bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impacts of agrochemical intensification on the assembly and reassembly of a mainland-island model metacommunity
Authors: Pelinson Rodolfo Mei , Strecht Bianca Rodrigues , Shimabukuro Erika Mayumi , Schiesari Luis Cesar 
Published: February 2021

ABSTRACTMany lentic aquatic environments are found embedded in agricultural fields, forming complex metacommunity structures. These habitats are vulnerable to contamination by agrochemicals, which can differentially affect local communities depending on the intensity and variability of species dispersal rates. We conducted a field experiment to assess how agrochemical intensification simulating the conversion of savannas into managed pastures and sugarcane fields affects freshwater community structure at different levels of spatial isolation. We constructed forty-five 1,200-L artificial ponds in a savanna landscape at three distances from a source wetland (30 m, 120 m, and 480 m). Ponds were spontaneously colonized by aquatic insects and amphibians and treated with no agrochemicals (‘savanna’ treatment), fertilizers (‘pasture’ treatment), or fertilizers and a single pulse of the insecticide fipronil and the herbicide 2,4-D (‘sugar cane’ treatment) following realistic dosages and application schedules. The experiment encompassed the entire rainy season. ‘Pasture’ communities were only slightly different from controls largely because two predatory insect taxa were more abundant in ‘pasture’ ponds. ‘Sugarcane’ communities strongly diverged from other treatments after the insecticide application, when a decrease in insect abundance indirectly benefitted amphibian populations. However, this effect had nearly disappeared by the end of the rainy season. The herbicide pulse had no effect on community structure. Spatial isolation changed community structure by increasing the abundance of non-predatory insects. However, it did not affect all predatory insects nor, surprisingly, amphibians. Therefore, spatial isolation did not change the effects of agrochemicals on community structure. Because agrochemical application frequently overlaps with the rainy season in many monocultures, it can strongly affect temporary pond communities. Ponds embedded in pastures might suffer mild consequences of fertilization by favoring the abundance of few predators throughbottom-upeffects. Ponds in sugarcane fields, however, might experience a decline in the insect population, followed by an increase in the abundance of amphibians tolerant to environmental degradation. Furthermore, we found no evidence that isolation by distance can change the general effects of chemical intensification, but future experiments should consider using real crop fields as the terrestrial matrix since they can represent different dispersal barriers.
Expression of recombinant cardosin B in tobacco BY2 cells: an alternative system for the production of active milk clotting enzymes
Authors: Folgado André , Abranches Rita 
Published: February 2021

AbstractCynara cardunculusL. or cardoon is a plant that is used as a source of milk clotting enzymes during traditional cheese manufacturing. This clotting activity is due to aspartic proteases (APs) found in the cardoon flower, named cyprosins and cardosins. APs from cardoon flowers display a great degree of heterogeneity, resulting in variable milk clotting activities and directly influencing the final product. Producing these APs using alternative platforms such as bacteria or yeast has proven challenging, which is hampering their implementation on an industrial scale. We have developed tobacco BY2 cell lines as an alternative plant-based platform for the production of cardosin B. These cultures successfully produced active cardosin B and a purification pipeline was developed to obtain isolated cardosin B. The enzyme displayed proteolytic activity towards milk caseins and milk clotting activity under standard cheese manufacturing conditions. We also identified an unprocessed form of cardosin B and further investigated its activation process. The use of protease-specific inhibitors suggested a possible role for a cysteine protease in cardosin B processing. Mass spectrometry analysis identified three cysteine proteases containing a granulin-domain as candidates for cardosin B processing. These findings suggest an interaction between these two groups of proteases and contribute to an understanding of the mechanisms behind the regulation and processing of plant APs. This work also paves the way for the use of tobacco BY2 cells as an alternative production system for active cardosins and represents an important advancement towards the industrial production of cardoon APs.
A plant-like mechanism coupling m6A reading to polyadenylation safeguards transcriptome integrity and developmental genes partitioning inToxoplasma
Authors: Farhat Dayana C. , Bowler Matthew , Communie Guillaume , Pontier Dominique , Belmudes Lucid , Mas Caroline , Corrao Charlotte , Couté Yohann , Bougdour Alexandre , Lagrange Thierry , Hakimi Mohamed-Ali , Swale Christopher 
Published: February 2021

AbstractCorrect 3’end processing of mRNAs is regarded as one of the regulatory cornerstones of gene expression. In a parasite that must answer to the high regulatory requirements of its multi-host life style, there is a great need to adopt additional means to partition the distinct transcriptional signatures of the closely and tandemly-arranged stage specific genes. In this study, we report on our findings inT. gondiiof an m6A-dependent 3’end polyadenylation serving as a transcriptional barrier at theseloci. We identify the core polyadenylation complex withinT. gondiiand establish CPSF4 as a reader for m6A-modified mRNAs, via a YTH domain within its C-terminus, a feature which is shared with plants. We bring evidence of the specificity of this interaction both biochemically, and by determining the crystal structure at high resolution of theT. gondiiCPSF4-YTH in complex with an m6A modified RNA. We show that the loss of m6A, both at the level of its deposition or its recognition was associated with an increase in aberrantly elongated chimeric mRNAs emanating from impaired transcriptional termination, a phenotype previously noticed in the plant modelArabidopsis thaliana. We bring Nanopore direct RNA sequencing-based evidence of the occurrence of transcriptional read-through breaching into downstream repressed stage-specific genes, in the absence of either CPSF4 or the m6A RNA methylase components in bothT. gondiiandA. thaliana. Taken together, our results shed light on an essential regulatory mechanism coupling the pathways of m6A metabolism directly to the cleavage and polyadenylation processes, one that interestingly seem to serve, in bothT. gondiiandA. thaliana, as a guardian against aberrant transcriptional read-throughs.Highlightsm6A is recognized in apicomplexan and plants by CPSF4, a member of the cleavage and polyadenylation complex machinery.The structural insight behind the specificity of the binding of m6A by the CPSF4 YTH subunit are solved by high resolution crystal structures.The m6A-driven 3’end polyadenylation pathway protects transcriptome integrity by restricting transcriptional read-throughs and RNA chimera formation in apicomplexan parasites and plants.
Migration Restores Hybrid Incompatibility Driven By Mitochondrial-Nuclear Sexual Conflict
Authors: Munasinghe Manisha , Haller Benjamin C. , Clark Andrew G. 
Published: February 2021

AbstractIn the mitochondrial genome, sexual asymmetry in transmission allows the accumulation of male-harming mutations since selection acts only on the effect of the mutation in females. Called the “Mother’s Curse”, this phenomenon induces a selective pressure for nuclear variants that compensate for this reduction in male fitness. Previous work has demonstrated the existence of these interactions and their potential to act as Dobzhansky–Muller incompatibilities, contributing to reproductive isolation between populations. However, it is not clear how readily they would give rise to and sustain hybrid incompatibilities. Here, we use computer simulations in SLiM 3 to investigate the consequences of sexually antagonistic mitochondrial-nuclear interactions in a subdivided population. We consider distinct migration schemes and vary the chromosomal location, and consequently the transmission pattern, of nuclear restorers. Disrupting these co-evolved interactions results in less-fit males, skewing the sex ratio toward females. Restoration of male fitness depends on both the chromosomal location of nuclear restorer loci and the migration scheme. Our results show that these interactions may act as Dobzhansky–Muller incompatibilities, but their strength is not enough to drive population isolation. Overall, this model shows the varied ways in which populations can respond to migration’s disruption of co-evolved mitochondrial-nuclear interactions.
A tale of two gradients: Differences between the left and right hemispheres predict semantic cognition and visual reasoning
Authors: del Jesus Gonzalez Alam Tirso Rene , Mckeown Brontë L. A. , Gao Zhiyao , Bernhardt Boris , de Wael Reinder Vos , Margulies Daniel S. , Smallwood Jonathan , Jefferies Elizabeth 
Published: February 2021

AbstractDecomposition of whole-brain functional connectivity patterns reveals a principal gradient that captures the separation of sensorimotor cortex from heteromodal regions in the default mode network (DMN); this gradient captures the systematic order of networks on the cortical surface. Functional homotopy is strongest in sensorimotor areas, and weakest in heteromodal cortices, suggesting there may be differences between the left and right hemispheres (LH/RH) in the principal gradient, especially towards its apex. This study characterised hemispheric differences in the position of large-scale cortical networks along the principal gradient, and their functional significance. We collected resting-state fMRI and semantic and non-verbal reasoning task performance in 175+ healthy volunteers. We then extracted the principal gradient of connectivity for each participant and tested which networks showed significant hemispheric differences in gradient value. We investigated the functional associations of these differences by regressing participants’ behavioural efficiency in tasks outside the scanner against their interhemispheric gradient difference for each network. LH showed a higher overall principal gradient value, consistent with its role in heteromodal semantic cognition. One frontotemporal control subnetwork was linked to individual differences in semantic cognition: when it was nearer heteromodal DMN on the principal gradient in LH, participants showed more efficient semantic retrieval. In contrast, when a dorsal attention subnetwork was closer to the heteromodal end of the principal gradient in RH, participants showed better visual reasoning. Lateralization of function may reflect differences in connectivity between control and heteromodal regions in LH, and attention and visual regions in RH.
Protein Friction and Filament Bending Facilitate Contraction of Disordered Actomyosin Networks
Authors: Tam Alexander K. Y. , Mogilner Alex , Oelz Dietmar B. 
Published: February 2021

AbstractWe use mathematical modelling and computation to investigate how protein friction facilitates contraction of disordered actomyosin networks. We simulate two-dimensional networks using an agent-based model, consisting of a system of force-balance equations for myosin motor proteins and semi-flexible actin filaments. A major advantage of our approach is that it enables direct calculation of the network stress tensor, which provides a quantitative measure of contractility. Exploiting this, we use repeated simulations of disordered networks to confirm that both protein friction and actin filament bending are required for contraction. We then use simulations of elementary two-filament assemblies to show that filament bending flexibility can generate contraction on the microscopic scale. Finally, we show that actin filament turnover is necessary to sustain contraction and prevent pattern formation. Simulations with and without turnover also exhibit contractile pulses. However, these pulses are aperiodic, suggesting that periodic pulsation can only be achieved by additional regulatory mechanisms.
Chemoenzymatic labeling of DNA methylation patterns for single-molecule epigenetic mapping
Authors: Gabrieli Tslil , Michaeli Yael , Avraham Sigal , Torchinsky Dmitry , Juhasz Matyas , Coruh Ceyda , Arbib Nissim , Zhou Zhaohui Sunny , Law Julie A. , Weinhold Elmar , Ebenstein Yuval 
Published: February 2021

ABSTRACTDNA methylation, specifically, methylation of cytosine (C) nucleotides at the 5-carbon position (5-mC), is the most studied and among the most significant epigenetic modifications. Here we developed a chemoenzymatic procedure to fluorescently label non-methylated cytosines in the CpG context allowing epigenetic profiling of single DNA molecules spanning hundreds of thousands of base pairs. For this method, a CpG methyltransferase was used to transfer an azide to cytosines from a syntheticS-adenosyl-l-methionine cofactor analog. A fluorophore was then clicked onto the DNA, reporting on the amount and position of non-methylated CpGs. We found that labeling efficiency was increased two-fold by the addition of a nucleosidase that degrades the inactive by-product of the azide-cofactor after labeling, and prevents its inhibitory effect. We first used the method to determine the decline in global DNA methylation in chronic lymphocytic leukemia patients and then performed whole genome methylation mapping of the model plantArabidopsis thaliana.Our genome maps show high concordance with published methylation maps produced by bisulfite sequencing. Although mapping resolution is limited by optical detection to 500-1000 base pairs, the labeled DNA molecules produced by this approach are hundreds of thousands of base pairs long, allowing access to long repetitive and structurally variable genomic regions.
Chromatin accessibility changes at intergenic regions associates with ovarian cancer drug resistance
Authors: Gallon John , Loomis Erick , Curry Edward , Martin Nicholas , Brody Leigh , Garner Ian , Brown Robert , Flanagan James M. 
Published: February 2021

AbstractWe have investigated how genomic distribution of chromatin accessibilities alter during acquisition of resistance to carboplatin-based chemotherapy using matched ovarian cell lines from high grade serous ovarian cancer (HGSOC) patients before and after becoming clinically resistant to platinum-based chemotherapy. Resistant lines show altered chromatin accessibility at intergenic regions, but less so at gene promoters. Super-enhancers, as defined by clusters of cis-regulatory elements, at these intergenic regions show chromatin changes that are associated with altered expression of linked genes, with enrichment for genes involved in the Fanconi anemia/BRCA DNA damage response pathway. Further, genome-wide distribution of platinum adducts associates with the chromatin changes observed and distinguish sensitive from resistant lines. In the resistant line, we observe fewer adducts around gene promoters and more adducts at intergenic regions. Thus, chromatin changes at intergenic regulators of gene expression are associated within vivoderived drug resistance and Pt-adduct distribution in patient-derived HGSOC drug resistance models.
Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy
Authors: Koide Hiroki , Kodera Noriyuki , Bisht Shveta , Takada Shoji , Terakawa Tsuyoshi 
Published: February 2021

ABSTRACTThe condensin protein complex compacts chromatin during mitosis using its DNA-loop extrusion activity. Previous studies proposed scrunching and loop-capture models as molecular mechanisms for the loop extrusion process, both of which assume the binding of double-strand (ds) DNA to the so-called hinge domain formed at the interface of the condensin subunits Smc2 and Smc4. However, how the hinge domain contacts dsDNA has remained unknown, potentially due to its conformational plasticity. Here, we conducted atomic force microscopy imaging of the budding yeast condensin holo-complex and used this data as basis for coarse-grained molecular dynamics simulations to model the hinge structure in a transient open conformation. We then simulated the dsDNA binding to open and closed hinge conformations, predicting that dsDNA binds to the outside surface when closed and to the outside and inside surfaces when open. Our simulations also suggested that the hinge can close around dsDNA bound to the inside surface. The conformational change of the hinge domain might be essential for the dsDNA binding regulation and play important roles in condensin-mediated DNA-loop extrusion.
An anaphase surveillance mechanism prevents micronuclei formation from mitotic errors
Authors: Orr Bernardo , Sousa Filipe De , Gomes Ana Margarida , Ferreira Luísa T. , Figueiredo Ana C. , Maiato Helder 
Published: February 2021

SummaryMicronuclei are a hallmark of cancer and other human disorders and have recently been implicated in chromothripsis, a series of massive genomic rearrangements that may drive tumor evolution and progression. Here we show that Aurora B kinase mediates a surveillance mechanism that integrates error correction during anaphase with spatial control of nuclear envelope reformation to protect against micronuclei formation during human cell division. Using high-resolution live-cell imaging of human cancer and non-cancer cells we found that anaphase lagging chromosomes are often transient and rarely formed micronuclei. This strong bias against micronuclei formation relied on a midzone-based Aurora B phosphorylation gradient that assisted the mechanical transduction of spindle forces at the kinetochore-microtubule interface required for anaphase error correction, while delaying nuclear envelope reformation on lagging chromosomes, independently of microtubules. Our results uncover a new layer of protection against genomic instability and provide a strategy for the rational design of micronuclei-targeting therapies.
HPWSs and employee performance in KIBS companies: a mediating–moderating analysis
Authors: Wojtczuk-Turek Agnieszka , Turek Dariusz 
Published: February 2021

PurposeThe purpose of this paper is to discuss relationships between high-performance work systems (HPWSs) and productive/counterproductive behaviours initiated and performed by employees. Using the ability, motivation and opportunities (AMO) theoretical framework, the authors described how an HPWS influences employee behaviours. The authors suggest that HPWSs could increase productive work behaviour and decrease counterproductive behaviours by mediating employees' affective commitment and moderating their self-efficacy.Design/methodology/approachThis study is based on data from 563 questionnaires, which were completed using the computer-assisted telephone interview method. The respondents were knowledge workers, representing companies of various sizes in the Knowledge-Intensive Business Service (KIBS) sector in Poland. Statistical verification of the mediation and moderation analyses was conducted with macro PROCESS (ver. 3.3).FindingsThis research confirmed a significant statistical relationship between all examined variables. It has been shown that HPWSs influence productive and counterproductive behaviours both directly and indirectly through mediation of affective commitment. The statistical analysis also confirmed the study’s hypothesis that self-efficacy moderates relationships between an HPWS and employee behaviours.Research limitations/implicationsThis study has two limitations: its cross-sectional design and the use of self-reported questionnaire data.Originality/valueThis study is the first to explore mediating mechanisms between HPWSs and employee performance in the context of the KIBS companies in Poland. The results indicate that HPWSs are important antecedents of productive and counterproductive behaviours among knowledge workers.
The roles of whistleblowing system and fraud awareness as financial statement fraud deterrent
Authors: Shonhadji Nanang , Maulidi Ach 
Published: February 2021

Purpose
This paper aims to provide new theoretical discussion about the role of whistleblowing system and fraud awareness as an effective deterrent for financial statement fraud.

Design/methodology/approach
The authors conducted surveys to 13 reputable public accounting firms in East Java, Indonesia.

Findings
It is well acknowledged, as fraud attacks grow more sophisticated, whistleblowing system and fraud awareness can be possible deterrents. By increasing employees’ fraud awareness, they do not only recognise fraud symptoms and typologies but also support to raise concerns in good faith and on reasonable grounds. This study also suggests the role of fraud awareness as a human capital investment that increase sensitivity on identifying fraud symptoms and discouraging participation in crimes.

Originality/value
This study produces new theoretical discussion about fraud prevention. Then this study also offers several aspects that can help organisation to establish effective whistleblowing systems and reporting mechanisms. Those aspects identified can encourage an individual to report malpractice or wrongdoing. This study also offers how fraud awareness can support the implementation of whistleblowing system in preventing fraudulent financial statements and other irregularities.
A typology of emerging farmers in three rural provinces of South Africa: what are the implications for the land redistribution policy?
Authors: Zantsi Siphe , Pienaar Louw Petrus , Greyling Jan C. 
Published: February 2021

PurposeUnderstanding diversity amongst potential beneficiaries of land redistribution is of critical importance for both design and planning of successful land reform interventions. This study seeks to add to the existing literature on farming types, with specific emphasis on understanding diversity within a sub-group of commercially oriented or emerging smallholders.Design/methodology/approachUsing a multivariate statistical analysis – principal component and cluster analyses applied to a sample of 442 commercially-oriented smallholders – five distinct clusters of emerging farmers are identified, using variables related to farmers' characteristics, income and expenditure and farm production indicators and willingness to participate in land redistribution. The five clusters are discussed in light of a predefined selection criteria that is based on the current policies and scholarly thinking.FindingsThe results suggest that there are distinct differences in farming types, and each identified cluster of farmers requires tailored support for the effective implementation of land reform. The identified homogenous sub-groups of smallholders, allows us to understand which farmers could be a better target for a successful land redistribution policy.Originality/valueMost of the existing typology studies in South Africa tend to focus on general smallholders and in the Eastern Cape province; this study extends the literature by focussing on specific prime beneficiaries of land reform in three provinces. This study uses a more detailed dataset than the Statistics general and agricultural household surveys.