bluuebunny/crossref_metadata_2025_split huggingface dataset:
Natural variations of SLG1 confer high-temperature tolerance in indica rice
Authors: Xu Yufang , Zhang Li , Ou Shujun , Wang Ruci , Wang Yueming , Chu Chengcai , Yao Shanguo 
Published: October 2020

AbstractWith global warming and climate change, breeding crop plants tolerant to high-temperature stress is of immense significance. tRNA 2-thiolation is a highly conserved form of tRNA modification among living organisms. Here, we report the identification ofSLG1(Slender Guy 1), which encodes the cytosolic tRNA 2-thiolation protein 2 (RCTU2) in rice.SLG1plays a key role in the response of rice plants to high-temperature stress at both seedling and reproductive stages. Dysfunction ofSLG1results in plants with thermosensitive phenotype, while overexpression ofSLG1enhances the tolerance of plants to high temperature.SLG1is differentiated between the two Asian cultivated rice subspecies,indicaandjaponica, and the variations at both promoter and coding regions lead to an increased level of thiolated tRNA and enhanced thermotolerance ofindicarice varieties. Our results demonstrate that the allelic differentiation ofSLG1confersindicarice to high-temperature tolerance, and tRNA thiolation pathway might be a potential target in the next generation rice breeding for the warming globe.
Intestinal release of biofilm-like microcolonies encased in calcium-pectinate beads increases probiotic properties of Lacticaseibacillus paracasei
Authors: Heumann Arnaud , Assifaoui Ali , Da Silva Barreira David , Thomas Charles , Briandet Romain , Laurent Julie , Beney Laurent , Lapaquette Pierre , Guzzo Jean , Rieu Aurélie 
Published: October 2020

AbstractIn this study, we show that calcium pectinate beads (CPB) allow the formation of 20 µm spherical microcolonies of the probiotic bacteria Lacticaseibacillus paracasei (formerly designated as Lactobacillus paracasei) ATCC334 with a high cell density, reaching more than 10 log (CFU/g). The bacteria within these microcolonies are well structured and adhere to a three-dimensional network made of calcium-pectinate through the synthesis of extracellular polymeric substances (EPS) and thus display a biofilm-like phenotype, an attractive property for their use as probiotics. During bacterial development in the CPB, a coalescence phenomenon arises between neighboring microcolonies accompanied by their peripheral spatialization within the bead. Moreover, the cells of L. paracasei ATCC334 encased in these pectinate beads exhibit increased resistance to acidic stress (pH 1.5), osmotic stress (4.5 M NaCl), the freeze-drying process and combined stresses, simulating the harsh conditions encountered in the gastrointestinal (GI) tract. In vivo, the oral administration of CPB-formulated L. paracasei ATCC334 in mice demonstrated that biofilm-like microcolonies are successfully released from the CPB matrix in the colonic environment. In addition, these CPB-formulated probiotic bacteria display the ability to reduce the severity of a DSS-induced colitis mouse model, with a decrease in colonic mucosal injuries, less inflammation, and reduced weight loss compared to DSS control mice. To conclude, this work paves the way for a new form of probiotic administration in the form of biofilm-like microcolonies with enhanced functionalities.
Application of a long short-term memory for deconvoluting conductance contributions at charged ferroelectric domain walls
Authors: Holstad Theodor S. , Ræder Trygve M. , Evans Donald M. , Småbråten Didirk R. , Krohns Stephan , Schaab Jakob , Yan Zewu , Bourret Edith , van Helvoort Antonius T. J. , Grande Tor , Selbach Sverre M. , Agar Joshua C. , Meier Dennis 
Published: October 2020

AbstractFerroelectric domain walls are promising quasi-2D structures that can be leveraged for miniaturization of electronics components and new mechanisms to control electronic signals at the nanoscale. Despite the significant progress in experiment and theory, however, most investigations on ferroelectric domain walls are still on a fundamental level, and reliable characterization of emergent transport phenomena remains a challenging task. Here, we apply a neural-network-based approach to regularize local I(V)-spectroscopy measurements and improve the information extraction, using data recorded at charged domain walls in hexagonal (Er0.99,Zr0.01)MnO3 as an instructive example. Using a sparse long short-term memory autoencoder, we disentangle competing conductivity signals both spatially and as a function of voltage, facilitating a less biased, unconstrained and more accurate analysis compared to a standard evaluation of conductance maps. The neural-network-based analysis allows us to isolate extrinsic signals that relate to the tip-sample contact and separating them from the intrinsic transport behavior associated with the ferroelectric domain walls in (Er0.99,Zr0.01)MnO3. Our work expands machine-learning-assisted scanning probe microscopy studies into the realm of local conductance measurements, improving the extraction of physical conduction mechanisms and separation of interfering current signals.
A method for differentiating human induced pluripotent stem cells toward functional cardiomyocytes in 96-well microplates
Authors: Balafkan Novin , Mostafavi Sepideh , Schubert Manja , Siller Richard , Liang Kristina Xiao , Sullivan Gareth , Bindoff Laurence A. 
Published: October 2020

AbstractThe capacity of pluripotent stem cells both for self-renewal and to differentiate into any cell type have made them a powerful tool for studying human disease. Protocols for efficient differentiation towards cardiomyocytes using defined, serum-free culture medium combined with small molecules have been developed, but thus far, limited to larger formats. We adapted protocols for differentiating human pluripotent stem cells to functional human cardiomyocytes in a 96-well microplate format. The resulting cardiomyocytes expressed cardiac specific markers at the transcriptional and protein levels and had the electrophysiological properties that confirmed the presence of functional cardiomyocytes. We suggest that this protocol provides an incremental improvement and one that reduces the impact of heterogeneity by increasing inter-experimental replicates. We believe that this technique will improve the applicability of these cells for use in developmental biology and mechanistic studies of disease.
Magnetic separation of peripheral nerve-resident cells underscores key molecular features of human Schwann cells and fibroblasts: an immunochemical and transcriptomics approach
Authors: Peng Kaiwen , Sant David , Andersen Natalia , Silvera Risset , Camarena Vladimir , Piñero Gonzalo , Graham Regina , Khan Aisha , Xu Xiao-Ming , Wang Gaofeng , Monje Paula V. 
Published: October 2020

AbstractNerve-derived human Schwann cell (SC) cultures are irreplaceable models for basic and translational research but their use can be limited due to the risk of fibroblast overgrowth. Fibroblasts are an ill-defined population consisting of highly proliferative cells that, contrary to human SCs, do not undergo senescence in culture. We initiated this study by performing an exhaustive immunological and functional characterization of adult nerve-derived human SCs and fibroblasts to reveal their properties and optimize a protocol of magnetic-activated cell sorting (MACS) to separate them effectively both as viable and biologically competent cells. We next used immunofluorescence microscopy imaging, flow cytometry analysis and next generation RNA sequencing (RNA-seq) to unambiguously characterize the post-MACS cell products. High resolution transcriptome profiling revealed the identity of key lineage-specific transcripts and the clearly distinct neural crest and mesenchymal origin of human SCs and fibroblasts, respectively. Our analysis underscored a progenitor- or stem cell-like molecular phenotype in SCs and fibroblasts and the heterogeneity of the fibroblast populations. In addition, pathway analysis of RNA-seq data highlighted putative bidirectional networks of fibroblast-to-SC signaling that predict a complementary, yet seemingly independent contribution of SCs and fibroblasts to nerve regeneration. In sum, combining MACS with immunochemical and transcriptomics approaches provides an ideal workflow to exhaustively assess the identity, the stage of differentiation and functional features of highly purified cells from human peripheral nerve tissues.
The silk of gorse spider mite Tetranychus lintearius represents a novel natural source of nanoparticles and biomaterials
Authors: Lozano-Pérez Antonio Abel , Pagán Ana , Zhurov Vladimir , Hudson Stephen D. , Hutter Jeffrey L. , Pruneri Valerio , Pérez-Moreno Ignacio , Grbic’ Vojislava , Cenis José Luis , Grbic’ Miodrag , Aznar-Cervantes Salvador 
Published: October 2020

AbstractSpider mites constitute an assemblage of well-known pests in agriculture, but are less known for their ability to spin silk of nanoscale diameters and high Young’s moduli. Here, we characterize silk of the gorse spider mite Tetranychus lintearius, which produces copious amounts of silk with nano-dimensions. We determined biophysical characteristics of the silk fibres and manufactured nanoparticles and biofilm derived from native silk. We determined silk structure using attenuated total reflectance Fourier transform infrared spectroscopy, and characterized silk nanoparticles using field emission scanning electron microscopy. Comparative studies using T. lintearius and silkworm silk nanoparticles and biofilm demonstrated that spider mite silk supports mammalian cell growth in vitro and that fluorescently labelled nanoparticles can enter cell cytoplasm. The potential for cytocompatibility demonstrated by this study, together with the prospect of recombinant silk production, opens a new avenue for biomedical application of this little-known silk.
Increasing temperatures accentuate negative fitness consequences of a marine parasite
Authors: Godwin Sean C. , Fast Mark D. , Kuparinen Anna , Medcalf Kate E. , Hutchings Jeffrey A. 
Published: October 2020

AbstractInfectious diseases are key drivers of wildlife populations and agriculture production, but whether and how climate change will influence disease impacts remains controversial. One of the critical knowledge gaps that prevents resolution of this controversy is a lack of high-quality experimental data, especially in marine systems of significant ecological and economic consequence. Here, we performed a manipulative experiment in which we tested the temperature-dependent effects on Atlantic salmon (Salmo salar) of sea lice (Lepeophtheirus salmonis)—a parasite that can depress the productivity of wild-salmon populations and the profits of the salmon-farming industry. We explored sea-louse impacts on their hosts across a range of temperatures (10, 13, 16, 19, and 22 °C) and infestation levels (zero, ‘low’ (mean abundance ± SE = 1.6 ± 0.1 lice per fish), and ‘high’ infestation (6.8 ± 0.4 lice per fish)). We found that the effects of sea lice on the growth rate, condition, and survival of juvenile Atlantic salmon all worsen with increasing temperature. Our results provide a rare empirical example of how climate change may influence the impacts of marine disease in a key social-ecological system. These findings underscore the importance of considering climate-driven changes to disease impacts in wildlife conservation and agriculture.
Modelling early events in Mycobacterium bovis infection using a co-culture model of the bovine alveolus
Authors: Lee Diane Frances , Stewart Graham Roger , Chambers Mark Andrew 
Published: October 2020

AbstractBovine tuberculosis (bTB), a zoonosis mainly caused byMycobacterium bovishas severe socio-economic consequences and impact on animal health. Host–pathogen interactions duringM. bovisinfection are poorly understood, especially early events which are difficult to follow in vivo. This study describes the utilisation of an in vitro co-culture model, comprising immortalised bovine alveolar type II (BATII) epithelial cells and bovine pulmonary arterial endothelial cells (BPAECs). When cultured at air–liquid interface, it was possible to follow the migration of liveM. bovisBacille Calmette-Guérin (BCG) and to observe interactions with each cell type, alongside cytokine release. Infection with BCG was shown to exert a detrimental effect primarily upon epithelial cells, with corresponding increases in IL8, TNFα, IL22 and IL17a cytokine release, quantified by ELISA. BCG infection increased expression of CD54, MHC Class I and II molecules in endothelial but not epithelial cells, which exhibited constitutive expression. The effect of peripheral blood mononuclear cell conditioned medium from vaccinated cattle upon apical-basolateral migration of BCG was examined by quantifying recovered BCG from the apical, membrane and basolateral fractions over time. The numbers of recovered BCG in each fraction were unaffected by the presence of PBMC conditioned medium, with no observable differences between vaccinated and naïve animals.
Efficient hybrid 3D system calibration for magnetic particle imaging systems using a dedicated device
Authors: von Gladiss Anselm , Graeser Matthias , Behrends André , Chen Xin , Buzug Thorsten M. 
Published: October 2020

AbstractImage reconstruction in magnetic particle imaging is often performed using a system matrix based approach. The acquisition of a system matrix is a time-consuming calibration which may take several weeks and thus, is not feasible for a clinical device. Due to hardware characteristics of the receive chain, a system matrix may not even be used in similar devices but has to be acquired for each imager. In this work, a dedicated device is used for measuring a hybrid system matrix. It is shown that the measurement time of a 3D system matrix is reduced by 96%. The transfer function of the receive chains is measured, which allows the use of the same system matrix in multiple devices. Equivalent image reconstruction results are reached using the hybrid system matrix. Furthermore, the inhomogeneous sensitivity profile of receive coils is successfully applied to a hybrid system matrix. It is shown that each aspect of signal acquisition in magnetic particle imaging can be taken into account using hybrid system matrices. It is favourable to use a hybrid system matrix for image reconstruction in terms of measurement time, signal-to-noise ratio and discretisation.
Ethiopia’s transforming wheat landscape: tracking variety use through DNA fingerprinting
Authors: Hodson D. P. , Jaleta M. , Tesfaye K. , Yirga C. , Beyene H. , Kilian A. , Carling J. , Disasa T. , Alemu S. K. , Daba T. , Misganaw A. , Negisho K. , Alemayehu Y. , Badebo A. , Abeyo B. , Erenstein O. 
Published: October 2020

AbstractEthiopia is the largest wheat producer in sub-Saharan Africa yet remains a net importer. Increasing domestic wheat production is a national priority. Improved varieties provide an important pathway to enhancing productivity and stability of production. Reliably tracking varietal use and dynamics is a challenge, and the value of conventional recall surveys is increasingly questioned. We report the first nationally representative, large-scale wheat DNA fingerprinting study undertaken in Ethiopia. Plot level comparison of DNA fingerprinting with farmer recall from nearly 4000 plots in the 2016/17 season indicates that only 28% of farmers correctly named wheat varieties grown. The DNA study reveals that new, rust resistant bread wheat varieties are now widely adopted. Germplasm originating from CGIAR centres has made a significant contribution. Corresponding productivity gains and economic benefits have been substantial, indicating high returns to investments in wheat improvement. The study provides an accurate assessment of wheat varietal status and sets a benchmark for national policy-makers and donors. In recent decades, the Ethiopian wheat landscape has transformed from local tetraploid varieties to widespread adoption of high yielding, rust resistant bread wheat. We demonstrate that DNA fingerprinting can be applied at scale and is likely to transform future crop varietal adoption studies.
Time to first treatment and P53 dysfunction in chronic lymphocytic leukaemia: results of the O-CLL1 study in early stage patients
Authors: Monti Paola , Lionetti Marta , De Luca Giuseppa , Menichini Paola , Recchia Anna Grazia , Matis Serena , Colombo Monica , Fabris Sonia , Speciale Andrea , Barbieri Marzia , Gentile Massimo , Zupo Simonetta , Dono Mariella , Ibatici Adalberto , Neri Antonino , Ferrarini Manlio , Fais Franco , Fronza Gilberto , Cutrona Giovanna , Morabito Fortunato 
Published: October 2020

AbstractChronic lymphocytic leukaemia (CLL) is characterised by a heterogeneous clinical course. Such heterogeneity is associated with a number of markers, including TP53 gene inactivation. While TP53 gene alterations determine resistance to chemotherapy, it is not clear whether they can influence early disease progression. To clarify this issue, TP53 mutations and deletions of the corresponding locus [del(17p)] were evaluated in 469 cases from the O-CLL1 observational study that recruited a cohort of clinically and molecularly characterised Binet stage A patients. Twenty-four cases harboured somatic TP53 mutations [accompanied by del(17p) in 9 cases], 2 patients had del(17p) only, and 5 patients had TP53 germ-line variants. While del(17p) with or without TP53 mutations was capable of significantly predicting the time to first treatment, a reliable measure of disease progression, TP53 mutations were not. This was true for cases with high or low variant allele frequency. The lack of predictive ability was independent of the functional features of the mutant P53 protein in terms of transactivation and dominant negative potential. TP53 mutations alone were more frequent in patients with mutated IGHV genes, whereas del(17p) was associated with the presence of adverse prognostic factors, including CD38 positivity, unmutated-IGHV gene status, and NOTCH1 mutations.
A framework to quantify controlled directed interactions in network physiology applied to cognitive function assessment
Authors: Marzbanrad Faezeh , Yaghmaie Negin , Jelinek Herbert F. 
Published: October 2020

AbstractThe complex nature of physiological systems where multiple organs interact to form a network is complicated by direct and indirect interactions, with varying strength and direction of influence. This study proposes a novel framework which quantifies directional and pairwise couplings, while controlling for the effect of indirect interactions. Simulation results confirm the superiority of this framework in uncovering directional primary links compared to previous published methods. In a practical application of cognitive attention and alertness tasks, the method was used to assess controlled directed interactions between the cardiac, respiratory and brain activities (prefrontal cortex). It revealed increased interactions during the alertness task between brain wave activity on the left side of the brain with heart rate and respiration compared to resting phases. During the attention task, an increased number of right brain wave interactions involving respiration was also observed compared to rest, in addition to left brain wave activity with heart rate. The proposed framework potentially assesses directional interactions in complex network physiology and may detect cognitive dysfunctions associated with altered network physiology.
Methylation of MGMT promoter does not predict response to temozolomide in patients with glioblastoma in Donostia Hospital
Authors: Egaña Larraitz , Auzmendi-Iriarte Jaione , Andermatten Joaquin , Villanua Jorge , Ruiz Irune , Elua-Pinin Alejandro , Aldaz Paula , Querejeta Arrate , Sarasqueta Cristina , Zubia Felix , Matheu Ander , Samprón Nicolas 
Published: October 2020

AbstractO6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status has been considered a prognostic factor in newly diagnosed glioblastoma (GBM). In this study, we evaluated the prognostic and predictive value of MGMT promoter methylation in patients with glioblastoma in Donostia Hospital. Surprisingly, methylation of MGMT promoter did not predict response to temozolomide in patients with glioblastoma in Donostia Hospital. Specifically, overall survival (OS) and progression-free survival (PFS) did not differ significantly by MGMT methylation status in our cohort. In contrast, both were longer in patients who received treatment, received more TMZ cycles, had a better general status and perform at least a partial resection. No association was detected between methylation of MGMT promoter and molecular markers such as ATRX, IDH, p53 and Ki67. These results indicate that MGMT methylation did not influence in patient survival in our cohort.
Targeting of the E3 ubiquitin-protein ligase HUWE1 impairs DNA repair capacity and tumor growth in preclinical multiple myeloma models
Authors: Kunz Viktoria , Bommert Kathryn S. , Kruk Jessica , Schwinning Daniel , Chatterjee Manik , Stühmer Thorsten , Bargou Ralf , Bommert Kurt 
Published: October 2020

AbstractExperimental evidence suggests that ubiquitin-protein ligases regulate a number of cellular processes involved in tumorigenesis. We analysed the role of the E3 ubiquitin-protein ligase HUWE1 for pathobiology of multiple myeloma (MM), a still incurable blood cancer. mRNA expression analysis indicates an increase in HUWE1 expression levels correlated with advanced stages of myeloma. Pharmacologic as well as RNAi-mediated HUWE1 inhibition caused anti-proliferative effects in MM cell lines in vitro and in an MM1.S xenotransplantation mouse model. Cell cycle analysis upon HUWE1 inhibition revealed decreased S phase cell fractions. Analyses of potential HUWE1-dependent molecular functions did not show involvement in MYC-dependent gene regulation. However, HUWE1 depleted MM cells displayed increased DNA tail length by comet assay, as well as changes in the levels of DNA damage response mediators such as pBRCA1, DNA-polymerase β, γH2AX and Mcl-1. Our finding that HUWE1 might thus be involved in endogenous DNA repair is further supported by strongly enhanced apoptotic effects of the DNA-damaging agent melphalan in HUWE1 depleted cells in vitro and in vivo. These data suggest that HUWE1 might contribute to tumour growth by endogenous repair of DNA, and could therefore potentially be exploitable in future treatment developments.