Myosin 5a transports cellular cargos along actin filaments towards the cell periphery. Its long lever plays a key role in determining the large size of its powerstoke, stepping distance along F-actin, ability to bear load and its regulation by Ca2+. Despite this, little is known about the physical properties of the lever and how they contribute to the mechanics of walking. Using a combination of cryo-electron microscopy and molecular dynamics simulations, we resolved the first structure of myosin 5a comprising the motor domain and full-length lever (subfragment-1) bound to actin. From the flexibility captured in the cryo-electron microscopy data, we were able to characterise the stiffness of the lever. Here, we demonstrate how the structure and flexibility of the lever contribute to the regulation and walking behaviour of myosin 5a. | Make paid
Understanding the impact of lipid nanoparticles' size on immunogenicity represents an important step for enabling the rapid development of novel vaccines against known or emergent diseases. Dynamic light scattering, also known as quasi-elastic light scattering or photon correlation spectroscopy, has established itself as an optimal analytical method to determine particle size due to its in-situ approach and fast measurements. However, its application to many systems of industrial relevance has been limited due to artifacts arising from multiple scattering. Results interpretation becomes severely compromised depending on the concentration of the system and the size of the particles. In this context, strong sample dilution is often required, bringing additional uncertainties to the formulation development process. Here, we show how advanced dynamic light scattering technology can filter out multiple scattering from the signal and yield fully accurate sizing measurements, regardless of the sample concentration. We illustrate this in a comparative study with standard dynamic light scattering using polystyrene beads as model suspension as well as a concentrated commercial lipid nanoparticle adjuvant (AddaVax). | Make paid
Biomolecular condensates form via phase transitions of condensate-specific biomacromolecules. Intrinsically disordered regions (IDRs) featuring the appropriate sequence grammar can contribute homotypic and heterotypic interactions to the driving forces for phase separation of multivalent proteins. At this juncture, experiments and computations have matured to the point where the concentrations of coexisting dense and dilute phases can be quantified for individual IDRs in complex milieus both in vitro and in vivo. For a macromolecule such as a disordered protein in a solvent, the locus of points that connects concentrations of the two coexisting phases defines a phase boundary or binodal. Often, only a few points along the binodal, especially in the dense phase, are accessible for measurement. In such cases and for quantitative and comparative analysis of parameters that describe the driving forces for phase separation, it is useful to fit measured or computed binodals to well-known mean-field free energies for polymer solutions. Unfortunately, the non-linearity of the underlying free energy functions makes it challenging to put mean-field theories into practice. Here, we present FIREBALL, a suite of computational tools designed to enable efficient construction, analysis, and fitting to experimental or computed data of binodals. We show that depending on the theory being used, one can also extract information regarding coil-to-globule transitions of individual macromolecules. Here, we emphasize the ease-of-use and utility of FIREBALL using examples based on data for two different IDRs. | Make paid
Cytochrome c oxidase (CcO) is an essential enzyme in mitochondrial and bacterial respiration. It catalyzes the four-electron reduction of molecular oxygen to water and harnesses the chemical energy to translocate four protons across biological membranes, thereby establishing the proton gradient required for ATP synthesis. The full turnover of the CcO reaction involves an oxidative phase, in which the reduced enzyme (R) is oxidized by molecular oxygen to the metastable oxidized OH state, and a reductive phase, in which OH is reduced back to the R state. During each of the two phases, two protons are translocated across the membranes. However, if OH is allowed to relax to the resting oxidized state (O), the redox equivalent to OH, its subsequent reduction to R is incapable of driving proton translocation. How the O state structurally differs from OH remains an enigma in modern bioenergetics. Here, with resonance Raman spectroscopy and serial femtosecond X-ray crystallography (SFX), we show that the heme a3 iron and CuB in the active site of the O state, like those in the OH state, are coordinated by a hydroxide ion and a water molecule, respectively. However, Y244, a residue covalently linked to one of the three CuB ligands and critical for the oxygen reduction chemistry, is in the neutral protonated form, which distinguishes O from OH, where Y244 is in the deprotonated tyrosinate form. These structural characteristics of O provide new insights into the proton translocation mechanism of CcO. | Make paid
Pseudouridine ({Psi}) is one of the most common post-transcriptional modifications in RNA and has been known to play significant roles in several crucial biological processes. The N1-methyl derivative of pseudouridine i.e N1-methylpseudouridine has also been reported to be important for the stability and function of RNA. Several studies suggest the importance of pseudouridine and N1-methylpseudouridine in mRNA therapeutics. The critical contribution of pseudouridine, especially that of its N1-methyl derivative in the efficiency of the COVID-19 mRNA vaccines, suggests the requirement to better understand the role of these modifications in the structure, stability and function of RNA. In the present study, we have investigated the consequences of the presence of these modifications in the stability of RNA duplex structures by analyzing different structural properties, hydration characteristics and energetics of these duplexes. We have previously studied the structural and thermodynamic properties of RNA duplexes with an internal {Psi}-A pair and reported the stabilizing effect of {Psi} over U (Deb, I. et al. Sci Rep 9, 16278 (2019)). Here, we have extended our work to understand the properties of RNA duplexes with an internal m1{Psi}-A pair and also theoretically demonstrate the effect of substituting internal U-G, U-U and U-C mismatches with the {Psi}-G, {Psi}-U and {Psi}-C mismatches and also with the m1{Psi}-G, m1{Psi}-U and m1{Psi}-C mismatches respectively, within dsRNA. Our results indicate the context-dependent stabilization of base stacking interactions by N1-methylpseudouridine compared to uridine and pseudouridine, presumably resulting from the increased molecular polarizability due to the presence of the methyl group. | Make paid
A crucial step in inbred plant breeding is the choice of mating design to derive high-performing inbred varieties while also maintaining a competitive breeding population to secure sufficient genetic gain in future generations. In practice, the mating design usually relies on crosses involving the best parental inbred lines to ensure high mean progeny performance. This excludes crosses involving lower performing but more complementary parents in terms of favorable alleles. We predicted crosses with putative outstanding progenies (high mean and high variance progeny distribution) using genomic prediction models to assess the value of top progeny. This study compared the benefits and drawbacks of seven genomic cross selection criteria (CSC) in terms of genetic gain for one trait and genetic diversity in the next generation. Six CSC were already published and we have proposed an improved CSC that can estimate the proportion of progeny above a threshold (e.g. the best parental line of the breeding population). We simulated mating designs optimized using different CSC and 835 elite parents from a real breeding program that were evaluated between 2000 and 2016. We applied constraints on parental contributions and genetic similarities between parents according to usual breeder practices. Our results showed that CSC based on progeny variance estimation increased the genetic value of superior progenies by up to 5% in the next generation compared to CSC based on the progeny mean estimation (i.e. parental genetic values) alone. It also increased the genetic gain (up to 4%) and/or maintained more genetic diversity at QTLs (up to 4% more genic variance when the marker effects were perfectly estimated). | Make paid
Loss of function mutations of the PINK1 kinase cause familial early-onset Parkinson's disease. PINK1 is activated upon mitochondrial damage to phosphorylate ubiquitin and Parkin to trigger removal of damaged mitochondria by autophagy (mitophagy). PINK1 also indirectly phosphorylates a subset of Rab GTPases including Rab8A. We have performed a siRNA screen of all human Ser/Thr kinases in HeLa cells and discovered the integrated stress response kinase EIF2AK1 (HRI) negatively regulates PINK1 following mitochondrial damage. We demonstrate that EIF2AK1 knockout cells enhance mitochondrial depolarization-induced stabilization of PINK1 and increased phosphorylation of ubiquitin and Rab8A. We confirm our findings in multiple human cell lines including SK-OV-3, U2OS and ARPE-19 cells. Knockdown of upstream components of the recently described mitochondrial-cytosol relay pathway, OMA1 and DELE1, enhanced PINK1 stabilisation and activation similar to EIF2AK1. Using the mito-QC mitophagy reporter in human cells, we observe that EIF2AK1 knockdown moderately increases PINK1-dependent mitophagy. Our findings indicate that EIF2AK1 is a negative regulator of PINK1 and suggest that inhibitors of EIF2AK1 could have therapeutic benefits in Parkinson's disease and related disorders of ageing. | Make paid
To elucidate the pathogenesis of vein of Galen malformations (VOGMs), the most common and severe congenital brain arteriovenous malformation, we performed an integrated analysis of 310 VOGM proband-family exomes and 336,326 human cerebrovasculature single-cell transcriptomes. We found the Ras suppressor p120 RasGAP (RASA1) harbored a genome-wide significant burden of loss-of-function de novo variants (p=4.79x10-7). Rare, damaging transmitted variants were enriched in Ephrin receptor-B4 (EPHB4) (p=1.22x10-5), which cooperates with p120 RasGAP to limit Ras activation. Other probands had pathogenic variants in ACVRL1, NOTCH1, ITGB1, and PTPN11. ACVRL1 variants were also identified in a multi-generational VOGM pedigree. Integrative genomics defined developing endothelial cells as a key spatio-temporal locus of VOGM pathophysiology. Mice expressing a VOGM-specific EPHB4 kinase-domain missense variant exhibited constitutive endothelial Ras/ERK/MAPK activation and impaired hierarchical development of angiogenesis-regulated arterial-capillary-venous networks, but only when carrying a second-hit allele. These results illuminate human arterio-venous development and VOGM pathobiology and have clinical implications. | Make paid
This study aimed to explore whether Lactococcus G423 could ameliorate growth performance of broilers by modulation of gut microbiota-metabolites based on the 16S rRNA and LC-MS. A total of 640 one-day-old AA broilers were randomly divided into 4 groups (Control, Lac_L, Lac_H, and ABX). Average daily gain, average daily feed intake, and feed conversion ratio were calculated on the 42nd day. The ileum content was harvested and immediately frozen in liquid nitrogen for 16S rRNA and LC-MS analyses. Then, the results of 16S rRNA analysis were confirmed by qPCR. Compared with the CON group, ADG significantly increased in the Lac_H group (P<0.05), and survival rate significantly decreased in the Lac_H, Lac_H, and ABX groups (all P<0.05). A significant difference in microbial diversity was found among the four groups. Compared with the CON group, the abundance rates of Firmicutes and Lactobacillus in the Lac_H group were significantly risen (P<0.05). The global and overview maps and membrane transport in the Lac_L, Lac_H, and ABX groups significantly changed versus those in the CON group (P<0.05). The results of LC-MS demonstrated that Lactococcus could significantly improve the levels of some metabolites, and these metabolites were involved in 5 metabolic pathways. Among them, the pathways of linoleic acid metabolism, phenylalanine metabolism, and pentose and glucuronate interconversions significantly changed (P<0.05). Lactococcus improved wight and survival rate of broilers through the gut microbiota, regulating the pathways of amino acid metabolism, lipid metabolism, bile acid metabolism, and carbohydrate metabolism. However, antibiotics may negatively influence the gut microbiota. | Make paid
Charged residues on the surface of proteins are critical for both protein stability and interactions. However, many proteins contain binding regions with a high net-charge that may destabilize the protein but are useful for binding to oppositely charged targets. We hypothesized that these domains would be marginally stable, as electrostatic repulsion would compete with favorable hydrophobic collapse during folding. Furthermore, by increasing the salt concentration we predict that these protein folds would be stabilized by mimicking some of the favorable electrostatic interactions that take place during target binding. We varied the salt and urea concentrations to probe the contributions of electrostatic and hydrophobic interactions for the folding of the 60-residue yeast SH3 domain found in Abp1p. The SH3 domain was significantly stabilized with increased salt concentrations according to the Debye-Huckel limiting law. Molecular dynamics and NMR show that sodium ions interact with all 15 acidic residues but do little to change backbone dynamics or overall structure. Folding kinetics experiments show that the addition of urea or salt primarily affects the folding rate, indicating that almost all the hydrophobic collapse and electrostatic repulsion occurs in the transition state. After the transition state formation, modest yet favorable short-range salt-bridges are formed along with hydrogen bonds, as the native state fully folds. Thus, hydrophobic collapse offsets electrostatic repulsion to ensure this highly charged binding domain can still fold and be ready to bind to its charged peptide targets, a property that is likely evolutionarily conserved over one billion years. | Make paid
Innate immune receptors that form complexes with secondary receptors, activating multiple signalling pathways, modulate cellular activation and play essential roles in regulating homeostasis and immunity. We have previously identified a variety of bovine C-type lectin-like receptors that possess similar functionality than their human orthologues. Mincle (CLEC4E), a heavily glycosylated monomer, is involved in the recognition of the mycobacterial component Cord factor (trehalose 6,6'-dimycolate). Here we characterise the bovine homologue of Mincle (boMincle), and demonstrate that the receptor is structurally and functionally similar to the human orthologue (huMincle), although there are some notable differences. In the absence of cross-reacting antibodies, boMincle-specific antibodies were created and used to demonstrate that, like the human receptor, boMincle is predominantly expressed by myeloid cells. BoMincle surface expression increases during the maturation of monocytes to macrophages. However, boMincle mRNA transcripts were also detected in granulocytes, B cells, and T cells. Finally, we show that boMincle binds to isolated bovine CD4+ T cells in a specific manner, indicating the potential to recognize endogenous ligands. This suggests that the receptor might also play a role in homeostasis in cattle. | Make paid
Nep1 is a protein essential for the formation of the eukaryotic and archaeal small ribosomal subunit. It is an enzyme responsible for the site-specific SAM-dependent methylation of pseudouridine ({Psi}) during the pre-rRNA processing. It possesses a non-trivial topology, namely, a 31 knot in the active site. Herein, we investigate the structure and mechanism of catalysis of Nep1 using a combination of bioinformatics, computational, and experimental methods. In particular, we address the issue of seemingly unfeasible deprotonation of {Psi} nucleobase in the active site of Nep1 by a distant aspartate residue (e.g., D101 in Nep1 of S. cerevisiae). Sequence alignment analysis across different organisms identifies a conserved serine/threonine residue that may play a role of a proton-transfer mediator (e.g., S233 in Nep1 from S. cerevisiae), facilitating the reaction. Two enzyme-substrate complexes, one based on an available crystal structure and the other generated by molecular docking, of representative eukaryotic (from S. cerevisiae) and archaeal (from A. fulgidus) Nep1 homologs are subjected to molecular dynamics (MD) simulations. The resulting trajectories confirm that the hydroxyl-containing amino acid can indeed adopt a position suitable for proton-shuttling, with the OH group located in between the proton donor and acceptor. However, during the MD simulations, a water molecule emerges from arrangements of the active site, which can assume the role of the proton-transfer mediator instead. To discern between these two alternative pathways, we evaluate the possible methylation mechanisms by quantum-chemical calculations based on density functional theory, using the cluster approach. The obtained energy profiles indicate that the most facile course of the reaction for both the yeast and archaeal enzymes is to engage the water molecule. These results are corroborated by agreement of the computed energy barriers with experimentally measured enzyme kinetics. Moreover, mutational studies show that, while aspartate D101 is crucial for the catalytic activity, serine S233 is irrelevant in this context, indirectly supporting the water-mediated proton transfer. Our findings comprehensively elucidate the mode of action of Nep1 and provide implication for understanding the catalytic mechanisms of other enzymes that involve a proton transfer in the active site over extended distances. | Make paid
Engineering B family DNA polymerases to utilize artificial nucleotides with unique large group labeling is limited by a general lack of understanding about the mechanism of the structural determinants that define substrate specificity. In this study, we report the engineering process of a natural DNA polymerase (KOD pol) from Thermococcus Kodakaraenis by using semi-rational design strategies. The essential residues around the active pocket and DNA binding site of KOD pol are characterized by using an established high-throughput microwell-based screening method. We obtained a five-mutant variant by performing site-directed saturation mutagenesis and combinatorial mutations of motif A and position 485, including two previously reported mutation sites (141/143) with inactive exonuclease activity. Then we selected more mutants, which were expected to increase the catalytic activity based on computational simulations, to perform experimental verification. By stepwise combinatorial mutation, we obtained an eleven-mutation variant E10 with over 25 times improvement of kinetic efficiency which has similar and satisfactory performances on both the BGI NGS platform (SE50) and MGI CoolMPSTM platform (PE100). The results indicated that E10 is a potential candidate for commercialization. The beneficial mutation sites identified in this study might be shared with other archaeal B-family DNA polymerases, which can provide a guide for the mutagenesis of other types of enzymes. | Make paid
Lipoprotein lipase (LPL) hydrolyzes triglycerides from circulating lipoproteins, releasing free fatty acids. Active LPL is needed to prevent hypertriglyceridemia, which is a risk factor for cardiovascular disease (CVD). Using cryogenic electron microscopy (cryoEM), we determined the structure of an active LPL dimer at 3.9 [A] resolution. This is the first structure of a mammalian lipase with an open, hydrophobic pore adjacent to the active site. We demonstrate that the pore can accommodate an acyl chain from a triglyceride. Previously, it was thought that an open lipase conformation was defined by a displaced lid peptide, exposing the hydrophobic pocket surrounding the active site. With these previous models after the lid opened, the substrate would enter the active site, be hydrolyzed and then released in a bidirectional manner. It was assumed that the hydrophobic pocket provided the only ligand selectivity. Based on our structure, we propose a new model for lipid hydrolysis, in which the free fatty acid product travels unidirectionally through the active site pore, entering and exiting opposite sides of the protein. By this new model, the hydrophobic pore provides additional substrate specificity and provides insight into how LPL mutations in the active site pore may negatively impact LPL activity, leading to chylomicronemia. Structural similarity of LPL to other human lipases suggests that this unidirectional mechanism could be conserved but has not been observed due to the difficulty of studying lipase structure in the presence of an activating substrate. We hypothesize that the air/water interface formed during creation of samples for cryoEM triggered interfacial activation, allowing us to capture, for the first time, a fully open state of a mammalian lipase. Our new structure also revises previous models on how LPL dimerizes, revealing an unexpected C-terminal to C-terminal interface. The elucidation of a dimeric LPL structure highlights the oligomeric diversity of LPL, as now LPL homodimer, heterodimer, and helical filament structures have been elucidated. This diversity of oligomerization may provide a form of regulation as LPL travels from secretory vesicles in the cell, to the capillary, and eventually to the liver for lipoprotein remnant uptake. We hypothesize that LPL dimerizes in this active C-terminal to C-terminal conformation when associated with mobile lipoproteins in the capillary. | Make paid
Due to the enhanced labeling capability of maleimide-based fluorescent probes in in vitro experiments, lysine-cysteine-lysine (KCK) tags are frequently added to proteins for visualization. Here we show that, although no noticeable changes were detected from in vivo fluorescence imaging and chromatin immunoprecipitation (ChIP) assays, the KCK-tag substantially altered DNA compaction rates by Bacillus subtilis ParB protein in in vitro single-molecule DNA flow-stretching experiments. Furthermore, our measurements and statistical analyses demonstrate that the KCK-tags also altered the ParB protein's response to nucleotide (cytidine triphosphate CTP or its nonhydrolyzable analog CTP{gamma}S) binding and the presence of the specific DNA binding sequence (parS). Remarkably, the appended KCK-tags are capable of even reversing the trends of DNA compaction rates upon different experimental conditions. DNA flow-stretching experiments for both fluorescently-labeled ParB proteins and ParB proteins with an N-terminal glutamic acid-cysteine-glutamic acid (ECE) tag support the notion that electrostatic interactions between charges on the tags and the DNA backbone are an underlying cause of the protein's property changes. While it is typically assumed that the short KCK-tag minimally perturbs protein function, our results demonstrate that this assumption must be carefully tested when using tags for protein labeling. | Make paid
Ephrin (EPH) receptors have been implicated in tumorigenesis and metastasis, but the functional understanding of mutations observed in human cancers is limited. We previously demonstrated reduced cell compartmentalisation for somatic EPHB1 mutations found in metastatic colorectal cancer cases. We, therefore, integrated pan-cancer and pan-EPH mutational data to prioritise recurrent EPHB1 mutations for functional studies to understand their contribution to cancer development and metastasis. Here, 79,151 somatic mutations in 9,898 samples of 33 different tumour types were analysed to find 3D-mutated cluster pairs and recurring hotspot mutations in EPH receptors. From these, 15 recurring EPHB1 mutations were stably expressed in colorectal cancer cells. Whereas the ligand-binding domain mutations C61Y, R90C, and R170W, the fibronectin domain mutation R351L, and the kinase domain mutation D762N displayed reduced to strongly compromised cell compartmentalisation, the kinase domain mutations R743W and G821R enhanced this phenotype. While mutants with reduced compartmentalisation also had reduced ligand-induced receptor phosphorylation, the enhanced compartmentalisation was not linked to receptor phosphorylation level. Phosphoproteome mapping pinpointed the PI3K pathway and PIK3C2B phosphorylation in cells harbouring mutants with reduced compartmentalisation. This is the first integrative study of pan-cancer EPH receptor mutations followed by in vitro validation, a robust way to identify cancer-causing mutations. | Make paid
Alzheimer's disease (AD) is the leading cause of dementia worldwide, but there are limited therapeutic options and no current cure. While the involvement of microglia in AD has been highly appreciated, the role of other innate and adaptive immune cells remains largely unknown, partly due to their scarcity and heterogeneity. This study aimed to study non-microglial immune cells in wild type and AD-transgenic mouse brains across different ages. Our results uncovered the presence of a unique CD8+ T cell population that were selectively increased in aging AD mouse brains, here referred to as ''disease-associated T cells (DATs)''. These DATs were found to express an elevated tissue-resident memory and Type I interferon-responsive gene signature. Further analysis of aged AD mouse brains showed that these CD8+ T cells were not present in peripheral or meningeal tissues. Preventing CD8+ T cell development in AD-transgenic mice via genetic deletion of beta-2 microglobulin (B2m) led to a reduction of amyloid-{beta} ; plaque formation in aged mice, and improved memory in AD-transgenic mice as early as four months of age. The integration of transcriptomic and epigenomic profiles at the single-cell level revealed potential transcription factors that reshape the regulomes of CD8+ T cells. These findings highlight a critical role for DATs in the progression of AD and provide a new avenue for treatment. | Make paid
While better management of loco-regional prostate cancer (PC) has greatly improved survival, advanced PC remains a major cause of cancer deaths. Novel, targetable, pathways that contribute to tumorigenesis in advanced PC could open new therapeutic options. The di-ganglioside GD2 is a target of FDA-approved antibody therapies in neuroblastoma, but any role of GD2 in PC is little explored. Here, we show that GD2 is expressed on a small subpopulation of tumor cells in a subset of PC patients, especially in metastatic PC. Variable levels of cell surface GD2 expression are seen in most PC cell lines, and the expression is highly upregulated by experimental induction of lineage progression or enzalutamide resistance in CRPC cell models. GD2+ fraction is enriched upon growth of PC cells as tumorspheres and GD2+ fraction is enriched in tumorsphere growth. CRISPR-Cas9 knockout (KO) of the rate-limiting GD2 biosynthetic enzyme GD3 Synthase (GD3S) in GD2-high CRPC cell models led to marked impairment of their in vitro oncogenic traits, reduced cancer stem cell and epithelial-mesenchymal transition marker expression and growth as bone-implanted xenograft tumors. Our results support a potential role of GD3S and its product GD2 in promoting PC tumorigenesis, likely by its recently demonstrated role in maintaining cancer stem cells and suggest the potential for GD2 targeting in advanced PC. | Make paid
The organization of the representational space underlying the neural coding of word meaning has long been a central question in cognitive science. Although there is general agreement that lexical semantic representations must make contact with sensory-motor and affective experiences in a non-arbitrary fashion, the nature of this relationship remains controversial. Many researchers have proposed that lexical concepts (i.e., word meanings) are represented primarily in terms of their experiential content, ultimately derived from sensory-motor and affective processes. However, the recent success of distributional language models in emulating human linguistic behavior has led to proposals that word co-occurrence information may play a more important role in the representation of concepts in the human brain. We investigated this issue by using representational similarity analysis (RSA) of semantic priming data. Participants performed a speeded lexical decision task in two sessions separated by approximately one week. All target words were presented once in each session, but each time they were preceded by a different prime word. Priming was computed for each target as the difference in RT between the two sessions. We evaluated eight models of semantic word representation in terms of their ability to predict the magnitude of the priming effect for each target: two based on experiential information, three based on distributional information, and three based on taxonomic information. Crucially, we used partial correlation RSA to account for intercorrelations between predictions from different models, which allowed us to assess, for the first time, the unique predictive power of experiential and distributional models. We found that semantic priming was driven primarily by experiential similarity between prime and target, with no evidence of an independent effect of distributional similarity. These results support experiential accounts of language representation and indicate that, despite their good performance at some linguistic tasks, distributional models do not encode the same kind of information used by the brain. | Make paid
This systematic review and meta-analysis examined the effects of neurofeedback training (NFT) on attentional performance in healthy adults. Six databases (PubMed, Scopus, Web of Science, PsycInfo, JDream3, and Ichu-shi) were searched up to June 2022 for randomized controlled trials (RCTs) comparing attentional performance following NFT to a control group. Risk of bias was determined using the Cochrane Collaboration's tool. We identified 41 RCTs for qualitative synthesis and 15 RCTs without high risk of bias (including 569 participants) for meta-analysis using a random-effects model. The overall effect of NFT on attentional performance was significant (standardized mean difference = 0.27, 95% confidence interval = 0.10-0.44). However, approximately half of the studies did not compare its effects with sham-NFT, and no significant pooled effect of NFT was found in the studies compared to a sham-NFT group. Furthermore, subgroup analyses revealed variable effects on individual attentional performance subsets (executive function, spatial orientation, and arousal). Future large-scale sham-controlled RCTs are needed to confirm the efficacy of NFT for improving attentional performance. | Make paid
Estrogen receptor-positive (ER+) breast cancer commonly disseminates to bone marrow, where interactions with mesenchymal stromal cells (MSCs) shape disease trajectory. We modeled these interactions with tumor-MSC co-cultures and used an integrated transcriptome-proteome-network-analyses workflow to identify a comprehensive catalog of contact-induced changes. Induced genes and proteins in cancer cells, some borrowed and others tumor-intrinsic, were not recapitulated merely by conditioned media from MSCs. Protein-protein interaction networks revealed the rich connectome between 'borrowed' and 'intrinsic' components. Bioinformatic approaches prioritized one of the 'borrowed' components, CCDC88A/GIV, a multi-modular metastasis-related protein which has recently been implicated in driving one of the hallmarks of cancers, i.e., growth signaling autonomy. MSCs transferred GIV protein to ER+ breast cancer cells (that lack GIV) through tunnelling nanotubes via connexin (Cx)43-facilitated intercellular transport. Reinstating GIV alone in GIV-negative breast cancer cells reproduced ~20% of both the 'borrowed' and the 'intrinsic' gene induction patterns from contact co-cultures; conferred resistance to anti-estrogen drugs; and enhanced tumor dissemination. Findings provide a multiomic insight into MSC[->]tumor cell intercellular transport and validate how transport of one such candidate, GIV, from the haves (MSCs) to have-nots (ER+ breast cancer) orchestrates aggressive disease states. | Make paid
Beneficial interactions with microorganisms are pivotal for crop performance and resilience. However, it remains unclear how heritable the microbiome is with respect to the host plant genotype and to what extent host genetic mechanisms can modulate plant-microbe interactions in the face of environmental stress. Here, we surveyed the root and rhizosphere microbiome of 129 accessions of locally adapted Zea mays, sourced from diverse habitats and grown under control and different stress conditions. We quantified treatment and host genotype effects on the microbiome. Plant genotype and source environment were predictive of microbiome composition. Genome wide association analysis identified host genetic variants linked to both rhizosphere microbiome composition and source environment. We identified transposon insertions in a candidate gene linked to both the abundance of a keystone microbe Massilia and source total soil nitrogen, finding mutant plants to show a reduction in lateral root density. We conclude that locally adapted maize varieties exert patterns of genetic control on their root and rhizosphere microbiomes that follow variation in their home environments, consistent with a role in tolerance to prevailing stress. | Make paid
Cell dynamics and biological function are governed by changing patterns of gene expression. Intricate gene interaction networks orchestrate these changes. Inferring these interactions from data is a notoriously difficult inverse problem. The majority of existing network inference methods work at the population level. They construct static representations of gene regulatory networks, and they do not naturally allow us to infer differences in gene regulation across heterogeneous cell populations. Here we build upon recent dynamical inference methods that model single cell dynamics using Markov processes, which leads to an information-theoretic approach, locaTE, which employs the localised transfer entropy to infer cell-specific, causal gene regulatory networks. LocaTE uses high-resolution estimates of dynamics and geometry of the cellular gene expression manifold to inform inference of regulatory interactions. We find that this approach is superior to static inference methods, often by a significant margin. We demonstrate that factor analysis can give detailed insights into the inferred cell-specific GRNs. In application to three experimental datasets, we demonstrate superior performance and additional insights compared to stancard static GRN inference methods. For example, we recover key transcription factors and regulatory interactions driving mouse primitive endoderm formation, pancreatic development, and haematopoiesis. For both simulated and experimental data, we find that locaTE provides a powerful, efficient and scalable network inference method that allows us to distil cell-specific networks from single cell data. | Make paid
Overexpression of EPS15 Homology Domain containing 1 (EHD1) has been linked to tumorigenesis but whether its core function as a regulator of intracellular traffic of cell surface receptors plays a role in oncogenesis remains unknown. We establish that EHD1 is overexpressed in Ewing sarcoma (EWS), with high EHD mRNA expression specifying shorter patient survival. ShRNA and CRISPR-knockout with mouse Ehd1 rescue established a requirement of EHD1 for tumorigenesis and metastasis. RTK antibody arrays identified the IGF-1R as a target of EHD1 regulation in EWS. Mechanistically, we demonstrate a requirement of EHD1 for endocytic recycling and Golgi to plasma membrane traffic of IGF-1R to maintain its surface expression and downstream signaling. Conversely, EHD1 overexpression-dependent exaggerated oncogenic traits require IGF-1R expression and kinase activity. Our findings define the RTK traffic regulation as a proximal mechanism of EHD1 overexpression-dependent oncogenesis that impinges on IGF-1R in EWS, supporting the potential of IGF-1R and EHD1 co-targeting. | Make paid
The intracellular bacterium Wolbachia is a common symbiont of many arthropods and nematodes, well studied for its impacts on host reproductive biology. However, its broad success as a vertically transmitted infection cannot be attributed to manipulations of host reproduction alone. Using the Drosophila melanogaster model and their natively associated Wolbachia strain "wMel", we show that Wolbachia infection supports fly development and buffers against nutritional stress. Wolbachia infection across several fly genotypes and a range of nutrient conditions resulted in reduced pupal mortality, increased adult emergence, and larger size. We determined that the exogenous supplementation of pyrimidines rescued these phenotypes in the Wolbachia-free, flies suggesting that Wolbachia plays a role in providing this metabolite that is normally limiting for fly growth. Additionally, Wolbachia was sensitive to host pyrimidine metabolism: Wolbachia titers increased upon transgenic knockdown of the Drosophila de novo pyrimidine synthesis pathway but not knockdown of the de novo purine synthesis pathway. We propose that Wolbachia acts as a nutritional symbiont to supplement fly development and enhance host fitness. | Make paid
The movement of animals is a central component of their behavioural strategies. Statistical tools for movement data analysis, however, have long been limited, and in particular, unable to account for past movement information except in a very simplified way. In this work, we propose MoveFormer, a new step-based model of movement capable of learning directly from full animal trajectories. While inspired by the classical step-selection framework and previous work on the quantification of uncertainty in movement predictions, MoveFormer also builds upon recent developments in deep learning, such as the Transformer architecture, allowing it to incorporate long temporal contexts. The model predicts an animals next movement step given its past movement history, including not only purely positional and temporal information, but also any available environmental covariates such as land cover or temperature. We apply our model to a diverse dataset made up of over 1550 trajectories from over 100 studies, and show how it can be used to gain insights about the importance of the provided context features, including the extent of past movement history. Our software, along with the trained model weights, is released as open source. | Make paid
BackgroundTrue flies (Diptera) are an ecologically important group that play a role in agriculture, public health and ecosystem functioning. As researchers continue to investigate this order, it is beneficial to link the growing occurrence data to biological traits. However, large-scale ecological trait data are not readily available for fly species. While some databases and datasets include fly data, many ecologically relevant traits for taxa of interest are not included. In this study we create a dataset containing ecological traits (habitat and diet) for fly species of Canada and Greenland having occurrence records on the Barcode of Life Data Systems (BOLD). We present a dataset containing trait information for 983 Diptera species. New InformationDiptera were chosen for the dataset based on the occurrence records available for Diptera species from Canada and Greenland on the Barcode of Life Data Systems (BOLD). Trait data were then compiled based on literature searches conducted from April 2021 - January 2023 and assigned at the lowest taxonomic level possible. Three biological traits were included: habitat, larval diet, and adult diet. The dataset contains traits for 983 species across 380 genera, 25 subfamilies, and 61 families. This dataset allows for assignment of traits to occurrence data for Diptera species and can be used for further research into the ecology, evolution, and conservation of this order. | Make paid
In comparisons between mutant and wild-type genotypes, transcriptome analysis can reveal the direct impacts of a mutation, together with the homeostatic responses of the biological system. Recent studies have highlighted that, when homozygous mutations are studied in non-isogenic backgrounds, genes from the same chromosome as a mutation often appear over-represented among differentially expressed (DE) genes. One hypothesis suggests that DE genes chromosomally linked to a mutation may not reflect true biological responses to the mutation but, instead, result from differences in representation of expression quantitative trait loci (eQTLs) between sample groups selected on the basis of mutant or wild-type genotype. This is problematic when inclusion of spurious DE genes in a functional enrichment study results in incorrect inferences of mutation effect. Here we show that chromosomally co-located differentially expressed genes (CC-DEGs) can also be observed in analyses of dominant mutations in heterozygotes. We define a method and a metric to quantify, in RNA-sequencing data, localised differential allelic representation (DAR) between groups of samples subject to differential expression analysis. We show how the DAR metric can predict regions prone to eQTL-driven differential expression, and how it can improve functional enrichment analyses through gene exclusion or weighting of gene-level rankings. Advantageously, this improved ability to identify probable eQTLs also reveals examples of CC-DEGs that are likely to be functionally related to a mutant phenotype. This situation was predicted by R.A. Fisher in 1930 as due to selection for advantageous linkage disequilibrium after chromosomal rearrangements. By comparing the genomes of zebrafish (Danio rerio) and medaka (Oryzias latipes), a teleost with a conserved ancestral karyotype, we find possible examples of chromosomal aggregation of CC-DEGs during evolution of the zebrafish lineage. The DAR metric provides a solid foundation for addressing the eQTL issue in new and existing datasets because it relies solely on RNA-sequencing data. | Make paid
Neurons in the neocortex exhibit astonishing morphological diversity which is critical for properly wiring neural circuits and giving neurons their functional properties. The extent to which the morphological diversity of excitatory neurons forms a continuum or is built from distinct clusters of cell types remains an open question. Here we took a data-driven approach using graph-based machine learning methods to obtain a low-dimensional morphological "bar code" describing more than 30,000 excitatory neurons in mouse visual areas V1, AL and RL that were reconstructed from a millimeter scale serial-section electron microscopy volume. We found a set of principles that captured the morphological diversity of the dendrites of excitatory neurons. First, their morphologies varied with respect to three major axes: soma depth, total apical and basal skeletal length. Second, neurons in layer 2/3 showed a strong trend of a decreasing width of their dendritic arbor and a smaller tuft with increasing cortical depth. Third, in layer 4, atufted neurons were primarily located in the primary visual cortex, while tufted neurons were more abundant in higher visual areas. Fourth, we discovered layer 4 neurons in V1 on the border to layer 5 which showed a tendency towards avoiding deeper layers with their dendrites. In summary, excitatory neurons exhibited a substantial degree of dendritic morphological variation, both within and across cortical layers, but this variation mostly formed a continuum, with only a few notable exceptions in deeper layers. | Make paid
Perinatal high fat diet (pHFD) exposure alters the development of vagal neurocircuits that control gastrointestinal (GI) motility and reduce stress resiliency in offspring. Descending oxytocin (OXT; prototypical anti-stress peptide) and corticotropin releasing factor (CRF; prototypical stress peptide) inputs from the paraventricular nucleus (PVN) of the hypothalamus to the dorsal motor nucleus of the vagus (DMV) modulate the GI stress response. How these descending inputs, and their associated changes to GI motility and stress responses, are altered following pHFD exposure are, however, unknown. The present study used retrograde neuronal tracing experiments, in vivo recordings of gastric tone, motility, and gastric emptying rates, and in vitro electrophysiological recordings from brainstem slice preparations to investigate the hypothesis that pHFD alters descending PVN-DMV inputs and dysregulates vagal brain-gut responses to stress. Compared to controls, rats exposed to pHFD had slower gastric emptying rates and did not respond to acute stress with the expected delay in gastric emptying. Neuronal tracing experiments demonstrated that pHFD reduced the number of PVNOXT neurons that project to the DMV, but increased PVNCRF neurons. Both in vitro electrophysiology recordings of DMV neurons and in vivo recordings of gastric motility and tone demonstrated that, following pHFD, PVNCRF-DMV projections were tonically active, and that pharmacological antagonism of brainstem CRF1 receptors restored the appropriate gastric response to brainstem OXT application. These results suggest that pHFD exposure disrupts descending PVN-DMV inputs, leading to a dysregulated vagal brain-gut response to stress. | Make paid