bluuebunny/crossref_metadata_2025_split huggingface dataset:
The cIAP ubiquitin ligases sustain type 3 γδ T and innate lymphoid cells during aging to allow normal cutaneous and mucosal responses
Authors: Rizk John , Mörbe Urs M. , Agerholm Rasmus , Ulmert Isabel , Tardos Elisa Catafal , Kadekar Darshana , Baglioni Maria V. , Viñals Monica Torrellas , Bekiaris Vasileios 
Published: May 2020

AbstractEnvironmental and molecular cues early in life are often associated with the permanent shaping of our immune system during adulthood. Although increasing, our knowledge of the signaling pathways that operate in early life and their temporal mode of action is limited. Herein, we demonstrate that the cellular inhibitor of apoptosis proteins 1 and 2 (cIAP1/2), which are E3 ubiquitin ligases and master regulators of the nuclear factor-kappa B (NF-κB) pathway, function during late neonatal and prepubescent life to sustain interleukin(IL)-17-producing gamma delta T cells (γδT17) and group 3 innate lymphoid cells (ILC3). We show that cell-intrinsic deficiency in cIAP1/2 at 3-4 weeks of life leads to downregulation of the transcription factors cMAF and RORγt, and failure to enter cytokine-induced cell cycle. This is followed by progressive loss of γδT17 cells and ILC3 while mice are aging. Mice deficient in cIAP1/2 have severely reduced γδT17 cells and ILC3, present with suboptimal γδT17 responses in the skin, lack small intestinal isolated lymphoid follicles and cannot control intestinal bacterial infection. Mechanistically, these effects appear to be dependent on overt activation of the non-canonical NF-κB pathway. Our data identify the cIAP E3 ubiquitin ligases as critical early life molecular switches for establishing effective type-3 immunity during aging.
Identification of conserved epitopes in SARS-CoV-2 spike and nucleocapsid protein
Authors: Forcelloni Sergio , Benedetti Anna , Dilucca Maddalena , Giansanti Andrea 
Published: May 2020

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which first occurred in Wuhan (China) in December 2019, is a novel virus that causes a severe acute respiratory disease. The virus spike glycoproteins and nucleocapsid proteins are the main targets for the development of vaccines and antiviral drugs, to control the disease spread. We herein study the structural order-disorder propensity and the rates of evolution of these two proteins to characterize their B cell and T cell epitopes, previously suggested to contribute to immune response caused by SARS-CoV-2 infections. We first analyzed the rates of evolution along the sequences of spike and nucleocapsid proteins in relation to the spatial locations of their epitopes. For this purpose, we compared orthologs from seven human coronaviruses: SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1. We then focus on the local, structural order-disorder propensities of the protein regions where the SARS-CoV-2 epitopes are located. We show that the vast majority of nucleocapsid protein epitopes overlap the RNA-binding and dimerization domains and some of them are characterized by low rates of evolutions. Similarly, spike protein epitopes are preferentially located in regions that are predicted to be ordered and well-conserved, in correspondence of the heptad repeats 1 and 2. Interestingly, both the receptor-binding motif to ACE2 and the fusion peptide of spike protein are characterized by high rates of evolution, probably to overcome host immunity. In conclusion, our results provide evidence for conserved epitopes that may help to develop long-lasting, broad-spectrum SARS-CoV-2 vaccines.
Identification ofAvramr1fromPhytophthora infestansusing long read and cDNA pathogen-enrichment sequencing (PenSeq)
Authors: Lin Xiao , Song Tianqiao , Fairhead Sebastian , Witek Kamil , Jouet Agathe , Jupe Florian , Witek Agnieszka I. , Karki Hari S. , Vleeshouwers Vivianne G. A. A. , Hein Ingo , Jones Jonathan D. G. 
Published: May 2020

SummaryPotato late blight, caused by the oomycete pathogenPhytophthora infestans, significantly hampers potato production. Recently, a newResistance to Phytophthora infestans(Rpi) gene,Rpi-amr1, was cloned from a wildSolanumspecies,Solanum americanum. Identification of the corresponding recognized effector (Avirulence, orAvr)genes fromP. infestansis key to elucidating their naturally occurring sequence variation, which in turn informs the potential durability of the cognate late blight resistance.To identify theP. infestanseffector recognized byRpi-amr1, we screened available effector libraries and used long read and cDNA pathogen-enrichment sequencing (PenSeq) on fourP. infestansisolates to explore the untested effectors.By using SMRT and cDNA PenSeq, we identified 47 highly expressed effectors fromP. infestans, including PITG_07569 which triggers a highly specific cell death response when transiently co-expressed withRpi-amr1inNicotiana benthamiana, suggesting thatPITG_07569isAvramr1.Here we demonstrate that long read and cDNA PenSeq enables the identification of full-length RxLR effector families, and their expression profile. This study has revealed key insights into the evolution and polymorphism of a complex RxLR effector family that is associated with the recognition byRpi-amr1.
Intraflagellar transport during the assembly of flagella of different length inTrypanosoma bruceiisolated from tsetse flies
Authors: Bertiaux Eloïse , Mallet Adeline , Rotureau Brice , Bastin Philippe 
Published: May 2020

AbstractMulticellular organisms assemble cilia and flagella of precise lengths differing from one cell to another, yet little is known about the mechanisms governing these differences. Similarly, protists assemble flagella of different lengths according to the stage of their life cycle. This is the case ofTrypanosoma bruceithat assembles flagella of 3 to 30 µm during its development in the tsetse fly. It provides an opportunity to examine how cells naturally modulate organelle length. Flagella are constructed by addition of new blocks at their distal end via intraflagellar transport (IFT). Immunofluorescence assays, 3-D electron microscopy and live cell imaging revealed that IFT was present in all life cycle stages. IFT proteins are concentrated at the base, IFT trains are located along doublets 3-4 & 7-8 and travel bidirectionally in the flagellum. Quantitative analysis demonstrated that the total amount of IFT proteins correlates with the length of the flagellum. Surprisingly, the shortest flagellum exhibited a supplementary large amount of dynamic IFT material at its distal end. The contribution of IFT and other factors to the regulation of flagellum length is discussed.Summary statementThis work investigated the assembly of flagella of different length during the development ofTrypanosoma bruceiin the tsetse fly, revealing a direct correlation between the amount of intraflagellar transport proteins and flagellum length.
A role for glutathione in buffering excess intracellular copper inStreptococcus pyogenes
Authors: Stewart Louisa J. , Ong Cheryl-lynn Y. , Zhang May M. , Brouwer Stephan , McIntyre Liam , Davies Mark R. , Walker Mark J. , McEwan Alastair G. , Waldron Kevin J. , Djoko Karrera Y. 
Published: May 2020

ABSTRACTCopper (Cu) is an essential metal for bacterial physiology but in excess it is bacteriotoxic. To limit Cu levels in the cytoplasm, most bacteria possess a transcriptionally-responsive system for Cu export. In the Gram-positive human pathogenStreptococcus pyogenes(Group AStreptococcus, GAS), this system is encoded by thecopYAZoperon. In this study, we demonstrate that the site of GAS infectionin vivorepresents a Cu-rich environment but inactivation of thecopACu efflux gene does not reduce virulence in a mouse model of invasive disease.In vitro, Cu treatment leads to multiple observable phenotypes, including defects in growth and viability, decreased fermentation, inhibition of glyceraldehyde 3-phosphate dehydrogenase (GapA) activity, and misregulation of metal homeostasis, likely as a consequence of mismetalation of non-cognate metal-binding sites. Surprisingly, the onset of these effects is delayed by ∼4 h even though expression ofcopZis upregulated immediately upon exposure to Cu. We further show that the onset of all phenotypes coincides with depletion of intracellular glutathione (GSH). Supplementation with extracellular GSH replenishes the intracellular pool of this thiol and suppresses all the observable effects of Cu treatment. Our results indicate that GSH contributes to buffering of excess intracellular Cu when the transcriptionally-responsive Cu export system is overwhelmed. Thus, while thecopYAZoperon is responsible for Cuhomeostasis, GSH has a role in Cutolerancethat allows bacteria to maintain metabolism even in the presence of an excess of this metal ion. This study advances fundamental understanding of Cu handling in the bacterial cytoplasm.IMPORTANCEThe control of intracellular metal availability is fundamental to bacterial physiology. In the case of copper (Cu), it is established that rising intracellular Cu levels eventually fill the metal-sensing site of the endogenous Cu-sensing transcriptional regulator, which in turn induces transcription of a copper export pump. This response caps intracellular Cu availability below a well-defined threshold and prevents Cu toxicity. Glutathione, abundant in many bacteria, is known to bind Cu and is long assumed to contribute to bacterial Cu handling. However, there is some ambiguity since neither its biosynthesis nor uptake is Cu-regulated. Furthermore, there is little experimental support for this role of glutathione beyond measurement of the effect of Cu on growth of glutathione-deficient mutants. Our work with Group AStreptococcusprovides new evidence that glutathione increases the threshold of intracellular Cu availability that can be tolerated by bacteria and thus advances fundamental understanding of bacterial Cu handling.
GATA-1-dependent histone H3K27ac mediates erythroid cell-specific interaction between CTCF sites
Authors: Kim Yea Woon , Kang Yujin , Kang Jin , Kim AeRi 
Published: May 2020

AbstractCTCF sites interact with each other in the chromatin environment, establishing domains. Our previous study showed that interaction between CTCF sites is cell type-specific around the β-globin locus and is dependent on erythroid specific activator GATA-1. To find out molecular mechanisms of the cell type-specific interaction, we directly inhibited GATA-1 binding to the β-globin enhancers by deleting its binding motifs and found that histone H3K27 acetylation (H3K27ac) was decreased at CTCF sites surrounding the β-globin locus, even though CTCF binding itself was maintained at the sites. Forced H3K27ac by TSA treatment or CBP/p300 KD affected the interactions between CTCF sites around the β-globin locus. Analysis of public ChIA-PET data revealed that H3K27ac is higher at CTCF sites forming short chromatin interactions than long interactions. The short interactions contain erythropoiesis-associated genes and GATA-1 binding sites in erythroid K562 cells. Depletion of GATA-1 reduced H3K27ac at CTCF sites near erythroid enhancers. These results indicate that GATA-1-dependent histone H3K27ac at neighboring CTCF sites mediates erythroid specific chromatin interaction between them.
Validation of suitable genes for normalization of diurnal gene expression studies inChenopodium quinoa
Authors: Maldonado-Taipe Nathaly , Sarange Dilan , Schmöckel Sandra , Jung Christian , Emrani Nazgol 
Published: May 2020

AbstractQuinoa depicts high nutritional quality and abiotic stress resistance attracting strong interest in the last years. To unravel the function of candidate genes for agronomically relevant traits, studying their transcriptional activities by RT-qPCR is an important experimental approach. The accuracy of such experiments strongly depends on precise data normalization. To date, validation of potential candidate genes for normalization of diurnal expression studies has not been performed inC. quinoa. We selected eight candidate genes based on transcriptome data and literature survey, including conventionally used reference genes. We used three statistical algorithms (BestKeeper, geNorm and NormFinder) to test their stability and added further validation by a simulation-based strategy. We demonstrated that using different reference genes, including those top ranked by stability, causes significant differences among the resulting diurnal expression patterns, and that our novel approach overcomes failures related to stability-based selection of reference genes. Our results show that isocitrate dehydrogenase enzyme (IDH-A) and polypyrimidine tract-binding protein (PTB) are suitable genes to normalize diurnal expression data of two different quinoa accessions. The validated reference genes obtained in this study will improve the accuracy of RT-qPCR data normalization and facilitate gene expression studies in quinoa.
Plasticity of the xylem vulnerability to embolism in poplar relies on quantitative pit properties rather than on pit structure
Authors: Lemaire Cédric , Quilichini Yann , Brunel-Michac Nicole , Santini Jérémie , Berti Liliane , Cartailler Julien , Conchon Pierre , Badel Éric , Herbette Stéphane 
Published: May 2020

AbstractKnowledge on variations of drought resistance traits are needed to predict the potential of trees to acclimate to coming severe drought events. Xylem vulnerability to embolism is a key parameter related to such droughts, and its phenotypic variability relies mainly on environmental plasticity. We investigated the structural determinants controlling the plasticity of vulnerability to embolism, focusing on the key elements involved in the air bubble entry in a vessel, especially the inter-vessel pits. Poplar saplings (Populus tremula x alba) grown in contrasted water availability or light exposure exhibited differences in vulnerability to embolism in a range of 0.76 MPa. We then characterized the structural changes related to qualitative and quantitative pit characteristics, from the pit structure to the organization of xylem vessels, using different microscopy techniques (TEM, SEM, light). X-ray microtomography analysis allowed observing the vessel vulnerability and testing some of the relationships between structural traits and vulnerability to embolism inside the xylem. The pit ultrastructure did not change, whereas the vessel dimensions increased with vulnerability to embolism and the grouping index and fraction of inter-vessel cell wall decreased with vulnerability to embolism. These findings holds when comparing trees or when comparing vessels inside the xylem. These results evidenced that plasticity of vulnerability to embolism occurs through changes in the quantitative pit properties such as pit area and vessel grouping rather than on the pit structure.
Functional Exploration of Heterotrimeric Kinesin-II in IFT and Ciliary Length Control inChlamydomonas
Authors: Li Shufen , Chen Wei , Wan Kirsty Y , Tao Hui , Liang Xin , Pan Junmin 
Published: May 2020

SUMMARYHeterotrimeric organization of kinesin-II is essential for its function in anterograde IFT in ciliogenesis. However, the molecular basis of forming this complex for its function is not well understood. In addition, the anterograde IFT velocity varies significantly in different organisms, but how motor speed affects ciliary length is not clear. We show thatChlamydomonaskinesin-II (CrKinesin-II) involves distinct mechanisms from mammals and C.elegansin its assembly to necessitate its function in IFT. Furthermore, chimeric CrKinesin-II with human kinesin-II motor domains functionedin vitroandin vivo, leading to a ~2.8-fold reduced anterograde IFT velocity and a similar fold reduction in IFT injection rate that supposedly correlates with ciliary assembly activity. However, the ciliary length was only mildly reduced (~15%). Modelling analyses suggest that such a non-linear scaling relationship between IFT velocity and ciliary length can be accounted for by limitation of the motors and/or its ciliary cargoes, e.g. tubulin.
The Ice Nucleating Protein InaZ is Activated by Low Temperature
Authors: Roeters Steven J. , Golbek Thaddeus W. , Bregnhøj Mikkel , Drace Taner , Alamdari Sarah , Roseboom Winfried , Kramer Gertjan , Šantl-Temkiv Tina , Finster Kai , Woutersen Sander , Pfaendtner Jim , Boesen Thomas , Weidner Tobias 
Published: May 2020

AbstractIce-nucleation active (INA) bacteria can promote the growth of ice more effectively than any other known material. Utilizing specialized ice-nucleating proteins (INPros), they obtain nutrients from plants by inducing frost damage and, when airborne in the atmosphere, they drive ice nucleation within clouds and may affect global precipitation patterns. Despite their evident environmental importance, the molecular mechanisms behind INPro-induced freezing have remained largely elusive. In the present study, we investigated the folding and the structural basis for interactions between water and the ice-nucleating protein InaZ from the INA bacteriumPseudomonas syringaestrain R10.79. Using vibrational sum-frequency generation and two-dimensional infrared spectroscopy, we demonstrate that the ice-active repeats of InaZ adopt a β-helical structure in solution and at water surfaces. In this configuration, hydrogen bonding between INPros and water molecules imposes structural ordering on the adjacent water network. The observed order of water increases as the interface is cooled to temperatures close to the melting point of water. Experimental SFG data combined with spectral calculations and molecular-dynamics simulations shows that the INPro reorients at lower temperatures. We suggest that the reorientation can enhance order-inducing water interactions and, thereby, the effectiveness of ice nucleation by InaZ.
Translocation of flexible and tensioned ssDNA throughin silicodesigned hydrophobic nanopores with two constrictions
Authors: Rattu Punam , Haynes Taylor , Wallace E. Jayne , Khalid Syma 
Published: May 2020

ABSTRACTProtein-inspired nanopores with hydrophobic constriction regions have previously been shown to offer some promise for DNA sequencing. Here we explore a series of pores with two hydrophobic constrictions. The impact of nanopore radius, the nature of residues that define the constriction region and the flexibility of the ssDNA is explored. Our results show that aromatic residues slow down DNA translocation, and in the case of short DNA strands, they cause deviations from a linear DNA conformation. When DNA is under tension, translocation is once again slower when aromatic residues are present in the constriction. However, the lack of flexibility in the DNA backbone provides a narrower window of opportunity for the DNA bases to be retained inside the pore via interaction with the aromatic residues, compared to more flexible strands. Consequently, there is more variability in translocation rates for strands under tension. DNA entry into the pores is correlated to pore width, but no such correlation between width and translocation rate is observed.
Thwarted enthusiasm: effects of workplace incivility on newcomer proactive behaviors
Authors: Lan Yuanyuan , Xia Yuhuan , Li Shuang , Wu Wen , Hui Jiaqi , Deng Hui 
Published: May 2020

PurposeThe purpose of this study is to explore the relationship between supervisor and coworkers’ workplace incivility and newcomer proactive behaviors. Drawing on conservation of resources (COR) theory, the authors examined resource depletion as a mediator and newcomer proactive personality, as well as their current organizational tenure as moderators of the relationship between workplace incivility toward newcomers and their proactive behaviors.Design/methodology/approachA time-lagged research design was used to test hypotheses with data covering 322 newcomers and their immediate supervisors in two subsidiaries of a large food processing company in China. Regression analysis using the PROCESS macro in SPSS is used to test the hypotheses.FindingsThe results show that workplace incivility toward newcomers is negatively related to their proactive behaviors. This relationship is mediated by resource depletion. Furthermore, newcomers’ proactive personality moderates the relationship between workplace incivility and resource depletion. Moreover, both the direct effect of workplace incivility on resource depletion and its indirect effect on newcomer proactive behaviors are moderated by the combination of newcomer proactive personality and their current organizational tenure.Originality/valueDrawing on COR theory, a theoretical framework is constructed that specifies the process through which workplace incivility affects proactive behaviors to expand collective understandings of workplace incivility in the newcomer context. Furthermore, the boundary conditions of the underlying process are investigated, which further enhances the contribution of this paper to the extant literature on workplace incivility.
Forest birds as diversity indicator in suburban and residential areas
Authors: Nelson Bryan Raveen , Mamat Mazrul Aswady , Cheeho Wong , Shahimi Salwa 
Published: May 2020

Purpose
Birds are biological indicators for environment health in which their sightings and abundance could reflect a certain situation or become evaluation tool for co-existence of another species. Here, the study aims to observe urban settlements with substantial forestation, may it be artificial or natural, and the occurrence of bird assemblage across time. Considering the foraging activity of birds hardcoded with sustainability, their spatial overlap resultant into service provision, which can mean, baseline occurrence or an expected encounter equates to support system for ecological vigour.

Design/methodology/approach
From this, birds could indicate external environment vulnerability related to climatic fluctuations, whereby documentation of their arrival across spatial-temporal regimes allowed us to understand their distribution between residential and forested areas.

Findings
Though urban birds are abundant and viewed less important for conservation, the existence of certain species such as long-tailed shrike and little green pigeon disclose the types of food they consume and, the other types of birds attracted to their prey. With regard, the sightings of these birds would mean an encounter with 20 or more other species at a bird watching occasion, though it is limited to the sightings of urban birds.

Originality/value
Subject to criteria for green space, attaining plenty of bird species provides understanding of food availability, the support services and opportunity for urban birds to thrive in midst the opportunity for resources such as food, perching grounds and sufficient numbers of counterparts to reproduce into healthy urban bird populations.