bluuebunny/crossref_metadata_2025_split huggingface dataset:
The herpes simplex virus type I deamidase enhances propagation but is dispensable for retrograde axonal transport into the nervous system
Authors: Stults Austin M. , Smith Gregory A. 
Published: July 2019

ABSTRACTUpon replication in mucosal epithelia and transmission to nerve endings, capsids of herpes simplex virus type I (HSV-1) travel retrograde within axons to peripheral ganglia where life-long latent infections are established. A capsid-bound tegument protein, pUL37, is an essential effector of retrograde axonal transport and also houses a deamidase activity that antagonizes innate immune signaling. In this report, we examined whether the deamidase of HSV-1 pUL37 contributes to the neuroinvasive retrograde axonal transport mechanism. We conclude that neuroinvasion is enhanced by the deamidase, but the critical contribution of pUL37 to retrograde axonal transport functions independently of this activity.IMPORTANCEHerpes simplex virus type 1 invades the nervous system by entering nerve endings and sustaining long-distance retrograde axonal transport to reach neuronal nuclei in ganglia of the peripheral nervous system. The incoming viral particle carries a deamidase activity on its surface that antagonizes antiviral responses. We examined the contribution of the deamidase to the hallmark neuroinvasive property of this virus.
Effects of long-term warming and enhanced nitrogen and sulfur deposition on microbial communities in a boreal peatland
Authors: Martí Magalí , Eiler Alexander , Buck Moritz , Bertilsson Stefan , Al-Soud Waleed Abu , Sørensen Søren , Nilsson Mats B. , Svensson Bo H. 
Published: July 2019

AbstractWith ongoing environmental change, it is important to understand ecosystem responses to multiple perturbations over long time scales atin situconditions. Here, we investigated the individual and combined effects of 18 years of warming and enhanced nitrogen and sulfate deposition on peat microbial communities in a nutrient-poor boreal mire. The three perturbations individually affected prokaryotic community composition, where nitrogen addition had the most pronounced effect, and its combination with the other perturbations led to additive effects. The functional potential of the community, characterized by shotgun metagenomics, was strongly affected by the interactive effects in the combined treatments. The responses in composition were also partly reflected in the functional gene repertoire and in altered carbon turnover, i.e. an increase of methane production rates as a result of nitrogen addition and a decrease with warming. Long-term nitrogen addition and warming-induced changes caused a shift fromSphagnum-dominated plant communities to vascular plant dominance, which likely transact with many of the observed microbial responses. We conclude that simultaneous perturbations do not always lead to synergistic effects, but can also counteract and even neutralize one another, and thus must be studied in combination when attempting to predict future characteristics and services of peatland ecosystems.
Identification of hidden population structure in time-scaled phylogenies
Authors: Volz Erik M. , Wiuf Carsten , Grad Yonatan H. , Frost Simon D.W. , Dennis Ann M. , Didelot Xavier 
Published: July 2019

AbstractPopulation structure influences genealogical patterns, however data pertaining to how populations are structured are often unavailable or not directly observable. Inference of population structure is highly important in molecular epidemiology where pathogen phylogenetics is increasingly used to infer transmission patterns and detect outbreaks. Discrepancies between observed and idealised genealogies, such as those generated by the coalescent process, can be quantified, and where significant differences occur, may reveal the action of natural selection, host population structure, or other demographic and epidemiological heterogeneities. We have developed a fast non-parametric statistical test for detection of cryptic population structure in time-scaled phylogenetic trees. The test is based on contrasting estimated phylogenies with the theoretically expected phylodynamic ordering of common ancestors in two clades within a coalescent framework. These statistical tests have also motivated the development of algorithms which can be used to quickly screen a phylogenetic tree for clades which are likely to share a distinct demographic or epidemiological history. Epidemiological applications include identification of outbreaks in vulnerable host populations or rapid expansion of genotypes with a fitness advantage. To demonstrate the utility of these methods for outbreak detection, we applied the new methods to large phylogenies reconstructed from thousands of HIV-1 partialpolsequences. This revealed the presence of clades which had grown rapidly in the recent past, and was significantly concentrated in young men, suggesting recent and rapid transmission in that group. Furthermore, to demonstrate the utility of these methods for the study of antimicrobial resistance, we applied the new methods to a large phylogeny reconstructed from whole genomeNeisseria gonorrhoeaesequences. We find that population structure detected using these methods closely overlaps with the appearance and expansion of mutations conferring antimicrobial resistance.
Highly efficient transgenesis withminiMosinCaenorhabditis briggsae
Authors: Ding Qiutao , Ren Xiaoliang , Li Runsheng , Chan Luyan , Ho Vincy WS , Bi Yu , Xie Dongying , Zhao Zhongying 
Published: July 2019

AbstractC. briggsaeas a companion species forC. eleganshas played an increasingly important role in study of evolution of development, gene regulation and genome. Aided by the isolation of its sister spices, it has recently been established as a model for speciation study. To take full advantage of the species for comparative study, an effective transgenesis method especially those with single copy insertion is important for functional comparison. Here we modified a transposon-based transgenesis methodology that had been originally developed inC. elegansbut worked marginally inC. briggsae. By incorporation of a heat shock step, the transgenesis efficiency inC. briggsaewith single copy insertion is comparable to that inC. elegans. We used the method to generate 54 independent insertions mostly consisting of a mCherry tag over theC. briggsaegenome. We demonstrated the use of the tags in identifying interacting loci responsible for hybrid male sterility betweenC. briggsaeandC. nigoniwhen combined with the GFP tags we generated previously. Finally, we demonstrated thatC. briggsaehas developed native immunity against theC. eleganstoxin, PEEL-1, but not SUP-35, making the latter a potential negative selection marker against extrachromosomal array.SummaryNematodeC. briggsaehas been used for comparative study againstC. elegansover decades. Importantly, a sister species has recently been identified, with whichC. briggsaeis able to mate and produce viable hybrid progeny. This opens the possibility of using nematode species as a model for speciation study for the first time. To take full advantage ofC. briggsaefor comparative study, an effective transgenesis method to generate single copy insertion is important especially for functional comparison. An attempt was made previously to generate single copy insertion with transposon-based transgenesis methodology, which had been originally developed inC. elegansbut with limited success inC. briggsae. Here we modified the transposon-based methodology by incorporation of a heat shock step, which allows us to achieve a much higher transgenesis efficiency inC. briggsaewith single copy insertion. We used the method to generate 54 independent insertions mostly consisting of a mCherry tag over theC. briggsaegenome. We demonstrated the use of the tags in identifying interacting loci responsible for hybrid male sterility betweenC. briggsaeandC. nigoniwhen combined with the GFP tags we generated previously. Finally, we demonstrated thatC. briggsaehas developed native immunity against theC. eleganstoxin, PEEL-1, but not SUP-35, making the latter a potential negative selection marker against extrachromosomal array. Taken together, the modified transgenesis methodology and the transgenic strains generated in this study are expected to further facilitateC. briggsaeas a model for comparative study or speciation study.
Haldane’s Probability of Mutant Survival is Not the Probability of Allele Establishment
Authors: Krukov Ivan , de Koning A.P. Jason 
Published: July 2019

ABSTRACTHaldane notably showed in 1927 that the probability of fixation for an advantageous allele is approximately 2s, for selective advantages. This widely known result is variously interpreted as either the fixation probability or the establishment probability, where the latter is considered the likelihood that an allele will survive long enough to have effectively escaped loss by drift. While Haldane was concerned with escape from loss by drift in the same paper, in this short note we point out that: 1) Haldane’s ‘probability of survival’ is analogous to the probability of fixation in a Wright-Fisher model (as also shown by others); and 2) This result is unrelated to Haldane’s consideration of how common an allele must be to ‘probably spread through the species’. We speculate that Haldane’s survival probability may have become misunderstood over time due to a conflation of terminology about surviving drift and ‘ultimately surviving’ (i.e., fixing). Indeed, we find that the probability of establishment remarkably appears to have been overlooked all these years, perhaps as a consequence of this misunderstanding. Using straightforward diffusion and Markov chain methods, we show that under Haldane’s assumptions, where establishment is defined by eventual fixation being more likely that extinction, the establishment probability is actually 4swhen the fixation probability is 2s. Generalizing consideration to deleterious, neutral, and adaptive alleles in finite populations, if establishment is defined by the odds ratio between eventual fixation and extinction,k, the general establishment probability is (1 +k)/ktimes the fixation probability. It is therefore 4swhenk= 1, or 3swhenk= 2 for beneficial alleles in large populations. Askis made large, establishment becomes indistinguishable from fixation, and ceases to be a useful concept. As a result, we recommend establishment be generally defined as when the odds of ultimate fixation are greater than for extinction (k= 1, following Haldane), or when fixation is twice as likely as extinction (k= 2).
Relevance of genomic evaluation for egg quality traits in layers
Authors: Picard Druet David , Varenne Amandine , Herry Florian , Hérault Frédéric , Allais Sophie , Burlot Thierry , Le Roy Pascale 
Published: July 2019

AbstractBackgroundGenomic evaluation, based on thousands of genetic markers, has become the standard evaluation methodology in dairy cattle breeding programs over the past few years. Despite the many differences between dairy cattle breeding and poultry breeding, genomic selection seems very promising for the avian sector, and studies are currently being conducted to optimize avian selection schemes. In this optimization perspective, one of the key parameters is to properly predict the accuracy of genomic evaluation in pure line layers.MethodsBoth genetic evaluation and genomic evaluation were performed on three candidate populations (male and female), using different sizes of phenotypic records on five egg quality traits and at two different ages. The methodologies used were BLUP & ssGBLUP, and variance-covariance matrices were estimated through REML. To estimate evaluation accuracy, the LR method was implemented. Four statistics were used to assess the relative accuracy of the estimated breeding values of candidates, their bias and dispersion, as well as the differences between genetic evaluation and genomic evaluation.ResultsIt was observed that genomic evaluation, whether performed on males or females, always proved more accurate than genetic evaluation. The gain was higher when phenotypic information was narrowed and an augmentation of the size of the reference population led to an increase in accuracy prediction, for what regards genomic evaluation. By taking into account the increase of selection intensity and the decrease of the generation interval induced by genomic selection, the expected annual genetic gain would be higher with ancestry-based genomic evaluation of male candidates than with genetic evaluation based on collaterals. This advantage of genomic selection over genetic selection requires to be studied in more details for female candidates.ConclusionsIn conclusion, in the population studied, genomic evaluation for egg quality traits of breeding birds at birth seems a promising strategy, at least for what regards males selection.
Protein interactions of Magnaporthe oryzae protein kinase CK2 and secondary data analysis of a large number of transcriptomes suggest chaperone-like activity is integral to its function
Authors: Zhang Lianhu , Zhang Dongmei , Liu Dan , Li Yuan , Li Hongchen , Wang Zonghua , Hansen Bjoern Oest , Olsson Stefan 
Published: July 2019

ABSTRACTCK2, a serine/threonine (S/T) kinase present in eukaryotic cells is known to have a vast number of substrates. We have recently shown that it localizes to nuclei and at pores between hyphal compartments in M. oryzae. We performed a pulldown-proteomics of M. oryzae CK2 catalytic subunit MoCKa to detect interacting proteins. The MoCKa pulldown was enriched for septa and nucleoli proteins and intrinsically disordered proteins (IDPs) containing a CK2 phosphorylation motif proposed to destabilize and unfold alpha helixes. This points to a function for CK2 phosphorylation and corresponding phosphatase dephosphorylation in the formation of functional protein-protein aggregates and protein-RNA/DNA binding. To test this as widely as possible we used secondary data downloaded from databases from a large range of M. oryzae experiments and also for a relatively closely related plant pathogenic fungus, Fusarium graminearum. We found that CKa expression was strongly positively correlated with S/T phosphatases as well as with disaggregase (HSP104, YDJ1, SSA1) and an autophagy indicating protein (ATG8). The latter points to increased protein aggregate formation at high levels of CKa expression. Our results suggest a general role for CK2 in aggregation and disaggregation of IDPs and their binding to proteins, DNA and RNA interactions.
Late Embryogenesis Abundant (LEA) proteins confer water stress tolerance to mammalian somatic cells
Authors: Czernik M , Fidanza A , Luongo FP , Valbonetti L , Scapolo PA , Patrizio P , Loi P 
Published: July 2019

AbstractLate Embryogenesis Abundant (LEA) proteins are commonly found in organisms capable of undergoing reversible dehydration - “anhydrobiosis”. Here, we have produced three LEA proteins: pTag-RAB17-GFP-N,Zea maysdehydrin-1dhn, expressed in the nucleo-cytoplasm; pTag-WCOR410-RFP,Tricum aestivumcold acclimation proteinWCOR410, binding to cellular membranes, and pTag-LEA-BFP,Artemia franciscanaLEA protein group 3 that targets the mitochondria. Somatic cells transfected with three LEA proteins were subjected to desiccation under controlled conditions, followed by rehydration, viability assessment and membrane/mitochondria functional tests were performed. Results shown that LEA protect cells from desiccation injury. Cells expressed all LEA proteins shown very high percentage of viable cells (58%) after four hour of desiccation compare to un-transfected cells (1% cell alive). Plasmalemma, cytoskeleton and mitochondria appeared unaffected in LEA-expressing cells, confirming their protective action during the entire desiccation and rehydration process. Here, we show that natural xeroprotectants (LEA proteins) transiently expressed in somatic cells confer them desiccation tolerance.
N-cadherin stabilises neural identity by dampening anti-neural signals
Authors: Punovuori K , Migueles RP , Malaguti M , Blin G , Macleod KG , Carragher NO , Pieters T , van Roy F , Stemmler MP , Lowell S 
Published: July 2019

AbstractA switch from E-to N-cadherin regulates the transition from pluripotency to neural identity but the mechanism by which cadherins regulate differentiation was previously unknown. Here we show that the acquisition of N-cadherin stabilises neural identity by dampening anti-neural signals. We use quantitative image-analysis to identify an effect of N-cadherin to promote neural differentiation independently of effects on cell cohesiveness. We reveal that cadherin switching diminishes the level of nuclear β-catenin, and that N-cadherin also dampens FGF activity and consequently stabilises neural fate. Finally, we compare the timing of cadherin switching and differentiationin vivoandin vitro, and find that this process becomes dysregulated duringin vitrodifferentiation. We propose that N-cadherin helps to propagate a stable neural identity throughout the emerging neuroepithelium, and that dysregulation of this process contributes to asynchronous differentiation in culture.
The tricellular vertex-specific adhesion molecule Sidekick facilitates polarised cell intercalation duringDrosophilaaxis extension
Authors: Finegan Tara M. , Hervieux Nathan , Nestor-Bergmann Alexander , Fletcher Alexander G. , Blanchard Guy B. , Sanson Bénédicte 
Published: July 2019

ABSTRACTIn epithelia, tricellular vertices are emerging as important sites for the regulation of epithelial integrity and function. Compared to bicellular contacts, however, much less knowledge is available. In particular, resident proteins at tricellular vertices were identified only at occluding junctions, with none known at adherens junctions. In a previous study, we discovered that inDrosophilaembryos, the adhesion molecule Sidekick (Sdk), well known in invertebrates and vertebrates for its role in the visual system, localises at tricellular vertices at the level of adherens junctions. Here, we survey a wide range ofDrosophilaepithelia and establish that Sdk is a resident protein at tricellular adherens junctions, the first of its kind. Clonal analysis suggests that pair-wise homophilic adhesion is necessary and sufficient for Sdk tricellular vertex localisation. Super-resolution imaging using structured illumination reveals that Sdk proteins form string-like structures at vertices. Postulating that Sdk may have a role in epithelia where adherens junctions are actively remodelled, we analysed the phenotype ofsdknull mutant embryos duringDrosophilaaxis extension, using quantitative methods. We find that apical cell shapes are strikingly abnormal insdkmutants. Moreover, adhesion at apical vertices is compromised in rearranging cells, with holes forming and persisting throughout axis extension. Finally, we show that polarized cell intercalation is decreased and abnormal insdkmutants. Mathematical modeling of the cell behaviours supports the conclusion that the T1 transitions of polarized cell intercalation are delayed insdkmutants. We propose that this delay, in combination with a change in the mechanical properties of the converging and extending tissue, causes the striking cell shape phenotype ofsdkmutant embryos.
Determinants of behavioral intentions towards a professional certification scheme at European level
Authors: Ruiz-Molina Maria-Eugenia , Gil-Saura Irene , Berenguer-Contri Gloria , Auch Christoph 
Published: July 2019

PurposeThe purpose of this paper is to analyze the effect of candidates’ perceptions of the attributes of a professional certification scheme based on competences, as well as personal factors, that may influence in the behavioral intentions toward such certification program, i.e. intention to participate in the certification process and willingness to pay for the certificate.Design/methodology/approachBased on a survey of 2,630 professionals about the “Certified Professional” program in eight European countries, the influence of the perceived attributes of the certification program and the personal characteristics of the potential candidates on their behavioral intentions are analyzed.FindingsDifficulty and fairness of the certification process, credibility, innovativeness, international recognition and future usefulness of the professional certificate influence positively on the candidate’s likelihood of applying for being certified and the willingness to pay. Young professionals not holding a university diploma show high probability to participate in the certification process and intention to pay for the certificate.Practical implicationsPromotional efforts to launch a professional certification scheme should concentrate in creating strong associations of the certificate with the notions of international prestige, credibility and usefulness to enhance employability and professional growth. Segmentation criteria to increase communication effectiveness are defined.Originality/valueIn recent years, there has been a proliferation of professional certification programs in competences, and literature has advocated the need to investigate the perceived value of such systems in terms of benefits and barriers perceived by potential applicants for accreditation. The present paper aims at addressing this research gap.
Women's career interruptions: an integrative review
Authors: Bian Xinyi , Wang Jia 
Published: July 2019

Purpose
The purpose of this integrative literature review was three-fold: to explore the phenomenon of women’s career interruptions as revealed by publications in the past two decades, to propose a new career decision tree model (CDTM) and to outline an agenda for future research.

Design/methodology/approach
The authors adopted the integrative literature review approach proposed by Torraco (2005, 2016) and used a mind mapping application called MindMeister to synthesize 64 identified articles.

Findings
The proposed CDTM can assist those who are interested in exploring individuals’ career decisions to think systematically about career influencers at different levels.

Originality/value
The CDTM is significantly different from existing career models and theories in that it explains women’s career interruptions in a context-sensitive manner. This model can assist human resource development professionals in analyzing the influencers of women’s career decisions and tackling individual problems level by level.
Determinants of peer-to-peer rental rating scores: the case of Airbnb
Authors: Zhu Liang , Cheng Mingming , Wong IpKin Anthony 
Published: July 2019

Purpose
This study aims to identify the key determinants of Airbnb rating scores.

Design/methodology/approach
This study is based on a sample of 127,257 listings across 43 cities. A total of 24 explanatory variables were identified, and they were further grouped into host verification information, communication, policy of renting, space, information about environment, price and experience of hosting. Both Tobit and ordered logit models were used to perform the analysis.

Findings
The results indicate that good communication, large space and provision of information about the listings’ environment have a positive effect on users’ satisfaction, whereas experience of hosting negatively influences users’ satisfaction.

Originality/value
This study contributes to the peer-to-peer accommodation literature by affording a more complete understanding about guest satisfaction and its determinants.