bluuebunny/crossref_metadata_2025_split huggingface dataset:
A partial pathogenicity chromosome inFusarium oxysporumis sufficient to cause disease and can be horizontally transferred
Authors: Li Jiming , Fokkens Like , Conneely Lee James , Rep Martijn 
Published: January 2020

AbstractDuring host colonization, plant pathogenic fungi secrete proteins, called effectors, to facilitate infection. Collectively, effectors may defeat the plant immune system, but usually not all effectors are equally important for infecting a particular host plant. InFusarium oxysporumf.sp.lycopersici, all known effector genes – also calledSIXgenes – are located on a single accessory chromosome which is required for pathogenicity and can also be horizontally transferred to another strain. To narrow down the minimal region required for virulence, we selected partial pathogenicity chromosome deletion strains by fluorescence-assisted cell sorting of a strain in which the two arms of the pathogenicity chromosome were labelled withGFPandRFP, respectively. By testing the virulence of these deletion mutants, we show that the complete long arm and part of the short arm of the pathogenicity chromosome are not required for virulence. In addition, we demonstrate that smaller versions of the pathogenicity chromosome can also be transferred to a non-pathogenic strain and they are sufficient to turn the non-pathogen into a pathogen. Surprisingly, originally non-pathogenic strains that had received a smaller version of the pathogenicity chromosome were much more aggressive than recipients with a complete pathogenicity chromosome. Whole genome sequencing analysis revealed that partial deletions of the pathogenicity chromosome occurred mainly close to repeats, and that spontaneous duplication of sequences in accessory regions is frequent both in chromosome deletion strains and in horizontal transfer (recipient) strains.Author SummaryFungal genomes can often be divided into a core genome, which is essential for growth, and an accessory genome which is dispensable. The accessory genome in fungi can be beneficial under some conditions. For example, in some plant-pathogenic fungi, virulence genes are present in the accessory genome, which enable these fungi to cause disease on certain hosts. InFusarium oxysporumf.sp.lycopersici, which infects tomato, all host-specific virulence genes are located on a single accessory chromosome. This ‘pathogenicity chromosome’ can be horizontally transferred between strains. Here, we found that many suspected virulence genes are in fact not required for virulence because strains without a large part of the pathogenicity chromosome, including these genes, showed no reduced virulence. In addition, we demonstrate that partial pathogenicity chromosomes can be horizontally transferred to a non-pathogen. Surprisingly, originally non-pathogenic strains that had received a partial pathogenicity chromosome were more virulent than strains that had received the complete pathogenicity chromosome.
CRISPR/Cas with ribonucleoprotein complexes and transiently selected telomere vectors allows highly efficient marker-free and multiple genome editing inBotrytis cinerea
Authors: Leisen Thomas , Bietz Fabian , Werner Janina , Wegner Alex , Schaffrath Ulrich , Scheuring David , Willmund Felix , Mosbach Andreas , Scalliet Gabriel , Hahn Matthias 
Published: January 2020

AbstractCRISPR/Cas has become the state-of-the-art technology for genetic manipulation in diverse organisms, enabling targeted genetic changes to be performed with unprecedented efficiency. Here we report on the first establishment of robust CRISPR/Cas editing in the important necrotrophic plant pathogenBotrytis cinereabased on the introduction of optimized Cas9-sgRNA ribonucleoprotein complexes (RNPs) into protoplasts. Editing yields were further improved by development of a novel strategy that combines RNP delivery with transiently stable telomeres containing vectors, which allowed temporary selection and convenient screening of marker-free editing. We demonstrate that this approach provides vastly superior editing rates compared to existing CRISPR/Cas-based methods in filamentous fungi, including the model plant pathogenMagnaporthe oryzae. The high performance of telomere vector-mediated coediting was demonstrated by random mutagenesis of codon 272 of thesdhBgene, a major determinant of resistance to succinate dehydrogenase inhibitor (SDHI) fungicides by in bulk replacement of the codon 272 with codons encoding all 20 amino acids. All exchanges were found at similar frequencies in the absence of selection but SDHI selection allowed the identification of novel amino acid substitutions which conferred differential resistance levels towards different SDHI fungicides. The increased efficiency and easy handling of RNP-based cotransformation is expected to greatly facilitate molecular research inB. cinereaand other fungi.
ILoReg enables high-resolution cell population identification from single-cell RNA-seq data
Authors: Smolander Johannes , Junttila Sini , Venäläinen Mikko S , Elo Laura L 
Published: January 2020

AbstractSingle-cell RNA-seq allows researchers to identify cell populations based on unsupervised clustering of the transcriptome. However, subpopulations can have only subtle transcriptomic differences and the high dimensionality of the data makes their identification challenging. We introduce ILoReg (https://github.com/elolab/iloreg), an R package implementing a new cell population identification method that achieves high differentiation resolution through a probabilistic feature extraction step that is applied before clustering and visualization.
Mechanochemical modelling of dorsal closure reveals emergent cell behaviour in tissue morphogenesis
Authors: Atzeni Francesco , Pasakarnis Laurynas , Mosca Gabriella , Smith Richard S. , Aegerter Christof M. , Brunner Damian 
Published: January 2020

AbstractTissue morphogenesis integrates cell type-specific biochemistry and architecture, cellular force generation and mechanisms coordinating forces amongst neighbouring cells and tissues. We use finite element-based modelling to explore the interconnections at these multiple biological scales in embryonic dorsal closure, where pulsed actomyosin contractility in adjacent Amnioserosa (AS) cells powers the closure of an epidermis opening. Based on ourin vivoobservations, the model implements F-actin nucleation periodicity that is independent of MyoII activity. Our model reveals conditions, where depleting MyoII activity nevertheless indirectly affects oscillatory F-actin behaviour, without the need for biochemical feedback. In addition, it questions the previously proposed role of Dpp-mediated regulation of the patterned actomyosin dynamics in the AS tissue, suggesting them to be emergent. Tissue-specific Dpp interference supports the model’s prediction. The model further predicts that the mechanical properties of the surrounding epidermis tissue feed back on the shaping and patterning of the AS tissue. Finally, our model’s parameter space reproduces mutant phenotypes and provides predictions for their underlying cause. Our modelling approach thus reveals several unappreciated mechanistic properties of tissue morphogenesis.
Development of high-throughput screening assays for profiling snake venom Phospholipase A2activity after high-resolution chromatographic fractionation
Authors: Still Kristina B.M. , Slagboom Julien , Kidwai Sarah , Xie Chunfang , Eisses Bastiaan , Vonk Freek J. , Somsen Govert W. , Casewell Nicholas R. , Kool Jeroen 
Published: January 2020

AbstractMany organisms, ranging from plants to mammals, contain phospholipase A2enzymes (PLA2s), which catalyze the production of lysophospholipids and fatty acid proinflammatory mediators. PLA2s are also common constituents of animal venoms, including bees, scorpions and snakes, and they cause a wide variety of toxic effects including neuro-, myo-, cyto-, and cardio-toxicity, anticoagulation and edema. The aim of this study was to develop a generic method for profiling enzymatically active PLA2s in snake venoms after chromatographic separation. For this, low-volume high-throughput assays for assessment of enzymatic PLA2activity were evaluated and optimized. Subsequently, the assays were incorporated into a nanofractionation platform that combines high-resolution fractionation of crude venoms by liquid chromatography (LC) with bioassaying in 384-well plate format, and parallel mass spectrometric (MS) detection for toxin identification. The miniaturized assays developed are based on absorbance or fluorescence detection (respectively, using cresol red or fluorescein as pH indicators) to monitor the pH drop associated with free fatty acid formation by enzymatically active PLA2s. The methodology was demonstrated for assessment of PLA2activity profiles of venoms from the snake speciesBothrops asper,Echis carinatus,Echis coloratus, Echis ocellatus,Oxyuranus scutellatusandDaboia russelii russelii.
Cell size regulation in budding yeast does not depend on linear accumulation of Whi5
Authors: Barber Felix , Amir Ariel , Murray Andrew W. 
Published: January 2020

AbstractCells must couple cell cycle progress to their growth rate to restrict the spread of cell sizes present throughout a population. Linear, rather than exponential, accumulation of Whi5, was proposed to provide this coordination by causing a higher Whi5 concentration in cells born at smaller size. We tested this model using the inducibleGAL1promoter to make the Whi5 concentration independent of cell size. At an expression level that equalizes the mean cell size with that of wild-type cells, the size distributions of cells with galactose-induced Whi5 expression and wild-type cells are indistinguishable. Fluorescence microscopy confirms that the endogenous andGAL1promoters produce different relationships between Whi5 concentration and cell volume without diminishing size control in the G1 phase. We also expressed Cln3 from the GAL1 promoter, finding that the spread in cell sizes for an asynchronous population is unaffected by this perturbation. Our findings contradict the previously proposed model for cell size control in budding yeast and demonstrate the need for a molecular mechanism that explains how cell size controls passage through Start.Author ContributionsFB performed the experiments, data analysis and simulations. All authors designed the experiments and wrote the manuscript.Significance StatementDespite decades of research, the question of how single cells regulate their size remains unclear. Here we demonstrate that a widely supported molecular model for the fundamental origin of size control in budding yeast is inconsistent with a set of experiments testing the model’s key prediction. We therefore conclude that the problem of cell size control in budding yeast remains unsolved. This work highlights the need for rigorous testing of future models of size control in order to make progress on this fundamental question.
Ribosome heterogeneity inDrosophila melanogastergonads through paralog-switching
Authors: Hopes Tayah , Norris Karl , Agapiou Michaela , McCarthy Charley G.P. , Lewis Philip A. , O’Connell Mary J , Fontana Juan , Aspden Julie L 
Published: January 2020

ABSTRACTRibosomes have long been thought of as homogeneous macromolecular machines, but recent evidence suggests they are heterogeneous and could be specialised to regulate translation. Here, we have characterised ribosomal protein heterogeneity across 4 tissues ofDrosophila melanogaster. We find that testes and ovaries contain the most heterogeneous ribosome populations, which occurs through a combination of paralog-enrichment and paralog-switching. We have solved structures of ribosomes purified fromin vivotissues by cryo-EM, revealing differences in precise ribosomal arrangement for testis and ovary 80S ribosomes. Differences in the amino acid composition of paralog pairs and their localisation on the ribosome exterior indicate paralog-switching could alter the ribosome surface, enabling different proteins to regulate translation. One testis-specific paralog-switching pair is also found in humans, suggesting this is a conserved site of ribosome heterogeneity. Overall, this work allows us to propose that mRNA translation might be regulated in the gonads through ribosome heterogeneity, providing a potential means of ribosome specialisation.
Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II logPChallenge
Authors: Işık Mehtap , Bergazin Teresa Danielle , Fox Thomas , Rizzi Andrea , Chodera John D. , Mobley David L. 
Published: January 2020

AbstractThe SAMPL Challenges aim to focus the biomolecular and physical modeling community on issues that limit the accuracy of predictive modeling of protein-ligand binding for rational drug design. In the SAMPL5 logDChallenge, designed to benchmark the accuracy of methods for predicting drug-like small molecule transfer free energies from aqueous to nonpolar phases, participants found it difficult to make accurate predictions due to the complexity of protonation state issues. In the SAMPL6 logPChallenge, we asked participants to make blind predictions of the octanol-water partition coefficients of neutral species of 11 compounds and assessed how well these methods performed absent the complication of protonation state effects. This challenge builds on the SAMPL6 pKaChallenge, which asked participants to predict pKavalues of a superset of the compounds considered in this logPchallenge. Blind prediction sets of 91 prediction methods were collected from 27 research groups, spanning a variety of quantum mechanics (QM) or molecular mechanics (MM)-based physical methods, knowledge-based empirical methods, and mixed approaches. There was a 50% increase in the number of participating groups and a 20% increase in the number of submissions compared to the SAMPL5 logDChallenge. Overall, the accuracy of octanol-water logPpredictions in SAMPL6 Challenge was higher than cyclohexane-water logDpredictions in SAMPL5, likely because modeling only the neutral species was necessary for logPand several categories of method benefited from the vast amounts of experimental octanol-water logPdata. There were many highly accurate methods: 10 diverse methods achieved RMSE less than 0.5 logPunits. These included QM-based methods, empirical methods, and mixed methods with physical modeling supported with empirical corrections. A comparison of physical modeling methods showed that QM-based methods outperformed MM-based methods. The average RMSE of the most accurate five MM-based, QM-based, empirical, and mixed approach methods based on RMSE were 0.92±0.13, 0.48±0.06, 0.47±0.05, and 0.50±0.06, respectively.
A signal of competitive dominance in mid-latitude herbaceous plant communities
Authors: Capitán José A. , Cuenda Sara , Ordóñez Alejandro , Alonso David 
Published: January 2020

AbstractUnderstanding the main determinants of species coexistence across space and time is a central question in ecology. However, ecologists still know little about the scales and conditions at which biotic interactions matter and how these interact with the environment to structure species assemblages. Here we use recent theory developments to analyze plant distribution and trait data across Europe and find that plant height clustering is related to both evapotranspiration and gross primary productivity. This clustering is a signal of interspecies competition between plants, which is most evident in mid-latitude ecoregions, where conditions for growth (reflected in actual evapotranspiration rates and gross primary productivities) are optimal. Away from this optimum, climate severity likely overrides the effect of competition, or other interactions become increasingly important. Our approach bridges the gap between species-rich competition theories and large-scale species distribution data analysis.
DrosophiladTBCE recruits tubulin around chromatin to promote mitotic spindle assembly
Authors: Métivier Mathieu , Gallaud Emmanuel , Pascal Aude , Gagné Jean-Philippe , Poirier Guy G. , Chrétien Denis , Gibeaux Romain , Richard-Parpaillon Laurent , Benaud Christelle , Giet Régis 
Published: January 2020

AbstractProper assembly of mitotic spindles requires microtubule nucleation at centrosomes but also around chromatin. In this study, we reveal a novel mechanism by which an enrichment of tubulin in the nuclear space following nuclear envelope breakdown promotes nucleation of spindle microtubules. This event mediated by the tubulin-specific chaperone dTBCE, depends on its tubulin binding CAP-Gly motif and is regulated by Ran. Live imaging, proteomic and biochemical analyses suggest that dTBCE is enriched in the nucleus at nuclear envelope breakdown and interacts with nuclear pore proteins and the Ran machinery to create an environment that facilitates subsequent tubulin enrichment. We propose that dTBCE-dependent increase in tubulin concentration in the nuclear space is an important mechanism for microtubule nucleation in organisms where compartmentalization prevents free diffusion of tubulin.
Networked psychostimulants: a web-based ethnographic study
Authors: Robitaille Caroline 
Published: January 2020

Purpose
The purpose of this paper is to understand contemporary psychostimulant use among members of online discussion fora. Two objectives are addressed: to describe accounts of practices related to psychostimulant use, and to examine how these pharmaceuticals may shape contemporary subjectivities.

Design/methodology/approach
This paper presents a qualitative analysis of three online discussion fora belonging to Reddit. Drawing on actor-network theory, psychostimulants are envisaged as networked actants to understand the underlying logics related to their use. Non-participant observation of r/Adderall was carried out over an 18-month period. A qualitative analysis of postings on the three selected fora was also performed.

Findings
For each discussion forum, a network comprised of human and non-human actors was observed: members of the forum, psychostimulants as objects and subreddits as agentic spaces. This study reveals the emergence of multiple subjectivities associated with psychostimulant use: productivity, wellness and enhancement‐related.

Practical implications
Findings open to a wider debate regarding public health’s and healthcare professionals’ understanding of psychostimulant use outside of the clinical setting and how this may contrast with how psychostimulant use is practiced in context.

Originality/value
This research shows new online socio-cultural spaces formed around psychostimulant use. Calling upon a web-based ethnographic approach, this research presents a new perspective on the contemporary use of psychostimulants.
Impacts of large-scale interior murals on hospital employees: a pharmacy department case study
Authors: McCunn Lindsay , Frey Cara 
Published: January 2020

Purpose
Trending in modern interior design frameworks is an integration of real and simulated (i.e. photographs, murals) elements of nature into buildings, and a number of interdisciplinary studies concern the effects of nature on various aspects of human functioning. The purpose of this paper is to measure employees’ self-reported levels of affective organizational commitment (AOC), perceived productivity, well-being, attention restoration and satisfaction at work to explore how each mural is conceptualized and to make recommendations to hospital administrators and facilities managers as they make decisions concerning mural design and placement. One hospital had a biophilic mural and the other had a bold abstract mural.

Design/methodology/approach
The research was carried out using post-occupancy evaluation and mixed-methods survey design.

Findings
Employees in both hospitals disagreed that their organizational commitment (OC), perceived productivity or well-being at work had improved since the new murals had been installed. Responses from both hospitals were also low concerning perceptions of attention restoration. Indeed, no significant differences between hospitals were found. Correlations among scales were found within hospitals that support published studies. More correlations occurred at the hospital where employees viewed the biophilic mural (e.g. between OC and perceived productivity, and between satisfaction with the physical environment and perceived productivity). At both sites, satisfaction with the physical environment correlated with OC.

Originality/value
The authors expected that those working within view of the biophilic mural would report stronger ratings of AOC, perceived productivity, well-being, attention restoration and satisfaction with the workplace than employees with a view of the abstract scene. No differences between groups were found; responses to psychosocial scale items asking about whether attitudes had improved after the retrofit were low or neutral for employees in either hospital. However, more correlations between scales that support existing literature were revealed for those working near the biophilic mural. Thus, the authors recommend architectural programming before a design change to gather insight on occupants’ preferences at work.
PDC-SiAlCN ceramic based wireless passive temperature sensors using integrated resonator/antenna up to 1100°C
Authors: Yu Yuxi , Han Bin , Xia Fansen 
Published: January 2020

PurposeThis paper aims to present wireless passive temperature sensors by using high-temperature stable polymer-derived silicoaluminum carbonitride (PDC-SiAlCN) ceramic materials.Design/methodology/approachIn this paper, a novel PDC-SiAlCN ceramic was synthesized by using polyvinylsilazne and aluminum-tri-sec-butoxide as precursors. Then, PDC-SiAlCN was used as the sensing material to fabricate sensors. The sensors are based on a cavity resonator and an integrated slot antenna. The resonant frequencies of the sensors are determined by the dielectric constants of PDC-SiAlCN ceramic, which monotonically increase versus temperature.FindingsThe effect of sensor dimension on the performance of the sensors was investigated using simulation and experimental methods. The using temperature, reliability and sensing distance of the sensors were studied experimentally. The sensors performed measurement up to 1100°C with excellent reliability and repeatability. The sensing distance varied from 38 to 14 mm when the temperature increasing from 20°C to 1100°C.Originality/valuePDC-SiAlCN ceramic based wireless passive temperature sensors have the advantage of seamless integration of slot antennas and resonators, which greatly reduces the size of the sensor, reduces the direction of antenna transmission and increases the transmission space. The sensors can be used for many harsh environment applications such as engine monitoring.