopolites, coxa of gonopod densely bristled, collum with two rows of long bristles, femur long, slender and with a spine. All these characters are absent in the present genus. In Streptogonopus, gonopod femorite is distinctly demarcated from post femorite region and solenomere is twisted with solenophore but in the present species, femorite is not be separated from post femorite region and solenomere is free from solenophore.

category: zoology


title: A new species of the genus Carlogonus (Spirostreptida: Harpagophoridae) from West Bengal, India.

abstract: A new species of Carlogonus, Carlogonus bengalensis is described from West Bengal, India. The adult is blackish brown in colour with a yellowish curved tail, round body with 60 segments, 55 mm in length, 5th segment of male bears a hump, telopodite of the gonopod long, flat and band like with a single curved antetorsal process, mesal process with a red spine, proplical lobe with a curved orange spine, inner surface of metaplical fold with sigilla, palette spatula like and a few blepharochatae at the apical margin. Male bears white pad on femur and tibia. Comparison was made with the "exaratus group" of the genus Carlogonus.


title: High-sensitivity detection of facial features on MRI brain scans with a convolutional network

abstract: Platforms and institutions that support MRI data sharing need to ensure that identifiable facial features are not present in shared images. Currently, this assessment requires manual effect as no auto-mated tools exist that can efficiently and accurately detect if an image has been "defaced". The scarcity of publicly available data with pre-served facial features, as well as the meager incentives to create such a cohort privately, have averted the development of face-detection models. Here, we introduce a framework to detect whether an input MRI brain scan has been defaced, with the ultimate goal of streamlining it within the submission protocols of MRI data archiving and sharing platforms. We present a binary (defaced/"nondefaced") classifier based on a custom convolutional neural network architecture. We train the model on 980 de-faced MRI scans from 36 different studies that are publicly available at OpenNeuro.org. To overcome the unavailability of nondefaced examples, we augment the dataset by inpainting synthetic faces into each training image. We show the adequacy of such a data augmentation in a cross-validation evaluation. We demonstrate the performance estimated with cross-validation matches that of an evaluation on a held-out dataset (N =581) preserving real faces, and obtain accuracy/sensitivity/speci-ficity scores of 0.978/0.983/0.972, respectively. Data augmentations are key to boosting the performance of models bounded by limited sample sizes and insufficient diversity. Our model contributes towards developing classifiers with[~] 100% sensitivity detecting faces, which is crucial to ensure that no identifiable data are inadvertently made public.

category: neuroscience


title: Interneuronal dynamics facilitate the initiation of cortical spreading depression

abstract:
Cortical spreading depression (CSD) is thought to precede migraine attacks with aura and is characterized by a slowly traveling wave of inactivity through cortical pyramidal cells. During CSD, pyramidal cells experience hyperexcitation with rapidly increasing firing rates, major changes in electrochemistry, and ultimately spike block that propagates slowly across the cortex. While the identifying characteristic of CSD is the pyramidal cell hyperexcitation and subsequent spike block, it is currently unknown how the dynamics of the cortical microcircuits and inhibitory interneurons affect the initiation of CSD.

We tested the contribution of cortical inhibitory interneurons to the initiation of spike block using a cortical microcircuit model that takes into account changes in ion concentrations that result from neuronal firing. Our results show that interneuronal inhibition provides a wider dynamic range to the circuit and generally improves stability against spike block.

Despite these beneficial effects, strong interneuronal firing contributed to rapidly changing extracellular ion concentrations, which facilitated hyperexcitation and led to spike block first in the interneuron and then in the pyramidal cell. In all cases, a loss of interneuronal firing triggered pyramidal cell spike block. However, preventing interneuronal spike block was insufficient to rescue the pyramidal cell from spike block. Our data thus demonstrate that while the role of interneurons in cortical microcircuits is complex, they are critical to the initiation of pyramidal cell spike block and CSD. We discuss the implications that localized effects on cortical interneurons have beyond the isolated microcircuit.


title: The neuroinflammatory interleukin-12 signaling pathway drives Alzheimer's disease-like pathology by perturbing oligodendrocyte survival and neuronal homeostasis

abstract: Alzheimers disease (AD) is characterized by deposition of pathological amyloid-{beta} (A{beta}) and tau protein aggregates and involves chronic neuroinflammation, ultimately leading to neurodegeneration and cognitive decline. Central in AD-related neuroinflammation is the proinflammatory interleukin-12 (IL-12)/IL-23 signaling pathway whose inhibition has been shown to attenuate pathology and cognitive defects in AD-like mice. In order to explore which cell types are involved in this neuroinflammatory cascade, we used single-nuclei RNA sequencing in AD-like APPPS1 mice lacking or harboring IL-12/IL-23 signaling. We found Il12b transcripts encoding the common p40 subunit of IL-12/IL-23 signaling to be expressed preferentially, but not exclusively, in microglia in an AD-specific manner. In contrast, transcripts for the other subunits of the IL-12 signaling pathway were expressed constitutively in neurons and oligodendrocytes irrespective of AD pathology, while transcripts for IL-23 were almost undetectable. Notably, genetic ablation of IL-12/IL-23 signaling did not affect the inflammatory gene expression profile of the AD-specific disease associated microglia (DAM), but reversed the loss of mature myelin-producing oligodendrocytes and alterations in neuronal homeostasis in APPPS1 mice. Taken together, our results reveal that IL-12, but not IL-23 is the main driver of AD-specific IL-12/IL-23 neuroinflammation, which alters neuronal and oligodendrocyte functions. Given that drugs targeting IL-12 already exist, our data may foster first clinical trials in AD subjects using this novel neuroimmune target.


title: The nematode worm C. elegans chooses between bacterial foods exactly as if maximizing economic utility

abstract: In value-based decision making, options are selected according to subjective values assigned by the individual to available goods and actions. Despite the importance of this faculty of the mind, the neural mechanisms of value assignments, and how choices are directed by them, remain obscure. To investigate this problem, we used a classic measure of utility maximization, the Generalized Axiom of Revealed Preference, to quantify internal consistency of food preferences in Caenorhabditis elegans, a nematode worm with a nervous system of only 302 neurons. Using a novel combination of microfluidics and electro-physiology, we found that C. elegans food choices fulfill the necessary and sufficient conditions for utility maximization, indicating that nematodes behave exactly as if they maintain, and attempt to maximize, an underlying representation of subjective value. Food choices are well-fit by a utility function widely used to model human consumers. Moreover, as in many other animals, subjective values in C. elegans are learned, a process we now find requires intact dopamine signaling. Differential responses of identified chemosensory neurons to foods with distinct growth potential are amplified by prior consumption of these foods, suggesting that these neurons may be part of a value-assignment system. The demonstration of utility maximization in an organism with no more than several hundred neurons sets a new lower bound on the computational requirements for maximization, and offers the prospect of an essentially complete explanation of value-based decision making at single neuron resolution.


title: The role of frontal cortex in multisensory decisions

abstract: To interpret the world and make accurate perceptual decisions, the brain must combine information across sensory modalities. For instance, it must combine vision and hearing to localize objects based on their image and sound. Probability theory suggests that evidence from multiple independent cues should be combined additively, and several studies support this hypothesis1-14. However, other studies suggest that mammals, particularly mice, can exhibit sensory bias during audiovisual integration15-19; furthermore, the cortical substrates of multisensory integration remain uncertain20. Here we show that to localize a stimulus, mice combine auditory and visual spatial cues additively, a computation supported by additive multisensory integration in frontal cortex. We developed an audiovisual localization task where mice turn a wheel to indicate the joint position of an image and a sound. Scanning optogenetic inactivation21-24 during stimulus presentation showed that visual cortex contributes unisensory information whereas frontal cortex contributes multisensory information to the mouses decision. Neuropixels recordings of >10,000 neurons indicated that neural activity in frontal area MOs (secondary motor cortex) reflects an additive combination of visual and auditory signals. An accumulator model2,25,26 applied to the sensory representations of MOs neurons reproduced both the observed choices and reaction times. Sensory signals in MOs were specific to trained mice, and indeed the same accumulator applied to naive mice failed to perform the task. These results suggest that frontal cortex adapts through learning to integrate information across sensory cortices, providing a signal that is then transformed into a binary decision by a downstream accumulator.


title: Mouse frontal cortex mediates additive multisensory decisions


title: Geraniol Enhances Inhibitory Inputs to Paraventricular Thalamic Nucleus and Induces Sedation in Mice

abstract:
Geraniol (GE), a plant-derived acyclic monoterpene, shows a wide variety of beneficial effects. Notably, recent studies have reported the potential sedative effects of GE in fish and rats. However, the mechanisms of GE in sedation remain elusive. Here, we found that GE reduced locomotion, relieved pentylenetetrazol (PTZ)-induced seizures, altered the electroencephalogram (EEG), and facilitated general anesthesia in mice. Meanwhile, GE decreased c-Fos expression and suppressed the calcium activity in the paraventricular thalamic nucleus (PVT). Microinjection of GE into the PVT reduced locomotion and facilitated propofol-induced anesthesia. Furthermore, the electrophysiology results showed that GE-induced dramatic membrane hyperpolarization and suppressed the neuronal activity of PVT neurons, mainly by prolonging spontaneous inhibitory postsynaptic currents and inducing tonic inhibitory currents via GABAA receptors. Our study revealed that GE enhances inhibitory inputs to PVT neurons and induces sedation in mice. These findings provide a potential candidate for further development of sedatives and anesthetics.

Graphic Summary

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/441289v1_ufig1.gif" ALT="Figure 1">
View larger version (37K):
org.highwire.dtl.DTLVardef@fd8424org.highwire.dtl.DTLVardef@1ee77caorg.highwire.dtl.DTLVardef@faab42org.highwire.dtl.DTLVardef@101b921_HPS_FORMAT_FIGEXP  M_FIG C_FIG


title: Systematic analysis of Epstein-Barr virus genes and their individual contribution to virus production and composition

abstract:
Epstein-Barr virus (EBV), a member of the large herpesvirus family is a very complex human{gamma} -herpesvirus. Its complexity with respect to viral gene regulation, its preferred latent life style and technical difficulties are major obstacles, which hinder efficient virus generation in vitro to mass-produce or establish recombinant wild-type EBV or mutant derivatives. To explore conditions optimizing and improving virus production, we established and tested an EBV gene library with 77 expression plasmids and a set of designed shRNAs. With this tool set we investigated the contributions of individual viral genes in the context of virus synthesis and virion functions. Engineered virus stocks were systematically analyzed with respect to physical and bioparticle concentration, virus titer and virus uptake by primary human B cells, EBVs target cells in vivo. To quantitate virus uptake by these cells, we developed a novel {beta}-lactamase-based assay that can monitor fusion events of the viral envelope with membranes of recipient cells at the level of single cells. Based on our findings, EBV does not encode a dominant regulator that governs virus production, but our results identified several EBV genes such as BALF4, BVLF1 and BKRF4, encoding a viral glycoprotein, a transcriptional regulator of late viral genes, and a possible tegument protein, respectively, that improve virus production regarding virus yield, virus composition and quality, and virus uptake by primary human B cells.

ImportanceFor more than 20 years HEK293 cells have been instrumental to produce virus stocks of recombinant EBV. The identification of this cell line as a source of infectious EB virions was unexpected because HEK293 cells are very distant from B cells and in particular plasma cells which produce EBV progeny in vivo. To our knowledge, no systematic analysis has addressed the fundamental question whether virus yield with respect to virus concentration, virion composition and functionality can be improved to produce recombinant EBV stocks in HEK293 cells. We tackled this question and analyzed 77 individual EBV genes for their possible contribution to virus yield. To analyze and compare different virus stocks we used established and developed novel assays to characterize important parameters of EB virions and their functions.

category: microbiology


title: Using Human Induced Pluripotent Stem Cell Derived Organoids to Identify New Pathologies in Patients with PDX1 Mutations

abstract: Two patients with mutations in PDX1 presented with pancreatic agenesis, chronic diarrhea and poor weight gain, the causes of which were not identified through routine clinical testing. We generated patient derived organoids as a novel diagnostic strategy and observed that PDX1188delC/188delC antral organoids convert to an intestinal phenotype, while intestinal organoids undergo gastric metaplasia with significant reduction in enteroendocrine cells. This prompted a re-examination of gastric and intestinal biopsies from both PDX1188delC/188delC patients, which recapitulated organoid phenotypes. Antral biopsies had increased parietal cells and lacked G-cells suggesting loss of antral identity. These patients will now be monitored for the progression of metaplasia. This study demonstrates the utility of organoids for patient diagnoses and treatment.

category: developmental biology


title: Variations in soil nutrient dynamics and bacterial communities in long-term tea monoculture production systems

abstract: Long-term monoculture agriculture systems could lead to soil degradation and yield decline. The ways in which soil microbiotas interact with one another, particularly in response to long-term tea monoculture systems are currently unclear. In this study, through the comparison of three independent tea plantations across eastern China composed of varying stand ages (from 3 years to 90 years after conversion from forest), we found that long-term tea monoculture led to significant increases in soil total organic carbon (TOC) and microbial nitrogen (MBN). Additionally, the structure, function and co-occurrence network of soil microbial communities were investigated by pyrosequencing 16S rRNA genes. The pyrosequencing analysis revealed that structures and functions of soil bacterial communities were significantly affected by different stand ages of tea plantations, but sampling sites and land-use conversion (from forest to tea plantation) still outcompeted stand age to control the diversity and structure of soil bacterial communities. Further RDA analysis revealed that the C and N availability improvement in tea plantation soils led to variation of structure and function in soil microbial communities. Moreover, co-occurrence network analysis of soil bacterial communities also demonstrated that interactions among soil bacteria taxa were strengthened with the increasing stand age of respective tea stands. Overall, this study provides a comprehensive understanding of the impact of long-term monoculture stand age on soil nutrient dynamics and bacterial communities in tea production.


title: Rcompadre and Rage - two R packages to facilitate the use of the COMPADRE and COMADRE databases and calculation of life history traits from matrix population models

abstract:
O_LIMatrix population models (MPMs) are an important tool for biologists seeking to understand the causes and consequences of variation in vital rates (e.g., survival, reproduction) across life cycles. Empirical MPMs describe the age- or stage-structured demography of organisms and usually represent the life history of a population during a particular time frame at a specific geographic location.
C_LIO_LIThe COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database are the most extensive resources for MPM data, collectively containing >12,000 individual projection matrices for >1,100 species globally. Although these databases represent an unparalleled resource for researchers, land managers, and educators, the current computational tools available to answer questions with MPMs impose significant barriers to potential COM(P)ADRE database users by requiring advanced knowledge to handle diverse data structures and program custom analysis functions.
C_LIO_LITo close this knowledge gap, we present two interrelated R packages designed to (i) facilitate the use of these databases by providing functions to acquire, quality control, and manage both the MPM data contained in COMPADRE and COMADRE, and a users own MPM data (Rcompadre), and (ii) present a range of functions to calculate life history traits from MPMs in support of ecological and evolutionary analyses (Rage). We provide examples to illustrate the use of both.
C_LIO_LIRcompadre and Rage will facilitate demographic analyses using MPM data and contribute to the improved replicability of studies using these data. We hope that this new functionality will allow researchers, land managers, and educators to unlock the potential behind the thousands of MPMs and ancillary metadata stored in the COMPADRE and COMADRE matrix databases, and in their own MPM data.
C_LI