title: Unveiling the neural correlates of habit in the dorsal striatum

abstract: We have recently reported sustained inhibition in the dorsomedial striatum (DMS) and sustained excitation in the dorsolateral striatum (DLS) during execution of a lever press sequence in a discrete-trials task promoting habit. This sustained dorsostriatal activity was present early on, and did not clearly change in step with improved performance over ten training sessions. Early onset of sequence-related neural activity could have resulted from rapid habitual learning promoted by presentation of lever cues, predicting reward availability and delivery. To test this hypothesis, we compared DLS and DMS spiking activity in the discrete trials habit-promoting task with two task variants that promote goal-directed behavior. Comparison of the three tasks revealed that mean neuronal spiking activity was generally sustained across the lever press sequence in the task promoting habit and characterized by overall excitation in DLS and inhibition in DMS relative to baseline. In contrast, mean activity differences in DLS and DMS were much less prominent, and most changes occurred transiently around individual lever presses, in the tasks promoting goal-directed behavior. These results indicate that sequence delineation cues, such as the lever cues in these studies, promote habitual behavior and that this habitual behavior is encoded in the striatum by cue-triggered sustained DLS excitation and DMS inhibition that likely reflects cue-elicited behavioral chunking.


title: Differentiation of exhausted CD8 T cells after termination of chronic antigen stimulation stops short of achieving functional T cell memory

abstract: T cell exhaustion is associated with failure to clear chronic infections and malignant cells. Defining the molecular mechanisms of T cell exhaustion and reinvigoration is essential to improving immunotherapeutic modalities. Analysis of antigen-specific CD8+ T cells before and after antigen removal in human hepatitis C virus (HCV) infection confirmed pervasive phenotypic, functional, and transcriptional differences between exhausted and memory CD8+ T cells. After viral cure, we observed broad phenotypic and transcriptional changes in clonally stable exhausted T-cell populations suggesting differentiation towards a memory-like profile. However, functionally, the cells showed little improvement and critical transcriptional regulators remained in the exhaustion state. Notably, T cells from chronic HCV infection that were exposed to antigen for shorter periods of time because of viral escape mutations were functionally and transcriptionally more similar to memory T cells from spontaneously resolved acute HCV infection. Thus, duration of T cell stimulation impacts the ability to recover from exhaustion, as antigen removal after long-term T cell exhaustion is insufficient for the development of key T cell memory characteristics.

category: immunology


title: Artificial mosaic brain evolution of relative telencephalon size improves cognitive performance in the guppy (Poecilia reticulata)

abstract: The telencephalon is a brain region believed to have played an essential role during cognitive evolution in vertebrates. However, till now, all the evidence on the evolutionary association between telencephalon size and cognition stem from comparative studies. To experimentally investigate the potential evolutionary association between cognitive abilities and telencephalon size, we used male guppies artificially selected for large and small telencephalon relative to the rest of the brain. In a detour task, we tested a functionally important aspect of executive cognitive ability; inhibitory control abilities. We found that males with larger telencephalon outperformed males with smaller telencephalon. They showed faster improvement in performance during detour training and were more successful in reaching the food reward without touching the transparent barrier. Together, our findings provide the first experimental evidence showing that evolutionary enlargements of relative telencephalon size confer cognitive benefits, supporting an important role for mosaic brain evolution during cognitive evolution.

category: ecology


title: Roads as ecological traps for giant anteaters

abstract:
Wildlife-vehicle collisions (WVC) represent a serious source of mortality for many species, threatening local populations persistence while also carrying a high economic and human safety cost. Animals may adapt their behaviour to road associated threats, but roadside resources can act as attractants, providing misleading signals about the quality of roadside habitats, ultimately acting as an ecological trap. Yet, the extent to which individuals modify their behaviour and space use to roads is largely unknown for most taxa. Using fine-scale movement data from 41 giant anteaters (Myrmecophaga tridactyla), tracked in the Brazilian Cerrado, we aimed to identify facets of movement behaviour that might exhibit plasticity to roads and traffic volume. Specifically, the analysis of daily and instantaneous movement speeds, home range characteristics, and crossing rates/times, allowed us to test for an effect of road proximity, traffic volume and natural linear features on movement behaviour. We found no effect of road proximity or traffic volume on space use or movement behaviour. While individuals tended to reduce their movement speed when approaching roads and crossed roads ~3 times less than would have been expected by random chance, none of the highways we monitored were impervious. The majority of tracked anteaters living near roads (<2km) crossed them, with higher crossing rates for males. Consequently, habitat near roads may function as an ecological trap where healthy individuals occupy the territories nearby or bisected by roads but eventually are road-killed given their regular crossings, leaving the territory vacant for subsequent occupation. Crucially, we found no evidence that anteaters actively searched for passage structures to cross the roads. This suggests that crossing structures alone are unlikely to mitigate WVC induced mortality. Our research reinforces the need to implement fencing, properly linked to existing passages, and minimising the amount of night-time driving to reduce the number of WVCs.

Article Impact StatementAnalyses of giant anteater movement show how roads act as ecological traps, reinforcing the need for fencing and reduced night-time driving.


title: A global map of human pressures on tropical coral reefs

abstract: As human activities on the worlds oceans intensify, mapping human pressures is essential to develop appropriate conservation strategies and prioritize investments with limited resources. Here, we map non-climatic pressures on coral reefs using the latest quantitative data layers on fishing, nitrogen and sediment pollution, coastal and industrial development, and tourism. Across 54,596 coral reef pixels worldwide, we identify the top-ranked local pressure and estimate a cumulative pressure index mapped at 0.05-degree ([~]5 km) resolution. Fishing was the most common top-ranked pressure followed by water pollution (nutrients and sediments), although there is substantial variation by regions. We also find that local pressures are similar inside and outside a proposed global portfolio of coral reef climate refugia. We provide the best available information to inform critical conservation strategies and ensure local pressures are effectively managed to increase the likelihood of the persistence of coral reefs to climate change.


title: The evolution of germ-soma specialization under different genetic and environmental effects

abstract: Division of labor exists at different levels of biological organization - from cell colonies to human societies. One of the simplest examples of the division of labor in multicellular organisms is germ-soma specialization, which plays a key role in the evolution of organismal complexity. Here we formulate and study a general mathematical model exploring the emergence of germ-soma specialization in colonies of cells. We consider a finite population of colonies competing for resources. Colonies are of the same size and are composed by asexually reproducing haploid cells. Each cell can contribute to activity and fecundity of the colony, these contributions are traded-off. We assume that all cells within a colony are genetically identical but gene expression is affected by variation in the microenvironment experienced by individual cells. Through analytical theory and evolutionary agent-based modeling we show that the shape of the trade-off relation between somatic and reproductive functions, the type and extent of variation in within-colony microenvironment, and, in some cases, the number of genes involved, are important predictors of the extent of germ-soma specialization. Specifically, increasing convexity of the trade-off relation, the number of different environmental gradients acting within a colony, and the number of genes (in the case of random microenvironmental effects) promote the emergence of germ-soma specialization. Overall our results contribute towards a better understanding of the role of genetic, environmental, and microenvironmental factors in the evolution of germ-soma specialization.

category: evolutionary biology


title: Reconstructing genotypes from GWAS Summary Statistics

abstract: The emergence of genomewide association studies (GWAS) has led to the creation of large repositories of human genetic variation, creating enormous opportunities for genetic research and worldwide collaboration. Methods that are based on GWAS summary statistics seek to leverage such records, overcoming barriers that often exist in individual-level data access while also offering significant computational savings. Here, we propose a novel framework that can reconstruct allelic and genotypic counts/frequencies for each SNP from case-control GWAS summary statistics. Our framework is simple and efficient without the need of any complicated underlying assumptions. Illustrating the great potential of this framework we also propose three summary-statistics-based applications implemented in a new software package (ReACt): GWAS meta-analysis (with and without sample overlap), case-case GWAS, and, for the first time, group polygenic risk score (PRS) estimation. We evaluate our methods against the current state-of-the-art on both synthetic data and real genotype data and show high performance in power and error control. Our novel group PRS method based on summary statistics could not be achieved prior to our proposed framework. We demonstrate here the potential applications and advantages of this approach. Our work further highlights the great potential of summary-statistics-based methodologies towards elucidating the genetic background of complex disease and opens up new avenues for research.

category: genetics


title: Reconstructing SNP Allele and Genotype Frequencies from GWAS Summary Statistics


title: Comparison Of The Drug Entrapment Efficiency Of Almond Gum (Badam Pisin) To Span-60 Niosomes By Folin-Ciocalteu Assay

abstract: Almond gum (Badam Gum/ Badam Pisin) is a natural polymer composed of mainly carbohydrates (>90%) which makes it a potential candidate in targeted drug delivery. It contains 46% L-arabinose which is known to have fluid entrapment capacity. Various methods of drug targeting against tumor have been developed but due to poor solubility in body fluids, the bioavailability of the drug is reduced and so is its effectiveness. Almond gum is known to be water-soluble so the required bioavailability will be achieved and the drug dosage will also be minimal. Since it is of natural origin side effects will be less compared to that of artificially prepared drugs. Studies show that almond gum is known to have various health benefits including increasing immunity and acting as a coolant. Terminalia catappa (Indian almond), the source of almond gum is abundant in the Indian subcontinent hence making it more economical than chemical surfactants. The objective of this study is to determine whether Almond gum has a higher drug entrapment efficiency than that of Niosomes.

category: bioengineering


title: Integrated spatial multi-omics reveals fibroblast fate during tissue repair

abstract: In the skin, tissue injury results in fibrosis in the form of scars composed of dense extracellular matrix deposited by fibroblasts. The therapeutic goal of regenerative wound healing has remained elusive in part because principles of fibroblast programming and adaptive response to injury remain incompletely understood. Here, we present a multimodal -omics platform for the comprehensive study of cell populations in complex tissue, which has allowed us to characterize the cells involved in wound healing across both time and space. We employ a stented wound model that recapitulates human tissue repair kinetics and multiple Rainbow transgenic lines to precisely track fibroblast fate during the physiologic response to injury. Through integrated analysis of single cell chromatin landscapes and gene expression states, coupled with spatial transcriptomic profiling, we are able to impute fibroblast epigenomes with temporospatial resolution. This has allowed us to define the mechanisms controlling cell fate during migration, proliferation, and differentiation following tissue injury and thereby reexamine the canonical phases of wound healing. These findings have broad implications for the study of tissue repair in complex organ systems.

category: bioinformatics


title: ARIC: Accurate and robust inference of cell type proportions from bulk gene expression or DNA methylation data

abstract: Quantifying the cell proportions, especially for rare cell types in some scenarios, is of great value to track signals related to certain phenotypes or diseases. Although some methods have been pro-posed to infer cell proportions from multi-component bulk data, they are substantially less effective for estimating rare cell type proportions since they are highly sensitive against feature outliers and collinearity. Here we proposed a new deconvolution algorithm named ARIC to estimate cell type proportions from bulk gene expression or DNA methylation data. ARIC utilizes a novel two-step marker selection strategy, including component-wise condition number-based feature collinearity elimination and adaptive outlier markers removal. This strategy can systematically obtain effective markers that ensure a robust and precise weighted {upsilon}-support vector regression-based proportion prediction. We showed that ARIC can estimate fractions accurately in both DNA methylation and gene expression data from different experiments. Taken together, ARIC is a promising tool to solve the deconvolution problem of bulk data where rare components are of vital importance.


title: Curvature-driven feedback on aggregation-diffusion of proteins in lipid bilayers

abstract: AO_SCPLOWBSTRACTC_SCPLOWMembrane bending is an extensively studied problem from both modeling and experimental perspectives because of the wide implications of curvature generation in cell biology. Many of the curvature generating aspects in membranes can be attributed to interactions between proteins and membranes. These interactions include protein diffusion and formation of aggregates due to protein-protein interactions in the plane of the membrane. Recently, we developed a model that couples the in-plane flow of lipids and diffusion of proteins with the out-of-plane bending of the membrane. Building on this work, here, we focus on the role of explicit aggregation of proteins on the surface of the membrane in the presence of membrane bending and diffusion. We develop a comprehensive framework that includes lipid flow, membrane bending energy, the entropy of protein distribution, and an explicit aggregation potential and derive the governing equations. We compare this framework to the Cahn-Hillard formalism to predict the regimes in which the proteins form patterns on the membrane. We demonstrate the utility of this model using numerical simulations to predict how aggregation and diffusion, coupled with curvature generation, can alter the landscape of membrane-protein interactions.

category: biophysics


title: Clusterin in Alzheimer's disease: an amyloidogenic inhibitor of amyloid formation

abstract: Clusterin is a heterodimeric glycoprotein (- and {beta}-chain), which has been described as an extracellular molecular chaperone. In humans, clusterin is an amyloid associated protein, co-localizing with fibrillar deposits in several amyloidoses, including Alzheimers disease. To clarify its potential implication in amyloid formation, we located aggregation-prone regions within the sequence of clusterin -chain, via computational methods. We had peptide-analogues of each region chemically synthesized and experimentally demonstrated that all of them can form amyloid-like fibrils. We also provide evidence that the same peptide-analogues can inhibit amyloid-{beta} fibril formation. These findings elucidate parts of the molecular mechanism in which clusterin inhibits amyloid formation. At the same time, they hint that molecular chaperones with amyloidogenic properties might have a role in the regulation of amyloid formation, essentially acting as functional amyloids.


title: Oncogenic RAS activity predicts response to chemotherapy and outcome in lung adenocarcinoma

abstract: Activating mutations in the driver oncogene KRAS occur in 32% of lung adenocarcinomas, leading to more aggressive disease and resistance to therapy in preclinical studies. However, the association between KRAS mutational status and patient outcome or response to treatment remains unclear, likely due to additional events modulating RAS pathways. To obtain a broader measure of RAS pathway activation beyond KRAS mutation only, we developed RAS84, a transcriptional signature optimised to capture RAS oncogenic activity in lung adenocarcinoma. Using RAS84 to classify lung cell lines, we show that RAS transcriptional activity outperforms KRAS mutation to predict resistance to chemotherapy drugs in vitro. We report that 84% of lung adenocarcinomas show clear transcriptional evidence of RAS oncogenic activation, falling into four groups characterised by coincident mutation of STK11/LKB1, TP53 or CDKN2A. Given that 65% of these RAS pathway active tumours do not have KRAS mutations, we find that the classifications developed when considering only KRAS mutant tumours have significance in a much broader cohort of patients. Critically, patients in the highest RAS activity groups show adverse clinical outcome and reduced response to chemotherapy. The stratification of patients using gene expression patterns linked to oncogenic RAS signalling activity instead of genetic alterations in cancer genes could ultimately help clinical decision making.

category: cancer biology


title: Temporal dynamics of base excision / single-strand break repair protein complex assembly and disassembly are modulated by the PARP1/NAD+/SIRT6 axis

abstract: Assembly and disassembly of DNA repair protein complexes at sites of DNA damage is essential to maintain genomic integrity. We investigated factors coordinating assembly of the base excision repair (BER) proteins, DNA polymerase {beta} (Pol{beta}) and XRCC1, to DNA lesion sites, identifying a new role for Pol{beta} in regulating XRCC1 disassembly from DNA repair complexes and conversely, demonstrating Pol{beta}s dependence on XRCC1 for complex assembly. RealPAR, a genetically-encoded probe for live cell imaging of poly(ADP-ribose) (PAR), reveals that Pol{beta} and XRCC1 require PAR for repair complex assembly and PAR degradation for disassembly. We find that BER complex assembly is further modulated by attenuation / augmentation of NAD+ biosynthesis. Finally, SIRT6 does not regulate PARP1 activation but impairs XRCC1 recruitment, leading to diminished Pol{beta} abundance at sites of DNA damage. These findings highlight coordinated yet independent roles for both PARP1 and SIRT6 and their regulation by NAD+ bioavailability to facilitate BER.


title: The Actin Bundling Protein Fascin Promotes Lung Cancer Growth and Metastasis by Enhancing Glycolysis and PFKFB3 Expression

abstract: Fascin is a pro-metastasis actin bundling protein upregulated in essentially all the metastatic carcinoma. It is believed that fascin promotes cancer cell migration and invasion by facilitating membrane protrusions such as filopodia and invadopodia. Aerobic glycolysis is a key feature of cancer metabolism that provides critical intermediate metabolites for tumor growth and cell proliferation. Here we report that fascin increase glycolysis in lung cancer to promote tumor growth and metastasis. Fascin promotes glycolytic flux by increasing the expression and activities of phosphofructose kinase 1 and 2 (PFK1 and 2). The glycolytic function of fascin depends on activation of YAP1 through its canonical actin bundling activity. Fascin promotes the binding of YAP1 to a TEAD1/4 binding motif located 30 bp upstream of the PFKFB3 transcription start site to activate its transcription. Our interrogation of the TCGA database suggest that the fascin-YAP1-PFKFB3 circuit is likely conserved across different types of cancer. We further showed that the glycolytic function of fascin is essential for promotion of lung cancer growth and metastasis. Importantly, pharmacological inhibitors of fascin could be used to suppress the YAP1-PFKFB3 signaling and inhibit glycolysis in cancer cell lines, organoid cultures and xenograft metastasis models. Taken together, our data reveal an important glycolytic role of fascin in lung cancer metabolism, and suggest that pharmacological inhibitors of fascin could be used to reprogram cancer metabolism in lung cancer and potentially other cancer with fascin upregulation.


title: Perfluorooctanoic Acid Induces Liver and Serum Dyslipidemia in Humanized PPARα Mice Fed an American Diet

abstract: Per- and polyfluoroalkyl substances (PFAS) are pervasive in the environment resulting in nearly universal detection in people. Human serum PFAS concentrations are strongly associated with increased serum low-density lipoprotein cholesterol (LDL-C), and growing evidence suggests an association with serum triacylglycerides (TG). Here, we tested the hypothesis that perfluorooctanoic acid (PFOA) dysregulates liver and serum triacylglycerides in human peroxisome proliferator activated receptor  (hPPAR)-expressing mice fed an American diet. Mice were exposed to PFOA (3.3 mg/l) in drinking water for 6 weeks resulting in a serum concentration of 48 {+/-} 9 g/ml. In male and female hPPAR mice, PFOA increased total liver TG and TG substituted with saturated and monounsaturated fatty acids. Lack of expression of hPPAR alone also increased total liver TG, and PFOA treatment had little effect on liver TG in null mice. In hPPAR mice, PFOA neither significantly increased nor decreased serum TG; however, there was a modest increase in TG associated with very low-density cholesterol particles in both sexes. Across studies, a non-monotonic effect of PFOA on serum TG is evident, with the serum PFOA concentration in this study falling near the "null point" between increasing and decreasing serum TG. Intriguingly, in female PPAR null mice, PFOA significantly increased serum TG, with a similar trend in males. PFOA also modified fatty acid and TG homeostasis-related gene expression in liver, in a hPPAR-dependent manner, but not in adipose. The results reveal the importance of context (serum concentration and genotype) in determining the effect of PFOA on lipid homeostasis.

category: pharmacology and toxicology


title: Plasticity of cold hardiness in the eastern spruce budworm, Choristoneura fumiferana

abstract: High latitude insect populations must cope with extreme conditions, particularly cold temperatures. Insects use a variety of cold hardiness mechanisms to withstand this temperature stress, and these can drive geographic distributions through overwintering mortality. The degree of cold hardiness can be altered by two evolved responses: phenotypic plasticity and local adaptation. Phenotypic plasticity can occur within or between generations (transgenerational plasticity; TGP), and local adaptation can evolve through directional selection in response to regional climatic differences. We used the eastern spruce budworm, Choristoneura fumiferana (Lepidoptera: Tortricidae) as a model to explore the role that variable winter temperatures play in inducing two aspects of plasticity in cold hardiness: TGP and local adaptation in phenotypic plasticity. This species is one of the most destructive boreal forest pests in North America, therefore accurately predicting overwintering survival is essential for effective management. While we found no evidence of TGP in cold hardiness, there was a long-term fitness cost to larvae that experienced repeated cold exposures. We also found evidence of local adaptation in both seasonal and short-term plasticity of cold hardiness. These findings provide evidence for the importance of phenotypic plasticity and local adaptation when modelling species distributions.

category: physiology


title: Cell layer-specific expression of the B-class MADS-box gene PhDEF drives petal tube or limb development in petunia flowers

abstract: Floral homeotic MADS-box transcription factors ensure the correct development of floral organs with all their mature features, i.e. organ shape, size, colour and cellular identity. Furthermore, all plant organs develop from clonally-independent cell layers, deriving from the meristematic epidermal (L1) and internal (L2 and L3) layers. How cells from these distinct layers acquire their floral identities and coordinate their growth to ensure reproducible organ development is unclear. Here we study the development of the Petunia x hybrida (petunia) corolla, which consists of five fused petals forming a tube and pigmented limbs. We present petunia flowers expressing the B-class MADS-box gene PhDEF in the epidermis or in the mesophyll of the petal only, that we called wico and star respectively. Strikingly, the wico flowers form a very small tube while their limbs are almost normal, and the star flowers form a normal tube but very reduced and unpigmented limbs. Therefore, the star and wico phenotypes indicate that in the petunia petal, the epidermis mainly drives limb growth and pigmentation while the mesophyll mainly drives tube growth. As a first step towards the identification of candidate genes involved in specification of petal layer identities and tube/limb development, we sequenced the star and wico whole petal transcriptome at three developmental stages. Among downregulated genes in star petals, we found the major regulator of anthocyanin biosynthesis ANTHOCYANIN 1 (AN1), and we showed that, in vitro, PhDEF directly binds to its terminator sequence, suggesting that it might regulate its expression. Altogether this study shows that layer-specific expression of PhDEF drives petunia tube or limb development in a highly modular fashion, which adds an extra layer of complexity to the petal development process.

category: plant biology


title: The Alzheimer's disease genetic risk factor BIN1 induces isoform-dependent neurotoxicity through early endosome defects

abstract: The Bridging Integrator 1 (BIN1) gene is a major susceptibility gene for Alzheimers disease (AD). Deciphering its pathophysiological role is challenging due to its numerous isoforms. Here we observed in Drosophila that human BIN1 isoform1 (BIN1iso1) overexpression, contrary to BIN1iso8 and BIN1iso9, induced an accumulation of endosomal vesicles and neurodegeneration. Systematic search for endosome regulators able to prevent BIN1iso1-induced neurodegeneration indicated that a defect at the early endosome level is responsible for the neurodegeneration. In human induced neurons (hiNs) and cerebral organoids, BIN1 knock-out resulted in the narrowing of early endosomes. This phenotype was rescued by BIN1iso1 but not BIN1iso9 expression. Finally, BIN1iso1 overexpression also led to an increase in the size of early endosomes and neurodegeneration in hiNs. Altogether, our data demonstrate that the AD susceptibility gene BIN1, and especially BIN1iso1, contributes to early-endosome size deregulation, which is an early pathophysiological hallmark of AD pathology.

category: neuroscience


title: The Alzheimer susceptibility gene BIN1 induces isoform-dependent neurotoxicity through early endosome defects


title: Impaired top-down auditory processing despite extensive single-neuron responses during human sleep

abstract: Sleep in all species is universally defined as a reversible, homeostatically-regulated state of a reduced behavioral responsiveness, with a high arousal threshold in response to external sensory stimulation1. However, it remains unclear whether sleep mainly gates motor output or affects responses along sensory pathways, and whether sleep primarily modulates specific aspects of the sensory response such as feedforward vs. feedback signaling2-7. Here, we simultaneously recorded polysomnography, iEEG, microwire LFPs, and neuronal spiking activity during wakefulness and sleep in 13 epilepsy patients implanted with clinical depth electrodes, while presenting auditory stimuli (e.g. click-trains, words, music). The results revealed robust spiking and induced LFP high-gamma (80-200Hz) power responses during both NREM and REM sleep across the lateral temporal lobe. The magnitude of the responses was only moderately attenuated in sleep, most notably for late responses beyond the early auditory cortex. Nonetheless, sleep responses maintained their tight locking with soundwave envelopes and their information content was only minimally affected. In contrast, a decrease in LFP alpha-beta (10-30Hz) power responses was prevalent in wakefulness but significantly disrupted in sleep. Entrainment to 40 Hz click-trains was comparable across REM sleep and wakefulness, but reduced in NREM sleep. In conclusion, our results establish the presence of extensive and robust auditory responses during sleep while LFP alpha-beta power decrease, likely reflecting top-down processes8-10, is deficient. More broadly, our findings suggest that feedback signalling is key to conscious sensory processing11-13.


title: TDP-43 represses cryptic exon inclusion in FTD/ALS gene UNC13A

abstract: A hallmark pathological feature of neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is the depletion of RNA-binding protein TDP-43 from the nucleus of neurons in the brain and spinal cord. A major function of TDP-43 is as a repressor of cryptic exon inclusion during RNA splicing. Single nucleotide polymorphisms (SNPs) in UNC13A are among the strongest genome-wide association study (GWAS) hits associated with FTD/ALS in humans, but how those variants increase risk for disease is unknown. Here we show that TDP-43 represses a cryptic exon splicing event in UNC13A. Loss of TDP-43 from the nucleus in human brain, neuronal cell lines, and iPSC-derived motor neurons resulted in the inclusion of a cryptic exon in UNC13A mRNA and reduced UNC13A protein expression. Remarkably, the top variants associated with FTD/ALS risk in humans are located in the cryptic exon harboring intron itself and we show that they increase UNC13A cryptic exon splicing in the face of TDP-43 dysfunction. Together, our data provide a direct functional link between one of the strongest genetic risk factors for FTD/ALS (UNC13A genetic variants) and loss of TDP-43 function.


title: The SPARC DRC: Building a resource for the autonomic nervous system community

abstract: The Data and Resource Center (DRC) of the NIH-funded SPARC program is developing databases, connectivity maps and simulation tools for the mammalian autonomic nervous system. The experimental data and mathematical models supplied to the DRC by the SPARC consortium are curated, annotated and semantically linked via a single knowledgebase. A data portal has been developed that allows discovery of data and models both via semantic search and via an interface that includes Google Map-like 2D flatmaps for displaying connectivity, and 3D anatomical organ scaffolds that provide a common coordinate framework for cross-species comparisons. We discuss examples that illustrate the data pipeline, which includes data upload, curation, segmentation (for image data), registration against the flatmaps and scaffolds, and finally display via the web portal, including the link to freely available online computational facilities that will enable neuromodulation hypotheses to be investigated by the autonomic neuroscience community and device manufacturers.


title: Pupil-linked arousal modulates trial-by-trial motor adaptation in humans

abstract: Pupil diameter, under constant illumination, is known to reflect individuals internal states, such as surprise about observation and environmental uncertainty. Despite the growing use of pupillometry in cognitive learning studies as an additional measure for examining internal states, few studies have used pupillometry in human motor learning studies. Here we provide the first detailed characterization of pupil diameter changes in a short-term reach adaptation paradigm. We measured pupil changes in 91 human participants while they adapted to abrupt, gradual, or switching force field conditions. Sudden increases in movement error caused by the introduction/reversal of the force field resulted in strong phasic pupil dilation during movement accompanied by a transient increase in tonic pre-movement baseline pupil diameter in subsequent trials. In contrast, clear changes in pupil responses were absent when the force field was gradually introduced, indicating that error drove the changes in pupil responses. Nevertheless, we found an association between baseline pupil diameter and awareness of the gradually-introduced perturbation assessed post-experimentally. In all experiments, we also found a strong co-occurrence of larger baseline pupil diameter and slower reaction and movement time after each set break. Interestingly, error-induced pupil responses gradually became insensitive after experiencing multiple reversals. Collectively, these results suggest that tonic baseline pupil diameter reflects ones belief about environmental uncertainty, whereas phasic pupil dilation during movement reflects surprise about a sensory outcome (i.e., movement error), and both effects are modulated by novelty. Our results provide a new approach for non-verbally assessing participants internal states during motor learning.


title: Pupil diameter tracked during motor adaptation in humans


title: Individual variability in the human connectome maintains selective cross-modal consistency and shares microstructural signatures

abstract: Individuals are different in their behavioural responses and cognitive abilities. Neural underpinnings of individual differences are largely unknown. Here, by using multimodal imaging data including diffusion MRI, functional MRI and MEG, we show the consistency of interindividual variation of connectivity across modalities. We demonstrated that regional differences in individual variability of structural and functional connectomes is characterized by higher variability in association cortices and lower variability in sensory and visual cortices. This pattern is consistent across all modalities at varying degrees as shown by significant alignment between functional and structural connectome variabilities at several clusters of brain regions. Variability in connectivity is associated with cortical myelin content and microstructural properties of connections. Our findings contribute to understanding of individual differences in functional and structural organization of brain and facilitate fingerprinting applications.


title: Taking aim at the perceptual side of motor learning: Exploring how explicit and implicit learning encode perceptual error information through depth vision

abstract:
Motor learning in visuomotor adaptation tasks results from both explicit and implicit processes, each responding differently to an error signal. While the motor output side of these processes is extensively studied, their visual input side is relatively unknown. We investigated if and how depth perception affects the computation of error information by explicit and implicit motor learning. Two groups of participants threw virtual darts at a virtual dartboard while receiving perturbed endpoint feedback. The Delayed group was allowed to re-aim and their feedback was delayed to emphasize explicit learning, while the Clamped group received clamped cursor feedback which they were told to ignore, and continued to aim straight at the target to emphasize implicit adaptation. Both groups played this game in a highly detailed virtual environment (Depth condition) and in an empty environment (No-Depth condition). The Delayed group showed an increase in error sensitivity under Depth relative to No-Depth conditions. In contrast, the Clamped group adapted to the same degree under both conditions. The movement kinematics of the Delayed participants also changed under the Depth condition, consistent with the target appearing more distant, unlike the Clamped group. A comparison of the Delayed behavioral data with a perceptual task from the same individuals showed that the effect of the Depth condition on the re-aiming direction was consistent with an increase in the scaling of the error distance and size. These findings suggest that explicit and implicit learning processes may rely on different sources of perceptual information.

New & NoteworthyWe leveraged a classic sensorimotor adaptation task to perform a first systematic assessment of the role of perceptual cues in the estimation of an error signal in the 3D space during motor learning. We crossed two conditions presenting different amounts of depth information, with two manipulations emphasizing explicit and implicit learning processes. Explicit learning responded to the visual conditions, consistent with perceptual reports, while implicit learning appeared to be independent of them.


title: Vaccine Hyporesponse Induced By Individual Antibiotic Treatment In Mice And Non-Human Primates Is Diminished Upon Recovery Of The Gut Microbiome

abstract:
Emerging evidence demonstrates a connection between microbiome composition and suboptimal response to vaccines (vaccine hyporesponse). Harnessing the interaction between microbes and the immune system could provide novel therapeutic strategies for improving vaccine response. Currently we do not fully understand the mechanisms and dynamics by which the microbiome influences vaccine response. Using both mouse and non-human primate models, we report that short-term oral treatment with a single antibiotic (vancomycin) results in disruption of the gut microbiome and this correlates with a decrease in systemic levels of antigen-specific IgG upon subsequent parenteral vaccination. We further show that recovery of microbial diversity before vaccination prevents antibiotic-induced vaccine hyporesponse, and that the antigen specific IgG response correlates with the recovery of microbiome diversity. RNA-sequencing analysis of small intestine, spleen, whole blood, and secondary lymphoid organs from antibiotic treated mice revealed a dramatic impact on the immune system, and a muted inflammatory signature is correlated with loss of bacteria from Lachnospiraceae, Ruminococcaceae, and Clostridiaceae. These results suggest that microbially modulated immune pathways may be leveraged to promote vaccine response and will inform future vaccine design and development strategies.

ImportanceAntibiotic-induced gut microbiome disruption has been linked to reduced vaccine efficacy. Despite these observations, there remains a knowledge gap in the specific mechanisms by which antibiotics and the gut microbiome influence vaccine efficacy. We aim to contribute to the fields growing mechanistic understanding by presenting a detailed analysis of antibiotic treatment and recovery as it relates to vaccine response and the microbiome. Using animal models, we show that short-term antibiotic treatment prior to vaccination results in diminished vaccine-specific immune responses, and that these are correlated with specific microbiome signatures. We also demonstrate the converse, in which gut microbiome recovery can result in improved vaccine response. We further reveal that antibiotics can significantly alter multiple relevant immune pathways and this alteration in immune tone may contribute to the vaccine hyporesponse. We expect our findings will enable the continued prosecution of the role of the microbiome in modulating the host immune system.


title: Genomic and epigenomic adaptation in SP-R210 (Myo18A) isoform-deficient macrophages

abstract: 1Macrophages play fundamental roles in regulation of inflammatory responses to pathogens, resolution of inflammation and tissue repair, and maintenance of tissue homeostasis. The long (L) and short (S) isoforms of SP-R210/MYO18A, a macrophage receptor for surfactant protein A (SP-A) and C1q, regulate basal and inflammatory macrophage phenotype at multiple gene expression, translational, and subcellular levels in addition to their SP-A and C1q-mediated functions; disruption of L renders macrophages hyper-inflammatory, although the underlying mechanism had previously been unexplored. We asked whether disruption of the L isoform led to the hyper-inflammatory state via alteration of global genomic responses. RNA sequencing analysis of SP-R210L(DN) macrophages revealed basal and influenza induced upregulation of genes associated with inflammatory pathways, including TLR, RIG-I, NOD, and cytoplasmic DNA signaling, whereas knockdown of both SP-R210 isoforms (L and S) only resulted in increased RIG-I and NOD signaling. Chromatin immunoprecipitation sequencing (ChIP-seq) analysis showed increased genome-wide deposition of the pioneer transcription factor PU.1 in SP-R210L(DN) compared to WT cells. ChIP-seq analysis of histone H3 methylation showed alterations in both repressive (H3K9me3 and H3K27me3) and transcriptionally active (H3K9me3) histone marks. Influenza A virus (IAV) infection, which stimulates an array of cytosolic and TLR-mediated antiviral mechanisms, resulted in differential redistribution between proximal promoter and distal sites and decoupling of PU.1 binding from Toll-like receptor regulated gene promoters in SP-R210L(DN) cells. Our findings suggest that SP-R210L-deficient macrophages are poised with an open PU.1-primed chromatin conformation to rapidly respond to inflammatory and metabolic stimuli.


title: Autophagy Induced by Palmitic Acid: a Brake in NAFLD Neutrophils

abstract:
Innate immune suppression and high blood fatty acid levels are the pathological basis of multiple metabolic diseases. Neutrophil vacuolation is an indicator of the immune status of patients, which is associated with autophagy-dependent granule degradation. Vacuolated neutrophils are observed in ethanol toxicity and septicemia patients due to the changes in their blood constituents, but how about the neutrophils in nonalcoholic fatty liver disease (NAFLD) patient is unknown. Here, we confirmed that an adhesion deficiency and an increased autophagy level existed in NAFLD neutrophils, and the three neutrophil granule subunits, namely, the azurophil granules, specific granules and gelatinase granules, could be engulfed by autophagosomes for degradation, and these autophagy-triggered granule degradation events were associated with vacuolation in palmitic acid (PA)-treated and NAFLD neutrophils. Concordantly, the adhesion-associated molecules CD11a, CD11b, CD18 and Rap1 on the three granule subunits were degraded during PA induced autophagy. Moreover, the cytosolic CD11a, CD11b, CD18 and Rap1 were targeted by Hsc70 and then delivered to lysosomal-like granules for degradation. Notably, in vitro and ex vivo, PA induced autophagy by inhibiting the p-PKC/PKD2 pathway. Overall, we showed that high blood PA level inhibited the p-PKC/PKD2 pathway to induce NAFLD neutrophil autophagy, which promoted the degradation of CD11a, CD11b, CD18 and Rap1 and further decreased the adhesion of neutrophils, thereby impairing the neutrophil function of NAFLD patients. This theory provides a new therapeutic strategy to improve the immune deficiency in NAFLD patients.

Visual Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/438261v1_ufig1.gif" ALT="Figure 1">
View larger version (61K):
org.highwire.dtl.DTLVardef@454a53org.highwire.dtl.DTLVardef@112a7e7org.highwire.dtl.DTLVardef@1cd397forg.highwire.dtl.DTLVardef@7a0058_HPS_FORMAT_FIGEXP  M_FIG C_FIG Key PointsO_LIVacuolation and adhesion deficiency of NAFLD neutrophils are associated with autophagy-dependent granule degradation
C_LIO_LIPA inhibits p-PKC/PKD2 to induce autophagy, which induces the degradation of CD11a, CD11b, CD18 and Rap1 and decreases neutrophil adhesion
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category: cell biology


title: Effect Of Telomerization On The Growth Patterns Of Adult Cutaneous Diploid Fibroblasts

abstract: The article describes effects of telomerization on proliferative activity in cultured cutaneous diploid fibroblasts obtained from an adult men aged 57 years. It is shown that the cells in the control culture initially divide quite actively, but starting from the 27th to the 40th passages, the rate of their division decreases and the time to reach the monolayer increases by about 2 times, and starting from the 42nd passage, the time to reach the monolayer increases by 4-10 times (up to 16-40 days). In a single case, an increase in the doubling time of control non-thelomerized cells was recorded up to 30 times (136 days). The introduction of the telomerase gene allowed cells maintain a high rate of cell division to about 45-47 passages. At the same time, the culture with the telomerase gene exceeds the control culture by 10 passages. Rate of growth the cells with telomerase gene after 48 and up to 57 passages slowed down by 10-18 times (up to 40-73 days). At the 47th passage in the control culture and at the 57th passage in the experimental culture, the cells practically stopped dividing and their number did not increase. The results show that the inclusion of the telomerase gene in adult fibroblasts does not always cancel the limit of cell divisions.


title: The global ocean size-spectrum from bacteria to whales

abstract:
It has long been hypothesized that aquatic biomass is evenly distributed among logarithmic body mass size-classes. Although this community structure has been observed locally among plankton groups, its generality has never been formally tested across all marine life, nor have its impacts by humans been broadly assessed. Here, we bring together data at the global scale to test the hypothesis from bacteria to whales. We find that biomass within most order of magnitude size-classes is indeed remarkably constant, near 1 Gt wet weight (1015 grams), but that bacteria and whales are markedly above and below this value, respectively. Furthermore, human impacts have significantly truncated the upper one-third of the spectrum. Size-spectrum theory has yet to provide an explanation for what is possibly lifes largest scale regularity.

One Sentence SummaryHuman activities have fundamentally altered one of lifes largest scale patterns; a global power law size distribution spanning bacteria to whales.


title: Phylomedicine of mutational processes in somatic cancer cell populations

abstract: Mutational processes in somatic cancer cell populations are constantly changing, leaving their signatures in the accumulated genomic variation in tumors. The inference of mutational signatures from the observed genetic variation enables spatiotemporal tracking of tumor mutational processes that evolve due to cellular environmental changes, mutations, and treatment regimes. Ultimately, mutational patterns illuminate the mechanistic understanding of their evolution in cancer progression. We show that the integration of cancer cell phylogeny with mutational signature deconvolution enables higher-resolution detection of gain and loss of mutational processes within the phylogeny. This approach to analyzing somatic genomic variations in 61 lung cancer patients revealed a high turn-over of mutational processes over time and closely related clonal lineages. Some mutational signatures (e.g., smoking-related) showed a higher propensity to be lost, whereas others (e.g., AID/APOBEC) were gained during lung tumors evolution. These observations shed light on the evolution of mutational processes in somatic cell evolution.


title: Stratification of Risk of Progression to Colectomy in Ulcerative Colitis using Measured and Predicted Gene Expression

abstract: An important goal of clinical genomics is to be able to estimate the risk of adverse disease outcomes. Between 5% and 10% of ulcerative colitis (UC) patients require colectomy within five years of diagnosis, but polygenic risk scores (PRS) utilizing findings from GWAS are unable to provide meaningful prediction of this adverse status. By contrast, in Crohns disease, gene expression profiling of GWAS-significant genes does provide some stratification of risk of progression to complicated disease in the form of a Transcriptional Risk Score (TRS). Here we demonstrate that both measured (TRS) and polygenic predicted gene expression (PPTRS) identify UC patients at 5-fold elevated risk of colectomy with data from the PROTECT clinical trial and UK Biobank population cohort studies, independently replicated in an NIDDK-IBDGC dataset. Prediction of gene expression from relatively small transcriptome datasets can thus be used in conjunction with transcriptome-wide association studies to stratify risk of disease complications.


title: A literature-derived knowledge graph augments the interpretation of single cell RNA-seq datasets

abstract: Technology to generate single cell RNA-sequencing (scRNA-seq) datasets and tools to annotate them have rapidly advanced in the past several years. Such tools generally rely on existing transcriptomic datasets or curated databases of cell type defining genes, while the application of scalable natural language processing (NLP) methods to enhance analysis workflows has not been adequately explored. Here we deployed an NLP framework to objectively quantify associations between a comprehensive set of over 20,000 human protein-coding genes and over 500 cell type terms across over 26 million biomedical documents. The resultant gene-cell type associations (GCAs) are significantly stronger between a curated set of matched cell type-marker pairs than the complementary set of mismatched pairs (Mann Whitney p < 6.15x10-76, r = 0.24; cohens D = 2.6). Building on this, we developed an augmented annotation algorithm that leverages GCAs to categorize cell clusters identified in scRNA-seq datasets, and we tested its ability to predict the cellular identity of 185 clusters in 13 datasets from human blood, pancreas, lung, liver, kidney, retina, and placenta. With the optimized settings, the true cellular identity matched the top prediction in 66% of tested clusters and was present among the top five predictions for 94% of clusters. Further, contextualization of differential expression analyses with these GCAs highlights poorly characterized markers of established cell types, such as CLIC6 and DNASE1L3 in retinal pigment epithelial cells and endothelial cells, respectively. Taken together, this study illustrates for the first time how the systematic application of a literature derived knowledge graph can expedite and enhance the annotation and interpretation of scRNA-seq data.

category: genomics


title: Statistical properties of the MetaCore network of protein-protein interactions

abstract: The MetaCore commercial database describes interactions of proteins and other chemical molecules and clusters in the form of directed network between these elements, viewed as nodes. The number of nodes goes beyond 40 thousands with almost 300 thousands links between them. The links have essentially bi-functional nature describing either activation or inhibition actions between proteins. We present here the analysis of statistical properties of this complex network applying the methods of the Google matrix, PageRank and CheiRank algorithms broadly used in the frame of the World Wide Web, Wikipedia, the world trade and other directed networks. We specifically describe the Ising PageRank approach which allows to treat the bi-functional type of protein-protein interactions. We also show that the developed reduced Google matrix algorithm allows to obtain an effective network of interactions inside a specific group of selected proteins. This method takes into account not only direct protein-protein interactions but also recover their indirect nontrivial couplings appearing due to summation over all the pathways passing via the global bi-functional network. The developed analysis allows to espablish an average action of each protein being more oriented to activation or inhibition. We argue that the described Google matrix analysis represents an efficient tool for investigation of influence of specific groups of proteins related to specific diseases.


title: matUtils: Tools to Interpret and Manipulate Mutation Annotated Trees

abstract: The vast scale of SARS-CoV-2 sequencing data has made it increasingly challenging to comprehensively analyze all available data using existing tools and file formats. To address this, we present a database of SARS-CoV-2 phylogenetic trees inferred with unrestricted public sequences, which we update daily to incorporate new sequences. Our database uses the recently-proposed mutation-annotated tree (MAT) format to efficiently encode the tree with branches labeled with parsimony-inferred mutations as well as Nextstrain clade and Pango lineage labels at clade roots. As of June 9, 2021, our SARS-CoV-2 MAT consists of 834,521 sequences and provides a comprehensive view of the virus evolutionary history using public data. We also present matUtils - a command-line utility for rapidly querying, interpreting and manipulating the MATs. Our daily-updated SARS-CoV-2 MAT database and matUtils software are available at http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/ and https://github.com/yatisht/usher, respectively.


title: A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees


title: Privacy Preserving RNA-Model Validation Across Laboratories

abstract: Reproducibility of results obtained using RNA data across labs remains a major hurdle in cancer research. Often, molecular predictors trained on one dataset cannot be applied to another due to differences in RNA library preparation and quantification. While current RNA correction algorithms may overcome these differences, they require access to all patient-level data, which necessitates the sharing of training data for predictors when sharing predictors. Here, we describe SpinAdapt, an unsupervised RNA correction algorithm that enables the transfer of molecular models without requiring access to patient-level data. It computes data corrections only via aggregate statistics of each dataset, thereby maintaining patient data privacy. Furthermore, SpinAdapt can correct new samples, thereby enabling evaluation of validation cohorts. Despite an inherent tradeoff between privacy and performance, SpinAdapt outperforms current correction methods that require patient-level data access. We expect this novel correction paradigm to enhance research reproducibility and patient privacy. Finally, SpinAdapt lays a mathematical framework that can be extended to other -omics modalities.


title: Detection of Junctional Ectopic Tachycardia by Central Venous Pressure

abstract: Central venous pressure (CVP) is the blood pressure in the venae cavae, near the right atrium of the heart. This signal waveform is commonly collected in clinical settings, and yet there has been limited discussion of using this data for detecting arrhythmia and other cardiac events. In this paper, we develop a signal processing and feature engineering pipeline for CVP waveform analysis. Through a case study on pediatric junctional ectopic tachycardia (JET), we show that our extracted CVP features reliably detect JET with comparable results to the more commonly used electrocardiogram (ECG) features. This machine learning pipeline can thus improve the clinical diagnosis and ICU monitoring of arrhythmia. It also corroborates and complements the ECG-based diagnosis, especially when the ECG measurements are unavailable or corrupted.


title: Real-time lens-free visualization of strong light scattering by biogenic guanine platelets

abstract: Microscopic observation system without lens has a potential to realize ubiquitous sensing network detecting micro/nano biological hazards to modern society because the lens-free imaging device can provide an extremely compact microscope. In addition to in slico micro-mirrors, liquid injectable organic micro-mirrors should be found and utilized for achieving the ideal imaging device for micro/nano objects. This study demonstrates a high contrast lens-free image of the projection from a biogenic guanine platelet floating in water. The fish guanine platelet generated intense and high directional diffraction as well as regular reflection of incident light. The light projection from guanine platelet individually formed an intense platelet-shaped image in real-time on CMOS image sensor arrays. A dynamic projection movie of the guanine platelet, the size of which was approximately 20 [~] 40 m x 5 [~] 10 m x 100 nm in thickness, was obtained in a small aqueous droplet whose height was less than 2 mm. The developed new lens-free technology using biogenic tiny platelet has an ability to portably visualize movements of the micro/nano objects interacting with the platelet. The compact lens-free inspection can contribute to keep our society in safe.


title: Autologous humanized mouse models of iPSC-derived tumors allow for the evaluation and modulation of cancer-immune cell interactions

abstract:
Modeling the tumor-immune cell interactions in humanized mice is complex and limits drug development. Here, we generated easily accessible tumor models by transforming either primary skin fibroblasts or iPSC-derived cell lines injected in immune-deficient mice reconstituted with human autologous immune cells. Our results showed that either fibroblastic, hepatic or neural tumors were all efficiently infiltrated and partially or totally rejected by autologous immune cells in humanized mice. Characterization of tumor immune infiltrates revealed high expression levels of the dysfunction markers Tim3 and PD-1 in T cells and an enrichment in regulatory T cell suggesting rapid establishment of an immunosuppressive microenvironment. Inhibition of PD-1 by Nivolumab in humanized mice resulted in an increased immune cell infiltration and a slight decrease in tumor growth. We expect these versatile and accessible cancer models will facilitate preclinical studies and the evaluation of autologous cancer immunotherapies across a range of different tumor cell types.

SIGNIFICANCE STATEMENTPreclinical models capable of providing an environment where human tumors are confronted with autologous immune cells are not easily accessible and limit drug development. As an alternative we generated genetically-defined tumor cell lines from primary and iPSC-derived cells for the evaluation of cancer-immune cell interactions in autologous humanized mice.


title: Quantitative resistance loci to southern rust mapped in a temperate maize diversity panel

abstract: Southern rust is a severe foliar disease of maize resulting from infection with the obligate biotrophic fungus, Puccinia polysora. The disease reduces photosynthetic productivity which reduces yields with the greatest yield losses (up to 50%) associated with earlier onset infections. Puccinia polysora urediniospores overwinter only in tropical and subtropical regions but cause outbreaks when environmental conditions favor initial infection. Increased temperatures and humidity during the growing season, combined with an increased frequency of moderate winters are likely to increase the frequency of severe southern rust outbreaks in the US corn belt. In summer 2020, a severe outbreak of Southern Rust was observed in eastern Nebraska (NE), USA. Disease incidence severity showed significant variation among maize genotypes. A replicated maize association panel planted in Lincoln, NE was scored for disease severity. Genome wide association studies identified four loci associated with significant quantitative variation in disease severity which were associated with candidate genes with plausible links to quantitative disease resistance and a transcriptome wide association study conducted identified additional associated genes. Together these results indicate substantial diversity in resistance to southern rust exists among current temperate adapted maize germplasm, including several candidate loci which may explain observed variation in resistance to southern rust.


title: Is it that simple? Linear mapping models in cognitive neuroscience

abstract: Many cognitive neuroscience studies use large feature sets to predict and interpret brain activity patterns. Feature sets take many forms, from human stimulus annotations to representations in deep neural networks. Of crucial importance in all these studies is the mapping model, which defines the space of possible relationships between features and neural data. Until recently, most encoding and decoding studies have used linear mapping models. Increased availability of large datasets and computing resources has allowed some researchers to employ more flexible nonlinear mapping models instead; however, the question of whether nonlinear mapping models can yield meaningful scientific insights remains debated. Here, we discuss the choice of a mapping model in the context of three overarching desiderata: predictive accuracy, interpretability, and biological plausibility. We show that, contrary to popular intuition, these desiderata do not map cleanly onto the linear/nonlinear divide; instead, each desideratum can refer to multiple research goals, each of which imposes its own constraints on the mapping model. Moreover, we argue that, instead of categorically treating the mapping models as linear or nonlinear, we should instead aim to estimate the complexity of these models. We show that, in many cases, complexity provides a more accurate reflection of restrictions imposed by various research goals. Finally, we outline several complexity metrics that can be used to effectively evaluate mapping models.


title: Beyond linear regression: mapping models in cognitive neuroscience should align with research goals


title: Electrical Propagation of Condensed and Diffuse Ions Along Actin Filaments

abstract: In this article, we elucidate the role of divalent ion condensation and high polarization of immobile water molecules in the condensed layer on the propagation of ionic calcium waves along actin filaments. We introduced a novel electrical triple layer model and used a non-linear Debye-Huckel theory with a non-linear, dissipative, electrical transmission line model to characterize the physicochemical properties of each monomer in the filament. This characterization is carried out in terms of an electric circuit model containing monomeric flow resistances and ionic capacitances in both the condensed and diffuse layers. In our studies, we characterized the biocylindrical actin filament model using a high resolution molecular structure. We considered resting and excited states of a neuron using representative mono and divalent electrolyte mixtures. Additionally, we used 0.05V and 0.15V voltage inputs to study ionic waves in voltage clamp experiments on actin filaments. Our results reveal that the physicochemical properties characterizing the condensed and diffuse layers lead to different electrical conduction mediums depending on the ionic species and the neuron state. This region specific propagation mechanism provides a more realistic avenue of delivery by way of cytoskeleton filaments for larger charged cationic species. This new direct path for transporting divalent ions might be crucial for many electrical processes that connect different compartments of the neuron to the soma.


title: Common ALS/FTD risk variants in UNC13A exacerbate its cryptic splicing and loss upon TDP-43 mislocalization

abstract:
Variants within the UNC13A gene have long been known to increase risk of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), two related neurodegenerative diseases defined by mislocalization of the RNA-binding protein TDP-43. Here, we show that TDP-43 depletion induces robust inclusion of a cryptic exon (CE) within UNC13A, a critical synaptic gene, resulting in nonsense-mediated decay and protein loss. Strikingly, two common polymorphisms strongly associated with ALS/FTD risk directly alter TDP-43 binding within the CE or downstream intron, increasing CE inclusion in cultured cells and in patient brains. Our findings, which are the first to demonstrate a genetic link specifically between loss of TDP-43 nuclear function and disease, reveal both the mechanism by which UNC13A variants exacerbate the effects of decreased nuclear TDP-43 function, and provide a promising therapeutic target for TDP-43 proteinopathies.

One-Sentence SummaryShared ALS/FTD risk variants increase the sensitivity of a cryptic exon in the synaptic gene UNC13A to TDP-43 depletion.


title: Reference transcriptomes of porcine peripheral immune cells created through bulk and single-cell RNA sequencing

abstract: Pigs are a valuable human biomedical model and an important protein source supporting global food security. The transcriptomes of peripheral blood immune cells in pigs were defined at the bulk cell-type and single cell levels. First, eight cell types were isolated in bulk from peripheral blood mononuclear cells (PBMCs) by cell sorting, representing Myeloid, NK cells and specific populations of T and B cells. Transcriptomes for each bulk population of cells were generated by RNA-seq with 10,974 expressed genes detected. Pairwise comparisons between cell types revealed specific expression, while enrichment analysis identified 1,885 to 3,591 significantly enriched genes across all 8 cell types. Gene Ontology analysis for the top 25% of significantly enriched genes (SEG) showed high enrichment of biological processes related to the nature of each cell type. Comparison of gene expression indicated highly significant correlations between pig cells and corresponding human PBMC bulk RNA-seq data available in Haemopedia. Second, higher resolution of distinct cell populations was obtained by single-cell RNA-sequencing (scRNA-seq) of PBMC. Seven PBMC samples were partitioned and sequenced that produced 28,810 single cell transcriptomes distributed across 36 clusters and classified into 13 general cell types including plasmacytoid dendritic cells (DC), conventional DCs, monocytes, B cell, conventional CD4 and CD8 {beta} T cells, NK cells, and {gamma}{delta} T cells. Signature gene sets from the human Haemopedia data were assessed for relative enrichment in genes expressed in pig cells and integration of pig scRNA-seq with a public human scRNA-seq dataset provided further validation for similarity between human and pig data. The sorted porcine bulk RNAseq dataset informed classification of scRNA-seq PBMC populations; specifically, an integration of the datasets showed that the pig bulk RNAseq data helped define the CD4CD8 double-positive T cell populations in the scRNA-seq data. Overall, the data provides deep and well-validated transcriptomic data from sorted PBMC populations and the first single-cell transcriptomic data for porcine PBMCs. This resource will be invaluable for annotation of pig genes controlling immunogenetic traits as part of the porcine Functional Annotation of Animal Genomes (FAANG) project, as well as further study of, and development of new reagents for, porcine immunology.


title: Biome-scale woody encroachment threatens conservation potential and sustainability of U.S. rangelands

abstract:
O_LIRangelands of the United States provide ecosystem services that sustain biodiversity and rural economies. Native tree encroachment is a long-standing conservation challenge to these landscapes. Still, its impact is often overlooked due to the slow pace of tree invasions and the positive public perception of trees.
C_LIO_LIRecent innovations in satellite remote sensing permit the tracking of tree encroachment and the corresponding impact on herbaceous production. We analyzed tree cover change and herbaceous production across 17 western states from 1990 to 2019.
C_LIO_LIWe show that tree encroachment is a dominant change agent in western U.S. rangelands; tree cover has increased by 50% (77,323 km2) over 30 years, with more than 25% of U.S. rangelands experiencing sustained tree cover expansion. Since 1990, roughly 300 Tg of herbaceous biomass has been lost, totaling $5 billion in foregone revenue to small agricultural producers.
C_LIO_LISynthesis and applications: The impact of tree encroachment to rangeland loss is similar in magnitude to row-crop conversion, another primary threat to U.S. rangelands. Prioritizing conservation efforts to prevent tree encroachment can bolster ecosystem and economic sustainability, particularly among privately-owned lands threatened by land-use conversion.
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title: Tree invasions threaten the conservation potential and sustainability of U.S.rangelands


title: Tree encroachment threatens the conservation potential and sustainability of U.S. rangelands


title: Species-area relationships emerge from multiple coexistence mechanisms

abstract: The increase of species richness with area is a universal phenomenon on Earth. How-ever, this observation contrasts with our poor understanding of how these species-area relationships (SARs) emerge from the collective effects of area, spatial heterogeneity, and local interactions. By combining a structuralist approach with five years of empirical observations in a highly-diverse Mediterranean grassland, we show that spatial hetero-geneity plays a little role in the accumulation of species richness with area in our system. Instead, as we increase the sampled area more species combinations are realized, and they coexist mainly due to direct pairwise interactions rather than by changes in single-species dominance or by indirect interactions. We also identify a small set of transient species with small population sizes that are consistently found across spatial scales. These findings empirically support the importance of the architecture of species interactions together with stochastic events for driving coexistence- and species-area relationships.


title: The spatial configuration of biotic interactions shapes coexistence-area relation-ships in an annual plant community


title: Coral symbionts exhibit a polycistronic flavodiiron gene leading to functional proteins in photosynthesis

abstract: Photosynthesis in cyanobacteria, green algae, and basal land plants is protected against excess reducing pressure on the photosynthetic chain by flavodiiron proteins (FLV) that dissipate photosynthetic electrons by reducing O2. In these organisms, the genes encoding FLV are always conserved in the form of a pair of two-type isozymes (FLVA and FLVB) that are believed to function in O2 photo-reduction as a heterodimer. While coral symbionts (dinoflagellates of the family Symbiodiniaceae) are the only algae to harbor FLV in photosynthetic red plastid lineage, only one gene is found in transcriptomes and its role and activity remain unknown. Here, we characterized the FLV genes in Symbiodiniaceae and found that its coding region is composed of tandemly repeated FLV sequences. By measuring the O2-dependent electron flow and P700 oxidation, we suggest that this atypical FLV is active in vivo. Based on the amino-acid sequence alignment and the phylogenetic analysis, we conclude that in coral symbionts, the gene pair for FLVA and FLVB have been fused to construct one coding region for a hybrid enzyme, which presumably occurred when or after both genes were inherited from basal green algae to the dinoflagellate. Immunodetection suggested the FLV polypeptide to be cleaved by a post-translational mechanism, adding it to the rare cases of polycistronic genes in eukaryotes. Our results demonstrate that FLV are active in coral symbionts with genomic arrangement that is unique to these species. The implication of these unique features on their symbiotic living environment is discussed.


title: Optogenetic control of receptors reveals distinct roles for actin- and Cdc42-dependent negative signals in chemotactic signal processing

abstract: During chemotaxis, neutrophils use cell surface G-Protein Coupled Receptors (GPCRs) to detect chemoattractant gradients1-4. The downstream signaling system is wired with multiple feedback loops that amplify weak inputs and promote spatial separation of cell front and rear activities1, 5-8. Positive feedback could promote rapid signal spreading9, yet information from the receptors is transmitted with high spatial fidelity, enabling detection of small differences in chemoattractant concentration across the cell1. How the signal transduction network achieves signal amplification while preserving spatial information remains unclear. The GTPase Cdc42 is a cell-front polarity coordinator that is predictive of cell turning, suggesting an important role in spatial processing10. To directly measure information flow from receptors to Cdc42, we paired zebrafish parapinopsina, an optogenetic GPCR that allows reversible ON/OFF receptor control with a spectrally compatible red/far red Cdc42 FRET biosensor. Using this new toolkit, we show that positive and negative signals downstream of G-proteins shape a rapid, dose-dependent Cdc42 response. Furthermore, F-actin and Cdc42 itself provide two distinct negative signals that limit the duration and spatial spread of Cdc42 activation, maintaining output signals local to the originating receptors.


title: Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ

abstract: Nuclear processes depend heavily on the organization of chromatin, whose subunits are cylinder-shaped complexes called nucleosomes. A subset of mammalian nucleosomes in situ resemble the canonical structure determined in vitro 24 years ago. The structure of nucleosomes in situ is otherwise poorly understood. Here we use cryo-ET and 3-D classification analysis to study the structure of yeast nucleosomes both in vitro and in situ. We show that the class averages of GFP-tagged yeast nucleosomes in vitro resemble canonical nucleosomes, with additional GFP densities. In contrast, none of the class averages of nucleosome-like particles in situ (inside cells) resemble canonical nucleosomes. The heterogeneous nature of the in situ class averages suggests that the intranuclear environment favors multiple conformations. Using the structural observations here and the results of previous genomics and biochemical studies, we propose a model in which the average yeast nucleosomes DNA is partially detached in situ.


title: Quantitative prey species detection in predator guts across multiple trophic levels by DNA shotgun sequencing

abstract:
O_LIMetabarcoding has revolutionized the study of ecological communities, but PCR bias hampers quantitative analyses, as required in studies of trophic interactions. Direct DNA shotgun sequencing can avoid the amplification step when unassembled reads are mapped to a reference database, enabling identification and quantification of prey items.
C_LIO_LITwo feeding bioassays tested the precision and accuracy of quantitative assessments with the coccinellids Harmonia axyridis and Hippodamia convergens, the chrysopid Chrysoperla externa, and the aphid Myzus persicae. Guts were dissected and the total DNA extracted was directly sent to sequence by Illumina HiSeq2500 (insert 350 bp, PE 250). Predator gut content reads were blasted against an arthropod mitochondrial DNA reference database for taxonomic assignment and the matches curated for false positive prey identification using a series of bioinformatics pipelines, mostly in R. Taxonomic assignment through KrakenUnique, which is based on the counts of unique k-mers, was compared.
C_LIO_LIIn a Prey Quantity bioassay, the number of prey reads was correlated to the amount of prey consumed and the elapsed time since consumption. In a Direct and Indirect Predation bioassay, prey was detectable in the predator 6 h after feeding (direct predation) and the preys prior prey was detectable 3 h after feeding (indirect predation). Detection of indirect predation was related to the species-specific decay rates of the two predators, but not to the order of predation.
C_LIO_LIWe demonstrate that degraded prey DNA was quantifiable across trophic levels with high accuracy (98.4% positive predictive value) and taxonomic resolution.
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title: The fluoride permeation pathway and anion recognition in Fluc family fluoride channels

abstract: Fluc family fluoride channels protect microbes against ambient environmental fluoride by undermining the cytoplasmic accumulation of this toxic halide. These proteins are structurally idiosyncratic, and thus the permeation pathway and mechanism have no analogy in other known ion channels. Although fluoride binding sites were identified in previous structural studies, it was not evident how these ions access aqueous solution, and the molecular determinants of anion recognition and selectivity have not been elucidated. Using x-ray crystallography, planar bilayer electrophysiology and liposome-based assays, we identify additional binding sites along the permeation pathway. We use this information to develop an oriented system for planar lipid bilayer electrophysiology and observe anion block at one of these sites, revealing insights into the mechanism of anion recognition. We propose a permeation mechanism involving alternating occupancy of anion binding sites that are fully assembled only as the substrate approaches.

category: biochemistry


title: Guidelines for obtaining an absolute blood flow index with laser speckle contrast imaging

abstract: Laser speckle contrast imaging (LSCI) is a technique broadly applied in research and clinical settings for full-field characterization of tissue perfusion. It is based on the analysis of speckle pattern contrast, which can be theoretically related to the decorrelation time - a quantitative measure of dynamics. A direct contrast to decorrelation time conversion, however, requires prior knowledge of specific parameters of the optical system and scattering media and thus is often impractical. For this reason, and because of the nature of some of the most common applications, LSCI is historically used to measure relative blood flow change. Over time, the belief that the absolute blood flow index measured with LSCI is not a reliable metric and thus should not be used has become more widespread. This belief has resulted from the use of LSCI to compare perfusion in different animal models and to obtain longitudinal blood flow index observations without proper consideration given to the stability of the measurement. Here, we aim to clarify the issues that give rise to variability in the repeatability of the quantitative blood flow index and to present guidelines on how to make robust absolute blood flow index measurements with conventional single-exposure LSCI. We also explain how to calibrate contrast to compare measurements from different systems and show examples of applications that are enabled by high repeatability.


title: First-principles model of optimal translation factors stoichiometry

abstract: Enzymatic pathways have evolved uniquely preferred protein expression stoichiometry in living cells, but our ability to predict the optimal abundances from basic properties remains underdeveloped. Here we report a biophysical, first-principles model of growth optimization for core mRNA translation, a multi-enzyme system that involves proteins with a broadly conserved stoichiometry spanning two orders of magnitude. We show that a parsimonious flux model constrained by proteome allocation is sufficient to predict the conserved ratios of translation factors through maximization of ribosome usage The analytical solutions, without free parameters, provide an interpretable framework for the observed hierarchy of expression levels based on simple biophysical properties, such as diffusion constants and protein sizes. Our results provide an intuitive and quantitative understanding for the construction of a central process of life, as well as a path toward rational design of pathway-specific enzyme expression stoichiometry.


title: Small but complete: liquid-liquid phase separation in minimalistic peptides

abstract:
Liquid-liquid phase separation (LLPS) of proteins mediates the assembly of biomolecular condensates involved in physiological and pathological processes. Identifying the minimalistic building blocks and the sequence determinant of protein phase separation is of urgent importance but remains challenging due to the enormous sequence space and difficulties of existing methodologies in characterizing the phase behavior of ultrashort peptides. Here we demonstrate computational tools to efficiently quantify the microscopic fluidity and density of liquid-condensates/solid-aggregates and the temperature-dependent phase diagram of peptides. Utilizing our approaches, we comprehensively predict the LLPS abilities of all 400 dipeptide combinations of coded amino acids based on 492 micro-second molecular dynamics simulations, and observe the occurrences of spontaneous LLPS. We identify 54 dipeptides that form solid-like aggregates and three categories of dipeptides with high LLPS propensity. Our predictions are validated by turbidity assays and differential interference contrast (DIC) microscopy on four representative dipeptides (WW, QW, GF, and VI). Phase coexistence diagrams are constructed to explore the temperature dependence of LLPS. Our results reveal that aromatic moieties are crucial for a dipeptide to undergo LLPS, and hydrophobic and polar components are indispensable. We demonstrate for the first time that dipeptides, minimal but complete, possess multivalent interactions sufficient for LLPS, suggesting that LLPS is a general property of peptides/proteins, independent of their sequence length. This study provides a computational and experimental approach to the prediction and characterization of the phase behavior of minimalistic peptides, and will be helpful for understanding the sequence-dependence and molecular mechanism of protein phase separation.

SignificanceProtein liquid-liquid phase separation (LLPS) is associated with human health and diseases. Identifying the minimalistic building blocks and sequence determinants of LLPS is of urgent importance but remains computationally challenging partially due to the lack of methodologies characterizing the liquid condensates. Herein we provide approaches to evaluate LLPS ability of dipeptides, and screen all 400 dipeptides by MD simulations combined with multi-bead-per-residue models which capture key interactions driving LLPS that are missing in one-bead-per-residue models. Three categories of LLPS dipeptides are identified and the experimentally-verified QW dipeptide is by far the smallest LLPS system. Our results suggest that dipeptides, minimal but complete, possess multivalent interactions sufficient for LLPS, and LLPS is a general property of peptides/proteins, independent of their length.


title: Dipeptides are minimalistic but sufficient for liquid-liquid phase separation


title: Discovery of Latent Drivers from Double Mutations in Pan-Cancer Data Reveal their Clinical Impact

abstract:
Background

Transforming patient-specific molecular data into clinical decisions is fundamental to personalized medicine. Despite massive advancements in cancer genomics, to date driver mutations whose frequencies are low, and their observable transformation potential is minor have escaped identification. Yet, when paired with other mutations in cis, such  latent driver mutations can drive cancer. Here, we discover potential  latent driver double mutations.

Method

We applied a statistical approach to identify significantly co-occurring mutations in the pan-cancer data of mutation profiles of [~]80,000 tumor sequences from the TCGA and AACR GENIE databases. The components of same gene doublets were assessed as potential latent drivers. We merged the analysis of the significant double mutations with drug response data of cell lines and patient derived xenografts (PDXs). This allowed us to link the potential impact of double mutations to clinical information and discover signatures for some cancer types.

Results

Our comprehensive statistical analysis identified 228 same gene double mutations of which 113 mutations are cataloged as latent drivers. Oncogenic activation of a protein can be through either single or multiple independent mechanisms of action. Combinations of a driver mutation with either a driver, a weak driver, or a strong latent driver have the potential of a single gene leading to a fully activated state and high drug response rate. Tumor suppressors require higher mutational load to coincide with double mutations compared to oncogenes which implies their relative robustness to losing their functions. Evaluation of the response of cell lines and patient-derived xenograft data to drug treatment indicate that in certain genes double mutations can increase oncogenic activity, hence a better drug response (e.g. in PIK3CA), or they can promote resistance to the drugs (e.g. in EGFR).

Conclusion

Our comprehensive analysis of same allele double mutations in cancer genome landscapes emphasizes that interrogation of big genomic data and integration with the results of large-scale small-molecule sensitivity data can provide deep patterns that are rare; but can still result in dramatic phenotypic alterations, and provide clinical signatures for some cancer types.

category: systems biology


title: Decisions in an Innate Behavioral Sequence

abstract: Innate behaviors are comprised of ordered sequences of component actions that progress to satisfy drives. We have characterized the structure of egg-laying behavior in Drosophila in detail and observed that the sequence is not merely comprised of motor acts but also acts of sensory exploration that govern the transitions between component actions. We have identified a cluster of internal sensory neurons that provide information about the progression of the egg during ovipositor burrowing, a behavior necessary for the subterraneous deposition of the egg. These neurons impart sensory feedback that allows burrowing to continue to egg deposition or to abort in favor of further exploration. Diminished activity of these neurons upon completed egg expulsion may initiate the transition to the final phase of egg-laying, allowing the cycle to repeat. Sensory feedback therefore plays a critical role at decision points between transitions affording innate behaviors with an adaptive flexibility.


title: DIFFERENCES IN THE EFFECTS ON HUMAN FOCUS OF MUSIC PLAYLISTS AND PERSONALIZED SOUNDSCAPES, AS MEASURED BY BRAIN SIGNALS.

abstract: The goal of this study was to investigate the effect of sounds on human focus and to identify the properties that contribute most to increasing and decreasing focus in people within their natural, everyday environment. Participants (N=62, 18-65y) performed various tasks on a tablet computer while listening to either no background sounds (silence), popular music playlists designed to increase focus (pre-recorded songs in a particular sequence), or engineered soundscapes that were personalized to individual listeners (digital audio composed in real-time based on input parameters such as heart rate, time of day, location, etc.). Sounds were delivered to participants through headphones while simultaneously their brain signals were recorded by a portable electroencephalography headband. Participants completed four one-hour long sessions at home during which different sound content played continuously. Using brain decoding technology, we obtained individual participant focus levels over time and used this data to analyze the effects of various properties of sound. We found that while participants were working, personalized soundscapes increased their focus significantly above silence (p=0.008), while music playlists did not have a significant effect. For the young adult demographic (18-36y), all sound content tested was significantly better than silence at producing focus (p=0.001-0.009). Personalized soundscapes increased focus the most relative to silence, but playlists of pre-recorded songs also increased focus significantly during specific time intervals. Ultimately we found that it is possible to accurately predict human focus levels that will be experienced in response to sounds a priori based on the sounds physical properties. We then applied this finding to compare between music genres and revealed that classical music, engineered soundscapes, and natural sounds were the best genres for increasing focus, while pop and hip-hop were the worst. These insights can enable human and artificial intelligence composers to produce increases or decreases in listener focus with high temporal (millisecond) precision. Future research will include real-time adaptation of sound libraries for other functional objectives beyond affecting focus, such as affecting listener enjoyment, stress, and memory.


title: Differences In The Effects On Human Focus Of Music Playlists And Personalized Soundscapes, As Measured By Brain Signals.


title: Modeling The Effect of Background Sounds on Human Focus Using Brain Decoding Technology


title: Egocentric Biases are Determined by the Precision of Self-related Predictions.

abstract: According to predictive processing theories, emotional inference involves simultaneously minimising discrepancies between predictions and sensory data relating to both ones own and others states, achievable by altering either ones own state (empathy) or perception of anothers state (egocentric bias) so they are more congruent. We tested a key hypothesis of these accounts, that predictions are weighted in inference according to their precision (inverse variance). If correct, more precise self-related predictions should bias perception of anothers emotional expression to a greater extent than less precise predictions. We manipulated predictions about upcoming own-pain (low or high magnitude) using cues that afforded either precise (a narrow range of possible magnitudes) or imprecise (a wide range) predictions. Participants judged pained facial expressions presented concurrently with own-pain to be more intense when own-pain was greater, and precise cues increased this biasing effect. Implications of conceptualising interpersonal influence in terms of predictive processing are discussed.


title: Focal fMRI signal enhancement with implantable inductively coupled detectors

abstract: Despite extensive efforts to increase the signal-to-noise ratio (SNR) of fMRI images for brain-wide mapping, technical advances of focal brain signal enhancement are lacking, in particular, for animal brain imaging. Emerging studies have combined fMRI with fiber optic-based optogenetics to decipher circuit-specific neuromodulation from meso to macroscales. Acquiring fMRI signal with high spatiotemporal resolution is needed to bridge cross-scale functional dynamics, but SNR of targeted cortical regions is a limiting factor. We have developed a multi-modal fMRI imaging platform with an implanted inductive coil detector. This detector boosts the tSNR of MRI images, showing a 2-3 fold sensitivity gain over conventional coil configuration. In contrast to the cryoprobe or array coils with limited spaces for implanted brain interface, this setup offers a unique advantage to study brain circuit connectivity with optogenetic stimulation and can be further extended to other multi-modal fMRI mapping schemes.


title: Pigs as a new behavioral model for studying Pavlovian eyeblink conditioning

abstract:
IntroPigs have been an increasingly popular preclinical model in nutritional neuroscience, as their anatomy, physiology, and nutrition requirements are highly comparable to those of humans. Eyeblink conditioning is one of the most well-validated behavioral paradigms in neuroscience to study underlying mechanisms of learning and memory formation in the cerebellum. Eyeblink conditioning has been performed in many species but has never been done on young pigs. Therefore, our aim here was to develop and validate an eyeblink conditioning paradigm in young pigs.

MethodEighteen intact male pigs were artificially reared from postnatal day 2 to 30. The eyeblink conditioning setup consisted of a sound-damping box with a hammock that pigs were placed in, which allowed the pig to remain comfortable yet maintain a typical range of head motion. In a delay conditioning paradigm, the conditional stimulus (CS) was a 550 ms blue light-emitting diode (LED), the unconditional stimulus (US) was a 50 ms eye air-puff, the CS-US interval was 500 ms. Starting at postnatal day 14, pigs were habituated for five days to the eyeblink conditioning setup, followed by 5 daily sessions of acquisition training (40 paired CS-US trials each day).

ResultsThe group-averaged amplitude of eyelid responses gradually increased over the course of the five days of training, indicating that pigs learned to make the association between the LED light CS and the air-puff US. A similar increase was found for the conditioned response (CR) probability: the group-averaged CR probability on session 1 was about 12% and reached a CR probability of 55% on day 5. The latency to CR peak time lacked a temporal preference in the first session, but clearly showed preference from the moment that animals started to show more CRs in session 2 and onwards whereby the eyelid was maximally closed exactly at the moment that the US would be delivered.

ConclusionWe concluded that 4-week-old pigs have the capability of performing in a cerebellar classical association learning task, demonstrating for the first time that eyeblink conditioning in young pigs has the potential to be a valuable behavioral tool to measure neurodevelopment.


title: Evidence or Confidence: What Really Accumulates During a Decision?

abstract: Assessing ones confidence in ones choices is of paramount importance to making adaptive decisions, and it is thus no surprise that humans excel in this ability. However, standard models of decision-making, such as the drift-diffusion model (DDM), treat confidence assessment as a post-hoc or parallel process that does not directly influence the choice - the latter depends only on accumulated evidence. Here, we pursue the alternative hypothesis that what is accumulated during a decision is confidence (that the to-be selected option is the best) rather than raw evidence. Accumulating confidence has the appealing consequence that the decision threshold corresponds to a desired level of confidence for the choice, and that confidence improvements can be traded off against the resources required to secure them. We show that most previous findings on perceptual and value-based decisions traditionally interpreted from an evidence-accumulation perspective can be explained more parsimoniously from our novel confidence-driven perspective. Furthermore, we show that our novel confidence-driven DDM (cDDM) naturally generalizes to any number of decisions - which is notoriously extemporaneous using traditional DDM or related models. Finally, we discuss future empirical evidence that could be useful in adjudicating between these alternatives.


title: Sex differences in behavioral and brainstem transcriptomic neuroadaptations following neonatal opioid exposure in outbred mice

abstract:
The opioid epidemic led to an increase in the number of Neonatal Opioid Withdrawal Syndrome (NOWS) cases in infants born to opioid-dependent mothers. Hallmark features of NOWS include weight loss, severe irritability, respiratory problems, and sleep fragmentation. Mouse models provide an opportunity to identify brain mechanisms that contribute to NOWS. Neonatal outbred Swiss Webster Cartworth Farms White (CFW) mice were administered morphine (15mg/kg, s.c.) twice daily for postnatal days (P) 1-14, an approximate of the third trimester of human gestation. Male and female mice underwent behavioral testing on P7 and P14 to determine the impact of opioid exposure on anxiety and pain sensitivity. Ultrasonic vocalizations (USVs) and daily body weights were also recorded. Brainstems containing pons and medulla were collected during morphine withdrawal on P14 for RNA-sequencing. Morphine induced weight loss from P2-14, which persisted during adolescence (P21) and adulthood (P50). USVs markedly increased at P7 in females, emerging earlier than males. On P7 and P14, both morphine exposed female and male mice displayed hyperalgesia on the hot plate and tail flick assays, with females having greater hyperalgesia than males. Morphine-exposed mice exhibited increased anxiety-like behavior in the open-field arena at P21. Transcriptome analysis of the brainstem (medulla plus pons), an area implicated in opioid withdrawal and NOWS, identified pathways enriched for noradrenergic signaling in females and males. We also found sex-specific pathways related to mitochondrial function and neurodevelopment in females and circadian entrainment in males. Sex-specific transcriptomic neuroadaptations implicate unique neurobiological mechanisms underlying NOWS-like behaviors.

SIGNIFICANCE STATEMENTNeonatal opioid withdrawal syndrome (NOWS) is a poorly understood condition that has both a genetic and environmental component and is thought to be mechanistically distinct from opioid withdrawal in adults. The development of murine models for measuring neurobehavioral responses is critical for informing the neurobiological adaptations underlying NOWS. Using outbred mice that more closely model human genetic variation, we discovered a surprising degree of sexual dimorphism in behavioral timing and severity of NOWS-model behaviors as well as transcriptomic adaptations in brain tissue that together suggest distinct mechanisms and sex-specific therapeutics for reversing withdrawal symptoms and restoring brain function.