bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating the effector suite profile of Australian Fusarium oxysporum isolates from agricultural and natural ecosystems
Authors: Achari Saidi R. , Kaur Jatinder K. , Mann Ross C. , Sawbridge Tim , Summerell Brett A. , Edwards Jacqueline 
Published: October 2020

AbstractPathogenic and putatively nonpathogenic isolates of Fusarium oxysporum are ubiquitously present in soils. Pathogenic isolates designated as formae speciales are very host specific. The genes that determine host‐specific pathogenicity may be expected to be similar between strains within a forma specialis. Three different pathways were used for mining putative effectors from 85 assembled genome sequences representing isolates from the agricultural and natural ecosystems. A total of 436 putative effectors were identified, of which 115 were present in all the isolates. The presence–absence phylogeny showed some clustering of isolates based on the ecosystems, while some clustered with isolates from different ecosystems. Isolates from the agricultural and natural ecosystems shared 358 putative effectors. Agricultural isolates had 78 unique putative effectors, while isolates from the natural ecosystems had no unique effectors. Isolates from the natural ecosystems had effectors that have previously been confirmed with virulence functions in other filamentous fungi, suggesting that the natural ecosystems may be acting as a reservoir for pathogenic isolates awaiting compatible hosts. They also possessed putative effectors with domains involved in polysaccharide degradation. The putative effectors in the natural ecosystem isolates may be important for both parasitic and ecological fitness. Further analysis of the three characterized ff. sp.—lycopersici, niveum, and pisi—revealed high conservation in the pathogenicity mechanism in F. oxysporum. However, each strain had unique putative effectors, which may be responsible for host specificity.
Service Design and Citizen Satisfaction with E‐Government Services: A Multidimensional Perspective
Authors: Chan Frank K. Y. , Thong James Y. L. , Brown Susan A. , Venkatesh Viswanath 
Published: October 2020

AbstractThis research examines the relationship between service design and citizen satisfaction with e‐government services. Based on a multidimensional conceptualization of service, we define three key service perceptions, each comprising different design characteristics, that jointly influence perceived service quality and citizen satisfaction with e‐government services. The service perceptions and their corresponding design characteristics are: (1) perceptions of a core service—accuracy, completeness, self‐service capability, and convenience; (2) perceptions of facilitating services—accessibility, privacy protection, security protection, and user support; and (3) perceptions of supporting services—personalization capability and transparency. We tested our research model using data from a two‐stage survey of 3,065 users of three e‐government services. The results showed that all design characteristics contributed to their respective service perceptions that influenced perceived service quality that in turn influenced citizen satisfaction. The finding of a three‐way interaction among the service perceptions supported their complementary role in influencing perceived service quality.
Quasi-Stationary Monte Carlo and The Scale Algorithm
Authors: Pollock Murray , Fearnhead Paul , Johansen Adam M. , Roberts Gareth O. 
Published: October 2020

SummaryThis paper introduces a class of Monte Carlo algorithms which are based on the simulation of a Markov process whose quasi-stationary distribution coincides with a distribution of interest. This differs fundamentally from, say, current Markov chain Monte Carlo methods which simulate a Markov chain whose stationary distribution is the target. We show how to approximate distributions of interest by carefully combining sequential Monte Carlo methods with methodology for the exact simulation of diffusions. The methodology introduced here is particularly promising in that it is applicable to the same class of problems as gradient-based Markov chain Monte Carlo algorithms but entirely circumvents the need to conduct Metropolis–Hastings type accept–reject steps while retaining exactness: the paper gives theoretical guarantees ensuring that the algorithm has the correct limiting target distribution. Furthermore, this methodology is highly amenable to ‘big data’ problems. By employing a modification to existing naive subsampling and control variate techniques it is possible to obtain an algorithm which is still exact but has sublinear iterative cost as a function of data size.
Covid‐19, Economic Growth and South African Fiscal Policy
Authors: Burger Philippe , Calitz Estian 
Published: October 2020

AbstractFollowing years of fast‐rising debt levels, we show that the Covid‐19 crisis worsened an already deteriorating fiscal position in South Africa. To restore fiscal sustainability in the aftermath of the crisis some commentators argue that higher government expenditure will grow GDP sufficiently to stabilise the debt/GDP ratio. We reject this, showing that although a real increase in expenditure stimulates economic growth (a short‐run, once‐off effect), the public expenditure/GDP ratio exceeds the level at which an increase in the ratio positively impacts growth. We then explore the past efforts of government to maintain or restore fiscal sustainability by estimating a fiscal reaction function using a Markov‐switching model. Following the impact of the Covid‐19 crisis on the budget, we subsequently establish the deficit, expenditure and revenue adjustments that the government will have to make to restore fiscal sustainability. Finally, we consider the merits of introducing a debt ceiling.
Evaluating strange forecasts: The curious case of football match scorelines
Authors: Reade J. James , Singleton Carl , Brown Alasdair 
Published: October 2020

AbstractThis study analyses point forecasts of exact scoreline outcomes for football matches in the English Premier League. These forecasts were made for distinct competitions and originally judged differently. We compare these with implied probability forecasts using bookmaker odds and a crowd of tipsters, as well as point and probability forecasts generated from a statistical model. From evaluating these sources and types of forecast, using various methods, we argue that regression encompassing is the most appropriate way to compare point and probability forecasts, and find that both these types of forecasts for football match scorelines generally add information to one another.
Perceived burdensomeness is a curvilinear, short‐term predictor of suicide ideation in a community sample of adults
Authors: Crosby Eric S. , Zuromski Kelly L. , Witte Tracy K. 
Published: October 2020

AbstractObjectiveOur primary aim was to test the Interpersonal Theory of Suicide's synergy hypothesis (i.e., the interaction between perceived burdensomeness and thwarted belongingness) in the proximal prediction of suicide ideation, while accounting for quadratic effects.MethodWe used MTurk to recruit participants (N = 478) with a lifetime history of suicidal thoughts and behaviors; they completed two batteries of self‐report questionnaires three days apart.ResultsContrary to the synergy hypothesis, only suicide ideation and the quadratic effect of perceived burdensomeness at Time 1 were significant predictors of suicide ideation at Time 2. The quadratic effect of perceived burdensomeness indicated a u‐shaped function, whereby scores at or above the 80th percentile on perceived burdensomeness at Time 1 had increasingly strong, positive associations with suicide ideation at Time 2, while scores under the 80th percentile were not predictive of suicide ideation at Time 2. Also, thwarted belongingness and suicide ideation at Time 1 were significant predictors of perceived burdensomeness at Time 2.ConclusionsThese findings add to a growing literature that does not support the synergy hypothesis and suggests the importance of including nonlinear terms when examining the Interpersonal Theory of Suicide's constructs.
Marginal nitrate leaching around the recommended nitrogen fertilizer rate in winter cereals
Authors: Vogeler Iris , Thomsen Ingrid Kaag , Jensen Johannes L. , Hansen Elly Møller 
Published: October 2020

AbstractOptimum nitrogen (N) fertilization, which aims for high productivity while minimizing N losses to the environment, requires a better understanding of the N leaching behaviour around the recommended N rate. A study was conducted with increasing N fertilization levels over 3 years (2016–2019) with early and timely sown winter cereals (rye and wheat) at two sites in Denmark with different climatic conditions. For winter rye N fertilizer application rates ranged from 0 to 258 kg N ha‒1, and for winter wheat from 0 to 300 kg ha‒1. Grain yields did not respond much to the N application above the recommended rate. Nitrate (NO3) leaching was very low in the first period, but increased in the second and third period. The effect of a potential N carry‐over on marginal N leaching (defined as the additional N leaching per unit of additional N fertilizer applied) is large. Under early sown winter rye, marginal N leaching is reduced from 36 to 14 kg N ha‒1 in the third period following N fertilization of the recommended rate of 170 kg N ha‒1 when carry‐over was accounted for, and under the timely sown winter rye from 68 to 24 kg N ha‒1. Our results show that marginal N leaching around the recommended rate is almost linear at the study site, when carry‐over is accounted for. Thus, the use of precision agriculture, with lower fertilization application rates to areas with high residual soil N, is less effective compared with sites, which have an exponential leaching behaviour.
The previously missing c. 2.9 Ga high‐K continental crust in West Gondwana revealed in Northeast Brazil
Authors: Ferreira Alanielson C. D. , Dantas Elton L. , Fuck Reinhardt A. 
Published: October 2020

Abstract2.9 Ga is an uncommon magmatic age in Archean evolution worldwide, especially in West Gondwana. We identified so far unknown 2.97–2.92 Ga high‐K calc‐alkaline magmatism in the Borborema Province, northeast Brazil. It appears to indicate that the transition to high‐K magmas occurred before c. 2.7 Ga in Earth's history. The 2.9 Ga protoliths were reworked and progressively changed composition to 2.65 Ga and 2.25 Ga higher‐K granites in early magmatic arcs. Therefore, despite several reworking events from the Archean to Proterozoic times, these rare relicts of K‐rich magmatism indicate that reworking of felsic components was significant for the growth and differentiation of continental crust from c. 2.9 Ga onwards in West Gondwana.
Phytochrome B and PCH1 protein dynamics store night temperature information
Authors: Murcia Germán , Enderle Beatrix , Hiltbrunner Andreas , Casal Jorge J. 
Published: October 2020

SUMMARYPlants experience temperature fluctuations during the course of the daily cycle, and although stem growth responds rapidly to these changes we largely ignore whether there is a short‐term memory of previous conditions. Here we show that nighttime temperatures affect the growth of the hypocotyl of Arabidopsis thaliana seedlings not only during the night but also during the subsequent photoperiod. Active phytochrome B (phyB) represses nighttime growth and warm temperatures reduce active phyB via thermal reversion. The function of PHOTOPERIODIC CONTROL OF HYPOCOTYL1 (PCH1) is to stabilise active phyB in nuclear bodies but, surprisingly, warmth reduces PCH1 gene expression and PCH1 stability. When phyB was active at the beginning of the night, warm night temperatures enhanced the levels of nuclear phyB and reduced hypocotyl growth rate during the following day. However, when end‐of‐day far‐red light minimised phyB activity, warm night temperatures reduced the levels of nuclear phyB and enhanced the hypocotyl growth rate during the following day. This complex growth pattern was absent in the phyB mutant. We propose that temperature‐induced changes in the levels of PCH1 and in the size of the physiologically relevant nuclear pool of phyB amplify the impact of phyB‐mediated temperature sensing.
In vivo imaging of tagged mRNA in plant tissues using the bacterial transcriptional antiterminator BglG
Authors: Peña Eduardo J. , Robles Luna Gabriel , Heinlein Manfred 
Published: October 2020

SummaryRNA transport and localization represent important post‐transcriptional mechanisms to determine the subcellular localization of protein synthesis. Plants have the capacity to transport messenger (m)RNA molecules beyond the cell boundaries through plasmodesmata and over long distances in the phloem. RNA viruses exploit these transport pathways to disseminate their infections and represent important model systems to investigate RNA transport in plants. Here, we present an in vivo plant RNA‐labeling system based on the Escherichia coli RNA‐binding protein BglG. Using the detection of RNA in mobile RNA particles formed by viral movement protein (MP) as a model, we demonstrate the efficiency and specificity of mRNA detection by the BglG system as compared with MS2 and λN systems. Our observations show that MP mRNA is specifically associated with MP in mobile MP particles but hardly with MP localized at plasmodesmata. MP mRNA is clearly absent from MP accumulating along microtubules. We show that the in vivo BglG labeling of the MP particles depends on the presence of the BglG‐binding stem–loop aptamers within the MP mRNA and that the aptamers enhance the coprecipitation of BglG by MP, thus demonstrating the presence of an MP:MP mRNA complex. The BglG system also allowed us to monitor the cell‐to‐cell transport of the MP mRNA, thus linking the observation of mobile MP mRNA granules with intercellular MP mRNA transport. Given its specificity demonstrated here, the BglG system may be widely applicable for studying mRNA transport and localization in plants.
Analysis of CACTA transposase genes unveils the mechanism of intron loss and distinct small RNA silencing pathways underlying divergent evolution of Brassica genomes
Authors: Liu Beibei , Iwata‐Otsubo Aiko , Yang Diya , Baker Robert L. , Liang Chun , Jackson Scott A. , Liu Shengyi , Ma Jianxin , Zhao Meixia 
Published: October 2020

SUMMARYIn comparison with retrotransposons, DNA transposons make up a smaller proportion of most plant genomes. However, these elements are often proximal to genes to affect gene expression depending on the activity of the transposons, which is largely reflected by the activity of the transposase genes. Here, we show that three AT‐rich introns were retained in the TNP2‐like transposase genes of the Bot1 (Brassica oleracea transposon 1) CACTA transposable elements in Brassica oleracea, but were lost in the majority of the Bot1 elements in Brassica rapa. A recent burst of transposition of Bot1 was observed in B. oleracea, but not in B. rapa. This burst of transposition is likely related to the activity of the TNP2‐like transposase genes as the expression values of the transposase genes were higher in B. oleracea than in B. rapa. In addition, distinct populations of small RNAs (21, 22 and 24 nt) were detected from the Bot1 elements in B. oleracea, but the vast majority of the small RNAs from the Bot1 elements in B. rapa are 24 nt in length. We hypothesize that the different activity of the TNP2‐like transposase genes is likely associated with the three introns, and intron loss is likely reverse transcriptase mediated. Furthermore, we propose that the Bot1 family is currently undergoing silencing in B. oleracea, but has already been silenced in B. rapa. Taken together, our data provide new insights into the differentiation of transposons and their role in the asymmetric evolution of these two closely related Brassica species.
Structural determinants for NF‐Y subunit organization and NF‐Y/DNA association in plants
Authors: Chaves‐Sanjuan Antonio , Gnesutta Nerina , Gobbini Andrea , Martignago Damiano , Bernardini Andrea , Fornara Fabio , Mantovani Roberto , Nardini Marco 
Published: October 2020

SUMMARYNF‐Y transcription factor comprises three subunits: NF‐YA, NF‐YB and NF‐YC. NF‐YB and NF‐YC dimerize through their histone fold domain (HFD), which can bind DNA in a non‐sequence‐specific fashion while serving as a scaffold for NF‐YA trimerization. Upon trimerization, NF‐YA specifically recognizes the CCAAT box sequence on promoters and enhancers. In plants, each NF‐Y subunit is encoded by several genes giving rise to hundreds of potential heterotrimeric combinations. In addition, plant NF‐YBs and NF‐YCs interact with other protein partners to recognize a plethora of genomic motifs, as the CCT protein family that binds CORE sites. The NF‐Y subunit organization and its DNA‐binding properties, together with the NF‐Y HFD capacity to adapt different protein modules, represent plant‐specific features that play a key role in development, growth and reproduction. Despite their relevance, these features are still poorly understood at the molecular level. Here, we present the structures of Arabidopsis and rice NF‐YB/NF‐YC dimers, and of an Arabidopsis NF‐Y trimer in complex with the FT CCAAT box, together with biochemical data on NF‐Y mutants. The dimeric structures identify the key residues for NF‐Y HFD stabilization. The NF‐Y/DNA structure and the mutation experiments shed light on HFD trimerization interface properties and the NF‐YA sequence appetite for the bases flanking the CCAAT motif. These data explain the logic of plant NF‐Y gene expansion: the trimerization adaptability and the flexible DNA‐binding rules serve the scopes of accommodating the large number of NF‐YAs, CCTs and possibly other NF‐Y HFD binding partners and a diverse audience of genomic motifs.
Cytochrome P450 CYP81A10v7 in Lolium rigidum confers metabolic resistance to herbicides across at least five modes of action
Authors: Han Heping , Yu Qin , Beffa Roland , González Susana , Maiwald Frank , Wang Jian , Powles Stephen B. 
Published: October 2020

SUMMARYRapid and widespread evolution of multiple herbicide resistance in global weed species endowed by increased capacity to metabolize (degrade) herbicides (metabolic resistance) is a great threat to herbicide sustainability and global food production. Metabolic resistance in the economically damaging crop weed species Lolium rigidum is well known but a molecular understanding has been lacking. We purified a metabolic resistant (R) subset from a field evolved R L. rigidum population. The R, the herbicide susceptible (S) and derived F2 populations were used for candidate herbicide resistance gene discovery by RNA sequencing. A P450 gene CYP81A10v7 was identified with higher expression in R vs. S plants. Transgenic rice overexpressing this Lolium CYP81A10v7 gene became highly resistant to acetyl‐coenzyme A carboxylase‐ and acetolactate synthase‐inhibiting herbicides (diclofop‐methyl, tralkoxydim, chlorsulfuron) and moderately resistant to hydroxyphenylpyruvate dioxygenase‐inhibiting herbicide (mesotrione), photosystem II‐inhibiting herbicides (atrazine and chlorotoluron) and the tubulin‐inhibiting herbicide trifluralin. This wide cross‐resistance profile to many dissimilar herbicides in CYP81A10v7 transgenic rice generally reflects what is evident in the R L. rigidum. This report clearly showed that a single P450 gene in a cross‐pollinated weed species L. rigidum confers resistance to herbicides of at least five modes of action across seven herbicide chemistries.
Targeted gene disruption of ATP synthases 6‐1 and 6‐2 in the mitochondrial genome of Arabidopsis thaliana by mitoTALENs
Authors: Arimura Shin‐ichi , Ayabe Hiroki , Sugaya Hajime , Okuno Miki , Tamura Yoshiko , Tsuruta Yu , Watari Yuta , Yanase Shungo , Yamauchi Takaki , Itoh Takehiko , Toyoda Atsushi , Takanashi Hideki , Tsutsumi Nobuhiro 
Published: October 2020

SUMMARYWe recently achieved targeted disruptions of cytoplasmic male sterility (CMS)‐associated genes in the mitochondrial genomes of rice and rapeseed by using mitochondria‐targeted transcription activator‐like effector nucleases (mitoTALENs). It was the first report of stable and heritable targeted gene modification of plant mitochondrial genomes. Here, we attempted to use mitoTALENs to disrupt two mitochondrial genes in the model plant Arabidopsis thaliana(Arabidopsis) using three different promoters and two types of TALENs. The targets were the two isoforms of the ATP synthase subunit 6 gene, atp6‐1 and atp6‐2. Each of these genes was successfully deleted and the mitochondrial genomes were recovered in a homoplasmic state. The nuclear genome also has a copy of atp6‐1, and we were able to confirm that it was the mitochondrial gene and not the nuclear pseudogene that was knocked out. Among the three mitoTALEN promoters tried, the RPS5A promoter was the most effective. Conventional mitoTALENs were more effective than single‐molecule mito‐compactTALENs. Targeted mitochondrial gene deletion was achieved by crossing as well as by floral‐dip transformation to introduce the mitoTALEN constructs into the nucleus. The gene disruptions were caused by large (kb‐size) deletions. The ends of the remaining sequences were connected to distant loci, mostly by illegitimate homologous recombinations between repeats.
Coordinated regulation of starch synthesis in maize endosperm by microRNAs and DNA methylation
Authors: Hu Yufeng , Li Yangping , Weng Jianfeng , Liu Hanmei , Yu Guowu , Liu Yinghong , Xiao Qianlin , Huang Huanhuan , Wang Yongbin , wei Bin , Cao Yao , Xie Ying , Long Tiandan , Li Hui , Zhang Junjie , Li Xinhai , Huang Yubi 
Published: October 2020

SUMMARYStarch synthesis is an essential feature of crop filling, but knowledge of the molecular mechanisms regulating the expression of starch synthesis genes (SSGs) is currently limited to transcription factors (TFs). Here, we obtained transcriptome, small RNAome, and DNA methylome data from maize (Zea mays) endosperms during multiple developmental stages and established a regulatory network atlas of starch synthesis. Transcriptome analysis showed a sharp transition at 9–10 days after pollination, when genes involved in starch and sucrose metabolism are upregulated and starch accumulates rapidly. Expression pattern analysis established a comprehensive network between SSGs and TFs. During maize endosperm development, the miRNAs with preferential repression of the expression of TFs, particularly the TFs regulating SSG expression, were extensively downregulated. Specifically, ZmMYB138 and ZmMYB115 affected the transcriptional activities of Du1/Wx and Ae1/Bt2 genes at their respective promoter regions. Remarkably, the two TFs were negatively regulated by the copious expression of Zma‐miR159k‐3p at the post‐transcriptional level. This suggests that miRNAs are important regulators of starch synthesis. Moreover, with the exclusion of the TFs, the expression of both SSGs and miRNAs was globally regulated by DNA methylation. Altogether, the present results (i) establish the regulatory functions of miRNAs and DNA methylation in starch synthesis and (ii) indicate that DNA methylation functions as a master switch.