title: High-throughput profiling of natural acquired humoral immune response to a large panel of known and novel full length ectodomain P. falciparum merozoite vaccine candidates under reduced malaria transmission.

abstract: Despite recent progress in the fight against malaria, it still remains a global health challenge necessitating development of intervention strategies. However, the search for malaria vaccine(s) has so far been very challenging. Multiple targets have been tested and so far only a few show promise with one having been endorsed by the WHO. In this study we explore the development of immunity in a low transmission setting, with very few documented re-infections, in order to understand the kinetics of the development and waning of immunity to current and novel blood-stage vaccine candidate antigens. To do this we performed a high-throughput measurement of natural acquired immunity against P. falciparum antigens utilizing a well-established micro-array platform based on the mammalian protein expression system. This large panel of known and novel recombinant full length ectodomain P. falciparum merozoite vaccine candidates were differently recognized by the immune system. Based on the overal spread of the data, some of these antigens induced the acquisition of high levels (1st tertile) of antibodies, among which included novel antigens such as PF3D7_1025300, PF3D7_1105800, PF3D7_1334400, PF3D7_0911300, PF3D7_1252300, PF3D7_1460600, PF3D7_1453100, PF3D7_0831400 and some induced low levels of antibodies (3rd tertile) while others induced moderate levels (4th tertile). In this longitudinal cohort with low level of malaria endemicity, acquisition of humoral immunity to these full length ectodomains P. falciparum antigens demonstrate different dynamics over-time, whereby it was either not acquired or if it was acquired it was either maintained or lost at different rates. These various identified novel antigens are potentially ideal candidates to be prioritized for further functional and or serological studies.


title: Pathogen profiling of Australian rabbits by metatranscriptomic sequencing

abstract:
Australia is known for its long history of using biocontrol agents, like myxoma virus and rabbit haemorrhagic disease virus (RHDV), to manage wild European rabbit populations. Interestingly, while undertaking RHDV surveillance of rabbits that were found dead we observed that approximately 40% of samples were negative for RHDV. To investigate whether other infectious agents are responsible for killing rabbits in Australia we subjected a subset of these RHDV-negative liver samples to metatranscriptomic sequencing. In addition, we investigated whether the host transcriptome data could provide additional differentiation between likely infectious versus non-infectious causes of death. We identified transcripts from several Clostridia species, Pasteurella multocida, Pseudomonas, and Eimeria stiedae in liver samples of several rabbits that had died suddenly, all of which are known to infect rabbits and are capable of causing fulminant disease. In addition, we identified Hepatitis E virus and Cyniclomyces yeast in some samples, both of which are not usually associated with severe disease. In one third of the sequenced liver samples, no infectious agent could be identified. While metatranscriptomic sequencing cannot provide definitive evidence of causation, additional host transcriptome analysis provided further insights to distinguish between pathogenic microbes and commensals or environmental contaminants. Interestingly, three samples where no pathogen could be identified showed evidence of upregulated host immune responses, while immune response pathways were not upregulated when E. stiedae, Pseudomonas, or yeast were detected. In summary, although no new putative rabbit pathogens were identified, this study provides a robust workflow for future investigations into rabbit mortality events.

ImportanceWe have observed that approximately 40% of rabbit liver samples submitted for RHDV testing (from rabbits that had died suddenly without obvious cause) are RHDV-negative. Interestingly, a similar finding was reported in pet rabbits in the United Kingdom. This raises the intriguing question of what else is killing rabbits, both in Australia and internationally? Using a metatranscriptomic sequencing approach, we found that Clostridiaceae, Pasteurella multocida, and Eimeria are frequently detected in cases of sudden rabbit death in Australia. While we did not identify any potential new pathogens that could be explored in the context of wild rabbit management, we have validated an approach to explore future mortality events of lagomorphs that may identify candidate novel biocontrols. Furthermore, our findings reaffirm the recommendation to follow good hygiene practices when handling rabbits, since domestic rabbits harboured several pathogens of potential public health significance, including Escherichia, Pasteurella multocida, and Hepatitis E virus.

category: microbiology


title: Xist expression impacts chromatin structure and YY1 mediated transcription of X-linked genes in hematopoietic progenitor cells

abstract: X chromosome inactivation (XCI) is a dosage compensation phenomenon that occurs in females. Initiation of XCI depends on Xist RNA, which triggers silencing of one of the two X chromosomes, except for genes that escape XCI. This inactive state is propagated during cell divisions with continuous Xist expression. How Xist impacts XCI maintenance remains an open question. Here, we delete Xist in hematopoietic cells of mice and report increased fraction of cycling hematopoietic progenitors and differentiation defects during hematopoiesis. Xist loss results in upregulation of a subset of X-linked genes, several of which escape XCI and have functions in hematopoiesis and immunity. We find that the underlying mechanism of transcriptional upregulation involves reduced H3K27me3 occupancy and increased chromatin accessibility which accommodate binding of YY1 transcription factor (TF). We propose that XCI maintenance defects in Xist deficient mice rely on the landscape of open chromatin sites, TF availability, and cell cycle stress in specific cellular context during hematopoiesis.

category: cell biology


title: Understanding West Nile virus spread: Mathematical modelling to determine the mechanisms with the most influence on infection dynamics.

abstract:
West Nile disease is a vector-borne disease caused by West Nile virus (WNV), involving mosquitoes as vectors and birds as maintenance hosts. Humans and other mammals can be infected via mosquito bites, developing symptoms ranging from mild fever to severe neurological infection. Due to the worldwide spread of WNV, human infection risk is high in several countries. Nevertheless, there are still several knowledge gaps regarding WNV dynamics. Several aspects of transmission taking place between birds and mosquitoes, such as the length of the infectious period in birds or mosquito biting rates, are still not fully understood, and precise quantitative estimates are still lacking for the European species involved. This lack of knowledge affects the precision of parameter values when modelling the infection, consequently resulting in a potential impairment of the reliability of model simulations and predictions. Further investigations are thus needed to better understand these aspects, but field studies, especially those involving several wild species, such as in the case of WNV, can be challenging. Thus, it becomes crucial to identify which mechanisms most influence the dynamics of WNV transmission. In the present work, we propose a sensitivity analysis to identify the parameters that have the largest impact on the spread of the infection. Based on a mathematical model simulating WNV spread into the Lombardy region (northern Italy), the basic reproduction number of the infection was estimated and used to quantify infection spread into mosquitoes and birds. Then, we quantified how variations in the duration of the infectious period in birds, the mosquito biting rate on birds, and the competence and susceptibility to infection of different bird species might affect WNV transmission. Our study highlights that all considered parameters can affect the spread of WNV, but the duration of the infectious period in birds and mosquito biting rate are the most impactful, highlighting the need for further studies to better estimate these parameters. In addition, our study suggests that a WNV outbreak is very likely to occur in all areas with suitable temperatures, highlighting the wide area where WNV represents a serious risk for public health.

Author SummaryInfectious communicable diseases are currently one of the main burdens for human beings and public health. The comprehension of their spread and maintenance is one of the main goals to facilitate their control and eradication, but due to the complexity of their cycles and transmission mechanisms, obtaining this information is often difficult and demanding. The control of vector-borne diseases in particular represents an important and very complex challenge for public health. Mathematical models are suitable tools to investigate disease dynamics and their transmission mechanisms. To build a suitable model that can simulate transmission dynamics, a reliable and precise estimate of parameters for measuring transmission mechanisms is fundamental. We thus propose a sensitivity analysis of four unknown epidemiological parameters (bird recovery rate, mosquito biting rate, avian susceptibility to infection and avian competence to infection) that play a crucial role in driving West Nile virus (WNV) infection to determine which of them have the greatest impact on infection spread. This analysis allows us to identify the investigated parameters that need the most accurate estimate and to further investigate mechanisms that majorly affect WNV spread.

category: ecology


title: TraDIS-validate: a method for curating ordered gene-replacement libraries

abstract: In recent years the availability of genome sequence information has grown logarithmically resulting in the identification of a plethora of uncharacterised genes. To address this gap in functional annotation, many high-throughput screens have been devised with the goal of uncovering novel gene functions. Gene-replacement libraries are one such tool that can be screened in a high-throughput way to link genotype and phenotype and are key community resources. However, for a phenotype to be attributed to a specific gene, there needs to be confidence in the genotype. Construction of large libraries can be laborious and occasionally errors will arise. Here, we present a rapid and accurate method for the validation of any ordered gene-replacement library. We applied our method (TraDIS-Validate) to the well-known Keio library of Escherichia coli gene-deletion mutants. Our method identified 3,718 constructed mutants out of a total of 3,728 confirmed isolates. TraDIS-validate therefore had a success rate of 99.7% for identifying the correct kanamycin cassette position. This dataset provides a benchmark for the purity of the Keio mutants and a screening method for mapping the position of an antibiotic resistance cassette in any ordered library.

category: genetics


title: Genomic Surveillance of Salmonella spp. in the Philippines, 2013-2014

abstract:
Increasing antimicrobial resistance (AMR) in Salmonella has been observed in the Philippines. This study aims to utilize whole genome sequencing (WGS) to characterize the population and AMR mechanisms of Salmonella captured by the Philippine Antimicrobial Resistance Surveillance Program (ARSP) and contrast to traditional laboratory methods.

We sequenced the whole genomes of 148 Salmonella Typhi (S. Typhi) and 65 non-typhoidal Salmonella (NTS) collected in the Philippines in 2013-2014. From the genome sequences, we determined the serotype, multilocus sequence type, presence of determinants of antimicrobial resistance and relatedness between isolates. We also compared the genotypic predictions of serotype and AMR to the phenotypic data.

AMR rates in S. Typhi were low, with sparse acquisition of mutations associated with reduced susceptibility to fluoroquinolones or extended-spectrum beta-lactamases (ESBL) genes. In contrast, three quarters of NTS isolates were insusceptible to at least one antimicrobial, with more than half carrying mutations and/or genes linked to resistance to fluoroquinolones. ESBL genes were detected in five genomes that also carried other AMR determinants. The population of S. Typhi was dominated by the likely endemic genotype 3.0, which also caused of a putative local outbreak susceptible to antibiotics. The main NTS clades were global epidemic S. Enteritidis ST11 and the monophasic variant of S. Typhimurium (I 4,[5],12:i:-) ST34, which had frequently been serotyped as S. Typhimurium in the laboratory.

This was the first time that Salmonella isolated from the Philippines were characterized by WGS and we provide evidence of its utility for ongoing surveillance at the ARSP.

category: genomics


title: Hypoxic response is driven by the BAF form of SWI/SNF

abstract: SWI/SNF has been shown to have important functions in hypoxia-mediated gene expression through roles of its catalytic and core subunits. Since SWI/SNF exists as three distinct assemblies, and usage of complex specific subunits of the complex can be expected to vary within a given cell under changing environmental conditions. It remains an open question as to the compositional makeup of SWI/SNF and the roles of individual complexes in gene expression and cell viability in a hypoxic environment. In our current study, we find that hypoxia regulates levels of unique subunits that define each complex. Protein levels of ARID2 and PBRM1, members of PBAF and BRD9, a member of ncBAF, are downregulated in hypoxic cells, while members of BAF complex are retained. Our studies further show that loss of ARID1A, ARID1B and DPF2, which are unique subunits of BAF, reduces induction of HIF target genes and ARID1A or DPF2 are important for cell survival during hypoxia. Collectively, our results provide evidence that levels of SWI/SNF forms are not static within cells, but can be dynamically altered as a response to environmental changes.

category: biochemistry


title: A Simple and Reproducible In-Vivo Rabbit Phonation Model for Glottic Insufficiency

abstract:
IntroductionGlottic insufficiency can result from neurologic injury, surgery, radiation, and the aging larynx. Treatment includes voice therapy, vocal fold injection augmentation, surgical medialization, or laryngeal reinnervation procedures. The objective of this study is to describe an in-vivo rabbit phonation model for glottic insufficiency that is simple and reproducible by means of unilateral cricothyroid muscle stimulation and high-speed video recordings of evoked phonation.

MethodsA non-randomized controlled trial utilizing seven New Zealand white rabbits was performed via a single operation including evoked phonation with bilateral and unilateral cricothyroid muscle stimulation conditions. The effect of stimulation method on glottic cycle, pitch and loudness was compared. Endoscopic recordings using 5,000 frames-per-second image capture technology and audiologic recordings were obtained for all phonation conditions. Primary outcome measures included means of maximum glottal area (MGA)/length pixel ratio, right and left amplitude/length pixel ratios, calculated cycle frequency, auditory recorded frequency, and maximum auditory intensity. Measurements were obtained via pixel counts using imageJ. Paired t-tests compared the average values obtained over five consecutive glottic cycles for each unilateral and bilateral stimulation during evoked phonation.

ResultsMean (median, IQR) MGA/length was significantly greater with unilateral, 20.30 (19.13, 10.97), vs bilateral, 9.62 (8.33, 2.58), stimulation (p=0.043). Mean frequency (median, IQR), 683.46 Hz (658.5, 197.1) vs 479.92 Hz (458.1, 112); (p=0.027) and mean maximum intensity, 83.5 dB (83.5, 1) vs 76.3 dB (74.5, 4); (p=0.013) were significantly reduced from bilateral to unilateral stimulation. There was no significant difference of mean right amplitude/length between bilateral and unilateral.

ConclusionThe described model demonstrates a simple and reproducible means of producing glottic insufficiency and represents a pathway for better understanding the biomechanics and pathophysiology of glottic insufficiency and offers the potential to compare treatment modalities through in-vivo study.

category: bioengineering


title: Novel ERR pan-agonists ameliorate heart failure through boosting cardiac fatty acid metabolism and mitochondrial function

abstract: Cardiac metabolic dysfunction is a hallmark of heart failure. Estrogen related receptors ERR and ERR{gamma} are essential regulators for cardiac metabolism. Therefore, activation of ERR could be a potential therapeutic intervention for heart failure. However, no natural or synthetic ERR agonist is available to demonstrate their pharmacological effect in vivo. Using a structure-based design approach, we designed and synthesized two structurally distinct pan-ERR agonists, SLU-PP-332 (332) and SLU-PP-915 (915), which significantly improved ejection fraction and ameliorated fibrosis against pressure overload-induced heart failure without affecting cardiac hypertrophy. Mechanistically, a broad-spectrum of metabolic genes were transcriptionally activated by ERR agonists, particularly genes involved in fatty acid metabolism and mitochondrial function, which were mainly mediated by ERR{gamma}. Metabolomics analysis showed significant normalization of metabolic profiles in fatty acid/lipid and TCA/OXPHOS metabolites by 915 in the mouse heart with 6-week pressure overload. Autophagy was also induced by ERR agonists in cardiomycoyte. On the other hand, ERR agonism led to downregulation of cell cycle and development pathways, which was partially mediated by E2F1 in cardiomyocyte. In summary, ERR agonists maintain oxidative metabolism, which confers cardiac protection against pressure overload-induced heart failure in vivo. Our results provided direct pharmacological evidence supporting the further development of ERR agonists as novel heart failure therapeutics in vivo.

category: pharmacology and toxicology


title: ScRNA-seq Identified the Metabolic Reprogramming of Human Colonic Immune Cells in Different Locations and Disease States

abstract: Different regions and states of the human colon are likely to have a distinct influence on immune cell functions. Here we studied the immunometabolic mechanisms for the spatial immune specialization and the dysregulated immune response during ulcerative colitis at single-cell resolution. We revealed that the macrophages and CD8+ T cells in the lamina propria (LP) of the human colon possessed an effector phenotype and were more activated, while their lipid metabolism was suppressed compared with those in the epithelial (Epi). Also, IgA+ plasma cells accumulated in lamina propria of the sigmoid colon were identified to be more metabolically activated versus those in the cecum and transverse colon, and the improved metabolic activity was correlated with the expression of CD27. In addition to the immunometabolic reprogramming caused by spatial localization colon, we found dysregulated cellular metabolism was related to the impaired immune functions of macrophages, dendritic cells, regulatory T cells, and ILCs in patients with ulcerative colitis. The cluster of OSM+ inflammatory monocytes was also identified to play its role in resistance to anti-TNF treatment, and we explored targeted metabolic reactions that could reprogram them to a normal state. Altogether, this study revealed a landscape of metabolic reprogramming of human colonic immune cells in different locations and disease states, and offered new insights into treating ulcerative colitis by immunometabolic modulation.

category: immunology


title: Extension of bacterial rDNA sequencing to concurrent epigenetic analysis and its application to 16S meta-epigenetics

abstract: Although polymerase chain reaction (PCR) amplification and sequencing of the 16S rDNA region has been used in a wide range of scientific fields, it does not provide DNA methylation information. We describe a simple add-on method to investigate 5-methylcytosine residues in the bacterial 16S rDNA region from clinical samples or flora. Single-stranded bacterial DNA after bisulfite conversion was preferentially amplified with multiple displacement amplification (MDA) at pH neutral, and the 16S rDNA region was analyzed using nested bisulfite PCR and sequencing. 16S rDNA bisulfite sequencing can provide clinically important bacterial DNA methylation status concurrently with intact 16S rDNA sequence information. We used this approach to identify novel methylation sites and a methyltransferase (M. MmnI) in Morganella morganii. Next, we analyzed bacterial flora from clinical specimens of small amount and identified different methylation motifs among Enterococcus faecalis strains. The method developed here, referred to as "add-on" to the conventional 16S rDNA analysis, is the most clinically used bacterial identification genetic test, which provides additional information that could not be obtained with the conventional method. Since the relationship between drug resistance in bacteria and DNA methylation status has been reported, bacterial epigenetic information would be useful in clinical testing as well. Our analysis suggests that M. MmnI has a promotive effect on erythromycin resistance. 16S rDNA bisulfite PCR and sequencing coupled with MDA at pH neutral is a useful add-on tool for analyzing 16S meta-epigenetics.


title: High-throughput detection and quantification of phosphatidylcholines and sphingomyelins from single cells by chip-based nanoelectrospray ionisation

abstract: Recent advances in single-cell genomics and transcriptomics technologies have transformed our understanding of cellular heterogeneity in growth, development, ageing and disease. Despite these advances, however, single-cell metabolite profiling (i.e., metabolomics) methods have comparatively lagged behind due to limitations in technology. We have developed a high-throughput method for the detection and quantification of a wide range of phosphatidylcholine (PC) and sphingomyelin (SM) species from single cells that combines fluorescence-assisted cell sorting (FACS) with automated chip-based nanoelectrospray ionisation (nanoESI) and shotgun lipidomics. We show herein that our method is capable of quantifying more than 50 different PC and SM species from single cells and can easily distinguish between cells of different lineages or cells treated with exogenous fatty acids. Moreover, our method can detect more subtle differences in the lipidome between cell lines of the same cancer type. Our approach has the capacity to be run in parallel with other single-cell technologies to deliver near-complete multi-omics data on cells with a similar phenotype and has the capacity to significantly advance our current knowledge on cellular heterogeneity.


title: Reconstructing cell interactions and state trajectories in pancreatic cancer stromal tumoroids

abstract: Interlineage communication within a cancer microenvironment can augment cancer cell behaviour and impact response to therapy. Patient-derived cancer organoids provide an opportunity to explore cancer cell biology, however it is a major challenge to generate a complex cancer microenvironment in vitro. Here, we established a stromal tumoroid culture system modeling pancreatic ductal adenocarcinoma (PDAC) that reconstitutes multilineage interactions between cancer, endothelial, and fibroblast cells and recapitulates several aspects of primary tumors. Whole-mount immunohistochemistry on cleared tumoroids reveals organized vessel, desmoplastic fibroblast, and glandular cancer cell phenotypes that emerge over time. Time-course scRNA-seq measurements show that tumoroid formation activates fibroblasts, altering the extracellular matrix (ECM) composition and inducing cancer cell signal-response signatures and metabolic state change. Comparison between tumoroids with normal or cancer associated fibroblasts (CAFs) reveals different ECM compositions, as well as differential effects on cancer cell behaviors and metabolism. We identify Syndecan 1 (SDC1) and Peroxisome proliferator-activated receptor gamma (PPARG) as receptor and metabolic nodes involved in cancer cell response to CAF signals, and blocking SDC1 disrupts cancer cell growth within the tumoroid. Tumoroids from multiple PDAC patients revealed co-existence of subpopulations associated with classical and basal phenotypes, and CAF-induced migration behaviors emerged in certain patient tumoroids. Comparisons between patient tumoroids revealed a multigene migration signature that develops over time reflecting a stress response mechanism that correlates with worse clinical outcome. Altogether, stromal tumoroids can be used to explore dynamic and reciprocal interactions between cancer, CAF and endothelial cell states, and our data provides new inroads into the discovery of personalized pancreatic cancer therapies.

category: cancer biology


title: Urinary single-cell sequencing captures intrarenal injury and repair processes in human acute kidney injury

abstract:
Acute kidney injury (AKI) is a major health issue, the outcome of which depends primarily on damage and reparative processes of tubular epithelial cells (TEC). Mechanisms underlying AKI remain incompletely understood, specific therapies are lacking and monitoring the course of AKI in clinical routine is confined to measuring urine output and plasma levels of filtration markers.

Here we demonstrate feasibility and potential of a novel approach to assess the cellular and molecular dynamics of AKI by establishing a robust urine-to-single cell RNA sequencing (scRNAseq) pipeline for excreted kidney cells via flow cytometry sorting. We analyzed 42,608 single cell transcriptomes of 40 urine samples from 32 AKI patients and compared our data with reference material from human AKI post-mortem biopsies and published mouse data. We demonstrate that TEC transcriptomes mirror intrarenal pathology and reflect distinct injury and repair processes, including oxidative stress, inflammation, and tissue rearrangement. We also describe an AKI-specific abundant urinary excretion of progenitor-like cells.

In conclusion, single cell transcriptomics of kidney cells excreted in urine provides non-invasive, unprecedented insight into cellular processes underlying AKI, thereby opening novel opportunities for target identification, AKI sub-categorization and monitoring of natural disease course and interventions.

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category: molecular biology


title: GWAS in the Southern African context

abstract: Researchers would generally adjust for the possible confounding effect of population structure by considering global ancestry proportions or top principle components. Alternatively, researchers would conduct admixture mapping to increase the power to detect variants with an ancestry effect. This is sufficient in simple admixture scenarios, however, populations from southern Africa can be complex multi-way admixed populations. Duan et al. (2018) first described local ancestry adjusted allelic (LAAA) analysis as a robust method for discovering association signals, while producing minimal false-positives. Their simulation study, however, was limited to a two-way admixed population. Realizing that their findings might not translate to other admixture scenarios, we simulated a three- and five-way admixed population to compare the LAAA model to other models commonly used in GWAS. We found that, given our admixture scenarios, the LAAA model identifies the most causal variants in most of the phenotypes we tested across both the three-way and five-way admixed populations. The LAAA model also produced a high number of false-positives which was potentially caused by the ancestry effect size that we assumed. Considering the extent to which the various models tested differed in their results and considering that the source of a given association is unknown, we recommend that researchers use multiple GWAS models when analysing populations with complex ancestry.


title: Purely enzymatic incorporation of an isotope-labeled adenine into RNA for the study of conformational dynamics by NMR

abstract: Solution NMR spectroscopy is a well-established tool with unique advantages for structural studies of RNA molecules. However, for large RNA sequences, the NMR resonances often overlap severely. A reliable way to perform resonance assignment and allow further analysis despite spectral crowding is the use of site-specific isotope labeling in sample preparation. While solid-phase oligonucleotide synthesis has several advantages, RNA length and availability of isotope-labeled building blocks are persistent issues. Purely enzymatic methods pose as an alternative and have been presented in the literature. In this study, we report on a method in which we exploit the preference of T7 RNA polymerase for nucleotide monophosphates over triphosphates for the 5 position, which allows 5-labeling of RNA. Successive ligation to an unlabeled RNA strand generates a site-specifically labeled RNA. We show the successful production of such an RNA sample for NMR studies, report on experimental details and expected yields, and present the surprising finding of a previously hidden set of peaks which reveals conformational exchange in the RNA structure. This study highlights the feasibility of site-specific isotope-labeling of RNA with enzymatic methods.


title: Prediction of range expansion and estimation of dispersal routes of water deer (Hydropotes inermis) in the transboundary region between China, the Russian Far East and the Korean Peninsula

abstract: Global changes may direct species expansion away from their current range. When such an expansion occurs, and a species colonizes a new region, it is important to monitor the habitat used by the species and use the information for updated management strategies. Water deer is listed as Vulnerable species in IUCN Red List and restricted to east central China and the Korean Peninsula. Since 2017 water deer has expanded its range towards northeast China and the Russian Far East. Our research focuses on data collected in northeast China and the Russian Far East during 2017-2021, with the purpose of providing support for a better understanding of habitat use and provide conservation suggestions. We used MaxEnt to model species niche and distribution and predict habitat suitability for water deer and applied the circuitscape to determine possible dispersal routes for the species. There is good quality habitat for water deer in the boundary area of the Yalu and Tumen River estuaries between China, North Korea, and the Russian Far East, as well as the east and west regions of the Korean Peninsula. Elevation, distance to cropland and water sources, and presence of wetlands were the variables that positively contributed to modelling the suitable habitats. Two possible dispersal routes were determined using the circuit theory, one was across the area from North Korea to the downstream Tumen transboundary region, and the other was across North Korea to the boundary region in China and along the tiger national park in northern China. A series of protected areas in North Korea, China, and Russia may support the dispersal of water deer. The establishment of a Northeast Asia landscape conservation network would help establish monitoring and conservation planning at a broad scale, and this study provides an example for the need for such a network


title: Hypothalamic astrocyte control systemic glucose metabolism and energy balance via regulation of extra-synaptic glutamate signaling

abstract: The hypothalamus is key in the control of energy balance. However, to this day strategies targeting hypothalamic neurons failed to provide viable option to treat most metabolic diseases. Conversely, the role of astrocytes in systemic metabolic control has remained largely unexplored. Here we show that obesity promotes anatomically restricted remodeling of hypothalamic astrocyte activity. In the paraventricular nucleus (PVN) of the hypothalamus, chemogenetic manipulation of astrocytes results in bidirectional control of neighboring neuron activity, autonomic outflow, glucose metabolism and energy balance. Such process recruits a mechanism involving the astrocytic control of ambient glutamate levels, which becomes defective in obesity. Positive or negative chemogenetic manipulation of PVN astrocyte Ca2+ signals respectively worsen or improves metabolic status of diet-induced obese mice. Collectively, these findings highlight a yet unappreciated role for astrocyte in the direct control of systemic metabolism and suggest potential targets for anti-obesity strategy.

category: physiology


title: Tissue-wide Effects Overrule Cell-intrinsic Gene Function in Cortical Projection Neuron Migration

abstract:
The mammalian neocortex is composed of diverse neuronal and glial cell classes that broadly arrange in six distinct laminae. Cortical layers emerge during development and defects in the developmental programs that orchestrate cortical lamination are associated with neurodevelopmental diseases. The developmental principle of cortical layer formation is based on concerted radial projection neuron migration, from their birthplace to their final target position. Radial migration occurs in defined sequential steps that are regulated by a large array of signaling pathways. However, based on genetic loss-of-function experiments, most studies have thus far focused on the role of cell-autonomous gene function. Yet, cortical neuron migration in situ is a complex process and migrating neurons traverse along diverse cellular compartments and environments. The role of tissue-wide properties and genetic state in radial neuron migration is however not well understood. Here, we utilized Mosaic Analysis with Double Markers (MADM) technology to either sparsely or globally delete gene function followed by quantitative single cell phenotyping. The MADM-based gene ablation paradigms in combination with computational modeling demonstrated that global tissue-wide effects predominate cell-autonomous gene function albeit in a gene-specific manner. Our results thus suggest that the genetic landscape in a tissue critically impacts the overall migration phenotype of individual cortical projection neurons. In a broader context our findings imply that global tissue-wide effects represent an essential component of the underlying etiology associated with focal malformations of cortical development (FMCD) in particular, and neurological diseases in general.

LAY SUMMARYThe assembly of the mammalian brain is a complex process and depends on tightly regulated developmental and genetic programs. The coordinated process of nerve cell (neuron) migration is essential to home neurons into their correct position which is vital for normal brain development. Disturbance of the neuron migration process at any point of development leads to severe brain malformations which result in devastating disease. To date, studies have mainly focused on cell-intrinsic gene functions controlling neuronal migration. Therefore, very little is known about the possible contribution of the cellular surrounding and tissue-wide effects. The scale and nature of such global tissue-wide effects remain completely unclear. We thus established genetic platforms based on Mosaic Analysis with Double Markers (MADM) to visualize and quantify tissue-wide effects in a defined genetic context and at single cell resolution. We found a critical predominant role of the genetic landscape and state of cellular environment affecting overall neuron migration properties. In a broader context our results suggest that global tissue-wide effects are a major component of the underlying etiology of neurological diseases such as focal malformations of cortical development (FMCD).

category: neuroscience


title: Postnatal environmental enrichment enhances memory by shaping hippocampal-prefrontal theta and gamma rhythms in diploid and trisomic female mice

abstract: Rich social, physical, and cognitively stimulating lifestyles have powerful effects on cognitive abilities, especially when they are experienced early in life. Cognitive therapies are widely used to attenuate cognitive impairment due to intellectual disability, but also aging and neurodegeneration, however the underlying neural mechanisms are poorly understood. Here we investigated the neural substrates of memory amelioration induced by postnatal environmental enrichment (EE) in diploid female mice and Ts65Dn female mice with partial trisomy of genes ortholog to human chromosome 21, a standard model of Down syndrome (DS, trisomy 21). We recorded neural activities in two brain structures key for cognitive function, the hippocampus and the prefrontal cortex, during rest, sleep and memory performance in mice reared in standard or enriched environments for 7 weeks post-weaning. We found that EE shaped hippocampal- prefrontal neural dynamics in diploid mice and rescued the same disrupted pathways in Ts65Dn mice. The neural activity changes detected in EE-reared wild-type mice combined task-independent adjustments (augmented hippocampal pyramidal activity and gamma synchrony across different brain states) and memory-dependent adjustments (enhanced theta-gamma coupling and ripples in the HPC). Therefore, both brain state adjustments and memory-associated adjustments are good candidates to underlie the beneficial effects of EE on cognition in diploid female mice. Concomitantly, EE attenuated hippocampal and prefrontal hypersynchrony in trisomic females, suggesting distinct neural mechanisms for the generation and rescue of healthy and pathological brain synchrony, respectively, by EE. These results put forward hippocampal hypersynchrony and hippocampal-prefrontal miscommunication as major neural mechanisms underlying the beneficial effects of EE for intellectual disability in DS.


title: Autism is associated with inter-individual variations of gray and white matter morphology

abstract:
BackgroundAlthough many studies have explored atypicalities in gray and white matter (GM, WM) morphology of autism, most of them rely on unimodal analyses that do not benefit from the likelihood that different imaging modalities may reflect common neurobiology. We aimed to establish multimodal brain patterns that differentiate between autism and typically developing (TD) controls and explore associations between these brain patterns and clinical measures.

MethodsWe studied 183 individuals with autism and 157 TD individuals (6-30 years) in a large deeply phenotyped autism dataset (EU-AIMS LEAP). Linked Independent Component Analysis was utilized to link all participants GM and WM images, and group comparisons of modality shared variances were examined. Subsequently, we performed a canonical correlation analysis to explore the aggregated effects between all multimodal GM-WM covariations and clinical profiles.

ResultsOne multimodal pattern was significantly related to autism. This pattern was primarily associated with GM in bilateral insula, frontal, pre- and post-central, cingulate, and caudate areas, and co-occurred with altered WM features in the superior longitudinal fasciculus. The canonical analysis showed a significant multivariate correlation primarily between multimodal brain patterns that involved variation of corpus callosum, and symptoms of social affect in the autism group.

ConclusionsOur findings demonstrate the assets of integrated analyses of GM and WM alterations to study the brain mechanisms that underpin autism, and show that the complex clinical autism phenotype can be interpreted by multimodal brain patterns that are spread across the brain involving both cortical and subcortical areas.


title: Discovery of therapeutic agents targeting PKLR for NAFLD using drug repositioning

abstract:
Background & AimsNon-alcoholic fatty liver disease (NAFLD) encompasses a wide spectrum of liver pathologies. However, not medical treatment has been approved for the treatment of the disease. In our previous study, we found PKLR could be a potential target for treatment of NALFD. Here, the aim is to investigate the effect of PKLR in in vivo model and perform drug repositioning to identify a drug candidate for treatment of NAFLD.

MethodsBiopsies from liver, muscle, white adipose tissue and heart were obtained from control and PKLR knockout mice fed with chow and high sucrose diets. Lipidomics as well as transcriptmics analyses were conducted using these tissue samples. In addition, a computational drug repositioning analysis was performed and drug candidates were identified. The drug candidates were finally tested in both in vitro and in vivo models to evaluated their toxicity and efficacy.

ResultsThe Pklr KO reversed the increased hepatic triglyceride level in mice fed with high sucrose diet and partly recovered the transcriptomic changes in liver as well as other three tissues. Both liver and white adipose tissues exhibited dysregulated circadian transcriptomic profiles, and these dysregulations were reversed by hepatic knockout of Pklr. In addition, 10 small molecule drugs were identified as potential inhibitor of PKLR by the drug repositioning pipeline, and two of them significantly inhibited both the PKLR expression and triglyceride level in in vitro model. Finally, the two selected small molecule drugs were evaluated in in vivo rat models and it was demonstrated that these drugs attenuated hepatic steatosis without side effect on other tissues.

ConclusionIn conclusion, our study provided biological insights about the critical role of PKLR in NAFLD progression and proposed a treatment strategy for NAFLD patients, which has been validated in preclinical experiment.

category: systems biology


title: Transition to siblinghood causes substantial and long-lasting physiological stress reactions in wild bonobos

abstract: In mammals with a slow ontogeny, the birth of a sibling marks a major developmental transition. Behavioral studies suggest that this event is stressful for the older offspring, but physiological evidence for this is lacking, and it remains unknown whether the birth of a sibling is stressful beyond mere weaning stress. Studying transition to siblinghood in wild bonobos, we investigated physiological changes in urinary cortisol (stress response), neopterin (cell-mediated immunity), and total triiodothyronine (metabolic rate), and related them to behavioral changes in mother-infant relationship and feeding (suckling, riding, proximity, body contact, independent foraging). With siblings birth, cortisol levels increased fivefold in the older offspring and remained elevated for seven months, independent of age. This was associated with diminished immunity but not with behavioral or metabolic changes. Our results indicate that transition to siblinghood is stressful beyond nutritional and social weaning and suggest that this effect is evolutionary old.

category: evolutionary biology


title: A five-fold expansion of the global RNA virome reveals multiple new clades of RNA bacteriophages

abstract: High-throughput RNA sequencing offers unprecedented opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA viral contigs. Via analysis of the 330k novel RNA-dependent RNA polymerases (RdRP), this expansion corresponds to a five-fold increase of RNA virus diversity. Extended RdRP phylogeny supports monophyly of the five established phyla, reveals two putative new bacteriophage phyla and numerous putative novel classes and orders. The dramatically expanded Lenarviricota phylum, consisting of bacterial and related eukaryotic viruses, now accounts for a third of the RNA virome diversity. Identification of CRISPR spacer matches and bacteriolytic proteins suggests that subsets of picobirnaviruses and partitiviruses, previously associated with eukaryotes, infect prokaryotic hosts. Gene content analysis revealed multiple domains previously not found in RNA viruses and implicated in virus-host interactions. This vast collection of new RNA virus genomes provides insights into RNA virus evolution and should become a major resource for RNA virology.


title: A network of cytosolic (co)chaperones promotes the biogenesis of mitochondrial signal-anchored outer membrane proteins

abstract: Signal-anchored (SA) proteins are anchored into the mitochondrial outer membrane (OM) via a single transmembrane segment at their N-terminus while the bulk of the proteins is facing the cytosol. These proteins are encoded by nuclear DNA, translated on cytosolic ribosomes, and are then targeted to the organelle and inserted into its OM by import factors. Recently, research on the insertion mechanisms of these proteins into the mitochondrial OM have gained a lot of attention. In contrast, the early cytosolic steps of their biogenesis are unresolved. Using various proteins from this category and a broad set of in vivo, in organello, and in vitro assays, we reconstituted the early steps of their biogenesis. We identified a subset of molecular (co)chaperones that interact with newly synthesized SA proteins, namely, Hsp70 and Hsp90 chaperones and co-chaperones from the Hsp40 family like Ydj1 and Sis1. These interactions were mediated by the hydrophobic transmembrane segments of the SA proteins. We further demonstrate that interfering with these interactions inhibits the biogenesis of SA proteins to varying extents. Finally, we could demonstrate direct interaction of peptides corresponding to the transmembrane segments of SA proteins with the (co)chaperones and reconstitute in vitro the transfer of such peptides from the Hsp70 chaperone to the mitochondrial Tom70 receptor. Collectively, this study unravels an array of cytosolic chaperones and mitochondrial import factors that facilitates the targeting and membrane integration of mitochondrial SA proteins.


title: Melanosomes degrade lipofuscin and precursors that are derived from photoreceptor membrane turnover in the retinal pigment epithelium--an explanation for the origin of the melanolipofuscin granule

abstract: The accumulation of the age pigment lipofuscin within the retinal pigment epithelium (RPE) is one the most remarkable changes observed in association with age-related macular degeneration (AMD) and Stargardt disease. Both aging and pathological processes lead to the accumulation of melanolipofuscin (MLF) granules, which have been reported to reflect the onset of AMD more accurately than lipofuscin. The underlying mechanism by which MLF forms is still not understood. We investigate the potential role that melanin plays in the degradation of lipofuscin and MLF in pigmented Abca4-/- mice following treatment with several NO generating drugs. Abca4-/- mice are generally used as models for lipofuscin-related eye diseases. We also induced melanogenesis in albino Abca4-/- mice via the over-expression of tyrosinase, the key enzyme involved in melanogenesis. We compared the ultrastructure of lipofuscinogensis in the RPE of pigmented and albino Abca4-/- mice. Fluorescence microscopy was employed for the quantification of lipofuscin. We found high amounts of unique thin (3-4 nm) lamellar membranes (TLMs) that were left over from the degradation of photoreceptor disc membranes by high-resolution electron microscopy. Accumulated TLMs were significantly more frequent in the RPE cells of the albinos than the pigmented mice, indicating that melanin plays a role in removing TLMs. The intravitreal injection of several NO generating drugs was found to reduce the amount of autofluorescent lipofuscin in the cytoplasm of RPE cells, particularly the MLF granules of pigmented Abca4-/- mice. No effect was observed in terms of lipofuscin removal in NO-exposed albino Abca4-/- mice. However, transfection with tyrosinase led to a reduction in the lipofuscin levels of artificially pigmented RPE cells in albino Abca4-/- mice following the formation of melanin. The results show for the first time that melanin plays an important, if not a key, role in the degradation of lipofuscin in RPE cells.


title: Perinatal Oxycodone Exposure Causes Long Term Sex-Dependent Changes in Sensory and Reward Processing in Adult Mice

abstract: In utero opioid exposure is associated with lower weight and a Neonatal Opioid Withdrawal Syndrome (NOWS) at birth, along with longer-term adverse neurodevelopmental outcomes and mood disorders. While NOWS is sometimes treated with continued opioids, clinical studies have not addressed if long-term neurobehavioral outcomes are worsened with continued postnatal exposure to opioids. In addition, pre-clinical studies comparing in utero only opioid exposure to continued post-natal opioid administration for withdrawal mitigation are lacking. Therefore, we implemented a rodent perinatal opioid exposure model of Oxycodone (Oxy) exposure for comparison of long-term consequences of Oxy exposure until birth (Short Oxy) to the impact of continued postnatal opioid exposure (Long Oxy) spanning gestation through birth and lactation. Short Oxy exposure was associated with a sex-specific increase in weight gain trajectory in adult male mice. Long Oxy exposure caused an increased weight gain trajectory in adult males, sex-dependent changes in morphine conditioned place preference, and alterations in nociceptive processing in females. Importantly, there was no evidence of long-term social behavioral deficits, anxiety, hyperactivity, or memory deficits following Short or Long Oxy exposure. Our findings suggest that offspring with prolonged opioid exposure experienced some long-term sequelae compared to pups with opioid cessation at birth. These results highlight the potential long-term consequences of opioid administration as a mitigation strategy for clinical NOWS symptomology and suggest alternatives should be explored.


title: Awake responses suggest inefficient dense coding in the mouse retina

abstract: The structure and function of the vertebrate retina have been extensively studied across species with an isolated, ex vivo preparation. Retinal function in vivo, however, remains elusive, especially in awake animals. Here we performed single-unit extracellular recordings in the optic tract of head-fixed mice to compare the output of awake, anesthetized, and ex vivo retinas. While the visual response properties were overall similar, we found that awake retinal output had 1) faster kinetics with less variability in the response latencies across different cell types; and 2) higher firing activity, by [~]20 Hz on average, for both baseline and visually evoked responses. Notably, unlike the other conditions, many awake ON cells did not increase firing in response to light increments due to high baseline activity near saturation. Instead, they encoded light intensity fluctuations primarily by decreasing firing upon light decrements. In either condition, the visual message remains the same: the more spikes, the higher light intensity. The awake response patterns, however, violate efficient coding principles, predicting that sensory systems should favor firing patterns minimizing energy consumption. Our findings suggest that the retina employs dense coding in vivo, rather than sparse efficient coding as suggested from previous ex vivo studies.


title: Synaptic basis of a sub-second representation of time

abstract: Temporal sequences of neural activity are essential for driving well-timed behaviors, but the underlying cellular and circuit mechanisms remain elusive. We leveraged the well-defined architecture of the cerebellum, a brain region known to support temporally precise actions, to explore theoretically whether the experimentally observed diversity of short-term synaptic plasticity (STP) at the input layer could generate neural dynamics sufficient for subsecond temporal learning. Simulated synaptic input generated a diverse set of transient, firing patterns in granule cells (GCs) that provided a temporal basis set for learning precisely timed pauses of Purkinje cell activity associated with delayed eyelid conditioning and Bayesian interval estimation. The learning performance across time intervals was influenced by the temporal bandwidth of the GC basis, which was determined by the input layer synaptic properties. The ubiquity of STP throughout the brain positions it as a general, tunable cellular mechanism for sculpting neural dynamics and fine-tuning behavior.


title: Conflict- and error-related theta activities are coupled to BOLD signals in different brain regions

abstract: Both conflict and error processing have been linked to the midfrontal theta power (4-8 Hz) increase as indicated by EEG studies and greater hemodynamic activity in the anterior midcingulate cortex (aMCC) as indicated by fMRI studies. Conveniently, the source of the midfrontal theta power was estimated in or nearby aMCC. However, previous studies using concurrent EEG and fMRI recordings in resting-state or other cognitive tasks observed only a negative relationship between theta power and BOLD signal in the brain regions typically showing task-related deactivations. In this study, we used a simultaneous EEG-fMRI technique to investigate a trial-by-trial coupling between theta power and hemodynamic activity during the performance of two conflict tasks. Independent component analysis (ICA) was applied to denoise the EEG signal and select individual midfrontal EEG components, whereas group ICA was applied to fMRI data to obtain a functional parcellation of the frontal cortex. Using a linear mixed- effect model, theta power was coupled with the peak of hemodynamic responses from various frontal, cingulate, and insular cortical sites to unravel the potential brain sources that contribute to conflict- and error-related theta variability. Although several brain regions exhibited conflict-related increases in hemodynamic activity, the conflict pre-response theta showed only a negative correlation to BOLD signal in the midline area 9 (MA9), a region exhibiting conflict-sensitive deactivation. Conversely, and more expectedly, error-related theta showed a positive relationship to activity in the aMCC. Our results provide novel evidence suggesting that the amplitude of pre-response theta reflects the process of active inhibition that suppresses the MA9 activity. This process is affected independently by the stimulus congruency, reaction times variance, and is susceptible to the time-on-task effect. Finally, it predicts the commitment of an omission error. Together, our findings highlight that conflict- and error-related theta oscillations represent fundamentally different processes.


title: Task-specific effects of biological sex and sex hormones on object recognition memories in a 6-hydroxydopamine-lesion model of Parkinson's disease in adult male and female rats

abstract:
Many patients with Parkinsons disease (PD) experience impairments in cognition and memory with few therapeutic options currently available to mitigate them. This has fueled interest in determining how factors including biological sex and sex hormones might modulate higher order function in PD. Previous studies have investigated this in female rats and in gonadally intact and gonadectomized males, with and without hormone replacement, that received bilateral neostriatal 6-hydroxydopamine (6-OHDA) lesions to model PD. Barnes maze and What Where When Episodic-like memory testing showed that 6-OHDA lesions disrupted spatial working and episodic memory functions in both sexes, and that in males, androgen-sensitive behaviors could be rescued in subjects where circulating androgen levels were diminished. Here we tested similar animal groups using the Novel Object Preference (NOP) and Object-in-Place (OiP) tasks. This revealed two entirely different patterns of sex and sex hormone influence. First, for both tasks, 6-ODHA lesions impaired object discrimination in males but not females. Further, for the NOP task, 6-OHDA lesions disrupted discrimination in males rats independently of hormone status. And finally, 6-OHDA lesions impaired OiP performance in males regardless of whether androgen levels were high or low but had no effect on discrimination in gonadectomized rats given 17{beta}-estradiol. Together with previous findings, these data identify the impacts of sex and sex hormones on cognition and memory in PD as behavioral task/behavioral domain specific. This specificity could explain why a cohesive clinical picture of endocrine impacts on higher order function in PD has remained elusive.

HIGHLIGHTSO_LI6-OHDA lesions impair Novel Object performance in male but not female rats.
C_LIO_LI6-OHDA lesions impair Object-in-Place performance in male but not female rats.
C_LIO_LIGonadectomy has no effect on 6-OHDA-induced deficits in Novel Object Preference.
C_LIO_LIEstrogen replacement prevents 6-OHDA-induced Object-in-Place deficits in males.
C_LI


title: Inducing a mental context for associative memory formation with real-time fMRI neurofeedback

abstract: Memory, one of the hallmarks of human cognition, can be modified when humans voluntarily modulate single neuron or neural population activity using neurofeedback. However, it is currently unknown whether memory is facilitated or impaired after such neural perturbation. In this study, participants memorized objects while we trained them with abstract neurofeedback to modulate their brain activity patterns in the ventral visual stream to represent either faces or houses. The neurofeedback created an implicit face or house context in the brain while memorizing the objects. The results revealed that participants created associations between each memorized object and its implicit context solely due to the neurofeedback manipulation. Our findings shed light onto how memory formation can be influenced by synthetic memory tags with neurofeedback and advance our understanding of mnemonic processing.


title: Sequential increase of PHGDH expression with Alzheimer's pathology and symptoms

abstract: We report consistent increases in phosphoglycerate dehydrogenase (PHGDH) expression in mouse models of Alzheimers disease (AD) (3xTg-AD) and related tauopathy (PS19), particularly in hippocampal astrocytes. Human single-cell RNA-sequencing data reveal a sequential increase of PHGDH expression in people with no, early, and late AD pathology, which is corroborated by protein mass spectrometry and immunohistochemical analyses of three independent cohorts. A sequential increase of PHGDH expression also correlates with increasing clinical AD symptoms and worsening cognitive decline in patients. The consistent increase of PHGDH expression in six AD cohorts (Mayo, ROSMAP, Mount Sinai, Baltimore, Amsterdam, and UCSD/UCI) corroborates with the recent report of PHGDH extracellular RNA in blood plasma as a candidate biomarker for early diagnosis of AD and offers a caution to the suggested use of L-serine as a potential therapy of AD.


title: Oligodendrocytes form paranodal bridges that generate chains of myelin sheaths vulnerable to degeneration with age

abstract: Myelin sheaths in the CNS are generated by the tips of oligodendrocyte processes, which wrap axons to accelerate action potential conduction, provide metabolic support and control excitability. Here we identify a distinct mode of myelination, conserved between zebrafish, mouse and human, in which oligodendrocytes extend myelin along individual axons by linking myelin sheaths across nodes of Ranvier (NoR). By forming thin extensions that cross NoR, which we term paranodal bridges, multiple sheaths can be connected to the soma by a single cytoplasmic process. Extensive in vivo live imaging-based analyses, complemented by serial electron microscopic reconstruction of paranodal bridges, revealed that many oligodendrocytes use this strategy to generate longer stretches of myelin along individual axons. In the mouse somatosensory cortex, paranodal bridges were particularly prevalent along the highly branched axons of parvalbumin expressing (PV) interneurons, which enabled oligodendrocytes to extend myelin sheaths around axon bifurcations. Sheaths at the distal ends of these chains of myelin degenerated more frequently in aged mice, suggesting that they may be more vulnerable to the aging brain environment. This previously undescribed and evolutionarily conserved feature of oligodendrocytes extends myelin coverage of individual axons without new oligodendrogenesis, which may reduce metabolic demand and preserve the fidelity of action potential propagation at axon branch points.


title: Dissociable misconfigurations of striatal functional connectivity profiles in smokers

abstract: Corticostriatal circuits are central to reward processing and reinforcement learning functions that often become dysregulated in substance use disorder (SUD) and drive compulsive drug use. Human neuroimaging research seeking to identify how corticostriatal circuits become altered in SUD has primarily focused on evaluating connectivity between cortex-striatum node-pairs. Yet, striatal nodes receive appreciable input from many cortical nodes, and the morphological and electrophysiological properties of striatal nodes dictate that combinational features of their multivariate "connectivity profiles" shape their activity more so than any individual cortical node. Here, we introduce an approach for quantifying and statistically evaluating different types of multivariate connectivity profile configuration differences (i.e., aggregate divergence, rank order arrangement, and entropy shift) that may reflect different forms of circuit plasticity, and apply it to nicotine dependent smokers (n=46) as an exemplar SUD. Foremost, we find evidence of significant connectivity profile misconfiguration throughout much of the striatum, suggesting that prior findings of abnormal connections between individual striatal-cortical node-pairs may only represent the "tip of the iceberg" of corticostriatal circuit alteration in nicotine dependence. Moreover, we find that dorsolateral and ventromedial striatum display distinct types of connectivity profile misconfiguration. Whereas dorsolateral striatum almost exclusively displays abnormal rank order arrangement that is present in both the nicotine sated and acutely abstinent states - indicative of a "trait" misconfiguration - ventromedial striatum almost exclusively displays abnormal aggregate divergence that only manifests during acute abstinence - indicative of a "state" misconfiguration. Further, we identify a unique striatal site in the right caudal ventral putamen that displays multiple forms of connectivity profile misconfiguration, where connections with cognitive processing cortical areas overtake those with motor/premotor control cortical areas as the strongest in the connectivity profile, and acute abstinence significantly strengthens this abnormal arrangement. Moreover, the interactive magnitude of these misconfigurations during acute abstinence is significantly linked to dependence severity. Collectively, the present findings underscore the need for increased examination of connectivity profile misconfigurations as a mechanism of SUD etiology and as a potential guide for identifying therapeutic intervention targets.


title: Botulinum neurotoxin accurately separates tonic vs phasic transmission and reveals heterosynaptic plasticity rules in Drosophila

abstract: In developing and mature nervous systems, diverse neuronal subtypes innervate common targets to establish and maintain functional neural circuits. A major challenge towards understanding the structural and functional architecture of neural circuits is to separate these inputs and determine their intrinsic and heterosynaptic relationships. The Drosophila larval neuromuscular junction is a powerful model system to study these questions, where two glutamatergic motor neurons, the strong phasic-like Is and weak tonic-like Ib, co-innervate individual muscle targets to coordinate locomotor behavior. However, complete neurotransmission from each input has never been electrophysiologically separated. We have developed a botulinum neurotoxin, BoNT-C, that eliminates both spontaneous and evoked neurotransmission without perturbing synaptic growth or structure, enabling the first approach that accurately isolates input-specific neurotransmission. Selective expression of BoNT-C in Is or Ib motor inputs disambiguates functional properties of each input. Importantly, the composite values of Is and Ib neurotransmission can be fully recapitulated by isolated physiology from each input. Finally, selective silencing by BoNT-C does not induce heterosynaptic structural or functional plasticity at the convergent input. Thus, BoNT-C establishes the first approach to cleanly separate neurotransmission between tonic vs phasic neurons and defines heterosynaptic plasticity rules in a powerful model glutamatergic circuit.


title: Predator odor (TMT) exposure potentiates interoceptive sensitivity to alcohol and increases GABAergic gene expression in the anterior insular cortex and nucleus accumbens in male rats

abstract: Post-traumatic stress disorder (PTSD) confers enhanced vulnerability to develop comorbid alcohol use disorder (AUD). Exposure to the scent of a predator, such as the fox odor TMT, has been used to model a traumatic stressor with relevance to PTSD symptomatology. Alcohol produces distinct interoceptive (subjective) effects that may influence vulnerability to problem drinking and AUD. As such, understanding the lasting impact of stressor on sensitivity to the interoceptive effects of alcohol is clinically relevant. The present study used a 2-lever, operant drug discrimination procedure to train male, Long-Evans rats to discriminate the interoceptive effects of alcohol (2 g/kg, i.g.) from water. Upon stable performance, rats underwent a 15-min exposure to TMT. Two weeks later, an alcohol dose-response curve was conducted to evaluate the lasting effects of the TMT stressor on the interoceptive effects of alcohol. The TMT group showed a leftward shift in ED50 of the dose response curve compared to controls, reflecting potentiated interoceptive sensitivity to alcohol. TMT exposure did not affect response rate. GABAergic signaling in both the anterior insular cortex (aIC) and the nucleus accumbens (Acb) is involved in the interoceptive effects of alcohol and stressor-induced adaptations. As such, follow-up experiments in alcohol-naive rats examined neuronal activation (as measured by c-Fos immunoreactivity) following TMT and showed that TMT exposure increased c-Fos expression in the aIC and the nucleus accumbens core (AcbC). 2 weeks after TMT exposure, Gad-1 gene expression was elevated in the aIC and Gat-1 was increased in the Acb compared to controls. Lastly, the alcohol discrimination and alcohol-naive groups displayed dramatic differences in stress reactive behaviors during the TMT exposure, suggesting that alcohol exposure may alter the behavioral response to predator odor. Together, these data suggest that predator odor stressor results in potentiated sensitivity to alcohol possibly through GABAergic adaptations in the aIC and Acb, which may be relevant to understanding PTSD-AUD comorbidity.


title: Targeting the fronto-parietal network using multifocal personalized transcranial alternating current stimulation to enhance motor sequence learning in healthy older adults

abstract:
BackgroundHealthy older adults show a decrease in motor learning capacity as well as in working memory (WM) performance. WM has been suggested to be involved in motor learning processes, such as sequence learning. Correlational evidence has shown the involvement of the fronto-parietal network (FPN), a network underlying WM processes, in motor sequence learning. However, causal evidence is currently lacking. Non-invasive brain stimulation (NIBS) studies have focused so far predominantly on motor related areas to enhance motor sequence learning while areas associated with more cognitive aspects of motor learning have not yet been addressed.

HypothesisIn this study, we aim to provide causal evidence for the involvement of WM processes and the underlying FPN in successful motor sequence learning by using a theta transcranial alternating current stimulation (tACS) paradigm targeting the FPN during motor sequence learning.

MethodsIn a cohort of 20 healthy older adults, we applied bifocal tACS in the theta range to the FPN during a sequence learning task. With the use of a double-blind, cross-over design, we tested the efficacy of active compared with sham stimulation. Two versions of the motor task were used: one with high and one with low WM load, to explore the efficacy of stimulation on tasks differing in WM demand. Additionally, the effects of stimulation on WM performance were addressed using an N-back task. The tACS frequency was personalized by means of EEG measuring the individual theta peak frequency during the N-back task.

ResultsThe application of personalized theta tACS to the FPN improved performance on the motor sequence learning task with high WM load (p <.001), but not with low WM load. Active stimulation significantly improved both speed (p <.001), and accuracy (p =.03) during the task with high WM load. In addition, the stimulation paradigm improved performance on the N-back task for the 2-back task (p = .013), but not for 1-back and 3-back.

ConclusionMotor sequence learning can be enhanced with the use of personalized bifocal theta tACS to the FPN when WM load is high. This indicates that the efficacy of this stimulation paradigm is dependent on the cognitive demand during the learning task and provides further causal evidence for the critical involvement of WM processes and the FPN in motor sequence learning in healthy older adults. These findings open new exciting possibilities to counteract the age-related decline in motor learning capacity and WM performance.


title: Structural insight into the individual variability architecture of the functional brain connectome

abstract: Human cognition and behaviors depend upon the brains functional connectomes, which vary remarkably across individuals. However, whether and how the functional connectome individual variability architecture is structurally constrained remains largely unknown. Using tractography- and morphometry-based network models, we observed the spatial convergence of structural and functional connectome individual variability, with higher variability in heteromodal association regions and lower variability in primary regions. We demonstrated that functional variability is significantly predicted by a unifying structural variability pattern and that this prediction follows a primary-to-heteromodal hierarchical axis, with higher accuracy in primary regions and lower accuracy in heteromodal regions. We further decomposed group-level connectome variability patterns into individual unique contributions and uncovered the structural-functional correspondence that is associated with individual cognitive traits. These results advance our understanding of the structural basis of individual functional variability and suggest the importance of integrating multimodal connectome signatures for individual differences in cognition and behaviors.


title: Structural insight into the individual variability architecture of the functional human brain connectome


title: Single-nucleus transcriptomic analysis reveals divergence of glial cells in peripheral somatosensory system between human and mouse

abstract: Glial cells play a crucial role in regulating physiological and pathological functions, such as sensation, infections, acute injuries, and chronic neurodegenerative disorders. Glial cells include astrocytes, microglia, and oligodendrocytes in the central nervous system (CNS) and satellite glial cells (SGCs) in the peripheral nervous system (PNS). Despite the understanding of glial subtypes and functional heterogeneity in animal models achieved by single-cell or single-nucleus RNA sequencing, no research has investigated the transcriptomic profiles of glial cells in the human PNS and spinal cord. Here, we used high-throughput single-nucleus RNA sequencing to map the cellular and molecular heterogeneity of SGCs in the human dorsal root ganglion (DRG) and astrocytes, microglia, and oligodendrocytes in the human spinal cord. To explore the conservation and divergence across species, we compared these human findings with those from mice. Additionally, the expression profiles of risk genes of common DRG and spinal cord diseases in glial cells were compared between humans and mice. As a result, little SGCs heterogeneity was found in both human and mouse DRG. In the human spinal cord, astrocytes, microglia, and oligodendrocytes were respectively divided into six distinct transcriptomic subclusters. In the mouse spinal cord, astrocytes, microglia, and oligodendrocytes were divided into six, five, and six distinct transcriptomic subclusters, respectively. The comparative results revealed substantial heterogeneity in all glial cells between humans and mice. Notably, we also identified transcriptomic heterogeneity in several classical genes and risk genes for neurological disorders across humans and mice. Together, the present data comprehensively profiled glial cell heterogeneity and provides a powerful resource for investigating the cellular basis of glial-related physiological and pathological conditions in peripheral somatosensory system.


title: Brain regional identity and cell type specificity landscape of human cortical organoid models

abstract:
In vitro models of corticogenesis using mouse and human pluripotent stem cells (PSC) have greatly improved our understanding of human brain development and disease. Among these, 3D cortical organoid systems are able to recapitulate some aspects of in vivo cytoarchitecture of the developing cortex.

Here, we tested three cortical organoid protocols for brain regional identity, cell type-specificity and neuronal maturation. Overall all protocols gave rise to organoids that displayed a time-dependent expression of neuronal maturation genes such as those involved in the establishment of synapses and neuronal function. We showed that three months old cortical organoids showed a pattern of gene expression that resembled late human embryonic cortex. Comparatively, directed differentiation methods without WNT activation gave rise to the highest degree of cortical regional identity in brain organoids. Whereas, default "intrinsic" brain organoid differentiation produced the broadest range of cell types such as neurons, astrocytes and hematopoietic-lineage derived microglia cells of the brain. These results suggest that cortical organoid models produce diverse outcomes in terms of brain regional identity and cell type specificity and emphasize the importance of selecting the correct model for the right application.


title: Effects of auditory sleep modulation approaches on brain oscillatory and cardiovascular dynamics

abstract: Sleep modulation techniques to elucidate the functional role of sleep brain oscillations in brain and body functions have gained large interest. Slow waves, the hallmark feature of deep non-rapid eye movement sleep, do potentially drive restorative effects on brain and cardiovascular functions. Auditory stimulation to modulate slow waves is a promising tool, however, directly comparing different auditory stimulation approaches within a night and analyzing induced dynamic brain and cardiovascular effects are yet missing. Here, we tested various auditory stimulation approaches in a windowed, 10 s ON (stimulations) followed by 10 s OFF (no stimulations), within-night stimulation design and compared them to a SHAM control condition. We report the results of three studies and a total of 51 included stimulation nights. We found a large and global increase in slow wave activity (SWA) in the stimulation window compared to SHAM. Furthermore, slow wave dynamics were most pronouncedly increased at the start of the stimulation and declined across the stimulation window. Beyond the changes in brain oscillations, we observed, for some conditions, a significant increase in the mean interval between two heartbeats within a stimulation window, indicating a slowing of the heart rate, and increased heart rate variability derived parasympathetic activity. Those cardiovascular changes were positively correlated with the change in SWA and thus, our findings provide mechanistic insight into the potential of auditory slow wave enhancement to modulate cardiovascular restorative conditions during sleep. However, future studies need to investigate whether the potentially increased restorative capacity through slow wave enhancements translates into a more rested cardiovascular system on the subsequent day.


title: Inferring monosynaptic connections from paired dendritic spine Ca2+ imaging and large-scale recording of extracellular spiking

abstract: Techniques to identify monosynaptic connections between neurons have been vital for neuroscience research, facilitating important advancements concerning network topology, synaptic plasticity, and synaptic integration, among others. Here, we introduce a novel approach to identify and monitor monosynaptic connections using high-resolution dendritic spine Ca2+ imaging combined with simultaneous large-scale recording of extracellular electrical activity by means of high-density microelectrode arrays (HD-MEAs). We introduce an easily adoptable analysis pipeline that associates the imaged spine with its presynaptic unit and test it on in vitro recordings. The method is further validated and optimized by simulating synaptically-evoked spine Ca2+ transients based on measured spike trains in order to obtain simulated ground-truth connections. The proposed approach offers unique advantages as i) it can be used to identify monosynaptic connections with an accurate localization of the synapse within the dendritic tree, ii) it provides precise information of presynaptic spiking, and iii) postsynaptic spine Ca2+ signals and, finally, iv) the non-invasive nature of the proposed method allows for long-term measurements. The analysis toolkit together with the rich data sets that were acquired are made publicly available for further exploration by the research community.


title: Contribution of individual excitatory synapses on dendritic spines to electrical signaling

abstract:
Even though dendritic spines are widely considered the elementary computational units of the brain, current understanding of the exact contribution of individual synapses on spines to the electrical signalling in neurons is incomplete. We combined the techniques of whole cell recording and voltage imaging to monitor directly unitary excitatory postsynaptic potentials evoked by two-photon glutamate uncaging (uEPSPs) on individual dendritic spines. We analysed the initiation, temporal summation, and propagation of uEPSPs from the spine head to the parent dendrite and to the cell body in neocortical pyramidal neurons. Our measurements show no significant attenuation of uEPSPs across the spine neck in different types of pyramidal neurons. This result implies that spine synapses are not electrically isolated from parent dendrites and that spines do not serve a meaningful electrical role. Using the same techniques, we next characterized temporal summation of uEPSPs induced at individual spine synapses by repetitive glutamate uncaging mimicking burst activity of presynaptic neurons. We found that pharmacological block of desensitization of AMPA receptors increased the amplitude of cumulative uEPSP response in the spines head and, consequently, in parent dendrite and soma. Thus, responses to high frequency repetitive quantal EPSPs are strictly limited in amplitude and waveform by AMPA receptor desensitization at the site of origin thereby preventing synaptic saturation.

Significance StatementWe used an electrochromic voltage-sensitive dye, which acts as a transmembrane optical voltmeter, to define the electrical role of dendritic spines, small membrane protrusions that receive most of the excitatory synaptic inputs in the brain. The data argue that spine synapses of investigated principal neurons are not electrically isolated from the parent dendrites. We also found that AMPA receptor desensitization restricts the amplitude of temporal summation during repetitive synaptic activation. These results facilitate our understanding of how a complex assembly of receptors and ion channels in spines are utilized to generate and process electrical signals and mediate plasticity in response to quantal release of chemical transmitters caused by patterned activity in presynaptic axons.


title: 2-Arachodonoylglycerol-mediated endocannabinoid signaling modulates mechanical hypersensitivity associated with alcohol withdrawal in mice

abstract: Alcohol use disorder (AUDs) commonly co-occurs in patients with chronic pain, and a major barrier to achieving abstinence and preventing relapse is the emergence of hyperalgesia during alcohol withdrawal. Elucidating novel therapeutic approaches to target hyperalgesia associated with alcohol withdrawal could have important implications for the treatment of AUD. Here we examined the role of 2-arachidonoylglycerol (2-AG)-mediated endocannabinoid (eCB) signaling in the regulation of hyperalgesia associated with alcohol withdrawal in mice and tested the hypothesis that pharmacological augmentation of 2-AG signaling could reduce hyperalgesia during withdrawal. After 72 hours of withdrawal from a continuous access two-bottle choice drinking paradigm, male and female mice exhibited increased mechanical but not thermal hypersensitivity, which normalized by 7 days. This effect was reversed by pretreatment with the monoacylglycerol lipase (MAGL) inhibitor JZL184, which elevates levels of 2-AG. The effects of JZL184 were prevented by coadministration of either a CB1 or CB2 antagonist. Inhibition of the 2-AG synthetic enzyme diacylglycerol lipase (DAGL) with DO34 exacerbated mechanical hypersensitivity during alcohol withdrawal, causing an earlier onset and persistent hypersensitivity even one week into withdrawal. Our findings demonstrate the critical role of 2-AG signaling in the bidirectional regulation of mechanical sensitivity during alcohol withdrawal, with enhancement of 2-AG levels reducing sensitivity, and inhibition of 2-AG synthesis exacerbating sensitivity. These data suggest 2-AG augmentation could represent a novel approach to the treatment of alcohol withdrawal-associated hyperalgesia and AUD in patients with comorbid pain disorders.


title: Sleep duration and brain structure - phenotypic associations and genotypic covariance

abstract:
The question of how much sleep is best for the brain attracts scientific and public interest, and there is concern that insuficient sleep leads to poorer brain health. However, it is unknown how much sleep is sufficient and how much is too much. We analyzed 51,295 brain magnetic resonnance images from 47,039 participants, and calculated the self-reported sleep duration associated with the largest regional volumes and smallest ventricles relative to intracranial volume (ICV) and thickest cortex. 6.8 hours of sleep was associated with the most favorable brain outcome overall. Critical values, defined by 95% confidence intervals, were 5.7 and 7.9 hours. There was regional variation, with for instance the hippocampus showing largest volume at 6.3 hours. Moderately long sleep (> 8 hours) was more strongly associated with smaller relative volumes, thinner cortex and larger ventricles than even very short sleep (< 5 hours), but effect sizes were modest. People with larger ICV reported longer sleep (7.5 hours), so not correcting for ICV yielded longer durations associated with maximal volume. Controlling for socioeconomic status, body mass index and depression symptoms did not alter the associations. Genetic analyses showed that genes related to longer sleep in short sleepers were related to shorter sleep in long sleepers. This may indicate a genetically controlled homeostatic regulation of sleep duration. Mendelian randomization analyses did not suggest sleep duration to have a causal impact on brain structure in the analyzed datasets. The findings challenge the notion that habitual short sleep is negatively related to brain structure.

Significance statementAccording to consensus recommendations, adults should sleep between 7 and 9 hours to optimize their health. We found that sleeping less than the recommended amount was associated with greater regional brain volumes relative to intracranial volume, and very short sleep was only weakly related to smaller volumes. Genetic analyses did not show causal effects of sleep duration on brain structure. Taken together, the results suggest that habitual short sleep is not an important contributor to lower brain volumes in adults on a group level, and that large individual dfferences in sleep need likely exist.


title: Perceptual consequences of interocular imbalances in the duration of temporal integration

abstract: Temporal differences in visual information processing between the eyes can cause dramatic misperceptions of motion and depth. Processing delays between the eyes cause the Pulfrich effect: oscillating targets in the frontal plane are misperceived as moving along near-elliptical motion trajectories in depth (Pulfrich, 1922). Here, we explain a previously reported but poorly understood variant: the anomalous Pulfrich effect. When this variant is perceived, the illusory motion trajectory appears oriented left- or right-side back in depth, rather than aligned with the true direction of motion. Our data indicate that this perceived misalignment is due to interocular differences in neural temporal integration periods, as opposed to interocular differences in delay. For oscillating motion, differences in the duration of temporal integration dampen the effective motion amplitude in one eye relative to the other. In a dynamic analog of the Geometric effect in stereo-surface-orientation perception (Ogle, 1950), the different motion amplitudes cause the perceived misorientation of the motion trajectories. Forced-choice psychophysical experiments, conducted with either different spatial frequencies and/or different onscreen motion damping in the two eyes, show that the perceived misorientation in depth is associated with the eye having greater motion damping. A target-tracking experiment provided more direct evidence that the anomalous Pulfrich effect is caused by interocular differences in temporal integration and delay. These findings highlight the computational hurdles posed to the visual system by temporal differences in sensory processing. Future work will explore how the visual system overcomes these challenges to achieve accurate perception.


title: Decision formation in parietal cortex transcends a fixed frame of reference

abstract: Neurons in the lateral intraparietal cortex (area LIP) represent the formation of a decision when it is linked to a specific action, such as an eye movement to a choice target. However, these neurons should be unable to represent a decision that transpires across actions that would disrupt this linkage. We investigated this limitation by recording simultaneously from many neurons. While intervening actions disrupt the representation by single neurons, the ensemble achieves continuity of the decision process by passing information from currently active neurons to neurons that will become active after the action. In this way, the representation of an evolving decision can be generalized across actions and transcends the frame of reference that specifies the neural response fields. The finding extends previous observations of receptive field remapping, thought to support the stability of perception across eye movements, to the continuity of a thought process, such as a decision.


title: An electrophysiological and behavioral model of Paramecium, the "swimming neuron"

abstract: Paramecium is a large unicellular organism that swims in fresh water using cilia. When stimulated by various means (mechanically, chemically, optically, thermally), it often swims backward then turns and swims forward again in a new direction: this is called the avoiding reaction. This reaction is triggered by a calcium-based action potential. For this reason, several authors have called Paramecium the "swimming neuron". Here we present an empirically constrained model of its action potential based on electrophysiology experiments on live immobilized paramecia, together with simultaneous measurement of ciliary beating using particle image velocimetry. Using these measurements and additional behavioral measurements of free swimming, we extend the electrophysiological model by coupling calcium concentration to kinematic parameters, turning it into a swimming model. In this way, we obtain a model of autonomously behaving Paramecium. Finally, we demonstrate how the modeled organism interacts with an environment, can follow gradients and display collective behavior. This work provides a modeling basis for investigating the physiological basis of autonomous behavior of Paramecium in ecological environments.


title: Normalization of aperiodic ECoG components indicates fine motor recovery after sensory cortical stroke in mice

abstract: Electrophysiological signatures of ischemic stroke might help to develop a deeper understanding of the mechanisms of recovery. Here, analyses of multichannel electrocorticography (ECoG) in awake mice demonstrated that the shape of power spectral density (PSD) is modulated in the vicinity of sensory cortical stroke. PSD consists of both rhythmic oscillatory and non-rhythmic, aperiodic components. The alteration of spectrum shape was reflected in a transient increase of aperiodic exponents, while the relative power and frequency of slow oscillations remained unchanged in the peri-infarct cortex. Exponents derived from motor areas significantly correlated with recovery of fine motor deficits of the contralateral forepaw thus indicating functional modifications of neuronal activity. In conclusion, aperiodic spectral exponents exhibited a unique spatiotemporal profile in the mouse cortex after stroke and might complement future studies providing a dynamic link from pathophysiology to behavior.


title: Structured and disordered regions of Ataxin-2 contribute differently to the specificity and efficiency of mRNP granule formation.

abstract: Ataxin-2 (ATXN2) is a gene implicated in spinocerebellar ataxia type II (SCA2), amyotrophic lateral sclerosis (ALS) and Parkinsonism. The encoded protein is a therapeutic target for ALS and related conditions. ATXN2 (or Atx2 in insects) can function in translational activation, translational repression, mRNA stability and in the assembly of mRNP-granules, a process mediated by intrinsically disordered regions (IDRs). Previous work has shown that the LSm (Like-Sm) domain of Atx2, which can help stimulate mRNA translation, antagonizes mRNP-granule assembly. Here we advance these findings through a series of experiments on Drosophila and human Ataxin-2 proteins. Results of Targets of RNA-Binding Proteins Identified by Editing (TRIBE), co-localization and immunoprecipitation experiments indicate that a polyA-binding protein (PABP) interacting, PAM2 motif of Ataxin-2 may be a major determinant of the mRNA and protein content of Ataxin-2 mRNP granules. Transgenic experiments in Drosophila indicate that while the Atx2-LSm domain may protect against neurodegeneration, structured PAM2- and unstructured IDR- interactions both support Atx2-induced cytotoxicity. Taken together, the data lead to a proposal for how Ataxin-2 interactions are remodelled during translational control and how structured and non-structured interactions contribute differently to the specificity and efficiency of RNP granule condensation as well as to neurodegeneration.


title: Pro-resolving lipid mediators within brain esterified lipid pools are reduced in female rats chronically exposed to traffic-related air pollution or genetically susceptible to Alzheimer's Disease phenotype

abstract: Traffic-related air pollution (TRAP) is a risk factor for Alzheimers disease (AD) where neuroinflammation underlies disease progression and pathogenesis. Unresolved inflammation in AD is known to be exacerbated by brain deficits in unesterified pro-resolving lipid mediators enzymatically synthesized from polyunsaturated fatty acids. Recently, we reported that in the brain, unesterified pro-resolving lipid mediators which are bioactive, can also be supplied from less bioactive esterified lipid pools such as neutral lipids (NLs) and phospholipids (PLs). It is not known whether esterified pro-resolving lipid mediators are affected by AD pathology and exacerbated by TRAP exposure. In the present study we addressed this data gap using TgF344-AD male and female rats that express human AD risk genes and their wildtype littermates exposed to filtered air (FA) or TRAP from 1 to 15 months of age. Esterified lipid mediators within NLs and PLs were quantified by mass-spectrometry. We observed a significant reduction in pro-resolving lipid mediators in both NLs and PLs of female TgF344-AD rats compared to wildtype controls. TRAP exposure also reduced pro-resolving lipids in the female brain, mainly in PL pools, but did not exacerbate changes observed in TgF344-AD rats. Minimal changes were observed in males. Our findings indicate that AD genotype and chronic TRAP exposure result in sex-specific deficits in brain esterified pro-resolving lipid mediators, the pool that supplies free and bioactive lipid mediators. These data provide new information on lipid-mediated mechanisms regulating impaired inflammation resolution in AD, and show for the first time that chronic TRAP exposure targets the same lipid network implicated in AD.


title: Variational phylodynamic inference using pandemic-scale data

abstract: The ongoing global pandemic has sharply increased the amount of data available to researchers in epidemiology and public health. Unfortunately, few existing analysis tools are capable of exploiting all of the information contained in a pandemic-scale data set, resulting in missed opportunities for improved surveillance and contact tracing. In this paper, we develop the variational Bayesian skyline (VBSKY), a method for fitting Bayesian phylodynamic models to very large pathogen genetic data sets. By combining recent advances in phylodynamic modeling, scalable Bayesian inference and differentiable programming, along with a few tailored heuristics, VBSKY is capable of analyzing thousands of genomes in a few minutes, providing accurate estimates of epidemiologically relevant quantities such as the effective reproduction number and overall sampling effort through time. We illustrate the utility of our method by performing a rapid analysis of a large number of SARS-CoV-2 genomes, and demonstrate that the resulting estimates closely track those derived from alternative sources of public health data.


title: Biomechanical dependence of SARS-CoV-2 infections

abstract: Older people have been disproportionately vulnerable to the current SARS-CoV-2 pandemic, with an increased risk of severe complications and death compared to other age groups. A mix of underlying factors has been speculated to give rise to this differential infection outcome, including changes in lung physiology, weakened immunity, and severe immune response. Our study focuses on the impact of biomechanical changes in lungs that occur as individuals age, i.e., the stiffening of the lung parenchyma and increased matrix fiber density. We used hydrogels with an elastic modulus of 0.2 and 50 kPa and conventional tissue culture surfaces to investigate how infection rate changes with parenchymal tissue stiffness in lung epithelial cells challenged with SARS-CoV-2 Spike (S) protein pseudotyped lentiviruses. Further, we employed electrospun fiber matrices to isolate the effect of matrix density. Given the recent data highlighting the importance of alternative virulent strains, we included both the native strain identified in early 2020 and an early S protein variant (D614G) that was shown to increase the viral infectivity markedly. Our results show that cells on softer and sparser scaffolds, closer resembling younger lungs, exhibit higher infection rates by the WT and D614G variant. This suggests that natural changes in lung biomechanics do not increase the propensity for SARS-CoV-2 infection and that other factors, such as a weaker immune system, may contribute to increased disease burden in the elderly.