title: Supervised spatial inference of dissociated single-cell data with SageNet

abstract: Spatially-resolved transcriptomics uncovers patterns of gene expression at supercellular, cellular, or subcellular resolution, providing insights into spatially variable cellular functions, diffusible morphogens, and cell-cell interactions. However, for practical reasons, multiplexed single cell RNA-sequencing remains the most widely used technology for profiling transcriptomes of single cells, especially in the context of large-scale anatomical atlassing. Devising techniques to accurately predict the latent physical positions as well as the latent cell-cell proximities of such dissociated cells, represents an exciting and new challenge. Most of the current approaches rely on an  autocorrelation assumption, i.e., cells with similar transcriptomic profiles are located close to each other in physical space and vice versa. However, this is not always the case in native biological contexts due to complex morphological and functional patterning. To address this challenge, we developed SageNet, a graph neural network approach that spatially reconstructs dissociated single cell data using one or more spatial references. SageNet first estimates a gene-gene interaction network from a reference spatial dataset. This informs the structure of the graph on which the graph neural network is trained to predict the region of dissociated cells. Finally, SageNet produces a low-dimensional embedding of the query dataset, corresponding to the reconstructed spatial coordinates of the dissociated tissue. Furthermore, SageNet reveals spatially informative genes by extracting the most important features from the neural network model. We demonstrate the utility and robust performance of SageNet using molecule-resolved seqFISH and spot-based Spatial Transcriptomics reference datasets as well as dissociated single-cell data, across multiple biological contexts. SageNet is provided as an open-source python software package at https://github.com/MarioniLab/SageNet.


title: A combinatorial anticancer drug screen identifies off-target effects of epigenetic chemical probes

abstract: Anticancer drug response is determined by genetic and epigenetic mechanisms. To identify the epigenetic regulators of anticancer drug response, we conducted a chemical epigenetics screen using chemical probes that target different epigenetic modulators. In this screen, we tested 31 epigenetic probes in combination with 14 mechanistically diverse anticancer agents and identified 8 epigenetic probes that significantly potentiate the cytotoxicity of TAK-243, a first-in-class ubiquitin-activating enzyme (UBA1) inhibitor evaluated in several solid and hematologic malignancies. These probes are TP-472, GSK-864, A-196, UNC1999, SGC-CBP30 and PFI-4 (and its related analogs GSK6853 and GSK5959), and they target BRD9/7, mutant IDH1, SUV420H1/2, EZH2/1, p300/CBP and BRPF1B, respectively. In contrast to epigenetic probes, negative control compounds did not have a significant impact on TAK-243 cytotoxicity. Potentiation of TAK-243 cytotoxicity was associated with reduced ubiquitylation and induction of apoptosis. Mechanistically, epigenetic probes exerted their potentiation by inhibiting the efflux transporter ABCG2 without inducing significant changes in the ubiquitylation pathways or ABCG2 expression levels. The identified probes shared chemical scaffold similarities with TAK-243 and could potentially interact with ABCG2 as assessed by docking analysis. Based on these data, we have developed a cell-based assay that can quantitatively evaluate ABCG2 inhibition by drug candidates. In conclusion, our study identifies epigenetic chemical probes that profoundly potentiate TAK-243 cytotoxicity through off-target ABCG2 inhibition. We also provide experimental evidence that several negative control compounds cannot exclude a subset of off-target effects of chemical probes. Finally, potentiation of TAK-243 cytotoxicity can serve as a quantitative measure of ABCG2-inhibitory activity.

category: pharmacology and toxicology


title: Stepwise origin and evolution of a transcriptional activator and repressor system integrating nutrient signaling in plants

abstract: Plants possess a unique transcriptional regulatory system in which two related MYB-related transcription factors (TFs) coordinate gene expression according to phosphate (Pi) and nitrogen (N) availability. The Phosphorus Starvation Response (PSR) type TFs are transcriptional activators integrating the cellular Pi sensing machinery and gene regulation majorly under Pi starvation. The Hypersensitivity To Low Pi-Elicited Primary Root Shortening (HRS) type TFs are transcriptional repressors integrating the Pi and N availability signals through different feedback loops. They are highly connected through multiple signaling loops to finetune the transcriptional responses according to nutrient availability. Molecular functions of these TFs are fairly uncovered in model systems; however, how plants evolved this activator-repressor system is currently unknown. In this study, using sensitive evolutionary analysis, we identified a stepwise origin of the PSR-HRS regulatory system in plants. The PSR TFs were originated before the split of Prasinodermophyta and Chlorophyta. The HRS TFs were originated later in the Streptrophycean algae. We also identified the asymmetric expansion of this TF repertoire in land plants majorly shaped by genome duplication and triplication events. The phylogenetic reconstruction coupled with motif analysis revealed that the origin of the specific accessory motifs is a major contributing factor in the functional divergence which led to the evolution of different sub-families preceding the angiosperm radiation. The spatiotemporal gene expression analysis in different developmental stages and nutrient availability conditions in angiosperms identified a critical role of expression divergence in shaping the functions of these TF families which is essential for adaptive plasticity of plants.

category: plant biology


title: Attentional rhythmic blink: Theta/Alpha balance in neural oscillations determines the rhythmicity in visual sampling

abstract: Brain oscillations in the theta (3-7 Hz) and alpha (7-13 Hz) bands are implicated in visual perception and attention. We show that in an attentional blink paradigm, where the task requires detecting two targets presented in rapid succession, perceptual performance varied with the rhythms at these two frequencies, which we name attentional rhythmic blink. In the absence of distractors, second target detection performance fluctuated at the theta rhythm, but the fluctuation frequency shifted toward alpha rhythm when distractors were interspersed with the targets. We further show, in magnetoencephalography experiments, that a change in the dominant frequency of ongoing neural oscillations accompanied those in perceptual performance, with the parietal theta being more pronounced in the no-distractor and the occipital alpha in the distractor conditions, respectively. We propose that perceptual rhythms may depend on the power balance between ongoing neural oscillations, determined by the task-specific demand.

category: neuroscience


title: Unilateral Perforant Path Transection Does Not Alter Lateral Entorhinal Cortical or Hippocampal CA3 Arc Expression

abstract: It is well established that degradation of perforant path fibers is associated with age-related cognitive dysfunction and CA3 hyperactivity. Whether this fiber loss triggers a cascade of other functional changes within the hippocampus circuit has not been causatively established, however. Thus, the current study evaluated the effect of perforant path fiber loss on neuronal activity in CA3 and layer II of the lateral entorhinal cortex (LEC) in relation to mnemonic similarity task performance. Expression of the immediate early gene Arc was quantified in rats that received a unilateral right hemisphere transection of the perforant path or sham surgery that cut the cortex but left the fibers intact. Behavior-related expression of Arc mRNA was measured to test the hypothesis that fiber loss leads to elevated activation of CA3 and LEC neurons, as previously observed in aged rats that were impaired on the mnemonic similarity task. Transection of perforant path fibers, which has previously been shown to lead to a decline in mnemonic similarity task performance, did not alter Arc expression. Arc expression in CA3, however, was correlated with task performance on the more difficult discrimination trials across both surgical groups. These observations further support a link between CA3 activity and mnemonic similarity task performance but suggest the reduced input from the entorhinal cortex to the hippocampus, as observed in old age, does not causatively elevate CA3 activity.


title: Dcifer: an IBD-based method to calculate genetic distance between polyclonal infections

abstract: An essential step toward reconstructing pathogen transmission and answering epidemiologically relevant questions from genomic data is obtaining pairwise genetic distance between infections. For recombining organisms such as malaria parasites, relatedness measures quantifying recent shared ancestry would provide a meaningful distance, suggesting methods based on identity by descent (IBD). While the concept of relatedness and consequently an IBD approach is fairly straightforward for individual parasites, the distance between polyclonal infections, which are prevalent in malaria, presents specific challenges and awaits a general solution that could be applied to infections of any clonality and accommodate multiallelic (e.g. microsatellite or microhaplotype) and biallelic (SNP) data. Filling this methodological gap, we present Dcifer (Distance for complex infections: fast estimation of relatedness), a method for calculating genetic distance between polyclonal infections, which is designed for unphased data, explicitly accounts for population allele frequencies and complexity of infection, and provides reliable inference. Dcifers IBD-based framework allows us to define model parameters that represent interhost relatedness and to propose corresponding estimators with attractive statistical properties. By using combinatorics to account for unobserved phased haplotypes, Dcifer is able to quickly process large datasets and estimate pairwise relatedness along with measures of uncertainty. We show that Dcifer delivers accurate and interpretable results and detects related infections with statistical power that is 2-4 times greater than that of approaches based on identity by state. Applications to real data indicate that relatedness structure aligns with geographic locations. Dcifer is implemented in a comprehensive publicly available software package.

category: genetics


title: Echtvar: Compressed variant representation for rapid annotation and filtering of SNPs and indels

abstract: Germline and somatic variants within an individual or cohort are interpreted with information from large cohorts. Annotation with this information becomes a computational bottleneck as population sets grow to terabytes of data. Here, we introduce echtvar, which efficiently encodes population variants and annotation fields into a compressed archive that can be used for rapid variant annotation and filtering. Most variants, including position and alleles are encoded into 32-bits-half the size of previous encoding schemes and at least 4 times smaller than a naive encoding. The annotations, stored separately, are also encoded and compressed. We show that echtvar is faster and uses less space than existing tools and that it can effectively reduce the number of candidate variants. We give examples on germ-line and somatic variants to document how echtvar can facilitate exploratory data analysis on genetic variants. Echtvar is available at https://github.com/brentp/echtvar under an MIT license.

category: bioinformatics


title: BioAct: Biomedical Knowledge Base Construction using Active Learning

abstract: Creating and curating knowledge resources has been a paramount activity in the biomedical domain. In recent years, automated methods for knowledge base construction have flourished and have enabled large scale construction and curation of such resources. In the biological domain, techniques such as next generation sequencing produce new data at exponential rate, making mere manual curation of knowledge resources simply unfeasible. The major technology to automate knowledge base construction is Information Extraction -- specifically tasks such as Named Entity Recognition or Relation Extraction. The major hurdle for IE methods is the availability of labelled data for training, which can be prohibitively expensive and challenging to obtain due to the need of domain experts. Active learning aims at minimizing the cost of manual labelling by only requiring it for smaller and more useful portions of the data. With this motivation, we devised a method to quickly construct highly curated datasets to enable biomedical knowledge base construction. The method, named BioAct, is based on a partnership between automatic annotation methods (leveraging SciBERT with other machine learning models) and subject matter experts and uses active learning to create training datasets in the biological domain. The main contribution of this work is twofold; in addition to the BioAct method itself, we publicly release an annotated dataset on antimicrobial resistance, produced by a team of subject matter experts using BioAct. Additionally, we simulate a knowledge base construction task using the MegaRes and CARD knowledge bases to provide insight and lessons learned about the usefulness of the annotated dataset for this task.


title: Scan-Centric, Frequency-Based Method for Characterizing Peaks from Direct Injection Fourier transform Mass Spectrometry Experiments

abstract: We introduce a novel, scan-centric method for characterizing peaks from direct injection multi-scan Fourier transform mass spectra of complex samples that utilizes frequency values derived directly from the spacing of raw m/z points in spectral scans. Our peak characterization method utilizes intensity independent noise removal and normalization of scan-level data to provide a much better fit of relative intensity to natural abundance probabilities for low abundance isotopologues that are not present in all of the acquired scans. Moreover, our method calculates both peak- and scan-specific statistics incorporated within a series of quality control steps that are designed to robustly derive peak centers, intensities and intensity ratios with their scan-level variances. These cross-scan characterized peaks are suitable for use in our previously published peak assignment methodology, Small Molecule Isotope Resolved Formula Enumeration (SMIRFE).


title: Chloroplasts in plant cells show active glassy behavior under low light conditions

abstract: Plants have developed intricate mechanisms to adapt to changing light conditions. Besides photo- and heliotropism - the differential growth towards light and the diurnal motion with respect to sunlight - chloroplast motion acts as a fast mechanism to change the intracellular structure of leaf cells. While chloroplasts move towards the sides of the plant cell to avoid strong light, they accumulate and spread out into a layer on the bottom of the cell at low light to increase the light absorption efficiency. Although the motion of chloroplasts has been studied for over a century, the collective organelle-motion leading to light adapting self-organized structures remains elusive. Here we study the active motion of chloroplasts under dim light conditions, leading to an accumulation in a densely packed quasi-2D layer. We observe burst-like re-arrangements and show that these dynamics resemble colloidal systems close to the glass transition by tracking individual chloroplasts. Furthermore, we provide a minimal mathematical model to uncover relevant system parameters controlling the stability of the dense configuration of chloroplasts. Our study suggests that the meta-stable caging close to the glass-transition in the chloroplast mono-layer serves a physiological relevance. Chloroplasts remain in a spread-out configuration to increase the light uptake, but can easily fluidize when the activity is increased to efficiently re-arrange the structure towards an avoidance state. Our research opens new questions about the role that dynamical phase transitions could play in self-organized intracellular responses of plant cells towards environmental cues.

category: biophysics


title: High total water loss driven by low-fat diet in desert-adapted mice

abstract: Availability of essential food resources is one of the most important drivers of survival and to persist in environments where critical resource abundance is changing, animals must either relocate or adapt in place. Testing an animals ability to respond to alternative conditions can reveal differences in physiological responses. We used flow-through respirometry to characterize metabolic phenotypes of the desert-adapted cactus mouse (Peromyscus eremicus) under diurnally variable environmental conditions that mimic the Sonoran Desert and treated mice with two different diets; a standard diet and a low-fat diet. We found significant diet-specific differences in the rate of water loss and serum electrolyte values. Mice fed the low-fat diet lost more water relative to those eating the standard diet and patterns of de novo lipogenesis are not limited by dietary composition. Our results are consistent with the hypothesis that diet contributes to water homeostasis. Compared to other desert animals, rodents have limited capacity to dissipate heat using evaporative cooling, limiting thermoregulatory performance at higher temperatures. We predict that a mismatch in physiological requirements and environmental conditions could significantly impact small mammal survival in desert environments if optimal foods become less abundant, as may be the case given climate change.

category: physiology


title: A high-efficiency scar-free genome editing toolkit for Acinetobacter baumannii

abstract:
Structured synopsisO_ST_ABSBackgroundC_ST_ABSThe current mutagenesis tools for Acinetobacter baumannii leave selection markers or residual sequences behind, or involve tedious counterselection and screening steps. Furthermore, they are usually adapted for model strains, rather than to multidrug resistant (MDR) clinical isolates.

ObjectivesTo develop a scar-free genome editing tool suitable for chromosomal and plasmid modifications in MDR A. baumannii AB5075.

MethodsWe prove the efficiency of our adapted genome editing system by deleting the multidrug efflux pumps craA and cmlA5, as well as curing plasmid p1AB5075. We then characterised the antibiotic sensitivity phenotype of the mutants compared to the wild type for chloramphenicol, tobramycin and amikacin by disc diffusion assays and determined their minimum inhibitory concentration for each strain.

ResultsWe successfully adapted the genome editing protocol to A. baumannii AB5075, achieving a double recombination frequency close to 100% and securing the construction of a mutant within 10 work days. Furthermore, we show that the {Delta}craA has a strong sensitivity to chloramphenicol, tobramycin and amikacin, whereas the {Delta}cmlA5 mutant does not show a significant decrease in viability for the antibiotics tested. On the other hand, the removal of p1AB5075 produced an increased sensitivity to tobramycin and amikacin.

ConclusionWe have adapted a highly efficient genome editing tool for A. baumannii and proved that craA has a broader substrate range than previously thought. On the other hand, whereas cmlA5 is annotated as a chloramphenicol efflux pump and is encoded within an aminoglycoside resistance island, it does not provide resistance to any of those compounds.

category: microbiology


title: Habitat preference influences response to changing agricultural landscapes in two long-horned bees.

abstract: Agricultural intensification and urban development have drastically influenced pollinators living in semi-natural grasslands. Pollinators are likely to have different responses to these land-use changes; some decline rapidly while others maintain or increase their populations. We predicted differences in interspecific response to land-use changes are partly attributed to differences in habitat preference. We examined the distribution and flower use patterns of two closely related Eucera species with different habitat preferences. Study sites were meadows surrounding traditional, intensified, and urbanised agricultural lands in the Osaka-Kobe metropolitan area, Japan. Forest-associated Eucera nipponensis were significantly fewer in consolidated and urbanised meadows than traditional meadows, whereas open land-associated E. spurcatipes exhibited the opposite. A significant negative relationship between their abundances was also found. Both species foraged on legume flowers most frequently (83.5%), but floral use pattern was significantly different in traditional and consolidated meadows. Bee species preferring stable habitats were vulnerable to land consolidation and urbanisation, while species associated with disturbed habitats maintained or increased population size in meadows with the land-use changes. Thus, recent land uses may have different impacts on species with different habitat preferences.

category: ecology


title: Triglyceride lipolysis driven by glucose restriction triggers liquid-crystalline phase transitions and proteome remodeling of lipid droplets

abstract: Lipid droplets (LDs) are reservoirs for triglycerides (TGs) and sterol-esters (SEs), but how these lipids are organized within LDs and influence its proteome remains unclear. Using in situ cryoelectron tomography, we show that glucose restriction triggers lipid phase transitions within LDs generating liquid-crystalline lattices inside them. Mechanistically this requires TG lipolysis, which decreases the LD TG:SE ratio, promoting SE transition to a liquid-crystalline phase. Molecular dynamics simulations reveal TG depletion promotes spontaneous TG and SE de-mixing in LDs, additionally altering the lipid packing of the phospholipid monolayer surface. Fluorescence imaging and proteomics further reveal that liquid-crystalline phases are associated with selective remodeling of the LD proteome. Some canonical LD proteins including Erg6 re-localize to the ER network, whereas others remain LD-associated. Model peptide LiveDrop also redistributes from LDs to the ER, suggesting liquid-crystalline-phases influence ER-LD inter organelle transport. Our data suggests glucose restriction drives TG mobilization, which alters the phase properties of LD lipids and selectively remodels the LD proteome.

category: cell biology


title: Context-dependent choice and evaluation in real-world consumer behavior

abstract: A body of work spanning neuroscience, economics, and psychology indicates that decisionmaking is context-dependent, which means that the value of an option depends not only on the option in question, but also on the other options in the choice set--or the  context. While context effects have been observed primarily in small-scale laboratory studies with tightly constrained, artificially constructed choice sets, it remains to be determined whether these context effects take hold in real-world choice problems, where choice sets are large and decisions driven by rich histories of direct experience. Here, we investigate whether valuations are context-dependent in real-world choice by analyzing a large restaurant rating dataset (Yelp.com) as well as two independent replication datasets which provide complementary operationalizations of restaurant choice. We find that users make fewer ratings-maximizing choices in choice sets with higher-rated options--a hallmark of context-dependent choice-- and that post-choice restaurant ratings also varied systematically with the ratings of unchosen restaurants. Furthermore, in a follow-up laboratory experiment using hypothetical choice sets matched to the real-world data, we find further support for the idea that subjective valuations of restaurants are scaled in accordance with the choice context, providing corroborating evidence for a general mechanistic-level account of these effects. Taken together, our results provide a potent demonstration of context-dependent choice in real-world choice settings, manifesting both in decisions and subjective valuation of options.


title: Differential genetic strategies of Burkholderia vietnamiensis and Paraburkholderia kururiensis for root colonization of Oryza sativa ssp. japonica and ssp. indica, as revealed by Tn-seq

abstract:
Burkholderia vietnamiensis LMG10929 (Bv) and Paraburkholderia kururiensis M130 (Pk) are bacterial rice growth-promoting models. Besides this common ecological niche, species of the Burkholderia genus are also found as opportunistic human pathogens while Paraburkholderia are mostly environmental and plant-associated species. Here, we compared the genetic strategies used by Bv and Pk to colonize two subspecies of their common host, Oryza sativa ssp. japonica (cv. Nipponbare) and ssp. indica (cv. IR64). We used high-throughput screening of transposon insertional mutant libraries (Tn-seq) to infer which genetic elements have the highest fitness contribution during root surface colonization at 7 days post inoculation. Overall, we detected twice more genes in Bv involved in rice roots colonization compared to Pk, including genes contributing to the tolerance of plant defenses, which suggests a stronger adverse reaction of rice towards Bv compared to Pk. For both strains, the bacterial fitness depends on a higher number of genes when colonizing indica rice compared to japonica. These divergences in host pressure on bacterial adaptation could be partly linked to the cultivars differences in nitrogen assimilation. We detected several functions commonly enhancing root colonization in both bacterial strains e.g., Entner-Doudoroff (ED) glycolysis. Less frequently and more strain-specifically, we detected functions limiting root colonization such as biofilm production in Bv and quorum sensing in Pk. The involvement of genes identified through the Tn-seq procedure as contributing to root colonization i.e., ED pathway, c-di-GMP cycling and cobalamin synthesis, was validated by directed mutagenesis and competition with WT strains in rice root colonization assays.

ImportanceBurkholderiaceae are frequent and abundant colonizers of the rice rhizosphere and interesting candidates to investigate for growth promotion. Species of Paraburkholderia have repeatedly been described to stimulate plant growth. However, the closely related Burkholderia genus hosts both beneficial and phytopathogenic species, as well as species able to colonize animal hosts and cause disease in humans. We need to understand to what extent the bacterial strategies used for the different biotic interactions differ depending on the host and if strains with agricultural potential could also pose a threat towards other plant hosts or humans. To start answering these questions, we used here transposon sequencing to identify genetic traits in Burkholderia vietnamiensis and Paraburkholderia kururiensis that contribute to the colonization of two different rice varieties. Our results revealed large differences in the fitness gene sets between the two strains and between the host plants, suggesting a strong specificity in each bacterium-plant interaction.


title: Prescribed fire selects for a pyrophilous soil subcommunity in a northern California mixed conifer forest.

abstract: Low intensity prescribed fire is a critical strategy for mitigating the effects of catastrophic wildfires. The above-ground response to fire has been well-documented, including many ecosystem benefits associated with prescribed burning, but fewer studies have directly addressed the effect of prescribed fire on soil organisms. We aimed to understand how soil microbial communities respond to prescribed fire and to determine the ecological processes driving their dynamics. We extensively sampled four plots for 17 months in a mixed conifer forest in northern California, USA; immediately following a low-intensity prescribed fire, a higher-intensity prescribed fire, and two no-burn control plots. We found that prescribed fire significantly altered the community structure for both fungi (ITS) and bacteria (16S), which was sustained throughout the time-series. By comparing our community profiling results with a model of neutral community assembly, we found that the presence of most taxa across all experimental conditions could be explained by neutral processes. However, combining threshold indicator taxa analysis and correlation network analysis with the neutral model identified a cohort of taxa that responded deterministically to prescribed fire. The subcommunity identified through this series of analyses includes both known and new pyrophilous taxa. Beyond this, our analyses revealed network modules within postfire communities which were responsive to fire-intensity. Taken together, these results lay the foundation for building a process-driven understanding of microbial community assembly in the context of the classical disturbance regime of fire.


title: Loss of PRMT2 in myeloid cells in normoglycemic mice phenocopies impaired regression of atherosclerosis in diabetic mice

abstract: Regression of atherosclerosis is impaired in diabetes. However, the factors mediating this effect remain incomplete. We identified Protein Arginine Methyltransferase 2 (PRMT2) as a protein whose expression in macrophages is reduced in hyperglycemia and diabetes. PRMT2 catalyzes arginine methylation to target proteins to modulate gene expression. Because PRMT2 expression is reduced in cells in hyperglycemia, we wanted to determine whether PRMT2 plays a causal role in the impairment of atherosclerosis regression in diabetes. We therefore examined the consequence of deleting PRMT2 in myeloid cells during regression of atherosclerosis in normal and diabetic mice. Remarkably, we found a significant impairment of atherosclerosis regression under normoglycemic conditions in mice lacking PRMT2 (Prmt2-/-) in myeloid cells that mimics the decrease in regression of atherosclerosis in WT mice under diabetic conditions. This was associated with increased plaque macrophage retention, as well as increased apoptosis and necrosis. PRMT2-deficient plaque CD68+ cells under normoglycemic conditions showed increased expression of genes involved in cytokine signaling and inflammation compared to WT. Consistently Prmt2-/- bone marrow derived macrophages (BMDMs) showed an increased response of pro-inflammatory genes to LPS, and a decreased response of inflammation resolving genes to IL-4. This increased response to LPS in Prmt2-/- BMDMs is via enhanced NF-kappa B activity. Thus, the loss of PRMT2 is causally linked to impaired atherosclerosis regression via a heightened inflammatory response in macrophages. That PRMT2 expression was lower in myeloid cells in plaques from human subjects with diabetes supports the relevance of our findings to human atherosclerosis.


title: Structure of the Dengue Virus RNA Promoter

abstract: Dengue virus, a single-stranded positive sense RNA virus, is the most prevalent mosquito-borne pathogen in the world. Like all RNA viruses, it uses conserved structural elements within its genome to control essential replicative steps. A 70 nucleotides stem-loop RNA structure (called SLA) found at the 5-end of the genome of all flaviviruses, functions as the promoter for viral replication. This highly conserved structure interacts with the viral polymerase NS5 to initiate RNA synthesis. Here we report the NMR structure of a monomeric SLA from Dengue virus serotype 1, assembled to high-resolution from independently folded structural elements. The DENV1 SLA has an L-shape structure, where the top and side helices are coaxially-stacked and the bottom helix is roughly perpendicular to them. Because the sequence is highly conserved among different flavivirus genomes, it is likely that the three-dimensional fold and local structure of SLA are also conserved among flaviviruses and required for efficient replication. This work provides structural insight into the Dengue promoter and provides the foundation for the discovery of new antiviral drugs that target this essential replicative step.

category: biochemistry


title: A universal sequencing read interpreter

abstract: Massively parallel DNA sequencing has led to the rapid growth of highly multiplexed experiments in biology. Such experiments produce unique sequencing results that require specific analysis pipelines to decode highly structured reads. However, no versatile framework that interprets sequencing reads for downstream biological analysis has been developed. Here we report INTERSTELLAR (interpretation, scalable transformation, and emulation of large-scale sequencing reads) that extracts data values encoded in theoretically any type of sequencing read and translates them into sequencing reads of any structure of choice. INTERSTELLAR first identifies sequence segments encoded in reads according to the users definition. Followed by error correction, values are extracted and compressed into an optimal space, which can be efficiently translated into sequencing reads of another structure. We demonstrated that INTERSTELLAR successfully extracted information from a range of sequencing reads and translated those of single-cell (sc)RNA-seq, scATAC-seq, and spatial transcriptomics to be analyzed by different software tools that have been developed for conceptually the same types of experiments. INTERSTELLAR will greatly facilitate the development of new sequencing-based experiments and sharing of data analysis pipelines.


title: Reproducible data integration and visualization of biological networks in R

abstract:
MotivationCollaborative workflows in network biology not only require the documentation of the performed analysis steps but also of the network data on which the decisions were based. However, replication of the entire workflow or tracking of the intermediate networks used for a particular visualization remains an intricate task. Also, the amount and heterogeneity of the integrated data requires instruments to explore and thus comprehend the results.

ResultsHere we demonstrate a collection of software tools and libraries for network data integration, exploration, and visualization to document the different stages of the workflow. The integrative steps are performed in R, and the entire process is accompanied by an interchangeable toolset for data exploration and network visualization.

AvailabilityThe source code of the performed workflow is available as R markdown scripts at https://github.com/frankkramer-lab/reproducible-network-visualization. A compiled HTML version is also hosted on Github pages at https://frankkramer-lab.github.io/reproducible-network-visualization.

Contactflorian.auer@informatik.uni-augsburg.de


title: rox: A statistical model for regression with missing values

abstract: AO_SCPLOWBSTRACTC_SCPLOWHigh-dimensional omics datasets frequently contain missing data points, which typically occur due to concentrations below the limit of detection (LOD) of the profiling platform. The presence of such missing values significantly limits downstream statistical analysis and result interpretation. Two common techniques to deal with this issue include the removal of samples with missing values, and imputation approaches which substitute the missing measurements with reasonable estimates. Both approaches, however, suffer from various shortcomings and pitfalls. In this paper, we present "rox", a novel statistical model for the analysis of omics data with missing values without the need for imputation. The model directly incorporates missing values as "low" concentrations into the calculation. We show the superiority of rox over common approaches on simulated data and on six metabolomics datasets. Fully leveraging the information contained in LOD-based missing values, rox provides a powerful tool for the statistical analysis of omics data.


title: Rye: genetic ancestry inference at biobank scale

abstract: Biobank projects around the world are generating genomic data for many thousands and even millions of individuals. Computational methods are needed to handle these massive data sets, including tools for genetic ancestry (GA) inference. Current methods for GA inference are generally accurate, but they are slow and do not scale to biobank-size genomic datasets. Here we present Rye - a new algorithm for GA inference at biobank scale. We compare the accuracy and runtime performance of Rye to the widely used RFMix and ADMIXTURE programs, and we apply it to a dataset of 488,221 genome-wide variant samples from the UK Biobank. Rye infers GA based on principal component analysis (PCA) of genomic variant samples from ancestral reference populations and query individuals. The algorithms accuracy is powered by Metropolis-Hastings optimization and its speed is provided by non-negative least squares (NNLS) regression. Rye produces highly accurate GA estimates for three-way admixed populations - African, European, and Native American - compared to RFMix and ADMIXTURE (R2 = 0.998 - 1.00), and shows 50x runtime improvement compared to ADMIXTURE on the UK Biobank dataset. Rye analysis of UK Biobank samples demonstrates how it can be used to infer GA at different levels of relatedness. We discuss user consideration and options for the use of Rye; the program and its documentation are distributed on the GitHub repository: https://github.com/healthdisparities/rye.


title: Impact of sequencing technologies on long non-coding RNA computational identification

abstract: The correct annotation of non-coding RNAs, especially long non-coding RNAs (lncRNAs), is still an important critial challenge in genome analyses. One crucial issue in lncRNA transcript annotation is the transcriptome resource that supports lncRNA loci. Long-read technologies now bring the potential to improve the quality of transcriptome annotation. Consequently, long non-coding RNAs (lncRNA) are probably the most benefited class of transcripts that would have improved annotation using this novel technology. However, there is a gap regarding benchmarking studies that highlighted if the direct use of lncRNA predictors in long-reads makes more precise identification of these transcripts. Considering that these lncRNA tools were not trained with these reads, we want to address: how is the performance of these tools? Are they also able to efficiently identify lncRNAs? We could provide evidence of where and how to make potential better approaches for the lncRNA annotation by understanding these issues. Keywords: Non-coding RNAs, high-throughput sequencing technologies, coding, methods, benchmarking, tools, NGS, transcripts


title: Heterotypic Endosomal Interactions Drive Emergent Early Endosomal Maturations

abstract: Endosomal trafficking in single cells entails the generation of membrane vesicles; their motor protein-mediated transport; morphological alterations such as tubulation, fusion and fission; as well as dynamic maintenance of various identities, defined by the lipid composition and localisation of specific proteins on their membranes. Endosomal maturation is a major feature of this process. It is classically described as endosomes shedding one specific protein and acquiring another, resulting in an identity change. This step governs the flux and the number of distinct endosomal populations. Many of the molecular players that characterise different compartments have been identified--for example, APPL1 on very early endosomes, and EEA1 on early endosomes. However, how an ensemble population of endosomes matures at a whole cell level has remained unstudied. Here, we describe a novel inter-endosomal interaction-based feed-forward mechanism that drives endosomal conversions and controls ensemble conversion rates at the whole cell level. Furthermore, using live-cell Forster Resonance Energy Transfer, we demonstrate that this process is underpinned by co-ordinated precedence in EEA1 binding via its N- and C-terminal domains, ensuring the biochemical maturation of these vesicles. Using simulations, we provide a quantitative framework to recapture the experimentally observed characteristics in the reaction scheme and the activity of EEA1. We demonstrate that the model of APPL1 to EEA1 endosomal maturation needs to be extended to include heterotypic interactions between endosomes that result in conversions, which form a significant fraction of events, in addition to the previously reported single endosome-centric maturation models. Based on these results, we motivate how temporal specificity emerges in an inherently stochastic system--namely, through a timekeeping mechanism via an N-terminal EEA1 trigger that enables deterministic outcomes in ensemble endosomal conversions.


title: Sustained morphine delivery suppresses bone formation and alters metabolic and circulating miRNA profiles in male C57BL/6J mice

abstract: Opioid use is detrimental to bone health, causing both indirect and direct effects on bone turnover. While the mechanisms of these effects are not entirely clear, recent studies have linked chronic opioid use to alterations in circulating miRNAs. Our aim was to develop a model of opioid-induced bone loss to understand bone turnover and identify candidate miRNA-mediated regulatory mechanisms. We evaluated the effects of sustained morphine treatment on the skeleton, metabolism, and body composition of male and female C57BL/6J mice by treating with vehicle (0.9% saline) or morphine (18 mg/kg) using subcutaneous osmotic minipumps for 25 days. Morphine-treated mice had higher energy expenditure and respiratory quotient, indicating a shift toward carbohydrate metabolism. Microcomputed tomography ({micro}CT) analysis indicated that male mice treated with morphine had reduced trabecular bone volume fraction (Tb.BV/TV) (15%) and Tb. bone mineral density (BMD) (14%) in the distal femur compared to vehicle. Conversely, bone microarchitecture was not changed in females after morphine treatment. Histomorphometric analysis demonstrated that in males, morphine reduced bone formation rate compared to vehicle, but osteoclast parameters were not different. Furthermore, morphine reduced bone formation marker gene expression in the tibia of males (Bglap and Dmp1). Circulating miRNA profile changes were evident in males, with 14 differentially expressed miRNAs associated with morphine treatment. Target analysis indicated hypoxia inducible factor (HIF) signaling pathway was targeted by miR-223-3p and fatty acid metabolism by miR-484, - 223-3p, and -328-3p. In summary, we have established a model where morphine leads to a lower trabecular bone formation in males. Further, understanding the mechanisms of bone loss from opioid treatment will be important for improving management of the adverse effects of opioids on the skeleton.


title: The rhizodynamics robot: Automated imaging system for studying long-term dynamic root growth

abstract: The study of plant root growth in real time has been difficult to achieve in an automated, high-throughput, and systematic fashion. Dynamic imaging of plant roots is important in order to discover novel root growth behaviors and to deepen our understanding of how roots interact with their environments. We designed and implemented the Generating Rhizodynamic Observations Over Time (GROOT) robot, an automated, high-throughput imaging system that enables time-lapse imaging of 90 containers of plants and their roots growing in a clear gel medium over the duration of weeks to months. The system uses low-cost, widely available materials. As a proof of concept, we employed GROOT to collect images of orchid root growth of multiple species over six months. Beyond imaging plant roots, our system is highly customizable and can be used to collect time-lapse image data of different container sizes and configurations regardless of what is being imaged, making it applicable to many fields that require longitudinal time-lapse recording.


title: Bone marrow haematopoietic stem cells influence liver homeostatic networks and cancer development after dietary intervention

abstract: In fatty liver disease, systemic homeostasis is perturbed. While pre-clinical models are used to understand its pathogenesis, translating this knowledge to patients is difficult. However, by focusing on the most preserved homeostasis systems between species and models, novel disease dimensions can be unearthed. We interrogated core liver gene co-expression networks in a mouse model of liver cancer following dietary challenge. Immunometabolic modules showed temporal changes under the influence of diet duration and aging. The behaviour of immune network in tumours mirrored their counterparts in non-tumour liver. A high immune response network was associated with a lower tumour burden in mice and humans. This module in mice was enriched for genes related to haematopoietic cell differentiation. Consistently, the bone marrow haematopoietic stem and progenitor cells response was reflective of the liver immune response. Linking haematopoiesis to hepatic homeostasis uncovers a hitherto unexplored dimension of tissue crosstalk that can inform pathogenesis.

category: systems biology


title: Bone marrow haematopoietic stem cells influence liver homeostatic networks and cancer development


title: Dopamine release at the time of a predicted aversive outcome causally controls the trajectory and expression of conditioned behavior

abstract:
BackgroundThe inability to predict when aversive stimuli will and will not occur in is a hallmark of anxiety and stress disorders. Dopamine release in the nucleus accumbens (NAc) is sufficient and necessary for aversive learning and has been linked to both anxiety and stress disorder symptomatology. Thus, understanding how dopamine controls associative learning in response to aversive stimuli is critical to understanding the role of dopamine in behavior in health and disease.

MethodsUsing an optical dopamine sensor combined with in-vivo fiber photometry in the NAc core of male and female C57BL/6J mice (N=38), we recorded dopamine responses to expected and omitted aversive outcomes during learning. We derived predictions from a theory-driven model of associative learning (Kutlu-Calipari-Schmajuk, KCS model) and tested the causality of these predictions using optogenetics.

ResultsDopamine release was evoked by the predicted omission of aversive stimuli in a fashion that cannot be explained by dopamine as a reward-based prediction signal. The magnitude of the dopamine response during omissions scaled with predictions about the probability of their occurrence; however, dopamine did not track the associative value of predictive cues. Finally, we showed that the observed effects are causal to learned behavior and can only be explained by dopamine signaling the perceived saliency of predicted aversive events.

ConclusionsWe elucidate the role of NAc core dopamine signaling in aversive learning in a theory-based and stimulus-specific fashion and offer potential avenues for understanding the neural mechanisms involved in anxiety and stress disorders.


title: Resilience to anxiety and anhedonia after predator scent stress is accompanied by increased nucleus accumbens mGlu5 in female rats

abstract: Despite the higher prevalence of post-traumatic stress disorder (PTSD) in women, the majority of preclinical neuroscience research has been conducted utilizing male subjects. We have found that male rats exposed to the predator scent 2,4,5-trimethyl-3-thiazoline (TMT) show heterogenous development of long-term anxiety-like behavior and conditioned fear to the TMT environment. Stress-Resilient males exhibit increased mGlu5 mRNA expression in the basolateral amygdala (BLA) and prefrontal cortex. Here we sought to determine whether the same behavioral and genetic responses would be observed in female rats exposed to TMT. Sprague-Dawley rats were exposed to TMT for ten minutes, while Controls were exposed to an unscented environment. Anxiety and anhedonia were assessed 7-14 days later with elevated plus maze (EPM), acoustic startle response (ASR), light/dark box, and sucrose preference test. TMT-exposed females spent less time in the EPM open arms and exhibited greater startle amplitude, and reduced sucrose intake compared to Controls. Median split analyses conducted on EPM and sucrose intake yielded phenotypes that displayed behavior in the light/dark box consistent with EPM and sucrose testing. Unlike male Susceptible rats, female Susceptible rats showed no freezing when re-exposed to the TMT context, nor did Resilient female rats present elevated BLA mGlu5 mRNA levels. Instead, Susceptible females had greater BLA mGlu5 than Resilient or Control rats. This work indicates that, as in humans, rats exhibit sex-dependent responses to stress. This translational animal model may provide insight into how females are uniquely affected by PTSD.


title: Bayesian interpolation for power laws in neural data analysis

abstract: Power laws arise in a variety of phenomena ranging from matter undergoing phase transition to the distribution of word frequencies in the English language. Usually, their presence is only apparent when data is abundant, and accurately determining their exponents often requires even larger amounts of data. As the scale of recordings in neuroscience becomes larger, an increasing number of studies attempt to characterise potential power-law relationships in neural data. In this paper, we aim to discuss the potential pitfalls that one faces in such efforts and to promote a Bayesian interpolation framework for this purpose. We apply this framework to synthetic data and to data from a recent study of large-scale recordings in mouse primary visual cortex (V1), where the exponent of a powerlaw scaling in the data played an important role: its value was argued to determine whether the populations stimulus-response relationship is smooth, and experimental data was provided to confirm that this is indeed so. Our analysis shows that with such data types and sizes as we consider here, the best-fit values found for the parameters of the power law and the uncertainty for these estimates are heavily dependent on the noise model assumed for the estimation, the range of the data chosen, and (with all other things being equal) the particular recordings. It is thus challenging to offer a reliable statement about the exponents of the power law. Our analysis, however, shows that this does not affect the conclusions regarding the smoothness of the population response to low-dimensional stimuli but casts doubt on those to natural images. We discuss the implications of this result for the neural code in the V1 and offer the approach discussed here as a framework that future studies, perhaps exploring larger ranges of data, can employ as their starting point to examine power-law scalings in neural data.


title: Theory of spontaneous persistent activity and inactivity in vivo reveals differential cortico-entorhinal functional connectivity

abstract: Persistent activity is thought to mediate working memory. While such stimulus evoked persistence is well studied, mechanisms of internally generated or spontaneous persistence in vivo are unknown. Further, current theories based on attractor dynamics focus on elevated activity as a memory substrate, while little attention has focused on the role of inactivity attractors. Here, we present a mean field model of functional interaction between large cortical networks that predicts both spontaneous persistent activity (SPA) and inactivity (SPI); the latter has never been seen before in experiments or models. We confirm these predictions using simultaneously recorded neocortical local field potential (LFP) and the membrane potential (Vm) of identified excitatory neurons from several brain areas in vivo during slow oscillations, especially from layer 3 of the medial (MECIII) and lateral entorhinal cortex (LECIII), which show SPA and SPI. By matching model and experimental statistics, we predict the relative strength of internal and external excitation in the LECIII and MECIII networks. Our predictions match anatomical data. Further, the model predicts, and the experiments confirm, that SPA and SPI are quantized by cortical UDS and follow the statistics of a history dependent Bernoulli process. These convergent, theory-experiment results thus reveal the differential nature of cortico-entorhinal functional connectivity, resulting in a unique pattern of persistent activity and persistent inactivity, a novel and energetically efficient memory substrate.


title: Single acoustic closed loop stimulation in mice to modulate hippocampo-thalamo-cortical activity and performance

abstract: Neural brain rhythms of sleep reflect neuronal activity underlying sleep-associated memory consolidation. The modulation of brain rhythms, for instance the sleep slow oscillation (SO) is used both to investigate neurophysiological mechanisms as well as to measure the impact on presumed functional correlates. In humans, auditory closed-loop stimulation targeted to the SO Up-state successfully enhanced the slow oscillation rhythm and phase-dependent spindle activity, although effects on memory retention have varied. Here, we aim to disclose relations between stimulation induced hippocampo-thalamo-cortical activity and retention performance on a hippocampus dependent task in mice. Closed-loop acoustic stimuli applied during four SO phases always acutely increased sharp wave ripple (SPWR) activity without disrupting non-rapid eye movement (NREM) sleep. Stimulation achieved an above chance preference index for stimuli delivered across a 3 h retention interval of sleep at the SO Up-state and at the Down-to-Up-state, but not at the Down-state nor late Up-state/Up-to Down-state. Results support the use of closed-loop acoustic stimulation in mice to investigate the inter-regional mechanisms underlying memory consolidation.


title: Probing neuronal functions with precise and targeted laser ablation in the living cortex: reply

abstract: In the comment on the article [Optica 8, 12 (2021)], the authors performed theoretical calculation to show that with a 1.1 NA objective and 140 fs laser pulses with single pulse energy of 2.2 nJ, and 80 MHz repetition rate, the focal point temperature rises 0.3 K and reaches equilibrium after 100 s in water. They suggest that the damage to brain tissue by laser could not be caused by thermal effects but rather by plasma-mediated chemical effects. To quantify the thermal accumulation due to the fs laser illumination in living animals, we used a thermocouple sensor to measure the temperature change in the vicinity of the laser focus at a depth of 300 m in the adult mouse cortex. Our results show that at 930 nm wavelength, 25 m from the laser focus, 19-300 mW laser can all lead to a brain tissue temperature rise of more than 0.3 K at 1 second and the maximum equilibrium temperature rise of more than 28 K. These experimental measurements are significantly higher than theoretically calculated values in the comment. These results suggest that the thermal accumulation effect of focused low-energy pulses from fs laser oscillators could contribute significantly to the collateral damage in the living brain.


title: A python-based package for long-lasting video acquisition and semi-automated detection of convulsive seizures in rodents

abstract:
BackgroundEpilepsy is a very invalidating pathology characterized by the unpredictable appearance of abnormal cerebral activity leading to seizures and co-morbidities. The ability to detect and even predict seizures is a major challenge and many research laboratories are using rodents models of epilepsy to unravel possible mechanisms. The gold standard to record and detect seizures is electroencephalography, but it is very invasive. For rodents used in research, video analysis is a very interesting approach but the major disadvantages are that it is time consuming, prone to human error, and not very reproducible. Commercial solutions for detailed phenotyping analysis on humans or rodents exist but they are costly. Some open source software programs are also available, they provide very interesting and precise behavior data, but none of them are made for high throughput analysis of a large number of video files generated by long lasting recordings.

New methodWe developed an open-source python-based package of two software programs that enable automated video acquisition and simple motion analysis associated with a spectral power analysis, which enable a semi-automated identification of convulsive seizures. The method needs cheap webcams and a computer or a server.

ResultsUsing two murine epilepsy models (Nav1.1 mutations), we have compared our motion analysis software to human visual inspection and found an 88.8% accuracy in convulsive seizures detection. We then compare our method to the gold standard electrocorticogram analysis and found a 93.2% accuracy. The motion analysis is also interesting to get a readout of the animal activity without the invasiveness of electromyogram recordings.

ConclusionsThis new method is easy to use, cost-effective and allows: 1) detection of convulsive seizures in a noninvasive way, 2) high speed analysis of a large number of video files with a good accuracy, and 3) automated acquisition and semi-automated analysis of a very large number of files.

HighlightsO_LINoninvasive semi-automated detection of convulsive seizures from videos
C_LIO_LIHigh speed of analysis with a good accuracy
C_LIO_LIAbility to acquire and analyze a very large number of files
C_LIO_LIEasy to use graphical interfaces
C_LIO_LICost-effective setup
C_LI


title: Visual working memory recruits two functionally distinct alpha rhythms in posterior cortex

abstract:
Oscillatory activity in the human brain is dominated by posterior alpha oscillations (8-14 Hz), which have been shown to be functionally relevant in a wide variety of cognitive tasks. Although posterior alpha oscillations are commonly considered a single oscillator anchored at an individual alpha frequency (IAF; [~]10 Hz), previous work suggests that IAF reflects a spatial mixture of different brain rhythms. In this study, we assess whether Independent Component Analysis (ICA) can disentangle functionally distinct posterior alpha rhythms in the context of visual short-term memory retention. Magnetoencephalography (MEG) was recorded in 33 subjects while performing a visual working memory task. Group analysis at sensor level suggested the existence of a single posterior alpha oscillator that increases in power and decreases in frequency during memory retention. Conversely, single-subject analysis of independent components revealed the existence of two dissociable alpha rhythms: one that increases in power during memory retention (Alpha1) and another one that decreases in power (Alpha2). Alpha1 and Alpha2 rhythms were differentially modulated by the presence of visual distractors (Alpha1 increased in power while Alpha2 decreased) and had an opposite relationship with accuracy (positive for Alpha1 and negative for Alpha2). In addition, Alpha1 rhythms showed a lower peak frequency, a narrower peak width, a greater relative peak amplitude and a more central source than Alpha2 rhythms. Together, our results demonstrate that modulations in posterior alpha oscillations during short-term memory retention reflect the dynamics of at least two distinct brain rhythms with different functions and spatiospectral characteristics.

Significance statementAlpha oscillations are the most prominent feature of the human brains electrical activity, and consist of rhythmic neuronal activity in posterior parts of the cortex. Alpha is usually considered a single brain rhythm that changes in power and frequency to support cognitive operations. We here show that posterior alpha entails at least two dissociable rhythms with distinct functions and characteristics. These findings could solve previous inconsistencies in the literature regarding the direction of task-related alpha power/frequency modulations and their relation to cognitive performance. In addition, the existence of two distinct posterior alpha rhythms could have important consequences for the design of neurostimulation protocols aimed at modulating alpha oscillations and subsequently cognition.


title: Neural oscillations across olfactory regions encode odorant information in the teleost olfactory system

abstract: Field potential oscillations in the olfactory system of vertebrates and invertebrates are prominent and well-studied, but their functions remain nevertheless enigmatic. Spatial networks are thought to play a role in olfactory discrimination in different species, but their analysis is frequently complicated by behavior, learning and respiration (sniffing). Here, we show that in a sniffing-free model (trout), the relevant feature for discriminating odorant identity is the information conveyed by the oscillatory activity in a spatially distributed network, including the olfactory bulb and the telencephalic regions Vv and Dp. Specifically, information-based methods based on spectral decoding, information sharing, and information redundancy distinguished odorant identity across spatially distant regions while classical spectral analyses did not. Our study demonstrates that olfactory oscillations are carriers of spatially distributed odor information across the teleost olfactory system.


title: A revised calcium-dependent model of theta-burst transcranial magnetic stimulation

abstract: Calcium dependency is presently an essential assumption in modelling the neuromodulatory effects of transcranial magnetic stimulation (TMS). Among the various neuromodulatory TMS protocols, theta-burst stimulation (TBS) at present is the fastest intervention to generate strong effects. A decade ago, Y.Z. Huang et al. developed a first neuromodulation model to explain the bidirectional effects of TBS based on postsynaptic intracellular calcium concentration elevation. We discover, however, that the published computer code is not consistent with the model formulations in the corresponding paper. Further analysis confirms that the computer model with an index confusion was used for fitting the experimental results, running the simulation, and plotting the corresponding figures in the original publication. This paper intends to fix the computer code and additionally create a non-convex optimisation solution for re-calibrating the model. After re-calibration, the revised model outperforms the initial model in accuracy describing the MEP amplitudes of TBS-induced after-effects under specific situations.


title: Immediate neural network impact after the loss of a semantic hub

abstract: The human brain extracts meaning from the world using an extensive neural system for semantic knowledge. Whether such broadly distributed systems1-3 crucially depend on or can compensate for the loss of one of their highly interconnected hubs4-6 is controversial4. The strongest level of causal evidence for the role of a brain hub is to evaluate its acute network-level impact following disconnection and any rapid functional compensation that ensues. We report rare neurophysiological data from two patients who underwent awake intracranial recordings during a speech prediction task immediately before and after neurosurgical treatment that required disconnection of the left anterior temporal lobe (ATL), a crucial hub for semantic knowledge4-6. Informed by a predictive coding framework, we tested three sets of hypotheses including diaschisis causing disruption in interconnected sites7 and incomplete or complete compensation by other language-critical and speech processing sites8-10. Immediately after ATL disconnection, we observed highly specific neurophysiological alterations in the recorded fronto-temporal network, including abnormally magnified high gamma responses to the speech sounds in auditory cortex. We also observed evidence for rapid compensation, seen as focal increases in effective connectivity involving language-critical sites in the inferior frontal gyrus and speech processing sites in auditory cortex. However, compensation was incomplete, in part because after ATL disconnection speech prediction signals were depleted in auditory cortex. This study provides direct causal evidence for a semantic hub in the human brain and shows striking neural impact and a rapid attempt at compensation in a neural network after the loss of one of its hubs.


title: Humoral signaling-mediated effects of unilateral brain injury: differences in the left-right sided afferent responses

abstract:
Disruption of neural tracts descending from the brain to the spinal cord after brain trauma and stroke causes postural and sensorimotor deficits. We previously showed that unilateral lesion to the sensorimotor cortex in rats with completely transected thoracic spinal cord produced asymmetry in hindlimb posture and withdrawal reflexes. Supraspinal signals to hindlimb muscles may be transmitted through the paravertebral chain of sympathetic ganglia that remain intact after the transection. We here demonstrated that prior transection of the spinal cord at the cervical level that was rostrally to segments with preganglionic sympathetic neurons, did not abolish formation of asymmetry in hindlimb posture and musculo-articular resistance to stretch after unilateral brain injury. Thus not the sympathetic system but humoral signals may mediate the effects of brain injury on the lumbar spinal circuits. The asymmetric responses in rats with transected spinal cords were eliminated by bilateral lumbar dorsal rhizotomy after the left-side brain injury, but resistant to deafferentation after the right-side brain lesion. Two mechanisms, one dependent on and one independent of afferent input may account for asymmetric hindlimb motor responses. Resistance to deafferentation may be due to sustained stretch- and effort-unrelated muscle contractions that is often observed in patients with central lesions. Left-right asymmetry is unusual feature of these mechanisms that both are activated by humoral signals.

Graphical Abstract

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title: Estimation of cochlear frequency selectivity using a convolution model of forward-masked compound action potentials

abstract: Frequency selectivity is a fundamental property of the peripheral auditory system; however, the invasiveness of auditory nerve (AN) experiments limits its study in the human ear. Compound action potentials (CAPs) associated with forward-masking have been suggested as an alternative means to assess cochlear frequency selectivity. Previous methods relied on an empirical comparison of AN and CAP tuning curves in animal models, arguably not taking full advantage of the information contained in forward-masked CAPs. In this work, we seek to provide a direct estimate of the quality factor characterizing AN frequency tuning using many forward-masked CAP responses. The method is based on a convolution model of the CAP that takes into account the masking of AN populations induced by notched-noise maskers with various notch widths and attenuations. The model produces masking patterns that, once convolved by a unitary response, predict forward-masked CAP waveforms. Model parameters, including those characterizing frequency selectivity, are fine-tuned by minimizing waveform prediction errors across the different masking conditions, yielding robust estimates. The method was applied to click-evoked CAPs at the round window of anesthetized chinchillas. The estimated quality factor Q10 as a function of center frequency is shown to closely match the average quality factor obtained from AN-fiber tuning curves, without the need for an empirical correction factor. Beyond the estimation of frequency selectivity, the proposed model proves to be accurate in predicting forward-masked CAP responses, and therefore could be extended to study more complex aspects of cochlear signal processing using a similar experimental approach.


title: CbpD crystal structure adds intrigue to substrate-specificity motifs in chitin-active lytic polysaccharide monooxygenases

abstract: Pseudomonas aeruginosa secretes diverse proteins via its Type 2 Secretion System, including a 39 KDa Chitin-Binding Protein, CbpD. CbpD was recently shown to be a lytic polysaccharide monooxygenase active on chitin, and to contribute substantially to virulence. To-date no structure of this virulence factor has been reported. Its first two domains are homologous to those found in the crystal structure of Vibrio cholerae GbpA, while the third domain is homologous to the NMR structure of the Cellvibrio japonicus CjLPMO10A CBM73 domain. We report the 3.0 [A] resolution crystal structure of CbpD solved by molecular replacement, which required ab initio models of each CbpD domain generated by the artificial intelligence deep learning structure prediction algorithm RoseTTAFold. The structure of CbpD confirms previously postulated chitin-specific motifs in the AA10 domain while challenging the deterministic effects of other postulated substrate specificity motifs. Additionally, the structure of CbpD shows that post translational modifications occur on the chitin binding surface. Moreover, the structure raises interesting possibilities about how Type 2 Secretion System substrates may interact with the secretion machinery and demonstrates the utility of new artificial intelligence protein structure prediction algorithms in making challenging structural targets tractable.


title: Crystal structure of the Rubella virus protease reveals a unique papain-like protease fold

abstract: Rubella is well-controlled due to an effective vaccine, but outbreaks are still occurring without any available antiviral treatments. There is still much to learn about the rubella virus (RUBV) papain-like protease (RubPro) that could be a potential drug target. This protease is crucial to RUBV replication, cleaving the non-structural polyprotein p200 into 2 multi-functional proteins, p150 and p90. Here we report a novel crystal structure of RubPro at 1.64 [A] resolution. It has a similar catalytic core structure to that of SARS-CoV-2 and foot-mouth-disease virus (FMDV) proteases. RubPro has well-conserved sequence motifs that are also found in its newly discovered Rubivirus relatives. The RubPro construct was shown to have protease activity in trans against a construct of RUBV protease-helicase and fluorogenic peptide. A protease-helicase construct was also cleaved in E. coli expression. RubPro was demonstrated to possess deubiquitylation activity, suggesting a potential role of RubPro in modulating the hosts innate immune responses. The structural and functional insights of the RubPro will advance our current understanding of its function and point to more structure-based research into the RUBV replication machinery, in hopes of developing antiviral therapeutics in the future.


title: Microbiota of the pregnant mouse: characterization of the bacterial communities in the oral cavity, lung, intestine, and vagina through culture and DNA sequencing

abstract:
Mice are frequently used as animal models for mechanistic studies of infection and obstetrical disease, yet characterization of the murine microbiota during pregnancy is lacking. The objective of this study was to therefore characterize the microbiotas of distinct body sites of the pregnant mouse that harbor microorganisms that could potentially invade the murine amniotic cavity leading to adverse pregnancy outcomes: vagina, oral cavity, intestine, and lung. The microbiotas of these body sites were characterized through anoxic, hypoxic, and oxic culture, as well as through 16S rRNA gene sequencing. With the exception of the vagina, the cultured microbiotas of each body site varied with atmosphere, with the greatest diversity in the cultured microbiota appearing under anoxic conditions. Only cultures of the vagina were able to recapitulate the microbiota observed from direct DNA sequencing of body site samples, primarily due to the dominance of two Rodentibacter strains. Identified as R. pneumotropicus and R. heylii, these isolates exhibited dominance patterns similar to those of Lactobacillus crispatus and L. iners in the human vagina. Whole genome sequencing of these Rodentibacter strains revealed shared genomic features, including the ability to degrade glycogen, an abundant polysaccharide in the vagina. In summary, we report body site specific microbiotas in the pregnant mouse with potential ecological parallels to those of humans. Importantly, our findings indicate that the vaginal microbiota of pregnant mice can be readily cultured, suggesting that mock vaginal microbiotas can be tractably generated and maintained for experimental manipulation in future mechanistic studies of host vaginal-microbiome interactions.

IMPORTANCEMice are widely utilized as animal models of obstetrical complications; however, the characterization of the murine microbiota has been neglected during pregnancy. Microorganisms from the vagina, oral cavity, intestine, and lung have been found in the intra-amniotic space, where their presence threatens the progression of gestation. Herein, we characterize the microbiotas of pregnant mice and establish the appropriateness of culture in capturing the microbiota at each site. The high relative abundance of Rodentibacter observed in the vagina is similar to that of Lactobacillus in humans, suggesting potential ecological parallels. Importantly, we report that the vaginal microbiota of the pregnant mouse can be readily cultured under hypoxic conditions, demonstrating that mock microbial communities can be utilized to test the potential ecological parallels between microbiotas in human and murine pregnancy, and to evaluate the relevance of the structure of these microbiotas for adverse pregnancy outcomes, especially intra-amniotic infection and spontaneous preterm birth.


title: Cadmium is detrimental to Caenorhabditis elegans via anetwork involving circRNA, lncRNA and phosphorylatedprotein

abstract:
Cadmium (Cd) as a heavy metal causes serious environmental pollution and multiple organ and system damage in human. However, little is known about the specific molecular mechanisms of the associated regulatory networks. In this study, we selected Caenorhabditis elegans (C. elegans) to investigate the effects of Cd exposure as it acts as an acknowledged and established genetic model organism. A total of 26 differentially-expressed circular RNA (DEcircRNAs), 143 lncRNAs (DElncRNAs), 69 microRNAs (DEmiRNAs) and 6209 mRNAs (DEmRNAs) were found and identified, which might influence reproductive function, aging processes and nervous system functions through regulating the levels of circRNAs and lncRNAs and the controlling of regulatory networks of circRNA/lncRNA-miRNA-mRNA. Based on quantitative PCR, four DEcircRNAs and three DElncRNAs were confirmed to have different expression levels between the Cd-treated and control group. Further, 5 protein-coding genes might be regulated by DElnRNAs through cis-acting and 114 by trans-acting elements. Additionally, 42 differentially regulative phosphopeptides were detected and 4 novel pairs of transcription factors (TFs)-kinase-substrate that might be influenced by Cd exposure were constructed by phosphoproteomics. Our findings suggest that Cd might influence multi-functions and the aging process of C. elegans and may inhibit the expression of TFs to reduce phosphorylated levels of the corresponding protein.

SynopsisCadmium exists widely in soil, water and air. This study manifested the regulatory network involving circRNA, lncRNA and phosphorylated protein in C.elegans after Cd exposure, which revealing the potential molecular mechanism underlying the toxic effect caused by Cd.

Graphic Abstract

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category: molecular biology


title: RET Signaling Persists in the Adult Intestine and Stimulates Motility by Limiting PYY Release from Enteroendocrine Cells

abstract:
Background & AimsRET receptor tyrosine kinase is necessary for enteric nervous system (ENS) development. Loss-of-function RET mutations cause Hirschsprung disease (HSCR), in which infants are born with aganglionic bowel. Despite surgical correction, HSCR patients often experience chronic defecatory dysfunction and enterocolitis, suggesting that RET is important after development. To test this hypothesis, we determined the location of postnatal RET and its significance in gastrointestinal (GI) motility.

MethodsRetCFP/+ mice and human transcriptional profiling data were studied to identify the enteric neuronal and epithelial cells that express RET. To determine whether RET signaling in these cells regulates adult gut motility in vivo, genetic and pharmacologic approaches were used to disrupt RET in either all RET-expressing cells, a major subset of enteric neurons, or intestinal epithelial cells.

ResultsDistinct subsets of enteric neurons and enteroendocrine cells expressed RET in the adult intestine. RET disruption in the intestinal epithelium, rather than in enteric neurons, slowed GI motility selectively in adult male mice. This effect was phenocopied by RET kinase inhibition. Most RET+ epithelial cells were either enterochromaffin cells that release serotonin (5-HT) or L-cells that release peptide YY (PYY), both of which can alter motility. RET kinase inhibition exaggerated PYY release in a nutrient-dependent manner without altering 5-HT secretion. PYY receptor blockade fully rescued dysmotility in mice lacking epithelial RET.

ConclusionRET signaling normally limits nutrient-dependent PYY release from L-cells and this activity is necessary for normal intestinal motility in male mice. These effects could contribute to post-operative dysmotility in HSCR, which predominantly affects males, and uncovers a mechanism that could be targeted to treat post-prandial GI dysfunction.

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org.highwire.dtl.DTLVardef@4c8e83org.highwire.dtl.DTLVardef@204d13org.highwire.dtl.DTLVardef@a429d8org.highwire.dtl.DTLVardef@1b75265_HPS_FORMAT_FIGEXP  M_FIG C_FIG


title: Cross-activation of the FGF, TGF-β and WNT pathways constrains BMP4-mediated induction of the Totipotent state in mouse embryonic stem cells.

abstract: Cell signaling induced cell fate determination is central to stem cell and developmental biology. Embryonic stem cells (ESC) are an attractive model for understanding the relationship between cell signaling and cell fates. Cultured mouse ESCs can exist in multiple cell states resembling distinct stages of early embryogenesis, such as Totipotent, Pluripotent, Primed and Primitive Endoderm. The signaling mechanisms regulating the Totipotent state acquisition and coexistence of these states are poorly understood. Here we identify BMP4 as an inducer of the Totipotent state. However, we discovered that BMP4-mediated induction of the Totipotent state is constrained by the cross-activation of FGF, TGF-{beta} and WNT pathways. We exploited this finding to enhance the proportion of Totipotent cells in ESCs by rationally inhibiting these cross-activated pathways using small molecules. Single-cell mRNA-sequencing further revealed that induction of the Totipotent state is accompanied by the suppression of both the Primed and Primitive Endoderm states. Furthermore, the reprogrammed Totipotent cells generated in culture have a molecular and functional resemblance to Totipotent cell stages of preimplantation embryos. Our findings reveal a novel BMP4 signaling mechanism in ESCs to regulate multiple cell states, potentially significant for managing stem cell heterogeneity in differentiation and reprogramming.

category: developmental biology


title: Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation

abstract:
BackgroundVascular endothelial cells are a mesoderm-derived lineage with many essential functions, including angiogenesis and coagulation. However, the gene regulatory mechanisms that underpin endothelial specialization are largely unknown, as are the roles of 3D chromatin organization in regulating endothelial cell transcription.

MethodsTo investigate the relationships between 3D chromatin organization and gene expression in endothelial cell differentiation, we induced endothelial cell differentiation from human pluripotent stem cells and performed Hi-C and RNA-seq assays at specific timepoints in differentiation.

ResultsOur analyses reveal that long-range intrachromosomal contacts increase over the course of endothelial cell differentiation, as do genomic compartment transitions between active and inactive states. These compartmental states are tightly associated with endothelial transcription. Dynamic topologically associating domain (TAD) boundaries strengthen and converge on an endothelial cell state, and nascent TAD boundaries are linked to the expression of genes that support endothelial cell specification. Relatedly, chromatin pairwise point interactions (DNA loops) increase in frequency during differentiation and are linked to the expression of genes with essential roles in vascular biology, including MECOM, TFPI, and KDR. To identify forms of regulation specific to endothelial cell differentiation, we compared the functional chromatin dynamics of endothelial cells with those of developing cardiomyocytes. Cardiomyocytes exhibit greater long-range cis interactions than endothelial cells, whereas endothelial cells have increased local intra-TAD interactions and much more abundant pairwise point interactions.

ConclusionsGenome topology changes dynamically during endothelial differentiation, including acquisition of long-range cis interactions and new TAD boundaries, interconversion of hetero- and euchromatin, and formation of DNA loops. These chromatin dynamics guide transcription in the development of endothelial cells and promote the divergence of endothelial cells from related cell types such as cardiomyocytes.


title: A general framework for species-abundance distributions: linking traits and dispersal to explain commonness and rarity

abstract: Species-abundance distributions (SADs) describe the spectrum of commonness and rarity in a community. Beyond the universal observation that most species are rare and only a few common, more-precise description of SAD shape is controversial. Furthermore, the mechanisms behind SADs and how they vary along environmental gradients remain unresolved. We lack a general non-neutral theory of SADs. Here we develop a trait-based framework, focusing on a local community coupled to the region by dispersal. The balance of immigration and exclusion determines abundances, which vary over orders-of-magnitude. Under stabilizing selection, the local trait-abundance distribution (TAD) reflects a transformation of the regional TAD. The left-tail of the SAD depends on scaling exponents of the exclusion function and the regional species pool. More-complex local dynamics can lead to multimodal TADs and SADs. Connecting SADs with trait-based ecological theory provides a way to generate more-testable hypotheses on the controls over commonness and rarity in communities.


title: Phylogenomic patterns of divergence and gene flow detail the evolution of reinforcement and hybrid speciation in Phlox wildflowers

abstract: AO_SCPLOWBSTRACTC_SCPLOWIt is becoming increasingly clear that the evolutionary histories of many groups of organisms are riddled with reticulation. Some clades of organisms appear to be hotspots of speciation by hybridization and gene flow. For example, there are two cases of reinforcement and up to nine cases of hypothesized hybrid speciation in the eastern standing Phlox (Polemoniaceae) wildflowers. However, the relationships of these taxa and the hypotheses about their evolution have received limited attention with genomic data. We performed a comprehensive phylogenomic study of the eastern standing Phlox to resolve their evolutionary relationships and test long-standing hypotheses about if and how hybridization and gene flow acted as creative forces in their diversification. Our phylogenomic analyses on genome-wide markers provides resolution into the evolutionary relationships of thirty-two eastern standing Phlox taxa, including well-supported non-monophyletic relationships across species complexes. Explicit tests for introgression support gene flow occurring alongside the evolution of one of the two cases of reinforcement, and patterns of divergence and gene flow support one of the five hypothesized homoploid hybrid speciation events. Additionally, comparative read mapping allowed assignment of putative subgenome ancestries for four allotetraploids hybrid species. Our findings demonstrate the utility and importance of phylogenomics in confirming hypothesized evolutionary histories of non-model systems and add to the growing evidence that gene flow across species boundaries can play a role in the generation of novel biodiversity.

category: evolutionary biology


title: Genomic underpinnings of population persistence in Isle Royale moose

abstract:
Island ecosystems provide models to assess the impacts of isolation on population persistence. However, most studies of persistence have focused on a single species, without comparisons to other organisms they interact with in the ecosystem. The simple predator-prey system of moose and gray wolves on Isle Royale provides allows a direct contrast of genetic variation in a prey species with their natural predator. Wolves on Isle Royale exhibited signs of severe inbreeding depression, which nearly drove the population to extinction in 2019. In the relative absence of wolves, the moose population has thrived and exhibits no obvious signs of inbreeding depression despite being isolated for [~]120 years and having low genetic diversity. Here, we examine the genomic underpinnings of population persistence in the Isle Royale moose population. We document high levels of inbreeding in the population, roughly as high as the wolf population at the time of its decline. However, inbreeding in the moose population manifests in the form of intermediate-length runs of homozygosity indicative of gradual inbreeding, contrasting with the severe recent inbreeding observed in the wolf population. Using simulations, we demonstrate that this more gradual inbreeding in the moose population has resulted in an estimated 50% purging of the inbreeding load, helping to explain the continued persistence of the population. However, we also document notable increases in genetic load, which could eventually threaten population viability over the long term. Finally, we document low diversity in mainland North American moose populations due to a severe founder event occurring near the end of the Holocene. Overall, our results demonstrate a complex relationship between inbreeding, genetic diversity, and population viability that highlights the importance of maintaining isolated populations at moderate size to avert extinction from genetic factors.

Significance statementIsolated wildlife populations face a high risk of extinction due in part to the deleterious consequences of inbreeding. Whether purifying natural selection can overcome these negative impacts by "purging" harmful recessive mutations is a topic of active debate. We characterized the extent of purging in an isolated moose population. Our results demonstrate signatures of gradual inbreeding in the population, ideal circumstances to facilitate purging. Using simulations, we demonstrate substantial potential for purging in the population, though we also show that fitness is reduced by small population size and inbreeding. Our findings provide insight into the mechanisms enabling persistence in isolated populations, with implications for conserving the growing number of isolated populations worldwide.


title: Resource sharing leads to the emergence of division of labour

abstract: Division of labour occurs in a broad range of organisms. Yet, how division of labour can emerge in the absence of pre-existing interindividual differences is poorly understood. Using a simple but realistic model, we show that in a group of initially identical individuals, division of labour emerges spontaneously if returning foragers share part of their resources with other group members. In the absence of resource sharing, individuals follow an activity schedule of alternating between foraging and other tasks. If non-foraging individuals are fed by other individuals, their alternating activity schedule becomes interrupted, leading to task specialisation and the emergence of division of labour. Furthermore, nutritional differences between individuals reinforce division of labour. Such differences can be caused by increased metabolic rates during foraging or by dominance interactions during resource sharing. Our model proposes a plausible mechanism for the self-organised emergence of division of labour in animal groups of initially identical individuals. This mechanism could also play a role for the emergence of division of labour during the major evolutionary transitions to eusociality and multicellularity.


title: Reconstructing physical cell interaction networks from single-cell data using Neighbor-seq

abstract: Cell-cell interactions are the fundamental building blocks of tissue organization and multicellular life. We developed Neighbor-seq, a method to identify and annotate the architecture of direct cell-cell interactions and relevant ligand-receptor signaling from the undissociated cell fractions in massively parallel single cell sequencing data. Neighbor-seq accurately identifies microanatomical features of diverse tissue types such as the small intestinal epithelium, terminal respiratory tract, and splenic white pulp. It also captures the differing topologies of cancer-immune-stromal cell communications in pancreatic and skin tumors, which are consistent with the patterns observed in spatial transcriptomic data. Neighbor-seq is fast and scalable. It draws inferences from routine single-cell data and does not require prior knowledge about sample cell-types or multiplets. Neighbor-seq provides a framework to study the organ-level cellular interactome in health and disease, bridging the gap between single-cell and spatial transcriptomics.

category: genomics


title: Defensiveness measurement in honey bees (Apis mellifera)and brain expression of associated genes after noxious stimulus

abstract: Honey bee (Apis mellifera sp.) colonies and individuals respond variably to disturbances. In this study, we examined the role of neural modulation and metabolism in constitutive and experience-dependent differences in defensive response. We compared brain gene expression in bees of identified gentle and defensive colonies in a standard assay. For neuromodulation, we examined membrane receptor genes for the biogenic amines dopamine (DOPR2), octopamine (OAR), and serotonin (5HT2a), and the enzyme gene in the synthesis pathway (THR). To examine neural metabolism, we assessed the Oxidative Phosphorylation Pathway "OXPHOS" gene expression (i.e., ND51 and ND20-LIKE). Bees of defensive colonies had a significantly lower expression of amine receptor, synthesis genes, and OXPHOS genes. Experience differences or exposure to nociceptive neurons activated by nocive stimuli (electric shock) led to differences in the expression of all genes except 5HT2a. The same target genes demonstrated an increase in expression levels after electric shock and sting response. We discuss the convergence of neuromodulation, neural metabolism

category: animal behavior and cognition


title: A Deep SE(3)-Equivariant Model for Learning Inverse Protein Folding

abstract: In this work, we establish a framework to tackle the inverse protein design problem; the task of predicting a proteins primary sequence given its backbone conformation. To this end, we develop a generative SE(3)-equivariant model which significantly improves upon existing autoregressive methods. Conditioned on backbone structure, and trained with our novel partial masking scheme and side-chain conformation loss, we achieve state-of-the-art native sequence recovery on structurally independent CASP13, CASP14, CATH4.2, and TS50 test sets. On top of accurately recovering native sequences, we demonstrate that our model captures functional aspects of the underlying protein by accurately predicting the effects of point mutations through testing on Deep Mutational Scanning datasets. We further verify the efficacy of our approach by comparing with recently proposed inverse protein folding methods and by rigorous ablation studies.


title: Maps of high density microsatellites accumulation in human genome

abstract: We systematically built more than 100,000 microsatellites landscape-maps with identifying 3,433 and 5,306 high density microsatellites accumulation (HDMA) peaks in the human reference genome (GRCh38, p13 version) and the first complete human genome (T2T-CHM13, 1.1 version) at 1 kilobase resolution. Intuitive HDMA peak-locus maps were constructed for every chromosome of the 2 genomes, revealing that these HDMA peaks are distributed regularly along every chromosome. Data mining and comparison of HDMA peaks illustrated that most of the HDMA peaks may play biological roles with highly variable genomic sequences. Therefore, comparing the variation of HDMA peaks will provide an unprecedented approach to study human genetic variation.


title: SATINN: An automated neural network-based classification of testicular sections allows for high-throughput histopathology of mouse mutants

abstract:
MotivationThe mammalian testis is a complex organ with a hierarchical organization that changes smoothly and stereotypically over time in normal adults. While testis histology is already an invaluable tool for identifying and describing developmental differences in evolution and disease, methods for standardized, digital image analysis of testis are needed to expand the utility of this approach.

ResultsWe developed SATINN (Software for Analysis of Testis Images with Neural Networks), a multi-level framework for automated analysis of multiplexed immunofluorescence images from mouse testis. This approach uses a convolutional neural network (CNN) to classify nuclei from seminiferous tubules into 7 distinct cell types with an accuracy of 94.2%. These cell classifications are then used in a second-level tubule CNN, which places seminiferous tubules into one of 7 distinct tubule stages with 90.4% accuracy. We further describe numerous cell- and tubule-level statistics that can be derived from wildtype testis. Finally, we demonstrate how the classifiers and derived statistics can be used to rapidly and precisely describe pathology by applying our methods to image data from two mutant mouse lines. Our results demonstrate the feasibility and potential of using computer-assisted analysis for testis histology, an area poised to evolve rapidly on the back of emerging, spatially-resolved genomic and proteomic technologies.

Availability and implementationScripts to apply the methods described here are available from http://github.com/conradlab/SATINN.


title: USAT: a Bioinformatic Toolkit to Facilitate Interpretation and Comparative Visualization of Tandem Repeat Sequences

abstract: Tandem repeats (TR), which are highly variable genomic variants, are widely used in individual identification, disease diagnostics and evolutionary studies. The recent advances of sequencing technologies and bioinformatic tools facilitate calling TR haplotypes. Both length-based and sequence-based TR alleles are used in different applications. However, sequence-based TR alleles could provide the highest precision to characterize TR haplotypes. Analysis of the differences between or among TR haplotypes, especially at the single nucleotide level, is the focus of TR haplotype characterization. In this study, we developed a Universal STR Allele Toolkit (USAT) for TR haplotype analysis, which includes allele size conversion, sequence comparison of haplotypes, figure plotting and comparison for allele distribution, and interactive visualization. An example application of USAT for analysis of the CODIS core STR loci with benchmarking human individuals demonstrated the capabilities of USAT. USAT has a user-friendly graphic interface and runs in all major computing operating systems at a fast speed with parallel computing enabled. In summary, USAT is able to facilitate the interpretation, visualization, and comparisons of TRs.


title: A Kinetic Map of the Influence of Biomimetic Lipid Membrane Models on Aβ42 Aggregation

abstract: The aggregation of the amyloid {beta} peptide (A{beta}) is one of the major molecular hallmarks of Alzheimers disease. Although A{beta} deposits have been mostly observed extracellularly, various studies have reported the presence of also intracellular A{beta} assemblies. Because these intracellular A{beta} aggregates might play a role in the onset and progression of Alzheimers disease, it is important to investigate their possible origins at different locations of the cell along the secretory pathway of the amyloid precursor protein (APP), from which A{beta} is derived by proteolytic cleavage. Since lipid bilayers have been shown to promote the aggregation of A{beta}, in this study we measure the effects of the lipid membrane composition on the in vitro aggregation kinetics of the 42-residue form of A{beta} (A{beta}42). By using small unilamellar vesicles modelling cellular membranes at different locations, including the inner and outer leaflets of the plasma membrane, late endosomes, the endoplasmic reticulum (ER), and the Golgi apparatus, we show that A{beta}42 aggregation is inhibited by the ER and Golgi membranes. These results provide a preliminary map of the possible effects of the membrane composition in different cellular locations on A{beta} aggregation, and suggest the presence of an evolutionary optimization of lipid composition to prevent the intracellular aggregation of A{beta}.