title: Transcriptomic mapping of the inter-individual variability of cellular stress response activation in primary human hepatocytes

abstract:
Background & AimsOne of the early key events of drug-induced liver injury (DILI) is the activation of adaptive stress responses, a cellular mechanism to overcome stress. Given the diversity of DILI outcomes and lack in understanding of population variability, we mapped the inter-individual variability in stress response activation to improve DILI prediction.

Approach & ResultsHigh-throughput transcriptome analysis of over 8,000 samples was performed in primary human hepatocytes of 50 individuals upon 8 to 24 h exposure to broad concentration ranges of stress inducers: tunicamycin to induce the unfolded protein response (UPR), diethyl maleate for the oxidative stress response, cisplatin for the DNA damage response and TNF for NF-{kappa}B signalling. This allowed investigation of the inter-individual variability in concentration-dependent stress response activation, where the average of benchmark concentrations (BMCs) had a maximum difference of 864, 13, 13 and 259-fold between different hepatocytes for UPR, oxidative stress, DNA damage and NF-{kappa}B signalling-related genes, respectively. Hepatocytes from patients with liver disease resulted in less stress response activation. Using a population mixed-effect framework, the distribution of BMCs and maximum fold change were modelled, allowing simulation of smaller or larger PHH panel sizes. Small panel sizes systematically under-estimated the variance and resulted in low probabilities in estimating the correct variance for the human population. Moreover, estimated toxicodynamic variability factors were up to 2-fold higher than the standard uncertainty factor of 101/2 to account for population variability during risk assessment, exemplifying the need of data-driven variability factors.

ConclusionsOverall, by combining high-throughput transcriptome analysis and population modelling, improved understanding of variability in stress response activation across the human population could be established, thereby contributing towards improved prediction of DILI.

category: pharmacology and toxicology


title: DENR/MCTS1 knockdown modulates repeat-associated non-AUG translation

abstract: Repeat associated non-AUG (RAN) translation of mRNAs containing repeat-expansion mutations produces toxic peptides in neurons of patients suffering from neurodegenerative diseases. Recent findings indicate that RAN translation in diverse model systems is not inhibited by cellular stressors that impair global translation through phosphorylation of the alpha subunit of eIF2, the essential eukaryotic translation initiation factor that brings the initiator tRNA to the 40S ribosome. Using in vitro, cell-based, and Drosophila models, we examined the role of alternative ternary complex factors that may function in place of eIF2, including eIF2A, eIF2D, and DENR/MCTS1. Among these factors, DENR knockdown had the greatest inhibitory effect on RAN translation of expanded GGGGCC and CGG repeat reporters, and its reduction improved survival of Drosophila expressing expanded GGGGCC repeats. Taken together, these data support a role for alternative initiation factors in RAN translation and suggest they may serve as novel therapeutic targets in neurodegenerative disease.

category: neuroscience


title: Rhes protein transits from neuron to neuron and facilitates mutant huntingtin spreading in the brain.

abstract: Rhes (RASD2) is a thyroid hormone-induced gene that regulates striatal motor activity and promotes neurodegeneration in Huntington disease (HD) and tauopathy. Previously, we showed that Rhes moves between cultured striatal neurons and transports the HD protein, polyglutamine-expanded huntingtin (mHTT) via tunneling nanotube (TNT)-like membranous protrusions. However, similar intercellular Rhes transport has not yet been demonstrated in the intact brain. Here, we report that Rhes induces TNT-like protrusions in the striatal medium spiny neurons (MSNs) and transported between dopamine-1 receptor (D1R)-MSNs and D2R-MSNs of intact striatum and organotypic brain slices. Notably, mHTT is robustly transported within the striatum and from the striatum to the cortical areas in the brain, and Rhes deletion diminishes such transport. Moreover, we also found transport of Rhes to the cortical regions following restricted expression in the MSNs of the striatum. Thus, Rhes is a first striatum-enriched protein demonstrated to move and transport mHTT between neurons and brain regions, providing new insights on interneuronal protein transport in the brain.


title: Efficient decoding of large-scale neural population responses with Gaussian-process multiclass regression

abstract: Neural decoding methods provide a powerful tool for quantifying the information content of neural population codes and the limits imposed by correlations in neural activity. However, standard decoding methods are prone to overfitting and scale poorly to high-dimensional settings. Here, we introduce a novel decoding method to overcome these limitations. Our approach, the Gaussian process multi-class decoder (GPMD), is well-suited to decoding a continuous low-dimensional variable from high-dimensional population activity, and provides a platform for assessing the importance of correlations in neural population codes. The GPMD is a multi-nomial logistic regression model with a Gaussian process prior over the decoding weights. The prior includes hyperparameters that govern the smoothness of each neurons decoding weights, allowing automatic pruning of uninformative neurons during inference. We provide a variational inference method for fitting the GPMD to data, which scales to hundreds or thousands of neurons and performs well even in datasets with more neurons than trials. We apply the GPMD to recordings from primary visual cortex in three different species: monkey, ferret, and mouse. Our decoder achieves state-of-the-art accuracy on all three datasets, and substantially outperforms independent Bayesian decoding, showing that knowledge of the correlation structure is essential for optimal decoding in all three species.


title: Highly sensitive genetically-encoded sensors for population and subcellular imaging of cAMP in vivo

abstract: Cyclic adenosine monophosphate (cAMP) integrates information from diverse G protein-coupled receptors, such as neuromodulator receptors, to regulate pivotal biological processes in a cellular- and subcellular-specific manner. However, in vivo cellular-resolution imaging of cAMP dynamics in neurons has not been demonstrated. Here, we screen existing genetically-encoded cAMP sensors, and further develop the best performer to derive three improved variants, called cAMPFIREs. These sensors exhibit up to ten-fold increased sensitivity to cAMP and a corrected, cytosolic distribution. cAMPFIREs are compatible with both ratiometric and fluorescence lifetime imaging, and can detect cAMP dynamics elicited by norepinephrine at physiologically-relevant, nanomolar concentrations. Imaging of cAMPFIREs in awake mice reveals tonic levels of cAMP in cortical neurons that are associated with wakefulness, and are differentially regulated in different subcellular compartments. Furthermore, enforced locomotion elicits neuron-specific, bidirectional cAMP dynamics, in part, mediated by norepinephrine. Finally, cAMPFIREs also function in Drosophila, suggesting that they have broad applicability for studying intracellular signaling in vivo.


title: Methylmalonic acid impairs cell respiration and glutamate uptake in C6 rat glioma cells

abstract: Methylmalonic acidemia is an organic acidemia caused by deficient activity of L-methylmalonyl-CoA mutase or its cofactor cyanocobalamin and it is biochemically characterized by an accumulation of methylmalonic acid (MMA) in tissue and body fluids of patients. The main clinical manifestations of this disease are neurological and observable symptoms during metabolic decompensation are encephalopathy, cerebral atrophy, coma, and seizures, which commonly appear in newborns. This study aimed to investigate the toxic effects of MMA in a glial cell line presenting astrocytic features. Astroglial C6 cells were exposed to MMA (0.1-10mM) for 24 or 48 hours and cell viability, glucose consumption and oxygen consumption rate, as well as glutamate uptake and ATP content were analyzed. The possible preventive effects of bezafibrate were also evaluated. MMA significantly reduced cell viability after 48-hour period and increased glucose consumption during the same period of incubation. Regarding the energy homeostasis, MMA significantly reduced respiratory parameters of cells after 48-hour exposition, indicating that cell metabolism is compromised at resting and reserve capacity state, which might influence the cell capacity to meet energetic demands. Glutamate uptake and ATP content were also compromised after exposition to MMA, which can be influenced energy metabolism impairment, affecting the functionality of the astroglial cells. Our findings suggest that these effects could be involved in the pathophysiology of neurological dysfunction of this disease.


title: Age-related neural dedifferentiation for individual stimuli: An across-participant pattern similarity analysis

abstract: Age-related neural dedifferentiation - reductions in the regional specificity and precision of neural representations - is proposed to compromise the ability of older adults to form sufficiently distinct neural representations to support episodic memory encoding. The computational model that spurred investigations of age-related neural dedifferentiation initially characterized this phenomenon as a reduction in the specificity of neural patterns for individual items or stimuli. Most investigations have focused on reductions in neural differentiation for patterns of neural activity associated with category level information, such as reduced neural selectivity between categories of visual stimuli (e.g., scenes, objects, and faces). Here, I report a novel across-participant pattern similarity analysis method to measure neural distinctiveness for individual stimuli that were presented to participants on a single occasion. Measures of item level pattern similarity during encoding showed a graded positive subsequent memory effect in younger, with no significant subsequent memory effect in older adults. These results suggest that age-related reductions in the distinctiveness of neural patterns for individual stimuli during age differences in memory encoding. Moreover, a measure of category level similarity demonstrated a significant subsequent memory effect associated with item recognition (regardless of an object source memory detail), whereas the effect in older was associated with source memory. These results converge with predictions of computational models of dedifferentiation showing age-related reductions in the distinctiveness of neural patterns across multiple levels of representation.


title: A thalamo-centric neural signature for restructuring negative self-beliefs

abstract: Negative self-beliefs are a core feature of psychopathology. Despite this, we have a limited understanding of the brain mechanisms by which negative self-beliefs are cognitively restructured. Using a novel paradigm, we had participants use Socratic questioning techniques to restructure self-beliefs during ultra-high resolution 7-Tesla functional magnetic resonance imaging (UHF fMRI) scanning. Cognitive restructuring elicited prominent activation in a fronto-striato-thalamic circuit, including the mediodorsal thalamus (MD), a group of deep subcortical nuclei believed to synchronize and integrate prefrontal cortex activity, but which has seldom been directly examined with fMRI due to its small size. Increased activity was also identified in the medial prefrontal cortex (MPFC), a region consistently activated by internally focused mental processing, as well as in lateral prefrontal regions associated with regulating emotional reactivity. Using Dynamic Causal Modelling (DCM), evidence was found to support the MD as having a strong excitatory effect on the activity of regions within the broader network mediating cognitive restructuring. Moreover, the degree to which participants modulated MPFC-to-MD effective connectivity during cognitive restructuring predicted their individual tendency to engage in repetitive negative thinking. Our findings represent a major shift from a cortico-centric framework of cognition and provide important mechanistic insights into how the MD facilitates key processes in cognitive interventions for common psychiatric disorders. In addition to relaying integrative information across basal ganglia and the cortex, we propose a multifaceted role for the MD whose broad excitatory pathways act to increase synchrony between cortical regions to sustain complex mental representations, including the self.


title: Mapping the human corticoreticular pathway with multimodal delineation of the gigantocellular reticular nucleus and high-resolution diffusion tractography

abstract:
The corticoreticular pathway (CRP) is a major motor tract that provides volitional input to the reticular formation motor nuclei and may be an important mediator of motor recovery after central nervous system damage. However, its cortical origins, trajectory and laterality are incompletely understood in humans. This study aimed to map the human CRP and generate an average CRP template in standard MRI space. Following recently established guidelines, we manually delineated the primary reticular formation motor nucleus (gigantocellular reticular nucleus [GRN]) using several group-mean MRI contrasts from the Human Connectome Project (HCP). CRP tractography was then performed with HCP diffusion-weighted MRI data (N=1,065) by selecting diffusion streamlines that reached both the frontal cortex and GRN. Corticospinal tract (CST) tractography was also performed for comparison. Results suggest that the human CRP has widespread origins, which overlap with the CST across most of the motor cortex and include additional exclusive inputs from the medial and anterior prefrontal cortices. The estimated CRP projected through the anterior and posterior limbs of the internal capsule before partially decussating in the midbrain tegmentum and converging bilaterally on the pontomedullary reticular formation. Thus, the CRP trajectory appears to partially overlap the CST, while being more distributed and anteromedial to the CST in the cerebrum before moving posterior to the CST in the brainstem. These findings have important implications for neurophysiologic testing, cortical stimulation and movement recovery after brain lesions. We expect that our GRN and tract maps will also facilitate future CRP research.

HIGHLIGHTSO_LIThe corticoreticular pathway (CRP) is a major tract with poorly known human anatomy
C_LIO_LIWe mapped the human CRP with diffusion tractography led by postmortem & animal data
C_LIO_LIThe CRP appears to originate from most of the motor cortices and further anterior
C_LIO_LIThe estimated CRP had distributed and bilateral projections to the brainstem
C_LIO_LIThese findings have important implications for motor recovery after brain lesions
C_LI


title: LyTS: A Lysosome Localized Complex of TMEM192 and STK11IP

abstract: The degradative and signaling functions of lysosomes are dependent on numerous peripherally associated proteins. Targeting of lysosomes to sites of need is controlled by adaptors that link lysosomes to both dynein and kinesin motors. SKIP is one such adaptor that promotes microtubule plus-end-directed movement through its interaction with Arl8 on the lysosome surface and kinesin-1. Sequence homology between SKIP and STK11IP (also known as LIP1) led us to investigate a potential role for STK11IP at lysosomes. After first establishing that STK11IP localizes to lysosomes, we identified TMEM192, an abundant lysosomal integral membrane protein, as the major binding partner of STK11IP and demonstrated that STK11IP depends on TMEM192 for both its lysosome localization as well as its stability. Depletion studies furthermore support a role for these proteins in the control of lysosome homeostasis. Collectively, these new results define a lysosome localized complex of TMEM192 and STK11IP that we have named LyTS ("lights").

category: cell biology


title: Mechanistic basis for SNX27-Retromer coupling to ESCPE-1 in promoting endosomal cargo recycling.

abstract: Sorting nexin-27 (SNX27)-Retromer is an endosomal sorting complex that orchestrates endosome-to-plasma membrane recycling of hundreds of internalized receptors, channels and transporters, enzymes and adhesion molecules. While SNX27-Retromer is essential for development, subtle functional defects are observed in human disease, most notably neurodegenerative and neurological disorders. Achieving a thorough mechanistic dissection of SNX27-Retromer is central to understanding endosomal sorting in health and disease. Here we combine biochemical, structural and cellular analyses to establish the mechanistic basis through which SNX27-Retromer couples to the membrane tubulating ESCPE-1 complex (Endosomal SNX-BAR sorting complex for promoting exit 1). We show that a conserved surface in the FERM (4.1/ezrin/radixin/moesin) domain of SNX27 directly binds acidic-Asp-Leu-Phe (aDLF) motifs in the disordered amino-termini of the SNX1 and SNX2 subunits of ESCPE-1. This interaction hands-over SNX27-Retromer captured integral membrane proteins into ESCPE-1 tubular profiles to promote their cell surface recycling. Through phylogenetic analysis, we reveal that SNX27:Retromer:ESCPE-1 assembly evolved in a stepwise manner during the early evolution of metazoans, which reflects the increasing complexity of endosomal sorting from the ancestral opisthokont to modern animals.


title: Interorganelle lipid flux revealed by enzymatic mass tagging in vivo

abstract: The distinct activities of cellular organelles are dependent on the proper function of their membranes. Coordinated membrane biogenesis of the different organelles necessitates interorganelle transport of lipids from their site of synthesis to their destination membranes. Several proteins and trafficking pathways have been proposed to participate in lipid distribution, but despite the basic importance of this process, in vivo evidence linking the absence of putative transport pathways to specific transport defects remains scarce. An obvious reason for this scarcity is the near absence of in vivo lipid trafficking assays. Here we introduce a versatile method named METALIC (Mass tagging-Enabled TrAcking of Lipids In Cells) to track interorganelle lipid flux inside living cells. In this strategy, two enzymes, one directed to a "donor" and the other to an "acceptor" organelle, add two distinct mass tags to lipids. Mass spectrometry-based detection of lipids bearing the two mass tags is then used as a proxy for lipid exchange between the two organelles. By applying this approach to ER and mitochondria, we show that the ERMES and Vps13-Mcp1 complexes have lipid transport activity in vivo, and unravel their relative contributions to ER-mitochondria lipid exchange.


title: Architecture and evolution of the cis-regulatory system of the echinoderm kirrelL gene

abstract: The gene regulatory network (GRN) that underlies echinoderm skeletogenesis is a prominent model of GRN architecture and evolution. KirrelL is an essential downstream effector gene in this network and encodes an Ig-superfamily protein required for the fusion of skeletogenic cells and the formation of the skeleton. In this study, we dissected the transcriptional control region of the kirrelL gene of the purple sea urchin, Strongylocentrotus purpuratus. Using plasmid- and BAC-based transgenic reporter assays, we identified key cis-regulatory elements (CREs) and transcription factor inputs that regulate Sp-kirrelL, including direct, positive inputs from two key transcription factors in the skeletogenic GRN, Alx1 and Ets1. We next identified kirrelL cis-regulatory regions from seven other echinoderm species that together represent all classes within the phylum. By introducing these heterologous regulatory regions into developing sea urchin embryos we provide evidence of their remarkable conservation across ~500 million years of evolution. We dissected in detail the kirrelL regulatory region of the sea star, Patiria miniata, and demonstrated that it also receives direct inputs from Alx1 and Ets1. Our findings identify kirrelL as a component of the ancestral echinoderm skeletogenic GRN. They support the view that GRN sub-circuits, including specific transcription factor-CRE interactions, can remain stable over vast periods of evolutionary history. Lastly, our analysis of kirrelL establishes direct linkages between a developmental GRN and an effector gene that controls a key morphogenetic cell behavior, cell-cell fusion, providing a paradigm for extending the explanatory power of GRNs.

category: developmental biology


title: Intervene or wait? Modelling the timing of intervention in conservation conflicts adaptive management under uncertainty.

abstract: The timing of biodiversity managers interventions can be critical to the success of conservation, especially in situations of conflict between conservation objectives and human livelihood, i.e., conservation conflicts. Given the uncertainty associated with complex social-ecological systems and the potentially irreversible consequences of delayed action for biodiversity and livelihoods, managers tend to simply intervene as soon as possible by precaution. However, refraining from intervening when the situation allows it can be beneficial, notably by saving critical management resources. Here, we introduce a strategy for managers to decide, based on monitoring, whether intervention is required or if waiting is possible. This study evaluates the performance of this waiting strategy compared to a strategy of unconditional intervention at every opportunity. We built an individual-based model of conservation conflict between a manager aiming to conserve an animal population and farmers aiming to maximize yield by protecting their crop from wildlife damage. We then simulated a budget-constrained adaptive management over time applying each strategy, while accounting for uncertainty around population dynamics and around decision-making of managers and farmers. Our results showed that when the decision for the manager to intervene was based on a prediction of population size trajectory, the waiting strategy performed at least as well as unconditional intervention while also allowing managers to save resources by avoiding unnecessary interventions. Under difficult budgetary constraints on managers, this waiting strategy ensured as high yields as unconditional intervention while significantly improving conservation outcomes by compensating managers lack of resources with the benefits accrued over waiting periods. This suggests that waiting strategies are worth considering in conservation conflicts, as they can facilitate equitable management with a more efficient use of management resources, which are often limiting in biodiversity conservation.

category: ecology


title: Intervene or wait? A model evaluating the timing of intervention in conservation conflicts adaptive management under uncertainty.


title: Exploring dimensions of biodiversity in Japanese ferns

abstract:
PremiseBiodiversity is often only measured with species richness. However, this ignores evolutionary history and is not sufficient for making conservation decisions. Here, we characterize multiple facets and drivers of biodiversity to understand how these relate to bioregions and conservation status in the ferns of Japan.

MethodsWe compiled a community dataset of 1,239 20 km x 20 km grid-cells including 672 taxa based on > 300,000 specimen records. We combined this with a phylogeny and functional traits to analyze taxonomic, phylogenetic, and functional diversity, and modeled biodiversity metrics in response to environmental factors and reproductive mode. Hierarchical clustering was used to delimit bioregions. Conservation status and threats were assessed by comparing the overlap of significantly diverse grid-cells with conservation zones and range maps of native Japanese deer.

ResultsTaxonomic richness was highest at mid-latitudes. Phylogenetic and functional diversity and phylogenetic endemism were highest in small southern islands. Relative phylogenetic and functional diversity were high at high and low latitudes, and low at mid-latitudes. Grid-cells were grouped into three (phylogenetic) or four (taxonomic) major bioregions. Temperature and apomixis were identified as drivers of biodiversity patterns. Conservation status was generally high for grid-cells with significantly high biodiversity, but the threat due to herbivory by deer was greater for taxonomic richness than other metrics.

ConclusionsOur integrative approach reveals previously undetected patterns and drivers of biodiversity in the ferns of Japan. Future conservation efforts should recognize that threats can vary by biodiversity metric and consider multiple multiple metrics when establishing conservation priorities.

category: evolutionary biology


title: Spatial phylogenetics of Japanese ferns: Patterns, processes, and implications for conservation


title: The Macromolecular MR Spectrum in Healthy Aging

abstract:
PurposeMobile macromolecules (MMs) from amino acids, cytosolic proteins and mobile lipids contribute a significant spectral background underlying the metabolite signals in the MR spectrum. A recent consensus recommends that MM contributions should be removed or included in modeling basis sets for determination of metabolite concentrations and/or metabolite ratios. The purpose of this study was to acquire the MM spectrum from healthy participants at a range of ages, and to investigate changes in the signals with age and sex groups.

MethodsInversion time (TI) series were acquired to determine an optimal inversion time to null the metabolite signals. Experiments were carried out using a single adiabatic hyperbolic-secant inversion pulse. After the preliminary experiment, 102 volunteers (49M/53F) between 20 and 69 years were recruited for in vivo data acquisition in the centrum semiovale (CSO) and posterior cingulate cortex (PCC). The protocol consisted of a T1-weighted MPRAGE for structural images, followed by PRESS localization using a voxel size of 30 x 26 x 26 mm3 with pre-inversion (TR/TI 2000/600 ms) and CHESS water suppression. Metabolite-nulled spectra were modeled using a reduced basis set (NAA, Cr, Cho, Glu) and a flexible spline baseline (0.1 ppm knot spacing) followed by subtraction of the modeled metabolite signals to yield a  clean MM spectrum, using the Osprey software. Pearsons correlation coefficient was calculated between integrals and age for the 14 MM signals between 0.9-4.2 ppm. One-way ANOVA was performed to determine differences between age groups. An independent t-test was carried out to determine differences between sexes. Relationships between brain tissues with age and sex groups were also measured.

ResultsMM spectra were successfully acquired in 99 (CSO) and 96 (PCC) of 102 subjects. No significant correlations were seen between age and MM integrals. One-way ANOVA also suggested no age-group differences for any MM peak (all p > 0.004). No differences were observed between sex groups. The voxels were segmented as 80 {+/-} 4% white matter, 18 {+/-} 4% gray matter, and 2 {+/-} 1% CSF for CSO and 28 {+/-} 4% white matter, 61 {+/-} 4% gray matter and 11 {+/-} 1% CSF for PCC. WM and GM showed a significant (p < 0.05) negative linear association with age in the WM-predominant CSO (R = -0.29) and GM-predominant PCC regions (R = -0.57) respectively while CSF increased significantly with age in both regions.

ConclusionOur findings indicate that the MM spectrum is stable across a large age range and between sexes, suggesting a pre-defined MM basis function can be used for linear combination modeling of metabolite data from different age and sex groups.

HighlightsO_LIA large publicly available MM-aging dataset is presented.
C_LIO_LIMacromolecule signals do not change with age between 20 and 70.
C_LIO_LIThere is no sex difference for macromolecule integrals.
C_LI

category: bioengineering


title: SNR-efficient distortion-free diffusion relaxometry imaging using ACcelerated Echo-train shifted EPTI (ACE-EPTI)

abstract:
PurposeTo develop an efficient acquisition technique for distortion-free diffusion MRI and diffusion-relaxometry.

MethodsA new ACcelerated Echo-train shifted Echo-Planar Time-resolved Imaging (ACE-EPTI) technique is developed to achieve high-SNR, distortion- and blurring-free diffusion and diffusion-relaxometry imaging. ACE-EPTI employs a newly designed variable density spatiotemporal encoding with self-navigation capability, that allows submillimeter in-plane resolution using only 3-shot. Moreover, an echo-train-shifted acquisition is developed to achieve minimal TE, together with an SNR-optimal readout length, leading to ~30% improvement in SNR efficiency over single-shot EPI. To recover the highly accelerated data with high image quality, a tailored subspace image reconstruction framework is developed, that corrects for odd/even-echo phase difference, shot-to-shot phase variation, and the B0 field changes due to field drift and eddy currents across different dynamics. After the phase-corrected subspace reconstruction, artifacts-free high-SNR diffusion images at multiple TEs are obtained with varying T2* weighting.

ResultsSimulation, phantom and in-vivo experiments were performed, which validated the 3-shot spatiotemporal encoding provides accurate reconstruction at submillimeter resolution. The use of echo-train shifting and optimized readout length improves the SNR-efficiency by 27-36% over single-shot EPI. The reconstructed multi-TE diffusion images were demonstrated to be free from distortion (susceptibility and eddy currents) and phase/field variation induced artifacts. These improvements of ACE-EPTI enable improved diffusion tensor imaging and rich multi-TE information for diffusion-relaxometry analysis.

ConclusionACE-EPTI was demonstrated to be an efficient and powerful technique for high-resolution diffusion imaging and diffusion-relaxometry, which provides high SNR, distortion- and blurring-free, and time-resolved multi-echo images by a fast 3-shot acquisition.


title: Context-Dependent Flux Coupling via Conserved Small-Molecule Regulatory Structures

abstract: Small-molecule regulation modulates enzyme activity and is widespread in metabolic networks. However, the organization of small-molecule regulatory networks and its generalized role is not well understood. We analyze the structure of the genome-wide Escherichia coli small-molecule regulatory network (SMRN) to reveal that it optimizes controllability in the metabolic network. This is achieved by conserved, highly overabundant incoherent feedforward loops. Using multi-omics data, we characterize loop examples in central carbon metabolism. These use signals from hypothesized flux-sensing metabolites phosphoenolpyruvate, -ketoglutarate, citrate, and malate to distinguish between glycolysis, gluconeogenesis, and glyoxylate shunt activity to differentially couple fluxes across these major modes of metabolism. Our results suggest that coupling of fluxes by direct modulation of enzyme activity is an emergent property of the SMRN that depends heavily on both regulatory structure and metabolic context via the metabolome, and further that flux sensing and coupling may be a global property of the metabolic network.


title: Benchmarking Computational Integration Methods for Spatial Transcriptomics Data

abstract: The increasing popularity of spatial transcriptomics has allowed researchers to analyze transcriptome data in its tissue samples spatial context. Various methods have been developed for detecting SV (spatially variable) genes, with distinct spatial expression patterns. However, the accuracy of using these SV genes in clustering has not been thoroughly studied. On the other hand, in single cell resolution sequencing data without spatial context, clustering analysis is usually done on highly variable (HV) genes. Here we investigate if integrating SV genes and HV genes from spatial transcriptomics data can improve clustering performance beyond using SV genes alone. We examined three methods that detect SV genes, including Giotto, spatialDE, and SPARK, and evaluated six methods that integrate different features measured from the same samples including MOFA+, scVI, Seurat v4, CIMLR, SNF, and the straightforward concatenation approach. We applied these methods on 19 real datasets from three different spatial transcriptomics technologies (merFISH, SeqFISH+, and Visium) as well as 20 simulated datasets of varying spatial expression conditions. Our evaluations show that MOFA+ and simple concatenation have good performances in general, despite the variations among datasets and spatial transcriptomics platforms. This work shows that integrating highly variable and spatially variable genes in the spatial transcriptomics data can improve clustering beyond using spatially variable genes only. It also provides practical guides on the choices of computational methods to accomplish this goal.

category: bioinformatics


title: The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation

abstract:
MotivationPangenomes provide novel insights for population and quantitative genetics, genomics, and breeding not available from studying a single reference genome. Instead, a species is better represented by a pangenome or collection of genomes. Unfortunately, managing and using pangenomes for genomically diverse species is computationally and practically challenging. We developed a trellis graph representation anchored to the reference genome that represents most pangenomes well and can be used to impute complete genomes from low density sequence or variant data.

ResultsThe Practical Haplotype Graph (PHG) is a pangenome pipeline, database (PostGRES & SQLite), data model (Java, Kotlin, or R), and Breeding API (BrAPI) web service. The PHG has already been able to accurately represent diversity in four major crops including maize, one of the most genomically diverse species, with up to 1000-fold data compression. Using simulated data, we show that, at even 0.1X coverage, with appropriate reads and sequence alignment, imputation results in extremely accurate haplotype reconstruction. The PHG is a platform and environment for the understanding and application of genomic diversity.

AvailabilityAll resources listed here are freely available. The PHG Docker used to generate the simulation results is https://hub.docker.com/ as maizegenetics/phg:0.0.27. PHG source code is at https://bitbucket.org/bucklerlab/practicalhaplotypegraph/src/master/. The code used for the analysis of simulated data is at https://bitbucket.org/bucklerlab/phg-manuscript/src/master/. The PHG database of NAM parent haplotypes is in the CyVerse data store (https://de.cyverse.org/de/) and named /iplant/home/shared/panzea/panGenome/PHG_db_maize/phg_v5Assemblies_20200608.db.

Contactpjb39@cornell.edu


title: Whole-tissue deconvolution and scRNAseq analysis identify altered endometrial cellular compositions and functionality associated with endometriosis

abstract:
The uterine lining (endometrium) exhibits a pro-inflammatory phenotype in women with endometriosis, resulting in pain, infertility, and poor pregnancy outcomes. The full complement of cell types contributing to this phenotype has yet to be identified, as most studies have focused on bulk tissue or select cell populations. Herein, through integrating whole-tissue deconvolution and single cell RNAseq, we comprehensively characterized immune and nonimmune cell types in endometrium of women with or without disease and their dynamic changes across the menstrual cycle. We designed metrics to evaluate specificity of deconvolution signatures that resulted in single cell identification of 13 novel signatures for immune cell subtypes in healthy endometrium. Guided by statistical metrics, we identified contributions of endometrial epithelial, endothelial, plasmacytoid dendritic cells, classical dendritic cells, monocytes, macrophages, and granulocytes to the endometrial pro-inflammatory phenotype, underscoring roles for nonimmune as well as immune cells to the dysfunctionality of this tissue.

Teaser SentenceCell type deconvolution and single cell RNAseq analysis identify altered endometrial cellular compositions in women with endometriosis


title: dsMTL - a computational framework for privacy-preserving, distributed multi-task machine learning

abstract: Multitask learning allows the simultaneous learning of multiple  communicating algorithms. It is increasingly adopted for biomedical applications, such as the modeling of disease progression. As data protection regulations limit data sharing for such analyses, an implementation of multitask learning on geographically distributed data sources would be highly desirable. Here, we describe the development of dsMTL, a computational framework for privacy-preserving, distributed multi-task machine learning that includes three supervised and one unsupervised algorithms. dsMTL is implemented as a library for the R programming language and builds on the DataSHIELD platform that supports the federated analysis of sensitive individual-level data. We provide a comparative evaluation of dsMTL for the identification of biological signatures in distributed datasets using two case studies, and evaluate the computational performance of the supervised and unsupervised algorithms. dsMTL provides an easy- to-use framework for privacy-preserving, federated analysis of geographically distributed datasets, and has several application areas, including comorbidity modeling and translational research focused on the simultaneous prediction of different outcomes across datasets. dsMTL is available at https://github.com/transbioZI/dsMTLBase (server-side package) and https://github.com/transbioZI/dsMTLClient (client-side package).


title: Redesigning the Eterna100 for the Vienna 2 folding engine

abstract: The rational design of RNA is becoming important for rapidly developing technologies in medicine and biochemistry. Recent work has led to the development of several RNA secondary structure design algorithms and corresponding benchmarks to evaluate their performance. However, the performance of these algorithms is linked to the nature of the underlying algorithms for predicting secondary structure from sequences. Here, we show that an online community of RNA design experts is capable of modifying an existing RNA secondary structure design benchmark (Eterna100) with minimal alterations to address changes in the folding engine used (Vienna 1.8 updated to Vienna 2.4). We tested this new Eterna100-V2 benchmark with five RNA design algorithms, and found that neural network-based methods exhibited reduced performance in the folding engine they were evaluated on in their respective papers. We investigated this discrepancy, and determined that structural features, previously classified as difficult, may be dependent on parameters inherent to the RNA energy function itself. These findings suggest that for optimal performance, future algorithms should focus on finding strategies capable of solving RNA secondary structure design benchmarks independently of the free energy benchmark used. Eterna100-V1 and Eterna100-V2 benchmarks and example solutions are freely available at https://github.com/eternagame/eterna100-benchmarking.


title: Tensor-decomposition--based unsupervised feature extraction in single-cell multiomics data analysis

abstract: Analysis of single-cell multiomics datasets is a novel topic and is considerably challenging because such datasets contain a large number of features with numerous missing values. In this study, we implemented a recently proposed tensor-decomposition (TD)-based unsupervised feature extraction (FE) technique to address this difficult problem. The technique can successfully integrate single-cell multiomics data composed of gene expression, DNA methylation, and accessibility. Although the last two have large dimensions, as many as ten million, containing only a few percentages of non-zero values, TD-based unsupervised FE can integrate three omics datasets without filling missing values. Together with UMAP, which is used frequently when embedding single-cell measurements into two-dimensional space, TD-based unsupervised FE can produce two-dimensional embedding coincident with classification when integrating single-cell omics datasets. Genes selected based on TD-based unsupervised FE were also significantly related to reasonable biological roles.


title: Gene function prediction in five model eukaryotes based on gene relative location through machine learning

abstract:
MotiviationThe function of most genes is unknown. The best results in gene function prediction are obtained with machine learning-based methods that combine multiple data sources, typically sequence derived features, protein structure and interaction data. Even though there is ample evidence showing that a genes function is not independent of its location, the few available examples of gene function prediction based on gene location relay on sequence identity between genes of different organisms and are thus subjected to the limitations of the relationship between sequence and function.

ResultsHere we predict thousands of gene functions in five eukaryotes (Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus and Homo sapiens) using machine learning models trained with features derived from the location of genes in the genomes to which they belong. To the best of our knowledge this is the first work in which gene function prediction is successfully achieved in eukaryotic genomes using predictive features derived exclusively from the relative location of the genes.

Contactfpazos@iibce.edu.uy

Supplementary informationhttp://gfpml.bnd.edu.uy


title: An Inter-strand Loop Extrusion Model

abstract: Loop extrusion convincingly describes how certain Structural Maintenance of Chromosome (SMC) proteins mediate the formation of large DNA loops. Yet, most of the existing computational models cannot reconcile recent in vitro observations showing that condensins can traverse each other, bypass large roadblocks and perform steps longer than its own size. To fill this gap, we propose a three-dimensional (3D) "trans-grabbing" model for loop extrusion which not only reproduces the experimental features of loop extrusion by one SMC complex, but also predicts the formation of so-called "Z-loops" via the interaction of two or more SMCs extruding along the same DNA substrate. By performing Molecular Dynamics simulations of this model we discover that the experimentally observed asymmetry in the different types of Z-loops is a natural consequence of the DNA tethering in vitro. Intriguingly, our model predicts this bias to disappear in absence of tethering and a third type of Z-loop, which has not yet been identified in experiments, to appear. Our model naturally explains road-block bypassing and the appearance of steps larger than the SMC size as a consequence of non-contiguous DNA grabbing. Finally, it is the first to our knowledge to address how Z-loops and bypassing might occur in a way that is broadly consistent with existing cis-only 1D loop extrusion models.

category: biophysics


title: Three-Dimensional Loop Extrusion


title: Stereo-specific Lasofoxifene Derivatives Reveal the Interplay between Estrogen Receptor Alpha Stability and Antagonistic Activity in ESR1 Mutant Breast Cancer Cells

abstract:
Chemical manipulation of estrogen receptor alpha ligand binding domain structural mobility tunes receptor lifetime and influences breast cancer therapeutic activities. Selective estrogen receptor modulators (SERMs) extend ER cellular lifetime, accumulation, and are antagonists in the breast and agonists in the uterine epithelium and/or in bone. Selective estrogen receptor degraders (SERDs) reduce ER cellular lifetime/accumulation and are pure antagonists. Activating somatic ESR1 mutations Y537S and D538G enable resistance to first-line endocrine therapies. SERDs have shown significant activities in ESR1 mutant setting while few SERMs have been studied. To understand whether chemical manipulation of ER cellular lifetime and accumulation influences antagonistic activity, we synthesized a series of methylpyrollidine lasofoxifene derivatives that maintained the drugs antagonistic activities while uniquely tuning ER cellular accumulation. These molecules were examined alongside a panel of antiestrogens in live cell assays of ER cellular accumulation, lifetime, SUMOylation, and transcriptional antagonism. High-resolution x-ray crystal structures of WT and Y537S ER ligand binding domain in complex with the methylated lasofoxifene derivatives, SERMs, and SERDs show that molecules that favor a highly buried helix 12 conformation achieve the greatest transcriptional suppression activities. Together these results show that chemical reduction of ER cellular lifetime does not necessarily correlate with transcriptional antagonism in ESR1 mutated breast cancer cells. Importantly, our approach shows how minor chemical additions modulate receptor cellular lifetime while maintaining other activities to achieve desired SERM or SERD profiles.

SIGNIFICANCEThis study shows that antiestrogens that enforce a wild-type-like antagonist conformation demonstrate improved therapeutic activities in hormone-resistant breast cancer cells harboring Y537S and D538G ESR1.

category: cancer biology


title: Aberrant accumulation of NIK promotes tumorigenicity by dysregulating post-translational modifications in breast cancer

abstract: Post-translational modifications and mRNA translation are frequently altered in human cancers. However, investigations to understand their roles in the cancer progression mechanism remain insufficient. In this research, we explored protein levels altered by translational or post-translational regulation by analyzing transcriptome and western blotting data of the highly malignant breast cancer cell lines. From these analyses, NIK was found to be upregulated at the protein level to predominantly activate the non-canonical NF-{kappa}B pathway in a breast cancer cell line. Furthermore, the increase in NIK protein production was attributed to the dysregulation of ubiquitin-proteasome system caused by a decrease in the translation of cIAP1. NIK upregulation contributed to tumorigenicity by regulating the expression of inflammatory response-related genes. Collectively, our study suggests that NIK is post-translationally modified and has the potential to be a therapeutic target and diagnostic marker for breast cancer.


title: The mechanical regulation of RNA binding protein hnRNPC in the failing heart

abstract: Cardiac pathologies are characterized by intense remodeling of the extracellular matrix (ECM) that eventually leads to heart failure. Cardiomyocytes respond to the ensuing biomechanical stress by re-expressing fetal contractile proteins via transcriptional and post-transcriptional processes, like alternative splicing (AS). Here, we demonstrate that the heterogeneous nuclear ribonucleoprotein C (hnRNPC) is upregulated and relocates to the sarcomeric Z-disk upon ECM pathological remodeling. We show that this is an active site of localized translation, where the ribonucleoprotein associates to the translation machinery. Alterations in hnRNPC expression and localization can be mechanically determined and affect the AS of numerous mRNAs involved in mechanotransduction and cardiovascular diseases, like Hippo pathway effector YAP1. We propose that cardiac ECM remodeling serves as a switch in RNA metabolism by impacting an associated regulatory protein of the spliceosome apparatus. These findings offer new insights on the mechanism of mRNAs homeostasis mechanoregulation in pathological conditions.

category: pathology


title: A Multi-Omics Human Liver Organoid Screening Platform for DILI Risk Prediction

abstract:
Background and AimsDrug-induced liver injury (DILI) is a prominent failure mode in drug development resulting in clinical trial failures and post-approval withdrawal. Improved in vitro models for DILI risk prediction that can model diverse genetics are needed to improve safety and reduce high attrition rates in drug development. In this study, we evaluated the utility of human liver organoids (HLOs) for high-throughput DILI risk prediction and in an organ-on-chip system. The recent clinical failure of inarigivir soproxil due to DILI underscores the need for improved models.

MethodsHLOs were adapted for high-throughput drug screening in dispersed-cell 384-well format and a collection of DILI-associated drugs were screened. HLOs were also adapted to a liver-chip system to investigate enhanced in vivo-like function. Both platforms were benchmarked for their ability to predict DILI using combined biochemical assays, microscopy-based morphological profiling, and transcriptomics.

ResultsDispersed HLOs retained DILI predictive capacity of intact HLOs and are amenable to high-throughput screening allowing for measurable IC50 values for cytotoxicity. Distinct morphological differences were observed in cells treated with drugs exerting differing mechanisms of action. HLOs on chips were shown to increase albumin production, CYP450 expression and also release ALT/AST when treated with known DILI drugs. Importantly, HLO liver chips were able to predict hepatotoxicity of tenofovir-inarigivir and showed steatosis and mitochondrial perturbation via phenotypic and transcriptomic analysis.

ConclusionsThe high throughput and liver-on-chip system exhibit enhanced in vivo-like function and demonstrate the utility of the platforms in early and late-stage drug development. Tenofovir-inarigivr associated hepatotoxicity was observed and highly correlates with the clinical manifestation of DILI.


title: Neurosecretory protein GL-induced fat accumulation is accompanied by repressing the immune-inflammatory response in the adipose tissue of mice

abstract: We have recently identified neurosecretory protein GL (NPGL), a small secretory protein expressed in the vertebrate hypothalamus, as an orexigenic factor with remarkable fat accumulation by overexpression of the NPGL precursor gene (Npgl) for two months. In the present study, we analyzed the effects of short-term Npgl overexpression for 18 days as the early stage of obesity to address the mechanisms underlying obese-like phenotype. Similar to previous studies, short-term Npgl overexpression stimulated food intake and fat accumulation in the white adipose tissues (WAT), whereas the masses of the brown adipose tissue, testis, liver, heart, and muscle remained unchanged. In addition, we observed increased blood insulin and leptin levels due to Npgl overexpression, while little changes were induced in blood glucose, free fatty acids, triglyceride, and cholesterol levels. Furthermore, transcriptome analysis of the inguinal WAT using RNA-sequencing technique revealed that overexpression of Npgl upregulated the genes involved in cytoskeleton regulation, whereas it decreased those involved in immune-inflammatory responses. These results suggest that NPGL plays a crucial role in enlarging adipocytes and suppressing inflammation to avoid metabolic abnormalities, eventually contributing to accelerating energy storage.

category: physiology


title: Mathematical modeling reveals a complex network of signaling and apoptosis pathways in the survival of memory plasma cells

abstract: The long-term survival of memory plasma cells is conditional on the signals provided by dedicated survival niches in the bone marrow organized by mesenchymal stromal cells. Recently, we could show that plasma cell survival requires secreted factors such as APRIL and direct contact to stromal cells, which act in concert to activate NF-kB- and PI3K-dependent signaling pathways to prevent cell death. However, the precise dynamics of the underlying regulatory network are confounded by the complexity of potential interaction and cross-regulation pathways. Here, based on flow-cytometric quantification of key signaling proteins in the presence or absence of the required survival signals, we generated a quantitative model of plasma cell survival. Our model emphasizes the non-redundant and essential nature of the two plasma cell survival signals APRIL and stromal cell contact, providing resilience to endoplasmic reticulum stress and mitochondrial stress, respectively. Importantly, the modeling approach allowed us to unify distinct data sets and derive a consistent picture of the intertwined signaling and apoptosis pathways regulating plasma cell survival.

category: systems biology


title: Sexual dimorphism in epilepsy and comorbidities in Dravet syndrome mice carrying a targeted deletion of exon 1 of the Scn1a gene

abstract:
ObjectiveDravet Syndrome (DS) is a catastrophic form of paediatric epilepsy associated with multiple comorbidities mainly caused by mutations in the SCN1A gene. DS progresses in three different phases termed febrile, worsening and stabilization stage. Mice that are haploinsufficient for Scn1a faithfully model each stage of DS, although various aspects have not been fully described, including the temporal appearance and sex differences of the epilepsy and comorbidities. The aim of the present study was to investigate the epilepsy landscape according to the progression of DS and the long-term co-morbidities in the Scn1a(+/-)tm1Kea DS mouse line that are not fully understood yet.

MethodsMale and female F1.Scn1a(+/+) and F1.Scn1a(+/-)tm1Kea mice were assessed in the hyperthermia model or monitored by video electroencephalogram (vEEG) and wireless video-EEG according to the respective stage of DS. Long-term comorbidities were investigated through a battery of behaviour assessments in [~]6 month-old mice.

ResultsAt P18, F1.Scn1a(+/-)tm1Kea mice showed the expected sensitivity to hyperthermia-induced seizures. Between P21 and P28, EEG recordings in F1.Scn1a(+/-)tm1Kea mice combined with video monitoring revealed a high frequency of SRS and SUDEP. Power spectral analyses of background EEG activity also revealed that low EEG power in multiple frequency bands was associated with SUDEP risk in F1.Scn1a(+/-)tm1Kea mice during the worsening stage of DS. Later, SRS and SUDEP rates stabilized and then declined in F1.Scn1a(+/-)tm1kea mice. SRS and SUDEP in F1.Scn1a(+/-)tm1kea mice displayed variations with the time of day and sex, with female mice displaying higher numbers of seizures and greater SUDEP risk. F1.Scn1a(+/-)tm1kea mice [~]6 month- old displayed fewer behavioural impairments than expected including hyperactivity, impaired exploratory behaviour and poor nest building performance.

SignificanceThese results reveal new features of this model that will optimize use and selection of phenotype assays for future studies on the mechanisms, diagnosis, and treatment of DS.

Key point boxO_LIScn1a(+/-)tm1kea DS mouse model faithfully reproduces the three stages of DS
C_LIO_LISex of F1.Scn1a(+/-)tm1kea mice influences the epilepsy phenotype
C_LIO_LIF1.Scn1a(+/-)tm1kea develop some of the long-term comorbidities of DS
C_LI


title: Pattern separation and tuning shift in human sensory cortex underlie fear memory

abstract: Animal research has recognized the role of the sensory cortex in fear memory and two key underlying mechanisms--pattern separation and tuning shift. We interrogated these mechanisms in the human sensory cortex in an olfactory differential conditioning study with a delayed (9-day) retention test. Combining affective appraisal and olfactory psychophysics with functional magnetic resonance imaging (fMRI) multivoxel pattern analysis and voxel-based tuning analysis over a linear odor-morphing continuum, we confirmed affective and perceptual learning and memory and demonstrated associative plasticity in the human olfactory (piriform) cortex. Specifically, the piriform cortex exhibited immediate and lasting enhancement in pattern separation (between the conditioned stimuli/CS and neighboring non-CS) and late-onset yet lasting tuning shift towards the CS, especially in anxious individuals. These findings highlight an evolutionarily conserved sensory cortical system of fear memory, which can underpin sensory encoding of fear/threat and confer a sensory mechanism to the neuropathophysiology of anxiety.


title: The brain uses invariant dynamics to generalize outputs across movements

abstract: The nervous system uses a repertoire of outputs to produce diverse movements. Thus, the brain must solve how to issue and transition the same outputs in different movements. A recent proposal states that network connectivity constrains the transitions of neural activity to follow invariant rules across different movements, which we term  invariant dynamics. However, it is unknown whether invariant dynamics are actually used to drive and generalize outputs across movements, and what advantage they provide for controlling movement. Using a brain-machine interface that transformed motor cortex activity into outputs for a neuroprosthetic cursor, we discovered that the same output is issued by different activity patterns in different movements. These distinct patterns then transition according to a model of invariant dynamics, leading to patterns that drive distinct future outputs. Optimal control theory revealed this use of invariant dynamics reduces the feedback input needed to control movement. Our results demonstrate that the brain uses invariant dynamics to generalize outputs across movements.


title: Tightly-coupled inhibitory and excitatory functional networks in the early visual cortex

abstract: Intracortical inhibition plays a critical role in shaping activity patterns in the mature cortex. However, little is known about the structure of inhibition in early development prior to the onset of sensory experience, a time when spontaneous activity exhibits long-range correlations predictive of mature functional networks. Here, using calcium imaging of GABAergic neurons in the early ferret visual cortex, we show that spontaneous activity in inhibitory neurons is already highly organized into distributed modular networks before visual experience. Inhibitory neurons exhibit spatially modular activity with long-range correlations and precise local organization that is in quantitative agreement with excitatory networks. Furthermore, excitatory and inhibitory networks are strongly co-aligned at both millimeter and cellular scales. These results demonstrate a remarkable degree of organization in inhibitory networks early in the developing cortex, providing support for computational models of self-organizing networks and suggesting a mechanism for the emergence of distributed functional networks during development.


title: MS-driven metabolic alterations are recapitulated in iPSC-derived astrocytes

abstract:
ObjectiveAstrocytes play a significant role in the pathology of Multiple Sclerosis (MS). Nevertheless, for ethical reasons, most of the studies in these cells were performed on the Experimental Autoimmune Encephalomyelitis model. As there are significant differences between human and mouse cells, we aimed here to better characterize astrocytes from patients with MS (PwMS), focusing mainly on mitochondrial function and cell metabolism.

MethodsWe obtained and characterized induced pluripotent stem cell (iPSC)-derived astrocytes from three PwMS and three unaffected controls and performed functional assays including electron microscopy, flow cytometry, cytokine measurement, gene expression, in situ respiration, and metabolomics.

ResultsWe detected several differences in MS astrocytes including: (i) enrichment of genes associated with mitophagy and neurodegeneration, (ii) increased mitochondrial fission and decreased mitochondrial to nuclear DNA ratio, indicating disruption of mitochondrial content, (iii) increased production of superoxide and MS-related proinflammatory chemokines, (iv) increased electron transport capacity and proton leak, in line with the increased oxidative stress, and (v) a distinct metabolic profile, with a deficiency in amino acid catabolism and increased sphingolipid metabolism, which have already been linked to MS.

InterpretationTo our knowledge, this is the first study thoroughly describing the metabolic profile of iPSC-derived astrocytes from PwMS, and validating this model as a powerful tool to study disease mechanisms and to perform non-invasive drug targeting assays in vitro. Our findings recapitulate several disease features described in patients and provide new mechanistic insights into the metabolic rewiring of astrocytes in MS, which could be targeted in future therapeutic studies.


title: MRI-Visible Perivascular Space (PVS) Changes with Long-Duration Spaceflight

abstract: Humans are exposed to extreme environmental stressors during spaceflight and return with alterations in brain structure and shifts in intracranial fluids. To date, no studies have evaluated the effects of spaceflight on perivascular spaces (PVSs) within the brain, which are believed to facilitate fluid drainage and brain homeostasis. Here, we examined how the number and morphology of magnetic resonance imaging (MRI)-visible PVSs are affected by spaceflight, including prior spaceflight experience. Fifteen astronauts underwent six T1-weighted 3T MRI scans, twice prior to launch and four times following their return to Earth after [~]6-month missions to the International Space Station. White matter MRI-visible PVS number and morphology were calculated using an established automated segmentation algorithm. We found that novice astronauts showed an increase in total PVS volume from pre- to post-flight, whereas experienced crewmembers did not (adjusted for age, sex, and time between landing and first MRI scan). Moreover, experienced astronauts exhibited a significant correlation between more previous flight days and greater PVS median length at baseline, suggesting that experienced astronauts exhibit holdover effects from prior spaceflight(s). There was also a significant positive correlation between pre- to post-flight increases in PVS median length and increases in right lateral ventricular volume. The presence of spaceflight associated neuro-ocular syndrome (SANS) was not associated with PVS number or morphology. Together, these findings demonstrate that spaceflight is associated with PVS morphological changes, and specifically that spaceflight experience is an important factor in determining PVS characteristics.


title: The connecting cilium inner scaffold provides a structural foundation to maintain photoreceptor integrity

abstract:
Retinal degeneration is a leading cause of human blindness due to progressive loss of ciliated photoreceptors cells. While this degradation can be associated with cohesion defects of the microtubule-based connecting cilium (CC) structure, the underlying mechanism is not understood. Here, using expansion microscopy and electron microscopy, we reveal the molecular architecture of the CC and demonstrate that microtubules are linked together by a CC-inner scaffold (CC-IS) containing POC5, CENTRIN and FAM161A. Monitoring CC-IS assembly during photoreceptor development in mouse reveals that it acts as a structural zipper, progressively bridging microtubule doublets and straightening the CC. Consistently, Fam161a mutations lead to a specific CC-IS loss and trigger microtubule doublets spreading, prior to outer segment collapse and photoreceptor degeneration, providing a molecular mechanism for retinitis pigmentosa disease.

One Sentence SummaryThe connecting cilium inner scaffold acts as a structural zipper granting photoreceptor integrity.


title: Molecular Basis for CPC-Sgo1 Interaction: Implications for Centromere Localisation and Function of the CPC

abstract: The Chromosomal Passenger Complex (CPC; consisting of Borealin, Survivin, INCENP and Aurora B kinase) and Shugoshin 1 (Sgo1) are key regulators of chromosome bi-orientation, a process essential for error-free chromosome segregation. Their functions rely on their ability to associate with centromeres. Two histone phosphorylations, histone H3 Thr3 (H3T3ph; directly recognised by Survivin) and histone H2A Thr120 (H2AT120ph; indirectly recognised via Sgo1), together with CPCs intrinsic ability to bind nucleosome, facilitate CPC centromere recruitment. The molecular basis for CPC-Sgo1 binding and how their direct interaction influences CPC centromere localisation and function are lacking. Here, using an integrative structure-function approach, we show that the histone H3-like Sgo1 N-terminal tail interacts with Survivin acting as a hot-spot for CPC-Sgo1 assembly, while downstream Sgo1 residues, mainly with Borealin contributes for high affinity interaction. Disruption of the Sgo1 N-terminal tail-Survivin interaction abolished CPC-Sgo1 assembly in vitro and perturbed centromere localisation and function of CPC. Our findings provide evidence that CPC binding to Sgo1 and histone H3 N-terminal tail are mutually exclusive, suggesting that these interactions will likely take place in a spatially/temporally restricted manner and provide a rationale for the Sgo1-mediated  kinetochore proximal centromere pool of CPC.


title: Renal Interstitial Cells Promote Nephron Regeneration by Secreting Prostaglandin E2

abstract: In organ regeneration, progrnitor and stem cells reside in their native microenvironment, which provides dynamic physical and chemical cues essential to their survival, proliferation and differentiation. However, what kind of cells provide a native microenvironment for renal progenitor cells has not been clarified. Here, single-cell sequencing of zebrafish kidney revealed that fabp10 was a marker of renal interstitial cells (RICs), and the Tg(fabp10a:GFP) transgenic line can specifically label RICs in zebrafish kidney. The formation of RICs and nephrons are closely accompanied during nephron regeneration. RICs form a network to wrap the renal progenitor cell aggregates. RICs in close contact with cell aggregates express cyclooxygenase 2 and secrete prostaglandin 2 (PGE2). Inhibiting PGE2 production prevented nephrogenesis by reducing the proliferation and differentiation of progenitor cell aggregates. PGE2 promoted maturation of the nephron by activating the WNT signaling pathway in progenitor cell aggregates in cooperation with Wnt4a. These findings suggest that RICs provide a necessary microenvironment for rapid nephrogenesis during nephron regeneration.


title: Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification

abstract: Stochastic mechanisms diversify cell fates during development. How cells randomly choose between two or more fates remains poorly understood. In the Drosophila eye, the random mosaic of two R7 photoreceptor subtypes is determined by expression of the transcription factor Spineless (Ss). Here, we investigated how cis-regulatory elements and trans factors regulate nascent transcriptional activity and chromatin compaction at the ss gene locus during R7 development. We find that the ss locus is in a compact state in undifferentiated cells. An early enhancer drives ss transcription in all R7 precursors to open the ss locus. In differentiating cells, transcription ceases and the ss locus stochastically remains open or compacts. In SsON R7s, ss is open and competent for activation by a late enhancer, whereas in SsOFF R7s, ss is compact and repression prevents expression. Our results suggest that a temporally dynamic antagonism, in which transcription drives decompaction and then compaction represses transcription, controls stochastic cell fate specification.


title: Decadal trend of plankton community change and habitat shoaling in the Arctic gateway recorded by planktonic foraminifera

abstract: The Fram Strait plays a crucial role in regulating the heat and sea-ice dynamics in the Arctic. In response to the ongoing global warming, the marine biota of this Arctic gateway is experiencing significant changes with increasing advection of Atlantic species. The footprint of this "Atlantification" has been identified in isolated observations across the plankton community, but a systematic, multi-decadal perspective on how regional climate change facilitates the invasion of Atlantic species and affects the ecology of the resident species is lacking. Here we evaluate a series of 51 depth-resolved plankton profiles collected in the Fram Strait during seven surveys between 1985 and 2015, using planktonic foraminifera as a proxy for changes in both the pelagic community composition and species vertical habitat depth. The time series reveals a progressive shift towards more Atlantic species, occurring independently of changes in local environmental conditions. We conclude that this trend is reflecting higher production of the Atlantic species in the "source" region, from where they are advected into the Fram Strait. At the same time, we observe that the ongoing extensive sea-ice export from the Arctic and associated cooling-induced decline in density and habitat shoaling of the subpolar Turborotalita quinqueloba, whereas the resident Neogloboquadrina pachyderma persists. As a result, the planktonic foraminiferal community and vertical structure in the Fram Strait shifts to a new state, driven by both remote forcing of the Atlantic invaders and local climatic changes acting on the resident species. The strong summer export of Arctic sea ice has so far buffered larger plankton transformation. We predict that if the sea-ice export will decrease, the Arctic gateway will experience rapid restructuring of the pelagic community, even in the absence of further warming. Such a large change in the gateway region will likely propagate into the Arctic proper.


title: Pyruvate:ferredoxin oxidoreductase and low abundant ferredoxins support aerobic photomixotrophic growth in cyanobacteria

abstract:
The decarboxylation of pyruvate is a central reaction in the carbon metabolism of all organisms. Both the pyruvate:ferredoxin oxidoreductase (PFOR) and the pyruvate dehydrogenase (PDH) complex catalyze this reaction. Whereas PFOR reduces ferredoxin, the PDH complex utilizes NAD+. Anaerobes rely on PFOR, which was replaced during evolution by the PDH complex found in aerobes. Cyanobacteria possess both. Our data challenge the view that PFOR is exclusively utilized for fermentation. Instead, we show, that the cyanobacterial PFOR is stable in the presence of oxygen in vitro and is required for optimal photomixotrophic growth under aerobic conditions while the PDH complex is inactivated under the same conditions. We found that cells rely on a general shift from utilizing NAD(H)-dependent to ferredoxin-dependent enzymes under these conditions.

The utilization of ferredoxins instead of NAD(H) saves a greater share of the Gibbs free energy, instead of wasting it as heat. This obviously simultaneously decelerates metabolic reactions as they operate closer to their thermodynamic equilibrium. It is common thought that during evolution, ferredoxins were replaced by NAD(P)H due to their higher stability in an oxidizing atmosphere. However, utilization of NAD(P)H could also have been favored due to a higher competitiveness because of an accelerated metabolism.


title: Excluding loci with substitution saturation improves inferences from phylogenomic data

abstract: The historical signal in nucleotide sequences becomes eroded over time by substitutions occurring repeatedly at the same sites. This phenomenon, known as substitution saturation, is recognized as one of the primary obstacles to deep-time phylogenetic inference using genome-scale data sets. We present a new test of substitution saturation and demonstrate its performance in simulated and empirical data. For some of the 36 empirical phylogenomic data sets that we examined, we detect substitution saturation in around 50% of loci. We found that saturation tends to be flagged as problematic in loci with highly discordant phylogenetic signals across sites. Within each data set, the loci with smaller numbers of informative sites are more likely to be flagged as containing problematic levels of saturation. The entropy saturation test proposed here is sensitive to high evolutionary rates relative to the evolutionary timeframe, while also being sensitive to several factors known to mislead phylogenetic inference, including short internal branches relative to external branches, short nucleotide sequences, and tree imbalance. Our study demonstrates that excluding loci with substitution saturation can be an effective means of mitigating the negative impact of multiple substitutions on phylogenetic inferences.


title: Abundant small RNAs in the reproductive tissues of the honey bee, Apis mellifera, are a plausible mechanism for epigenetic inheritance and parental manipulation of gene expression

abstract: Polyandrous social insects such as the honey bee are prime candidates for parental manipulation of gene expression in offspring. Although there is good evidence for parent-of-origin effects in honey bees the epigenetic mechanisms that underlie these effects remain a mystery. Small RNA molecules such as miRNAs, piRNAs and siRNAs play important roles in transgenerational epigenetic inheritance and in the regulation of gene expression during development. Here we present the first characterisation of small RNAs present in honey bee reproductive tissues: ovaries, spermatheca, semen, fertilised and unfertilised eggs, and testes. We show that semen contains fewer piRNAs relative to eggs and ovaries, and that piRNAs and miRNAs which map antisense to genes involved in DNA regulation and developmental processes are differentially expressed between tissues. tRNA fragments are highly abundant in semen and have a similar profile to those seen in semen in other animals. Intriguingly we find abundant piRNAs that target the sex determination locus, suggesting that piRNAs may play a role in honey bee sex determination. We conclude that small RNAs play a fundamental role in honey bee gametogenesis and reproduction and provide a plausible mechanism for parent-of origin-effects on gene expression and reproductive physiology.

category: genomics


title: Three-dimensional microenvironment regulates gene expression, function, and tight junction dynamics of iPSC-derived blood-brain barrier microvessels

abstract: The blood-brain barrier (BBB) plays a pivotal role in brain health and disease. In the BBB, brain microvascular endothelial cells (BMECs) are connected by tight junctions which regulate paracellular transport, and express specialized transporter systems which regulate transcellular transport. However, existing in vitro models of the BBB display variable physiological accuracy across a wide range of characteristics including gene/protein expression and barrier function. Here, we use an isogenic family of fluorescently-labeled iPSC-derived BMEC-like cells (iBMECs) and brain pericyte-like cells (iPCs) within two-dimensional confluent monolayers (2D) and three-dimensional (3D) tissue-engineered microvessels to explore how 3D microenvironment regulates gene expression and function of the in vitro BBB. We show that 3D microenvironment (shear stress, cell-ECM interactions, and cylindrical geometry) increases BBB phenotype and endothelial identity, and alters angiogenic and cytokine responses in synergy with pericyte co-culture. Tissue-engineered microvessels incorporating junction-labeled iBMECs enable study of the real-time dynamics of tight junctions during homeostasis and in response to physical and chemical perturbations.


title: Identification and Interaction Analysis of Molecular Markers in Myocardial Infarction by Integrated Bioinformatics Analysis

abstract: Myocardial infarction (MI) is the leading cardiovascular diseases in worldwide, yet relatively little is known about the genes and signaling pathways involved in MI progression. The present investigation aimed to elucidate potential crucial candidate genes and pathways in MI. expression profiling by high throughput sequencing dataset (GSE132143) was downloaded from the Gene Expression Omnibus (GEO) database, which included data from 20 MI samples and 12 normal control samples. Differentially expressed genes (DEGs) were identified using t-tests in the DESeq2 R package. These DEGs were subsequently investigated by Gene Ontology (GO) and pathway enrichment analysis, a protein-protein interaction (PPI) network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network were constructed and analyzed. Hub genes were validated by receiver operating characteristic curve (ROC) analysis. In total, 958 DEGs were identified, of which 480 were up regulated and 478 were down regulated. GO and pathway enrichment analysis results revealed that the DEGs were mainly enriched in, immune system, neuronal system, response to stimulus, and multicellular organismal process. A PPI network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network was constructed by using Cytoscape software, and CFTR, CDK1, RPS13, RPS15A, RPS27, NOTCH1, MRPL12, NOS2, CCDC85B and ATN1 were identified as the hub genes. Our results highlight the important roles of the genes including CFTR, CDK1, RPS13, RPS15A, RPS27, NOTCH1, MRPL12, NOS2, CCDC85B and ATN1 in MI pathogenesis or therapeutic management.


title: Functionally Graded Flexural Rigidity Improves FlightPerformance in Flapping Wing Insects

abstract: Insect wings are heterogeneous structures, with flexural rigidity varying one to two orders of magnitude over the wing surface. This heterogeneity influences the deformation the flapping wing experiences during flight. However, it is not well understood how this flexural rigidity gradient affects wing performance. Here, we develop a simplified 2D model of a flapping wing as a pitching, plunging airfoil using the assumed mode method and unsteady vortex lattice method to model the structural and fluid dynamics, respectively. We conduct parameter studies to explore how variable flexural rigidity affects mean lift production, power consumption and the forces required to flap the wing. We find that there is an optimal flexural rigidity distribution that maximizes lift production; this distribution generally corresponds to a 3:1 ratio between the wings flapping and natural frequencies, though the ratio is sensitive to flapping kinematics. For hovering flight, the optimized flexible wing produces 20% more lift and requires 15% less power compared to a rigid wing but needs 20% higher forces to flap. Even when flapping kinematics deviate from those observed during hover, the flexible wing outperforms the rigid wing in terms of aerodynamic force generation and power across a wide range of flexural rigidity gradients. Peak force requirements and power consumption are inversely proportional with respect to flexural rigidity gradient, which may present a trade-off between insect muscle size and energy storage requirements. The model developed in this work can be used to efficiently investigate other spatially variant morphological or material wing features moving forward.


title: Investigation of Chordwise Functionally Graded Flexural Rigidity in Flapping Wings Using a Two-Dimensional Pitch-Plunge Model


title: Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation

abstract: How type 2 Topoisomerase (TopoII) proteins relax and simplify the topology of DNA molecules is one of the most intriguing open questions in genome and DNA biophysics. Most of the existing models neglect the dynamics of TopoII which is characteristics for proteins searching their targets via facilitated diffusion. Here, we show that dynamic binding of TopoII speeds up the topological relaxation of knotted substrates by enhancing the search of the knotted arc. Intriguingly, this in turn implies that the timescale of topological relaxation is virtually independent of the substrate length. We then discover that considering binding biases due to facilitated diffusion on looped substrates steers the sampling of the topological space closer to the boundaries between different topoisomers yielding an optimally fast topological relaxation. We discuss our findings in the context of topological simplification in vitro and in vivo.


title: Preclinical models of human multiple myeloma subgroups

abstract: Multiple myeloma (MM), a tumor of germinal center (GC)-experienced plasma cells, comprises distinct genetic subgroups, such as the t(11;14)/CCND1 and the t(4;14)/MMSET subtype. We have generated subgroup-specific MM models by the GC B cell-specific co-activation of Ccnd1 or MMSET with a constitutively active Ikk2 mutant, mimicking the secondary NF{kappa}B activation frequently seen in human MM. Ccnd1/Ikk2ca and MMSET/Ikk2ca mice developed a pronounced, clonally restricted plasma cell outgrowth with age, accompanied by serum M spikes, bone marrow insufficiency and bone lesions. The transgenic plasma cells could be propagated in vivo and showed transcriptional profiles resembling their human counterparts. Thus, we show that Ccnd1 and MMSET cooperate with NF{kappa}B in MM pathogenesis, considering for the first time the genetic heterogeneity of MM for the generation of preclinical models.


title: Alterations in rhythmic and non-rhythmic resting-state EEG activity and their link to cognition in older age

abstract: While many structural and biochemical changes in the brain have been previously associated with aging, the findings concerning electrophysiological signatures, reflecting functional properties of neuronal networks, remain rather controversial. To try resolve this issue, we took advantage of a large population study (N=1703) and comprehensively investigated the association of multiple EEG biomarkers (power of alpha and theta oscillations, individual alpha peak frequency (IAF), the slope of 1/f power spectral decay), aging, and aging and cognitive performance. Cognitive performance was captured with three factors representing processing speed, episodic memory, and interference resolution. Our results show that not only did IAF decline with age but it was also associated with interference resolution over multiple cortical areas. To a weaker extent, 1/f slope of the PSD showed age-related reductions, mostly in frontal brain regions. Finally, alpha power was negatively associated with the speed of processing in the right frontal lobe, despite the absence of age-related alterations. Our results thus demonstrate that multiple electrophysiological features, as well as their interplay, should be considered when investigating the association between age, neuronal activity, and cognitive performance.


title: Retinoschisin deficiency induces persistent aberrant waves of activity affecting neuroglial signaling in the retina

abstract:
Genetic disorders which present during development make treatment strategies particularly challenging because there is a need to disentangle primary pathophysiology from downstream dysfunction caused at key developmental stages. To provide a deeper insight into this question, we studied a mouse model of X-linked juvenile retinoschisis (XLRS), an early onset inherited condition caused by mutations in the RS1 gene encoding retinoschisin (RS1) and characterized by cystic retinal lesions and early visual deficits. Using an unbiased approach in expressing the fast intracellular calcium indicator GCaMP6f in neuronal, glial, and vascular cells of the retina of mice lacking RS1, we found that initial cyst formation is paralleled by the appearance of aberrant spontaneous neuro-glial signals as early as postnatal day 13. These presented as glutamate-driven wavelets of neuronal activity and sporadic radial bursts of activity by Muller glia, spanning all retinal layers and disrupting light-induced signaling. This study highlights a critical role for RS1 in early retinal development with a potential to disrupt circuit formation to central targets. Additionally, it confers a functional role to RS1 beyond the scope of an adhesion molecule and identifies an early onset for dysfunction, a potential temporal target for therapeutic intervention and diagnosis.

Significance Statement/ HighlightsO_LIPhotoreceptor inner segments express Rs1 at P5, after which RS1 protein is detected in the inner segments by P9 and throughout the retina at later ages, with structural abnormalities observed by optical coherence tomography at P13 in Rs1 mutant mouse models.
C_LIO_LIAberrant glutamate-driven wavelets identified by GCaMP6f-based analyses are a novel pathophysiological feature of RS1 deficient mice that emerge after maximal RS1 expression.
C_LIO_LIMuller glia display abnormal radial glutamate-driven coordinated and sporadic bursts of activity in RS1-deficient mice.
C_LIO_LIThese data identify a novel pathophysiological feature of RS1-deficient mice and define a window where treatments might be most effective.
C_LI

Graphical Abstract

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title: The STAT5-IRF4-BATF pathway drives heightened epigenetic remodeling in naïve CD4+ T cell responses of older adults

abstract: T cell aging is a complex process combining the emergence of cellular defects with activation of adaptive mechanisms. Generation of T cell memory is impaired, while a low-inflammatory state is induced, in part due to effector T cells. To determine whether age-associated changes in T cell fate decisions occur early after T cell activation, we profiled the longitudinal transcriptional and epigenetic landscape induced by TCR stimulation comparing naive CD4+ T cells from young and older adults. In spite of attenuated TCR signaling, activation-induced remodeling of the epigenome increased with age, culminating in heightened BATF and BLIMP1 activity. Single cell studies, integrating ATAC-seq and RNA-seq data, identified increases in dysfunctional and in effector T cells and a decrease in BACH2-expressing memory cell precursors. STAT5 activation, in part due to a decline in HELIOS and aberrant IL-2 receptor expression, accounted for the induction of transcription factor networks favoring effector cell differentiation.

category: immunology


title: Fear of parasitism affects the functional role of ecosystem engineers

abstract: Fear is an integrated part of predator-prey interactions with cascading effects on the structure and function of ecosystems. Fear of parasitism holds a similar ecological potential but our understanding of the underlying mechanisms in host-parasite interactions is limited by lack of empirical examples. Here, we experimentally test if blue mussels Mytilus edulis respond behaviourally to the mere presence of infective transmission stages of the trematode Himasthla elongata by ceasing filtration activity, thereby avoiding infection. Our results show that blue mussels reduced clearance rates by more than 30% in presences of parasites. The reduced filtration activity resulted in lower infection rates in experimental mussels. The identified parasite-specific avoidance behaviour can be expected to play a significant role in regulating the ecosystem engineering function of blue mussels in coastal habitats.


title: Advanced Age Has Dissociable Effects on Hippocampal CA1 and CA3 Ripples

abstract:
Sharp-wave/ripples are brief, high-frequency events in hippocampal subregions CA3 and CA1 that occur during rest or pauses in behavior. Ripples detected in CA1 have lower frequency in aged compared to young rats. Although CA1 ripples are theorized to manifest from CA3, ripple dynamics in CA3 have not been examined in aged animals. The current study obtained simultaneous recordings between CA1 and CA3 in young and aged rats to examine sharp-wave/ripple characteristics in both regions in relation to age. While CA1 ripple frequency was reduced with age, there were no age differences in CA3 ripples. In aged, but not young, rats there was also a significant increase in the probability of CA3 and CA1 ripples co-occurring between the pre- and post-behavior rest epochs. Moreover, in both age groups, CA1 ripples that co-occurred with a CA3 ripple had increased frequency, power, and duration. These findings suggest age differences in CA1 are not due to altered afferent input from CA3, but instead reflect distinct mechanisms of ripple generation with age.

HIGHLIGHTSO_LICA1 ripple frequency is reduced with age.
C_LIO_LICA3 ripple characteristics do not change with age.
C_LIO_LIIn aged rats only, CA3-CA1 ripple co-occurrence increased following behavior.
C_LIO_LICA1 ripples that co-occurred with CA3 had greater frequency, power, and duration.
C_LI

category: animal behavior and cognition


title: Multimodal measurements of phototoxicity in nonlinear optical microscopy

abstract: Nonlinear optical imaging modalities, such as two-photon microscopy and stimulated Raman scattering (SRS) microscopy, make use of pulsed-laser excitation with high peak intensity that can perturb the native state of cells. In this study, we investigated the short and long-term effects of pulsed laser induced phototoxicity. We used bulk RNA sequencing, quantitative measurement of cell proliferation, and measurement of the generation of reactive oxygen species (ROS) to assess phototoxic effects, at different time scales, for a range of laser excitation settings relevant to SRS imaging. We define a range of laser excitation settings for which there was no significant ROS generation, differential gene expression, or change in proliferation rates of mouse Neuro2A cells. Changes in proliferation rate and ROS generation were observed under imaging conditions with an excitation intensity of over 600 mW/m2. Repeated imaging of the same field of view at this excitation intensity of over 600 mW/m2 resulted in visual damage to N2A cells. Laser induced perturbations in live cells may impact downstream measurements of cell state including subsequent imaging or molecular measurements. This study provides guidance for imaging parameters that minimize photo-induced perturbations in SRS microscopy to ensure accurate interpretation of experiments with time-lapse imaging or with paired measurements of imaging and sequencing on the same cells.


title: Accurate and automated high-coverage identification of chemically cross-linked peptides with MaxLynx

abstract: Cross-linking combined with mass spectrometry (XL-MS) provides a wealth of information about the 3D structure of proteins and their interactions. We introduce MaxLynx, a novel computational proteomics workflow for XL-MS integrated into the MaxQuant environment. It is applicable to non-cleavable and MS-cleavable cross linkers. For both we have generalized the Andromeda peptide database search engine to efficiently identify cross-linked peptides. For non-cleavable peptides, we implemented a novel di-peptide Andromeda score, which is the basis for a computationally efficient N-squared search engine. Additionally, partial scores summarize the evidence for the two constituents of the di-peptide individually. A posterior error probability based on total and partial scores is used to control false discovery rates. For MS-cleavable cross linkers a scoring of signature peaks is combined with the conventional Andromeda score on the cleavage products. The MaxQuant 3D-peak detection was improved to ensure more accurate determination of the monoisotopic peak of isotope patterns for heavy molecules, which cross-linked peptides typically are. A wide selection of filtering parameters can replace manual filtering of identifications, which is often necessary when using other pipelines. On benchmark datasets of synthetic peptides, MaxLynx outperforms all other tested software on data for both types of cross linkers as well as on a proteome-wide dataset of cross-linked D. melanogaster cell lysate. The workflow also supports ion-mobility enhanced MS data. MaxLynx runs on Windows and Linux, contains an interactive viewer for displaying annotated cross-linked spectra and is freely available at https://www.maxquant.org/.


title: ΔGunfold leaderless, a package for high-throughput analysis of translation initiation regions (TIRs) at the transcriptome scale and for leaderless mRNA optimization

abstract:
BackgroundTranslation initiation is an essential step for fidelity of gene expression, in which the ribosome must bind to the translation initiation region (TIR) and position the initiator tRNA in the P-site (1). For this to occur correctly, the TIR encompassing the ribosome binding site (RBS) needs to be highly accessible (2-5). {Delta}Gunfold is a metric for computing accessibility of the TIR, but there is no automated way to compute it manually with existing software/tools limiting throughput.

Results{Delta}Gunfold leaderless allows users to automate the {Delta}Gunfold calculation to perform high-throughput analysis. Importantly,{Delta} Gunfold leaderless allows calculation of TIRs of both leadered mRNAs and leaderless mRNAs which lack a 5 UTR and which are abundant in bacterial, archaeal, and mitochondrial transcriptomes (4, 6, 7). The ability to analyze leaderless mRNAs also allows one additional feature where users can computationally optimize leaderless mRNA TIRs to maximize their gene expression (8, 9).

ConclusionsThe {Delta}Gunfold leaderless package facilitates high-throughput calculations of TIR accessibility, is designed to calculate TIR accessibility for leadered and leaderless mRNA TIRs which are abundant in bacterial/archaeal/organellar transcriptomes and allows optimization of leaderless mRNA TIRs for biotechnology.


title: Binary outcomes of enhancer activity underlie stable random monoallelic expression

abstract: Mitotically stable random monoallelic gene expression (RME) is documented for a small percentage of autosomal genes. Here we investigated the role of enhancers in the RME of natural killer (NK) cell receptor genes. Enhancers were accessible and enriched in H3K27ac on silent and active alleles alike, decoupling enhancer activation and expression. Enhancers controlled gene expression frequency, as predicted by the binary model of enhancer action, and enhancer deletion converted the broadly expressed Nkg2d into an RME gene, recapitulating natural variegation. The results suggested that RME is a consequence of general enhancer properties and therefore many genes may be subject to some degree of RME, which was borne out by analysis of a panel of genes previously thought to be universally expressed within defined hematopoietic lineages: Nkg2d, Cd45, Cd8a and Thy1. We propose that previously documented RME is an extreme on a continuum of intrinsically probabilistic gene expression.

category: molecular biology


title: DNA damage signaling regulates cohesin stabilization and promotes meiotic chromosome axis morphogenesis

abstract:
A hallmark of meiosis is the reorganization of chromosomes as linear arrays of chromatin loops around a chromosome axis comprised of cohesins and regulatory proteins. Defective axis morphogenesis impairs homolog pairing, synapsis, and recombination. We find that axis assembly in C. elegans is promoted by DNA Damage Response (DDR) signaling activated at meiotic entry. Central to this regulation is downregulation of the cohesin release factor WAPL-1 by the DDR transducer kinase ATM-1, which is activated by the meiotic kinase CHK-2. Additional cohesin regulators, including ECO-1 and PDS-5, also contribute to stabilizing axis-associated cohesins. We find that downregulation of WAPL by ATM also promotes cohesin enrichment at DNA damage foci in cultured mammalian cells. Our findings reveal that the DDR and Wapl play conserved roles in cohesin regulation in meiotic prophase and proliferating cells.

One-Sentence SummaryDNA Damage Response kinase ATM phosphorylates WAPL to promote meiotic chromosome axis assembly and DNA repair


title: Aβ oligomers trigger necroptosis-mediated neurodegeneration via microglia activation in Alzheimer's disease.

abstract: Alzheimers disease (AD) is a major adult-onset neurodegenerative condition with no available treatment. Compelling reports point amyloid-{beta} (A{beta}) as the main etiologic agent that triggers AD. Although there is extensive evidence of detrimental crosstalk between A{beta} and microglia that contributes to neuroinflammation in AD, the exact mechanism leading to neuron death remains unknown. Using postmortem human AD brain tissue, we show that A{beta} pathology is associated with the necroptosis effector pMLKL. Moreover, we found that the burden of A{beta}o correlates with the expression of key markers of necroptosis activation. Additionally, inhibition of necroptosis by pharmacological or genetic means, reduce neurodegeneration and memory impairment triggered by A{beta}o in mice. Since microglial activation is emerging as a central driver for AD pathogenesis, we then tested the contribution of microglia to the mechanism of A{beta}o-mediated necroptosis activation in neurons. Using an in vitro model, we show that conditioned medium from A{beta}o-stimulated microglia elicited necroptosis in neurons through activation of TNF- signaling, triggering extensive neurodegeneration. Notably, necroptosis inhibition provided significant neuronal protection. Together, these findings suggest that A{beta}o-mediated microglia stimulation in AD contributes to necroptosis activation in neurons and neurodegeneration. As necroptosis is a druggable degenerative mechanism, our findings might have important therapeutic implications to prevent the progression of AD.


title: Vectofusin-1 based T-cell transduction approach for developing murine CAR-T cells for cancer.

abstract: Gene transfer into human and murine T-cells using viral-based approaches has several promising therapeutic applications including the production of chimeric antigen receptor T-cell (CAR-T) therapy. The generation of murine CAR-T is paramount to test and validate immunocompetent mouse models for CAR-T therapy. Several viral transduction enhancers already exist for gene therapy with few limitations. In this study, we tested vectofusin-1, a short cationic peptide, as a soluble transduction enhancer for gammaretroviral transduction for the generation of anti-CD19 murine CAR-T. We found that in comparison to Retronectin, Vectofusin-1 is an equally optimal transduction enhancer for the generation of murine CAR-T cells.

category: genetics