bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hybrid seed incompatibility in Capsella is connected to chromatin condensation defects in the endosperm
Authors: Dziasek Katarzyna , Simon Lauriane , Placette Clément Lafon , Laenen Benjamin , Wärdig Cecilia , Santos-González Juan , Slotte Tanja , Köhler Claudia 
Published: September 2020

AbstractHybridization of closely related plant species is frequently connected to endosperm arrest and seed failure, for reasons that remain to be identified. In this study, we investigated the molecular events accompanying seed failure in hybrids of the closely related species pairCapsella rubellaandC. grandiflora. Mapping of QTLs for the underlying cause of hybrid incompatibility in Capsella revealed three QTLs that were close to pericentromeric regions. This prompted us to investigate whether there are specific changes in heterochromatin associated with interspecific hybridizations. Indeed, we found that chromatin was less condensed in the endosperm, while the embryo was not affected. Loss of chromosome condensation was connected with a strong loss of CHG and CHH methylation and mitotic abnormalities. Genome-wide sequencing of hybrid endosperm revealed that the chromosome loss was random and was likely a consequence of reduced chromatin condensation. Consistent with reduced DNA methylation in hybrid endosperm, we found a disproportionate deregulation of genes located close to pericentromeric regions. Among those deregulated genes there were many potential targets of the AGAMOUS-LIKE transcription factor PHERES1, suggesting that reduced DNA methylation allows PHERES1 to hyperactivate its targets. Since the identified QTLs were also associated with pericentromeric regions, we conclude that relaxation of heterochromatin in response to interspecies hybridization exposes and activates loci leading to hybrid seed failure.
Low immunogenicity of malaria pre-erythrocytic stages can be overcome by vaccination
Authors: Müller Katja , Gibbins Matthew P. , Reyes-Sandoval Arturo , Hill Adrian V. S. , Draper Simon J. , Matuschewski Kai , Silvie Olivier , Hafalla Julius Clemence R. 
Published: September 2020

ABSTRACTVaccine discovery and development critically depends on predictive assays, which prioritise protective antigens. Immunogenicity is considered one important criterion for progression of candidate vaccines to further clinical evaluation, including phase I/II trials. Here, we tested this assumption in an infection and vaccination model for malaria pre-erythrocytic stages. We engineeredPlasmodium bergheiparasites that harbour a well-characterised epitope for stimulation of CD8+ T cells either as an antigen in the circumsporozoite protein (CSP), the surface coat protein of extracellular sporozoites or in the upregulated in sporozoites 4 (UIS4), a major protein associated with the parasitophorous vacuole membrane (PVM) that surrounds the intracellular exo-erythrocytic forms (EEF). We show that the antigen origin results in profound differences in immunogenicity with a sporozoite antigen eliciting robust and superior antigen-specific CD8+ T cell responses, whilst an EEF antigen evokes poor responses. However, despite their contrasting immunogenic properties, both sporozoite and EEF antigens gain access to antigen presentation pathways in hepatocytes, as recognition and targeting by vaccine-induced, antigen-specific effector CD8+ T cells results in high levels of protection when targeting both antigens. Our study is the first demonstration that poor immunogenicity of EEF antigens does not preclude their susceptibility to antigen-specific CD8+ T cell killing. Our findings that antigen immunogenicity is an inadequate predictor of vaccine susceptibility have wide-ranging implications on antigen prioritisation for the design and testing of next-generation pre-erythrocytic malaria vaccines.
Evaluating Inositol phospholipid interactions with Inward Rectifier Potassium Channels and characterising their role in Disease
Authors: Pipatpolkai Tanadet , Corey Robin A. , Proks Peter , Ashcroft Frances M. , Stansfeld Phillip J. 
Published: September 2020

AbstractMembrane proteins are frequently modulated by specific protein-lipid interactions. The activation of human inward rectifying potassium (hKir) channels by phosphoinositides (PI) has been well characterised. Here, we apply a coarse-grained molecular dynamics free-energy perturbation (CG-FEP) protocol to capture the energetics of binding of PI lipids to hKir channels. By using either a single- or multi-step approach, we establish a consistent value for the binding of PIP2to hKir channels, relative to the binding of the bulk phosphatidylcholine phospholipid. Furthermore, by perturbing amino acid side chains on hKir6.2, we show that the neonatal diabetes mutation E179K increases PIP2affinity, while the congenital hyperinsulinism mutation K67N results in a reduced affinity. We show good agreement with electrophysiological data where E179K exhibits a reduction in neomycin sensitivity, implying that PIP2binds more tightly E179K channels. This illustrates the application of CG-FEP to compare affinities between lipid species, and for annotating amino acid residues.
Structural characterization of LsrK to target quorum sensing and comparison between X-ray and homology model
Authors: Medarametla Prasanthi , Laitinen Tuomo , Poso Antti 
Published: September 2020

ABSTRACTQuorum sensing is being investigated as an alternative therapeutic strategy in antibacterial drug discovery to combat bacterial resistance. LsrK is an autoinducer-2 kinase, playing a key role in the phosphorylation of autoinducer-2 (AI-2) signalling molecules involved in quorum sensing. Inhibiting LsrK could result in reduced pathogenicity by interfering with the quorum sensing signalling. Previously, we have generated homology models to identify LsrK inhibitors using structure-based virtual screening and successfully found the first class of LsrK inhibitors. While conducting these studies, the crystal structure of LsrK was released providing us an opportunity to inspect the reliability and quality of our models. Structural analysis of crystal structure and homology models revealed the consistencies of constructed models with crystal structure in the structural fold and binding site. Further, binding characteristics and conformational changes are investigated using molecular dynamics. These simulations provided us insights into the protein function and flexibility that need to be considered during the structure-based drug design studies targeting LsrK.
Population stratification in GWAS meta-analysis should be standardized to the best available reference datasets
Authors: Sarmanova Aliya , Morris Tim , Lawson Daniel John 
Published: September 2020

AbstractPopulation stratification has recently been demonstrated to bias genetic studies even in relatively homogeneous populations such as within the British Isles. A key component to correcting for stratification in genome-wide association studies (GWAS) is accurately identifying and controlling for the underlying structure present in the sample. Meta-analysis across cohorts is increasingly important for achieving very large sample sizes, but comes with the major disadvantage that each individual cohort corrects for different population stratification. Here we demonstrate that correcting for structure against an external reference adds significant value to meta-analysis. We treat the UK Biobank as a collection of smaller studies, each of which is geographically localised. We provide software to standardize an external dataset against a reference, provide the UK Biobank principal component loadings for this purpose, and demonstrate the value of this with an analysis of the geographically sampled ALSPAC cohort.
Local postsynaptic signalling on slow time scales in reciprocal olfactory bulb granule cell spines matches asynchronous release
Authors: Jodar Tiffany Ona , Lage-Rupprecht Vanessa , Abraham Nixon M. , Rose Christine R. , Egger Veronica 
Published: September 2020

AbstractIn the vertebrate olfactory bulb (OB), axonless granule cells (GC) mediate self- and lateral inhibitory interactions between mitral/tufted cells via reciprocal dendrodendritic synapses. Locally triggered release of GABA from the large reciprocal GC spines occurs on both fast and slow time scales, possibly enabling parallel processing during olfactory perception. Here we investigate local mechanisms for asynchronous spine output.To reveal the temporal and spatial characteristics of postsynaptic ion transients, we imaged spine and adjacent dendrite Ca2+- and Na+-signals with minimal exogenous buffering by the respective fluorescent indicator dyes upon two-photon uncaging of DNI-glutamate in OB slices from juvenile rats. Both postsynaptic fluorescence signals decayed slowly, with average half durations in the spine head of t1/2_Δ[Ca2+]i~500 ms and t1/2_Δ[Na+]i~1000 ms. We also analysed the kinetics of already existing data of postsynaptic spine Ca2+-signals in response to glomerular stimulation in OB slices from adult mice, either WT or animals with partial GC glutamate receptor deletions (NMDAR: GluN1 subunit; AMPAR: GluA2 subunit). In a large subset of spines the fluorescence signal had a protracted rise time (average time to peak ~400 ms, range 20 ms - >1000 ms). This slow rise was independent of Ca2+entry via NMDARs, since similarly slow signals occurred in ΔGluN1 GCs. Additional Ca2+entry in ΔGluA2 GCs (with AMPARs rendered Ca2+-permeable), however, resulted in larger ΔF/Fs that rose yet more slowly.Thus GC spines appear to dispose of several local mechanisms to promote asynchronous GABA release, which are reflected in the time course of mitral/tufted cell recurrent inhibition.
Twinfilin1 controls lamellipodial protrusive activity and actin turnover during vertebrate gastrulation
Authors: Devitt Caitlin C. , Lee Chanjae , Cox Rachael M. , Papoulas Ophelia , Alvarado José , Marcotte Edward M. , Wallingford John B. 
Published: September 2020

AbstractThe dynamic control of the actin cytoskeleton is a key aspect of essentially all animal cell movements. Experiments in single migrating cells andin vitrosystems have provided an exceptionally deep understanding of actin dynamics. However, we still know relatively little of how these systems are tuned in cell-type specific ways, for example in the context of collective cell movements that sculpt the early embryo. Here, we provide an analysis of the actin severing and depolymerization machinery during vertebrate gastrulation, with a focus on Twinfilin1. We confirm previous results on the role of Twf1 in lamellipodia and extend those findings by linking Twf1, actin turnover, and cell polarization required for convergent extension during vertebrate gastrulation.
The p97-UBXN1 complex regulates aggresome formation
Authors: Mukkavalli Sirisha , Klickstein Jacob Aaron , Ortiz Betty , Juo Peter , Raman Malavika 
Published: September 2020

AbstractThe recognition and disposal of misfolded proteins are essential for the maintenance of cellular homeostasis. Perturbations in the pathways that promote degradation of aberrant proteins contribute to a variety of protein aggregation disorders broadly termed proteinopathies. It is presently unclear how diverse disease-relevant aggregates are recognized and processed for degradation. The p97 AAA-ATPase in combination with a host of adaptor proteins functions to identify ubiquitylated proteins and target them for degradation by the ubiquitin-proteasome system or through autophagy. Mutations in p97 cause multi-system proteinopathies; however, the precise defects underlying these disorders are unclear given the large number of pathways that rely on p97 function. Here, we systematically investigate the role of p97 and its adaptors in the process of formation of aggresomes which are membrane-less structures containing ubiquitylated proteins that arise upon proteasome inhibition. We demonstrate that p97 mediates both aggresome formation and clearance in proteasome-inhibited cells. We identify a novel and specific role for the p97 adaptor UBXN1 in the process of aggresome formation. UBXN1 is recruited to ubiquitin-positive aggresomes and UBXN1 knockout cells are unable to form a single aggresome, and instead display dispersed ubiquitin aggregates. Furthermore, loss of p97-UBXN1 results in the increase in Huntingtin polyQ aggregates both in mammalian cells as well as in aC.elegansmodel of Huntington’s Disease. Together our work identifies evolutionarily conserved roles for p97 and its adaptor UBXN1 in the disposal of protein aggregates.
The impact of stomatal kinetics on diurnal photosynthesis and water use efficiency under fluctuating light
Authors: Eyland David , van Wesemael Jelle , Lawson Tracy , Carpentier Sebastien 
Published: September 2020

AbstractDynamic light conditions require continuous adjustments of stomatal aperture. As stomatal conductance (gs) kinetics are a magnitude slower than photosynthesis (A), they are hypothesized to be key to plant productivity and water use efficiency. Using step-changes in light intensity, we studied the diversity of light-induced gskinetics in relation to stomatal anatomy in five banana genotypes (Musaspp.) and modelled the impact onAand intrinsic water use efficiency (iWUE). Banana generally exhibited a strong limitation ofAby gs, indicating a priority for water saving. Significant genotypic differences in gskinetics and gs-based limitations ofAwere observed. For two contrasting genotypes the impact of differential gskinetics onAandiWUE was further investigated under realistic diurnally fluctuating light conditions and at whole-plant level. Genotype-specific stomatal kinetics observed at the leaf level were corroborated at whole-plant level, suggesting that despite differences in gscontrol at different locations in the leaf and across leaves, genotype-specific responses are still maintained. However, under diurnally fluctuating light conditions gsspeediness had only a momentary impact on the diurnaliWUE and carbon gain. During the afternoon there was a setback in kinetics: the absolute gsand the gsresponses to light were damped, strongly limitingAand the diurnaliWUE. We conclude that the impact of the differential gskinetics on the limitation ofAwas dependent on the target light intensity, the magnitude of change, the gsprior to the intensity change and particularly the time of the day.One sentence summaryGenotype-specific stomatal rapidity is for the first time validated at whole-plant level, but under fluctuating light the impact of stomatal dynamics depends on other factors like the time of the day.
Dendritic localization of mRNA inDrosophilaMushroom Body Output Neurons
Authors: Mitchell Jessica , Smith Carlas S. , Titlow Josh , Otto Nils , van Velde Pieter , Booth Martin , Davis Ilan , Waddell Scott 
Published: September 2020

AbstractMemory-relevant neuronal plasticity is believed to require local translation of new proteins at synapses. Understanding this process requires the visualization of the relevant mRNAs within these neuronal compartments. Here we used single-molecule fluorescencein situhybridization (smFISH) to localize mRNAs at subcellular resolution in the adultDrosophilabrain. mRNAs for subunits of nicotinic acetylcholine receptors and kinases could be detected within the dendrites of co-labelled Mushroom Body Output Neurons (MBONs) and their relative abundance showed cell-specificity. Moreover, aversive olfactory learning produced a transient increase in the level ofCaMKIImRNA within the dendritic compartments of the γ5β′2a MBONs. Localization of specific mRNAs in MBONs before and after learning represents a critical step towards deciphering the role of dendritic translation in the neuronal plasticity underlying behavioural change inDrosophila.
Biomechanical Modeling of a Bone Tunnel Enlargement Post ACL Reconstruction
Authors: Borjali Amirhossein , Mohseni Mahdi , Chizari Mahmoud 
Published: September 2020

AbstractBackgroundBone tunnel enlargement is considered as a potential problem following ACL reconstruction and can cause a fixation failure and complicate its revision surgery. This study evaluates post tibial tunnel expansion in ACL reconstruction using an interference screw.MethodsA series of in-vitro experimental tests on animal bone and tissues were used to simulate post ACL reconstruction. The study believes an unbalanced lateral force can cause a local enlargement on the contact zone inside the tunnel. Grayscale X-ray images were used to assess the screw alignment inside the tunnel.ResultsThey showed a slight misalignment between the screw and the tunnel axis as the tendon strands moved along the side of the tunnel, and the screw had partial contact with the tendon and bone along the tunnel. According to the results, increased stress in the tunnel wall causes tunnel enlargement. Although the tunnel created away from the tibial central axis produced a higher strength, it results in higher stress on the wall of the tunnel which can increase the risk of tunnel expansion.ConclusionsThe current study believes the use of an unguided interference screw insertion potentially increases risks of the misaligned fixation and cause a tunnel enlargement. This risk may be controlled by restricting the post-operative rehabilitation.
Redundancy Circuits of the Commissural Pathways in Human and Rhesus Macaque Brains
Authors: Ghulam-Jelani Zulfar , Barrios-Martinez Jessica , Eguiluz-Melendez Aldo , Gomez Ricardo , Anania Yury , Yeh Fang-Cheng 
Published: September 2020

AbstractIt has been hypothesized that the human brain has traded redundancy for efficiency, but the structural existence has not been identified to examine this claim. Here, we report three redundancy circuits of the commissural pathways in primate brains, namely the orbitofrontal, temporal, and occipital redundancy circuits of the anterior commissure and corpus callosum. Each redundancy circuit has two distinctly separated routes connecting a common pair of cortical regions. We mapped their trajectories in human and rhesus macaque brains using individual and population-averaged tractography. The dissection results confirmed the existence of these redundancy circuits connecting the orbitofrontal lobe, amygdala, and visual cortex. The volume analysis showed a significant reduction in the orbitofrontal and occipital redundancy circuits of the human brain, whereas the temporal redundancy circuit had a substantial organizational difference between the human and rhesus macaque. Our overall findings suggest that the human brain is more efficient in the commissural pathway, as shown by the significantly reduced volume of the anterior commissure which serves as the backup connections for the corpus callosum. This reduction of the redundancy circuit may explain why humans are more vulnerable to psychiatric brain disorders stemming from the corpus callosum compared to non-human primates.SignificanceWe report and describe the connection routes of three redundancy circuits of the commissural pathways in human and rhesus macaque brains and compare their volumes. Our tractography and dissection studies confirmed that the human brain has smaller redundancy circuits. This is the first time such redundancy circuits of the commissural pathways have been identified, and their differences quantified in human and rhesus macaque to verify the redundancy-efficiency tradeoff hypothesis. The findings provide new insight into the topological organization of the human brain and may help understand the circuit mechanism of brain disorders involving these pathways.
HPM Live μ for a full CLEM workflow
Authors: Heiligenstein Xavier , de Beer Marit , Heiligenstein Jérôme , Eyraud Frédérique , Manet Laurent , Schmitt Fabrice , Lamers Edwin , Lindenau Joerg , Lindert Mariska Kea-te , Salamero Jean , Raposo Graça , Sommerdijk Nico , Belle Martin , Akiva Anat 
Published: September 2020

ABSTRACTWith the development of advanced imaging methods that took place in the last decade, the spatial correlation of microscopic and spectroscopic information - known as multimodal imaging or correlative microscopy (CM) - has become a broadly applied technique to explore biological and biomedical materials at different length scales. Among the many different combinations of techniques, Correlative Light and Electron Microscopy (CLEM) has become the flagship of this revolution.Where light (mainly fluorescence) microscopy can be used directly for the live imaging of cells and tissues, for almost all applications, electron microscopy (EM) requires fixation of the biological materials. Although sample preparation for EM is traditionally done by chemical fixation and embedding in a resin, rapid cryogenic fixation (vitrification) has become a popular way to avoid the formation of artefacts related to the chemical fixation/embedding procedures. During vitrification, the water in the sample transforms into an amorphous ice, keeping the ultrastructure of the biological sample as close as possible to the native state. One immediate benefit of this cryo-arrest is the preservation of protein fluorescence, allowing multi-step multi-modal imaging techniques for CLEM.To further explore the potential of cryo-fixation, we developed a high-pressure freezing (HPF) system that allows vitrification under different environmental parameters and applied it in different CLEM workflows. In this chapter, we introduce our novel HPF live μ instrument with a focus on its coupling to a light microscope. We elaborate on the optimization of sample preservation and the time needed to capture a biological event, going from live imaging to cryo-arrest using HPF. We will address the adaptation of HPF to novel correlation workflows related to the forthcoming transition from imaging 2D (cell monolayers) to imaging 3D samples (tissue) and the associated importance of homogeneous deep vitrification. Lastly, we will discuss the potential of our HPM within CLEM protocols especially for correlating live imaging using the Zeiss LSM900 with electron microscopy.
Detecting local changes in chromatin architecture with false discovery control
Authors: Koch Hillary , Yang Tao , Imakaev Maxim , Hardison Ross C. , Li Qunhua 
Published: September 2020

AbstractHi-C experiments are a powerful means to describe the organization of chromatin interactions genome-wide. By using Hi-C data to identify differentially organized genomic regions, relationships between this organization, gene expression, and cell identity may be established. However, Hi-C data exhibit a unique and challenging spatial structure, as genomic loci can show strong correlations when they are nearby in 3D space within the nucleus or 1D space along the chromosome. Consequently, the development of methods that can accurately detect differences between Hi-C samples while controlling false discoveries has remained difficult. To meet this need, we introduce a spatial modeling approach based on sliding window statistics. Using polymer simulations, we illustrate the improved power and precision of our method to identify differentially interacting genomic regions. We further demonstrate our method’s ability to reveal biologically meaningful changes in chromatin architecture through two data analyses concerning the loss of architectural and chromatin remodeling proteins.