Miracle-dz/UniFAR-FTUs huggingface dataset:
Community attitudes on genetic research of gender identity, sexual orientation, and mental health

Biological sex is an important factor in mental health, and a non-binary view of how variation in sex and gender influence mental health represents a new research frontier that may yield new insights. The recent acceleration of research into sexual orientation, gender identity, and mental health has generally been conducted without sufficient understanding of the opinions of sexual and gender minorities (SGM) toward this research. We surveyed 768 individuals, with an enrichment of LGBTQ+ stakeholders, for their opinions regarding genetic research of SGM and mental health. We found that the key predictors of attitudes toward genetic research specifically on SGM are 1) general attitudes toward genetic and mental health research 2) tolerance of SGM and associated behaviors 3) non-cisgender stakeholder status and 4) age of the respondent. Non-heterosexual stakeholder status was significantly associated with increased willingness to participate in genetic research if a biological basis for gender identity were discovered. We also found that non-stakeholders with a low tolerance for SGM indicated their SGM views would be positively updated if science showed a biological basis for their behaviors and identities. These findings represent an important first step in understanding and engaging the LGBTQ+ stakeholder community in the context of genetic research.
A highly scalable method for joint whole genome sequencing and gene expression profiling of single cells

Understanding how genetic variation alters gene expression - how genotype affects phenotype - is a central challenge in biology. To address this question in complex cell mixtures, we developed Direct Nuclear Tagmentation and RNA-sequencing (DNTR-seq), which enables whole genome and mRNA sequencing jointly in single cells. When applied to biobanked leukemia samples, DNTR-seq readily identified minor subclones within patients, as well as cell-type specific gene editing such as T-cell receptor rearrangements. mRNA-seq quality is equal to RNA-only methods, and the high yield combined with low positional bias of the genomic library preparation allows detection of sub-megabase aberrations at ultra low coverage of 0.5-3M read pairs per genome. Since each cell library is individually addressable, rare subpopulations can be re-sequenced at increased depth, allowing multi-tiered study designs where depth of sequencing is informed by previous results. In addition, the direct tagmentation protocol enables coverage-independent estimation of ploidy, which can be used to unambiguously identify cell singlets. Thus, DNTR-seq directly links each cell’s state to its corresponding genome at a scale enabling routine analysis of heterogeneous tumors and other complex tissues.
Angioplasty-induced epigenomic remodeling entails BRD4 and EZH2 hierarchical regulations

Atherosclerosis is commonly treated with angioplasty which, however, evokes neointimal hyperplasia (IH) and recurrent stenotic diseases. Epigenomic investigation was lacking on post-angioplasty IH. The histone acetylation reader BRD4 and H3K27me3 writer EZH2 are potent epigenetic factors; their relationship is little understood. Through genome-wide survey in the rat angioplasty model, we studied BRD4 and EZH2 functional regulations involved in IH. We performed chromatin immunoprecipitation sequencing (ChIPseq) using rat carotid arteries. While H3K27me3 ChIPseq signal prevalently intensified in balloon-injured (vs uninjured) arteries, BRD4 and H3K27ac became more enriched at Ezh2. Indeed, BRD4-siRNA or CRISPR-deletion of BRD4-associated enhancer abated the smooth muscle cell (SMC) expression of EZH2, and SMC-specific BRD4 knockout in BRD4fl/fl; Myh11CreERT2 mice reduced both H3K27me3 and IH in wire-injured femoral arteries. In accordance, post-angioplasty IH was exacerbated and mitigated, respectively, by lentiviral expression and pharmacological inhibition of EZH2/1; EZH2 (or EZH1) loss- and gain-of-function respectively attenuated and aggravated pro-IH SMC proliferative behaviors. Furthermore, while H3K27me3 ChIPseq signal magnified at P57 and ebbed at Ccnd1 and Uhrf1 after injury, silencing either EZH2 or EZH1 in SMCs up-regulated P57 and down-regulated Ccnd1 and Uhrf1. In summary, our results reveal an upsurge of EZH2/H3K27me3 after angioplasty, BRD4’s control over EZH2 expression, and non-redundant EZH2/1 functions. As such, this study unravels angioplasty-induced loci-specific H3K27me3/ac redistribution in the epigenomic landscape rationalizing BRD4/EZH2-governed pro-IH regulations.
Biodiversity mediates the effects of stressors but not nutrients on litter decomposition

Understanding the consequences of ongoing biodiversity changes for ecosystems is a pressing challenge. Controlled biodiversity-ecosystem function experiments with random biodiversity loss scenarios have demonstrated that more diverse communities usually provide higher levels of ecosystem functioning. However, it is not clear if these results predict the ecosystem consequences of environmental changes that cause non-random alterations in biodiversity and community composition. We synthesized 69 independent studies reporting 660 observations of the impacts of two pervasive drivers of global change (chemical stressors and nutrient enrichment) on animal and microbial decomposer diversity and litter decomposition. Using meta-analysis and structural equation modelling, we show that declines in decomposer diversity and abundance explain reduced litter decomposition in response to stressors but not to nutrients. While chemical stressors generally reduced biodiversity and ecosystem functioning, detrimental effects of nutrients occurred only at high levels of nutrient inputs. Thus, more intense environmental change does not always result in stronger responses, illustrating the complexity of ecosystem consequences of biodiversity change. Overall, these findings provide strong empirical evidence for significant real-world biodiversity-ecosystem functioning relationships when human activities decrease biodiversity. This highlights that the consequences of biodiversity change for ecosystems are nontrivial and depend on the kind of environmental change.
Organ-specific propensity drives patterns of gene expression evolution

The origins of multicellular physiology are tied to evolution of gene expression. Genes can shift expression as organisms evolve, but how ancestral expression influences altered descendant expression is not well understood. To examine this, we amalgamated 1,903 RNA-seq datasets from 182 research projects, including 6 organs in 21 vertebrate species. Quality control eliminated project-specific biases, and expression shifts were reconstructed using gene-family-wise phylogenetic Ornstein–Uhlenbeck models. Expression shifts following gene duplication result in more drastic changes in expression properties. The expression properties were tightly coupled with protein evolutionary rate, depending on whether and how gene duplication occurred. Fluxes in expression patterns among organs were nonrandom, forming modular connections which were reshaped by gene duplication. Thus, if expression shifted, ancestral expression in some organs induces a strong propensity for expression in particular organs in descendants. This supports a major role for what might be termed “preadaptive” pathways of gene expression evolution.
Interspecific plant competition mediates the metabolic and ecological signature of a plant-herbivore interaction under warming and elevated CO2

Biotic interactions shape community evolution, but we lack mechanistic insights on how metabolic and ecological processes under climate change are altered by biotic interactions.We used a two-trophic model community consisting of the aphidDysaphis plantagineafeeding on the forbPlantago lanceolata, and a grass competitorLolium perennethat does not experience herbivory by the aphid. Monocultures and mixtures were exposed to the herbivory treatment and to three relevant simulated environmental changes as prevalent under current climate change (increased temperature, CO2, and increased temperature and CO2)Elevated CO2reduced the nitrogen content ofP. lanceolata, while simultaneous increases of CO2and temperature modified the plant metabolic component and the magnitude of these responses in different directions. Elevated CO2enhanced defence systems inP. lanceolata, but these effects were not altered by warming. Interspecific plant competition did, however, neutralise these responses. There were no indirect effects of climate change on aphid population growth despite changes in plant defense, nutritional quality and biomass induced by our environmental change scenarios.We thus demonstrate interactions between abiotic and biotic processes on plant metabolite profiles, but more importantly, that climate change effect on a selection of the metabolic pathways are altered by herbivory and competition. Our experiment under semi-natural conditions thus demonstrates the non-additive and often neutralizing effects of biotic interactions on plant metabolism and species performance under climate-associated environmental change.
Systemic mutational rescue in Escherichia coli elicited by a valency dependent, high affinity protein DNA interaction

The controlled formation of sequence specific DNA protein complexes is a fundamental feature of most genetic transactions. Studies of the impact of point mutations on the function of individual components, such as repressors, remains a key aspect of many Systems and Synthetic Biology research programmes. One of the most dramatic systemic consequences of a point mutation is exhibited by the monomeric DNA methyltransferases M.HhaI and M.EcoRII, where substitution of a single, catalytic cysteine by either glycine or alanine, creates a lethal gain of function phenotype. In vivo expression of these point mutants promotes the deposition of high affinity nucleoprotein complexes that arrest replication in vivo, causing cell death. Interestingly, it appears that a systemic response to expression of these mutant enzymes is dramatically enhanced when they are expressed as synthetic dimers. A previously unreported form of “mutational rescue” appears to be triggered as a result of networked crosslinking of host cell DNA resulting from an increased valency of nucleoprotein complex formation. This finding may have significance for developing molecular interventions for the controlled regulation of genome function and for the development of novel antimicrobial and anticancer strategies.
Resolving Cell Cycle Speed in One Snapshot with a Live-Cell Fluorescent Reporter

Cell proliferation changes concomitantly with fate transitions during reprogramming, differentiation, regeneration, and oncogenesis. Methods to resolve cell cycle length heterogeneity in real-time are currently lacking. Here, we describe a genetically encoded fluorescent reporter that captures live cell cycle speed using a single measurement. This reporter is based on the color-changing Fluorescent Timer (FT) protein, which emits blue fluorescence when newly synthesized before maturing into a red fluorescent protein. We generated a mouse strain expressing an H2B-FT fusion reporter from a universally active locus, and demonstrate that faster-cycling cells can be distinguished from slower-cycling ones based on the intracellular fluorescence ratio between the FT’s blue and red states. Using this reporter, we reveal the native cell cycle speed distributions of fresh hematopoietic cells, and demonstrate its utility in analyzing cell proliferation in solid tissues. This system is broadly applicable for dissecting functional heterogeneity associated with cell cycle dynamics in complex tissues.
How to use random walks for modeling the movement of wild animals

Animal movement has been identified as a key feature in understanding animal behavior, distribution and habitat use and foraging strategies among others. At the same time, technological improvements now allow for generating large datasets of high sampled GPS data over a long period of time. However, such datasets often remain unused or used only in part due to the lack of practical models that can directly infer the desired features from raw GPS locations and the complexity of existing approaches. Some of them being disputed for their lack of rational or biological justifications in their design. We propose a simple model of individual movement with explicit parameters based on essential features of animal behavior. The main thrust was to stick to empirical observations, rather than using black-box models that could possibly perform very well while providing little insight from an ecological perspective. We used a simple model, based on a two-dimensional biased and correlated random walk with three forces related to advection, attraction and immobility of the animal. These forces can be directly estimated using individual raw GPS data. The performance of the model is assessed through 5 statistics that describe the spatial features of animal movement. We demonstrate the approach by using GPS data of 5 roe deer with high frequency sampling. We show that combining the three forces significantly improves the model performance. We also found that the model’s parameters are not affected by the sampling rate of the GPS, suggesting that our model could also be used with low frequency sampling GPS devices. Additionally, the practical design of the model was verified for detecting spatial feature abnormalities (such as voids) and for providing estimates of density and abundance of wild animals. Our results show that a simple and practicable random walk template can account for the spatial complexity of wild animals. Integrating even more additional features of animal movement, such as individuals’ interactions or environmental repellents, could help to better understand the spatial behavior of wild animals.
Force-dependent Piezo1 recruitment to focal adhesions regulates adhesion maturation and turnover specifically in non-transformed cells

Piezo1 is a mechanosensitive Ca2+-permeable channel that has been implicated in a number of mechanosensing processes. It is diffusive on plasma membranes and activated by local membrane tension changes yet recent data suggest that Piezo1 activity is tightly coupled to the integrin-mediated actin cytoskeleton through a poorly understood mechanism. In our studies, we found that Piezo1 stably localizes to RGD matrix adhesions in normal but not in transformed cells. Piezo1 binding requires contractility and triggers local Ca2+ entry during adhesion formation and turnover. In transformed cells, Piezo1 level does not affect adhesion morphology; and there is no detectable Ca2+ influx around adhesions. Based upon these findings, we suggest that Piezo1 is a novel component of integrin-based adhesions in non-transformed cells and contributes to the distinct mechanosensing and Ca2+ signaling in normal vs transformed cells. Concentration of Piezo1 at adhesions is a key factor underlying Piezo1’s physiological functions.
A microscopy-based kinetic analysis of yeast vacuolar protein sorting

The yeast Saccharomyces cerevisiae is amenable to studying membrane traffic by live-cell fluorescence microscopy. We used this system to explore two aspects of cargo protein traffic through prevacuolar endosome (PVE) compartments to the vacuole. First, at what point during Golgi maturation does a biosynthetic vacuolar cargo depart from the maturing cisternae? To address this question, we modified a regulatable fluorescent secretory cargo by adding a vacuolar targeting signal. Traffic of the vacuolar cargo requires the GGA clathrin adaptors, which arrive during the early-to-late Golgi transition. Accordingly, the vacuolar cargo begins to exit the Golgi near the midpoint of maturation, significantly before exit of a secretory cargo. Second, how are cargoes delivered from PVE compartments to the vacuole? To address this question, we tracked biosynthetic and endocytic cargoes after they had accumulated in PVE compartments. The results imply that stable PVE compartments repeatedly deliver material to the vacuole by a kiss-and-run mechanism.
Tumour purity as a prognostic factor in colon cancer

Tumour purity is defined as the proportion of cancer cells in the tumour tissue. The impact of tumour purity on colon cancer (CC) prognosis, genetic profile and microenvironment has not been thoroughly accessed. Therefore, clinical and transcriptomic data from three public datasets, GSE17536/17537, GSE39582, and TCGA were retrospectively collected (n = 1248). Tumour purity of each sample was inferred by a computational method based on transcriptomic data. Stage III and MMR-deficient (dMMR) CC patients showed a significantly lower tumour purity. Low purity CC conferred worse survival and tumour purity was identified as an independent prognostic factor. Moreover, high tumour purity CC patients benefited more from adjuvant chemotherapy. Subsequent genomic analysis found that the mutation burden was negatively associated with tumour purity with only APC and KRAS significantly more mutated in high purity CC. However, no somatic copy number alteration event was correlated with tumour purity. Furthermore, immune-related pathways and immunotherapy-associated markers (PD-1, PD-L1, CTLA-4, LAG-3, and TIM-3) were highly enriched in low purity samples. Notably, the relative proportion of M2 macrophages and neutrophils, which indicated worse survival in CC, was negatively associated with tumour purity. Therefore, tumour purity exhibited potential value for CC prognostic stratification as well as adjuvant chemotherapy benefit prediction. The relative worse survival in low purity CC may attribute to higher mutation frequency in key pathways and purity related microenvironmental changing. Summary Low purity colon cancer patients conferred worse survival and benefited less from adjuvant chemotherapy. The mutation burden was negatively associated with tumour purity. Low purity samples exhibited intense immune phenotype with more M2 macrophages and neutrophils infiltration.
The meaning of the Michaelis-Menten constant: Km describes a steady-state

Often, in vitro or in vivo enzyme-mediated catalytic events occur far from equilibrium and, therefore, substrate affinity measured as the inverse of ES ⇄ E+S dissociation equilibrium constant (Kd) has a doubtful physiological meaning; in practice it is almost impossible to determine Kd (except using stopped-flow or other sophisticated methodologies). The Michaelis-Menten constant (Km), the concentration of substrate ([S]) providing half of enzyme maximal activity, is not the (Kd). In the simple E+S ⇄ ES → E+P or in more complex models describing S conversion into P, Km must be considered the constant defining the steady state at any substrate concentration. Enzyme kinetics is based on initial rate determination, i.e. in the linear part of the S to P conversion when the concentration of [ES] remains constant while steady state occurs. We also show that Systems Biology issues such as the time required to respond to a system perturbation, is more dependent on k1, the kinetic constant defining substrateenzyme association, than on Km. Whereas Km is instrumental for biochemical basic and applied approaches, in any physiological condition, an important parameter to be considered is the substrate association rate (k1).
Contrasting Gene Decay in Subterranean Vertebrates: Insights from Cavefishes and Fossorial Mammals

Abstract Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxes functional constraints. Subterranean vertebrates are outstanding models to analyze this process, and gene decay can serve as a readout. We sought to understand some general principles on the extent and tempo of the decay of genes involved in vision, circadian clock, and pigmentation in cavefishes. The analysis of the genomes of two Cuban species belonging to the genus Lucifuga provided evidence for the largest loss of eye-specific genes and nonvisual opsin genes reported so far in cavefishes. Comparisons with a recently evolved cave population of Astyanax mexicanus and three species belonging to the Chinese tetraploid genus Sinocyclocheilus revealed the combined effects of the level of eye regression, time, and genome ploidy on eye-specific gene pseudogenization. The limited extent of gene decay in all these cavefishes and the very small number of loss-of-function mutations per pseudogene suggest that their eye degeneration may not be very ancient, ranging from early to late Pleistocene. This is in sharp contrast with the identification of several vision genes carrying many loss-of-function mutations in ancient fossorial mammals, further suggesting that blind fishes cannot thrive more than a few million years in cave ecosystems.
From taxonomic to functional dark diversity: exploring the causes of potential biodiversity and its implications for conservation

Dark diversity is an emerging and promising concept proposed to estimate the recruitment potential of natural communities and guide conservation and restoration policies. It represents all the species that could be present in a community due to favourable environmental conditions, but are currently lacking. To date, experimental approaches only measured taxonomic dark diversity, mainly based on species coexistence, which relies partly on neutral processes. Thus, these approaches may fail to identify the biodiversity which is lacking for deterministic reasons, and can hence hardly bring out suitable restoration methods. Here, we propose a novel method to estimate dark diversity, which is based on more deterministic coexistence: the coexistence of species’ functional features. We adapted the Beals’ co-occurrence index using functional groups, and we estimated functional dark diversity based on coexistence of functional groups. We then made use of functional dark diversity to address a persistent issue of restoration ecology: how does passive rewilding impact the ecological integrity of recovered communities? We compared spontaneous, secondary woodlands with ancient forests, in terms of taxonomic and functional dark diversity of vascular plants and spiders. Our results indicated that functional dark diversity does not equate to taxonomic dark diversity. Considering plants, recent woodlands surprisingly harboured less functional dark diversity than ancient forests, while they had a very similar amount of taxonomic dark diversity. Concerning spiders, recent woodlands harboured a similar amount of functional dark diversity as ancient forests, but more taxonomic dark diversity. Also, the composition of functional dark diversity differed between forest types, shedding light on their past assembly processes and unveiling their potential for conservation and effective restoration. Synthesis and applications. Functional dark diversity brings novel perspectives for ecological diagnostic and restoration. Combined to taxonomic dark diversity, it enables to identify easily the deterministic constrains which limit the re-assembly of ecological communities after land-use changes and to predict the realistic, possible establishments of functional features. Here, we showed that spontaneous woodlands can have very similar, sometimes even higher, ecological integrity than that of ancient forests, and hence may be valuable habitats to be conserved from an ecological perspective.