title: Combinatorial interactions of Hox genes establish appendage diversity of the amphipod crustacean Parhyale hawaiensis

abstract:
Hox genes establish regional identity along the anterior-posterior axis in diverse animals. Changes in Hox expression can induce striking homeotic transformations, where one region of the body is transformed into another. Previous work in Drosophila has demonstrated that Hox cross-regulatory interactions are crucial for maintaining proper Hox expression. One major mechanism is the phenomenon of "posterior prevalence", wherein anterior Hox genes are repressed by more posterior Hox genes. Loss of posterior Hox expression under this model would predict posterior-to-anterior transformations, as is frequently observed in Drosophila. While posterior prevalence is thought to occur in many animals, studies of such Hox cross-regulation have focused on a limited number of organisms. In this paper, we examine the cross-regulatory interactions of three Hox genes, Ultrabithorax (Ubx), abdominal-A (abd-A), and Abdominal-B (Abd-B) in patterning thoracic and abdominal appendages in the amphipod crustacean Parhyale hawaiensis. Studies of Hox function in Parhyale have previously revealed two striking phenotypes which differed markedly from what a "posterior prevalence" model would predict, including non-contiguous and anterior-to-posterior transformations. We probe the logic of Parhyale Hox cross-regulation by using CRISPR/Cas9 to systematically examine all combinations of Ubx, abd-A, and Abd-B loss of function in Parhyale. By analyzing homeotic phenotypes and examining the expression of additional Hox genes, we reveal Hox cross-regulatory interactions in Parhyale. From these data, we also demonstrate that some Parhyale Hox genes function combinatorially to specify posterior limb identity, rather than abiding by a posterior prevalence mechanism. These results provide evidence that combinatorial Hox interactions may be responsible for the tremendous body plan diversity of crustaceans.

Graphical Abstract

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title: Zinc as a non-hormonal contraceptive: a better alternative to the copper intrauterine device (IUD)

abstract:
Long-acting and reversible contraceptives (LARC) are the most widely used form of female contraception worldwide, however they have significant side-effects that often result in early removal. Most LARCs are hormonal, but the use of exogenous hormones is not suitable for all women and causes side-effects in many others. The copper IUD (CuIUD) is the only non-hormonal LARC, but a large proportion of users suffer severe side effects. This study proposes the use of zinc as a suitable alternative to the CuIUD.

A rat intrauterine device (IUD) model was established to test the efficacy of a zinc IUD (ZnIUD) against a CuIUD, and a control nylon IUD. The IUD was surgically implanted into one uterine horn while the other remained untreated. Both the ZnIUD and CuIUD resulted in significantly fewer implantation sites compared to untreated horns. There was no significant difference between treated and untreated horns in the control nylon IUD group. Histological assessment revealed damage and inflammation in the endometrium of CuIUD treated horns, but only minor epithelial damage in ZnIUD treated horns, closely resembling the normal appearance of the control horns. This suggests ZnIUDs may not share the side-effect profile of the CuIUD. To test the long-term efficacy of the ZnIUD, rats had a ZnIUD surgically implanted into both horns and cohoused with males for 3 months. These rats mated regularly but did not get pregnant, confirming the long-term effectiveness of the ZnIUD. Reversibility of the ZnIUD was also established, as removal of the ZnIUD after 3 months resulted in no significant difference in the number of implantation sites between treated and untreated horns.

This study demonstrated the contraceptive efficacy of zinc and its potential as a LARC. The ZnIUD had minimal histological impact on the endometrium compared to the current copper standard, indicating that IUDs containing zinc may offer highly effective contraception while causing fewer side effects.

category: developmental biology


title: Ecological diversity exceeds evolutionary diversity in model ecosystems

abstract: Understanding community saturation is fundamental to ecological theory. While investigations of the diversity of evolutionary stable states (ESSs) are widespread, the diversity of communities that have yet to reach an evolutionary endpoint is poorly understood. We use Lotka-Volterra dynamics and trait-based competition to compare the diversity of randomly assembled communities to the diversity of the ESS. We show that, with a large enough founding diversity (whether assembled at once or through sequential invasions), the number of long-time surviving species exceeds that of the ESS. However, the excessive founding diversity required to assemble a saturated community increases rapidly with the dimension of phenotype space. Additionally, traits present in communities resulting from random assembly are more clustered in phenotype space compared to random, though still markedly less ordered than the ESS. By combining theories of random assembly and ESSs we bring a new viewpoint to both the saturation and random assembly literature.

category: ecology


title: Long-term temperature trend in Kamchatka supports expansion of harmful algae

abstract: Ocean coastal ecosystems are changing, and global shifts in temperature lead to the expansion and intensification of harmful algae. In conjunction with anthropogenic effects it may result in future exacerbation of harmful algal blooms. Here we use the 2002-2020 years record of surface ocean temperature data retrieved from Sentinel-2 satellite to examine the recent temperature trend in Avacha Bay, Kamchatka Peninsula. Satellite analysis demonstrated a temperature increase trend in ocean surface water during spring and summer months and detected algal bloom in July 2020 preceding a mass death of marine benthic life in September-October 2020. Using 16S rRNA and 18S rRNA gene amplicon nanopore-based sequencing, we analyzed microbial and microalgal communities in the water samples from area of 2020 algal blooms. Our results suggest the presence of potentially toxic and bloom-forming algae from genera related to former HABs (harmful algal blooms) in the Avacha Bay region. A better understanding of the potentially toxic algae phytoplankton composition in the shifting temperature environment and time-series monitoring of HABs is of utmost importance for scientific community. We suggest that satellite analysis in combination with eDNA monitoring by nanopore-based sequencing represents promising option to detect potentially toxic algae and follow bloom development.


title: Mark loss can strongly bias demographic rates in multi-state models: a case study with simulated and empirical datasets

abstract:
O_LIThe development of methods for individual identification in wild species and the refinement of Capture-Mark-Recapture (CMR) models during the past decades has greatly improved the assessment of population demographic rates to answer ecological and conservation questions. In particular, multistate models, with their flexibility for the analysis of complex study systems, have become popular in the ecological community. However, despite the extensive use of these models, little attention has been paid to the effect of common violations of the CMR model assumptions, such as mark loss and the often-associated recycling of remarked individuals.
C_LIO_LITo explore this knowledge gap we used a wide range of simulation scenarios reflecting frequently encountered real case studies inspired from the survival rates of 700 vertebrates species. We estimated the effects of mark loss and recycled individuals on parameter estimates using a multi-state Cormack-Jolly-Seber (MSCJS) framework. We explored parameter bias through simulations of a metapopulation system with different capture and survival rates. We also illustrated how mark loss can be easily estimated and accounted for using an empirical long-term (10 years) CMR dataset of bats, individually identified using both PIT tag technology as marks that can be lost, and multi-locus genotypes as  permanent marks.
C_LIO_LIThe results from our simulated scenarios demonstrated that the occurrence of bias and the parameters concerned were highly dependent on the study system, and no general rules on parameter behaviour can be established a priori. The model structure and the interdependency among parameters make it challenging to predict how bias could affect estimates.
C_LIO_LIOur results highlight the need to assess the effect of mark loss when using MSCJS models. Ignoring such violations of model assumptions can have important implications for ecological inferences and conservation policies. In general, the use of permanent marks (e.g. genotype), should always be preferred when modelling of population dynamics and if not possible, combining two types of temporary marks (e.g. PIT tags, bands) should be considered.
C_LI


title: Habitat resource overlap in two broad-ranged sympatric Neotropical forest eagles

abstract: Quantifying resource partitioning between co-occurring species has important ecological and evolutionary implications. Yet, few studies compare resource overlap in both geographic and environmental space. We test whether the habitat requirements of two closely related Neotropical forest eagles, the crested eagle (Morphnus guianensis) and harpy eagle (Harpia harpyja), differ at fine and coarse resolutions across their shared geographic range. Using landcover and topographic covariates, we quantified resource overlap first using higher resolution (30 arc-sec data) generalized linear models (GLMs), and second using coarser-grain (2.5 arc-min data) environmental ordination. The distribution of both eagles was largely explained by canopy species richness and structural complexity with evergreen forest, but with differing responses to landcover and topography, particularly with the harpy eagle more likely in areas of dense evergreen forest. Both eagles were negatively associated with mosaic forest, with this relationship stronger for the crested eagle. Harpy eagle distribution was restricted by higher elevation and terrain roughness, compared to the crested eagle, whose distribution was more restricted by canopy species richness and structure. From the GLMs, resource overlap was > 92 % in geographical space but reduced to 64 % in environmental space. From ordination, resource overlap was 76 % in environmental space, with randomization tests supporting equivalent environmental space for both eagles. Our results suggest that at the biogeographical scale, crested and harpy eagles share environmental space, but there may be subtle differences in fine-scale habitat preference. We recommend habitat resource overlap be assessed in both geographical and environmental space at multiple resolutions to capture the inherent variability in environmental conditions available to co-occurring species.


title: sdmTMB: an R package for fast, flexible, and user-friendly generalized linear mixed effects models with spatial and spatiotemporal random fields

abstract:
O_LIGeostatistical data--spatially referenced observations related to some continuous spatial phenomenon-- are ubiquitous in ecology and can reveal ecological processes and inform management decisions. However, appropriate models to analyze these data, such as generalized linear mixed effects models (GLMMs) with Gaussian random fields, are often computationally intensive and challenging to implement, interpret, and evaluate.
C_LIO_LIHere, we introduce the R package sdmTMB, which implements predictive-process SPDE- (stochastic partial differential equation) based spatial and spatiotemporal models. Estimation is conducted via maximum marginal likelihood with Template Model Builder (TMB) but can be extended to penalized likelihood or Bayesian inference. We describe the statistical model, illustrate the packages use through two case studies, and compare the functionality, speed, and interface to related software.
C_LIO_LIWe highlight advantages of using sdmTMB for this class of models: (1) sdmTMB provides a flexible interface familiar to users of glm(), lme4, glmmTMB, or mgcv; (2) estimation is often faster than alternatives; (3) sdmTMB provides simple out-of-sample cross validation; (4) non-stationary processes (time-varying and spatially varying coefficients) are easily constructed with a formula interface; and (5) sdmTMB includes features not available as a combination in related packages (e.g., delta/hurdle models, penalized smoothers and break-point effects, anisotropy, abundance index standardization).
C_LIO_LIWe hope that sdmTMBs user-friendly interface will open this useful class of models to a wider audience within species distribution modelling and beyond.
C_LI


title: Sexual selection on female copulatory devices in an insect with nuptial gifts

abstract: Genitalia are rapidly evolving structures, often driven by sexual conflict and/or sexual selection (especially in males) for coercive, attractive, or stimulatory traits that increase fertilization success. In systems where males make large investments in offspring (i.e., paternal care or nuptial gifts) females may be subject to strong sexual selection, sometimes resulting in the evolution of female ornaments or genital adaptations that increase acquisition of mates and/or male goods and services. In Hemiandrus, short-tailed (reduced ovipositor) ground weta, where males feed their mates spermatophylax gifts, females possess a secondary genitalic device (the accessory organ) that is necessary for successful copulation. Females may compete for access to these gifts in order to avoid starvation because following the mating season, they enter a months-long maternal care period without eating. Thus, the accessory organ may be a sexually selected device involved in the acquisition of spermatophylax meals. Here, we test this hypothesis in female ground weta Hemiandrus pallitarsis by determining whether an increase in mating frequency (estimated from microsatellite analysis of stored sperm) increases lifetime reproductive success (the Bateman gradient). Additionally, we test if the accessory organ is under directional sexual selection by measuring its relationship with female mating success. As predicted, there was both positive Bateman gradients for females, suggestive of sexual selection, and evidence of directional sexual selection on accessory organ length. Although organ length did not correlate well with female fecundity (eggs in abdomen), it may increase mating success by indicating maternal condition and thus quality of her offspring care.

category: evolutionary biology


title: Facultative parthenogenesis in an asexual stick insect: re-evolution of sex or vestigial sexual capacity?

abstract: Transitions from obligate sex to obligate parthenogenesis have occurred repeatedly across the tree of life. Whether these transitions occur abruptly or via a transient phase of facultative parthenogenesis is rarely known. We discovered and characterised facultatively parthenogenetic populations of the North American stick insect Timema douglasi, a species in which only obligately parthenogenetic populations were known so far. These populations comprised three genetic lineages. Females from all lineages were capable of parthenogenesis (with variable efficiency) but their propensity to reproduce sexually after mating varied extensively. In all three lineages, parthenogenesis resulted in the complete loss of heterozygosity in a single generation. Obligately parthenogenetic Timema have also lost all heterozygosity, suggesting that parthenogenesis evolved via a gradual capacity increase while conserving the proximate mechanism. It is unclear whether the populations we discovered have re-evolved sex (via re-expression of existing pathways), or whether they are vestigial sexual populations in a species where all other lineages have evolved obligate parthenogenesis already. We speculate that facultative parthenogenesis may often be transient and be replaced by obligate strategies (either sex or parthenogenesis) because of a trade-off between the efficiency of the two reproductive modes.


title: Ecological and evolutionary consequences of selective interspecific information use

abstract: II.AbstactThe ecology of social information use has been studied in many intra- and interspecific contexts, while the evolutionary consequences of social information use remain less understood. Furthermore, selective social information use, where individuals are discriminative in their decision-making on how to use social information, has been overlooked in interspecific context. In particular, the intentional decision to reject a behavioural trait observed via social information, has gained less attention, although it has recently been shown to occur in various taxa. We develop an individual-based simulation model to explore in which circumstances social information use leads to different coevolutionary outcomes among populations of two species. The initial phenotypes and the balance between costs of competition and benefits of social information use determine whether selection leads to trait divergence, convergence or coevolutionary arms race between two species. Based on existing literature, we propose that selective decisions of individuals, including active rejection, may have far-reaching fitness consequences, potentially leading to similar evolutionary consequences among the populations of the information source and the user as predicted by our model. Overall, we argue that the eco-evolutionary consequences of selective interspecific social information use may be much more prevalent than thus far considered.


title: A spatial genome aligner for multiplexed DNA-FISH

abstract: Multiplexed fluorescence in situ hybridization (FISH) has emerged as a powerful approach for analyzing 3D genome organization, but it is eminently challenging to derive chromosomal conformations from noisy fluorescence signals. Tracing chromatin is not straightforward as chromosomes lack conserved shapes for reference checking whether an observed fluorescence signal belongs to a chromatin fiber or not. Here we report a spatial genome aligner that parses true chromatin signal from noise by aligning signals to a DNA polymer model. We demonstrate that this spatial genome aligner can efficiently reconstruct chromosome architectures from DNA-FISH data across multiple scales and determine chromosome ploidies de novo in interphase cells. Reprocessing of previous whole-genome chromosome tracing data with this method revealed the spatial aggregation of sister chromatids in S/G2 phase cells in asynchronous mouse embryonic stem cells, and uncovered extranumerary chromosomes that remain tightly paired in post-mitotic neurons of the adult mouse cortex. Our spatial genome aligner may facilitate the adaption of multiplexed DNA-FISH by the community.

category: genomics


title: circRAB3IP modulates cell proliferation by reorganizing gene expression and mRNA processing in a paracrine manner

abstract: Circular RNAs are endogenous long-lived and abundant non-coding species. Despite their prevalence, only few circRNAs have been dissected mechanistically to date. Here, we catalogued nascent RNA-enriched circRNAs from primary human cells and functionally assign a role to circRAB3IP in sustaining cellular homeostasis. We combined "omics" and functional experiments to show how circRAB3IP depletion deregulates hundreds of genes, suppresses cell cycle progression, and induces senescence-associated gene expression changes. Conversely, excess circRAB3IP delivered to endothelial cells via extracellular vesicles suffices for accelerating their division. We attribute these effects to the interplay between circRAB3IP and the general splicing factor SF3B1, which impacts transcript usage of cell cycle-related genes. Together, our findings link the maintenance of cell homeostasis to the tightly regulated titers of a single circRNA.


title: A chromosome-level assembly of the "Cascade" hop (Humulus lupulus) genome provides insights into Cannabaceae evolution

abstract:
O_LIWe present a chromosome-level assembly of the Cascade hop (Humulus lupulus L. var. lupulus) genome. The hop genome is large (2.8 Gb) and complex, and early attempts at assembly resulted in fragmented assemblies. Recent advances have made assembly of the hop genome more tractable, transforming the extent of investigation that can occur.
C_LIO_LIThe chromosome-level assembly of Cascade was developed by scaffolding the previously-reported Cascade assembly generated with PacBio long-read sequencing, and polishing with Illumina short-read DNA sequencing. We developed gene models and repeat annotations, and used a controlled bi-parental mapping population to identify significant sex-associated markers. We assess molecular evolution in gene sequences, gene family expansion and contraction, and time divergence using Bayesian inference.
C_LIO_LIWe identified the putative sex chromosome in the female genome based on significant sex-associated markers from the bi-parental mapping population. While the estimate of repeat content (~64%) is similar to the hemp genome, syntenic blocks in hop contain a greater percentage of LTRs. Hop is enriched for disease resistance-associated genes in syntenic gene blocks and expanded gene families.
C_LIO_LIThe Cascade chromosome-level assembly will inform cultivation strategies and serve to deepen our understanding of the hop genomic landscape, benefiting hop researchers and the Cannabaceae genomics community.
C_LI


title: A chromosome-level assembly of the "Cascade" hop (Humulus lupulus) genome uncovers signatures of molecular evolution and improves time of divergence estimates for the Cannabaceae family


title: A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships

abstract:
Chromatin contacts are essential for gene-expression regulation, however, obtaining a high-resolution genome-wide chromatin contact map is still prohibitively expensive owing to large genome sizes and the quadratic scale of pairwise data. Chromosome conformation capture (3C) based methods such as Hi-C have been extensively used to obtain chromatin contacts. However, since the sparsity of these maps increases with an increase in genomic distance between contacts, long-range or trans chromatin contacts are especially challenging to sample.

Here, we created a high density reference genome-wide chromatin contact map using a meta-analytic approach. We integrate 3600 Human, 6700 Mouse, and 500 Fly 3C experiments to create species-specific meta-3C contact maps with 304 billion, 193 billion, and 19 billion contacts in respective species. We validate that meta-3C are uniquely powered to capture functional chromatin contacts in both cis and trans. Unlike individual experiments, meta-3C gene contacts predict gene coexpression for long-range and trans chromatin contacts. Similarly, for long-range cis-regulatory interactions, meta-3C contacts outperform both all individual experiments, providing an improvement over the conventionally used linear genomic distance-based association. Assessing between species, we find patterns of chromatin contacts conservation in both cis and trans and strong associations with coexpression even in species for which 3C data is lacking.

We have generated an integrated chromatin interaction network which complements a large number of methodological and analytic approaches focused on improved specificity or interpretation. This high-depth "super-experiment" is surprisingly powerful in capturing long-range functional relationships of chromatin interactions, which are now able to predict coexpression, expression quantitative trait loci (eQTL), and cross-species relationships.


title: Discordant genotype calls across technology platforms elucidate variants with systematic errors in next-generation sequencing

abstract: Large-scale next-generation sequencing (NGS) datasets have been transformative for informing clinical variant interpretation and as reference panels for statistical and population genetic efforts. While such resources are often treated as ground truth, we find that in widely used reference datasets such as the Genome Aggregation Database (gnomAD), some variants pass gold standard filters yet are systematically different in their genotype calls across sequencing technologies. The inclusion of such discordant sites in study designs involving multiple sequencing platforms (e.g. whole genome and/or different whole-exome captures) could bias results and lead to false-positive hits in association studies due to technological artifacts rather than a true relationship to the phenotype. Here, we describe this phenomenon of discordant genotype calls across sequencing technologies, characterize the error mode of wrong calls, provide a blacklist of discordant sites identified in gnomAD that should be treated with caution in analyses, and present a metric and machine learning classifier trained on gnomAD data to identify likely discordant variants in other datasets. We find that different NGS technologies have different sets of variants at which this problem occurs but that there are characteristic variant features that can be used to predict discordant behavior. Discordant sites are largely shared across ancestry groups, though different populations are powered for discovery of different variants. We find that the most common error mode is that of a variant being heterozygous for one platform and homozygous for the other, with heterozygous in the genomes and homozygous reference in the exomes making up the majority of miscalls.


title: Bursts of genomic instability potentiate phenotypic and genomic diversification in Saccharomyces cerevisiae

abstract: How microbial cells leverage their phenotypic potential to survive in a changing environment is a complex biological problem, with important implications for pathogenesis and species evolution. Stochastic phenotype switching, a particularly fascinating adaptive approach observed in numerous species across the tree of life, introduces phenotypic diversity into a population through mechanisms which have remained difficult to define. Here we describe our investigations into the mechanistic basis of colony morphology phenotype switching which occurs in populations of a pathogenic isolate of Saccharomyces cerevisiae, YJM311. We observed that clonal populations of YJM311 cells produce variant colonies that display altered morphologies and, using whole genome sequence analysis, discovered that these variant clones harbored an exceptional collection of karyotypes newly altered by de novo structural genomic variations (SVs). Overall, our analyses indicate that copy number alterations, more often than changes in allelic identity, provide the causative basis of this phenotypic variation. Individual variants carried between 1 and 16 de novo copy number variations, most of which were whole chromosomal aneuploidies. Notably, the inherent stability of the diploid YJM311 genome is comparable to that of domesticated laboratory strains, indicating that the collections of SVs harbored by variant clones did not arise by a chronic chromosomal instability (CIN) mechanism. Rather, variant clones acquired these complex karyotypic configurations simultaneously, during stochastic and transient episodes of punctuated systemic genomic instability (PSGI). Surprisingly, we found that the majority of these highly altered variant karyotypes were propagated with perfect fidelity in long-term passaging experiments, demonstrating that high aneuploidy burdens can often be conducive with prolonged genomic instability. Together, our results demonstrate that colony morphology switching in YJM311 is driven by a stochastic process in which genome stability and plasticity are integrally coupled to phenotypic heterogeneity. Consequently, this system simultaneously introduces both phenotypic and genomic variation into a population of cells, which can, in turn perpetuate population diversity for many generations thereafter.


title: Stress-induced transcriptional readthrough into neighboring genes is linked to intron retention

abstract: Exposure to certain stresses leads to readthrough transcription. Here we found that readthrough transcription often proceeds into the proximal gene downstream, in a phenomenon termed "read-in". Using polyA-selected RNA-seq data from mouse fibroblasts, we identified widespread read-in in heat shock, oxidative and osmotic stress conditions. We found that read-in genes share distinctive genomic characteristics; they are extremely short, and highly GC rich. Furthermore, using ribosome footprint profiling we found that translation of read-in genes is significantly reduced. Strikingly, read-in genes show extremely high levels of intron retention during stress, mostly in their first intron, which is not explained by features usually associated with intron retention, such as short introns and high GC content. Finally, we found that first introns in read-in genes have weaker splice sites. Our data portray a relationship between read-in and intron retention, suggesting it may have co-evolved to facilitate reduced translation of read-in genes during stress.


title: Dynamic interaction of bacterial cellulose synthase subunit D (BcsD) in type I bacterial cellulose synthase

abstract: Cellulose is a promising biological material for supporting sustainable human life. This natural polymer is synthesized by cellulose synthase, a protein complex in the cell membrane. Cellulose synthase in bacteria is a hetero-subunit complex, and its subunit organization varies widely depending on the species. In the type I bacterial cellulose synthase complex, the BcsD (bacterial cellulose synthase D) protein is believed to play an important role in producing cellulose with long slender fiber morphology and high crystallinity, given the phenotype of the bcsD-deficient mutant and the specific existence of the type I operon in bacterial species synthesizing crystalline cellulose microfibrils such as Acetobacter. In this study, we successfully established a heterogeneously expressed Bcs protein in Escherichia coli as an experimental model and conducted biochemical studies for the BcsD protein and the other three major subunits of bacterial cellulose synthase, BcsA, BcsB, and BcsC. It has been shown that the BcsD protein interacts with the functionally required minimal subunits of the BcsAB complex, as well as the BcsC protein. Furthermore, it was shown that BcsD interacts with the BcsAB complex in two modes: direct protein-protein interactions and indirect interactions through the product cellulose. The former and latter modes represent the basal and active states of the type I bacterial cellulose synthase, respectively. This dynamic behavior of the BcsD protein is important for the type I bacterial cellulose synthase complex to regulate the crystallization process of cellulose.

category: biochemistry


title: Dynamic interaction of BcsD subunit in type I bacterial cellulose synthase


title: Modulation of RNA binding properties of the RNA helicase UPF1 by its activator UPF2

abstract: The NMD helicase UPF1 is a prototype of the superfamily 1 (SF1) of RNA helicases that bind RNA with high affinity and translocate on it in an ATP-dependent manner. Previous studies showed that UPF1 has a low basal catalytic activity that is greatly enhanced upon binding of its interaction partner, UPF2. Activation of UPF1 by UPF2 entails a large conformational change that switches the helicase from an RNA-clamping mode to an RNA-unwinding mode. The ability of UPF1 to bind RNA was expected to be unaffected by this activation mechanism. Here we show, using a combination of biochemical and biophysical methods, that binding of UPF2 to UPF1 drastically reduces the affinity of UPF1 for RNA, leading to a release of the bound RNA. Although UPF2 is capable of binding RNA in vitro, our results suggest that dissociation of the UPF1-RNA complex is not a consequence of direct competition in RNA binding but rather an allosteric effect that is likely mediated by the conformational change induced by binding of the helicase to its activator. We discuss these results in light of transient interactions forged during mRNP assembly, particularly in the UPF1-dependent mRNA decay pathways.


title: Treatment with an Antigen-Specific Dual Microparticle System Reverses Advanced Multiple Sclerosis in Mice

abstract:
Antigen-specific therapies hold promise for treating autoimmune diseases such as multiple sclerosis while avoiding the deleterious side effects of systemic immune suppression. In this study, an antigen-specific dual-sized microparticle (dMP) immunotherapy reversed hind limb paralysis when administered in mice with advanced experimental autoimmune encephalomyelitis (EAE). Treatment reduced central nervous system (CNS) immune cell infiltration, demyelination and inflammatory cytokine levels. Mechanistic insights using single-cell RNA sequencing showed that treatment impacted the MHC II antigen presentation pathway in dendritic cells, macrophages, B cells and microglia, not only in the draining lymph nodes, but strikingly also in the spinal cord. CD74 and cathepsin S were among the common genes downregulated in most antigen presenting cell (APC) clusters, with B cells also having numerous MHC II genes reduced. Efficacy of the treatment diminished when B cells were absent, suggesting their impact in this therapy, in concert with other immune populations. Activation and inflammation were reduced in both APCs and T cells. This promising antigen-specific therapeutic approach advantageously engaged essential components of both innate and adaptive autoimmune responses, and capably reversed paralysis in advanced EAE without the use of broad immunosuppressant.

Significance StatementMultiple sclerosis (MS) is a debilitating autoimmune disease that can lead to paralysis. We demonstrate an antigen-specific microparticle treatment can reverse hind limb paralysis when administered in advanced EAE. Single-cell RNA-sequencing and flow cytometry analysis provide evidence the treatment acts by diminishing Ag presentation in APCs, including B cells in the CNS and the draining lymph nodes. Thus, the antigen-specific dual-sized microparticle treatment is a promising therapy even in advanced EAE, and potentially MS.

category: bioengineering


title: Variants identify sarcomere inter-protein contacts distinguishing inheritable cardiac muscle diseases

abstract: Human ventriculum myosin ({beta}mys) powers contraction sometimes while complexed with myosin binding protein C (MYBPC3) on the myosin thick filament. The latter regulates {beta}mys activity through inter-protein contacts. Single nucleotide variants (SNVs) change protein sequence in {beta}mys or MYBPC3. They cause inheritable heart disease. When a SNV modified domain locates to an inter-protein contact it affects complex coordination. Domains involved, one in {beta}mys and the other in MYBPC3, form coordinated domains called co-domains. Co-domains are bilateral implying the potential for a shared impact from SNV modification in either domain suggesting their joint response to a common perturbation assigns location. Human population genetic divergence is the common systemic perturbation. A general contraction model with a neural/Bayes network design reveals SNV probabilities specifying correlations between domain members using 2D correlation genetics (2D-CG). It reveals co-domain locations in three common human heart diseases caused by SNVs, familial hypertrophic cardiomyopathy (FHC), dilated cardiomyopathy (DCM), and left ventricle non-compaction (LVN). Co-domain maps for DCM and LVN link MYBPC3 with two levels of myosin heads on the myosin thick filament surface implying these myosin dimers form the super-relaxed state (SRX). The FHC co-domain map involves just one myosin dimer implying the myosins do not form SRX. Comparing co-domain maps for FHC, DCM, and LVN phenotypes suggests SRX disruption involves a co-domain between MYBPC3 regulatory domain and the myosin regulatory light chain (RLC) N-terminus. The general contraction model scenarios, constructed from feed-forward neural networks, were explored with the purpose to understand how to interpret them mechanistically with basic natural language characteristics. These characteristics emerge from dependencies among inputs coded in hidden layer width and depth when they are deciphered using 2D-CG. In this application, the thick filament structural states emerge for FHC, DCM, and LVN phenotypes defining thick filament structural state joining the other standard characteristics of phenotype and pathogenicity. Emergent natural language interpretations for general network contraction models are on the horizon.

category: bioinformatics


title: Repositioning linifanib as a potent anti-necroptosis agent for sepsis

abstract:
BackgroundSepsis is a systemic inflammatory syndrome (SIRS) caused by acute microbial infection with high mortality rate. The role of tumour necrosis factor  (TNF-)-induced necroptosis in promoting the pathophysiology of sepsis has been identified. Effective prevention of necroptosis is expected to improve the prognosis of sepsis patients.

MethodsWe conducted bioinformatics prediction of candidate drugs by analyzing differentially expressed genes of sepsis patients extracted from GEO database, combining library of integrated network-based cellular signatures (LINCS) L1000 perturbation database. Biological experiments based on TNF--induced necroptosis in cellular and mouse model were performed to verify the protection of candidate drugs from SIRS. Cell viability was measured by CellTiter-Glo luminescent ATP assay. Effects of linifanib on necroptosis were investigated by western blotting, immunoprecipitation, and in vitro RIPK1 kinase assay. Survival curve analysis of SIRS mice treated by linifanib was performed.

ResultsA total of 16 candidate drugs was screened out through bioinformatics analysis. Our experiments demonstrated that linifanib effectively protected cells from necroptosis and rescued the death of SIRS mice from shock induced by TNF-. In vitro, linifanib directly suppressed RIPK1 kinase activity. In vivo, linifanib effectively reduced the overexpressed level of IL-6, a good marker of severity during severe sepsis, in the lung of SIRS mice.

ConclusionWe provide preclinical evidence for the potential clinical utility of linifanib in sepsis. Study of drug repositioning using bioinformatical predictions combined with experimental validations provides novel strategies for the development of sepsis drug.


title: PLO3S : Protein LOcal Surficial Similarity Screening

abstract: The study of protein molecular surfaces enable to better understand and predict protein interactions. Different methods have been developed in computer vision to compare surfaces that can be applied to protein molecular surfaces. The present work proposes a method using the the Wave Kernel Signature : Protein LOcal Surficial Similarity Screening (PLO3S). The descriptor of the PLO3S method is a local surface shape descriptor projected on a unit sphere mapped onto a 2D plane and called Surface Wave Interpolated Maps (SWIM). PLO3S allows to rapidly compare protein surface shapes through local comparisons to filter large protein surfaces datasets in protein structures virtual screening protocols.


title: Extraction and analysis of methylation features from Pacific Biosciences SMRT reads using MeStudio

abstract:
MotivationDNA methylation is the most relevant epigenetic information, present in eukaryotes and prokaryotes, and is related to several biological phenomena, from cellular differentiation to control of gene flow, pathogenesis and virulence. The widespread use of third-generation sequencing technologies allows direct and easy detection of genome-wide methylation profiles, offering increasing opportunities to understand and exploit the epigenomics landscape.

ResultsWe introduce MeStudio, a pipeline which allows to analyse and combine genome-wide methylation profiles with genomic features. Outputs report the presence of DNA methylation in coding sequences, noncoding sequences, intergenic sequences, and sequences upstream to CDS. We show the usage and performances of MeStudio on a set of single-molecule real time sequencing outputs from the bacterial species Sinorhizobium meliloti.

Availability and ImplementationMeStudio is written in Python, Bash and C and is freely available under an open source GPLv3 license at https://github.com/combogenomics/MeStudio

Supplementary informationSupplementary data are available at Bioinformatics online.

Contactcombo.unifi@gmail.com


title: Effective holistic characterization of small molecule effects using heterogeneous biological networks

abstract:
Drug discovery is the practice of identifying chemical entities with activities useful for treating human diseases. Despite substantial advancements in biotechnologies such as assays for detecting promising hits and computational methods for identifying targets to pursue, the success rate of novel therapeutics in the clinic is rapidly declining. The two most common reasons for drug attrition in clinical trials are efficacy, in that the drug is not capable of treating the disease, and safety, in which the compound is too toxic to patients and does not outweigh any purported benefits. Here we describe the use of an integrated human interactome network to describe the complete picture of drug behavior in biological systems and lead to more promising therapeutic candidate generation. The Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun multiscale drug discovery, repurposing, and design was enhanced to include drugs/compounds, proteins, diseases/indications, Gene Ontology entities, and drug side effects, accompanied with various known associations between them, and interactomic signatures were generated for all compounds using the node2vec algorithm for the purpose of relating them in the context of diseases for which they are approved. The results indicate there is significant biological information available in the side effect profile of a drug and they can be used to better relate drugs in terms of their therapeutic behavior. Side effects were also predicted for all compounds in the platform; known drug-side effect associations were recovered at rates ten times higher than what can be expected with random chance. The network architecture was also investigated in the context of protein pathways, where drug distance to various pathways served as the features for input to a random forest machine learning model in the context of indications they are associated to treat, with interesting results highlighted for mental disorders and cancer metastasis. This pipeline highlights the ability of CANDO to accurately relate drugs in a multitarget interactomic context, and paves the way for predicting novel putative drug candidates using the information gleaned from not only their side effect profiles, but their impacts on protein pathways as well.

Significance StatementOur study outlines the capability of our drug discovery, repurposing, and design platform known as CANDO to more accurately describe small molecule therapeutic behavior in biological systems via the use of heterogeneous networks. This includes the ability to predict indications as well as side effects for compounds without clinical data, ultimately advancing the science of drug discovery.


title: SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data

abstract: Single-cell DNA sequencing (scDNA-seq) has enabled the identification of single nucleotide somatic variants and the reconstruction of cell phylogenies. However, statistical phylogenetic models for cell phylogeny reconstruction from raw sequencing data are still in their infancy. Here we present SIEVE (SIngle-cell EVolution Explorer), a statistical method for the joint inference of somatic variants and cell phylogeny under the finite-sites assumption from scDNA-seq reads. SIEVE leverages raw read counts for all nucleotides at candidate variant sites, and corrects the acquisition bias of branch lengths. In our simulations, SIEVE outperforms other methods both in phylogenetic accuracy and variant calling accuracy. We apply SIEVE to three scDNA-seq datasets, for colorectal (CRC) and triple-negative breast cancer (TNBC), one of them generated by us. On simulated data, SIEVE reliably infers homo-and heterozygous somatic variants. The analysis of real data uncovers that double mutant genotypes are rare in CRC but unexpectedly frequent in TNBC samples.


title: PPML-Omics: a Privacy-Preserving federated Machine Learning system protects patients' privacy from omic data

abstract:
Modern machine learning models towards various tasks with omic data analysis give rise to threats of privacy leakage of patients involved in those datasets. Despite the advances in different privacy technologies, existing methods tend to introduce too much noise, which hampers model accuracy and usefulness. Here, we built a secure and privacy-preserving machine learning (PPML) system by combining federated learning (FL), differential privacy (DP) and shuffling mechanism.

We applied this system to analyze data from three sequencing technologies, and addressed the privacy concern in three major tasks of omic data, namely cancer classification with bulk RNA-seq, clustering with single-cell RNA-seq, and the integration of spatial gene expression and tumour morphology with spatial transcriptomics, under three representative deep learning models. We also examined privacy breaches in depth through privacy attack experiments and demonstrated that our PPML-Omics system could protect patients privacy. In each of these applications, PPML-Omics was able to outperform state-of-the-art systems under the same level of privacy guarantee, demonstrating the versatility of the system in simultaneously balancing the privacy-preserving capability and utility in omic data analysis. Furthermore, we gave the theoretical proof of the privacy-preserving capability of PPML-Omics, suggesting the first mathematically guaranteed model with robust and generalizable empirical performance.


title: Mult-iomic integrated curvature study on pan-cancer genomic data

abstract: In this work, we introduce a new mathematical framework based on network curvature to extract significant cancer subtypes from multi-omics data. This extends our previous work that was based on analyzing a fixed single-omics data class (e,g, CNA, gene expression, etc.). Notably, we are able to show that this new methodology provided us with significant survival differences on Kaplan-Meier curves across almost every cancer that we considered. Moreover, the variances in Ollivier-Ricci curvature was explored to investigate its usefulness in network topology analysis as this curvature may be capturing subtle functional changes between various cancer subtypes.


title: Multi-omic integrated curvature study on pan-cancer genomic data


title: Charge transfer of unconfined regions in quasi-periodic quantum wells : DNA nanostructure study

abstract: This study presents a quantum well model using transfer matrix to analyse the charge transfer characteristic in DNA nanostructure sequences. The unconfined state or unbound state above the quantum well are used to investigate the carrier behaviours in nanostructure of semiconductor. Similar analysis and simulations can be applied to the understanding of charge transfer in DNA nanostructure with sequence of periodic and quasi-periodic sequences. The model was validated with experiments using photoreflectance spectroscopy on nanostructure in semiconductor superlattice. In addition, the results published by the study of Thermoelectric effect and its dependence on molecular length and sequence in single DNA molecules[1] were used to compare with the simulations by the quantum well model. The results show agreement and can provide new insight into charge transfer and transport in DNA nanostructure with different types of sequences.

category: biophysics


title: Model biomolecular condensates have heterogeneous structure quantitatively dependent on the interaction profile of their constituent macromolecules

abstract: Biomolecular condensates play numerous roles in cells by selectively concentrating client proteins while excluding others. These functions are likely to be sensitive to the spatial organization of the scaffold proteins forming the condensate. We use coarse-grained molecular simulations to show that model intrinsically-disordered proteins phase separate into a heterogeneous, structured fluid characterized by a well-defined length scale. The proteins are modelled as semi-flexible polymers with punctate, multifunctional binding sites in good solvent conditions. Their dense phase is highly solvated with a spatial structure that is more sensitive to the separation of the binding sites than their affinity. We introduce graph theoretic measures to show that the proteins are heterogeneously distributed throughout the dense phase, an effect that increases with increasing binding site number, and exhibit multi-timescale dynamics. The simulations predict that the structure of the dense phase is modulated by the location and affinity of binding sites distant from the termini of the proteins, while sites near the termini more strongly affect its phase behaviour. The relations uncovered between the arrangement of weak interaction sites on disordered proteins and the material properties of their dense phase can be experimentally tested to give insight into the biophysical properties and rational design of biomolecular condensates.


title: NADK upregulation is an essential metabolic adaptation that enables breast cancer metastatic colonization

abstract: Metabolic reprogramming and metabolic plasticity allow cancer cells to fine-tune their metabolism to adapt to the ever-changing environments of the metastatic cascade, for which lipid metabolism and oxidative stress are of particular importance. Continuous production of NADPH, a cornerstone of both lipid and redox homeostasis, is essential for proliferation and cell survival suggesting that cancer cells may require larger pools of NADPH to efficiently metastasize. NADPH is recycled through reduction of NADP+ by several enzymatic systems in cells; however, de novo NADP+ is synthesized only through one known enzymatic reaction, catalysed by NAD+ kinase (NADK). Here, we show that NADK is upregulated in metastatic breast cancer cells enabling de novo production of NADP(H) and the expansion of the NADP(H) pools thereby increasing the ability of these cells to adapt to the oxidative challenges of the metastatic cascade and efficiently metastasize. Mechanistically, we found that metastatic signals lead to a histone H3.3 variant-mediated epigenetic regulation of the NADK promoter, resulting in increased NADK levels in cells with metastatic ability. Together, our work presents a previously uncharacterized role for NADK as an important contributor to breast cancer progression and suggests that NADK constitutes an important and much needed therapeutic target for metastatic breast cancers.

category: cancer biology


title: AMP-kinase mediates adaptation of glioblastoma cells to conditions of the tumour microenvironment

abstract:
AMP-activated protein kinase (AMPK) is a central cellular energy sensor that regulates metabolic activity. We hypothesised that in glioblastoma (GB), AMPK plays a pivotal role in balancing metabolism under conditions of the tumour microenvironment, which is characterised by fluctuating and often low nutrient and oxygen availability. Impairment of this network could thus interfere with tumour progression.

AMPK activity was modulated genetically by CRISPR/Cas9-based double knockout (DKO) of the catalytic 1 and 2 subunits in human GB cells and effects were confirmed by pharmacological AMPK inhibition using BAY3827 and an inactive control compound in primary GB cell lines.

We found that metabolic adaptation of GB cells under energy stress conditions (hypoxia, glucose deprivation) was dependent on AMPK and accordingly that, AMPK DKO cells were more vulnerable to glucose-deprivation or inhibition of glycolysis and sensitised to hypoxia-induced cell death. This effect was rescued by reexpression of the AMPK 2 subunit. Similar results were observed using the selective pharmacological AMPK inhibitor BAY3827. Mitochondrial biogenesis was regulated AMPK-dependently with a reduced mitochondrial mass and mitochondrial membrane potential in AMPK DKO GB cells. In vivo, AMPK DKO GB cells showed impaired tumour growth and tumour formation in CAM assays as well as in an orthotopic glioma mouse model.

Our study highlights the importance of AMPK for GB cell adaptation towards energy depletion and emphasises the role of AMPK for tumour formation in vivo. Moreover, we identified mitochondria as central downstream effectors of AMPK signalling. The development of AMPK inhibitors could open opportunities for the treatment of hypoxic tumours.


title: CRISPR-induced exon skipping of β-catenin reveals tumorigenic mutants driving distinct subtypes of liver cancer

abstract: CRISPR/Cas9-driven cancer modeling studies are based on disruption of tumor suppressor genes (TSGs) by small insertions or deletions (indels) that lead to frame-shift mutations. In addition, CRISPR/Cas9 is widely used to define the significance of cancer oncogenes and genetic dependencies in loss-of function studies. However, how CRISPR/Cas9 influences gain-of-function oncogenic mutations is elusive. Here, we demonstrate that single guide RNA targeting exon 3 of {beta}-catenin results in exon skipping and generates gain-of-function isoforms in vivo. CRISPR/Cas9-mediated exon skipping of {beta}-catenin induces liver tumor formation in synergy with YAPS127A in mice. We define two distinct exon skipping-induced tumor subtypes with different histological and transcriptional features. Notably, ectopic expression of two exon-skipped {beta}-catenin transcript isoforms together with YAPS127A phenocopies the two distinct subtypes of liver cancer. Moreover, we identify similar {beta}-catenin exon skipping events in hepatocellular carcinoma (HCC) patients. Collectively, our findings advance our understanding of {beta}-catenin-related tumorigenesis and reveal that CRISPR/Cas9 can be repurposed, in vivo, to study gain-of-function mutations of oncogenes in cancer.


title: S6K1 phosphorylates Cdk1 and MSH6 to regulate DNA repair.

abstract: The mTORC1 substrate, S6 Kinase 1 (S6K1), is involved in the regulation of cell growth, ribosome biogenesis, glucose homeostasis and adipogenesis. Accumulating evidence has suggested a role for mTORC1 signaling in the DNA damage response. This is mostly based on the findings that mTORC1 inhibitors sensitized cells to DNA damage. However, a direct role of the mTORC1-S6K1 signaling pathway in DNA repair and the mechanism by which this signaling pathway regulates DNA repair is unknown. In this study, we discovered a novel role for S6K1 in regulating DNA repair through the coordinated regulation of the cell cycle, homologous recombination (HR) DNA repair (HRR) and mismatch DNA repair (MMR) mechanisms. Here we show that S6K1 orchestrates DNA repair by phosphorylation of Cdk1 at serine 39, causing G2/M cell cycle arrest enabling homologous recombination and by phosphorylation of MSH6 at serine 309, enhancing MMR. Moreover, breast cancer cells harboring RPS6KB1 gene amplification show increased resistance to several DNA damaging agents and S6K1 expression is associated with poor survival of breast cancer patients treated with chemotherapy. Our findings reveal an unexpected function of S6K1 in the DNA repair pathway, serving as a tumorigenic barrier by safeguarding genomic stability.


title: LAMC2 marks a tumor-initiating cell population with an aggressive signature in pancreatic cancer

abstract: Tumor-initiating cells (TIC), also known as cancer stem cells, are considered a specific subpopulation of cells necessary for cancer initiation and metastasis. Here, we report a LAMC2-positive cell population, which is endowed with enhanced self-renewal capacity, and is sufficient for tumor initiation, differentiation, and driving metastasis. Mechanistically, mRNA profiling of these cells indicate a prominent squamous signature, and differentially activated pathways critical for tumor growth and metastasis, including deregulation of the TGF-{beta} signaling pathway. Treatment with Vactosertib, a new small molecule inhibitor of transforming growth factor-{beta} (TGF-{beta}) type I receptor (activin receptor-like kinase-5, ALK5), completely abrogated the lung metastasis, primarily originating from LAMC2 expressing cells. Our results prompt further study of this TIC population in pancreatic cancer and exploration as a potential therapeutic target and/or biomarker.


title: Integrative single cell and spatial transcriptomic analysis reveal reciprocal microglia - plasma cell crosstalk in the mouse brain during chronic Trypanosoma brucei infection

abstract: Human African trypanosomiasis, or sleeping sickness, is caused by the protozoan parasite Trypanosoma brucei and induces profound reactivity of glial cells and neuroinflammation when the parasites colonise the central nervous system. However, the transcriptional and functional responses of the brain to chronic T. brucei infection remain poorly understood. By integrating single cell and spatial transcriptomics of the mouse brain, we identified that glial responses triggered by infection are readily detected in the proximity to the circumventricular organs, including the lateral and 3rd ventricle. This coincides with the spatial localisation of both slender and stumpy forms of T. brucei. Furthermore, in silico predictions and functional validations led us to identify a previously unknown crosstalk between homeostatic Cx3cr1+ microglia and Cd138+ plasma cells mediated by IL-10 and B cell activating factor (BAFF) signalling. This study provides important insights and resources to improve understanding of the molecular and cellular responses in the brain during infection with African trypanosomes.

category: pathology


title: Leaf nitrogen does not explain changes in soybean radiation-use efficiency in vegetative and early reproductive stages

abstract:
Ontogenic changes in soybean radiation-use efficiency (RUE) have been attributed to variation in specific leaf nitrogen (SLN) based only on data collected during seed filling. We evaluated this hypothesis using data on leaf area, absorbed photosynthetically active radiation (APAR), aboveground dry matter (ADM), and plant nitrogen (N) concentration collected during the entire crop season from seven field experiments conducted in a stress-free environment. Each experiment included a full N treatment that received ample N fertilizer and a zero N treatment that relied on N fixation and soil N mineralization. We estimated RUE based on changes in ADM between sampling times and associated APAR, accounting for changes in biomass composition. The SLN and RUE exhibited different seasonal patterns: a bell-shaped pattern with a peak around the beginning of seed filling, and a convex pattern followed by an abrupt decline during late seed filling, respectively. The level of N supply influenced SLN more than RUE via changes in leaf N concentration, with small changes in specific leaf weight. Changes in SLN explained the decline in RUE during seed filling but failed to predict changes in RUE in earlier stages. A simple approach based on phenological stages may give more realistic estimates of RUE before seed filling, improving crop growth and yield prediction via crop models and remote sensing.

HighlightChanges in radiation-use efficiency during soybean vegetative and early reproductive stages are not related to specific leaf nitrogen.

category: physiology


title: Deep Phenotyping and Lifetime Trajectories Reveal Limited Effects of Longevity Regulators on the Aging Process in C57BL/6J Mice

abstract:
Current concepts regarding the biology of aging are based on studies aimed at identifying factors regulating natural lifespan. However, lifespan as a sole proxy measure for aging can be of limited value because it may be restricted by specific sets of pathologies, rather than by general physiological decline. Here, we employed large-scale phenotyping to analyze hundreds of phenotypes and thousands of molecular markers across tissues and organ systems in a single study of aging male C57BL/6J mice. For each phenotype, we established lifetime profiles to determine when age-dependent phenotypic change is first detectable relative to the young adult baseline. We examined central genetic and environmental lifespan regulators (putative anti-aging interventions, PAAIs; the following PAAIs were examined: mTOR loss-of-function, loss-of-function in growth hormone signaling, dietary restriction) for a possible countering of the signs and symptoms of aging. Importantly, in our study design, we included young treated groups of animals, subjected to PAAIs prior to the onset of detectable age-dependent phenotypic change. In parallel to our studies in mice, we assessed genetic variants for their effects on age-sensitive phenotypes in humans. We observed that, surprisingly, many PAAI effects influenced phenotypes long before the onset of detectable age-dependent changes, rather than altering the rate at which these phenotypes developed with age. Accordingly, this subset of PAAI effects does not reflect a targeting of age-dependent phenotypic change. Overall, our findings suggest that comprehensive phenotyping, including the controls built in our study, is critical for the investigation of PAAIs as it facilitates the proper interpretation of the mechanistic mode by which PAAIs influence biological aging.

HighlightsO_LIPhenotyping at scale defines lifetime trajectories of age-dependent changes in C57BL/6J mice
C_LIO_LICentral genetic and environmental lifespan regulators (putative anti-aging interventions; PAAIs) influence age-sensitive phenotypes (ASPs) often long before the appearance of age-dependent changes in these ASPs
C_LIO_LICorresponding genetic variants in humans also have age-independent effects
C_LIO_LIMany PAAI effects shift the baseline of ASPs rather than slowing their rate of change
C_LI


title: Establishing a reproducible approach for the controllable deposition and maintenance of plants cells with 3D bioprinting

abstract: Capturing cell-to-cell and cell-to-environment signals in a defined 3 dimensional (3D) microenvironment is key to study cellular functions, including cellular reprogramming towards tissue regeneration. A major challenge in current culturing methods is that these methods cannot accurately capture this multicellular 3D microenvironment. In this study, we established the framework of 3D bioprinting with plant cells to study cell viability, cell division, and cell identity. We established long-term cell viability for bioprinted Arabidopsis root cells and soybean meristematic cells. To analyze the large image datasets generated during these long-term viability studies, we developed an open source high-throughput image analysis pipeline. Furthermore, we showed the cell cycle re-entry of the isolated Arabidopsis and soybean cells leading to the formation of microcalli. Finally, we showed that the identity of isolated cells of Arabidopsis roots expressing endodermal markers maintained longer periods of time. The framework established in this study paves the way for a general use of 3D bioprinting for studying cellular reprogramming and cell cycle re-entry towards tissue regeneration.

category: plant biology


title: Complex developmental and transcriptional dynamics underlie pollinator-driven evolutionary transitions in nectar spur morphology in Aquilegia (columbine)

abstract:
PremiseDetermining the developmental programs underlying morphological variation is key to elucidating the evolutionary processes that generated the stunning biodiversity of the angiosperms. Here, we characterize the developmental and transcriptional dynamics of the elaborate petal nectar spur of Aquilegia (columbine) in species with contrasting pollination syndromes and spur morphologies.

MethodsWe collected petal epidermal cell number and length data across four Aquilegia species, two with the short, curved nectar spurs of the bee-pollination syndrome, and two with the long, straight spurs of the hummingbird syndrome. We also performed RNA-seq on A. brevistyla (bee) and A. canadensis (hummingbird) distal and proximal spur compartments at multiple developmental stages. Finally, we intersected these datasets with a previous QTL mapping study on spur length and shape to identify new candidate loci.

ResultsThe differential growth between the proximal and distal surfaces of curved spurs is primarily driven by differential cell division. However, independent transitions to straight spurs in the hummingbird syndrome have evolved by increasing differential cell elongation between spur surfaces. The RNA-seq data reveal these tissues to be transcriptionally distinct, and point to auxin signaling as being involved with the differential cell elongation responsible for the evolution of straight spurs. We identify several promising candidate genes for future study.

ConclusionsOur study, taken together with previous work in Aquilegia, reveals the complexity of the developmental mechanisms underlying trait variation in this system. The framework we have establish here will lead to exciting future work examining candidate genes and processes involved in the rapid radiation of the genus.


title: Polymer nanoparticles pass the plant interface

abstract:
As agriculture strives to feed an ever-increasing number of people, it must adapt to cope with climate change. It is also clear that our biosphere is suffering from an increasing burden of anthropogenic waste which includes minute plastic particles. It is not yet known whether plants will accumulate such micro- and nanoplastic materials, nor how their surface properties might influence uptake. Therefore, we prepared well-defined block copolymer nanoparticles with a range of different sizes (Dh = 20 - 100 nm) and surface chemistries by aqueous dispersion polymerisation using different functional macro chain transfer agents. A BODIPY fluorophore was then incorporated via hydrazone formation and uptake of these fluorescent nanoparticles into intact roots and protoplasts of Arabidopsis thaliana was investigated using confocal microscopy. Where uptake was seen, it was inversely proportional to nanoparticle size. Positively charged particles accumulated around root surfaces and were not taken up by roots or protoplasts, whereas negatively charged nanoparticles accumulated slowly in protoplasts and roots, becoming prominent over time in the xylem of intact roots. Neutral nanoparticles exhibited early, rapid penetration into plant roots and protoplasts, but lower xylem loads relative to the negative nanoparticles. These behaviours differ from those recorded in animal cells and our results show that, despite robust cell walls, plants are vulnerable to nanoplastic particles in the water and soil. The data form both a platform for understanding plastic waste in the farmed environment, and may also be used constructively for the design of precision delivery systems for crop protection products.

Significance StatementSustainable food production must keep pace with the growing global population, as well as adapt to climate change and other anthropogenic insults. It has become clear that micro-and nanoscale plastics are accumulating in all parts of the biosphere and we have set out to study how vulnerable plants are to such waste. We show that the size and surface properties of the designed plastics significantly affect both their speed of uptake and distribution within intact roots. Crucially, it is clear that rigid cell walls around plant cells are no barrier to the smallest particles and these pass into the plants vasculature. Our results relate to plastic waste but can also be used to develop precision vehicles for crop protection.


title: Animal-reliance bias in publishing is a potential barrier to scientific progress

abstract: Publication of scientific findings is a fundamental part of the research process that pushes innovation and generates policies and interventions that benefit society, but it is not without biases. Publication bias is generally recognized as journals preference for publishing studies based on the direction and magnitude of results. However, early evidence of a new type of bias related to publication has emerged in which editorial policy and/or peer reviewers or editors request that animal data be provided to validate studies produced using nonanimal human biology-based approaches. We describe herein "animal-reliance bias" in publishing: a reliance on or preference for animal-based methods where they may not be necessary or where nonanimal-based methods may be suitable, which affects the likelihood of a manuscript being accepted for publication. To gather evidence of the occurrence of this emerging type of publication bias, we set out to collect the experiences and perceptions of scientists and reviewers related to animal- and nonanimal-based experiments during peer review. To this end, we created a survey with 33 questions that was completed by 90 respondents working in several areas in the biological and biomedical fields. Twenty-one survey respondents indicated that they have carried out animal-based experiments for the sole purpose of anticipating reviewer requests. Thirty-one survey respondents indicated that they have been asked by peer reviewers to add animal experimental data to their nonanimal study; 14 of these felt that it was sometimes justified, and 11 did not think the request was justified. The data presented strongly support the occurrence of animal-reliance bias and indicates that status quo and conservatism biases may explain such attitudes by peer reviewers and editors. To our knowledge, this is the first study to recognize the existence of animal-reliance bias in publishing and provides the basis for developing strategies to prevent this practice from happening.

category: scientific communication and education


title: Improving patient survival by direct targeting of chimeric protein-protein interaction networks

abstract: Protein fusions produced by the "slippage" of two genes or by chromosomal translocations are essential diagnostic biomarkers of cancer. Fusions produce novel protein-protein interactions, which eliminate other interactions by changing protein domains in such fusions. The impact of these changes disseminates along protein-protein interaction networks, thereby altering cancer-promoting activity and creating cancer phenotypes. Currently, for most patients, the determination of appropriate drugs is totally empirical. As such, a personalized therapy approach based on unique patient genomic markers is needed. In this study, we considered 672 aliquot IDs containing 3091 fusions from The Cancer Genome Atlas (TCGA), accounting for 25 cancer sub-types assigned as leukemias, lymphomas, sarcomas, melanoma, glioblastoma and carcinomas. Protein-protein interaction maps showed distinct patterns according to cancer sub-type, reflected as different phenotypic traits. We induced site-directed percolations, i.e., critical transitions, by selective knockouts of genes encoding proteins in a given interaction network so as to identify breakdown points. The number of genes that needed to be knocked out in a site-directed manner before inducing a breakdown ranged from 1-7 based on whether the fusion protein was part of a network hub. Quantitatively, in leukemia, lymphoma, melanoma and glioblastoma, breakdown was achieved in 218 fusion networks when only higher degree hubs were percolated, and in 280 networks when a combination of higher and lower degree hubs was targeted, with an FDR < 0.05. These were subsequently addressed in survival studies. We found that patient survival may be improved by considering  breakdown points as drug targets.

category: systems biology


title: Protein synthesis inhibition and loss of homeostatic functions in astrocytes from an Alzheimer's disease mouse model: a role for ER-mitochondria interaction.

abstract: Deregulation of protein synthesis and ER stress/unfolded protein response (ER stress/UPR) have been reported in astrocytes. However, the relationships between protein synthesis deregulation and ER stress/UPR, as well as their role in the altered homeostatic support of Alzheimers disease (AD) astrocytes remain poorly understood. Previously, we reported that in astrocytic cell lines from 3xTg-AD mice (3Tg-iAstro) protein synthesis was impaired and ER-mitochondria distance was reduced. Here we show that impaired protein synthesis in 3Tg-iAstro is associated with an increase of p-eIF2 and downregulation of GADD34. Although mRNA levels of ER stress/UPR markers were increased two-three-fold, we found neither activation of PERK nor downstream induction of ATF4 protein. Strikingly, the overexpression of a synthetic ER-mitochondrial linker resulted in a reduced protein synthesis and augmented p-eIF2 without any effect on ER stress/UPR marker genes. In vivo, in hippocampi of 3xTg-AD mice, reduced protein synthesis, increased p-eIF2 and downregulated GADD34 protein were found, while no increase of p-PERK or ATF4 proteins was observed, suggesting that in AD astrocytes, both in vitro and in vivo, phosphorylation of eIF2 and impairment of protein synthesis are PERK-independent. Next, we investigated the ability of 3xTg-AD astrocytes to support metabolism and function of other cells of the central nervous system. Astrocyte conditioned medium (ACM) from 3Tg-iAstro cells significantly reduced protein synthesis rate in primary hippocampal neurons. When added as a part of pericyte/endothelial cell (EC)/astrocyte 3D co-culture, 3Tg-iAstro, but not WT-iAstro, severely impaired formation and ramification of tubules. Finally, a chemical chaperone 4-phenylbutyric acid (4-PBA) rescued protein synthesis, p-eIF2 levels in 3Tg-iAstro cells and tubulogenesis in pericyte/EC/3Tg-iAstro co-culture. Collectively, our results suggest that a PERK-independent, p-eIF2-associated impairment of protein synthesis compromises astrocytic homeostatic functions and this may be caused by the altered ER-mitochondria interaction.

category: neuroscience


title: The general anesthetic isoflurane inhibits calcium activity in cerebrovascular endothelial cells and disrupts vascular tone

abstract: Calcium signaling in cerebrovascular endothelial cells (CVECs) has been identified to play key physiological and pathological roles in blood brain barrier function and neurovascular coupling, which involve dynamic changes in vessel diameter. However, there are no studies that measured correlated changes in vessel diameter and calcium activity in CVECs in vivo. In this study, we used the general anesthetic isoflurane (ISO) to induce a maximally dilated state in cortical blood vessels and measured the effects of the manipulation on CVEC calcium reporter activity in awake Cdh5BAC-GCaMP mice by use of two-photon fluorescence microscopy through thinned skull cranial windows. For the first time, we report dual effects of ISO on calcium activity in cerebral blood vessels of different diameter. During anesthesia induction ISO exposure triggered a short latency synchronous increase in calcium activity, followed by a period of activity suppression in small, medium, and large diameter vessels. Furthermore, during anesthesia maintenance calcium activity was desynchronized, and the relationship between vascular tone and calcium activity was disrupted in all vessel types. Based on these results we propose that there is a feedback mechanism between intracellular calcium fluctuations in CVECs and the maintenance of cerebrovascular tone.


title: Subjective cognitive decline predicts lower cingulo-opercular network functional connectivity in individuals with lower neurite density in the forceps minor

abstract: Cognitive complaints of attention/concentration problems are highly frequent in older adults with subjective cognitive decline (SCD). Functional connectivity in the cingulo-opercular network (CON-FC) supports cognitive control, tonic alertness, and visual processing speed. Thus, those complaints in SCD may reflect a decrease in CON-FC. Frontal white-matter tracts such as the forceps minor exhibit age- and SCD-related alterations and, therefore, might influence the CON-FC decrease in SCD. Here, we aimed to determine whether SCD predicts an impairment in CON-FC and whether neurite density in the forceps minor modulates that effect. To do so, we integrated cross-sectional and longitudinal analyses of multimodal data in a latent growth curve modeling approach. Sixty-nine healthy older adults (13 males; 68.33 {+/-} 7.95 years old) underwent resting-state functional and diffusion-weighted magnetic resonance imaging, and the degree of SCD was assessed at baseline with the memory functioning questionnaire (greater score indicating more SCD). Forty-nine of the participants were further enrolled in two follow-ups, each about 18 months apart. Baseline SCD did not predict CON-FC after three years or its rate of change (p-values > 0.092). Notably, however, the forceps minor neurite density did modulate the relation between SCD and CON-FC (intercept; b = 0.20, 95% confidence interval, CI, [0.03, 0.37], p = 0.020), so that SCD predicted a greater CON-FC decrease in older adults with relatively lower neurite density in the forceps minor. The neurite density of the forceps minor, in turn, negatively correlated with age. These results suggest that CON-FC alterations in SCD are dependent upon the forceps minor neurite density. Moreover, these results imply modifiable age-related factors that could help delay or mitigate both age and SCD-related effects on brain connectivity.


title: Pharmacological manipulations of physiological arousal and sleep-like slow waves modulate sustained attention

abstract: Sustained attention describes our ability to keep a constant focus on a given task. This ability is modulated by our physiological state of arousal. Although lapses of sustained attention have been linked with dysregulations of arousal, the underlying physiological mechanisms remain unclear. An emerging body of work proposes that the intrusion during wakefulness of sleep-like slow waves, a marker of the transition toward sleep, could mechanistically account for attentional lapses. This study aimed to expose, via pharmacological manipulations of the monoamine system, the relationship between the occurrence of sleep-like slow waves and the behavioural consequences of sustained attention failures. In a double-blind, randomised-control trial, 32 healthy participants received methylphenidate, atomoxetine, citalopram or placebo during four separate experimental sessions. During each session, electroencephalography (EEG) was used to measure neural activity whilst participants completed a visual task requiring sustained attention. Methylphenidate, which increases wake-promoting dopamine and noradrenaline across cortical and subcortical areas, improved behavioural performance whereas atomoxetine, which increases dopamine and noradrenaline predominantly over frontal cortices, led to more impulsive responses. Additionally, citalopram, which increases sleep-promoting serotonin, led to more missed trials. Based on EEG recording, citalopram was also associated with an increase in sleep-like slow waves. Importantly, compared to a classical marker of arousal such as alpha power, only slow waves differentially predicted both slower and faster responses in a region-specific fashion. These results suggest that a decrease in arousal can lead to local sleep intrusions during wakefulness which could be mechanistically linked to impulsivity and sluggishness.


title: Synthetic torpor triggers a neuroprotective and regulated mechanism in the rat brain, leading to the reversibility of Tau protein hyperphosphorylation.

abstract:
Hyperphosphorylated Tau protein (PPTau) is the hallmark of tauopathic neurodegeneration. During "synthetic torpor" (ST), a transient hypothermic state which can be induced in rats by the local pharmacological inhibition of the Raphe Pallidus, a reversible brain Tau hyperphosphorylation occurs. The aim of the present study was to elucidate the - as yet unknown - molecular mechanisms underlying this process, at both a cellular and systemic level. Different phosphorylated forms of Tau and the main cellular factors involved in Tau phospho-regulation were assessed by western blot in the parietal cortex and hippocampus of rats induced in ST, at either the hypothermic nadir or after the recovery of euthermia. Pro- and anti-apoptotic markers, as well as different systemic factors which are involved in natural torpor, were also assessed. Finally, the degree of microglia activation was determined through morphometry. Overall, the results show that ST triggers a regulated biochemical process which can counteract PPTau formation starting, unexpectedly, from the hypothermic nadir. In particular, at the nadir, the glycogen synthase kinase-{beta} was largely inhibited in both regions, the antiapoptotic factor AKT was significantly activated in the hippocampus, and melatonin plasma levels were significantly increased, while a transient neuroinflammation was observed during the recovery period. Together, the present data suggest that ST can trigger a previously undescribed latent and regulated physiological process, that is able to cope with brain PPTau formation.

Graphical abstract

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title: A Spinal Circuit That Transmits Innocuous Cool Sensations

abstract: Temperature information is precisely processed in the nervous system. While progress has been made in identifying molecular thermosensors in the periphery, the neural circuits that process temperature information in the central nervous system remain unknown. Here we have identified an essential node in the neural circuitry for innocuous cool sensations. We found that a population of excitatory interneurons co-expressing Calbindin1 and Lbx1 (Calb1Lbx1) in the dorsal horn of the spinal cord is activated by innocuous cool temperatures. Genetic ablation or silencing of spinal Calb1Lbx1 neurons causes loss of innocuous cool but not noxious cold sensations. Further Brainbow labeling with expansion microscopy and electrophysiology showed that a small cluster of spinal Calb1Lbx1 interneurons in lamina I and the outer layer of lamina II represents the cooling-transmission neurons. These neurons receive monosynaptic connections from TRPM8+ primary sensory neurons and amplify the activity of cool-sensitive spinoparabrachial projection neurons. Our findings reveal a microcircuit in the dorsal spinal cord that specifically transmits innocuous cool sensations.


title: Sex-specific effects of chronic paternal stress on offspring development are partially mediated via mothers.

abstract: Paternal stress exposure is known to impact the development of stress-related behaviors in offspring. Previous work has highlighted the importance of sperm mediated factors, such as RNAs, in transmitting the effects of parental stress. However, a key unanswered question is whether mothers behavior could drive or modulate the transmission of paternal stress effects on offspring development. Here we investigate how chronic variable stress in Balb/C mice influences the sex-specific development of anxiety- and depression-like neural and behavioral development in offspring. Moreover, we examined how stressed fathers influenced mate maternal investment towards their offspring and how this may modulate the transmission of paternal stress effects on offspring. We show that paternal stress leads to sex-specific effects on offspring behavior. Males that are chronically stressed sire female offspring that show increased anxiety and depression-like behaviors. However, male offspring of stressed fathers show reductions in anxiety- and depression-behaviors and are generally more exploratory. Moreover, we show that females mated with stressed males gain less weight during pregnancy and provide less care towards their offspring which additionally influenced offspring development. These data indicate that paternal stress can influence offspring development directly and indirectly via changes in mothers, with implications for divergent development between male and female offspring.


title: Intact maternal buffering of stress response in infant rats despite altered responsivity towards maternal olfactory cues in the valproic acid model of autism-like behavior

abstract: Disrupted processing of social cues and altered social behaviors are among the core symptoms of autism spectrum disorders (ASDs), and they emerge as early as the first year of life. These differences in sensory abilities may affect the ability of children with ASDs to securely attach to a caregiver and experience caregiver buffering of stress. Prenatal exposure to valproic acid (VPA) has been used to model some aspects of ASDs in rodents. Here, we asked whether prenatal VPA exposure altered infant rats behavioral responsivity to maternal olfactory cues in an odor preference test and affected maternal buffering of infants stress responsivity to shock. In the odor preference test, one-week old rats treated with VPA during pregnancy appeared to have impaired social recognition and/or may be less motivated to approach social odors in early infancy. These effects were particularly prominent in female pups. In two-week old rats, VPA-exposed pups and saline-exposed pups showed similar preferences for home cage bedding. Although VPA-exposed pups may initially have a deficit in this attachment-related behavior they do recover typical responses to home cage bedding in later infancy. Both control and VPA-exposed pups showed robust stress hormone responses to repeated shocks, an effect which was blocked when a calm mother was present during shock exposure. No sex differences in the effect of maternal presence on the stress response to shock and no interactions between sex and prenatal drug exposure were observed. Although VPA-exposed pups may show impaired responsivity to maternal cues in early infancy, maternal presence is still capable of regulating the stress response in VPA-exposed pups. In this study we demonstrate the importance of utilizing multiple batteries of tests in assessing behavior, dissecting the behavior on one test into different components. Our results inform about the underlying behavioral characteristics of some of the ASD phenotypes, including sex differences reported by clinical studies, and could shed light on potential opportunities for intervention.


title: Microglial TNFα orchestrates brain phosphorylation during the sleep period and controls homeostatic sleep.

abstract: The time we spend asleep is adjusted to previous time spent awake, and therefore believed to be under tight homeostatic control. Here, we establish microglia as a new cellular component of the sleep homeostat circuit. By using quantitative phosphoproteomics we demonstrate that microglia-derived TNF controls thousands of phosphorylation sites during the sleep period. Substrates of microglial TNF comprise sleep-promoting kinases and numerous synaptic proteins, including a subset whose phosphorylation status codes sleep need and determines sleep duration. As a result, lack of microglial TNF attenuates the build-up of sleep need, as measured by slow wave activity, and prevents immediate compensation for loss of sleep. Together, we propose that microglia control sleep homeostasis by releasing TNF that acts at the neuronal circuitry through dynamic control of phosphorylation.


title: Sex-specific role of the circadian transcription factor NPAS2 in opioid tolerance, withdrawal, and analgesia

abstract: Opioids like fentanyl are the mainstay treatment for chronic pain. Unfortunately, opioids high addiction liability has led to the current opioid crisis. This is in part related to long-term use side-effects, including analgesic tolerance (gradual decrease in analgesia), and physical dependence (withdrawal symptoms upon opioid interruption), causing dose-escalation and preventing usage interruption. Altered circadian rhythmicity and sleep patterns are common in patients on opioid therapy. Prior research showed intricate bidirectional interactions between circadian rhythmicity, opioid analgesic efficacy, and side-effects. However, underlying mechanisms are largely unknown. Neuronal PAS domain protein 2 (NPAS2) is a circadian transcription factor that is highly expressed in structures of the central nervous system that modulate pain and opioids. In this study, we used male and female mice expressing non-functional NPAS2 (NPAS2 deficient, NPAS2-/-) to investigate the role of NPAS2 in fentanyl analgesia, tolerance, hyperalgesia, and dependence. In NPAS2-/- mice, we found that thermal pain thresholds, acute analgesia, and tolerance to a fixed dose of fentanyl were largely like wild-type mice. However, female NPAS2-/- mice augmented behavioral state of analgesic tolerance and exhibited significantly more behavioral symptoms of physical dependence. Conversely, only male NPAS2-/- mice had increased fentanyl-induced hypersensitivity, when compared to matched-sex littermate controls. Together, our findings suggest sex-specific effects of NPAS2 signaling in the regulation of fentanyl-induced tolerance, hyperalgesia, and dependence.


title: Robust Estimation of 1/f Activity Improves Oscillatory Burst Detection

abstract:
Neural oscillations often occur as transient bursts with variable amplitude and frequency dynamics. Quantifying these effects is important for understanding brain-behaviour relationships, especially in continuous datasets. To robustly measure bursts, rhythmical periods of oscillatory activity must be separated from arrhythmical background 1/f activity, which is ubiquitous in electrophysiological recordings. The Better OSCillation (BOSC) framework achieves this by defining a power threshold above the estimated background 1/f activity, combined with a duration threshold. Here we introduce a modification to this approach called fBOSC which uses a spectral parametrisation tool to accurately model background 1/f activity in neural data. fBOSC (which is openly available as a MATLAB toolbox) is robust to power spectra with oscillatory peaks and can also model non-linear spectra. Through a series of simulations, we show that fBOSC more accurately models the 1/f power spectrum compared with existing methods. fBOSC was especially beneficial where power spectra contained a "knee" below [~]0.5-10 Hz, which is typical in neural data. We also found that, unlike other methods, fBOSC was unaffected by oscillatory peaks in the neural power spectrum. Moreover, by robustly modelling background 1/f activity, the sensitivity for detecting oscillatory bursts was standardised across frequencies (e.g. theta- and alpha-bands). Finally, using openly available resting state magnetoencephalography and intracranial electrophysiology datasets, we demonstrate the application of fBOSC for oscillatory burst detection in the theta-band. These simulations and empirical analyses highlight the value of fBOSC in detecting oscillatory bursts, including in datasets that are long and continuous with no distinct experimental trials.

Graphical abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/485674v2_ufig1.gif" ALT="Figure 1">
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org.highwire.dtl.DTLVardef@96bd80org.highwire.dtl.DTLVardef@733458org.highwire.dtl.DTLVardef@17184d1org.highwire.dtl.DTLVardef@1c6cca5_HPS_FORMAT_FIGEXP  M_FIG C_FIG To determine a power threshold for burst detection, the Better OSCillation framework (BOSC) estimates background 1/f activity by modelling neural power spectra. Here we introduce a modification, termed fBOSC, to more robustly estimate 1/f activity in situations with prominent oscillatory peaks and/or the presence of a non-linear "knee" in the power spectrum. This was shown to standardise burst detection across frequency bands in both simulated and empirical data.


title: Single-cell Transcriptomic Atlas of the Human Substantia Nigra in Parkinson's Disease

abstract: Parkinsons disease (PD) is a common and complex neurodegenerative disorder. Loss of neuromelanin-containing dopaminergic (DA) neurons in the substantia nigra (SN) is a hallmark of PD neuropathology; the etiology of PD remains unclear. Single-cell (-nucleus) RNA sequencing (sc or snRNAseq) has significantly advanced our understanding of neurodegenerative diseases including Alzheimers, but limited progress has been made in PD. Here we generated by far the largest snRNAseq data of high-quality 315,867 nuclei from the human SN including 9 healthy controls and 23 idiopathic PD cases across different Braak stages. Clustering analysis identified major brain cell types including DA neurons, excitatory neurons, inhibitory neurons, glial cells, endothelial, pericytes, fibroblast and T-cells in the human SN. By combining immunostaining and validating against the datasets from independent cohorts, we identified three molecularly distinct subtypes of DA-related neurons, including a RIT2-enriched population, in human aged SN. All DA neuron subtypes degenerated in PD, whereas the composition of non-neuronal cell clusters including major glial types showed little change. Our study delineated cell-type-specific PD-linked gene expression in the SN and their alterations in PD. Examination of cell-type-based transcriptomic changes suggests the complexity and diversity of molecular mechanisms of PD. Analysis of the remaining DA neurons of the three subtypes from PD demonstrated alterations of common gene sets associated with neuroprotection. Our findings highlight the heterogeneity of DA neurons in the human SN and suggest molecular basis for vulnerability and resilience of human DA neurons in PD. Our cohort thus provides a valuable resource for dissecting detailed mechanisms of DA neuron degeneration and identifying new neuroprotective strategies for PD.


title: Enhanced short-wavelength sensitivity in the blue-tongued skink,Tiliqua rugosa

abstract:
The complex visually mediated behaviors of diurnal lizards are enabled by a retina typically containing five types of opsins with the potential for tetrachromatic color vision. Despite lizards using a wide range of color signals, the limited variation in photoreceptor spectral sensitivities across lizards suggests only weak selection for species-specific, spectral tuning of photoreceptors. Some species, however, have enhanced short wavelength sensitivity, which likely helps with the detection of signals rich in ultraviolet and short wavelengths. In this study, we examined the visual system of Tiliqua rugosa, which has a UV/blue tongue, to determine the spectral sensitivity of the eye and to gain insight into this species visual ecology. Electroretinograms coupled with spectral stimulation showed peak sensitivity at 560 nm with high similarity to other lizards at wavelengths greater than 530 nm. However, at shorter wavelengths, sensitivity is enhanced leading to a spectral sensitivity curve that is 28 nm broader (full width at half height) than other lizards studied so far. The width of the curve is partially explained by a population of photoreceptors that respond more strongly to low temporal frequencies with possible peaks in sensitivity between 460 and 470 nm suggesting that they are SWS2 photoreceptors. The lack of a peak in sensitivity at 360 nm at low temporal frequencies and under a monochromatic light that suppresses the response of LWS photoreceptors, suggests that the SWS1 photoreceptors are red-shifted. In addition, the yellow and green oil droplets that are common in other diurnal lizards appear to be missing and instead, only transparent and pale-yellow oil droplets are present. LWS photoreceptors are likely paired with pale-yellow oil droplets to produce LWS photoreceptors with wider spectral sensitivity curves than in other lizards. Opsin sequencing reveals SWS1, SWS2, RH1, RH2 and LWS opsin genes that are very similar to the visual opsins detected in the green anole, Anolis carolinensis, suggesting there is little change in the spectral sensitivity of photoreceptors compared to other diurnal lizards. Since we only obtained a partial sequence of the SWS1 opsin, we were unable to determine whether amino acid substitution at tuning sites could have played a role in red-shifting the SWS1 photoreceptor spectral sensitivity. Photoreceptor densities are typically higher in central and ventral retinal regions than in the dorsal retina suggesting that higher spatial sampling is necessary at eye level and above the animal than on the ground. However, the SWS1 photoreceptors do not follow this pattern potentially due to their low abundance making them less relevant to high acuity visual tasks. Our findings demonstrate that there are possibly multiple mechanisms acting synergistically in the visual system of T. rugosa to enhance short wavelength sensitivity between 360 and 530 nm. While it is tempting to suggest that this is an adaptation to facilitate the detection of the blue tongues of conspecifics, additional experiments are necessary to determine its ecological relevance.

Summary statementColor vision and the distribution of photoreceptor subtypes in T. rugosa