bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measurement of infection efficiency of a major wheat pathogen using time-resolved imaging of disease progress
Authors: Karisto P. , Dora S. , Mikaberidze A. 
Published: May 2018

AbstractInfection efficiency is a key epidemiological parameter that determines the proportion of pathogen spores able to infect and cause lesions once they have landed on a susceptible plant tissue. In this study, we present an improved method to measure infection efficiency of Zymoseptoria tritici using a replicated greenhouse experiment. Z. tritici is a fungal pathogen that infects wheat leaves and causes Septoria tritici blotch (STB), a major disease of wheat worldwide.We devised an original experimental setup, where we (i) attached living wheat leaves to metal plates allowing for time-resolved imaging of disease progress in planta. Since lesions were continuously appearing, expanding and merging during the period of up to three weeks, daily measurements were necessary for accurate counting of lesions. We also (ii) used reference membranes to characterize the density and the spatial distribution of inoculated spores on leaf surfaces. In this way, we captured the relationship between the number of lesions and the number of viable spores deposited on the leaves and estimated the infection efficiency of about 4 % from the slope of this relationship.Our study provides a proof of principle for an accurate and reliable measurement of infection efficiency of Z. tritici. The method opens opportunities for determining the genetic basis of the component of quantitative resistance that suppresses infection efficiency. This knowledge would improve breeding for quantitative resistance against STB, a control measure considered more durable than deployment of major resistance genes.
Equivalence of the Erlang Seir Epidemic Model and the Renewal Equation
Authors: Champredon David , Dushoff Jonathan , Earn David J.D. 
Published: May 2018

AbstractMost compartmental epidemic models can be represented using the Euler-Lotka renewal equation (RE). The value of the RE is not widely appreciated in the epidemiological modelling community, perhaps because its equivalence to standard models has not been presented rigorously in non-trivial cases. Here, we provide analytical expressions for the intrinsic generation interval distribution that must be used in the RE in order to yield epidemic dynamics that are identical to those of the susceptible-exposed-infectious-recovered (SEIR) compartmental model with Erlang-distributed latent and infectious periods. This class of models includes the standard (exponentially-distributed) SIR and SEIR models as special cases.
The apical region of the herpes simplex virus major capsid protein promotes capsid maturation
Authors: Ruhge Laura L. , Huet Alexis G. E. , Conway James F. , Smith Gregory A. 
Published: May 2018

ABSTRACTThe herpesvirus capsid assembles in the nucleus as an immature procapsid precursor built around viral scaffold proteins. The event that initiates procapsid maturation is unknown, but it is dependent upon activation of the VP24 internal protease. Scaffold cleavage triggers angularization of the shell and its decoration with the VP26 and pUL25 capsid-surface proteins. In both the procapsid and mature angularized capsid, the apical region of the major capsid protein (VP5) is surface exposed. We investigated whether the VP5 apical region contributes to intracellular transport dynamics following entry into primary sensory neurons and also tested the hypothesis that conserved negatively-charged amino acids in the apical region contribute to VP26 acquisition. To our surprise neither hypothesis proved true. Instead, mutation of glutamic acid residues in the apical region delayed viral propagation and induced focal capsid accumulations in nuclei. Examination of capsid morphogenesis based on epitope unmasking, capsid composition, and ultrastructural analysis indicated that these clusters consisted of procapsids. The results demonstrate that, in addition to established events that occur inside the capsid, the exterior capsid shell promotes capsid morphogenesis and maturation.
The potassium channel KCNJ13 is essential for smooth muscle cytoskeletal organization during mouse tracheal tubulogenesis
Authors: Yin Wenguang , Kim Hyun-Taek , Wang ShengPeng , Gunawan Felix , Wang Lei , Kishimoto Keishi , Zhong Hua , Roman Dany , Preussner Jens , Guenther Stefan , Graef Viola , Buettner Carmen , Grohmann Beate , Looso Mario , Morimoto Mitsuru , Mardon Graeme , Offermanns Stefan , Stainier Didier Y.R. 
Published: May 2018

AbstractTubulogenesis is essential for the formation and function of internal organs. One such organ is the trachea, which allows gas exchange between the external environment and the lungs. However, the cellular and molecular mechanisms underlying tracheal tube development remain poorly understood. Here, we show that the potassium channel KCNJ13 is a critical modulator of tracheal tubulogenesis. We identify Kcnj13 in an ethylnitrosourea forward genetic screen for regulators of mouse respiratory organ development. Kcnj13 mutants exhibit a shorter trachea as well as defective smooth muscle (SM) cell alignment and polarity. KCNJ13 is essential to maintain ion homeostasis in tracheal SM cells, which is required for actin polymerization. This process appears to be mediated, at least in part, through activation of the actin regulator AKT, as pharmacological increase of AKT phosphorylation ameliorates the Kcnj13 mutant trachea phenotypes. These results provide insights into the role of ion homeostasis in cytoskeletal organization during tubulogenesis.
Agent-Based Modeling Reveals Possible Mechanisms for Observed Aggregation Cell Behaviors inMyxococcus xanthus
Authors: Zhang Zhaoyang , Igoshin Oleg A. , Cotter Christopher R. , Shimkets Lawrence J. 
Published: May 2018

AbstractMyxococcus xanthusis a soil bacterium that serves as a model system for biological self-organization. Cells form distinct, dynamic patterns depending on environmental conditions. An agent-based model (ABM) was used to understand howM. xanthuscells aggregate into multicellular mounds in response to starvation. In this model, each cell is modeled as an agent, represented by a point-particle and characterized by its position and moving direction. At low agent density, the model recapitulates the dynamic patterns observed by experiments and a previous biophysical model. To study aggregation at high cell density, we extended the model based on the recent experimental observation that cells exhibit biased movement towards aggregates. We tested two possible mechanisms for this biased movement and demonstrate that a chemotaxis model with adaptation can reproduce the observed experimental results leading to the formation of stable aggregates. Furthermore, our model reproduces the experimentally observed patterns of cell alignment around aggregates.Author summaryCollective self-organization of cells into multicellular structures is important for lifestyle of many bacterial species.Myxococcus xanthusbacterium is a model system for studying this self-organization. In this work, we investigate how in response to starvationM. xanthuscells aggregate into multicellular mounds. A recent study identified the key cellular behaviors that are necessarily for the aggregation but the mechanisms of these behaviors remained unclear. To uncover these mechanisms, we developed a computational model that simulates interactions among a large number of cells. The results demonstrate that the observed bias in the cell reversal times as they move towards the aggregates can be explained by chemotaxis model. In this model cells secrete a chemical signal and respond to it via a partially-adapting biochemical network. The resulting aggregation dynamics are in good agreement with the experiments. Furthermore, chemotaxis signaling model reproduces the experimentally observed patterns of cell alignment around aggregates. On the other hand, an alternative model, based on contact-dependent signaling between cells, fails to aid in aggregation. Thus our models make important predictions about the cellular interactions that drives multicellular aggregation and can serve as a basis to investigate a wider range of developmental mutant strains.
Dorsal/NF-κB exhibits a dorsal-to-ventral mobility gradient in the Drosophila embryo
Authors: Al Asafen Hadel , Clark Natalie M. , Goyal Etika , Jacobsen Thomas , Dima Sadia Siddika , Chen Hung-Yuan , Sozzani Rosangela , Reeves Gregory T. 
Published: May 2018

AbstractMorphogen-mediated patterning is a highly dynamic developmental process. To obtain an accurate understanding of morphogen gradient formation and downstream gene expression, biophysical parameters such as protein mobilities must be quantifiedin vivo. The dorsal-ventral (DV) patterning of earlyDrosophilaembryos by the NF-κB homolog Dorsal (Dl) is an excellent system for understanding morphogen gradient formation. Dl gradient formation is controlled by the inhibitor Cactus/IκB (Cact), which regulates the nuclear import and diffusion of Dl protein. However, quantitative measurements of Dl mobility and binding are currently lacking. Here, we use scanning fluorescence correlation spectroscopy to quantify the mobility of GFP-tagged Dl. We find that the DNA binding of Dl-GFP, which affects its mobility, varies along the DV axis, with highest DNA binding on the ventral side. Moreover, we also observe that the time scale for Dl-GFP to exit the nucleus is longer in the ventral and lateral regions of the embryo, which is consistent with stronger DNA binding. Using analysis of mutant alleles ofdltagged with GFP, we conclude that Dl-GFP/Cact interactions in the nuclei are responsible for the variation in Dl-GFP/DNA binding along the DV axis, which impacts our understanding of the spatial range of the Dl gradient and the robustness and precision of downstream gene expression. Thus, our results highlight the complexity of morphogen gradient dynamics and the ability of quantitative measurements of biophysical interactions to drive biological discovery.
A high-density carbon fiber neural recording array technology
Authors: Massey Travis L , Santacruz Samantha R , Hou Jason F , Pister Kristofer SJ , Carmena Jose M , Maharbiz Michel M 
Published: May 2018

Abstract.Objective: Microwire and Utah-style neural recording arrays are the predominant devices used for cortical neural recording, but the implanted electrodes cause a significant adverse biological response and suffer from well-studied performance degradation. Recent work has demonstrated that carbon fiber electrodes do not elicit this same adverse response, but these existing designs are not practically scalable to hundreds or thousands of recording sites. We present technology that overcomes these issues while additionally providing fine electrode pitch for spatial oversampling.Approach: We present a 32-channel carbon fiber monofilament-based intracortical neural recording array fabricated through a combination of bulk silicon microfabrication processing and microassembly. This device represents the first truly two-dimensional carbon fiber neural recording array. The density, channel count, and size scale of this array are enabled by an out-of-plane microassembly technique in which individual fibers are inserted through metallized and isotropically conductive adhesive-filled holes in an oxide-passivated microfabricated silicon substrate.Main results: Five-micron diameter fibers are spaced at a pitch of 38 microns, four times denser than state of the art one-dimensional arrays. The fine diameter of the carbon fibers affords both minimal cross-section and nearly three orders of magnitude greater lateral compliance than standard tungsten microwires. Typical 1 kHz impedances are on the order of hundreds of kiloohms, and successful in vivo recording is demonstrated in the motor cortex of a rat. 22 total units are recorded on 20 channels, with unit SNR ranging from 0.85 to 4.2.Significance: This is the highest density microwire-style electrode array to date, and this fabrication technique is scalable to a larger number of electrodes and allows for the potential future integration of microelectronics. Large-scale carbon fiber neural recording arrays are a promising technology for reducing the inflammatory response and increasing the information density, particularly in neural recording applications where microwire arrays are already used.
Acute-phase CD4+ T cell responses targeting invariant viral regions are associated with control of live-attenuated simian immunodeficiency virus
Authors: Sutton Matthew S. , Ellis-Connell Amy , Moriarty Ryan V. , Balgeman Alexis J. , Gellerup Dane , Barry Gabrielle , Weiler Andrea M. , Friedrich Thomas C. , O’Connor Shelby L. 
Published: May 2018

AbstractWe manipulated SIVmac239Δnef, a model of MHC-independent viral control, to evaluate characteristics of effective cellular responses mounted by Mauritian cynomolgus macaques (MCMs) who express the M3 MHC haplotype that has been associated with poor control of pathogenic SIV. We created SIVΔnef-8x to test the hypothesis that effective SIV-specific T cell responses targeting invariant viral regions can emerge in the absence of immunodominant CD8+ T cell responses targeting variable epitopes, and that control is achievable in individuals lacking known protective MHC alleles. Full proteome IFNγ ELISPOT assays identified six newly targeted immunogenic regions following SIVΔnef-8x infection of M3/M3 MCMs. We deep sequenced circulating virus and found that four of the six newly targeted regions rarely accumulated mutations. Six animals infected with SIVΔnef-8x targeted at least one of the four invariant regions and had a lower set point viral load compared to two animals that did not target any invariant regions. We found that MHC class II molecules restricted all four of the invariant peptide regions, while the two variable regions were restricted by MHC class I molecules. Therefore, in the absence of immunodominant CD8+ T cell responses that target variable regions during SIVmac239Δnef infection, individuals without ‘protective’ MHC alleles developed predominantly CD4+ T cell responses specific for invariant regions that may improve control of virus replication. Our results provide some evidence that antiviral CD4+ T cells during acute SIV infection can contribute to effective viral control and should be considered in strategies to combat HIV infection.ImportanceStudies defining effective cellular immune responses to human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) have largely focused on a rare population that express specific MHC class I alleles and control virus replication in the absence of antiretroviral treatment. This leaves in question whether similar effective immune responses can be achieved in the larger population. The majority of HIV-infected individuals mount CD8+ T cell responses that target variable viral regions that accumulate high-frequency escape mutations. Limiting T cell responses to these variable regions and targeting invariant viral regions, similar to observations in rare ‘elite controllers’, may provide an ideal strategy for the development of effective T cell responses in individuals with diverse MHC genetics. Therefore, it is paramount to determine whether T cell responses can be redirected towards invariant viral regions in individuals without ‘protective’ MHC alleles and if these responses improve control of virus replication.
Two-photon imaging induces brain heating and calcium microdomain hyperactivity in cortical astrocytes
Authors: Schmidt Elke , Oheim Martin 
Published: May 2018

ABSTRACTUnraveling how neural networks process and represent sensory information and how this cellular dynamics instructs behavioral output is a main goal in current neuroscience. Two-photon activation of optogenetic actuators and fluorescence calcium (Ca2+) imaging with genetically encoded Ca2+ indicators allow, respectively, the all-optical stimulation and readout of activity from genetically identified cell populations. However, these techniques expose the brain to high near-infrared light doses raising the concern of light-induced adverse effects on the biological phenomena being studied. Combing Ca2+ imaging of GCaMP6f-expressing cortical astrocytes as a sensitive readout for photodamage and an unbiased machine-based event detection, we demonstrate the subtle build-up of aberrant microdomain Ca2+ signals in fine astroglial processes. Illumination conditions routinely being used in biological two-photon microscopy (920-nm excitation, 100-fs regime, ten mW average power) increased the frequency of microdomain Ca2+ events, but left their amplitude, area and duration rather unchanged. This increase in local Ca2+ activity was followed by Ca2+ transients in the otherwise silent soma. Ca2+ hyperactivity occurred without overt morphological damage. Surprisingly, at the same average power, continuous-wave 920-nm illumination was as damaging as fs pulses, indicating a linear, heating-mediated (rather than a highly non-linear) damage mechanism. In an astrocyte-specific IP3-receptor knock-out mouse (IP3R2-KO), Near-infrared light-induced Ca2+ microdomains signals persisted in the small processes, underpinning their resemblance to physiological IP3R2-independent Ca2+ signals, while somatic activity was abolished. Contrary to what has generally been believed in the field, shorter pulses and lower average power are advantageous to alleviate photodamage and allow for longer useful recording windows.SIGNIFICANCE STATEMENTImaging the fine structure and function of the brain has become possible with two-photon microscopy that uses ultrashort-pulsed infrared laser light for better tissue penetration. The high peak energy of these light pulses has raised concerns about photodamage resulting from multi-photon processes. Here, we show that the time-averaged rather than the peak laser power matters. At wavelengths and with laser powers now commonly used in neuroscience brain damage occurs as a consequence of direct infrared light absorption, i.e., heating. To counteract brain heating we explore a strategy that uses even shorter, more energetic pulses but a lower time-averaged laser power to produce the same image quality while making two-photon microscopy less invasive.
Ecdysone signaling promotes expression of multifunctional RNA binding proteins essential for ovarian germline stem cell self-renewal inDrosophila
Authors: Finger Danielle S. , Holt Vivian V. , Ables Elizabeth T. 
Published: May 2018

ABSTRACTSteroid hormones promote stem cell self-renewal in many tissues; however, the molecular mechanisms by which hormone signaling is integrated with niche-derived signals are largely uncharacterized. In theDrosophilaovary, the steroid hormone ecdysone promotes germline stem cell (GSC) self-renewal. Despite strong evidence that ecdysone modulates the reception of bone morphogenetic protein (BMP) signals in GSCs, transcriptional targets of ecdysone signaling that facilitate BMP reception are unknown. Here, we report that ecdysone signaling promotes the expression of the heterogeneous nuclear ribonucleoproteins (hnRNPs)squid,hephaestus,Hrb27C, andHrb87Fin GSCs. These hnRNPs functionally interact with ecdysone signaling to control GSC number and are cell autonomously required in GSCs for their maintenance. We demonstrate that hnRNPs promote GSC self-renewal by binding to transcripts essential for proper BMP signaling, including the BMP receptorsthickveinsandpunt. Our findings support the model that stem cells coordinate local and long-range signals at the transcriptional and post-transcriptional levels to maintain self-renewal in response to physiological demand.GRAPHICAL ABSTRACTEcdysone signaling regulates distinct hnRNPs that bind to BMP signaling targets to control GSC self-renewal.SUMMARY STATEMENTEcdysone signaling promotes expression of heterogeneous ribonucleoproteins that modulate BMP-dependent germline stem cell self-renewal in theDrosophilaovary.
Putting hands to rest: efficient deep CNN-RNN architecture for chemical named entity recognition with no hand-crafted rules
Authors: Korvigo Ilia , Holmatov Maxim , Zaikovskii Anatolii , Skoblov Mikhail 
Published: May 2018

AbstractChemical named entity recognition (NER) is an active field of research in biomedical natural language processing. To facilitate the development of new and superior chemical NER systems, BioCreative released the CHEMDNER corpus, an extensive dataset of diverse manually annotated chemical entities. Most of the systems trained on the corpus rely on complicated hand-crafted rules or curated databases for data preprocessing, feature extraction and output post-processing, though modern machine learning algorithms, such as deep neural networks, can automatically design the rules with little to none human intervention. Here we explored this approach by experimenting with various deep learning architectures for targeted tokenisation and named entity recognition. Our final model, based on a combination of convolutional and stateful recurrent neural networks with attention-like loops and hybrid word-and character-level embeddings, reaches near human-level performance on the testing dataset with no manually asserted rules. To make our model easily accessible for standalone use and integration in third-party software, we’ve developed a Python package with a minimalistic user interface.
Protein biocargo of citrus fruit-derived vesicles reveals heterogeneous transport and extracellular vesicles populations
Authors: Pocsfalvi Gabriella , Turiák Lilla , Ambrosone Alfredo , del Gaudio Pasquale , Puska Gina , Fiume Immacolata , Silvestre Teresa , Vékey Károly 
Published: May 2018

AbstractCellular vesicles are membrane-enclosed organelles that transport material inside and outside the cell. Plant-derived vesicles are receiving increasing attention due to their potential as nanovectors for the delivery of biologically active substances. We aimed to expand our understanding about the heterogeneity and the protein biocargo of citrus fruit juice sac cell-derived vesicles. Micro- and nanosized vesicle fractions were isolated from four citrus species,C. sinensis,C. limon,C. paradisiandC. aurantium, characterized using physicochemical methods and protein cargos were compared using label-free quantitative shotgun proteomics. In each sample approximately 600-800 proteins were identified. Orthologues of most of the top-ranking proteins have previously been reported in extracellular vesicles of mammalian origin. Patellin-3-like, clathrin heavy chain, heat shock proteins, 14-3-3 protein, glyceraldehyde-3-phosphate dehydrogenase and fructose-bisphosphate aldolase 6 were highly expressed in all citrus vesicle fractions. The presence of membrane channel aquaporin on the other hand characteristic of the nanovesicle fractions. Bioinformatics revealed more than hundred protein orthologues potentially implicated in vesicular trafficking. In particular, CCV, COPI and COPII coat proteins indicates the presence of highly heterogeneous populations of intracellular transport vesicles. Moreover, the different hydrolases and oxidoreductases transported within the citrus fruit-derived vesicles can be responsible for the various biological activities possessed by the preparations.AbbreviationsEVsextracellular vesicles;MVsmicrovesicles;NVsnanovesicles;PMplasma membrane;UCultracentrifugation;CCVclathrin coated vesicles;COPIcoat protein I;COPIIcoat protein II