Miracle-dz/UniFAR-FTUs huggingface dataset:
Unicolonal aggression within and among local population of the invasive ant, Tapinoma melanocephalum in Viti Levu, Fiji

Invasive species are among the most significant threats to biodiversity, especially in insular areas. These species drastically alter ecosystem structures and functioning and may cause local extinctions. Among them, structure-infesting ants represent a subset of major pest problems in urban environments, where they represent violation of esthetic and economic thresholds, and have potential influences on human health. Some invasive ants exhibit an extraordinary form of social organisation, called unicoloniality, whereby individuals mix freely among physically separated nests. This form of social organization has highly attributed to their success. Among these ants spreading world-wide, Tapinoma melanocephalum (ghost ant) represents an understudied model. This is a tramp ant of African or Oriental origin, which appears to be a disturbance specialist and in many locations is absent from undisturbed natural habitats. But, this species is widely distributed all around Fiji, especially on the main island of Viti Levu. In this context, we test the pattern of aggression and genetic structure of seven distant populations from Viti Levu; within nests and among nests within the populations. Ants within and among populations showed no aggressive interactions. This pattern led to an assumption that there may have been only one introduction which led to existence of one main supercolony. This study has provided evidence that unicoloniality can be maintained in invasive ants with very little genetic differentiation and has the ability to discriminate between nest mates and nonnests mates through changing cuticular hydrocarbons.
Phylogeny- and morphology-based recognition of new species in the spider-parasitic genus Gibellula (Hypocreales, Cordycipitaceae) from Thailand

Abstract Thailand is known to be a part of what is called the Indo-Burma biodiversity hotspot, hosting a vast array of organisms across its diverse ecosystems. This is reflected by the increasing number of new species described over time, especially fungi. However, a very few fungal species from the specialized spider-parasitic genus Gibellula have ever been reported from this region. A survey of invertebrate-pathogenic fungi in Thailand over several decades has led to the discovery of a number of fungal specimens with affinities to this genus. Integration of morphological traits into multi-locus phylogenetic analysis uncovered four new species: G. cebrennini, G. fusiformispora, G. pigmentosinum, and G. scorpioides. All these appear to be exclusively linked with torrubiella-like sexual morphs with the presence of granulomanus-like asexual morph in G. pigmentosinum and G. cebrennini. A remarkably high host specificity of these new species towards their spider hosts was revealed, and for the first time, evidence is presented for manipulation of host behavior in G. scorpioides.
Evaluation of Combined Effect of Micronutrients (ZnSO4 + Borax) and Fungicides to Control the Purple Blotch Complex of Onion (Allium cepa)

Ten different treatments viz. T0 = Control, T1 = Micronutrients (ZnSO4 + Borax), T2 = Rovral 50 WP + Micronutrients, T3 = Dithane M-45 + Micronutrients, T4 = Ridomil Gold + Micronutrients, T5 = Cupravit + Micronutrients, T6 = Rovral 50 WP, T7 = Dithane M-45, T8 = Ridomil Gold and T9 = Cupravit were evaluated against the purple blotch complex disease of onion caused by Alternaria porri and Stemphylium vesicarium in field condition for bulb yield. In lab condition, all the tested chemical fungicides (Rovral 50 WP, Dithane M-45, Ridomil Gold MZ-72 and Cupravit 50 WP) significantly reduced mycelial growth of both pathogens. Among the fungicides, Rovral 50 WP @ 0.2% reduced the highest radial mycelial growth followed by Dithane M-45 @ 0.45% and Ridomil Gold MZ-72 @ 0.2% compared to control. In field experiment, application of Rovral 50 WP @ 0.2% along with micronutrients showed significant effect in reducing disease incidence and severity which significantly increased bulb yield and yield contributing characters.
Temporal trait plasticity and neighborhood crowding predict the growth of tropical trees

Functional traits and neighborhood composition have been used to predict tree growth dynamics. Temporal changes in trait values (temporal trait plasticity) is one of the mechanisms for adaptive plastic response to environmental change. However, the consequence of temporal change in trait values and neighborhoods on the growth performance of individuals has rarely been investigated. We, therefore tested the effect of temporal changes in trait values and neighborhood crowding on the growth rate of individuals in a tropical forest using a dataset containing individual level growth and functional trait data for Ficus individuals. We collected trait and size data at two time points (2010 and 2017) for 472 individuals of 15 Ficus species in Xishuangbanna tropical forest dynamics plot, southwest China. We used linear mixed effect model to predict the effect of temporal trait plasticity and neighborhood crowding on the relative growth rate of individuals using these data. We found significant temporal changes in individuals’ functional traits suggesting a shift in ecological strategies from being functionally acquisitive to conservative. We also found differences in neighborhood crowding between the two census years indicating that the strength of individual interactions might change over time. The temporal changes in trait values and neighborhood crowding were found to predict better the relative growth rate of individuals, compared to static trait or crowding values in the initial and final censuses. We also found major axes of tree functional strategies in a principal component analysis, highlighting potentially adaptive trait differences. Our results in general highlight to consider the temporal dimension of functional traits and biotic interactions, as our result suggest that growth-trait relationships may vary between time points, allowing us to understand the demographic response of species to temporal environmental change.
Acute depletion of METTL3 identifies a role for N6-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome

RNA N6-methyladenosine (m6A) modification plays important roles in multiple aspects of RNA regulation. m6A is installed co-transcriptionally by the METTL3/14 complex, but its direct roles in RNA processing remain unclear. Here we investigate the presence of m6A in nascent RNA of mouse embryonic stem cells (mESCs). We find that around 10% m6A peaks are in introns, often close to 5’-splice sites. RNA m6A peaks significantly overlap with RBM15 RNA binding sites and the histone modification H3K36me3. Interestingly, acute dTAG depletion of METTL3 reveals that inclusion of m6A-bearing alternative introns/exons in the nascent transcriptome is disrupted. For terminal or variable-length exons, m6A peaks are generally located upstream of a repressed 5’-splice site, and downstream of an enhanced 5’-splice site. Intriguingly, genes with the most immediate effects on splicing include several components of the m6A pathway, suggesting an autoregulatory function. Our findings demonstrate a direct crosstalk between m6A machinery and the regulation of RNA processing.
Scribble controls social behaviors through the regulation of the ERK/Mnk1 pathway

Social behavior is a basic domain affected in several neurodevelopmental disorders. Indeed, deficits in social interest, interactions and recognition represent core symptoms of Autism Spectrum Disorder but are also found associated with a heterogeneous set of neuropsychiatric and rare disorders. The SCRIB gene that codes for the polarity protein SCRIBBLE has been identified as a risk gene for spina bifida, the most common type of open neural tube defect, found at high frequencies in autistic patients, as other congenital anomalies, while the deletions/mutations of the 8q24.3 region encompassing SCRIB genes is associated with multisyndromic and rare disorders. Nonetheless, the potential link between SCRIB and ASD-relevant social phenotypes has not been investigated yet. Hence, we performed an extensive behavioral characterization of the circletail line that carries a mutated version of Scrib. Scribcrc/+ mice displayed reduced social interest, lack of preference for social novelty and social reward, and reduced social habituation while other behavioral domains were unaltered. Social deficits were associated with reduced hippocampal volume, upregulation of ERK phosphorylation in specific hippocampal regions, together with increased c-Fos activity in the same brain areas. Importantly, the social alterations were rescued by both direct and indirect pERK inhibition. These results support a specific link between polarity genes, social behaviors and hippocampal functionality, thus suggesting a role for SCRIB in the etiopathology of neurodevelopmental disorders. Furthermore, our data demonstrate the crucial role of the MAPK/ERK signaling pathway, in underlying the social deficits induced by SCRIB mutation, thus supporting its relevance as a therapeutic target.
Physiological System Dysregulation in Gene Expression Correlates Negatively with Age

We attempted to identify gene expression systems that dysregulate with age in human peripheral blood samples across five public datasets. Dysregulation of gene ontology (GO)-defined systems was measured using the Mahalanobis distance (DM), a measure of multivariant aberrance. We expected many weak positive DM-age correlations, indicating loss of homeostatic control. Out of the 5180 GO terms tested, we found 230 systems that replicated in at least three datasets. Surprisingly, all 230 systems showed negative DM-age correlations, in contrast to findings with clinical biomarkers. These systems were mostly metabolic functions related to small molecules and nitrogen compounds, transport functions, biosynthetic processes and response to stress functions. These results suggest a loss of responsiveness in these gene expression systems during the aging process, and contrast to some previous literature showing increased gene expression heterogeneity with age.
DTFLOW: Inference and Visualization of Single-cell Pseudo-temporal Trajectories Using Diffusion Propagation

One of the major challenges in single-cell data analysis is the determination of cellular developmental trajectories using single-cell data. Although substantial studies have been conducted in recent years, more effective methods are still strongly needed to infer the developmental processes accurately. In this work we devise a new method, named DTFLOW, for determining the pseudo-temporal trajectories with multiple branches. This method consists of two major steps: namely a new dimension reduction method (i.e. Bhattacharyya kernel feature decomposition (BKFD)) and a novel approach, named Reverse Searching on kNN Graph (RSKG), to identify the underlying multi-branching processes of cellular differentiations. In BKFD we first establish a stationary distribution for each cell to represent the transition of cellular developmental states based on the random walk with restart algorithm and then propose a new distance metric for calculating pseudo-times of single-cells by introducing the Bhattacharyya kernel matrix. The effectiveness of DTFLOW is rigorously examined by using four single-cell datasets. We compare the efficiency of the new method with two state-of-the-art methods. Simulation results suggest that our proposed method has superior accuracy and strong robustness properties for constructing pseudo-time trajectories. Availability: DTFLOW is implemented in Python and available at https://github.com/statway/DTFLOW.
Detection of sexually antagonistic transmission distortions in trio datasets

Sex dimorphisms are widespread in animals and plants, for morphological as well as physiological traits. Understanding the genetic basis of sex dimorphism and its evolution is crucial for understanding biological differences between the sexes. Genetic variants with sex-antagonistic effects on fitness are expected to segregate in populations at the early phases of sexual dimorphism emergence. Detecting such variants is notoriously difficult, and the few genome-scan methods employed so far have limited power and little specificity. Here, we propose a new framework to detect a signature of sexually antagonistic selection. We rely on trio datasets where sex-biased transmission distortions can be directly tracked from parents to offspring, and allows identifying signal of sexually antagonistic transmission distortions in genomic regions. We report the genomic location and recombination pattern surrounding 66 regions detected as potentially under sexually antagonist selection. We find an enrichment of genes associated with embryonic development within these regions. Last, we highlight two candidates regions for sexually antagonistic selection in humans.
Single-Cell RNAseq of Out-of-Thaw Mesenchymal Stromal Cells Shows Striking Tissue-of-Origin Differences and Inter-donor Cell-Cycle Variations

Mesenchymal stromal cells (MSCs) from a variety of tissue sources are widely investigated in clinical trials, and the MSCs are often administered immediately after thawing the cryopreserved product. While previous reports have examined the transcriptome of freshly-cultured MSCs from some tissues, little is known about the single-cell transcriptomic profiles of out-of-thaw MSCs from different tissue sources. Such understanding could help determine which tissue origins and delivery methods are best suited for specific indications. Here, we characterized cryopreserved MSCs, immediately post-thaw, from bone marrow (BM) and cord tissue (CT), using single-cell RNA sequencing (scRNA-seq). We show that out-of-thaw BM-vs. CT-MSCs have significant differences in gene expression. Gene-set enrichment analyses implied divergent functional potential. In addition, we show that MSC-batches can vary significantly in cell cycle status, suggesting different proliferative vs. immunomodulatory potentials. Our results provide a comprehensive single-cell transcriptomic landscape of clinically and industrially relevant MSC products. Highlights Single cell gene expression comparison between Bone-marrow derived MSCs and Cord-tissue derived MSCs Donor effects and cell heterogeneity on tissue-specific MSC gene expression Single Cell Pooling Enhances Differential Expression Analysis for Bone marrow and Cord tissue MSC samples Gene ontology reveals tissue specific unique molecular function and pathways
Optogenetic stimulation of lateral hypothalamic orexin/dynorphin inputs in the ventral tegmental area potentiates mesolimbic dopamine neurotransmission and promotes reward-related behaviours

Reward and reinforcement processes are critical for survival and propagation of genes. While numerous brain systems underlie these processes, a cardinal role is ascribed to mesolimbic dopamine. However, ventral tegmental area (VTA) dopamine neurons receive complex innervation and various neuromodulatory factors, including input from lateral hypothalamic orexin/hypocretin neurons which also express and co-release the neuropeptide, dynorphin (LHox/dyn). Dynorphin in the VTA induces aversive conditioning through the Kappa opioid receptor (KOR) and decreases dopamine when administered intra-VTA. Exogenous application of orexin or orexin 1 receptor (OXR1) antagonists in the VTA bidirectionally modulates dopamine-driven motivation and reward-seeking behaviours, including the attribution of motivational value to primary rewards and associated conditioned stimuli. However, the effect of endogenous stimulation of LHox/dyn-containing projections to the VTA and the potential contribution of co-released dynorphin on mesolimbic dopamine and reward related processes remains uncharacterised. We combined optogenetic, electrochemical, and behavioural approaches to examine this. We found that optical stimulation of LHox/dyn inputs in the VTA potentiates mesolimbic dopamine neurotransmission in the nucleus accumbens (NAc) core, produces real time and place preference, and increases the incentive value attributed to a Pavlovian food cue. LHox/dyn potentiation of NAc dopamine release and real time place preference was completely blocked by an OXR1 antagonist. Thus, rewarding effects associated with optical stimulation of LHox/dyn inputs in the VTA are predominantly driven by orexin rather than dynorphin.
LIONirs: flexible Matlab toolbox for fNIRS data analysis

Background Functional near-infrared spectroscopy (fNIRS) is a suitable tool for recording brain function in pediatric or challenging populations. As with other neuroimaging techniques, the scientific community is engaged in an evolving debate regarding the most adequate methods for performing fNIRS data analyses. New method We introduce LIONirs, a neuroinformatics toolbox for fNIRS data analysis, designed to follow two main goals: (1) flexibility, to explore several methods in parallel and verify results using 3D visualization; (2) simplicity, to apply a defined processing pipeline to a large dataset of subjects by using the MATLAB Batch System. Results Within the graphical user interfaces (DisplayGUI), the user can reject noisy intervals and correct artifacts, while visualizing the topographical projection of the data onto the 3D head representation. Data decomposition methods are available for the identification of relevant signatures, such as brain responses or artifacts. Multimodal data recorded simultaneously to fNIRS, such as physiology, electroencephalography or audio-video, can be visualized using the DisplayGUI. The toolbox includes several functions that allow one to read, preprocess, and analyze fNIRS data, including task-based and functional connectivity measures. Comparison with existing methods Several good neuroinformatics tools for fNIRS data analysis are currently available. None of them emphasize multimodal visualization of the data throughout the preprocessing steps and multidimensional decomposition, which are essential for understanding challenging data. Furthermore, LIONirs provides compatibility and complementarity with other existing tools by supporting common data format. Conclusions LIONirs offers a flexible platform for basic and advanced fNIRS data analysis, shown through real experimental examples. Highlights The LIONirs toolbox is designed for fNIRS data inspection and visualization. Methods are integrated for isolation of relevant activity and correction of artifacts. Multimodal auxiliary, EEG or audio-video are visualized alongside the fNIRS data. Task-based and functional connectivity measure analysis tools are available. The code structure allows to automated and standardized analysis of large data set. Graphical abstract
Striatal BOLD and midfrontal theta power express motivation for action

Action selection is biased by the valence of anticipated outcomes. To assess the mechanisms by which these motivational biases are expressed and controlled, we measured simultaneous EEG-fMRI during a motivational Go/NoGo learning task (N=36), leveraging the temporal resolution of EEG and subcortical access of fMRI. VmPFC BOLD encoded cue valence, importantly predicting trial-by-trial valence-driven response speed differences and EEG theta power around cue onset. In contrast, striatal BOLD encoded selection of active Go responses and correlated with theta power around response time. Within trials, theta power ramped in the fashion of an evidence accumulation signal for the value of making a ‘Go’ response, capturing the faster responding to reward cues. Our findings reveal a dual nature of midfrontal theta power, with early components reflecting the vmPFC contribution to motivational biases, and late components reflecting their striatal translation into behavior, in line with influential recent “value of work” theories of striatal processing.
A thousand metagenome-assembled genomes of Akkermansia reveal new phylogroups and geographical and functional variations in human gut

The present study revealed the genomic architecture of Akkermansia in human gut by analyzing 1,119 near-complete metagenome-assembled genomes, 84 public available genomes, and 1 newly sequenced A. glycaniphila strain. We found that 1) the genomes of Akkermansia formed 4 species (including 2 candidate species) with distinct interspecies similarity and differed genomic characteristics, and 2) the population of A. muciniphila was structured by 3 previously identified phylogroups (Amuc I, II, and III) referring to 1,132 genomes and 1 new phylogroup (defined as Amuc IV) that contained 62 genomes. Amuc III was presented in Chinese population and Amuc IV was mainly distributed in western populations. A large number of gene of functions, pathways, and carbohydrate active enzymes that specifically associated to phylogroups. Our findings based on over a thousand genomes strengthened the previous knowledge and provided new insights into the population structure and ecology of Akkermansia in human gut.
TTAPE-Me dye is not selective to cardiolipin and responds to main anionic phospholipids unspecifically

Identification, visualization and quantitation of cardiolipin (CL) in biological membranes is of great interest due to important structural and physiological roles of this lipid. Selective fluorescent detection of CL using non-covalently bound fluorophore TTAPE-Me (1,1,2,2-tetrakis[4-(2-trimethylammonioethoxy)-phenylethene) has been recently proposed. However, this dye was only tested on wild-type mitochondria or liposomes containing neglegible amounts of other anionic lipids, such as PG and PS. No clear preference of TTAPE-Me for binding to CL compared to PG and PS was found in our experiments. The shapes of the emission spectra for these anionic phospholipids were also found to be indistinguishable. Our experiments and complementary molecular dynamics simulations suggest that fluorescence intensity of TTAPE-Me is regulated by dynamic equilibrium between emitting dye, bound to anionic lipids by means of unspecific electrostatic attraction, and non-emitting dye aggregates in aqueous solution. Therefore, TTAPE-Me is not suitable for detection, visualization and localization of CL in the presence of PS and PG present in physiological amounts in the membranes of eukaryotic and prokaryotic cells, respectively.
The inhibitory activity of GlyT2 targeting bioactive lipid analgesics are influenced by formation of a deep lipid cavity

The human glycine transporter GlyT2 (SLC6A5) has emerged as a promising drug target for the development of new analgesics to manage chronic pain. N-acyl amino acids inhibit GlyT2 through binding to an allosteric binding site to produce analgesia in vivo with minimal overt side effects. In this paper we use a combination of medicinal chemistry, electrophysiology, and computational modelling to explore the molecular basis of GlyT2 inhibition at the allosteric site. We show how N-acyl amino acid head group stereochemistry, tail length and double bond position promote enhanced inhibition by deep penetration into the binding pocket. This work provides new insights into the interaction of lipids with transport proteins and will aid in future rational design of novel GlyT2 inhibitors.