bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlative Organelle Microscopy: fluorescence guided volume electron microscopy of intracellular processes
Authors: Loginov Sergey , Fermie Job , Fokkema Jantina , Agronskaia Alexandra V. , de Heus Cilia , Blab Gerhard A. , Klumperman Judith , Gerritsen Hans C. , Liv Nalan 
Published: March 2021

AbstractIntracellular processes depend on a strict spatial and temporal organization of proteins and organelles. Directly linking molecular to nanoscale ultrastructural information is therefore crucial to understand cellular physiology. Volume or 3-dimensional (3D) correlative light and electron microscopy (volume-CLEM) holds unique potential to explore cellular physiology at high-resolution ultrastructural detail across cell volumes. Application of volume-CLEM is however hampered by limitations in throughput and 3D correlation efficiency. Addressing these limitations, we here describe a novel pipeline for volume-CLEM that provides high-precision (<100nm) registration between 3D fluorescence microscopy (FM) and 3D electron microscopy (EM) data sets with significantly increased throughput. Using multi-modal fiducial nanoparticles that remain fluorescent in epoxy resins and a 3D confocal fluorescence microscope integrated in a Focused Ion Beam Scanning Electron Microscope (FIB.SEM), our approach uses FM to target extremely small volumes of even single organelles for imaging in volume-EM, and obviates the need for post correlation of big 3D datasets. We extend our targeted volume-CLEM approach to include live-cell imaging, adding information on the motility of intracellular membranes selected for volume-CLEM. We demonstrate the power of our approach by targeted imaging of rare and transient contact sites between endoplasmic reticulum (ER) and lysosomes within hours rather than days. Our data suggest that extensive ER-lysosome and mitochondria-lysosome interactions restrict lysosome motility, highlighting the unique capabilities of our integrated CLEM pipeline for linking molecular dynamic data to high-resolution ultrastructural detail in 3D.SignificanceWe have developed a correlative imaging pipeline to(i)correlate 3D-FM to volume-EM data with high precision, directly bridging the FM and EM resolutions(ii)achieve high-throughput volume-CLEM by targeted EM imaging of a single organelle sized region-of-interest, pre-identified by FM(iii)link live-cell fluorescence imaging of cultured mammalian cells to high-throughput volume-CLEM(iv)quantitatively study structure-function relations at subcellular scale(v)link rare (e.g. membrane contact sites) and transient (e.g. organelle interactions) cellular events to 3D ultrastructure.The targeted volume-CLEM pipeline provides a unique prospect for multi-modal correlative intracellular analysis combining dynamic interaction (live-cell imaging), functional state (live-cell imaging), molecular localization (FM), and 3D-ultrastructure (FIB.SEM) at nanometer scale.
Type 2 innate immunity regulates hair follicle homeostasis to controlDemodexpathosymbionts
Authors: Ricardo-Gonzalez Roberto R. , Kotas Maya E. , Tenvooren Iliana , Marquez Diana M. , Fassett Marlys S. , Lee Jinwoo , Daniel Scott G. , Bittinger Kyle , Díaz Roberto Efraín , Fraser James S. , Ansel K. Mark , Spitzer Matthew H. , Liang Hong-Erh , Locksley Richard M. 
Published: March 2021

AbstractAllergic skin diseases are common, but basal roles for type 2 immunity in cutaneous homeostasis are incompletely understood. Here, we show that skin group 2 innate lymphoid cells (ILC2s) are the predominant resident cells that secretes IL-13, which attenuates epithelial cell proliferation during anagen throughout the hair follicle (HF), including in HF stem cells. Although HF are normal in the absence of type 2 immunity, colonization with the commensal mite,Demodex musculi,results in epithelial proliferation and aberrant hair follicle morphology accompanied by loss of stable commensalism with massive infestation and expansion of inflammatory ILC2s and other immune cells. Topical anti-parasitic agents, but not broad-spectrum antibiotics, reversed the phenotype. CommensalDemodexcolonization of mammalian hair follicles is ubiquitous, including in humans, revealing an unanticipated role for ILC2s and type 2 immunity for skin homeostasis in the normal environment.One Sentence SummaryDynamic regulation of skin physiology by Type 2 innate immunity regulates healthy commensalism by parasiticDemodexmites.
Staphylococcus aureusα-toxin induces acid sphingomyelinase release from a human endothelial cell line
Authors: Krones David , Rühling Marcel , Becker Katrin Anne , Kunz Tobias C. , Sehl Carolin , Paprotka Kerstin , Gulbins Erich , Fraunholz Martin 
Published: March 2021

AbstractStaphylococcus aureus(S. aureus) is well known to express a plethora of toxins of which the pore-forming hemolysin A (α-toxin) is the best-studied cytolysin. Pore-forming toxins (PFT) permeabilize host membranes during infection thereby causing concentration-dependent effects in host cell membranes ranging from disordered ion fluxes to cytolysis. Host cells possess defense mechanisms against PFT attack, resulting in endocytosis of the breached membrane area and delivery of repair vesicles to the insulted plasma membrane as well as a concurrent release of membrane repair enzymes. Since PFTs from several pathogens have been shown to recruit membrane repair components, we here investigated whether staphylococcal α-toxin is able to induce these mechanisms in endothelial cells. We show thatS. aureusα-toxin induced increase in cytosolic Ca2+in endothelial cells, which was accompanied by p38 MAPK phosphorylation. Toxin challenge led to increased endocytosis of an extracellular fluid phase marker as well as increased externalization of LAMP1-positive membranes suggesting that peripheral lysosomes are recruited to the insulted plasma membrane. We further observed that thereby the lysosomal protein acid sphingomyelinase (ASM) was released into the cell culture medium. Thus, our results show that staphylococcal α-toxin triggers mechanisms in endothelial cells, which have been implicated in membrane repair after damage of other cell types by different toxins.
DecipheringBrassicaplant defence responses to cabbage white butterfly egg-associated molecular patterns
Authors: Caarls Lotte , Bassetti Niccoló , van Doesburg Femke , Verbaarschot Patrick , van Loon Joop J.A. , Schranz M. Eric , Fatouros Nina E. 
Published: March 2021

AbstractBrassicaplants activate a strong hypersensitive response (HR)-like necrosis underneath eggs of cabbage white butterflies, but their molecular response to eggs is poorly understood. Here, we developed a method to generate egg wash to identify potential insect egg-associated molecular patterns (EAMPs) inducing HR-like necrosis. We found that egg wash, containing compounds fromPieriseggs, induced a similar response as eggs. We show that wash of hatched eggs, of egg glue, and of accessory reproductive glands (ARG) that produce this glue, also induced HR-like necrosis, whereas removal of the glue from eggs resulted in a reduced response. Eggs ofPierisbutterflies induced callose deposition, production of reactive oxygen species and cell death inB. nigraandB. rapaleaf tissue, also in plants that did not express HR-like necrosis. Finally, only washes fromPieriseggs induced defence genes and ethylene production, whereas egg wash of a generalist moth did not. Our results indicate that EAMPs are in the egg glue and that the response inB. nigrais specific toPierisspecies. Our study expands knowledge on theBrassica-Pieris-egg interaction, and paves the way for identification of EAMPs inPierisegg glue and corresponding receptor inBrassicaspp.
Innate immune signaling in trophoblast and decidua organoids defines differential antiviral defenses at the maternal-fetal interface
Authors: Yang Liheng , Semmes Eleanor C. , Ovies Cristian , Megli Christina , Permar Sallie , Gilner Jennifer B. , Coyne Carolyn B. 
Published: March 2021

AbstractInfections at the maternal-fetal interface can directly harm the fetus and induce complications that adversely impact pregnancy outcomes. Innate immune signaling by both fetal-derived placental trophoblasts and the maternal decidua must provide antimicrobial defenses at this critical interface without compromising its integrity. Here, we developed matched trophoblast and decidua organoids from human placentas to define the relative contributions of these cells to antiviral defenses at the maternal-fetal interface. We demonstrate that trophoblast and decidua organoids basally secrete distinct immunomodulatory factors, including the constitutive release of the antiviral type III interferon IFN- λ2 from trophoblast organoids, and differentially respond to viral infections through the induction of organoid-specific factors. Lastly, we define the differential susceptibility of trophoblast and decidua organoids to human cytomegalovirus (HCMV) and the transcriptional and immunological responses of these organoids to HCMV infection. Our findings establish matched trophoblast and decidua organoids as ex vivo models to study vertically transmitted infections and highlight differences in innate immune signaling by fetal-derived trophoblasts and the maternal decidua.
Interactions and information: Exploring task allocation in ant colonies using network analysis
Authors: Swain Anshuman , Williams Sara D. , Di Felice Louisa J. , Hobson Elizabeth A. 
Published: March 2021

ABSTRACTIn animal societies, individuals may take on different roles to fulfil their own needs and the needs of their groups. Ant colonies display high levels of organisational complexity, with ants fulfilling different roles at different timescales (what is known astask allocation). Factors affecting task allocation can be at the individual level (e.g., physiology), or at the group level (e.g., the network of interactions). We focus on group level processes by exploring the relationship between interaction networks, task allocation and task switching using a previously published dataset (Mersch et al., 2013) tracking the behaviour of sixCamponotus fellahcolonies over 41 days. In our new analyses, our goal was to better explain the noisy process of task switching beyond simple age polyethism. First, we investigated the architecture of interaction networks using node (individual) level network measures and their relation to the individual’s task – foraging, cleaning or nursing – and whether or not the ant switched tasks. We then explored how noisy information propagation was among ants, as a function of the colony composition (how many ants carried out which tasks), through the information-theoretic metric ofEffective Information. Our results show that interaction history was tied to task allocation: ants who switched to a task are more likely to have interacted with other ants carrying out that task. The degree to which interactions related to task allocation, as well as the noise in those interactions, depended on which groups of ants were interacting. Overall, we showed that colony cohesion was stable even as ant-level network measures varied more for ants when they switched functional groups; thus, ant colonies maintained a high level of information flow as determined by network analysis, and ant functional groups played different roles in maintaining colony cohesion through varied information flows.HighlightsWe analysed the interaction networks of sixCamponotus fellahcoloniesWe tested how centrality and information flow were tied to task switchingNode-level network metrics and the information theoretic measure ofEffective Informationexplained differences among functional groupsInteractions were correlated with task switching, but the strength of the correlation differed across functional groups
HPMCP-coated microcapsules containing the Ctx(Ile21)-Ha antimicrobial peptide reduces the mortality rate caused by resistantSalmonellaEnteritidis in poultry
Authors: Roque Borda Cesar Augusto , Pereira Larissa Pires , Lopes Guastalli Elisabete Aparecida , Soares Nilce Maria , Mac-Lean Priscilla Ayleen Bustos , D’Alessandro Salgado Douglas , Meneguin Andréia Bagliotti , Chorilli Marlus , Vicente Eduardo Festozo 
Published: March 2021

ABSTRACTThe constant use of synthetic antibiotics as growth promoters can cause great bacterial resistance in chicks. Consequently, the use of these drugs has been restricted in different countries. Antimicrobial peptides have gained relevance in recent years due to their minimal capacity for bacterial resistance and does not generate toxic residues that harm the environment and human health. In this work, Ctx(Ile21)-Ha antimicrobial peptide was employed, due to its previously reported largely antimicrobial potential, to evaluate its application effect in laying chicks challenged withSalmonellaEnteritidis, resistant to nalidixic acid and spectinomycin. For this, Ctx(Ile21)-Ha was synthesized, microencapsulated and coated with hypromellose phthalate (HPMCP) to be release in the intestine. Two different doses (3.2 and 6.4 µg of Ctx(Ile21)-Ha per kg of isoproteic and isoenergetic poultry feed) were included in the chicks’ food and administered for 28 days. Antimicrobial activity, effect and response as treatment were evaluated. Statistical results were analyzed in detail and indicate that the formulated Ctx(Ile21)-Ha peptide had a positive and significant effect in relation to the reduction of chick mortality. There was a significant difference in laying chick weight between the control and microencapsulation treatment groups as a function of time. Therefore, the microencapsulated Ctx(Ile21)-Ha antimicrobial peptide may be an interesting and promising option in the substitution of conventional antibiotics.
Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases
Authors: Trigg Shelly A. , Venkataraman Yaamini R. , Gavery Mackenzie R. , Roberts Steven B. , Bhattacharya Debashish , Downey-Wall Alan , Eirin-Lopez Jose M. , Johnson Kevin M. , Lotterhos Katie E. , Puritz Jonathan B. , Putnam Hollie M. 
Published: March 2021

AbstractThere is a growing focus on the role of DNA methylation in the ability of marine invertebrates to rapidly respond to changing environmental factors and anthropogenic impacts. However, genome-wide DNA methylation studies in non-model organisms are currently hampered by limited understanding of methodological biases. Here we compare three methods for quantifying DNA methylation at single base-pair resolution — Whole Genome Bisulfite Sequencing (WGBS), Reduced Representation Bisulfite Sequencing (RRBS), and Methyl-CpG Binding Domain Bisulfite Sequencing (MBDBS) — using multiple individuals from two reef-building coral species with contrasting environmental sensitivity. All methods reveal substantially greater methylation inMontipora capitata(11.4%) than the more sensitivePocillopora acuta(2.9%). The majority of CpG methylation in both species occurs in gene bodies and flanking regions. In both species, MBDBS has the greatest capacity for detecting CpGs in coding regions at our sequencing depth, however MBDBS may be influenced by intra-sample methylation heterogeneity. RRBS yields robust information for specific loci albeit without enrichment of any particular genome feature and with significantly reduced genome coverage. Relative genome size strongly influences the number and location of CpGs detected by each method when sequencing depth is limited, illuminating nuances in cross-species comparisons. As genome-wide methylation differences, supported by data across bisulfite sequencing methods, may contribute to environmental sensitivity phenotypes in critical marine invertebrate taxa, these data provide a genomic resource for investigating the functional role of DNA methylation in environmental tolerance.
Self-organization of a doubly asynchronous irregular network state for spikes and bursts
Authors: Vercruysse Filip , Naud Richard , Sprekeler Henning 
Published: March 2021

AbstractCortical pyramidal cells (PCs) have a specialized dendritic mechanism for the generation of bursts, suggesting that these events play a special role in cortical information processing.In vivo, bursts occur at a low, but consistent rate. Theory suggests that this network state increases the amount of information they convey. However, because burst activity relies on a threshold mechanism, it is rather sensitive to dendritic input levels. In spiking network models, network states in which bursts occur rarely are therefore typically not robust, but require fine-tuning. Here, we show that this issue can be solved by a homeostatic inhibitory plasticity rule in dendrite-targeting interneurons that is consistent with experimental data. The suggested learning rule can be combined with other forms of inhibitory plasticity to self-organize a network state in which both spikes and bursts occur asynchronously and irregularly at low rate. Finally, we show that this network state creates the network conditions for a recently suggested multiplexed code and thereby indeed increases the amount of information encoded in bursts.Author summaryThe language of the brain consists of sequences of action potentials. These sequences often contain bursts, short “words” consisting of a few action potentials in rapid succession. Bursts appear to play a special role in the brain. They indicate whether a stimulus was perceived or missed, and they are very effective drivers of synaptic plasticity, the neural substrate of learning. Bursts occur rarely, but consistently, a condition that is thought to maximize the amount of information they can communicate. In our article, we argue that this condition is far from self-evident, but requires very special circumstances. We show that these circumstances can be reached by homeostatic inhibitory plasticity in certain inhibitory neuron types. This may sound complicated, but basically works just like a thermostat. When bursts occur too often, inhibition goes up and suppresses them. When they are too rare, inhibition goes down and thereby increases their number. In computer simulations, we show that this simple mechanism can create circumstances akin to those in the brain, and indeed allows bursts to convey information effectively. Whether this mechanism is indeed used by the brain now remains to be tested by our experimental colleagues.
EHMT2 Controls Transcriptional Noise and the Developmental Switch after Gastrulation in the Mouse Embryo
Authors: Zeng Tie-Bo , Pierce Nicholas , Liao Ji , Singh Purnima , Zhou Wanding , Szabó Piroska E. 
Published: March 2021

ABSTRACTEmbryos that carry zygotic or parental mutations inEhmt2, the gene encoding the main euchromatic histone H3K9 methyltransferase, EHMT2, exhibit variable developmental delay. We asked the question whether the delayed embryo is different transcriptionally from the normally developing embryo when they reach the same developmental stage. We collected embryos carrying a series of genetic deficiencies in theEhmt2gene and performed total RNA sequencing of somite stage-matched individual embryos. We applied novel four-way comparisons to detect differences between normal versus deficient embryos, and between 12-somite and 6-somite embryos. Importantly, we also identified developmental changes in transcription that only occur during the development of the normal embryo. We found that at the 6-somite stage, gastrulation-specific genes were not precisely turned off in theEhmt2−/−embryos, and genes involved in organ growth, connective tissue development, striated muscle development, muscle differentiation, and cartilage development were not precisely switched on in theEhmt2−/−embryos. Zygotic EHMT2 reduced transcriptional variation of developmental switch genes and at some repeat elements at the six-somite stage embryos. Maternal EHMT2-mutant embryos also displayed great transcriptional variation consistent with their variable survival, but transcription was normal in developmentally delayed parental haploinsufficient embryos, consistent with their good prospects. Global profiling of transposable elements in the embryo revealed that specific repeat classes responded to EHMT2. DNA methylation was specifically targeted by EHMT2 to LTR repeats, mostly ERVKs. Long noncoding transcripts initiated from those misregulated ‘driver’ repeats inEhmt2−/−embryos, and extended to several hundred kilobases, encompassing a multitude of additional, similarly misexpressed ‘passenger repeats.’ These findings establish EHMT2 as an important regulator of the transition between gastrulation programs and organ specification programs and of variability.
Self-Supervised Deep Learning Encodes High-Resolution Features of Protein Subcellular Localization
Authors: Kobayashi Hirofumi , Cheveralls Keith C. , Leonetti Manuel D. , Royer Loic A. 
Published: March 2021

AbstractElucidating the diversity and complexity of protein localization is essential to fully understand cellular architecture. Here, we presentcytoself, a deep-learning approach for fully self-supervised protein localization profiling and clustering.cytoselfleverages a self-supervised training scheme that does not require pre-existing knowledge, categories, or annotations. Trainingcytoselfon images of 1,311 endogenously labeled proteins from the OpenCell database reveals a highly resolved protein localization atlas that recapitulates major scales of cellular organization, from coarse classes such as nuclear, cytoplasmic and vesicular, to the subtle localization signatures of individual protein complexes. We quantitatively validatecytoself’s ability to cluster proteins into organelles and protein complex clusters using a clustering score, and show thatcytoselfattains higher scores than previous unsupervised or self-supervised approaches. Finally, to better understand the inner workings of our model, we dissect the emergent features from which our clustering is derived, interpret these features in the context of the fluorescence images, and analyze the performance contributions of the different components of our approach.
Clinically relevant mutations of mycobacterial GatCAB inform regulation of translational fidelity
Authors: Li Yang-Yang , Cai Rong-Jun , Yang Jia-Ying , Hendrickson Tamara L. , Xiang Ye , Javid Babak 
Published: March 2021

AbstractMost bacteria employ a two-step indirect tRNA aminoacylation pathway for the synthesis of aminoacylated tRNAGlnand tRNAAsn. The heterotrimeric enzyme GatCAB performs a critical amidotransferase reaction in the second step of this pathway. We have previously demonstrated in mycobacteria that this two-step pathway is error-prone and translational errors contribute to adaptive phenotypes such as antibiotic tolerance. Furthermore, we identified clinical isolates of the globally important pathogenMycobacterium tuberculosiswith partial loss-of-function mutations ingatA, and demonstrated that these mutations result in high, specific rates of translational error and increased rifampicin tolerance. However, the mechanisms by which these clinically-derived mutations ingatAimpact GatCAB function was unknown. Here, we describe biochemical and biophysical characterization ofM. tuberculosisGatCAB, containing either wild-typegatAor one of twogatAmutants from clinical strains. We show that these mutations have minimal impact on enzymatic activity of GatCAB; however, they result in destabilization of the GatCAB complex as well as that of the ternary asparaginyl-transamidosome. Stabilizing complex formation with the solute trehalose increases specific translational fidelity of not only the mutant strains, but also of wild-type mycobacteria. Therefore, our data suggest that alteration of GatCAB stability may be a mechanism for modulation of translational fidelity.