title: Evolution and systematics of the Aculeata and kin (Hymenoptera),with emphasis on the ants (Formicoidea: {dagger}@@@idae fam. nov., Formicidae).

abstract: Fossils provide unique opportunity to understand the tempo and mode of evolution and are essential for modeling the history of lineage diversification. Here, we interrogate the Mesozoic fossil record of the Aculeata, with emphasis on the ants (Formicidae), and conduct an extended series of ancestral state estimation exercises on distributions of tip-dated combined-evidence phylogenies. We developed and illustrated from ground-up a series of 576 morphological characters which we scored for 144 extant and 431 fossil taxa, including all families of Aculeata, Trigonaloidea, Evanioidea, and {dagger}Ephialtitoidea. We used average posterior probability support to guide composition of a target matrix of 303 taxa, for which we integrated strongly filtered ultraconserved element (UCE) data for 115 living species. We also implemented reversible jump MCMC (rjMCMC) and hidden state methods to model complex behavioral characters to test hypotheses about the pathway to obligate eusociality. In addition to revising the higher classification of all sampled groups to family or subfamily level using estimated character polarities to diagnose nodes across the phylogeny, we find that the mid-Cretaceous genera {dagger}Camelomecia and {dagger}Camelosphecia form a clade which is robustly supported as sister to all living and fossil Formicidae. For this reason, we name this extinct clade as {dagger}@@@idae fam. nov. and provide a definition for the expanded Formicoidea. Based on our results, we recognize three major phases in the early evolution of the ants: (1) origin of Formicoidea as ground-adapted huntresses during the Late Jurassic in the "stinging aggressor" guild (Aculeata) among various lineages of "sneaking parasitoids" (non-aculeate Vespina); (2) the first formicoid radiation during the Early Cretaceous, by the end of which all major extant linages originated; and (3) turnover of the Formicoidea at the end-Cretaceous leading to the second formicoid radiation. We conclude with a concentrated series of considerations for future directions of study with this dataset and beyond.


title: Comparison of Transcranial Doppler Ultrasound with Computational Fluid Dynamics: Responses to Physiological Stimuli

abstract: Few studies have compared transcranial Doppler (TCD) ultrasound with independent techniques such as computational fluid dynamics (CFD) simulations, particularly in response to stimuli. We compared TCD cerebral blood flow velocity in healthy participants with subject-specific CFD simulations to determine differences in techniques. Twelve participants underwent head and neck imaging with 3 Tesla magnetic resonance angiography. Velocity waveforms in the middle cerebral artery (MCA) were measured with TCD while velocity and diameter in the neck arteries were measured with duplex ultrasound at rest, hypercapnia and exercise. Subject-specific CFD simulations were developed for each condition, with velocity waveforms extracted in the same region as TCD. We found that absolute TCD velocities were significantly higher than CFD data, and non-significantly correlated across all conditions (r range 0.030-0.377, all P>0.05). However, relative changes from rest to hypercapnia and exercise generally exhibited significant positive correlations (r range 0.448-0.770), with the strongest correlation being average velocity change from rest to exercise (r=0.770, P<0.01). We have found that although absolute MCA velocity measurements from different sources vary, relative velocity changes yield stronger correlations regardless of source. Our findings indicate relative responses to physiological stimuli, along with absolute data, should be considered for analyzing cerebral blood flow velocity.

category: bioengineering


title: Ribosome profiling reveals the translational landscape and allele-specific translation efficiency in rice

abstract: Translational regulation is a critical step in the process of gene expression and governs the synthesis of proteins from mRNAs. Many studies have revealed the translational regulation in plants in response to various environmental stimuli. However, there has been no comprehensive landscape of translational regulation and allele-specific translation efficiency in multiple tissues of plants, especially in rice, a main staple crop feeding nearly half of the world population. Here, we used RNA-seq and Ribo-seq data to analyze the transcriptome and translatome of an elite hybrid rice SY63 and its parental varieties ZS97 and MH63. The results revealed that gene expression patterns varied more significantly between tissues than between varieties at both transcriptional and translational levels. Besides, we identified 3,392 upstream open reading frames (uORFs), and most of the uORF-containing genes were enriched for transcription factors. Only 668 long non-coding RNAs could be translated into peptides. Finally, we discovered numerous genes with allele-specific translation efficiency in SY63, and further demonstrated that some cis-regulatory elements (secondary structures of mRNAs and the binding of miRNAs) may contribute to allelic divergence in translation efficiency. Overall, our findings may improve the understanding of translational regulation in rice and provide information for the molecular basis of breading research.

category: bioinformatics


title: Odysseia: Genetic Regulatory Feature Analysis with Interpretable Classification Machine Learning Models

abstract: With rapid progress of robust single-cell transcriptome sequencing since last decade, numerous complex mechanisms underlying cell development has been revealed. Single-cell RNA sequencing (scRNA-seq) analysis is widely accepted as the main approach to define cell stages and phenotypes. As conversion of somatic cells into induced pluripotency cells succeeded, identification key genetic factors(GFs) with scRNA-seq for cell reprogramming in biological research and regenerative medicine fields gained increasing attention. Herein, we describe Odysseia, an interpretable machine learning classifier based single-cell gene expression profile(scGEP) analysis system, that assesses importances of genetic regulatory features in differentiating cell states(CSs). Furthermore, extracted factors, when combining with regulatory network analysis, can help to find key GFs in classifying CSs and possibly inducing CS conversions. Analyzed three published scRNA-seq datasets used to study divergent cell types, Odysseia correctly extracted GFs acclaimed to be capable of inducing CS conversions. Overall, Odysseia provides an automated alternative to obtain guidance information while explicating mechanism to engineer cellular phenotypes.


title: CXCR2 inhibition enables NASH-HCC immunotherapy

abstract:
ObjectiveHepatocellular carcinoma (HCC) is increasingly associated with non-alcoholic steatohepatitis (NASH). HCC immunotherapy offers great promise; however, recent data suggests NASH-HCC may be less sensitive to conventional immune checkpoint inhibition (ICI). We hypothesised that targeting neutrophils using a CXCR2 small molecule inhibitor may sensitise NASH-HCC to ICI therapy.

DesignNeutrophil infiltration was characterised in human HCC and mouse models of HCC. Late-stage intervention with anti-PD1 and/or a CXCR2 inhibitor was performed in murine models of NASH-HCC. The tumour immune microenvironment was characterised by imaging mass cytometry, RNA-seq and flow cytometry.

ResultsNeutrophils expressing CXCR2, a receptor crucial to neutrophil recruitment in acute-injury, are highly represented in human NASH-HCC. In models of NASH-HCC lacking response to ICI, the combination of a CXCR2 antagonist with anti-PD1 suppressed tumour burden and extended survival. Combination therapy increased intratumoral XCR1+ dendritic cell activation and CD8+ T cell numbers which are associated with anti-tumoral immunity, this was confirmed by loss of therapeutic effect upon genetic impairment of myeloid cell recruitment, neutralisation of the XCR1-ligand XCL1 or depletion of CD8+ T cells. Therapeutic benefit was accompanied by an unexpected increase in tumour-associated neutrophils (TANs) which switched from a pro-tumor to anti-tumour progenitor-like neutrophil phenotype. Reprogrammed TANs were found in direct contact with CD8+ T cells in clusters that were enriched for the cytotoxic anti-tumoural protease granzyme B. Neutrophil reprogramming was not observed in the circulation indicative of the combination therapy selectively influencing TANs.

ConclusionCXCR2-inhibition induces reprogramming of the tumour immune microenvironment that promotes ICI in NASH-HCC.

Significance of this studyWhat is already known on this subject? O_LIImmune checkpoint inhibition therapy is emerging as a promising new therapy for the treatment of advanced hepatocellular carcinoma (HCC).
C_LIO_LIOnly a minority of HCC patients will respond to immune checkpoint inhibition (ICI) therapy and recent data suggest that HCC on the background of NASH may have reduced sensitivity to this treatment strategy.
C_LIO_LINeutrophils are a typical myeloid component of the liver in NASH and are found either within the HCC tumour microenvironment or in a peritumoural location.
C_LIO_LINeutrophils have considerable phenotypic plasticity and can exist in both tumour promoting and tumour suppressing states.
C_LIO_LINeutrophils may have the ability to influence ICI therapy.
C_LI

What are the new findings? O_LICXCR2+ neutrophils are found in human NASH and within the tumour of both human and mouse models of NASH-HCC.
C_LIO_LIThe resistance of NASH-HCC to anti-PD1 therapy is overcome by co-treatment with a CXCR2 small molecule inhibitor, with evidence of reduced tumour burden and extended survival.
C_LIO_LIAnti-PD1 and CXCR2 inhibitor combine to selectively reprogramme tumour-associated neutrophils (TANs) from a pro- to an anti-tumour phenotype.
C_LIO_LIReprogrammed TANs proliferate locally within Granzyme B+ immune clusters that contain physically associating CD8+ T cells and antigen presenting cells.
C_LIO_LIConventional XCR1+ dendritic cells (cDC1s) are found to be elevated in anti-PD1 and CXCR2 inhibitor treated HCCs and together with CD8+ T cells are required for therapeutic benefit.
C_LI How might it impact on clinical practice in the foreseeable future?

O_LITANs can be selectively manipulated to adopt an anti-tumour phenotype which unlocks their potential for cancer therapy. The ability of CXCR2 antagonism to combine with ICI therapy to bring about enhanced therapeutic benefit in NASH-HCC (and potentially in HCC of other aetiologies) warrents clinical investigation.
C_LI

category: cancer biology


title: Cryo-electron tomography of Birbeck granules reveals the molecular mechanism of langerin lattice formation

abstract: Langerhans cells are specialized antigen-presenting cells localized within the epidermis and mucosal epithelium. Upon contact with Langerhans cells, pathogens are captured by the C- type lectin langerin and internalized into a structurally unique vesicle known as a Birbeck granule. Although the immunological role of Langerhans cells and Birbeck granules have been extensively studied, the mechanism by which the characteristic zippered membrane structure of Birbeck granules is formed remains elusive. In this study, we observed isolated Birbeck granules using cryo-electron tomography and reconstructed the 3D structure of the repeating unit of the honeycomb lattice of langerin at 6.4 [A] resolution. We found that the interaction between the two langerin trimers was mediated by docking the flexible loop at residues 258-263 into the secondary carbohydrate-binding cleft. Mutations within the loop inhibited Birbeck granule formation and the internalization of HIV pseudovirus. These findings suggest a molecular mechanism for membrane zippering during Birbeck granule biogenesis and provide insight into the role of langerin in the defense against viral infection.

category: immunology


title: Mitoquinone mesylate targets SARS-CoV-2 and associated lung inflammation through host pathways

abstract:
To date, there is no effective oral antiviral against SARS-CoV-2 that is also anti-inflammatory. Herein, we show that the mitochondrial antioxidant mitoquinone/mitoquinol mesylate (Mito-MES), a dietary supplement, has potent antiviral activity against SARS-CoV-2 and its variants of concern in vitro and in vivo. Mito-MES had nanomolar in vitro antiviral potency against the Beta and Delta SARS-CoV-2 variants as well as the murine hepatitis virus (MHV-A59). Mito-MES given in SARS-CoV-2 infected K18-hACE2 mice through oral gavage reduced viral titer by nearly 4 log units relative to the vehicle group. We found in vitro that the antiviral effect of Mito-MES is attributable to its hydrophobic dTPP+ moiety and its combined effects scavenging reactive oxygen species (ROS), activating Nrf2 and increasing the host defense proteins TOM70 and MX1. Mito-MES was efficacious reducing increase in cleaved caspase-3 and inflammation induced by SARS-CoV2 infection both in lung epithelial cells and a transgenic mouse model of COVID-19. Mito-MES reduced production of IL-6 by SARS-CoV-2 infected epithelial cells through its antioxidant properties (Nrf2 agonist, coenzyme Q10 moiety) and the dTPP moiety. Given established safety of Mito-MES in humans, our results suggest that Mito-MES may represent a rapidly applicable therapeutic strategy that can be added in the therapeutic arsenal against COVID-19. Its potential long-term use by humans as diet supplement could help control the SARS-CoV-2 pandemic, especially in the setting of rapidly emerging SARS-CoV-2 variants that may compromise vaccine efficacy.

One-Sentence SummaryMitoquinone/mitoquinol mesylate has potent antiviral and anti-inflammatory activity in preclinical models of SARS-CoV-2 infection.

category: microbiology


title: In vitro evolution of Listeria monocytogenes reveals selective pressure for loss of SigB and AgrA function at different incubation temperatures.

abstract:
The alternative sigma factor B ({sigma}B) contributes to the stress tolerance of the foodborne pathogen Listeria monocytogenes by upregulating the General Stress Response. We previously showed that {sigma}B loss-of-function mutations arise frequently in strains of L. monocytogenes, and suggested that mild stresses might favour the selection of such mutations. In this study, we performed in vitro evolution experiments (IVEE) where L. monocytogenes was allowed to evolve over 30 days at elevated (42{degrees}C) or lower (30{degrees}C) incubation temperatures. Isolates purified throughout the IVEE revealed the emergence of sigB operon mutations at 42{degrees}C. However, at 30{degrees}C independent alleles in the agr locus arose, resulting in the inactivation of the Agr quorum sensing. Colonies of both sigB- and agr- strains exhibited a greyer colouration on 7-days-old agar plates compared with the parental strain. Scanning electron microscopy revealed a more complex colony architecture in the wild type than in the mutant strains. sigB- strains outcompeted the parental strain at 42{degrees}C, but not at 30{degrees}C, whilst agr- strains showed a small increase in competitive fitness at 30{degrees}C. Analysis of 40,080 L. monocytogenes publicly available genome sequences revealed a high occurrence rate of premature stop codons in both the sigB and agrCA loci. An analysis of a local L. monocytogenes strain collection revealed 5 out of 168 strains carrying agrCA alleles. Our results suggest that the loss of {sigma}B or Agr confer an increased competitive fitness in some specific conditions and this likely contributes to the emergence of these alleles in strains of L. monocytogenes.

ImportanceTo withstand environmental aggressions L. monocytogenes upregulates a large regulon through the action of the alternative sigma factor B ({sigma}B). However, {sigma}B becomes detrimental for L. monocytogenes growth under mild stresses, which confer a competitive advantage to {sigma}B loss-of-function alleles. Temperatures of 42{degrees}C, a mild stress, are often employed in mutagenesis protocols of L. monocytogenes and promote the emergence of {sigma}B loss-of-function alleles in the sigB operon. In contrast, lower temperatures of 30{degrees}C promote the emergence of Agr loss-of-function alleles, a cell-cell communication mechanism in L. monocytogenes. Our findings demonstrate that loss-of-function alleles emerge spontaneously in laboratory-grown strains. These alleles rise in the population as a consequence of the trade-off between growth and survival imposed by the activation of {sigma}B in L. monocytogenes. Additionally, our results demonstrate the importance of identifying unwanted hitchhiker mutations in newly constructed mutant strains.

category: molecular biology


title: Quantitative Evaluation of Nonlinear Methods for Population Structure Visualization & Inference

abstract: Population structure (also called genetic structure and population stratification) is the presence of a systematic difference in allele frequencies between sub-populations in a population as a result of non-random mating between individuals. It can be informative of genetic ancestry, and in the context of medical genetics it is an important confounding variable in genome wide association studies. Recently, many nonlinear dimensionality reduction techniques have been proposed for the population structure visualization task. However, an objective comparison of these techniques has so far been missing from the literature. In this paper, we discuss the previously proposed nonlinear techniques and some of their potential weaknesses. We then propose a novel quantitative evaluation methodology for comparing these nonlinear techniques, based on populations for which pedigree is either known a-priori through artificial selection or simulation. Based on this evaluation metric, we find graph-based algorithms such as t-SNE and UMAP to be superior to PCA, while neural network based methods fall behind.


title: The gene signatures of human alpha cells in types 1 and 2 diabetes indicate disease-specific pathways of alpha cell dysfunction

abstract: Glucagon secretion is perturbed in both type 1 and type 2 diabetes (T1D, T2D) the pathophysiological changes at the level of individual pancreatic alpha cells are still largely obscure. Using recently-curated single-cell RNA data from human donors with either T1D or T2D and appropriate controls, we leveraged alpha cell transcriptomic alterations consistent with both common and discrete pathways. Firstly, altered expression of genes associated with alpha cell identity (ARX, MAFB) was common to both diseases. In contrast, increased expression of cytokine-regulated genes and genes involved in glucagon biosynthesis and processing were apparent in T1D, whereas mitochondrial genes associated with reactive oxygen species generation (COX7B, NQO2) were dysregulated in alpha cells from T2D patients. Conversely, T1D alpha cells displayed alterations in genes associated with autoimmune-induced ER stress (ERLEC1, HSP90) whilst those from T2D patients showed changes in glycolytic and citrate cycle genes (LDH, PDHB, PDK4) which were unaffected in T1D. These findings suggest that despite some similarities related to loss-of-function, the alterations of alpha cells present important disease-specific signatures, suggesting that they are secondary to the main pathogenic events characteristic to each disease, namely immune-mediated-or metabolic-mediated-stress in respectively T1D and T2D.

category: physiology


title: Intermittent Fasting Mitigates Vascular and Neuronal Pathologies in a Mouse Model of Vascular Dementia

abstract: Chronic cerebral hypoperfusion (CCH) is an important pathophysiological mechanism of vascular cognitive impairment (VCI). The heterogeneous effects of CCH complicate establishing single target therapies against VCI and its more severe form, vascular dementia (VaD). Intermittent fasting (IF) has multiple targets and is neuroprotective across a range of disease conditions including stroke, but its effects against CCH-induced neurovascular pathologies remain to be elucidated. We therefore assessed the effect of IF against CCH-associated neurovascular pathologies and investigated underlying mechanisms. Male C57BL/6 mice were subjected to either ad libitum feeding (AL) or IF (16 hours of fasting per day) for 4 months. In both groups, CCH was experimentally induced by the bilateral common carotid artery stenosis (BCAS) method. Sham operated groups were used as controls. Measures of leaky microvessels, blood brain barrier (BBB) permeability, protein expression of tight junctions, extracellular matrix components and white matter changes were determined to investigate the effect of IF against CCH-induced neurovascular pathologies. IF alleviated CCH-induced neurovascular pathologies by reducing the number of leaky microvessels, BBB breakdown, loss of tight junctional proteins and vascular endothelial growth factors. In addition, IF mitigated the severity of white matter lesions, maintained myelin basic protein levels, while concurrently reducing hippocampal neuronal cell death. Furthermore, IF reduced CCH-induced increase in levels of matrix metalloproteinase (MMP)-2 and its upstream activator MT1-MMP, which are involved in the breakdown of the extracellular matrix that is a core component of the BBB. Additionally, we observed that IF reduced CCH-induced increase in the oxidative stress marker malondialdehyde, and increased antioxidant markers glutathione and superoxide dismutase. Combined, our data suggests that IF attenuates neurovascular damage, metalloproteinase and oxidative stress-associated pathways, and cell death in the brain following CCH in a mouse model of VCI. Although IF has yet to be assessed in human patients with VaD, our data suggest that IF may be an effective means of preventing the onset or suppressing the development of neurovascular pathologies in VCI and VaD.

category: neuroscience


title: Single-Case Disconnectome Lesion-symptom Mapping: Identifying Two Subtypes of Limb Apraxia

abstract:
Influential theories of skilled action posit that distinct cognitive mechanisms and neuroanatomic substrates support meaningless gesture imitation and tool use pantomiming, and poor performance on these tasks are hallmarks of limb apraxia. Yet prior research has primarily investigated brain-behavior relations at the group level; thus, it is unclear whether we can identify individuals with isolated impairments in meaningless gesture imitation or tool use pantomiming whose performance is associated with a distinct neuroanatomic lesion profile. The goal of this study was to test the hypothesis that individuals with disproportionately worse performance in meaningless gesture imitation would exhibit cortical damage and white matter disconnection in left fronto-parietal brain regions, whereas individuals with disproportionately worse performance in tool use pantomiming would exhibit cortical damage and white matter disconnection in left temporo-parietal brain regions. Fifty-eight participants who experienced a left cerebrovascular accident took part in a meaningless gesture imitation task, a tool use pantomiming task, and a T1 structural MRI. Two participants were identified who had relatively small lesions and disproportionate impairments on one task relative to the other, as well as below-control-level performance on one task and not the other. Using these criteria, one participant was disproportionately impaired at meaningless gesture imitation, and the other participant was disproportionately impaired at pantomiming tool use. Graph theoretic analysis of each participants structural disconnectome demonstrated that disproportionately worse meaningless gesture imitation performance was associated with disconnection among the left inferior parietal lobule, the left superior parietal lobule, and the left middle and superior frontal gyri, whereas disproportionately worse tool use pantomiming performance was associated with disconnection between left temporal and parietal regions. Our results demonstrate that relatively focal lesions to specific portions of the Tool Use Network can be associated with distinct limb apraxia subtypes.

HighlightsO_LIDistinct subtypes of apraxia are supported by distinct neuroanatomic substrates.
C_LIO_LIFronto-parietal lesions are associated with meaningless imitation deficits.
C_LIO_LITemporo-parietal lesions are associated with tool use pantomiming deficits.
C_LIO_LIStructural connectivity among cortical areas supports a distributed praxis system.
C_LI


title: Multiple bumps can enhance robustness to noise in continuous attractor networks

abstract: A central function of continuous attractor networks is encoding coordinates and accurately updating their values through path integration. To do so, these networks produce localized bumps of activity that move coherently in response to velocity inputs. In the brain, continuous attractors are believed to underlie grid cells and head direction cells, which maintain periodic representations of position and orientation, respectively. These representations can be achieved with any number of activity bumps, and the consequences of having more or fewer bumps are unclear. We address this knowledge gap by constructing 1D ring attractor networks with different bump numbers and characterizing their responses to three types of noise: fluctuating inputs, spiking noise, and deviations in connectivity away from ideal attractor configurations. Across all three types, networks with more bumps experience less noise-driven deviations in bump motion. This translates to more robust encodings of linear coordinates, like position, assuming that each neuron represents a fixed length no matter the bump number. Alternatively, we consider encoding a circular coordinate, like orientation, such that the network distance between adjacent bumps always maps onto 360 degrees. Under this mapping, bump number does not significantly affect the amount of error in the coordinate readout. Our simulation results are intuitively explained and quantitatively matched by a unified theory for path integration and noise in multi-bump networks. Thus, to suppress the effects of biologically relevant noise, continuous attractor networks should employ more bumps when encoding linear coordinates; this advantage disappears when encoding circular coordinates. Our findings provide motivation for the presence of multiple bumps in the mammalian grid network.


title: Negative Impact of Daily Screen Use on Inhibitory Control Network in Preadolescence: A Two Year Follow-Up Study

abstract: The COVID pandemic has made an unprecedented shift in childrens daily lives. Children are increasingly spending time with screens to learn and connect with others. As online environment rapidly substitutes in-person experience, understanding childrens neuropsychological trajectories associated with screen experiences is important. Given previous findings suggesting that excessive screen use can lead children to seek more immediate rewards over delayed outcomes, we hypothesized that the increased screen time delays the development of inhibitory control. By analyzing neuropsychological data for 8,334 children (9-11ys) from the ABCD Study Data, we found that children with longer screen time showed a higher reward orientation and a weaker inhibitory control system (i.e., fronto-striatal circuitry) in the brain. Importantly, the interaction of screen experience with the reward sensitivity negatively influences the development of inhibitory control system in the brain over two years, implying possible long-term negative impacts of increased daily screen time on neuropsychological development in children. The results further demonstrated that screen time especially influences the dorsal striatum connectivity, which suggests that the effect of daily screen use is more of a habitual seeking behavior. The results together provide neural and behavioral evidence on the negative impact of daily screen use on developing children.


title: Uncovering circuit mechanisms of current sinksand sources with biophysical simulations ofprimary visual cortex

abstract: Local field potential (LFP) recordings reflect the dynamics of the current source density (CSD) in brain tissue. The synaptic, cellular and circuit contributions to current sinks and sources are ill-understood. We investigated these in mouse primary visual cortex using public Neuropixels recordings and a detailed circuit model based on simulating the Hodgkin-Huxley dynamics of numerous cortical neurons belonging to 17 cell types. The model simultaneously captured spiking and CSD responses and demonstrated a two-way dissociation: Firing rates are altered with minor effects on the CSD pattern by adjusting synaptic weights, and CSD is altered with minor effects on firing rates by adjusting synaptic placement on the dendrites. We describe how thalamocortical inputs and recurrent connections sculpt specific sinks and sources early in the visual response, whereas cortical feedback crucially alters them in later stages. Our findings show that CSD analysis provides powerful constraints for modeling beyond those from considering spikes.


title: The phase of sensorimotor mu and beta oscillations has the opposite effect on corticospinal excitability

abstract: Neural oscillations in the primary motor cortex (M1) shape corticospinal excitability. Power and phase of ongoing mu (8-13 Hz) and beta (14-30 Hz) activity may mediate motor cortical output. However, the functional dynamics of both mu and beta phase and power relationships and their interaction, are largely unknown. Here, we employ recently developed real-time targeting of the mu and beta rhythm, to apply phase-specific brain stimulation and probe motor corticospinal excitability non-invasively. For this, we used instantaneous read-out and analysis of ongoing oscillations, targeting four different phases (0{degrees}, 90{degrees}, 180{degrees}, and 270{degrees}) of mu and beta rhythms with suprathreshold single-pulse transcranial magnetic stimulation (TMS) to M1. Ensuing motor evoked potentials (MEPs) in the right first dorsal interossei muscle were recorded. Twenty healthy adults took part in this double-blind randomized crossover study. Mixed model regression analyses showed significant phase-dependent modulation of corticospinal output by both mu and beta rhythm. Strikingly, these modulations exhibit a double dissociation. MEPs are larger at the mu trough and rising phase and smaller at the peak and falling phase. For the beta rhythm we found the opposite behavior. Also, mu power, but not beta power, was positively correlated with corticospinal output. Power and phase effects did not interact for either rhythm, suggesting independence between these aspects of oscillations. Our results provide insights into real-time motor cortical oscillation dynamics, which offers the opportunity to improve the effectiveness of TMS by specifically targeting different frequency bands.


title: High Cellular Uptake Gene Delivery Platform with Chitosan and L-arginine Complex for Cancer Treatment

abstract: Gene therapy outperforms chemotherapy in limiting the harm to human body. A major impediment to the progress of gene therapy is a lack of proper carriers. Chitosan, derived from shellfish, is a desirable candidate for nucleic acid delivery because of its outstanding biodegradability and biocompatibility. However, previous works show that chitosan has poor cell membrane permeability. In this study, we synthesize a complex delivery system for gene therapy by compounding chitosan with L-arginine, and test the encapsulation, uptake, and cancer cell treatment power. Encapsulation efficiency of the chitosan/L-arginine complex (CA) can reach more than 90% in weight. Flow cytometry reveal that siRNA delivered by the complex can be taken in by cells 10 times better than free siRNA and 2 times better than chitosan alone. Confocal imaging confirmed the high cellular uptake, and siRNA tests in HeLa cells indicate the successful silencing of the target gene (RRM2). The complex serves as a gene delivery system that is capable of loading and delivering a variety of genetic materials in which the specific nucleic acid molecule to be delivered could be altered at will.


title: Dynamic Generalised Additive Models (DGAM) for forecasting discrete ecological time series

abstract:
O_LIGeneralised Additive Models (GAMs) are increasingly popular for describing smooth nonlinear relationships between predictors and response variables. GAMs are particularly relevant in ecology for representing hierarchical functions for discrete responses that encompass complex features including zero-inflation, bounding and uneven sampling. However, GAMs are less useful for producing forecasts as their smooth functions provide unstable predictions outside the range of training data.
C_LIO_LIWe introduce Dynamic Generalised Additive Models (DGAMs), where the GAM linear predictor is jointly estimated with unobserved dynamic components to model time series that evolve as a function of nonlinear predictor associations and latent temporal processes. These models are particularly useful for multivariate series, as they can estimate hierarchical smooths while learning complex temporal associations via dimension-reduced latent factor processes. We implement our models in the mvgam R package, which uses the mgcv and rjags packages to construct smoothing splines and estimate unobserved parameters in a probabilistic framework.
C_LIO_LIUsing simulations, we illustrate how our models outperform competing formulations in realistic ecological forecasting tasks while identifying important smooth predictor functions. We use a real-world case study to highlight some of mvgams key features, which include functions for: calculating correlations among series latent trends, performing model selection using rolling window forecasts, online data augmentation via a recursive particle filter, and visualising probabilistic uncertainties for smooths and predictions.
C_LIO_LIDynamic GAMs (DGAM) offer a solution to the challenge of forecasting discrete time series while estimating ecologically relevant nonlinear predictor associations. Our Bayesian latent factor approach will be particularly useful for exploring competing dynamic ecological models that encompass hierarchical smoothing structures while providing forecasts with robust uncertainties, tasks that are becoming increasingly important in applied ecology.
C_LI

category: ecology


title: Arabidopsis histone H3 lysine 9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to repress KNAT1 and KNAT2

abstract: Arabidopsis KRYPTONITE/SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 4 (KYP/SUVH4), SUVH5 and SUVH6 are H3K9 methyltransferases and they are redundantly involved in silencing of transposable elements (TEs). A recent study indicated that KYP/SUVH5/6 can directly interact with the histone deacetylase HDA6 to synergistically regulate TE expression. However, the function of KYP/SUVH5/6 in plant development is still unclear. The ASYMMETRIC LEAVES1 (AS1) and AS2 form a transcription complex, which is involved in leaf development by repressing the homeobox genes KNOTTED-LIKE FROM ARABIDOPSIS THALIANA 1 (KNAT1) and KNAT2. In this study, we found that KYP and SUVH5/6 directly interact with AS1-AS2 to repress KNAT1 and KNAT2 by altering histone H3 acetylation and H3K9 dimethylation levels. In addition, KYP can directly target on the promoters of KNAT1 and KNAT2, and the binding of KYP is dependent on AS1. Furthermore, the genome-wide occupancy profile of KYP indicated that KYP is enriched in the promoter regions of coding genes, and the binding of KYP is positively correlated with that of AS1 and HDA6. Together, these results indicate that Arabidopsis H3K9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to alter histone H3 acetylation and H3K9 dimethylation from the KNAT1 and KNAT2 loci.

category: plant biology


title: Initiation of aboveground organ primordia depends on combined action of auxin, ERECTA family genes, and PINOID.

abstract:
Leaves and flowers are produced by the shoot apical meristem (SAM) at a certain distance from its center, a process that requires the hormone auxin. The amount of auxin and the pattern of its distribution in the initiation zone determine the size and spatial arrangement of organ primordia. Auxin gradients in the SAM are formed by PIN-FORMED (PIN) auxin efflux carriers whose polar localization in the plasma membrane depends on the protein kinase PINOID (PID).

Previous work determined that ERECTA family genes (ERfs) control initiation of leaves. ERfs are plasma membrane receptors that enable cell-to-cell communications by sensing extracellular small proteins from Epidermal Patterning Factor/EPF-like (EPF/EPFL) family. Here, we investigate whether ERfs regulate initiation of organs by altering auxin distribution or signaling. Genetic and pharmacological data suggest that ERfs do not regulate organogenesis through PINs while transcriptomics data show ERfs do not alter primary transcriptional responses to auxin.

Our results indicate that in the absence of ERf signaling, the peripheral zone cells inefficiently initiate leaves in response to auxin signals and that increased accumulation of auxin in the er erl1 erl2 SAM can partially rescue organ initiation defects. We propose that both auxin and ERfs are essential for leaf initiation, and that they have common downstream targets. Genetic data also indicate that the role of PID in initiation of cotyledons and leaves cannot be attributed solely to regulation of PIN polarity, and PID is likely to have other functions in addition to regulation of auxin distribution.

Summary statementAuxin is unable to promote cotyledon and leaf initiation in the absence of signaling by ERECTA family receptor kinases and the kinase PINOID.


title: An Agrobacterium strain auxotrophic for methionine is useful for switchgrass transformation

abstract: Auxotrophic strains of Agrobacterium tumefaciens can contribute to the development of more efficient transformation systems, especially for crops historically considered recalcitrant. Homologous recombination was used to derive methionine auxotrophs of two common A. tumefaciens strains, LBA4404 and EHA105. The EHA105 strains were more efficient for switchgrass transformation, while both the EHA105 and LBA4404 strains worked equally well for the rice control. Event quality, as measured by transgene copy number, was not affected by auxotrophy, but was higher for the LBA4404 strains than the EHA105 strains. Ultimately, the use of auxotrophs reduced bacterial overgrowth during co-cultivation, with a concomitant decrease in the need for antibiotics. In turn, reduced overgrowth allowed longer co-cultivation periods, with a trend towards higher transformation frequencies for switchgrass, but not for rice.


title: Domestication and lowland adaptation of coastal preceramic maize from Paredones, Peru

abstract:
Archaeological cobs from Paredones and Huaca Prieta (Peru) are phenotypically indistinguishable from modern maize. This contrasts with the earliest Mexican macro-specimens from Guila Naquitz and San Marcos, which are phenotypically intermediate even though they date more recently in time. These observations suggest at least two alternative scenarios, one in which maize was domesticated earlier than previously thought in the lowland Mesoamerica, followed by rapid lowland dispersal to Peru, and another in which maize was independently domesticated in South America and subsequently lost, as current evidence supports a single origin for all modern maize. To gain insights into the origins of ancient Peruvian maize, we sequenced DNA from three Paredones specimens dating 6775 to 5000 calibrated years before present (BP) and conducted comparative analyses with two teosinte subspecies (Zea mays ssp. mexicana and parviglumis) and extant maize, including highland and lowland landraces from Mesoamerica and South America. We show that Paredones maize originated from the same domestication event as Mexican maize and was domesticated by 6775 BP, implying rapid dispersal followed by improvement. Paredones maize show minimal levels of gene flow from mexicana, smaller than those observed in teosinte parviglumis. It also harbors significantly fewer alleles previously found to be adaptive to highlands, but not of alleles adaptive to lowlands, supporting a lowland migration route. Our overall results imply that Paredones maize originated in Mesoamerica, arrived in Peru without mexicana introgression through a rapid lowland migration route, and underwent improvements in both Mesoamerica and South America.

Significance StatementThe coastal Peruvian preceramic sites of Paredones and Huaca Prieta provide the earliest known maize macro-remains. Found more than 3,800 km away from the maize center of origin and presenting a phenotypically modern cob constitution relative to their antiquity, these specimens represent a paradox for understanding maize evolution and dispersal. We show that Paredones maize originated in Mesoamerica, like all known maize, and arrived in South America without introgression from the teosinte mexicana. Since modern maize has substantial contributions from mexicana, it raises the question of when mexicana introgression spread to South America. Paredones maize preferentially shares adaptive allelic diversity with lowland Mesoamerican samples, suggesting a migration route probably associated with a coastal corridor previously identified with archeological findings.


title: Local light signalling at the leaf tip drives remote differential petiole growth through auxin-gibberellin dynamics

abstract: Although plants are immobile, many of their organs are flexible to move in response to environmental cues. In dense vegetation plants detect neighbours through far-red light perception with their leaf tip. They respond remotely, with asymmetrical growth between the abaxial and adaxial sides of the leafstalk, the petiole. This results in upward movement that brings the leaf blades into better lit zones of the canopy. The plant hormone auxin is required for this response, but it is not understood how non-differential leaf tip-derived auxin can remotely regulate movement. Here we show that remote light signalling promotes auxin accumulation in the abaxial petiole by reinforcing an intrinsic auxin transport directionality. In the petiole, auxin elicits a response of both auxin as well as a second growth promoter; gibberellin. We show that this dual regulation is necessary for hyponastic leaf movement in response to light. Our results reveal how plants can spatially relay information about neighbour proximity from their sensory leaf tips to the petiole base, thus driving adaptive growth.


title: Chloroplast genome assemblies and comparative analyses of major Vaccinium berry crops

abstract:
BackgroundVaccinium is an economically important genus of berry crops in the family Ericaceae. Given the numerous hybridizations and polyploidization events among Vaccinium species, the taxonomy of this genus has remained uncertain and the subject of long debate. Therefore, the availability of more genomic resources for Vaccinium can provide useful tools for phylogenetic resolution, species identification, authentication of berry food products, and a framework for genetic engineering.

ResultsIn this study, we assembled five Vaccinium chloroplast sequences representing the following berry types: northern highbush blueberry (V. corymbosum), southern highbush blueberry (V. corymbosum hybrids), rabbiteye blueberry (V. virgatum), lowbush blueberry (V. angustifolium), and bilberry (V. myrtillus). Two complete plastid genomes were achieved using long-read PacBio sequencing, while three draft sequences were obtained using short-read Illumina sequencing. Comparative analyses also included other previously available Vaccinium chloroplast sequences, especially the commercially important species V. macrocarpon (cranberry). The Vaccinium chloroplast genomes exhibited a circular quadripartite structure, with an overall highly conserved synteny and sequence identity among them. Despite their high similarity, we identified some polymorphic regions in terms of expansion/contraction of inverted repeats, gene copy number variation, simple sequence repeats, and single nucleotide polymorphisms. Phylogenetic analysis revealed multiple origins of highbush blueberry plastomes, likely due to the hybridization events during northern and southern highbush blueberry domestication.

ConclusionsOur results enrich the genomic data availability for new Vaccinium species by sequencing and assembling the chloroplast DNA of major economically important berry types. Additional whole plastome analyses including more samples and wild species will be useful to obtain a refined knowledge of the maternal breeding history of blueberries and increase phylogenetic resolution at low taxonomic levels.


title: Are tropical hummingbird pollination networks resistant to experimental extirpation of a common flowering plant?

abstract: Plants and pollinators are experiencing parallel declines worldwide, despite theory predicting that pollination networks should withstand disturbance due to redundancy of pollinators, rarity of interactions between specialists, and flexible pollinator foraging behavior (rewiring). Experiments evaluating the stability of plant-pollinator networks may help resolve this incongruity but remain uncommon. In this study, we simulated the extirpation of a hummingbird-pollinated understory plant, Heliconia tortuosa, from tropical forest fragments using a replicated Before-After-Control-Impact experimental design while quantifying hummingbird space use (383 hummingbird captures and 72 radio-tagged individuals), floral visitation rates (6474 visits from >19,000 observation hours), and plant pollination success (529 flowers). To complement this experimental approach, we also examined these responses across a natural gradient in H. tortuosa density. We expected that declines of H. tortuosa would either result in (i) network collapse, in which hummingbirds vacate fragments and compromise the reproductive success of other flowering plants, or (ii) increased hummingbird reliance on alternative resources, leading to sustained fragment use. We also hypothesized that landscape and local context (i.e., connectivity to additional forest area and alternative resource abundance) could mediate hummingbird responses to H. tortuosa declines; for example, connectivity could facilitate hummingbird visitation to areas of reduced food availability. In our removal experiment, hummingbird persistence and plant pollination success were remarkably resistant to loss of H. tortuosa, a locally common plant species representing >40% of the available nectar resources on average. However, naturally low H. tortuosa densities were associated with reduced floral visitation rates and decreased pollination. Although landscape context (connectivity) led to higher hummingbird abundance, we found little evidence that connectivity or resource availability mediated hummingbird responses to declines in H. tortuosa availability. The exact mechanisms enabling short-term hummingbird persistence after resource removal remain unclear, as we did not discover evidence of rewiring. Physiological adaptations (e.g., torpor and insectivory), may have contributed to hummingbird resilience, perhaps alongside high movement abilities that facilitated visitation to spatially dispersed floral resources. With the important caution that short-term experiments may not realistically emulate natural extinction processes, our study provides partial support for theoretical predictions that pollination networks may be relatively robust to plant species loss.


title: Plastomes of Garcinia mangostana L. and comparative analysis with other Garcinia species

abstract: The two varieties of mangosteen (Garcinia mangostana L.) cultivated in Malaysia are known as Manggis and Mesta. The latter is preferred for its flavor, texture, and seedlessness. Here, we report a complete plastome (156,580 bp) of the Mesta variety which was obtained through a hybrid assembly approach using PacBio and Illumina sequencing reads. It encompasses a large single-copy (LSC) region (85,383 bp) and a small single-copy (SSC) region (17,137 bp) that are separated by 27,230 bp of inverted repeat (IR) regions at both ends. The plastome comprises 128 genes, namely 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The plastome of the Manggis variety (156,582 bp) obtained from reference-guided assembly of Illumina reads was found to be nearly identical to Mesta except for two indels and the presence of a single nucleotide polymorphism (SNP). Comparative analyses with other publicly available Garcinia plastomes, including G. anomala, G. gummi-gutta, G. mangostana var. Thailand, G. oblongifolia, G. paucinervis, and G. pedunculata found that the gene content, gene order, and gene orientation were highly conserved among the Garcinia species. Phylogenomic analysis divided the six Garcinia plastomes into three groups with the Mesta and Manggis varieties clustered closer to G. anomala, G. gummi-gutta, and G. oblongifolia, while the Thailand variety clustered with G. pedunculata in another group. These findings serve as future references for the identification of species or varieties and facilitate phylogenomic analysis of lineages from the Garcinia genus to better understand their evolutionary history.


title: Neprosin belongs to the glutamic peptidase family G3 based on in silico evidence

abstract: Neprosin was first discovered in the insectivorous tropical pitcher plants of Nepenthes species as a novel protease with prolyl endopeptidase (PEP) activity. Neprosin has two uncharacterized domains of neprosin activation peptide and neprosin. A previous study has shown neprosin activity in hydrolyzing proline-rich gliadin, a gluten component that triggers celiac disease. In this study, we performed in silico structure-function analysis to investigate the catalytic mechanism of neprosin. Neprosin sequences lack the catalytic triad and motifs of PEP family S9. Protein structures of neprosins from Nepenthes x ventrata (NvNpr) and N. rafflesiana (NrNpr1) were generated by ab initio methods and comparatively assessed to obtain high-quality models. Structural alignment of models to experimental structures in the Protein Data Bank (PDB) found a high structural similarity to glutamic peptidases. Further investigations reveal other resemblances to the glutamic peptidases with low optimum pH that activates the enzyme via autoproteolysis for maturation. Two highly conserved glutamic acid residues, which are stable according to the molecular dynamics simulation, can be found at the active site of the substrate cleft. Protein docking demonstrated that mature neprosins bind well with potent antigen I-gliadin at the putative active site. Taken together, neprosins represent a new glutamic peptidase family, with a putative catalytic dyad of two glutamic acids. This study illustrates a hypothetical enzymatic mechanism of the neprosin family and demonstrates the useful application of an accurate ab initio protein structure prediction in the structure-function study of a novel protein family.


title: Neprosin belongs to a new family of glutamic peptidase family based on in silico evidence


title: Mitochondrial Genome of Garcinia mangostana L. variety Mesta

abstract: Fruits of Garcinia mangostana L. (mangosteen) are rich in nutrients with xanthones found in the pericarp having great pharmaceutical potential. Mangosteen variety Mesta is only found in Malaysia, which tastes sweeter than the common Manggis variety in Southeast Asia. In this study, we report the complete mitogenome of G. mangostana L. variety Mesta with a total sequence length of 371,235 bp of which 1.7% could be of plastid origin. The overall GC content of the mitogenome is 43.8%, comprising 29 protein-coding genes, 3 rRNA genes, and 21 tRNA genes. Repeat and tandem repeat sequences accounted for 5.8% and 0.15% of the Mesta mitogenome, respectively. There are 333 predicted RNA-editing sites in Mesta mitogenome. These include the RNA-editing events that generated the start codon of nad1 gene and the stop codon of ccmFC gene. Phylogenomic analysis with a maximum likelihood method showed that the mitogenome of mangosteen variety Mesta was grouped under Malpighiales order. This is the first complete mitogenome from the Garcinia genus for future evolutionary studies.


title: Phylogeny of the genus Dolichopus Latreille, 1796 and testing for phylogenetic signal in morphological characters and morphometric data

abstract:
Four groups of characters were used to evaluate phylogenetic relationships among 50 species of the genus Dolichopus: 810 nucleotide characters (for cytochrome oxidase I), 18 continuous characters generated from a geometric morphometric analysis of wing shape, 12 relative characters of the leg morphometry and 42 traditional morphological characters. Subsequently, the common database was used to construct a phylogenetic genus tree and to study the presence of a phylogenetic signal in each group. In this study it was shown that the following characters have a significant phylogenetic signal: the thickening of the costal vein at the insertion point with R1, the color of the fore coxa, the presence of male secondary sexual characters on the forelegs, the color of the femora, the presence of long cilia on the hind femora, and the color of the lower postocular cilia. Traits of male wing shape, such us the relative position of the apex of M1+2, the location of the posterior cossvein, the origin of the radial veins, and the position of the anal vein base, also showed a high phylogenetic signal. In addition, in males, the relative lengths of the first segment of the fore and mid tarsi showed a clear correlation with molecular data, which were interconnected with the presence of males leg modifications. In females, morphometric traits exhibited a less significant phylogenetic signal than in males, although, in most cases, the same traits evinced a high phylogenetic signal.

StatementsWe (corresponding authors) certify that we have participated sufficiently in the conception and design of this work and the analysis of the data (wherever applicable), as well as the writing of the manuscript, to take public responsibility for it. We believe the manuscript represents valid work. We have reviewed the final version of the manuscript and approve it for publication. Neither has the manuscript nor one with substantially similar content under my authorship been published nor is being considered for publication elsewhere, except as described in an attachment. Furthermore, we attest that we will produce the data upon which the manuscript is based for examination by the editors or their assignees, if requested.

The present paper has not been submitted to another journal. All co-authors are aware of the present submission. All co-authors agree to the publication. The work was funded by RFBR and NSFC according to the research project No 20-54-53005.

category: zoology


title: Zebrafish Neuromesodermal Progenitors Undergo a Critical State Transition in vivo

abstract: The transition state model of cell differentiation proposes that a transient window of gene expression stochasticity precedes entry into a differentiated state. As this has been assessed primarily in vitro, we sought to explore whether it can also be observed in vivo. Zebrafish neuromesodermal progenitors (NMps) differentiate into spinal cord and paraxial mesoderm at the late somitogenesis stages. We observed an increase in gene expression variability at the 24 somite stage (24ss) prior to their differentiation. From our analysis of a published 18ss scRNA-seq dataset, we showed that the NMp population possesses a signature consistent with a population undergoing a critical transition. By building in silico composite gene expression maps from our image data, we were able to assign an  NM index to each in silico NMp based on the cumulative expression of its neural and mesodermal markers. With the NM index distributions, we demonstrated that cell population heterogeneity of the NMps peaked at 24ss. We then incorporated stochasticity and non-autonomy into a genetic toggle switch model and uncovered the existence of rebellious cells, which we then confirmed by reexamining the composite maps. Taken together, our work supports the transition state model within an endogenous cell fate decision making event.

category: developmental biology


title: Stepwise remodelling and subcompartment formation in individual vesicles by three ESCRT-III proteins

abstract: The endosomal sorting complex required for transport (ESCRT) is a multi-protein complex involved in several membrane remodelling processes. Different approaches have been used to dissect the mechanism by which ESCRT proteins produce scission in the membranes. However, the underlying mechanisms generating the membrane deformations remain poorly understood. In this study, giant unilamellar vesicles (GUVs), microfluidic technology and micropipette aspiration are combined to continuously follow the ESCRT-III-mediated membrane remodelling on the single-vesicle level for the first time. With this approach, we identify different mechanisms by which a minimal set of three ESCRT-III proteins from the phagocytic parasite Entamoeba histolytica reshape the membrane. These proteins modulate the membrane stiffness and spontaneous curvature to regulate the bud size and generate intraluminal vesicles in GUVs even in the absence of ATP. We show that the bud stability depends on the protein concentration and membrane tension. The approach introduced here should open the road to diverse applications in synthetic biology for establishing artificial cells with several membrane compartments.

category: biophysics


title: CD81 partners with CD44 in promoting exosome biogenesis, tumor cluster formation, and lung metastasis in triple negative breast cancer

abstract: Tumor-initiating cells with reprogramming plasticity are thought to be essential for cancer development and metastatic regeneration in many cancers; however, the molecular mechanisms are not fully understood. This study reports that CD81, a tetraspanin protein marker of small extracellular vesicles (exosomes), functions as a binding partner of CD44 and facilitates self-renewal of tumor initiating cells. Using machine learning-assisted protein structure modeling, co-immunoprecipitation, and mutagenesis approaches, we further demonstrate that CD81 interacts with CD44 on the cellular membrane through their extracellular regions. In-depth global and phosphoproteomic analyses of clustering tumor cells unveils endocytosis-related signature pathways of proteins and phosphorylation patterns regulated by CD81 and CD44 specifically or shared between two. Notably, CRISPR Cas9-mediated depletion of either CD44 or CD81 results in loss of both proteins in cancer cell-secreted exosomes, a state which abolishes exosome-induced self-renewal of recipient cells for mammosphere formation. CD81 is expressed in >80% of human circulating tumor cells (CTCs) and specifically enriched in clustered CTCs along with CD44 isolated from breast cancer patients. Mimicking the phenotypes of CD44 deficiency, loss of CD81 also inhibits tumor cluster aggregation, tumorigenesis, and lung metastasis of triple negative breast cancer (TNBC), supporting the clinical significance of CD81 in association with patient outcomes. Our study highlights the novel role of CD81 and its partnership with CD44 in cancer exosomes, self-renewal, CTC clustering, and metastasis initiation of TNBC.


title: Targeting TRIP13 in Wilms Tumor with Nuclear Export Inhibitors

abstract: Wilms tumor (WT) is the most common renal malignancy of childhood. Despite improvements in the overall survival, relapse occurs in ~15% of patients with favorable histology WT (FHWT). Half of these patients will succumb to their disease. Identifying novel targeted therapies in a systematic manner remains challenging in part due to the lack of faithful preclinical in vitro models. We established ten short-term patient-derived WT cell lines and characterized these models using low-coverage whole genome sequencing, whole exome sequencing and RNA-sequencing, which demonstrated that these ex-vivo models faithfully recapitulate WT biology. We then performed targeted RNAi and CRISPR-Cas9 loss-of-function screens and identified the nuclear export genes (XPO1 and KPNB1) as strong vulnerabilities. We observed that these models are sensitive to nuclear export inhibition using the FDA approved therapeutic agent, selinexor (KPT-330). Selinexor treatment of FHWT suppressed TRIP13 expression, which was required for survival. We further identified in vitro and in vivo synergy between selinexor and doxorubicin, a chemotherapy used in high risk FHWT. Taken together, we identified XPO1 inhibition with selinexor as a potential therapeutic option to treat FHWTs and in combination with doxorubicin, leads to durable remissions in vivo.


title: An apical membrane complex controls rhoptry exocytosis and invasion in Toxoplasma

abstract: Apicomplexan parasites possess secretory organelles called rhoptries that undergo regulated exocytosis upon contact with the host. This process is essential for the parasitic lifestyle of these pathogens and relies on an exocytic machinery sharing structural features and molecular components with free-living ciliates. Here, we performed a Tetrahymena-based transcriptomic screen to uncover novel exocytic factors in Ciliata and Apicomplexa. We identified membrane-bound proteins, named CRMPs, forming part of a large complex essential for rhoptry secretion and invasion in Toxoplasma. In contrast to previously described rhoptry exocytic factors, TgCRMPs are not required for the assembly of the rhoptry secretion machinery and only transiently associated with the exocytic site - prior to invasion. CRMPs and their partners contain putative host cell-binding domains, and CRMPa shares similarity to GPCR proteins. We propose that the CRMP complex acts as host-molecular sensor to ensure that rhoptry exocytosis occurs when the parasite contacts the host cell.

category: cell biology


title: Kinetochore- and chromosome-driven transition of microtubules into bundles promotes spindle assembly

abstract: Mitotic spindle assembly is crucial for chromosome segregation and relies on bundles of microtubules that extend from the poles and overlap in the middle. However, how these structures form remains poorly understood. Here we show that overlap bundles arise through a network-to-bundles transition driven by kinetochores and chromosomes. STED super-resolution microscopy revealed that PRC1-crosslinked microtubules initially form loose arrays, which become rearranged into bundles. Kinetochores promote microtubule bundling by lateral binding via CENP-E/kinesin-7 in an Aurora B-regulated manner. Bundle separation is driven by steric interactions of the bundle-associated chromosomes at the spindle midplane since spindles with uncondensed or uncongressed chromosomes are narrower. In agreement with experiments, theoretical modeling suggests that bundles arise through competing attractive and repulsive mechanisms. Finally, perturbation of overlap bundles led to inefficient correction of erroneous kinetochore-microtubule attachments. Thus, kinetochores and chromosomes drive coarsening of a uniform microtubule array into overlap bundles, which promote not only spindle formation but also chromosome segregation fidelity.


title: TraB is a novel component of the ER-Mitochondria contact site (EMCS) with dual roles in ER-Mitochondrial tethering and mitophagy

abstract: ER-mitochondria contact sites (EMCSs) are important for mitochondrial function. Here, we have identified a novel eukaryotic EMCS complex, comprising a family of uncharacterised mitochondrial outer-membrane proteins, TraB1 and the ER protein, VAP27-1. In Arabidopsis, there are two TraB1 isoforms and the trab1a/trab1b double mutant exhibits abnormal mitochondrial morphology, strong starch accumulation and impaired energy metabolism, indicating that these proteins are essential for normal mitochondrial function. Moreover, TraB1 proteins also interact with ATG8 in order to regulate mitochondrial degradation (mitophagy). The turnover of depolarised mitochondria is significantly reduced in both trab1a/b and VAP27 mutants (vap27-1/3/4/6) under mitochondrial stress conditions, with an increased population of dysfunctional mitochondria present in the cytoplasm. Consequently, plant recovery after stress is significantly perturbed. A similar phenotype is found in both autophagy mutants (atg5 and atg7), suggesting that TraB1 regulated mitophagy and ER-mitochondrial tethering are two closely related processes, necessary for normal mitochondrial function. Taken together, we ascribe a dual role to TraB1 which is a novel component of the EMCS complex in eukaryotes, regulating both tethering of the mitochondria to the ER and mitophagy.


title: Prediction of sex-determination mechanisms in avian primordial germ cells using RNA-seq analysis

abstract: Avian sex is determined by various factors, such as the dosage of DMRT1 and cell-autonomous mechanisms. While the sex-determination mechanism in gonads is well analyzed, the mechanism in germ cells remains unclear. In this study, we explored the gene expression profiles of male and female primordial germ cells (PGCs) during embryogenesis in chickens to predict the mechanism of sex-determination. Male and female PGCs were isolated from blood and gonads with a purity > 96% using flow cytometry and analyzed using RNA-seq. Prior to settlement in the gonads, female circulating PGCs (cPGCs) obtained from blood displayed sex-biased expression. Gonadal PGCs (gPGCs) also displayed sex-biased expression, and the number of female-biased genes detected was higher than male-biased genes. The female-biased genes in gPGCs were enriched in some metabolic processes. To reveal the mechanisms underlying the transcriptional regulation of female-biased genes in gPGCs, we performed stimulation tests. Stimulation with retinoic acid against cultured gPGCs derived from male embryos resulted in the upregulation of several female-biased genes. Overall, our results suggest that sex determination of avian PGCs possess aspects of both cell-autonomous and somatic cell regulation. Moreover, it appears that sex determination occurs earlier in females than in males.


title: Meiotic DNA breaks activate a streamlined phospho-signaling response that largely avoids protein level changes

abstract: Meiotic cells introduce a large number of programmed DNA breaks into their genome to stimulate meiotic recombination and ensure controlled chromosome inheritance and fertility. An intricate checkpoint network involving key kinases and phosphatases coordinates the repair of these DNA breaks during meiosis, but the precise DNA break-dependent phosphorylation targets remain poorly understood. It is also unknown whether meiotic DNA breaks change gene expression akin to the canonical DNA-damage response. To address these questions, we analyzed the meiotic DNA break response in Saccharomyces cerevisiae using multiple systems-level approaches. We identified 332 DNA break-dependent phosphorylation sites, vastly expanding the number of known DNA break-dependent phosphorylation events during meiotic prophase. Only about half of these events occurred in recognition motifs for the known meiotic checkpoint kinases Mec1 (ATR), Tel1 (ATM) and Mek1 (CHK2), suggesting that additional kinases contribute to the meiotic DNA break response. Surprisingly, the numerous changes in phosphorylation were accompanied by very few changes in protein levels despite a clearly detectable transcriptional response. To explain this dichotomy, we show that meiotic entry lowers the expression baseline of many mRNAs enough so that subsequent break-dependent mRNA production has no measurable effects on the largely stable proteome.


title: The evolution of recombination in self-fertilizing organisms

abstract: Cytological data from flowering plants suggest that the evolution of recombination rates is affected by the mating system of organisms, as higher chiasma frequencies are often observed in self-fertilizing species compared with their outcrossing relatives. Understanding the evolutionary cause of this effect is of particular interest, as it may shed light on the selective forces favoring recombination in natural populations. While previous models showed that inbreeding may have important effects on selection for recombination, existing analytical treatments are restricted to the case of loosely linked loci and weak selfing rates, and ignore the effect of genetic interference (Hill-Robertson effect), known to be an important component of selection for recombination in randomly mating populations. In this article, we derive general expressions quantifying the stochastic and deterministic components of selection acting on a mutation affecting the genetic map length of a whole chromosome along which deleterious mutations occur, valid for arbitrary selfing rates. The results show that selfing generally increases selection for recombination caused by interference among mutations as long as selection against deleterious alleles is sufficiently weak. While interference is often the main driver of selection for recombination under tight linkage or high selfing rates, deterministic effects can play a stronger role under intermediate selfing rates and high recombination, selecting against recombination in the absence of epistasis, but favoring recombination when epistasis is negative. Individual-based simulation results indicate that our analytical model often provides accurate predictions for the strength of selection on recombination under partial selfing.

category: evolutionary biology


title: Genetic immune escape landscape in primary and metastatic cancer

abstract: Immune surveillance escape is a hallmark of tumorigenesis1. Multiple studies have characterized the immune escape landscape across several untreated early-stage primary cancer types2-4. However, whether late-stage treated metastatic tumors present differences in genetic immune escape (GIE) prevalence and dynamics remains unclear. Here, we performed a pan-cancer characterization of GIE prevalence across six immune escape pathways in 6,457 uniformly processed Whole Genome Sequencing (WGS) tumor samples including 58 cancer types from 1,943 primary untreated patients and 4,514 metastatic patients. To effectively address the complexity of the Human Leukocyte Antigen (HLA-I) locus and to characterize its tumor status, we developed LILAC, an open-source integrative framework. We demonstrate that one in four tumors harbor GIE alterations, with high mechanistic and frequency variability across cancer types. GIE prevalence is highly consistent between primary and metastatic tumors for most cancer types with few exceptions such as prostate and thyroid carcinomas that have increased immune evasion frequencies in metastatic tumors. Positive selection analysis revealed that GIE alterations are frequently selected for in tumor evolution and that focal LOH of HLA-I, unlike non-focal LOH of HLA-I, tends to lose the HLA allele that presents the largest neoepitope repertoire. We also unraveled tumor genomic features contributing to immune escape incidence, including DNA repair deficiency, APOBEC activity, tobacco associated mutation load and viral DNA integration. Finally, there is a strong tendency for mid and high tumor mutation burden (TMB) tumors to preferentially select LOH of HLA-I for GIE whereas hypermutated samples favor global immune evasion strategies. Our results indicate that genetic immune escape is generally a pre-metastatic event during tumor evolution and that tumors adapt different strategies depending on their neoepitope burden.

category: genomics


title: A three-dimensional human adipocyte model of fatty acid-induced obesity

abstract: Obesity prevalence has reached pandemic proportions, leaving individuals at high risk for the development of diseases such as cancer and type 2 diabetes. In obesity, to accommodate excess lipid storage, adipocytes become hypertrophic, which is associated with an increased pro-inflammatory cytokine secretion and dysfunction of metabolic processes such as insulin signaling and lipolysis. Targeting adipocyte dysfunction is an important strategy to prevent the development of obesity-associated disease. However, it is unclear how accurately animal models reflect human biology, and the long-term culture of human hypertrophic adipocytes in an in vitro 2D monolayer is challenging due to the buoyant nature of adipocytes. Here we describe the development of a human 3D in vitro disease model that recapitulates hallmarks of obese adipocyte dysfunction. First, human primary adipose-derived stromal cells are embedded in hydrogel, and infiltrated into a thin cellulose scaffold. The thin microtissue profile allows for efficient assembly and image-based analysis. After adipocyte differentiation, the scaffold is stimulated with oleic or palmitic acid to mimic caloric overload. Using functional assays, we demonstrated that this treatment induced important obese adipocyte characteristics such as a larger lipid droplet size, increased basal lipolysis, insulin resistance and activation of macrophages through adipocyte-conditioned media. This 3D disease model mimics physiologically relevant hallmarks of obese adipocytes, to enable investigations into the mechanisms by which dysfunctional adipocytes contribute to disease.


title: Comparing algorithms for assessing upper limb use with inertial measurement units

abstract: The various existing measures to quantify upper limb use from wrist-worn inertial measurement units (IMU) can be grouped into three categories: (a) Thresholded activity counting, (b) Gross movement score and (c) machine learning. While machine learning algorithms are a promising approach to detect upper limb use, there is currently no knowledge of the information used by these methods, and the data-related factors that influence their performance. A comparison of existing methods was carried out using data from a previous study which was collected from 10 unimpaired and 5 hemiparetic subjects, with annotation to identify periods of functional and non-functional upper limb use. Intra-subject random forest machine learning measures were found to classify upper limb use more accurately than other measures. The random forest measure uses information about the orientation and the amount of movement of the forearm to detect upper limb use. The types of movements and the proportion of functional data included in training/testing set influences the performance of machine learning measures. This study presents the first step towards understanding and optimizing machine learning methods for upper limb use assessment using wearable sensors.


title: Uncertainty Quantification in Variable Selection for Genetic Fine-Mapping using Bayesian Neural Networks

abstract: In this paper, we propose a new approach for variable selection using a collection of Bayesian neural networks with a focus on quantifying uncertainty over which variables are selected. Motivated by fine-mapping applications in statistical genetics, we refer to our framework as an "ensemble of single-effect neural networks" (ESNN) which generalizes the "sum of single-effects" regression framework by both accounting for nonlinear structure in genotypic data (e.g., dominance effects) and having the capability to model discrete phenotypes (e.g., case-control studies). Through extensive simulations, we demonstrate our methods ability to produce calibrated posterior summaries such as credible sets and posterior inclusion probabilities, particularly for traits with genetic architectures that have significant proportions of non-additive variation driven by correlated variants. Lastly, we use real data to demonstrate that the ESNN framework improves upon the state-of-the-art for identifying true effect variables underlying various complex traits.


category: genetics


title: StabMap: Mosaic single cell data integration using non-overlapping features

abstract: Currently available single cell -omics technologies capture many unique features with different biological information content. Data integration aims to place cells, captured with different technologies, onto a common embedding to facilitate downstream analytical tasks. Current horizontal data integration techniques use a set of common features, thereby ignoring non-overlapping features and losing information. Here we introduce StabMap, a mosaic data integration technique that stabilises mapping of single cell data by exploiting the non-overlapping features. StabMap is a flexible approach that first infers a mosaic data topology, then projects all cells onto supervised or unsupervised reference coordinates by traversing shortest paths along the topology. We show that StabMap performs well in various simulation contexts, facilitates disjoint mosaic data integration, and enables the use of novel spatial gene expression features for mapping dissociated single cell data onto a spatial transcriptomic reference.


title: A nucleation-and-growth model for the packaging of genome in linear virus-like particles: impact of multiple packaging signals

abstract:
Inspired by recent experiments on the spontaneous assembly of virus-like particles from a solution containing a synthetic coat protein and double-stranded DNA, (1) we put forward a kinetic model that has as main ingredients a stochastic nucleation and a deterministic growth process. The efficiency and rate of the packaging of the DNA turn out to strongly increase by introducing proteins onto the DNA template that are modified using CRISPR-Cas techniques to bind specifically at predesignated locations, mimicking assembly signals in viruses. Our model shows that treating these proteins as nucleation-inducing diffusion barriers is sufficient to explain experimentally observed increase in encapsulation efficiency, but only if the nucleation rate is sufficiently high. We find an optimum in the encapsulation kinetics for conditions where the number of packaging signals is equal to the number of nucleation events that can occur during time required to fully encapsulate the DNA template, presuming that the nucleation events can only take place adjacent to a packaging signal. Our theory is in satisfactory agreement with the available experimental data.

SIGNIFICANCEThe rate and efficiency of the encapsulation of double-stranded DNA by synthetic coat proteins was recently found to be strongly enhanced by the presence of specifically positioned protein molecules on the DNA that mimic so-called packaging signals. We present a kinetic theory based on the initial stochastic nucleation and subsequent deterministic elongation of the protein coat with the aim to explain these findings. We find that equidistantly placed nucleation sites that also act as diffusion barriers on the DNA have profound and non-trivial effects, and they can either slow down or speed up encapsulation, depending on how fast nucleation is on the time scale of the elongation process. Our findings may contribute to the rational design of linear virus-like particles.


title: The effect of carbamazepine on bone structure and strength in control and Osteogenesis Imperfecta (Col1a2 +/p.G610C) mice

abstract: The inherited brittle bone disease osteogenesis imperfecta (OI) is commonly caused by COL1A1 and COL1A2 mutations that disrupt the collagen I triple helix. This causes intracellular endoplasmic reticulum (ER) retention of the misfolded collagen and can result in a pathological ER stress response. A therapeutic approach to reduce this toxic mutant load could be to stimulate mutant collagen degradation by manipulating autophagy and/or ER-associated degradation. Since carbamazepine (CBZ) both stimulates autophagy of misfolded collagen X and improves skeletal pathology in a metaphyseal chondrodysplasia model, we tested the effect of CBZ on bone structure and strength in 3 week-old male OI Col1a2 +/p.G610C and control mice. Treatment for 3 or 6 weeks with CBZ, at the dose effective in metaphyseal chondrodysplasia, provided no therapeutic benefit to Col1a2 +/p.G610C mouse bone structure, strength, or composition, measured by micro-computed tomography, three point bending tests and Fourier-transform infrared microspectroscopy. In control mice however, CBZ treatment for 6 weeks impaired femur growth and led to lower femoral cortical and trabecular bone mass. These data, showing the negative impact of CBZ treatment on the developing mouse bones, raise important issues which must be considered in any human clinical applications of CBZ in growing individuals.

category: pathology


title: Automatic Generation of Interactive Multidimensional Phase Portraits

abstract: Mathematical models formally and precisely represent biological mechanisms with complex dynamics. To understand the possible behaviors of such systems, phase portrait diagrams can be used to visualize their overall global dynamics across a domain. However, producing these phase portrait diagrams is a laborious process reserved to mathematical experts. Here, we developed a computational methodology to automatically generate phase portrait diagrams to study biological dynamical systems based on ordinary differential equations. The method only needs as input the variables and equations describing a multidimensional biological system and it automatically outputs for each pair of dependent variables a complete phase portrait diagram, including the critical points and their stability, the nullclines of the system, and a vector space of the trajectories. Crucially, the portraits generated are interactive, and the user can move the visualized planar slice, change parameters with sliders, and add trajectories in the phase and time domains, after which the diagrams are updated in real time. The method is available as a user-friendly graphical interface or can be accessed programmatically with a Mathematica package. The generated portraits and particular views can be saved as computable notebooks preserving the interactive functionality, an approach that can be adopted for reproducible science and interactive pedagogical materials. The method, code, and examples are freely-available at https://lobolab.umbc.edu/autoportrait.

category: systems biology


title: Multisensory interactions on auditory and somatosensory information in expert pianists

abstract: Fine-tuned sensory functions are bases of efficient motor control and learning and typically characterize skilled individuals. Although numerous studies demonstrated enhanced unimodal sensory functions at both neural and behavioral levels in skilled individuals, little is known about their multisensory interaction, especially multisensory integration and selective attention that involve volitional control of information derived from multiple sensory organs. Here, we show unique multisensory interaction functions of expert pianists. Expert pianists and musically untrained individuals performed five sets of intensity discrimination tasks at the auditory and somatosensory modalities with different conditions: (1) auditory stimulus, (2) somatosensory stimulus, (3) congruent auditory and somatosensory stimuli (i.e., multisensory integration), (4) auditory and task-irrelevant somatosensory stimuli, and (5) somatosensory and task-irrelevant auditory stimuli. In the fourth and fifth conditions, participants were instructed to ignore a task-irrelevant stimulus and to pay attention to a task-relevant stimulus (i.e., selective attention). The unimodal intensity discrimination of the pianists was superior to that of the nonmusicians at the auditory modality but not at the somatosensory modality. While the discrimination perception was superior in the condition (3) compared to the better one of the individual unimodal conditions (i.e., conditions 1 and 2) only in the pianists, the task-irrelevant somatosensory stimulus worsened the auditory discrimination more in the pianists than the nonmusicians. These findings indicate efficient processing of multisensory information in expert pianists, which enables to benefit from multisensory integration of the auditory and somatosensory information, but exacerbates top-down selective inhibition of somatosensory information during auditory processing.


title: Performance reserves in brain-imaging-based phenotype prediction

abstract: Machine learning studies have shown that various phenotypes can be predicted from structural and functional brain images. However, in most such studies, prediction performance ranged from moderate to disappointing. It is unclear whether prediction performance will substantially improve with larger sample sizes or whether insufficient predictive information in brain images impedes further progress. Here, we systematically assess the effect of sample size on prediction performance using sample sizes far beyond what is possible in common neuroimaging studies. We project 3-9 fold improvements in prediction performance for behavioral and mental health phenotypes when moving from one thousand to one million samples. Moreover, we find that moving from single imaging modalities to multimodal input data can lead to further improvements in prediction performance, often on par with doubling the sample size. Our analyses reveal considerable performance reserves for neuroimaging-based phenotype prediction. Machine learning models may benefit much more from extremely large neuroimaging datasets than currently believed.


title: Manipulation-specific activity in motor and somatosensory cortex as mice handle food

abstract: Food-handling offers unique yet largely unexplored opportunities to investigate how cortical activity relates to forelimb movements in a natural, ethologically essential, and kinematically rich form of manual dexterity. To determine these relationships, we recorded spiking activity in mouse forelimb M1 and S1 and tongue/jaw M1. Activity in all areas was strongly modulated in close association with discrete active manipulation events that occurred intermittently as mice fed. Each areas activity was also partly distinct in its overall timing and phasic/tonic temporal profile, attributable to area-specific composition of activity classes. Forelimb position could be accurately predicted from activity in all three regions. These results thus establish that cortical activity during food-handling is manipulation-specific, distributed, and broadly similar across multiple cortical areas, while also exhibiting area- and submovement-specific relationships with the fast kinematic hallmarks of this form of complex, free-object-handling manual dexterity.


title: Active exploration of a novel environment drives the activation of the hippocampus-amygdala complex of domestic chicks.

abstract:
In birds, like in mammals, the hippocampus critically mediates spatial navigation through the formation of a spatial map. This study investigates the impact of active exploration of a novel environment on the hippocampus of young domestic chicks, during formation of a new spatial map. Chicks that were free to actively explore the novel environment exhibited a significantly higher neural activation (measured by c-Fos expression), compared to those that passively observed the novel environment from a restricted area. The difference was limited to the anterior and the dorsolateral parts of the intermediate hippocampus. Furthermore, the nucleus taeniae of the amygdala showed a higher c-Fos expression in the active exploration group than the passive observation group. In both brain regions, brain activation correlated with the number of locations that chicks visited during the test. This suggest that the increase of c-Fos expression in the hippocampus is related to increased firing rates of spatially coding neurons. Furthermore, our study indicates a functional linkage of the hippocampus and nucleus taeniae of the amygdala in processing spatial information. Overall, with the present study, we confirm that, in birds like in mammals, exploration of novel environments activates hippocampus, which is likely related to the formation of new spatial representations.

Summary statementActive exploration of a novel environment induces stronger activation of hippocampus and taeniae of domestic chicks than pure visual, passive exploration from a restricted area.


title: Persistent horizontal and vertical, MR-induced nystagmus in resting state Human Connectome Project data

abstract:
ObjectiveStrong magnetic fields from magnetic resonance (MR) scanners induce a Lorentz force that contributes to vertigo and persistent nystagmus. Prior studies have reported a predominantly horizontal direction for healthy subjects in a 7 Tesla (T) MR scanner, with slow phase velocity (SPV) dependent on head orientation. Less is known about vestibular signal behavior for subjects in a weaker, 3T magnetic field, the standard strength used in the Human Connectome Project (HCP). The purpose of this study is to characterize the form and magnitude of nystagmus induced at 3T.

MethodsForty-two subjects were studied after being introduced head-first, supine into a Siemens Prisma 3T scanner. Eye movements were recorded in four separate acquisitions over 20 minutes. A biometric eye model was fit to the recordings to derive rotational eye position and then SPV. An anatomical template of the semi-circular canals was fit to the T2 anatomical image from each subject, and used to derive the angle of the B0 magnetic field with respect to the vestibular apparatus.

ResultsRecordings from 37 subjects yielded valid measures of eye movements. The population-mean SPV {+/-} SD for the horizontal component was -1.38 {+/-} 1.27 deg/sec, and vertical component was -0.93 {+/-} 1.44 deg/sec, corresponding to drift movement in the rightward and downward direction. Although there was substantial inter-subject variability, persistent nystagmus was present in half of subjects with no significant adaptation over the 20 minute scanning period. The amplitude of vertical drift was correlated with the roll angle of the vestibular system, with a non-zero vertical SPV present at a 0 degree roll.

InterpretationNon-habituating vestibular signals of varying amplitude are present in resting state data collected at 3T.


title: Olfactory responses of Drosophila are encoded in the organization of projection neurons

abstract: The projection neurons (PNs), reconstructed from electron microscope (EM) images of the Drosophila olfactory system, offer a detailed view of neuronal anatomy, providing glimpses into information flow in the brain. About 150 PNs constituting 51 glomeruli in the antennal lobe (AL) are bundled together in the axonal extension, routing the olfactory signal received at the AL to the mushroom body (MB) calyx and the lateral horn (LH). Here we quantify the neuronal organization by inter-PN distances and examine its relationship with the odor types sensed by Drosophila. The homotypic PNs that constitute glomeruli in AL are tightly bundled and stereotyped in position; however, such a glomerular-like PN organization in AL is no longer sustained in the higher brain center. Instead, odor-type dependent clusters consisting of multiple different homotypes become more prevalent in MB calyx and LH. We find that there are statistically significant associations between the spatial organization among a group of homotypic PNs and certain stereotyped behavioral responses. In particular, pheromone-encoding homotypes are segregated from other neurons not only in LH but also in MB calyx. Our findings suggest that before neural computation in the inner brain, some of the olfactory responses are already encoded either by the homotype or in the spatial organization of PNs, illuminating that the labeled-line strategy is at work in the Drosophila olfactory system.


title: Categorical bias as a crucial parameter in visual working memory: the effect of memory load and retention interval

abstract: Visual information can be stored as continuous as well as categorical representations in visual working memory (VWM) to guide subsequent behavior. Yet it is still unclear what determines whether VWM is represented as continuous or categorical information, or as a mix of both. Recent studies have shown that color VWM representations adjust flexibly depending on the number of memory items as well as the duration that these items need to be maintained for. The current study aims to extend and replicate these crucial effects. In a delayed estimation task, participants memorized one to four colored objects presented at different spatial locations, followed by a delay of 100, 500, 1,000, or 2,000 ms. Next, a probe indicated the location of the color that participants needed to report. We measured the extent to which responses were biased in the direction of prototypical colors. Crucially, we implemented this categorical bias in an extension to the classic mixture model (Zhang & Luck 2008) in which the center of the error distribution is a crucial parameter that characterizes the extent to which VWM is biased by color categories. We found that VWM shows a strong categorical bias in all cases, and that this bias increases with increasing memory load; strikingly, this effect of memory load on categorical bias is stronger at longer intervals (1,000 ms or longer), as compared to shorter intervals, yet it peaks for intermediate memory loads as opposed to the highest memory load. Overall, our results suggest that when visual information needs to be maintained for one second or longer, VWM becomes more reliant on categorical representations as memory load increases.


title: Structural and functional alterations of neuromuscular synapses in a mouse model of ACTA1 congenital myopathy

abstract:
Mutations in skeletal muscle -actin (Acta1) cause a variety of myopathies. In a mouse model of congenital myopathy, heterozygous Acta1 (H40Y) knock-in (Acta1+/Ki) mice exhibit features of human nemaline myopathy, including premature lethality, severe muscle weakness, reduced mobility, and the presence of nemaline rods in muscle fibers. In this study, we investigated the structure and function of the neuromuscular junction (NMJ) in the Acta1+/Ki mice. We found marked impairments in NMJ structure in the mutant mice, including fragmented endplates and nerve terminals, reduced density of acetylcholine receptors (AChRs) on endplate membranes, reduced nerve occupancy at endplates, and increased numbers of muscle fiber subsynaptic nuclei. We compared the NMJs in three different types of muscles - the extensor digitorum longus (EDL, composed of fast-twitch muscle fibers), soleus (Sol, enriched in slow-twitch fibers) and the triangularis sterni muscle (TS, a mixed fiber type muscle). Among these three types of muscles, EDL was affected to the greatest extent, suggesting that fast-twitch fibers may be most susceptible to NMJ fragmentation in Acta1+/Ki nemaline myopathy.

Electrophysiological analysis of mutant NMJs showed a reduced quantal size (reduced mEPP amplitude), increased mEPP frequency, and increased quantal content, but normal EPP amplitude compared to wild type (WT) NMJs. The results suggest that affected synapses may have undergone homeostatic compensation to maintain normal levels of neurotransmitter release. In addition, paired-pulse facilitation was reduced and synaptic depression under repetitive nerve stimulation was enhanced, indicating shortterm synaptic plasticity was compromised in the mutant mice.

Key pointsO_LIMice heterozygous for an Acta1 (H40Y) knock-in mutation exhibit clinical features of human nemaline myopathy. We report structural and functional alterations of neuromuscular synapses in these mutant mice. The NMJ impairments include endplate fragmentation, reduced endplate nerve occupancy, and increased numbers of subsynaptic nuclei in muscle fibers.
C_LIO_LINeuromuscular synaptic transmission was compromised - demonstrating both increased quantal content and changes in short-term synaptic plasticity.
C_LIO_LIIncreases in spontaneous neurotransmitter release and quantal content suggest homeostatic compensation of synapses to maintain normal transmitter release in the mutant NMJs.
C_LI


title: A key role of orientation in the coding of visual motion direction

abstract: Despite the fundamental importance of visual motion processing, our understanding of how the brain represents basic aspects of motion is incomplete. While it is generally believed that direction is the main representational feature of motion, motion processing is also influenced by non-directional orientation signals that are present in most motion stimuli. Here, we aimed to test whether this non-directional motion axis determines motion perception even when orientation is completely absent from the stimulus. Using stimuli with and without orientation signals, we found that serial dependence in a simple motion direction estimation task was predominantly determined by the orientation of the previous motion stimulus. Moreover, the observed attraction profiles closely matched the characteristic pattern of serial attraction found in orientation perception. Evidently, the sequential integration of motion signals depends solely on the orientation of motion, indicating a fundamental role of non-directional orientation in the coding of visual motion direction.