bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amblyomma mixtumfree-living stages: Summer and winter use, preference, and niche width in an agroecosystem (Yopal, Casanare, Colombia)
Authors: Forero-Becerra Elkin , Acosta Alberto , Benavides Efraín , Hidalgo Marylin 
Published: December 2020

AbstractStudying a species’ tolerance to an ecosystem’s environmental conditions and its selection of available resources is relevant in ecological and evolutionary terms. Moreover, formulation of effective control strategies implicitly includes the study of habitat use and preference and niche width in anthropogenically transformed natural landscapes. Here, we evaluated whether the use, habitat preference, and niche range of theAmblyomma mixtumtick changed between stages, habitats, and seasons (summer-winter 2019) on a farm in Yopal (Casanare, Colombia). To this end, the presence and relative abundance of larvae, nymphs, and free-living adults was quantified in four different habitats according to the type of vegetation cover (Riparian Forest, Cocoa Crop, King Grass Crop, and Star Grass Paddock). Habitat availability was calculated, environmental variables were analyzed, and various indices of habitat use and preference and niche width were calculated.A. mixtum’s habitat use and preference and niche width changed between stages, habitat types, and time of the year. The total abundance ofA. mixtumwas an order of magnitude greater in summer than winter. Nymphs and larvae dominated it in the summer and adults in the winter. In summer, all the stages used the four habitats. In winter, the larvae did not use two habitats (Riparian Forest and Cocoa Crop); nymphs did not use the cocoa crop.A. mixtumadults used all the habitats in both seasons. In summer, the nymphs and larvae preferred three of the four habitats (King Grass Crop, Star Grass Paddock, and Cocoa Crops), while adults preferred the King Grass Crop. In winter, the nymphs and larvae preferred the King Grass Crop and Star Grass Paddock, while the adults preferred the King Grass Crop. The value of the niche width index was high for larvae, nymphs, and adults in summer, while it was high only for adults in winter.A. mixtumis exposed to significant daily, seasonal, and multiannual variations in relative humidity (minimum 30%), ambient temperature (minimum 18°C), solar radiation (maximum 800 W/m2), and precipitation (maximum 481 mm/month). Thus, the localA. mixtumpopulation could rapidly acclimatize to changing habitats (unstable or temporary) under fluctuating environmental conditions (e.g., King Grass Crop). However, the winter flood season in Yopal could exceedA. mixtum’s adaptive capacity during its most vulnerable stages. Mathematically, a low number of femaleA. mixtum, surviving the most demanding environmental conditions, could sufficiently ensure the population’s persistence, which, coupled with the vast host range, could facilitate the ticks stages’ dispersal among habitats to complete their life cycle.A. mixtum’s population control should be carried out during its season of greater vulnerability (winter), when the population is low, particularly the females.
Cisplatin-inducible death receptor 5 antisense long non-coding RNA modulates cell cycle and proliferation in HeLa cells
Authors: Gürer Dilek Cansu , Erdoğan İpek , Ahmadov Ulvi , Sweef Osama , Akgül Bünyamin 
Published: December 2020

AbstractCisplatin is a chemotherapeutic drug with pleiotropic effects known to modulate the expression of long non-coding RNAs (lncRNAs). With the annotation of many novel lncRNAs, it is imperative to employ a more comprehensive approach to identify cisplatin-mediated changes in the expression of lncRNAs. Next generation sequencing (NGS)-based profiling of total RNAs from cisplatin-treated HeLa cells identified 3489 expressed lncRNAs, of which 1930 and 1051 were up- and downregulated upon cisplatin treatment, respectively. For functional analyses, we selected one of the cisplatin inducible lncRNAs situated antisense to the death receptor 5 and thus named death receptor 5 antisense lncRNA (DR5-AS). Knock-down of DR5-AS lncRNA caused a morphological change in cell shape without inducing any cell death. A second round of NGS-based profiling of total RNAs from DR5-AS-silenced cells revealed differential expression of genes associated with the immune system and cell cycle. Further analyses showed that DR5-AS reduces cell proliferation and causes a cell cycle arrest at S and G2/M phases. These results suggest that cisplatin-mediated reduction in cell proliferation and cell cycle may be mediated by long non-coding RNAs.SignificanceCisplatin is known to induce DNA-damage-induced cell death, which is used in combination chemotherapies in various cancer types. However, many patients develop resistance to cisplatin, which involves both protein-coding and noncoding genes. Although a number of long noncoding RNAs are linked to cisplatin resistance, a more comprehensive study is required. In this study, we took advantage of next-generation-sequencing based lncRNA profiling to unveil the extent of cisplatin inducible lncRNAs in HeLa cells. Additionally, we functionally characterized one of the cisplatin-inducible lncRNA, death receptor 5 antisense. Interestingly, this spesific lncRNA modulates cell morphology, proliferation and cell cycle without affecting cell death.
Vangl2 regulates the dynamics of Wnt cytonemes in vertebrates
Authors: Brunt Lucy , Greicius Gediminas , Evans Benjamin D , Virshup David M , Wedgwood Kyle CA , Scholpp Steffen 
Published: December 2020

AbstractThe Wnt signalling network regulates cell proliferation and cell differentiation as well as migration and polarity in development of multicellular organisms. However, it is still unclear how distribution of Wnt ligands is precisely controlled to fulfil all of these different functions. Here, we show that the four-pass transmembrane protein Vangl2 occupies a central role in determining the distribution of Wnt by cytonemes in vertebrate tissue. In zebrafish epiblast cells, mouse intestinal telocytes and human gastric cancer cells, activation of Vangl2 leads to the generation of fewer but extremely long cytonemes, which start to branch and deliver Wnt protein to multiple cells. The Vangl2-activated cytonemes increase Wnt/β-catenin signalling in the surrounding cells. Concordantly, inhibition of Vangl2 function leads to the formation of shorter cytonemes and reduced paracrine Wnt/β-catenin signal activation. A mathematical model simulating the observed Vangl2 functions on cytonemes in zebrafish gastrulation predicts an anterior shift of the morphogenetic signalling gradient, altered tissue patterning, and a loss of the sharpness of tissue domains. We confirmed these predictions during anteroposterior patterning in the zebrafish neural plate. In summary, we show that Vangl2 - a core member of the PCP signalling component - is fundamental to paracrine Wnt/β-catenin signalling by controlling cytoneme behaviour in vertebrate development and tissue homeostasis.
Ecm29-dependent proteasome localization regulates cytoskeleton remodeling at the immune synapse
Authors: Ibañez-Vega Jorge , Valle Felipe Del , Saez Juan José , Diaz Jheimmy , Soza Andrea , Yuseff María Isabel 
Published: December 2020

AbstractThe formation of an immune synapse (IS) enables B cells to capture membrane-tethered antigens, where cortical actin cytoskeleton remodeling regulates cell spreading and depletion of F-actin at the centrosome promotes the recruitment of lysosomes to facilitate antigen extraction. How B cells regulate both pools of actin, remains poorly understood. We report here that decreased F-actin at the centrosome and IS relies on the distribution of the proteasome, regulated by Ecm29. Silencing Ecm29 decreases the proteasome pool associated to the centrosome of B cells and shifts its accumulation to the cell cortex and IS. Accordingly, Ecm29-silenced B cells display increased F-actin at the centrosome, impaired centrosome and lysosome repositioning to the IS and defective antigen extraction and presentation. Ecm29-silenced B cells, which accumulate higher levels of proteasome at the cell cortex, display decreased actin retrograde flow in lamellipodia and enhanced spreading responses. Our findings support a model where B the asymmetric distribution of the proteasome, mediated by Ecm29, coordinates actin dynamics at the centrosome and the IS, promoting lysosome recruitment and cell spreading.
Receptor-linked environment-sensitive probe monitors the local membrane environment surrounding the insulin receptor
Authors: Umebayashi Miwa , Takemoto Satoko , Reymond Luc , Sundukova Mayya , Hovius Ruud , Bucci Annalisa , Heppenstall Paul A. , Yokota Hideo , Johnsson Kai , Riezman Howard 
Published: December 2020

AbstractFunctional membrane proteins in the plasma membrane are suggested to have specific membrane environments that play important roles to maintain and regulate the function of proteins. However, the local membrane environments of membrane proteins remain largely unexplored due to the lack of techniques allowing to monitor them in living cells. We have developed a method to probe the local membrane environment surrounding a membrane protein in the plasma membrane by covalently tethering a solvatochromic, environment-sensitive dye, Nile red, to a membrane protein via a flexible linker. Our direct imaging reported on the spatio-temporal properties of membrane fluidity of the local environment surrounding the insulin receptor. The local environment was distinct from the average plasma membrane fluidity and was quite dynamic and heterogeneous. Upon addition of insulin, the local membrane environment surrounding the receptor increased in fluidity in an insulin receptor-kinase dependent manner. This new technology should allow researchers to examine changes in membrane properties caused by receptor activation and devise ways to address the role of these changes in physiological processes.
Single cell analysis of blood mononuclear cells stimulated through CD3 and CD28 shows collateral activation of B and NK cells and demise of monocytes
Authors: Lawlor Nathan , Nehar-Belaid Djamel , Grassmann Jessica D.S. , Stoeckius Marlon , Smibert Peter , Stitzel Michael L. , Pascual Virginia , Banchereau Jacques , Williams Adam , Ucar Duygu 
Published: December 2020

AbstractImmune cell activation assays have been widely used for immune monitoring and for understanding disease mechanisms. However, these assays are typically limited in scope. A holistic study of circulating immune cell responses to different activators is lacking. Here we developed a cost-effective high-throughput multiplexed single-cell RNA-seq combined with epitope tagging (CITE-seq) to determine how classic activators of T cells (anti-CD3 coupled with anti-CD28) or monocytes (LPS) alter the cell composition and transcriptional profiles of peripheral blood mononuclear cells (PBMCs) from healthy human donors. Anti-CD3/CD28 treatment activated all classes of lymphocytes either directly (T cells) or indirectly (B and NK cells) but reduced monocyte numbers. Activated T and NK cells expressed senescence and effector molecules, whereas activated B cells transcriptionally resembled autoimmune disease- or age-associated B cells (e.g., CD11c, T-bet). In contrast, LPS specifically targeted monocytes and induced two main states: early activation characterized by the expression of chemoattractants and a later pro-inflammatory state characterized by expression of effector molecules. These data provide a foundation for future immune activation studies with single cell technologies (https://czi-pbmc-cite-seq.jax.org/).Graphical abstract
A hypothesis for theta rhythm frequency control in CA1 microcircuits
Authors: Skinner Frances K , Rich Scott , Lunyov Anton R , Lefebvre Jeremie , Chatzikalymniou Alexandra P 
Published: December 2020

ABSTRACTComputational models of neural circuits with varying levels of biophysical detail have been generated in pursuit of an underlying mechanism explaining the ubiquitous hippocampal theta rhythm. However, within the theta rhythm are at least two types with distinct frequencies associated with different behavioural states, an aspect that must be considered in pursuit of these mechanistic explanations. Here, using our previously developed excitatory-inhibitory network models that generate theta rhythms, we investigate the robustness of theta generation to intrinsic neuronal variability by building a database of heterogeneous excitatory cells and implementing them in our microcircuit model. We specifically investigate the impact of three key ‘building block’ features of the excitatory cell model that underlie our model design: these cells’ rheobase, their capacity for post-inhibitory rebound, and their spike-frequency adaptation. We show that theta rhythms at various frequencies can arise dependent upon the combination of these building block features, and we find that the speed of these oscillations are dependent upon the excitatory cells’ response to inhibitory drive, as encapsulated by their phase response curves. Taken together, these findings support a hypothesis for theta frequency control that includes two aspects: (i) an internal mechanism that stems from the building block features of excitatory cell dynamics; (ii) an external mechanism that we describe as ‘inhibition-based tuning’ of excitatory cell firing. We propose that these mechanisms control theta rhythm frequencies and underlie their robustness.
Bacteriophage infection produces membrane vesicles inEscherichia colivia both explosive cell lysis and membrane blebbing
Authors: Mandal Pappu K. , Ballerin Giulia , Nolan Laura M. , Petty Nicola K. , Whitchurch Cynthia B. 
Published: December 2020

AbstractMembrane Vesicles (MVs) are membrane-bound spherical nanostructures that prevail in all three domains of life. In Gram-negative bacteria, MVs are thought to be produced through blebbing of the outer membrane and are often referred to as outer membrane vesicles (OMVs). We have recently described another mechanism of MV biogenesis inPseudomonas aeruginosathat involves explosive cell lysis events which shatters cellular membranes into fragments that rapidly anneal into MVs. Interestingly, MVs are often observed within preparations of lytic bacteriophage, however the source of these MVs and their association with bacteriophage infection has not been explored. In this study we aimed to determine if MV biogenesis is associated with lytic bacteriophage infection. Live super-resolution microscopy demonstrated that explosive cell lysis ofE. colicells infected with either bacteriophage T4 or T7, produced MVs derived from shattered membrane fragments. Infection by either bacteriophage was also associated with the formation of membrane blebs on intact bacteria. TEM revealed multiple classes of MVs within phage lysates, consistent with multiple mechanisms of MV biogenesis. These findings suggest that bacteriophage infection may be a major contributor to the abundance of bacterial MVs in nature.
Temporal resolution relates to sensory hyperreactivity independently of stimulus detection sensitivity in individuals with autism spectrum disorder
Authors: Yaguchi Ayako , Atsumi Takeshi , Fukatsu Reiko , Ide Masakazu 
Published: December 2020

AbstractBackgroundResearchers have been focused on perceptual characteristics of autism spectrum disorder (ASD) in terms of sensory hyperreactivity. Previously, we demonstrated that temporal resolution, which is the accuracy in differentiating the order of two successive vibrotactile stimuli, is associated with the severity of sensory hyperreactivity (Ide et al. 2019). Herein, we examined whether an increase in the perceptual intensity of a tactile stimulus, despite its short duration, is derived from high temporal resolution and a high frequency of sensory temporal summation.MethodSixteen participants with ASD and fifteen typically developing (TD) participants performed two psychophysical experimental tasks, and we evaluated the detectable duration of vibrotactile stimuli with the same amplitude and temporal resolution. Sensory hyperreactivity was estimated using a self-reported questionnaire.ResultsThere was no relationship between temporal resolution and the duration of detectable stimuli in either group. However, the ASD group showed more severe sensory hyperreactivity in daily life than the TD group did, and ASD participants with severe sensory hyperreactivity tended to have high temporal resolution but not high sensitivity for detectable duration.ConclusionContrary to our hypothesis, there might be different processing between temporal resolution and sensitivity for stimulus detection. Sensory reactivity in daily life would not be based on sensitivity for stimulus detection measured in an experimental task, and we suggest that atypical temporal processing would affect sensory reactivity in ASD. Keywords (within 6 keywords): Temporal resolution, Temporal summation, Autism spectrum disorder, Hyperreactivity, Gap detection
On-chipperivascular niche with patient-derived glioma cells
Authors: Gerigk Magda , Bulstrode Harry , Shi HaoTian Harvey , Tönisen Felix , Cerutti Camilla , Morrison Gillian , Rowitch David , Huang Yan Yan Shery 
Published: December 2020

AbstractGlioblastoma multiforme (GBM), is the most common and the most aggressive type of primary brain malignancy. Glioblastoma stem-likecells (GSCs) are able to migrate in vascular niches within or away from the tumour mass, increasing tumour resistance to patient treatments and contributing to relapses. To study individual GSCs migration and their interactions with the microenvironment in the vasculature, there is a need to develop a model of human blood vesselsin vitro. Herein, we report a systematic study on the interaction between patient-derived glioma stem-likecell lines with different organotypic perivascular niche models. A microfluidic chip integrated with an extracellular matrix was fabricated to support the culture of rounded microvessels, formed with endothelial cells from three different organs, (1) human brain microvascular endothelial cells (hCMEC/D3), (2) human umbilical vein endothelial cells (HUVECs) and, (3) human lung microvascular endothelial cells (HMVEC-L). Three-dimensional (3D) cell culture retains selected adherent and tight junction markers of the endothelial cells, and the stemness-related genes of GSCs. We optimized the experimental protocol to perform qPCR, and western blot on the co-cultured GSCs with endothelial cells forming microvessels. Endpoint biological assays showed upregulation of neovascularization-related genes in endothelial cells (e.g., angiopoietins, vascular endothelial growth factor receptors) resulted after their co-culture with GBM cells. Moreover, we measured cancer cell speed and polarization during migration towards the endothelial cell formed vessel by live-cell imaging showing that organotypic (brain cancer cells – brain endothelial microvessel) interactions differ from those within non-tissue specific vascular niches. The development and optimization of this 3D microfluidic device could provide the next level of complexity of anin vitrosystem to study the influence of glioma cells on normal brain endothelium. More importantly, it enables the possibility to conduct comparative studies to dissect the influence of 3D culture, microvessel architecture and organotypic vessel types on glioma cells’ stemness and migration.
Nodal root diameter and node number in maize (Zea mays L.) interact to influence plant growth under nitrogen stress
Authors: Schneider Hannah M. , Yang Jennifer T. , Brown Kathleen M. , Lynch Jonathan P. 
Published: December 2020

AbstractUnder nitrogen limitation, plants increase resource allocation to root growth relative to shoot growth. The utility of various root architectural and anatomical phenotypes for nitrogen acquisition are not well understood. Nodal root number and root cross-sectional area were evaluated in maize in field and greenhouse environments. Nodal root number and root cross-sectional area were inversely correlated under both high and low nitrogen conditions. Attenuated emergence of root nodes, as opposed to differences in the number of axial roots per node, was associated with substantially reduced root number. Greater root cross-sectional area was associated with a greater stele area and number of cortical cell files. Genotypes that produced few, thick nodal roots rather than many, thin nodal roots had deeper rooting and better shoot growth in low nitrogen environments. Fewer nodal roots offset the respiratory and nitrogen costs of thicker diameter roots, since total nodal root respiration and nitrogen content was similar for genotypes with many, thin and few, thick nodal roots. We propose that few, thick nodal roots may enable greater capture of deep soil nitrogen and improve plant performance under nitrogen stress. The interaction between an architectural and anatomical trait may be an important strategy for nitrogen acquisition. Understanding trait interactions among different root nodes has important implications in for improving crop nutrient uptake and stress tolerance.
RgCop-A regularized copula based method for gene selection in single cell rna-seq data
Authors: Lall Snehalika , Ray Sumanta , Bandyopadhyay Sanghamitra 
Published: December 2020

AbstractGene selection in unannotated large single cell RNA sequencing (scRNA-seq) data is important and crucial step in the preliminary step of downstream analysis. The existing approaches are primarily based on high variation (highly variable genes) or significant high expression (highly expressed genes) failed to provide stable and predictive feature set due to technical noise present in the data. Here, we proposeRgCop, a novelregularizedcopula based method for gene selection from large single cell RNA-seq data.RgCoputilizes copula correlation (Ccor), a robust equitable dependence measure that captures multivariate dependency among a set of genes in single cell expression data. We raise an objective function by adding al1regularization term withCcorto penalizes the redundant co-efficient of features/genes, resulting non-redundant effective features/genes set. Results show a significant improvement in the clustering/classification performance of real life scRNA-seq data over the other state-of-the-art.RgCopperforms extremely well in capturing dependence among the features of noisy data due to the scale invariant property of copula, thereby improving the stability of the method. Moreover, the differentially expressed (DE) genes identified from the clusters of scRNA-seq data are found to provide an accurate annotation of cells. Finally, the features/genes obtained fromRgCopcan able to annotate the unknown cells with high accuracy.AvailabilityCorresponding software is available in:https://github.com/Snehalikalall/RgCopContactsumanta.ray@cwi.nl
Proteomic and functional analyses of the periodic membrane skeleton in neurons
Authors: Zhou Ruobo , Han Boran , Nowak Roberta , Lu Yunzhe , Heller Evan , Xia Chenglong , Chishti Athar H. , Fowler Velia M. , Zhuang Xiaowei 
Published: December 2020

AbstractActin, spectrin, and associated molecules form a membrane-associated periodic skeleton (MPS) in neurons. The molecular composition and functions of the MPS remain incompletely understood. Here, using co-immunoprecipitation and mass spectrometry, we identified hundreds of candidate MPS-interacting proteins that span diverse functional categories. We validated representative proteins in several of these categories, including previously unknown MPS structural components, as well as motor proteins, cell adhesion molecules, ion channels, and signaling proteins, demonstrating periodic distributions of ∼20 proteins in neurons using super-resolution imaging. Genetic perturbations of the MPS and its interacting proteins further suggested functional roles of the MPS in axon-axon and axon-dendrite interactions and in axon diameter regulation, and implicated the involvement of MPS interactions with cell adhesion molecules and non-muscle myosin in these roles. These results provide new insights into the interactome of the MPS, and suggest new functions of the MPS in neurons.