title: Size matters: an analytical study on the role of tissue size in spatiotemporal distribution of morphogens unveils a transition between different reaction-diffusion regimes

abstract: The reaction-diffusion model constitutes one of the most influential mathematical models to study distribution of morphogens in tissues. Despite its widespread use, the effect of finite tissue size on model-predicted spatiotemporal morphogen distributions has not been completely elucidated. In this study, we analytically investigated the spatiotemporal distributions of morphogens predicted by a reaction-diffusion model in a finite 1D domain, as a proxy for a biological tissue, and compared it with the solution of the infinite-domain model. We explored the reduced parameter, the tissue length in units of a characteristic reaction-diffusion length, and identified two reaction-diffusion regimes separated by a crossover tissue size estimated in [~]3.3 characteristic reaction-diffusion lengths. While above this crossover the infinite-domain model constitutes a good approximation, it breaks below this crossover, whereas the finite-domain model faithfully describes the entire parameter space. We evaluated whether the infinite-domain model renders accurate estimations of diffusion coefficients when fitted to finite spatial profiles, a procedure typically followed in Fluorescence Recovery After Photobleaching (FRAP) experiments. We found that the infinite-domain model overestimates diffusion coefficients when the domain is smaller than the crossover tissue size. Thus, the crossover tissue size may be instrumental in selecting the suitable reaction-diffusion model to study tissue morphogenesis.


title: Extended Graphical Lasso for Multiple Interaction Networks for High Dimensional Computational Data

abstract:
There has been a spate of interest in association networks in biological and medical research, for example, genetic interaction networks. In this paper, we propose a novel method, the extended joint hub graphical lasso (EDOHA), to estimate multiple related interaction networks for high dimensional omics data across multiple distinct classes. To be specific, we construct a convex penalized log likelihood optimization problem and solve it with an alternating direction method of multipliers (ADMM) algorithm. The proposed method can also be adapted to estimate interaction networks for high dimensional compositional data such as microbial interaction networks. The performance of the proposed method in the simulated studies shows that EDOHA has remarkable advantages in recognizing class-specific hubs than the existing comparable methods. We also present three applications of real datasets. Biological interpretations of our results confirm those of previous studies and offer a more comprehensive understanding of the underlying mechanism in disease.

Author summaryReconstruction of multiple association networks from high dimensional omics data is an important topic, especially in biology. Previous studies focused on estimating different networks and detecting common hubs among all classes. Integration of information over different classes of data while allowing difference in the hub nodes is also biologically plausible. Therefore, we propose a method, EDOHA, to jointly construct multiple interaction networks with capacity in finding different hub networks for each class of data. Simulation studies show the better performance over conventional methods. The method has been demonstrated in three real world data.

category: systems biology


title: Extended Graphical Lasso for Multiple Interaction Networks for High Dimensional Omics Data


title: A mixture of generative models strategy helps humans generalize across tasks

abstract: What role do generative models play in generalization of learning in humans? Our novel multi-task prediction paradigm--where participants complete four sequence learning tasks, each being a different instance of a common generative family--allows the separate study of within-task learning (i.e., finding the solution to each of the tasks), and across-task learning (i.e., learning a task differently because of past experiences). The very first responses participants make in each task are not yet affected by within-task learning and thus reflect their priors. Our results show that these priors change across successive tasks, increasingly resembling the underlying generative family. We conceptualize multi-task learning as arising from a mixture-of-generative-models learning strategy, whereby participants simultaneously entertain multiple candidate models which compete against each other to explain the experienced sequences. This framework predicts specific error patterns, as well as a gating mechanism for learning, both of which are observed in the data.

category: neuroscience


title: Complement Decay-Accelerating Factor is a modulator of influenza A virus lung immunopathology

abstract:
Clearance of viral infections, such as SARS-CoV-2 and influenza A virus (IAV), must be fine-tuned to eliminate the pathogen without causing immunopathology. As such, an aggressive initial innate immune response favors the host in contrast to a detrimental prolonged inflammation. The complement pathway bridges innate and adaptive immune system and contributes to the response by directly clearing pathogens or infected cells, as well as recruiting proinflammatory immune cells and regulating inflammation. However, the impact of modulating complement activation in viral infections is still unclear. In this work, we targeted the complement decay-accelerating factor (DAF/CD55), a surface protein that protects cells from non-specific complement attack, and analyzed its role in IAV infections. We found that DAF modulates IAV infection in vivo, via an interplay with the antigenic viral proteins hemagglutinin (HA) and neuraminidase (NA), in a strain specific manner. Our results reveal that, contrary to what could be expected, DAF potentiates complement activation, increasing the recruitment of neutrophils, monocytes and T cells. We also show that viral NA acts on the heavily sialylated DAF and propose that it exacerbates complement activation, leading to lung immunopathology. Remarkably, this mechanism has no impact on viral loads but rather on the host resilience to infection and may have direct implications in zoonotic influenza transmissions.

Author summaryExacerbated complement activation and immune deregulation are at the basis of several pathologies induced by respiratory viruses. Here, we report that complement decay-accelerating factor (DAF), which inhibits complement activation in healthy cells, increases disease severity upon Influenza A virus (IAV) infection. Remarkably, DAF interaction with IAV proteins, hemagglutinin (HA) and neuraminidase (NA), resulted in excessive complement activation and recruitment of innate and adaptive immune cells, without affecting viral loads. Furthermore, we observed that viral NA directly cleaves DAF and promotes complement activation, providing a possible link between IAV-DAF interaction and pathology. Therefore, our results unveil a novel pathway that could modulate disease severity, which may help to understand the increased pathogenicity of zoonotic and pandemic IAV infections.

category: microbiology


title: The global redox-responsive transcriptional regulator Rex represses fermentative metabolism and is required for Listeria monocytogenes pathogenesis

abstract:
The Gram-positive bacterium Listeria monocytogenes is the causative agent of the foodborne disease listeriosis, one of the deadliest bacterial infections known. In order to cause disease, L. monocytogenes must properly coordinate its metabolic and virulence programs in response to rapidly changing environments within the host. However, the mechanisms by which L. monocytogenes senses and adapts to the many stressors encountered as it transits through the gastrointestinal (GI) tract and disseminates to peripheral organs are not well understood. In this study, we investigated the role of the redox-responsive transcriptional regulator Rex in L. monocytogenes growth and pathogenesis. Rex is a conserved canonical transcriptional repressor that monitors the intracellular redox state of the cell by sensing the ratio of reduced and oxidized nicotinamide adenine dinucleotides (NADH and NAD+, respectively). Here, we demonstrated that L. monocytogenes Rex represses fermentative metabolism and is therefore required for optimal growth in the presence of oxygen. We also show that Rex represses the production of virulence factors required for survival and invasion of the GI tract, as a strain lacking rex was more resistant to acidified bile and invaded host cells better than wt. Consistent with these results, Rex was dispensable for colonizing the GI tract and disseminating to peripheral organs in an oral listeriosis model of infection. However, Rex-dependent regulation was required for colonizing the spleen and liver, and L. monocytogenes lacking the Rex repressor were nearly sterilized from the gallbladder. Taken together, these results demonstrated that Rex functions as a repressor of fermentative metabolism and suggests a role for Rex-dependent regulation in L. monocytogenes pathogenesis. Importantly, the gallbladder is the bacterial reservoir during listeriosis, and our data suggest redox sensing and Rex-dependent regulation are necessary for bacterial survival and replication in this organ.

AUTHOR SUMMARYListeriosis is a foodborne illness caused by Listeria monocytogenes and is one of the deadliest bacterial infections known, with a mortality rate of up to 30%. Following ingestion of contaminated food, L. monocytogenes disseminates from the gastrointestinal (GI) tract to peripheral organs, including the spleen, liver, and gallbladder. In this work, we investigated the role of the global redox-responsive regulator Rex in L. monocytogenes growth and pathogenesis. We demonstrated that Rex derepression coordinates expression of genes necessary in the GI tract during infection, including fermentative metabolism, bile resistance, and invasion of host cells. Accordingly, Rex was dispensable for colonizing the GI tract of mice during an oral listeriosis infection. Interestingly, Rex-dependent regulation was required for bacterial replication in the spleen, liver, and gallbladder. Taken together, our results demonstrate that Rex-mediated redox sensing and transcriptional regulation are important for L. monocytogenes metabolic adaptation and virulence.


title: Screening of the antimicrobial activity of marine sponge extracts from Martinique.

abstract: Marine sponges are known for their antimicrobial, antifungal, and cytotoxic activity. In this study, the activity of aqueous and ethanoic extracts of 3 sponges from Martinique were tested on 5 bacterial strains: Bascillus cereus (CIP 783), Echerichia coli (CIP 54127), Pseudomonas aeruginosa (CIP A22), Staphylococcus aureus (CIP 67.8) and Staphylococcus saprophyticus (CIP 76125). The antimicrobial activity of Agelas clathrodes, Desmapsamma anchorata, and Verongula rigida, was demonstrated using the disc diffusion method and by determining the minimum inhibitory concentration and the minimum bactericidal concentration. The ethanoic extract of Agelas clathrodes had an inhibitory activity specifically on Staphylococcus aureus and Staphylococcus saprophyticus. No activity was observed for the other extracts. Further chemical analyses will be carried out in order to identify the active molecules of these sponges.


title: VAMPIRE: A model blood cell trait focused annotation tool for interpretation and prioritization of complex trait genome-wide association study results

abstract: Genome-wide association studies (GWAS) have identified hundreds of thousands of genetic variants associated with complex diseases and traits. However, most variants are noncoding and not clearly linked to genes, making it challenging to interpret these GWAS signals. We present a systematic variant-to-function study, prioritizing the most likely functional elements of the genome for experimental follow-up, for >148,000 variants identified for hematological traits. Specifically, we developed VAMPIRE: Variant Annotation Method Pointing to Interesting Regulatory Effects, an interactive web application implemented in R Shiny (http://shiny.bios.unc.edu/vampire/). This tool efficiently integrates and displays information from multiple complementary sources, including epigenomic signatures from blood cell relevant tissues or cells, functional and conservation summary scores, variant impact on protein and gene expression, chromatin conformation information, as well as publicly available GWAS and phenome-wide association study (PheWAS) results. Leveraging data generated from independently performed functional validation experiments, we demonstrate that our prioritized variants, genes, or variant-gene links are significantly more likely to be experimentally validated. This study not only has important implications for systematic and efficient revelation of functional mechanisms underlying GWAS variants for hematological traits, but also provides a prototype that can be adapted to many other complex traits, paving the path for efficient variant to function (V2F) analyses.

category: genetics


title: From GWAS Variant to Function: a Study of ~148,000 Variants for Blood Cell Traits.


title: Exceptional origin activation revealed by comparative analysis in two laboratory yeast strains

abstract:
We performed a comparative analysis of replication origin activation by genome-wide single-stranded DNA mapping in two common laboratory strains of Saccharomyces cerevisiae challenged by hydroxyurea (HU), an inhibitor of the ribonucleotide reductase. By doing so we gained understanding of the impact on origin activation by three factors: replication checkpoint control, DNA sequence polymorphisms, and relative positioning of origin and transcription unit. Our analysis recapitulated the previous finding that the majority of origins are subject to checkpoint control by the Rad53 kinase when cells were treated with HU. In addition, origins either subject to Rad53 checkpoint control or impervious to it are largely concordant between the two strains. However, these two strains also produced different dynamics of origin activation. First, the W303-RAD53 cells showed a significant reduction of fork progression than A364a-RAD53 cells. This phenotype was accompanied by an elevated level of Rad53 phosphorylation in W303-RAD53 cells. Second, W303-rad53K227A checkpoint-deficient cells activated a greater number of origins accompanied by global reduction of ssDNA across all origins compared to A364a-rad53K227A cells; and this is correlated with lower expression level of the mutant protein in W303 than in A364a. We also show that sequence polymorphism in the consensus motifs of the replication origins plays a minor role in determining origin usage. Remarkably, eight strain-specific origins lack the canonical 11-bp consensus motif for autonomously replicating sequences in either strain background. Finally, we identified a new class of origins that are only active in checkpoint-proficient cells, which we named "Rad53-dependent origins". The only discernible feature of these origins is that they tend to overlap with an open reading frame, suggesting previously unexplored connection between transcription and origin activation. Our study presents a comprehensive list of origin usage in two diverse yeast genetic backgrounds, fine-tunes the different categories of origins with respect to checkpoint control, and provokes further exploration of the interplay between origin activation and transcription.

Author SummaryComparative analysis of origins of replication in two laboratory yeast strains reveals new insights into origin activation, regulation and dependency on the Rad53 checkpoint kinase.

category: genomics


title: Parallel processing of working memory and temporal information by distinct types of cortical projection neurons

abstract: It is unclear how different types of cortical projection neurons work together to support diverse cortical functions. We examined the discharge characteristics and inactivation effects of intratelencephalic (IT) and pyramidal tract (PT) neurons--two major types of cortical excitatory neurons that project to cortical and subcortical structures, respectively--in the medial prefrontal cortex of mice performing a delayed response task. We found that IT neurons, but not PT neurons, convey significant working memory-related signals. We also found that the inactivation of IT neurons, but not PT neurons, impairs behavioral performance. In contrast, PT neurons convey far more temporal information than IT neurons during the delay period. Our results indicate a division of labor between IT and PT projection neurons in the prefrontal cortex for the maintenance of working memory and for tracking the passage of time, respectively.


title: Metagenomes from the Loxahatchee wildlife refuge in the Florida Everglades

abstract:
The Florida Everglades ecosystem represents a significant wetlands area and serves as a terrestrial carbon reservoir mediated in large part by microorganisms. Shotgun metagenome sequencing provides a snapshot of microbial diversity and the frequency of metabolic and functional gene content. Here, we present an analysis of 20 sediment samples collected from the Arthur R. Marshall Loxahatchee National Wildlife Refuge to characterize the taxonomic and functional potential of the microbial and viral communities, and reconstructed metagenome-assembled genomes. A total of 122 medium-quality and 6 high-quality MAGs are reported, three of which likely represent a novel species within the class Dehalococcoidia.

The most abundant phyla of bacteria and archaea were Proteobacteria and Euryarchaeota, respectively. Caudovirales was the most abundant viral order. Significant differences in taxonomic composition and diversity were observed among collection sites. Additionally, water samples were analyzed for pH, total nitrogen, total organic carbon, elements (P, K, Mg, Fe, Mn, Pb, Ca, S), chloride, electric conductivity, orthophosphate, nitrate, and ammonia, while the sediment samples were analyzed for carbon, nitrogen, and pH. Differences in measured aquatic and sediment analytes revealed significant correlations with numerous phyla. Significant correlations were observed between estimated gene frequencies of both aquatic and sediment analytes, most notably between kup/kdpB and dsrA/cysC with potassium and sulfur, respectively, as well as phoD/phnX and cysC with pH. Together, these data provide an important view into the functional and metabolic potential encoded within the sediment microbial communities in the Florida Everglades.


title: Cardiac Specific Overexpression of Transcription Factor EB (TFEB) in Normal Hearts Induces Pathologic Cardiac Hypertrophy and Lethal Cardiomyopathy

abstract: TFEB promotes lysosomal biogenesis, autophagy, and lysosomal exocytosis. The present study characterized the consequence of inducible TFEB overexpression in cardiomyocytes in vivo. We generated cardiomyocyte-specific doxycycline inducible (Tet off) mice to achieve spatial and temporal control of TFEB overexpression, by crossing TFEB transgenic mice with mice harboring the tTA transgene (TFEB/tTA). Two weeks after doxycycline removal, an 8-fold increase in TFEB protein expression was observed in transgenic hearts. Heart weight normalized to tibia length was increased by 2.5-fold following TFEB overexpression (TFEB/tTA), characterized by induction of markers of pathological hypertrophy, such as Nppa, Nppb and Acta1, progressive contractile dysfunction and cardiac dilatation. Overexpression of TFEB resulted in premature death, associated with high degree AV block. Reversal of TFEB overexpression normalized cardiac structure and function. Mitochondrial respiration and ATP levels were preserved after 2-weeks of TFEB induction, despite reduced mitochondrial (OXPHOS) protein expression, mtDNA content, and altered mitochondrial morphology. Signaling through mTOR was induced in TFEB/tTA mice, and when inhibited by rapamycin treatment for 4 weeks, partially offset left ventricular dysfunction. Transcriptome analysis revealed early suppression of mitochondrial metabolic pathways, induction of fibrosis and altered calcium signaling. MCOLN1, a lysosomal calcium release channel, the calcineurin target RCAN1.4, and the mitochondrial calcium uniporter (MCU) were strikingly induced in TFEB/tTA mice. In summary, persistent overexpression of TFEB at high levels (8-fold protein upregulation) in cardiomyocytes promotes pathologic cardiac hypertrophy via suppression of mitochondrial bioenergetic pathways and activation of pro-fibrotic and calcium regulatory pathways.

category: cell biology


title: Tdrd3 regulates the progression of meiosis II through translational control of Emi2 mRNA in mouse oocytes

abstract: After completion of meiosis I, the oocyte immediately enters meiosis II and forms a metaphase II (MII) spindle without an interphase, which is fundamental for generating a haploid gamete. Here, we identify tudor domain-containing protein 3 (Tdrd3) as a novel regulator of oocyte meiosis. Although early mitotic inhibitor 2 (Emi2) protein has been shown to ensure the meiosis I to II transition and the subsequent MII spindle formation by inhibiting the anaphase-promoting complex/cyclosome (APC/C), how it accumulates after meiosis I has remained unresolved. We isolated Tdrd3 as a protein directly binding to Emi2 mRNA. In GV-stage mouse oocytes, Emi2 mRNA assembled into RNA granules containing Tdrd3, while cyclin B1 mRNA, which was translated in early meiosis I, formed different granules. Knockdown of Tdrd3 attenuated Emi2 synthesis in meiosis II without affecting cyclin B1 synthesis in meiosis I. Moreover, Tdrd3-deficient oocytes entered interphase and failed to form an MII spindle after completion of meiosis I. Taken together, our results indicate the importance of Tdrd3-mediated translational control of Emi2 mRNA, which promotes Emi2 synthesis in meiosis II, for the progression of meiosis.

category: developmental biology


title: Restricted nucleation and piRNA-mediated establishment of H3K9me3-dependent heterochromatin during embryogenesis in Drosophila miranda

abstract: Heterochromatin is a key architectural feature of eukaryotic genomes, crucial for silencing of repetitive elements and maintaining genome stability. Heterochromatin shows stereotypical enrichment patterns around centromeres and repetitive sequences, but the molecular details of how heterochromatin is established during embryogenesis are poorly understood. Here, we map the genome-wide distribution of H3K9me3-dependent heterochromatin in individual embryos of D. miranda at precisely staged developmental time points. We find that canonical H3K9me3 enrichment patterns are established early on before cellularization, and mature into stable and broad heterochromatin domains through development. Intriguingly, initial nucleation sites of H3K9me3 enrichment appear as early as embryonic stage3 (nuclear cycle 9) over transposable elements (TE) and progressively broaden, consistent with spreading to neighboring nucleosomes. The earliest nucleation sites are limited to specific regions of a small number of TE families and often appear over promoter regions, while late nucleation develops broadly across most TEs. Early nucleating TEs are highly targeted by maternal piRNAs and show early zygotic transcription, consistent with a model of co-transcriptional silencing of TEs by small RNAs. Interestingly, truncated TE insertions lacking nucleation sites show significantly reduced enrichment across development, suggesting that the underlying sequences play an important role in recruiting histone methyltransferases for heterochromatin establishment.


title: NECAB2 orchestrates an endosomal pathway of mitochondrial quality control at striatal synapses

abstract: Synaptic signaling depends on ATP generated by mitochondria. Due to extensive connectivity, the striatum is especially vulnerable to mitochondrial dysfunction and thus requires efficient mitochondrial quality control and repair. We found that global knockout of the neuronal calcium-binding protein 2 (NECAB2) in the mouse causes loss of striatal synapses and behavioral phenotypes related to striatal dysfunction such as reduced motivation and altered sensory gating. Striatal mitochondria from Necab2 knockout mice are more abundant and smaller. They are characterized by increased respiration and superoxide production resulting in oxidative stress. This accumulation of dysfunctional mitochondria is caused by a defective assembly of mitochondria with early endosomes in a pathway that involves the small GTPase Rab5 and its guanine nucleotide exchange factor Alsin/ALS2. NECAB2 therefore participates in an endosomal pathway of mitochondrial stress response and repair important for striatal function.


title: NECAB2 participates in an endosomal pathway of mitochondrial stress response at striatal synapses


title: Corticotropin-releasing factor distribution in the brain of the brown anole lizard

abstract: Corticotropin-releasing factor (CRF) is best known for its involvement in peripheral glucocorticoid release across vertebrate species. However, CRF is also produced and released throughout various brain regions to regulate central aspects of the stress response. While these various CRF populations have been described extensively in mammals, less is known about their distributions in other amniotes, and only a handful of studies have ever examined CRF distributions in reptiles. Out study is the first to map CRF cell and fiber distributions in the brain of a lizard, the brown anole (Anolis sagrei). Our results indicate that brown anole CRF distributions are highly similar to those in snakes and turtles. However, unlike in these other reptile species, we find immunofluorescent CRF neurons in a few additional brown anole locations, most notably the supraoptic nucleus. The CRF distribution in the present study is also similar to published CRF descriptions in mammals and birds, although our findings, as well as the other published reports in reptiles, collectively suggest that reptiles possess a slightly more restricted distribution of CRF cell populations than do mammals and birds.


title: Laminar dynamics of beta bursts in human motor cortex

abstract: Modulation of motor cortical activity in the beta frequency range is one of the strongest and most studied movement-related neural signals. At the single trial level, beta band activity is often characterized by transient bursting events rather than slowly modulating oscillations, suggesting a more rapid, information-encoding functional role than previously believed. Insight into how beta bursts are generated in sensorimotor circuits can provide important constraints to theories about their functional role for movement control. To this end, we leverage and extend recent developments in high precision MEG for temporally resolved laminar analysis of burst activity, combined with a neocortical circuit model that simulates the biophysical generators of the electrical currents which drive beta bursts. This approach pinpoints the generation of beta bursts in human motor cortex to distinct excitatory synaptic inputs to deep and superficial cortical layers, which drive current flow in opposite directions. These laminar dynamics of beta bursts in motor cortex align with prior invasive animal recordings within the somatosensory cortex, and suggest a conserved mechanism for somatosensory and motor cortical beta bursts. More generally, we demonstrate the ability for uncovering the laminar dynamics of event-related neural signals in human non-invasive recordings.


title: Cholecystokinin 1 Receptor (Cck1R) Activates mTORC1 signaling and is Protective to Purkinje cells in SCA Mice

abstract: Spinocerebellar Ataxias (SCAs) are a group of genetic diseases characterized by progressive ataxia and neurodegeneration, often in cerebellar Purkinje neurons. A SCA1 mouse model, Pcp2-ATXN1[30Q]D776, has severe ataxia in absence of progressive Purkinje neuron degeneration and death. Previous RNA-seq analyses identified cerebellar up-regulation of the peptide hormone Cholecystokinin (Cck) in Pcp2-ATXN1[30Q]D776 mice. Importantly, absence of Cck1 receptor (Cck1R) in Pcp2-ATXN1[30Q]D776 mice confers a progressive disease with Purkinje neuron death. A Cck1R agonist, A71623 administered to Pcp2-ATXN1[30Q]D776;Cck-/- and Pcp2-AXTN1[82Q] mice dampened Purkinje neuron pathology and associated deficits in motor performance. In addition, A71623 administration improved motor performance of Pcp2-ATXN2[127Q] SCA2 mice. Moreover, the Cck1R agonist A71623 corrected mTORC1 signaling and improved expression of calbindin in cerebella of AXTN1[82Q] and ATXN2[127Q] mice. These results indicate that manipulation of the Cck-Cck1R pathway is a potential therapeutic target for treatment of diseases involving Purkinje neuron degeneration.


title: Cholecystokinin 1 Receptor (Cck1R) Normalizes mTORC1 signaling and is Protective to Purkinje cells in SCA Mice


title: Molecular origin of somatostatin-positive neuron vulnerability

abstract: Reduced somatostatin (SST) and SST-positive (SST+) neurons are hallmarks of neurological disorders and associated with mood disturbances, but their origin are unknown. Chronic psychosocial stress induces behavioral emotionality deficits and deregulates unfolded protein response (UPR) of the endoplasmic reticulum (ER) preferentially in SST+ neurons. Here we confirm that chronic stress increases ER stress levels in SST+ neurons of mouse prefrontal cortex, and show that genetically suppressing ER stress in SST+ neurons, but not in pyramidal neurons, normalized psychosocial stress-induced behavioral emotionality. Forced expression of SST precursor protein (preproSST), mimicking psychosocial stress-induced early proteomic changes, induces ER stress, whereas mature SST or processing-incompetent preproSST does not. Biochemical analyses further show that psychosocial stress induces SST protein aggregation under elevated ER stress conditions. These results demonstrate that SST processing is a SST+ neuron-intrinsic vulnerability factor under conditions of sustained or over-activated UPR in the ER, hence negatively impacting SST+ neuron functions.


title: Cerebellum controls timing of periaqueductal grey encoding of fear memory and expression of fear conditioned behaviour

abstract:
The pivotal role of the periaqueductal grey (PAG) in fear learning is reinforced by the identification of neurons in rat ventral PAG (vPAG) that encode fear memory through signalling the onset and offset of an auditory conditioned stimulus during presentation of the unreinforced conditioned tone during retrieval. Some units only display CS+ onset or offset responses and the two signals differ in extinction sensitivity, suggesting they are independent of each other. In addition, understanding cerebellar contributions to survival circuits is advanced by the discovery that: (i) reversible inactivation of the medial cerebellar nucleus (MCN) during fear consolidation leads in subsequent retrieval to: (a) disruption of the temporal precision of vPAG offset, but not onset responses to the unreinforced conditioned tone, and (b) an increase in duration of freezing behaviour. And (ii) chemogenetic manipulation of the MCN-vPAG projection during fear acquisition: (a) reduces the occurrence of fear- related ultrasonic vocalisations and (b) during subsequent retrieval, slows the extinction rate of fear- related freezing. These findings show that the cerebellum is part of the survival network that regulates fear memory processes at multiple timescales and in multiple ways; raising the possibility that dysfunctional interactions in the cerebellar-survival network may underlie fear-related disorders and comorbidities.

Impact StatementCerebellar-periaqueductal grey interactions contribute to fear conditioned processes and, as such, provide a novel target for treating psychological conditions including post-traumatic stress disorder.


title: Deep behavioral phenotyping of mouse autism models using open-field behavior

abstract: AO_SCPLOWBSTRACTC_SCPLOWAutism is noted for both its genotypic and phenotypic diversity. Repetitive action, resistance to environmental change, and motor disruptions vary from individual to individual. In animal models, conventional behavioral phenotyping captures such fine-scale variations incompletely. Here we use advances in computer vision and deep learning to develop a framework for characterizing mouse behavior on multiple time scales using a single popular behavioral assay, the open field test. We observed male and female C57BL/6J mice to develop a dynamic baseline of adaptive behavior over multiple days. We then examined two rodent models of autism, a cerebellum-specific model, L7-Tsc1, and a whole-brain knockout model, Cntnap2. Both Cntnap2 knockout and L7-Tsc1 mutants showed forelimb lag during gait. L7-Tsc1 mutants showed complex defects in multi-day adaptation, lacking the tendency of wild-type mice to spend progressively more time in corners of the arena. In L7-Tsc1 mutant mice, failure-to-adapt took the form of maintained ambling, turning, and locomotion, and an overall decrease in grooming. Adaptation in Cntnap2 knockout mice more broadly resembled that of wild-type. L7-Tsc1 mutant and Cntnap2 knockout mouse models showed different patterns of behavioral state occupancy. Our automated pipeline for deep phenotyping successfully captures model-specific deviations in adaptation and movement as well as differences in the detailed structure of behavioral dynamics.


title: Role of the ubiquitin ligase ITCH in clathrin-mediated endocytosis of the epidermal growth factor receptor

abstract: Once activated by ligand, epidermal growth factor receptor (EGFR) is endocytosed in clathrin-coated pits. ITCH is an E3 ubiquitin ligase that interacts with and ubiquitinates several proteins involved in clathrin-mediated endocytosis (CME) including endophilin. To further investigate the function of ITCH in EGFR endocytosis, the internalization of fluorescent EGF was measured in ITCH-/- HeLa cells. In the absence of ITCH, there was a significant decrease in the CME of EGF. Rescue experiments using wild-type ITCH confirmed the importance of the protein for normal EGF uptake. ITCH point mutations that disrupt the interaction of ITCH with endophilin failed to rescue the defects in EGFR uptake, as did a non-catalytic form of ITCH. ITCH-/- cells also displayed a delay in the rate of phospho-EGFR degradation as well as prolonged ERK1/2 signaling. Our study uncovers a pathway regulating EGFR trafficking and reveals for the first time that the protein ITCH is required for CME of EGFR.


title: A unified genealogy of modern and ancient genomes

abstract: The sequencing of modern and ancient genomes from around the world has revolutionised our understanding of human history and evolution1,2. However, the general problem of how best to characterise the full complexity of ancestral relationships from the totality of human genomic variation remains unsolved. Patterns of variation in each data set are typically analysed independently, and often using parametric models or data reduction techniques that cannot capture the full complexity of human ancestry3,4. Moreover, variation in sequencing technology5,6, data quality7 and in silico processing8,9, coupled with complexities of data scale10, limit the ability to integrate data sources. Here, we introduce a non-parametric approach to inferring human genealogical history that overcomes many of these challenges and enables us to build the largest genealogy of both modern and ancient humans yet constructed. The genealogy provides a lossless and compact representation of multiple datasets, addresses the challenges of missing and erroneous data, and benefits from using ancient samples to constrain and date relationships. Using simulations and empirical analyses, we demonstrate the power of the method to recover relationships between individuals and populations, as well as to identify descendants of ancient samples. Finally, we show how applying a simple non-parametric estimator of ancestor geographical location to the inferred genealogy recapitulates key events in human history. Our results demonstrate that whole-genome genealogies are a powerful means of synthesising genetic data and provide rich insights into human evolution.


title: Inferring population histories for ancient genomes using genome-wide genealogies

abstract: Ancient genomes anchor genealogies in directly observed historical genetic variation, and contextualise ancestral lineages with archaeological insights into their geography and lifestyles. We introduce an extension of the Relate algorithm to incorporate ancient genomes and reconstruct the joint genealogies of 14 previously published high-coverage ancients and 278 present-day individuals of the Simons Genome Diversity Project. As the majority of ancient genomes are of lower coverage and cannot be directly built into genealogies, we additionally present a fast and scalable method, Colate, for inferring coalescence rates between low-coverage genomes without requiring phasing or imputation. Our method leverages sharing patterns of mutations dated using a genealogy to construct a likelihood, which is maximised using an expectation-maximisation algorithm. We apply Colate to 430 ancient human shotgun genomes of >0.5x mean coverage. Using Relate and Colate, we characterise dynamic population structure, such as repeated partial population replacements in Ireland, and gene-flow between early farmer and European hunter-gatherer groups. We further show that the previously reported increase in the TCC/TTC mutation rate, which is strongest in West Eurasians among present-day people, was already widespread across West Eurasia in the Late Glacial Period ~10k - 15k years ago, is strongest in Neolithic and Anatolian farmers, and is remarkably well predicted by the coalescence rates between other genomes and a 10,000-year-old Anatolian individual. This suggests that the driver of this signal originated in ancestors of ancient Anatolia >14k years ago, but was already absent by the Mesolithic and may indicate a genetic link between the Near East and European hunter-gatherer groups in the Late Paleolithic.


title: Reexamination of N-terminal domains of Syntaxin-1 in vesicle fusion from central murine synapses

abstract: Syntaxin-1 (STX1) and Munc18-1 are two requisite components of synaptic vesicular release machinery, so much so synaptic transmission cannot proceed in their absence. They form a tight binary complex through two major binding modes: one through STX1s N-peptide, the other through STX1s closed conformation driven by its Habc-domain. However, physiological roles of these two reportedly different binding modes in synapses are still controversial. Here we characterized the roles of STX1s N-peptide, Habc-domain, and open conformation with and without N-peptide deletion using our STX1-null mouse model system and exogenous reintroduction of STX1A mutants. We show, on the contrary to the general view, that the Habc-domain is absolutely required and N-peptide is dispensable for synaptic transmission. However, STX1s N-peptide plays a regulatory role, particularly in the Ca2+-sensitivity and the short-term plasticity of vesicular release, whereas STX1s open conformation governs the vesicle fusogenicity. Strikingly, we also show that neurotransmitter release still proceeds when both the interaction modes between STX1 and Munc18-1 are presumably intervened together, necessitating a refinement of the conceptualization of STX1-Munc18-1 interaction.


title: An HB40 - JUNGBRUNNEN1 - GA 2-OXIDASE regulatory module for gibberellin homeostasis in Arabidopsis

abstract: The phytohormones gibberellins (GAs) play fundamental roles in almost every aspect of plant growth and development. Although there is good knowledge about GA biosynthetic and signaling pathways, factors contributing to the mechanisms homeostatically controlling GA levels remain largely unclear. Here, we demonstrate that homeobox transcription factor HB40 of the HD-Zip family in Arabidopsis thaliana regulates GA content at two additive control levels. We show that HB40 expression is induced by GA and in turn reduces the levels of endogenous bioactive GAs by a simultaneous reduction of GA biosynthesis and increased GA deactivation. Hence, HB40 overexpression leads to typical GA-deficiency traits, such as small rosettes, reduced plant height, delayed flowering, and male sterility. In contrast, a loss-of-function hb40 mutation enhances GA-controlled growth. Genome-wide RNA-sequencing combined with molecular-genetic analyses revealed that HB40 directly activates transcription of JUNGBRUNNEN1 (JUB1), a key TF repressing growth by suppressing GA biosynthesis and signaling. HB40 also represses genes encoding GA 2-oxidases (GA2oxs) which are major GA catabolic enzymes. The effect of HB40 is ultimately mediated through induction of nuclear growth-repressing DELLA proteins. Our results thus uncover an important role of the HB40/JUB1/GA2ox/DELLA network in controlling GA homeostasis during plant growth.

category: plant biology


title: Sucrose synthase activity is not required for cellulose biosynthesis in Arabidopsis

abstract: Biosynthesis of plant cell walls requires UDP-glucose as the substrate for cellulose biosynthesis, and as an intermediate for the synthesis of other matrix polysaccharides. The sucrose cleaving enzyme sucrose synthase (SUS) is thought to have a central role in UDP-glucose biosynthesis, and a long held and much debated hypothesis postulates that SUS is required to supply UDP-glucose to cellulose biosynthesis. To investigate the role of SUS in cellulose biosynthesis of Arabidopsis thaliana we characterized mutants in which four, or all six Arabidopsis SUS genes were disrupted. These sus mutants showed no growth phenotypes, vascular tissue cell wall defects or changes in cellulose content. Moreover, the UDP-glucose content of rosette leaves of the sextuple sus mutants was increased by approximately 20% compared to wild type. It can thus be concluded that cellulose biosynthesis is able to employ alternative UDP-glucose biosynthesis pathway(s), and thereby the model of SUS requirement for cellulose biosynthesis in Arabidopsis can be refuted.


title: IRONMAN Tunes Responses to Iron Deficiency in Concert with Environmental pH

abstract:
Iron (Fe) is an essential mineral element which governs the composition of natural plant communities and limits crop yield in agricultural ecosystems due to its extremely low availability in most soils, particularly at alkaline pH. To extract sufficient Fe from the soil under such conditions, some plants including Arabidopsis thaliana secrete Fe-mobilizing phenylpropanoids, which mobilize sparingly soluble Fe hydroxides by reduction and chelation. We show here that ectopic expression of the IRONMAN peptides IMA1 and IMA2 improves growth on calcareous soil by inducing the biosynthesis and secretion of the catecholic coumarin fraxetin (7,8-dihydroxy-6-methoxycoumarin) through increased expression of MYB72 and SCOPOLETIN 8-HYDROXYLASE (S8H), a response which is strictly dependent on elevated environmental pH (pHe). By contrast, transcription of the cytochrome P450 family protein CYP82C4, catalyzing the subsequent hydroxylation of fraxetin to sideretin, which forms less stable complexes with iron, was strongly repressed under such conditions. Luciferase reporter assays in transiently transformed protoplasts showed that IMA1/IMA2 peptides are translated and modulate the expression of CYP82C4 and MYB72 by acting as transcriptional coactivators. It is concluded that IMA peptides regulate processes supporting Fe uptake at both acidic and elevated pH by controlling gene expression upstream of or in concert with a putative pHe signal to adapt the plant to the prevailing edaphic conditions. This regulatory pattern confers tolerance to calcareous soils by extending the pH range in which Fe can be efficiently absorbed from the soil. Altering the expression of IMA peptides provides a novel route for generating plants adapted to calcareous soils.

One sentence summaryEctopic expression of IRONMAN peptides improves growth under iron-limiting conditions by inducing responses to limited iron availability in accordance with the environmental pH.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Wolfgang Schmidt (wosh@gate.sinica.edu.tw).


title: Drought is a stronger driver of plant morphology and nutritional composition than warming in two common pasture species

abstract: Under warmer and drier future conditions, global livestock and dairy production are threatened by impacts on the productivity and nutritional quality of pastures. However, morphological and nutritional adjustments within plants in response to warming and drought vary among species and less is known how these relate to production and forage quality. To investigate this, we grew two common pasture species, tall fescue (Festuca arundinacea: grass) and lucerne (Medicago sativa: legume), in a climate-controlled facility, under different temperatures (ambient and elevated) and watering regimes (well-watered and droughted). We found that drought had a strong negative impact on biomass production, morphology and nutritional quality while warming only significantly affected both species when response metrics were considered in concert, although to a lesser degree than the drought. Furthermore, interactions between warming and drought were only seen for lucerne, with the greatest reduction in biomass and most dead material and dry matter content. In tall fescue, drought had bigger impacts on nutritional composition than morphological traits, while in lucerne, drought affected all morphological traits and most nutritional parameters. These findings suggest that in future climate scenarios, drought may be a stronger driver of changes in the morphology and nutritional composition of pasture grasses and legumes, compared to modest levels of warming.


title: LC-MS Based Draft Map of the Arabidopsis thaliana Nuclear Proteome and Protein Import in Pattern Triggered Immunity

abstract: Despite its central role as the ark of genetic information and gene expression the plant nucleus is surprisingly understudied. We isolated nuclei from the Arabidopsis thaliana dark grown cell culture left untreated and treated with flg22 and nlp20, two elicitors of pattern triggered immunity (PTI) in plants, respectively. An LC-MS based discovery proteomics approach was used to measure the nuclear proteome fractions. An enrichment score based on the relative abundance of cytoplasmic, mitochondrial and golgi markers in the nuclear protein fraction allowed us to curate the nuclear proteome producing high quality catalogs of around 3,000 nuclear proteins under untreated and both PTI conditions. The measurements also covered low abundant proteins including more than 100 transcription factors and transcriptional co-activators. Protein import into the nucleus in plant immunity is known. Here we sought to gain a broader impression of this phenomenon employing our proteomics data and found 157 and 73 proteins to be putatively imported into the nucleus upon stimulus with flg22 and nlp20, respectively. Furthermore, the abundance of 93 proteins changed significantly in the nucleus following elicitation of immunity. These results suggest promiscuous ribosome assembly and retrograde signaling from the mitochondrion to the nucleus including Prohibitins and Cytochrome C, in the two forms of PTI.


title: PAMP-triggered Genetic Reprogramming Involves Widespread Alternative Transcription Initiation and an Immediate Transcription Factor Wave

abstract: Immune responses triggered by pathogen-associated molecular patterns (PAMPs) are key to pathogen defense, but drivers of the genetic reprogramming required to reach the immune state remain incompletely understood in plants. Here, we report a time-course study of the establishment of PAMP-triggered immunity (PTI) using cap analysis of gene expression (CAGE). Our results show that as much as 15% of all PAMP response genes display alternative transcription initiation. In several cases, use of alternative TSSs may be regulatory as it determines inclusion of target peptides or protein domains, or occurrence of upstream open reading frames (uORFs) in mRNA leader sequences. We also find that 60% of PAMP-response genes respond much earlier than previously thought. In particular, a previously unnoticed cluster of rapidly and transiently PAMP-induced genes is enriched in transcription factors whose functions, previously associated with biological processes as diverse as abiotic stress adaptation and stem cell activity, appear to converge on growth restriction. Furthermore, some examples of known potentiators of PTI, in one case under direct MAP kinase control, support the notion that the rapidly induced transcription factors could constitute direct links to PTI signaling pathways and drive gene expression changes underlying establishment of the immune state.


title: Distinct metabolic flux modes through the tricarboxylic acid cycle in mesophyll and guard cells revealed by GC-MS-based 13C-positional isotopomer analysis

abstract:
O_LI13C-Metabolic flux analysis (13C-MFA) have greatly contributed to revealing the regulation of plant metabolism. However, mass spectrometry (MS) approaches have hitherto been limited in their power to deduce flux information due to lack of positional information.
C_LIO_LIHere we established an MS-based 13C-positional isotopomer labelling approach and performed a multi-species/cell-types analysis based on previous 13C-MFA to compare flux modes through the tricarboxylic acid (TCA) cycle and associated pathways in mesophyll (MCs) and guard cells (GCs).
C_LIO_LIBoth cell types showed high 13C-enrichment in pyruvate. However, GCs and sink MCs, but not source MCs showed high 13C-incorporation into Glu/Gln following provision of 13C-sucrose. Only GCs showed higher 13C-enrichment in the carbon 1 atom of Gln, which is derived from PEPc-mediated CO2 fixation. Increased 13C-enrichment in the carbon 1 of Glu was also observed in both trxo1 and ntra ntrb mutants, but not in wild type Arabidopsis plants, following provision of 13C-glucose.
C_LIO_LIOur results suggest that the mitochondrial thioredoxin system restricts the fluxes from PEPc and glycolysis to Glu in illuminated MCs and reveal that fluxes throughout the TCA cycle of GCs resemble those of sink MCs but operate different non-cyclic flux modes to support Gln synthesis in the light.
C_LI


title: Transcriptome sequence reveals candidate genes involving in the post-harvest hardening of trifoliate yam Dioscorea dumetorum

abstract: Storage ability of D. dumetorum is restricted by a severe phenomenon of post-harvest hardening which starts 72h after harvest and renders tubers inedible. Previous work has only focused on the biochemistry changes affecting the PHH on D. dumetorum. To the best of our knowledge nobody has identified candidate genes responsible for hardness on D. dumetorum. Here, transcriptome analysis of D. dumetorum tubers was performed, 4 months after emergence (4MAE), after harvest (AH), 3 days AH (3DAH) and 14 days AH (14DAH) on four accessions using RNA-Seq. In total between AH and 3DAH, 165, 199,128 and 61 differentially expressed genes (DEGs) were detected in Bayangam 2, Fonkouankem 1, Bangou 1 and Ibo sweet 3 respectively. Functional analysis of DEGs revealed that genes encoding for cellulose synthase A, xylan O-acetyltransferase chlorophyll a/b binding protein 1,2,3,4 and transcription factor MYBP were found predominantly and significantly up-regulated 3DAH, implying that genes were potentially involved in the post-harvest hardening. A hypothetical mechanism of this phenomenon and its regulation has been proposed. These findings provide the first comprehensive insights into genes expression in yam tubers after harvest and valuable information for molecular breeding against the post-harvest hardening. A hypothetical mechanism of this phenomenon and its regulation has been proposed. These findings provide the first comprehensive insights into genes expression in yam tubers after harvest and valuable information for molecular breeding against the post-harvest hardening.


title: Cerebellar tDCS alters the perception of optic flow

abstract: Studies have shown that the cerebellar vermis is involved in the perception of motion. However, it is unclear how the cerebellum influences motion perception. tDCS is a non-invasive brain stimulation technique that can reduce (through cathodal stimulation) or increase neuronal excitability (through anodal stimulation). To explore the nature of the cerebellar involvement on large-field global motion perception (i.e., optic flow-like motion), we applied tDCS on the cerebellar midline while participants performed an optic flow motion discrimination task. Our results show that anodal tDCS improves discrimination threshold for optic flow perception, but only for left-right motion in contrast to up-down motion discrimination. This result was evident within the first 10 minutes of stimulation and was also found post-stimulation. Cathodal stimulation did not have any significant effects on performance in any direction. The results show that discrimination of planar optic flow can be improved with tDCS of the cerebellar midline and provide further support for the role of the human midline cerebellum in the perception of optic flow.


title: Disentangling the relative importance of spatio-temporal parameters and host selectivity in shaping AMF communities in temperate forests

abstract: Many woody and herbaceous plants in temperate forests cannot establish and survive in the absence of mycorrhizal associations. Here, we address and hierarchize how Glomeromycota, a group of soil-borne fungi, forming a ubiquitous type of mycorrhiza, varied in a temperate forest patch in Germany with time, space, plant hosts but also the proximity to Glomeromycota-associating woody species. The communities of Glomeromycota in our study were non-random. We observed that space had a greater impact on fungal community structure than either time or proximity to Glomeromycota-associating trees but unlike host identity did not alter Glomeromycotan richness. The set of parameters which we addressed has rarely been studied together and we believe that the resulting ranking could ease prioritizing some of them to include in future surveys. Glomeromycota are crucial for the establishment of understory plants in temperate forests making it desirable to further explore how they vary in time and space.

category: ecology


title: Understanding distribution and occupancy of Himalayan Monal in Uttarkashi district, Uttarakhand

abstract: The Himalayan Monal is a conservation priority species in its entire distribution range. Its population is declining in many areas due to various anthropogenic threats. The information on species distribution and its abundance is lacking in many areas which are vital for conservation and management planning. Hence, through the present study, we have assessed the abundance and occupancy of Himalayan monal in Uttarkashi district (Uttarakhand). We used camera traps and conventional sign surveys for documenting the species during 2018-2019. We installed a total of 69 camera traps (2819 trap nights) and surveyed 54 trails (650 km) which represents entire habitat and topographic variability of the landscape. The occupancy and detection probability was modelled using the habitat variables. The top model showed that occupancy probability of Himalayan monal was positively influenced by the slope ({beta} =27.52 {+/-}16.25) and negatively influenced by Reserve Forest (RF) ({beta}= -8.14 SE {+/-} 4.99). The observed naive occupancy of Himalayan Monal was 0.69 in the study area, which was slightly lower than the estimated occupancy. However, in the null model, the site occupancy estimated was found to be 0.82{+/-}0.08 and with detection probability 0.23{+/-}0.03. The overall abundance of monal was estimated about 171.58 {+/-}10.2 in the study area with an average density of 0.62/ km2. The activity pattern analysis indicates that monal remains very active between 6.00 hrs -12.00 hrs and relatively less active during mid-day when humans are most active 11.30 hrs-16.30 hrs. The present study is a first attempt to estimate occupancy and abundance using camera traps as well as sign survey for the species primarily from non-Protected Area (PA). We found that Himalayan monal is abundant outside the PAs, which is a good indication for its long-term viability and also identified areas for conservation and management prioritization in Uttarkashi.


title: Change of information by positive frequency-dependent selection in two very different models (laser-like and chirality of shell-coiling in the snail Partula suturalis)

abstract:
Although according to the second law of thermodynamics the world tends toward maximum disorder, over millions of years evolution has given rise to an enormous variety of complex organisms. To explain this, one must assume that natural selection is a process of information acquisition. Since some years an information theory of selection exists that can quantify this change and thus helps to understand the apparent contradiction between the existence of biological complexity and the tendency toward disorder that generally prevails in nature. Here I apply this theory to examples of frequency-dependent selection (this means: in which phenotype frequency determines its fitness).

The snail Partula suturalis gave an evolutionary and ecologically unique and hence very valuable example of this type of selection before it became extinct about thirty years ago on its native island. Spatially separated populations with left- and right-coiled shells occurred on Moorea, but also hybridization zones. Since both types of shells were the same except for chirality, the question is whether selection happened at all. The inheritance of this character is monogenic and in this respect simple, but is complicated by the fact that it is the maternal genotype, not the own, that determines the phenotype. This causes that for the calculation of the information change by selection not the genotype or phenotype frequencies are sufficient, but one must consider their combination. The simulation shows that frequency-dependent selection in P. suturalis indeed increased information.

It has already been shown that selection can also be important outside animate nature, for example in the generation of laser light, which has extraordinary properties: it is monochromatic, monoaxial and monophasic. Phase selection is frequency(=density)-dependent and therefore of interest here. In selection theory the mean fitness {omega} is of special significance. In a laser-like model, in modeling phase selection, we find that {omega}=1+A2, where A2 is the the light intensity or the square of the amplitude, respectively. During selection, {omega} increases and, in parallel, since selection is a process of information acquisition, so does the information. Because of the connection between {omega} and A2 this also means for the laser-like model that - assuming a constant number of photons - a larger amplitude always means more information (less entropy).

category: evolutionary biology


title: Identification of differentially distributed gene expression and distinct sets of cancer-related genes identified by changes in expression mean and variability

abstract: There is increasing evidence that changes in the variability or overall distribution of gene expression are important both in normal biology and in diseases, particularly cancer. Genes whose expression differs in variability or distribution without a difference in mean are ignored by traditional differential expression-based analyses. Using a Bayesian hierarchical model that provides tests for both differential variability and differential distribution for bulk RNA-seq data, we report here an investigation into differential variability and distribution in cancer. Analysis of eight paired tumour-normal datasets from The Cancer Genome Atlas confirms that differential variability and distribution are able to identify cancer-related genes. We further demonstrate that differential variability identifies cancer-related genes that are missed by differential expression analysis, and that differential expression and differential variability identify functionally distinct sets of genes. These results suggest that differential variability analysis may provide insights into genetic aspects of cancer that would not be revealed by differential expression, and that differential distribution analysis may allow for more comprehensive identification of cancer-related genes than analyses based on changes in mean or variability alone.


title: Identification of differentially distributed gene expression and distinct sets of cancer-related genes identified by changes in mean and variability


title: N-terminal extensions strengthen hydrophobic inter-subunit interactions between HU's C-terminal domains to frustrate heterodimer formation

abstract: HU is a nucleoid-associated protein (NAP) that helps bacterial chromosomal DNA to remain compact. Escherichia coli contains two homologs of HU that are ~ 70 % identical: HU-A and HU-B. The early log phase, late log phase, and stationary phase of E. coli growth are reported to be dominated, respectively, by HU-AA homodimers, HU-BB homo-dimers, and HU-AB heterodimers. Here, we show that the formation of HU-AB heterodimers occurs to a much lower degree in HU chains that have a displaced N-terminus, whether through addition of an N-terminal affinity (polyhistidine) tag, or fusion of a fluorescent protein. A combination of mass spectrometry, spectroscopy, chromatography, and electrophoresis (exploring glutaraldehyde crosslinking of subunits) was used to study the mixing, co-expression, unfolding and refolding of HU-AA and HU-BB homodimers. The data suggests that, in HU polypeptides with N-terminal extension, whereas inter-subunit contacts between the alpha helical N-terminal domains (NTDs) undergo facile unfolding and dissociation, inter-subunit contacts between the beta sheet- and IDR-dominated C-terminal domains (CTDs) fail to do so, due to persistence of hydrophobic inter-subunit interactions between two beta sheets. This persistence causes HU to remain nominally dimeric even after substantive unfolding, and frustrates subunit exchange and heterodimer formation.

category: biochemistry


title: Input-Output Slope Curve Estimation in Neural Stimulation Based on Optimal Sampling Principles

abstract: This paper discusses some of the practical limitations and issues, which exist for the input-output (IO) slope curve estimation (SCE) in neural, brain and spinal, stimulation techniques. The drawbacks of the SCE techniques by using existing uniform sampling and Fisher-information-based optimal IO curve estimation (FO-IOCE) methods are elaborated. A novel IO SCE technique is proposed with a modified sampling strategy and stopping rule which improve the SCE performance compared to these methods. The effectiveness of the proposed IO SCE is tested on 1000 simulation runs in transcranial magnetic stimulation (TMS), with a realistic model of motor evoked potentials (MEPs). The results show that the proposed IO SCE method successfully satisfies the stopping rule, before reaching the maximum number of TMS pulses in 79.5% of runs, while the estimation based on the uniform sampling technique never converges and satisfies the stopping rule. At the time of successful termination, the proposed IO SCE method decreases the 95th percentile (mean value in the parentheses) of the absolute relative estimation errors (AREs) of the slope curve parameters up to 7.45% (2.2%), with only 18 additional pulses on average compared to that of the FO-IOCE technique. It also decreases the 95th percentile (mean value in the parentheses) of the AREs of the IO slope curve parameters up to 59.33% (16.71%), compared to that of the uniform sampling method. The proposed IO SCE also identifies the peak slope with higher accuracy, with the 95th percentile (mean value in the parentheses) of AREs reduced by up to 9.96% (2.01%) compared to that of the FO-IOCE method, and by up to 46.29% (13.13%) compared to that of the uniform sampling method.

category: bioinformatics


title: MultiMAP: Dimensionality Reduction and Integration of Multimodal Data

abstract: Multimodal data is rapidly growing in many fields of science and engineering, including single-cell biology. We introduce MultiMAP, an approach for dimensionality reduction and integration of multiple datasets. MultiMAP recovers a single manifold on which all of the data resides and then projects the data into a single low-dimensional space so as to preserve the structure of the manifold. It is based on a framework of Riemannian geometry and algebraic topology, and generalizes the popular UMAP algorithm1 to the multimodal setting. MultiMAP can be used for visualization of multimodal data, and as an integration approach that enables joint analyses. MultiMAP has several advantages over existing integration strategies for single-cell data, including that MultiMAP can integrate any number of datasets, leverages features that are not present in all datasets (i.e. datasets can be of different dimensionalities), is not restricted to a linear mapping, can control the influence of each dataset on the embedding, and is extremely scalable to large datasets. We apply MultiMAP to the integration of a variety of single-cell transcriptomics, chromatin accessibility, methylation, and spatial data, and show that it outperforms current approaches in preservation of high-dimensional structure, alignment of datasets, visual separation of clusters, transfer learning, and runtime. On a newly generated single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) and single-cell RNA-seq (scRNA-seq) dataset of the human thymus, we use MultiMAP to integrate cells along a temporal trajectory. This enables the quantitative comparison of transcription factor expression and binding site accessibility over the course of T cell differentiation, revealing patterns of transcription factor kinetics.


title: CONSTAX2: Improved taxonomic classification of environmental DNA markers

abstract:
CONSTAX - the CONSensus TAXonomy classifier - was developed for accurate and reproducible taxonomic annotation of fungal rDNA amplicons and is based upon a consensus approach of RDP, SINTAX and UTAX algorithms. CONSTAX2 can be used to classify prokaryotes and incorporates BLAST-based classifiers to reduce classification errors. Additionally, CONSTAX2 implements a conda-installable, command line tool with improved classification metrics, faster training, multithreading support, capacity to incorporate external taxonomic databases, new isolate matching and high-level taxonomy tools, replete with documentation and example tutorials.

Availability and ImplementationCONSTAX2 is available at https://github.com/liberjul/CONSTAXv2, and is packaged for Linux and MacOS from Bioconda. A tutorial and documentation are available at https://constax.readthedocs.io/en/latest/.


title: Slow chromatin dynamics enhances promoter accessibility to transcriptional condensates

abstract: Enhancers are DNA sequences at a long genomic distance from target genes. Recent experiments suggest that enhancers are anchored to the surfaces of condensates of transcription machinery and that the loop extrusion process enhances the transcription level of their target genes. Here we theoretically study the polymer dynamics driven by the loop extrusion of the linker DNA between an enhancer and the promoter of its target gene to calculate the contact probability of the promoter to the transcription machinery in the condensate. Our theory predicts that when the loop extrusion process is active, the contact probability increases with increasing linker DNA length. This finding reflects the fact that the relaxation time, with which the promoter stays in proximity to the surface of the transcriptional condensate, increases as the length of the linker DNA increases. This contrasts the equilibrium case for which the contact probability between the promoter and the transcription machineries is smaller for longer linker DNA lengths.

category: biophysics


title: Cardiac fibroblast mechanoresponse guides anisotropic organization of hiPSC-derived cardiomyocytes in vitro

abstract: The human myocardium is a mechanically active tissue typified by anisotropic organization of the resident cells (cardiomyocytes (CMs) and cardiac fibroblasts (cFBs)) and the extracellular matrix (ECM). Upon ischemic injury, the anisotropic tissue is replaced by disorganized scar tissue, eventually resulting in loss of coordinated contraction. Efforts to re-establish tissue anisotropy in the injured myocardium are hampered by a lack of understanding on how CM and/or cFB structural organization is affected by the two major physical cues inherent in the myocardium: ECM organization and cyclic mechanical strain. Herein, we investigate the singular and combined effect of ECM (dis)organization and cyclic strain in a 2D human in vitro co-culture model of the myocardial microenvironment. We show that (an)isotropic ECM protein patterning can guide the orientation of CMs and cFBs, both in mono- and co-culture. Subsequent application of uniaxial cyclic strain - mimicking the local anisotropic deformation of beating myocardium - causes no effect when applied parallel to the anisotropic ECM. However, when cultured on isotropic substrates, cFBs, but not CMs, orient away from the direction of cyclic uniaxial strain (strain avoidance). In contrast, CMs show strain avoidance via active remodeling of their sarcomeres only when co-cultured with at least 30% cFBs. Paracrine signaling or N-cadherin-mediated communication between CMs and cFBs were no contributing factors, but our findings suggest that the mechanoresponsive cFBs provide structural guidance for CM orientation and elongation. Our study therefore highlights a synergistic mechanobiological interplay between CMs and cFBs in shaping tissue organization, which is of relevance for regenerating functionally organized myocardium.


title: Human pluripotent stem cell-derived cardiomyocytes align under cyclic strain when guided by cardiac fibroblasts


title: Deciphering the molecular mechanism of the cancer formation by chromosome structural dynamics

abstract: Cancer reflects the dysregulation of the underlying gene network, which is intimately related to the 3D genome organization. Numerous efforts have been spent on experimental characterizations of the structural alterations in cancer genomes. However, there is still a lack of genomic structural-level understanding of the temporal dynamics for cancer initiation and progression. Here, we use a landscape-switching model to investigate the chromosomal structural transition during the can-cerization and reversion processes. We find that the chromosome undergoes a non-monotonic structural shape-changing pathway with initial expansion followed by compaction during both of these processes. Furthermore, our analysis reveals that the chromosome with a more expanded structure than those at both the normal and cancer cell during cancerization exhibits a sparse contact pattern, which shows significant structural similarity to the one at the embryonic stem cell in many aspects, including the trend of contact probability declining with the genomic distance, the global structural shape geometry and the spatial distribution of loci on chromosome. We show that cell cancerization and reversion are highly irreversible processes in terms of the chromosomal structural transition pathways, spatial repositioning of chromosomal loci and hysteresis loop of contact evolution analysis. Our model draws a molecular-scale picture of cell cancerization, which contains initial reprogramming towards the stem cell followed by differentiation towards the cancer cell, accompanied by an initial increase and subsequent decrease of cell stemness.


title: DNA translocase repositions a nucleosome by the lane-switch mechanism

abstract:
Translocases such as DNA/RNA polymerases, replicative helicases, and exonucleases are involved in eukaryotic DNA transcription, replication, and repair. Since eukaryotic genomic DNA wraps around histone core complexes and forms nucleosomes, translocases inevitably encounter nucleosomes. Previous studies have shown that a histone core complex repositions upstream (downstream) when SP6RNA or T7 RNA polymerase (bacterial exonuclease, RecBCD) partially unwraps nucleosomal DNA. However, the molecular mechanism of the downstream repositioning remains unclear. In this study, we identify the lane-shift mechanism for downstream nucleosome repositioning via coarse-grained molecular dynamics simulations, which we validated by restriction enzyme digestion assays and deep sequencing assays. In this mechanism, after a translocase unwraps nucleosomal DNA up to the site proximal to the dyad, the remaining wrapped DNA switches its binding region (lane) to that vacated by the unwrapping, and the downstream DNA rewraps, completing downstream repositioning. This mechanism may have crucial implications for transcription through nucleosomes, histone recycling, and nucleosome remodeling.

SIGNIFICANCEEukaryotic chromosomes are composed of repeating subunits termed nucleosomes. Thus, proteins that translocate along the chromosome, DNA translocases, inevitably collide with nucleosomes. Previous studies revealed that a translocase repositions a nucleosome upstream or downstream upon their collision. Though the molecular mechanisms of the upstream repositioning have been extensively studied, that of downstream repositioning remains elusive. In this study, we performed coarse-grained molecular dynamics simulations, proposed the lane-shift mechanism for downstream repositioning, and validated this mechanism by restriction enzyme digestion assays and deep sequencing assays. This mechanism has broad implications for how translocases deal with nucleosomes for their functions.


title: Anthracyclins increase free PUFAs and etherPEs with PUFAs as potential hallmarks of lipid peroxidation and ferroptosis

abstract: Metabolic and personalized interventions in cancer treatment require a better under-standing of the relationship between the induction of cell death and metabolism. Consequently, we treated three primary liver cancer cell lines with two anthracyclins (doxorubicin and idarubin) and studied the changes of the lipidome. We found that both anthracyclins in the three cell lines increased the levels of polyunsaturated fatty acids (PUFAs) and alkylacylglycerophosphoethano-lamines (etherPEs) with PUFAs. As PUFAs and alkylacylglycerophospholipids with PUFAs are fundamental in lipid peroxidation during ferroptotic cell death, our results suggests supplementa-tion with PUFAs and/or etherPEs with PUFAs as a potential general adjuvant of anthracyclins. In contrast, neither the markers of de novo lipogenesis nor cholesterol lipids presented the same trend in all cell lines and treatments. In agreement with previous research, this suggests that modulation of the metabolism of cholesterol could be considered a specific adjuvant of anthracyclins depend-ing on the type of tumor and the individual. Finally, we discuss the changes in the lipidome in re-lation to the endoplasmic reticulum stress and the sensitivity to anthracyclins of the different cells. In conclusion, our results suggest that the modulation of different lipid metabolic pathways may be considered for generalized and personalized metabochemotherapies.

category: cancer biology


title: Single cell transcriptome mapping identifies a local innate B cell population driving local antibody production and chronic rejection after lung transplantation

abstract: Bronchiolitis obliterans syndrome (BOS) due to chronic rejection is the main reason for poor outcomes after lung transplantation (LTx). We and others have recently identified B cells as major contributors to BOS after LTx. The extent of B cell heterogeneity, however, as well as those B cell populations that determine chronic rejection of the lung, remain entirely unclear. Here, we provide a map of cell population heterogeneity and their gene expression patterns during chronic rejection after orthotopic LTx in mice. Out of a total of 14 major comprehensive cell clusters, corresponding to 11 known major cell subpopulations, Mzb1-expressing plasma cells (PCs) were the most prominently increased cell population in lungs with BOS. Scgb1a1-expressing bronchial epithelial cells were depleted, while Cd14-expressing monocytes and Pdgfra-expressing fibroblasts were enriched in BOS grafts. These findings were validated in two different cohorts of human BOS after LTx. MZB1-IgG-double positive PCs infiltrated the airways of patients with BOS, while they were absent from healthy lungs. IgG, but not IgA, IgD, IgE or IgM, were significantly increased in bronchoalveolar lavage from BOS patients, compared with LTx patients who did not develop BOS. Pseudotime and trajectory analysis revealed that a Bhlhe41, Cxcr3, Itgb1-triple positive-B cell subset, also expressing classical markers of the innate-like B-1 B cell population, served as the progenitor pool for Mzb1+ PCs. This progenitor B cell subset accounted for the increase in IgG2c expression and production in BOS lung grafts. Importantly, Aicda-/- mice, which lack all isotypes of Ig (except IgM) were protected from the onset of BOS after LTx. In summary, we provide a detailed atlas of cell population changes of chronic rejection after LTx. We have identified IgG-positive PCs and their progenitors - an innate B cell subpopulation characterized by a specific subset of markers - as the major source of local antibody production and a major contributor to both mouse and human BOS after LTx.

category: physiology


title: A systems-level analysis of dynamic total-body PET data reveals complex skeletal energy metabolism networks in vivo

abstract:
Bone is now regarded to be a key regulator of a number of metabolic processes, in addition to the regulation of mineral metabolism. However, our understanding of complex bone metabolic interactions at a systems level remains rudimentary, limiting our ability to assess systemic mechanisms underlying diseases and develop novel therapeutics. In vitro molecular biology and bioinformatics approaches have frequently been used to understand the mechanistic changes underlying disease at the cell level, however, these approaches lack the capability to interrogate dynamic multi-bone metabolic interactions in vivo. Here we present a novel and integrative approach to understand complex bone metabolic interactions in vivo using total-body positron emission tomography (PET) network analysis of murine 18F-FDG scans, as a biomarker of glucose metabolism signature in bones. In this report we show that different bones within the skeleton have a unique glucose metabolism and form a complex metabolic network. These data could have important therapeutic implications in the management of the metabolic syndrome and skeletal disease. The application of our approach to clinical and preclinical total-body PET studies promises to reveal further physiological and pathological tissue interactions, which simplistic PET standard uptake values analysis fail to interrogate, extending beyond skeletal metabolism, due to the diversity of PET radiotracers available and under development as well as the advent of clinical total-body PET systems.

One Sentence SummaryBones form a complex metabolic network.


title: AGL16 negatively modulates stress response to balance with growth

abstract: Sensile plants constantly experience environmental stresses in nature. They must have evolved effective mechanisms to balance growth with stress response. Here we report the MADS-box transcription factor AGL16 acting as a negative regulator in stress response. Loss-of-AGL16 confers resistance to salt stress in seed germination, root elongation, and soil-grown plants, while elevated AGL16 expression confers the opposite phenotypes compared with wild type. However, the sensitivity to ABA in seed germination is inversely correlated with AGL16 expression level. Transcriptomic comparison revealed that the improved salt resistance of agl16 mutant was largely attributed to enhanced expression of stress responsive transcriptional factors and genes involved in ABA signaling and ion homeostasis. We further demonstrated that AGL16 directly binds to the CArG motifs in the promoter of HKT1;1, HsfA6a, and MYB102 and represses their expression. Genetic analyses with double mutants also support that HsfA6a and MYB102 are target genes of AGL16. Taken together, our results show that AGL16 acts as negative regulator transcriptionally suppressing key components in stress response and may play a critical role in balancing stress response with growth.


title: Plant trait heterosis is quantitatively associated with expression heterosis of plastid ribosomal proteins

abstract:
The use of hybrids is widespread in agriculture, yet the molecular basis for hybrid vigor (heterosis) remains obscure. To identify molecular components that may contribute to the known higher photosynthetic capacity of maize hybrids, we analyzed proteomic and transcriptomic data from seedling leaf tissues of the hybrid, B73xMo17, and its inbred parents. Subunits of complexes required for protein synthesis in the chloroplast and for the light reactions of photosynthesis were expressed above mid-parent and high-parent levels, respectively. Nuclear and plastid-encoded subunits were expressed similarly and in a dominant pattern with B73 as the high-parent for most proteins. The reciprocal hybrid displayed the same pattern with B73 still the dominant parent. Protein expression patterns were mostly the same in the adult leaf blade. To rank the relevance of expression differences to trait heterosis, we compared seedling leaf protein levels to adult plant heights of 15 hybrids. Expression heterosis (hybrid/mid-parent expression levels) was most positively correlated with plant height heterosis (hybrid/mid-parent plant height) for the plastid-encoded and nuclear-encoded chloroplast ribosomal proteins; the cytosolic ribosomal proteins were slightly less correlated. Ethylene biosynthetic enzymes were expressed below mid-parent levels in the hybrids, and the ethylene biosynthesis mutant, acs2/acs6, largely phenocopied the hybrid proteome, indicating that a reduction in ethylene biosynthesis may mediate the differences between inbreds and their hybrids. Levels of jasmonic acid biosynthetic enzymes were reduced in both acs2/acs6 and the hybrid, and expression heterosis levels of these proteins were the most negatively correlated with plant height heterosis.

Significance StatementHeterosis (hybrid vigor) boosts the productivity and resilience of crops and livestock above the levels of both parents, yet its underlying mechanisms remain unknown. We analyzed expression patterns of proteins in maize hybrids and their inbred parents. Differences in several molecular machines and biochemical pathways were found and quantitatively assessed using a panel of 15 hybrids. Seedling leaf chloroplast ribosomal proteins were able to quantitatively infer levels of adult plant heterosis. Expression levels of biosynthetic enzymes for the stress hormone, ethylene, were reduced in hybrids as was previously reported for the dicot Arabidopsis. Mutation of these genes in a maize inbred caused the proteome to resemble a hybrid. Repression of ethylene biosynthesis may be a conserved component of heterosis physiology.


title: The role of network connectivity on epileptiform activity

abstract: A number of potentially important mechanisms have been identified as key players to generate epileptiform activity, such as genetic mutations, activity-dependent alteration of synaptic functions, and functional network reorganization at the macroscopic level. Here we study how network connectivity at cellular level can affect the onset of epileptiform activity, using computational model networks with different wiring properties. The model suggests that networks connected as in real brain circuits are more resistant to generate seizure-like activity. The results suggest new experimentally testable predictions on the cellular network connectivity in epileptic individuals, and highlight the importance of using the appropriate network connectivity to investigate epileptiform activity with computational models.


title: Audiovisual adaptation is expressed in spatial and decisional codes

abstract: The brain adapts dynamically to the changing sensory statistics of its environment. The neural circuitries and representations that support this cross-sensory plasticity remain unknown. We combined psychophysics and model-based representational fMRI and EEG to characterize how the adult human brain adapts to misaligned audiovisual signals. We show that audiovisual adaptation moulds regional BOLD-responses and fine-scale activity patterns in a widespread network from Heschls gyrus to dorsolateral prefrontal cortices. Crucially, audiovisual recalibration relies on distinct spatial and decisional codes that are expressed with opposite gradients and timecourses across the auditory processing hierarchy. Early activity patterns in auditory cortices encode sounds in a continuous space that flexibly adapts to misaligned visual inputs. Later activity patterns in frontoparietal cortices code decisional uncertainty consistent with these spatial transformations. Our findings demonstrate that regions throughout the auditory processing hierarchy multiplex spatial and decisional codes to adapt flexibly to the changing sensory statistics in the environment.


title: THE COMPLEX HODOLOGICAL ARCHITECTURE OF THE MACAQUE DORSAL INTRAPARIETAL AREAS AS EMERGING FROM NEURAL TRACERS AND DW-MRI TRACTOGRAPHY

abstract: In macaque monkeys, dorsal intraparietal areas are involved in several daily visuo-motor actions. However, their border and sources of cortical afferents remain loosely defined. Through a retrograde tracer and MRI diffusion-based tractography study here we show a complex organization of the dorsal bank of the IPS, which can be subdivided into a rostral area PEip, projecting to the spinal cord, and a caudal area MIP lacking such projections. Both areas include a rostral and a caudal sector, emerging from their ipsilateral, gradient-like connectivity profiles. As tractography estimations, we used the cross-sectional volume of the white matter bundles connecting each area with other parietal and frontal regions, after selecting ROIs corresponding to the injection sites of retrograde tracers. A quantitative analysis between the proportions of cells projecting to all sectors of PEip and MIP along the continuum of the dorsal bank of the IPS and tractography revealed a significant correlation between the two data sets for most connections. Moreover, tractography revealed "false positive" but plausible streamlines awaiting histological validation.


title: Simulating homeostatic, allostatic and goal-directed forms of interoceptive control using Active Inference

abstract:
The adaptive regulation of bodily and interoceptive parameters, such as body temperature, thirst and hunger is a central problem for any biological organism. Here, we present a series of simulations using the framework of Active Inference to formally characterize interoceptive control and some of its dysfunctions. We start from the premise that the goal of interoceptive control is to minimize a discrepancy between expected and actual interoceptive sensations (i.e., a prediction error or free energy). Importantly, living organisms can achieve this goal by using various forms of interoceptive control: homeostatic, allostatic and goal-directed. We provide a computationally-guided analysis of these different forms of interoceptive control, by showing that they correspond to distinct generative models within Active Inference. Furthermore, we illustrate how these generative models may support empirical research, by predicting physiological and brain signals that may accompany both adaptive and maladaptive interoceptive control.

HighlightsO_LIWe use Active Inference to provide formal models of interoceptive control
C_LIO_LIWe model homeostatic, allostatic and goal-directed forms of interoceptive control
C_LIO_LIOur simulations illustrate both adaptive interoceptive control and its dysfunctions
C_LIO_LIWe discuss how the models can aid empirical research on interoception
C_LI


title: Ketamine disrupts gaze patterns during face viewing in the common marmoset

abstract: Faces are stimuli of critical importance for primates. The common marmoset (Callithrix jacchus) is a promising model for investigations of face processing, as this species possesses oculomotor and face processing networks resembling those of macaques and humans. Face processing is often disrupted in neuropsychiatric conditions such as schizophrenia (SZ) and thus it is important to recapitulate underlying circuitry dysfunction preclinically. The N-Methyl-D-aspartate (NMDA) non-competitive antagonist ketamine has been used extensively to model the cognitive symptoms of SZ. Here, we investigated the effects of a subanesthetic dose of ketamine on oculomotor behaviour in marmosets during face viewing. Four marmosets received systemic ketamine or saline injections while viewing phase-scrambled or intact videos of conspecifics faces. To evaluate effects of ketamine on scan paths during face viewing, we identified regions of interest in each face video, and classified locations of saccade onsets and landing positions within these areas. A preference for the snout over eye regions was observed following ketamine administration. In addition, regions in which saccades landed could be significantly predicted by saccade onset region in the saline but not the ketamine condition. No significant drug effects were observed for phase-scrambled videos. Effects on saccade control were limited to a reduction in saccade amplitudes during viewing of scrambled videos. Thus, ketamine induced a significant disruption of scan paths during viewing of conspecific faces but limited effects on saccade motor control. These findings support the use of ketamine in marmosets for investigating changes in neural circuits underlying social cognition in neuropsychiatric disorders.


title: Artificial Neurovascular Network (ANVN) to Study the Accuracy Vs. Efficiency Trade-Off in an Energy Dependent Neural Network

abstract:
AbstractArtificial feedforward neural networks perform a wide variety of classification and function approximation tasks with high accuracy. Unlike their artificial counterparts, biological neural networks require a supply of adequate energy delivered to single neurons by a network of cerebral microvessels. Since energy is a limited resource, a natural question is whether the cerebrovascular network is capable of ensuring maximum performance of the neural network while consuming minimum energy? Should the cerebrovascular network also be trained, along with the neural network, to achieve such an optimum?

In order to answer the above questions in a simplified modeling setting, we constructed an Artificial Neurovascular Network (ANVN) comprising a multilayered perceptron (MLP) connected to a vascular tree structure. The root node of the vascular tree structure is connected to an energy source, and the terminal nodes of the vascular tree supply energy to the hidden neurons of the MLP. The energy delivered by the terminal vascular nodes to the hidden neurons determines the biases of the hidden neurons. The "weights" on the branches of the vascular tree depict the energy distribution from the parent node to the child nodes. The vascular weights are updated by a kind of "backpropagation" of the energy demand error generated by the hidden neurons.

We observed that higher performance was achieved at lower energy levels when the vascular network was also trained along with the neural network. This indicates that the vascular network needs to be trained to ensure efficient neural performance. We observed that below a certain network size, the energetic dynamics of the network in the per capita energy consumption vs. classification accuracy space approaches a fixed-point attractor for various initial conditions. Once the number of hidden neurons increases beyond a threshold, the fixed point appears to vanish, giving place to a line of attractors. The model also showed that when there is a limited resource, the energy consumption of neurons is strongly correlated to their individual contribution to the networks performance.

Author summaryThe limited availability of resources contributed to a significant role in shaping evolution. The brain is also no different. It is known to have tremendous computing power at a significantly lower cost than artificial computing systems. The artificial neural networks aim typically at minimizing output error and maximizing accuracy. A biological network like the brain has an added constraint of energy availability, which might force it to choose an optimal solution that provides the best possible accuracy while consuming minimum energy. The intricate vascular network which ensures adequate energy to the brain might be a systematically trained layout rather than a hard-wired anatomical structure. Through this work, we intend to explore how the artificial neural network would behave if it were made dependent on an energy supply network and how the training of the energy supply network would influence the performance of the neural network. Our model concluded that training of a vascular energy network is highly desirable, and when the size of the neural network is small, the energy consumed by each neuron is a direct readout on its contribution to the network performance.


title: Human primed endothelial colony forming cells exert neuroprotective effects in the growth restricted newborn piglet

abstract:
The fetal brain is particularly vulnerable to the detrimental effects of fetal growth restriction (FGR) with subsequent abnormal neurodevelopment being common. There are no current treatments to protect the FGR newborn from lifelong neurological disorders. This study examines whether pure fetal mesenchymal stem cells and endothelial colony forming cells (ECFC) from the human term placenta are neuroprotective through modulating neuroinflammation and supporting the brain vasculature. We determined that one dose of these primed ECFCs (pECFC) on the first day of life to the newborn FGR piglet improved damaged vasculature, restored the neurovascular unit, reduced brain inflammation and improved adverse neuronal and white matter changes present in the FGR newborn piglet brain. These findings could not be reproduced using mesenchymal stromal cells alone. These results demonstrate pECFC treatment exerts beneficial effects on multiple cellular components in the FGR brain and act as a neuroprotectant.

One Sentence SummaryStem cell treatment improves brain outcomes in the growth restricted newborn


title: FIBRIN POLYMER ON THE SURFACE OF BIOMATERIAL IMPLANTS DRIVES THE FOREIGN BODY REACTION

abstract: ABSTRACTImplantation of biomaterials and medical devices in the body triggers the foreign body reaction (FBR) which is characterized by macrophage fusion at the implant surface leading to the formation of foreign body giant cells and the development of the fibrous capsule enveloping the implant. While adhesion of macrophages to the surface is an essential step in macrophage fusion and implanted biomaterials are known to rapidly acquire a layer of host proteins, a biological substrate that is responsible for this process in vivo is unknown. Here we show that mice with genetically-imposed fibrinogen deficiency display a dramatic reduction of macrophage fusion on implanted biomaterials and are protected from the formation of fibrin-containing granulation tissue, a precursor of the fibrous capsule. Furthermore, macrophage fusion on biomaterials implanted in FibAEK mice that express a mutated form of fibrinogen incapable of thrombin-mediated polymerization was strongly reduced. Surprisingly, despite the lack of fibrin, the capsule was formed in FibAEK mice, although it had a different composition and distinct mechanical properties than that in wild-type mice. Specifically, while mononuclear -SMA-expressing macrophages embedded in the capsule of both strains of mice secreted collagen, the amount of collagen and its density in the tissue of FibAEK mice was reduced. These data identify fibrin polymer as a key biological substrate driving the development of the FBR.

category: immunology


title: Reporter gene assay for membrane fusion of extracellular vesicles

abstract: AbstractExtracellular vesicles (EVs) secreted by living cells are expected to deliver biological cargo molecules, including RNA and proteins, to the cytoplasm of recipient cells. There is an increasing need to understand the mechanism of intercellular cargo delivery by EVs. However, the lack of a feasible bioassay has hampered our understanding of the biological processes of EV uptake, membrane fusion, and cargo delivery to recipient cells. Here, we describe a reporter gene assay that can measure the membrane fusion efficiency of EVs during cargo delivery to recipient cells. When EVs containing tetracycline transactivator (tTA)-fused tetraspanins are internalized by recipient cells and fuse with cell membranes, the tTA domain is exposed to the cytoplasm and cleaved by protease to induce tetracycline responsive element (TRE)-mediated reporter gene expression in recipient cells. This assay (designated as EV-mediated tetraspanin-tTA delivery assay, ETTD assay), enabled us to assess the cytoplasmic cargo delivery efficiency of EVs in recipient cells. With the help of a vesicular stomatitis virus-derived membrane fusion protein, the ETTD assay could detect significant enhancement of cargo delivery efficiency of EVs. Furthermore, the ETTD assay could evaluate the effect of potential cargo delivery enhancers/inhibitors. Thus, the ETTD assay may contribute to a better understanding of the underlying mechanism of the cytoplasmic cargo delivery by EVs.