title: Gut IgA Enhances Systemic IgG Responses to Pneumococcal Vaccines Through the Commensal Microbiota

abstract: The gut microbiota enhances systemic immunoglobulin G (IgG) responses to vaccines. However, it is unknown whether this effect involves IgA, a mucosal antibody that coats intestinal microbes. Here we found that gut IgA increased peripheral IgG responses to pneumococcal vaccines, as these responses were profoundly impaired in mice with global or mucosa-restricted IgA deficiency. The positive effect of IgA on vaccine-induced IgG production implicated gut bacteria. Indeed, IgG responses to pneumococcal vaccines were also defective in ex-germ free mice recolonized with gut microbes from mouse or human IgA-deficient donors. IgA exerted this IgG-enhancing effect by constraining the systemic translocation of intestinal commensal antigens, which caused chronic immune activation, including T cell overexpression of programmed death-1. This immune inhibitory receptor hindered vaccine-specific IgG production by eliciting functional B cell unresponsiveness, which was reverted by anti-programmed death-1 treatment. Thus, gut IgA is functionally interconnected with systemic IgG via intestinal microbes.


title: The predictive potential of key adaptation parameters and proxy fitness traits between benign and stressful thermal environments

abstract: Understanding the adaptive potential of a species is key when predicting whether a species can contend with climate change. Adaptive capacity depends on the amount of genetic variation within a population for relevant traits. However, genetic variation changes in different environments, making it difficult to predict whether a trait will respond to selection when not measured directly in that environment. Here, we investigated how genetic variances, and phenotypic and genetic covariances, between a fitness trait and morphological traits changed between thermal environments in two closely-related Drosophila. If morphological traits strongly correlate with fitness, they may provide an easy-to-measure proxy of fitness to aid in understanding adaptation potential. We used a parent-offspring quantitative genetic design to test the effect of a benign (23{degrees}C) and stressful (28{degrees}C) thermal environment on genetic variances of fecundity and wing size and shape, and their phenotypic and genetic covariances. We found genetic variances were higher within the stressful environment for fecundity but lower within the stressful environment for wing size. We did not find evidence for significant phenotypic correlations. Phenotypic and genetic correlations did not reveal a consistent pattern between thermal environments or within or between species. This corroborates previous research and reiterates that conclusions drawn in one environment about the adaptive potential of a trait, and the relationship of that trait with fitness, cannot be extrapolated to other environments or within or between closely-related species. This confirms that researchers should use caution when generalising findings across environments in terms of genetic variation and adaptive potential.

category: evolutionary biology


title: New Segmentation and Feature Extraction Algorithm for the Classification of White Blood Cells in Peripheral Smear Images

abstract: This article addresses a new method for the classification of white blood cells (WBCs) using image processing techniques and machine learning methods. The proposed method consists of three steps: detecting the nucleus and cytoplasm, extracting features, and classification. At first, a new algorithm is designed to segment the nucleus. For the cytoplasm to be detected, only a part of it located inside the convex hull of the nucleus is involved in the process. This attitude helps us overcome the difficulties of segmenting the cytoplasm. In the second phase, three shapes and four novel color features are devised and extracted. Finally, by using an SVM model, the WBCs are classified. The segmentation algorithm can detect the nucleus with a dice similarity coefficient of 0.9675. The proposed method can categorize WBCs in Raabin-WBC, LISC, and BCCD datasets with accuracies of 94.65 %, 92.21 %, and 94.20 %, respectively. It is worth mentioning that the hyperparameters of the classifier are fixed only with the Raabin-WBC dataset, and these parameters are not readjusted for LISC and BCCD datasets. The obtained results demonstrate that the proposed method is robust, fast, and accurate.

category: bioengineering


title: New Segmentation and Feature Extraction Algorithm for Classification of White Blood Cells in Peripheral Smear Images


title: Low effective mechanical advantage of giraffes' limbs during walking reveals trade-off between limb length and locomotor performance

abstract:
Giraffes (Giraffa camelopardalis) possess specialised locomotor morphology, namely elongate and gracile distal limbs. Whilst this contributes to their overall height (and enhanced feeding behaviour), we propose that the combination of long limb segments and modest muscle lever arms results in low effective mechanical advantage (EMA, the ratio of in-lever to out-lever moment arms), when compared with other cursorial mammals. To test this, we used a combination of experimentally measured kinematics and ground rection forces (GRFs), musculoskeletal modelling, and inverse dynamics to calculate giraffe forelimb EMA during walking. Giraffes walk with an EMA of 0.34 ({+/-}0.05 S.D.), with no evident association with speed within their walking gait. Giraffe EMA was markedly below the expectations extrapolated from other mammals ranging from 0.03 - 297 kg, and provides further evidence that EMA plateaus or even diminishes in mammals exceeding horse size. We further tested the idea that limb segment length is a factor which determines EMA, by modelling the GRF and muscle moment arms in the extinct giraffid Sivatherium giganteum and the other extant giraffid Okapia johnstoni. Giraffa and Okapia shared similar EMA, despite a 4-6 fold difference in body mass (Okapia EMA = 0.38). In contrast Sivatherium, sharing a similar body mass to Giraffa, had greater EMA (0.59), which we propose reflects behavioural differences, such athletic performance. Our modelling approach suggests that limb length is a determinant of GRF moment arm magnitude, and that unless muscle moment arms scale isometrically with limb length, tall mammals are prone to low EMA.

Significance StatementGiraffes are the tallest living animals - using their height to access food unavailable to their competitors. It is not clear how their specialized anatomy impacts their athletic ability. We made musculoskeletal models of the forelimbs from a giraffe and two close relatives, and used motion-capture and forceplate data to measure how efficient they are when walking in a straight line. A horse for example, uses just 1 unit of muscle force to oppose 1 unit of force on the ground. Giraffe limbs however are comparatively disadvantaged - their muscles must develop 3 units of force to oppose 1 unit of force at the ground. This explains why giraffes walk and run at relatively slow speeds.

category: biophysics


title: Nucleosome induced homology recognition in chromatin

abstract: One of the least understood properties of chromatin is the ability of its similar regions to recognise each other through weak interactions. Theories based on electrostatic interactions between helical macromolecules suggest that the ability to recognize sequence homology is an innate property of the non-ideal helical structure of DNA. However, this theory does not account for nucleosomal packing of DNA. Can homologous DNA sequences recognize each other while wrapped up in the nucleosomes? Can structural homology arise at the level of nucleosome arrays? Here we present a theoretical investigation of the recognition-potential-well between chromatin fibers sliding against each other. This well is different to the one predicted and observed for bare DNA; the minima in energy do not correspond to literal juxtaposition, but are shifted by approximately half the nucleosome repeat length. The presence of this potential-well suggests that nucleosome positioning may induce mutual sequence recognition between chromatin fibers and facilitate formation of chromatin nanodomains. This has implications for nucleosome arrays enclosed between CTCF-cohesin boundaries, which may form stiffer stem-like structures instead of flexible entropically favourable loops. We also consider switches between chromatin states, e.g., through acetylation/deacetylation of histones, and discuss nucleosome-induced recognition as a precursory stage of genetic recombination.


title: Chromoanagenesis landscape in 10,000 TCGA patients

abstract: During the past decade, whole-genome sequencing of tumor biopsies and individuals with congenital disorders highlighted the phenomenon of chromoanagenesis, a single chaotic event of chromosomal rearrangement. Chromoanagenesis was shown to be frequent in many types of cancers, to occur in early stages of cancer development, and significantly impact the tumors nature. However, an in-depth, cancer-type dependent analysis has been somewhat incomplete due to the shortage in whole genome sequencing of cancerous samples. In this study, we extracted data from The Pan-Cancer Analysis of Whole Genome (PCAWG) and The Cancer Genome Atlas (TCGA) to construct a machine learning algorithm that can detect chromoanagenesis with high accuracy (86%). The algorithm was applied to ~10,000 TCGA cancer patients. We utilize the chromoanagenesis assignment results, to analyze cancer-type specific chromoanagenesis characteristics in 20 TCGA cancer types. Our results unveil prominent genes affected in either chromoanagenesis or non-chromoanagenesis tumorigenesis. The analysis reveals a mutual exclusivity relationship between the genes impaired in chromoanagenesis versus non-chromoanagenesis cases. We offer the discovered characteristics as possible targets for cancer diagnostic and therapeutic purposes.

category: cancer biology


title: Crystal structures of the σ2 receptor template large-library docking for selective chemotypes active in vivo

abstract: The {sigma}2 receptor is a poorly understood transmembrane receptor that has attracted intense interest in many areas of biology including cancer imaging, Alzheimers disease, schizophrenia, and neuropathic pain. However, little is known regarding the molecular details of the receptor, and few highly selective ligands are available. Here, we report the crystal structure of the {sigma}2 receptor in complex with the clinical drug candidate roluperidone and the probe compound PB28. These structures, in turn, templated a large-scale docking screen of 490 million make-on-demand molecules. Of these, 484 compounds were synthesized and tested, prioritizing not only high-ranking docked molecules, but also those with mediocre and poor scores. Overall, 127 compounds with binding affinities superior to 1 M were identified, all in new chemotypes, 31 of which had affinities superior to 50 nM. Intriguingly, hit rate fell smoothly and monotonically with docking score. Seeking to develop selective and biologically active probe molecules, we optimized three of the original docking hits for potency and for selectivity, achieving affinities in the 3 to 48 nM range and to up to 250-fold selectivity vs. the {sigma}1 receptor. Crystal structures of the newly discovered ligands bound to the {sigma}2 receptor were subsequently determined, confirming the docked poses. To investigate the contribution of the {sigma}2 receptor in pain processing, and to distinguish it from the contribution of the {sigma}1 receptor, two potent {sigma}2-selective and one potent {sigma}1/{sigma}2 non-selective ligand were tested for efficacy in a mouse model of neuropathic pain. All three ligands demonstrated timedependent decreases in mechanical hypersensitivity in the spared nerve injury model, supporting a role for the {sigma}2 receptor in nociception, and a possible role for {sigma}1/{sigma}2 polypharmacology. This study illustrates the opportunities for rapid discovery of in vivo active and selective probes to study under-explored areas of biology using structurebased screens of diverse, ultra-large libraries following the elucidation of protein structures.

category: pharmacology and toxicology


title: Topographic divergence of atypical cortical asymmetry and regional atrophy patterns in temporal lobe epilepsy: a worldwide enigma study

abstract: AO_SCPLOWBSTRACTC_SCPLOWTemporal lobe epilepsy (TLE), a common drug-resistant epilepsy in adults, is primarily a limbic network disorder associated with predominant unilateral hippocampal pathology. Structural MRI has provided an in vivo window into whole-brain grey matter pathology in TLE relative to controls, by either mapping (i) atypical inter-hemispheric asymmetry or (ii) regional atrophy. However, similarities and differences of both atypical asymmetry and regional atrophy measures have not been systematically investigated. Here, we addressed this gap using the multi-site ENIGMA-Epilepsy dataset comprising MRI brain morphological measures in 732 TLE patients and 1,418 healthy controls. We compared spatial distributions of grey matter asymmetry and atrophy in TLE, contextualized their topographies relative to spatial gradients in cortical microstructure and functional connectivity, and examined clinical associations using machine learning. We identified a marked divergence in the spatial distribution of atypical inter-hemispheric asymmetry and regional atrophy mapping. The former revealed a temporo-limbic disease signature while the latter showed diffuse and bilateral patterns. Our findings were robust across individual sites and patients. Cortical atrophy was significantly correlated with disease duration and age at seizure onset, while degrees of asymmetry did not show a significant relationship to these clinical variables. Our findings highlight that the mapping of atypical inter-hemispheric asymmetry and regional atrophy tap into two complementary aspects of TLE-related pathology, with the former revealing primary substrates in ipsilateral limbic circuits and the latter capturing bilateral disease effects. These findings refine our notion of the neuropathology of TLE and may inform future discovery and validation of complementary MRI biomarkers in TLE.

category: neuroscience


title: Induced neural progenitor cells and iPS-neurons from major depressive disorder patients show altered bioenergetics and electrophysiological properties

abstract: The molecular pathomechanisms of major depressive disorder (MDD) are still not completely understood. Here, we follow the hypothesis, that mitochondria dysfunction which is inevitably associated with bioenergetic disbalance is a risk factor that contributes to the susceptibility of an individual to develop MDD. Thus, we investigated molecular mechanisms related to mitochondrial function in induced neuronal progenitor cells (NPCs) which were reprogrammed from fibroblasts of eight MDD patients and eight non-depressed controls. We found significantly lower maximal respiration rates, altered cytosolic basal calcium levels, and smaller soma size in NPCs derived from MDD patients. These findings are partially consistent with our earlier observations in MDD patient-derived fibroblasts. Furthermore, we differentiated MDD and control NPCs into iPS-neurons and analysed their passive biophysical and active electrophysiological properties to investigate whether neuronal function can be related to altered mitochondrial activity and bioenergetics. Interestingly, MDD patient-derived iPS-neurons showed significantly lower membrane capacitance, a less hyperpolarized membrane potential, increased Na+ current density and increased spontaneous electrical activity. Our findings indicate that functional differences evident in fibroblasts derived from MDD patients are partially present after reprogramming to induced-NPCs, might relate to altered function of iPS-neurons and thus might be associated with the aetiology of major depressive disorder.


title: Nuclei are mobile processors enabling specialization in a gigantic single-celled syncytium

abstract: In multicellular organisms, the specification, coordination, and compartmentalization of cell types enable the formation of complex body plans. However, some eukaryotic protists such as slime molds generate diverse and complex structures while remaining in a multinucleated syncytial state. It is unknown if different regions of these giant syncytial cells have distinct transcriptional responses to environmental encounters, and if nuclei within the cell diversify into heterogeneous states. Here we performed spatial transcriptome analysis of the slime mold Physarum polycephalum in the plasmodium state under different environmental conditions, and used single-nucleus RNA-sequencing to dissect gene expression heterogeneity among nuclei. Our data identifies transcriptome regionality in the organism that associates with proliferation, syncytial substructures, and localized environmental conditions. Further, we find that nuclei are heterogenous in their transcriptional profile, and may process local signals within the plasmodium to coordinate cell growth, metabolism, and reproduction. To understand how nuclei variation within the syncytium compares to heterogeneity in single-nucleated cells, we analyzed states in single Physarum amoebal cells. We observed amoebal cell states at different stages of mitosis and meiosis, and identified cytokinetic features that are specific to nuclei divisions within the syncytium. Notably, we do not find evidence for predefined transcriptomic states in the amoebae that are observed in the syncytium. Our data shows that a single-celled slime mold can control its gene expression in a region-specific manner while lacking cellular compartmentalization, and suggests that nuclei are mobile processors facilitating local specialized functions. More broadly, slime molds offer the extraordinary opportunity to explore how organisms can evolve regulatory mechanisms to divide labor, specialize, balance competition with cooperation, and perform other foundational principles that govern the logic of life.

category: cell biology


title: Genome-wide mutational signatures of immunological diversification in normal lymphocytes

abstract:
A lymphocyte suffers many threats to its genome, including programmed mutation during differentiation, antigen-driven proliferation and residency in diverse microenvironments. After developing protocols for single-cell lymphocyte expansions, we sequenced whole genomes from 717 normal naive and memory B and T lymphocytes and hematopoietic stem cells. Lymphocytes carried more point mutations and structural variation than stem cells, accruing at higher rates in T than B cells, attributable to both exogenous and endogenous mutational processes. Ultraviolet light exposure and other sporadic mutational processes generated hundreds to thousands of mutations in some memory lymphocytes. Memory B cells acquired, on average, 18 off-target mutations genome-wide for every one on-target IGV mutation during the germinal center reaction. Structural variation was 16-fold higher in lymphocytes than stem cells, with ~15% of deletions being attributable to off-target RAG activity.

One Sentence SummaryThe mutational landscape of normal lymphocytes chronicles the off-target effects of programmed genome engineering during immunological diversification and the consequences of differentiation, proliferation and residency in diverse microenvironments.

category: genomics


title: Tissue fixation effects on human retinal lipid analysis by MALDI imaging and LC-MS/MS technologies

abstract: Imaging mass spectrometry (IMS) allows the location and abundance of lipids to be mapped across tissue sections of human retina. For reproducible and accurate information, sample preparation methods need to be optimized. Paraformaldehyde fixation of a delicate multilayer structure like human retina facilitates the preservation of tissue morphology by forming methylene bridge cross-links between formaldehyde and amine/ thiols in biomolecules; however, retina sections analyzed by IMS are typically fresh-frozen. To determine if clinically significant inferences could be reliably based on fixed tissue, we evaluated the effect of fixation on analyte detection, spatial localization, and introduction of artefactual signals. Hence, we assessed the molecular identity of lipids generated by matrix-assisted laser desorption ionization (MALDI-IMS) and liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) for fixed and fresh-frozen retina tissues in positive and negative ion modes. Based on MALDI-IMS analysis, more lipid signals were observed in fixed compared to fresh-frozen retina. More potassium adducts were observed in fresh-frozen tissues than fixed as the fixation process caused displacement of potassium adducts to protonated and sodiated species in ion positive ion mode. LC-MS/MS analysis revealed an overall decrease in lipid signals due to fixation that reduced glycerophospholipids and glycerolipids and conserved most sphingolipids and cholesteryl esters. The high quality and reproducible information from untargeted lipidomics analysis of fixed retina informs on all major lipid classes, similar to fresh-frozen retina, and serves as a steppingstone towards understanding of lipid alterations in retinal diseases.

category: biochemistry


title: ROR and RYK extracellular region structures suggest that receptor tyrosine kinases have distinct WNT-recognition modes

abstract: SUMMARYWNTs play key roles in development and disease, by binding both Frizzled (FZD) seven-pass transmembrane receptors and numerous co-receptors that include the ROR and RYK receptor tyrosine kinases (RTKs). We describe crystal structures and WNT-binding characteristics of extracellular regions from the Drosophila ROR and RYK orthologs Nrk (neurospecific receptor tyrosine kinase) and Derailed-2 (Drl-2). RORs bind WNTs though a FZD-related cysteine-rich domain (CRD), and RYKs through a WNT-inhibitory factor (WIF) domain. Our structures suggest that neither the Nrk CRD nor the Drl-2 WIF domain can accommodate the acyl chain typically attached to WNTs. The Nrk CRD contains a deeply buried bound fatty acid, unlikely to be exchangeable with a WNT acyl chain. The Drl-2 WIF domain lacks the lipid-binding site seen in WIF-1. We also show that DWnt-5, which regulates Drosophila ROR and RYK orthologs, lacks an acyl chain. Together with analysis of WNT/receptor interaction sites, these structures provide new insight into how WNTs recruit their RTK co-receptors into signaling complexes.


title: Why does Δ9-Tetrahydrocannabinol act as a partial agonist of cannabinoid receptors?

abstract: Cannabinoid receptor 1 (CB1) is a therapeutically relevant drug target for controlling pain, obesity, and other central nervous system disorders. However, full agonists and antagonists of CB1 have been reported to cause serious side effects in patients. Therefore, partial agonists have emerged as a viable alternative to full agonists and antagonists as they avoid overstimulation and side effects. One of the key bottlenecks in the design of partial agonists is the lack of understanding of the molecular mechanism of partial agonism. In this study, we examine two mechanistic hypotheses for the origin of partial agonism in cannabinoid receptors and explain the mechanistic basis of partial agonism exhibited by {Delta}9-Tetrahydrocannabinol (THC). In particular, we inspect whether partial agonism emerges from the ability of THC to bind in both agonist and antagonist binding pose or from its ability to only partially activate the receptor. Extensive molecular dynamics simulations and the Markov state model capture the THC binding in both antagonist, and agonist binding poses in CB1 receptor. Furthermore, we observe that binding of THC in the agonist binding pose leads to rotation of toggle switch residues and causes partial outward movement of intracellular transmembrane helix 6 (TM6). Our simulations also suggest that the alkyl side chain of THC plays a crucial role in determining partial agonism by stabilizing the ligand in the agonist and antagonist-like poses within the pocket. This study provides us fundamental insights into the mechanistic origin of the partial agonism of THC.


title: Imaging protein conformational space in liquid water

abstract: Recent developments in electron-transparent materials have paved the way for liquid-phase electron microscopy (LPEM) leading to an unprecedented understanding of the structure and dynamics of specimens in their liquid environment. Image reconstruction in liquid-state poses several challenges, and most importantly, it undermines the single-particle analysis assumption that the three-dimensional objects captured on the image sensor are identical. We propose the combination of all-atom simulations with LPEM to complement structural studies with dynamic investigations. In this work, we exploited LPEM to image the dynamics of particles undergoing Brownian motion, using their natural rotation to access the particle structural landscape for reconstructing its architecture in 3D using tomographic techniques. We have selected two test cases for our approach according to prior data accessibility and physiological environment factors: apoferritin and archaeal RNA polymerase. We show that the adopted approach allows to achieve sub-nanometer spatial resolutions of protein structures, either imaging proteins one by one and assessing different conformational states or combining several proteins into one statistical conformational ensemble.


title: Analysis of the mechanism of Aldo-keto reductase dependent cis-platin resistance in HepG2 based on transcriptomic and NADH metabolic analysis

abstract: Aldo-keto oxidoreductase (AKR) inhibitors could reverse several cancer cells resistance to Cis-platin, but their role in resistance remains unclear. Our RNA-seq results showed de novo NAD biosynthesis-related genes, and NAD(P)H-dependent oxidoreductases were significantly upregulated in Cis-platin-resistant HepG2 hepatic cancer cells (HepG2-RC cells) compared with HepG2 cells. Knockdown of AKR1Cs could increase Cis-platin sensitivity in HepG2-RC cells about two-fold. Interestingly, the AKR1C inhibitor meclofenamic acid could increase Cis-platin sensitivity of HepG2-RC cells about eight-fold, indicating that knockdown of AKR1Cs only partially reversed the resistance. Meanwhile, the amount of total NAD and the ratio of NADH/NAD+ were increased in HepG2-RC cells compared with HepG2 cells. The increased NADH could be explained as a directly operating antioxidant to scavenge radicals induced by Cis-platin. We report here that NADH, which is produced by NAD(P)H-dependent oxidoreductases, plays a key role in the AKR-associated Cis-platin resistance of HepG2 hepatic cancer cells.


title: STDP and the distribution of preferred phases in the whisker system

abstract:
Rats and mice use their whiskers to probe the environment. By rhythmically swiping their whiskers back and forth they can detect the existence of an object, locate it, and identify its texture. Localization can be accomplished by inferring the position of the whisker. Rhythmic neurons that track the phase of the whisking cycle encode information about the azimuthal location of the whisker. These neurons are characterized by preferred phases of firing that are narrowly distributed. Consequently, pooling the rhythmic signal from several upstream neurons is expected to result in a much narrower distribution of preferred phases in the downstream population, which however has not been observed empirically. Here, we show how spike timing dependent plasticity (STDP) can provide a solution to this conundrum. We investigated the effect of STDP on the utility of a neural population to transmit rhythmic information downstream using the framework of a modeling study. We found that under a wide range of parameters, STDP facilitated the transfer of rhythmic information despite the fact that all the synaptic weights remained dynamic. As a result, the preferred phase of the downstream neuron was not fixed, but rather drifted in time at a drift velocity that depended on the preferred phase, thus inducing a distribution of preferred phases. We further analyzed how the STDP rule governs the distribution of preferred phases in the downstream population. This link between the STDP rule and the distribution of preferred phases constitutes a natural test for our theory.

Author summaryThe distribution of preferred phases of whisking neurons in the somatosensory system of rats and mice presents a conundrum: a simple pooling model predicts a distribution that is an order of magnitude narrower than what is observed empirically. Here, we suggest that this non-trivial distribution may result from activity-dependent plasticity in the form of spike timing dependent plasticity (STDP). We show that under STDP, the synaptic weights do not converge to a fixed value, but rather remain dynamic. As a result, the preferred phases of the whisking neurons vary in time, hence inducing a non-trivial distribution of preferred phases, which is governed by the STDP rule. Our results imply that the considerable synaptic volatility which has long been viewed as a difficulty that needs to be overcome, may actually be an underlying principle of the organization of the central nervous system.


title: Increased signal to noise ratios within experimental field trials by regressing spatially distributed soil properties as principal components.

abstract:
Environmental variability poses a major challenge to any field study. Researchers attempt to mitigate this challenge through replication. Thus, the ability to detect experimental signals is determined by the degree of replication and the amount of environmental variation, noise, within the experimental system. A major source of noise in field studies comes from the natural heterogeneity of soil properties which create micro-treatments throughout the field. To make matters worse, the variation within different soil properties is often non-randomly distributed across a field. We explore this challenge through a sorghum field trial dataset with accompanying plant, microbiome and soil property data. Diverse sorghum genotypes and two watering regimes were applied in a split-plot design. We describe a process of identifying, estimating, and controlling for the effects of spatially distributed soil properties on plant traits and microbial communities using minimal degrees of freedom. Importantly, this process provides a tool with which sources of environmental variation in field data can be identified and removed, improving our ability to resolve effects of interest and to quantify subtle phenotypes.

IMPORTANCEData from field experiments are notoriously noisy. Proper field designs with high replication aid in mitigating this challenge, yet true biological correlations are still often masked by environmental variability. This work identifies soil property composition as a spatially distributed source of variance to three types of characteristics: plant phenotype, microbiome composition, and leaf traits. We show that once identified, spatial principal component regression was able to account for these effects so that more precise estimates of experimental factors were obtained. This generalizable method is applicable to diverse field experiments.

category: systems biology


title: A type I interferon response defines a conserved microglial state required for effective phagocytosis

abstract: Microglia, the innate immune cells of the brain, are exquisitely sensitive to dynamic changes in the neural environment. Using single cell RNA sequencing of the postnatal somatosensory cortex during topographic remapping, we identified a type I interferon (IFN-I) responsive microglia population that expanded with this developmental stressor. Using the marker gene IFITM3 we found that IFN-I responsive microglia were engulfing whole neurons. Loss of IFN-I signaling (Ifnar1-/-) resulted in dysmorphic  bubble microglia with enlarged phagolysosomal compartments. We also observed a reduction in dead cells and an accumulation of neurons with double strand DNA breaks, a marker of cell stress. Conversely, IFN-I gain of function in zebrafish was sufficient to drive microglial engulfment of whole neurons. We identified IFITM3+ microglia in two murine disease models: SARS-CoV-2 infection and the 5xFAD model of Alzheimers disease. These data reveal a novel role for IFN-I signaling in regulating efficient neuronal clearance by microglia.


title: A type I interferon response defines a conserved microglial state required for effective neuronal phagocytosis


title: A behavioral paradigm for measuring perceptual distances in mice

abstract: Perceptual similarities between a specific stimulus and other stimuli of the same modality provide valuable information about the structure and geometry of sensory spaces. While typically a subject of behavioral experiments in humans, perceptual similarities, or distances, are rarely measured in other species. However, understanding the neural computations responsible for sensory representations requires the monitoring and sometime manipulating of neural activity, which is more readily achieved in other experimental models. Here we develop a behavioral paradigm that allows for the quantifying of perceptual similarity between sensory stimuli using mouse olfaction as a model system.


title: Enhancing the darkside: Asymmetric gain of cone photoreceptors underpins discrimination of visual scenes based on their skewness

abstract: Psychophysical data indicates humans can discriminate visual scenes based on their skewness - the ratio of dark and bright patches within a visual scene. It was also shown that on a phenomenological level this skew discrimination is described by the so-called Blackshot mechanism, which accentuates strong negative contrasts within a scene. Here we demonstrate that the underlying computation starts as early as the cone phototransduction cascade whose gain is higher for strong negative contrasts than for strong positive contrasts. We recorded from goldfish cone photoreceptors and found that the asymmetry in the phototransduction gain leads to higher amplitude of the responses to negatively than to positively skewed light stimuli. This asymmetry in the amplitude was present in the photocurrent, voltage response and cone synaptic output. These results highlight the importance of the early photoreceptor non-linearity for perception. Additionally, we found that stimulus skewness leads to a subtle change in photoreceptor kinetics. For negatively skewed stimuli, the cones impulse response functions peak later than for positively skewed stimulus. However, stimulus skewness does not affect the cones overall integration time.


title: A four-point measurement probe for brain tissue conductivity and permittivity characterization

abstract: We present a measurement probe consisting of four platinum electrodes fused into soda-lime glass. The probe is based on a four-terminal sensing technique that uses separate pairs of current-carrying and voltage-sensing electrodes and performs more accurate measurements than the simpler and more usual two-terminal sensing technique. The electrodes are aranged within an area of 1 mm2 allowing for local characterization of different brain tissues. The operation of the probe is demonstrated in situ on post mortem porcine brain tissue by measuring the impedance spectra of grey and white matter in a frequency range of 1 kHz < f < 1 MHz. The conductivity and relative permittivity are derived from the impedance spectra using the geometry factor of the probe. The geometry factor is obtained experimentally by measuring the impedances of an electrolytical dilution series with known conductivities. The obtained conductivity of grey matter is in the order of 0.11 S/m and of white matter is in the order of 0.07 S/m over the acquired frequency range.


title: Morphine exposure bidirectionally alters c-Fos expression in a sex-, age-, and brain region-specific manner during adolescence

abstract: Drug and alcohol use during adolescence is common, and data in both humans and preclinical animal models clearly indicate drug exposure during adolescence increases the risk of substance use and other mental health disorders later in life. Adolescence is a period of social, emotional, and cognitive development, and is characterized by increased exploratory behavior, risk-taking, and peer-centered social interactions. These are thought to be behavioral manifestations of developmental plasticity in  reward regions of the brain. Human data indicate that adolescence is not a unitary developmental period, but rather different neural and behavioral sequelae can be observed in early vs. late adolescence. However, most studies with rodent models examine a single adolescent age compared to a mature adult age, and often only in males. Herein, we sought to determine whether the acute response to the opioid morphine would also differ across adolescence, and by sex. By quantifying c-Fos positive cells, a proxy for neural activity, at different stages during adolescence (pre-, early, mid-, and late adolescence) and in multiple reward regions (prefrontal cortex, nucleus accumbens, caudate/putamen), we determined that acute morphine can either reduce or increase c-Fos expression dependent on adolescent age, sex, and brain region. These data suggest that heterogeneity in the consequences of adolescent opioid exposure may be due to the interaction between age- and sex-specific developmental profiles of reward processing in individual brain regions. In future studies, it will be important to add age within adolescence as an independent variable to fully capture the consequences of healthy or abnormal reward-related neural development.


title: PTPRU, a quiescence-induced receptor tyrosine phosphatase negatively regulates osteogenic differentiation of human mesenchymal stem cells

abstract: Bone marrow mesenchymal stem cells (MSCs) are heterogeneous osteo-progenitors that are mainly responsible for bone regeneration and homeostasis. In vivo, a subpopulation of bone marrow MSCs persists in a quiescent state, providing a source of new cells for repair. Previously, we reported that induction of quiescence in hMSCs in vitro skews their differentiation potential in favour of osteogenesis while suppressing adipogenesis. Here, we uncover a new role for a protein tyrosine phosphatase, receptor type U (PTPRU) in repressing osteogenesis during quiescence. A 75 kD PTPRU protein isoform was found to be specifically induced during quiescence and down-regulated during cell cycle reactivation. Using siRNA-mediated knockdown, we report that in proliferating hMSC, PTPRU preserves self-renewal, while in quiescent hMSC, PTPRU not only maintains reversibility of cell cycle arrest but also suppresses expression of osteogenic lineage genes. Knockdown of PTPRU in proliferating or quiescent hMSC de-represses osteogenic markers, and enhances induced osteogenic differentiation. We also show that PTPRU positively regulates a {beta}-catenin-TCF transcriptional reporter. Taken together, our study suggests a role for a quiescence-induced 75kD PTPRU isoform in modulating bone differentiation in hMSC, potentially involving the Wnt pathway.


title: Large-scale deployment and establishment of Wolbachia into the Aedes aegypti population in Rio de Janeiro, Brazil.

abstract: Traditional methods of vector control have proven insufficient to reduce the alarming incidence of Dengue, Zika and chikungunya in endemic countries. The bacterium symbiont Wolbachia has emerged as an efficient pathogen-blocking and self-dispersing agent that reduces the vectorial potential of Aedes aegypti populations and potentially impairs arboviral disease transmission. In this work, we report the results of a large-scale Wolbachia intervention in Ilha do Governador, Rio de Janeiro, Brazil. wMel-infected adults were released across residential areas between August 2017 and March 2020. Over 131 weeks, including release and post-release phases, we monitored the wMel prevalence in field specimens, and analyzed introgression profiles of two assigned intervention areas, RJ1 and RJ2. Our results revealed that wMel successfully invaded both areas, reaching overall infection rates of 50-70% in RJ1, and 30-60% in RJ2 by the end of the monitoring period. At the neighborhood-level, wMel introgression was heterogeneous in both RJ1 and RJ2, with some profiles sustaining a consistent increase in infection rates and others failing to elicit the same. Correlation analysis revealed a weak overall association between RJ1 and RJ2 (r = 0.2849, P = 0.0236), and an association at a higher degree when comparing different deployment strategies, vehicle or backpack-assisted, within RJ1 (r = 0.4676, P < 0.0001) or RJ2 (r = 0.6263, P < 0.0001). The frequency knockdown resistance (kdr) alleles in wMel-infected specimens from both areas was consistently high over this study. Altogether, these findings corroborate that wMel can be successfully deployed at large-scale as part of vector control intervention strategies, and provide the basis for imminent disease impact studies in Southeastern Brazil.

category: ecology


category: microbiology


title: Ecological basis and genetic architecture of crypsis polymorphism in the desert clicker grasshopper (Ligurotettix coquilletti)

abstract: Color polymorphic species can offer exceptional insight into the ecology and genetics of adaptation. Although the genetic architecture of animal coloration is diverse, many color polymorphisms are associated with large structural variants and maintained by biotic interactions. Grasshoppers are exceptionally polymorphic in both color and karyotype, making them excellent models for understanding the ecological drivers and genetic underpinnings of color variation. Banded and uniform morphs of the desert clicker grasshopper (Ligurotettix coquilletti) are found across the western deserts of North America. To address the hypothesis that predation maintains local color polymorphism and shapes regional crypsis variation, we surveyed morph frequencies and tested for covariation with two predation environments. Morphs coexisted at intermediate frequencies at most sites, consistent with local balancing selection. Morph frequencies covaried with the appearance of desert substrate - an environment used only by females - indicating that ground-foraging predators are major agents of selection on crypsis. We next addressed the hypothesized link between morph variation and genome structure. To do so, we designed an approach for detecting inversions and indels using only RADseq data. The banded morph was perfectly correlated with a large putative indel. Remarkably, indel dominance differed among populations, a rare example of dominance evolution in nature.


title: How marine currents and environment shape plankton genomic differentiation: a mosaic view from Tara Oceans metagenomic data

abstract: Plankton seascape genomics show different trends from large-scale weak differentiation to micro-scale structures. Prior studies underlined the influence of environment and seascape on a few single species differentiation and adaptation. However, these works generally focused on few single species, sparse molecular markers, or local scales. Here, we investigate the genomic differentiation of plankton at macro-scale in a holistic approach using Tara Oceans metagenomic data together with a reference-free computational method to reconstruct the FST-based genomic differentiation of 113 marine planktonic species using metavariant species (MVS). These MVSs, modelling the species only by their polymorphism, include a wide range of taxonomic groups comprising notably 46 Maxillopoda/Copepoda, 24 Bacteria, 5 Dinoflagellates, 4 Haptophytes, 3 Cnidarians, 3 Mamiellales, 2 Ciliates, 1 Collodaria, 1 Echinoidea, 1 Pelagomonadaceae, 1 Cryptophyta and 1 Virus. The analyses showed that differentiation between populations was significantly lower within basins and higher in bacteria and unicellular eukaryotes compared to zooplantkon. By partitioning the variance of pairwise-FSTmatrices, we found that the main drivers of genomic differentiation were Lagrangian travel time, salinity and temperature. Furthermore, we classified MVSs into parameter-driven groups and showed that taxonomy poorly determines which environmental factor drives genomic differentiation. This holistic approach of plankton genomic differentiation for large geographic scales, a wide range of taxa and different oceanic basins, offers a systematic framework to analyse population genomics of non-model and undocumented marine organisms.


title: Translational control of polyamine metabolism by CNBP is required for Drosophila locomotor function

abstract:
Microsatellite expansions of CCTG repeats in the CNBP gene leads to accumulation of toxic RNA and have been associated to DM2. However, it is still unclear whether the dystrophic phenotype is also linked to CNBP decrease, a conserved CCHC-type zinc finger RNA binding protein that regulates translation and is required for mammalian development.

Here we show that depletion of Drosophila CNBP in muscles causes age-dependent locomotor defects that are correlated with impaired polyamine metabolism. We demonstrate that the levels of ornithine decarboxylase (ODC) and polyamines are significantly reduced upon dCNBP depletion. Of note, we show a reduction of the CNBP-polyamine axis in muscle from DM2 patients. Mechanistically, we provide evidence that dCNBP controls polyamine metabolism through binding dOdc mRNA and regulating its translation. Remarkably, the locomotor defect of dCNBP-deficient flies is rescued by either polyamine supplementation or dOdc1 overexpression. We suggest that this dCNBP function is evolutionarily conserved in vertebrates with relevant implications for CNBP-related pathophysiological conditions.

GRAPHICAL ABSTRACT

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/441910v2_ufig1.gif" ALT="Figure 1">
View larger version (35K):
org.highwire.dtl.DTLVardef@a8c31corg.highwire.dtl.DTLVardef@1a18260org.highwire.dtl.DTLVardef@76a3d4org.highwire.dtl.DTLVardef@fdd041_HPS_FORMAT_FIGEXP  M_FIG C_FIG CNBP controls muscle function by regulating the polyamine metabolism

O_LILack of dCNBP impairs locomotor function through ODC-polyamine downregulation
C_LIO_LIdCNBP binds dOdc mRNA and regulates its translation
C_LIO_LIPolyamine supplementation or dOdc1 reconstitution rescues locomotor defects
C_LIO_LICNBP-ODC-polyamine levels are reduced in muscle of DM2 patients
C_LI

category: genetics


title: Simple degradable cyclodextrin polyester with chelator-based crosslinker for stent-based drug delivery

abstract: Cyclodextrins are a class of molecules which inclusion complexes with small hydrophobic drugs, and has historically been used to improve solubility and bioavailability of labile drugs in pharmaceutical applications. More recently, polymerized cyclodextrin has been applied in various applications as implantable drug delivery depots and as medical device coatings (e.g. polymeric hernia meshes) due to their ability to sustain and control drug delivery as well as prevent biofouling. Cyclodextrin polymers as coatings for metal medical devices, like screws or stents, is less explored; due to the high mechanical property mismatch between polymers and metals, a polymer coating is liable to delaminate easily, especially during device deformation. Novel methods for facilitating attachment to metal substrates have been explored, but coating longevity is still an issue, and these methods typically require the use of multiple reagents and complex methods. We report here the development and characterization of a cyclodextrin polymer with a chelator-based crosslinker with respect to appearance, chemistry, drug release profiles, erosion, pH-dependence. We found that increasing the crosslinking ratio (crosslinker:cyclodextrin) slowed down degradation and decreased drug loading as well. Drug release of the anti-restenotic drug sirolimus proceeded for over 4 weeks. The ability of the polymer to stably coat metal stents was verified, and the coating procedure is a simple, single step protocol.


title: Movement-Preceding Neural Activity under Parametrically Varying Levels of Time Pressure

abstract: Self-initiated movements are known to be preceded by the readiness potential or RP, a gradual increase in surface-negativity of cortical potentials that can begin up to 1 second or more before movement onset. The RP has been extensively studied for decades, and yet we still lack a clear understanding of its functional role. Attempts to model the RP as an accumulation-to-bound process suggest that this signal is a by-product of time-locking to crests in neural noise rather than the outcome of a pre-conscious decision to initiate a movement. One parameter of the model accounts for the imperative to move now, with cued movements having a strong imperative and purely spontaneous movements having no imperative. Two different variants of the model have been proposed, and both predict a decrease in the (negative) amplitude of the early RP as the imperative grows stronger. In order to test this empirically, we conducted an experiment where subjects produced self-initiated movements under varying levels of time pressure, and we investigated the amplitude, shape, and latency of the RP as a function of the imperative to move, operationalised as a time limit. We identified distinct changes in the amplitude of the early RP that grew non-linearly as the time limit grew shorter. Thus these data did not support the prediction made by the model. In addition, our results confirm that the shape of the RP is not stereotypically negative, being either positive or absent in about half of the subjects.


title: Spatiotemporal patterns of neuronal subtype genesis suggest hierarchical development of retinal diversity

abstract: How do neuronal subtypes emerge during development? Recent molecular studies have expanded our knowledge of existing neuronal diversity. However, the genesis of neuronal subtypes remains elusive and previous studies have been limited by a lack of quantitative methods for simultaneous detection of subtype diversity in situ. The bipolar interneurons of the mammalian retina represent a diverse neuronal class, characterized by distinct functions, morphologies, and recently discovered transcriptional profiles. Here, we developed a comprehensive spatiotemporal map of bipolar subtype genesis in the retina. Combining multiplexed detection of 16 RNA markers with timed delivery of EdU and BrdU, we analyzed more than 30,000 single cells in full retinal sections to classify all bipolar subtypes and their birthdates. We found that bipolar subtype birthdates are ordered and follow a centrifugal developmental axis. Spatial analysis revealed a striking oscillatory wave pattern of bipolar subtype birthdates, and lineage analyses suggest clonal restriction on homotypic subtype production. These results inspired a hierarchical model of neuronal subtype genesis in the mammalian retina, with the wave pattern of subtype birthdates arising from early asymmetric cell divisions among founding retinal progenitor cells. Our results provide an outline of the developmental logic that generates diverse neuronal subtypes, and establishes a framework for studying subtype diversification.

category: developmental biology


title: Marker-assisted mapping enables effective forward genetic analysis in the arboviral vector Aedes aegypti, a species with vast recombination deserts

abstract: Aedes aegypti is a major vector of arboviruses that cause dengue, chikungunya, yellow fever and Zika. Although recent success in reverse genetics has facilitated rapid progress in basic and applied research, integration of forward genetics with modern technologies remains challenging in this important species, as up-to-47% of its chromosome is refractory to genetic mapping due to extremely low rate of recombination. Here we report the development of a marker-assisted-mapping (MAM) strategy to readily screen for and genotype only the rare but informative recombinants, drastically increasing both the resolution and signal-to-noise ratio. Using MAM, we mapped a transgene that was inserted in a >100 Mb recombination desert and a sex-linked spontaneous red-eye (re) mutation just outside the region. We subsequently determined, by CRISPR/Cas9-mediated knockout, that cardinal is the causal gene of re, which is the first forward genetic identification of a causal gene in Ae. aegypti. This study provides the molecular foundation for using gene-editing to develop versatile and stable genetic sexing methods by improving upon the current re-based genetic sexing strains. MAM does not require densely populated markers and can be readily applied throughout the genome to facilitate the mapping of genes responsible for insecticide- and viral-resistance. By enabling effective forward genetic analysis, MAM bridges a significant gap in establishing Ae. aegypti as a model system for research in vector biology. As large regions of suppressed recombination are also common in other plant and animal species including those of economic significance, MAM will have broad applications beyond vector biology.


title: WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

abstract: Evidence of whole-genome duplications (WGDs) and subsequent karyotype changes has been detected in most major lineages of life on Earth. To clarify the complex resulting multiple-layered patterns of gene collinearity in genome analyses there is a need for convenient and accurate toolkits. To meet this need, we introduce here WGDI (Whole-Genome Duplication Integrated analysis), a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidizations and cross-species genome alignments. WGDI supports three main workflows (polyploid inference, hierarchical inference of genomic homology, and ancestral chromosomal karyotyping) that can improve detection of WGD and characterization of related events. It incorporates a more sensitive and accurate collinearity detection algorithm than previous softwares, and can accelerate WGD-related karyotype research. As a freely available toolkit at GitHub (https://github.com/SunPengChuan/wgdi), WGDI outperforms similar tools in terms of efficiency, flexibility and scalability. In an illustrative example of its application, WGDI convincingly clarified karyotype evolution in Aquilegia coerulea and Vitis vinifera following WGDs and rejected the hypothesis that Aquilegia contributed as a parental lineage to the allopolyploid origin of core dicots.

category: bioinformatics


title: Volumetric Semantic Instance Segmentation of the Plasma Membrane of HeLa Cells

abstract: In this work, the unsupervised volumetric semantic segmentation of the plasma membrane of HeLa cells as observed with Serial Block Face Scanning Electron Microscopy is described. The resin background of the images was segmented at different slices of a 3D stack of 518 slices with 8, 192 x 8, 192 pixels each. The background was used to create a distance map which helped identify and rank the cells by their size at each slice. The centroids of the cells detected at different slices were linked to identify them as a single cell that spanned a number of slices. A subset of these cells, i.e., largest ones and those not close to the edges were selected for further processing. The selected cells were then automatically cropped to smaller regions of interest of 2, 000 x 2, 000 x 300 voxels that were treated as cell instances. Then, for each of these volumes the nucleus was segmented and the cell was separated from any neighbouring cells through a series of traditional image processing steps that followed the plasma membrane. The segmentation process was repeated for all the regions selected. For one cell for which the ground truth was available, the algorithm provided excellent results in Accuracy (AC) and Jaccard Index (JI): Nucleus: JI = 0.9665, AC= 0.9975, Cell and Nucleus JI = 0.8711, AC = 0.9655, Cell only JI = 0.8094, AC = 0.9629. A limitation of the algorithm for the plasma membrane segmentation was the presence of background, as in cases of tightly packed cells. When tested for these conditions, the segmentation of the nuclear envelope was still possible. All the code and data are released openly through GitHub, Zenodo and EMPIAR.


title: Germline Sex Determination regulates sex-specific signaling between germline stem cells and their niche

abstract: The establishment of sexual identity in germ cells is critical for the development of male and female germline stem cells (GSCs) and production of sperm vs. eggs. Thus, this process is essential for sexual reproduction and human fertility. Germ cells depend on signals from the somatic gonad to determine their sex, but in organisms such as flies, mice and humans, the sex chromosome genotype of the germ cells is also important for germline sexual development. How somatic signals and germ cell-intrinsic cues act together to regulate germline sex determination is a key question about which little is known. We have found that JAK/STAT signaling in the GSC niche promotes male identity in germ cells and GSCs, in part by activating expression of the epigenetic reader Phf7. We have also found that JAK/STAT signaling is blocked in XX (female) germ cells through the intrinsic action of the sex determination gene Sex lethal, which preserves female identity. Thus, an important function of germline sexual identity is to control how GSCs respond to signals in their niche environment.


title: Glucose Uptake as an Alternative to Stop-Flow Respirometry for Measuring Metabolic Rate in Danio rerio Larvae

abstract:
Respirometry is the current gold-standard for measuring metabolic rate. However, there is a growing need for metabolic rate measurements suitable for developmental studies, particularly in Danio rerio, where many important developmental stages occur at < 4 mm. While many metabolic studies rely on respirometry, the cost and complexity of the equipment limits its appeal in non-specialist labs, and background respiration becomes increasingly problematic as the size of the organism reduces. Here, glucose uptake was compared to stop-flow respirometry as an alternative measure of metabolic rate more suitable to the small scale required for developmental studies. A Passing-Bablok regression revealed the rate of glucose uptake can be considered equivalent to oxygen consumption as a measure of metabolic rate in Danio rerio larvae within a 95% limit of agreement. Therefore, glucose uptake is a valid alternative to the gold-standard in small organisms where conventional respirometry is problematic.

Summary statementThe rate of glucose uptake is a valid alternative to respirometry for metabolic rate measurements in small larval fish.

category: physiology


title: Subsynaptic positioning of AMPARs by LRRTM2 controls synaptic strength

abstract: Recent evidence suggests that nanoorganization of proteins within synapses may control the strength of communication between neurons in the brain. The unique subsynaptic distribution of glutamate receptors, which cluster in nanoalignment with presynaptic sites of glutamate release, supports this idea. However, testing it has been difficult because mechanisms controlling subsynaptic organization remain unknown. Reasoning that transcellular interactions could position AMPA receptors, we targeted a key transsynaptic adhesion molecule implicated in controlling AMPAR number, LRRTM2, using engineered, rapid proteolysis. Severing the LRRTM2 extracellular domain led quickly to nanoscale de-clustering of AMPARs away from release sites, not prompting their escape from synapses until much later. This rapid remodeling of AMPAR position produced significant deficits in evoked, but not spontaneous, postsynaptic receptor activation. These results dissociate receptor numbers from their nanopositioning in determination of synaptic function, and support the novel concept that adhesion molecules acutely position AMPA receptors to dynamically control synaptic strength.


title: Hematopoietic differentiation is characterized by a transient peak of cell-to-cell gene expression variability in normal and pathological conditions.

abstract: Hematopoietic differentiation has been metaphorically represented as linear trajectories with discrete steps from hematopoietic stem cells to mature cells. While the transcriptional state of cells at the beginning or at the end of these trajectories are well described from bulk analysis, what happens in the intermediate states has remained elusive until the use of single cell approaches. Applying Shannon entropy to measure cell-to-cell variability among cells at the same stage of differentiation, we observed a transient peak of gene expression variability in all the hematopoietic differentiation pathways. Strikingly, genes with the highest entropy variation in a given differentiation pathway matched genes known as pathway-specific, whereas genes with the highest expression variation were common to all pathways. Finally, we showed that the level of cell-to-cell variation is increased in the most immature compartment of hematopoiesis in myelodysplastic syndromes. These data suggest that differentiation could be better conceptualized as a dynamical stochastic process with a transient stage of cellular indetermination.


title: Hematopoietic differentiation is characterized by a transient peak of entropy at a single cell level.


title: Dynamics and heterogeneity of Erk-induced immediate-early gene expression

abstract: Many canonical signaling pathways exhibit complex time-varying responses, yet how minutes-timescale pulses of signaling interact with the dynamics of transcription and gene expression remains poorly understood. Erk-induced immediate early gene (IEG) expression is a model of this interface, exemplifying both dynamic pathway activity and a rapid, potent transcriptional response. Here, we quantitatively characterize IEG expression downstream of dynamic Erk stimuli in individual cells. We find that IEG expression responds rapidly to acute changes in Erk activity, but only in a sub-population of stimulus-responsive cells. We find that while Erk activity partially predicts IEG expression, a majority of response heterogeneity is independent of Erk and can be rapidly tuned by different mitogenic stimuli and parallel signaling pathways. We extend our findings to an in vivo context, the mouse epidermis, where we observe heterogenous immediate-early gene accumulation in both fixed tissue and single-cell RNA-sequencing data. Our results demonstrate that signaling dynamics can be faithfully transmitted to gene expression and suggest that the signaling-responsive population is an important parameter for interpreting gene expression responses.


title: Unraveling the stepwise maturation of the yeast telomerase

abstract: Telomerases elongate the ends of chromosomes required for cell immortality through their reverse transcriptase activity. By using the model organism Saccharomyces cerevisiae we defined the order in which the holoenzyme matures. First, a longer precursor of the telomerase RNA, TLC1 is transcribed and exported into the cytoplasm, where it associates with the protecting Sm-ring, the Est- and the Pop-proteins. This partly matured telomerase is re-import into the nucleus via Mtr10 and a novel TLC1-import factor, the karyopherin Cse1. Remarkably, while mutations in all known transport factors result in short telomere ends, mutation in CSE1 bypasses this defect and become Type I like survivors. Interestingly, both import receptors contact the Sm-ring for nuclear import, which therefore resembles a quality control step in the maturation process of the telomerase. The re-imported immature TLC1 is finally trimmed into the ~1150 nucleotide long mature form. TMG-capping of TLC1 finalizes maturation, leading to mature telomerase.


title: A somatic piRNA pathway regulates epithelial-to-mesenchymal transition of chick neural crest cells

abstract: In the metazoan germline, Piwi proteins play an essential regulatory role in maintenance of stemness and self-renewal by piRNA-mediated repression of transposable elements. To date, the activity of Piwi proteins and the piRNA pathway in vertebrates was believed to be confined to the gonads. Our results reveal expression of Piwil1 in a vertebrate somatic cell type, the neural crest-a migratory embryonic stem cell population. We show that Piwil1 is expressed at low levels throughout chick neural crest development, peaking just before neural crest cells undergo an epithelial-to-mesenchymal transition to leave the neural tube and migrate into the periphery. Importantly, loss of Piwil1 impedes neural crest emigration. Small RNA sequencing reveals somatic piRNAs with sequence signatures of an active ping pong loop. Coupled with Piwil1 knockout RNA-seq, our data suggest that Piwil1 regulates expression of the transposon derived gene ERNI in the chick dorsal neural tube, which in turn suppresses Sox2 expression to precisely control the timing of neural crest specification and emigration. Our work provides mechanistic insight into a novel function of the piRNA pathway as a regulator of somatic development in vertebrates.


title: Enhancing and inhibitory motifs have coevolved to regulate CD4 activity

abstract: CD4+ T cells use T cell receptor (TCR)-CD3 complexes, and CD4, to respond to peptide antigens within MHCII molecules (pMHCII). We report here that, through [~]435 million years of evolution in jawed vertebrates, purifying selection has shaped motifs in the extracellular, transmembrane, and intracellular domains of eutherian CD4 that both enhance pMHCII responses and are coevolving with residues in an intracellular motif that inhibits pMHCII responses. Importantly, while CD4 interactions with the Src kinase, Lck, are classically viewed as the key determinant of CD4s contribution to pMHCII responses, we found that without the inhibitory motif CD4-Lck interactions are not necessary for robust responses to pMHCII. In summary, motifs that mediate events on the outside and inside of CD4+ T cells coevolved to finetune the relay of pMHCII-specific information across the membrane. These results have implications for the evolution and function of complex transmembrane receptors and for biomimetic engineering.

category: immunology


title: Evolutionary history and origin of Tre1 superfamily shed light on its role in regulating blood brain barrier.

abstract: Understanding how the evolutionary relationship between immune cells and the blood-brain is important to devise therapeutic strategies that can regulate their critical function. In vertebrates, immune cells follow either a paracellular or transcellular pathway to infiltrate the BBB. In drosophila glial cells form the BBB that regulates the access of immune-like cells to the drosophila brain. However, it is still not known which route immune-like cells follow to infiltrate the drosophila brain. In vertebrates, paracellular migration is dependent on PECAM1, while transcellular migration is dependent on the expression of CAV1. Interestingly drosophila genome lacks both genes. Tre1 superfamily (Tre1, Moody, and Dmel_CG4313) play a diverse role in regulating transepithelial migration in drosophila. However, its evolutionary history and origin are not yet known. We performed phylogenetic analysis, together with HH search, positive selection, and ancestral reconstruction to investigate the Tre1 family Interestingly we found that Tre1 exists in mollusks, insects, ambulacria, and sclaidphora. Moody is shown to be a more ancient protein and it existed since cnidaria emergence and has a homolog (GPCR84) in mammals. The third family member (Dmel_CG4313) only exists in insects. The origin of the family seems to be related to the rhodopsin-like family and in particular family . We found that opsin is the nearest receptor to have a common ancestor with the Tre1 superfamily that seems to have diverged in sponges. We investigated the positive selection of the Tre1 family using PAML. Tre1 seems to have evolved under negative selection, whereas Moody has evolved during positive selection. The sites that we found under positive selection are Likely to play a role in the speciation of function in the case of Moody. We have identified an SH3, in Tre1 and, moody and Dmel_CG4313. Sh3 is known to play a fundamental role in regulating actin movement in a Rho-dependent manner. We suggest that Tre1 could be playing an important role in paracellular diapedesis in drosophila.


title: Forward and Reverse Genetic Dissection of Morphogenesis Identifies Filament-Competent Candida auris Strains

abstract:
Candida auris is an emerging healthcare-associated pathogen of global concern. Although this organism does not display the same morphological plasticity as the related fungal pathogen Candida albicans, recent reports have identified numerous C. auris isolates that grow in cellular aggregates or filaments. However, the genetic circuitry governing C. auris morphology remains largely uncharacterized. Here, we developed an Agrobacterium-mediated transformation system to generate mutants exhibiting aggregating or filamentous cell morphologies. Aggregating strains were associated with disruption of homologs of Saccharomyces cerevisiae chitinase and chitin synthase regulatory proteins, including components of the Regulation of ACE2 Morphogenesis (RAM) pathway, while disruption of a homolog of the S. cerevisiae ELM1 gene resulted in a novel filamentous strain of C. auris. To facilitate targeted genetic manipulation, we developed a transiently expressed Cas9 and sgRNA expression system for use in C. auris. Transformation using this system significantly increased the efficiency of homologous recombination and targeted integration of a reporter cassette in all four clades of C. auris. Using this system, we generated targeted deletion mutants to confirm the roles of RAM and Elm1 proteins in regulating C. auris morphogenesis. Overall, our findings provide novel insights into the genetic regulation of aggregating and filamentous morphogenesis in C. auris. Furthermore, the genetic manipulation tools described here will allow for inexpensive and efficient manipulation of the C. auris genome.

ImportanceCandida auris is an emerging and often multi-drug resistant fungal pathogen responsible for outbreaks globally. Current difficulties in performing genetic manipulation in this organism remain a barrier to understanding C. auris biology. Homologous recombination approaches can result in less than 1% targeted integration of a reporter cassette, emphasizing the need for new genetic tools specific for manipulating C. auris. Here, we adapted Agrobacterium-mediated transformation and a transient Cas9 and sgRNA expression system for use in forward and reverse genetic manipulation of C. auris. We demonstrated the efficacy of each system by uncovering genes underlying cellular morphogenesis in C. auris. We identified a novel filamentous mutant of C. auris, demonstrating that this organism has maintained the capacity for filamentous growth. Our findings provide additional options for improving the genetic tractability of C. auris, which will allow for further characterization of this emerging pathogen.


title: Neural dynamics between anterior insular cortex and right supramarginal gyrus dissociate genuine affect sharing from automatic responses to pretended pain

abstract: Empathy for pain engages both shared affective responses and self-other distinction. In this study, we addressed the highly debated question of whether neural responses previously linked to affect sharing could result from the perception of salient affective displays. Moreover, we investigated how affect sharing and self-other distinction interact to determine our response to a pain that is either perceived as genuine or pretended (while in fact both were acted for reasons of experimental control). We found stronger activations in regions associated with affect sharing (anterior insula, aIns, and anterior mid-cingulate cortex, aMCC) as well as with affective self-other distinction (right supramarginal gyrus, rSMG), in participants watching video clips of genuine vs. pretended facial expressions of pain. Using dynamic causal modeling (DCM), we then assessed the neural dynamics between the right aIns and rSMG in these two conditions. This revealed a reduced inhibitory effect on the aIns to rSMG connection for genuine compared to pretended pain. For genuine pain only, brain-to-behavior regression analyses highlighted a linkage between this inhibitory effect on the one hand, and pain ratings as well as empathic traits on the other. These findings imply that if the pain of others is genuine and thus calls for an appropriate empathic response, neural responses in the aIns indeed seem related to affect sharing and self-other distinction is engaged to avoid empathic over-arousal. In contrast, if others merely pretend to be in pain, the perceptual salience of their painful expression results in neural responses that are down-regulated to avoid inappropriate affect sharing and social support.


title: Neurodegenerative and functional signatures of the cerebellar cortex in m.3243A>G patients

abstract:
Mutations of the mitochondrial DNA are an important cause of inherited diseases that can severely affect the tissues homeostasis and integrity. The m.3243A>G mutation is the most commonly observed across mitochondrial disorders and is linked to multisystemic complications, including cognitive deficits. In line with in vitro experiments demonstrating the m.3243A>Gs negative impact on neuronal energy production and integrity, m.3243A>G patients show cerebral gray matter tissue changes. However, its impact on the most neuron-dense, and therefore energy-consuming brain structure - the cerebellum - remains elusive.

In this work, we used high resolution structural and functional data acquired using 7 Tesla MRI to characterize the neurodegenerative and functional signatures of the cerebellar cortex in m.3243A>G patients. Our results reveal altered tissue integrity within distinct clusters across the cerebellar cortex, apparent by their significantly reduced volume and longitudinal relaxation rate compared to healthy controls, indicating macroscopic atrophy and microstructural pathology. Spatial characterization reveals that these changes occur especially in regions related to the frontoparietal brain network that is involved in information processing and selective attention. In addition, based on resting-state fMRI data, these clusters exhibit reduced functional connectivity to frontal and parietal cortical regions, especially in patients characterized by (i) a severe disease phenotype and (ii) reduced information processing speed and attention control.

Combined with our previous work, these results provide insight into the neuropathological changes and a solid base to guide longitudinal studies aimed to track disease progression.


title: Determination of HLA-DR level in cytotoxic T lymphocytes: a new validated tool to predict breast cancer response to treatment

abstract:
BackgroundNeoadjuvant chemotherapy (NACT) is the usual treatment for locally-advanced breast cancer (BC). However, more than half of the patients lack an effective response to this treatment. Thus, its urgent to find predictive biomarkers. Recently, we proposed the HLA-DR expression level in cytotoxic T lymphocytes (CTLs) as a robust biomarker to select, in advance, patients that will actually benefit from NACT.

Patients and MethodsA total of 202 BC patients, 102 of which submitted to NACT, were enrolled in this study. 61 biopsies and 41 blood samples collected pre-NACT and 100 non-NACT tumor samples were immunophenotyped by flow cytometry. Both NACT and non-NACT patients were followed up for 34 months. Blood-isolated immune cells were cultured with BC cell lines in a 3D system.

ResultsHere we confirmed that HLA-DR level in CTLs is a highly sensitive and specific biomarker to predict BC response to NACT, reflected in circulation and independent of the patients age, BC subtype and other tumor-immunological features. Therefore, we developed a predictive probability model, based on the determination of HLA-DR level in tumor-infiltrating CTLs, that could be used to guide therapeutic decisions. Interestingly, this biomarker was also associated with progression-free survival, regardless the treatment. Contrary to HLA-DRnegative CTLs, HLA-DR+ CTLs were able to reduce the viability of tumor cells, in culture, in agreement with their higher expression of activation, proliferation and cytotoxicity-related molecules. Tissue-residency and memory markers were also increased in HLA-DR+ CTLs. These anti-tumor features of HLA-DR+ CTLs may justify the clinical observations.

ConclusionHLA-DR level in CTLs is a validated and independent biomarker to predict response to NACT which allow the establishment of a clinical meaningful tool to select in advance patients that will truly benefit from this treatment. Intriguingly, it may be further used as a biomarker of BC patients general prognosis.

Highlights- HLA-DR level in cytotoxic T cells is an independent predictive factor of breast cancer response to NACT
- A predictive probability model based on this biomarker was developed as a new tool to improve treatment decisions
- HLA-DR level in cytotoxic T cells is also reflected systemically
- HLA-DR level in cytotoxic T cells is also a prognostic factor, associated with progression-free survival
- HLA-DR+ cytotoxic T cells exhibit several phenotypic and functional anti-tumor characteristics


title: The impact of multiple species invasion on soil and plant communities increases with invader diversity

abstract: Despite increasing evidence indicating that invasive species are harming ecological systems and processes, impacts of multiple invasions, and the linkages between these events and changes in vegetation and soil are inadequately documented and remain poorly understood. Addressing multiple invasions would help to highlight high priority invaders and would aid in designing more effective control strategies, contributing to environmental restoration and sustainability. In this work, we tested the impact of three concurring invasive plant species, Amorpha fruticosa, Fraxinus pennsylvanica and Acer negundo, on soil conditions and native plant diversity. The research was conducted in riparian ecosystem and included the following treatments: (1) co-occurrence of the three invasive plant species, (2) occurrence of a single invasive species, and (3) control, i.e., absence of invasive species. Our findings revealed that the impact of invasive plants on soil properties and native plant diversity is magnified by their co-occurrence. Soil in mixed plots (those populated with all three invaders) contained much higher levels of nitrifying bacteria (NB), organic matter (Om), nitrogen (N), and carbon (C) as well as lower carbon to nitrogen ratio (C:N) levels, compared to single species invaded plots and control plots. Mixed plots were also characterized by reduced native plant diversity compared to single species invaded and control plots. Differences in soil conditions and native plant diversity revealed the interactive potential of invasive plants in depleting biodiversity, and thus in affecting ecological and biogeochemical processes. Our results highlight the need to study the impact of multispecies invasion and suggest that sites in riparian areas affected by co-occurring invaders, should be prioritized for ecosystem restoration.


title: The effects of epistasis and linkage on the invasion of locally beneficial mutations and the evolution of genomic islands

abstract: We study local adaptation of a peripheral population by investigating the fate of new mutations using a haploid two-locus two-allele continent-island migration model. We explore how linkage, epistasis, and maladaptive gene flow affect the invasion probability of weakly beneficial de-novo mutations that arise on the island at an arbitrary physical distance to a locus that already maintains a stable migration-selection polymorphism. By assuming a slightly supercritical branching process, we deduce explicit conditions on the parameters that permit a positive invasion probability and we derive approximations for it. They show how the invasion probability depends on the additive and epistatic effects of the mutant, on its linkage to the polymorphism, and on the migration rate. We use these approximations together with empirically motivated distributions of epistatic effects to analyze the influence of epistasis on the expected invasion probability if mutants are drawn randomly from such a distribution and occur at a random physical distance to the existing polymorphism. We find that the invasion probability generally increases as the epistasis parameter increases or the migration rate decreases, but not necessarily as the recombination rate decreases. Finally, we shed light on the size of emerging genomic islands of divergence by exploring the size of the chromosomal neighborhood of the already established polymorphism in which 50% or 90% of the successfully invading mutations become established. These  window sizes always decrease in a reverse sigmoidal way with stronger migration and typically increase with increasing epistatic effect.

category: evolutionary biology


title: Diverse mechanisms for epigenetic imprinting in mammals

abstract: Genomic imprinting and X chromosome inactivation (XCI) require epigenetic mechanisms to direct allele-specific expression. Despite their critical roles in embryonic development, how universal epigenetic regulators coordinate these specific tasks from single locus to chromosome-scale remains understudied. Here, we systematically disrupted multiple essential epigenetic pathways within polymorphic F1 zygotes to examine postimplantation effects on canonical and non-canonical genomic imprinting as well as X chromosome inactivation. We find that DNA methylation and Polycomb group repressors are both indispensable for autosomal imprinting, albeit at distinct gene sets. Moreover, the extraembryonic ectoderm relies on a broader spectrum of unique imprinting mechanisms, including non-canonical targeting of maternal endogenous retrovirus (ERV) driven promoters by G9a. We further utilize our data to identify Polycomb dependent and independent gene clusters on the imprinted X chromosome, which appears to reflect distinct domains of Xist-mediated suppression. Our data has allowed us to assemble a comprehensive inventory of the epigenetic mechanisms utilized in eutherian mammals to maintain parent-specific imprinting, including an expanded view of the placental lineage that comprises multiple unique pathways.


title: Missingness Adapted Group Informed Clustered (MAGIC)-LASSO: A novel paradigm for prediction in data with widespread non-random missingness

abstract: The availability of large-scale biobanks linking rich phenotypes and biological measures are a powerful opportunity for scientific discovery. However, real-world collections frequently have extensive non-random missing data. Machine learning methods are able to predict missing data but performance is significantly impaired by block-wise missingness inherent to many biobanks. To address this, we developed Missingness Adapted Group-wise Informed Clustered LASSO (MAGIC-LASSO) which performs hierarchical clustering of variables based on missingness followed by sequential Group LASSO within clusters. Variables are pre-filtered for missingness and balance between training and target sets with final models built using stepwise inclusion of features ranked by completeness. This research has been conducted using the UK Biobank (n>500k) to predict unmeasured Alcohol Use Disorders Identification Test (AUDIT.) The phenotypic correlation between measured and predicted total score was 0.67 while genetic correlations between independent subjects was >0.86, demonstrating the method has significant accuracy and utility.


title: Multi-animal pose estimation and tracking with DeepLabCut

abstract: Estimating the pose of multiple animals is a challenging computer vision problem: frequent interactions cause occlusions and complicate the association of detected keypoints to the correct individuals, as well as having extremely similar looking animals that interact more closely than in typical multi-human scenarios. To take up this challenge, we build on DeepLabCut, a popular open source pose estimation toolbox, and provide high-performance animal assembly and tracking--features required for robust multi-animal scenarios. Furthermore, we integrate the ability to predict an animals identity directly to assist tracking (in case of occlusions). We illustrate the power of this framework with four datasets varying in complexity, which we release to serve as a benchmark for future algorithm development.

category: animal behavior and cognition


title: An inexpensive, high-precision, modular spherical treadmill setup optimized for Drosophila experiments

abstract:
To pursue a more mechanistic understanding of the neural control of behavior, many neuroethologists study animal behavior in controlled laboratory environments. One popular approach is to measure the movements of restrained animals while presenting controlled sensory stimulation. This approach is especially powerful when applied to genetic model organisms, such as Drosophila melanogaster, where modern genetic tools enable unprecedented access to the nervous system for activity monitoring or targeted manipulation. While there is a long history of measuring the behavior of body- and head-fixed insects walking on an air-supported ball, the methods typically require complex setups with many custom components. Here we present a compact, simplified setup for these experiments that achieves high-performance at low cost.

The simplified setup combines existing hardware and software solutions with new component designs. We replaced expensive optomechanical and custom machined components with off-the-shelf and 3D-printed parts. We built the system around an inexpensive camera that achieves 180 Hz imaging and use an inexpensive tablet computer for presenting view-angle-corrected stimuli updated through a local network. We quantify the performance of the integrated system and characterize the visually guided behavior of flies in response to a range of visual stimuli. The improved system is thoroughly documented. This publication is accompanied by CAD files, parts lists, source code, and step-by-step instructions for setting up the system and analyzing behavioral data. We detail a complete ~$.300 system, including a cold-anesthesia tethering stage, that is ideal for hands-on teaching laboratories. This represents a nearly 50-fold cost reduction as compared to a typical system used in research laboratories, yet is fully featured and yields excellent performance.

We report the current state of this system, which started with a one-day teaching lab for which we built seven parallel setups and continues towards a setup in our lab for larger-scale analysis of visual-motor behavior in flies. Because of the simplicity, compactness, and low cost of this system, we believe that high-performance measurements of tethered insect behavior should now be widely accessible and suitable for integration into many systems. This access enables broad opportunities for comparative work across labs, species, and behavioral paradigms.


title: Characterizing stored red blood cells using ultra-high throughput holographic cytometry

abstract: Holographic cytometry is introduced as an ultra-high throughput implementation of quantitative phase image based on off-axis interferometry of cells flowing through parallel microfluidic channels. Here, it is applied for characterizing morphological changes of red blood cells during storage under regular blood bank condition. The approach allows high quality phase imaging of a large number of cells greatly extending our ability to study cellular phenotypes using individual cell images. Holographic cytology measurements show multiple physical traits of the cells, including optical volume and area, which are observed to consistently change over the storage time. In addition, the large volume of cell imaging data can serve as training data for machine learning algorithms. For the study here, logistic regression is used to classify the cells according to the storage time points. The results of the classifiers demonstrate the potential of holographic cytometry as a diagnostic tool.

category: bioengineering


title: The Split-Belt Rimless Wheel

abstract: Split-belt treadmill training, common in stroke rehabilitation and motor learning experiments, reveals a mechanism through which energy can be extracted from the environment. People can extract net positive work from a split-belt treadmill by lengthening their step onto the fast belt. To understand how leg angles and belt speed differences affect energy transfer between the treadmill and the person during split-belt walking, we simulated a split-belt rimless wheel that alternates rotating on fast and slow treadmill belts. We found that the split-belt rimless wheel can passively walk steadily forward under a range of conditions, extracting enough energy from the treadmill to overcome losses during collisions. The simulated wheel can tolerate both speed disturbances and ground height variability, and it can even capture enough energy to walk uphill. We also built a physical split-belt rimless wheel robot, demonstrating the feasibility of energy extraction during split-belt treadmill walking. In comparing the wheel solutions to human split-belt gait, we found that humans do not maximize positive work performed by the treadmill; costs associated with balance and free vertical moments likely limit adaptation. This study characterizes the mechanics and energetics of split-belt walking, demonstrating that energy capture through intermittent contacts with the two belts is possible when the belt speed difference is paired with an asymmetry in leg angles at step-to-step transitions. This study demonstrates a novel way of harnessing energy through individual rotations rather than continuous contact and offers a simple model framework for understanding human choices during split-belt walking.


title: A comparison of tools for copy-number variation detection in germline whole exome and whole genome sequencing data

abstract:
BackgroundCopy-number variations (CNVs) have important clinical implications for several diseases and cancers. The clinically relevant CNVs are hard to detect because CNVs are common structural variations that define large parts of the normal human genome. CNV calling from short-read sequencing data has the potential to leverage available cohort studies and allow full genomic profiling in the clinic without the need for additional data modalities. Questions regarding performance of CNV calling tools for clinical use and suitable sequencing protocols remain poorly addressed, mainly because of the lack of good reference data sets.

MethodsWe reviewed 50 popular CNV calling tools and included 11 tools for benchmarking in a unique reference cohort encompassing 39 whole genome sequencing (WGS) samples paired with analysis by the current clinical standard --SNP-array based CNV calling. Additionally, for nine of these samples we performed whole exome sequencing (WES) performed, in order to address the effect of sequencing protocol on CNV calling. Furthermore, we included Gold Standard reference sample NA12878, and tested 12 samples with CNVs confirmed by multiplex ligation-dependent probe amplification (MLPA).

ResultsTool performance varied greatly in the number of called CNVs and bias for CNV lengths. Some tools had near-perfect recall of CNVs from arrays for some samples, but poor precision. Filtering output by CNV ranks from tools did not salvage precision. Several tools had better performance patterns for NA12878, and we hypothesize that this is the result of overfitting during the tool development.

ConclusionsWe suggest combining tools with the best recall: GATK gCNV, Lumpy, DELLY, and cn.MOPS. These tools also capture different CNVs. Further improvements in precision requires additional development of tools, reference data sets, and annotation of CNVs, potentially assisted by the use of background panels for filtering of frequently called variants.


title: AutoGGN: A Gene Graph Network AutoML tool for Multi-Omics Research

abstract: Omics data identifies biological characteristics from genetic to phenotypic levels during the life span. Molecular interaction networks have a fundamental impact on life activities. Integrating omics data and molecular interaction networks will help researchers delve into comprehensive information underlying the data. Here, we proposed a new multimodal method called AutoGGN to aggregate multi-omics data and molecular interaction networks based on graph convolutional neural networks. We evaluated AutoGGN using two different tasks: cancer type classification and single-cell stage classification. On both tasks, AutoGGN showed better performance compared to other methods, the trend is relevant to the ability of utilizing much more information from biological data. The phenomenon indicated AutoGGN has the potential to incorporate valuable information from molecular interaction networks and multi-omics data effectively. Furthermore, in order to provide a better understanding of the mechanism of prediction results, we assessed the explanation using SHAP module and identified the key genes contributing to the prediction of classification, which will provide insights for the downstream design of biological experiments.


title: AutoGGN: A Gene Graph Network AutoML Tool for Multi-Omics Research


title: 3C-seq-captured chromosome conformation of the hyperthermophilic archaeon Thermofilum adornatum

abstract:
Three-dimensional structure of chromosomes displays diverse patterns across the tree of life, with compartments, interaction domains and loops being quite universally observed. The archaeal kingdom remains understudied to this extent so far, despite representing an interesting area from evolutionary and other perspectives.

Here we describe the spatial chromosomal organization of a hyperthermophilic crenarchaeon Thermofilum adornatum strain 1910b based on high-throughput chromosome conformation capture (3C-seq) approach. The chromosome contact map showed a curved secondary diagonal almost orthogonal to the main one. No evidence of chromosome loops was present. We were able to identify boundaries of different strengths between chromosome interaction domains (CIDs) albeit moderate. The plaid-like patterns previously reported for Sulfolobus archaea were not observed. However, the calculation of A/B compartments divided the genome into 2 domains that were different by the density of predicted highly expressed genes and location of origins.

Further comparison of these domains with whole-genome gene expression profiles will allow to test whether these domains represent expression-associated compartments. If so, it is possible that they represent primitive compartments evolutionarily older than the plaid patterns of Sulfolobus and higher eukaryotes. Further exploration of 3D chromatin in all branches of archaeal diversity will elucidate the evolution of the links between structural and functional organization in live organisms.


title: HyMM: Hybrid method for disease-gene prediction by integrating multiscale module structures

abstract:
MotivationIdentifying disease-related genes is important for the study of human complex diseases. Module structures or community structures are ubiquitous in biological networks. Although the modular nature of human diseases can provide useful insights, the mining of information hidden in multiscale module structures has received less attention in disease-gene prediction.

ResultsWe propose a hybrid method, HyMM, to predict disease-related genes more effectively by integrating the information from multiscale module structures. HyMM consists of three key steps: extraction of multiscale modules, gene rankings based on multiscale modules and integration of multiple gene rankings. The statistical analysis of multiscale modules extracted by three multiscale-module-decomposition algorithms (MO, AS and HC) shows that the functional consistency of the modules gradually improves as the resolution increases. This suggests the existence of different levels of functional relationships in the multiscale modules, which may help reveal disease-gene associations. We display the effectiveness of multiscale module information in the disease-gene prediction and confirm the excellent performance of HyMM by 5-fold cross-validation and independent test. Specifically, HyMM with MO can more effectively enhance the ability of disease-gene prediction; HyMM (MO, RWR) and HyMM (MO, RWRH) are especially preferred due to their excellent comprehensive performance, and HyMM (AS, RWRH) is also good choice due to its local performance. We anticipate that this work could provide useful insights for disease-module analysis and disease-gene prediction based on multi-scale module structures.

Availabilityhttps://github.com/xiangiu0208/HvMM

Contactlimin@mail.csu.edu.cn

Supplementary informationSupplementary data are available at Bioinformatics online.


title: Sequence-based correction of barcode bias in massively parallel reporter assays

abstract: Massively parallel reporter assays (MPRA) are a high-throughput method for evaluating in vitro activities of thousands of candidate cis-regulatory elements (CREs). In these assays, candidate sequences are cloned upstream or downstream of a reporter gene tagged by unique DNA sequences. However, tag sequences may themselves affect reporter gene expression and lead to major potential biases in the measured cis-regulatory activity. Here, we present a sequence-based method for correcting tag sequence-specific effects and demonstrate that our method can significantly reduce this source of variation, and improve the identification of functional regulatory variants by MPRAs. We also show that our model captures sequence features associated with post-transcriptional regulation of mRNA. Thus, this new method helps to not only improve detection of regulatory signals in MPRA experiments but also to design better MPRA protocols.