title: Emergent collective locomotion in an active polymer model of entangled worm blobs

abstract: Numerous worm and arthropod species form physically-connected aggregations in which interactions among individuals give rise to emergent macroscale dynamics and functionalities that enhance collective survival. In particular, some aquatic worms such as the California blackworm (Lumbriculus variegatus) entangle their bodies into dense blobs to shield themselves against external stressors and preserve moisture in dry conditions. Motivated by recent experiments revealing emergent locomotion in blackworm blobs, we investigate the collective worm dynamics by modeling each worm as a self-propelled Brownian polymer. Though our model is two-dimensional, compared to real three-dimensional worm blobs, we demonstrate how a simulated blob can collectively traverse temperature gradients via the coupling between the active motion and the environment. By performing a systematic parameter sweep over the strength of attractive forces between worms, and the magnitude of their directed self-propulsion, we obtain a rich phase diagram which reveals that effective collective locomotion emerges as a result of finely balancing a tradeoff between these two parameters. Our model brings the physics of active filaments into a new meso- and macroscale context and invites further theoretical investigation into the collective behavior of long, slender, semi-flexible organisms.


title: Sequence determines the switch in the fibril forming regions in the low complexity FUS protein and its variants

abstract:
Residues spanning distinct regions of the low-complexity domain of the RNA-binding protein, Fused in Sarcoma (FUS-LC), form fibril structures with different core morphologies. NMR experiments show that the 214 residue FUS-LC forms a fibril with an S-bend (core-1, residues 39-95), while the rest of the protein is disordered. In contrast, the fibrils of the C-terminal variant (FUS-LC-C; residues 111-214) has a U-bend topology (core-2, residues 112-150). Absence of the U-bend in FUS-LC implies that the two fibril cores do not coexist. Computer simulations show that these perplexing findings could be understood in terms of the population of sparsely-populated fibril-like excited states in the monomer. The propensity to form core-1 is higher compared to core-2. We predict that core-2 forms only in truncated variants that do not contain the core-1 sequence. At the monomer level, sequence-dependent enthalpic effects determine the relative stabilities of the core-1 and core-2 topologies.

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category: biophysics


title: Sequence Determines the Switch in the Fibril Forming Regions in the Low-Complexity FUS Protein and Its Variants


title: The potential for mobile demersal fishing to reduce carbon storage and sequestration in seabed sediments

abstract: Subtidal marine sediments are one of the planets primary carbon stores and strongly influence the oceanic sink for atmospheric CO2. By far the most pervasive human activity occurring on the seabed is bottom trawling and dredging for fish and shellfish. A global first-order estimate suggested mobile demersal fishing activities may cause 160-400 Mt of organic carbon (OC) to be remineralised annually from seabed sediment carbon stores. There are, however, many uncertainties in this calculation. Here, we discuss the potential drivers of change in seabed OC stores due to mobile demersal fishing activities and conduct a systematic review, synthesising studies where this interaction has been directly investigated. Mobile demersal fishing would be expected to reduce OC in seabed stores, albeit with site-specific variability. Reductions would occur due to lower production of flora and fauna, the loss of fine flocculent material, increased sediment resuspension, mixing and transport, and increased oxygen exposure. This would be offset to some extent by reduced faunal bioturbation and respiration, increased off-shelf transport and increases in primary production from the resuspension of nutrients. Studies which directly investigated the impact of demersal fishing on OC stocks had mixed results. A finding of no significant effect was reported in 51% of 59 experimental contrasts; 41% reported lower OC due to fishing activities, with 8% reporting higher OC. In relation to remineralisation rates within the seabed, 14 experimental contrasts reported that demersal fishing activities decreased remineralisation, with four reporting higher remineralisation rates. The direction of effects was related to sediment type, impact duration, study design and local hydrography. More evidence is urgently needed to accurately quantify the impact of anthropogenic physical disturbance on seabed carbon in different environmental settings, and incorporate full evidence-based carbon considerations into global seabed management.

category: ecology


title: Skilful decadal-scale prediction of fish habitat and distribution shifts

abstract: Many fish and marine organisms are responding to our planets changing climate by shifting their distribution (i.e. where they are found). Such shifts can drive conflicts at the international scale and are highly problematic for the communities and businesses that depend on these living marine resources for income and nutrition. Advances in climate prediction mean that in some regions the state of the ocean, and thereby the drivers of these shifts, can be skilfully forecast up to a decade ahead. However, the potential for these forecasts to benefit ocean-dependent communities has yet to be realised. Here we show for the first time that marine climate predictions can be used to generate decadal-scale forecasts of shifts in the habitat and distribution of marine fish species, as exemplified by Atlantic mackerel, bluefin tuna and blue whiting. We show statistically significant forecast skill of individual years that outperform both persistence and climatological baseline forecasts for lead times of 3-10 years: multi-year averages perform even better, yielding correlation coefficients in excess of 0.90 in some cases. We also show that the habitat shifts underling recent conflicts over Atlantic mackerel fishing rights could have been foreseen on similar timescales. Our results show that climate predictions can be translated into information directly relevant to stakeholders and we anticipate that this tool will be critical in foreseeing, adapting to and coping with the challenges of a changing and variable future climate, particularly in the most ocean-dependent nations and communities.


title: A geospatial mapping pipeline for ecologists

abstract: Geospatial modelling can give fundamental insights in the biogeography of life, providing key information about the living world in current and future climate scenarios. Emerging statistical and machine learning approaches can help us to generate new levels of predictive accuracy in exploring the spatial patterns in ecological and biophysical processes. Although these statistical models cannot necessarily represent the essential mechanistic insights that are needed to understand global biogeochemical processes under ever-changing environmental conditions, they can provide unparalleled predictive insights that can be useful for exploring the variation in biophysical processes across space. As such, these emerging tools can be a valuable approach to complement existing mechanistic approaches as we aim to understand the biogeography of Earths ecosystems. Here, we present a comprehensive methodology that efficiently handles large datasets to produce global predictions. This mapping pipeline can be used to generate quantitative, spatially explicit predictions, with a particular emphasis on spatially-explicit insights into the evaluation of model uncertainties and inaccuracies.


title: Single Cell Transcriptomics Reveals Cell Type Specific Diversification in Human Heart Failure

abstract: Heart failure represents a major cause of morbidity and mortality worldwide. Single cell transcriptomics have revolutionized our understanding of cell composition and associated gene expression across human tissues. Through integrated analysis of single cell and single nucleus RNA sequencing data generated from 45 individuals, we define the cell composition of the healthy and failing human heart. We identify cell specific transcriptional signatures of heart failure and reveal the emergence of disease associated cell states. Intriguingly, cardiomyocytes converge towards a common disease associated cell state, while fibroblasts and myeloid cells undergo dramatic diversification. Endothelial cells and pericytes display global transcriptional shifts without changes in cell complexity. Collectively, our findings provide a comprehensive analysis of the cellular and transcriptomic landscape of human heart failure, identify cell type specific transcriptional programs and states associated with disease, and establish a valuable resource for the investigation of human heart failure.

category: genomics


title: The Thousand Polish Genomes Project- a national database of Polish variant allele frequencies

abstract:
Although Slavic populations account for over 3.5% of world inhabitants, no centralized, open source reference database of genetic variation of any Slavic population exists to date. Such data are crucial for either biomedical research and genetic counseling and are essential for archeological and historical studies. Polish population, homogenous and sedentary in its nature but influenced by many migrations of the past, is unique and could serve as a good genetic reference for middle European Slavic nations.

The aim of the present study was to describe first results of analyses of a newly created national database of Polish genomic variant allele frequencies. Never before has any study on the whole genomes of Polish population been conducted on such a large number of individuals (1,079).

A wide spectrum of genomic variation was identified and genotyped, such as small and structural variants, runs of homozygosity, mitochondrial haplogroups and Mendelian inconsistencies. The allele frequencies were calculated for 943 unrelated individuals and released publicly as The Thousand Polish Genomes database. A precise detection and characterisation of rare variants enriched in the Polish population allowed to confirm the allele frequencies for known pathogenic variants in diseases, such as Smith-Lemli-Opitz syndrome (SLOS) or Nijmegen breakage syndrome (NBS). Additionally, the analysis of OMIM AR genes led to the identification of 22 genes with significantly different cumulative allele frequencies in the Polish (POL) vs European NFE population. We hope that The Thousand Polish Genomes database will contribute to the worldwide genomic data resources for researchers and clinicians.


title: Identifying Protein Complexes in Protein-protein Interaction Data using Graph Convolution Network

abstract: Protein complexes are groups of two or more polypeptide chains that join together to build noncovalent networks of protein interactions. A number of means of computing the ways in which protein complexes and their members can be identified from these interaction networks have been created. While most of the existing methods identify protein complexes from the protein-protein interaction networks (PPIs) at a fairly decent level, the applicability of advanced graph network methods has not yet been adequately investigated. In this paper, we proposed various graph convolutional networks (GCNs) methods to improve the detection of the protein functional complexes. We first formulated the protein complex detection problem as a node classification problem. Second, the Neural Overlapping Community Detection (NOCD) model was applied to cluster the nodes (proteins) using a complex affiliation matrix. A representation learning approach, which combines the multi-class GCN feature extractor (to obtain the features of the nodes) and the mean shift clustering algorithm (to perform clustering), is also presented. We have also improved the efficiency of the multi-class GCN network to reduce space and time complexities by converting the dense-dense matrix operations into dense-spares or sparse-sparse matrix operations. This proposed solution significantly improves the scalability of the existing GCN network. Finally, we apply clustering aggregation to find the best protein complexes. A grid search was performed on various detected complexes obtained by applying three well-known protein detection methods namely ClusterONE, CMC, and PEWCC with the help of the Meta-Clustering Algorithm (MCLA) and Hybrid Bipartite Graph Formulation (HBGF) algorithm. The proposed GCN-based methods were tested on various publicly available datasets and provided significantly better performance than the previous state-of-the-art methods. The code and data used in this study are available from https://github.com/Analystharsh/GCN_complex_detection

category: bioinformatics


title: The disease associated Tau35 fragment has an increased propensity to aggregate compared to full-length tau

abstract: Tau35 is a truncated form of tau found in human brain in a subset of tauopathies. Tau35 expression in mice recapitulates key features of human disease, including progressive increase in tau phosphorylation, along with cognitive and motor dysfunction. The appearance of aggregated tau suggests that Tau35 may have structural properties distinct from those of other tau species that could account for its pathological role in disease. To address this hypothesis, we performed a structural characterization of monomeric and aggregated Tau35 and compared the results to those of two longer isoforms, 2N3R and 2N4R tau. We used small angle X-ray scattering to show that Tau35, 2N3R and 2N4R tau all behave as disordered monomeric species but Tau35 exhibits higher rigidity. In the presence of the poly-anion heparin, Tau35 increases thioflavin T fluorescence significantly faster and to a greater extent than full-length tau, demonstrating a higher propensity to aggregate. We used atomic force microscopy, transmission electron microscopy and X-ray fiber diffraction to demonstrate that Tau35 aggregates are morphologically similar to previously reported tau fibrils but they are more densely packed. These data increase our understanding of the aggregation inducing properties of clinically relevant tau fragments and their potentially damaging role in the pathogenesis of human tauopathies.


title: Dissociable Multi-scale Patterns of Development in Personalized Brain Networks

abstract: The brain is organized into networks at multiple resolutions, or scales, yet studies of functional network development typically focus on a single scale. Here, we derived personalized functional networks across 29 scales in a large sample of youths (n=693, ages 8-23 years) to identify multi-scale patterns of network re-organization related to neurocognitive development. We found that developmental shifts in inter-network coupling systematically adhered to and strengthened a functional hierarchy of cortical organization. Furthermore, we observed that scale-dependent effects were present in lower-order, unimodal networks, but not higher-order, transmodal networks. Finally, we found that network maturation had clear behavioral relevance: the development of coupling in unimodal and transmodal networks dissociably mediated the emergence of executive function. These results delineate maturation of multi-scale brain networks, which varies according to a functional hierarchy and impacts cognitive development.

category: neuroscience


title: Rescuing epileptic and behavioral alterations in a Dravet syndrome mouse model by inhibiting eEF2K

abstract: Dravet Syndrome is a severe childhood pharmacoresistant epileptic disorder caused mainly by mutations in the SCN1A gene, which encodes for the 1 subunit of the type I voltage-gated sodium channel (NaV1.1), that cause imbalance between excitation and inhibition in the brain. We recently found that eEF2K knock out mice displayed enhanced GABAergic transmission and tonic inhibition and were less susceptible to epileptic seizures. In Scn1a+/- mice, a mouse model of the Dravet syndrome, we found that the activity of eEF2K/eEF2 pathway was enhanced. Then, we demonstrated that both genetic deletion and pharmacological inhibition of eEF2K were able to reduce the epileptic phenotype of Scn1a+/- mice. Interestingly we also found that motor coordination defect, memory impairments, and stereotyped behavior of the Scn1a+/- mice were reverted by eEF2K deletion. The analysis of spontaneous inhibitory postsynaptic currents (sIPSCs) suggested that the rescue of the pathological phenotype was driven by the potentiation of GABAergic synapses. Our data indicate that pharmacological inhibition of eEF2K could represent a novel therapeutic intervention for treating epilepsy and related comorbidities in the Dravet syndrome.


title: The characteristics of the HIV-1 Env glycoprotein contribute to viral pathogenesis

abstract:
The understanding of HIV-1 pathogenesis and clinical progression is incomplete because of the variable contribution of host, immune and viral factors. The involvement of viral factors has been investigated in extreme clinical phenotypes from rapid progressors to long-term non-progressors (LTNPs). Among HIV-1 proteins, the envelope glycoprotein complex (Env) has concentrated many studies for its important role in the immune response and in the first steps of viral replication. In this study, we analyzed the contribution of 41 Envs from 24 patients with different clinical progression rates and viral loads (VLs), LTNP-Elite Controllers (LTNP-ECs); Viremic LTNPs (vLTNPs), and non-controllers individuals contemporary to LTNPs or recent, named Old and Modern progressors. We analyzed the Env expression, the fusion and cell-to-cell transfer capacities as well as viral infectivity. The sequence and phylogenetic analysis of Envs were also performed. In every functional characteristic, the Envs from subjects with viral control (LTNP-ECs and vLTNPs) showed significant lower performance compared to those from the progressor individuals (Old and Modern). Regarding sequence analysis, the variable loops of the gp120 subunit of the Env (i.e., V2, V4 and mainly V5) of the progressor individuals showed longer and more glycosylated sequences than controller subjects. Therefore, HIV-1 Envs presenting poor viral functions and shorter sequences were associated with viremic control and the non-progressor clinical phenotype, whereas functional Envs were associated with the lack of virological control and progressor clinical phenotypes. These correlations support the central role of Env genotypic and phenotypic characteristics in the in vivo HIV-1 infection and pathogenesis.

IMPORTANCEThe role of the virus in the pathogenesis of HIV-1 infection has not been investigated in isolates from individuals with different progression rates. In this work, we studied the properties of the envelope glycoprotein complex (Env) in individuals with different progression rates to elucidate its role in pathogenesis. We estimated the Env expression, the CD4 binding, the fusion and cell-to-cell viral transfer capacities that affect the infectivity of the viral Envs in recombinant viruses. The Envs from individuals which control viral replication and lack clinical progression (LTNP-ECs and vLTNPs) showed lower functional capacities than from subjects with clinical progression (Old and Modern). The functional increase of the Envs characteristics was associated with an increase in viral infectivity and in increased length of variable loops and the number of glycosylation sites of the Env (gp120/SU). These results support the concept that viral characteristics contribute to viral infection and pathogenesis.

category: microbiology


title: Recruitment of Scc2/4 to double strand breaks depends on γH2A and DNA end resection

abstract: Homologous recombination (HR) enables cells to overcome the threat of DNA double strand breaks (DSB), allowing for repair without the loss of genetic information. Central to the HR repair process is the de novo loading of Cohesin around a DSB by its loader complex Scc2/4. Although Cohesins accumulation at these sites has been well studied, the prerequisites leading to Scc2/4 recruitment during the repair process are still elusive. Here we investigate which factors are required for recruitment of Scc2 around DSBs in Saccharomyces cerevisiae. To address this question, we combined ChIP-qPCR with a GAL-inducible HO-endonuclease system to generate a site specific DSB in vivo. We find that Scc2 recruitment relies on yH2A and Tel1, but as opposed to Cohesin, not on Mec1. We further demonstrate that binding of Scc2 depends on and coincides with DNA end resection. Although affected by the impact on resection, this recruitment of Scc2 is not directly facilitated by the RSC, SWR1 or INO80 complexes. Our results shed light on the intricate DSB repair cascade leading to the recruitment of Scc2/4 and the subsequent loading of Cohesin.

category: cell biology


title: The preeminent role of directional selection in generating extreme morphological change in Glyptodonts (Cingulata; Xenarthra)

abstract: The prevalence of stasis on macroevolution has been classically taken as evidence of the strong role of stabilizing selection in constraining morphological evolution. Rates of evolution calculated over longer time scales tend to fall below the expected under genetic drift, suggesting that the signal for directional selection is erased at longer time scales. Here we investigated the rates of morphological evolution of the skull in a fossil lineage that underwent extreme morphological modification, the glyptodonts. Contrary to what was expected, we show here that directional selection was the main process during the evolution of glyptodonts. Furthermore, the reconstruction of selection patterns shows that traits selected to generate a glyptodont morphology are markedly different from those operating on extant armadillos. Changes in both direction and magnitude of selection are probably tied to glyptodonts invasion of a specialist-herbivore adaptive zone. These results suggest that directional selection might have played a more important role in the evolution of extreme morphologies than previously imagined.

category: evolutionary biology


title: Phylodynamic inference for emerging viruses using segregating sites

abstract: Epidemiological models are commonly fit to case data to estimate model parameters and to infer unobserved disease dynamics. More recently, epidemiological models have also been fit to viral sequence data using phylodynamic inference approaches that generally rely on the reconstruction of viral phylogenies. However, especially early on in an expanding viral population, phylogenetic uncertainty can be substantial and methods that require integration over this uncertainty can be computationally intensive. Here, we present an alternative approach to phylodynamic inference that circumvents the need for phylogenetic tree reconstruction. Our "tree-free" approach instead relies on quantifying the number of segregating sites observed in sets of sequences over time and using this trajectory of segregating sites to infer epidemiological parameters within a Sequential Monte Carlo (SMC) framework. Using forward simulations, we first show that epidemiological parameters and processes leave characteristic signatures in segregating site trajectories, demonstrating that these trajectories have the potential to be used for phylodynamic inference. We then show using mock data that our proposed approach accurately recovers key epidemiological quantities such as the basic reproduction number and the timing of the index case. Finally, we apply our approach to SARS-CoV-2 sequence data from France, estimating a reproductive number of approximately 2.2 and an introduction time of mid-January 2021, consistent with estimates from epidemiological surveillance data. Our findings indicate that "tree-free" phylodynamic inference approaches that rely on simple population genetic summary statistics can play an important role in estimating epidemiological parameters and reconstructing infectious disease dynamics, especially early on in an epidemic.


title: Ecological inference using data from accelerometers needs careful protocols

abstract:
O_LIAccelerometers in animal-attached tags have proven to be powerful tools in behavioural ecology, being used to determine behaviour and provide proxies for movement-based energy expenditure. Researchers are collecting and archiving data across systems, seasons and device types. However, in order to use data repositories to draw ecological inference, we need to establish the error introduced according to sensor type and position on the study animal and establish protocols for error assessment and minimization.
C_LIO_LIUsing laboratory trials, we examine the absolute accuracy of tri-axial accelerometers and determine how inaccuracies impact measurements of dynamic body acceleration (DBA), as the main acceleration-based proxy for energy expenditure. We then examine how tag type and placement affect the acceleration signal in birds using (i) pigeons Columba livia flying in a wind tunnel, with tags mounted simultaneously in two positions, (ii) back- and tail-mounted tags deployed on wild kittiwakes Rissa tridactyla. Finally, we (iii) present a case study where two generations of tag were deployed using different attachment procedures on red-tailed tropicbirds Phaethon rubricauda foraging in different seasons.
C_LIO_LIBench tests showed that individual acceleration axes required a two-level correction (representing up to 4.3% of the total value) to eliminate measurement error. This resulted in DBA differences of up to 5% between calibrated and uncalibrated tags for humans walking at different speeds. Device position was associated with greater variation in DBA, with upper- and lower back-mounted tags in pigeons varying by 9%, and tail- and back-mounted tags varying by 13% in kittiwakes. Finally, DBA varied by 25% in tropicbirds between seasons, which may be attributable to tag attachment procedures.
C_LIO_LIAccelerometer accuracy, tag placement, and attachment details critically affect the signal amplitude and thereby the ability of the system to detect biologically meaningful phenomena. We propose a simple method to calibrate accelerometers that should be used prior to deployments and archived with resulting data, suggest a way that researchers can assess accuracy in previously collected data, and caution that variable tag placement and attachment can increase sensor noise and even generate trends that have no biological meaning.
C_LI

category: animal behavior and cognition


title: Directional Cell Migration Guided by a Strain Gradient

abstract: Strain gradients, the percentage of the deformation changed across a continuous field by applying forces, have been observed in developing tissues due to the inherent heterogeneity of the mechanical properties. The directional movement of cells are essential for proper cell localization, and it is well-established that cells establish directional migration in responses to gradients of chemicals, rigidity, density of extracellular matrices, and topography of substrates. However, it is unclear whether strain gradients imposed on cells due to tissue growth are sufficient to drive directional cell migration. In this work, we develop a programmable uniaxial cell stretch device coupled with geometrical constraints to create controllable strain gradients on cells. We demonstrate that single rat embryonic fibroblasts (REFs) respond to very small strain gradients. In a gradient level of 4% per mm, 60%-70% of the REFs prefer to migrate towards the lower strain side in both the static and the 0.1 Hz cyclic stretch conditions. We confirm that such responses to strain gradient is distinct from durotaxis or haptotaxis. Moreover, by using the YFP-Paxillin reporter, we discover that the directional migration of the cells is initiated by increasing focal adhesion contact areas and higher rate of protrusion formation in the lower strain side of the cell. Together, in this work we establish strain gradient as a novel cue to regulate directional cell migration and may provide new insights in development and tissue repairs.

category: bioengineering


title: DnoisE: Distance denoising by Entropy. An open-source parallelizable alternative for denoising sequence datasets

abstract: DNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons are generated during amplification and sequencing procedures and constitute one of the major sources of concern for the interpretation of metabarcoding results. Several denoising programs have been implemented to detect and eliminate these errors. However, almost all denoising software currently available has been designed to process non-coding ribosomal sequences, most notably prokaryotic 16S rDNA. The growing number of metabarcoding studies using coding markers such as COI or RuBisCO demands a re-assessment and calibration of denoising algorithms. Here we present DnoisE, the first denoising program designed to detect erroneous reads and merge them with the correct ones using information from the natural variability (entropy) associated to each codon position in coding barcodes. We have developed an open-source software using a modified version of the UNOISE3 algorithm. DnoisE implements different merging procedures as options, and can incorporate codon entropy information either retrieved from the data or supplied by the user. In addition, the algorithm of DnoisE is parallelizable, greatly reducing run times on computer clusters. Our program also allows different input file formats, so it can be readily incorporated into existing metabarcoding pipelines.


title: metaboprep: an R package for pre-analysis data description and processing.

abstract:
MotivationMetabolomics is an increasingly common part of health research and there is need for pre-analytical data processing. Researchers typically need to characterize the data and to exclude errors within the context of the intended analysis. While some pre-processing steps are common, there is currently a lack of standardization and reporting transparency for these procedures.

ResultsHere we introduce metaboprep, a standardized data processing workflow to extract and characterize high quality metabolomics data sets. The package extracts data from pre-formed worksheets, provides summary statistics and enables the user to select samples and metabolites for their analysis based on a set of quality metrics. A report summarizing quality metrics and the influence of available batch variables on the data is generated for the purpose of open disclosure. Where possible, we provide users flexibility in defining their own selection thresholds.

Availability and implementationmetaboprep is an open-source R package available at https://github.com/MRCIEU/metaboprep

Contactd.a.hughes@bristol.ac.uk or laura.corbin@bristol.ac.uk


title: Forward Entrainment: Evidence, Controversies, Constraints, and Mechanisms

abstract: We define forward entrainment as that part of the entrainment process that outlasts the entraining stimulus. In this study, we examine conditions under which one may or may not observe forward entrainment. In part 1, we review and evaluate studies that have observed forward entrainment using a variety of psychophysical methods (detection, discrimination and reaction times), different target stimuli (tones, noise, gaps), different entraining sequences (sinusoidal, rectangular or sawtooth waveforms), a variety of physiological measures (MEG, EEG, ECoG, CSD), in different modalities (auditory and visual), across modalities (audiovisual and auditory-motor), and in different species. In part 2, we review those studies that have failed to observe forward entrainment, with emphasis on evaluating the methodological and stimulus design differences that may clarify the contrasting findings across these two classes of studies. In part 3, we describe those experimental conditions under which we ourselves have failed to observe forward entrainment, and provide new data on use of complex envelope patterns as entraining stimuli, show data on intersubject variability, and provide new findings on psychometric functions that characterize the strength of forward entrainment at different SNRs. In part 4 we theorize on potential mechanisms, describe how neurophysiological and psychophysical studies approach the study of entrainment, and caution against drawing direct causal inferences between the two without compelling evidence beyond correlative measures.


title: Rate-Based Decoding of Images from Multi-Region, High Resolution, Electrode Recordings In the Mouse Visual System

abstract: 1We hypothesize that deep networks are superior to linear decoders at recovering visual stimuli from neural activity. Using high-resolution, multielectrode Neuropixels recordings, we verify this is the case for a simple feed-forward deep neural network having just 7 layers. These results suggest that these feed-forward neural networks and perhaps more complex deep architectures will give superior performance in a visual brain-machine interface.


title: Neurotoxic astrocytic glypican-4 drives APOE4-dependent tau pathology

abstract: The aggregation of tau proteins into insoluble filaments and the spread of these filaments across brain regions are the major drivers of neurodegeneration in tauopathies, including in Alzheimers disease (AD). Apolipoprotein E4 (APOE4), a crucial genetic risk factor for late-onset AD, has been shown to exacerbate tau pathology in mouse models. However, the exact mechanisms through which APOE4 induces tau pathology remains unknown. Here, we report that the astrocyte-secreted protein glypican-4 (GPC-4), which we identify as a novel binding partner of APOE4, drives tau pathology. We discovered that GPC-4 preferentially interacts with APOE4 in comparison to APOE2, considered to be a protective allele to AD, and post-mortem APOE4-carrying AD brains highly express GPC-4 in neurotoxic astrocytes. The astrocyte-secreted GPC-4 induced both tau accumulation and propagation in vitro. CRISPR/dCas9 mediated activation of GPC-4 in a tauopathy mouse model robustly induced tau pathology. Using in vitro Tau FRET-biosensor cells, human iPSCs-derived astrocytes and an in vivo mouse model, we found that APOE4-induced tau pathology was greatly diminished in the absence of GPC-4. We further show that APOE4-mediated surface trafficking of APOE receptor low-density lipoprotein receptor-related protein 1 (LRP1) through GPC-4 can be a gateway to tau spreading. Together, our data comprehensively demonstrate that APOE4-induced tau pathologies are directly mediated by GPC-4.


title: Astrocyte-secreted glypican-4 drives APOE4-dependent tau pathology


title: Global analysis of the specificities and targets of endoribonucleases from E. coli toxin-antitoxin systems

abstract:
Toxin-antitoxin systems are widely distributed genetic modules typically featuring toxins that can inhibit bacterial growth and antitoxins that can reverse inhibition. Although Escherichia coli encodes 11 toxins with known or putative endoribonuclease activity, the target of most of these toxins remain poorly characterized. Using a new RNA-seq pipeline that enables the mapping and quantification of RNA cleavage with single-nucleotide resolution, we characterize the targets and specificities of 9 endoribonuclease toxins from E. coli. We find that these toxins use low-information cleavage motifs to cut a significant proportion of mRNAs in E. coli, but not tRNAs or the rRNAs from mature ribosomes. However, all the toxins, including those that are ribosome-dependent and cleave only translated RNA, inhibit ribosome biogenesis. This inhibition likely results from the cleavage of ribosomal protein transcripts, which disrupts the stoichiometry and biogenesis of new ribosomes and causes the accumulation of aberrant ribosome precursors. Collectively, our results provide a comprehensive, global analysis of endoribonuclease-based toxin-antitoxin systems in E. coli and support the conclusion that, despite their diversity, each disrupts translation and ribosome biogenesis.

ImportanceToxin-antitoxin systems are widespread genetic modules found in almost all bacteria that can regulate their growth and may play prominent roles in phage defense. Escherichia coli encodes 11 TA systems in which the toxin is a known or predicted endoribonuclease. The targets and cleavage specificities of these endoribonucleases have remained largely uncharacerized, precluding an understanding of how each impacts cell growth and an assessment of whether they have distinct or overlapping targets. Using a new and broadly applicable RNA-seq pipeline, we present a global analysis of 9 endoribonulease toxins from E. coli. We find that each uses a relatively low-information cleavage motif to cut a large proportion of mRNAs in E. coli, but not tRNAs or mature rRNAs. Notably, although the precise set of targets varies, each toxin efficiently disrupts ribosome biogenesis, primarily by cleaving the mRNAs of ribosomal proteins. In sum, the analyses presented provide new, comprehensive insights into the cleavage specificities and targets of almost all endoribonuclease toxins in E. coli. Despite different specificities, our work reveals a striking commonality in function as each toxin disrupts ribosome biogenesis and translation.


title: Genomic and functional characterization of Pseudomonas aeruginosa-targeting bacteriophages isolated from hospital wastewater

abstract: Pseudomonas aeruginosa infections can be difficult to treat and new therapeutic approaches are needed. Bacteriophage therapy is a promising alternative to traditional antibiotics, but large numbers of isolated and characterized phages are lacking. We collected 23 genetically and phenotypically diverse P. aeruginosa isolates from people with cystic fibrosis (CF) and clinical infections, and characterized their genetic, phenotypic, and prophage diversity. We then used these isolates to screen and isolate 14 new P. aeruginosa-targeting phages from hospital wastewater. Phages were characterized with genome sequencing, comparative genomics, and lytic activity screening against all 23 bacterial host isolates. For four different phages, we evolved bacterial mutants that were resistant to phage infection. We then used genome sequencing and functional analysis of the resistant mutants to study their mechanisms of phage resistance as well as changes in virulence factor production and antibiotic resistance, which differed from corresponding parent bacterial isolates. Finally, we tested two phages for their ability to kill P. aeruginosa grown in biofilms in vitro, and observed that both phages reduced viable bacteria in biofilms by least one order of magnitude. One of these phages also showed activity against P. aeruginosa biofilms grown on CF airway epithelial cells. Overall, this study demonstrates how systematic genomic and phenotypic characterization can be deployed to develop bacteriophages as precision antibiotics.


title: Functional diversity increases the efficacy of phage combinations

abstract: Phage therapy is a promising alternative to traditional antibiotics for treating bacterial infections. Such phage-based therapeutics typically contain multiple phages, but how the efficacy of phage combinations scales with phage richness, identity and functional traits is unclear. Here, we experimentally tested the efficacy of 827 unique phage combinations ranging in phage richness from 1 to 12 phages. The efficacy of phage combinations increased with phage richness. However, complementarity between functionally diverse phages allowed efficacy to be maximised at lower levels of phage richness in functionally diverse combinations. These findings suggest that phage functional diversity is the key property of effective phage combinations, enabling the design of simple but effective phage therapies that overcome the practical and regulatory hurdles that limit development of more diverse phage therapy cocktails.


title: Legionella pneumophila targets autophagosomes and promotes host autophagy during late infection

abstract:
Autophagy is a fundamental eukaryotic process that mediates clearance of unwanted molecules and facilitates nutrient release. The bacterial pathogen Legionella pneumophila establishes an intracellular niche within phagocytes by manipulating host cellular processes, such as autophagy. Effector proteins translocated by L. pneumophilas Dot/Icm type IV secretion system have been shown to suppress autophagy. However evidence suggests that overall inhibition of autophagy may be detrimental to the bacterium. As autophagy contributes to cellular homeostasis and nutrient acquisition, L. pneumophila may translocate effectors that promote autophagy for these benefits. Here, we show that effector protein Lpg2411 binds phosphatidylinositol-3-phosphate lipids and preferentially binds autophagosomes. Translocated Lpg2411 accumulates late during infection and co-localizes with the autophagy receptor p62 and ubiquitin. Furthermore, autophagy is inhibited to a greater extent in host cells infected with a mutant strain lacking Lpg2411 compared to those infected with wild-type L. pneumophila, indicating that Lpg2411 stimulates autophagy to support the bacteriums intracellular lifestyle.

SummaryLegionella pneumophila translocates several effector proteins that inhibit autophagic processes. In this study, we find that the effector protein Lpg2411 targets autophagosomes during late stages of infection and promotes autophagy.


title: Reconstruction of nitrogenase predecessors suggests origin from maturase-like enzymes

abstract:
The evolution of biological nitrogen fixation, uniquely catalyzed by nitrogenase enzymes, has been one of the most consequential biogeochemical innovations over lifes history. Though understanding the early evolution of nitrogen fixation has been a longstanding goal from molecular, biogeochemical, and planetary perspectives, its origins remain enigmatic. In this study, we reconstructed the evolutionary histories of nitrogenases, as well as homologous maturase proteins that participate in the assembly of the nitrogenase active-site cofactor but are not able to fix nitrogen. We combined phylogenetic and ancestral sequence inference with an analysis of predicted functionally divergent sites between nitrogenases and maturases to infer the nitrogen-fixing capabilities of their shared ancestors. Our results provide phylogenetic constraints to the emergence of nitrogen fixation and are consistent with a model wherein nitrogenases emerged from maturase-like predecessors. Though the precise functional role of such a predecessor protein remains speculative, our results highlight evolutionary contingency as a significant factor shaping the evolution of a biogeochemically essential enzyme.

SIGNIFICANCE STATEMENTThe origin of nitrogenase-catalyzed nitrogen fixation was a transformative event in lifes history, garnering long-term study from molecular, biogeochemical, and planetary perspectives. Reconstruction of ancestral nitrogenases suggests that the protein sequence space capable of yielding a nitrogen-fixing enzyme in the past was likely more constrained than previously thought. Specifically, here we show that nitrogenases likely evolved from ancestors that resemble maturases, homologs that today participate in nitrogenase cofactor assembly, contrary to the commonly accepted view that maturases evolved from a nitrogenase ancestor. We further submit that the molecular architecture that may have been required for nitrogenase origins was unlikely to have been shaped by the same environmental drivers often implicated in the evolution of nitrogen fixation. If this decoupling is found to be a recurring pattern in metabolic origins, then the presented results would undercut the common, systems-focused rationale of using ancient environmental conditions to explain the timing of critical and singular biogeochemical innovations in lifes past.


title: Reconstruction of nitrogenase predecessors suggests origin from maturase-like proteins


title: Early adaptation in a microbial community is dominated by mutualism-enhancing mutations

abstract: Species interactions drive species evolution while evolution shapes these interactions. The resulting eco-evolutionary dynamics, their outcomes and their repeatability depend on how adaptive mutations available to community members affect fitness and ecologically relevant traits. However, the diversity of adaptive mutations available to community members is not well characterized, and we do not know how this diversity is affected by the ecological milieu. Here we use barcode lineage tracking to address this gap in a competitive mutualism between the yeast Saccharomyces cerevisiae and the alga Chlamydomonas reinhardtii. We find that yeast has access to many adaptive mutations with diverse ecological consequences, in particular, those that increase and reduce the yields of both species. The presence of alga does not change which mutations are adaptive in yeast (i.e., there is no fitness trade-off for yeast between growing alone or with alga), but rather shifts selection to favor yeast mutants that increase the yields of both species and make the mutualism stronger. Thus, in the presence of alga, we find that yeast repeatably evolves to become more cooperative, even though cooperativity is not directly favored by natural selection in our system. Our results demonstrate that ecological interactions not only alter the trajectory of evolution but also dictate its repeatability; in particular, weak mutualisms can repeatably evolve to become stronger.


title: Mutualism-enhancing mutations dominate early adaptation in a microbial community


title: Comparison and evaluation of statistical error models for scRNA-seq

abstract: Heterogeneity in single-cell RNA-seq (scRNA-seq) data is driven by multiple sources, including biological variation in cellular state as well as technical variation introduced during experimental processing. Deconvolving these effects is a key challenge for preprocessing workflows. Recent work has demonstrated the importance and utility of count models for scRNA-seq analysis, but there is a lack of consensus on which statistical distributions and parameter settings are appropriate. Here, we analyze 58 scRNA-seq datasets that span a wide range of technologies, systems, and sequencing depths in order to evaluate the performance of different error models. We find that while a Poisson error model appears appropriate for sparse datasets, we observe clear evidence of overdispersion for genes with sufficient sequencing depth in all biological systems, necessitating the use of a negative binomial model. Moreover, we find that the degree of overdispersion varies widely across datasets, systems, and gene abundances, and argues for a data-driven approach for parameter estimation. Based on these analyses, we provide a set of recommendations for modeling variation in scRNA-seq data, particularly when using generalized linear models or likelihood-based approaches for preprocessing and downstream analysis.


title: Long-range single-molecule mapping of chromatin modification in eukaryotes

abstract: The epigenetic modifications of histones are essential markers related to the development and pathogenesis of diseases, including human cancers. Mapping histone modification has emerged as the widely used tool for studying epigenetic regulation. However, existing approaches are limited by fragmentation and short-read sequencing represent the average chromatin status in samples and cannot provide information about the long-range chromatin states. We leveraged the advantage of long read sequencing to develop a method "BIND&MODIFY" for profiling the histone modification of individual DNA fibers. Our approach is based on the recombinant fused protein A-M.EcoGII, which tethers the methyltransferase M.EcoGII to the protein binding sites and locally labels the neighboring DNA regions through artificial methylations. We demonstrated that the aggregated BIND&MODIFY signal matches the bulk-level ChIP-seq and CUT&TAG, verify the single-molecule heterogenous histone modification status, and quantify the correlation between distal elements. This method could be an essential tool in future third-generation sequencing ages.


title: Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples

abstract: Archived formalin-fixed paraffin-embedded (FFPE) samples are the global standard format for preservation of the majority of biopsies in both basic research and translational cancer studies, and profiling chromatin accessibility in the archived FFPE tissues is fundamental to understanding gene regulation. Accurate mapping of chromatin accessibility from FFPE specimens is challenging because of the high degree of DNA damage. Here, we first showed that standard ATAC-seq can be applied to purified FFPE nuclei but yields lower library complexity and a smaller proportion of long DNA fragments. We then present FFPE-ATAC, the first highly sensitive method for decoding chromatin accessibility in FFPE tissues that combines Tn5-mediated transposition and T7 in vitro transcription. The FFPE-ATAC generates high-quality chromatin accessibility profiles with 500 nuclei from a single FFPE tissue section, enables the dissection of chromatin profiles from the regions of interest with the aid of hematoxylin and eosin (H&E) staining, and reveals disease-associated chromatin regulation from the human colorectal cancer FFPE tissue archived for more than 10 years. In summary, the approach allows decoding of the chromatin states that regulate gene expression in archival FFPE tissues, thereby permitting investigators, to better understand epigenetic regulation in cancer and precision medicine.


title: Local CpG density affects the trajectory of age-associated epigenetic changes

abstract: DNA methylation is an epigenetic mark associated with gene repression and genome stability. Its pattern in the genome is disrupted with age and these changes can be used to statistically predict age with epigenetic clocks. Rates of aging inferred from these clocks correlate with human health. However, the molecular mechanisms underpinning age-associated DNA methylation changes are unknown. Local DNA sequence plays a strong role in programming DNA methylation levels at individual loci independently of age, but its influence on age-associated DNA methylation changes is unknown. We analysed longitudinal human DNA methylation trajectories at 345,895 CpGs from 600 individuals aged between 67 and 80 to understand the factors responsible for age-associated epigenetic changes at individual CpGs in the genome. We show that changes in methylation with age are especially apparent at 8,322 low CpG density loci. Using SNP data from the same individuals we demonstrate that DNA methylation trajectories are affected by local sequence polymorphisms at 1,487 loci with low CpG density. More generally, we find that local CpG density is a strong determinant of a CpGs methylation trajectory and that CpGs located in low CpG density regions are particularly prone to change. Overall, our results demonstrate that local DNA sequence influences age-associated DNA methylation changes in humans in vivo. We suggest that this occurs because interactions between CpGs reinforce maintenance of methylation patterns in CpG dense regions.

category: genetics


title: Pharmacokinetic Effects of Combined Exposure to Nicotine and THC via E-Cigarettes in Pregnant Rats

abstract:
Nicotine and cannabis are two of the most commonly consumed licit and illicit drugs during pregnancy, often consumed together via e-cigarettes. Vaping is assumed to be a safer alternative than traditional routes of consumption, yet the potential consequences of prenatal e-cigarette exposure are largely unknown, particularly when these two drugs are co-consumed. In a novel co-exposure model, pregnant Sprague-Dawley rats received nicotine (36 mg/mL), THC (100 mg/mL), the combination, or the vehicle via e-cigarettes daily from gestational days 5-20, mimicking the first and second human trimesters. Maternal blood samples were collected throughout pregnancy to measure drug and metabolite levels, and core body temperatures before and after exposure were also measured. Pregnant dams exposed to combined nicotine and THC had lower plasma nicotine and cotinine levels than those exposed to nicotine alone; similarly, the combined exposure group also had lower plasma THC and THC metabolite (THC-OH and THC-COOH) levels than those exposed to THC alone. Prenatal nicotine exposure gradually decreased basal core body temperatures each day, with chronic exposure, whereas exposure to THC alone decreased temperatures during the individual sessions. Despite these physiological effects, no changes were observed in food or water intake, weight gain, or basic litter outcomes. These data suggest that combined exposure to nicotine and THC elicits both separate and interactive physiological effects of nicotine and THC on pregnant dams. These data and use of this model can help improve education for pregnant mothers about prenatal e-cigarette use and has important implications for public policy.

HIGHLIGHTSO_LIRepeated prenatal nicotine exposure via e-cigarettes gradually decreased temperatures
C_LIO_LIPrenatal THC exposure via e-cigarettes decreased temperatures during intoxication
C_LIO_LICombined prenatal exposure via e-cigarettes altered plasma drug and metabolite levels
C_LIO_LIThis co-exposure model elicits separate and interactive effects of nicotine and THC
C_LI

category: pharmacology and toxicology


title: MuscleNET: Mapping Electromyography to kinematic and dynamic biomechanical variables by machine learning

abstract:
ObjectiveThis paper proposes machine learning models for mapping surface electromyography (sEMG) signals to regression of joint angle, joint velocity, joint acceleration, joint torque, and activation torque.

ApproachThe regression models, collectively known as MuscleNET, take one of four forms: ANN (Forward Artificial Neural Network), RNN (Recurrent Neural Network), CNN (Convolutional Neural Network), and RCNN (Recurrent Convolutional Neural Network). Inspired by conventional biomechanical muscle models, delayed kinematic signals were used along with sEMG signals as the machine learning models input; specifically, the CNN and RCNN were modeled with novel configurations for these input conditions. The models inputs contain either raw or filtered sEMG signals, which allowed evaluation of the filtering capabilities of the models. The models were trained using human experimental data and evaluated with different individual data.

Main resultsResults were compared in terms of regression error (using the root-mean-square) and model computation delay. The results indicate that the RNN (with filtered sEMG signals) and RCNN (with raw sEMG signals) models, both with delayed kinematic data, can extract underlying motor control information (such as joint activation torque or joint angle) from sEMG signals in pick-and-place tasks. The CNNs and RCNNs were able to filter raw sEMG signals.

SignificanceAll forms of MuscleNET were found to map sEMG signals within 2 ms, fast enough for real-time applications such as the control of exoskeletons or active prostheses. The RNN model with filtered sEMG and delayed kinematic signals is particularly appropriate for applications in musculoskeletal simulation and biomechatronic device control.

category: systems biology


title: Unsupervised characterization of dynamic functional connectivity reveals age-associated differences in temporal stability and connectivity states during rest and task

abstract: Understanding brain functions as an outcome of underlying neuro-cognitive network mechanisms in rest and task requires accurate spatiotemporal characterization of the relevant functional brain networks. Recent endeavours of the Neuroimaging community to develop the notion of dynamic functional connectivity is a step in this direction. A key goal is to detect what are the important events in time that delimits how one functional brain network defined by known patterns of correlated brain activity transitions into a "new" network. Such characterization can also lead to more accurate conceptual realization of brain states, thereby, defined in terms of time-resolved correlations. Nonetheless, identifying the canonical temporal window over which dynamic functional connectivity is operational is currently based on an ad-hoc selection of sliding windows that can certainly lead to spurious results. Here, we introduce a data-driven unsupervised approach to characterize the high dimensional dynamic functional connectivity into dynamics of lower dimensional patterns. The whole-brain dynamic functional connectivity states bearing functional significance for task or rest can be explored through the temporal correlations, both short and long range. The present study investigates the stability of such short- and long-range temporal correlations to explore the dynamic network mechanisms across resting state, movie viewing and sensorimotor action tasks requiring varied degrees of attention. As an outcome of applying our methods to the fMRI data of a healthy ageing cohort we could quantify whole-brain temporal dynamics which indicates naturalistic movie watching task is closer to resting state than the sensorimotor task. Our analysis also revealed an overall trend of highest short range temporal network stability in the sensorimotor task, followed by naturalistic movie watching task and resting state that remains similar in both young and old adults. However, the stability of neurocognitive networks in the resting state in young adults is higher than their older counterparts. Thus, healthy ageing related differences in quantification of network stability along task and rest provides a blueprint of how our approach can be used for cohort studies of mental health and neurological disorders.


title: Motion/direction-sensitive thalamic neurons project extensively to the middle layers of primary visual cortex

abstract: The motion/direction-sensitive and location-sensitive neurons are two major functional types in mouse visual thalamus that project to the primary visual cortex (V1). It has been proposed that the motion/direction-sensitive neurons mainly target the superficial layers in V1, in contrast to the location-sensitive neurons which mainly target the middle layers. Here, by imaging calcium activities of motion/direction-sensitive and location-sensitive axons in V1, we find no evidence for these cell-type specific laminar biases at population level. Furthermore, using a novel approach to reconstruct single-axon structures with identified in vivo response types, we show that, at single-axon level, the motion/direction-sensitive axons have middle layer preferences and project more densely to the middle layers than the location-sensitive axons. Overall, our results demonstrate that Motion/direction-sensitive thalamic neurons project extensively to the middle layers of V1, challenging the current view of the thalamocortical organizations in the mouse visual system.


title: Pre-trial predictors of conflict response efficacy in human dorsolateral prefrontal cortex

abstract: The ability to perform motor actions depends, in part, on the brains initial state, that is, the ensemble firing rate pattern prior to the initiation of action. We hypothesized that the same principle would apply to cognitive functions as well. To test this idea, we examined a unique set of single unit data collected in human dorsolateral prefrontal (dlPFC) cortex. Data were collected in a conflict task that interleaves Simon (motor-type) and Eriksen (flanker-type) conflict trials. In dlPFC, variability in pre-trial firing rate predicted the ability to resolve conflict, as inferred from reaction times. Ensemble patterns that predicted faster Simon reaction times overlapped slightly with those predicting Erikson performance, indicating that the two conflict types are associated with near-orthogonal initial states, and suggesting that there is a weak abstract or amodal conflict preparatory state in this region. These codes became fully orthogonalized in the response state. We interpret these results in light of the initial state hypothesis, arguing that the firing patterns in dlPFC immediately preceding the start of a task predispose it for the efficient implementation of cognitive action.


title: Inside Information: Systematic within-node connectivity changes observed across tasks or groups

abstract: Mapping the human connectome and understanding its relationship to brain function holds tremendous clinical potential. The connectome has two fundamental components: the nodes and the connections between them. While much attention has been given to deriving atlases and measuring the connections between nodes, there have been no studies examining the networks within nodes. Here we demonstrate that each node contains significant connectivity information, that varies systematically across task-induced states and subjects, such that measures based on these variations can be used to classify tasks and identify subjects. The results are not specific for any particular atlas but hold across different atlas resolutions. To date, studies examining changes in connectivity have focused on edge changes and assumed there is no useful information within nodes. Our findings illustrate that for typical atlases, within-node changes can be significant and may account for a substantial fraction of the variance currently attributed to edge changes.


title: Cellular toxicity of iHAP1 and DT-061 does not occur through PP2A-B56 targeting

abstract: PP2A is an abundant phosphoprotein phosphatase that acts as a tumor suppressor. For this reason, compounds able to activate PP2A are attractive anticancer agents. The small molecule compounds iHAP1 and DT-061 have recently been reported by Leonard et al. (2020) and Morita et al. (2020) in Cell to selectively stabilize specific PP2A-B56 complexes which mediate cell killing. Here, we show that this is not the case and question key findings in these papers. Through genome wide CRISPR-Cas9 screens, we uncover the biological pathways targeted by these compounds. We find that iHAP1 directly blocks microtubule assembly both in vitro and in vivo and thus acts as a microtubule poison. In contrast, DT-061 disrupts both the Golgi apparatus and the endoplasmic reticulum and we directly visualize DT-061 in cytoplasmic granules that co-localize with Golgi markers. Our work demonstrates that iHAP1 and DT-061 cannot be used for dissecting PP2A-B56 biology.


title: Large-scale deregulation of gene expression by artificial light at night in tadpoles of common toads

abstract: Artificial light at night (ALAN) affects numerous physiological and behavioural mechanisms in various species by potentially disturbing circadian timekeeping systems. Although gene-specific approaches have already shown the deleterious effect of ALAN on the circadian clock, immunity and reproduction, large-scale transcriptomic approaches with ecologically relevant light levels are still lacking to assess the global impact of ALAN on biological processes. Moreover, studies have focused mainly on variations in gene expression during the night in the presence of ALAN but never during the day. In a controlled laboratory experiment, transcriptome sequencing of Bufo bufo tadpoles revealed that ALAN affected gene expression at both night and daytime with a dose-dependent effect and globally induced a downregulation of genes. ALAN effects were detected at very low levels of illuminance (0.1 lux) and affected mainly genes related to the innate immune system and, to a lesser extend to lipid metabolism. These results indicate that a broad range of physiological pathways is impacted at the molecular level by very low levels of ALAN potentially resulting in reduced survival under environmental immune challenges.


title: Sea Surface Temperatures Drive Historical Demography of Deep-Sea Fishes

abstract: Demographic histories are largely understood to be a product of their environment, as populations expand or contract in response to major environmental changes. Deep-pelagic fishes inhabit one of the most temporally and spatially stable habitats on the planet, so they may be resistant to the demographic instability commonly reported in other marine habitats, but their demographic histories are poorly understood. We reconstructed the demographic histories of thirteen species of deep-pelagic fishes using mitochondrial and nuclear DNA sequence data. We uncovered widespread evidence of demographic expansion in our study species, a counterintuitive result bases on the nature of the deep-pelagic. The frequency-based methods detected potential demographic changes in eleven species, while the Extended Bayesian Skyline Plots were more conservative and identified population expansion in five species. The dates of expansion largely coincide with periods of warm sea-surface temperature at the northern and southern boundaries for the ranges these species inhabit. We suggest that this is the result of the pelagic larval phase shared by most deep-pelagic fishes, where the larvae inhabit the upper 200 meters. Changes in sea surface conditions likely alter the suitability of the habitat in a given region for the larval phase, affecting the species range and in turn population size. These results are critical to our understanding of how the deep-pelagic fish community will respond to future climatic changes.


title: Myths and mechanisms: RecBCD and Chi hotspots as determinants of self vs. non-self

abstract: Bacteria face a challenge when DNA enters their cells by transformation, mating, or phage infection. Should they treat this DNA as an invasive foreigner and destroy it, or consider it one of their own and potentially benefit from incorporating new genes or alleles to gain useful functions? It is frequently stated that the short nucleotide sequence Chi (5 GCTGGTGG 3) recognized by RecBCD helicase-nuclease allows Escherichia coli to distinguish self (i.e., E. coli) DNA from non-self (i.e., any other) DNA and to destroy non-self DNA, and that Chi is "over-represented" in the E. coli genome. We show here that these dogmas are incorrect and apparently based on false assumptions. We note Chis wide-spread occurrence and activity in distantly related species. We illustrate multiple, highly non-random features of the genomes of coli and coliphage P1 that account for Chis high frequency and genomic position, leading us to propose that P1 selects for Chis enhancement of recombination, whereas E. coli selects for the preferred codons in Chi. We discuss other, substantiated mechanisms for self vs. non-self determination involving RecBCD and for RecBCDs destruction of DNA that cannot recombine, whether foreign or domestic.


title: Reflective mirror-based line-scan adaptive optics OCT

abstract: Line-scan OCT, incorporated with adaptive optics (AO), offers high resolution, speed and sensitivity for imaging retinal structure and function in vivo. Here, we introduce its implementation with reflective mirror-based afocal telescopes, optimized for imaging light-induced retinal activity (optoretinography) and weak retinal reflections at the cellular scale. A non-planar optical design was followed based on previous recommendations with key differences specific to a line-scan geometry. The three beam paths fundamental to an OCT system - illumination/sample, detection, and reference - were modeled in Zemax optical design software to yield theoretically diffraction-limited performance over a 2.2 deg. field-of-view and 1.5 D vergence range at the eyes pupil. The performance for imaging retinal structure was exemplified by cellular-scale visualization of retinal ganglion cells, macrophages, foveal cones, and rods in human observers. The performance for functional imaging was exemplified by resolving the light-evoked optical changes in foveal cone photoreceptors where the spatial resolution was sufficient for cone spectral classification at an eccentricity 0.3 deg. from the foveal center. This enabled the first in vivo demonstration of reduced S-cone (short-wavelength cone) density in the human foveola, thus far observed only in ex vivo histological preparations. Together, the feasibility for high resolution imaging of retinal structure and function demonstrated here holds significant potential for basic science and translational applications.


title: Multiplexed identification of RAS paralog imbalance as a driver of lung cancer growth

abstract: Oncogenic KRAS mutations occur in approximately 30% of lung adenocarcinoma. Despite several decades of effort, oncogenic KRAS-driven lung cancer remains difficult to treat, and our understanding of the positive and negative regulators of RAS signaling is incomplete. To uncover the functional impact of diverse KRAS-interacting proteins on lung cancer growth in vivo, we used multiplexed somatic CRISPR/Cas9-based genome editing in genetically engineered mouse models with tumor barcoding and high-throughput barcode sequencing. Through a series of CRISPR/Cas9 screens in autochthonous lung tumors, we identified HRAS and NRAS as key suppressors of KRASG12D-driven tumor growth in vivo and confirmed these effects in oncogenic KRAS-driven human lung cancer cell lines. Mechanistically, RAS paralogs interact with oncogenic KRAS, suppress KRAS-KRAS interactions, and reduce downstream ERK signaling. HRAS mutations identified in KRAS-driven human tumors partially abolished this effect. Comparison of the tumor-suppressive effects of HRAS and NRAS in KRAS- and BRAF-driven lung cancer models confirmed that RAS paralogs are specific suppressors of oncogenic KRAS-driven lung cancer in vivo. Our study outlines a technological avenue to uncover positive and negative regulators of oncogenic KRAS-driven cancer in a multiplexed manner in vivo and highlights the role of RAS paralog imbalance in oncogenic KRAS-driven lung cancer.

category: cancer biology


title: Melanopic stimulation does not affect psychophysical threshold sensitivity for luminance flicker

abstract: In addition to the cone photoreceptors the retina contains intrinsically photosensitive retinal ganglion cells (ipRGCs). These cells express the photopigment melanopsin and are known to be involved in reflexive visual functions such as pupil response and photo-entrainment of the circadian rhythm. It is possible that the ipRGCs contribute to conscious visual perception, either by providing an independent signal to the geniculo-striate pathway, or by interacting with and thus modifying signals arising from "classical" retinal ganglion cells that combine and contrast cone input. Here, we tested for the existence of an interaction by asking if a 350% change in melanopsin stimulation alters psychophysical sensitivity for the detection of luminance flicker. In Experiment 1, we tested for a change in the threshold for detecting luminance flicker in three participants after they adapted to backgrounds with different degrees of tonic melanopsin stimulation. In Experiments 2 and 3, this test was repeated, but now for luminance flicker presented on a transient pedestal of melanopsin stimulation. Across the three experiments, no effect of melanopsin stimulation upon threshold flicker sensitivity was found. Our results suggest that even large changes in melanopsin stimulation do not affect near-threshold, cone-mediated visual perception.


title: Sensory attenuation for external events is produced by a competition for attentional resources

abstract: Self-produced stimuli appear attenuated compared to stimuli generated by others. This effect is known as sensory attenuation (Blakemore et al., 1999). Here, we asked whether an attentional prioritization for the tactile modality during a goal-directed hand movement leads to sensory attenuation for sounds. We presented stimuli in a virtual reality setup that allowed to manipulate the time of tactile feedback when pressing a virtual button. We found that a tactile impulse was perceived as more intense in the moment the hand pushed the button (N = 29). In a second experiment (N = 25), participants pushed a button and estimated the intensity of sounds. We found sensory attenuation for sounds only when tactile feedback was provided at the time the movement goal was reached. These data indicate that sensory attenuation for sounds occurs because tactile attention is boosted towards the movement goal, leaving reduced attentional resources for the auditory modality.


title: Motor attention to the tactile modality induces sensory attenuation for sounds


title: Tactile pre-motor attention induces sensory attenuation for sounds


title: Meta-strategy learning in physical problem-solving: the effect of embodied experience

abstract:
Embodied cognition suggests that our bodily experiences broadly shape our cognitive capabilities. We study how embodied experience affects the abstract physical problem-solving strategies people use in a virtual task where embodiment does not affect action capabilities. We compare how groups with different embodied experience - 25 children and 35 adults with congenital limb differences versus 45 children and 40 adults born with two hands - perform this task, and find that while there is no difference in overall competence, the groups use different cognitive strategies to find solutions. People born with limb differences think more before acting, but take fewer attempts to reach solutions. Conversely, development affects the particular actions children use, as well as their persistence with their current strategy. Our findings suggest that while development alters action choices and persistence, differences in embodied experience drive strategic changes in the acquisition of cognitive strategies for balancing acting with thinking.

Statement of RelevanceTheories of embodied cognition suggest our cognitive and perceptual capabilities are shaped by how our bodies constrain our interactions with the world; however, these tasks often study short-term effects or setups where body differences impact task solutions. Here we compare the performance of children and adults with and without congenital limb differences (missing hands/upper limbs) on a virtual physical problem-solving task, where both groups had equal motor capabilities for interacting with the world. Across ages, participants with limb differences solved these tasks as proficiently as those without limb differences, but took fewer attempts to come to solutions, with more time spent thinking between attempts. This suggests that early life differences in embodied experience cause changes in individuals "cognitive strategies" for allocating time between thinking and acting.


title: Lifelong learning of cognitive strategies for physical problem-solving: the effect of embodied experience


title: Therapeutic targeting of SETD2-deficient cancer cells with the small-molecule compound RITA

abstract:
The histone methyltransferase SETD2 and its associated histone mark H3 lysine 36 trimethylation (H3K36me3) are frequently lost in certain cancer types, identifying SETD2 as an important therapeutic target. Here we show that SETD2-deficient cancer cells are profoundly sensitive to the compound RITA, resulting in significant p53 induction and apoptosis. This is further associated with defects in DNA replication, leading to delays in S-phase progression, increased recruitment of replication stress markers, and reduced replication fork progression. RITA sensitivity is linked to the phenol sulphotransferase SULT1A1, which we find to be highly upregulated in cells that lack SETD2. Depletion of SULT1A1 or addition of the phenol sulphotransferase inhibitor DCNP abolishes these phenotypes and suppresses the sensitivity of SETD2-deficient cancer cells, identifying SULT1A1 activity to be critical in mediating the potent cytotoxicity of RITA against SETD2-deficient cells. These findings define a novel therapeutic strategy for targeting the loss of SETD2 in cancer.

Significance StatementThe histone-modifying enzyme SETD2 has emerged as an important tumour suppressor in a number of different cancer types, identifying it as a promising therapeutic target. The concept of synthetic lethality, a genetic interaction in which the simultaneous loss of two genes or pathways that regulate a common essential process renders the cell nonviable, is a valuable tool for killing cancer cells that have known mutations. In this study, we conducted a synthetic lethality screen for compounds that specifically target SETD2-deficient cancer cells. The top hit, a compound called RITA, reduces cell viability and induces cell death only in the context of SETD2 loss, thereby highlighting a potential novel therapeutic strategy for treating SETD2-deficient cancers.


title: Short-term diet intervention alters the small non-coding RNA (sncRNA) landscape of human sperm

abstract: Offspring health outcomes are often linked with epigenetic alterations triggered by maternal nutrition and intrauterine environment. Strong experimental data also link paternal preconception nutrition with pathophysiology in the offspring, but the mechanism(s) routing the effects of paternal exposures remain elusive. Animal experimental models have highlighted small non-coding RNAs (sncRNAs) as potential regulators of paternal effects, though less is known about the existence of similar mechanisms in human sperm. Here, we first characterised the baseline sncRNA landscape of human sperm, and then studied the effects of a 6-week diet intervention on their expression profile. Baseline profiling identified 5tRFs, miRNAs and piRNAs to be the most abundant sncRNA subtypes, primarily expressed from regulatory elements like UTRs, CpG-rich regions and promoters. Expression of a subset of these sncRNAs varied with age, BMI and sperm quality of the donor. Diet intervention enriched in vitamin D and omega-3 fatty acids showed a marked increase of these nutrients in circulation and altered the sperm sncRNA expression. These included 3 tRFs, 15 miRNAs and 112 piRNAs, with gene targets involved in fatty acid metabolism, vitamin D response (LXR/RXR activation, TGF-beta and Wnt signaling), and transposable elements. These findings provide evidence that human sperms are sensitive to alterations in exposures such as diet, and sncRNAs capture the epigenetic imprint of this change. Hence changes to paternal nutrition during preconception may improve sperm quality and offspring health outcomes. To benefit future research, we developed iDad_DB, an open access database of baseline and diet-altered sncRNA in human male germline.


title: Heterogeneous substrate binding in a glutamate transporter homologue

abstract: Integral membrane glutamate transporters couple the concentrative substrate transport to ion gradients. There is a wealth of structural and mechanistic information about this family. Recent studies revealed transport rate heterogeneity in an archaeal homologue GltPh, inconsistent with simple kinetic models, but its structural and mechanistic determinants remain undefined. In a mutant GltPh, which exclusively populates the outward-facing state, we demonstrate the co-existence of at least two sub-states in slow equilibrium binding the substrate with different apparent affinities. Wild-type GltPh shows similar binding properties, and modulation of the sub-state equilibrium correlates with transport rates. Following binding, the low-affinity sub-state of the mutant is transient. Consistently, cryo-EM on samples frozen within seconds after substrate addition reveals the presence of structural classes with perturbed helical packing of the extracellular half of the transport domain in regions adjacent to the binding site. In contrast, an equilibrated structure does not show such classes. The structure at 2.2 [A] resolution details a pattern of waters in the intracellular half of the domain and resolves classes with subtle differences in the substrate-binding site. We hypothesize that the rigid cytoplasmic half of the domain mediates substrate and ion recognition and coupling, while the extracellular labile half sets the affinity and dynamic properties.


title: Lung adenocarcinoma cell-derived exosomal miR-328 promote osteoclastogenesis by targeting Nrp2

abstract: Bone metastasis of lung cancer and detailed mechanisms are still elusive, and the roles of exosomes derived from lung adenocarcinoma cells in this process have attracted much attention. In this study, we found that A549 cell-derived exosomes (A549-Exos) promoted osteogenesis and bone resorption in vitro. Furthermore, A549-Exos target bone in vivo and promoted bone resorption in vivo. Mechanistically, A549-Exosomal miR-328 promoted bone resorption by targeting Nrp2 and A549-ExosmiR-328 Inhibitors inhibited bone resorption in vivo. Thus, A549-Exosomal miR-328 promote osteoclastogenesis by targeting Nrp2 and A549-ExosmiR-328 Inhibitors may serve as a potential nanomedicine for the treatment of bone metastasis.


title: Non-invasive imaging of gene expression and protein secretion dynamics in living mice

abstract: The topology of gene expression and protein localization is a crucial characteristic of life, where the spatiotemporal dynamic of secretory proteins instruct higher order organization, including the orchestration of developmental and adaptive programs. However tools to non-invasively interrogate the fate of secretory proteins in vivo are scarce. Here we introduce a genetic tagging strategy for in vivo imaging of the secretion and expression dynamics of secretory proteins in living animals. Applying this to a prototypical liver-derived secretory protein, we demonstrate that this approach, combined with optical in-vivo imaging, uncovers extrahepatic prothrombin expression in multiple novel anatomical sites (including testes, placenta, brain, kidney, heart and lymphatic system) and in emerging tumors, resulting in significant amounts of tumor-derived prothrombin in the blood with procoagulant properties. Syngeneic cell lines from this mouse model enable unravelling regulatory mechanisms in high resolution, and in a scalable format ex vivo. Beyond discovering new functions of proteins in a targeted manner, this model allows identifying rheostats in the cross-talk between gene expression and availability of a secretory protein. It is also a valuable resource for uncovering novel (tissue-specific) therapeutic vulnerabilities.


title: Non-invasive imaging of gene expression and protein secretion dynamics in living mice uncovers ectopic prothrombin expression as driver of thrombosis in cancer


title: Non-invasive imaging of gene expression and protein secretion dynamics in living mice: identification of ectopic prothrombin expression as driver of thrombosis in cancer


title: Rapid evolution of the functionally conserved gap gene giant in Drosophila

abstract: Developmental processes in multicellular organisms, and the outcomes they produce, are often evolutionarily conserved. Yet phylogenetic conservation of developmental outcomes is not reflected in functional preservation of the genes regulating these processes, a phenomenon referred to as developmental system drift (1, 2). Little is known about the evolutionary forces producing change in the molecular details of regulatory genes and their networks while preserving development outcomes. Here we address this void in knowledge by systematically swapping the Drosophila melanogaster coding and noncoding regions of the essential gap gene, giant, a key regulator of embryonic pattern formation, with orthologous sequences drawn from both closely and distantly related species within the genus. Employing sensitized genetic complementation assays, the loss of a transgenes ability to restore viability occurs across phylogeny at every interspecific level of comparison and includes both coding and noncoding changes. Epistasis is present as well -- both between coding and noncoding sequences and, in a dramatic example of change-of-sign epistasis, between the only two coding substitutions separating two very closely related species. A continuous process of functional divergence hidden under conserved phylotypic developmental outcomes requires reconsideration of the prevailing view that the essential genes in conserved regulatory networks are protected from the driving forces of evolutionary change.


title: A Mouse Model of Brittle Cornea Syndrome caused by mutation in Zfp469.

abstract:
Brittle Cornea Syndrome (BCS) is a rare recessive condition characterised by extreme thinning of the cornea and sclera. BCS results from loss-of-function mutations in the poorly understood genes ZNF469 or PRDM5. In order to determine the function of ZNF469 and to elucidate pathogenic mechanisms, we used genome editing to recapitulate a human ZNF469 BCS mutation in the orthologous mouse gene, Zfp469. Ophthalmic phenotyping showed that homozygous Zfp469 mutation causes significant central and peripheral corneal thinning arising from reduced stromal thickness. Expression of key components of the corneal stroma in primary keratocytes from Zfp469BCS/BCS mice is affected, including decreased Col1a1 and Col1a2 expression. This alters the type I:type V collagen ratio and results in collagen fibrils with smaller diameter and increased fibril density in homozygous mutant corneas, correlating with decreased biomechanical strength in the cornea. Cell-derived matrices generated by primary keratocytes show reduced deposition of type I collagen offering an in vitro model for stromal dysfunction. Work remains to determine whether modulating ZNF469 activity will have therapeutic benefit in BCS or in conditions such as keratoconus where the cornea thins progressively.

Summary statementA mouse model of Brittle Cornea Syndrome was created to elucidate molecular mechanisms underlying pathology of this rare connective tissue disorder in which extremely thin corneas rupture, causing irreversible blindness.


title: Identifying cellular-to-phenotype associations by elucidating hierarchical relationships in high-dimensional cytometry data

abstract: High-throughput single cell technologies hold the promise of discovering novel cellular relationships with disease. However, analytical workflows constructed for these technologies to associate cell proportions with disease often employ unsupervised clustering techniques that overlook the valuable hierarchical structures that have been used to define cell types. We present treekoR, a framework that empirically recapitulates these structures, facilitating multiple quantifications and comparisons of cell type proportions. Our results from twelve case studies reinforce the importance of quantifying proportions relative to parent populations in the analyses of cytometry data -- as failing to do so can lead to missing important biological insights.


title: Cryo-EM structure of alpha-synuclein fibrils amplified by PMCA from PD and MSA patient brains

abstract:
Synucleinopathies are neurodegenerative diseases related to the aggregation of the protein alpha-synuclein (aSyn). Among these diseases, Parkinsons disease (PD) and multiple system atrophy (MSA) are most prevalent. aSyn can readily form different fibrillar polymorphs, if exposed to an air-water interface or by templating with pre-existing fibrils. We here report the structures of three fibrillar polymorphs that were obtained after seeding monomeric aSyn with PD and MSA patients brain homogenates using protein misfolding cyclic amplification (PMCA). Seeding with a control brain homogenate did not produce fibrils, and seeding with other in vitro generated fibrillar polymorphs as a control faithfully produced polymorphs of a different type. The here determined fibril structures from PD and MSA brain tissue represent new folds, which partly resemble that of previously reported in vitro generated fibrils from Y39 phosphorylated aSyn protein. The relevance of these fibrils for synucleinopathies in humans remains to be further investigated.

Impact StatementNeurodegenerative diseases such as Parkinsons disease (PD) and Multiple System Atrophy (MSA) are suspected to be causatively related to the prion-like propagation of aggregates of the protein alpha-synuclein (aSyn). The fibril structures reported here were obtained after seeding from diseased human brain homogenate and differ from all previously published aSyn fibril arrangements. In case these fibrils would turn out to be the long sought causative agents of these diseases, their structures might lead to the development of therapeutic strategies to modify these diseases and to a better understanding of the mechanistic processes that lead to neurodegeneration and spreading of the diseases.


title: Cerebellar Control of a Unitary Head Direction Sense

abstract: Head direction (HD) cells, key neuronal elements in the mammalians navigation system, are hypothesized to act as a continuous attractor network, in which temporal coordination between cell members is maintained under different brain states or external sensory conditions, resembling a unitary neural representation of direction. Whether and how multiple identified HD signals in anatomically separate HD cell structures are part of a single and unique attractor network is currently unknown. By manipulating the cerebellum, we identified pairs of thalamic and retrosplenial HD cells that lose their temporal coordination in the absence of external sensory drive, while the neuronal coordination within each of these brain regions remained intact. Further, we show that distinct cerebellar mechanisms are involved in the stability of direction representation depending on external sensory conditions. These results put forward a new role for the cerebellum in mediating stable and coordinated HD neuronal activity toward a unitary thalamocortical representation of direction.


title: Centriole distal-end proteins CP110 and Cep97 influence cartwheel growth at the proximal-end of centrioles

abstract: Centrioles are composed of a central cartwheel tethered to nine-fold symmetric microtubule (MT) blades. The centriole cartwheel and MTs are thought to grow from opposite ends of these organelles, so it is unclear how they coordinate their assembly. We previously showed that an oscillation of Polo-like kinase 4 (Plk4) helps to initiate and time the growth of the cartwheel at the proximal end. Here, we show that CP110 and Cep97 form a complex close to the distal-end of the centriole MTs whose levels rise and fall as the new centriole MTs grow, entrained by the core Cdk/Cyclin oscillator that drives the nuclear divisions in these embryos. These CP110/Cep97 dynamics, however, do not appear to time the period of centriole MT growth directly. Instead, we find that changing the levels of CP110/Cep97 alters the Plk4 oscillation and the growth of the cartwheel at the proximal end. These findings reveal an unexpected crosstalk between factors normally concentrated at opposite ends of the growing centrioles, which may help to coordinate centriole growth.


title: Centriole distal-end proteins CP110 and Cep97 influence centriole cartwheel growth at the proximal-end


title: Glycocalyx engineering with heparan sulfate mimetics attenuates Wnt activity during adipogenesis to promote glucose uptake and metabolism.

abstract:
Adipose tissue (AT) plays a crucial role in maintaining me tabolic homeostasis by storing lipids and glucose from circulation as intracellular fat. As peripheral tissues like AT become insulin resistant, decompensation of blood glucose levels occurs causing type 2 diabetes (T2D). Currently, glycocalyx modulating as a pharmacological treatment strategy to improve glucose homeostasis in T2D patients is underexplored. Here, we show a novel role for cell surface heparan sulfate (HS) in establishing glucose uptake capacity and metabolic utilization in differentiated adipocytes. Using a combination of chemical and genetic interventions, we identified that HS modulates this metabolic phenotype by attenuating levels of Wnt signaling during adipogenesis. By engineering the glycocalyx of preadipocytes with exogenous synthetic HS mimetics, we were able to enhance glucose clearance capacity after differentiation through modulation of Wnt ligand availability. These findings establish the cellular glycocalyx as a possible new target for therapeutic intervention in T2D patients by enhancing glucose clearance capacity independent of insulin secretion.

SIGNIFICANCEMetabolic disorders associated with the Western-style diet, such as type 2 diabetes, are among the main drivers of mortality in the US and globally, with more than 380 million people currently affected by this disease worldwide. However, treatment options for type 2 diabetes are currently limited to management of caloric uptake and expenditure, with none able to reverse the condition long-term. The ability to reprogram adipose tissues to improve their overall capacity to clear glucose may provide one such opportunity. Here we provide evidence that glycocalyx remodeling in pre-adipocytes with heparan sulfate mimetics will alter their differentiation program by modulating Wnt signaling to produce adipocytes with increased glucose uptake and utilization.


title: RESEPT: tissue architecture inference and visualization from spatially resolved transcriptomics

abstract: Spatially resolved transcriptomics provides a new way to define spatial contexts and understand biological functions in complex diseases. Although some computational frameworks can characterize spatial context via various clustering methods, the detailed spatial architectures and functional zonation often cannot be revealed and localized due to the limited capacities of associating spatial information. We present RESEPT, a deep-learning framework for characterizing and visualizing tissue architecture from spatially resolved transcriptomics. Given inputs as gene expression or RNA velocity, RESEPT learns a three-dimensional embedding with a spatial retained graph neural network from the spatial transcriptomics. The embedding is then visualized by mapping as color channels in an RGB image and segmented with a supervised convolutional neural network model. Based on a benchmark of sixteen 10x Genomics Visium spatial transcriptomics datasets on the human cortex, RESEPT infers and visualizes the tissue architecture accurately. It is noteworthy that, for the in-house AD samples, RESEPT can localize cortex layers and cell types based on a pre-defined region-or cell-type-specific genes and furthermore provide critical insights into the identification of amyloid-beta plaques in Alzheimers disease. Interestingly, in a glioblastoma sample analysis, RESEPT distinguishes tumor-enriched, non-tumor, and regions of neuropil with infiltrating tumor cells in support of clinical and prognostic cancer applications.


title: Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning


title: Non-equilibrium conditions inside rock pores drive fission, maintenance and selection of coacervate protocells

abstract: Key requirements for the first cells on Earth include the ability to compartmentalize and evolve. Compartmentalization spatially localizes biomolecules from a dilute pool and an evolving cell which grows and divides permits mixing and propagation of information to daughter cells. Complex coacervate microdroplets are excellent candidates as primordial cells with the ability to partition and concentrate molecules into their core and support primitive and complex biochemical reactions. However, the evolution of coacervate protocells by fusion, growth and fission has not yet been demonstrated. In this work, a primordial environment initiated the evolution of coacervate-based protocells. Gas bubbles inside heated rock pores perturb the coacervate protocell distribution and drive the growth, fusion, division and selection of coacervate microdroplets. This setting provides a primordial non-equilibrium environment. Our findings describe how common gas bubbles within heated rock pores induce the early evolution processes of coacervate-based protocells, providing a compelling scenario for the evolution of membrane-free coacervate microdroplets on the early Earth.


title: Ovarian cysts and granulosa cell tumors develop after sublethal total body irradiation in mice

abstract:
BackgroundLocalized and total body irradiation are used to treat certain cancers and also used prior to transplantation of stem cells or organs. However, the use of radiation also induces collateral damage to the cells of healthy tissue. Although the acute damage of radiation to oocytes is well known, the long-term effects induced by radiation to stromal cells and their relationship with age are still unclear.

MethodsA total of 206 two-month-old female mice were whole-body exposed to gamma rays at doses of 0, 0.5, 1, 2, or 4 Gy, respectively. The mice were sacrificed at 3.5, 9, 12, or 18 months of age and pathological changes including cysts and tumors were assessed in the ovary and other organs.

ResultsThe overall incidence of visible pathological changes of mice receiving irradiation was 33.7% in the ovary, but much lower in the liver, spleen, lung, thymus, and skin. Among these, the ovarian cyst formation rate was 24.7%, and tumor lesions were 10.2%, respectively, compared to 5% cyst formation and no tumor lesions among control, unirradiated mice. Statistical analysis showed that cyst formation was age, but not dose-dependent, whereas the formation of tumor lesions was dependent on both age and radiation dose. Pathology analysis indicated that most ovarian cysts originated from follicles and both tumor lesions analyzed originated from granulosa cells.

ConclusionOvaries are highly susceptible to the effects of radiation. Long-term damage is increased after total body irradiation in mice, manifested by higher incidences of cyst formation and tumor lesions. The ovarian stromal-derived granulosa cells might play an essential role in these changes.