bluuebunny/crossref_metadata_2025 huggingface dataset:
Population genomics ofPocilloporacorals: insights from RAD-sequencing
Authors: Aurelle Didier , Pratlong Marine , Oury Nicolas , Haguenauer Anne , Gélin Pauline , Magalon Hélène , Adjeroud Mehdi , Romans Pascal , Vidal-Dupiol Jeremie , Claereboudt Michel , Noûs Camille , Reynes Lauric , Toulza Eve , Bonhomme François , Mitta Guillaume , Pontarotti Pierre
Published: May 2021

Scleractinian corals are of great ecological interest as ecosystem engineer species. Accordingly, there is a wealth of studies on their adaptive abilities facing climate change. Such studies should rely on precise species and population delimitation. Nevertheless species delimitation in corals can be hindered by the lack of adequate genetic markers, by hybridization, and by morphological plasticity. Here we applied RAD sequencing to the study of species delimitation and genetic structure in populations ofPocilloporaspp. from Oman and French Polynesia with the objectives to test primary species hypotheses based on mitochondrial DNA sequencing, and to study the genetic structure among sampling sites inside species. Regarding the varying levels of missing data observed among samples we tested different filtering strategy. The main genetic differentiation was observed between samples from Oman and French Polynesia, which also corresponded to different mitochondrial lineages and species hypotheses. In Oman, we did not observe any clear differentiation according to the main mitochondrial lineages considered here, nor between sampling sites. In French Polynesia where a single mitochondrial lineage was studied, we did not evidence any differentiation according to sampling sites. These results provide an additional example of the importance of using independent nuclear markers for the study of species delimitation. Our analyses also allowed the identification of clonal lineages in our samples, and to take them into account in our interpretations. We used simulations to study the impact of clonal reproduction on the distribution of statistics of genetic diversity and genetic structure among loci.
A universal pocket in Fatty acyl-AMP ligases ensures redirection of fatty acid pool away from Coenzyme A-based activation
Authors: Patil Gajanan S. , Kinatukara Priyadarshan , Mondal Sudipta , Shambhavi Sakshi , Patel Ketan D. , Pramanik Surabhi , Dubey Noopur , Narasimhan Subhash , Madduri Murali Krishna , Pal Biswajit , Gokhale Rajesh S. , Sankaranarayanan Rajan
Published: May 2021

Fatty acyl-AMP ligases (FAALs) channelize fatty acids towards biosynthesis of virulent lipids in mycobacteria and other pharmaceutically or ecologically important polyketides and lipopeptides in other microbes. They do so by bypassing the ubiquitous coenzyme A-dependent activation and rely on the acyl carrier protein-tethered 4’-phosphopantetheine (holo-ACP). The molecular basis of how FAALs strictly reject chemically identical and abundant acceptors like coenzyme A (CoA) and acceptholo-ACP unlike other members of the ANL superfamily remains elusive. We show FAALs have plugged the promiscuous canonical CoA-binding pockets and utilize highly selective alternative binding sites. These alternative pockets can distinguish adenosine 3’, 5’-bisphosphate-containing CoA fromholo-ACP and thus FAALs can distinguish between CoA andholo-ACP. These exclusive features helped identify the omnipresence of FAAL-like proteins and their emergence in plants, fungi, and animals with unconventional domain organisations. The universal distribution of FAALs suggests they are parallelly evolved with FACLs for ensuring a CoA-independent activation and redirection of fatty acids towards lipidic metabolites.
The gut parasiteNosema ceranaeimpairs olfactory learning in bumblebees
Authors: Gómez-Moracho Tamara , Durand Tristan , Lihoreau Mathieu
Published: May 2021

Pollinators are exposed to numerous parasites and pathogens when foraging on flowers. These biological stressors may affect critical cognitive abilities required for foraging. Here, we tested whether exposure toNosema ceranae, one of the most widespread parasite of honey bees also found in wild pollinators, impacts cognition in bumblebees. We investigated different forms of olfactory learning and memory using conditioning of the proboscis extension reflex. Seven days after feeding parasite spores, bumblebees showed lower performance in absolute and differential learning, and reversal learning than controls. Long-term memory was also slightly reduced. The consistent effect ofN. ceranaeexposure across different types of olfactory learning indicates that its action was not specific to particular brain areas or neural processes. We discuss the potential mechanisms by whichN. ceranaeimpairs bumblebee cognition and the broader consequences for populations of pollinators.
Pivotal Roles for Ribonucleases inStreptococcus pneumoniaePathogenesis
Authors: Sinha Dhriti , Frick Jacob , Clemmons Kristen , Winkler Malcolm E. , De Lay Nicholas R.
Published: May 2021

RNases perform indispensable functions in regulating gene expression in many bacterial pathogens by processing and/or degrading RNAs. Despite the pivotal role of RNases in regulating bacterial virulence factors, the functions of RNases have not yet been studied in the major human respiratory pathogenStreptococcus pneumoniae(pneumococcus). Here, we sought to determine the impact of two conserved RNases, the endoribonuclease RNase Y and exoribonuclease polynucleotide phosphorylase (PNPase), on the physiology and virulence ofS. pneumoniaeserotype 2 strain D39. We report that RNase Y and PNPase are essential for pneumococcal pathogenesis as both deletion mutants showed strong attenuation of virulence in murine models of invasive pneumonia. Genome-wide transcriptomic analysis revealed that nearly 200 mRNA transcripts were significantly up-regulated, whereas the abundance of several pneumococcal sRNAs, including the Ccn (CiaRControlledNoncoding RNA) sRNAs, were altered in the Δrnymutant relative to the wild-type strain. Additionally, lack of RNase Y resulted in pleiotropic phenotypes that included defects in pneumococcal cell morphology and growthin vitro. In contrast, Δpnpmutants showed no growth defectin vitro, but differentially expressed a total of 40 transcripts including the tryptophan biosynthesis operon genes and numerous 5’-cis-acting regulatory RNAs, a majority of which were previously shown to impact pneumococcal disease progression in mice using the serotype 4 strain TIGR4. Altogether our data suggest that RNase Y exerts a global impact on pneumococcal physiology, while PNPase-mediates virulence phenotypes, likely through sRNA regulation.

IMPORTANCE

Streptococcus pneumoniaeis a notorious human pathogen that adapts to conditions in distinct host tissues and responds to host cell interactions by adjusting gene expression. Ribonucleases (RNases) are key players that modulate gene expression by mediating the turnover of regulatory and protein-coding transcripts. Here, we characterized two highly conserved RNases, RNase Y and PNPase, and evaluated their impact on the S. pneumoniaetranscriptome for the first time. We show that PNPase influences the levels of a narrow set of mRNAs, but a large number of regulatory RNAs primarily implicated in virulence control, whereas RNase Y has a more sweeping effect on gene expression, altering levels of transcripts involved in diverse cellular processes including cell division, metabolism, stress response, and virulence. This study further reveals that RNase Y regulates expression of genes governing competence by mediating the turnover ofCiaR-controlled-noncoding (Ccn) sRNAs.
A short report on optimization of nucleic acid probes by DNA microarray synthesis and next generation sequencing
Authors: Nong Mikkelsen Rachel Yuan , Mikkelsen Tarjei Sigurd
Published: May 2021

This manuscript has been withdrawn by bioRxiv as it was submitted and made public without the full consent of all the authors. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author
Glioblastoma mutations impair ligand discrimination by EGFR
Authors: Hu Chun , Leche Carlos A. , Kiyatkin Anatoly , Stayrook Steven E. , Ferguson Kathryn M. , Lemmon Mark A.
Published: May 2021

The epidermal growth factor receptor (EGFR) is frequently mutated in human cancer, and is an important therapeutic target. EGFR inhibitors have been successful in lung cancer, where the intracellular tyrosine kinase domain is mutated, but not in glioblastoma multiforme (GBM) – where mutations (or deletions) occur exclusively in the EGFR extracellular region. Wild-type EGFR is known to elicit distinct signals in response to different growth factor ligands, exhibiting biased agonism. We recently showed that individual ligands stabilize distinct receptor dimer structures, which signal with different kinetics to specify outcome. EGF induces strong symmetric dimers that signal transiently to promote proliferation. Epiregulin (EREG) induces weak asymmetric dimers that generate sustained signaling and differentiation. Intriguingly, several GBM mutation hotspots coincide with residues that define the asymmetric and symmetric dimer structures. Here, we show that common extracellular GBM mutations prevent EGFR from distinguishing between EGF and EREG based on dimer structure and stability – allowing strong dimers to form with both ligands. Crystal structures show that the R84K mutation symmetrizes EREG-driven dimers, whereas the A265V mutation remodels key dimerization sites. Our results suggest that modulating EGFR’s biased agonism plays an important role in GBM, and suggest new approaches for ‘correcting’ aberrant EGFR signaling in cancer.
Comparison of unit resolution versus high-resolution accurate mass for parallel reaction monitoring
Authors: Heil Lilian R. , Remes Philip M. , MacCoss Michael J.
Published: May 2021

Parallel reaction monitoring (PRM) is an increasingly popular alternative to selected reaction monitoring (SRM) for targeted proteomics. PRM’s strengths over SRM are that it monitors all product ions in a single spectrum, thus eliminating the need to select interference-free product ions prior to data acquisition, and that it is most frequently performed on high-resolution instruments, such as quadrupole-orbitrap and quadrupole-time of flight instruments. Here, we show that the primary advantage of PRM is the ability to monitor all transitions in parallel, and that high-resolution data are not necessary to obtain high quality quantitative data. We run the same scheduled PRM assay, measuring 432 peptides from 126 plasma proteins, multiple times on a Orbitrap Eclipse Tribrid mass spectrometer, alternating separate liquid chromatography-tandem mass spectrometry runs between the high resolution Orbitrap and the unit resolution linear ion trap for PRM. We find that both mass analyzers have similar technical precision, and that the linear ion trap’s superior sensitivity gives it better lower limits of quantitation on over 62% of peptides in the assay.

Abstract graphic
Transcriptomic and rRNA:rDNA signatures of environmental vs. entericEnterococcus faecalisisolates under oligotrophic freshwater conditions
Authors: Suttner Brittany , Kim Minjae , Johnston Eric R. , Orellana Luis H. , Ruiz-Perez Carlos A. , Rodriguez-R Luis M. , Hatt Janet K. , Brown Joe , Santo Domingo Jorge W. , Konstantinidis Konstantinos T.
Published: May 2021

The use of enterococci as a fecal indicator bacterial group for public health risk assessment has been brought into question by recent studies showing that “naturalized” populations ofE. faecalisexist in the extraenteric environment in a viable but not culturable (VBNC) state. The extent to which these naturalized or VBNCE. faecaliscan confound water quality monitoring is unclear. To determine if strains isolated from different habitats display different survival strategies and responses, we compared the decay patterns of threeE. faecalisisolates from the natural environment (environmental strains) against three human gut isolates (enteric strains) in laboratory mesocosms that simulate an oligotrophic, aerobic freshwater environment. Our results showed similar overall decay rates between enteric and environmental isolates based on viable plate and qPCR counts. However, the enteric isolates exhibited a spike in rRNA:rDNA ratios between days 1 and 3 of the mesocosm incubations that was not observed in environmental isolates, which could indicate a different stress response. Nevertheless, there was no strong evidence of differential expression of genes thought to be related to habitat adaptation in the accompanying mesocosm metatranscriptomes when compared between environmental and enteric isolates. Overall, our results provide novel information on how rRNA levels may vary over different metabolic states (i.e., alive vs. VBNC) for this important indicator bacteria. We also observed some evidence for habitat adaptation inE. faecalis; however, this adaptation may not be substantial or consistent enough for integration in water quality monitoring.

IMPORTANCE

Enterococci are commonly used worldwide to monitor environmental fecal contamination and public health risk for waterborne diseases. However, some species within this group can enter an inactive, viable but not culturable (VBNC) state that make it difficult to accurately quantify during routine monitoring. Furthermore, lower-risk, environmental enterococci strains may also confound water quality estimates. We developed an rRNA:rDNA viability assay forE. faecalis(a predominant species within this fecal group) and tested it against both enteric and environmental isolates in freshwater mesocosms to assess whether this approach can serve as a more sensitive water quality monitoring tool. We were unable to reliably distinguish the different isolate types using this assay under the conditions tested here; thus, environmental strains should continue to be counted during routine water monitoring. However, this assay could be useful for distinguishing more recent (i.e., higher risk) fecal pollution because rRNA levels significantly decreased after one week in all isolates.
A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance
Authors: Bourassa Lori , Perchetti Garrett A. , Phung Quynh , Lin Michelle J. , Mills Margaret G. , Roychoudhury Pavitra , Harmon Kimberly G. , Reed Jonathan C. , Greninger Alexander L.
Published: May 2021

More than one year into a global pandemic, SARS-CoV-2 is now defined by a variety of rapidly evolving variant lineages. Several FDA authorized molecular diagnostic tests have been impacted by viral variation, while no reports of viral variation affecting antigen test performance have occurred to date. While determining the analytical sensitivity of the Quidel Sofia SARS Antigen FIA test (Sofia 2), we uncovered a high viral load specimen that repeatedly tested negative by this antigen test. Whole genome sequencing of the specimen uncovered two mutations, T205I and D399N, present in the nucleocapsid protein of the isolate. All six SARS-CoV-2 positive clinical specimens available in our laboratory with a D399N nucleocapsid mutation and CT < 31 were not detected by the Sofia 2 but detected by the Abbott BinaxNOW COVID-19 Ag Card, while clinical specimens with the T205I mutation were detected by both assays. Testing of recombinant SARS-CoV-2 nucleocapsid with these variants demonstrated an approximate 1000-fold loss in sensitivity for the Quidel Sofia SARS Antigen FIA test associated with the D399N mutation, while the BinaxNOW and Quidel Quickvue SARS Antigen tests were unaffected by the mutation. The D399N nucleocapsid mutation has been relatively uncommon to date, appearing in only 0.02% of genomes worldwide at time of writing. Our results demonstrate how routine pathogen genomics can be integrated into the clinical microbiology laboratory to investigate diagnostic edge cases, as well as the importance of profiling antigenic diversity outside of the spike protein for SARS-CoV-2 diagnostics.
Chronic Aryl Hydrocarbon Receptor Activity Phenocopies Smoking-induced Skeletal Muscle Impairment
Authors: Thome Trace , Miguez Kayla , Willms Alexander , de Souza Angela R. , Chandran Vijayendran , Burke Sarah S. , Goddard Yana , Baglole Carolyn , Anagnostou Maria-Eleni , Bourbeau Jean , Thomas Jagoe R. , Morais Jose , Taivassalo Tanja , Ryan Terence , Hepple Russell T.
Published: May 2021

Background

COPD patients exhibit skeletal muscle atrophy, denervation, and reduced mitochondrial oxidative capacity. Whilst chronic tobacco smoke exposure is implicated in COPD muscle impairment, the mechanisms involved are ambiguous. The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that activates detoxifying pathways with numerous exogenous ligands, including tobacco smoke. Whereas transient AHR activation is adaptive, chronic activation can be toxic. On this basis, we tested the hypothesis that chronic smoke-induced AHR activation causes adverse muscle impact.

Methods

We used clinical patient muscle samples, andin vitro(C2C12 myotubes) andin vivomodels (mouse), to perform gene expression, mitochondrial function, muscle and neuromuscular junction morphology, and genetic manipulations (adeno-associated virus-mediated gene transfer).

Results

16 weeks tobacco smoke exposure in mice caused: muscle atrophy, neuromuscular junction degeneration, and reduced oxidative capacity. Similarly, smoke exposure reprogrammed the muscle transcriptome, with down-regulation of mitochondrial and neuromuscular junction genes. In mouse and human patient specimens, smoke exposure increased muscle AHR signaling. Mechanistically, experiments in cultured myotubes demonstrated that smoke condensate activated the AHR, caused mitochondrial impairments, and induced an AHR-dependent myotube atrophy. Finally, to isolate the role of AHR activity, expression of a constitutively active AHR mutant without smoke exposure caused atrophy and mitochondrial impairments in cultured myotubes, and muscle atrophy and neuromuscular junction degeneration in mice.

Conclusions

These results establish that chronic AHR activity, as occurs in smokers, phenocopies the atrophy, mitochondrial impairment and neuromuscular junction degeneration caused by chronic tobacco smoke exposure.
Relief of ParB autoinhibition by parS DNA catalysis and ParB recycling by CTP hydrolysis promote bacterial centromere assembly
Authors: Antar Hammam , Soh Young-Min , Zamuer Stefano , Bock Florian P. , Anchimiuk Anna , De Los Rios Paolo , Gruber Stephan
Published: May 2021

Three-component ParABS systems are widely distributed factors for plasmid partitioning and chromosome segregation in bacteria. ParB protein acts as an adaptor between the 16 bp centromericparSDNA sequences and the DNA segregation ATPase ParA. It accumulates at high concentrations at and near aparSsite by assembling a partition complex. ParB dimers form a DNA sliding clamp whose closure atparSrequires CTP binding. The mechanism underlying ParB loading and the role of CTP hydrolysis however remain unclear. We show that CTP hydrolysis is dispensable for Smc recruitment toparSsites inBacillus subtilisbut is essential for chromosome segregation by ParABS in the absence of Smc. Our results suggest that CTP hydrolysis contributes to partition complex assembly via two mechanisms. It recycles off-target ParB clamps to allow for new attempts atparStargeting and it limits the extent of spreading fromparSby promoting DNA unloading. We also propose a model for howparSDNA catalyzes ParB clamp closure involving a steric clash between ParB protomers binding to opposingparShalf sites.
Engineered protein-small molecule conjugates empower selective enzyme inhibition
Authors: Lewis Andrew K. , Harthorn Abbigael , Johnson Sadie M. , Lobb Roy R. , Hackel Benjamin J.
Published: May 2021

Summary

Specific, potent ligands drive precision medicine and fundamental biology. Proteins, peptides, and small molecules constitute effective ligand classes. Yet greater molecular diversity would aid the pursuit of ligands to elicit precise biological activity against challenging targets. We demonstrate a platform to discover protein-small molecule (PriSM) hybrids to combine unique pharmacophore activities and shapes with constrained, efficiently engineerable proteins. A fibronectin protein library was yeast displayed with a single cysteine coupled to acetazolamide via a maleimide-poly(ethylene glycol) linker. Magnetic and flow cytometric sorts enriched specific binders to carbonic anhydrase isoforms. Isolated PriSMs exhibited potent, specific inhibition of carbonic anhydrase isoforms with superior efficacy to acetazolamide or protein alone including an 80-fold specificity increase and 9-fold potency gain. PriSMs were engineered with multiple linker lengths, protein conjugation sites, and sequences against two different isoforms, which reveals platform flexibility and impacts of molecular designs. PriSMs advance the molecular diversity of efficiently engineerable ligands.
Mapping the Central and Peripheral Projections of Lung Innervating Sensory Neurons
Authors: Su Yujuan , Barr Justinn , Jaquish Abigail , Xu Jinhao , Verheyden Jamie M , Sun Xin
Published: May 2021

While best known as the gas exchange organ, the lung is also critical for sensing and responding to the aerosol environment in part through interaction with the nervous system. The rich diversity of lung innervating neurons remains poorly understood. Here, we interrogated the cell body location, projection pattern and targets of lung-innervating sensory neurons. Retrograde tracing from the lung labeled neurons primarily in the vagal ganglia, in a spatially distributed population expressing markers includingVglut2, Trpv1, Tac1, Calb1orPiezo2. Centrally, they project to the nucleus of the solitary tract in the brainstem. Peripherally, they project along the branching airways and terminate on airway smooth muscles, vasculature including lymphatics, and selected alveoli. Notably, a discrete population of Calb1+ neurons preferentially innervate pulmonary neuroendocrine cells, a demonstrated airway sensor population. This comprehensive illustration of the properties of lung innervating sensory neurons serves as a foundation for understanding their function in lung.
Detecting natural selection in trait-trait coevolution
Authors: Jiang Daohan , Zhang Jianzhi
Published: May 2021

No phenotypic trait evolves independently of all other traits, but the cause of trait-trait coevolution is poorly understood. While the coevolution could arise simply from pleiotropic mutations that simultaneously affect the traits concerned, it could also result from multivariate natural selection favoring certain trait relationships. To gain a general mechanistic understanding of trait-trait coevolution, we examine the evolution of 220 cell morphology traits across 16 natural strains of the yeastSaccharomyces cerevisiaeand the evolution of 24 wing morphology traits across 110 fly species of the family Drosophilidae, along with the variations of these traits among gene deletion or mutation accumulation lines (a.k.a. mutants). For numerous trait pairs, the phenotypic correlation among evolutionary lineages differs significantly from that among mutants. Specifically, we find hundreds of cases where the evolutionary correlation between traits is strengthened or reversed relative to the mutational correlation, which, according to our population genetic simulation, is likely caused by multivariate selection. Furthermore, we detect selection for enhanced modularity of the yeast traits analyzed. Together, these results demonstrate that trait-trait coevolution is shaped by natural selection and suggest that the pleiotropic structure of mutation is not optimal. Because the morphological traits analyzed here are chosen largely because of their measurability and thereby are not expected to be biased with regard to natural selection, our conclusion is likely general.
Factors that affect the rates of adaptive and non-adaptive evolution at the gene level in humans and chimpanzees
Authors: Soni Vivak , Eyre-Walker Adam
Published: May 2021

The rate of amino acid substitution has been shown to be correlated to a number of factors including the rate of recombination, the age of the gene, the length of the protein, mean expression level and gene function. However, the extent to which these correlations are due to adaptive and non-adaptive evolution has not been studied in detail, at least not in hominids. We find that the rate of adaptive evolution is significantly positively correlated to the rate of recombination, protein length and gene expression level, and negatively correlated to gene age. The correlations remain significant when each factor is controlled for in turn, except when controlling for expression in an analysis of protein length; and they also remain significant, or marginally significant, when biased gene conversion is controlled for. However, the positive correlations could be an artefact of population size contraction. We also find that the rate of non-adaptive evolution is negatively correlated to each factor, and all these correlations survive controlling for each other and biased gene conversion. Finally, we examine the effect of gene function on rates of adaptive and non-adaptive evolution; we confirm that virus interacting proteins (VIPs) have higher rates of adaptive and lower rates of non-adaptive evolution, but we also demonstrate that there is significant variation in the rate of adaptive and non-adaptive evolution between GO categories when removing VIPs. We estimate that the VIP/non-VIP axis explains about 5-8x more of the variance in evolutionary rate than GO categories.
Cell-type-specific silence in thalamocortical circuits precedes hippocampal sharp-wave ripples
Authors: Chambers Anna R. , Berge Christoffer Nerland , Vervaeke Koen
Published: May 2021

Memory consolidation requires the encoding of neocortical memory traces, which is thought to occur during hippocampal oscillations called sharp-wave ripples (SWR). Evidence suggests that the hippocampus communicates memory-related neural patterns across distributed cortical circuits via its major output pathways. Here, we sought to understand how this information is processed in the retrosplenial cortex (RSC), a primary target circuit. Using patch-clamp recordings from mice during quiet wakefulness, we found that SWR-aligned synaptic modulation is widespread but weak, and that spiking responses are sparse. However, using cell type and projection-specific two-photon calcium imaging and optogenetics, we show that, starting 1-2 seconds before SWR, superficial inhibition in RSC is reduced, along with thalamocortical input. We propose that pyramidal dendrites experience a period of decreased local inhibition and subcortical interference in a seconds-long time window preceding hippocampal SWR. This may aid communication of weak and sparse SWR-aligned excitation between the hippocampus and neocortex, and promote the selective strengthening of memory-related connections.
SARS-CoV-2 B.1.1.7 and B.1.351 variants of concern induce lethal disease in K18-hACE2 transgenic mice despite convalescent plasma therapy
Authors: Horspool Alexander M. , Ye Chengjin , Wong Ting Y. , Russ Brynnan P. , Lee Katherine S. , Winters Michael T. , Bevere Justin R. , Kieffer Theodore , Martinez Ivan , Sourimant Julien , Greninger Alexander , Plemper Richard K. , Denvir James , Cyphert Holly A. , Torrelles Jordi , Martinez-Sobrido Luis , Damron F. Heath
Published: May 2021

SARS-CoV-2 variants of concern (VoCs) are impacting responses to the COVID-19 pandemic. Here we present a comparison of the SARS-CoV-2 USA-WA1/2020 (WA-1) strain with B.1.1.7 and B.1.351 VoCs and identify significant differences in viral propagationin vitroand pathogenicityin vivousing K18-hACE2 transgenic mice. Passive immunization with plasma from an early pandemic SARS-CoV-2 patient resulted in significant differences in the outcome of VoC-infected mice. WA-1-infected mice were protected by plasma, B.1.1.7-infected mice were partially protected, and B.1.351-infected mice were not protected. Serological correlates of disease were different between VoC-infected mice, with B.1.351 triggering significantly altered cytokine profiles than other strains. In this study, we defined infectivity and immune responses triggered by VoCs and observed that early 2020 SARS-CoV-2 human immune plasma was insufficient to protect against challenge with B.1.1.7 and B.1.351 in the mouse model.
Early flowering in oilseed-typeBrassica rapaplants results from nonsense-mediated mRNA decay (NMD) ofBrFLC2
Authors: Kim Sujeong , Kim Jin A , Kang Hajeong , Kim Dong-Hwan
Published: May 2021

ManyBrassicaspecies require vernalization (long-term winter-like cooling) for transition to the reproductive stage. In the past several decades, scientific efforts have been made to discern the molecular mechanisms underlying vernalization in many species. Thus, to identify the key regulators required for vernalization inBrassica rapaL., we constructed a linkage map composed of 7,833 single nucleotide polymorphism (SNP) markers using the late-flowering Chinese cabbage (B. rapaL. ssp.pekinensis) inbred line ‘Chiifu’ and the early-flowering yellow sarson (B. rapaL. ssp.trilocularis(Roxb.)) line ‘LP08’ and identified a single major QTL on the upper-arm of the chromosome A02. In addition, we compared the transcriptomes of the lines ‘Chiifu’ and ‘LP08’ at five vernalization time points, including both non-vernalized and post-vernalization conditions. We observed thatBrFLC2was significantly downregulated in the early flowering ‘LP08’ and had two deletion sites around theBrFLC2genomic region compared with theBrFLC2genomic region in ‘Chiifu.’ In the present study, we also demonstrate that early flowering in ‘LP08’ line is attributed to the low expression ofBrFLC2, which is caused by nonsense-mediated mRNA decay (NMD). Therefore, this study provides a better understanding of the molecular mechanisms underlying floral transition inB. rapa.

One sentence summary

NMD-mediated degradation ofBrFLC2mRNA transcripts is the main cause of rapid flowering of oilseed-typeB. rapa‘LP08’ plants.
The role of Federal crop insurance for farms and ranches that sell through local food markets
Authors: Jablonski Becca B.R. , Hadrich Joleen , Bauman Allie
Published: May 2021

Purpose

The Agriculture Improvement Act of 2018 directed the United States Department of Agriculture (USDA) Risk Management Association to investigate a policy targeted to farms and ranches that sell through local food markets. However, there is no available research that quantitatively documents the extent to which local food producers utilize Federal crop insurance.

Design/methodology/approach

The authors utilize 2013–2016 USDA Agricultural Resource Management Survey data to compare farms and ranches with sales through local food markets to those with and without Federal crop insurance expenditure, as well as the distribution of Federal crop expenditure, across market channels and scales.

Findings

There is a little variation in Federal crop insurance expenditure across market channels, defined as direct-to-consumer only sales, intermediated sales, and a combination of direct-to-consumer and intermediated sales. Rather, the results show that scale is the primary predictor of Federal crop insurance expenditure; larger operations are more likely to have nonzero Federal crop insurance expenses.

Originality/value

This article provides the first national research to document descriptive statistics of the utilization of Federal crop insurance by US farms and ranches that utilize local food market channels.
Exploring engagement with health apps: the emerging importance of situational involvement and individual characteristics
Authors: Flaherty Sarah Jane , McCarthy Mary , Collins Alan M. , McCafferty Claire , McAuliffe Fionnuala M.
Published: May 2021

Purpose

Health apps offer a potential approach to support healthier food behaviours but a lack of sufficient engagement may limit effectiveness. This study aims to use a user engagement theoretical lens to examine the factors that influence app engagement over time and may prompt disengagement.

Design/methodology/approach

A phenomenological exploration of the lived experience was used. Women from a lower socioeconomic background (based on the occupation and employment status of the household’s primary income earner) were randomly assigned to use one of two apps for a minimum of eight weeks. Multiple data collection methods, including accompanied shops, researcher observations, interviews, participant reflective accounts and questionnaires, were used at different time-points to examine engagement. Theoretical thematic analysis was conducted to explore the engagement experience and relevant social, personal and environmental influences.

Findings

Healthy food involvement appears to drive app engagement. Changes in situational involvement may contribute to fluctuation in engagement intensity over time as the saliency of personal goals change. Negatively valenced engagement dimensions may contribute to the overall expression of engagement. A lack of congruency with personal goals or an imbalance between perceived personal investment and value was expressed as the primary reasons for disengagement.

Research limitations/implications

Situational involvement may act as a trigger of different engagement phases. There is a need to better distinguish between enduring and situational involvement in engagement research.

Practical implications

Individual characteristics may shape engagement and propensity for disengagement, which highlights the practical importance of incorporating tailored features into app design.

Originality/value

Findings broaden the current conceptualisation of engagement within the digital space and prompt a reconsideration of the role of situational involvement and negatively valenced dimensions throughout the engagement process.
Internal communication and the development of customer-oriented behavior among frontline employees
Authors: Ferdous Ahmed Shahriar , Polonsky Michael , Bednall David Hugh Blore
Published: May 2021

Purpose

Frontline employees (FLEs) are a key source of competitive advantage for organizations and have a significant impact on the quality of customer–firm interactions. This study aims to use the stimulus-organism-response (S-O-R) model as a theoretical lens to examine whether internal communication (IC) (stimulus) evokes FLEs’ organizational identification (emotional) and job satisfaction (cognitive), and whether these in turn shape FLE customer-oriented behavior (response). The study also tested whether these mediated relationships are moderated by perceived communication formalization.

Design/methodology/approach

The hypothesized mediated and moderated effects were tested using data collected from a cross-sectional survey of 293 full-time salespeople working for a large general insurance company.

Findings

Both organizational identification and job satisfaction simultaneously mediate the relationship between IC and customer-oriented behavior. Perceived communication formalization was found to weaken the mediated relationship between IC and customer-oriented behavior, but only when this is via job satisfaction.

Research limitations/implications

This study has shown that where IC is positively viewed by FLEs, it can be leveraged as a key driver by organizations to evoke simultaneous positive emotional and cognitive reactions, leading to increased customer-oriented behavior.

Practical implications

This study informs both theory and practice related to effective IC among customer-contact FLEs.

Originality/value

The study shows how IC can simultaneously produce two simultaneous emotional and cognitive reactions leading to FLE customer-oriented behavior and how these mediated relationships can be moderated by perceived communication formalization. The study used the S-O-R model as the theoretical lens to test these relationships.
Student satisfaction from the influence of the built environment, price fairness and teaching care: a study at a community-supported university
Authors: Benetti Corrêa da Silva Marcelo , Matte Juliana , Bebber Suélen , Dalla Santa de Carvalho Mayron , de Atayde Moschen Suane , Fachinelli Ana Cristina
Published: May 2021

Purpose

This study aims to test and analyze factors that may influence the satisfaction of university students, specifically, from the built environment, price fairness and teaching care.

Design/methodology/approach

A survey was conducted with 250 students from a university in southern Brazil. The data were analyzed by structural equation modeling.

Findings

The main results proved that the built environment, price fairness and teaching care have a significant and positive influence on the satisfaction of university students.

Practical implications

The factors presented explanation power for student satisfaction, which shows that they are essential aspects and, therefore, must be observed by universities to satisfy their students.

Originality/value

The study identifies the impact of factors such as the environment, price and teaching service on student satisfaction.
Modern-day slavery? The work-life conflict of domestic workers in Nigeria
Authors: Adisa Toyin Ajibade , Adekoya Olatunji David , Okoya Olajumoke
Published: May 2021

Purpose

The trend of domestic employment thrives almost in every society. It is most common in developing countries and Nigeria is no exception. This paper aims to examine the nature of the role of a domestic worker in Nigeria and the work-life conflict issues involved in such work.

Design/methodology/approach

This study uses a qualitative research approach to examine the nature of the role of domestic workers and the associated work-life conflict issues.

Findings

The findings show that the nature of the jobs of domestic workers in Nigeria gives rise to a situation of modern-day slavery in which an employee works without a formal employment contract, with little or no rights to private time. Long and unstructured working hours, employers’ perceptions about domestic workers and a huge workload fuel and exacerbate work-life conflict amongst domestic workers in Nigeria.

Research limitations/implications

The extent to which the findings of this research can be generalised is constrained by the limited and selected sample of the research and the research context.

Practical implications

The primacy of the employer over the employee in domestic employment means that both time and work-based conflicts continue to buffer work-life conflict if domestic workers’ working hours remain unscheduled and their employers’ perceptions about them remain unchanged. This invariably has a negative impact on the domestic workers’ health and productivity. Therefore, domestic employment should be regulated by law and domestic workers should be treated like other formal employees.

Originality/value

This study contributes to the debates on the work-life conflict by highlighting the nature of the role of domestic workers in a non-western context, Nigeria and provides a nuanced insight into the work-life conflict issues involved in such work. The findings add conceptual thought and empirical evidence to the debate on work-life conflict.
A new Painlevé integrable Broer-Kaup system: symmetry analysis, analytic solutions and conservation laws
Authors: Kumar Sachin , Gupta Rajesh Kumar , Kumari Pinki
Published: May 2021

Purpose

This study aims to find the symmetries and conservation laws of a new Painlevé integrable Broer-Kaup (BK) system with variable coefficients. This system is an extension of dispersive long wave equations. As the system is generalized and new, it is essential to explore some of its possible aspects such as conservation laws, symmetries, Painleve integrability, etc.

Design/methodology/approach

This paper opted for an exploratory study of a new Painleve integrable BK system with variable coefficients. Some analytic solutions are obtained by Lie classical method. Then the conservation laws are derived by multiplier method.

Findings

This paper presents a complete set of point symmetries without any restrictions on choices of coefficients, which subsequently yield analytic solutions of the series and solitary waves. Next, the authors derive every admitted non-trivial conservation law that emerges from multipliers.

Research limitations/implications

The authors have found that the considered system is likely to be integrable. So some other aspects such as Lax pair integrability, solitonic behavior and Backlund transformation can be analyzed to check the complete integrability further.

Practical implications

The authors develop a time-dependent Painleve integrable long water wave system. The model represents more specific data than the constant system. The authors presented analytic solutions and conservation laws.

Originality/value

The new time-dependent Painleve integrable long water wave system features some interesting results on symmetries and conservation laws.
How does China’s information and communications technology infrastructure investment promote economic growth?
Authors: Liu Kerry
Published: May 2021

Purpose

This study aims to analyse the effects of China’s information and communications technology (ICT) infrastructure investment on economic growth.

Design/methodology/approach

Using a panel data set of China’s 30 regions during 2010–2015, this study uses the generalized method of moments (GMM) methods.

Findings

This study finds that compared with “old-type” infrastructure investment such as transport infrastructure and utility infrastructure, there is a time lag but greater effect from ICT infrastructure investment on growth and this relation is non-linear. Also, the human capital factor plays an enhancing role.

Originality/value

This study is the first of its kind that examines the relationship between ICT infrastructure investment and growth in China.
The connection between leader behaviour and employee sickness absence in public administration
Authors: Buzeti Jernej
Published: May 2021

Purpose

The purpose of this study is to find the connection between leader behaviour and employee sickness absence in public administration.

Design/methodology/approach

The research data was collected with the help of an online questionnaire. The SPSS statistical programme and structural equation modelling in AMOS were used to analyse the data.

Findings

The research was conducted in public administration institutions, and 3,220 employees from public administration were included in the research sample. The author found a negative one-way relationship between certain types of behaviour and sickness absence. The author defines leader behaviour as a multidimensional construct in which each dimension represents a separate cluster of leader behavioural characteristics. Leaders’ “progressiveness” is the most important dimension, and a one-point increase in “progressiveness” (five-point scale) leads to a reduction of 2.8 days in sickness absence for one employee.

Research limitations/implications

The author focused only on one segment of factors (the behaviour of leaders) that affects sickness absence. To explain the maximum possible measure of the variability in sickness absence, it would be best to include several different influencing factors.

Practical implications

The study represents a structured model of the link between sickness absence and leader behaviour. With the model, it is possible to determine which behavioural forms of leaders influence sickness absence, where leader behaviour is treated as a complex whole, and not as an individual behavioural characteristic.

Originality/value

The study addresses calls for research on the relationship between leader behaviour and employee sickness absence within countries.
Adaptive neural network-based path tracking control for autonomous combine harvester with input saturation
Authors: Zhang Yuexin , Wang Lihui , Liu Yaodong
Published: May 2021

Purpose

To reduce the effect of parameter uncertainties and input saturation on path tracking control for autonomous combine harvester, a path tracking controller is proposed, which integrates an adaptive neural network estimator and a saturation-aided system.

Design/methodology/approach

First, to analyze and compensate the influence of external factors, the vehicle model is established combining a dynamic model and a kinematic model. Meanwhile, to make the model simple, a comprehensive error is used, weighting heading error and position error simultaneously. Second, an adaptive neural network estimator is presented to calculate uncertain parameters which eventually improve the dynamic model. Then, the path tracking controller based on the improved dynamic model is designed by using the backstepping method, and its stability is proved by the Lyapunov theorem. Third, to mitigate round-trip operation of the actuator due to input saturation, a saturation-aided variable is presented during the control design process.

Findings

To verify the tracking accuracy and environmental adaptability of the proposed controller, numerical simulations are carried out under three different cases, and field experiments are performed in harvesting wheat and paddy. The experimental results demonstrate the tracking errors of the proposed controller that are reduced by more than 28% with contrast to the conventional controllers.

Originality/value

An adaptive neural network-based path tracking control is proposed, which considers both parameter uncertainties and input saturation. As far as we know, this is the first time a path tracking controller is specifically designed for the combine harvester with full consideration of working characteristics.
Robotic milling of complex NURBS surface with fixed cutter axis control method
Authors: Z.Q. Wang , X.Q. Liu , X.R. Wang , C.Y. Li , N. Yang , T.S. Lin , P. He
Published: May 2021

Purpose

This papers aims to provide a fixed cutter axis control (F-CAC) industrial robot (IR) milling for NURBS surfaces with large fluctuation, which can avoid over-cut and interference during IR milling in contrast to variable cutter axis control (V-CAC) IR milling.

Design/methodology/approach

After the design of a target surface, the IR reciprocating milling trajectory can be obtained using NURBS mapping projection method. A set of interpolation points of the reciprocating trajectory can be calculated using the equi-chord interpolation method. Combining with F-CAC method and curvature estimation, the IR reciprocating trajectory of the tool center point (TCP) without over-cut can be obtained. The programs corresponding to posture control using F-CAC can be generated by IR kinematics.

Findings

In contrast to the V-CAC milling method, the F-CAC method can machine successfully the NURBS surfaces with large fluctuation. The simulation and machining proves that F-CAC is feasible and effective to machine NURBS surface with large fluctuation without over-cut phenomenon. The F-CAC has wide application in carving and woodworking industry at present.

Originality/value

The F-CAC method is very practical and effective for IR milling of complex NURBS surfaces with large fluctuation without over-cut and interference phenomenon.