bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergence of stealth polymorphs that escape α-synuclein amyloid monitoring, take over and acutely spread in neurons
Authors: De Giorgi Francesca , Laferrière Florent , Zinghirino Federica , Faggiani Emilie , Lends Alons , Bertoni Mathilde , Yu Xuan , Grélard Axelle , Morvan Estelle , Habenstein Birgit , Dutheil Nathalie , Doudnikoff Evelyne , Daniel Jonathan , Claverol Stéphane , Qin Chuan , Loquet Antoine , Bezard Erwan , Ichas François 
Published: February 2020

AbstractThe conformational strain diversity characterizing α-synuclein (α-syn) amyloid fibrils is possibly at the origin of the different clinical presentations of synucleinopathies. Experimentally, various α-syn fibril polymorphs have been obtained from distinct fibrillization conditions by altering the medium constituents and were selected by amyloid monitoring using the probe Thioflavin T (ThT). We report here that besides classical ThT positive products, fibrillization in saline simultaneously gives rise to competing fibril polymorphs that are invisible to ThT (stealth polymorphs), and that can take over. Due to competition, spontaneous generation of such stealth polymorphs bears on the apparent fibrillization kinetics and on the final plateau values. Their emergence has thus been ignored so far or mistaken for fibrillization inhibitions/failures. Compared to their ThT-positive counterparts, and as judged from their chemical shift resonances fingerprint, these new stealth polymorphs present a yet undescribed atomic organization and show an exacerbated propensity (approx. 20-fold) towards self-replication in cortical neurons. They also trigger a long distance synucleinopathic spread along nigro-striatal projectionsin vivo. In order to rapidly screen fibrillization products for the presence of such stealth polymorphs, we designed a simple multiplexed assay that can be easily and rapidly operated. This assay allows us to demonstrate the sustainability of the conformational replication of these novel and particularly invasive strains. It should also be of help to avoid erroneous upstream interpretations of fibrillization rates based on sole ThT, and to expedite further structural and functional characterization of stealth amyloid assemblies.One Sentence Summarystealth α-synuclein fibrils take over
Fibronectin-Based Nanomechanical Biosensors to Map 3D Strains in Live Cells and Tissues
Authors: Shiwarski Daniel J. , Tashman Joshua W. , Tsamis Alkiviadis , Bliley Jacqueline M. , Blundon Malachi A. , Aranda-Michel Edgar , Jallerat Quentin , Szymanski John M. , McCartney Brooke M. , Feinberg Adam. W. 
Published: February 2020

AbstractMechanical forces are integral to a wide range of cellular processes including migration, differentiation and tissue morphogenesis; however, it has proved challenging to directly measure strain at high spatial resolution and with minimal tissue perturbation. Here, we fabricated, calibrated, and tested a fibronectin (FN)-based nanomechanical biosensor (NMBS) that can be applied to cells and tissues to measure the magnitude, direction, and dynamics of strain from subcellular to tissue length-scales. The NMBS is a fluorescently-labeled, ultrathin square lattice FN mesh with spatial resolution tailored by adjusting the width and spacing of the lattice fibers from 2-100 µm. Time-lapse 3D confocal imaging of the NMBS demonstrated strain tracking in 2D and 3D following mechanical deformation of known materials and was validated with finite element modeling. Imaging and 3D analysis of the NMBS applied to single cells, cell monolayers, and Drosophila ovarioles demonstrated the ability to dynamically track microscopic tensile and compressive strains in various biological applications with minimal tissue perturbation. This fabrication and analysis platform serves as a novel tool for studying cells, tissues, and more complex systems where forces guide structure and function.
TheLanatatrichome mutation increases stomatal conductance and reduces leaf temperature in tomato
Authors: Gasparini Karla , Souto Ana Carolina R. , da Silva Mateus F. , Costa Lucas C. , Figueiredo Cássia Regina Fernandes , Martins Samuel C. V. , Peres Lázaro E. P. , Zsögön Agustin 
Published: February 2020

ABSTRACTBackground and aimsTrichomes are epidermal structures with an enormous variety of ecological functions and economic applications. Glandular trichomes produce a rich repertoire of secondary metabolites, whereas non-glandular trichomes create a physical barrier against biotic and abiotic stressors. Intense research is underway to understand trichome development and function and enable breeding of more resilient crops. However, little is known on how enhanced trichome density would impinge on leaf photosynthesis, gas exchange and energy balance.MethodsPrevious work has compared multiple species differing in trichome density, instead here we analyzed monogenic trichome mutants in a single tomato genetic background (cv. Micro-Tom). We determined growth parameters, leaf spectral properties, gas exchange and leaf temperature in thehairs absent(h),Lanata(Ln) andWoolly(Wo) trichome mutants.Key resultsShoot dry mass, leaf area, leaf spectral properties and cuticular conductance were not affected by the mutations. However, theLnmutant showed increased carbon assimilation (A) possibly associated with higher stomatal conductance (gs), since there were no differences in stomatal density or stomatal index between genotypes. Leaf temperature was furthermore reduced inLnin the early hours of the afternoon.ConclusionsWe show that a single monogenic mutation can increase glandular trichome density, a desirable trait for crop breeding, whilst concomitantly improving leaf gas exchange and reducing leaf temperature.HIGHLIGHTA monogenic mutation in tomato increases trichome density and optimizes gas exchange and leaf temperature
The FUSED LEAVES1/ADHERENT1Regulatory Module Is Required For Maize Cuticle Development And Organ Separation
Authors: Liu Xue , Bourgault Richard , Strable Josh , Galli Mary , Chen Zongliang , Dong Jiaqiang , Molina Isabel , Gallavotti Andrea 
Published: February 2020

ABSTRACTIn land plants all aerial epidermal cells are covered by the cuticle, an extracellular hydrophobic layer. The cuticle represents a primary barrier between cells and the external environment, provides protection against abiotic and biotic stresses, and prevents organ fusion during development. Here we report the cloning and characterization of a classic mutant of maize calledadherent1(ad1), first described a century ago, and we show thatAD1encodes a 3-KETOACYL-CoA SYNTHASE involved in the deposition of cuticular wax on the epidermis of leaves and inflorescences.ad1mutants show decreased amounts of various wax components as well as a range of organ fusion defects during vegetative and reproductive development. Accordingly, we find thatAD1is strongly expressed in the epidermis of various developing organs where it is directly regulated by the MYB transcription factor FUSED LEAVES1 (FDL1), which in turn controls a series of additional genes involved in cuticle formation. Altogether, our results identify a major pathway of cuticle biosynthesis essential for the development of maize plants, and a key regulatory module that is conserved across monocot and eudicot species.One sentence summaryThe classic maize mutantadherent1, first isolated a century ago, is affected in an enzyme responsible for cuticle formation that is regulated by the MYB transcription factor FUSED LEAVES1.
scTenifoldNet: a machine learning workflow for constructing and comparing transcriptome-wide gene regulatory networks from single-cell data
Authors: Osorio Daniel , Zhong Yan , Li Guanxun , Huang Jianhua Z. , Cai James J. 
Published: February 2020

AbstractConstructing and comparing gene regulatory networks (GRNs) from single-cell RNA sequencing (scRNAseq) data has the potential to reveal critical components in the underlying regulatory networks regulating different cellular transcriptional activities. Here, we present a robust and powerful machine learning workflow—scTenifoldNet—for comparative GRN analysis of single cells. The scTenifoldNet workflow, consisting of principal component regression, low-rank tensor approximation, and manifold alignment, constructs and compares transcriptome-wide single-cell GRNs (scGRNs) from different samples to identify gene expression signatures shifting with cellular activity changes such as those associated with pathophysiological processes and responses to environmental perturbations. We used simulated data to benchmark scTenifoldNet’s performance, and then applied scTenifoldNet to several real data sets. In real-data applications, scTenifoldNet identified highly specific changes in gene regulation in response to acute morphine treatment, an antibody anticancer drug, gene knockout, double-stranded RNA stimulus, and amyloid-beta plaques in various types of mouse and human cells. We anticipate that scTenifoldNet can help achieve breakthroughs through constructing and comparing scGRNs in poorly characterized biological systems, by deciphering the full cellular and molecular complexity of the data.HighlightsscTenifoldNet is a machine learning workflow built upon principal component regression, low-rank tensor approximation, and manifold alignmentscTenifoldNet uses single-cell RNA sequencing (scRNAseq) data to construct single-cell gene regulatory networks (scGRNs)scTenifoldNet compares scGRNs of different samples to identify differentially regulated genesReal-data applications demonstrate that scTenifoldNet accurately detects specific signatures of gene expression relevant to the cellular systems tested.Short abstractWe present scTenifoldNet—a machine learning workflow built upon principal component regression, low-rank tensor approximation, and manifold alignment—for constructing and comparing single-cell gene regulatory networks (scGRNs) using data from single-cell RNA sequencing (scRNAseq). scTenifoldNet reveals regulatory changes in gene expression between samples by comparing the constructed scGRNs. With real data, scTenifoldNet identifies specific gene expression programs associated with different biological processes, providing critical insights into the underlying mechanism of regulatory networks governing cellular transcriptional activities.
Oomycete metabolism is highly dynamic and reflects lifestyle adaptations
Authors: Rodenburg Sander Y.A. , de Ridder Dick , Govers Francine , Seidl Michael F. 
Published: February 2020

SUMMARYPathogen-host symbiosis drives metabolic adaptations. Animal and plant pathogenic oomycetes are thought to adapt their metabolism to facilitate interactions with their hosts. Here, we performed a large-scale comparison of oomycete metabolism and uncovered considerable variation in oomycete metabolism that could be linked to differences in lifestyle. Pathway comparisons revealed that plant pathogenic oomycetes can be divided in two parts; a conserved part and an accessory part. The accessory part could be associated with the degradation of plant compounds produced during defence responses. Obligate biotrophic oomycetes have smaller metabolic networks, and this group displays converged evolution by repeated gene losses affecting the same metabolic pathways. A comparison of the metabolic networks of obligate biotrophic oomycetes with those of plant pathogenic oomycetes as a whole revealed that the losses of metabolic enzymes in biotrophs are not random and that the network of biotrophs contracts from the periphery inwards. Our analyses represent the first metabolism-focused comparison of oomycetes at this scale and will contribute to a better understanding of the evolution and relationship between metabolism and lifestyle adaptation.ORIGINALITY & SIGNFICANCE STATEMENTThe intimate interaction between pathogens and their hosts exerts strong selection pressure leading to rapid adaptation. How this shapes the metabolism of pathogens is largely unknown. Here, we used comparative genomics to systematically characterize the metabolisms of animal and plant pathogenic oomycetes, a group of eukaryotes comprising many important animal and plant pathogens with significant economic and ecological impact. Core- and pan-genome as well as metabolic network analyses of distantly related oomycetes and their non-pathogenic relatives revealed considerable lifestyle- and lineage-specific adaptations. Extreme lifestyle adaptation could be observed in the metabolism of obligate biotrophic oomycetes – a group of pathogens that require a living host for proliferation. The metabolic networks of obligate biotrophic oomycetes reflect profound patterns of reductive evolution, converging to a loss the same metabolic enzymes during acquisition of an obligate parasitic lifestyle. These findings contribute to a be better understanding of oomycete evolution and the relationship between metabolism and lifestyle adaptation.
Emergence of ribozyme and tRNA-like structures from mineral-rich muddy pools on prebiotic earth
Authors: Roy Suvam , Bapat Niraja V. , Derr Julien , Rajamani Sudha , Sengupta Supratim 
Published: February 2020

AbstractThe RNA world hypothesis, although a viable one regarding the origin of life on earth, has so far failed to provide a compelling explanation for the synthesis of RNA molecules with catalytic functions, from free nucleotides via abiotic processes. To tackle this long-standing problem, we develop a realistic model for the onset of the RNA world, using experimentally determined rates for polymerization reactions. We start with minimal assumptions about the initial state that only requires the presence of short oligomers or just free nucleotides and consider the effects of environmental cycling by dividing a day into a dry, semi-wet and wet phases that are distinguished by the nature of reactions they support. Long polymers, with maximum lengths sometimes exceeding 100 nucleotides, spontaneously emerge due to a combination of non-enzymatic, non-templated polymer extension and template-directed primer extension processes. The former helps in increasing the lengths of RNA strands, whereas the later helps in producing complementary copies of the strands. Strands also undergo hydrolysis in a structure-dependent manner that favour breaking of bonds connecting unpaired nucleotides. We identify the most favourable conditions needed for the emergence of ribozyme and tRNA-like structures and double stranded RNA molecules, classify all RNA strands on the basis of their secondary structures and determine their abundance in the population. Our results indicate that under suitable environmental conditions, non-enzymatic processes would have been sufficient to lead to the emergence of a variety of ribozyme-like molecules with complex secondary structures and potential catalytic functions.
MPRAudit Quantifies the Fraction of Variance Described by Unknown Features in Massively Parallel Reporter Assays
Authors: Siegel David A. , Le Tonqueze Olivier , Biton Anne , Erle David J. , Zaitlen Noah 
Published: February 2020

AbstractTransformative advances in molecular technologies, such as massively parallel reporter assays (MPRAs) and CRISPR screens, can efficiently characterize the effects of genetic and genomic variation on cellular phenotypes. Analysis approaches to date have focused on identifying individual genomic regions or genetic variants that perturb a phenotype of interest. In this work, we develop a wholistic framework (MPRAudit) to determine the global contribution of sequence to phenotypic variation across subsets of the entire experiment, opening the door to myriad novel analyses. For example, MPRAudit can reliably estimate the upper limit of predictive performance, the fraction of variation attributed to specific biological categories, and the total contribution of experimental noise. We demonstrate through simulation and application to several types of real MPRA data sets how MPRAudit can lead to an improved understanding of experimental quality, molecular biology, and guide future research. Applying MPRAudit to real MPRA data, we observe that sequence variation is the primary driver of outcome variability, but that known biological categories explain only a fraction of this variance. We conclude that our understanding of how sequence variation impacts phenotype, even at the level of MPRAs, remains open to further scientific discovery.
A critical period terminates the differentiation of olfactory sensory neurons
Authors: Jafari Shadi , Alenius Mattias 
Published: February 2020

AbstractDevelopment generates a vast number of neuron types and classes. When and how neuronal differentiation end is poorly understood. Here, we show thatDrosophilaolfactory sensory neurons (OSNs) matures during a critical period and reveal that the differentiation termination mechanism is similar to the mammalian odorant receptor (OR) choice mechanism. We first showed that initiation ofDrosophilaOR expression required heterochromatin opening and a H3K9me3 demethylase,Kdm4b. Further genetic studies demonstrated thatLsd1andsu(var)3-9, similar to mouse, were required to balance heterochromatin in order to stabilize OR expression. Expression analysis showed thatLsd1, su(var)3-9increased andKdm4bdecreased during the first two days after eclosion. We further showed that environment changes during the period, but not after, caused permanent transformed Lsd1, su(var)3-9 and Kdm4b expression and altered OR gene regulation. These results together suggest the last step in OSN terminal differentiation to be a gene regulatory critical period.
Functional specialization of human salivary glands and origins of proteins intrinsic to human saliva
Authors: Saitou Marie , Gaylord Eliza , Xu Erica , May Alison , Neznanova Lubov , Nathan Sara , Grawe Anissa , Chang Jolie , Ryan William , Ruhl Stefan , Knox Sarah M. , Gokcumen Omer 
Published: February 2020

SUMMARYSalivary proteins are essential for maintaining health in the oral cavity and proximal digestive tract and serve as a diagnostic window into human disease. However, their precise organ origins remain unclear. Through transcriptomic analysis of major adult and fetal salivary glands, and integration with the saliva proteome and transcriptomes of 28+ organs, we linked human saliva proteins to their source, identified salivary gland-specific genes, and uncovered fetal- and adult-specific gene repertoires. Our results also provide new insights into the degree of gene retention during maturation and suggest that functional diversity between adult gland-types is driven by specific dosage combinations of hundreds of transcriptional regulators rather than a few gland-specific factors. Finally, we demonstrate the hitherto unrecognized heterogeneity of the human acinar cell lineage. Our results pave the way for future investigations into glandular biology and pathology, as well as saliva’s use as a diagnostic fluid.
Suppression of canonical TGF-β signaling enables GATA4 to interact with H3K27me3 demethylase JMJD3 to promote cardiomyogenesis
Authors: Riching Andrew S. , Danis Etienne , Zhao Yuanbiao , Cao Yingqiong , Chi Congwu , Bagchi Rushita A. , Klein Brianna J. , Xu Hongyan , Kutateladze Tatiana G. , McKinsey Timothy A. , Buttrick Peter M. , Song Kunhua 
Published: February 2020

SummaryDirect reprogramming of fibroblasts into cardiomyocytes (CMs) represents a promising strategy to regenerate CMs lost after ischemic heart injury. Overexpression ofGATA4,HAND2,MEF2C,TBX5, miR-1, and miR-133 (GHMT2m) along with transforming growth factor beta (TGF-β) inhibition efficiently promotes reprogramming. However, the mechanisms by which TGF-β blockade promotes cardiac reprogramming remain unknown. Here, we identify interactions between the histone H3 lysine 27 trimethylation (H3K27me3) – demethylase JMJD3, the SWI/SNF remodeling complex subunit BRG1, and cardiac transcription factors. Furthermore, canonical TGF-β signaling regulates the interaction between GATA4 and JMJD3. TGF-β activation impairs the ability of GATA4 to bind target genes and prevents demethylation of H3K27 at cardiac gene promoters during cardiac reprogramming. Finally, a mutation inGATA4(V267M) exhibits reduced binding to JMJD3 and impaired cardiomyogenesis. Thus, we have identified an epigenetic mechanism wherein canonical TGF-β pathway activation impairs cardiac gene programming by interfering with GATA4-JMJD3 interactions.
Nanoscale Molecular Characterisation of Hair Cuticles using Integrated AFM-IR
Authors: Fellows A. P. , Casford M. T. L. , Davies P. B. 
Published: February 2020

AbstractThe nanometre-scale topography and chemical structure of hair cuticles has been investigated by vibrational spectroscopy and imaging in two spectral regions. The combination of Atomic Force Microscopy with a tuneable infrared laser (AFM-IR) circumvents the diffraction limit that has impaired traditional infrared spectroscopy, facilitating surface spectroscopy at ultra-spatial resolution. The variation in protein and lipid content of the cuticle cell surface approaching its edge, as well as the exposed layered structure of the cell at the edge itself, was investigated. Furthermore, the contribution of cystine-related products to the cuticle layers was determined. The variation of protein, lipid and cystine composition in the observed layers, as well as the measured dimensions of each, correspond closely to that of the epicuticle, A-layer, exocuticle and endocuticle layers of the cuticle cell sub-structure.Statement of SignificanceUsing AFM-IR to analyse the nanoscale cuticle features is both significant and novel in the field. Thus far, the great majority of work on the chemical investigation of the structure of hair has been limited to bulk measurements, or subject to the diffraction limit associated with traditional IR spectroscopies and microscopies. AFM-IR circumvents this diffraction limit and allows nanometre-scale, localised chemical investigation with high surface selectivity. While non-chemical investigations, e.g. those using Transmission Election Microscopy, have previously shown cuticles to have a layered substructure, AFM-IR sheds light on significant chemical variations of protein and lipid compositions within such layers, enabling their quantification.
Microtubule instability driven by longitudinal and lateral strain propagation
Authors: Igaev Maxim , Grubmüller Helmut 
Published: February 2020

AbstractTubulin dimers associate longitudinally and laterally to form metastable microtubules (MTs). MT disassembly is preceded by subtle structural changes in tubulin fueled by GTP hydrolysis. These changes render the MT lattice unstable, but it is unclear exactly how they affect lattice energetics and strain. We performed long-time atomistic simulations to interrogate the impacts of GTP hydrolysis on tubulin lattice conformation, lateral inter-dimer interactions, and (non-)local lateral coordination of dimer motions. The simulations suggest that most of the hydrolysis energy is stored in the lattice in the form of longitudinal strain. While not significantly affecting lateral bond stability, the stored elastic energy results in more strongly confined and correlated dynamics of GDP-tubulins, thereby entropically destabilizing the MT lattice.
Nanoscale pattern extraction from relative positions of sparse 3D localisations
Authors: Curd Alistair P. , Leng Joanna , Hughes Ruth E. , Cleasby Alexa J. , Rogers Brendan , Trinh Chi , Baird Michelle A. , Takagi Yasuharu , Tiede Christian , Sieben Christian , Manley Suliana , Schlichthaerle Thomas , Jungmann Ralf , Ries Jonas , Shroff Hari , Peckham Michelle 
Published: February 2020

AbstractWe present a method for extracting high-resolution ordered features from localisation microscopy data by analysis of relative molecular positions in 2D or 3D. This approach allows pattern recognition at sub-1% protein detection efficiencies, in large and heterogeneous samples, and in 2D and 3D datasets. We used this method to infer ultrastructure of the nuclear pore, the cardiomyocyte Z-disk, DNA origami structures and the centriole.