title: Distinct Protofilament-scale Dynamics Define the Differential Remodeling of Microtubule Arrays

abstract:
The dynamic reorganization of microtubule-based cellular structures, such as the spindle and the axoneme, fundamentally depends on the dynamics of individual polymers within multimicrotubule arrays. A major class of enzymes, implicated in both the complete demolition and fine size control of microtubule-based arrays, are depolymerizing kinesins. How different depolymerases differently remodel microtubule arrays is poorly understood. A major technical challenge in addressing this question is that existing optical or electron-microscopy methods lack the spatial-temporal resolution to observe the dynamics of individual microtubules within larger arrays. Here we use Atomic Force Microscopy (AFM) to image depolymerizing arrays at single microtubule and protofilament resolution. We discover previously unseen modes of microtubule array destabilization by conserved depolymerases. We find that the kinesin-13 MCAK mediates asynchronous protofilament depolymerization and lattice-defect propagation, whereas the kinesin-8 Kip3p promotes synchronous protofilament depolymerization. Unexpectedly, MCAK can depolymerize the highly stable axonemal doublets, but Kip3p cannot. We propose that distinct protofilament-level activities underlie the functional dichotomy of depolymerases, resulting in either large-scale destabilization or length regulation of microtubule arrays. Our work establishes AFM as a powerful strategy to visualize microtubule dynamics within arrays and reveals how nanometer-scale substrate specificity leads to differential remodeling of micron-sized cytoskeletal structures.

SIGNIFICANCE STATEMENTOne cannot help but marvel at the precise organization of microtubule polymers in cellular structures such as the axoneme and the spindle. However, our understanding of the biochemical mechanisms that sculpt these arrays comes largely from in vitro experiments with a small number (one or two) of microtubules. This is somewhat akin to studying the architecture of multilane highways by studying one-lane streets. Here we directly visualize depolymerizing microtubule arrays at individual microtubule and protofilament resolution using Atomic Force Microscopy. Our results reveal differences in microtubule depolymerase activity and provide insights into how these differences in enzymatic activity on the nanometer scale can result in the differential remodeling of multi-microtubule arrays on the micron-length scale.


title: Atomic Force Microscopy Reveals Distinct Protofilament-scale Structural Dynamics in Depolymerizing Microtubule Arrays

category: biophysics


title: Exogenous phosphatidic acid reduces acetaminophen-induced liver injury in mice by activating hepatic interleukin-6 signaling through inter-organ crosstalk

abstract: We previously demonstrated that endogenous phosphatidic acid (PA) promotes liver regeneration after acetaminophen (APAP) hepatotoxicity in mice. Based on that, we hypothesized that exogenous PA is also beneficial. To test that, we treated mice with a toxic APAP dose at 0 h, followed by PA or vehicle at multiple timepoints. We then collected blood and liver at 6, 24, and 52 h. Post-treatment with PA protected against liver injury at 6 h, and the combination of PA and N-acetyl-cysteine (NAC) further reduced injury compared to NAC alone. Interestingly, PA had no effect on major early mechanisms of APAP toxicity, including APAP bioactivation, oxidative stress, JNK activation, and mitochondrial damage. However, transcriptomics revealed that PA activated interleukin-6 (IL-6) signaling in the liver, and IL-6 was increased in serum from PA-treated mice. Furthermore, PA did not protect against APAP in IL-6-deficient mice. In addition, IL-6 expression increased 18-fold in adipose tissue after PA, indicating that adipose tissue is a likely source of the increased IL-6 due to PA treatment. Surprisingly, however, exogenous PA did not alter regeneration, despite the widely accepted role of IL-6 in liver repair. These data reinforce the protective role of IL-6 in APAP hepatotoxicity, provide new insight into the role of IL-6 in liver regeneration, and indicate that exogenous PA or PA derivatives may one day be a useful adjunct treatment for APAP overdose with NAC.

category: pharmacology and toxicology


title: Sting orchestrates the crosstalk between polyunsaturated fatty acids metabolism and inflammatory responses

abstract: Inflammatory disorders are major health issues in which immune function and metabolic homeostasis are concertedly altered. Yet, the molecular mechanisms coordinating innate and metabolic pathways in homeostatic conditions are poorly understood. Here, we unveil a negative regulatory feedback loop involving the Stimulator of interferon genes (Sting) and the Fatty acid desaturase 2 (Fads2). At steady state, Sting regulates FA metabolism by repressing the activity of the Fads2 enzyme responsible for the desaturation of polyunsaturated FAs (PUFAs). Importantly, Sting activation increased Fads2 activity, while antagonizing Fads2 enhanced Sting activation, promoting the establishment of an anti-viral state. Remarkably, the cross-regulation between Sting and Fads2 is mediated by the cyclic GMP-AMP (cGAMP) Sting agonist and PUFAs. Indeed, we found that PUFAs inhibit Sting activation, while Sting agonists bind Fads2. Thus, our study identifies Sting as a master regulator of FA metabolism, and PUFAs as modulators of Sting-dependent inflammation. The interplay between Fads2 and Sting determines the fine-tuning of inflammatory responses, but comes at the expense of metabolic alterations, which are critical to consider in human pathologies associated with aberrant Sting activation.

category: immunology


title: A WDR35-dependent coatomer transports ciliary membrane proteins from the Golgi to the cilia

abstract: Intraflagellar transport (IFT) is a highly conserved mechanism for motor-driven transport of cargo within cilia, but how this cargo is selectively transported to cilia and across the diffusion barrier is unclear. WDR35/IFT121 is a component of the IFT-A complex best known for its role in ciliary retrograde transport. In the absence of WDR35, small mutant cilia form but fail to enrich in diverse classes of ciliary membrane proteins. In Wdr35 mouse mutants, the IFT-A peripheral components are degraded and core components accumulate at the transition zone. We reveal deep sequence homology and structural similarity of WDR35 and other IFT-As to the coatomer COPI proteins a and {beta}', and demonstrate an accumulation of  coat-less vesicles which fail to fuse with Wdr35 mutant cilia. Our data provides the first in situ evidence of a novel coatomer function for WDR35 likely with other IFT-A proteins in delivering ciliary membrane cargo from the Golgi necessary for cilia elongation.

category: cell biology


title: Narratives: fMRI data for evaluating models of naturalistic language comprehension

abstract: The "Narratives" collection aggregates a variety of functional MRI datasets collected while human subjects listened to naturalistic spoken stories. The current release includes 345 subjects, 891 functional scans, and 27 diverse stories of varying duration totaling ~4.6 hours of unique stimuli (~43,000 words). This data collection is well-suited for naturalistic neuroimaging analysis, and is intended to serve as a benchmark for models of language and narrative comprehension. We provide standardized MRI data accompanied by rich metadata, preprocessed versions of the data ready for immediate use, and the spoken story stimuli with time-stamped phoneme- and word-level transcripts. All code and data are publicly available with full provenance in keeping with current best practices in transparent and reproducible neuroimaging.

category: neuroscience


title: Herpes Simplex Virus Co-Infection Facilitates Rolling Circle Replication of the Adeno-Associated Virus Genome

abstract:
Adeno-associated virus (AAV) genome replication only occurs in the presence of a co-infecting helper virus such as adenovirus type 5 (AdV5) or herpes simplex virus type 1 (HSV-1). AdV5-supported replication of the AAV genome has been described to occur in a strand-displacement rolling hairpin replication (RHR) mechanism initiated at the AAV 3 inverted terminal repeat (ITR) end. It has been assumed that the same mechanism applies to HSV-1-supported AAV genome replication. Using nanopore sequencing as a novel, high-throughput approach to study viral genome replication we demonstrate the formation of double-stranded head-to-tail concatemers of AAV genomes in the presence of HSV-1, thus providing evidence for an unequivocal rolling circle replication (RCR) mechanism. This stands in contrast to the textbook model of AAV genome replication when HSV-1 is the helper virus.

SIGNIFICANCEEfficient adeno-associated virus (AAV) replication requires the presence of helper factors, which can be provided by co-infecting helper viruses such as adenoviruses or herpesviruses. AAV replication has been described to occur as a rolling hairpin replication mechanism. However, we show that during a herpes simplex virus type 1 (HSV-1) supported replication, AAV rolling circle-like replication intermediates are formed. Thus, this study stands in contrast to the textbook model of AAV genome replication. Additionally, we introduce nanopore sequencing as a novel, high-throughput approach to study viral genome replication in unprecedented detail.

category: microbiology


title: Drosophila glue protects from predation

abstract: Animals can be permanently attached to a substrate in terrestrial environments at certain stages of their development. Pupa adhesion has evolved multiple times in insects and is thought to maintain the animal in a place where it is not detectable by predators. Here, we investigate whether pupa adhesion in Drosophila can also protect the animal by preventing potential predators from detaching the pupa. We measured the adhesion of Drosophila species sampled from the same area and found that pupa adhesion varies among species, which can be explained by different glue production strategies. Then, we compared attached and manually detached pupae in both field and laboratory assays to investigate the role of pupa adhesion to prevent predation. First, we found that attached pupae remain on site 30 % more than detached pupae in the field after three days, probably because they are less predated. Second, we observed that attached pupae are less efficiently predated by ants in the laboratory: they are not carried back to the ant nest and more ants are needed to consume them onsite. Our results show that pupa adhesion can prevent the animal from being taken away by predators and is crucial for Drosophila fly survival.

category: evolutionary biology


title: Evolution of a virus-like architecture and packaging mechanism in a repurposed bacterial protein

abstract: Viruses are ubiquitous pathogens of global impact. Prompted by the hypothesis that their earliest progenitors recruited host proteins for virion formation, we have used stringent laboratory evolution to convert a bacterial enzyme lacking affinity for nucleic acids into an artificial nucleocapsid that efficiently packages and protects multiple copies of its own encoding mRNA. Revealing remarkable convergence on the molecular hallmarks of natural viruses, the accompanying changes reorganized the protein building blocks into an interlaced 240-subunit icosahedral capsid impermeable to nucleases, while emergence of a robust RNA stem-loop packaging cassette ensured high encapsidation yields and specificity. In addition to evincing a plausible evolutionary pathway for primordial viruses, these findings highlight practical strategies for developing non-viral carriers for diverse vaccine and delivery applications.

category: biochemistry


title: A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process

abstract: SARS-CoV-2 is the causative agent of COVID-19. The dimeric form of the viral main protease is responsible for the cleavage of the viral polyprotein in 11 sites, including its own N and C-terminus. Although several mechanisms of self-cleavage had been proposed for SARS-CoV, the lack of structural information for each step is a setback to the understanding of this process. Herein, we used X-ray crystallography to characterize an immature form of the main protease, which revealed major conformational changes in the positioning of domain-three over the active site, hampering the dimerization and diminishing its activity. We propose that this form preludes the cis-cleavage of N-terminal residues within the dimer, leading to the mature active site. Using fragment screening, we probe new cavities in this form which can be used to guide therapeutic development. Furthermore, we characterized a serine site-directed mutant of the main protease bound to its endogenous N and C-terminal residues during the formation of the tetramer. This quaternary form is also present in solution, suggesting a transitional state during the C-terminal trans-cleavage. This data sheds light in the structural modifications of the SARS-CoV-2 main protease during maturation, which can guide the development of new inhibitors targeting its intermediary states.


title: Brucella ovis cysteine biosynthesis contributes to peroxide stress survival and fitness in the intracellular niche

abstract: Brucella ovis is an ovine intracellular pathogen with tropism for the male genital tract. To establish and maintain infection, B. ovis must survive stressful conditions inside host cells, including low pH, nutrient limitation, and reactive oxygen species. These same conditions are often encountered in axenic cultures during stationary phase. Studies of stationary phase may thus inform understanding of Brucella infection biology, yet the genes and pathways that are important in Brucella stationary phase physiology remain poorly defined. We measured fitness of a barcoded pool of B. ovis Tn-himar mutants as a function of growth phase and identified cysE as a determinant of fitness in stationary phase. CysE catalyzes the first step in cysteine biosynthesis from serine, and we provide genetic evidence that two related enzymes, CysK1 and CysK2, function redundantly to catalyze cysteine synthesis at steps downstream of CysE. Deleting either cysE ({Delta}cysE) or both cysK1 and cysK2 ({Delta}cysK1 {Delta}cysK2) results in premature entry into stationary phase, reduced culture yield and sensitivity to exogenous hydrogen peroxide. These phenotypes can be chemically complemented by cysteine or glutathione. {Delta}cysE and {Delta}cysK1 {Delta}cysK2 strains have no defect in host cell entry in vitro but have significantly diminished intracellular fitness between 2 and 24 hours post infection. Our study has uncovered unexpected redundancy at the CysK step of cysteine biosynthesis in B. ovis, and demonstrates that cysteine anabolism is a determinant of peroxide stress survival and fitness in the intracellular niche.


title: Are specialised ABC transporters responsible for the circularisation of type I circular bacteriocins?

abstract: DisclaimerThe authors have withdrawn their manuscript whilst they perform further analysis to verify some interpretations and conclusions. Therefore, the authors do not wish this work to be cited as a reference. If you have any questions, please contact the corresponding author.


title: Development of a novel hybrid alphavirus-SARS-CoV-2 particle for rapid in vitro screening and quantification of neutralization antibodies, viral variants, and antiviral drugs

abstract: Timely development of vaccines and antiviral drugs is critical to control the COVID-19 pandemic 1-6. Current methods for quantifying vaccine-induced neutralizing antibodies involve the use of pseudoviruses, such as the SARS-CoV-2 spike protein (S) pseudotyped lentivirus7-14. However, these pseudoviruses contain structural proteins foreign to SARS-CoV-2, and require days to infect and express reporter genes15. Here we describe the development of a new hybrid alphavirus-SARS-CoV-2 (Ha-CoV-2) particle for rapid and accurate quantification of neutralization antibodies and viral variants. Ha-CoV-2 is a non-replicating SARS-CoV-2 virus-like particle, composed of SARS-CoV-2 structural proteins (S, M, N, and E) and a RNA genome derived from a fast expressing alphavirus vector 16. We demonstrated that Ha-CoV-2 can rapidly and robustly express reporter genes in target cells within 3-6 hours. We further validated Ha-CoV-2 for rapid quantification of neutralization antibodies, viral variants, and antiviral drugs. In addition, as a proof-of-concept, we assembled and compared the relative infectivity of a panel of 10 Ha-CoV-2 variant isolates (D614G, P.1, B.1.1.207, B.1.351, B.1.1.7, B.1.429, B.1.258, B.1.494, B.1.2, B.1.1298), and demonstrated that these variants in general are 2-10 fold more infectious. Furthermore, we quantified the anti-serum from an infected and vaccinated individual; the one dose vaccination with Moderna mRNA-1273 has greatly increased the anti-serum titer for approximately 6 fold. The post-vaccination serum has also demonstrated various neutralizing activities against all 9 variants tested. These results demonstrated that Ha-CoV-2 can be used as a robust platform for rapid quantification of neutralizing antibodies against SARS-CoV-2 and its variants.


title: Tyrosinase from mushroom Agaricus bisporus as an inhibitor of the Hepatitis C virus

abstract: Tyrosinases from both a commercial semi-purified Agaricus bisporus protein extract and directly isolated from white mushroom have been demonstrated to show antiviral activity against the Hepatitis C virus for the first time. The well-known tyrosinase from A. bisporus (TyrAB) of 45kDa and a newly discovered 50-kDa isoform from this tyrosinase (Tyr50kDa) have been tested. Cell toxicity and antiviral activity of tyrosinases in cultured Huh 5-2 liver tumor cells transfected with a replicon system (a plasmid that includes all non-structural Hepatitis C virus proteins and replicates autonomously) was determined. Native TyrAB was able to inhibit the replication of the hepatitis C virus without inducing toxicity in liver cells. In addition, the post-translational isoform of Tyr50kDa showed higher antiviral capacity than the former (up to 10 times greater), also exhibiting 10 times higher activity than the commercial drug Ribavirin(R). This antiviral activity was directly proportional to the enzymatic activity of tyrosinases, since no antiviral capacity was observed for the inactive enzymes. The tyrosinases approach could represent a new antiviral inhibition mechanism, through a catalytic mechanism of selective hydroxylation of key role tyrosine residues in viral proteases. The tyrosinases directly extracted from fresh mushrooms (containing both tyrosinases) showed similar antiviral activity and, therefore, might provide low-cost drugs for the treatment of hepatitis C.


title: Isolation and characterization of Pseudomonas chlororaphis strain ST9 and its potential as a bioinoculant for agriculture

abstract: The development of biotechnologies based on beneficial microorganisms for improving soil fertility and crop yields could help addressing many current agriculture challenges, such as food security, climate change, pests control, soil depletion while decreasing the use of chemical fertilizers and pesticides. Plant Growth Promoting (PGP) microbes can be used as probiotics in order to increase plant tolerance/resistance to abiotic/biotic stresses and in this context strains belonging to the Pseudomonas chlororaphis group have shown to have potential as PGP candidates. In this work a new P. chlororaphis isolate is reported and tested for (i) in vitro PGP features, (ii) whole genome sequence analysis, and (iii) its effects on root microbiome, plant growth and on the expression of different plant genes in greenhouse experiments. The potential use of this P. chlororaphis strain as a plant probiotic is discussed.


title: Shared population-level dynamics in monkey premotor cortex during solo action, joint action and action observation

abstract:
Studies of neural population dynamics of cell activity from monkey motor areas during reaching show that it mostly represents the generation and timing of motor behavior. We compared neural dynamics in dorsal premotor cortex (PMd) during the performance of a visuomotor task executed individually or cooperatively and during an observation task. In the visuomotor conditions, monkeys applied isometric forces on a joystick to guide a visual cursor in different directions, either alone or jointly with a conspecific. In the observation condition, they observed the cursors motion guided by the partner. We found that in PMd neural dynamics were widely shared across action execution and observation, with cursor motion directions more accurately discriminated than task types. This suggests that PMd encodes spatial aspects irrespective of specific behavioral demands. Furthermore, our results suggest that largest components of premotor population dynamics, which have previously been suggested to reflect a transformation from planning to movement execution, may rather reflect higher cognitive-motor processes, such as the covert representation of actions and goals shared across tasks that require movement and those that do not.

HIGHLIGHTSO_LIIn PMd neural dynamics is shared across action execution and mere observation
C_LIO_LITask directional features are more accurately discriminated than action types
C_LIO_LISpatial aspects are encoded in PMd independently from specific behavioral demands
C_LIO_LIPMd dynamics largely reflect higher cognitive-motor processes rather than strictly motor-related functions
C_LI


title: Are indigenous territories effective natural climate solutions? A neotropical analysis using matching methods and geographic discontinuity designs.

abstract: Indigenous Territories (ITs) with less centralized forest governance than Protected Areas (PAs) may represent cost-effective natural climate solutions to meet the Paris agreement. However, the literature has been limited to examining the effect of ITs on deforestation, despite the influence of anthropogenic degradation. Thus, little is known about the temporal and spatial effect of allocating ITs on carbon stocks dynamics that account for losses from deforestation and degradation. Using Amazon Basin countries and Panama, this study aims to estimate the temporal and spatial effects of ITs and PAs on carbon stocks. To estimate the temporal effects, we use annual carbon density maps, matching analysis, and linear mixed models. Furthermore, we explore the spatial heterogeneity of these estimates through geographic discontinuity designs, allowing us to assess the spatial effect of ITs and PAs boundaries on carbon stocks. The temporal effects highlight that allocating ITs preserves carbon stocks and buffer losses as PAs in Panama and Amazon Basin countries. The geographic discontinuity designs reveal that ITs boundaries secure more extensive carbon stocks than their surroundings, and this difference tends to increase towards the least accessible areas, suggesting that indigenous land use in neotropical forests may have a temporarily and spatially stable impact on carbon stocks. Our findings imply that ITs in neotropical forests support Nationally Determined Contributions (NDCs) under the Paris Agreement. Thus, Indigenous peoples must become recipients of countries results-based payments.

category: ecology


title: Variation and process of life history evolution in insular dwarfism as revealed by a natural experiment

abstract:
BackgroundIslands offer a classic topic for evolutionary studies. Few other subjects have historically raised as much fascination as the island large mammals that having evolved into dwarfs. Consensus has been gained that multivariate ecological causes are behind those changes, but what remains largely unexplored are the processes involved. Recent studies focused on associated change of body size and life history (age of reproduction, growth rate, longevity) - a key to understand the process of insular dwarfism. The Japanese Archipelago offers worldwide a unique natural experiment, as in its numerous islands of different sizes the same group of organisms, deer, have evolved into different sizes. We investigated eight deer populations exhibiting body size variation, both extant and fossil, to clarify the effect of insularity on life history traits.

ResultsWe applied several methods to both extant and extinct populations for resolving life history change among deer populations. Skeletochronology using lines of arrested growth successfully reconstructed body growth curves and revealed a gradual change in the growth trajectories reflecting degree of insularity: slower growth with prolonged growth periods in more isolated deer populations. An extensive examination of bone microstructure further corroborated it, and clearly indicated much slower growth and later somatic maturity in fossil insular deer, which had been isolated for more than 1.5 Myr. Finally, mortality patterns revealed by demographic analysis varied among deer populations and life history of insular populations shifted toward "slow-life" of K-strategists.

ConclusionWe clarified the evolutionary and ecological process behind insular dwarfism, which occurred in conjunction with life history shifts. The process initiated with phenotypic plasticity responding to the resource-limitation on predator-free islands after the settlements of islanders. Under the insular environments, natural selection favored K-selected animals and the life history traits were genetically fixed. Extreme K-strategy found in fossil dwarfs on islands would make them vulnerable to anthropogenic changes, that would explain termination of insular dwarfs after human arrival on islands.


title: Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes

abstract: Ciliates are unicellular eukaryotes with both a germline genome and a somatic genome in the same cytoplasm. The somatic macronucleus (MAC), responsible for gene expression, is not sexually transmitted but develops from a copy of the germline micronucleus (MIC) at each sexual generation. In the MIC genome of Paramecium tetraurelia, genes are interrupted by tens of thousands of unique intervening sequences, called Internal Eliminated Sequences (IESs), that have to be precisely excised during the development of the new MAC to restore functional genes. To understand the evolutionary origin of this peculiar genomic architecture, we sequenced the MIC genomes of nine Paramecium species (from [~]100 Mb in P. aurelia species to > 1.5 Gb in P. caudatum). We detected several waves of IES gains, both in ancestral and in more recent lineages. While the vast majority of IESs are single-copy in present-day genomes, we identified several families of mobile IESs, including non-autonomous elements acquired via horizontal transfer, that generated tens to thousands of new copies. These observations provide the first direct evidence that transposable elements can account for the massive proliferation of IESs in Paramecium. The comparison of IESs of different evolutionary ages indicates that, over time, IESs shorten and diverge rapidly in sequence while they acquire features that allow them to be more efficiently excised. We nevertheless identified rare cases of IESs that are under strong purifying selection across the aurelia clade. The cases examined contain or overlap cellular genes that are inactivated by excision during development, suggesting conserved regulatory mechanisms. Similar to the evolution of introns in eukaryotes, the evolution of Paramecium IESs highlights the major role played by selfish genetic elements in shaping the complexity of genome architecture and gene expression.

category: genomics


title: Functional architecture of the pancreatic islets: First responder cells drive the first-phase  response

abstract: Insulin-secreting {beta}-cells are functionally heterogeneous. Whether there exist cells driving the first-phase calcium response in individual islets, has not been examined. We examine  first responder cells, defined by the earliest [Ca2+] response during first-phase [Ca2+] elevation, distinct from previously identified "hub" and "leader" cells. First responder cells showed characteristics of high membrane excitability and lower electrical coupling to their neighbors. The first-phase response time of {beta}-cells in the islet was spatially organized, dependent on the cells distance to the first responder cell, and consistent over time up to [~]24 h. When first responder cells were laser ablated, the first-phase [Ca2+] was slowed down, diminished, and discoordinated compared to random cell ablation. Cells that were next earliest to respond often took over the role of the first responder upon ablation. In summary, we discover and characterize a distinct first responder {beta}-cell state, critical for the islet first-phase response to glucose.


title: MaPPeRTrac: A Massively Parallel, Portable, and Reproducible Tractography Pipeline

abstract: Large-scale diffusion MRI tractography remains a significant challenge. Users must orchestrate a complex sequence of instructions that requires many software packages with complex dependencies and high computational cost. We developed MaPPeRTrac, a probabilistic tractography pipeline that simplifies and vastly accelerates this process on a wide range of high performance computing (HPC) environments. It fully automates the entire tractography pipeline, from management of raw MRI machine data to edge density imaging (EDI) of the structural connectome. Dependencies are containerized with Docker or Singularity and de-coupled from code to enable rapid proto-typing and modification. Data artifacts are strictly organized with the Brain Imaging Data Structure (BIDS) to ensure that they are findable, accessible, interoperable, and reusable following FAIR principles. The pipeline takes full advantage of HPC resources using the Parsl parallel programming frame-work, resulting in the creation of connectome datasets of unprecedented size. MaPPeRTrac is publicly available and tested on commercial and scientific hardware, so that it may accelerate brain connectome research for a broader user community.


title: 4sUDRB-sequencing for genome-wide transcription bursting quantification in breast cancer cells

abstract: Epigenetics maintains cell-identity specific gene-expression patterns. However, within a population of isogenic cells of the same identity, a substantial variability in gene expression and responsiveness is still observed. Transcription bursting is a substantial source of this gene-expression variability or  noise, contributing to phenotypic heterogeneity and potentially driving both physiological and pathological processes such as differentiation or tumorigenesis and drug resistance. Identification of transcription-bursting dynamics at a genome-wide scale has been restricted to inferring bursts in mRNA production computationally from the heterogeneity of mRNA levels in single cell transcriptomic data. Systematic characterisation of the genomic and epigenetic chromatin context of genes with defined transcription bursting behaviour has been incomplete. Here, we measured the bursting of transcription itself by genome-wide nascent RNA sequencing of breast cancer MCF-7 cells upon synchronisation of transcription with a transcription elongation inhibitor and by calibration using live cell imaging of nascent PP7-tagged GREB1 transcription. Comparing across the entire genome, we find transcription bursting to be ubiquitous, with burst sizes of up to 160 transcripts. Transcription bursting is strongly correlated with steady state gene expression between genes, whereas both burst frequency and nascent transcript degradation only correlate weakly. Individual genes deviate strongly from this trend and engage both in anomalous burst size and frequency. We find that the presence of the TATA box or Inr sequence within gene promoters are significantly associated with a larger burst size, as are promoter-associated YY1 and E2F1 transcription-factor binding motifs. Enrichment of the transcription start site with epigenetic marks such as H3K79me2 and H3K27ac is also strongly associated with the transcription burst size. Finally, we show that in these MCF-7 breast-cancer cells, genes with a larger transcription burst size exhibit a larger immediate transcriptional response following endocrine drug treatment. Our genome-wide transcription-bursting analysis method paves the way to elucidate the dynamic role of epigenetic regulation on dynamic transcription in pathophysiology.

category: molecular biology


title: Maize (Zea mays L.) nucleoskeletal proteins regulate nuclear envelope remodeling and function in stomatal complex development and pollen viability.

abstract: In eukaryotes, the nuclear envelope (NE) encloses chromatin and separates it from the rest of the cell. The Linker of Nucleoskeleton and Cytoskeleton (LINC) complex physically bridges across the NE, linking nuclear and cytoplasmic components. In plants, these LINC complexes are beginning to be ascribed roles in cellular and nuclear functions, including chromatin organization, regulation of nuclei shape and movement, and cell division. Homologs of core LINC components, KASH and SUN proteins, have previously been identified in maize. Here, we characterized the presumed LINC-associated maize nucleoskeletal proteins NCH1 and NCH2, homologs of members of the plant NMCP/CRWN family, and MKAKU41, homologous to AtKAKU4. All three proteins localized to the nuclear periphery when transiently and heterologously expressed as fluorescent protein fusions in Nicotiana benthamiana. Overexpression of MKAKU41 caused dramatic changes in the organization of the nuclear periphery, including nuclear invaginations that stained positive for non-nucleoplasmic markers of the inner and outer NE, and the ER. The severity of these invaginations was altered by changes in LINC connections and the actin cytoskeleton. In maize, MKAKU41 appeared to share genetic functions with other LINC components, including control of nuclei shape, stomatal complex development, and pollen viability. Overall, our data show that NCH1, NCH2, and MKAKU41 have characteristic properties of LINC-associated plant nucleoskeletal proteins, including interactions with NE components suggestive of functions at the nuclear periphery that impact the overall nuclear architecture.


title: Coalescent-based species delimitation meets deep learning: Insights from a highly fragmented cactus system

abstract: Delimiting species boundaries is a major goal in evolutionary biology. An increasing body of literature has focused on the challenges of investigating cryptic diversity within complex evolutionary scenarios of speciation, including gene flow and demographic fluctuations. New methods based on model selection, such as approximate Bayesian computation, approximate likelihoods, and machine learning are promising tools arising in this field. Here, we introduce a framework for species delimitation using the multispecies coalescent model coupled with a deep learning algorithm based on convolutional neural networks (CNNs). We compared this strategy with a similar ABC approach. We applied both methods to test species boundary hypotheses based on current and previous taxonomic delimitations as well as genetic data (sequences from 41 loci) in Pilosocereus aurisetus, a cactus species complex with a sky-island distribution and taxonomic uncertainty. To validate our method, we also applied the same strategy on data from widely accepted species from the genus Drosophila. The results show that our CNN approach has high capacity to distinguish among the simulated species delimitation scenarios, with higher accuracy than ABC. For the cactus dataset, a splitter hypothesis without gene flow showed the highest probability in both CNN and ABC approaches, a result agreeing with previous taxonomic classifications and in line with the sky-island distribution and low dispersal features of P. aurisetus. Our results highlight the cryptic diversity within the P. aurisetus complex and show that CNNs are a promising approach for distinguishing complex evolutionary histories, even outperforming the accuracy of other model-based approaches such as ABC.


title: RgCop-A regularized copula based method for gene selection in single cell rna-seq data

abstract:
Gene selection in unannotated large single cell RNA sequencing (scRNA-seq) data is important and crucial step in the preliminary step of downstream analysis. The existing approaches are primarily based on high variation (highly variable genes) or significant high expression (highly expressed genes) failed to provide stable and predictive feature set due to technical noise present in the data. Here, we propose RgCop, a novel regularized copula based method for gene selection from large single cell RNA-seq data. RgCop utilizes copula correlation (Ccor), a robust equitable dependence measure that captures multivariate dependency among a set of genes in single cell expression data. We raise an objective function by adding a l1 regularization term with Ccor to penalizes the redundant co-efficient of features/genes, resulting non-redundant effective features/genes set. Results show a significant improvement in the clustering/classification performance of real life scRNA-seq data over the other state-of-the-art. RgCop performs extremely well in capturing dependence among the features of noisy data due to the scale invariant property of copula, thereby improving the stability of the method. Moreover, the differentially expressed (DE) genes identified from the clusters of scRNA-seq data are found to provide an accurate annotation of cells. Finally, the features/genes obtained from RgCop can able to annotate the unknown cells with high accuracy.

AvailabilityCorresponding software is available in: https://github.com/Snehalikalall/RgCop

Contactsumanta.ray@cwi.nl

category: bioinformatics


title: Multi-class Cancer Classification and Biomarker Identification using Deep Learning

abstract:
Genetic data is important for analysing cellular functions whose disruption gives rise to various kinds of cancer. The intricacies of gene interaction are captured in various kinds of data for cancer detection through sequencing technology, but diagnosis, prognosis and treatment are still hard. Advent of machine learning helped researchers in supervised and unsupervised learning tasks along with gene identification but resourcefulness has not been overtly satisfactory. This research revolves around multi-class cancer classification, feature extraction and relevant gene identification through deep learning methods for 12 different types of cancers using RNA-SEQ from The Cancer Genome Atlas.

It has been constrained by hardware resource availability and within them the experiments that have been performed have shown promising results. Stacked De-noising Autoencoders were used for feature extraction and biomarker identification while 1D Convolutional Neural Networks for classification. Classification was performed with extracted features and relevant genes, which gave average performance of around 94% and 95% respectively. We were able to identify generic cancer-related pathways and their associated genes through Stacked De-noising Auto-encoders generated weight matrix and features. The common pathways include WNT Signalling Pathway, Angiogenesis. Moreover, across all pathways some recurrent genes were observed, namely: PIK3C2G, PCDHB8, WNT10A and these genes were found, in literature, to be involved in multiple types of cancer.

The proposed approach shows superior performance and promise against traditional techniques used by bioinformatics community, in terms of accuracy and relevant gene identification.


title: Upregulation of DNA repair genes and cell extrusion underpin the remarkable radiation resistance of Trichoplax adhaerens.

abstract: Trichoplax adhaerens is the simplest multicellular animal with tissue differentiation and somatic cell turnover. Like all other multicellular organisms, it should be vulnerable to cancer, yet there have been no reports of cancer in T. adhaerens, or any other placozoan. We investigated the cancer resistance of T. adhaerens, discovering that they are able to tolerate high levels of radiation damage (218.6 Gy). To investigate how T. adhaerens survive levels of radiation that are lethal to other animals, we examined gene expression after the X-ray exposure, finding overexpression of genes involved in DNA repair and apoptosis including the MDM2 gene. We also discovered that T. adhaerens extrudes clusters of inviable cells after X-ray exposure. T. adhaerens is a valuable model organism for studying the molecular, genetic and tissue-level mechanisms underlying cancer suppression.

category: cancer biology


title: Red-beet betalain pigment inhibits amyloid-β aggregation and toxicity in amyloid-β expressing Caenorhabditis elegans model

abstract:
BACKGROUNDBetalain pigments are mainly produced by plants in the order Caryophyllales. Recent interest in the biological functions of betalain pigments has increased with antioxidant, anti-inflammatory, and anticancer activities reported.

RESULTSWe investigated the effects of betalain pigments derived from red-beet on amyloid-{beta} (A{beta}) aggregation, a cause of Alzheimers disease. Inhibition of A{beta} aggregation against A{beta}40 and A{beta}42 by betalain pigments in vitro was demonstrated by the Thioflavin T fluorescence assay, circular dichroism spectroscopy analysis and transmission electron microscopic observations. Moreover, we examined the ability of betalain pigments to interfere with A{beta} toxicity by using the transgenic Caenorhabditis elegans strain CL2006, which expresses the human A{beta}42 protein intracellularly within the body wall muscle and responds to A{beta}-toxicity with paralysis. Treatment with 50 M betalain pigments significantly delayed the paralysis of Caenorhabditis elegans.

CONCLUSIONThese results suggest that betalain pigments reduce A{beta}-induced toxicity by inhibiting A{beta} aggregation and may lead to their use as inhibitors of A{beta} aggregation.


title: Effector-independent brain network for auditory-motor integration: fMRI evidence from singing and cello playing

abstract:
Many everyday tasks share high-level sensory goals but differ in the movements used to accomplish them. One example of this is musical pitch regulation, where the same notes can be produced using the vocal system or a musical instrument controlled by the hands. Cello playing has previously been shown to rely on brain structures within the singing network for performance of single notes, except in areas related to primary motor control, suggesting that the brain networks for auditory feedback processing and sensorimotor integration may be shared (Segado et al. 2018). However, research has shown that singers and cellists alike can continue singing/playing in tune even in the absence of auditory feedback (Chen et al. 2013, Kleber et al. 2013), so different paradigms are required to test feedback monitoring and control mechanisms. In singing, auditory pitch feedback perturbation paradigms have been used to show that singers engage a network of brain regions including anterior cingulate cortex (ACC), anterior insula (aINS), and intraparietal sulcus (IPS) when compensating for altered pitch feedback, and posterior superior temporal gyrus (pSTG) and supramarginal gyrus (SMG) when ignoring it (Zarate et al. 2005, 2008). To determine whether the brain networks for cello playing and singing directly overlap in these sensory-motor integration areas, in the present study expert cellists were asked to compensate for or ignore introduced pitch perturbations when singing/playing during fMRI scanning. We found that cellists were able to sing/play target tones, and compensate for and ignore introduced feedback perturbations equally well. Brain activity overlapped for singing and playing in IPS and SMG when compensating, and pSTG and dPMC when ignoring; differences between singing/playing across all three conditions were most prominent in M1, centered on the relevant motor effectors (hand, larynx). These findings support the hypothesis that pitch regulation during cello playing relies on structures within the singing network and suggests that differences arise primarily at the level of forward motor control.

HighlightsO_LIExpert cellists were asked to compensate for or ignore introduced pitch perturbations when singing/playing during fMRI scanning.
C_LIO_LICellists were able to sing/play target tones, and compensate for and ignore introduced feedback perturbations equally well.
C_LIO_LIBrain activity overlapped for singing and playing in IPS and SMG when compensating, and pSTG and dPMC when ignoring.
C_LIO_LIDifferences between singing/playing across were most prominent in M1, centered around the relevant motor effectors (hand, larynx)
C_LIO_LIFindings support the hypothesis that pitch regulation during cello playing relies on structures within the singing network with differences arising primarily at the level of forward motor control
C_LI


title: In vivo visualization of pig vagus nerve 'vagotopy' using ultrasound

abstract:
BackgroundPlacement of the clinical vagus nerve stimulating cuff is a standard surgical procedure based on anatomical landmarks, with limited patient specificity in terms of fascicular organization or vagal anatomy. As such, the therapeutic effects are generally limited by unwanted side effects of neck muscle contractions, demonstrated by previous studies to result from stimulation of 1) motor fibers near the cuff in the superior laryngeal and 2) motor fibers within the cuff projecting to the recurrent laryngeal.

ObjectiveThe use of patient-specific visualization of vagus nerve fascicular organization could better inform clinical cuff placement and improve clinical outcomes.

MethodsThe viability of ultrasound, with the transducer in the surgical pocket, to visualize vagus nerve fascicular organization (i.e. vagotopy) was characterized in a pig model. Ultrasound images were matched to post-mortem histology to confirm the utility of ultrasound in identifying fascicular organization.

ResultsHigh-resolution ultrasound accurately depicted the vagotopy of the pig vagus nerve intra-operatively, as confirmed via histology. The stereotypical pseudo-unipolar cell body aggregation at the nodose ganglion was identifiable, and these sensory afferent fascicular bundles were traced down the length of the vagus nerve. Additionally, the superior and recurrent laryngeal nerves were identified via ultrasound.

ConclusionsIntraoperative visualization of vagotopy and surrounding nerves using ultrasound is a novel approach to optimize stimulating cuff placement, avoid unwanted activation of motor nerve fibers implicated in off-target effects, and seed patient-specific models of vagal fiber activation to improve patient outcomes.


title: Multidimensional brain-age prediction reveals altered brain developmental trajectory in psychiatric disorders

abstract: Neuroimaging-based brain-age prediction has emerged as an important new approach for studying brain development. However, brain regions change in different ways and at different rates. Unitary brain-age indices used in previous studies represent developmental status averaged across the whole brain and therefore do not capture the divergent developmental trajectories of various brain structures. Importantly, this staggered developmental unfolding, determined by genetics and postnatal experience, is implicated in the progression of psychiatric and neurological disorders. Here we propose an analytic method for computing a multidimensional brain-age index (MBAI) that provides regional age predictions. Using a database of 556 subjects (ages 8-21) that includes psychiatric and neurological patients as well as healthy controls, we conducted robust regression and cluster analyses to identify clusters of imaging features with distinct developmental trajectories. We then built machine-learning models to obtain brain-age predictions from each of the identified clusters to form the MBAI. Our results show that the MBAI provides a flexible analysis of region-specific brain-age changes that are invisible to unidimensional brain-age prediction methods. Importantly, brain ages computed from region-specific feature clusters contain complementary information and demonstrate differential ability to classify disorder groups (e.g., specific phobia, depression, ADHD) from healthy controls. Compared to unidimensional brain-age indices, we show that the MBAI is sensitive to alterations in brain structures and captures distinct regional change patterns which may serve as biomarkers that may contribute to our understanding of healthy and pathological brain development and to the characterization, diagnosis, and, potentially, treatment of various disorders.


title: Mapping the probability of forest snowdisturbances in Finland

abstract: The changing forest disturbance regimes emphasize the need for improved damage risk information. Here, our aim was to (1) improve the current understanding of snow damage risks by assessing the importance of abiotic factors, particularly the modelled snow load on trees, versus forest properties in predicting the probability of snow damage, (2) produce a snow damage probability map for Finland. We also compared the results for winters with typical snow load conditions and a winter with exceptionally heavy snow loads. To do this, we used damage observations from the Finnish national forest inventory (NFI) to create a statistical snow damage occurrence model, spatial data layers from different sources to use the model to predict the damage probability for the whole country in 16 x 16 m resolution. Snow damage reports from forest owners were used for testing the final map. Our results showed that best results were obtained when both abiotic and forest variables were included in the model. However, in the case of the high snow load winter, the model with only abiotic predictors performed nearly as well as the full model and the ability of the models to identify the snow damaged stands was higher than in other years. The results showed patterns of forest adaptation to high snow loads, as spruce stands in the north were less susceptible to damage than in southern areas and long-term snow load reduced the damage probability. The model and the derived wall-to-wall map were able to discriminate damage from no-damage cases on a good level. The damage probability mapping approach identifies the drivers of snow disturbances across forest landscapes and can be used to spatially estimate the current and future disturbance risks in forests, informing practical forestry and decision-making and supporting the adaptation to the changing disturbance regimes.


title: Assembly and Validation of Two Gap-free Reference Genomes for Xian/indica Rice Reveals Insights into Plant Centromere Architecture

abstract: Rice (Oryza sativa), a major staple throughout the world and a model system for plant genomics and breeding, was the first crop genome completed almost two decades ago. However, all sequenced genomes to date contain gaps and missing sequences. Here, we report, for the first time, the assembly and analyses of two gap-free reference genome sequences of the elite O. sativa xian/indica rice varieties  Zhenshan 97 (ZS97) and  Minghui 63 (MH63) that are being used as a model system to study heterosis. Gap-free reference genomes also provide global insights into the structure and function of centromeres. All rice centromeric regions share conserved centromere-specific satellite motifs but with different copy numbers and structures. Importantly, we demonstrate that >1,500 genes are located in centromere regions, of which ~15.6% are actively transcribed. The generation and release of both the ZS97 and MH63 gap-free genomes lays a solid foundation for the comprehensive study of genome structure and function in plants and breed climate resilient varieties for the 21st century.


title: Preclinical drug response metric based on cellular response phenotype provides better pharmacogenomic variables with phenotype relevance

abstract:
Background and PurposeAssessment of drug response is typically performed by constructing a dose-response curve of viability and summarizing it to a representative value. However, this is limited by its dependency on the assay duration and lack of reflections regarding actual cellular response phenotypes. To resolve these limitations, we considered contribution of each response phenotype upon a drug treatment to the overall growth behavior.

Experimental ApproachThe differential equation of phenotype population dynamics was solved analytically without numerical computation. By using the properly figured population dynamics, we explored how the conventional assessment method itself affects the assessment result of drug response, in the context of drug screening. Alternative phenotype metric was compared with the conventional metrics through evaluation of the publicly available drug response data.

Key ResultsThe conventional assessment showed several limitations in the comparative analysis of drug response: a significant time-dependency, and ambiguities in assessment results based on a dose-response curve. Instead, the alternative phenotype metrics provide time-independent phenotype rates of change, that contain all the information of the drug response at a given dose, and better classification including the mechanism underlying growth inhibition.

Conclusion and ImplicationsThe conventional dose-response curve is useful for a visual presentation of overall drug responses upon a certain molecular feature qualitatively. In contrast, the phenotype metric is better for assessing therapeutic effectiveness, and would improve preclinical pharmacogenomic analysis through its relevance to a response phenotype.

Bullet point summaryO_ST_ABSWhat is already knownC_ST_ABSO_LIDrug response is investigated by constructing a dose-response curve in wide range.
C_LIO_LIConventional assessment metrics of drug response lack reflections regarding actual cellular response phenotypes.
C_LI

What this study addsO_LILimitations of conventional assessments are due to time-dependency of dose-response curve and customary summarization.
C_LIO_LIPhenotype metric evaluate a single dose-response that is time-independent and phenotype-relevant.
C_LI

Clinical significanceO_LIPhenotype metric would improve pharmacogenomic analysis with better classification and phenotype-relevance of drug response.
C_LIO_LIImprovement in preclinical pharmacology would bring better translation and useful information in clinical studies.
C_LI


title: Constructing neural network models from brain data reveals representational transformations underlying adaptive behavior

abstract: The human ability to adaptively implement a wide variety of tasks is thought to emerge from the dynamic transformation of cognitive information. We hypothesized that these transformations are implemented via conjunctive activations in conjunction hubs - brain regions that selectively integrate sensory, cognitive, and motor activations. We used recent advances in using functional connectivity to map the flow of activity between brain regions to construct a task-performing neural network model from fMRI data during a cognitive control task. We verified the importance of conjunction hubs in cognitive computations by simulating neural activity flow over this empirically-estimated functional connectivity model. These empirically-specified simulations produced above-chance task performance (motor responses) by integrating sensory and task rule activations in conjunction hubs. These findings reveal the role of conjunction hubs in supporting flexible cognitive computations, while demonstrating the feasibility of using empirically-estimated neural network models to gain insight into cognitive computations in the human brain.


title: CLN5 and CLN3 function as a complex to regulate endolysosome function

abstract:
CLN5 is a soluble endolysosomal protein whose function is poorly understood. Mutations in this protein cause a rare neurodegenerative disease, Neuronal Ceroid Lipofuscinosis. We previously found that depletion of CLN5 leads to dysfunctional retromer, resulting in the degradation of the lysosomal sorting receptor, sortilin. However, how a soluble lysosomal protein can modulate the function of a cytosolic protein, retromer, is not known. In this work, we show that deletion of CLN5 not only results in retromer dysfunction, but also in impaired endolysosome fusion events. This results in delayed degradation of endocytic proteins and in defective autophagy. CLN5 modulates these various pathways by regulating downstream interactions between CLN3, an endolysosomal integral membrane protein whose mutations also result in Neuronal Ceroid Lipofuscinosis, Rab7A, and a subset of Rab7A effectors. Our data supports a model where CLN3 and CLN5 function as an endolysosome complex regulating various functions.

Summary StatementWe have previously demonstrated that CLN3 is required for efficient endosome-to-trans Golgi Network (TGN) trafficking of sortilin by regulating retromer function. In this work, we show that CLN5, which interacts with CLN3, regulates retromer function by modulating key interactions between CLN3, Rab7A, retromer, and sortilin. Therefore, CLN3 and CLN5 serve as endosomal switch regulating the itinerary of the lysosomal sorting receptors.


title: Genomic signature of shifts in selection and alkaline adaptation in highland fish

abstract:
Understanding how organisms adapt to aquatic life at high altitude is fundamental in evolutionary biology. This objective has been addressed primarily related to hypoxia adaptation by recent comparative studies, whereas highland fish has also long suffered extreme alkaline environment, insight into the genomic basis of alkaline adaptation has rarely been provided. Here, we compared the genomes or transcriptomes of 15 fish species, including two alkaline tolerant highland fish species and their six alkaline intolerant relatives, three alkaline tolerant lowland fish species and four alkaline intolerant species. We found putatively consistent patterns of molecular evolution in alkaline tolerant species in a large number of shared orthologs within highland and lowland fish taxa. Remarkably, we identified consistent signatures of accelerated evolution and positive selection in a set of shared genes associated with ion transport, apoptosis, immune response and energy metabolisms in alkaline tolerant species within both highland and lowland fish taxa. This is one of the first comparative studies that began to elucidate the consistent genomic signature of alkaline adaptation shared by highland and lowland fish. This finding also highlights the adaptive molecular evolution changes that support fish adapting to extreme environments at high altitude.

Significance StatementLittle is known about how wild fish responds to extreme alkaline stress besides hypoxia at high altitude. Comparative genomics has begun to elucidate the genomic basis of alkaline adaptation in lowland fish, such as killifish, but insight from highland fish has lagged behind. The common role of adaptive molecular evolution during alkaline adaptation in highland and lowland fish has rarely been discussed. We address this question by comparing 15 fish omics data. We find numbers of shared orthologs exhibited consistent patterns of molecular evolution in alkaline tolerant species relative to intolerant species. We further identify remarkably consistent signatures of rapidly evolving and positive selection in a substantial shared core of genes in both highland and lowland alkaline tolerant species.


title: Cytoplasmic and nuclear Sw-5b NLR act both independently and synergistically to dictate full host defense against tospovirus infection

abstract:
O_LIPlant intracellular nucleotide binding-leucine-rich repeat (NLR) receptors play critical roles in mediating host immunity to pathogen attack. We use tomato Sw-5b::tospovirus as a model system to study the specific role of the compartmentalized plant NLR in dictating host defense against virus at different infection steps.
C_LIO_LIWe demonstrated here that tomato NLR Sw-5b translocates to cytoplasm and nucleus, respectively, to play different roles in inducing host resistances against Tomato spotted wilt tospovirus (TSWV) infection. The cytoplasmic Sw-5b functions to induce a strong cell death response to inhibit TSWV replication. This host response is, however, insufficient to block viral intercellular and long-distance movement. The nucleus-localized Sw-5b triggers a host defense that weakly inhibits viral replication but strongly impedes virus intercellular and systemic movement. Furthermore, the cytoplasmic and nuclear Sw-5b act synergistically to dictate full host defense to TSWV infection.
C_LIO_LIWe further demonstrated that the extended N-terminal Solanaceae domain (SD) of Sw-5b plays critical roles in cytoplasm/nucleus partitioning. Sw-5b nucleotide-binding leucine-rich repeat (NB-LRR) controls its cytoplasm localization. Strikingly, the SD but not coil-coil (CC) domain is crucial for Sw-5b receptor to translocate from cytoplasm to nucleus to trigger the immunity. The SD was found to interact with importins. Silencing both importin  and {beta} expression disrupted Sw-5b nucleus translocation and host immunity against TSWV systemic infection.
C_LIO_LICollectively, our findings suggest that Sw-5b bifurcates disease resistances by cytoplasm/nucleus partitioning to block different infection steps of TSWV. The findings also identified a new regulatory role of extra domain of a plant NLR in mediating host innate immunity.
C_LI

category: plant biology


title: Ultrasensitivity and bistability in covalent modification cycles with positive autoregulation

abstract: Switch-like behaviours in biochemical networks are of fundamental significance in biological signal processing, and exist as two distinct types: ultra-sensitivity and bistability. Here we propose two new models of a reversible covalent-modification cycle with positive autoregulation (PAR) - a motif structure that is thought to be capable of both ultrasensitivity and bistability in different parameter regimes. These new models appeal to a modelling framework that we call complex complete, which accounts fully for the molecular complexities of the underlying signalling mechanisms. Each of the two new models encodes a specific molecular mechanism for PAR. We demonstrate that the modelling simplifications for PAR models that have been used in previous work, which rely on a Michaelian approximation for the enzyme-mediated reactions, are unable to accurately recapitulate the qualitative signalling responses supported by our  full complex-complete models. Strikingly, we show that the parameter regimes in which ultrasensitivity and bistability obtain in the complex-complete framework contradict the predictions made by the Michaelian simplification. Our results highlight the critical importance of accurately representing the molecular details of biochemical signalling mechanisms, and strongly suggest that the Michaelian approximation may be inadequate for predictive models of enzyme-mediated chemical reactions with added regulations.

category: systems biology


title: An open source platform for presenting dynamic visual stimuli

abstract:
Operant behavior procedures often rely on visual stimuli to cue the initiation or secession of a response, and to provide a means for discriminating between two or more simultaneously available responses. While primate and human studies typically use LCD or OLED monitors and touch screens, rodent studies use a variety of methods to present visual cues ranging from traditional incandescent light bulbs, single LEDs, and, more recently, touch screen monitors. Commercially available systems for visual stimulus presentation are costly, challenging to customize, and are typically closed source. We developed an open-source, highly-modifiable visual stimulus presentation platform that can be combined with a 3D-printed operant response device. The device uses an eight by eight matrix of LEDs, and can be expanded to control much larger LED matrices. Implementing the platform is low-cost (<$70 USD per device in the year 2020). Using the platform, we trained rats to make nosepoke responses and discriminate between two distinct visual cues in a location-independent manner. This visual stimulus presentation platform is a cost-effective way to implement complex visually-guided operant behavior, including the use of moving or dynamically changing visual stimuli.

Significance StatementThe design of an open source and low cost device for presenting visual stimuli is described. It is capable of presenting complex visual patterns and dynamically changing stimuli. A practical demonstration of the device is also reported, from an experiment in which rats performed a luminance based visual discrimination. The device has utility for studying visual processing, psychophysics, and decision making in a variety of species.


title: Remdesivir-Ivermectin combination displays synergistic interaction with improved in vitro antiviral activity against SARS-CoV-2

abstract: A key element for the prevention and management of COVID-19 is the development of effective therapeutics. Drug combination strategies of repurposed drugs offer several advantages over monotherapies, including the potential to achieve greater efficacy, the potential to increase the therapeutic index of drugs and the potential to reduce the emergence of drug resistance. Here, we report on the in vitro synergistic interaction between two FDA approved drugs, remdesivir and ivermectin resulting in enhanced antiviral activity against SARS-CoV-2. These findings warrant further investigations into the clinical potential of this combination, together with studies to define the underlying mechanism.


title: Modelling of SHMT1 riboregulation predicts dynamic changes of serine and glycine levels across cellular compartments

abstract: Human serine hydroxymethyltransferase (SHMT) regulates the serine-glycine one carbon metabolism and plays a role in cancer metabolic reprogramming. Two SHMT isozymes are acting in the cell: SHMT1 encoding the cytoplasmic isozyme, and SHMT2 encoding the mitochondrial one. Here we present a molecular model built on experimental data reporting the interaction between SHMT1 protein and SHMT2 mRNA, recently discovered in lung cancer cells. Using a stochastic dynamic model, we show that RNA moieties dynamically regulate serine and glycine concentration, shaping the system behaviour. For the first time we observe an active functional role of the RNA in the regulation of the serine-glycine metabolism and availability, which unravels a complex layer of regulation that cancer cells exploit to fine tune amino acids availability according to their metabolic needs. The quantitative model, complemented by an experimental validation in the lung adeno-carcinoma cell line H1299, exploits RNA molecules as metabolic switches of the SHMT1 activity. Our results pave the way for the development of RNA-based molecules able to unbalance serine metabolism in cancer cells.


title: Authentication of In Situ Measurements for Thoracic Aortic Aneurysms in Mice

abstract: Aortic diameter is a standard parameter for defining disease severity of thoracic aortic aneurysms. In mouse studies, aortic diameters can be measured in situ directly, but this approach has a potential confounder of underestimation due to the absence of physiological arterial blood pressure. In the present study, we developed an in situ approach for authentic aortic measurements. Thoracic aortic aneurysms were induced by beta-aminopropionitrile (BAPN, 0.5% wt/vol) administration in 4-week-old male C57BL/6J mice. Ultrasonography was performed to examine aortic dimensions, and mice with thoracic aortic dilatations were terminated subsequently. After saline perfusion through the left ventricle, periaortic tissues were removed to expose thoracic aortas. Optimal cutting temperature (OCT) compound was injected via the left ventricle to maintain aortic patency. In situ aortic images were captured pre- and post-OCT injection. In mice with severe thoracic aortic aneurysms, smaller aortic diameters were observed prior to OCT injection compared to ultrasound measurements, while aortic diameters in situ after OCT were comparable to diameters measured using ultrasound. A telemetry system demonstrated that maximal luminal pressures during 150 ul of OCT injection were 90 mmHg. Immunostaining for CD31 revealed that endothelial cells were preserved in the intima after OCT injection. These results indicate that OCT injection does not cause aortic damages due to excess pressures. In conclusion, in situ imaging with OCT injection provides authentic aortic measurements without overt aortic damage in mice with thoracic aortic aneurysms.

category: pathology


title: Sustained antibody response to ZIKV infection induced by NS1 protein is accompanied by the progressive appearance of autoreactive antibodies and cross-reactive B cell clones.

abstract: Besides antigen-specific responses to viral antigens, humoral immune response in virus infection can generate polyreactive and autoreactive antibodies. Dengue and Zika virus infections have been linked to antibody-mediated autoimmune disorders including Guillain-Barre syndrome. A unique feature of flaviviruses is the secretion of non-structural protein 1 (NS1) by infected cells. NS1 is highly immunogenic and antibodies targeting NS1 can have both protective and pathogenic roles. In the present study, we investigated the humoral immune response to Zika virus NS1 and found NS1 to be an immunodominant viral antigen associated with the presence of autoreactive antibodies. Through single B cell cultures, we coupled binding assays and BCR sequencing, confirming the immunodominance of NS1. Of note, we demonstrate the presence of self-reactive clones in germinal centers after both infection and immunization, some of which clones presenting cross-reactivity with NS1. Sequence analysis of anti-NS1 B cell clones showed sequence features associated with pathogenic autoreactive antibodies. Our findings demonstrate NS1 immunodominance at the cellular level as well as a potential role for NS1 in ZIKV associated autoimmune manifestations.


title: SARS-CoV-2 infecting the inner ear results in potential hearing damage at the early stage or prognosis of COVID-19 in rodents

abstract:
ObjectivesIn order to find out the association between the sensorineural hearing loss and COVID-19, we detected the expression ACE2 and TMPRSS2 in the mouse the hamster.

DesignUsing the public data from NCBI and GISAID, we assessed the expression of ACE2 and TMPRSS2 at the transcriptomic, DNA, and protein levels of ACE2 in the brain, inner ear, and muscle from the golden Syrian hamster (Mesocricetus auratus) and mouse (Mus musculus).

ResultsWe identified ACE2 and TMPRSS2 expressed at different level in the inner ear and brain at DNA and transcriptomic levels of both mouse and the hamster. The protein expression shows a similar pattern of the brain and inner ear, while the expression of ACE2 from the inner ear was relatively higher than it from the muscle.

ConclusionSARS-CoV-2 could infect the hearing system potentially and SSNHL could be a characteristic to detect asymptomatic patients of COVID-19.


title: Role of hypothalamic MAPK/ERK signaling in diabetes remission induced by the central action of fibroblast growth factor 1

abstract: The capacity of the brain to elicit sustained remission of hyperglycemia in rodent models of type 2 diabetes following intracerebroventricular (icv) injection of fibroblast growth factor 1 (FGF1) is well established. Here, we show that following icv FGF1 injection, hypothalamic signaling by extracellular signal-regulated kinases 1 and 2 (ERK1/2), members of the mitogen-activated protein kinase (MAPK) family is induced for at least 24h. Further, we show that in diabetic Lepob/ob mice, this prolonged response is required for the sustained antidiabetic action of FGF1, since it is abolished by sustained (but not acute) pharmacologic blockade of hypothalamic MAPK/ERK signaling. We also demonstrate that FGF1 R50E, a FGF1 mutant that activates FGF receptors but induces only transient hypothalamic MAPK/ERK signaling, fails to mimic the sustained glucose lowering induced by FGF1. These data identify sustained activation of hypothalamic MAPK/ERK signaling as playing an essential role in the mechanism underlying diabetes remission induced by icv FGF1 administration.


title: Evaluating performance of existing computational models in predicting CD8+ T cell pathogenic epitopes and cancer neoantigens

abstract: T cell recognition of a cognate peptide-MHC complex (pMHC) presented on the surface of infected or malignant cells, is of utmost importance for mediating robust and long-term immune responses. Accurate predictions of cognate pMHC targets for T Cell Receptors (TCR) would greatly facilitate identification of vaccine targets for both pathogenic diseases as well as personalized cancer immunotherapies. Predicting immunogenic peptides therefore has been at the centre of intensive research for the past decades but has proven challenging. Although numerous models have been proposed, performance of these models has not been systematically evaluated and their success rate in predicting epitopes in the context of human pathology, has not been measured and compared. In this study, we evaluated the performance of several publicly available models, in identifying immunogenic CD8+ T cell targets in the context of pathogens and cancers. We found that for predicting immunogenic peptides from an emerging virus such as SARS-CoV-2, none of the models perform substantially better than random or offer considerable improvement beyond HLA ligand prediction. We also observed suboptimal performance for predicting cancer neoantigens. Through investigation of potential factors associated with ill performance of models, we highlight several data- and model-associated issues. In particular, we observed that cross-HLA variation in the distribution of immunogenic and non-immunogenic peptides in training data of the models seem to substantially confound the predictions. We additionally compared key parameters associated with immunogenicity between pathogenic peptides and cancer neoantigens and observed evidence for differences in the thresholds of binding affinity and stability, which suggested the need to modulate different features in identifying immunogenic pathogen vs. cancer peptides. Overall, we demonstrate that accurate and reliable prediction of immunogenic CD8+ T cell targets remains unsolved, thus we hope our work will guide users and model developers regarding potential pitfalls and unsettled questions in existing immunogenicity predictors.


title: Host-generalist fungal pathogens of seedlings may maintain forest diversity via host-specific impacts and differential susceptibility among tree species

abstract:
O_LIHost-specialized pathogens are credited with the maintenance of tropical forest diversity under the Janzen-Connell hypothesis. Yet, in diverse forests, selection may favor pathogens with broad host ranges given their passive dispersal and the relative rarity of tree species.
C_LIO_LIWe surveyed the host associations of potential pathogens isolated from symptomatic seedlings in the forests in Panama and used inoculations to assess: (i) the pathogenicity and host ranges of 27 fungal isolates, and (ii) differences among tree species in susceptibility.
C_LIO_LIThirty-one of the 33 non-singleton OTUs isolated from seedlings are multi-host. All 31 multi-host OTUs exhibit low to moderate specialization, and we observed phylogenetically overdispersed host use for 19 OTUs. The pathogenicity of 10 isolates was experimentally confirmed; nine caused disease in seedlings in multiple families. However, the outcome of infection differs among tree species susceptible to a given multi-host pathogen. Furthermore, some tree species were seemingly resistant to all fungi tested, while others were susceptible to multiple fungi. Tree species adapted to environments with lower disease pressure were most likely to exhibit disease.
C_LIO_LIOur results suggest that generalist pathogens contribute to the maintenance of local and regional forest diversity via host-specific impacts and the exclusion of disease-sensitive trees from disease-prone habitats.
C_LI


title: Automated Analysis of Low-Field Brain MRI in Cerebral Malaria

abstract: A central challenge of medical imaging studies is to extract biomarkers that characterize disease pathology or outcomes. Modern automated approaches have found tremendous success in high-resolution, high-quality magnetic resonance images (MRI). These methods, however, may not translate to low resolution images acquired on MRI scanners with lower magnetic field strength. In low-resource settings where low-field scanners are more common and there is a shortage of radiologists to manually interpret MRI scans, it is critical to develop automated methods that can augment or replace manual interpretation, while accommodating reduced image quality. We present a fully automated framework for translating radiological diagnostic criteria into image-based biomarkers, inspired by a project in which children with cerebral malaria were imaged using low-field 0.35 Tesla MRI. We integrate multi-atlas label fusion, which leverages high-resolution images from another sample as prior spatial information, with parametric Gaussian hidden Markov models based on image intensities, to create a robust method for determining ventricular cerebrospinal fluid volume. We also propose normalized image intensity and texture measurements to determine the loss of gray-to-white matter tissue differentiation and sulcal effacement. These integrated biomarkers have excellent classification performance for determining severe brain swelling due to cerebral malaria.


title: Genetic epidemiology of variants associated with immune escape from global SARS-CoV-2 genomes

abstract: Many antibody and immune escape variants in SARS-CoV-2 are now documented in literature. The availability of SARS-CoV-2 genome sequences enabled us to investigate the occurrence and genetic epidemiology of the variants globally. Our analysis suggests that a number of genetic variants associated with immune escape have emerged in global populations.


title: Differential Dynamic Behavior of Prefusion Spike Proteins of SARS Coronaviruses 1 and 2

abstract: The coronavirus spike protein, which binds to the same human receptor in both SARS-CoV-1 and 2, has been implied to be a potential source of their differential transmissibility. However, the mechanistic details of spike protein binding to its human receptor remain elusive at the molecular level. Here, we have used an extensive set of unbiased and biased microsecond-level all-atom molecular dynamics (MD) simulations of SARS-CoV-1 and 2 spike proteins to determine the differential dynamic behavior of prefusion spike protein structure in the two viruses. Our results indicate that the active form of the SARS-CoV-2 spike protein is more stable than that of SARS-CoV-1 and the energy barrier associated with the activation is higher in SARS-CoV-2. Our results also suggest that not only the receptor binding domain (RBD) but also other domains such as the N-terminal domain (NTD) could play a role in the differential binding behavior of SARS-CoV-1 and 2 spike proteins.


title: TCR meta-clonotypes for biomarker discovery with tcrdist3: identification of public, HLA-restricted SARS-CoV-2 associated TCR features

abstract: As the mechanistic basis of adaptive cellular antigen recognition, T cell receptors (TCRs) encode clinically valuable information that reflects prior antigen exposure and potential future response. However, despite advances in deep repertoire sequencing, enormous TCR diversity complicates the use of TCR clonotypes as clinical biomarkers. We propose a new framework that leverages antigen-enriched repertoires to form meta-clonotypes - groups of biochemically similar TCRs - that can be used to robustly identify and quantify functionally similar TCRs in bulk repertoires. We apply the framework to TCR data from COVID-19 patients, generating 1831 public TCR meta-clonotypes from the 17 SARS-CoV-2 antigen-enriched repertoires with the strongest evidence of HLA-restriction. Applied to independent cohorts, meta-clonotypes targeting these specific epitopes were more frequently detected in bulk repertoires compared to exact amino acid matches, and 59.7% (1093/1831) were more abundant among COVID-19 patients that expressed the putative restricting HLA allele (FDR < 0.01), demonstrating the potential utility of meta-clonotypes as antigen-specific features for biomarker development. To enable further applications, we developed an open-source software package, tcrdist3, that implements this framework and facilitates flexible workflows for distance-based TCR repertoire analysis.


title: Drs2 regulates TRAPPIII in Atg9 transport: exposing the interplay of P4-ATPases and Multisubunit Tethering Complexes

abstract: Multisubunit Tethering Complexes (MTCs) are a set of conserved protein complexes that tether transported vesicles at the acceptor membrane. Interactions with other components of the trafficking machinery regulate MTCs through mechanisms that are just partially understood. Here we systematically investigate the interactome that regulates the function of MTCs. We found that P4-ATPases, a family of lipid transporters involved in the biogenesis of vesicles, interact with MTCs that participate in the anterograde and retrograde transport at the Golgi, such as TRAPPIII. We used the lipid flippase Drs2 as a model to investigate the mechanism and biological relevance of such interplay during the transport of Atg9 vesicles. Binding to the N-terminal tail of Drs2 stabilizes TRAPPIII on membrane compartments loaded with Atg9 and it is required for the delivery of Atg9 during selective autophagy, a role that is independent of previously reported functions of the P4-ATPase. This mechanism relies on the I(S/R)TTK motif nested in the N-terminal tail cavity of Drs2, a motif that is required for the interaction with MTCs.


title: Neuronal cascades shape whole-brain functional dynamics at rest

abstract:
At rest, mammalian brains display remarkable spatiotemporal complexity, evolving through recurrent brain states on a slow timescale of the order of tens of seconds. While the phenomenology of the resting state dynamics is valuable in distinguishing healthy and pathological brains, little is known about its underlying mechanisms. Here, we identify neuronal cascades as a potential mechanism. Using full-brain network modeling, we show that neuronal populations, coupled via a detailed structural connectome, give rise to large-scale cascades of firing rate fluctuations evolving at the same time scale of resting-state networks. The ignition and subsequent propagation of cascades depend upon the brain state and connectivity of each region. The largest cascades produce bursts of Blood-Oxygen-Level-Dependent (BOLD) co-fluctuations at pairs of regions across the brain, which shape the simulated resting-state network dynamics.We experimentally confirm these theoretical predictions. We demonstrate the existence and stability of intermittent epochs of functional connectivity comprising BOLD co-activation bursts in mice and human fMRI. We then provide evidence for the existence and leading role of the neuronal cascades in humans with simultaneous EEG/fMRI recordings. These results show that neuronal cascades are a major determinant of spontaneous fluctuations in brain dynamics at rest.

1 Significance StatementFunctional connectivity and its dynamics are widely used as a proxy of brain function and dysfunction. Their neuronal underpinnings remain unclear. Using connectome-based modeling, we link the fast microscopic neuronal scale to the slow emergent whole-brain dynamics. We show that cascades of neuronal activations spontaneously propagate in resting state-like conditions. The largest neuronal cascades result in the co-fluctuation of Blood-Oxygen-Level-Dependent signals at pairs of brain regions, which in turn translate to stable brain states. Thus, we provide a theoretical framework for the emergence and the dynamics of resting-state networks. We verify these predictions in empirical mouse fMRI and human EEG/fMRI datasets measured in resting states conditions. Our work sheds light on the multiscale mechanisms of brain function.


title: A small increase in CHEK1 activity leads to the arrest of the first zygotic division in human

abstract: The first mitotic division in mammalian zygotes is unique. The fertilized egg reactivates its cell cycle, and the maternal and paternal genomes start to reprogram to become totipotent. The first division is very sensitive to a range of perturbations, particularly the DNA damage, leading to the embryo's failure to enter the first mitosis. We discovered that a point mutation in the human CHEK1 gene resulted in an Arginine 442 to Glutamine change at the C-terminus of the CHEK1 protein. CHEK1 R442Q mutation caused the zygote to arrest just before the first division. Heterozygote individuals appeared to be healthy except that the female carriers are infertile. Expressing the corresponding mouse mutant Chk1 protein in zygotes also caused arrest before the first mitosis. Treating Chk1 R442Q mouse zygotes with low concentrations of CHEK1 inhibitor enabled the embryos to overcome the cell cycle arrest and resume normal development. Our results revealed an unexpected zygote mitotic checkpoint, which is extremely sensitive to the CHEK1 kinase activity. The fine-tuning of the DNA damage checkpoint permits the arrested one-cell embryos to overcome the first mitotic block and develop into healthy animals. These findings have important implications in assisted human reproduction.

category: developmental biology


title: X-MOL: large-scale pre-training for molecular understanding and diverse molecular analysis

abstract: In silico modelling and analysis of small molecules substantially accelerates the process of drug development. Representing and understanding molecules is the fundamental step for various in silico molecular analysis tasks. Traditionally, these molecular analysis tasks have been investigated individually and separately. In this study, we presented X-MOL, which applies large-scale pre-training technology on 1.1 billion molecules for molecular understanding and representation, and then, carefully designed fine-tuning was performed to accommodate diverse downstream molecular analysis tasks, including molecular property prediction, chemical reaction analysis, drug-drug interaction prediction, de novo generation of molecules and molecule optimization. As a result, X-MOL was proven to achieve state-of-the-art results on all these molecular analysis tasks with good model interpretation ability. Collectively, taking advantage of super large-scale pre-training data and super-computing power, our study practically demonstrated the utility of the idea of "mass makes miracles" in molecular representation learning and downstream in silico molecular analysis, indicating the great potential of using large-scale unlabelled data with carefully designed pre-training and fine-tuning strategies to unify existing molecular analysis tasks and substantially enhance the performance of each task.


title: Pairs of compensatory frameshifting mutations contribute to evolution of protein-coding sequences in vertebrates and insects

abstract: Insertions and deletions of lengths not divisible by 3 in protein-coding sequences cause frameshifts that usually induce premature stop codons and may carry a high fitness cost. However, this cost can be partially offset by a second compensatory indel restoring the reading frame. The role of such pairs of compensatory frameshifting mutations (pCFMs) in evolution has not been studied systematically. Here, we use whole-genome alignments of protein coding genes of 100 vertebrate species, and of 122 insect species, studying the prevalence of pCFMs in their divergence. We detect a total of 619 candidate pCFM-genes; 11 of them pass stringent quality filtering, including three human genes: RAB36, ARHGAP6 and NCR3LG1. In some instances, amino acid substitutions closely predating or following pCFMs restored the biochemical similarity of the frameshifted segment to the ancestral amino acid sequence, possibly reducing or negating the fitness cost of the pCFM. Typically, however, the resulting sequence bore no biochemical similarity to the ancestral one, indicating that pCFMs can uncover radically novel regions of protein space. In total, pCFMs represent an appreciable and previously overlooked source of novel variation in amino acid sequences.


title: SARS-CoV-2 mutations among minks show reduced lethality and infectivity to humans

abstract: SARS-CoV-2 infection in minks has become a serious problem, as the virus may mutate and reinfect humans; some countries have decided to cull minks. Here, the virus sequencing data in minks were analysed and compared to those of human-virus. Although the mink-virus maintained the characteristics of human-virus, some variants rapidly mutated, adapting to minks. Some mink-derived variants infected humans, which accounted for 40% of the total SARS-CoV-2 cases in the Netherlands. These variants appear to be less lethal and infective compared to those in humans. Variants that have mutated further among minks were not found in humans. Such mink-viruses might be suitable for vaccination for humans, such as in the case of the smallpox virus, which is less infective and toxic to humans.


title: The chirality of the mitotic spindle provides a passive mechanical response to forces and depends on microtubule motors and crosslinkers

abstract: Forces produced by motor proteins and microtubule dynamics within the mitotic spindle are crucial for proper chromosome segregation. In addition to linear forces, rotational forces or torques are present in the spindle, reflected in the left-handed twisted shapes of microtubule bundles that make the spindle chiral. However, the biological role and molecular origins of spindle chirality are unknown. By developing methods for measuring spindle twist, we show that spindles are most chiral near the metaphase-to-anaphase transition. To assess the role of chirality in maintaining spindle robustness under force, we compressed the spindles along their axis. This resulted in stronger left-handed twist, suggesting that the twisted shape allows for a mechanical response to forces. Inhibition or depletion of motor proteins that perform chiral stepping, Eg5/kinesin-5, Kif18A/kinesin-8, MKLP1/kinesin-6, and dynein, decreased the left-handed twist or led to right-handed twist, implying that these motors regulate the twist by rotating microtubules within their antiparallel overlaps or at the spindle pole. Right-handed twist was also observed after the depletion of the microtubule nucleator augmin, indicating its contribution to the twist through the nucleation of antiparallel bridging microtubules. The uncovered switch from left-handed to right-handed twist reveals the existence of competing mechanisms that promote twisting in opposite directions. As round spindles were more twisted than elongated ones, we infer that bending and twisting moments are generated by similar molecular mechanisms and propose a physiological role for spindle chirality in allowing the spindle to absorb mechanical load.


title: The chirality of the mitotic spindle provides a mechanical response to forces and depends on microtubule motors and augmin


title: The mechanism of SARS-CoV-2 nucleocapsid protein recognition by the human 14-3-3 proteins

abstract:
The coronavirus nucleocapsid protein (N) controls viral genome packaging and contains numerous phosphorylation sites located within unstructured regions. Binding of phosphorylated SARS-CoV N to the host 14-3-3 protein in the cytoplasm was reported to regulate nucleocytoplasmic N shuttling. All seven isoforms of the human 14-3-3 are abundantly present in tissues vulnerable to SARS-CoV-2, where N can constitute up to ~1% of expressed proteins during infection. Although the association between 14-3-3 and SARS-CoV-2 N proteins can represent one of the key host-pathogen interactions, its molecular mechanism and the specific critical phosphosites are unknown. Here, we show that phosphorylated SARS-CoV-2 N protein (pN) dimers, reconstituted via bacterial co-expression with protein kinase A, directly associate, in a phosphorylation-dependent manner, with the dimeric 14-3-3 protein, but not with its monomeric mutant. We demonstrate that pN is recognized by all seven human 14-3-3 isoforms with various efficiencies and deduce the apparent KD to selected isoforms, showing that these are in a low micromolar range. Serial truncations pinpointed a critical phosphorylation site to Ser197, which is conserved among related zoonotic coronaviruses and located within the functionally important, SR-rich region of N. The relatively tight 14-3-3/pN association can regulate nucleocytoplasmic shuttling and other functions of N via occlusion of the SR-rich region, while hijacking cellular pathways by 14-3-3 sequestration. As such, the assembly may represent a valuable target for therapeutic intervention.

HighlightsSARS-CoV-2 nucleocapsid protein (N) binds to all seven human 14-3-3 isoforms. This association with 14-3-3 strictly depends on phosphorylation of N. The two proteins interact in 2:2 stoichiometry and with the Kd in a M range. Affinity of interaction depends on the specific 14-3-3 isoform. Conserved Ser197-phosphopeptide of N is critical for the interaction.


title: IWS1 phosphorylation by AKT3 controls nuclear export of type I IFN mRNAs and sensitivity to oncolytic viral infection, by regulating the alternative RNA splicing of U2AF2.

abstract: AKT-phosphorylated IWS1 promotes Histone H3K36 trimethylation and alternative RNA splicing of target genes, including the U2AF65 splicing factor-encoding U2AF2. The predominant U2AF2 transcript, upon IWS1 phosphorylation block, lacks the RS-domain-encoding exon 2, and encodes a protein which fails to bind Prp19. Here we show that although both U2AF65 isoforms bind intronless mRNAs containing cytoplasmic accumulation region elements (CAR-E), only the RS domain-containing U2AF65 recruits Prp19 and promotes their nuclear export. The loading of U2AF65 to CAR-Elements was RS domain-independent, but RNA PolII-dependent. Virus- or poly(I:C)-induced type I IFNs are encoded by genes targeted by the pathway. IWS1 phosphorylation-deficient cells therefore, express reduced levels of IFN1/IFN{beta}1 proteins, and exhibit enhanced sensitivity to infection by multiple cytolytic viruses. Enhanced sensitivity of IWS1-deficient cells to Vesicular Stomatitis Virus and Reovirus resulted in enhanced apoptotic cell death via caspase activation. Inhibition of this pathway may therefore sensitize cancer cells to oncolytic viruses.


title: Enhancing bioreactor arrays for automated measurements and reactive control with ReacSight

abstract: New small-scale, low-cost bioreactors provide researchers with exquisite control of environmental parameters of microbial cultures over long durations, allowing them to perform sophisticated, high-quality quantitative experiments that are particularly useful in systems biology, synthetic biology and bioengineering. However, existing setups are limited in their automated measurement capabilities, primarily because sensitive and specific measurements require bulky, expensive, stand-alone instruments. Here, we present ReacSight, a generic and flexible strategy to enhance bioreactor arrays for automated measurements and reactive experiment control. On the hardware side, ReacSight leverages a pipetting robot for sample collection, handling and loading. On the software side, ReacSight provides a versatile instrument control architecture and a generic event system for reactive experiment control. ReacSight is ideally suited to integrate open-source, open-hardware components but can also accommodate closed-source, GUI-only components (e.g. cytometers). We use ReacSight to assemble a platform for cytometry-based characterization and reactive optogenetic control of parallel yeast continuous cultures. Using a dedicated bioreactor array, we showcase its capabilities on three applications. First, we achieve parallel real-time control of gene expression with light in different bioreactors. Second, we explore the impact of nutrient scarcity on fitness and cellular stress using well-controlled, high-information content competition assays. Third, we exploit nutrient scarcity to achieve dynamic control over the composition of a two-strain consortium. To illustrate the genericity of ReacSight, we also assemble an equivalent platform using the optogenetic-ready, open-hardware and commercially available Chi.Bio bioreactors.

category: synthetic biology