title: Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next?

abstract: Accurate prediction of tumor progression is key for adaptive therapy and precision medicine. Cancer progression models (CPMs) can be used to infer dependencies in mutation accumulation from cross-sectional data and provide predictions of tumor progression paths. However, their performance when predicting complete evolutionary trajectories is limited by violations of assumptions and the size of available data sets. Instead of predicting full tumor progression paths, here we focus on short-term predictions, more relevant for diagnostic and therapeutic purposes. We examine whether five distinct CPMs can be used to answer the question "Given that a genotype with n mutations has been observed, what genotype with n + 1 mutations is next in the path of tumor progression?" or, shortly, "What genotype comes next?". Using simulated data we find that under specific combinations of genotype and fitness landscape characteristics CPMs can provide predictions of short-term evolution that closely match the true probabilities, and that some genotype characteristics can be much more relevant than global features. Application of these methods to 25 cancer data sets shows that their use is hampered by a lack of information needed to make principled decisions about method choice. Fruitful use of these methods for short-term predictions requires adapting methods use to local genotype characteristics and obtaining reliable indicators of performance; it will also be necessary to clarify the interpretation of the methods results when key assumptions do not hold.


title: HTSlib - C library for reading/writing high-throughput sequencing data

abstract:
AbstractO_ST_ABSBackgroundC_ST_ABSSince the original publication of the VCF and SAM formats, an explosion of software tools have been created to process these data files. To facilitate this a library was produced out of the original SAMtools implementation, with a focus on performance and robustness. The file formats themselves have become international standards under the jurisdiction of the Global Alliance for Genomics and Health.

FindingsWe present a software library for providing programmatic access to sequencing alignment and variant formats. It was born out of the widely used SAMtools and BCFtools applications. Considerable improvements have been made to the original code plus many new features including newer access protocols, the addition of the CRAM file format, better indexing and iterators, and better use of threading.

ConclusionSince the original Samtools release, performance has been considerably improved, with a BAM read-write loop running 5 times faster and BAM to SAM conversion 13 times faster (both using 16 threads, compared to Samtools 0.1.19).

Widespread adoption has seen HTSlib downloaded over a million times from GitHub and conda. The C library has been used directly by an estimated 900 GitHub projects and has been incorporated into Perl, Python, Rust and R, significantly expanding the number of uses via other languages. HTSlib is open source and is freely available from htslib.org under MIT / BSD license.

Contactsamtools@sanger.ac.uk

category: bioinformatics


title: Paracrine signalling between intestinal epithelial and tumour cells induces a regenerative programme

abstract: Tumours are complex ecosystems composed of different types of cells that communicate and influence each other. While the critical role of stromal cells in affecting tumour growth is well established, the impact of mutant cancer cells on healthy surrounding tissues remains poorly defined. Here, we uncovered a paracrine mechanism by which intestinal cancer cells reactivate foetal and regenerative Yap-associated transcriptional programs in neighbouring wildtype epithelial cells, rendering them adapted to thrive in the tumour context. We identified the glycoprotein Thrombospondin-1 (THBS1) as the essential factor that mediates non-cell autonomous morphological and transcriptional responses. Importantly, Thbs1 is associated with bad prognosis in several human cancers. This study reveals the THBS1-YAP axis as the mechanistic link mediating paracrine interactions between epithelial cells in intestinal tumours.

category: cancer biology


title: Under-Oil Autonomously Regulated Oxygen Microenvironments: A Goldilocks Principle-Based Approach For Microscale Cell Culture

abstract: Oxygen levels in vivo are autonomously regulated by a supply-demand balance, which can be altered in disease states. However, the oxygen levels of in vitro cell culture systems, particularly microscale cell culture, are typically dominated by either supply or demand. Further, the oxygen microenvironment in these systems are rarely monitored or reported. Here, we present a method to establish and dynamically monitor autonomously regulated oxygen microenvironments (AROM) using an oil overlay in an open microscale cell culture system. Using this method, the oxygen microenvironment is dynamically regulated via a supply-demand balance of the system. We simulate the kinetics of oxygen diffusion in multiliquid-phase microsystems on COMSOL Multiphysics and experimentally validate the method using a variety of cell types including mammalian, fungal and bacterial cells. Finally, we demonstrate the utility of this method to establish a co-culture between primary intestinal epithelial cells and a highly prevalent human gut species Bacteroides uniformis.

category: bioengineering


title: Combining an alarmin HMGN1 peptide with PD-L1 blockade facilitates stem-like CD8+ T cell expansion and results in robust antitumor effects

abstract:
BackgroundThe expansion of intratumoral stem-like CD8+ T (Tstem) cells provides a potential approach to improving the therapeutic efficacy of immune checkpoint blockade (ICB). Thus, here we demonstrate a strategy to facilitate Tstem cell expansion by combining an alarmin high-mobility group nucleosome binding domain 1 (HMGN1) peptide with programmed death-ligand 1 (PD-L1) blockade.

MethodsThe antitumor effects of HMGN1, anti-PD-L1 antibody, and their combined treatment were monitored in the B16F10, LLC, Colon26, or the EO771 tumor-bearing mice. The comprehensive immunologic analyses, such as high-dimensional flow cytometry, transcriptome analysis, and single-cell RNA sequencing, were used to investigate the cellular and molecular mechanisms of antitumor immune responses after treatments.

ResultsThe HMGN1 peptide synergizes with PD-L1 blockade in augmenting the number of mature DCs enriched in immunoregulatory molecules (mregDCs) in tumors, and enhancing their MHC class I antigen-presenting program, which is correlated with the expansion of intratumoral Tstem cells, specifically promoting the Tstem cells but restricting terminally exhausted CD8+ T (Tex) cells, owing to the regulatory molecules expressed on mregDCs.

ConclusionOur results indicate that HMGN1 peptide serves as an immunoadjuvant to promote effective anti-PD-L1 immunotherapy and implicate that mregDCs play a role beyond facilitating Tstem cell expansion.

category: immunology


title: Excitatory Deep Brain Stimulation Quenches Parkinsonian Signs in the Basal Ganglia and Thalamus

abstract: Parkinsons disease (PD) is associated with abnormal {beta} band oscillations (13-30 Hz) in the cortico-basal ganglia circuits. Abnormally increased striato-pallidal inhibition and strengthening the synaptic coupling between subthalamic nucleus (STN) and globus pallidus externa (GPe), due to the loss of dopamine, are considered as the potential sources of {beta} oscillations in the basal ganglia. Deep brain stimulation (DBS) of the basal ganglia subregions is known as a way to reduce the pathological {beta} oscillations and motor deficits related to PD. Despite the success of the DBS, its underlying mechanism is poorly understood and, there is controversy about the inhibitory or excitatory role of the DBS in the literature. Here, we utilized a computational network model of basal ganglia which consists of STN, GPe, globus pallidus interna (GPi), and thalamic neuronal population. This model can reproduce healthy and pathological {beta} oscillations similar to what has been observed in experimental studies. Using this model, we investigated the effect of DBS to understand whether its effect is excitatory or inhibitory. Our results show that the excitatory DBS (EDBS) is able to quench the pathological synchrony and {beta} oscillations, while, applying inhibitory DBS (IDBS) failed to quench the PD signs. In light of simulation results, we conclude that the effect of the DBS on its target is excitatory.

category: neuroscience


title: Long SARS-CoV-2 nucleocapsid sequences in blood monocytes collected soon after hospital admission

abstract: Many viruses infect circulating mononuclear cells thereby facilitating infection of diverse organs. Blood monocytes (PBMC) are being intensively studied as immunologic and pathologic responders to the new SARS-CoV-2 virus (CoV19) but direct evidence showing CoV19 in monocytes is lacking. Circulating myeloid cells that take up residence in various organs can harbor viral genomes for many years in lymphatic tissues and brain, and act as a source for re-infection and/or post-viral organ pathology. Because nucleocapsid (NC) proteins protect the viral genome we tested PBMC from acutely ill patients for the diagnostic 72bp NC RNA plus adjacent longer (301bp) transcripts. In 2/11 patient PBMC, but no uninfected controls, long NCs were positive as early as 2-6 days after hospital admission as validated by sequencing. Pathogenic viral fragments, or the infectious virus, are probably disseminated by rare myeloid migratory cells that incorporate CoV19 by several pathways. Predictably, these cells carried CoV19 to heart and brain educing the late post-viral pathologies now evident.

category: microbiology


title: Universality in biodiversity patterns: Variation in species-temperature and species-productivity relationships reveals a prominent role of productivity in diversity gradients

abstract: Temperature and productivity appear as universal positive correlates of species richness. However, the strength and the shape of species-temperature (STR) and species-productivity (SPR) relationships vary widely, and the causes of this variation are poorly known. We analysed (1) published species richness data for multiple taxa sampled in various regions and (2) different clades within vertebrate classes globally, to test for the effects of spatial scale and characteristics of examined taxa and regions on the strength and direction of STRs and SPRs. There are striking differences in the variation of the relationships among types of data, between ectotherms and endotherms and also between STRs and SPRs. Some sources of this variation are of statistical nature (e.g. the relationships are stronger if the range of temperature or productivity variation is wider), but non-statistical sources are more important and illuminate the processes responsible for the origin of biodiversity patterns. The SPRs are generally stronger and less variable than STRs, and SPR variation is weakly related to the explored factors - the SPRs are stronger in warmer regions in ectotherms, while clade size is the only factor consistently affecting the strength of the SPR in endotherms. In contrast, STRs are weaker and more variable, and this variation is linked to region characteristics - most importantly, STRs are stronger in the regions where temperature positively correlates with productivity, indicating that productivity plays a role even in the STRs. The effect of temperature on species richness is thus complex and context-dependent, while productivity is a more universal driver of species richness patterns, largely independent of particular characteristics of given region or taxon. Productivity thus appears as the main proximate driver of species richness patterns, probably due to its effect on the limits of the number of viable populations which can coexist in a given environment.

category: ecology


title: Whole plastid genome-based phylogenomics supports an inner placement of the O. insectifera group rather than a basal position in the rapidly diversifying Ophrys genus (Orchidaceae)

abstract: Some lineages of the Orchid genus Ophrys exhibit among the highest diversification rates reported so far. As a consequence of a such intense and rapid evolution, the systematics and the taxonomy of this genus remains unclear. A hybrid assembly approach based-on long- and short-read genomic data allowed us to outperform classical methods to successfully assemble whole plastid genomes for two new Ophrys species: O. aymoninii and O. lutea. Along with three other previously Ophrys plastid genome sequences, we then reconstructed the first whole plastome-based molecular phylogeny including representatives of the three mains recognized Ophrys lineages. Our results support the placement of the O. insectifera clade as sister group of  non-basal Ophrys rather than a basal position. Our findings corroborate recent results obtained from genomic data (RAD-seq and transcriptomes) but contrast with previous ones. These results therefore confirm that molecular phylogenetic hypotheses based on a limited number of loci (e.g. nrITS, matK, rbcL) may have provided a biased picture of phylogenetic relationships within Ophrys and possibly other plant taxa.

category: evolutionary biology


title: HAYSTAC: A Bayesian framework for robust and rapid species identification in high-throughput sequencing data

abstract: Identification of specific species in metagenomic samples is critical for several key applications, yet many tools available require large computational power and are often prone to false positive identifications. Here we describe High-AccuracY and Scalable Taxonomic Assignment of MetagenomiC data (HAYSTAC), which can estimate the probability that a specific taxon is present in a metagenome. HAYSTAC provides a user-friendly tool to construct databases, based on publicly available genomes, that are used for competitive reads mapping. It then uses a novel Bayesian framework to infer the abundance and statistical support for each species identification, and provide per-read species classification. Unlike other methods, HAYSTAC is specifically designed to efficiently handle both ancient and modern DNA data, as well as incomplete reference databases, making it possible to run highly accurate hypothesis-driven analyses (i.e., assessing the presence of a specific species) on variably sized reference databases while dramatically improving processing speeds. We tested the performance and accuracy of HAYSTAC using simulated Illumina libraries, both with and without ancient DNA damage, and compared the results to other currently available methods (i.e., Kraken2/Braken, MALT/HOPS, and Sigma). HAYSTAC identified fewer false positives than both Kraken2/Braken and MALT in all simulations, and fewer than Sigma in simulations of ancient data. It uses less memory than Kraken2/Braken as well as MALT both during database construction and sample analysis. Lastly, we used HAYSTAC to search for specific pathogens in two published ancient metagenomic datasets, demonstrating how it can be applied to empirical datasets. HAYSTAC is available from https://github.com/antonisdim/HAYSTAC


title: Is photosynthetic enhancement sustained through three years of elevated CO2 in a 175 year old oaks?

abstract: Current carbon cycle models attribute rising atmospheric CO2 as the major driver of the increased terrestrial carbon sink, but with substantial uncertainties. The photosynthetic response of trees to elevated atmospheric CO2 is a necessary step, but not the only one, for sustaining the terrestrial carbon uptake, but can vary diurnally, seasonally and with duration of CO2 exposure. Hence we sought to quantify the photosynthetic response of the canopy-dominant species, Quercus robur, in a mature deciduous forest to elevated CO2 (eCO2) (+150 mol mol-1 CO2) over the first three years of a long-term free air CO2 enrichment facility at the Birmingham Institute of Forest Research in central England (BIFoR FACE). Over three thousand measurements of leaf gas exchange and related biochemical parameters were conducted in the upper canopy to assess the diurnal and seasonal responses of photosynthesis during the 2nd and 3rd year of eCO2 exposure. Measurements of photosynthetic capacity via biochemical parameters, derived from CO2 response curves, (Vcmax and Jmax) together with leaf nitrogen concentrations from the pre-treatment year to the 3 rd year of eCO2 exposure, were examined. We hypothesized an initial enhancement in light-saturated net photosynthetic rates (Asat) with CO2 enrichment of {approx}37% based on theory but also expected photosynthetic capacity would fall over the duration of the study. Over the three-year period, Asat of upper-canopy leaves was 33 {+/-} 8 % higher (mean and standard error) in trees grown in eCO2 compared with ambient CO2 (aCO2), and photosynthetic enhancement decreased with decreasing light. There were no significant effects of CO2 treatment on Vcmax or Jmax, nor leaf nitrogen. Our results suggest that mature Q. robur may exhibit a sustained, positive response to eCO2 without photosynthetic downregulation, suggesting that, with adequate nutrients, there will be sustained enhancement in C assimilated by these mature trees. Further research will be required to understand the location and role of the additionally assimilated carbon.

category: plant biology


title: A pH-eQTL interaction at the RIT2-SYT4 Parkinson's disease risk locus in the substantia nigra

abstract: Parkinsons disease (PD) causes severe motor and cognitive disabilities that result from the progressive loss of dopamine neurons in the substantia nigra. The rs12456492 variant in the RIT2 gene has been repeatedly associated with increased risk for Parkinsons disease. From a transcriptomic perspective, a meta-analysis found that RIT2 gene expression is correlated with pH in the human brain. To assess these pH associations in relation to PD risk, we examined the two datasets that assayed rs12456492, gene expression, and pH in the postmortem human brain. Using the BrainEAC dataset, we replicate the positive correlation between RIT2 gene expression and pH in the human brain (n=100). Furthermore, we found that the relationship between expression and pH is influenced by rs12456492. When tested across ten brain regions, this interaction is specifically found in the substantia nigra. A similar association was found for the co-localized SYT4 gene. In addition, SYT4 associations are stronger in a combined model with both genes, and the SYT4 interaction appears to be specific to males. In the GTEx dataset, the pH associations involving rs12456492 and expression of either SYT4 and RIT2 was not seen. This null finding may be due to the short postmortem intervals (PMI) of the GTEx tissue samples. In the BrainEAC data, we tested the effect of PMI and only observed the interactions in the longer PMI samples. These previously unknown associations suggest novel mechanistic roles for rs12456492, RIT2, and SYT4 in the regulation of pH in the substantia nigra.


title: Network alignment and similarity reveal atlas-based topological differences in structural connectomes

abstract:
The interactions between different brain regions can be modeled as a graph, called connectome, whose nodes correspond to parcels from a predefined brain atlas. The edges of the graph encode the strength of the axonal connectivity between regions of the atlas which can be estimated via diffusion Magnetic Resonance Imaging (MRI) tractography. Herein, we aim at providing a novel perspective on the problem of choosing a suitable atlas for structural connectivity studies by assessing how robustly an atlas captures the network topology across different subjects in a homogeneous cohort. We measure this robustness by assessing the alignability of the connectomes, namely the possibility to retrieve graph matchings that provide highly similar graphs. We introduce two novel concepts. First, the graph Jaccard index (GJI), a graph similarity measure based on the well-established Jaccard index between sets; the GJI exhibits natural mathematical properties that are not satisfied by previous approaches. Second, we devise WL-align, a new technique for aligning connectomes obtained by adapting the Weisfeiler-Lehman (WL) graph-isomorphism test. We validated the GJI and WL-align on data from the Human Connectome Project database, inferring a strategy for choosing a suitable parcellation for structural connectivity studies. Code and data are publicly available.

AUTHOR SUMMARYAn important part of our current understanding of the structure of the human brain relies on the concept of brain network, which is obtained by looking at how different brain regions are connected with each other. In this paper we present a strategy for choosing a suitable parcellation of the brain for structural connectivity studies by making use of the concepts of network alignment and similarity. To do so, we design a novel similarity measure between weighted networks called graph Jaccard index, and a new network alignment technique called WL-align. By assessing the possibility to retrieve graph matchings that provide highly similar graphs, we show that morphology- and structure-based atlases define brain networks which are more topologically robust across a wide range of resolutions.


title: A native chemical chaperone in the human eye lens

abstract: Cataract is one of the most prevalent protein aggregation disorders and still the most common cause of vision loss worldwide. The metabolically quiescent core region of the human lens lacks cellular or protein turnover; it has therefore evolved remarkable mechanisms to resist light-scattering protein aggregation for a lifetime. We now report that one such mechanism involves an unusually abundant lens metabolite, myo-inositol, suppressing aggregation of lens crystallins. We quantified aggregation suppression using our previously well-characterized in vitro aggregation assays of oxidation-mimicking human {gamma}D-crystallin variants and investigated myo-inositols molecular mechanism of action using solution NMR, negative-stain TEM, differential scanning fluorometry, thermal scanning Raman spectroscopy, turbidimetry in redox buffers, and free thiol quantitation. Unlike many known chemical chaperones, myo-inositols primary target was neither the native nor the unfolded state of the protein, nor the final aggregated state, but rather the rate-limiting bimolecular step on the aggregation pathway. Given recent metabolomic evidence that it is severely depleted in human cataractous lenses compared to age-matched controls, we suggest that maintaining or restoring healthy levels of myo-inositol in the lens may be a simple, safe, and globally accessible strategy to prevent or delay lens opacification due to age-onset cataract.

category: biophysics


title: Ecdysone coordinates plastic growth with robust pattern in the developing wing

abstract: Animals develop in unpredictable, variable environments. In response to environmental change some aspects of development adjust to generate plastic phenotypes. Other aspects of development, however, are buffered against environmental change to produce robust phenotypes. How organ development is coordinated to accommodate both plastic and robust developmental responses is poorly understood. Here, we demonstrate that the steroid hormone ecdysone coordinates both plasticity of organ size and robustness of organ pattern in the developing wings of the fruit fly Drosophila melanogaster. Using fed and starved larvae that lack prothoracic glands, which synthesise ecdysone, we show that nutrition regulates growth both via ecdysone and via an ecdysone-independent mechanism, while nutrition regulates patterning only via ecdysone. We then demonstrate that growth shows a graded response to ecdysone concentration, while patterning shows a threshold response. Collectively, these data support a model where nutritionally-regulated ecdysone fluctuations confer plasticity by regulating disc growth in response to basal ecdysone levels, and confers robustness by initiating patterning only once ecdysone peaks exceeds a threshold concentration. This could represent a generalizable mechanism through which hormones coordinate plastic growth with robust patterning in the face of environmental change.

category: developmental biology


title: Experimental evolution to identify undescribed mechanisms of resistance to a novel cationic peptide antibiotic

abstract: A key strategy for resolving the antibiotic resistance crisis is the development of new drugs with antimicrobial properties. The engineered cationic antimicrobial peptide WLBU2 (also known as PLG0206) is a promising broad-spectrum antimicrobial compound that has completed Phase I clinical studies. It has activity against Gram-negative and Gram-positive bacteria including infections associated with biofilm. No definitive mechanisms of resistance to WLBU2 have been identified. Here, we used experimental evolution under different levels of mutation supply and whole genome sequencing (WGS) to detect the genetic pathways and probable mechanisms of resistance to this peptide. We propagated populations of wild-type and mutator Pseudomonas aeruginosa in the presence of WLBU2 and performed WGS of evolved populations and clones. Populations that survived WLBU2 treatment acquired a minimum of two mutations, making the acquisition of resistance more difficult than for most antibiotics, which can be tolerated by mutation of a single target. Major targets of resistance to WLBU2 included the orfN and pmrB genes, previously described to confer resistance to other cationic peptides. More surprisingly, mutations that increase aggregation such as the wsp pathway were also selected despite the ability of WLBU2 to kill cells growing in a biofilm. The results show how the experimental evolution and WGS can identify genetic targets and actions of new antimicrobial compounds and predict pathways to resistance of new antibiotics in clinical practice.


title: Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants

abstract: The SARS-CoV-2 Spike protein needs to be in an open-state conformation to interact with ACE2 as part of the viral entry mechanism. We utilise coarse-grained normal-mode analyses to model the dynamics of Spike and calculate transition probabilities between states for 17081 Spike variants. Our results correctly model an increase in open-state occupancy for the more infectious D614G via an increase in flexibility of the closed-state and decrease of flexibility of the open-state. We predict the same effect for several mutations on Glycine residues (404, 416, 504, 252) as well as residues K417, D467 and N501, including the N501Y mutation, explaining the higher infectivity of the B.1.1.7 and 501.V2 strains. This is, to our knowledge, the first use of normal-mode analysis to model conformational state transitions and the effect of mutations thereon. The specific mutations of Spike identified here may guide future studies to increase our understanding of SARS-CoV-2 infection mechanisms and guide public health in their surveillance efforts.


title: Activation of the type 3 secretion system of enteropathogenic E. coli leads to reprogrammingof its lipid metabolism

abstract:
The cell envelope of gram-negative bacteria is a complex structure, essential for bacterial survival and for resistance to many antibiotics. Channels that cross the bacterial envelope and the host cell membrane form secretion systems that are activated upon attachment to host, enabling bacteria to inject effector molecules into the host cell, required for bacterial-host interaction. The type III secretion system (T3SS) is critical for the virulence of several pathogenic bacteria, including enteropathogenic E. coli (EPEC). The EPEC T3SS activation is associated with repression of carbon storage regulator (CsrA), resulting in gene expression remodeling, which is known to affect EPEC central carbon metabolism and contributes to the adaptation to a cell-adherent lifestyle in a poorly understood manner. We reasoned that the changes in bacterial envelope upon attachment to host and the activation of a secretion system may involve a modification of the lipid composition of bacterial envelope. Accordingly, we performed a lipidomics analysis on mutant strains that simulate T3SS activation. We saw a shift in glycerophospholipid metabolism towards the formation of lysophospholipids, attributed to corresponding upregulation of the phospholipase pldA and the acyltransferase ygiH upon T3SS activation in EPEC. We also detected a shift from menaquinones and ubiquinones to undecaprenyl lipids, concomitant to abnormal synthesis of O-antigen. The remodeling of lipid metabolism is mediated by CsrA and associated with increased bacteria cell size and Zeta potential, and a corresponding alteration in EPEC permeability to vancomycin, increasing the sensitivity of T3SS-activated strains and of adherent wild type EPEC to the antibiotic.

ImportanceThe characterization of EPEC membrane lipid metabolism upon attachment to host is an important step towards a better understanding the shift of EPEC, a notable human pathogen, from a planktonic to adherent life style. It may also apply to other pathogenic bacteria that use this secretion system. We predict that upon attachment to host cells the lipid remodeling upon T3SS activation contributes to bacterial fitness and promotes host colonization, and show that it is associated with increased cell permeability and higher sensitivity to vancomycin.

To the best of our knowledge, this is the first demonstration of a bacterial lipid remodeling due to activation of a secretion system.


title: Activation of the type 3 secretion system of enteropathogenic E. coli leads to remodeling of its membrane composition

category: systems biology


title: Activation of the type 3 secretion system of enteropathogenic E. coli leads to remodeling of its membrane composition and function


title: A new family of structurally conserved fungal effectors displays epistatic interactions with plant resistance proteins

abstract:
Recognition of a pathogen avirulence (AVR) effector protein by a cognate plant resistance (R) protein triggers a set of immune responses that render the plant resistant. Pathogens can escape this so-called Effector-Triggered Immunity (ETI) by different mechanisms including the deletion or loss-of-function mutation of the AVR gene, the incorporation of point mutations that allow recognition to be evaded while maintaining virulence function, and the acquisition of new effectors that suppress AVR recognition. The Dothideomycete Leptosphaeria maculans, causal agent of oilseed rape stem canker, is one of the few fungal pathogens where suppression of ETI by an AVR effector has been demonstrated. Indeed, AvrLm4-7 suppresses Rlm3- and Rlm9- mediated resistance triggered by AvrLm3 and AvrLm5-9, respectively. The presence of AvrLm4-7 does not impede AvrLm3 and AvrLm5-9 expression, and the three AVR proteins do not appear to physically interact. To decipher the epistatic interaction between these L. maculans AVR effectors, we determined the crystal structure of AvrLm5-9 and obtained a 3D model of AvrLm3, based on the crystal structure of Ecp11-1, a homologous AVR effector candidate from Fulvia fulva. Despite a lack of sequence similarity, AvrLm5-9 and AvrLm3 are structural analogues of AvrLm4-7 (structure previously characterized). Structure-informed sequence database searches identified a larger number of putative structural analogues among L. maculans effector candidates, including the AVR effector AvrLmS-Lep2, all produced during the early stages of oilseed rape infection, as well as among effector candidates from other phytopathogenic fungi. These structural analogues are named LARS (for Leptosphaeria AviRulence and Suppressing) effectors. Remarkably, transformants of L. maculans expressing one of these structural analogues, Ecp11-1, triggered oilseed rape immunity in several genotypes carrying Rlm3. Furthermore, this resistance could be suppressed by AvrLm4-7. These results suggest that Ecp11-1 shares a common activity with AvrLm3 within the host plant which is detected by Rlm3, or that the Ecp11-1 structure is sufficiently close to that of AvrLm3 to be recognized by Rlm3.

Author summaryAn efficient strategy to control fungal diseases in the field is genetic control using resistant crop cultivars. Crop resistance mainly relies on gene-for-gene relationships between plant resistance (R) genes and pathogen avirulence (AVR) genes, as defined by Flor in the 1940s. However, such gene-for-gene relationships can increase in complexity over the course of plant-pathogen co-evolution. Resistance against the plant-pathogenic fungus Leptosphaeria maculans by Brassica napus and other Brassica species relies on the recognition of effector (AVR) proteins by R proteins; however, L. maculans produces an effector that suppresses a subset of these specific resistances. Using a protein structure approach, we revealed structural analogy between several of the resistance-triggering effectors, the resistance-suppressing effector, and effectors from other plant-pathogenic species in the Dothideomycetes and Sordariomycetes classes, defining a new family of effectors called LARS. Notably, cross-species expression of one LARS effector from Fulvia fulva, a pathogen of tomato, in L. maculans resulted in recognition by several resistant cultivars of oilseed rape. These results highlight the need to integrate knowledge on effector structures to improve resistance management and to develop broad-spectrum resistances for multi-pathogen control of diseases.


title: Asymmetric chromatin capture and nuclear envelopes separate chromosomes in fused cells during mitosis

abstract: Hybrid cells derived through fertilization or somatic cell fusion recognize and separate chromosomes of different origin. The underlying mechanisms are unknown but could prevent aneuploidy and tumor formation. Here, we acutely induce fusion between Drosophila neural stem cells (neuroblasts; Nbs) and differentiating ganglion mother cells (GMCs) in vivo to define how epigenetically distinct chromatin is recognized and segregated. We find that Nb-GMC hybrid cells align both endogenous (neuroblast-origin) and ectopic (GMC-origin) chromosomes at the metaphase plate through centrosome derived dual-spindles. Mixing of endogenous and ectopic chromatin is prevented through an asymmetric, microtubule-dependent chromatin capture mechanism during interphase and physical boundaries imposed by nuclear envelopes. Although hybrid cells fail to accurately segregate ectopic chromatin, hybrid cells neither reduce the lifespan nor form visible tumors in host flies. We propose that Nb-GMC derived hybrid cells utilize asymmetric centrosome activity in interphase and nuclear envelopes to physically separate epigenetically distinct chromatin.

category: cell biology


title: Population dynamics and ranging behaviors of provisioned silvered langur (Trachypithecus cristatus) in Peninsular Malaysia

abstract: Tourists are attracted to the Bukit Melawati Kuala Selangor (BMKS) of Peninsular Malaysia, a small hill park, both for its status as a historical site and the free-ranging silvered langurs (Trachypithecus cristatus) that come for provisioning. We assessed the population trends and group sizes of T. cristatus over 10 years in the BMKS and examined their ranging patterns. Comparisons of observed populations between 2005 (190 individuals) and 2017 (193 individuals) revealed the stable demography and group sizes of the six T. cristatus groups in the BMKS. Based on a total of 185 location points of the six groups in 2017, their mean ranging area was 3.6 ha with a range of 0.86 to 6.93 ha with extensive spatial overlap. We also found a significant positive relationship between the six groups ranges and group sizes in 2017. Additionally, qualitative ecological comparisons with a previous study on T. cristatus in 1965 (before provisioning) suggest that the artificial food supply in the study area could modify the population dynamics and socioecology of T. cristatus. The modifications might alter their range size and territoriality in the BMKS. Overall, we found that provisioning had negative effects on the ecology of T. cristatus in the BMKS. Therefore, modifying management policies, such as banning feeding and implementing educational programs, may contribute to their proper conservation.


title: RAD51AP1 mediates RAD51 activity through nucleosome interaction

abstract:
RAD51 Associated Protein 1 (RAD51AP1) is a key protein in the homologous recombination DNA repair pathway (HR). Loss of RAD51AP1 leads to defective HR, genome instability and telomere erosion. RAD51AP1 physically interacts with the RAD51 recombinase and promotes RAD51-mediated capture of the donor DNA, synaptic complex assembly and displacement-loop formation when tested with synthetic, nucleosome-free DNA substrates in vitro. In cells, however, DNA is packaged into chromatin, posing an additional barrier to the complexities of the HR reaction. How RAD51AP1 functions as an HR activator in the context of chromatin has remained unclear.

In this study, we show that RAD51AP1 binds to Nucleosome Core Particles (NCPs). We identified a C-terminal region in RAD51AP1 and its previously mapped DNA binding domain as critical for mediating the association between RAD51AP1 and both the NCP and the histone octamer. We show that RAD51AP1 is capable of promoting duplex DNA capture and initiating joint-molecule formation with the NCP and chromatinized template DNA, respectively. Together, our results suggest that RAD51AP1 directly assists the RAD51-mediated search of donor DNA in chromatin. We present a model, in which RAD51AP1 anchors the DNA template through affinity for its nucleosomes to the RAD51-ssDNA nucleoprotein filament.

category: biochemistry


title: A MYT1L Syndrome mouse model recapitulates patient phenotypes and reveals altered brain development due to disrupted neuronal maturation

abstract: Human genetics have defined a new autism-associated syndrome caused by loss-of-function mutations in MYT1L, a transcription factor known for enabling fibroblast-to-neuron conversions. However, how MYT1L mutation causes autism, ADHD, intellectual disability, obesity, and brain anomalies is unknown. Here, we develop a mouse model of this syndrome. Physically, Myt1l haploinsufficiency causes obesity, white-matter thinning, and microcephaly in the mice, mimicking clinical phenotypes. During brain development we discovered disrupted gene expression, mediated in part by loss of Myt1l gene target activation, and identified precocious neuronal differentiation as the mechanism for microcephaly. In contrast, in adults we discovered that mutation results in failure of transcriptional and chromatin maturation, echoed in disruptions in baseline physiological properties of neurons. This results in behavioral anomalies including hyperactivity, muscle weakness and fatigue, and social alterations with more severe phenotypes in males. Overall, our findings provide insight into the mechanistic underpinnings of this disorder and enable future preclinical studies.


title: A unified theory of E/I synaptic balance, quasicritical neuronal avalanches and asynchronous irregular spiking

abstract:
Neuronal avalanches and asynchronous irregular (AI) firing patterns have been thought to represent distinct frameworks to understand the brain spontaneous activity. The former is typically present in systems where there is a balance between the slow accumulation of tension and its fast dissipation, whereas the latter is accompanied by the balance between synaptic excitation and inhibition (E/I). Here, we develop a new theory of E/I balance that relies on two homeostatic adaptation mechanisms: the short-term depression of inhibition and the spike-dependent threshold increase. First, we turn off the adaptation and show that the so-called static system has a typical critical point commonly attributed to self-organized critical models. Then, we turn on the adaptation and show that the network evolves to a dynamic regime in which: (I) E/I synapses balance regardless of any parameter choice; (II) an AI firing pattern emerges; and (III) neuronal avalanches display power laws. This is the first time that these three phenomena appear simultaneously in the same network activity. Thus, we show that the once thought opposing frameworks may be unified into a single dynamics, provided that adaptation mechanisms are in place. In our model, the AI firing pattern is a direct consequence of the hovering close to the critical line where external inputs are compensated by threshold growth, creating synaptic balance for any E/I weight ratio.

HighlightsO_LIAsynchronous irregular (AI) firing happens together with power-law neuronal avalanches under self-organized synaptic balance.
C_LIO_LISelf-organization towards the critical and balanced state (with AI and power-law avalanches) occur via short-term inhibition depression and firing threshold adaptation.
C_LIO_LIThe avalanche exponents match experimental findings.
C_LIO_LIThe adaptation time scales drive the self-organized dynamics towards different firing regimes.
C_LI

Author summaryTwo competing frameworks are employed to understand the brain spontaneous activity, both of which are backed by computational and experimental evidence: globally asynchronous and locally irregular (AI) activity arises in excitatory/inhibitory balanced networks subjected to external stimuli, whereas avalanche activity emerge in excitable systems on the critical point between active and inactive states. Here, we develop a new theory for E/I networks and show that there is a state where synaptic balance coexists with AI firing and power-law distributed neuronal avalanches. This regime is achieved through the introducing of short-term depression of inhibitory synapses and spike-dependent threshold adaptation. Thus, the system self-organizes towards the balance point, such that its AI activity arises from quasicritical fluctuations. The need for two independent adaptive mechanisms explains why different dynamical states are observed in the brain.


title: ZIKV disrupts fetal outcome, placental ultrastructure and drug transporter expression in mice

abstract: Congenital Zika virus (ZIKV) infection can induce fetal brain abnormalities. Here, we investigated whether maternal ZIKV infection affects placental physiology and metabolic transport potential and impacts the fetal outcome, regardless of viral presence in the fetus at term. Low (103 PFU-ZIKVPE243; low ZIKV) and high (5x107 PFU-ZIKVPE243; high ZIKV) virus titers were injected into immunocompetent (ICompetent C57BL/6) and immunocompromised (ICompromised A129) mice at gestational day (GD) 12.5 for tissue collection at GD18.5 (term). High ZIKV elicited fetal death rates of 66% and 100%, whereas low ZIKV induced fetal death rates of 0% and 60% in C57BL/6 and A129 dams, respectively. All surviving fetuses exhibited intrauterine growth restriction (IUGR) and decreased placental efficiency. High-ZIKV infection in C57BL/6 and A129 mice resulted in virus detection in maternal spleens and placenta, but only A129 fetuses presented virus RNA in the brain. Nevertheless, pregnancies in both strains produced fetuses with decreased head sizes (p<0.05). Low-ZIKV-A129 dams had higher IL-6 and CXCL1 levels (p<0.05), and their placentas showed increased CCL-2 and CXCL-1 contents (p<0.05). In contrast, low-ZIKV-C57BL/6 dams had an elevated CCL2 serum level and increased type I and II IFN expression in the placenta. Notably, less abundant microvilli and mitochondrial degeneration were evidenced in the placental labyrinth zone (Lz) of ICompromised and high-ZIKV-ICompetent mice but not in low-ZIKV-C57BL/6 mice. In addition, decreased placental expression of the drug transporters P-glycoprotein (P-gp) and breast cancer resistance protein (Bcrp) and the lipid transporter Abca1 was detected in all ZIKV-infected groups, but Bcrp and Abca1 were only reduced in ICompromised and high-ZIKV ICompetent mice. Our data indicate that gestational ZIKV infection triggers specific proinflammatory responses and affects placental turnover and transporter expression in a manner dependent on virus concentration and maternal immune status. Placental damage may impair proper fetal-maternal exchange function and fetal growth/survival, likely contributing to congenital Zika syndrome.

category: physiology


title: ZIKV disrupts placental ultrastructure and drug transporter expression in mice


title: Mangroves are an overlooked hotspot of insect diversity despite low plant diversity

abstract: We here compare the tropical arthropod fauna across a freshwater swamp and six different forest types (rain-, swamp, dry-coastal, urban, freshwater swamp, mangroves) based on 140,000 barcoded specimens belonging to ca. 8,500 species. Surprisingly, we find that mangroves, a globally imperiled habitat that had been expected to be species-poor for insects, are an overlooked hotspot for insect diversity despite having low plant diversity. Our study reveals a species-rich mangrove insect fauna (>3,000 species) that is distinct (>50% of species are mangrove-specific), and has high species turnover across Southeast and East Asia. For most habitats, plant diversity is a good predictor for insect diversity, but mangroves are an exception and compensate for a comparatively low number of phytophagous and fungivorous insect species by supporting an unusually rich community of predators whose larvae feed in the productive mudflats. For the remaining tropical habitats, the insect communities have diversity patterns that are largely congruent across guilds. The discovery of such a sizeable and distinct insect fauna in a globally threatened habitat underlines how little is known about global insect biodiversity.


title: Combinations of Indole based alkaloids from Mitragyna speciosa (Kratom) and cisplatin inhibit cell proliferation and migration of Nasopharyngeal carcinoma cell lines

abstract:
Ethnopharmacological relevanceMitragyna speciosa (Korth.) or kratom is a medicinal plant indigenous to Southeast Asia. The leaves of M. speciosa is used as a medication in pain management including cancer related pain, in a similar way as opioids and cannabis. Despite its well-known analgesic effect, there is a scarce of information on the cancer-suppressing potential of M. speciosa and its active constituents.

Aim of the studyTo assess the potential applicability of M. speciosa alkaloids (mitragynine, speciociliatine or paynantheine) as chemosensitizers for cisplatin in Nasopharyngeal carcinoma (NPC) cell lines.

Materials and MethodsThe cytotoxic effects of the extracts, fractions and compounds were determined by conducting in vitro cytotoxicity assays. Based on the cytotoxic screening, the alkaloid extract of M. speciosa exhibited potent inhibitory effect on the NPC cell line HK-1, and therefore, was chosen for further fractionation and purification. NPC cell lines HK-1 and C666-1 were treated with combinations of cisplatin and M. speciosa alkaloids in 2D monolayer culture. The effect of the drug combination on cell migration was tested using in vitro wound healing and spheroid invasion assays.

ResultsIn our bioassay guided isolation, both methanolic and alkaloid extracts showed mild to moderate cytotoxic effect against the HK-1 cell line. Both NPC cell lines were insensitive to single agent and combination treatments of the M. speciosa alkaloids. However, mitragynine and speciociliatine sensitised the HK-1 and C666-1 to cisplatin ~4- and >5-fold, respectively in 2D monolayer culture. The combination of mitragynine and cisplatin also significantly inhibited cell migration of the NPC cell lines. Similarly, combination of mitragynine and cisplatin inhibited growth and invasion of HK-1 spheroids in a dose-dependent manner. Moreover, the spheroids did not rapidly develop resistance to the drug combinations at high concentrations over 10 days.

ConclusionCollectively, data shows that both mitragynine and speciociliatine could be potential chemosensitizers for cisplatin. Further extensive drug mechanistic studies and investigations in animal models are necessary to delineate the applicability of M. speciosa alkaloids for NPC therapy.


title: The Wood Image Analysis and Dataset (WIAD): open-access visual analysis tools to advance the ecological data revolution

abstract:
O_LIEcological data is collected and shared at an increasingly rapid pace, but it is often shared in inconsistent and untraceable processed forms. Images of wood contain a wealth of information such as colours and textures but are most commonly reduced to ring-width measurements before they can be shared in various common file formats. Archiving digital images of wood samples in libraries, that have been developed for ecological analysis and are publicly available, remains the exception.
C_LIO_LIWe developed the Wood Image Analysis and Dataset (WIAD) an open-source application including a web-interface to integrate basic visual analysis of wood samples, such as increment cores, thin sections or x-ray films, basic data processing, and archiving of the images and derived data to facilitate transparency and reproducibility in studies using visual characteristics of wood.
C_LIO_LIWIAD provides user-friendly tools to manipulate images of wood samples, mark and measure wood characteristics such as growth increments, density fluctuations, early- and latewood widths, and fire scars, and to visualise, process, and archive images, metadata, and the derived data.
C_LIO_LIWIAD constitutes a step towards the reproducible automation of tree-ring analysis, while establishing an open-source foundation to create improved community developed repositories which would enable novel ecological studies harnessing the wealth of existing visual data.
C_LI


title: Absence of electroencephalographic evidence of implicit action-effect intentional binding with varying effect probability

abstract: The subjective experience of an attraction in time of an action, and the event caused by the action, is known as the intentional binding phenomenon. Intentional binding is a robust phenomenon and has previously been associated with subjective sense of agency, but recent studies have shown that binding can take place in the absence of action intentions. In this study, we tested possible electrophysiological equivalents to the intentional binding phenomenon under a simple action-effect task, where pressing of a button caused tones to occur at different pitches or delays with different probabilities. Changing the probabilities of the effect of an action has in some previous studies shown to influence the intentional binding phenomenon. We tested whether changes in action-effect probability gave rise to differences in movement related cortical potentials (MRCP) slopes, peak latency and auditory event related potential (aERP) changes of amplitude or latency of the N1, P2, P3 and N4 components of the central aERP, of which some has been related to sense of agency or intentional binding. We also tested differences in MRCP across the whole scalp prior to movements, and to differences in aERP across the whole scalp after the tone is played. We found no electrophysiological indications of intentional binding when action-effect contingencies were changed in accordance with conditions that have given rise to intentional binding in previous experiments. Our results are in line with several recent studies that have questioned whether intentional binding follows all voluntary actions and can be related to sense of agency at all.


title: Length-length and length-weight relationships for four small pelagic fishes in the Kuroshio-Oyashio current system

abstract: Length-length relationships and length-weight relationships were estimated for four small pelagic fishes (Japanese sardine Sardinops melanostictus, Japanese anchovy Engraulis japonicus, chub mackerel Scomber japonicus, and spotted mackerel Scomber australasicus) in the Kuroshio-Oyashio current system. Fish samples were collected from surface-midwater trawl surveys and commercial purse-seine fisheries between September and October of 2020 in the western North Pacific. Total length (TL), fork length (FL), and standard length (SL) were measured to 0.01 cm, and whole body weight (W) was measured to the nearest 0.01 g for each individual. All length-length relationships (TL-FL, TL-SL, and FL-SL) were highly significant (p < 0.0001), with r2 > 0.98 in all species. Length-weight relationships (W-TL, W-FL, and W-SL) were also highly significant (p < 0.0001), with r2> 0.98 in all species. This study provides a useful reference for biological studies and stock assessments of these small pelagic fishes.


title: Rate-of-change analysis in palaeoecology revisited: a new approach

abstract:
AO_SCPLOWBSTRACTC_SCPLOWDynamics in the rate of compositional change (rate-of-change; RoC) of biotic or abiotic assemblages preserved in palaeoecological sequences, are thought to reflect changes due to exogenous drivers such as climate and human forcing as well as endogenous factors linked to local dynamics and biotic interactions. However, changes in sedimentation rates and sampling strategies can result in an uneven distribution of time intervals and are known to affect RoC estimates. Furthermore, there has been relatively little exploration of the implications of these challenges in quantifying RoC in palaeoecology.

Here, we introduce R-Ratepol - an easy-to-use R package - that provides a robust numerical technique for detecting and summarising RoC patterns in complex multivariate time-ordered stratigraphical sequences. First, we compare the performance of common methods of estimating RoC and detecting periods of high RoC (peak-point) using simulated pollen-stratigraphical data with known patterns of compositional change and temporal resolution. In addition, we propose a new method of binning with a moving window, which shows a more than 5-fold increase in the correct detection of peak-points compared to the more traditional way of using individual levels.

Next, we apply our new methodology to four representative European pollen sequences and show that our approach also performs well in detecting periods of significant compositional change during known onsets of human activity, early land-use transformation, and changes in fire frequency.

Expanding the approach using R-Ratepol to open-access paleoecological datasets in global databases, such as Neotoma, will allow future palaeoecological and macroecological studies to quantify major changes in biotic composition or in sets of abiotic variables across broad spatio-temporal scales.


title: Sex-specific body mass ageing trajectories in adult Asian elephants

abstract: In species with marked sexual dimorphism and where one sex undergoes stronger intrasexual competition, that sex is expected to age earlier or quicker. Here, we utilise a unique, longitudinal dataset of a semi-captive population of Asian elephants (Elephas maximus), a species with marked male-biased intrasexual competition, with males being larger and living shorter, and test the hypothesis that males show earlier and/or faster body mass ageing than females. We show sex-specific body mass ageing trajectories: adult males gained weight up to the age of 48 years old, followed by a decrease in body mass until natural death. In contrast, adult females gained body mass with age until a body mass decline in the last year of life. Our study shows that sex-specific life-histories shape ageing patterns, consistent with the predictions of the classical theory of ageing.


title: Consensus clustering for Bayesian mixture models

abstract: Cluster analysis is an integral part of precision medicine and systems biology, used to define groups of patients or biomolecules. Consensus clustering is an ensemble approach that is widely used in these areas, which combines the output from multiple runs of a non-deterministic clustering algorithm. Here we consider the application of consensus clustering to a broad class of heuristic clustering algorithms that can be derived from Bayesian mixture models (and extensions thereof) by adopting an early stopping criterion when performing sampling-based inference for these models. While the resulting approach is non-Bayesian, it inherits the usual benefits of consensus clustering, particularly in terms of computational scalability and providing assessments of clustering stability/robustness. In simulation studies, we show that our approach can successfully uncover the target clustering structure, while also exploring different plausible clusterings of the data. We show that, when a parallel computation environment is available, our approach offers significant reductions in runtime compared to performing sampling-based Bayesian inference for the underlying model, while retaining many of the practical benefits of the Bayesian approach, such as exploring different numbers of clusters. We propose a heuristic to decide upon ensemble size and the early stopping criterion, and then apply consensus clustering to a clustering algorithm derived from a Bayesian integrative clustering method. We use the resulting approach to perform an integrative analysis of three 'omics datasets for budding yeast and find clusters of co-expressed genes with shared regulatory proteins. We validate these clusters using data external to the analysis. These clusters can help assign likely function to understudied genes, for example GAS3 clusters with histones active in S-phase, suggesting a role in DNA replication. Our approach can be used as a wrapper for essentially any existing sampling-based Bayesian clustering implementation, and enables meaningful clustering analyses to be performed using such implementations, even when computational Bayesian inference is not feasible, e.g. due to poor exploration of the target density (often as a result of increasing numbers of features) or a limited computational budget that does not along sufficient samples to drawn from a single chain. This enables researchers to straightforwardly extend the applicability of existing software to much larger datasets, including implementations of sophisticated models such as those that jointly model multiple datasets.


title: Identifying mutant-specific multi-drug combinations using Comparative Network Reconstruction

abstract:
Inhibition of aberrant signaling with target inhibitors is an important treatment strategy in cancer, but unfortunately responses are often short-lived. Multi-drug combinations have the potential to mitigate this, but to avoid toxicity such combinations must be selective and the dosage of the individual drugs should be as low as possible. Since the search space of multi-drug combinations is enormous, an efficient approach to identify the most promising drug combinations and dosages is needed.

Here, we present a pipeline to prioritize promising multi-drug combinations. We performed a limited set of drug perturbations in an isogenic cell line pair with and without an activating PI3K mutation, and recorded their signaling states and cell viability. We used these data to reconstruct mutant specific signaling networks and map the short term signaling response to longer term changes in cell viability. The resulting models then allowed us to predict the effect of unseen multi-drug combinations, at arbitrary drug-concentrations, on cell viability. Our initial aim was to find combinations that selectively reduce the viability of the PI3K mutant cells, but our models indicated that such combinations do not exist for this cell line pair. However, we were able to validate 25 of the 30 low-dose multi-drug combinations that we predicted to be anti-selective. Our pipeline thus enables a powerful strategy to rapidly map the efficacy and possible selectivity of drug combinations, hence significantly speeding up the pace at which we can explore the vast space of combination therapies.


title: Motor planning brings human primary somatosensory cortex into movement-specific preparatory states

abstract:
Motor planning plays a critical role in producing fast and accurate movement. Yet, the neural processes that occur in human primary motor and somatosensory cortex during planning, and how they relate to those during movement execution, remain poorly understood. Here we used 7T functional magnetic resonance imaging (fMRI) and a delayed movement paradigm to study single finger movement planning and execution. The inclusion of no-go trials and variable delays allowed us to separate what are typically overlapping planning and execution brain responses. Although our univariate results show widespread deactivation during finger planning, multivariate pattern analysis revealed finger-specific activity patterns in contralateral primary somatosensory cortex (S1), which predicted the planned finger action. Surprisingly, these activity patterns were as informative as those found in contralateral primary motor cortex (M1). Control analyses ruled out the possibility that the detected information was an artifact of subthreshold movements during the preparatory delay. Furthermore, we observed that finger-specific activity patterns during planning were highly correlated to those during execution. These findings reveal that motor planning activates the specific S1 and M1 circuits that are engaged during the execution of a finger press, while activity in both regions is overall suppressed. We propose that preparatory states in S1 may improve movement control through changes in sensory processing or via direct influence of spinal motor neurons.

Significance statementMotor planning is important for good behavioral performance, yet it is unclear which neural processes underlie the preparation of the nervous system for an upcoming movement. Using high-resolution functional neuroimaging, we investigated how motor planning for finger presses changes the activity state in primary motor and primary somatosensory cortex, and how brain responses during planning and execution relate to each other. We show that planning leads to finger-specific activation in both M1 and S1, which is highly similar to the finger-specific activity patterns elicited during execution. Our findings suggest that S1 is being specifically prepared for an upcoming action, either to actively contribute to the outflowing motor command or to enable action-specific sensory gating.


title: Motor planning brings human primary somatosensory cortex into action-specific preparatory states


title: Behavioral rebound following isolation of attention

abstract: Stable sensory perception is achieved through balanced excitatory-inhibitory interactions of lateralized sensory processing. In real world experience, sensory processing is rarely equal across lateralized processing regions, resulting in continuous rebalancing. Using lateralized attention as a case study, we predicted rebalancing lateralized processing following prolonged spatial attention imbalance could cause a gain in attention the opposite direction. In neurotypical human adults, we isolated covert attention to one visual field with a 30-minute attention-demanding task and found an increase in attention in the opposite visual field after manipulation. We suggest a gain in lateralized attention in the previously unattended visual field is due to an overshoot through attention rebalancing. The offline post-manipulation effect is suggestive of long-term potentiation affecting behavior. Our finding of visual field specific attention rebound could be critical for the development of clinical rehabilitation for patients with a unilateral lesion and lateralized attention deficits. This proof-of-concept study initiates the examination of overshoot following the release of imbalance in other lateralized control and sensory domains, important in our basic understanding of lateralized processing.


title: Impact of blindness onset on the representation of sound categories in occipital and temporal cortices

abstract: How does blindness onset impact on the organization of cortical regions coding for the deprived and the remaining senses? We show that the coding of sound categories in the occipital cortex is enhanced and more stable within and across blind individuals when compared to sighted controls, while a reverse group difference is found in the temporal cortex. Importantly, occipital and temporal regions share a more similar representational structure in blind people, suggesting an interplay between the reorganization of occipital and temporal regions following visual deprivation. We suggest that early, and to some extent late blindness, induces network-level reorganization of the neurobiology of auditory categories by concomitantly increasing/decreasing the respective computational load of occipital/temporal regions. These results highlight the interactive nature of regional brain development in case of sensory deprivation.


title: Conformational dynamics of auto-inhibition in the ER calcium sensor STIM1

abstract: The dimeric ER Ca2+ sensor STIM1 controls store-operated Ca2+ entry (SOCE) through the regulated binding of its CRAC activation domain (CAD) to Orai channels in the plasma membrane. In resting cells, the STIM1 CC1 domain interacts with CAD to suppress SOCE, but the structural basis of this interaction is unclear. Using single-molecule Forster resonance energy transfer (smFRET) and protein crosslinking approaches, we show that CC1 interacts dynamically with CAD in a domain-swapped configuration with an orientation predicted to sequester its Orai- binding region adjacent to the ER membrane. Following ER Ca2+ depletion and release from CAD, cysteine crosslinking indicates that the two CC1 domains become closely paired along their entire length in the active Orai-bound state. These findings provide a structural basis for the dual roles of CC1: sequestering CAD to suppress SOCE in resting cells and propelling it towards the plasma membrane to activate Orai and SOCE after store depletion.


title: Targeted DamID in C. elegans reveals a role for LIN-22 and NHR-25 in epidermal cell differentiation

abstract:
Transcription factors are key players in gene networks controlling cell fate specification during development. In multicellular organisms, they can display complex patterns of expression and binding to their targets, which necessitates tissue-specific characterisation of transcription factor-target interactions. Here, we focus on C. elegans seam cell development, which is used as a model of robust epidermal stem cell patterning. Despite our knowledge of multiple transcription factors playing a role in epidermal development, the composition of the gene network underlying cell fate patterning remains largely unknown. We introduce Targeted DamID (TaDa) that allows tissue-specific transcription factor target identification in intact C. elegans animals without cell isolation. We employ this method to recover putative targets in the epidermis for two transcription factors, the HES1 homologue LIN-22 and the NR5A1/2 nuclear hormone receptor NHR-25. Using single-molecule FISH (smFISH), we validate TaDa predictions and reveal a role for these transcription factors in promoting cell differentiation, as well as an unusual link between a HES factor and the Wnt signalling pathway.

Our results expand our understanding of the epidermal gene network and highlight the power of TaDa to dissect the architecture of tissue-specific gene regulatory networks.


title: Genome architecture shapes evolutionary adaptation to DNA replication stress

abstract: In haploid budding yeast, evolutionary adaptation to constitutive DNA replication stress alters three genome maintenance modules: DNA replication, the DNA damage checkpoint, and sister chromatid cohesion. We asked how these trajectories depend on a populations genome architecture by comparing the adaptation of haploids to that diploids and recombination deficient haploids. In all three genome architectures, adaptation happens within 1000 generations at rates that are linearly correlated with the initial fitness defect of the ancestors. Mutations in individual genes are selected at different frequencies in different architectures, but the benefits these mutations confer are similar in all three architectures, and combinations of these mutations reproduce the fitness gains of evolved populations. Despite the differences in the selected mutations, the evolutionary trajectories target the same three functional modules in all architectures revealing a common evolutionary response to DNA replication stress.


title: Probing T-cell response by sequence-based probabilistic modeling

abstract:
With the increasing ability to use high-throughput next-generation sequencing to quantify the diversity of the human T cell receptor (TCR) repertoire, the ability to use TCR sequences to infer antigen-specificity could greatly aid potential diagnostics and therapeutics. Here, we use a machine-learning approach known as Restricted Boltzmann Machine to develop a sequence-based inference approach to identify antigen-specific TCRs. Our approach combines probabilistic models of TCR sequences with clone abundance information to extract TCR sequence motifs central to an antigen-specific response. We use this model to identify patient personalized TCR motifs that respond to individual tumor and infectious disease antigens, and to accurately discriminate specific from non-specific responses. Furthermore, the hidden structure of the model results in an interpretable representation space where TCRs responding to the same antigen cluster, correctly discriminating the response of TCR to different viral epitopes. The model can be used to identify condition specific responding TCRs. We focus on the examples of TCRs reactive to candidate neoantigens and selected epitopes in experiments of stimulated TCR clone expansion.

Author SummaryLarge repertoires of immune cells, such as T cells, are increasingly made available by high-throughput sequencing. Exploiting such datasets to infer how T-cell respond to antigens could help design vaccines and adoptive T-cell therapies. We here propose an approach based on probabilistic machine learning to identify and characterize responding T cells. After learning, this approach is able to distinguish clones that specifically respond to different antigen stimulations. The model parameters and the low-dimensional representations of the T-cell sequences identify sequence motifs underlying T-cell recognition at the molecular level. The approach is illustrated on repertoire data describing in vitro stimulation of T cells by cancer-related neoantigens, as well as on data for common infectious diseases.


title: NetGenes: A database of essential genes predicted using features from interaction networks

abstract: Essential gene prediction models built so far are heavily reliant on sequence-based features and the scope of network-based features has been narrow. Previous work from our group demonstrated the importance of using network-based features for predicting essential genes with high accuracy. Here, we applied our approach for the prediction of essential genes to organisms from the STRING database and hosted the results in a standalone website. Our database, NetGenes, contains essential gene predictions for 2700+ bacteria predicted using features derived from STRING protein-protein functional association networks. Housing a total of 3.5M+ genes, NetGenes offers various features like essentiality scores, annotations and feature vectors for each gene. NetGenes is available at https://rbc-dsai-iitm.github.io/NetGenes/


title: Towards a unified theory of plant photosynthesis and hydraulics

abstract: The global carbon and water cycles are governed by the coupling of CO2 and water vapour exchanges through the leaves of terrestrial plants, controlled by plant adaptations to balance carbon gains and hydraulic risks. We introduce a trait-based optimality theory that unifies the treatment of stomatal responses and biochemical acclimation of plants to environments changing on multiple timescales. Tested with experimental data from 18 species, our model successfully predicts the simultaneous decline in carbon assimilation rate, stomatal conductance, and photosynthetic capacity during progressive soil drought. It also correctly predicts the dependencies of gas exchange on atmospheric vapour pressure deficit, temperature, and CO2. Model predictions are also consistent with widely observed empirical patterns, such as the distribution of hydraulic strategies. Our unified theory opens new avenues for reliably modelling the interactive effects of drying soil and rising atmospheric CO2 on global photosynthesis and transpiration.


title: HUMAN ADENOVIRUS TYPE 4 COMPRISES TWO MAJOR PHYLOGROUPS WITH DISTINCT REPLICATIVE FITNESS AND VIRULENCE PHENOTYPES

abstract:
Human adenovirus type 4 (HAdV-E4) is the only type (and serotype) classified within species Human mastadenovirus E that has been isolated from a human host to the present. Recent phylogenetic analysis of whole genome sequences of strains representing the spectrum of intratypic genetic diversity described to date identified two major evolutionary lineages designated phylogroups (PG) I, and II, and validated the early clustering of HAdV-E4 genomic variants into two major groups by low resolution restriction fragment length polymorphism analysis. In this study we expanded our original analysis of intra- and inter-PG genetic variability, and used a panel of viruses representative of the spectrum of genetic diversity described for HAdV-E4 to examine the magnitude of inter- and intra-PG phenotypic diversity using an array of cell-based assays and a cotton rat model of HAdV respiratory infection. Our proteotyping of HAdV-E strains using concatenated protein sequences in selected coding regions including E1A, E1B-19K and -55K, DNA polymerase, L4-100K, various E3 proteins, and E4-34K confirmed that the two clades encode distinct variants/proteotypes at most of these loci. Our in vitro and in vivo studies demonstrated that PG I and PG II differ in their growth, spread, and cell killing phenotypes in cell culture and in their pulmonary pathogenic phenotypes. Surprisingly, the differences in replicative fitness documented in vitro between PGs did not correlate with the differences in virulence observed in the cotton rat model. This body of work is the first reporting phenotypic correlates of naturally occurring intratypic genetic variability for HAdV-E4.

IMPORTANCEHuman adenovirus type 4 (HAdV-E4) is a prevalent causative agent of acute respiratory illness of variable severity and of conjunctivitis and comprises two major phylogroups that carry distinct coding variations in proteins involved in viral replication and modulation of host responses to infection. Our data show that PG I and PG II are intrinsically different regarding their ability to grow and spread in culture and to cause pulmonary disease in cotton rats.

This is the first report of phenotypic divergence among naturally occurring known genetic variants of a HAdV type of medical importance. This research reveals readily detectable phenotypic differences between strains representing phylogroups I and II, and it introduces a unique experimental system for the elucidation of the genetic basis of adenovirus fitness and virulence and thus for increasing our understanding of the implications of intratypic genetic diversity in the presentation and course of HAdV-E4-associated disease.


title: Mesophotic gorgonian corals evolve multiple times and faster than deep and shallow lineages

abstract: 1.Mesophotic Coral Ecosystems (MCEs) develop on a unique environment, where abrupt environmental changes take place. Using a time-calibrated molecular phylogeny (mtDNA: mtMutS), we examined the lineage membership of mesophotic gorgonian corals (Octocorallia: Cnidaria) in comparison to shallow and deep-sea lineages of the wider Caribbean-Gulf of Mexico and the Tropical Eastern Pacific. Our results show mesophotic gorgonians originating multiple times from old deep-sea octocoral lineages, whereas shallow-water species comprise younger lineages. The mesophotic gorgonian fauna in the studied areas are related to their zooxanthellate shallow-water counterparts in only two clades (Gorgoniidae and Plexauridae), where the shallow-deep gradient could serve as a driver of diversification. Interestingly, mesophotic clades have diversified faster than either shallow or deep clades. One of this groups with fast diversification is the family Ellisellidae, a major component of the mesophotic gorgonian coral assemblage worldwide.


title: BLOCKADE OF M4 MUSCARINIC RECEPTORS ON STRIATAL CHOLINERGIC INTERNEURONS NORMALIZES STRIATAL DOPAMINE RELEASE IN A MOUSE MODEL OF DYT1-TOR1A DYSTONIA

abstract: Trihexyphenidyl (THP), a non-selective muscarinic receptor (mAChR) antagonist, is commonly used for the treatment of dystonia associated with TOR1A, otherwise known as DYT1 dystonia. A better understanding of the mechanism of action of THP is a critical step in the development of better therapeutics with fewer side effects. We previously found that THP normalizes the deficit in striatal dopamine (DA) release in a mouse model of TOR1A dystonia (Tor1a+/{Delta}E knockin (KI) mice), revealing a plausible mechanism of action for this compound, considering that abnormal DA neurotransmission is consistently associated with many forms of dystonia. However, the mAChR subtype(s) that mediate the rescue of striatal dopamine release remain unclear. In this study we used a combination of pharmacological challenges and cell-type specific mAChR conditional knockout mice of either sex to determine which mAChR subtypes mediate the DA release-enhancing effects of THP. We determined that THP acts in part at M4 mAChR on striatal cholinergic interneurons to rescue DA release in both Tor1a+/+ and Tor1a+/{Delta}E KI mice. Further, we found that the subtype selective M4 antagonist VU6021625 recapitulates the effects of THP. These data implicate a principal role for M4 mAChR located on striatal cholinergic interneurons in the mechanism of action of THP and suggest that subtype selective M4 mAChR antagonists may be effective therapeutics with fewer side effects than THP for the treatment of TOR1A dystonia.

category: pharmacology and toxicology


title: Designing an irreversible metabolic switch for scalable induction of microbial chemical production

abstract: Bacteria can be harnessed to synthesise high-value chemicals. A promising strategy for increasing productivity uses inducible control systems to switch metabolism from growth to chemical synthesis once a large population of cell factories are generated. However, use of expensive chemical inducers limits scalability of this approach for biotechnological applications. Switching using cheap nutrients is an appealing alternative, but their tightly regulated uptake and consumption again limits scalability. Here, using mathematical models of fatty acid uptake in E. coli as an exemplary case study, we unravel how the cells native regulation and program of induction can be engineered to minimise inducer usage. We show that integrating positive feedback loops into the circuitry creates an irreversible metabolic switch, which, requiring only temporary induction, drastically reduces inducer usage. Our proposed switch should be widely applicable, irrespective of the product of interest, and brings closer the realization of scalable and sustainable microbial chemical production.

category: synthetic biology


title: Sugarcane Nitrogen and Irrigation Level Prediction Based on UAV-Captured Multispectral Image at Elongation Stage

abstract:
IntroductionSugarcane is the main industrial crop for sugar production; its growth status is closely related to fertilizer, water, and light input. Unmanned aerial vehicle (UAV)-based multispectral imagery is widely used for high-throughput phenotyping because it can rapidly predict crop vigor. This paper mainly studied the potential of multispectral images obtained by low-altitude UAV systems in predicting canopy nitrogen (N) content and irrigation level for sugarcane.

MethodsAn experiment was carried out on sugarcane fields with three irrigation levels and five nitrogen levels. A multispectral image at a height of 40 m was acquired during the elongation stage, and the canopy nitrogen content was determined as the ground truth. N prediction models, including partial least square (PLS), backpropagation neural network (BPNN), and extreme learning machine (ELM) models, were established based on different variables. A support vector machine (SVM) model was used to recognize the irrigation level.

ResultsThe PLS model based on band reflectance and five vegetation indices had better accuracy (R=0.7693, root mean square error (RMSE)=0.1109) than the BPNN and ELM models. Some spectral information from the multispectral image had obviously different features among the different irrigation levels, and the SVM algorithm was used for irrigation level classification. The classification accuracy reached 77.8%.

ConclusionLow-altitude multispectral images could provide effective information for N prediction and water irrigation level recognition.


title: Urban fox squirrels exhibit tolerance to humans but respond to stimuli from natural predators

abstract: Animals in urban areas that experience frequent exposure to humans often behave differently than those in less urban areas, such as exhibiting less vigilance or anti-predator behavior. These behavioral shifts may be an adaptive response to urbanization, but it may be costly if animals in urban areas also exhibit reduced anti-predator behavior in the presence of natural predators. In trials with only a human observer as the stimulus, urban squirrels exhibited reduced vigilance and anti-predator behavior compared to those in less urban areas. Next, we exposed squirrels in multiple urban and less urban sites to acoustic playbacks of a control stimulus (non-predatory bird calls), a natural predator (hawk), and dogs and recorded their vigilance and three different anti-predator behaviors when a human approached them while either broadcasting one of these three playbacks or no playbacks at all. Squirrels at urban sites also did not differ in their behavioral responses to the playbacks from possible predators (hawks or dogs) when they were compared to those at less urban sites exposed to these playbacks. Urban squirrels also exhibited increased vigilance and anti-predator behavior when exposed to a human paired with hawk playbacks compared to the control playbacks. Together, our results indicate that urban squirrels did perceive and assess risk to the natural predator appropriately despite exhibiting increased tolerance to humans. These results provide little support for the hypothesis that increased tolerance to humans causes animals to lose their fear of natural predators.

category: animal behavior and cognition


title: Neural heterogeneity promotes robust learning

abstract:
The brain has a hugely diverse, heterogeneous structure. Whether or not heterogeneity at the neural level plays a functional role remains unclear, and has been relatively little explored in models which are often highly homogeneous. We compared the performance of spiking neural networks trained to carry out tasks of real-world difficulty, with varying degrees of heterogeneity, and found that it substantially improved task performance. Learning was more stable and robust, particularly for tasks with a rich temporal structure. In addition, the distribution of neuronal parameters in the trained networks closely matches those observed experimentally. We suggest that the heterogeneity observed in the brain may be more than just the byproduct of noisy processes, but rather may serve an active and important role in allowing animals to learn in changing environments.

SummaryNeural heterogeneity is metabolically efficient for learning, and optimal parameter distribution matches experimental data.


title: Genetic polymorphism of CYP2C19 and subcortical variability in the human adult brain

abstract: Pharmacogenetic studies have shown involvement of cytochrome P450 enzymes in the metabolism of psychotropic drugs. However, expression and activity on endogenous substrates in the brain may underlie a constitutive role of these enzymes beyond drug metabolism. CYP2C19, which is expressed in the human fetal brain during neurodevelopment, shows affinity for endogenous compounds including monoaminergic neurotransmitters, steroid hormones, and endocannabinoids. In this study (N=608), we looked at the genetic polymorphism of CYP2C19 and its potential associations with structural phenotypes of subcortical brain volume with structural imaging. Using two independent volume estimation techniques, we found converging evidence for a positive association between CYP2C19 activity scores, as inferred from the genotype, and basal ganglia and hippocampal volume. This association was present only in female individuals, raising the possibility that effects on brain morphology may arise through a mechanism involving the metabolism of estrogen steroids.


title: Water stress and nitrogen supply affect floral traits and pollination in the white mustard, <Sinapis alba> (Brassicaceae)

abstract: Changes in environmental conditions are likely to have a complex effect on the growth of plants, their phenology, plant-pollinator interactions, and reproductive success. The current world is facing an ongoing climate change along with other human-induced environmental changes. Most research has focused on the impact of increasing temperature as a major driving force for climate change, but other factors may have important impacts on plant traits and pollination too and these effects may vary between different seasons. In addition, it is likely that the effects of multiple environmental factors, such as increasing temperature, water stress, and nitrogen enrichment are not independent. Therefore, we tested the impact of three key factors - season, water, and nitrogen supply - on plant traits, pollination, and seed production in Sinapis alba (Brassicaceae). Plants were grown in three seasons with two levels of water and nitrogen supply in a factorial design. We collected data on multiple vegetative and floral traits and assessed the response of pollinators in the field. Additionally, we evaluated the effect of growing conditions on seed set in plants exposed to pollinators and in hand-pollinated plants. Our results show that water stress impaired vegetative growth, decreased flower production, reduced visitation by pollinators and seed set, while nitrogen availability played an important role in nectar production. Seasonality modulated the effect of water and nitrogen availability on vegetative and floral traits and strongly affected flowering phenology and flower production. We demonstrated that changes in water and nitrogen availability alter plant vegetative and floral traits, which impacts flower visitation and consequently plant reproduction. We conclude that ongoing environmental changes such as altered precipitation regimes and nitrogen enrichment may thus affect plant-pollinator interactions with negative consequences for the reproduction of wild plants and insect-pollinated crops.


title: Genetics of white color and iridophoroma in "Lemon Frost" leopard geckos

abstract: The squamates (lizards and snakes) are close relatives of birds and mammals, with more than 10,000 described species that display extensive variation in a number of important biological traits, including coloration, venom production, and regeneration. Due to a lack of genomic tools, few genetic studies in squamates have been carried out. The leopard gecko1, Eublepharis macularius, is a popular companion animal, and displays a variety of coloration patterns. We took advantage of a large breeding colony and used linkage analysis, synteny, and homozygosity mapping to investigate a spontaneous semi-dominant mutation, "Lemon Frost", that produces white coloration and causes skin tumors (iridophoroma). We localized the mutation to a single locus which contains a strong candidate gene, SPINT12,3, a tumor suppressor implicated in human skin cutaneous melanoma (SKCM) and over-proliferation of epithelial cells in mice and zebrafish4-16. Our work establishes the leopard gecko as a tractable genetic system and suggests that a tumor suppressor in melanocytes in humans can also suppress tumor development in iridophores in lizards.

category: genetics


title: Genomic Copy Number Signatures Based Classifiers for Subtype Identification in Cancer

abstract:
Copy number aberrations (CNA) are one of the most important classes of genomic mutations related to oncogenetic effects. In the past three decades, a vast amount of CNA data has been generated by molecular-cytogenetic and genome sequencing based methods. While this data has been instrumental in the identification of cancer-related genes and promoted research into the relation between CNA and histo-pathologically defined cancer types, the heterogeneity of source data and derived CNV profiles pose great challenges for data integration and comparative analysis. Furthermore, a majority of existing studies have been focused on the association of CNA to pre-selected "driver" genes with limited application to rare drivers and other genomic elements.

In this study, we developed a bioinformatics pipeline to integrate a collection of 44,988 high-quality CNA profiles of high diversity. Using a hybrid model of neural networks and attention algorithm, we generated the CNA signatures of 31 cancer subtypes, depicting the uniqueness of their respective CNA landscapes. Finally, we constructed a multi-label classifier to identify the cancer type and the organ of origin from copy number profiling data. The investigation of the signatures suggested common patterns, not only of physiologically related cancer types but also of clinico-pathologically distant cancer types such as different cancers originating from the neural crest. Further experiments of classification models confirmed the effectiveness of the signatures in distinguishing different cancer types and demonstrated their potential in tumor classification.

category: bioinformatics


title: Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes


title: Multi-color fluorescence fluctuation spectroscopy in living cells via spectral detection

abstract: Signaling pathways in biological systems rely on specific interactions between multiple biomolecules. Fluorescence fluctuation spectroscopy provides a powerful toolbox to quantify such interactions directly in living cells. Cross-correlation analysis of spectrally separated fluctuations provides information about inter-molecular interactions but is usually limited to two fluorophore species. Here, we present scanning fluorescence spectral correlation spectroscopy (SFSCS), a versatile approach that can be implemented on commercial confocal microscopes, allowing the investigation of interactions between multiple protein species at the plasma membrane. We demonstrate that SFSCS enables cross-talk-free cross-correlation, diffusion and oligomerization analysis of up to four protein species labeled with strongly overlapping fluorophores. As an example, we investigate the interactions of influenza A virus (IAV) matrix protein 2 with two cellular host factors simultaneously. We furthermore apply raster spectral image correlation spectroscopy for the simultaneous analysis of up to four species and determine the stoichiometry of ternary IAV polymerase complexes in the cell nucleus.


title: Neural precursor grafts restore motor and non-motor functions in parkinsonian macaques

abstract:
Parkinsons disease (PD) evolves over an extended and variable period in humans; several years prior to the onset of classical motor symptoms, cognitive deficits as well as sleep and biological rhythm disorders develop and worsen with disease progression, significantly impacting the quality of life of patients. The gold standard MPTP macaque model of PD recapitulates the progression of motor and non-motor symptoms over contracted periods of time.

Here, this multidisciplinary and multiparametric study follows, in five animals, the steady progression of motor and non-motor symptoms and describes their reversal following bilateral grafts of neural precursors in diverse functional domains of the basal ganglia.

Results show unprecedented recovery from cognitive symptoms in addition to a strong clinical motor recuperation. Both motor and cognitive recovery and partial circadian rhythm recovery correlate with the degree of graft integration into the host environment as well as with in-vivo levels of striatal dopaminergic innervation and function.

Given inter-individuality of disease progression and recovery the present study underlines the importance of longitudinal multidisciplinary assessments in view of clinical translation and provides empirical evidence that integration of neural precursors following transplantation efficiently restores function at multiple levels in parkinsonian non-human primates.

One Sentence SummaryEmpirical evidence that cell therapy efficiently reverts cognitive and clinical motor symptoms in the non-human primate model of Parkinsons disease.


title: Induced Cognitive Impairments Reversed by Grafts of Neural Precursors: a Longitudinal Study in a Macaque Model of Parkinson's Disease


title: Optimized guide RNA selection recommendations for using spCas9 gene editing in human hematopoietic stem and progenitor cells

abstract:
Ribonucleoproteins (RNPs) are frequently applied for therapeutic gene editing as well as fundamental research, because the method is fast, viral free, and does not rely on clonal selection.

We evaluated various parameters to genetically engineer human hematopoietic stem progenitor cells (HSPCs) using spCas9-RNPs and achieve gene editing efficiencies up to 80%. We find that single guide RNA (sgRNA) design is critical to achieve high gene editing efficiencies. However, finding effective sgRNAs for HSPCs can be challenging, while the contribution of numerous in silico models is unclear.

Here we established a time- and cost-efficient in vitro transcribed sgRNA screening model in K562 cells to identify sgRNAs that are effective in HSPCs using RNP delivery. We show that this simple screening method outperforms all in silico prediction models. Our data demonstrates that most in silico sgRNA prediction models are ineffective and we make recommendations to potentially improve their accuracy.

We report that gene editing is equally efficient in distinct CD34+ HSPC subpopulations. Furthermore, no effects on cell proliferation, differentiation or in vitro hematopoietic lineage commitment were observed. Finally, no upregulation of p21 expression was found, suggesting unperturbed HSPC homeostasis.

Key pointsO_LIIn vitro transcribed single sgRNAs (IVTsgRNA) screening in K562 outperforms in silico modeling
C_LIO_LIHematopoietic stem and progenitor cells are equally targeted by Ribonucleoproteins (RNPs)
C_LIO_LIHematopoietic stem and progenitor cells show no induction of p21 expression or effects on differentiation, proliferation and lineage commitment
C_LI

Graphical abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/423329v2_ufig1.gif" ALT="Figure 1">
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category: molecular biology


title: A multi-level model analysis of lipolysis and fatty acid release from adipocytes in vitro and from adipose tissue invivo

abstract: Lipolysis and the release of fatty acids to supply energy fuel to other organs, such as between meals, during exercise, and starvation, are fundamental functions of the adipose tissue. The intracellular lipolytic pathway in adipocytes is activated by adrenaline and noradrenaline, and inhibited by insulin. Circulating fatty acids are elevated in type 2 diabetic individuals. The mechanisms behind this elevation are not fully known, and to increase the knowledge a link between the systemic circulation and intracellular lipolysis is key. However, data on lipolysis and knowledge from in vitro systems have not been linked to corresponding in vivo data and knowledge in vivo. Here, we use mathematical modelling to provide such a link. We examine mechanisms of insulin action by combining in vivo and in vitro data into an integrated mathematical model that can explain all data. Furthermore, the model can describe independent data not used for training the model. We show the usefulness of the model by simulating new and more challenging experimental setups in silico, e.g. the extracellular concentration of fatty acids during an insulin clamp, and the difference in such simulations between individuals with and without type 2 diabetes. Our work provides a new platform for model-based analysis of adipose tissue lipolysis, under both non-diabetic and type 2 diabetic conditions.


title: A Theory of Synaptic Transmission

abstract: Rapid and precise neuronal communication is enabled through a highly synchronous release of signaling molecules neurotransmitters into the synaptic cleft within just milliseconds of the action potential. Yet neurotransmitter release lacks a theoretical framework that is both phenomenologically accurate and mechanistically realistic. Here, we formulate an analytic theory of the action-potential-triggered neurotransmitter release at a chemical synapse. The theory captures general principles of synaptic transmission while generating concrete predictions for particular synapses. A universal scaling in synaptic transmission is established, and demonstrated through a collapse of experimental data from different synapses onto a universal curve. The theory shows how key characteristics of synaptic function - plasticity, fidelity, and efficacy - emerge from molecular mechanisms of neurotransmitter release machinery.