Miracle-dz/UniFAR-FTUs huggingface dataset:
Coping with Pleistocene climatic fluctuations: demographic responses in remote endemic reef fishes

Elucidating demographic history during the settlement of ecological communities is crucial for properly inferring the mechanisms that shape patterns of species diversity and their persistence through time. Here, we used genomic data and coalescent-based approaches to elucidate for the first time the demographic dynamics associated with the settlement by endemic reef fish fauna of one of the most remote peripheral islands of the Pacific Ocean, Rapa Nui (Easter Island). We compared the demographic history of nine endemic species in order to explore their demographic responses to Pleistocene climatic fluctuations. We found that Rapa Nui endemic species share a common demographic history as signatures of population expansions were retrieved for almost all of the species studied here, and synchronous demographic expansions initiated during the last glacial period were recovered for more than half of the studied species. These results suggest that eustatic fluctuations associated with Milankovitch cycles have played a central role in species demographic histories and in the final stage of the community assembly of many Rapa Nui reef fishes. Specifically, sea level low stands resulted in the maximum reef habitat extension for Rapa Nui endemic species; we discuss the potential role of seamounts in allowing endemic species to cope with Pleistocene climatic fluctuations, and we highlight the importance of local historical processes over regional ones. Overall, our results shed light on the mechanisms by which endemism arises and is maintained in peripheral reef fish fauna.
Recurrent plasticity mechanisms for perceptual decisions in the human brain

Learning and experience are critical for making successful decisions in the face of inherently ambiguous and noisy information. Yet, the human brain computations that mediate this perceptual learning skill remain highly debated, as fMRI at standard resolution does not allow us to discern whether learning alters sensory encoding or top-down influences. Here, we capitalize on the sub-millimetre resolution of ultra-high field imaging to interrogate the finer-scale computations that mediate perceptual learning in the human brain. Combining 7T laminar imaging with orientation discrimination training, we demonstrate learning-dependent changes in superficial V1 layers, suggesting that training alters read-out rather than input signals in the visual cortex. Further, training enhances feedforward connectivity between superficial V1 layers and middle layers of posterior parietal cortex. Our findings propose that the brain learns to translate sensory information to perceptual decisions via recurrent processing within visual cortex and enhanced connectivity from sensory to decision-related areas.
Comparative morphological and transcriptomic analyses reveal novel chemosensory genes in the poultry red mite, Dermanyssus gallinae and knockdown by RNA interference

Detection of chemical cues via chemosensory receptor proteins are essential for most animals, and underlies critical behaviors, including location and discrimination of food resources, identification of sexual partners and avoidance of predators. The current knowledge of how chemical cues are detected is based primarily on data acquired from studies on insects, while our understanding of the molecular basis for chemoreception in acari, mites in particular, remains limited. The poultry red mite (PRM), Dermanyssus gallinae, is one of the most important blood-feeding ectoparasites of poultry. Unlike other ectoparasites on animals, PRM feeds mainly at night. During daytime, these animals hide themselves in crevices around the poultry house. The diversity in habitat usage, as well as the demonstrated host finding and avoidance behaviors suggest that PRM relies on their sense of smell to orchestrate complex behavioral decisions. Comparative transcriptome analyses revealed the presence of candidate variant ionotropic receptors (IRs), odorant binding proteins (OBPs), niemann-pick proteins type C2 (NPC2) and sensory neuron membrane proteins (SNMPs). Some of these proteins were highly and differentially expressed in the forelegs of PRM. Rhodopsin-like G protein-coupled receptors (GPCRs) were also identified, while insect-specific odorant receptors (ORs) and odorant co-receptors (ORcos) were not detected. Furthermore, using scanning electron microscopy (SEM), the tarsomeres of all legs pairs were shown to be equipped with sensilla chaetica with or without tip pores, while wall-pored olfactory sensilla chaetica were restricted to the distal-most tarsomeres of the forelegs. Further, using the conserved odorant binding protein (OBP) as a test case, the results showed that RNA interference (RNAi) can be induced in D. gallinae chemosensory tissues. This study is the first to describe the presence of chemosensory genes in any Dermanyssidae family. It is also the first report of chemosensory gene knockdown by RNAi in any mite species and demonstrate that their diminutive size, less than 1 mm, is not a major impediment when applying gene knockdown approaches. Our findings make a significant step forward in understanding the chemosensory abilities of D. gallinae.
Zoledronate Extends Health Span and Survival via the Mevalonate Pathway in a FOXO-dependent Manner

Increased longevity has not been paralleled by extended healthspan, resulting in more years spent with multiple diseases in older age. As such, interventions to improve healthspan are urgently required. Zoledronate is a nitrogen containing bisphosphonate, which inhibits the farnesyl pyrophosphate synthase (FPPS) enzyme, central to the mevalonate pathway. It is already used clinically to prevent fractures in osteoporotic patients, who have been reported to derive unexpected and unexplained survival benefits. In this study we show that zoledronate has beneficial effects on both lifespan and healthspan using Drosophila as a model. We found that zoledronate extended lifespan, improved climbing activity and reduced intestinal epithelial dysplasia and permeability in aged flies. Mechanistic studies showed that zoledronate conferred resistance to oxidative stress and reduced accumulation of X-ray-induced DNA damage via inhibition of FPPS. Moreover, zoledronate inhibited pAKT in the mTOR pathway and functioned via dFOXO, a molecule associated with increased longevity, downstream of the mevalonate pathway. Taken together, our work indicates that zoledronate, a drug already widely used and dosed only once a year to prevent osteoporosis, modulates important mechanisms of ageing. Its repurposing holds great promise as a treatment to improve healthspan.
Robust survival-based RNAi using in tandem silencing of adenine phosphoribosyltransferase

RNA interference (RNAi) enables flexible and dynamic interrogation of entire gene families or essential genes without the need for exogenous proteins, unlike CRISPR-Cas technology. Unfortunately, isolation of plants undergoing potent gene silencing requires laborious design, visual screening, and physical separation for downstream characterization. Here, we developed a novel APT-based RNAi technology (APTi) in Physcomitrella patens that simultaneously improves upon the multiple limitations of current RNAi techniques. APTi exploits the pro-survival output of transiently silencing the APT gene in the presence of 2-fluoradenine, thereby establishing survival itself as a reporter of RNAi. To maximize silencing efficacy of gene targets we created vectors that facilitate insertion of any gene target sequence in tandem with the APT silencing motif. The APTi approach resulted in a homogenous population of P. patens mutants specific for our gene target, with zero surviving background plants within 8 days. The observed mutants directly corresponded to a maximal 93% reduction of the tested target protein, substantially exceeding previous dsRNA methods. The positive selection nature of APTi represents a fundamental improvement in RNAi technology and will contribute to the growing demand for technologies amenable to high-throughput phenotyping. One-sentence summary Generation of dsRNA targeting the APT gene in tandem with a target gene enables positive selection of strongly silencing plants.
Runs of homozygosity in killer whale genomes provide a global record of demographic histories

Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we investigated whether variation in killer whale (Orcinus orca) demographic history is reflected in genome‐wide heterozygosity and ROH length distributions, using a global data set of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific‐Atlantic parentage. We first reconstructed demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We found a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (<1 Mb), reflecting high background relatedness due to coalescence of haplotypes deep within the pedigree. In contrast, longer and therefore younger ROH (>1.5 Mb) were found in low latitude populations, and populations of known conservation concern. These include a Scottish killer whale, for which 37.8% of the autosomes were comprised of ROH >1.5 Mb in length. The fate of this population, in which only two adult males have been sighted in the past five years, and zero fecundity over the last two decades, may be inextricably linked to its demographic history and consequential inbreeding depression.
The Development of Cognitive Control in Children with Autism Spectrum Disorders or Obsessive-Compulsive Disorder: A Longitudinal fMRI study

Repetitive behavior is a core symptom of Autism Spectrum Disorder (ASD) and Obsessive-Compulsive Disorder (OCD), and has been associated with impairments in cognitive control. However, it is unclear how cognitive control and associated neural circuitry relate to the development of repetitive behavior in children with these disorders. In a multicenter, longitudinal study (TACTICS; Translational Adolescent and Childhood Therapeutic Interventions in Compulsive Syndromes), the development of cognitive control was assessed during late childhood using a longitudinal fMRI design with a modified stop-signal task in children with ASD or OCD, and typically developing (TD) children (baseline: N=122 (8-12y), follow-up: N=72 (10-14y), average interval: 1.2y). Stop-signal reaction time (SSRT) decreased over development, regardless of diagnosis. Repetitive behavior in children with ASD and OCD was not associated with performance on the stop-signal task. There were no whole-brain between-group differences in brain activity, but ROI-analyses showed increases in activity in right precentral gyrus over development for children with OCD. In sum, even though subtle differences were observed in the development of brain activity in children with OCD, the findings overall suggest that the development of cognitive control, as assessed by the stop signal task, is similar in children with and without ASD or OCD.
Identifying the spatial and temporal dynamics of molecularly-distinct glioblastoma sub-populations

Glioblastomas (GBMs) are the most aggressive primary brain tumours and have no known cure. Each individual tumour comprises multiple sub-populations of genetically-distinct cells that may respond differently to targeted therapies and may contribute to disappointing clinical trial results. Image-localized biopsy techniques allow multiple biopsies to be taken during surgery and provide information that identifies regions where particular sub-populations occur within an individual GBM, thus providing insight into their regional genetic variability. These sub-populations may also interact with one another through a competitive or cooperative nature; it is important to ascertain the nature of these interactions, as they may have implications for responses to targeted therapies. We combine genetic information from biopsies with a mechanistic model of interacting GBM sub-populations to characterise the nature of interactions between two commonly occurring GBM sub-populations, those with EGFR and PDGFRA genes amplified. We study population levels found across image-localized biopsy data from a cohort of 25 patients and compare this to model outputs under competitive, cooperative and neutral interaction assumptions. We explore other factors affecting the observed simulated sub-populations, such as selection advantages and phylogenetic ordering of mutations, which may also contribute to the levels of EGFR and PDGFRA amplified populations observed in biopsy data.
Analysis of the mutation dynamics of SARS-CoV-2 reveals the spread history and emergence of RBD mutant with lower ACE2 binding affinity

Monitoring the mutation dynamics of SARS-CoV-2 is critical for the development of effective approaches to contain the pathogen. By analyzing 106 SARS-CoV-2 and 39 SARS genome sequences, we provided direct genetic evidence that SARS-CoV-2 has a much lower mutation rate than SARS. Minimum Evolution phylogeny analysis revealed the putative original status of SARS-CoV-2 and the early-stage spread history. The discrepant phylogenies for the spike protein and its receptor binding domain proved a previously reported structural rearrangement prior to the emergence of SARS-CoV-2. Despite that we found the spike glycoprotein of SARS-CoV-2 is particularly more conserved, we identified a receptor binding domain mutation that leads to weaker ACE2 binding capability based on in silico simulation, which concerns a SARS-CoV-2 sample collected on 27th January 2020 from India. This represents the first report of a significant SARS-CoV-2 mutant, and requires attention from researchers working on vaccine development around the world. Highlights Based on the currently available genome sequence data, we provided direct genetic evidence that the SARS-COV-2 genome has a much lower mutation rate and genetic diversity than SARS during the 2002-2003 outbreak. The spike (S) protein encoding gene of SARS-COV-2 is found relatively more conserved than other protein-encoding genes, which is a good indication for the ongoing antiviral drug and vaccine development. Minimum Evolution phylogeny analysis revealed the putative original status of SARS-CoV-2 and the early-stage spread history. We confirmed a previously reported rearrangement in the S protein arrangement of SARS-COV-2, and propose that this rearrangement should have occurred between human SARS-CoV and a bat SARS-CoV, at a time point much earlier before SARS-COV-2 transmission to human. We provided first evidence that a mutated SARS-COV-2 with reduced human ACE2 receptor binding affinity have emerged in India based on a sample collected on 27th January 2020.
Distal-less genes Dlx1/Dlx2 repress oligodendrocyte genesis through transcriptional inhibition of Olig2 expression in the developing vertebrate forebrain

In this study, we demonstrate that mouse DLX2 binds to the Olig2 gene locus in mouse embryonic forebrain in vivo. We further confirm the specificity and the transcriptional repressive effect of the binding in vitro. Furthermore, loss of Dlx1/2 function leads to increased Olig2 expression in the ventral embryonic mouse forebrain in vivo. As well, we demonstrate that chicken DLX1 binds to one chicken Olig2 gene domain in vitro, and overexpression of Dlx1 is sufficient to repress Olig2 expression in the developing chicken forebrain in ovo. Chicken DLX1 with a mutation eliminating its DNA binding ability is unable to bind to the Olig2 probe in vitro, and abrogates its repressive function on Olig2 expression in ovo. Our results establish that Dlx1/2 is both necessary and sufficient to repress oligodendrocyte specification mediated via direct transcriptional inhibition of Olig2 expression in the developing vertebrate forebrain.
MicroHapDB: A Portable and Extensible Database of All Published Microhaplotype Marker and Frequency Data

Microhaplotypes are the subject of significant interest in the forensics community as a promising multi-purpose forensic DNA marker for human identification. Microhaplotype markers are composed of multiple SNPs in close proximity, such that a single NGS read can simultaneously genotype the individual SNPs and phase them in aggregate to determine the associated donor haplotype. Abundant throughout the human genome, numerous recent studies have sought to discover and rank microhaplotype markers according to allelic diversity within and among populations. Microhaplotypes provide an appealing alternative to STR markers for human identification and mixture deconvolution, but can also be optimized for ancestry inference or combined with phenotype SNPs for prediction of externally visible characteristics in a multiplex NGS assay. Designing and evaluating panels of microhaplotypes is complicated by the lack of a convenient database of all published data, as well as the lack of population allele frequency data spanning disparate marker collections. We present MicroHapDB, a comprehensive database of published microhaplotype marker and frequency data, as a tool to advance the development of microhaplotype-based human forensics capabilities. We also present population allele frequencies derived from 26 global population samples for all microhaplotype markers published to date, facilitating the design and interpretation of custom multi-source panels. We submit MicroHapDB as a resource for community members engaged in marker discovery, population studies, assay development, and panel and kit design.
Improved genetically encoded near-infrared fluorescent calcium ion indicators for in vivo imaging

Near-infrared (NIR) genetically-encoded calcium ion (Ca2+) indicators (GECIs) can provide advantages over visible wavelength fluorescent GECIs in terms of reduced phototoxicity, minimal spectral cross-talk with visible-light excitable optogenetic tools and fluorescent probes, and decreased scattering and absorption in mammalian tissues. Our previously reported NIR GECI, NIR-GECO1, has these advantages but also has several disadvantages including lower brightness and limited fluorescence response compared to state-of-the-art visible wavelength GECIs, when used for imaging of neuronal activity. Here, we report two improved NIR GECI variants, designated NIR-GECO2 and NIR-GECO2G, derived from NIR-GECO1. We characterized the performance of the new NIR GECIs in cultured cells, acute mouse brain slices, and C. elegans and Xenopus laevis in vivo. Our results demonstrate that NIR-GECO2 and NIR-GECO2G provide substantial improvements over NIR-GECO1 for imaging of neuronal Ca2+ dynamics.
Lamin B2 follows lamin A/C- mediated nuclear mechanics and cancer cell invasion efficacy

Interstitial tumor cell invasion depends upon complex mechanochemical adaptation of both cell body and the rigid nucleus in response to extracellular tissue topologies. Nuclear mechanics during cell migration through confined environments is controlled by A-type lamins, however, the contribution of B-type lamins to the deformability of the nucleus remains unclear. Using systematic expression regulation of different lamin isoforms, we applied multi-parameter wet-lab and in silico analysis to test their impact on nuclear mechanics, shape regulation, and cancer cell migration. Modulation of lamin A/C and B2 but not B1 isoforms controlled nuclear deformation and viscoelasticity, whereby lamin B2 generally followed lamin A/C-mediated effects. Cell migration rates were altered by 5 to 9-fold in dense collagen environments and synthetic devices, with accelerated rates after lamin downregulation and reverse effects after lamin upregulation, with migration rates strongly depending on nuclear shape change. These findings implicate cooperation of lamin B2 with lamin A/C in regulating nuclear mechanics for shape adaptation and migration efficacy. Summary Nuclear deformability during cancer cell invasion and metastasis is critically regulated by lamin A. Here, researchers showed that lamin B2 also contributes to nuclear mechanics, implicating cooperating lamin networks regulating nuclear integrity, migration efficacy, and metastatic tumor progression.
Vegetation and Microbes Interact to Preserve Organic Matter in Wooded Peatlands

Peatlands have persisted as massive carbon sinks over millennia, even during past periods of climate change. The commonly accepted theory of abiotic controls (mainly anoxia and low temperature) over carbon decomposition cannot explain how vast low-latitude wooded peatlands consistently accrete peat under warm and seasonally unsaturated conditions. Similarly, that theory cannot accurately project the decomposition rate in boreal peatlands where warming and drought have decreased Sphagnum and increased shrub expansion. Here, by comparing composition and ecological traits of microbes between Sphagnum- and shrub-dominated peatlands, we present a previously unrecognized natural course that curbs carbon loss against climate change. Slow-growing microbes decisively dominate the studied wooded peatlands, concomitant with plant-induced, high recalcitrant carbon and phenolics. The slow-growing microbes inherently metabolize organic matter slowly. However, the fast-growing microbes that dominate our Sphagnum site (most boreal peatlands as well) decomposed labile carbon >30 times faster than the slow-growing microbes. We show that the high-phenolic shrub/tree induced shifts in microbial composition may compensate for positive effects of temperature and/or drought on metabolism over time in peatlands. This biotic self-sustaining process that modulates abiotic controls on carbon cycling may help better project long-term climate-carbon feedbacks in peatlands.
Integrative and Conjugative Elements (ICE) and Associated Cargo Genes within and across Hundreds of Bacterial Genera

Horizontal gene transfer mediated by integrative and conjugative elements (ICE) is considered an important evolutionary mechanism of bacteria. It allows organisms to quickly evolve new phenotypic properties including antimicrobial resistance (AMR) and virulence. The rate of ICE-mediated cargo gene exchange has not yet been comprehensively studied within and between bacterial taxa. In this paper we report a big data analysis of ICE and associated cargo genes across over 200,000 bacterial genomes representing 1,345 genera. Our results reveal that half of bacterial genomes contain one or more known ICE features (“ICE genomes”), and that the associated genetic cargo may play an important role in the spread of AMR genes within and between bacterial genera. We identify 43 AMR genes that appear only in ICE genomes and never in non-ICE genomes. A further set of 95 AMR genes are found >5x more often in ICE versus non-ICE genomes. In contrast, only 29 AMR genes are observed more frequently (at least 5:1) in non-ICE genomes compared to ICE genomes. Analysis of NCBI antibiotic susceptibility assay data reveals that ICE genomes are also over-represented amongst phenotypically resistant isolates, suggesting that ICE processes are critical for both genotypic and phenotypic AMR. These results, as well as the underlying big data resource, are important foundational tools for understanding bacterial evolution, particularly in relation to important bacterial phenotypes such as AMR.