title: Characterization of prefusion-F-specific antibodies elicited by natural infection with human metapneumovirus

abstract: Human metapneumovirus (hMPV) is a major cause of acute respiratory tract infections in infants and the elderly for which there are no approved vaccines or antibody therapies. The viral fusion (F) glycoprotein is required for entry and is the primary target of neutralizing antibodies, however, little is known about the humoral immune response generated by humans as a result of natural infection. Here, we use stabilized hMPV F proteins to interrogate memory B cells from two elderly donors. We obtained over 700 paired non-IgM antibody sequences representing 563 clonotypes, indicative of a highly polyclonal antibody response to hMPV F in these individuals. Characterization of 136 of these monoclonal antibodies revealed broad recognition of the hMPV F surface, with potent neutralizing antibodies targeting each antigenic site. Cryo-EM structures of two neutralizing antibodies reveal the molecular basis for recognition of two prefusion-specific epitopes at the membrane-distal apex of hMPV F. Collectively these results provide new insights into the humoral response to hMPV infection in the elderly and will guide development of novel vaccine antigens.


title: Zebrafish cornea formation and homeostasis reflect robustness in camera-type eye biology, regardless of its environment

abstract: The cornea is the transparent tissue covering the camera-type eyes. This position makes this tissue prone to environmental aggressions, and physical alteration can have a drastic negative impact on sight. The current knowledge on zebrafish corneal physiology is too scarce to get an understanding on its strategy to maintain a clear sight in aquatic environment. In this study, we focus on corneal formation and maturation in zebrafish. After describing the morphological changes taking place from 3 days post fertilization to adulthood, we analyzed cell proliferation. We show that label retaining cells appear just before 1 month of age. Our cell proliferation study, combined to the study of Pax6a and krtt1c19e expression, demonstrate a long maturation process. This process ends with a solid patterning of corneal innervation. Finally, corneal abrasion wound healing process recapitulates the maturation process, via a plasticity period. Altogether, our study decipher the maturation steps of an aquatic cornea. These findings will facilitate the use of zebrafish as model of corneal physiology studies.

category: developmental biology


title: Wild common crossbills produce redder body feathers when their wings are clipped

abstract:
The animal signaling theory posits that conspicuous colorations exhibited by many animals have evolved as reliable signals of individual quality. Red carotenoid-based ornaments may depend on enzymatic transformations (oxidation) of dietary yellow carotenoids, which could occur in the inner mitochondrial membrane (IMM). Thus, carotenoid ketolation and cell respiration could share the same biochemical pathways. Accordingly, the level of trait expression (redness) would directly reveal the efficiency of individuals metabolism and hence, the bearer quality in an unfalsifiable way. Different avian studies have described that the flying effort may induce oxidative stress. A redox metabolism modified during the flight could thus influence the carotenoid conversion rate and, ultimately, animal coloration. Here, we aimed to infer the link between red carotenoid-based ornament expression and flight metabolism by increasing flying effort in wild male common crossbills Loxia curvirostra (Linnaeus). In this order, 295 adult males were captured during winter in an Iberian population. Half of the birds were experimentally handicapped through wing feather clipping to increase their flying effort, the other half being used as a control group. The rump feathers were also plucked in all the birds to stimulate plumage regrown of a small surface during a short time-lapse. Thirty-four birds with fully grown rump feathers could be recaptured in the subsequent weeks. Among them, male crossbills with experimentally impaired flying capacity showed redder rump feathers than controls. This result would support the hypothesis that the flying metabolism influences the redox enzymatic reactions required for converting yellow dietary carotenoids to red ketocarotenoids.

Summary statementCarotenoid-based colorations may depend on pigment enzymatic transformations linked to mitochondrial function. The flight metabolism could influence this. Here, common crossbills with clipped wings produced redder feathers than controls.

category: evolutionary biology


title: Social Learning of a Spatial Task by Observation Alone

abstract: Interactions between conspecifics are central to the acquisition of useful memories in the real world. Observational learning, i.e., learning a task by observing the success or failure of others, has been reported in many species, including rodents. However, previous work in rats with NMDA-receptor blockade has shown that even extensive observation of an unexplored space through a clear barrier is not sufficient to generate a stable hippocampal representation of that space. This raises the question of whether rats can learn a spatial task in a purely observed space from watching a conspecific, and if so, does this somehow stabilize their hippocampal representation? To address these questions, we designed an observational spatial task in a two-part environment that is nearly identical to that of the aforementioned electrophysiological study, in which an observer rat watches a demonstrator animal to learn the location of a hidden reward. Our results demonstrate that rats do not need to physically explore an environment to learn a reward location, provided a conspecific demonstrates where it is. We also show that the behavioral memory is not affected by NMDA receptor blockade, suggesting that the spatial representation underlying the behavior has been consolidated by observation alone.

category: animal behavior and cognition


title: ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2

abstract:
MotivationThe advent of long-read sequencing technologies has increased demand for the visualisation and interpretation of transcripts. However, tools that perform such visualizations remain inflexible and lack the ability to easily identify differences between transcript structures. Here, we introduce ggtranscript, an R package that provides a fast and flexible method to visualize and compare transcripts. As a ggplot2 extension, ggtranscript inherits the functionality and familiarity of ggplot2 making it easy to use.

Availability and implementationggtranscript is available at https://github.com/dzhang32/ggtranscript, DOI: https://doi.org/10.5281/zenodo.6374061

category: bioinformatics


title: Sorting of plant mitochondrial and plastid heteroplasmy is extremely rapid and depends on MSH1 activity

abstract: Because mitochondrial and plastid genomes exist at high cellular copy numbers, new mutations result in the co-occurrence of multiple alleles within a cell or individual, a phenomenon known as heteroplasmy. The extent to which heteroplasmies are transmitted across generations or eliminated through a sorting process involving successive genetic "bottlenecks" is not well understood in plants, in part because their low mutation rates make these variants so infrequent. We previously found that disruption of MutS Homolog 1 (MSH1), a nuclear gene involved in plant organellar DNA repair, results in numerous de novo point mutations, providing an unprecedented opportunity to explore the inheritance of these variants. Here, we used droplet digital PCR to quantitatively track the inheritance of single nucleotide variants (SNVs) in mitochondrial and plastid genomes of both wild-type Arabidopsis and msh1 mutants. We found that heteroplasmic sorting was rapid for both organelles, greatly exceeding the rates at which mitochondrial heteroplasmies are eliminated in animals. In msh1 mutants, plastid SNVs usually reached fixation or were lost within a single generation, indicating an effective transmission bottleneck size (N) of ~1. In contrast, mitochondrial heteroplasmies often persisted across generations but still exhibited a relatively narrow transmission bottleneck (N {approx} 4). Restoring MSH1 function in mitochondria increased the rate of heteroplasmic sorting (N {approx} 1.3), potentially due to its hypothesized role in promoting gene conversion as a mechanism of DNA repair, which is expected to homogenize genome copies within a cell. We also found that heteroplasmic sorting favored GC base pairs. Therefore, recombinational repair and gene conversion in plant organellar genomes may accelerate the elimination of heteroplasmies and bias the outcome of this sorting process.

category: plant biology


title: Glutathione-mediated plant response to high-temperature

abstract: Climate change induce global warming and intense heat waves that affect plant development and productivity. Among the molecular perturbations that high temperature induces in living cells is the accumulation of reactive oxygen species (ROS), which can damage macromolecules of the cell and perturb the cellular redox state. To cope with deleterious effects of ROS, plant, as other organisms, have developed strategies to scavenge ROS and to regulate their redox state. Among those, glutathione plays a major role in maintaining the cellular redox state and the function of key antioxidant enzymes like peroxidases. Here, we investigated the contribution of the redox systems in plant adaptation to high temperature. We studied two different high temperature regimes: a rise of ambient temperature to 27{degrees}C inducing a plant developmental adaptation program called thermomorphogenesis, and a 37{degrees}C treatment mimicking intense heat wave and affecting plant viability. Using the genetically encoded redox marker roGFP, we show that high temperature regimes lead to cytoplasm and nuclear oxidation and impact profoundly the glutathione pool rather than the glutathione redox state. Moreover, plant can restore the pool within a few hours, which likely contribute to plant adaptation to high temperature. However, conditional glutathione deficient mutants fail to adapt to intense heat waves or to induce thermomorphogenesis, suggesting that glutathione is involved in both heat adaptation mechanisms. We also evaluate by RNAseq analyses, how plant change its genome expression signature upon heat stress and identified a marked genome expression deviation in mutant deficient in glutathione antioxidant which might contribute to its sensitivity to high temperature. Thus, we define glutathione as a major antioxidant molecule acting in the adaptation of plant to rise of temperature.


title: Noise facilitates entrainment of a population of uncoupled limit cycle oscillators

abstract:
Many biological oscillators share two properties: they are subject to stochastic fluctuations (noise) and they must reliably adjust their period to changing environmental conditions (entrainment). While noise seems to distort the ability of single oscillators to entrain, in populations of oscillators noise allows entrainment for a wider range of input amplitudes and periods. Here, we investigate, how this effect depends on the noise intensity and the number of oscillators in the population. We have found that, if a population consists of a sufficient number of oscillators, increasing noise intensity leads to faster entrainment after a phase change of the input signal (jet lag) and increases sensitivity to low-amplitude input signals.

SIGNIFICANCELive is characterized by rhythms, such as daily changes in activity or the heartbeat. These rhythms are reflected in molecular oscillations generated at the level of individual cells. These oscillations are inherently noisy, but still cells reliably synchronize to external signals and provide reliable timing for other biological processes. Here, we show how noise can be beneficial to cell populations in terms of synchronization to external signals. Specifically, noise can increase the sensitivity to weak external signals and speed up adjustment to jet-lag-like perturbations.

category: systems biology


title: Deciphering the fibre-orientation independent component of R2* (R2,iso*) in the human brain with a single multi-echo gradient-recalled-echo measurement under varying microstructural conditions

abstract: The effective transverse relaxation rate (R2*) is sensitive to the microstructure of the human brain, e.g. the g-ratio characterising the relative myelination of axons. However, R2* depends on the orientation of the fibres relative to the main magnetic field degrading its reproducibility and that of any microstructural derivative measure. To decipher its orientation-independent part (R2,iso*), a second-order polynomial in time (M2) can be applied to single multi-echo gradient-recalled-echo (meGRE) measurements at arbitrary orientation. The linear-time dependent parameter, {beta}1, of M2 can be biophysically related to R2,iso* when neglecting the signal from the myelin water (MW) in the hollow cylinder fibre model (HCFM). Here, we examined the effectiveness of M2 using experimental and simulated data with variable g-ratio and fibre dispersion. We showed that the fitted {beta}1 effectively estimates R2,iso*when using meGRE with long maximum echo time (TEmax {approx} 54 ms) but its microscopic dependence on the g-ratio was not accurately captured. This error was reduced to less than 12% when accounting for the MW contribution in a newly introduced biophysical expression for {beta}1. We further used this new expression to estimate the MW fraction (0.14) and g-ratio (0.79) in a human optic chiasm. However, the proposed method failed to estimate R2,iso* for a typical in-vivo meGRE protocol (TEmax {approx} 18 ms). At this TEmax and around the magic angle, the HCFM-based simulations failed to explain the R2*-orientation-dependence. In conclusion, estimation of R2,iso* with M2 in vivo requires meGRE protocols with very long TEmax {approx} 54 ms.

category: neuroscience


title: Age-related differences in functional network segregation in the context of sex and reproductive stage

abstract:
Age is accompanied by differences in the organization of functional brain networks, which impact behavior in adulthood. Functional networks tend to become less segregated and more integrated with age. However, sex differences in network segregation declines with age are not well-understood. Further, network segregation in the context of female reproductive stage is relatively understudied, though unmasking such relationships would be informative for elucidating biological mechanisms that contribute to sex-specific differences in aging. In the current work, we used data from the Cambridge Centre for Ageing and Neuroscience (Cam-CAN) repository to evaluate differences in resting-state network segregation as a product of sex and reproductive stage. Reproductive stage was categorized using the Stages of Reproductive Aging Workshop (STRAW+10) criteria. Replicating prior work, we investigated the following functional networks: auditory, cerebellar-basal ganglia, cingulo-opercular task control, default mode, dorsal attention, fronto-parietal task control, salience, sensory somatomotor mouth, sensory somatomotor hand, ventral attention, and visual. First, our results mirror findings from previous work indicating that network segregation is lower with increasing age. Second, when analyzing associations between network segregation and age within each sex separately, we find differences between females and males. Finally, we report significant effects of reproductive stage on network segregation, though these findings are likely driven by age. Broadly, our results suggest that impacts of sex are important to evaluate when investigating network segregation differences across adulthood, though further work is needed to determine the unique role of menopause and sex hormones on the organization of functional brain networks within aging females.

Key PointsO_LISegregation of functional brain networks declines with increasing age
C_LIO_LIAge-segregation relationships are modified by biological sex
C_LIO_LIReproductive stage may impact sex differences in brain network organization
C_LI


title: Context-independent expression of spatial code in hippocampus

abstract: Hippocampus plays a crucial role in formation and retrieval of spatial memory across mammals and episodic memory in humans. Episodic as well as spatial memories can be retrieved irrespectively of subjects awake behavioral state and independently of its actual spatial context. The nature of hippocampal network activity during such out-context retrieval has not been described so far, though. Theoretically, context-independent spatial memory retrieval suggests a shift from the hippocampal spatial representations coding the actual- to the remembered context. In this study we show in rats that CA3 neuronal population can switch spontaneously across representations and transiently activate another stored familiar spatial pattern without a direct external sensory cuing. This phenomenon qualitatively differs from the well described sharp wave-related pattern reactivations during immobility. Here it occurred under theta oscillatory state during an active exploration and reflected the preceding experience of sudden environment change. The respective out-context coding spikes appeared later in the theta cycle than the in-context ones. Finally, the experience induced as well an emergence of population vectors with a co-expression of both codes segregated into different phases of the theta cycle.


title: STEPS 4.0: Fast and memory-efficient molecular simulations of neurons at the nanoscale

abstract: AO_SCPLOWBSTRACTC_SCPLOWRecent advances in computational neuroscience have demonstrated the usefulness and importance of stochastic, spatial reaction-diffusion simulations. However, ever increasing model complexity renders traditional serial solvers, as well as naive parallel implementations, inadequate. This paper introduces a new generation of the STochastic Engine for Pathway Simulation (STEPS) project, denominated STEPS 4.0, and its core components which have been designed for improved scalability, performance, and memory efficiency. STEPS 4.0 aims to enable novel scientific studies of macroscopic systems such as whole cells while capturing their nanoscale details. This class of models is out of reach for serial solvers due to the vast quantity of computation in such detailed models, and also out of reach for naive parallel solvers due to the large memory footprint. Based on a distributed mesh solution, we introduce a new parallel stochastic reaction-diffusion solver and a deterministic membrane potential solver in STEPS 4.0. The distributed mesh, together with improved data layout and algorithm designs, significantly reduces the memory footprint of parallel simulations in STEPS 4.0. This enables massively parallel simulations on modern HPC clusters and overcomes the limitations of the previous parallel STEPS implementation. Current and future improvements to the solver are not sustainable without proper software engineering practices. For this reason, we also give an overview of how the STEPS codebase and the development environment have been updated to follow modern software development practices. We benchmark performance improvement and memory footprint on three published models with different complexities, from a simple spatial stochastic reaction-diffusion model, to a more complex one that is coupled to a deterministic membrane potential solver to simulate the calcium burst activity of a Purkinje neuron. Simulation results of these models suggest that the new solution dramatically reduces the per-core memory consumption by more than a factor of 30, while maintaining similar or better performance and scalability.


title: NDR1/2 kinases regulate membrane trafficking, enable efficient autophagy and prevent neurodegeneration

abstract:
Autophagy is essential for neuronal development and its deregulation contributes to neurodegenerative diseases. NDR1 and NDR2 are highly conserved kinases implicated in neuronal development, mitochondrial health and autophagy, but how they affect mammalian brain development in vivo is not known. Using single and double Ndr1/2 knockout mouse models we show that, dual, but not individual loss of Ndr1/2 in neurons causes neurodegeneration during brain development, but also in adult mice. Proteomic and phosphoproteomic comparisons between Ndr1/2 knockout and control brains revealed novel kinase substrates and indicated that endocytosis is significantly affected in the absence of NDR1/2. We validated the endocytic protein, Raph1/Lpd1 as a novel NDR1/2 substrate and showed that both NDR1/2 and Raph1 are critical for endocytosis and membrane recycling. In NDR1/2 knockout brains, we observed prominent accumulation of transferrin receptor, p62 and ubiquitinated proteins, indicative of a major impairment of protein homeostasis. Furthermore, the levels of LC3-positive autophagosomes were reduced in knockout neurons, implying that reduced autophagy efficiency mediates p62 accumulation and neurotoxicity. Mechanistically, pronounced mislocalisation of the transmembrane autophagy protein ATG9A at the neuronal periphery, impaired axonal ATG9A trafficking and increased ATG9A surface levels further confirm defects in membrane trafficking and could underlie the impairment in autophagy. We provide novel insight into the roles of NDR1/2 kinases in maintaining neuronal health.

HighlightsO_LIDual neuronal Ndr1 and Ndr2 knockout during development or in adult mice causes neurodegeneration.
C_LIO_LIPhosphoproteomics comparison of Ndr1/2 knockouts with control littermates shows endocytosis and membrane trafficking to be affected and reveals novel substrates.
C_LIO_LIRaph1/Lamellipodin is a novel NDR1/2 substrate that is required for TfR endocytosis.
C_LIO_LINdr1/2 knockout brains exhibit a severe defect in ubiquitinated protein clearance and reduced autophagy.
C_LIO_LINDR1/2 and Raph1 are required for the trafficking of the only transmembrane autophagy protein, ATG9A.
C_LI


title: Excitatory-Inhibitory Recurrent Dynamics Produce Robust Visual Grids and Stable Attractors

abstract:
Spatially modulated grid cells has been recently found in the rat secondary visual cortex (V2) during activation navigation. However, the computational mechanism and functional significance of V2 grid cells remain unknown, and a theory-driven conceptual model for experimentally observed visual grids is missing. To address the knowledge gap and make experimentally testable predictions, here we trained a biologically-inspired excitatory-inhibitory recurrent neural network (E/I-RNN) to perform a two-dimensional spatial navigation task with multisensory (e.g., velocity, acceleration, and visual) input. We found grid-like responses in both excitatory and inhibitory RNN units, and these grid responses were robust with respect to the choices of spatial cues, dimensionality of visual input, activation function, and network connectivity. Dimensionality reduction analysis of population responses revealed a low-dimensional torus-like manifold and attractor, showing the stability of grid patterns with respect to new visual input, new trajectory and relative speed. We found that functionally similar receptive fields with strong excitatory-to-excitatory connection appeared within fully connected as well as structurally connected networks, suggesting a link between functional grid clusters and structural network. Additionally, multistable torus-like attractors emerged with increasing sparsity in inter- and intra-subnetwork connectivity. Finally, irregular grid patterns were found in a convolutional neural network (CNN)-RNN architecture while performing a visual sequence recognition task. Together, our results suggest new computational mechanisms of V2 grid cells in both spatial and non-spatial tasks.

HighlightsO_LIGrid patterns emerge in trained RNNs with multisensory inputs
C_LIO_LIGrid patterns are robust to the RNN input and network connectivity
C_LIO_LIPopulation responses show emergent ring-like manifolds and attractors
C_LIO_LIGrid-like patterns persist in RNNs while performing a non-spatial task.
C_LI


title: Zfp503/Nlz2 is Required for RPE Differentiation and Optic Fissure Closure

abstract:
PurposeUveal coloboma is a congenital eye malformation caused by failure of the optic fissure to close in early human development. Despite significant progress in identifying genes whose regulation is important for executing this closure, mutations are detected in a minority of cases using known gene panels, implying additional genetic complexity. We have previously shown knock down of znf503 (the ortholog of mouse Zfp503) in zebrafish causes coloboma. Here we characterize Zfp503 knock out (KO) mice and evaluate transcriptomic profiling of mutant vs. wild-type (WT) retinal pigment epithelium (RPE)/Choroid.

MethodsZfp503 KO mice were generated by gene targeting using homologous recombination. Embryos were characterized grossly and histologically. Patterns and level of developmentally relevant proteins/genes were examined with immunostaining/in situ hybridization. The transcriptomic profile of E11.5 KO RPE/choroid was compared to that of WT.

ResultsZfp503 is dynamically expressed in developing mouse eyes and that loss of its expression results in uveal coloboma. KO embryos exhibit altered mRNA levels and expression patterns of several key transcription factors involved in eye development, including Otx2, Mitf, Pax6, Pax2, Vax1 and Vax2, resulting in reduced melanin pigmentation in the presumptive RPE and its differentiation into neural-retina-like lineages. Comparison of RNA-Seq data from wild type and KO E11.5 embryos demonstrated reduced expression of melanin-related genes and significant overlap with genes known to be dynamically regulated at the optic fissure.

ConclusionsThese results demonstrate a critical role of Zfp503 in RPE differentiation and in optic fissure closure.


title: Molecular characterization of cell types in the squid Loligo vulgaris

abstract: Cephalopods have long been getting a lot of attention for their fascinating behavioral abilities and for the complexity of their nervous systems that set them apart from other mollusks. Because of the great evolutionary distance that separates vertebrates from mollusks, it is evident that higher cognitive features have evolved independently in this clade although they sometimes resemble cognitive functions of vertebrates. Alongside their complex behavioral abilities, cephalopods have evolved specialized cells and tissues, such as the chromatophores for camouflage or suckers to grasp prey. Gaining a better understanding of the biology of various species of cephalopods can significantly improve our knowledge of how these animals evolved and better identify the mechanisms that drive the astonishing faculties of their nervous systems. In this study, we performed single-cell transcriptomics of whole heads of Loligo vulgaris pre-hatchlings. We characterized the different cell types in the head of these animals and explored the expression patterns of core cell type markers by hybridization chain reaction. We were able to thoroughly describe some major components of the squid nervous that play important roles for the maintenance, development and sensory function in the nervous system of these animals.


title: Effects of haemosporidian co-infection and parasitemia on reproductive strategies in a polymorphic species

abstract: Host-parasite interactions play a significant role in evolution. Parasite infections impose fitness costs that can trigger trade-off responses in host reproductive strategies. Individuals can invest limited resources in parasite defense, such as stimulating the immune system, or perform terminal reproductive investment. Here, we investigated how haemosporidian co-infection and parasitemia influence different reproductive strategies in a polymorphic bird species (the white-throated sparrow, Zonotrichia albicollis). We provided an account of the impacts of co-infection and parasitemia on host reproductive success and reproductive strategies in response to parasite infection. We tested the effect of co-infection and parasitemia on reproductive success (fledgling number, extra-pair paternity, ratio social/genetic offspring) and the effect of parental infection on nestling quality (mean nestling growth rate and body condition). We found that co-infection increases reproductive extra-pair paternity and nestling mean body condition. Parental high parasitemia positively impacts the ratio of genetic offspring belonging to the social father and has mixed results on nestling quality. We observed that co-infection in females and parasitemia in males might trigger a switch in reproductive strategy towards a terminal investment for co-infected individuals. In contrast, high parasitemia in females negatively impacted their offspring fitness, possibly due to the reallocation of resources for fighting the infection.

category: ecology


title: High Quality Phasing Using Linked-Read Whole Genome Sequencing of Patient Cohorts Informs Genetic Understanding of Complex Traits

abstract: Phasing of heterozygous alleles is critical for interpretation of cis-effects of disease-relevant variation. For population studies, phase is often inferred from external data but read-based phasing approaches that span long genomic distances would be more accurate because they enable both genotype and phase to be obtained from a single dataset. To demonstrate how read-based phasing can provide functional insights, we sequenced 477 individuals with Cystic Fibrosis (CF) using linked-read sequencing. We benchmark read-based phasing with different short- and long-read sequencing technologies, prioritize linked-read technology as the most informative and produce a benchmark phase call set from reference sample HG002 for the community. The 477 samples display an average phase block N50 of 4.39 Mb. We use these samples to construct a graph representation of CFTR haplotypes, which facilitates understanding of complex CF alleles. Fine-mapping and phasing of the chr7q35 trypsinogen locus associated with CF meconium ileus demonstrates a 20 kb deletion and a PRSS2 missense variant p.Thr8Ile (rs62473563) independently contribute to meconium ileus risk (p=0.0028, p=0.011, respectively) and are PRSS2 pancreas eQTLs (p=9.5e-7 and p=1.4e-4, respectively), explaining the mechanism by which these polymorphisms contribute to CF. Phase enables access to haplotypes that can be used for genome graph or reference panel construction, identification of cis-effects, and for understanding disease associated loci. The phase information from linked-reads provides a causal explanation for variation at a CF-relevant locus which also has implications for the genetic basis of non-CF pancreatitis to which this locus has been reported to contribute.

category: genetics


title: Genome sequence of 12 Vigna species as a knowledge base of stress tolerance and resistance

abstract: Harnessing plant genetic resources including wild plants enables exploitation of agronomically unfavorable lands to secure food in the future. The genus Vigna, family Fabaceae, consists of many species of such kind, as they are often adapted to harsh environments including marine beach, arid sandy soil, acidic soil, limestone karst and marshes. Here we report long-read assemblies of 12 Vigna species, achieving 95% or higher BUSCO scores. The comparative analyses discovered a new class of WUSCHEL-related homeobox (WOX) transcription factor superfamily that are incorporated into LTR retrotransposons and have dramatically amplified in some species of the genus Vigna. Except WOX transcription factors, however, gene contents are highly conserved among Vigna species with few copy number variations. On the other hand, transcriptome data provided some insights that transcriptional alterations played more important roles in evolution of stress tolerance in the genus Vigna. The whole genome sequences presented in this study will facilitate understanding genetic mechanisms of stress tolerance and application for developing new crops that are adapted to unfavorable environments.

category: genomics


title: Pangenomics provides insights into the role of synanthropy in barn swallow evolution

abstract: Insights into the evolution of non-model organisms are often limited by the lack of reference genomes. As part of the Vertebrate Genomes Project, we present a new reference genome and a pangenome produced with High-Fidelity long reads for the barn swallow Hirundo rustica. We then generated a reference-free multialignment with other bird genomes to identify genes under selection. Conservation analyses pointed at genes enriched for transcriptional regulation and neurodevelopment. The most conserved gene is CAMK2N2, with a potential role in fear memory formation. In addition, using all publicly available data, we generated a comprehensive catalogue of genetic markers. Genome-wide linkage disequilibrium scans identified potential selection signatures at multiple loci. The top candidate region comprises several genes and includes BDNF, a gene involved in stress response, fear memory formation, and tameness. We propose that the strict association with humans in this species is linked with the evolution of pathways typically under selection in domesticated taxa.


title: Telomere-to-telomere human DNA replication timing profiles

abstract: The spatiotemporal organization of DNA replication produces a highly robust and reproducible replication timing profile. Sequencing-based methods for assaying replication timing genome-wide have become commonplace, but regions of high repeat content in the human genome have remained refractory to analysis. Here, we report the first telomere-to-telomere replication timing profiles in human, using the T2T-CHM13 genome assembly and sequencing data for five cell lines. We find that replication timing can be successfully assayed in centromeres and large blocks of heterochromatin. Centromeric regions replicate in mid-to-late S-phase and contain replication-timing peaks at a similar density to other genomic regions, while distinct families of heterochromatic satellite DNA differ in their bias for replicating in late S-phase. The high degree of consistency in centromeric replication timing across chromosomes within each cell line prompts further investigation into the mechanisms dictating that some cell lines replicate their centromeres earlier than others, and what the consequences of this variation are.


title: Resistance of mitochondrial DNA to chemical-induced germline mutations is independent of mitophagy in C. elegans

abstract: Mitochondrial DNA (mtDNA) is prone to mutation in aging and over evolutionary time, yet the processes that regulate the accumulation of de novo mtDNA mutations and modulate mtDNA heteroplasmy are not fully elucidated. Mitochondria lack certain DNA repair processes, which could contribute to polymerase error-induced mutations and increase susceptibility to chemical-induced mtDNA mutagenesis. We conducted error-corrected, ultra-sensitive Duplex Sequencing to investigate the effects of two known nuclear genome mutagens, cadmium and Aflatoxin B1, on germline mtDNA mutagenesis in Caenorhabditis elegans. After 1,750 generations, we detected 2,270 single nucleotide mutations. Heteroplasmy is pervasive in C. elegans and mtDNA mutagenesis is dominated by C:G [->] A:T mutations generally attributed to oxidative damage, yet there was no effect of either exposure on mtDNA mutation frequency, spectrum, or trinucleotide context signature. Mitophagy may play a role in eliminating mtDNA damage or deleterious mutations, and mitophagy-deficient mutants pink-1 and dct-1 accumulated significantly higher levels of mtDNA damage compared to wild-type C. elegans after exposures. However, there were only small differences in overall mutation frequency, spectrum, or trinucleotide context signature compared to wild-type after 3,050 generations, across all treatments. These findings suggest mitochondria harbor additional previously uncharacterized mechanisms that regulate mtDNA mutational processes across generations.


title: vcferr: Development, Validation, and Application of a SNP Genotyping Error Simulation Framework

abstract:
MotivationGenotyping error can impact downstream SNP-based analyses. Simulating various modes and and levels of error can help investigators better understand potential biases caused by miscalled genotypes.

ResultsWe have developed and validated vcferr, a tool to probabilistically simulate genotyping error and missigness in VCF files. We demonstrate how vcferr could be used to address a research question by introducing varying levels of error of different type into a sample in a simulated pedigree, and assessed how kinship analysis degrades as a function of kind and type of error.

Software Availabilityvcferr is available for installation on PyPi (https://pypi.org/project/vcferr/). The software is released under the MIT license with source code available on GitHub (https://github.com/signaturescience/vcferr).


title: Growth instabilities shape morphology and genetic diversity of cellular aggregates

abstract: Cellular aggregates assume an incredible variety of shapes ranging from circular molds to irregular tumors. While we understand many of the mechanisms responsible for these spatial patterns, little is known about how the shape of an aggregate influences its ecology and evolution. Here, we investigate this relationship in the context of microbial colonies grown on hard agar plates. This a well-studied system that exhibits a transition from smooth circular disks to more irregular and rugged shapes as either the nutrient concentration or cellular motility is decreased. Starting from a mechanistic model of colony growth, we identify two dimensionless quantities that determine how morphology and genetic diversity of the population depend on the model parameters. Our simulations further reveal that population dynamics cannot be accurately described by the commonly-used surface growth models. Instead, one has to explicitly account for the emergent growth instabilities and demographic fluctuations. Overall, our work links together environmental conditions, colony morphology, and evolution. This link is essential for a rational design of concrete, biophysical perturbations to steer evolution in the desired direction.

category: biophysics


title: Learning of probabilistic punishment as a model of anxiety produces changes in action but not punishment encoding in the dmPFC and VTA

abstract: Previously, we developed a novel model for anxiety during motivated behavior by training rats to perform a task where actions executed to obtain a reward were probabilistically punished and observed that after learning, neuronal activity in the ventral tegmental area (VTA) and dorsomedial prefrontal cortex (dmPFC) encode the relationship between action and punishment risk (Park & Moghaddam, 2017). Here we used male and female rats to expand on the previous work by focusing on neural changes in the dmPFC and VTA that were associated with the learning of probabilistic punishment, and with anxiolytic treatment with diazepam after learning. We find that adaptive neural responses of dmPFC and VTA during the learning of anxiogenic contingencies are independent from the punishment experience and occur primarily during the peri-action period. Our results further identify peri-action ramping of VTA neural activity, and VTA-dmPFC correlated activity, as potential markers for the anxiolytic properties of diazepam.


title: Primate dopamine neurons activated in rewarding environment by tonic disinhibition from amygdala

abstract: Seeking out good and avoiding bad objects is critical for survival. In practice, objects are rarely good every time or everywhere, but only at the right time or place. Whereas the basal ganglia (BG) are known to mediate goal-directed behavior, for example, saccades to rewarding objects, it remains unclear how such simple behaviors are rendered contingent on higher-order factors, including environmental context. Here we show that amygdala neurons are sensitive to environments and regulate dopamine (DA) neurons via an inhibitory projection to substantia nigra pars reticulata (SNr) neurons. We combined optogenetics and multi-channel recording to demonstrate that rewarding environments induce tonic firing changes in DA neurons. These tonic responses are mediated by disinhibition via GABAergic projection onto DA neurons from SNr, which in turn are suppressed by inhibitory projection from the amygdala. Thus, the amygdala provides an additional source of learning to BG circuits, namely contingencies imposed by the environment.


title: Glial dysregulation in human brain in Fragile X-related disorders

abstract: AbstractWhile large trinucleotide repeat expansions at the FMR1 locus cause Fragile X Syndrome (FXS), smaller "premutations" are associated with the late-onset condition Fragile X-associated tremor/ataxia syndrome (FXTAS), which shows very different clinical and pathological features, with no clear molecular explanation for these marked differences. One prevailing theory posits that the premutation uniquely causes neurotoxic increases in FMR1 mRNA (i.e., 4-8-fold increases), but evidence to support this hypothesis is largely derived from analysis of peripheral blood. We applied single- nucleus RNA-sequencing to post-mortem frontal cortex and cerebellum from 9 individuals with Fragile X mutations as well as age and sex matched controls (n=6) to assess cell-type specific molecular neuropathology. We found robust reduction of FMR1 mRNA in FXS as expected, with modest but significant upregulation ([~]1.3 fold) of FMR1 in glial clusters associated with premutation expansions. In premutation cases we identified alterations in glia number in cortex and cerebellum. Differential expression analysis demonstrated altered cortical oligodendrocyte development, while gene ontology analysis revealed alterations in neuroregulatory roles of glia, such as glial modulation of neurotransmission and synaptic structure. We identified significant enrichment of known FMR1 protein target genes in differentially expressed gene lists in FXS as well as the premutation, suggesting FMR1 protein target pathways may represent a shared source of dysfunction in both conditions despite opposite FMR1 mRNA changes. These findings challenge existing dogma regarding FXTAS and implicate glial dysregulation as a critical facet of premutation pathophysiology, representing novel therapeutic targets directly derived from the human condition.


title: High-resolution epigenetic profiling identifies novel regulators of COPD in human lung fibroblasts

abstract:
Patients with chronic obstructive pulmonary disease (COPD) are still waiting for curative treatments. Considering the environmental cause of COPD (e.g., cigarette smoke) and disease phenotypes, including stem-cell senescence and impaired differentiation, we hypothesized that COPD will be associated with altered epigenetic signaling in lung cells. We generated genome-wide DNA methylation maps at single CpG resolution of primary human lung fibroblasts (HLFs) isolated from distal parenchyma of ex-smoker controls and COPD patients, with both mild and severe disease. The epigenetic landscape is markedly changed in lung fibroblasts across COPD stages, with DNA methylation changes occurring predominantly in regulatory regions, including promoters and enhancers. RNA sequencing of matched fibroblasts demonstrated dysregulation of genes involved in proliferation, DNA repair, and extracellular matrix organization. Notably, we identified epigenetic and transcriptional dysregulation already in mild COPD patients, providing unique insights into early disease. Integration of profiling data identified 110 candidate regulators of disease phenotypes, including epigenetic factors. Using phenotypic screens, we verified the regulator capacity of multiple candidates and linked them to repair processes in the human lung.

Our study provides first integrative high-resolution epigenetic and transcriptomic maps of human lung fibroblasts across stages of COPD. We reveal novel transcriptomic and epigenetic signatures associated with COPD onset and progression and identify new candidate regulators involved in the pathogenesis of chronic respiratory diseases. The presence of various epigenetic factors among the candidates demonstrates that epigenetic regulation in COPD is an exciting research field that holds promise for novel therapeutic avenues for patients.

category: cell biology


title: The hidden intricacies of aquaporins: Remarkable details in a common structural scaffold

abstract: Evolution turned aquaporins (AQPs) into the most efficient facilitators of passive water flow through cell membranes at no expense of solute discrimination. In spite of a plethora of solved AQP structures, many structural details remain hidden. Here, by combining extensive sequence- and structural-based analysis of a unique set of 20 non-redundant high-resolution structures and molecular dynamics simulations of 4 representatives, we identify key aspects of AQP stability, gating, selectivity, pore geometry and oligomerization, with a potential impact on channel functionality. We challenge the general view of AQPs possessing a continuous open water pore and depict that AQPs selectivity is not exclusively shaped by pore lining residues but also by the relative arrangement of transmembrane helices. Moreover, our analysis reveals that hydrophobic interactions constitute the main determinant of protein thermal stability. Finally, we establish a novel numbering scheme of the conserved AQP scaffold facilitating direct comparison and prediction of potential structural effects of e.g. disease-causing mutations. Additionally, our results pave the way for the design of optimized AQP water channels to be utilized in biotechnological applications.


title: A novel cis-element enabled bacterial uptake by plant cells

abstract: The root nodule symbiosis (RNS) of plants with nitrogen-fixing bacteria is phylogenetically restricted to a single clade of flowering plants, which calls for yet unidentified trait acquisitions and genetic changes in the last common ancestor. Here we discovered - within the promoter of the transcription factor gene Nodule Inception (NIN) - a cis-regulatory element (PACE), exclusively present in members of this clade. PACE was essential for restoring infection threads (ITs) in nin mutants of the legume Lotus japonicus. PACE sequence variants from RNS-competent species appeared functionally equivalent. Evolutionary loss or mutation of PACE is associated with loss of this symbiosis. During early stages of nodule development, PACE dictates gene expression in a spatially restricted domain containing cortical cells carrying ITs. Consistent with its expression domain, PACE-driven NIN expression restored the formation of cortical ITs, also when engineered into the NIN promoter of tomato. Our data pinpoint PACE as a key evolutionary invention that connected NIN to a pre-existing symbiosis signal transduction cascade that governs the intracellular accommodation of arbuscular mycorrhiza fungi and is conserved throughout land plants. This connection enabled bacterial uptake into plant cells via intracellular support structures like ITs, a unique and unifying feature of this symbiosis.


title: Genotype by microbiome interactions have large effects on growth in Lotus japonicus

abstract: Biological interactions between plants and their root microbiomes are pivotal for plant growth. Even though the plant genotype [G], soil microbiome [C], and growth conditions (environment) [E] are core factors shaping the root microbiome, their relationships remain unclear. We disentangled the effects of G, C, E, and their interactions on the Lotus root microbiome and plant growth using a cross-inoculation approach that reconstructed the interactions between nine Lotus accessions and four soil microbiomes under two different environmental conditions. We found that a large proportion of the root microbiome composition was determined by C and E and that G-related (G, G x C, and G x E) effects were significant but small. In contrast, the interactions between G and C had a more pronounced effect on plant shoot growth than C alone. Our findings indicate that most microbiome variations controlled by C have little effect on the plant phenotype, whereas G x C interactions have more significant effects. Plant genotype-dependent interactions with soil microbes warrant more attention in efforts to optimize crop yield and resilience.


title: Classification of Movement-Related Oscillations in sEEG Recordings with Machine Learning

abstract:
Previous electrophysiological research has characterized canonical oscillatory patterns associated with movement mostly from recordings of primary sensorimotor cortex. Less work has attempted to decode movement based on electrophysiological recordings from a broader array of brain areas such as those sampled by stereoelectroencephalography (sEEG). Here we decoded movement using a linear support vector machine (SVM). We were able to accurately classify sEEG spectrograms during a keypress movement in a task versus those during the inter-trial interval. Furthermore, the important time-frequency patterns for this classification recapitulated findings from previous studies that used non-invasive electroencephalography (EEG) and electrocorticography (ECoG) and identified brain regions that were not associated with movement in previous studies. Specifically, we found these previously described patterns: beta (13 - 30 Hz) desynchronization, beta synchronization (rebound), pre-movement alpha (8 - 15 Hz) modulation, a post-movement broadband gamma (60 - 90 Hz) increase and an event-related potential. These oscillatory patterns were newly observed in a wide range of brain areas accessible with sEEG that are not accessible with other electrophysiology recording methods. For example, the presence of beta desynchronization in the frontal lobe was more widespread than previously described, extending outside primary and secondary motor cortices. We provide evidence for a system of putative motor networks that exhibit unique oscillatory patterns by describing the anatomical extent of the movement-related oscillations that were observed most frequently across all sEEG contacts.

Significance StatementSeveral major motor networks have been previously delineated in humans, however, much less is known about the population-level oscillations that coordinate this neural circuitry, especially in cortex. Therapies that modulate brain circuits to treat movement disorders, such as deep brain stimulation (DBS), or use brain signals to control movement, such as brain-computer interfaces (BCIs), rely on our basic scientific understanding of this movement neural circuitry. In order to bridge this gap, we used stereoelectroencephalography (sEEG) collected in human patients being monitored for epilepsy to assess oscillatory patterns during movement.


title: Health hazards posed by ionizing radiation to human space missions and newly developing methodologies to investigate them

abstract: Ionizing radiation is one of the main threats to human space exploration beyond low Earth orbit (BLEO). It is thus of primary importance to determine safe career dose limits for astronauts involved in BLEO missions. In this work the average equivalent doses received by a hypothetical human crew are established using the data of several robotic missions to the Moon and to Mars. The probabilities of the occurrence of deterministic effects due to radiation that could impair the success of a mission or lower the life expectancy of astronauts are evaluated using statistical methods. The limits of the obtained results concerning deterministic and stochastic effects basing on statistical methods are discussed. The conclusion is that new strategies are necessary in order to predict the insurgence of stochastic effects. We argue that the use of the so-called 3D models or organoids could be a good candidate of such a strategy that will be complementary to in vitro 2D models and animal models. Organoids are in fact able to recapitulate several relevant features of the real human organs and their in vivo surroundings. Yet, the main problem of detecting the onset of cancer in the human body remains outstanding. To this purpose, we propose here to combine organoid techniques with those of precision oncology and molecular medicine. Exactly these disciplines have greatly contributed in the recent time to the understanding of the patterns of cancer formation in several cases of tumors. Precision oncology and molecular medicine provide powerful markers to track down the events leading to tumorigenesis following exposure to radiation in organoids.


title: Inflammaging in human photoexposed skin: Early onset of senescence and imbalanced epidermal homeostasis across the decades.

abstract: Inflammaging is a theory of aging which purports that low-level chronic inflammation leads to cellular dysfunction and premature aging of surrounding tissue. Skin is susceptible to inflammaging because it is the first line of defense from the environment, particularly solar radiation. To better understand the impact of aging and photoexposure on epidermal biology we performed a systems biology-based analysis of photoexposed face and arm and photoprotected buttock sites from women between the ages of 20s to 70s. Biopsies were analyzed by histology, transcriptomics, and proteomics and skin surface biomarkers collected from tape strips. We identified morphological changes with age of epidermal thinning, rete ridge pathlength loss, and stratum corneum thickening. The SASP biomarkers IL-8 and IL-1RA/IL1- were consistently elevated in face across age and cis/trans-urocanic acid were elevated in arms and face with age. In older arms, the DNA damage response biomarker 53BP1 showed higher puncti numbers in basal layers and epigenetic aging was accelerated. Genes associated with differentiation and senescence show increasing expression in the 30s whereas genes associated with hypoxia and glycolysis increase in the 50s. Proteomics comparing 60s vs 20s confirmed elevated levels of differentiation and glycolytic related proteins. Representative immunostaining for proteins of differentiation, senescence, and oxygen sensing/hypoxia shows similar relationships. This systems biology-based analysis provides a body of evidence that young photoexposed skin is undergoing inflammaging. We propose the presence of chronic inflammation in young skin contributes to an imbalance of epidermal homeostasis that leads to a prematurely aged appearance during later life.


title: Transcriptional control of nucleus accumbens neuronal excitability by Retinoid X Receptor Alpha tunes sensitivity to drug rewards

abstract: The complex nature of the transcriptional networks underlying addictive behaviors suggests intricate cooperation between diverse gene regulation mechanisms that go beyond canonical activity-dependent pathways. Here we implicate in this process a novel nuclear receptor transcription factor, Retinoid X Receptor Alpha (RXR), which we identified bioinformatically as associated with addiction-like behaviors. In the nucleus accumbens (NAc) of male and female mice, we show that, while its own expression remains unaltered after cocaine exposure, RXR controls plasticity- and addiction-relevant transcriptional programs in both dopamine receptor D1- and D2-expressing medium spiny neurons, which in turn modulate intrinsic excitability and synaptic activity of these NAc cell types. Behaviorally, bidirectional viral and pharmacological manipulation of RXR regulates drug reward sensitivity in both non-operant and operant paradigms. Together, this study demonstrates a key role for NAc RXR in promoting drug addiction, and paves the way for future studies of rexinoid signaling in psychiatric disease states.


title: Local translation provides the asymmetric distribution of CaMKII required for associative memory formation

abstract: How compartment-specific local proteomes are generated and maintained is inadequately understood, particularly in neurons, which display extreme asymmetries. Here we show that local enrichment of Ca2+/calmodulin-dependent protein kinase II (CaMKII) in axons of Drosophila mushroom body neurons is necessary for cellular plasticity and associative memory formation. Enrichment is achieved via enhanced axoplasmic translation of CaMKII mRNA, through a mechanism requiring the RNA-binding protein Mub and a 23-base Mub-recognition element in the CaMKII 3UTR. Perturbation of either dramatically reduces axonal, but not somatic, CaMKII protein without altering the distribution or amount of mRNA in vivo and both are necessary and sufficient to enhance axonal translation of reporter mRNA. Together, these data identify elevated levels of translation of an evenly distributed mRNA as a novel strategy for generating subcellular biochemical asymmetries. They further demonstrate the importance of distributional asymmetry in the computational and biological functions of neurons.


title: Activation of the CA2-vCA1 pathway reverses social discrimination dysfunction in Shank3B knockout mice

abstract: Social memory dysfunction is a feature of several neuropsychiatric and neurodevelopmental disorders. Mutation or deletion of the SHANK3 gene, which codes for a synaptic scaffolding protein, has been linked to autism spectrum disorder (ASD) and Phelan-McDermid syndrome, conditions associated with impairments in social memory. Shank3B knockout (KO) mice exhibit several behavioral abnormalities that may be analogous to symptoms of ASD, including social discrimination deficits. The CA2 region of the hippocampus integrates numerous afferents and sends a major output to the ventral CA1 (vCA1), circuitry that plays an important role in social memory. Despite finding few differences in excitatory afferents to the CA2 in Shank3B KO mice, chemogenetic activation of CA2 excitatory neurons restored social recognition function to wildtype (WT) levels. Specific activation of the CA2-vCA1 circuitry had a similar effect. Neuronal oscillations in the theta, gamma and, sharp wave ripple ranges have been linked to social memory, but we observed no differences in these measures between WT and Shank3B KO mice in the vCA1 in response to social stimuli. However, activation of CA2 excitatory neurons enhanced vCA1 theta power in Shank3B KO mice, concurrent with behavioral improvements. These findings suggest that stimulating adult circuitry in a mouse model with neurodevelopmental impairments can be sufficient to invoke latent function, particularly with respect to social memory dysfunction. The extent to which vCA1 network oscillations in the theta range are responsible for rescued behavioral function remains unknown.


title: Sparcl1/Hevin drives inflammatory and neuropathic pain through astrocyte and NMDA receptor signaling

abstract: Hevin/Sparcl1 is an astrocyte-secreted protein and regulates synapse formation in the brain. Here we show that astrocytic hevin signaling plays a critical role in maintaining chronic pain. Compared to wild-type mice, hevin-null mice exhibited normal mechanical and heat sensitivity but reduced inflammatory pain. Interestingly, hevin is required for the maintenance of nerve injury-induced neuropathic pain (mechanical allodynia), and hevin-null mice have faster recovery than wild-type mice from neuropathic pain after nerve injury. Intrathecal injection of wild-type hevin but not a hevin mutant that is no longer synaptogenic was sufficient to induce persistent mechanical allodynia in naive mice and further enhanced neuropathic pain in animals with nerve injury. In hevin-null mice with nerve injury, AAV-mediated re-expression of hevin, but not mutant hevin, in GFAP-expressing spinal cord astrocytes could reinstate neuropathic pain. Mechanistically, hevin is crucial for spinal cord NMDA receptor (NMDAR) signaling, as NMDA-induced mechanical allodynia and inward currents in spinal cord lamina II neurons is reduced in hevin-null mice. Hevin potentiated NMDA currents mediated by the GluN2B-containing NMDARs. Furthermore, intrathecal injection of a neutralizing antibody against hevin alleviated acute inflammatory pain and persistent neuropathic pain. Secreted hevin was detected in mouse cerebrospinal fluid (CSF) and nerve injury significantly increased CSF hevin abundance. Finally, neurosurgery caused rapid (< 10 hours) and substantial increases (~20 fold) in HEVIN levels in human CSF. Collectively, our findings support a critical role of hevin and astrocytes in the maintenance of chronic pain. Neutralizing of secreted hevin with monoclonal antibody may provide a new therapeutic strategy for treating chronic pain and NMDAR-medicated neurodegeneration.


title: Large-Scale Benchmarking of Diverse Artificial Vision Models in Prediction of 7T Human Neuroimaging Data

abstract: Rapid simultaneous advances in machine vision and cognitive neuroimaging present an unparalleled opportunity to (re)assess the current state of artificial models of the human visual system. Here, we perform a large-scale benchmarking analysis of 85 modern deep neural network models (e.g. CLIP, BarlowTwins, Mask-RCNN) to characterize with robust statistical power how differences in architecture and training task contribute to the prediction of human fMRI activity across 16 distinct regions of the human visual system. We find: one, that even stark architectural differences (e.g. the absence of convolution in transformers and MLP-mixers) have very little consequence in emergent fits to brain data; two, that differences in task have clear effects-with categorization and self-supervised models showing relatively stronger brain predictivity across the board; three, that feature reweighting leads to substantial improvements in brain predictivity, without overfitting - yielding model-to-brain regression weights that generalize at the same level of predictivity to brain responses over 1000s of new images. Broadly, this work presents a lay-of-the-land for the emergent correspondences between the feature spaces of modern deep neural network models and the representational structure inherent to the human visual system.


title: Individual differences in late positive potential amplitude and theta power predict cue-induced eating

abstract:
Both the brains affective and cognitive systems are known to regulate cue-induced behaviors. Although it is established that individual differences in affective processing of food-related cues predict cue-induced eating, we have yet to investigate how both affective and cognitive mechanisms act in tandem to regulate cue-induced eating. We recorded electroencephalogram (EEG) from 59 adults while they viewed emotional & food-related images that preceded the delivery of food rewards (candies) or nonfood objects (beads). We measured the amplitude of the late positive potential (LPP) in response to images and power in the theta (4-8 Hz) frequency band after the candy or bead was dispensed to the participant. We found that individuals with larger LPP responses to food cues than to pleasant images (C>P group) ate significantly more during the experiment than did those with the opposite response pattern (P>C group, p < 0.001). Furthermore, we found that individuals with higher theta power after dispensation of the candy than of the bead ({theta}CA>{theta}BE) ate significantly more than did those with the opposite response pattern ({theta}BE>{theta}CA, p < 0.001). Finally, we found that the crossed P>C and {theta}BE>{theta}CA group ate less (p < 0.001) than did the other three groups formed by crossing the LPP and theta group assignments, who exhibited similar eating behavior on average (p = 0.662). These findings demonstrate that motivational salience and cognitive control converge to independently confer vulnerability or resilience to cue-induced behaviors, underscoring the need for individualized treatments to mitigate maladaptive behaviors.

HIGHLIGHTSO_LILPP responses to motivationally salient stimuli predict cue-induced eating.
C_LIO_LITheta power in the presence of food rewards predicts cue-induced eating.
C_LIO_LIThe LPP & theta may inform the development of personalized weight-loss interventions.
C_LI


title: Lassa virus glycoprotein nanoparticles elicit a neutralizing antibody that defines a new site of vulnerability

abstract: Lassa virus is endemic in large parts of West Africa and causes a hemorrhagic fever. Recent years have seen several serious outbreaks of Lassa fever with high mortality rates. A vaccine to curtail infection is urgently needed. The development of a recombinant protein vaccine has been hampered by the instability of soluble Lassa virus glycoprotein complex (GPC) trimers, which disassemble into monomeric subunits after expression. Here we use two-component protein nanoparticles to stabilize GPC in a trimeric conformation and present twenty prefusion GPC trimers on the surface of an icosahedral nanoparticle. Cryo-EM studies of assembled GPC nanoparticles demonstrated a well-ordered structure and yielded a high-resolution structure of an unliganded GPC. These nanoparticles induced potent humoral immune responses in rabbits and protective immunity against a lethal Lassa virus challenge in guinea pigs. We isolated a neutralizing antibody which was mapped to the putative receptor-binding site, revealing a novel site of vulnerability on GPC.

category: immunology


title: Detection of interphylum transfers of the magnetosome gene cluster in magnetotactic bacteria

abstract: Magnetosome synthesis in magnetotactic bacteria (MTB) is regarded as a very ancient evolutionary process that dates back to deep-branching phyla. MTB belonging to one of such phyla, Nitrospirota, contain the classical genes for the magnetosome synthesis (e.g., mam, mms) and man genes, which were considered to be specific for this group. However, the recent discovery of man genes in MTB from the Thermodesulfobacteriota phylum has raised several questions about the inheritance of these genes in MTB. In this work, three new man genes containing MTB genomes affiliated with Nitrospirota and Thermodesulfobacteriota, were obtained. By applying reconciliation with these and the previously published MTB genomes, we demonstrate that the last common ancestor of all Nitrospirota was most likely not magnetotactic as assumed previously. Instead, our findings suggest that the genes for magnetosome synthesis were transmitted to the phylum Nitrospirota by horizontal gene transfer (HGT), which is the first case of the interphylum transfer of magnetosome genes detected to date. Furthermore, we provide evidence for the HGT of magnetosome genes from the Magnetobacteriaceae to the Dissulfurispiraceae family within Nitrospirota. Thus, our results imply a more significant role of HGT in the MTB evolution than deemed before and challenge the hypothesis of the ancient origin of magnetosome synthesis.

category: microbiology


title: Hyperbolic Geometry-Based Deep Learning Methods to Produce Population Trees from Genotype Data

abstract:
The production of population-level trees using the genomic data of individuals is a fundamental task in the field of population genetics. Typically, these trees are produced using methods like hierarchical clustering, neighbor joining, or maximum likelihood. However, such methods are non-parametric: they require all data to be present at the time of tree formation, and the addition of new data points necessitates the regeneration of the entire tree, a potentially expensive process. They also do not easily integrate with larger workflows. In this study, we aim to address these problems by introducing parametric deep learning methods for tree formation from genotype data. Our models specifically create continuous representations of population trees in hyperbolic space, which has previously proven highly effective in embedding hierarchically structured data. We present two different architectures - a multi-layer perceptron (MLP) and a variational autoencoder (VAE) - and we analyze their performance using a variety of metrics along with comparisons to established tree-building methods. Both models tested produce embedding spaces that reflect human evolutionary history. In addition, we demonstrate the generalizability of these models by verifying that addition of new samples to an existing tree occurs in a semantically meaningful manner. Finally, we use Dasguptas Cost to compare the quality of trees generated by our models to those produced by established methods. Despite the fact that the benchmark methods are directly fit on the evaluation data, our models are able to outperform some of these and achieve highly comparable performance overall.

Author summaryTree production is a vital task in population genetics, but current approaches fall prey to several common shortfalls. Most notably, they lack the ability to add new data points after tree generation, and they are often difficult to use in larger pipelines. By leveraging cutting-edge advances pairing deep learning with hyperbolic geometry, we develop multiple models designed to rectify these issues. Through experiments on a dataset of humans from globally widespread ancestries, we demonstrate the generalizability of our models to new data, and we also show strong empirical performance with respect to currently used methods. In addition, we show that the data representations produced by our models are semantically meaningful and reflect known facts about human evolutionary history. Finally, we discuss the additional benefits our models could provide, including improved visualization, greater privacy preservation, and improved integration with downstream machine learning tasks. In conclusion, we present models that are accurate, flexible, and generalizable, with the potential to facilitate a variety of further applications.


title: Model-free Prediction Test with Application to Genomics Data

abstract: Testing the significance of prediction in a regression model is one of the most important topics in statistics. This problem is especially difficult without any parametric assumptions on the data. This paper aims to test the null hypothesis that, given confounding variables Z, X does not significantly contribute to the prediction of Y under the model-free setting, where X and Z are possibly high dimensional. We propose a general framework that first fits nonparametric regression models on the Y|X and Y|(X, Z), then compares the prediction power of the two models. The proposed method allows us to leverage the strength of the most powerful regression algorithms developed from the modern machine learning community. The p-value for the test can be easily obtained by permutation. In simulations, we find that the proposed method is more powerful compared to existing methods. The proposed method allows us to draw biologically meaningful conclusions from two gene expression data analyses without strong distributional assumptions: (a) testing prediction power of sequencing RNA for the proteins in CITE-seq data, and (b) identification of spatially variable genes in spatially resolved transcriptomics data.


title: CoCoA: Conditional Correlation Models with Association Size

abstract: SO_SCPLOWUMMARYC_SCPLOWMany scientific questions can be formulated as hypotheses about conditional correlations. For instance, in tests of cognitive and physical performance, the trade-off between speed and accuracy motivates study of the two variables together. A natural question is whether speed-accuracy coupling depends on other variables, such as sustained attention. Classical regression techniques, which posit models in terms of covariates and outcomes, are insufficient to investigate the effect of a third variable on the symmetric relationship between speed and accuracy. In response, we propose CoCoA (Conditional Correlation Model with Association Size), a likelihood-based statistical framework to estimate the conditional correlation between speed and accuracy as a function of additional variables. We propose novel measures of the association size, which are analogous to effect sizes on the correlation scale, while adjusting for confound variables. In simulation studies, we compare likelihood-based estimators of conditional correlation to semi-parametric estimators adapted from genome association studies, and find that the former achieves lower bias and variance under both ideal settings and model assumption misspecification. Using neurocognitive data from the Philadelphia Neurodevelopmental Cohort, we demonstrate that greater sustained attention is associated with stronger speed-accuracy coupling in a complex reasoning task while controlling for age. By highlighting conditional correlations as the outcome of interest, our model provides complementary insights to traditional regression modelling and partitioned correlation analyses.


title: Multimodal microscale mechanical mapping of cancer cells in complex microenvironments

abstract: The mechanical phenotype of the cell is critical for survival following deformations due to confinement and fluid flow. One idea is that cancer cells are plastic and adopt different mechanical phenotypes under different geometries that aid in their survival. Thus, an attractive goal, is to disrupt the cancer cells ability to adopt multiple mechanical states. To begin to address this question, we aimed to quantify the diversity of these mechanical states using in vitro biomimetics to mimic in vivo 2D and 3D extracellular matrix environments. Here, we used two modalities Brillouin microscopy ([~]GHz) and broadband frequency (3-15kHz) optical tweezer microrheology to measure microscale cell mechanics. We measured the response of intracellular mechanics of cancer cells cultured in 2D and 3D environments where we modified substrate stiffness, dimensionality (2D versus 3D), and presence of fibrillar topography. We determined that there was good agreement between two modalities despite the difference in timescale of the two measurements. These findings on cell mechanical phenotype in different environments confirm a correlation between modalities that employ different mechanisms at different temporal scales (Hz-kHz vs. GHz). We also determined that observed heterogeneity in cell shape that is more closely linked to the cells mechanical state. We also determined that individual cells in multicellular spheroids exhibit a lower degree of mechanical heterogeneity when compared to single cells cultured in monodisperse 3D cultures. Moreover, the observed decreased heterogeneity among cells in spheroids suggested that there is mechanical cooperativity between cells that make up a single spheroid.


title: Deciphering TP53 mutant Cancer Evolution with Single-Cell Multi-Omics

abstract: TP53 is the most commonly mutated gene in human cancer, typically occurring in association with complex cytogenetics and dismal outcomes. Understanding the genetic and non-genetic determinants of TP53-mutation driven clonal evolution and subsequent transformation is a crucial step towards the design of rational therapeutic strategies. Here, we carry out allelic resolution single-cell multi-omic analysis of haematopoietic stem/progenitor cells (HSPC) from patients with a myeloproliferative neoplasm who transform to TP53-mutant secondary acute myeloid leukaemia (AML), a tractable model of TP53-mutant cancer evolution. All patients showed dominant TP53  multi-hit HSPC clones at transformation, with a leukaemia stem cell transcriptional signature strongly predictive of adverse outcome in independent cohorts, across both TP53-mutant and wild-type AML. Through analysis of serial samples and antecedent TP53-heterozygous clones, we demonstrate a hitherto unrecognised effect of chronic inflammation, which supressed TP53 wild-type HSPC whilst enhancing the fitness advantage of TP53 mutant cells. Our findings will facilitate the development of risk-stratification, early detection and treatment strategies for TP53-mutant leukaemia, and are of broader relevance to other cancer types.

category: cancer biology


title: Natural variation identifies new effectors of water use efficiency in Arabidopsis.

abstract: Water use efficiency (WUE) is the ratio of biomass gained per unit of water consumed; thus, it can be altered by genetic factors that affect either side of the ratio. In the present study, we exploited natural variation for WUE as an unbiased approach to discover loci affecting either biomass accumulation or water use as factors affecting WUE. Genome-wide association (GWAS) analysis using integrated WUE measured through carbon isotope discrimination ({delta}13C) of Arabidopsis thaliana accessions identified genomic regions associated with WUE. Reverse genetic analysis of 70 candidate genes selected based on the GWAS results and transcriptome data identified 25 genes affecting WUE as measured by gravimetric and {delta}13C analyses. Mutants of four genes had higher WUE than wild type, while mutants of the other 21 genes had lower WUE. The differences in WUE were caused by either altered biomass or water consumption (or both). Stomatal density was not a primary cause of altered WUE in these mutants. Leaf surface temperatures indicated that transpiration differed for mutants of 16 genes, but generally biomass accumulation had greater effect on WUE. The genes we identified are involved in diverse cellular processes including hormone and calcium signaling, meristematic activity, photosynthesis, flowering time, leaf/vasculature development, and cell wall composition; however, none of them had been previously linked to WUE or traits related to plant water relations. Thus, our study successfully identified new effectors of WUE that can be used to understand the genetic basis of WUE and improve crop productivity.


title: Profiling the diversity of agonist-selective effects on the proximal proteome environment of G protein-coupled receptors

abstract: G protein-coupled receptors (GPCRs) regulate many aspects of physiology and represent actionable targets for drug discovery. These receptors translate ligand-dependent input into a cellular response by remodeling protein interaction networks that are exquisitely organized both spatially and temporally. APEX-based proximity biotin labeling combined with quantitative mass spectrometry has emerged as a powerful approach for capturing all aspects of this dynamic ligand-dependent cellular re-organization. However, a major challenge in this approach is the extraction of salient information from these highly complex datasets. Here, we describe a computational framework for analyzing proximity labeling datasets that reliably predicts the subcellular location of GPCRs and deconvolutes spatial and temporal components of protein interaction network organization. Focusing on the mu-opioid receptor and its activation with distinct agonist drugs, we demonstrate the applicability of this framework to resolve agonist-specific differences in receptor localization and trafficking as well as the protein interaction networks it engages. Using this approach, we discover two novel protein network components which produce widespread, yet distinct, effects on G protein-dependent signaling. While the framework is broadly applicable to proximity biotin labeling datasets, it holds specific promise for further rationalizing GPCR drug discovery efforts by providing an unbiased assessment of ligand-dependent effects, and by enabling the discovery of additional network components for consideration as novel therapeutic targets.


title: The pre-Bötzinger complex is necessary for the expression of post-inspiration

abstract: The mammalian three-phase respiratory motor pattern of inspiration, post-inspiration and expiration is expressed in spinal and cranial motor nerve activities. This pattern is generated by a hierarchical brainstem-wide pre-motor network. However, the local rhythmogenic circuit of the pre-Botzinger complex (pre-BotC) was established as the  noeud vitale necessary and sufficient to initiate inspiration. In present study, we tested the effect of unilateral and bilateral inactivation of the pre-BotC (microinjection of the GABAA receptor agonist isoguvacine 10 mM, 50 nl) on respiratory motor activities in an in situ perfused brainstem preparation of rat. As expected, bilateral inactivation of the pre-BotC triggered cessation of phrenic (PNA), hypoglossal (HNA) and vagal (VNA) nerve activities for 15-20 min. Partial recovery from bilateral isoguvacine injection was characterized by erratic activity in all recorded motor nerves reminiscent to patterns observed after disturbed excitatory-inhibitory balance within the local pre-BotC circuit. Surprisingly, ipsilateral isoguvacine injections into the pre-BotC triggered transient (6-8 min) cessation of inspiratory and post-inspiratory VNA (p<0.001) and suppressed inspiratory HNA by -70 {+/-} 15% (p<0.01), while inspiratory PNA burst frequency increased by 46 {+/-} 30% (p<0.01). Taken together, these observations confirm the role of the pre-BotC as the  noeud vitale of the mammalian respiratory network in situ and highlight a significant role for the pre-BotC in the expression of vagal post-inspiratory and inspiratory activity.


title: Post-activation depression produces extensor H-reflex suppression following flexor afferent conditioning

abstract: Suppression of the extensor H-reflex by flexor afferent conditioning is thought to be produced by a long-lasting inhibition of extensor Ia-afferent terminals via primary afferent depolarization (PAD) activated by GABAA receptors. Considering the recent finding that PAD does not produce presynaptic inhibition of Ia-afferent terminals, we examined if H-reflex suppression is instead mediated by post-activation depression of the test extensor Ia-afferents triggered by PAD-evoked spikes and/or by a long-lasting inhibition of the extensor motoneurons. A brief conditioning vibration of the flexor tendon suppressed both the extensor soleus H-reflex and the tonic discharge of soleus motor units for 300 ms, indicating that part of the H-reflex suppression was mediated by a long-lasting inhibition of the extensor motoneurons. When activating the flexor afferents electrically to produce conditioning, the soleus H-reflex was also suppressed for 300 ms, but only when a short-latency reflex was evoked in the soleus muscle by the conditioning input itself. In mice, a similar short-latency reflex was evoked when optogenetic or afferent activation of GABAergic (GAD2+) neurons produced PAD large enough to evoke orthodromic spikes in the test Ia-afferents, causing post-activation depression of subsequent monosynaptic excitatory-post-synaptic potentials. The time course of this post-activation depression and related H-reflex suppression (lasting 2 s) was like rate-dependent depression that is also due to post-activation depression. We conclude that extensor H-reflex inhibition by brief flexor afferent conditioning is produced by both post-activation depression of extensor Ia-afferents and long-lasting inhibition of extensor motoneurons, rather than from PAD directly inhibiting Ia afferent terminals.


title: PAF1 modulates innate immunity by both activation and repression of gene expression.

abstract: Sitting at the interface of gene expression and host-pathogen interaction, polymerase associated factor 1 complex (PAF1C) is a rising player in the innate immune response. The complex localizes to the nucleus and associates with chromatin to modulate RNA polymerase II (RNAPII) elongation of gene transcripts. Performing this function at both proximal and distal regulatory elements, PAF1C interacts with many host factors across such sites, along with several viral proteins during infection. Therefore, translating the ubiquity of PAF1C into specific impacts on immune gene expression remains especially relevant. Advancing this, we treat PAF1 knockout cells with a slate of immune stimuli to identify key trends in PAF1-dependent gene expression. From our transcriptomic data, we confirm PAF1 is an activator of traditional immune response pathways as well as other cellular pathways correlated with pathogen defense. We also highlight key aspects of variability in our data and refine how PAF1 contributes to both gene activation and suppression. Finally, employing motif analysis, we predict gene regulatory elements strongly associated with PAF1, including those implicated in an immune response. Combining these elements corroborates the previously identified functions of PAF1C while fostering new avenues for its study as a regulator of innate immunity.

category: molecular biology


title: Digitizing the coral reef: machine learning of underwater spectral images enables dense taxonomic mapping of benthic habitats

abstract: Existing coral reef survey methods struggle to accurately capture the taxonomic detail within the complex spatial structure of benthic communities. We propose a workflow to leverage underwater hyperspectral transects and two machine learning algorithms to produce dense habitat maps of 1150 m2 of reefs across the Curacao coastline. All 500+ million pixels were assigned to 43 labels at taxonomic family, genus or species level for corals, algae, sponges, or to substrate labels such as sediment, turf algae and cyanobacterial mats. With low annotation effort (2% pixels) and no external data, this workflow enables accurate (Fbeta 87%) survey-scale mapping, with unprecedented thematic and spatial detail. Our assessments of the composition and configuration of 23 transect communities showed high consistency. The dense habitat maps reveal the inadequacies of point sampling methods to accurately describe reef benthic communities. Digitizing the reef habitat structure enables validation and novel analysis of pattern and scale in coral reef ecology.


title: Molecular basis of DNA recognition by the HMG-box-C1 module of Capicua

abstract: The HMG-box protein Capicua (CIC) is an evolutionarily conserved transcriptional repressor with key functions in development and disease-associated processes. CIC binds DNA using an exclusive mechanism that requires both its HMG-box and a separate domain called C1, but how these domains cooperate to recognize specific DNA sequences is not known. Here we report the crystal structure of the human CIC HMG-box and C1 domains in complex with an 18-base-pair DNA oligomer containing a consensus octameric CIC binding site. We find that both protein domains adopt independent tri-helical structures that pack against opposite sides of the DNA helix. The C1 domain in particular folds into a helix-turn-helix (HTH) structure that resembles the FF phosphoprotein binding domain. It inserts into the major groove of the DNA and plays a direct role in enhancing both the affinity and sequence specificity of CIC DNA binding. Our results reveal a unique bipartite protein module, ensuring highly specific DNA recognition by CIC, and show how this mechanism is disrupted by cancer mutations affecting either the HMG-box or C1 domains.

category: biochemistry


title: The Modular μSiM Reconfigured: Integration of Microfluidic Capabilities to Study in vitro Barrier Tissue Models under Flow

abstract: Microfluidic approaches to study tissue barriers have emerged to address the lack of fluid flow in conventional "open-well" Transwell-like devices. However, microfluidic techniques have not achieved widespread usage in bioscience laboratories because they are not fully compatible with traditional, tried-and-true experimental protocols. To advance barrier tissue research, there is a need for a platform that combines the advantages of both conventional open-well and microfluidic systems. Here, we develop a plug-and-play flow module to add on-demand microfluidic capabilities to a modular microfluidic system featuring a silicon membrane "m-SiM" as an open-well device with live-cell imaging capabilities. The magnetic latching assembly of our design enables bi-directional reconfiguration between open-well and fluidic modes. This design feature allows users to conduct an experiment in an open-well format with established protocols and then add or remove microfluidic capabilities as desired. Our work also provides an experimentally-validated flow model to help select desired flow conditions based on the experimental needs. As a proof-of-concept, we demonstrate flow-induced alignment of endothelial cells and visualize different phases of neutrophil transmigration across an endothelial monolayer under flow. We anticipate that our reconfigurable design will be adopted by both engineering and bioscience laboratories due to the compatibility with standard open-well protocols and the simple flow addition capabilities.

category: bioengineering


title: An environmentally ultrasensitive fluorine-19 NMR probe for monitoring protein conformational equilibria

abstract: Limited chemical shift dispersion represents a major barrier to studying multi-state equilibria of large membrane proteins by 19F NMR. We describe a novel monofluoroethyl 19F probe with a dramatically larger chemical shift dispersion than existing probes. The improved conformational sensitivity and line shape enabled the detection of hidden states of a critical membrane transporter, guiding subsequent structural elucidation by single-particle cryo-electron microscopy.


title: Containing Cancer with Personalized Minimum Effective Dose

abstract: Resistance to treatment is a challenge in many cancer therapies. This is partly due to the heterogeneous nature of tumors, where drug-sensitive and drug-resistant cells compete for the same resources. This competition is largely shaped by cancer treatment. The rapid reduction of drug-sensitive cell population during therapy with a maximum-tolerated dose relaxes competitive stress on the drug-resistant cell population, promoting relapse. Therefore, maintaining a high level of drug-sensitive cell population with a treatment break or lower dose can impose effective competitive stress on drug-resistant cell populations. Adaptive therapy (AT) exploits the competition between cancer cells. However, given the heterogeneous treatment response of individual patients, determining a personalized optimal treatment that can fine-tune competitive stress remains challenging. Using a deterministic model of cancer cell population competition, this study defines an effective dose window (EDW) as a range of doses that conserve sufficient sensitive cells, while maintaining the tumor volume below a threshold (e.g., initial tumor volume), to maintain a sustained competition against resistant cells. As a proof of concept, we sought to determine the EDW for a small cohort of patients with melanoma (n=8). We first fitted the model to longitudinal tumor response data from each patient. We performed structural and practical identifiability analyses to confirm the reproducibility and uniqueness of the estimated parameters. Then, we considered a subset of the cohort with uniquely identifiable parameters and estimated patient-specific EDW. We demonstrated that if the dose belongs to the EDW, the tumor volume for each patient could be indefinitely contained either using continuous or AT strategy. Using the optimal control theory, we concluded that the lower bound of the EDW approximates the minimum effective dose (MED) for containing cancer. Taken together, using tumor biomarker data, this study provides a proof of concept that there may exist a patient-specific EDW that keeps the tumor below a threshold (e.g., initial volume) by maintaining sustained competition on resistant cells.


title: Effect of TSS on anti-CVB3 through TLR3 pathway

abstract:
Toll-like receptors (TLRs) can recognize molecular patterns associated with microorganisms and induce immune responses. TLR3 is responsible for recognizing viruses and making hosts resistant to Coxsackie B3 (CVB3) infection. In this study, we found that Tectorigenin Sodium Sulfonate (TSS) has a TLR3 inhibitory effect and exerts strong anti-CVB3 activity through the TLR3 pathway both in vivo and in vitro. Balb/c mice were infected by ip injection of CVB3 virus, and subcutaneously injected with TSS at 264mg{middle dot}Kg-1{middle dot}d-1 for 7 d. The life extension rate of CVB3-infected mice was up to 46.67%, and the mean time to death was prolonged from 6.00 {+/-} 0.47 d to 8.80 {+/-} 2.78 d (P < 0.01). TSS was also able to reduce the level of weight loss in mice, significantly reduce the symptoms of myocarditis caused by CVB3, reduce the virus titer in the heart, improve the spleen and thymus index, and enhance immune function. We further explored the underlying mechanism of TSS in CVB3-infected HT-29 cells and mice: TSS reduced TLR3 expression and downregulated its downstream TRIF, TRAF6, IRF3, NF-{kappa} B. MAPK, AP1 expression, reduced expression of IFN-{beta}IL-6TNF-. TSS has strong anti-CVB3 activity in vitro and in vivo and has the effect of inhibiting the activation of TLR3 pathway.

IMPORTANCETSS is expected to be an antiviral drug for the treatment of CVB3 infection. Its regulatory effect on the immune system provides a new approach for antiviral research.

category: pharmacology and toxicology


title: Mutated Tumor Suppressors Follow Oncogenes Profile by the Gene Hypermethylation of Partners in the Protein Interaction Networks

abstract:
As a result of current advances in the analysis of patient sequencing data, many tumors have been characterized in a personalized manner. Such data can also be used to characterize genes that act as either oncogenes or tumor suppressors. These include "defective" tumor suppressor genes which may function as driver oncogenes that play a key role in cancer proliferation due to various genetic alterations, specifically, chromosomal translocations. In this study, we considered protein networks, mutations, methylation data and cancer fusions to classify tumor suppressors that may convert into oncogenes. Moreover, we developed a novel network-based parameter called the  preferential attachment score to categorize genes as oncogenes and/or tumor suppressors. Such classification was achieved using a naive Bayes computation approach. We used an ABC-MCMC method for selecting features for training our classification algorithm. We then performed a survey of tumor suppressors and oncogenes from the perspective of somatic mutations and network properties for 691 TCGA cases. For comparative purposes, we chose currently well-established methods, such as MutSigCV, OncodriveCLUST, Oncodrive-FM, 20/20+, ActiveDriver, MuSiC, TUSON, OncodriveFML, and found that our algorithm outperformed these other tolls, with 93.3% efficiency. Based on 691 TCGA cohorts, we found that tumor suppressors presented the highest mutation frequency in most tumor types, relative to oncogenes. Using protein-protein interaction data, we found that essential proteins, tumor suppressors and oncogenes had higher degrees of connectivity and betweenness centrality, relative to normal proteins. Similarly, tumor suppressors and oncogenes had lower clustering coefficients, as well as shortest path distances (FDR < 0.05). Finally, most mutated tumor suppressors integrate hyper-methylated partners in the protein interaction networks of 3091 fusions, following the patterns of oncogenes (43%). Thus, these results further characterize cancer oncogenes and tumor suppressors in the context of deep analysis of cancer network alterations.

AvailabilitySource scripts are available at https://github.com/somnathtagore/NBC and the resource is available at http://ontum.md.biu.ac.il/index.html


title: Single Cell Profiling of CD45+ Spinal Cord Cells Reveals Microglial and B Cell Heterogeneity and Crosstalk Following Spinal Cord Injury

abstract: It is well established that immune cells play crucial roles after spinal cord injury (SCI). However, our knowledge of the contributions of various immune cells to injury progression and repair is incomplete. These gaps in understanding hamper development of SCI therapeutics. In the current study, using single-cell RNA sequencing, and transcriptomic analysis, the populations of resident and circulating CD45+ immune cells present within the uninjured and injured mouse spinal cord were identified. In the uninjured and subacutely-injured (7 day) spinal cord, most CD45+ cells were microglia while in chronic SCI (60 day) B cells predominated. Examination of microglia and B cell clusters showed subtype-specific alterations after SCI, including the presence of both immature and mature B cells chronically. Analysis of the expression of signaling partners in B cells and microglia identified injury-related microglia-B-cell interactions. This sequencing resource establishes unidentified interactions revealing new mechanisms to target inflammatory responses for SCI repair.


title: Cell type profiling in salamanders identifies innovations in vertebrate forebrain evolution

abstract: The evolution of advanced cognition in vertebrates is associated with two independent innovations in the forebrain: the six-layered neocortex in mammals and the dorsal ventricular ridge (DVR) in sauropsids (reptiles and birds). How these novelties arose in vertebrate ancestors remains unclear. To reconstruct forebrain evolution in tetrapods, we built a cell type atlas of the telencephalon of the salamander Pleurodeles waltl. Our molecular, developmental, and connectivity data indicate that parts of the sauropsid DVR trace back to tetrapod ancestors. In contrast, the salamander dorsal pallium is devoid of cellular and molecular characteristics of the mammalian neocortex, yet shares similarities with entorhinal cortex and subiculum. Our findings chart the series of innovations that resulted in the emergence of the sauropsid DVR, and the mammalian six-layered neocortex.