title: Spd-2 Gene Duplication Suggests Cell-Type Specific Assembly Mechanisms of Pericentriolar Material

abstract:
Centrosomes are multi-protein complexes that function as the major microtubule organizing center (MTOC) for the cell. While centrosomes play tissue-specific MTOC functions, little is known about how particular centrosome proteins are regulated across cell types to achieve these different functions. To investigate this cell type-specific diversity, we searched for gene duplications of centrosome genes in the Drosophila lineage with the aim of identifying centrosome gene duplications where each copy evolved for specialized functions. Through in depth functional analysis of a Spd-2 gene duplication in the Willistoni group, we discovered differences in the regulation of PCM in somatic and male germline cells. The parental gene, Spd-2A, is expressed in somatic cells, where it can function to organize pericentriolar material (PCM) and the mitotic spindle in larval brain neuroblasts. Spd-2A is absent during male meiosis, and even when ectopically expressed in spermatocytes it fails to rescue PCM and spindle organization. In contrast, the new gene duplicate, Spd-2B, is expressed specifically in spermatocytes. During male meiosis, Spd-2B localizes to centrosomes, organizes PCM and spindles, and is sufficient for proper male fertility. Experiments using chimeric transgenes reveal that differences in the C-terminal tails of Spd-2A and Spd-2B are responsible for these functional changes. Thus, Spd-2A and Spd-2B have evolved complementary functions by specializing for distinct subsets of cells. Together, our results demonstrate that somatic cells and male germline cells have fundamentally different requirements for PCM, suggesting that PCM proteins such as Spd-2 is differentially regulated across cell types to satisfy distinct requirements.

HighlightsO_LISpd-2 gene duplication in the Willistoni group is rapidly evolving
C_LIO_LIParent gene Spd-2A is expressed in somatic cells, whereas the gene duplicate Spd-2B is expressed in spermatocytes
C_LIO_LISpd-2A organizes pericentriolar material during somatic cell mitosis
C_LIO_LISpd-2B is specialized for pericentriolar material organization during male meiosis
C_LI


title: The Ribb-osome: Ribbon boosts ribosomal protein gene expression to coordinate organ form and function

abstract: Cell growth is well defined for the late (post-embryonic) stages of development, but evidence for early (embryonic) cell growth during post-mitotic morphogenesis is quite limited. Here, we identify early cell growth as a key characteristic of tubulogenesis in the Drosophila embryonic salivary gland (SG). A BTB/POZ domain nuclear factor, Ribbon (Rib), mediates this early cell growth. Rib binds the transcription start site of nearly every SG-expressed ribosomal protein gene (RPG) and is required for full expression of all RPGs tested. Rib binding to RPG promoters in vitro is weak and not sequence-specific, suggesting that specificity is achieved through co-factor interactions. Consistent with this hypothesis, we demonstrate Ribs ability to physically interact with each of the three known contributors to RPG transcription. Surprisingly, Rib-dependent early cell growth in another tubular organ--the embryonic trachea--is not mediated by direct RPG transcription. These findings support a model of early cell growth sustained by transcriptional regulatory networks customized for organ form and function.

category: developmental biology


title: The number of Follicle Stem Cells in a Drosophila ovariole.

abstract: A paper by Reilein et al (2017) presented several fundamental new insights into the behavior of adult Follicle Stem Cells (FSCs) in the Drosophila ovary, including evidence that each ovariole hosts a large number of FSCs (14-16) maintained by population asymmetry (Reilein et al., 2017), rather than just two FSCs, dividing with largely individually asymmetric outcomes, as originally proposed (Margolis and Spradling, 1995; Nystul and Spradling, 2007). Fadiga and Nystul (2019) contest some of these conclusions on the basis of their repetition of a multicolor lineage strategy used by Reilein et al (2017) and repetition of earlier single-color lineage analysis. Here we outline a number of shortcomings in the execution and interpretation of those experiments that, in our opinion, undermine their conclusions. The central issue of general relevance concerns the importance of comprehensively analyzing all stem cell lineages, independent of any pre-conceptions, in order to identify all constituents and capture heterogeneous behaviors.


title: Evolutionarily divergent mTOR remodels the translatome to drive rapid wound closure and regeneration

abstract: An outstanding mystery in biology is why some species, such as the axolotl, can scarlessly heal and regenerate tissues while most mammals cannot. Here, we demonstrate that rapid activation of protein synthesis is a unique, and previously uncharacterized, feature of the injury response critical for limb regeneration in the axolotl (A. mexicanum). By applying polysome sequencing, we identify hundreds of transcripts, including antioxidants and ribosome components, which do not change in their overall mRNA abundance but are selectively activated at the level of translation from pre-existing mRNAs in response to injury. In contrast, we show that protein synthesis is not activated in response to digit amputation in the non-regenerative mouse. We further identify the mTORC1 pathway as a key upstream signal that mediates this regenerative translation response in the axolotl. Inhibition of this pathway is sufficient to suppress translation and axolotl regeneration. Surprisingly, although mTOR is highly evolutionarily conserved, we discover unappreciated expansions in mTOR protein sequence among urodele amphibians. By engineering an axolotl mTOR in human cells, we demonstrate that this change creates a hypersensitive kinase that may allow axolotls to maintain this pathway in a highly labile state primed for rapid activation. This may underlie metabolic differences and nutrient sensing between regenerative and non-regenerative species that are key to regeneration. Together, these findings highlight the unanticipated impact of the translatome on orchestrating the early steps of wound healing in highly regenerative species and provide a missing link in our understanding of vertebrate regenerative potential.


title: Fruit colour and range size interact to influence diversification

abstract:
AimDifferent fruit colours are associated with dispersal by different frugivores, largely based on colour vision type. Frugivore mobility affects overall range size for the plant being dispersed. Here we determine the interaction between different fruit colours, range sizes, and diversification rates by testing two hypotheses: That (1) fruit colours attractive to birds have larger range sizes due to their higher dispersal ability, and that (2) different frugivore disperser groups, bird or mammal, leads to different diversification rate at different range size, where intermediate range size leads to the highest diversification rate.

LocationGlobal.

Time periodContemporary (or present)

Major taxa studiedPalms (Arecaceae)

MethodsUsing model selection, we identified three groups of colours with similar diversification rate and likely disperser. Range sizes were estimated and categorized species as small, intermediate, or large-ranged. For model selection and to determine the relationship beween fruit color, range size and diversification rate we used Multi-State Speciation and Extinction (MuSSE) models.

ResultsSpecies with intermediate range size had the highest net diversification for all three fruit colour groups. Bird-dispersed palms more likely diversified at small than at large range size while mammal-dispersed palms more likely diversified at larger range size than small. Fruit colours associated with mammal dispersal had more large-ranged species than colours associated with bird dispersal.

Main conclusionsThe associated between intermediate range size and higher diversification rate indicates that spatial factors that affect diversification at small and large range sizes result in higher diversification at intermediate ranges. We find striking differences in diversification rate within each range size category between fruit color groups. This suggests that the relationship between diversification rate and range size depends on the specific frugivorous dispersers and their dispersal patterns. This study reveals how fruit traits alter dispersal patterns and how that, in turn, influences diversification.

category: ecology


title: Relative importance of region, seasonality and weed management practices effects on the functional structure of weed communities in French vineyards

abstract: Winegrowers have diversified their weed management practices over the last two decades changing the structure and the composition of weed communities. Complementary to taxonomic studies, trait-based approaches are promising ways for a better understanding of weed communities responses to environmental and agronomic filters. In the present study, the impact of climate, soil characteristics, seasons and weed management practices (chemical weeding, tillage and mowing) were assessed on weed communities in three French wine-growing regions (Champagne, Languedoc and Rhone valley). These agro-environmental gradients structuring weed communities according to their combination of traits were highlighted using multivariate analysis (RLQ). The impacts of these filters on Community Weighted Means (CWM) and the Community Weighted Variance (CWV) of weed communities were analysed using mixed and null modelling. Our results showed that spatio-temporal and weed management practices variables explained from 13% to 48% of the total variance of CWM (specific leaf area, maximum height, seed mass, flowering onset and duration and lateral spread). Region, seasonality and management practices explained 53%, 28% and 19% of CWM marginal variance, respectively. Weed management impacted CWM and CWV through two main gradients: (i) a soil disturbance gradient with high mechanical disturbance of soil in tilled plots and low mechanical disturbance in chemically weeded plots and (ii) a vegetation cover gradient with high vegetation abundance in mowed plots compared to more bare soils in tilled and chemically weeded plots. Chemically weeded communities showed trait values of ruderal strategies (low seed mass, small-stature) in Languedoc. Mowed plots were associated with more competitive strategies (higher seed mass, higher stature and lower SLA) in Languedoc. Tillage favoured communities with high seed mass that increases the viability of buried seeds and high lateral spread values associated to the ability to resprout after tillage in Languedoc and Champagne. This study demonstrated that trait-based approach can be successfully applied to perennial cropping systems such as vineyards, in order to understand community assembly to better guide weed management practices.


title: Warming in the land of the midnight sun: breeding birds may suffer greater heat stress at high- vs low-Arctic sites

abstract: Rising global temperatures are expected to increase reproductive costs for wildlife as greater thermoregulatory demands interfere with essential breeding activities such as parental care. However, predicting the temperature threshold where reproductive performance is negatively impacted remains a significant hurdle. Using a novel thermoregulatory polygon approach, we predicted the threshold temperature at which an Arctic songbird-the snow bunting (Plectrophenax nivalis)-would need to reduce activity and perform below the 4-times basal metabolic rate (BMR) required to sustain nestling provisioning to avoid overheating. We then compared this threshold to operative temperatures recorded at high (82{degrees}N) and low (64{degrees}N) Arctic sites to estimate how heat constraints translate into site-specific impacts on sustained activity level. We predict buntings would become behaviourally constrained at operative temperatures above 11.7{degrees}C, whereupon they must reduce provisioning rates to maintain thermal balance. Low Arctic sites had larger fluctuations in solar radiation, producing consistent daily periods when operative temperatures exceeded 11.7{degrees}C. However, high-latitude birds faced entire, consecutive days where parents would not be able to sustain required provisioning rates. These data indicate that Arctic warming is likely already disrupting the breeding performance of cold-specialist birds, but also suggests counterintuitive and severe negative impacts of warming at high-latitude breeding locations.


title: Supervised continuous land cover change detection in a critically endangered shrubland ecosystem

abstract: Existing efforts to continuously land cover change using satellite image time-series have mostly focused on forested ecosystems in the tropics and northern hemisphere. The notable difference in reflectance that occurs following deforestation allows land cover change to be detected with relative accuracy. Less progress has been made in detecting change in low productivity, disturbanceprone vegetation such as grasslands and shrublands, where natural dynamics can be difficult to distinguish from habitat loss. Renosterveld is a hyperdiverse, critically endangered shrubland ecosystem in South Africa with less than 5-10% of its original extent remaining in small, highly fragmented patches. I demonstrate that direct classification of satellite image time series using neural networks can accurately detect the transformation of Renosterveld within a few days of its occurrence, and that trained models are suitable for operational continuous monitoring. A dataset of precisely dated vegetation change events between 2016 and 2021 was obtained from daily, high resolution Planet labs satellite data. This dataset was then used to train and evaluate 1D convolutional neural networks and Transformers to continuously detect land cover change events in multivariate time-series of vegetation activity of Sentinel 2 satellite data as it becomes available. The best model correctly identified 89% of land cover change events at the pixel-level, achieving a f-score of 0.93, a 79% improvement over the f-score of 0.52 achieved using a method designed for forested ecosystems based on trend analysis. Models have been deployed to operational use and are producing updated detections of habitat loss every 10 days. There is great potential for supervised approaches to continuous monitoring of habitat loss in ecosystems with complex natural dynamics. A key limiting step is the development of accurately dated datasets of land cover change events with which to train machine learning classifiers.


title: Continuous land cover change detection in a critically endangered shrubland ecosystem using neural networks


title: Comparative analysis of zooplankton diversity in freshwaters: What can we gain from metagenomic analysis?

abstract: Molecular genetic approaches applied to environmental DNA have great potential for biodiversity research and ecosystem monitoring. A metagenome contains genetic information from all organisms captured in an environmental sample. It has been primarily used to study bacteria and archaea, but promising reports focusing on metazoan diversity are emerging. However, methodological uncertainties remain, and studies are required to validate the power and the limitations of such an approach when applied to macro-eukaryotes. Here, we analyzed water sample metagenomes to estimate zooplankton diversity in 22 freshwater lakes across Eastern Canada. We tested the coherence of data based on morphologically identified zooplankton taxa and molecular genetic data derived from shotgun sequencing of environmental DNA collected at the same time. RV coefficients showed a significant correlation between the relative abundance of zooplankton families derived from small subunit rRNA genes extracted from the metagenomes and morphologically identified zooplankton. However, differences in congruence with morphological counts were detected when varied bioinformatic approaches were applied to presence-absence data. This study presents one of the first diversity assessments of a group of aquatic metazoans using metagenomes and validates the coherence of the community composition derived from genetic and classical species surveys. Overall, our results suggest that metagenomics has the potential to be further developed to describe metazoan biodiversity in aquatic ecosystems, and to advance this area we provide key recommendations for workflow improvement.


title: A spatial fingerprint of land-water linkage of biodiversity uncovered by remote sensing and environmental DNA

abstract: Aquatic and terrestrial ecosystems are tightly connected via spatial flows of organisms and resources. Such land-water linkages integrate biodiversity across ecosystems and suggest a spatial association of aquatic and terrestrial biodiversity. However, knowledge about this spatial extent is limited. By combining satellite remote sensing (RS) and environmental DNA (eDNA) extraction from river water across a 740-km2 mountainous catchment, we identify a characteristic spatial land-water fingerprint. Specifically, we find a spatial association of riverine eDNA diversity with RS spectral diversity of terrestrial ecosystems upstream, peaking at a 400 m distance yet still detectable up to a 3.3 km radius. Our findings testify that biodiversity patterns in rivers can be linked to the functional diversity of surrounding terrestrial ecosystems and provide a dominant scale at which these linkages are strongest. Such spatially explicit information is necessary for a functional understanding of land-water linkages and provides a reference scale for adequate conservation and landscape management decisions.


title: A decade of stability for wMel Wolbachia in natural Aedes aegypti populations

abstract:
Mosquitoes carrying Wolbachia endosymbionts are being released in many countries for arbovirus control. The wMel strain of Wolbachia blocks Aedes-borne virus transmission and can spread throughout mosquito populations by inducing cytoplasmic incompatibility. Aedes aegypti mosquitoes carrying wMel were first released into the field in Cairns, Australia, over a decade ago, and with wider releases have resulted in the near elimination of local dengue transmission. The long-term stability of Wolbachia effects is critical for ongoing disease suppression, requiring tracking of phenotypic and genomic changes in Wolbachia infections following releases. We used a combination of field surveys, phenotypic assessments, and Wolbachia genome sequencing to show that wMel has remained stable in its effects for up to a decade in Australian Ae. aegypti populations. Phenotypic comparisons of wMel-infected and uninfected mosquitoes from near-field and long-term laboratory populations suggest limited changes in the effects of wMel on mosquito fitness. Treating mosquitoes with antibiotics used to cure the wMel infection had limited effects on fitness in the next generation, supporting the use of tetracycline for generating uninfected mosquitoes without off-target effects. wMel has a temporally stable within-host density and continues to induce complete cytoplasmic incompatibility. A comparison of wMel genomes from pre-release (2010) and nine years post-release (2020) populations show few genomic differences and little divergence between release locations, consistent with the lack of phenotypic changes. These results indicate that releases of Wolbachia-infected mosquitoes for population replacement are likely to be effective for many years, but ongoing monitoring remains important to track potential evolutionary changes.

Author summaryWolbachia are endosymbionts that can block the transmission of arboviruses by mosquitoes. Aedes aegypti mosquitoes carrying the wMel strain of Wolbachia have been released in  population replacement interventions, which aim to establish wMel in mosquito populations, thereby reducing their ability to spread disease. Wolbachia population replacement programs began only a decade ago, raising uncertainty about their long-term effectiveness. Here we provide a comprehensive assessment of the long-term stability of wMel from the very first Wolbachia population replacement release. We show that there is no evidence for changes in the phenotypic effects of wMel in mosquitoes, and confirm that the wMel genome has changed very little in the decade since field releases began. wMel remains at high levels within mosquitoes, suggesting that its ability to block virus transmission has been retained. Our data provides confidence that Wolbachia population replacement releases will provide ongoing protection against arbovirus transmission.

category: evolutionary biology


title: H3K9me1/2 methylation limits the lifespan of C. elegans

abstract: Histone methylation plays crucial roles in the development, gene regulation and maintenance of stem cell pluripotency in mammals. Recent work shows that histone methylation is associated with aging, yet the underlying mechanism remains unclear. In this work, we identified a class of histone 3 lysine 9 mono-/dimethyltransferase genes (met-2, set-6, set-19, set-20, set-21, set-32 and set-33), mutations in which induce synergistic lifespan extension in the long-lived DAF-2 (IGF-1 receptor) mutant in C. elegans. These histone methyltransferase plus daf-2 double mutants not only exhibited an average lifespan nearly three times that of wild-type animals and a maximal lifespan of approximately 100 days, but also significantly increased resistance to oxidative and heat stress. Synergistic lifespan extension depends on the transcription factor DAF-16 (FOXO). mRNA-seq experiments revealed that the mRNA levels of class I DAF-16 target genes, which are activated by DAF-16, were further elevated in the double mutants. Among these genes, F35E8.7, nhr-62, sod-3, asm-2 and Y39G8B.7 are required for the lifespan extension of the daf-2;set-21 double mutant. In addition, treating daf-2 animals with the H3K9me1/2 methyltransferase G9a inhibitor also extends lifespan and increases stress resistance. Therefore, investigation of DAF-2 and H3K9me1/2 methyltransferase deficiency-mediated synergistic longevity will contribute to a better understanding of the molecular mechanisms of aging and therapeutic applications.

category: genetics


title: Formation and recycling of an active epigenetic mark mediated by cell cycle-specific RNAs

abstract: The mechanisms by which epigenetic modifications are established in gene regulatory regions of active genes remain poorly understood. The data presented show that the establishment and recycling of a major epigenetic mark, the acetylated form of the replacement histone H2A.Z, is regulated by cell cycle-specific long noncoding RNAs encoded in regions adjacent to the promoters of active genes. These transcripts, termed SPEARs (S Phase EArly RNAs), are induced in early S phase: their expression precedes that of the downstream genes on which they exert their regulatory action. SPEARs drive the modification and deposition of the acetylated form of histone H2A.Z by bringing together the replacement histone and the histone acetyl transferase TIP60. This widespread bimodal pathway constitutes a novel RNA-mediated mechanism for the establishment of epigenetic marks and cell-specific epigenetic profiles, thereby providing a unifying explanation for the accuracy and persistence of epigenetic marks on chromatin.


title: Regulation of defective mitochondrial DNA accumulation and transmission in C. elegans by the programmed cell death and aging pathways

abstract: The heteroplasmic state of eukaryotic cells allows for cryptic accumulation of defective mitochondrial genomes (mtDNA). "Purifying selection" mechanisms operate to remove such dysfunctional mtDNAs. We found that activators of programmed cell death (PCD), including the CED-3 and CSP-1 caspases, the BH3-only protein CED-13, and PCD corpse engulfment factors, are required in C. elegans to attenuate germline abundance of a 3.1 kb mtDNA deletion mutation, uaDf5, which is normally stably maintained in heteroplasmy with wildtype mtDNA. In contrast, removal of CED-4/Apaf1 or a mutation in the CED-4-interacting prodomain of CED-3, do not increase accumulation of the defective mtDNA, suggesting induction of a non-canonical germline PCD mechanism or non-apoptotic action of the CED-13/caspase axis. We also found that the abundance of germline mtDNAuaDf5 reproducibly increases with age of the mothers. This effect is transmitted to the offspring of mothers, with only partial intergenerational removal of the defective mtDNA. In mutants with elevated mtDNAuaDf5 levels, this removal is enhanced in older mothers, suggesting an age-dependent mechanism of mtDNA quality control. Indeed, we found that both steady-state and age-dependent accumulation rates of uaDf5 are markedly decreased in long-lived, and increased in short-lived, mutants. These findings reveal that regulators of both PCD and the aging program are required for germline mtDNA quality control and its intergenerational transmission.


title: Benchmarking phasing software with a whole-genome sequenced cattle pedigree

abstract:
BackgroundAccurate haplotype reconstruction is required in many applications in quantitative and population genomics. Different phasing methods are available but their accuracy must be evaluated for samples with different properties (population structure, marker density, etc.). We herein took advantage of whole-genome sequence data available for a Holstein cattle pedigree containing 264 individuals, including 98 trios, to evaluate several population-based phasing methods. This data represents a typical example of a livestock population, with low effective population size, high levels of relatedness and long-range linkage disequilibrium.

ResultsAfter stringent filtering of our sequence data, we evaluated several population-based phasing programs including one or more versions of AlphaPhase, ShapeIT, Beagle, Eagle and FImpute. To that end we used 98 individuals having both parents sequenced for validation. Their haplotypes reconstructed based on Mendelian segregation rules were considered the gold standard to assess the performance of population-based methods in two scenarios. In the first one, only these 98 individuals were phased, while in the second one, all the 264 sequenced individuals were phased simultaneously, ignoring the pedigree relationships. We assessed phasing accuracy based on switch error counts (SEC) and rates (SER), lengths of correctly phased haplotypes and pairwise SNP phasing accuracies (the probability that a pair of SNPs is correctly phased as a function of their distance). For most evaluated metrics or scenarios, the best software was either ShapeIT4.1 or Beagle5.2, both methods resulting in particularly high phasing accuracies. For instance, ShapeIT4.1 achieved a median SEC of 50 per individual and a mean haplotype block length of 24.1 Mb in the second scenario. These statistics are remarkable since the methods were evaluated with a map of 8,400,000 SNPs, and this corresponds to only one switch error every 40,000 phased informative markers. When more relatives were included in the data, FImpute3.0 reconstructed extremely long segments without errors.

ConclusionsWe report extremely high phasing accuracies in a typical livestock sample of 100 sequenced individuals. ShapeIT4.1 and Beagle5.2 proved to be the most accurate, particularly for phasing long segments. Nevertheless, most tools achieved high accuracy at short distances and would be suitable for applications requiring only local haplotypes.

category: genomics


title: Unravelling complex molecular mechanisms in pine with genome-wide association analysis and gene co-expression networks

abstract: The authors have withdrawn this manuscript because they decided to change the phenotypic characteristics to be evaluated, considering the more significant contribution to the field. Therefore, the authors do not want this work to be cited as a reference for the project. If you have any questions, please contact the corresponding author.


title: Electro-mechanical transfection for non-viral primary immune cell engineering

abstract:
Non-viral approaches to transfection have emerged a viable option for gene transfer. Electro-mechanical transfection involving use of electric fields coupled with high fluid flow rates is a scalable strategy for cell therapy development and manufacturing. Unlike purely electric field-based or mechanical-based delivery methods, the combined effects result in delivery of genetic material at high efficiencies and low toxicity. This study focuses on delivery of reporter mRNA to show electro-mechanical transfection can be used successfully in human T cells. Rapid optimization of delivery to T cells was observed with efficiency over 90% and viability over 80%. Confirmation of optimized electro-mechanical transfection parameters was assessed in multiple use cases including a 50-fold scale up demonstration. Transcriptome and ontology analysis show that delivery, via electro-mechanical transfection, does not result in gene dysregulation. This study demonstrates that non-viral electro-mechanical transfection is an efficient and scalable method for cell and gene therapy engineering and development.

One Sentence SummaryThis study demonstrates that non-viral electro-mechanical transfection is an efficient and scalable method for development of engineered cellular therapies.

category: bioengineering


title: High spatial resolution analysis using indentation mapping differentiates biomechanical properties of normal vs. degenerated mouse articular cartilage

abstract: Characterizing the biomechanical properties of articular cartilage is crucial to understanding processes of tissue homeostasis vs. degeneration. In mouse models, however, limitations are imposed by their small joint size and thin cartilage surfaces. Here we present a 3D automated surface mapping system and methodology that allows for mechanical characterization of mouse cartilage with high spatial resolution. We performed repeated indentation mappings, followed by cartilage thickness measurement via needle probing, at 31 predefined positions distributed over the medial and lateral femoral condyles of healthy mice. High-resolution 3D x-ray microscopy (XRM) imaging was used to validate tissue thickness measurements. The automated indentation mapping was reproducible, and needle probing yielded cartilage thicknesses comparable to XRM imaging. When comparing healthy vs. degenerated cartilage, topographical variations in biomechanics were identified, with altered thickness and stiffness (instantaneous modulus) across condyles and within anteroposterior sub-regions. This quantitative technique comprehensively characterized cartilage function in mice femoral condyle cartilage. Hence, it has the potential to improve our understanding of tissue structure-function interplay in mouse models of repair and disease.


title: Categorization of prophage genes in Bacillus subtilis 168 and assessing their relative importance through RNA-seq gene expression analysis

abstract: Bacteriophage evolves to control the population of fast-growing bacterial cells, without which explosion in bacterial population may induce unimaginable harm to diverse ecosystems. But, bacteriophage also "hide" in bacterial genomes when nutritional and environmental circumstances are unfavourable. This involves the integration of phage genome into the host genome at appropriate genomic loci in a process known as lysogeny. This work sought to delineate the prophages present in the annotated genome of Bacillus subtilis 168, and assess their relative importance through RNA-seq expression analysis. Firstly, examination of the annotated genome of the model Gram-positive bacterium revealed five distinct prophage regions: SPBeta, prophage 6, PBSX, prophage 3 region, and prophage 1 region. All prophage regions contain host genes, which suggests that host transposase activity have swapped in host genes for phage genes in the prophage genome. Given the significant number of phage genes that have been swapped into each of the prophage genome, all prophage regions are deemed to be defective. BLAST analysis further highlighted that many of the prophages in B. subtilis are extinct given that they do not have ancestral or daughter brethren. However, RNA-seq transcriptome analysis of B. subtilis turned out an interesting paradox indicative of the important role that host transposase have in swapping in host promoters for prophage genes. Specifically, a significant number of prophage genes are highly expressed, which is implausible given that phage genes should be transcriptionally silent. The result and phenomenon further suggests the relative facile nature in which host promoters could be swapped in for phage genes, which is indicative of presence of genomic motifs in prophage genome recognizable by host transposase. Existence of such sequence motifs is thus indicative of possible co-evolution of transposase and phages where transposases were originally a part of the phage genome, which latter "jumped out" into the host genome to aid the swapping in of host genes into the prophage genome for augmenting prophage genetic repertoire in the face of changing environmental conditions. Overall, it is not uncommon for bacterial species to harbour multiple prophages. But, lysogeny may not be a viable option for long-term preservation of prophage genetic repertoire given that host transposase would inevitable swap in host genes at random locations in the prophage genome.

category: bioinformatics


title: Chronumental: time tree estimation from very large phylogenies

abstract: Phylogenetic trees are an important tool for interpreting sequenced genomes, and their interrelationships. Estimating the date associated with each node of such a phylogeny creates a "time tree", which can be especially useful for visualising and analysing evolution of organisms such as viruses. Several tools have been developed for time-tree estimation, but the sequencing explosion in response to the SARS-CoV-2 pandemic has created phylogenies so large as to prevent the application of these previous approaches to full datasets. Here we introduce Chronumental, a tool that can rapidly infer time trees from phylogenies featuring large numbers of nodes. Chronumental uses stochastic gradient descent to identify lengths of time for tree branches which maximise the evidence lower bound under a probabilistic model, implemented in a framework which can be compiled into XLA for rapid computation. We show that Chronumental scales to phylogenies featuring millions of nodes, with chronological predictions made in minutes, and is able to accurately predict the dates of nodes for which it is not provided with metadata.


title: PepSeA: Peptide Sequence Alignment and Visualization Tools to Enable Lead Optimization

abstract: Therapeutic peptides offer potential advantages over small molecules in terms of selectivity, affinity, and their ability to target "undruggable" proteins that are associated with a wide range of pathologies. Despite their importance, there are currently no adequate molecular design capabilities that inform medicinal chemistry decisions on peptide programs. More specifically, SAR (Structure-Activity Relationship) analysis and visualization of linear, cyclic, and cross-linked peptides containing non-natural motifs, which are widely used in drug discovery. To bridge this gap, we developed PepSeA (Peptide Sequence Alignment and Visualization), an open-source, freely available package of sequence-based tools (https://github.com/Merck/PepSeA). PepSeA enables multi-sequence alignment of non-natural amino acids and enhanced HELM (Hierarchical Editing Language for Macromolecules) visualization. Via stepwise SAR analysis of a ChEMBL peptide dataset, we demonstrate PepSeAs power to accelerate decision making in lead optimization campaigns in pharmaceutical settings. PepSeA represents an initial attempt to expand cheminformatics capabilities for therapeutic peptides and to enable rapid and more efficient design-make-test cycles.


title: MPDB: a unified multi-domain protein structure database integrating structural analogue detection

abstract: With the development of protein structure prediction methods and biological experimental determination techniques, the structure of single-domain proteins can be relatively easier to be modeled or experimentally solved. However, more than 80% of eukaryotic proteins and 67% of prokaryotic proteins contain multiple domains. Constructing a unified multi-domain protein structure database will promote the research of multi-domain proteins, especially in the modeling of multi-domain protein structures. In this work, we develop a unified multi-domain protein structure database (MPDB). Based on MPDB, we also develop a server with two functional modules: (1) the culling module, which filters the whole MPDB according to input criteria; (2) the detection module, which identifies structural analogues of the full-chain according to the structural similarity between input domain models and the protein in MPDB. The module can discover the potential analogue structures, which will contribute to high-quality multi-domain protein structure modeling.


title: Spatial Probabilistic Mapping of Metabolite Ensembles in Mass Spectrometry Imaging

abstract: Mass spectrometry imaging (MSI) vows to enable simultaneous spatially-resolved investigation of hundreds of metabolites in tissue sections, but it still relies on poorly defined ion images for data interpretation. Here, we outline moleculaR, a computational framework (https://github.com/CeMOS-Mannheim/moleculaR) that introduces probabilistic mapping and point-for-point statistical testing of metabolites in tissue. It enables collective molecular projections and consequently spatially-resolved investigation of ion milieus, lipid pathways or user-defined biomolecular ensembles within the same image.


title: Structure Insight into Photosystem I Octamer from Cyanobacteria

abstract: Diversity of photosystem oligomers is essential to understand how photosynthetic organisms adopted to light conditions. Given by the structural and physiological significance, the assemblies of PSI supercomplex is of great interest in both chloroplast and cyanobacteria recently. In this study, two novel photosystem I supercomplexes were isolated for the first time from the low light incubated culture of filamentous cyanobacterium Anabaena sp. PCC 7120. These complexes were defined as PSI hexamers and octamers through biochemical and biophysical characterization. Their 77K emission spectra indicated that the red forms of chlorophylls seemed not to be affected during oligomerization. By cryo-EM single particle analysis, a near-atomic (7.0 [A]) resolution structure of PSI octamer was resolved, and the molecular assemblies of stable PSI octamer was revealed.

category: biophysics


title: Patient-derived zebrafish xenograft models reveal ferroptosis as a fatal and druggable weakness in metastatic uveal melanoma

abstract: Uveal melanoma (UM) is the most common intraocular melanoma, derived from transformed melanocytes of the uvea. Although treatment of primary UM is usually successful, there is a high risk (up to 50%) of liver metastasis with negligible long-term survival. There are currently no reproducible patient-derived animal models that faithfully recapitulate the latter stages of metastatic dissemination of UM, hindering the discovery of curative treatments. To overcome this problem and to accelerate the development of new metastatic UM treatments, we developed a patient-derived zebrafish xenograft (zf-PDX) model, using spheroid cultures generated from metastatic and primary UM tissues. Engrafted UM cells derived from these spheroid cultures give rise to metastatic lesions and recapitulate the molecular features of UMs and their potential drug sensitivity. Importantly, harnessing this versatile model, we reveal a high sensitivity of circulating UM cells to ferroptosis induction in vivo by Erastin and RSL3. Our findings are further corroborated by supportive analysis of patient data implicating ferroptosis as a new, and druggable, target for the treatment of metastatic UM patients, specifically in those with BAP1 loss in the tumor.

category: cancer biology


title: Sequence dependencies and mutation rates of localized mutational processes in cancer

abstract:
BackgroundCancer mutations accumulate through replication errors and DNA damage coupled with incomplete repair. Individual mutational processes often show strong sequence and regional preferences. As a result, some sequence contexts mutate at much higher rates than others. Mutational hotspots, with recurrent mutations across cancer samples, represent genomic positions with elevated mutation rates, often caused by highly localized mutational processes.

ResultsWe analyze the mutation rates of all 11-mer genomic sequence contexts using the PCAWG set of 2,583 pan-cancer whole genomes. We further associate individual mutations and contexts to mutational signatures and estimate their relative mutation rates. We show that hotspots generally identify highly mutable sequence contexts. Using these, we show that some mutational signatures are enriched in hotspot sequence contexts, corresponding to well-defined sequence preferences for the underlying localized mutational processes. This includes signature 17b (of unknown etiology) and signatures 62 (POLE), 7a (UV), and 72 (linked to lymphomas). In some cases, the mutation rate increases further when focusing on certain genomic regions, such as signature 62 in poised promoters, where the mutation is increased several thousand folds over the overall data set average.

ConclusionWe summarize our findings in a catalog of localized mutational processes, their sequence preferences, and their estimated mutation rates.


title: Qualitative and quantitative top-down proteomics of human colorectal cancer cell lines identified 23000 proteoforms and revealed drastic proteoform-level differences between metastatic and non-metastatic cancer cells

abstract:
Understanding cancer metastasis at the proteoform level is crucial for discovering new protein biomarkers for cancer diagnosis and drug development. Proteins are the primary effectors of function in biology and proteoforms from the same gene can have drastically different biological functions. Here, we present the first qualitative and quantitative top-down proteomics (TDP) study of a pair of isogenic human metastatic and non-metastatic colorectal cancer (CRC) cell lines (SW480 and SW620). This study pursues a global view of human CRC proteome before and after metastasis in a proteoform specific manner. We identified 23,319 proteoforms of 2,297 genes from the CRC cell lines using capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS), representing nearly one order of magnitude improvement in the number of proteoform identifications from human cell lines compared to literature data. We identified 111 proteoforms containing single amino acid variants (SAAVs) using a proteogenomic approach and revealed drastic differences between the metastatic and non-metastatic cell lines regarding SAAVs profiles. Quantitative TDP analysis unveiled statistically significant differences in proteoform abundance between the SW480 and SW620 cell lines on a proteome scale for the first time. Ingenuity Pathway Analysis (IPA) disclosed that many differentially expressed genes at the proteoform level had diversified functions and were closely related to cancer. Our study represents a milestone in TDP towards the definition of human proteome in a proteoform specific manner, which will transform basic and translational biomedical research.

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title: Computational analysis reveals similarities and differences between SCLC subtypes

abstract: Small cell lung cancer (SCLC) is a neuroendocrine malignancy with dismal survival rates. Previous studies have revealed inter and intra tumoral heterogeneity of SCLC driven by neuroendocrine differentiation and multiple gene expression signatures have been proposed to classify the distinct SCLC molecular subtypes However, few questions remain unanswered: a) how many SCLC subtypes exist? b) how similar or different are these subtypes?, c) which gene list(s) can be used to identify those specific subtypes? Here, we show that irrespective of the three gene sets (33 genes, 50 genes, 105 genes) proposed in different studies to classify SCLC into different subtypes, the markers of phenotypic heterogeneity in SCLC form a "teams" like pattern of co-expressed modules. Moreover, the 105 geneset could classify SCLC cell lines into five clusters, three of which can be distinctly mapped to the SCLC-A, SCLC-N and SCLC-Y subtypes. Intriguingly, we noticed a high degree of similarity in the transcriptional landscape of two non-neuroendocrine subtypes: SCLC-Y and SCLC-I*, as well as in their enrichment of EMT. Thus, our analysis elucidates the landscape of phenotypic heterogeneity enabling diverse SCLC subtypes.


title: Specific ATPases drive compartmentalized glycogen utilization in rat skeletal muscle

abstract: Glycogen is a key energy substrate in excitable tissue and especially in skeletal muscle fibers it contributes with a substantial, but also local energy production. A heterogenic subcellular distribution of three distinct glycogen pools in skeletal muscle is proved by transmission electron microscopy (TEM), which is thought to represent the requirements for local energy stores at the subcellular level. Here, we show that the three main energy-consuming ATPases in skeletal muscles (Ca2+-, Na+,K+-, and myosin ATPases) utilize different local pools of glycogen. These results clearly demonstrate compartmentalized glycogen metabolism and emphasize that spatially distinct pools of glycogen particles act as energy substrate for separated energy requiring processes, suggesting a new paradigm for understanding glycogen metabolism in working muscles, muscle fatigue and metabolic disorders.

category: physiology


title: European Vintage tomatoes galore: a result of farmers combinatorial assorting/swapping of a few diversity rich loci

abstract:
A comprehensive collection of 1,254 tomato accessions corresponding to European heirlooms and landraces, together with modern varieties, early domesticates and wild relatives, were analyzed by genotyping by sequencing. A continuous genetic gradient between the vintage and modern varieties was observed. European vintage tomatoes displayed very low genetic diversity, with only 298 loci out of 64,943 variants being polymorphic at the 95% threshold. European vintage tomatoes could be classified in several genetic groups. Two main clusters consisting of Spanish and Italian accessions showed a higher genetic diversity than the rest varieties, suggesting that these regions might be independent secondary centers of diversity and with a different history. Other varieties seem to be the result of a more recent complex pattern of migrations and hybridizations among the European regions. Several polymorphic loci were associated in a GWAS with fruit morphological traits in the European vintage collection, and the corresponding alleles were found to contribute to the distinctive phenotypic characteristic of the genetic varietal groups. The few highly polymorphic loci associated with morphological traits in an otherwise diversity-poor genome suggests a history of balancing selection, in which tomato farmers maintained the morphological variation by applying a high selective pressure within different varietal types.

HighlightThe high phenotypic diversity observed among European vintage varieties was created by traditional farmers by combining very few polymorphic loci subjected to balancing selection.

category: plant biology


title: Whole-genome sequence and methylome profiling of the almond (Prunus dulcis  D.A.Webb) cultivar Nonpareil

abstract: Almond (Prunus dulcis [Mill.] D.A. Webb) is an economically important, specialty nut crop grown almost exclusively in the United States. Breeding and improvement efforts worldwide have led to the development of key, productive cultivars, including  Nonpareil, which is the most widely grown almond cultivar. Thus far, genomic resources for this species have been limited, and a whole-genome assembly for  Nonpareil is not currently available despite its economic importance and use in almond breeding worldwide. We generated a 615.89X coverage genome sequence using Illumina, PacBio, and optical mapping technologies. Gene prediction revealed 27,487 genes using MinION Oxford nanopore and Illumina RNA sequencing, and genome annotation found that 68% of predicted models are associated with at least one biological function. Further, epigenetic signatures of almond, namely DNA cytosine methylation, have been implicated in a variety of phenotypes including self-compatibility, bud dormancy, and development of non-infectious bud failure. In addition to the genome sequence and annotation, this report also provides the complete methylome of several key almond tissues, including leaf, flower, endocarp, mesocarp, fruit skin, and seed coat. Comparisons between methylation profiles in these tissues revealed differences in genome-wide weighted percent methylation and chromosome-level methylation enrichment. The raw sequencing data are available on NCBI Sequence Read Archive, and the complete genome sequence and annotation files are available on NCBI Genbank. All data can be used without restriction.


title: Implementation of a novel optogenetic tool in mammalian cells based on a split T7 RNA polymerase

abstract: Optogenetic tools are widely used to control gene expression dynamics both in prokaryotic and eukaryotic cells. These tools are used in a variety of biological applications from stem cell differentiation to metabolic engineering. Despite some tools already available in bacteria, no light-inducible system currently exists to orthogonally control gene expression in mammalian cells. Such a tool would be particularly important in synthetic biology, where orthogonality is advantageous to achieve robust activation of synthetic networks. Here we implement, characterize and optimize a new orthogonal optogenetic tool in mammalian cells based on a previously published system in bacteria called Opto-T7RNAPs. The tool consists of a split T7 RNA polymerase coupled with the blue light-inducible magnets system (mammalian OptoT7 - mOptoT7). In our study we exploited the T7 polymerases viral origins to tune our systems expression level, reaching up to 20-fold change activation over the dark control. mOptoT7 is used here to generate mRNA for protein expression, shRNA for protein inhibition and Pepper aptamer for RNA visualization. Moreover, we show that mOptoT7 can mitigate gene expression burden when compared to other optogenetic constructs. These properties make mOptoT7 a new powerful tool to use when orthogonality and viral-like RNA species are desired in both synthetic biology and basic science applications.

category: synthetic biology


title: Phylogeography of Lanius senator reveals conflicts between alpha taxonomy, subspecies ranges and genetics.

abstract: Implementing the effort in understanding biogeographic distribution patterns and taxonomic limits within animal groups is crucial for addressing several challenges of modern zoology. Although avian phylogeography has been deeply investigated within Western Palearctic, several families, such as shrikes, still display complicated or neglected biogeographic patterns both between and within species, thus requiring further investigations. The Woodchat Shrike (Lanius senator) is a long-distance migratory species that exhibits three morphologically well-recognizable subspecies, whose boundaries have never been molecularly investigated. Here, we aimed to define the phylogeographic structure of Lanius senator throughout its breeding range and assess the genetic coherence with the phenotypically described subspecies. We assembled a collection of 34 samples mainly from breeding populations of each subspecies and analyzed them at four mtDNA and two nuDNA markers. We did not find a clear phylogenetic structure with nuclear Ornithine Decarboxylase (ODC) and myoglobin intron 2 (MYO), while all the four mtDNA loci (i.e., ND2, COI, cytb and Control Region) highlighted two main haplogroups, one including both the nominate subspecies L. s. senator and L. s. badius and the second consistent with L. s. niloticus only from the easternmost part of the range. Surprisingly, individuals phenotypically assigned to L. s. niloticus from Israel were genetically assigned to the senator/badius haplogroup. Moreover, genetic distances showed intermediate values between inter-intraspecies diversity usually found in Passerines. We estimated a divergence time among the two haplogroups around 800 kya (549 - 1.259 kya HPD). Our findings showed a mismatch in subspecies assignment using morphology and genetic information and a marked differentiation between the eastern L.s. niloticus and all the other L. senator populations.

category: zoology


title: Cognitive and affective Theory of Mind double dissociation after parietal and temporal lobe tumors

abstract: Extensive neuroimaging literature suggests that understanding others thoughts and emotions engages a wide network encompassing parietal, temporal and medial frontal brain areas. However, the causal role played by these regions in social inferential abilities is still unclear. Moreover very little is known about ToM deficits in brain tumours and whether potential anatomical substrates are comparable to those identified in fMRI literature. This study evaluated the performance of 105 tumour patients, before and immediately after brain surgery, on a cartoon-based non-verbal task evaluating Cognitive (Intention Attribution) and Affective (Emotion Attribution) ToM, as well as a non-social control condition (Causal Inference). Across multiple analyses, we found converging evidence of a double dissociation between patients with right superior parietal damage, selectively impaired in Intention Attribution, and those with right antero-medial temporal lesion, exhibiting deficits only in Emotion attribution. Instead, patients with damage to the frontal cortex were impaired in all kinds of inferential processes, including those from the non-social control conditions. Overall, our data provides novel reliable causal evidence of segregation between different aspects of the ToM network from both the cognitive and also the anatomical point of view.

category: neuroscience


title: A miniature kinematic coupling device for mouse head fixation

abstract:
Head-fixation is a common technique in the preparation of subjects for neuroscience experiments. Accurate alignment, stability, and repeatability during fixation provide experimental consistency, thus enabling the subject to return to the same position over time to provide meaningful data. Head restraint systems inspired by kinematic clamps have been developed to allow micron scale repositioning across imaging epochs in rats. Here we report the development of a light-weight, implantable kinematic coupling (clamp) system that is wearable by mice, and enables repeated positioning to submicron accuracy across imaging epochs. This system uses a stainless steel headplate and a Maxwell-style three-groove kinematic mounting system with magnetic force clamping load. Spheres on the dorsal surface of the headplate provide contact points for vee-groove kinematic features machined into a tabletop mount. Evaluation of the clamp using multiphoton microscopy revealed submicron precision in registration accuracy and stability, allowing cellular resolution calcium imaging in awake, behaving mice. These results indicate that miniaturized implantable kinematic clamps for mice could be valuable for future experiments which require repositioning of subjects across time and different instruments.

HighlightsO_LIDevelopment of a kinematic clamp for mice for precise repositioning in chronic studies.
C_LIO_LIHeadplate and clamp provide stability for cellular resolution imaging during behavior.
C_LIO_LIRuby contact features enable submicron registration repeatability.
C_LI


title: Single nuclear transcriptional signatures of dysfunctional brain vascular homeostasis in Alzheimer's disease

abstract: Brain perfusion and normal blood brain barrier integrity are reduced early in Alzheimers disease (AD). We performed single nucleus RNA sequencing of vascular cells isolated from AD and control brains to characterise pathological transcriptional signatures. We found that endothelial cells (EC) are enriched for expression of genes associated with susceptibility to AD. EC transcriptional signatures identified mechanisms for impaired {beta}-amyloid clearance. Evidence for immune activation was found with upregulation of interferon signalling genes in EC and in pericytes (PC). Transcriptional signatures suggested dysregulation of vascular homeostasis and angiogenesis with upregulation of pro-angiogenic signals (HIF1A) and metabolism in EC, but downregulation of homeostatic growth factor pathways (VEGF, EGF, insulin) in EC and PC and of extracellular matrix genes in fibroblasts (FB). Our genomic dissection of vascular cell risk gene enrichment suggests a potentially causal role for EC and defines transcriptional signatures associated with microvascular dysfunction in AD.


title: FiberNeat: unsupervised streamline clustering and white matter tract filtering in latent space

abstract: Whole-brain tractograms generated from diffusion MRI digitally represent the white matter structure of the brain and are composed of millions of streamlines. Such tractograms can have false positive and anatomically implausible streamlines. To obtain anatomically relevant streamlines and tracts, supervised and unsupervised methods can be used for tractogram clustering and tract extraction. Here we propose FiberNeat, an unsupervised white matter tract filtering method. FiberNeat takes an input set of streamlines that could either be unlabeled clusters or labeled tracts. Individual clusters/tracts are projected into a latent space using nonlinear dimensionality reduction techniques, t-SNE and UMAP, to find spurious and outlier streamlines. In addition, outlier streamline clusters are detected using DBSCAN and then removed from the data in streamline space. We performed quantitative comparisons with expertly delineated tracts. We ran FiberNeat on 131 participants data from the ADNI3 dataset. We show that applying FiberNeat as a filtering step after bundle segmentation improves the quality of extracted tracts and helps improve tractometry.


title: FiberNeat: Unsupervised White Matter Tract Filtering


title: Spindle - slow oscillation coupling correlates with memory performance and connectivity changes in a hippocampal network after sleep

abstract: After experiences are encoded, post-encoding reactivations during sleep have been proposed to mediate long-term memory consolidation. Spindle-slow oscillation coupling during NREM sleep is a candidate mechanism through which a hippocampal-cortical dialogue may strengthen a newly formed memory engram. Here, we investigated the role of fast spindle- and slow spindle-slow oscillation coupling in the consolidation of spatial memory in humans with a virtual water maze task involving allocentric and egocentric learning strategies. Furthermore, we analyzed how resting-state functional connectivity evolved across learning, consolidation, and retrieval of this task using a data-driven approach. Our results show task-related connectivity changes in the executive control network, the default mode network, and the hippocampal network at post-task rest. The hippocampal network could further be divided into two subnetworks of which only one showed modulation by sleep. Decreased functional connectivity in this subnetwork was associated with higher spindle-slow oscillation coupling power, which was also related to better memory performance at test. Overall, this study contributes to a more holistic understanding of the functional resting-state networks and the mechanisms during sleep associated to spatial memory consolidation.


title: KIBRA-PKCγ signaling pathway modulates memory performance in mice and humans

abstract: Human memory is a polygenic cognitive trait that is fundamental to individual competence. Genome-wide association studies (GWAS) have identified KIBRA as a novel gene associated with human memory performance. KIBRA interacts with AMPA receptors (AMPARs) and proteins essential for synaptic plasticity. The deletion of Kibra in mice impairs synaptic plasticity and learning and memory. However, the molecular basis through which KIBRA regulates dynamic AMPAR trafficking underlying synaptic plasticity is still unknown. Here we report that KIBRA interacts with the neuronal specific kinase PKC{gamma} to modulate AMPAR trafficking upon learning, and KIBRA-PKC{gamma} signaling pathway also associates with human memory performance. We find PKC{gamma} is an essential kinase that phosphorylates AMPARs upon learning, and the loss of KIBRA in mouse brain impedes PKC{gamma}-AMPAR interaction. Activation of PKC{gamma} enables KIBRA to recruit phosphorylated AMPARs to the synapse to promote LTP and learning. We further performed transcriptomic and genetic analyses in human postmortem brain samples, and behavioral and fMRI evaluations in living human subjects, to demonstrate the genetic interactions between KIBRA and PRKCG on memory performance and memory associated physiological engagement of the hippocampal memory system. Overall, our results support that the KIBRA-PKC{gamma} signaling pathway is crucial for modulating memory performance in mice and humans.


title: In vivo MR spectroscopy reflects synapse density in a Huntington's disease mouse model

abstract:
Striatal medium spiny neurons are highly susceptible in Huntingtons disease (HD), resulting in progressive synaptic perturbations that lead to neuronal dysfunction and death. Non-invasive imaging techniques, such as proton magnetic resonance spectroscopy (1H-MRS), are used in HD mouse models and patients with HD to monitor neurochemical changes associated with neuronal health. However, the association between brain neurochemical alterations and synaptic dysregulation is unknown, limiting our ability to monitor potential treatments that may affect synapse function. We conducted in vivo longitudinal 1H-MRS in the striatum followed by ex-vivo analyses of excitatory synapse density of two synaptic circuits disrupted in HD, thalamo-striatal (T-S) and cortico-striatal (C-S) pathways, to assess the relationship between neurochemical alterations and changes in synapse density. We used the zQ175(Tg/0) HD mouse model as well as zQ175 mice lacking one allele of CK2(zQ175(Tg/0):CK2(+/-)), a kinase previously shown to regulate synapse function in HD. Longitudinal analyses of excitatory synapse density showed early and sustained reduction in T-S synapses in zQ175 mice, preceding C-S synapse depletion, which was rescued in zQ175:CK2(+/-). Changes in T-S and C-S synapses were accompanied by progressive alterations in numerous neurochemicals between WT and HD mice. Linear regression analyses showed C-S synapse number positively correlated with 1H-MRS-measured levels of GABA while T-S synapse number positively correlated with levels of alanine, phosphoethanolamine and lactate, and negatively correlated with total creatine levels.

These associations suggest that these neurochemical concentrations measured by 1H-MRS may facilitate monitoring circuit-specific synaptic dysfunction in the zQ175 mouse model and in other HD pre-clinical studies.

Significance StatementThe pathogenic events of many neurodegenerative diseases including HD are triggered by reductions in number of synapses. Therefore, in vivo measures that reflect synapse number represent a powerful tool to monitor synaptic changes in numerous brain disorders. In this study, we showed that non-invasive in vivo 1H-MRS reflects excitatory synapse number in the striatum of the zQ175 mouse model of HD. The combination of longitudinal 1H-MRS and immunofluorescence synapse detection revealed that distinct neurochemical levels significantly correlated with different striatal glutamatergic synaptic input pathways, suggesting that 1H-MRS could distinguish circuit-dependent synapse changes in HD. These results provide potential neurochemical biomarkers to monitor synaptic changes in future pre-clinical trials with HD models.


title: Altered Salience Network Connectivity in 6-Week-Old Infants at Risk for Autism

abstract: Converging evidence implicates disrupted brain connectivity in autism spectrum disorder (ASD); however, the mechanisms linking altered connectivity early in development to the emergence of ASD symptomatology remain poorly understood. Here we examined whether atypicalities in the Salience Network (SN) - an early-emerging neural network involved in orienting attention to the most salient aspects of ones internal and external environment - may predict the development of ASD markers such as reduced social attention and atypical sensory processing. Six-week-old infants at high-risk for ASD exhibited stronger SN connectivity with sensorimotor regions; low-risk infants demonstrated stronger SN connectivity with prefrontal regions involved in social attention. Infants with higher connectivity with sensorimotor regions had lower connectivity with prefrontal regions, suggesting a direct tradeoff between attention to basic sensory versus socially-relevant information. Early alterations in SN connectivity predicted subsequent ASD symptomatology, providing a plausible mechanistic account for the unfolding of atypical developmental trajectories associated with ASD risk.


title: Hand and face somatotopy shown using MRI-safe vibrotactile stimulation with a novel Soft Pneumatic Actuator (SPA)-Skin interface

abstract: The exact somatotopy of the human facial representation in the primary somatosensory cortex (S1) remains debated. One reason that progress has been hampered is due to the methodological challenge of how to apply automated vibrotactile stimuli to face areas in a manner that is: 1) reliable despite differences in the curvatures of face locations; and 2) MR-compatible and free of MR-interference artefacts when applied in the MR head-coil. Here we overcome this challenge by using soft pneumatic actuator (SPA) technology. SPAs are made of a soft silicon material and can be in- or deflated by means of airflow, have a small diameter, and are flexible in structure, enabling good skin contact even on curved body surfaces (as on the face). To validate our approach, we first mapped the well-characterised S1 finger layout using this novel device and confirmed that tactile stimulation of the fingers elicited characteristic somatotopic finger activations in S1. We then used the device to automatically and systematically deliver somatosensory stimulation to different face locations. We found that the forehead representation was least distant from the representation of the hand. Within the face representation, we found that the lip representation is most distant from the forehead representation, with the chin represented in between. Together, our results demonstrate that this novel MR compatible device produces robust and clear somatotopic representational patterns using vibrotactile stimulation through SPA-technology.


title: Three water restriction schedules used in rodent behavioral tasks transiently impair growth and differentially evoke a stress hormone response without causing dehydration

abstract: Water restriction is commonly used to motivate rodents to perform behavioral tasks; however, its on hydration and stress hormone levels are unknown. Here, we report daily body weight and bi-weekly packed red blood cell volume and corticosterone in adult male rats across 80 days for three commonly used water restriction schedules. We also assessed renal adaptation to water restriction using post-mortem histological evaluation of renal medulla. A control group received ad libitum water. After one week of water restriction, rats on all restriction schedules resumed similar levels of growth relative to the control group. Nominal hydration was observed, and water restriction did not drive renal adaptation. An intermittent restriction schedule was associated with an increase in corticosterone relative to the control group. Our results suggest that the water restriction schedules used here will maintain welfare in rats. However, intermittent restriction evokes a stress response which could affect behavioral and neurobiological results. Our results also suggest that stable motivation in behavioral tasks may only be achieved after one week of restriction.


title: EEG microstate dynamics indicate a U-shaped path to propofol-induced loss of consciousness

abstract:
It is commonly believed that the stream of consciousness is not continuous but parsed into transient brain states manifesting themselves as discrete spatiotemporal patterns of global neuronal activity. Electroencephalographical (EEG) microstates are proposed as the neurophysiological correlates of these transiently stable brain states that last for fractions of seconds. To further understand the link between EEG microstate dynamics and consciousness, we continuously recorded high-density EEG in 23 surgical patients from their awake state to unconsciousness, induced by step-wise increasing concentrations of the intravenous anesthetic propofol. Besides the conventional parameters of microstate dynamics, we introduce a new method that estimates the complexity of microstate sequences. The brain activity under the surgical anesthesia showed a decreased sequence complexity of the stereotypical microstates, which became sparser and longer-lasting. However, we observed an initial increase in microstates temporal dynamics and complexity with increasing depth of sedation leading to a distinctive "U-shape" that may be linked to the paradoxical excitation induced by moderate levels of propofol. Our results support the idea that the brain is in a metastable state under normal conditions, balancing between order and chaos in order to flexibly switch from one state to another. The temporal dynamics of EEG microstates indicate changes of this critical balance between stability and transition that lead to altered states of consciousness.

HighlightsO_LIEEG microstates capture discrete spatiotemporal patterns of global neuronal activity
C_LIO_LIWe studied their temporal dynamics in relation to different states of consciousness
C_LIO_LIWe introduce a new method to estimate the complexity of microstates sequences
C_LIO_LIWith moderate sedation complexity increases then decreases with full sedation
C_LIO_LIComplexity of microstate sequences is sensitive to altered states of consciousness
C_LI


title: White matter microstructural integrity across the adult lifespan: Combined perspective of diffusion tensor and kurtosis imaging

abstract: Studies of healthy brain aging have reported diffusivity patterns associated with white matter degeneration using diffusion tensor imaging (DTI), which assumes that diffusion measured at the typical b-value (approximately 1000 s/mm2) is Gaussian. Diffusion kurtosis imaging (DKI) is an extension of DTI that measures non-Gaussian diffusion (kurtosis) to better capture microenvironmental changes by incorporating additional data at a higher b-value. In this study, using UK Biobank data (b values of 1000 and 2000 s/mm2), we investigate (1) the extent of novel information gained from adding diffusional kurtosis to diffusivity observations in aging, and (2) how conventional DTI metrics in aging compare with diffusivity metrics derived from DKI, which are corrected for kurtosis. We find a general pattern of lower kurtosis alongside higher diffusivity among older adults. We also find differences between diffusivity metrics derived from DTI and DKI, emphasizing the importance of accounting for non-Gaussian diffusion. This work highlights the utility of measuring diffusional kurtosis as a simple addition to conventional diffusion imaging of aging.


title: Neurons in human pre-supplementary motor area encode key computations for value-based choice

abstract: Adaptive behavior in real-world environments demands that choices integrate over several variables, including the novelty of the options under consideration, their expected value, and uncertainty in value estimation. We recorded neurons from the human pre-supplementary motor area (preSMA), ventromedial prefrontal cortex (vmPFC) and dorsal anterior cingulate to probe how integration over decision variables occurs during decision-making. In contrast to the other areas, preSMA neurons not only represented separate pre-decision variables for each choice option, but also encoded an integrated utility signal and, subsequently, the decision itself. Conversely, post-decision related encoding of variables for the chosen option was more widely distributed and especially prominent in vmPFC. Our findings position the human preSMA as central to the implementation of value-based decisions.


title: Inhibiting adult neurogenesis differentially affects spatial learning in females and males

abstract: Adult hippocampal neurogenesis has been implicated in the spatial processing functions of the hippocampus but ablating neurogenesis does not consistently lead to behavioral deficits in spatial tasks. Parallel studies have shown that adult-born neurons also regulate behavioral responses to stressful and aversive stimuli. We therefore hypothesized that spatial functions of adult-born neurons may be more prominent under conditions of stress, and may differ between males and females given established sex differences in stress responding. To test this we trained intact and neurogenesis-deficient rats in the spatial water maze at temperatures that vary in their degree of aversiveness. At standard temperatures (25{degrees}C) ablating neurogenesis did not alter learning and memory in either sex, consistent with prior work. However, in cold water (16{degrees}C), ablating neurogenesis had divergent sex-dependent effects: relative to intact rats, male neurogenesis-deficient rats were slower to escape and female neurogenesis-deficient rats were faster. Neurogenesis promoted temperature-related changes in search strategy in females, but it promoted search strategy stability in males. Females displayed greater recruitment of the dorsal hippocampus than males, particularly at 16{degrees}C. However, blocking neurogenesis did not alter activity-dependent immediate-early gene expression in either sex. Finally, morphological analyses of retrovirally-labelled neurons revealed greater experience-dependent plasticity in new neurons in males. Neurons had comparable morphology in untrained rats but 16{degrees}C training increased spine density, and 25{degrees}C training caused shrinkage of mossy fiber presynaptic terminals, specifically in males. Collectively, these findings indicate that neurogenesis functions in memory are prominent under conditions of stress, they provide the first evidence for sex differences in the behavioral function of newborn neurons, and they suggest possibly distinct roles for neurogenesis in cognition and mental health in males and females.


title: Spontaneous emergence of music detectors in a deep neural network trained for natural sound recognition

abstract:
Music exists in almost every society, has universal acoustic features, and is processed by distinct neural circuits in humans even with no experience of musical training. These characteristics suggest an innateness of the sense of music in our brain, but it is unclear how this innateness emerges and what functions it has. Here, using an artificial deep neural network that models the auditory information processing of the brain, we show that units tuned to music can spontaneously emerge by learning natural sound detection, even without learning music. By simulating the responses of network units to 35,487 natural sounds in 527 categories, we found that various subclasses of music are strongly clustered in the embedding space, and that this clustering arises from the music-selective response of the network units. The music-selective units encoded the temporal structure of music in multiple timescales, following the population-level response characteristics observed in the brain. We confirmed that the process of generalization is critical for the emergence of music-selectivity and that music-selectivity can work as a functional basis for the generalization of natural sound, thereby elucidating its origin. These findings suggest that our sense of music can be innate, universally shaped by evolutionary adaptation to process natural sound.

One-sentence summaryMusic-selectivity can arise spontaneously in deep neural networks trained for natural sound detection without learning music.


title: Spontaneous emergence of music detectors in a deep neural network


title: Long-term effects of network-based fMRI neurofeedback training for sustained attention

abstract: Neurofeedback allows for learning voluntary control over ones own brain activity, aiming to enhance cognition and clinical symptoms. A recent study improved sustained attention temporarily by training healthy participants to up-regulate the differential activity of the sustained attention network (SAN) minus the default mode network (DMN). However, long-term learning effects of functional magnetic resonance imaging (fMRI) neurofeedback training remain under-explored. Here, we evaluate the effects of network-based fMRI neurofeedback training for sustained attention by assessing behavioral and brain measures before, one day after, and two months after training. The behavioral measures include task as well as questionnaire scores, and the brain measures include activity and connectivity during self-regulation runs without feedback (i.e., transfer runs) and during resting-state runs. Neurally, we found that participants maintained their ability to control the differential activity during follow-up sessions. Also, the training-induced increase in FC between the DMN and occipital gyrus was maintained during follow-up transfer runs. In contrast, the training-induced increased FC between DMN and occipital gyrus was not observed during follow-up resting-state runs. Behaviorally, we found that enhanced sustained attention right after training returned to baseline level during follow-up. The discrepancy between lasting regulation-related brain changes but transient behavioral and resting-state effects raises the question of how neural changes induced by neurofeedback training translate to potential behavioral improvements. Since neurofeedback directly targets brain measures to indirectly improve behavior long-term, a better understanding of the brain-behavior associations during and after neurofeedback training is needed to develop its full potential as a promising scientific and clinical tool.


title: Natural killer-like B cells promote Th17 cell differentiation and exacerbate rheumatoid arthritis

abstract: B cells are important participants in the pathogenesis of rheumatoid arthritis (RA). Besides classical B cells, novel B cell subsets are continually to be identified in recent years. Natural killer-like B (NKB) cells, a newly recognized B cell subset, are proved to be actively involved in the anti-infection immunity. However, their role in RA and the potential mechanism remain elusive. Here, we showed that NKB cells were expanded dramatically in collagen-induced arthritis (CIA) mice, demonstrating dynamic changes during the disease progression. These cells promoted CD4+ effector T cell proliferation and Th17 cell differentiation in vitro, while adoptive transfer of these cells exacerbated the arthritis severity of CIA mice. RNA Sequencing revealed that NKB cells displayed distinct differential gene expression profile under RA circumstance, potential perpetuating the disease progression. Moreover, the frequencies of NKB cells were significantly increased in RA patients, positively correlated with the clinical and immunological features. After effective therapy, these cells could be recovered to normal levels. Taken together, our results preliminarily revealed the pathogenic role of NKB cells in RA by promoting Th17 proinflammatory responses. Targeting these cells might provide potential therapeutic strategies for this persistent disease.

category: immunology


title: Deep Phenotypic Analysis of Blood and Lymphoid T and NK Cells from HIV+ Controllers and Non-Controllers

abstract: T and natural killer (NK) cells are effector cells with key roles in anti-HIV immunity, including in lymphoid tissues, the major site of HIV persistence. In this study, we used 42-parameter CyTOF to conduct deep phenotyping of paired blood- and lymph node (LN)-derived T and NK cells from three groups of HIV+ aviremic individuals: elite controllers, and antiretroviral therapy (ART)-suppressed individuals who had started therapy during chronic vs. acute infection, the latter of which is associated with better outcomes. We found that acute-treated individuals are enriched for specific subsets of T and NK cells, including blood-derived CD56-CD16+ NK cells previously associated with HIV control, and LN-derived CD4+ T follicular helper cells with heightened expansion potential. An in-depth comparison of the features of the cells from blood vs. LNs of individuals from our cohort revealed that T cells from blood were more activated than those from LNs. By contrast, LNs were enriched for follicle-homing CXCR5+ CD8+ T cells, which expressed increased levels of inhibitory receptors and markers of survival and proliferation as compared to their CXCR5-counterparts. In addition, a subset of memory-like CD56brightTCF1+ NK cells was enriched in LNs relative to blood. These results together suggest unique T and NK cell features in acute-treated individuals, and highlight the importance of examining effector cells not only in blood but also the lymphoid tissue compartment, where the reservoir mostly persists, and where these cells take on distinct phenotypic features.


title: A simple strategy for sample annotation error detection in cytometry datasets

abstract: Mislabeling samples or data with the wrong participant information can impact study integrity and lead investigators to draw inaccurate conclusions. Quality control to prevent these types of errors is commonly embedded into the analysis of genomic datasets, but a similar identification strategy is not standard for cytometric data. Here, we present a method for detecting sample identification errors in cytometric data using expression of HLA class I alleles. We measured HLA-A*02 and HLA-B*07 expression in 3 longitudinal samples from 41 participants using a 33-marker CyTOF panel designed to identify major immune cell types. 3/123 samples (2.4%) showed HLA allele expression that did not match their longitudinal pairs. Furthermore, these same three samples cytometric signature did not match qPCR HLA class I allele data, suggesting that they were accurately identified as mismatches. We conclude that this technique is useful for detecting sample labeling errors in cytometric analyses of longitudinal data. This technique could also be used in conjunction with another method, like GWAS or PCR, to detect errors in cross-sectional data. We suggest widespread adoption of this or similar techniques will improve the quality of clinical studies that utilize cytometry.


title: RNA sensing via LGP2 is essential for the induction of a type I IFN response in ADAR1 deficiency

abstract: RNA editing by the enzyme Adenosine Deaminase Acting on RNA 1 (ADAR1) is an important mechanism by which cells avoid innate immune responses to some endogenous RNAs. In ADAR1-deficient cells, unedited self RNAs can form base-paired structures that resemble viral RNAs and inadvertently activate antiviral innate immune pathways that lead to the induction of type I interferon (IFN). Rare mutations in ADAR1 cause Aicardi-Goutieres Syndrome (AGS), a severe childhood autoinflammatory syndrome that is characterized by chronic and excessive type I IFN production and developmental delay. Conversely, ADAR1 dysfunction and consequent type I IFN production helps restrict tumor growth and potentiates the activity of some chemotherapy drugs. Induction of type I IFN in ADAR1-deficient cells is thought to be due to triggering of the cytosolic RIG-I-like receptor (RLR), MDA5, by unedited self RNAs. Here, we show that another RLR, LGP2, also has an essential role. We demonstrate that ADAR1-deficient human cells fail to mount a type I IFN response in the absence of LGP2 and this involves the canonical function of LGP2 as an RNA sensor and facilitator of MDA5-dependent signaling. Further, we show that the sensitivity of tumor cells to ADAR1 loss requires the presence of LGP2. Finally, we find that type I IFN induction in tumor cells depleted of ADAR1 and treated with some chemotherapeutics is fully dependent on the expression of LGP2. These findings highlight a central role for LGP2 in self RNA sensing with important clinical implications for the treatment of AGS as well as for the potential application of ADAR1-directed anti-tumor therapy.


title: Signaling from the RNA sensor RIG-I is regulated by ufmylation

abstract:
The RNA binding protein RIG-I is a key initiator of the antiviral innate immune response. The signaling that mediates the antiviral response downstream of RIG-I is transduced through the adaptor protein MAVS and results in the induction of type I and III interferons (IFN). This signal transduction occurs at endoplasmic reticulum (ER)-mitochondrial contact sites, to which RIG-I and other signaling proteins are recruited following their activation. RIG-I signaling is highly regulated to prevent aberrant activation of this pathway and dysregulated induction of IFN. Previously, we identified UFL1, the E3 ligase of the ubiquitin-like modifier conjugation system called ufmylation, UFL1, as one of the proteins recruited to membranes at ER-mitochondrial contact sites in response to RIG-I activation. Here, we show that UFL1, as well as the process of ufmylation, promote IFN induction in response to RIG-I activation. We find that following RNA virus infection, UFL1 is recruited to the membrane targeting protein 14-3-3{varepsilon}, and that this complex is then recruited to activated RIG-I to promote downstream innate immune signaling. Importantly, we found that 14-3-3{varepsilon} has an increase in UFM1-conjugation following RIG-I activation. Additionally, loss of cellular ufmylation prevents the interaction of 14-3-3{varepsilon} with RIG-I, which abrogates the interaction of RIG-I with MAVS and thus downstream signal transduction that induces IFN. Our results define ufmylation as an integral regulatory component of the RIG-I signaling pathway and as a post-translational control for IFN induction.

SignificanceThe viral RNA sensor RIG-I initiates the antiviral innate immune response by activating a signaling cascade that induces interferon. Activation of the RIG-I signaling pathway is highly regulated to quickly mount a protective immune response while preventing dysregulation that can lead to excessive inflammation or autoimmune disorders. Here, we characterize one such mechanism of regulation. We describe that UFL1, an E3 ligase for the ubiquitin-like modifier conjugation system called ufmylation, is important to promote RIG-I signaling. Using molecular approaches, we show that ufmylation promotes RIG-I interaction with the membrane targeting protein 14-3-3{varepsilon}. As such, ufmylation positively regulates RIG-I recruitment to its signaling adaptor proteins MAVS for induction of interferon in response to RNA virus infection.


title: Inducible transcriptional condensates drive 3D genome reorganization in the heat shock response

abstract: Mammalian developmental and disease-associated genes concentrate large quantities of the transcriptional machinery by forming membrane-less compartments known as transcriptional condensates. However, it is unknown whether these structures are evolutionarily conserved, capable of stress-inducible gene activation or involved in 3D genome reorganization. Here, we identify inducible transcriptional condensates in the yeast heat shock response (HSR). HSR condensates are biophysically dynamic spatiotemporal clusters of the sequence-specific transcription factor Heat shock factor 1 (Hsf1) with Mediator and RNA Pol II. Uniquely, HSR condensates drive the coalescence of multiple Hsf1 target genes, even those located on different chromosomes. Binding of the chaperone Hsp70 to a site on Hsf1 represses clustering, while an intrinsically disordered region on Hsf1 promotes condensate formation and intergenic interactions. Mutation of both Hsf1 determinants reprograms HSR condensates to become mammalian-like: constitutively active without intergenic coalescence. These results suggest that transcriptional condensates are ancient and flexible compartments of eukaryotic gene control.

category: molecular biology


title: Single-molecule imaging suggests compact and spliceosome dependent organization of long introns

abstract: Intron removal from pre-mRNAs is a critical step in the processing of RNA polymerase II transcripts, required to create translation competent mRNAs. In humans, introns account for large portions of the pre-mRNA, with intronic sequences representing about 95% of most pre-mRNA. Intron length varies considerably; introns can be as short as a few to hundreds of thousands of nucleotides in length. How nascent long intronic RNA is organized during transcription to facilitate the communication between 5 and 3 splice-sites required for spliceosome assembly however is still poorly understood. Here, we use single-molecule fluorescent RNA in situ hybridization (smFISH) to investigate the spatial organization of co- and post-transcriptional long introns in cells. Using two long introns within the POLA1 pre-mRNA as a model, we show that introns are packaged into compact assemblies, and when fully transcribed, are organized in a looped conformation with their ends in proximity. This organization is observed for nascent and nucleoplasmic pre-mRNAs and requires spliceosome assembly, as disruption of U2 snRNP binding results in introns with separated 5 and 3 ends. Moreover, interrogating the spatial organization of partially transcribed co-transcriptional POLA1 intron 35 indicates that the 5 splice site is maintained proximal to the 3 splice site during transcription, supporting a model that 5 splice site tethering to the elongating polymerase might contribute to spliceosome assembly at long introns. Together, our study reveals details of intron and pre-mRNA organization in cells and provides a tool to investigate mechanisms of splicing for long introns.

category: cell biology


title: Sex differences in migraine: A twin study

abstract: Migraine is a neurological disorder with a prominent sex difference such that two thirds of sufferers are female. The mechanisms behind the preponderance of migraine in women have yet to be elucidated. With data on 51,872 participants from the Swedish Twin Registry, we report results from two distinct analyses intended to clarify the degree to which genetic and environmental factors contribute to sex differences in migraine. First, we fit a sex-limitation model to determine if quantitative genetic differences (i.e., is migraine equally heritable across men and women) and/or qualitative genetic differences (i.e., are different genes involved in migraine across men and women) were present. Next, we used a multilevel logistic regression model to compare the prevalence of migraine in individuals from opposite-sex and same-sex twin pairs to determine whether differences in the prenatal hormone environment contribute to migraine risk. In the final analytic sample, women were found to have a significantly higher rate of migraine without aura relative to men (17.6% vs 5.5%). The results from an ADE sex-limitation model indicate that migraine is equally heritable in men and women, with a broad sense heritability of .45, (95% CI = .40 - .50), while results from a reduced AE sex-limitation model provide subtle evidence for differences in the genes underlying migraine across men and women. The logistic regression analysis revealed a significant increase in migraine risk for females with a male co-twin relative to females with a female co-twin (OR = 1.51, 95% CI = 1.26 - 1.81). These results suggest that the prominent sex difference in migraine prevalence is not entirely accounted for by genetic factors, while demonstrating that masculinization of the prenatal environment may increase migraine risk for females. This effect points to a potential prenatal neuroendocrine factor in the development of migraine.


title: Ultra-cheap and scalable epigenetic age predictions with TIME-Seq

abstract: Epigenetic "clocks" based on DNA methylation (DNAme) are the most robust and widely employed aging biomarker. They have been built for numerous species and reflect gold-standard interventions that extend lifespan. However, conventional methods for measuring epigenetic clocks are expensive and low-throughput. Here, we describe Tagmentation-based Indexing for Methylation Sequencing (TIME-Seq) for ultra-cheap and scalable targeted methylation sequencing of epigenetic clocks and other DNAme biomarkers. Using TIME-Seq, we built and validated inexpensive epigenetic clocks based on genomic and ribosomal DNAme in hundreds of mice and human samples. We also discover it is possible to accurately predict age from extremely low-cost shallow sequencing (e.g., 10,000 reads) of TIME-Seq libraries using scAge, a probabilistic age-prediction algorithm originally applied to single cells. Together, these methods reduce the cost of DNAme biomarker analysis by more than two orders of magnitude, thereby expanding and democratizing their use in aging research, clinical trials, and disease diagnosis.


title: Spatial-temporal analysis of nanoparticles in live tumor spheroids impacted by cell origin and density

abstract: Nanoparticles hold great preclinical promise in cancer therapy but continue to suffer attrition through clinical trials. Advanced, three dimensional (3D) cellular models such as tumor spheroids can recapitulate elements of the tumor environment and are considered the superior model to evaluate nanoparticle designs. However, there is an important need to better understand nanoparticle penetration kinetics and determine how different cell characteristics may influence this nanoparticle uptake. A key challenge with current approaches for measuring nanoparticle accumulation in spheroids is that they are often static, losing spatial and temporal information which may be necessary for effective nanoparticle evaluation in 3D cell models. To overcome this challenge, we developed an analysis platform, termed the Determination of Nanoparticle Uptake in Tumor Spheroids (DONUTS), which retains spatial and temporal information during quantification, enabling evaluation of nanoparticle uptake in 3D tumor spheroids. Outperforming linear profiling methods, DONUTS was able to measure silica nanoparticle uptake to 10 {micro}m accuracy in both isotropic and irregularly shaped cancer cell spheroids. This was then extended to determine penetration kinetics, first by a forward-in-time, center-in-space model, and then by mathematical modelling, which enabled the direct evaluation of nanoparticle penetration kinetics in different spheroid models. Nanoparticle uptake was shown to inversely relate to particle size and varied depending on the cell type, cell stiffness and density of the spheroid model. The automated analysis method we have developed can be applied to live spheroids in situ, for the advanced evaluation of nanoparticles as delivery agents in cancer therapy.


title: Brain-inspired spiking neural network controller for a neurorobotic whisker system

abstract: It is common for animals to use self-generated movements to actively sense the surrounding environment. For instance, rodents rhythmically move their whiskers to explore the space close to their body. The mouse whisker system has become a standard model to study active sensing and sensorimotor integration through feedback loops. In this work, we developed a bioinspired spiking neural network model of the sensorimotor peripheral whisker system, modelling trigeminal ganglion, trigeminal nuclei, facial nuclei, and central pattern generator neuronal populations. This network was embedded in a virtual mouse robot, exploiting the Neurorobotics Platform, a simulation platform offering a virtual environment to develop and test robots driven by brain-inspired controllers. Eventually, the peripheral whisker system was properly connected to an adaptive cerebellar network controller. The whole system was able to drive active whisking with learning capability, matching neural correlates of behaviour experimentally recorded in mice.