bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of ‘relict’ western lineage of citrus tristeza virus virulent genotype in decliningArunachal Wakro orange
Authors: Datta Sibnarayan , Das Bidisha , Budhauliya Raghvendra , Gopalakrishnan Reji , Muaka Vanlalh , Meghvansi Mukesh K , Rahman Safior , Dwivedi Sanjai K , Veer Vijay 
Published: August 2020

ABSTRACTEastern Himalayan foothills are known to have optimal agro-climatic conditions for production of quality citrus fruits including oranges. Among the citrus growing regions of eastern Himalayas, Wakro in the far eastern state of Arunachal Pradesh is known for its superior quality oranges, popular as theWakro orangeor theArunachal orange, which has been included in Geographical Indication Registry by the Government of India. However, during last few years, Arunachal orange orchards have been experiencing severe infestation of aphid associated with rapid decline disease, causing catastrophe to the farmers as well as state economy. Therefore, in 2015, an intensive survey of severely affected orange orchards was carried out to investigate the aetiological factors of citrus decline. RNA samples extracted from leaf and aphid specimens collected from Wakro orchards were subjected to CTV detection through 3’-UTR specific RT-PCR. Subsequently, ORF1 and CP genetic regions were amplified and clonal-sequencing was performed. Although, BLAST search showed close homology of the present sequences with other virulent genotype VT sequences, detailed phylogenetic analysis demonstrated affinity and clustering of present sequences with VT sequences belonging to the ‘western’ lineage. This finding is considerably distinct from CTV sequences reported from citrus growing orchards in India and other neighbouring countries. Additionally, low diversity of CP gene sequences, recombination patterns and presence of sequence segments identical to the present ones in other CTV genotypes was also revealed. Collectively, these observations indicate pristine and primeval nature of present CTV sequences, corroborating well with the proposed origin of CTV in this part of the globe. We here report our finding of western lineage of CTV virulent genotype VT, which is distinct from CTV molecular epidemiology in other parts of India and discuss the implications of these findings.
The relationship between hippocampal-dependent task performance and hippocampal grey matter myelination and iron content
Authors: Clark Ian A. , Callaghan Martina F. , Weiskopf Nikolaus , Maguire Eleanor A. 
Published: August 2020

AbstractIndividual differences in scene imagination, autobiographical memory recall, future thinking and spatial navigation have long been linked with hippocampal structure in healthy people, although evidence for such relationships is, in fact, mixed. Extant studies have predominantly concentrated on hippocampal volume. However, it is now possible to use quantitative neuroimaging techniques to model different properties of tissue microstructure in vivo such as myelination and iron. Previous work has linked such measures with cognitive task performance, particularly in older adults. Here we investigated whether performance on scene imagination, autobiographical memory, future thinking and spatial navigation tasks was associated with hippocampal grey matter myelination or iron content in young, healthy adult participants. MRI data were collected using a multi-parameter mapping protocol (0.8mm isotropic voxels) from a large sample of 217 people with widely-varying cognitive task scores. We found little evidence that hippocampal grey matter myelination or iron content was related to task performance. This was the case using different analysis methods (voxel-based quantification, partial correlations), when whole brain, hippocampal regions of interest, and posterior:anterior hippocampal ratios were examined, and across different participant sub-groups (divided by gender, task performance). Variations in hippocampal grey matter myelin and iron levels may not, therefore, help to explain individual differences in performance on hippocampal-dependent tasks, at least in young, healthy individuals.
Assessment of Structural Units Deletions in the Archaeal Oligosaccharyltransferase AglB
Authors: Pedebos Conrado , Verli Hugo 
Published: August 2020

AbstractOligosaccharyltransferases (OSTs) are enzymes that catalyze the transfer of a glycan chain to an acceptor protein. Their structure is composed by a transmembrane domain and a periplasmic / C-terminal domain, which can be divided into structural units. TheArchaeoglobus fulgidusOST, AfAglB, has unique structural units with unknown functions. Here, we evaluate the stability role proposed for AfAglB units by employing molecular modelling and molecular dynamics simulations, to examine the effect of single and double deletions in the enzyme structure. Our results show a strong effect on the dynamics of the C-terminal domain for the mutated systems with increased fluctuations near the deleted areas. Conformational profile and stability are deeply affected, mainly in the double unit deletion, modifying the enzyme behavior and binding interfaces. Coordination at the catalytic site was not disrupted, indicating that the mutated enzymes could retain activity at some level. Hotspots of variation were identified and rationalized with previous data. Our data shows that structural units may provide stabilization interactions, contributing for integrity of the wild-type enzyme at high temperatures. By correlating our findings to structural units mutagenesis experimental data available, it was observed that structural units deletion can interfere with OSTs stability and dynamics but it is not directly related to catalysis. Instead, they may influence the OST structural integrity, and, potentially, thermostability. This work offers a basis for future experiments involving OSTs structural and functional characterization, as well as for protein engineering.
Amino acids whose intracellular levels change most during aging alter chronological lifespan of fission yeast
Authors: Rallis Charalampos , Mülleder Michael , Smith Graeme , Au Yan Zi , Ralser Markus , Bähler Jürg 
Published: August 2020

AbstractAmino acid deprivation or supplementation can affect cellular and organismal lifespan, but we know little about the role of concentration changes in free, intracellular amino acids during aging. Here, we determine free amino-acid levels during chronological aging of non-dividing fission yeast cells. We compare wild-type with long-lived mutant cells that lack the Pka1 protein of the protein kinase A signalling pathway. In wild-type cells, total amino-acid levels decrease during aging, but much less so inpka1mutants. Two amino acids strongly change as a function of age: glutamine decreases, especially in wild-type cells, while aspartate increases, especially inpka1mutants. Supplementation of glutamine is sufficient to extend the chronological lifespan of wild-type but not ofpka1Δcells. Supplementation of aspartate, on the other hand, shortens the lifespan ofpka1Δbut not of wild-type cells. Our results raise the possibility that certain amino acids are biomarkers of aging, and their concentrations during aging can promote or limit cellular lifespan.
Brain activity fluctuations propagate as waves traversing the cortical hierarchy
Authors: Gu Yameng , Sainburg Lucas E. , Kuang Sizhe , Han Feng , Williams Jack W. , Liu Yikang , Zhang Nanyin , Zhang Xiang , Leopold David A. , Liu Xiao 
Published: August 2020

AbstractThe brain exhibits highly organized patterns of spontaneous activity as measured by resting-state fMRI fluctuations that are being widely used to assess the brain’s functional connectivity. Some evidence suggests that spatiotemporally coherent waves are a core feature of spontaneous activity that shapes functional connectivity, though this has been difficult to establish using fMRI given the temporal constraints of the hemodynamic signal. Here we investigated the structure of spontaneous waves in human fMRI and monkey electrocorticography. In both species, we found clear, repeatable, and directionally constrained activity waves coursed along a spatial axis approximately representing cortical hierarchical organization. These cortical propagations were closely associated with activity changes in distinct subcortical structures, particularly those related to arousal regulation, and modulated across different states of vigilance. The findings demonstrate a neural origin of spatiotemporal fMRI wave propagation at rest and link it to the principal gradient of resting-state fMRI connectivity.
Distributed source modeling of intracranial stereoelectroencephalographic measurements
Authors: Lin Fa-Hsuan , Lee Hsin-Ju , Ahveninen Jyrki , Jääskeläinen Iiro P. , Yu Hsiang-Yu , Lee Cheng-Chia , Chou Chien-Chen , Kuo Wen-Jui 
Published: August 2020

AbstractIntracranial stereoelectroencephalography (sEEG) provides unsurpassed sensitivity and specificity for human neurophysiology. However, sEEG group analyses are complicated because the electrode implantations differ greatly across individuals. Here, using an auditory experiment as the test case, we developed a distributed, anatomically realistic sEEG source-modeling approach for within- and between-subject analyses. In addition to intracranial event-related potentials (iERP), we also estimated the sources of high broadband gamma activity (HBBG), a putative correlate of local neural firing. The source models accounted for a significant portion of the variance of the sEEG measurements in leave-one-out cross-validation. After logarithmic transformations, the sensitivity and signal-to-noise ratio were linearly inversely related to the minimal distance between the brain location and electrode contacts (slope≈-3.6). The HGGB source estimates were remarkably consistent with analyses of intracranial-contact data. In conclusion, distributed sEEG source modeling provides a powerful neuroimaging tool, which facilitates anatomically-normalized group analyses of both iERP and HBBG.
Coronatine contributesPseudomonas cannabinapv.alisalensisvirulence by overcoming both stomatal and apoplastic defenses in dicot and monocot plants
Authors: Sakata Nanami , Ishiga Takako , Masuo Shunsuke , Hashimoto Yoshiteru , Ishiga Yasuhiro 
Published: August 2020

AbstractP. cannabinapv.alisalensis(Pcal) is a causative agent of bacterial blight of crucifer including cabbage, radish, and broccoli. Importantly,Pcalcan infect not only a wide range of Brassicaceae, but also green manure crops such as oat. However,Pcalvirulence mechanisms have not been investigated and are not fully understood. We focused on coronatine (COR) function, which is one of the well-knownP. syringaepv. tomatoDC3000 virulence factors, inPcalinfection processes on both dicot and monocot plants. Cabbage and oat plants dip-inoculated with aPcalKB211 COR mutant (ΔcmaA) exhibited reduced virulence compared toPcalWT. Moreover, ΔcmaAfailed to reopen stomata on both cabbage and oat, suggesting that COR facilitatesPcalentry through stomata into both plants. Furthermore, cabbage and oat plants syringe-infiltrated with ΔcmaAalso showed reduced virulence, suggesting that COR is involved in overcoming not only stomatal-based defense, but also apoplastic defense. Indeed, defense related genes, includingPR1andPR2, were highly expressed in plants inoculated with ΔcmaAcompared toPcalWT, indicating that COR suppresses defense-related genes of both cabbage and oat. Additionally, SA accumulation increases after ΔcmaAinoculation compared toPcalWT. Taken together, COR contributes to cause disease by suppressing stomatal-based defense and apoplastic defense in both dicot and monocot plants. This is the first study to investigate COR functions in the interaction ofPcaland different host plants (dicot and monocot plants) using genetically and biochemically defined COR deletion mutants.Author summaryDisease outbreaks caused by newPseudomonas syringaeisolates are problems worldwide.P. cannabinapv.alisalensis(Pcal) causes bacterial blight on a wide range of cruciferous plants and bacterial brown spot on oat plants. AlthoughP. syringaedeploys a variety of virulence factors,Pcalvirulence factors have not been investigated. We focused on coronatine (COR) function, which is one of the well-knownP. syringaevirulence factors. COR is a non-host-specific phytotoxin and contributes toP. syringaegrowth and lesion formation or expansion in several host plants. COR function has been mainly studied in the model pathogenP. syringaepv.tomatoDC3000 and model the plantArabidopsis thaliana. Thus, COR roles inPcalinfection especially on monocot plants have not been well studied. Therefore, we investigated COR role inPcalinteraction with both dicot and monocot plants. Here, we revealed that COR functions as a multifunctional suppressor to managePcalvirulence on both plants.
Low replication stress leads to specific replication timing advances associated to chromatin remodelling in cancer cells
Authors: Courtot Lilas , Bournique Elodie , Maric Chrystelle , Guitton-Sert Laure , Madrid-Mencía Miguel , Pancaldi Vera , Cadoret Jean-Charles , Hoffmann Jean-Sébastien , Bergoglio Valérie 
Published: August 2020

ABSTRACTDNA replication is well orchestrated in mammalian cells through a tight regulation of the temporal order of replication origin activation, named the replication timing, a robust and conserved process in each cell type. Upon low replication stress, the slowing of replication forks induces delayed replication of fragile regions leading to genetic instability. The impact of low replication stress on the replication timing in different cellular backgrounds has not been explored yet. Here we analysed the whole genome replication timing in a panel of 6 human cell lines under low replication stress. We first demonstrated that cancer cells were more impacted than non-tumour cells. Strikingly, we unveiled an enrichment of specific replication domains undergoing a switch from late to early replication in some cancer cells. We found that advances in replication timing correlate with heterochromatin regions poorly sensitive to DNA damage signalling while being subject to an increase of chromatin accessibility. Finally, our data indicate that, following release from replication stress conditions, replication timing advances can be inherited by the next cellular generation, suggesting a new mechanism by which cancer cells would adapt to cellular or environmental stress.
Nucleotide substitutions during speciation may explain substitution rate variation
Authors: Janzen Thijs , Bokma Folmer , Etienne Rampal S. 
Published: August 2020

ABSTRACTAlthough molecular mechanisms associated with the generation of mutations are highly conserved across taxa, there is widespread variation in mutation rates between evolutionary lineages. When phylogenies are reconstructed based on nucleotide sequences, such variation is typically accounted for by the assumption of a relaxed molecular clock, which is just a statistical distribution of mutation rates without much underlying biological mechanism. Here, we propose that variation in accumulated mutations may be partly explained by an elevated mutation rate during speciation. Using simulations, we show how shifting mutations from branches to speciation events impacts inference of branching times in phylogenetic reconstruction. Furthermore, the resulting nucleotide alignments are better described by a relaxed than by a strict molecular clock. Thus, elevated mutation rates during speciation potentially explain part of the variation in substitution rates that is observed across the tree of life.
Understanding metabolic behaviour in whole-cell model output
Authors: Landon Sophie , Chalkley Oliver , Breese Gus , Grierson Claire , Marucci Lucia 
Published: August 2020

SummaryWhole-cell modelling is a newly expanding field that has many applications in lab experiment design and predictive drug testing. Although whole-cell model output contains a wealth of information, it is complex and high dimensional, thus hard to interpret. Here, we present an analysis pipeline that combines machine learning, dimensionality reduction and network analysis to interpret and visualise metabolic reaction fluxes from a set of single gene knockouts simulated in theMycoplasma genitaliumwhole-cell model. We found that the reaction behaviours show trends that correlate with phenotypic classes of the simulation output, highlighting particular cellular subsystems that malfunction after gene knockouts. From a graphical representation of the metabolic network, we saw that there is a set of reactions that can be used as markers of a phenotypic class, showing their importance within the network. Our analysis pipeline can support the understanding of the complexity ofin silicocells without detailed knowledge of the constituent parts, which can help to understand the effects of gene knockouts, and, as whole-cell models become more widely built and used, aid genome design.
Multigenerational downregulation of insulin/IGF-1 signalling in adulthood improves lineage survival, reproduction, and fitness inC. eleganssupporting the developmental theory of ageing
Authors: Duxbury Elizabeth ML , Carlsson Hanne , Sales Kris , Sultanova Zahida , Immler Simone , Chapman Tracey , Maklakov Alexei A 
Published: August 2020

AbstractAdulthood-only downregulation of insulin/IGF-1 signalling (IIS), an evolutionarily conserved pathway regulating resource allocation between somatic maintenance and reproduction, increases lifespan without fecundity cost in the nematode,Caenorhabditis elegans. However, long-term multigenerational effects of reduced IIS remain unexplored and are proposed to carry costs for offspring quality. To test this hypothesis, we ran a mutation accumulation (MA) experiment and downregulated IIS in half of the 400 MA lines by silencingdaf-2gene expression using RNA interference (RNAi) across 40 generations. Contrary to the prediction, adulthood-onlydaf-2RNAi reduced extinction of MA lines both under UV-induced and spontaneous mutation accumulation. Fitness of the surviving UV-induced MA lines was higher underdaf-2RNAi. Reduced IIS increased intergenerational F1 offspring fitness under UV stress but had no quantifiable transgenerational effects. Functionalhrde-1was required for the benefits of multigenerationaldaf-2RNAi. Overall, we found net benefit to fitness from multigenerational reduction of IIS and the benefits became more apparent under stress. Because reduceddaf-2expression during development carries fitness costs, we suggest that our findings are best explained by the developmental theory of ageing, which maintains that the decline in the force of selection with age results in poorly regulated gene expression in adulthood.
Direct non-destructive total reflection X-ray fluorescence elemental determinations in zirconium alloy samples
Authors: Sanyal Kaushik , Kanrar Buddhadev , Dhara Sangita , Sibilia Mirta , Sengupta Arijit , Karydas Andreas Germanos , Mishra Nand Lal 
Published: August 2020

The development of a direct non-destructive synchrotron-radiation-based total reflection X-ray fluorescence (TXRF) analytical methodology for elemental determinations in zirconium alloy samples is reported for the first time. Discs, of diameter 30 mm and about 1.6 mm thickness, of the zirconium alloys Zr-2.5%Nb and Zircalloy-4 were cut from plates of these alloys and mirror polished. These specimens were presented for TXRF measurements directly after polishing and cleaning. The TXRF measurements were made at the XRF beamline at Elettra synchrotron light source, Trieste, Italy, at two different excitation energies, 1.9 keV and 14 keV, for the determinations of low- and high-Z elements, respectively. The developed analytical methodology involves two complementary quantification schemes, i.e. using either the fundamental parameter method or relative sensitivity based method, allowing quantification of fifteen minor and trace elements with respect to Zr with very good precision and accuracy. In order to countercheck the TXRF analytical results, some samples were analyzed using the DC arc carrier distillation atomic emission spectrometry technique also, which shows an excellent agreement with the results of the TXRF-based methodology developed in this work. The present work resulted in a non-destructive TXRF elemental characterization methodology of metal and alloy samples avoiding the cumbersome dissolution and matrix separation which are normally required in other techniques and traditional methods of TXRF determination. In addition, the production of analytical waste could also be avoided to a large extent. Although the work was carried out for specific applications in the nuclear industry, it is equally suitable for other such samples in different industrial applications.
Disability awareness arena in Sweden: voices of learning toward community facilities, universal design and disability perspective
Authors: Lundälv Jörgen , Ehrlington Henrik , Johansen Andreas 
Published: August 2020

Purpose
The purpose of this study is to describe knowledge, awareness and experience of different employees in a Swedish municipality (City of Gothenburg) concerning the disability perspective, accessibility and universal design in practice.

Design/methodology/approach
This study is based on an online survey. A total of 119 different employees responded to the survey. The data was analyzed from a mixed-method approach, using descriptive statistics and textual analysis. The study also included personal interviews with 19 employees in the City of Gothenburg.

Findings
A total of 521 employees in the City of Gothenburg participated in disability awareness exercises (DAE) at the Disability Awareness Arena to gain greater knowledge and insight on disability perspectives in different environments and services. Of these, 119 people representing different professions in soft and hard services and companies participated in the survey; and 19 people participated in personal interviews. The study showed that a vast majority of them were very satisfied and they have developed and practiced their new knowledge and attitude toward disability and accessibility.

Research limitations/implications
One limitation in this study is that it has investigated the experiences and effects of the DAE 6–12 months after its implementation. Therefore, it is not possible to analyze long-term effects that the DAE can have in practice.

Originality/value
To the best of the authors’ knowledge, no prior study of these issues has been conducted in Sweden. This study is deemed to have significant social benefit because of the steadily increasing demand for disability simulations, awareness of disability perspective and accessibility in municipality settings. No other study has addressed the importance of the DAE in these perspectives. DAE is defined in this article as a unique concept for promoting the usage of the disability perspective in the everyday workplace.