title: Characterization of an α-glucosidase enzyme conserved in Gardnerella spp. isolated from the human vaginal microbiome

abstract: Gardnerella spp. in the vaginal microbiome are associated with bacterial vaginosis, a dysbiosis in which a lactobacilli dominant microbial community is replaced with mixed aerobic and anaerobic bacteria including Gardnerella species. The co-occurrence of multiple Gardnerella species in the vaginal environment is common, but different species are dominant in different women. Competition for nutrients, particularly glycogen present in the vaginal environment, could play an important role in determining the microbial community structure. Digestion of glycogen into products that can be taken up and further processed by bacteria requires the combined activities of several enzymes collectively known as amylases, which belong to glycoside hydrolase family 13 (GH13) within the CAZy classification system. GH13 is a large and diverse family of proteins, making prediction of their activities challenging. SACCHARIS annotation of the GH13 family in Gardnerella resulted in identification of protein domains belonging to eight subfamilies. Phylogenetic analysis of predicted amylase sequences from 26 Gardnerella genomes demonstrated that a putative -glucosidase-encoding sequence, CG400_06090, was conserved in all species in the genus. The predicted -glucosidase enzyme was expressed, purified and functionally characterized. The enzyme was active on a variety of maltooligosaccharides over a broad pH range (4.0 - 8) with maximum activity at pH 7. The Km, kcat and kcat/Km values for the substrate 4-nitrophenyl -D-glucopyranoside were 8.3 M, 0.96 min-1 and 0.11 M-1min-1 respectively. Glucose was released from maltose, maltotriose, maltotetraose and maltopentaose, but no products were detected on thin layer chromatography when the enzyme was incubated with glycogen. Our findings show that Gardnerella spp. produce an -glucosidase enzyme that may contribute to the complex and multistep process of glycogen metabolism by releasing glucose from maltooligosaccharides.


title: Nance-Horan Syndrome-like 1 protein negatively regulates Scar/WAVE-Arp2/3 activity and inhibits lamellipodia stability and cell migration.

abstract: Cell migration is important for development and its aberrant regulation contributes to many diseases. The Scar/WAVE complex is essential for Arp2/3 mediated lamellipodia formation during mesenchymal cell migration and several coinciding signals activate it. However, so far, no direct negative regulators are known. We have identified Nance-Horan Syndrome-like 1 protein (NHSL1) as a novel, direct binding partner of the Scar/WAVE complex, which co-localise at protruding lamellipodia. This interaction is mediated by the Abi SH3 domain and two binding sites in NHSL1. Furthermore, active Rac binds to NHSL1 at two regions that mediate leading edge targeting of NHSL1. Surprisingly, NHSL1 inhibits cell migration through its interaction with the Scar/WAVE complex. Mechanistically, NHSL1 may reduce cell migration efficiency by impeding Arp2/3 activity, as measured in cells using a novel Arp2/3 FRET-FLIM biosensor, resulting in reduced F-actin density of lamellipodia, and consequently impairing the stability of lamellipodia protrusions.

category: cell biology


title: An optimal lysis time maximizes bacteriophage fitness in quasi-continuous culture

abstract: Optimality models have a checkered history in evolutionary biology. While optimality models have been successful in providing valuable insight into the evolution of a wide variety of biological traits, a common objection is that optimality models are overly simplistic and ignore organismal genetics. We revisit evolutionary optimization in the context of a major bacteriophage life history trait, lysis time. Lysis time refers to the period spanning phage infection of a host cell and its lysis, whereupon phage progeny are released. Lysis time, therefore, directly determines phage fecundity assuming progeny assembly rate is maximized. Noting that previous tests of lysis time optimality rely on batch culture, we implemented a quasi-continuous culture system to observe productivity of a panel of isogenic phage {lambda} mutants differing in lysis time. We report that {lambda} phage productivity in our experiments is maximized around an optimal lysis time of 63 min, which is the lysis time of the {lambda} "wildtype" strain. We discuss this finding in light of recent results that lysis time variation is also minimized in the {lambda} "wildtype" strain.

category: evolutionary biology


title: Spike frequency adaptation supports network computations on temporally dispersed information

abstract: For solving tasks such as recognizing a song, answering a question, or inverting a sequence of symbols, cortical microcircuits need to integrate and manipulate information that was dispersed over time during the preceding seconds. Creating biologically realistic models for the underlying computations, especially with spiking neurons and for behaviorally relevant integration time spans, is notoriously difficult. We examine the role of spike frequency adaptation in such computations and find that it has a surprisingly large impact. The inclusion of this well known property of a substantial fraction of neurons in the neocortex -- especially in higher areas of the human neocortex -- moves the performance of spiking neural network models for computations on network inputs that are temporally dispersed from a fairly low level up to the performance level of the human brain.

category: neuroscience


title: Predicting Cortical Signatures of Consciousness using Dynamic Functional Connectivity Graph-Convolutional Neural Networks

abstract: Decoding the levels of consciousness from cortical activity recording is a major challenge in neuroscience. Using clustering algorithms, we previously demonstrated that resting-state functional MRI (rsfMRI) data can be split into several clusters also called "brain states" corresponding to "functional configurations" of the brain. Here, we propose to use a selfsupervised machine learning method based on artificial neural networks to predict functional brain states across levels of consciousness from rsfMRI. The Functional Connectivity (FC) matrices reflect the brain-state dynamic at a given time. Because it is key to consider the FC topologies, a specific graph-Convolutional Neural Network (gCNN), namely BrainNetCNN, is considered to predict the brain states in awake and anesthetized nonhuman primates. To avoid the circularity that remains in the training stage, where the target is composed of pseudo-labels, recent self-supervised techniques are implemented. Using a linear probe for the prediction, the network achieves a prediction accuracy consistent with state-of-the-art methods lying in [0.655, 0.759] depending on the experimental settings. To put forward the interest of such a representation, the transition probabilities and the set of connections found to be important for predicting a brain state are computed. This latter is directly linked with the level of consciousness. The results demonstrate that deep learning methods are not only able to predict brain states but also provide additional insight into cortical signatures of consciousness with potential clinical consequences for the monitoring of anesthesia and the diagnosis of disorders of consciousness.


title: Leaf shape and size variation in bur oaks: An empirical study and simulation of sampling strategies

abstract:
PREMISELeaf shape and size figure strongly in trees adaptation to their environments. Oaks are notoriously variable in leaf morphology. Our study examines the degree to which within-tree, among-tree, and among-site variation contribute to latitudinal variation in leaf shape and size of bur oak (Quercus macrocarpa: Fagaceae), one of North Americas most geographically widespread oak species.

METHODSSamples were collected from four sites each at northern, central, and southern latitudes of the bur oak range. Ten leaf size traits were measured, and variance in these traits and eight ratios based on these traits was partitioned into tree, population, and latitude components. We then parameterized a series of leaf collection simulations using empirical covariance among leaves on trees and trees at sites. We used the simulations to assess the efficiency of different collecting strategies for estimating among-population differences in leaf shape and size.

KEY RESULTSLeaf size measurements were highly responsive to latitude. Site contributed more than tree to total variation in leaf morphology. Simulations suggest that power to detect among-site variance in leaf shape and size can be estimated most efficiently with increases in either leaves per tree (10-11 leaves from each of 5 trees) or trees per site (5 leaves from each of 10+ trees).

CONCLUSIONSOur study demonstrates the utility of simulating sampling and controlling for variance in sampling for leaf morphology, whether the questions being addressed are ecological, evolutionary, or taxonomic. Simulation code is provided as an R package (traitsPopSim) to help researchers plan morphological sampling strategies.

category: plant biology


title: Root specific plasticity induced by paclobutrazol confers improved deficit irrigation tolerance and agronomic performance in maize

abstract: Drought stress in maize often results in poor growth and reduced yield. Antioxidants play vital role in management of abiotic stresses. Drought or water deficit are detrimental to young seedlings establishment and transition from vegetative to reproductive growth in maize. Paclobutrazol (PBZ) has been widely used to confer abiotic stress tolerance in plants, however, its impact on root developmental attributes in maize and their relevance in drought management are least understood. Comprehensive experiments over a three year period (2017-2019) under early deficit (EDI) and terminal deficit (TDI) irrigation with or without paclobutrazol (PBZ) were conducted on five maize varieties (DDKL, DKC-9144, PG-2475, PG-2320 and Bio-9621). Plant shoot and root growth kinetics, phenological changes and physiological perturbations including antioxidant profile coupled with molecular regulation of root traits, showed DKC-9144 as best variety in terms of plant fitness and reproductive performance under deficit irrigation. Root developmental rates were key contributors towards improved plant biomass and cob yield under deficit irrigation tolerance. Structural equation modelling (SEM) demonstrated specific contribution of different root types (crown, brace and seminal roots) in maize towards improving water use efficiency, cob yield and plant height. From SEM, seminal root surface area and root length are proposed desired traits to improve water use efficiency and cob yield in DKC-9144 under deficit irrigation. Bi-variate analyses of twenty key traits of plant fitness and agronomic importance showed a strong correlation (r) between root traits and improved growth performance and yield stability indices.


title: Beta-adrenergic receptor signaling regulates ER-mitochondria contacts

abstract: Interactions between the endoplasmic reticulum (ER) and mitochondria (Mito) are crucial for many cellular functions, and their interaction levels change dynamically depending on the cellular environment. Little is known about how the interactions between these organelles are regulated within the cell. Here we screened a compound library to identify chemical modulators for ER-Mito contacts. Multiple agonists of G-protein coupled receptors (GPCRs), beta-adrenergic receptors ({beta}-ARs) in particular, scored in this screen. Analyses in multiple orthogonal assays validated that GPCR activation promotes physical and functional interactions between the two organelles. Furthermore, we have elucidated potential downstream effectors mediating GPCR-induced ER-Mito contacts. Given the role of GPCRs in sensing various extracellular signals and subsequently eliciting appropriate cellular responses, our data provide significant insights into the roles of ER-Mito contacts in maintaining cellular homeostasis and in responding to physiological demands or stresses.


title: G protein-coupled receptor signaling regulates ER-mitochondria contacts


title: Origin of Novel Coronavirus (COVID-19): A Computational Biology Study using Artificial Intelligence

abstract: Origin of the COVID-19 virus (SARS-CoV-2) has been intensely debated in the scientific community since the first infected cases were detected in December 2019. The disease has caused a global pandemic, leading to deaths of thousands of people across the world and thus finding origin of this novel coronavirus is important in responding and controlling the pandemic. Recent research results suggest that bats or pangolins might be the hosts for SARS-CoV-2 based on comparative studies using its genomic sequences. This paper investigates the SARS-CoV-2 origin by using artificial intelligence (AI) and raw genomic sequences of the virus. More than 300 genome sequences of COVID-19 infected cases collected from different countries are explored and analysed using unsupervised clustering methods. The results obtained from various AI-enabled experiments using clustering algorithms demonstrate that all examined SARS-CoV-2 genomes belong to a cluster that also contains bat and pangolin coronavirus genomes. This provides evidence strongly supporting scientific hypotheses that bats and pangolins are probable hosts for SARS-CoV-2. At the whole genome analysis level, our findings also indicate that bats are more likely the hosts for the COVID-19 virus than pangolins.

category: bioinformatics


title: Upregulated-flotillins and sphingosine kinase 2 derail vesicular trafic to stabilize AXL and promote epithelial-mesenchymal transition

abstract:
Altered endocytosis and vesicular trafficking are major players during tumorigenesis. Flotillin overexpression, a feature observed in many invasive tumors, and identified as a marker of poor prognosis, induces a deregulated endocytic and trafficking pathway called Upregulated Flotillin-Induced Trafficking (UFIT). Here, we found that, in non tumoral mammary epithelial cells, induction of the UFIT pathway promotes epithelial-to-mesenchymal transition (EMT) and accelerates the endocytosis of several transmembrane receptors, including AXL, in flotillin-positive late endosomes. AXL overexpression, frequently observed in cancer cells, is linked to EMT and metastasis formation. In flotillin-overexpressing non-tumoral mammary epithelial cells and in invasive breast carcinoma cells, we found that the UFIT-pathway-mediated AXL endocytosis allows its stabilization and depends on sphingosine-kinase 2, a lipid kinase recruited in flotillin-rich plasma membrane-domains and endosomes.

Thus, the deregulation of vesicular trafficking following flotillin upregulation, and through sphingosine kinase 2, emerges as a new mechanism of AXL overexpression and EMT-inducing signaling pathway activation.


title: Dietary intervention improves health metrics and life expectancy of the genetically obese DU6 (Titan) mouse

abstract: Suitable animal models are essential for translational research, especially in the case of complex, multifactorial conditions, such as obesity. The outbred mouse line Titan (DU6) results from the worlds longest selection experiment for high body mass and was previously described as a model for metabolic healthy (benign) obesity. The present study deeper characterized the geno- and phenotypes of this outbred mouse line and tested its suitability as an interventional obesity model. In contrast to previous findings, our data suggests that Titan mice are metabolically unhealthy obese and short-lived. Line-specific patterns of genetic invariability are in accordance with observed phenotypic traits. Titan mice show modifications in the liver transcriptome, proteome and epigenome that are linked to metabolic (dys)regulations. However, dietary intervention partially reversed the metabolic phenotype in Titan mice and significantly extended their life expectancy. Therefore, the Titan mouse line is a valuable resource for translational and interventional obesity research.

category: physiology


title: Multi-scale modeling shows that dielectric differences make NaV channels faster than KV channels

abstract:
The generation of action potentials in excitable cells requires different activation kinetics of voltage gated Na (NaV) and K (KV) channels. NaV channels activate much faster and allow the initial Na+ influx that generates the depolarizing phase and propagates the signal. Recent experimental results suggest that the molecular basis for this kinetic difference is an amino acid side chain located in the gating pore of the voltage sensor domain, which is a highly conserved isoleucine in KV channels, but an equally highly conserved threonine in NaV channels. Mutagenesis suggests that the hydrophobicity of this side chain in Shaker KV channels regulates the energetic barrier that gating charges need to overcome to move through the gating pore, and ultimately the rate of channel opening. We use a multi-scale modeling approach to test this hypothesis. We use high resolution molecular dynamics to study the effect of the mutation on polarization charge within the gating pore. We then incorporate these results in a lower resolution model of voltage gating to predict the effect of the mutation on the movement of gating charges. The predictions of our hierarchical model are fully consistent with the tested hypothesis, thus suggesting that the faster activation kinetics of NaV channels comes from a stronger dielectric polarization by threonine (NaV channel) produced as the first gating charge enters the gating pore, compared to isoleucine (KV channel).

eTOC SummaryVoltage-gated Na+ channels activate faster than K+ channels in excitable cells. Catacuzzeno et al. develop a model that shows how the dielectric properties of a divergent side-chain produce this difference in speed.

category: biophysics


title: Predicting Parallelism and Quantifying Divergence in Experimental Evolution

abstract: The degree that the environment determines what genes contribute towards adaptation is a fundamental question in microbial evolution. Microbial populations are often experimentally passaged in different environments and sequenced in order to identify candidates for adaptation in a particular environment. However, there remains the need to develop an appropriate statistical framework to identify genes that acquired more mutations in one environment over the other (i.e., divergent evolution). Here we demonstrate how the evolutionary outcomes among replicate populations in the same environment, known as parallel evolution, can be leveraged to construct an intuitive statistical test for identifying the genes that contribute towards divergent evolution. To accomplish this task, we examined publicly available evolve-and-resequence experiment datasets and found that the distribution of mutation counts among genes can be predicted using an ensemble of independent Poisson random variables. Building on this result, we propose that the degree of divergent evolution at a given gene between populations from two different environments can be modeled as the difference between two Poisson random variables, known as the Skellam distribution. We then propose and apply a statistical test to identify specific genes that contribute towards divergent evolution. IMPORTANCE: There is currently no existing framework that can be leveraged to identify genes that contribute towards divergent evolution in microbial evolution experiments. To correct for this absence, we investigated the distribution of mutation counts among genes in order to identify an appropriate null model. Our observations suggest that divergent evolution within a given gene can be modeled as the difference in the total number of mutations observed between two environments. This quantity is described by a probability distribution known as the Skellam distribution, providing an appropriate statistical test for researchers seeking to identify the set of genes that contribute towards divergent evolution in evolution experiments.


title: Immune landscape of a genetically-engineered murine model of glioma relative to human glioma by single-cell sequencing

abstract:
BackgroundThis study focuses on the evaluation of intratumoral immune infiltrates of the Qk/trp53/Pten (QPP) triple-knockout mouse model of glioblastoma with the purpose of establishing its relevance compared to the human disease. This included an analysis at the single cell level, of immune cells composition in both spontaneous and implanted mouse tumors and of samples obtained from human tumor resections.

MethodsWe analyzed a cohort of fifteen spontaneous QPP mice, nine implanted QPP mice and 10 glioma patients by standard immune profiling methods such as IHC. Of those, we analyzed three spontaneous QPP mice, three implanted QPP mice, and 10 glioma patients by single cell RNA sequencing.

ResultsIn the QPP samples we identified a predominantly myeloid cell population of monocytes, macrophages, and microglia, with minor populations of T, B, and NK cells. When comparing spontaneous and implanted mouse samples, we found that there were more neutrophil, T and NKT cells in the implanted model. In human samples, most of the lymphoid and myeloid compartments were immunosuppressive. While the complexity of the myeloid cell populations is preserved between the QPP model and the human disease, we observed significantly more immune-stimulatory populations in the implanted mouse model.

ConclusionsWe found that, despite differences at the subpopulation level, the immunosuppressive nature of the immune system in glioma, is recapitulated in our mouse model. Although we observed differences in the proportions of immune infiltrates derived from the spontaneous and implanted mouse models and in LGG compared to GBM, the major constituents are present in all cases and these differences may be caused by various etiological or pathogenic influences on tumor-immune interactions.

Key PointsO_LINew GBM mouse model for immunotherapy
C_LIO_LISingle cell profiling of the immune systems in human and mouse GBM
C_LI

category: cancer biology


title: The scaffold protein IQGAP1 links heat-induced stress signals to alternative splicing regulation in gastric cancer cells

abstract: In response to oncogenic signals, Alternative Splicing (AS) regulators such as SR and hnRNP proteins show altered expression levels, subnuclear distribution and/or post-translational modification status, but the link between signals and these changes remains unknown. Here, we report that a cytosolic scaffold protein, IQGAP1, performs this task in response to heat-induced signals. We show that in gastric cancer cells, a nuclear pool of IQGAP1 acts as a tethering module for a group of spliceosome components, including hnRNPM, a splicing factor critical for the response of the spliceosome to heat-shock. IQGAP1 controls hnRNPMs sumoylation, subnuclear localization and the relevant response of the AS machinery to heat-induced stress. Genome-wide analyses reveal that IQGAP1 and hnRNPM co-regulate the AS of a cell cycle-related RNA regulon in gastric cancer cells, thus favouring the accelerated proliferation phenotype of gastric cancer cells. Overall, we reveal a missing link between stress signals and AS regulation.

category: molecular biology


title: High temperature inhibits cnidarian-dinoflagellate symbiosis establishment through nitric oxide signaling

abstract: Disclaimer StatementThe authors have withdrawn their manuscript after further experiments based on reviewer comments did not support the conclusions of the paper. Therefore, the authors do not wish this work to be cited as reference for the project. The authors thank the anonymous reviewer for a critical assessment. If you have any questions, please contact the corresponding authors.

category: microbiology


title: Hyperbolic odorant mixtures as a basis for more efficient signaling between flowering plants and bees

abstract: Animals use odors in many natural contexts, for example, for finding mates or food, or signaling danger. Most analyses of natural odors search for either the most meaningful components of a natural odor mixture, or they use linear metrics to analyze the mixture compositions. However, we have recently shown that the physical space for complex mixtures is  hyperbolic, meaning that there are certain combination of variables that have a disproportionately large impact on perception and that these variables have specific interpretation in terms of metabolic processes taking place inside the flower and fruit that produce the odors. Here we show that the statistics of odorants and odorant mixtures produced by inflorescences (Brassica rapa) are also better described with a hyperbolic rather than a linear metric, and that combinations of odorants in the hyperbolic space are better predictors of the nectar and pollen resources sought by bee pollinators than the standard Euclidian combinations. We also show that honey bee and bumble bee antennae can detect most components of the B. rapa odor space, and the strength of responses correlates with positions of odorants in the hyperbolic space. In sum, a hyperbolic representation can be used to guide investigation of how information is represented at different levels of processing in the CNS.

category: animal behavior and cognition


title: A centrifuge-based method for identifying novel genetic traits that affect root-substrate adhesion in Arabidopsis thaliana

abstract: The physical presence of roots and the compounds they release affect the cohesion between roots and their environment. However, the plant traits that are important for these interactions are unknown and most methods that quantify the contributions of these traits are time-intensive and require specialist equipment and complex substrates. Our lab developed an inexpensive, high-throughput phenotyping assay that quantifies root-substrate adhesion in Arabidopsis thaliana. We now report that this method has high sensitivity and versatility for identifying different types of traits affecting root-substrate adhesion including root hair morphology, vesicle trafficking pathways and root exudate composition. We describe a practical protocol for conducting this assay and introduce its use in a forward genetic screen to identify novel genes affecting root-substrate interactions. This assay is a powerful tool for identifying and quantifying genetic contributions to cohesion between roots and their environment.


title: Cell-extracellular matrix interactions in the fluidic phase direct the topology and polarity of self-organized epithelial structures

abstract: In vivo, cells are surrounded by extracellular matrix (ECM). To build organs from single cells, it is generally believed that ECM serves as scaffolds to coordinate cell positioning and differentiation. Nevertheless, how cells utilize cell-ECM interactions for the spatiotemporal coordination to different ECM at the tissue scale is not fully understood. Here, using in vitro assay with engineered MDCK cells expressing H2B-mCherry (nucleus) and gp135/Podocalyxin-GFP (apical marker), we show in multi-dimensions that such coordination for epithelial morphogenesis can be determined by cell-soluble ECM interaction in the fluidic phase. The coordination depends on the native topology of ECM components such as sheet-like basement membrane (BM) and type I collagen (COL) fibers: scaffold formed by BM (COL) facilitates a close-ended (open-ended) coordination that leads to the formation of lobular (tubular) epithelium. Further, cells form apicobasal polarity throughout the entire lobule/tubule without a complete coverage of ECM at the basal side, and time-lapse two-photon scanning imaging reveals the polarization occurring early and maintained through the lobular expansion. During polarization, gp135-GFP was converged to the apical surface collectively in the lobular/tubular structures, suggesting possible intercellular communications. Under suspension culture, the polarization was impaired with multi-lumen formation in the tubules, implying the importance of ECM biomechanical microenvironment. Our results suggest a biophysical mechanism for cells to form polarity and coordinate positioning at tissue scale, and in engineering epithelium through cell-soluble ECM interaction and self-assembly.


title: Disease-relevant single cell photonic signatures identify S100β stem cells and their myogenic progeny in vascular lesions

abstract: A hallmark of subclinical atherosclerosis is the accumulation of vascular smooth muscle cell (SMC)-like cells leading to intimal thickening and lesion formation. While medial SMCs contribute to vascular lesions, the involvement of resident vascular stem cells (vSCs) remains unclear. We evaluated single cell photonics as a discriminator of cell phenotype in vitro before the presence of vSC within vascular lesions was assessed ex vivo using supervised machine learning and further validated using lineage tracing analysis. Using a novel lab-on-a-Disk (Load) platform, label-free single cell photonic emissions from normal and injured vessels ex vivo were interrogated and compared to freshly isolated aortic SMCs, cultured Movas SMCs, macrophages, B-cells, S100{beta}+ mVSc, bone marrow derived mesenchymal stem cells (MSC) and their respective myogenic progeny across five broadband light wavelengths ({lambda}465 - {lambda}670 {+/-} 20 nm). We found that profiles were of sufficient coverage, specificity, and quality to clearly distinguish medial SMCs from different vascular beds (carotid vs aorta), discriminate normal carotid medial SMCs from lesional SMC-like cells ex vivo following flow restriction, and identify SMC differentiation of a series of multipotent stem cells following treatment with transforming growth factor beta 1 (TGF-{beta}1), the Notch ligand Jaggedl, and Sonic Hedgehog using multivariate analysis, in part, due to photonic emissions from enhanced collagen III and elastin expression. Supervised machine learning supported genetic lineage tracing analysis of S100{beta}+ vSCs and identified the presence of S100{beta}+ vSC-derived myogenic progeny within vascular lesions. We conclude disease-relevant photonic signatures may have predictive value for vascular disease.


title: Slowly evolving dopaminergic activity modulates the moment-to-moment probability of movement initiation.

abstract: Clues from human movement disorders have long suggested that the neurotransmitter dopamine plays a key role in motor control, but how the endogenous dopaminergic system regulates movement is unknown. Here we show dynamic dopaminergic signaling over seconds-long timescales controls movement timing in mice. Animals were trained to initiate licking after a self-timed interval following a start-timing cue. The movement time was variable from trial-to-trial, as expected from previous studies. Surprisingly, dopaminergic signals ramped-up over seconds between the start-timing cue and the self-timed movement, with variable dynamics that predicted the movement time on single trials. Steeply rising signals preceded early lick-initiation, whereas slowly rising signals preceded later initiation. Higher baseline signals also predicted earlier self-timed movements. Optogenetic activation of dopamine neurons during self-timing did not trigger immediate movements, but rather caused systematic early-shifting of movement initiation, whereas inhibition caused late-shifting, as if modulating the probability of movement. Consistent with this view, the dynamics of the endogenous dopaminergic signals quantitatively predicted the moment-by-moment probability of movement initiation on single trials. These results reveal a causal role for dynamic dopaminergic signaling unfolding over seconds in modulating the decision of when to move.


title: Fear Conditioning Potentiates the Hippocampal CA1 Commissural Pathway In vivo and Increases Awake Phase Sleep

abstract: The hippocampus is essential for spatial learning and memory. To assess learning we used contextual fear conditioning (cFC), where animals learn to associate a place with aversive events like foot-shocks. Candidate memory mechanisms for cFC are long-term potentiation and long-term depression, but there is little direct evidence of them operating in the hippocampus in vivo following cFC. Also, little is known about the behavioral state changes induced by cFC. To address these issues, we recorded local field potentials in freely behaving mice by stimulating in the left dorsal CA1 region and recording in the right dorsal CA1 region. Synaptic strength in the commissural pathway was monitored by measuring field excitatory postsynaptic potentials (fEPSPs) before and after cFC. After cFC, the commissural pathways synaptic strength was potentiated. Although recordings occurred during the wake phase of the light/dark cycle, the mice slept more in the post-conditioning period than in the pre-conditioning period. Relative to awake periods, in non-rapid eye movement (NREM) sleep the fEPSPs were larger in both pre- and post-conditioning periods. We also found a significant negative correlation between the animals speed and fEPSP size. Therefore, to avoid confounds in the fEFSP potentiation estimates, we controlled for speed-related and sleep-related fEPSP changes and still found that cFC induced long-term potentiation, but no significant long-term depression. Synaptic strength changes were not found in the control group that simply explored the fear-conditioning chamber, indicating that exploration of the novel place did not produce the measurable effects caused by cFC. These results show that following cFC, the CA1 commissural pathway is potentiated, likely contributing to the functional integration of the left and right hippocampi in fear memory consolidation. In addition, the cFC paradigm produces significant changes in an animals behavioral state, which are observable as proximal changes in sleep patterns.


title: Time-limited alterations in cortical activity of a Knock-in mice model of KCNQ2-related Developmental and Epileptic Encephalopathy

abstract: De novo missense variants in the KCNQ2 gene encoding the Kv7.2 subunit of the voltage-gated potassium Kv7/M channel are the main cause of Developmental and Epileptic Encephalopathy (DEE). KCNQ2 related-DEE is characterized by pharmaco-resistant neonatal seizures associated with a developmental delay. While seizures usually resolve some weeks or months after birth, cognitive/behavioral deficits persist. To better understand the cellular mechanisms underlying KCNQ2-associated network dysfunction and their progression over time, we investigated in vivo, using local field potential recordings of freely moving animals, and ex-vivo in layers II/III and V of motor cortical slices, using patch-clamp recordings, the electrophysiological properties of pyramidal cells from a heterozygous knock-in (KI) mouse model carrying the p.T274M pathogenic variant during neonatal, post-weaning and juvenile developmental stages. We found that KI mice displayed spontaneous seizures preferentially at post-weaning rather than at juvenile stages. At the cellular level, the variant led to a reduction in M current density/chord conductance and to an increase in neuronal excitability. These alterations were observed already during the neonatal period in pyramidal cells of layers II / III and during post-weaning stage in pyramidal cells of layer V. Moreover there was an increase in the frequency of spontaneous network driven events mediated by GABA receptors in the layers II/III suggesting that the excitability of some interneurons was also increased. However, all these alterations were time limited and no more observed in layers II/III and V of juvenile mice. At this stage, M-current density and neuronal excitability were not different from the measurements made in juvenile wild-type mice. Thus our data indicate that the action of the variant on neuronal activity is developmentally regulated and that some cellular mechanisms leading to the recovery of Kv7/M channels function took place during brain maturation of KI mice. These results raise the possibility that the age related seizure remission observed in KCNQ2-related DEE patient results also from a time limited alteration of Kv7 channels activity and neuronal excitability.


title: Using singleton densities to detect recent selection in Bos taurus

abstract:
Many quantitative traits are subject to polygenic selection, where several genomic regions undergo small, simultaneous changes in allele frequency that collectively alter a phenotype. The widespread availability of genome data, along with novel statistical techniques, has made it easier to detect these changes. We apply one such method, the  Singleton Density Score, to the Holstein breed of Bos taurus to detect recent selection (arising up to around 740 years ago). We identify several genes as candidates for targets of recent selection, including some relating to cell regulation, catabolic processes, neural-cell adhesion and immunity. We do not find strong evidence that three traits that are important to humans - milk protein content, milk fat content, and stature - have been subject to directional selection. Simulations demonstrate that since B. taurus recently experienced a population bottleneck, singletons are depleted so the power of SDS methods are reduced. These results inform on which genes underlie recent genetic change in B. taurus, while providing information on how polygenic selection can be best investigated in future studies.

Impact statementMany traits of ecological or economic importance (including height, disease propensity, climatic adaptation) are  polygenic. That is, they are affected by a large number of genetic variants, with each one only making a small contribution to a trait, but collectively influence variation. As selection acts on all of these variants simultaneously, it only changes the frequency of each one by a small amount, making it hard to detect such selection from genome data. This situation has changed in recent years, with the proliferation of whole-genome data from many individuals, along with the development of methods to detect the subtle effects of polygenic selection. Here, we use data from 102 genomes from domesticated cattle (Bos taurus) that has experienced intense artificial selection since domestication, and test whether we can detect signatures of recent selection (arising up to 740 years ago). Domesticated species are appealing for this kind of study, as they are subject to extensive genome sequencing studies, and genetic variants can be related to traits under selection. We carried out our analysis in two parts. We first performed a genome-wide scan to find individual genetic regions that show signatures of recent selection. We identify some relating to cell regulation, catabolic processes, neural-cell adhesion and immunity. In the second part, we then analysed genetic regions associated with three key traits: milk protein content, milk fat content, and stature. We tested whether these regions collectively showed a signature of selection, but did not find a significant result in either case. Simulations suggest that the domestication history of cattle affected the power of these methods. We end with a discussion on how to best detect polygenic selection in future studies.


title: A normative account of confirmation bias during reinforcement learning

abstract: Reinforcement learning involves updating estimates of the value of states and actions on the basis of experience. Previous work has shown that in humans, reinforcement learning exhibits a confirmatory bias: when updating the value of a chosen option, estimates are revised more radically following positive than negative reward prediction errors, but the converse is observed when updating the unchosen option value estimate. Here, we simulate performance on a multi-arm bandit task to examine the consequences of a confirmatory bias for reward harvesting. We report a paradoxical finding: that confirmatory biases allow the agent to maximise reward relative to an unbiased updating rule. This principle holds over a wide range of experimental settings and is most influential when decisions are corrupted by noise. We show that this occurs because on average, confirmatory biases lead to overestimating the value of more valuable bandits, and underestimating the value of less valuable bandits, rendering decisions overall more robust in the face of noise. Our results show how apparently suboptimal learning policies can in fact be reward-maximising if decisions are made with finite computational precision.


title: The immunosuppression of macrophages underlies the cardioprotective effects of catestatin (CST)

abstract: Hypertension (HTN) is associated with inflammation and excessive production of catecholamines. Hypertensive patients have reduced plasma levels of Catestatin (CST), a bioactive cleavage product of the prohormone Chromogranin A (CgA). In mouse models, HTN symptoms can be reduced by administration of CST, but the role of CST in the regulation of cardiovascular function is unknown. In this study, we generated mice with knockout (KO) of the region of the CgA gene coding for CST (CST-KO) and found that CST-KO mice are not only hypertensive as predicted, but also display left ventricular hypertrophy, have marked macrophage infiltration of the heart and adrenal gland, and have elevated levels of pro-inflammatory cytokines and catecholamines. Intraperitoneal injection with CST reversed these phenotypes, and ischemic pre-conditioning-induced cardioprotection was also abolished in CST-KO mice. Experiments with chlodronate depletion of macrophages and bone-marrow transfer showed that macrophages produce CST and that the anti-hypertensive effects of CST are mediated in part via CSTs immunosuppression of macrophages as a form of feedback inhibition. The data thus implicate CST as a key autocrine attenuator of the cardiac inflammation in HTN by reducing macrophage inflammation.


title: Exploiting KRAS-driven Ferroaddiction in Cancer Through Ferrous Iron-Activatable Drug Conjugates (FeADC)

abstract: KRAS mutations cause a quarter of cancer mortality and most are undruggable. Several inhibitors of the MAPK pathway are FDA approved but poorly tolerated at dosages required to adequately extinguish RAS/RAF/MAPK signaling. We found that oncogenic KRAS signaling induces ferrous iron (Fe2+) accumulation early in and throughout KRAS-mediated transformation. We used an FDA-approved MEK inhibitor to produce a prototypical Ferrous Iron-Activatable Drug Conjugate (FeADC) which achieved potent MAPK blockade in tumor cells while sparing normal tissues. This innovation allowed sustainable, effective treatment of tumor bearing animals, with tumor-selective drug activation producing superior systemic tolerability. Ferrous iron accumulation is an exploitable feature of KRAS transformation and FeADCs hold promise for improving treatment of KRAS-driven solid tumors.


title: Preferred Conformations in the Intrinsically Disordered Region of Human CPEB3, a Functional Amyloid Linked to Memory Consolidation

abstract:
While implicated in neurodegenerative diseases, amyloids are also essential to some physiological processes, including memory consolidation by neuronal-specific isoforms of the Cytoplasmic Polyadenylation Element Binding (CPEB) protein family. CPEB mediates memory persistence by the formation of self-sustaining amyloid assemblies through its intrinsically disordered region (IDR). Here, we characterize the atomic level conformation and ps-ns dynamics of the 426-residue IDR of human CPEB3 (hCPEB3), which has been associated with episodic memory in humans, by NMR spectroscopy. We found that the first 29 residues: M1QDDLLMDKSKTQPQPQQQQRQQQQPQP29, adopt a helical+disordered motif. Residues 86-93: P83QQPPPP93, and 166-175: P166PPPAPAPQP175 form polyproline II (PPII) helices. While the (VG)5 repeat motif is completely disordered, residues 200-250 adopt three partially populated -helices. Residues 345-355, which comprise the nuclear localization signal (NLS), form a modestly populated -helix and border a phosphoTyr which may mediate STAT5B binding. These findings allow us to suggest a model for nascent hCPEB3 structural transitions at single residue resolution, advancing that amyloid breaker residues, like proline, are a key difference between functional versus pathological amyloids. Besides revealing some aspects of the molecular basis of memory, these findings could aid the future development of treatments for post-traumatic stress disorder.

Areas: Biophysics, Structural Biology, Biochemistry & Neurosciences.

category: biochemistry


title: Synergistic neural integration is greater downstream of recurrent information flow in organotypic cortical cultures

abstract:
The directionality of network information flow dictates how networks process information. A central component of information processing in both biological and artificial neural networks is their ability to perform synergistic integration-a type of computation. We established previously that synergistic integration varies directly with the strength of feedforward information flow. However, the relationships between both recurrent and feedback information flow and synergistic integration remain unknown. To address this, we analyzed the spiking activity of hundreds of neurons in organotypic cultures of mouse cortex. We asked how empirically observed synergistic integration varied with local functional network structure that was categorized into motifs with varying recurrent and feedback information flow. We found that synergistic integration was elevated in motifs with greater recurrent information flow beyond that expected from the local feedforward information flow. Feedback information flow was interrelated with feedforward information flow and was associated with decreased synergistic integration. Our results indicate that synergistic integration is distinctly influenced by the directionality of local information flow.

Author SummaryNetworks compute information. That is, they modify inputs to generate distinct outputs. These computations are an important component of network information processing. Knowing how the routing of information in a network influences computation is therefore crucial. Here we asked how a key form of computation--synergistic integration--is related to the direction of local information flow in networks of spiking cortical neurons. Specifically, we asked how information flow between input neurons (i.e., recurrent information flow) and information flow from output neurons to input neurons (i.e., feedback information flow) was related to the amount of synergistic integration performed by output neurons. We found that greater synergistic integration occurred where there was more recurrent information flow. And, lesser synergistic integration occurred where there was more feedback information flow relative to feedforward information flow. These results show that computation, in the form of synergistic integration, is distinctly influenced by the directionality of local information flow. Such work is valuable for predicting where and how network computation occurs and for designing networks with desired computational abilities.


title: Prevalence of Major Limb Loss (MLL) in Post conflict Acholi sub-region of Northern Uganda: Cross sectional study

abstract:
BACKGROUNDThere is a widely reported preponderance of major limb loss in Northern Uganda, which is believed to have been caused in large part by prolonged civil war. Access to rehabilitation facilities is extremely limited, and there has never been a study to understand how many people have major limb loss, nor how many of them have had access to medical or rehabilitative services.

AIMThe first prevalence study of disability and major limb loss in the region, and evaluated spatial patterns of cases of MLL.

DESIGNCross-sectional survey.

SETTINGThis research was undertaken in a community setting (at subjects homes).

POPULATION7,864 randomly selected households throughout the Acholi Sub-Region of Northern Uganda.

METHODSThis study comprised two questionnaires, the first to be completed by the head of every sampled household (n=7,864), and the second by any member of the household with major limb loss (n=181). Household locations were examined for spatial autocorrelation using Morans I statistic. The {chi}2 goodness of fit statistic was used to profile those with major limb loss in comparison with the underlying population.

RESULTSWe conservatively estimate that there are c.10,117 people with major limb loss in the region who require long-term rehabilitation services (c.0.5% of the population), and c.150,512 people with disabilities other than MLL (c.8.2% of the population). People with major limb loss are spread throughout the region (as opposed to clustered in specific locations) and are disproportionately male, older and less well educated than the general population.

CONCLUSIONThis research demonstrates, for the first time, the extent of the inadequacy of long-term rehabilitation services for those with major limb-loss in the study area. We provide new insight into the reasons that people are not accessing medical and rehabilitative services, and propose a way forward through the successful demonstration of an  outreach clinic model.

CLINICAL REHABILITATION IMPACTThe discovery of the spatial pattern of those with major limb loss, alongside the demonstration of the clinical outreach model, provides a compelling argument for the need of more such services and associated policy frameworks in remote and rural regions in the Global South.

TIDIER ChecklistWe confirm that this manuscript conforms to the STROBE Checklist for Cross-Sectional Studies

category: scientific communication and education


title: Human DICER helicase domain recruits PKR and modulates its antiviral activity

abstract:
The antiviral innate immune response mainly involves type I interferon (IFN) in mammalian cells. The contribution of the RNA silencing machinery remains to be established, but several recent studies indicate that the ribonuclease DICER can generate viral siRNAs in specific conditions. It has also been proposed that type I IFN and RNA silencing could be mutually exclusive antiviral responses. In order to decipher the implication of DICER during infection of human cells with alphaviruses such as the Sindbis virus and Semliki forest virus, we determined its interactome by proteomics analysis. We show that DICER specifically interacts with several double-stranded RNA binding proteins and RNA helicases during viral infection. In particular, proteins such as DHX9, ADAR-1 and the protein kinase RNA-activated (PKR) are enriched with DICER in virus-infected cells. We demonstrate that the helicase domain of DICER is essential for this interaction and that its deletion confers antiviral properties to DICER in an RNAi-independent, PKR-dependent, manner.

Author summaryWhile RNAi has been recognized as an efficient antiviral defense system in organisms such as plants and insects, its physiological importance in mammals remains to be determined. DICER is an enzyme involved in cleaving long double-stranded RNAs and is essential for RNAi induction. Using mass spectrometry analysis, we determined its interactome in human cells and showed that RNA binding proteins such as PKR are specifically enriched upon infection with the Sindbis virus or the Semliki forest virus. We determined that the N terminal helicase domain of the DICER protein acts as a platform to recruit these factors during infection and that its deletion confers an antiviral activity to DICER.


title: The cIAP ubiquitin ligases sustain type 3 γδ T and innate lymphoid cells during aging to allow normal cutaneous and mucosal responses

abstract: Environmental and molecular cues early in life are often associated with the permanent shaping of our immune system during adulthood. Although increasing, our knowledge of the signaling pathways that operate in early life and their temporal mode of action is limited. Herein, we demonstrate that the cellular inhibitor of apoptosis proteins 1 and 2 (cIAP1/2), which are E3 ubiquitin ligases and master regulators of the nuclear factor-kappa B (NF-{kappa}B) pathway, function during late neonatal and prepubescent life to sustain interleukin(IL)-17-producing gamma delta T cells ({gamma}{delta}T17) and group 3 innate lymphoid cells (ILC3). We show that cell-intrinsic deficiency in cIAP1/2 at 3-4 weeks of life leads to downregulation of the transcription factors cMAF and ROR{gamma}t, and failure to enter cytokine-induced cell cycle. This is followed by progressive loss of {gamma}{delta}T17 cells and ILC3 while mice are aging. Mice deficient in cIAP1/2 have severely reduced {gamma}{delta}T17 cells and ILC3, present with suboptimal {gamma}{delta}T17 responses in the skin, lack small intestinal isolated lymphoid follicles and cannot control intestinal bacterial infection. Mechanistically, these effects appear to be dependent on overt activation of the non-canonical NF-{kappa}B pathway. Our data identify the cIAP E3 ubiquitin ligases as critical early life molecular switches for establishing effective type-3 immunity during aging.

category: immunology


title: RBFOX2 Is Critical For Maintaining Alternative Polyadenylation And Mitochondrial Health In Rat Myoblasts

abstract: RBFOX2, which has a well-established role in alternative splicing, is linked to heart diseases. However, it is unclear whether RBFOX2 has other roles in RNA processing that can influence gene expression/function in muscle cells, contributing to disease pathology. Here, we employed both 3-end and nanopore cDNA sequencing to reveal a previously unrecognized role for RBFOX2 in maintaining alternative polyadenylation (APA) signatures in myoblasts. We found that RBFOX2-mediated APA modulates both mRNA levels and isoform expression of a collection of genes including contractile and mitochondrial genes. We identified the key muscle-specific contractile gene, Tropomyosin 1 and essential mitochondrial gene, Slc25a4 as APA targets of RBFOX2. Unexpectedly, depletion of RBFOX2 adversely affected mitochondrial health in myoblasts that is in part mediated by disrupted APA of mitochondrial gene Slc25a4. Mechanistically, we found that RBFOX2 regulation of Slc25a4 APA is mediated through consensus RBFOX2 binding motifs near the distal polyadenylation site enforcing the use of the proximal polyadenylation site. In sum, our results unveiled a new role for RBFOX2 in fine tuning expression levels of mitochondrial and contractile genes via APA in myoblasts relevant to heart diseases.


title: Novel analysis of drug-drug interactions reveals the appearance of non-linear dose dependence under the single drug treatment

abstract: The accurate prediction of new interactions between drugs is important for avoiding unknown (mild or severe) adverse reactions to drug combinations. The development of effective in silico methods for evaluating drug interactions based on gene expression data requires an understanding of how various drugs alter gene expression. Current computational methods for the prediction of drug-drug interactions (DDIs) utilize data for known DDIs to predict unknown interactions. However, these methods are limited in the absence of known predictive DDIs. To improve DDIs interpretation, a recent study has demonstrated strong non-linear (i.e., dosedependent) effects of DDIs. In this study, we present a new unsupervised learning approach involving tensor decomposition (TD)-based unsupervised feature extraction (FE) in 3D. We utilize our approach to reanalyze available gene expression profiles for Saccharomyces cerevisiae. We found that non-linearity is possible, even for single drugs. Thus, non-linear dose-dependence cannot always be attributed to DDIs. Our analysis provides a basis for the design of effective methods for evaluating DDIs.


title: NDI: A platform-independent data interface and database for neuroscience physiology and imaging experiments

abstract: Collaboration in neuroscience is impeded by the difficulty of sharing primary data, results, and software across labs. Here we introduce Neuroscience Data Interface (NDI), a platform-independent standard that allows an analyst to use and create software that functions independently from the format of the raw data or the manner in which the data is organized into files. The interface is rooted in a simple vocabulary that describes common apparatus and storage devices used in neuroscience experiments. Results of analyses - and analyses of analyses - are stored as documents in a scalable, queryable database that stores the relationships and history among the experiment elements and documents. The interface allows the development of an application ecosystem where applications can focus on calculation rather than data format or organization. This tool can be used by individual labs to exchange and analyze data, and it can serve to curate neuroscience data for searchable archives.


title: Microtubule re-organization during female meiosis in C. elegans

abstract:
The female meiotic spindles of most animals are acentrosomal and undergo striking morphological changes while transitioning from metaphase to anaphase. The ultra-structure of acentrosomal spindles, and how changes to this structure correlate with such dramatic spindle rearrangements remains largely unknown.

To address this, we applied light microscopy, large-scale electron tomography and mathematical modeling of female meiotic C. elegans spindles undergoing the transition from metaphase to anaphase. Combining these approaches, we find that meiotic spindles are dynamic arrays of short microtubules that turn over on second time scales. The results show that the transition from metaphase to anaphase correlates with an increase in the number of microtubules and a decrease in their average length. Detailed analysis of the tomographic data revealed that the length of microtubules changes significantly during the metaphase-to-anaphase transition. This effect is most pronounced for those microtubules located within 150 nm of the chromosome surface. To understand the mechanisms that drive this transition, we developed a mathematical model for the microtubule length distribution that considers microtubule growth, catastrophe, and severing. Using Bayesian inference to compare model predictions and data, we find that microtubule turn-over is the major driver of the observed large-scale reorganizations. Our data suggest that in metaphase only a minor fraction of microtubules, those that are closest to the chromosomes, are severed. The large majority of microtubules, which are not in close contact with chromosomes, do not undergo severing. Instead, their length distribution is fully explained by growth and catastrophe alone. In anaphase, even microtubules close to the chromosomes show no signs of cutting. This suggests that the most prominent drivers of spindle rearrangements from metaphase to anaphase are changes in nucleation and catastrophe rate. In addition, we provide evidence that microtubule severing is dependent on the presence of katanin.


title: Unraveling the interaction between doxorubicin and DNA origami nanostructures for customizable chemotherapeutic drug release

abstract: Doxorubicin (DOX) is a common drug in cancer chemotherapy, and its high DNA-binding affinity can be harnessed in preparing DOX-loaded DNA nanostructures for targeted delivery and therapeutics. Although DOX has been widely studied, the existing literature of DOX-loaded DNA-carriers remains limited and incoherent. Here, based on an in-depth spectroscopic analysis, we characterize and optimize the DOX loading into different 2D and 3D scaffolded DNA origami nanostructures (DONs). In our experimental conditions, all DONs show similar DOX binding capacities (one DOX molecule per two to three base pairs), and the binding equilibrium is reached within seconds, remarkably faster than previously acknowledged. To characterize drug release profiles, DON degradation and DOX release from the complexes upon DNase I digestion was studied. For the employed DONs, the relative doses (DOX molecules released per unit time) may vary by two orders of magnitude depending on the DON superstructure. In addition, we identify DOX aggregation mechanisms and spectral changes linked to pH, magnesium, and DOX concentration. These features have been largely ignored in experimenting with DNA nanostructures, but are probably the major sources of the incoherence of the experimental results so far. Therefore, we believe this work can act as a guide to tailoring the release profiles and developing better drug delivery systems based on DNA-carriers.


title: Recombination in Sarbecovirus lineage and mutations/insertions in spike protein linked to the emergence and adaptation of SARS-CoV-2

abstract: The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan city, China in December 2019 and thereafter its spillover across the world has created a global pandemic and public health crisis. Researchers across the world are involved in finding the origin and evolution of SARS-CoV-2, its transmission route, molecular mechanism of interaction between SARS-CoV-2 and host cells, and the cause of pathogenicity etc. In this paper, we shed light on the origin, evolution and adaptation of SARS-CoV-2 into human systems. Our phylogenetic/evolutionary analysis supported that bat-CoV-RaTG13 is the closest relative of human SARS-CoV-2, outbreak of SARS-CoV-2 took place via inter-intra species mode of transmission, and host-specific adaptation occurred in SARS-CoV-2. Furthermore, genome recombination analysis found that Sarbecoviruses, the subgenus containing SARS-CoV and SARS-CoV-2, undergo frequent recombination. Multiple sequence alignment (MSA) of spike proteins revealed the insertion of four amino acid residues "PRRA" (Proline-Arginine-Arginine-Alanine) into the SARS-CoV-2 human strains. Structural modeling of spike protein of bat-CoV-RaTG13 also shows a high number of mutations at one of the receptor binding domains (RBD). Overall, this study finds that the probable origin of SARS-CoV-2 is the results of intra-species recombination events between bat coronaviruses belonging to Sarbecovirus subgenus and the insertion of amino acid residues "PRRA" and mutations in the RBD in spike protein are probably responsible for the adaptation of SARS-CoV-2 into human systems. Thus, our findings add strength to the existing knowledge on the origin and adaptation of SARS-CoV-2, and can be useful for understanding the molecular mechanisms of interaction between SARS-CoV-2 and host cells which is crucial for vaccine design and predicting future pandemics.


title: β-catenin perturbations control differentiation programs in mouse embryonic stem cells

abstract: The Wnt/{beta}-catenin pathway is involved in development, cancer and embryonic stem cell (ESC) maintenance; its dual role in stem cell self-renewal and differentiation is still controversial. Here, by applying an in vitro system enabling inducible gene expression control, we report that moderate induction of transcriptionally active exogenous {beta}- catenin in {beta}-catenin null mouse ESCs promotes epiblast-like cell (EpiLC) derivation in vitro. Instead, in wild type cells moderate chemical pre-activation of the Wnt/{beta}-catenin pathway promotes EpiLC in vitro derivation. Finally, we suggest that moderate {beta}- catenin levels in {beta}-catenin null mouse ESCs favour early stem cell commitment towards mesoderm if the exogenous protein is induced only in the  ground state of pluripotency condition, or endoderm if the induction is maintained during the differentiation. Overall, our results confirm previous findings about the role of {beta}-catenin in pluripotency and differentiation, while indicating a role for its doses in promoting specific differentiation programs.


title: Identifying Behavioral Structure from Deep Variational Embeddings of Animal Motion

abstract: AO_SCPLOWBSTRACTC_SCPLOWQuantification and detection of the hierarchical organization of behavior is a major challenge in neuroscience. Recent advances in markerless pose estimation enable the visualization of highdimensional spatiotemporal behavioral dynamics of animal motion. However, robust and reliable technical approaches are needed to uncover underlying structure in these data and to segment behavior into discrete hierarchically organized motifs. Here, we present an unsupervised probabilistic deep learning framework that identifies behavioral structure from deep variational embeddings of animal motion (VAME). By using a mouse model of beta amyloidosis as a use case, we show that VAME not only identifies discrete behavioral motifs, but also captures a hierarchical representation of the motifs usage. The approach allows for the grouping of motifs into communities and the detection of differences in community-specific motif usage of individual mouse cohorts that were undetectable by human visual observation. Thus, we present a novel and robust approach for quantification of animal motion that is applicable to a wide range of experimental setups, models and conditions without requiring supervised or a-priori human interference.


title: Phagosome resolution regenerates lysosomes and maintains the degradative capacity in phagocytes

abstract:
Phagocytes engulf unwanted particles into phagosomes that then fuse with lysosomes to degrade the enclosed particles. Ultimately, phagosomes must be recycled to help recover membrane resources that were consumed during phagocytosis and phagosome maturation, a process referred to as phagosome resolution. Little is known about phagosome resolution, which may proceed through exocytosis or membrane fission. Here, we show that bacteria-containing phagolysosomes in macrophages undergo fragmentation through vesicle budding, tubulation, and constriction. Phagosome fragmentation requires cargo degradation, the actin and microtubule cytoskeletons, and clathrin. We provide evidence that lysosome reformation occurs during phagosome resolution since the majority of phagosome-derived vesicles displayed lysosomal properties. Importantly, we show that clathrin-dependent phagosome resolution is important to maintain the degradative capacity of macrophages challenged with two waves of phagocytosis. Overall, our work suggests that phagosome resolution contributes to lysosome recovery and to maintain the degradative power of macrophages to handle multiple waves of phagocytosis.

SummaryPhagocytes engulf particles into phagolysosomes for degradation. However, the ultimate fate of phagolysosomes is undefined. Lancaster, Fountain et al. show that phagosomes fragment to reform lysosomes in a clathrin-dependent manner. This process helps maintain the degradative capacity of phagocytes for subsequent rounds of phagocytosis.


title: The plate-to-rod transition in trabecular bone loss is elusive

abstract: Changes in trabecular micro-architecture are key to our understanding of osteoporosis. Previous work focusing on structure model index (SMI) measurements have concluded that disease progression entails a shift from plates to rods in trabecular bone, but SMI is heavily biased by bone volume fraction. As an alternative to SMI, we proposed the Ellipsoid Factor (EF) as a continuous measure of local trabecular shape between plate-like and rod-like extremes. We investigated the relationship between EF distributions, SMI and bone volume fraction of the trabecular geometry in a murine model of disuse osteoporosis as well as from human vertebrae of differing bone volume fraction. We observed a moderate shift in EF median (at later disease stages in mouse tibia) and EF mode (in the vertebral samples with low bone volume fraction) towards a more rod-like geometry, but not in EF maximum and minimum. These results support the notion that the plate to rod transition does not coincide with the onset of bone loss and is considerably more moderate, when it does occur, than SMI suggests. A variety of local shapes not straightforward to categorise as rod or plate exist in all our trabecular bone samples.


title: BACPHLIP: Predicting bacteriophage lifestyle from conserved protein domains

abstract: Bacteriophages are broadly classified into two distinct lifestyles: temperate and virulent. Temperate phages are capable of a latent phase of infection within a host cell (lysogenic cycle), whereas virulent phages directly replicate and lyse host cells upon infection (lytic cycle). Accurate lifestyle identification is critical for determining the role of individual phage species within ecosystems and their effect on host evolution. Here, we present BACPHLIP, a BACterioPHage LIfestyle Predictor. BACPHLIP detects the presence of a set of conserved protein domains within an input genome and uses this data to predict lifestyle via a Random Forest classifier that was trained on a dataset of 634 phage genomes. On an independent test set of 423 phages, BACPHLIP has an accuracy of 98%, greatly exceeding that of the previously existing tools (79%). BACPHLIP is freely available on GitHub (https://github.com/adamhockenberry/bacphlip) and the code used to build and test the classifier is provided in a separate repository (https://github.com/adamhockenberry/bacphlip-model-dev) for users wishing to interrogate and re-train the underlying classification model.


title: Protozoa populations are ecosystem engineers that shape prokaryotic community structure and function of the rumen microbial ecosystem

abstract: Unicellular eukaryotes are an integral part of many microbial ecosystems communities where they are known to interact with their surrounding prokaryotic community - either as predators or as a mutualistic habitat. Within the rumen, one of the most complex host-associated microbial habitats, ciliate protozoa represent the main micro-eukaryotes, accounting for up to 50% of the microbial biomass. Nonetheless, the extent of the ecological effect of protozoa on the microbial community and on the rumen metabolic output remains largely understudied. To assess the role of protozoa on the rumen ecosystem, we established an ex-vivo system in which distinct protozoa sub-communities were introduced to native rumen prokaryotic community. We show that the different protozoa communities exert a strong and differential impact on the composition of the prokaryotic community, as well as its function including methane production. Furthermore, the presence of protozoa increases prokaryotic diversity with a differential effect on specific bacterial populations such as Gammaproteobacteria, Prevotella and Spirochetes. Our results suggest that protozoa mitigate the effect of competitive exclusion between bacterial species, thereby contributing to the maintenance of prokaryotic diversity in the rumen. Our findings put forward the rumen protozoa populations as potentially important ecosystem engineers for future microbiome modulation strategies.


title: SpacePHARER: Sensitive identification of phages from CRISPR spacers in prokaryotic hosts

abstract: SpacePHARER (CRISPR Spacer Phage-Host Pair Finder) is a sensitive and fast tool for de novo prediction of phage-host relationships via identifying phage genomes that match CRISPR spacers in genomic or metagenomic data. SpacePHARER gains sensitivity by comparing spacers and phages at the protein level, optimizing its scores for matching very short sequences, and combining evidence from multiple matches, while controlling for false positives. We demonstrate SpacePHARER by searching a comprehensive spacer list against all complete phage genomes.


title: A role for Hmga2 in the early-stage transition of neural stem-progenitor cell properties during mouse neocortical development

abstract: During the early stage of mammalian neural development, neuroepithelial cells (NECs) proliferate and increase their pool size before switching their fate to become neurogenic radial glial cells (RGCs). The timing of this expansion-to-neurogenic phase transition is strictly regulated so as to determine the proper number of progenitors and differentiated cell types that constitute the brain. The molecular mechanism underlying this switch has remained poorly understood, however. We have now performed a transcriptomic analysis of NECs and RGCs and found that the expression of Hmga2 gene, which encodes a chromatin-associated protein, peaks at the expansion-to-neurogenic phase transition. By the use of our newly established method to manipulate NECs before neural tube closure, we found that knockdown of Hmga2 in NECs delayed the change in their transcriptomic profile and suppressed the onset of neurogenesis in the neocortex. Our study thus uncovers a key molecular player in the generation of neurogenic progenitors in the developing mouse neocortex.

category: developmental biology


title: Interplay of folded domains and the disordered low-complexity domain in mediating hnRNPA1 phase separation

abstract:
Liquid-liquid phase separation underlies the membrane-less compartmentalization of cells. Intrinsically disordered low-complexity domains (LCDs) often mediate phase separation, but how their phase behavior is modulated by folded domains is incompletely understood. Here, we interrogate the interplay between folded and disordered domains of the RNA-binding protein hnRNPA1. The LCD of hnRNPA1 is sufficient for mediating phase separation in vitro. However, we show that the folded RRM domains and a folded solubility-tag modify the phase behavior, even in the absence of RNA. Notably, the presence of the folded domains reverses the salt dependence of the driving force for phase separation relative to the LCD alone. Small-angle X-ray scattering experiments and coarse-grained MD simulations show that the LCD interacts transiently with the RRMs and/or the solubility-tag in a salt-sensitive manner, providing a mechanistic explanation for the observed salt-dependent phase separation. These data point to two effects from the folded domains: (1) electrostatically mediated interactions that compact hnRNPA1 and contribute to phase separation, and (2) increased solubility at higher ionic strengths mediated by the folded domains. The interplay between disordered and folded domains can modify the dependence of phase behavior on solution conditions and can obscure signatures of physicochemical interactions underlying phase separation.

Graphical abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=192 SRC="FIGDIR/small/096966v2_ufig1.gif" ALT="Figure 1">
View larger version (34K):
org.highwire.dtl.DTLVardef@119029borg.highwire.dtl.DTLVardef@fa274borg.highwire.dtl.DTLVardef@129deaaorg.highwire.dtl.DTLVardef@1d98f66_HPS_FORMAT_FIGEXP  M_FIG hnRNPA1 phase separation is highly salt sensitive.

Phase separation of the low-complexity domain (LCD) of hnRNPA1 increases with NaCl. In contrast, phase separation of full-length hnRNPA1 is saltsensitive. At low NaCl concentrations, electrostatic RRM-LCD interactions occur and can contribute positively to phase separation, but they are screened at high NaCl concentrations. The folded domains solubilize hnRNPA1 under these conditions and prevent phase separation.

C_FIG


title: Viral manipulation of a mechanoresponsive signalling axis disassembles processing bodies

abstract:
Processing bodies (PBs) are ribonucleoprotein granules that suppress cytokine mRNA translation that are targeted for disassembly by many viruses. Kaposis sarcoma-associated herpesvirus is the etiological agent of the inflammatory endothelial cancer, Kaposis sarcoma, and a PB-regulating virus. The virus encodes Kaposin B (KapB), which induces actin stress fibres (SFs) and cell spindling as well as PB disassembly. We now show that KapB-mediated PB disassembly requires actin rearrangements, RhoA effectors and the mechanoresponsive transcription activator, YAP. Moreover, ectopic expression of active YAP or exposure of ECs to mechanical forces caused PB disassembly in the absence of KapB and mechanoresponsive PB disassembly also required YAP. Using the viral protein KapB, we identified a new consequence of the exposure of cells to mechanical forces that alter actin dynamics and activate YAP, namely the disassembly of PBs.

ImportanceFor the first time, we demonstrate that processing bodies (PBs), cytoplasmic sites of RNA decay, are regulated by mechanical signaling events that alter actin dynamics and that this requires the mechanoresponsive transcription factor, YAP. Using the overexpression of a viral protein called KapB, known previously to mediate PB disassembly, we show that actin stress fibers (SFs) and the mechanoresponsive transcription factor, YAP, are required for PB loss. We also show that other established mechanical signals (shear stress or stiff extracellular matrix) that lead to the formation of SFs and activate YAP also cause PB disassembly. This is important because it means that KapB activates, from the inside out, a pathway that links cell shape to post-transcriptional gene regulation via cytoplasmic PBs.


title: Viral manipulation of mechanoresponsive signaling disassembles processing bodies


title: Impaired spatial learning and suppression of sharp wave ripples by cholinergic activation at the goal location

abstract: The hippocampus plays a central role in long-term memory formation, and different hippocampal network states are thought to have different functions in this process. These network states are controlled by neuromodulatory inputs, including the cholinergic input from the medial septum. Here, we used optogenetic stimulation of septal cholinergic neurons to understand how cholinergic activity affects different stages of spatial memory formation in a reward-based navigation task in mice. We found that optogenetic stimulation of septal cholinergic neurons (1) impaired memory formation when activated at goal location but not during navigation; (2) reduced sharp wave-ripple (SWR) incidence at goal location; and (3) reduced SWR incidence and enhanced the-ta-gamma oscillations during sleep. These results underscore the importance of appropriate timing of cholinergic input in long-term memory formation, which might help explain the limited success of cholinesterase inhibitor drugs in treating memory impairment in Alzheimers disease.


title: The effect of vascular health factors on white matter microstructure mediates age-related differences in executive function performance

abstract: Even within healthy aging, vascular risk factors can detrimentally influence cognition, with executive functions (EF) particularly vulnerable. Fronto-parietal white matter (WM) connectivity in part, supports EF and may be particularly sensitive to vascular risk. Here, we utilized structural equation modeling in 184 healthy adults (aged 20-94 years of age) to test the hypotheses that: 1) fronto-parietal WM microstructure mediates age effects on EF; 2) higher blood pressure (BP) and white matter hyperintensity (WMH) burden influences this association. All participants underwent comprehensive cognitive and neuropsychological testing including tests of processing speed, executive function (with a focus on tasks that require switching and inhibition) and completed an MRI scanning session that included FLAIR imaging for semi-automated quantification of white matter hyperintensity burden and diffusion-weighted imaging for tractography. Structural equation models were specified with age (as a continuous variable) and blood pressure predicting within-tract WMH burden and fractional anisotropy predicting executive function and processing speed. Results indicated that fronto-parietal white matter of the genu of the corpus collosum, superior longitudinal fasciculus, and the inferior frontal occipital fasciculus (but not cortico-spinal tract) mediated the association between age and EF. Additionally, increased systolic blood pressure and white matter hyperintensity burden within these white matter tracts contribute to worsening white matter health and are important factors underlying age-brain-behavior associations. These findings suggest that aging brings about increases in both BP and WMH burden, which may be involved in the degradation of white matter connectivity and in turn, negatively impact executive functions as we age.


title: StrVCTVRE: A supervised learning method to predict the pathogenicity of human genome structural variants

abstract:
BackgroundWhole genome sequencing resolves many clinical cases where standard diagnostic methods have failed. However, at least half of these cases remain unresolved after whole genome sequencing. Structural variants (SVs; genomic variants larger than 50 base pairs) of uncertain significance are the genetic cause of a portion of these unresolved cases. As sequencing methods using long or linked reads become more accessible and structural variant detection algorithms improve, clinicians and researchers are gaining access to thousands of reliable SVs of unknown disease relevance. Methods to predict the pathogenicity of these SVs are required to realize the full diagnostic potential of long-read sequencing.

ResultsTo address this emerging need, we developed StrVCTVRE to distinguish pathogenic SVs from benign SVs that overlap exons. In a random forest classifier, we integrated features that capture gene importance, coding region, conservation, expression, and exon structure. We found that features such as expression and conservation are important but are absent from SV classification guidelines. We leveraged multiple resources to construct a size-matched training set of rare, putatively benign and pathogenic SVs. StrVCTVRE performs accurately across a wide SV size range on independent test sets, which will allow clinicians and researchers to eliminate about half of SVs from consideration while retaining a 90% sensitivity.

ConclusionsWe anticipate clinicians and researchers will use StrVCTVRE to prioritize SVs in patients where no SV is immediately compelling, empowering deeper investigation into novel SVs to resolve cases and understand new mechanisms of disease. StrVCTVRE runs rapidly and is available at https://compbio.berkeley.edu/proj/strvctvre/.

category: genomics


title: CSI-Microbes: Identifying cell-type specific intracellular microbes from single-cell RNA-seq data

abstract: Despite recent reports of microbes living within tumor cells, the identification of intracellular microbes remains an open and important challenge. Here we introduce CSI-Microbes (computational identification of Cell type Specific Intracellular Microbes), a computational approach for the discovery of cell-type specific intracellular microbial taxa from single-cell RNA sequencing of host cells. It is first validated on two gold-standard datasets of human immune cells exposed to Salmonella. Next, CSI-Microbes is tested on Merkel cell and colorectal carcinoma where it identifies both reported and previously unknown tumor-specific intracellular microbes. Finally, CSI-Microbes is applied to analyze the intracellular microbiome of thirteen lung tumors where it identifies four tumors with bacterial taxa enriched in tumor cells and two tumors with bacterial taxa enriched in stroma or immune cells. Notably, the infected tumor cells down-regulate pathways associated with anti-microbial response and antigen processing and presentation, testifying to the functional significance of bacterial presence.


title: Selective B cell depletion upon intravenous infusion of replication-incompetent anti-CD19 CAR lentivirus

abstract: Anti-CD19 CAR-T therapy for B cell malignancies has shown clinical success, but a major limitation is the logistical complexity and high cost of manufacturing autologous cell products. If engineered for improved safety, direct infusion of viral gene transfer vectors to initiate in vivo CAR-T transduction, expansion and anti-tumor activity could provide an alternative, universal approach. To explore this approach we administered approximately 20 million replication-incompetent VSV-G lentiviral particles carrying an anti-CD19CAR-2A-GFP transgene comprising either an FMC63 (human) or 1D3 (murine) anti-CD19 binding domain, or a GFP-only control transgene, to wild-type C57BL/6 mice by tail vein infusion. The dynamics of immune cell subsets isolated from peripheral blood were monitored at weekly intervals. We saw emergence of a persistent CAR-transduced CD3+ T cell population beginning week 3-4 that reached a maximum of 13.5 +/-0.58% (mean +/-SD) and 7.8 +/-0.76% of the peripheral blood CD3+ T cell population in mice infused with ID3-CAR or FMC63-CAR lentivector, respectively, followed by a rapid decline in each case of the B cell content of peripheral blood. Complete B cell aplasia was apparent by week 5 and was sustained until the end of the protocol (week 8). No significant CAR positive populations were observed within other immune cell subsets or other tissues. These results indicate that direct IV infusion of conventional VSV-G pseudotyped lentiviral particles carrying a CD19 CAR transgene can transduce T cells that then fully ablate endogenous B cells in wild type mice.


title: Regulation by the pitcher plant Sarracenia purpurea of the structure of its inquiline food web

abstract: AO_SCPLOWBSTRACTC_SCPLOWPhytotelmata, the water-filled habitats in pitcher plants, bromeliad tanks, and tree-holes, host multitrophic food webs that are model experimental systems for studying food-web structure and dynamics. However, the plant usually is considered simply as an inert container, not as an interacting part of the food web. We used a manipulative field experiment with a response-surface design to determine effects of nutrient enrichment (multiple levels of NH4NO3, PO4, and captured prey), top predator (removed or present), and the plant itself (with or without plastic tubes inserted into the pitchers to isolate the food web from the plant) on the macrobial food web within the modified leaves ("pitchers") of the carnivorous pitcher plant Sarracenia purpurea. Connection to the plant, addition of NH4NO3 and removal of the top predator significantly increased the food webs saturation, defined as its trophic depth and number of interactions. No effects on food-web saturation resulted from addition of PO4 or supplemental prey. Plants such as S. purpurea that create phytotelmata are more than inert containers and their inhabitants are more than commensal inquilines. Rather, both the plant and the inquilines are partners in a complex network of interactions.

category: ecology


title: BioViz Connect: Web application linking CyVerse science gateway resources to genomic visualization in the Integrated Genome Browser

abstract: Genomics researchers do better work when they can interactively explore and visualize data. However, due to the vast size of experimental datasets, researchers are increasingly using powerful, cloud-based systems to process and analyze data. These remote systems, called science gateways, offer user-friendly, Web-based access to high performance computing and storage resources, but typically lack interactive visualization capability. In this paper, we present BioViz Connect, a middleware Web application that links the CyVerse science gateway to the Integrated Genome Browser (IGB), a highly interactive native application implemented in Java that runs on the users personal computer. Using BioViz Connect, users can (i) stream data from the CyVerse data store into IGB for visualization, (ii) improve the IGB user experience for themselves and others by adding IGB specific metadata to CyVerse data files, including genome version and track appearance, and (iii) run compute-intensive visual analytics functions on CyVerse infrastructure to create new datasets for visualization in IGB or other applications. To demonstrate how BioViz Connect facilitates interactive data visualization, we describe an example RNA-Seq data analysis investigating how heat and desiccation stresses affect gene expression in the model plant Arabidopsis thaliana. Lastly, we discuss limitations of the technologies used and suggest opportunities for future work. BioViz Connect is available from https://bioviz.org.


title: The legacy of C4 evolution in the hydraulics of C3 and C4 grasses

abstract: The anatomical reorganization required for optimal C4 photosynthesis should also impact plant hydraulics. Most C4 plants possess large bundle-sheath cells and high vein density, which should also lead to higher leaf hydraulic conductance (Kleaf) and capacitance. Paradoxically, the C4 pathway reduces water demand and increases water-use-efficiency, creating a potential mis-match between supply capacity and demand in C4 plant water relations. We use phylogenetic analyses, physiological measurements, and models to examine the reorganization of hydraulics in closely-related C4 and C3 grasses. Evolutionarily young C4 lineages have higher Kleaf, capacitance, turgor-loss-point, and lower stomatal conductance than their C3 relatives. In contrast, species from older C4 lineages show decreased Kleaf and capacitance, indicating that over time, C4 plants have evolved to optimize hydraulic investments while maintaining C4 anatomical requirements. The initial "over-plumbing" of C4 plants disrupts the positive correlation between maximal assimilation rate and Kleaf, decoupling a key relationship between hydraulics and photosynthesis generally observed in vascular plants.


title: Optimal coordination and reorganization of photosynthetic properties in C4 grasses

abstract: C3 and C4 are major functional types in terrestrial biosphere models, with photosynthesis traits as important input parameters. The evolution of C4 required reorganizations of Calvin-Benson-cycle and coordination of C4-cycle enzymes, resulting in divergences of physiological traits between C3 and C4. In addition, photosynthesis further optimized after the evolution of C4 causing diversification within C4 lineages due to different evolutionary histories. We combined optimality modeling, physiological measurements and phylogenetic analysis to examine how various aspects of C4 photosynthetic machinery were reorganized and coordinated within C4 lineages and as compared to closely-related C3 in grasses. Optimality models and measurements indicated a higher maximal electron transport to maximal Rubisco carboxylation ratio (Jmax/Vcmax) in C4 than C3, consistent with the optimal prediction to maximize photosynthesis. The coordination between Calvin-Benson and C4 cycles (Vpmax/Vcmax), however, is in line with the optimal modeling results under 200 ppm, as opposed to current CO2. Such inconsistencies can be explained by a slowly declining assimilation rate beyond optimal Vpmax/Vcmax. Although rapid coordination occurred early in C4 evolution, C4 is still under optimizing processes and photosynthetic measures have continued to increase across time. Lastly, better understandings of Jmax/Vcmax, Vpmax/Vcmax and fluorescence-based-electron-transport proffer enhanced approaches to parameterize terrestrial biosphere models.


title: Cross-attractor repertoire provides new perspective on structure-function relationship in the brain

abstract: The brain is a complex system exhibiting ever-evolving activity patterns without any external inputs or tasks. Such intrinsic dynamics (or lack thereof) are thought to play crucial roles in typical as well as atypical cognitive functioning. Linking the ever-changing intrinsic dynamics to the rather static anatomy is a challenging endeavor. Dynamical systems models are important tools for understanding how structure and function are linked in the brain. Here, we provide a novel modeling framework to examine such structure-function relations. Our deterministic approach complements previous modeling frameworks, which typically focus on noise-driven (or stochastic) dynamics near a single attractor. We examine the overall organizations of and coordination between all putative attractors. Using our approach, we first provide evidence that examining cross-attractor coordination between brain regions could better predict human functional connectivity than examining noise-driven near-attractor dynamics. Further, we observed that structural connections across scales modulate the energy costs of such cross-attractor coordination. Overall, our work provides a systematic framework for characterizing intrinsic brain dynamics as a web of cross-attractor transitions and associated energy costs. The framework may be used to predict transitions and energy costs associated with experimental or clinical interventions.


title: Dopamine influences attentional rate modulation in Macaque posterior parietal cortex

abstract: Cognitive neuroscience has made great strides in understanding the neural substrates of attention, but our understanding of its neuropharmacology remains incomplete. Although dopamine has historically been studied in relation to frontal functioning, emerging evidence suggests important dopaminergic influences in parietal cortex. We recorded single- and multi-unit activity whilst iontophoretically administering dopaminergic agonists and antagonists while rhesus macaques performed a spatial attention task. Out of 88 units, 50 revealed activity modulation by drug administration. Dopamine inhibited firing rates according to an inverted-U shaped dose-response curve and increased gain variability. Dopamine modulated attention-related rate changes and Fano Factors in broad and narrow-spiking units, respectively. D1 receptor antagonists diminished firing rates according to a monotonic function and interacted with attention modulating gain variability in broad-spiking units. Finally, both drugs decreased the pupil light reflex. These data show that dopamine shapes neuronal responses and modulates attentional processing in parietal cortex.


title: Topography of Hippocampal Connectivity with Sensorimotor Cortex Revealed by Optimizing Smoothing Kernel and Voxel Size

abstract: Studies of the hippocampus use smaller voxel sizes and smoothing kernels than cortical activation studies, typically using a multivoxel seed with specified radius for connectivity analysis. This study identified optimal processing parameters for evaluating hippocampal connectivity with sensorimotor cortex (SMC), comparing effectiveness by varying parameters during both activation and connectivity analysis. Using both 3mm and 4mm isovoxels, smoothing kernels of 6-10mm were evaluated on the amplitude and extent of motor activation and hippocampal connectivity with SMC. Psychophysiological interactions identified hippocampal connectivity with SMC during volitional movements, and connectivity effects from multivoxel seeds were compared with alternate methods; a structural seed represented the mean connectivity map from all voxels within a region, whereas a functional seed represented the regional voxel with maximal SMC connectivity. With few exceptions, the same parameters were optimal for activation and connectivity. Larger isovoxels showed larger activation volumes in both SMC and the hippocampus; connectivity volumes from structural seeds were also larger, except from the posterior hippocampus. Regardless of voxel size, the 10mm smoothing kernel generated larger activation and connectivity volumes from structural seeds, as well as larger beta estimates at connectivity maxima; structural seeds also produced larger connectivity volumes than multivoxel seeds. Functional seeds showed lesser effects from voxel size and smoothing kernels. Optimal parameters revealed topography in structural seed connectivity along both the longitudinal axis and mediolateral axis of the hippocampus. These results indicate larger voxels and smoothing kernels improve sensitivity for detecting both cortical activation and hippocampal connectivity.


title: Spatially resolved gene regulatory and disease vulnerability map of the adult Macaque cortex

abstract: Single cell approaches have increased our knowledge about the cell type composition of the non-human primate (NHP), but a detailed characterization of area-specific regulatory features remains outstanding. We generated single-cell chromatin accessibility (single-cell ATAC) and transcriptomic data of 358,237 cells from prefrontal cortex (PFC), primary motor cortex (M1) and primary visual cortex (V1) of adult cynomolgus monkey brain, and integrated this dataset with Stereo-seq (Spatio-Temporal Enhanced REsolution Omics-sequencing) of the corresponding cortical areas to assign topographic information to molecular states. We identified area-specific chromatin accessible sites and their targeted genes, including the cell type-specific transcriptional regulatory network associated with excitatory neurons heterogeneity. We reveal calcium ion transport and axon guidance genes related to specialized functions of PFC and M1, identified the similarities and differences between adult macaque and human oligodendrocyte trajectories, and mapped the genetic variants and gene perturbations of human diseases to NHP cortical cells. This resource establishes a transcriptomic and chromatin accessibility combinatory regulatory landscape at a single-cell and spatially resolved resolution in NHP cortex.


title: SYNAPTIC RELEASE POTENTIATION AT AGING AUDITORY RIBBON SYNAPSES

abstract: Age-related hidden hearing loss is often described as a cochlear synaptopathy that results from a progressive degeneration of the inner hair cell (IHC) ribbon synapses. The functional changes occurring at these synapses during aging are not fully understood. Here, we characterized this aging process in IHCs of C57BL/6J mice, a strain which is known to carry a cadherin23 mutation and experiences early hearing loss with age. These mice, while displaying a large increase in auditory brainstem thresholds due to 50 % loss of IHC synaptic ribbons at middle age (postnatal day 365), paradoxically showed enhanced acoustic startle reflex suggesting a hyperacusis-like response. The auditory defect was associated with a large shrinkage of the IHCs cell body and a drastic enlargement of their remaining presynaptic ribbons which were facing enlarged postsynaptic AMPAR clusters. Presynaptic Ca2+ microdomains and the capacity of IHCs to sustain high rates of exocytosis were largely increased, while on the contrary the expression of the fast repolarizing BK channels, known to negatively control transmitter release, was decreased. This age-related synaptic plasticity in IHCs suggested a functional potentiation of synaptic transmission at the surviving synapses, a process that could partially compensate the decrease in synapse number and underlie hyperacusis.