bluuebunny/crossref_metadata_2025_split huggingface dataset:
Are marine biodiversity hotspots still blackspots for barcoding?
Authors: Mugnai Francesco , Meglécz Emese ,   CoMBoMed group, Costantini Federica , Abbiati Marco , Bavestrello Giorgio , Bertasi Fabio , Bo Marzia , Capa María , Chenuil Anne , Colangelo Marina Antonia , De Clerck Olivier , Gutiérrez José Miguel , Lattanzi Loretta , Leduc Michèle , Martin Daniel , Matterson Kenan Oguz , Mikac Barbara , Plaisance Laetitia , Ponti Massimo , Riesgo Ana , Rossi Vincent , Turicchia Eva , Waeschenbach Andrea , Wangensteen Owen S 
Published: July 2021

AbstractMarine biodiversity underpins ecosystem health and societal well-being. Preservation of biodiversity hotspots is a global challenge. Molecular tools, like DNA barcoding and metabarcoding, hold great potential for biodiversity monitoring, possibly outperforming more traditional taxonomic methods. However, metabarcoding-based biodiversity assessments are limited by the availability of sequences in barcoding reference databases; a lack thereof results in high percentages of unassigned sequences. In this study we (i) present the current status of known vs. barcoded marine species at a global scale based on online taxonomic and genetic databases; and (ii) compare the current status with data from ten years ago. Then we analyzed occurrence data of marine animal species from five Large Marine Ecosystems (LMEs) classified as biodiversity hotspots, to identify any consistent disparities in COI barcoding coverage between geographic regions and at phylum level. Barcoding coverage varied among LMEs (from 36.8% to 62.4% COI-barcoded species) and phyla (from 4.8% to 74.7% COI-barcoded species), with Porifera, Bryozoa and Platyhelminthes being highly underrepresented, compared to Chordata, Arthropoda and Mollusca. We demonstrate that although barcoded marine species increased from 9.5% to 14.2% since the last assessment in 2011, about 15,000 (corresponding to 7.8% increase) new species were described from 2011 to 2021. The next ten years will thus be crucial to enroll concrete collaborative measures and long term initiatives (e.g., Horizon 2030, Ocean Decade) to populate barcoding libraries for the marine realm.
Experimental evolution of Vibrio cholerae: Identification of genes involved in motility in presence of polymyxin B
Authors: Giacomucci Sean , Vincent Antony T. , Duperthuy Marylise 
Published: July 2021

AbstractVibrio cholerae is the bacteria responsible for the cholera disease and a natural inhabitant of aquatic environments. Biofilm formation is important for human colonization and environmental survival. Motility is essential for adhesion and biofilm formation by V. cholerae. In a previous study, we showed that motility and biofilm formation are altered in the presence of sub-inhibitory concentrations of polymyxin B in V. cholerae. In this study, we performed an experimental evolution to identify genes rescuing the motility in the presence of polymyxin B. Mutations in 5 genes have been identified: ihfA, vacJ (mlaA), mlaF, dacB and ccmH. The details of these mutations, their potential impact on the function of the proteins they encode and on the motility in presence of polymyxin B are discussed.
Novel strains ofKlebsiella africanaandKlebsiella pneumoniaein Australian Fruit Bats (Pteropus poliocephalus)
Authors: McDougall Fiona K. , Wyres Kelly L. , Judd Louise M. , Boardman Wayne S.J. , Holt Kathryn E. , Power Michelle L. 
Published: July 2021

AbstractOver the past decade human associated multidrug resistant (MDR) and hypervirulentKlebsiella pneumoniaelineages have been increasingly detected in wildlife. This study investigated the occurrence ofK. pneumoniaespecies complex (KpSC) in grey-headed flying foxes (GHFF), an Australian fruit bat. Thirty-nine KpSC isolates were cultured from 275 GHFF faecal samples (14.2%), comprisingK. pneumoniae(sensu stricto) (n=30),Klebsiella africana(n=8) andKlebsiella variicolasubsp.variicola(n=1). The majority (79.5%) of isolates belonged to novel sequence types (ST), including two novelK. africanaSTs. This is the first report ofK. africanaoutside of Africa and in a non-human host. A minority (15.4%) of GHFF KpSC isolates shared STs with human clinicalK. pneumoniaestrains, of which, none belonged to MDR clonal lineages that cause frequent nosocomial outbreaks, and no isolates were characterised as hypervirulent. The occurrence of KpSC isolates carrying acquired antimicrobial resistance genes in GHFF was low (1.1%), with threeK. pneumoniaeisolates harbouring both fluoroquinolone and trimethoprim resistance genes. This study indicates that GHFF are not reservoirs for MDR and hypervirulent KpSC strains, but they do carry novelK. africanalineages. The health risks associated with KpSC carriage by GHFF are deemed low for the public and GHFF.
Chemoproteomic profiling reveals cellular targets of nitro-fatty acids
Authors: Fang Mingyu , Huang Kuan Hsun , Tu Wei-Ju , Chen Yi-Ting , Pan Pei-Yun , Hsiao Wan-Chi , Ke Yi-Yu , Tsou Lun K. , Zhang Mingzi M. 
Published: July 2021

AbstractNitro-fatty acids are a class of endogenous electrophilic lipid mediators with anti-inflammatory and cytoprotective effects in a wide range of inflammatory and fibrotic disease models. While these beneficial biological effects of nitro-fatty acids are mainly attributed to their ability to form covalent adducts with proteins, only a small number of proteins are known to be nitro-alkylated and the scope of protein nitro-alkylation remains undetermined. Here we describe the synthesis and application of a clickable nitro-fatty acid probe for the detection and first global identification of mammalian proteins that are susceptible to nitro-alkylation. 184 high confidence nitro-alkylated proteins were identified in human macrophages, majority of which are novel targets of nitro-fatty acids, including Extended synaptotagmin 2 (ESYT2), Signal transducer and activator of transcription 3 (STAT3), Toll-like receptor 2 (TLR2), Retinoid X receptor alpha (RXRα) and Glucocorticoid receptor (NR3C1). In particular, we showed that 9-nitro-oleate covalently modified and inhibited dexamethasone binding to NR3C1. Bioinformatic analyses revealed that nitro-alkylated proteins are highly enriched in endoplasmic reticulum and transmembrane proteins, and are overrepresented in lipid metabolism and transport pathways. This study significantly expands the scope of protein substrates targeted by nitro-fatty acids in living cells and provides a useful resource towards understanding the pleiotropic biological roles of nitro-fatty acids as signaling molecules or as multi-target therapeutic agents.
The transcription factor Xrp1 orchestrates both reduced translation and cell competition upon defective ribosome assembly or function
Authors: Kiparaki Marianthi , Khan Chaitali , Marco Virginia Folgado , Chuen Jacky , Baker Nicholas E. 
Published: July 2021

ABSTRACTRibosomal Protein (Rp) gene haploinsufficiency affects overall translation rate, leads to cell elimination by competition with wild type cells in mosaic tissues, and sometimes leads to accumulation of protein aggregates. The changes in ribosomal subunit levels observed are not sufficient for these effects, which all depend on the AT-hook, bZip domain protein Xrp1. In Rp+/− cells, Xrp1 reduced global translation through PERK-dependent phosphorylation of eIF2α. eIF2α phosphorylation was sufficient to reduce translation in, and also enable cell competition of, otherwise wild type cells. Unexpectedly, however, many other defects reducing ribosome biogenesis or function (depletion of TAF1B, eIF2, eIF4G, eIF6, eEF2, eEF1α1, or eIF5A), also increased eIF2α phosphorylation and enabled cell competition. In all cases this was through the Xrp1 expression that was induced, placing Xrp1 as the downstream instigator of cell competition that also contributed to overall translation deficits. In the absence of Xrp1, translation differences between cells were not themselves sufficient to trigger cell competition. Thus, Xrp1, which is shown here to be a sequence-specific transcription factor, is the master regulator that triggers cell competition and other consequences of multiple ribosomal stresses.
Cellular remodeling and JAK inhibition promote zygotic gene expression in theCionagermline
Authors: Ohta Naoyuki , Christiaen Lionel 
Published: July 2021

AbstractDuring development, remodeling of the cellular transcriptome and proteome underlies cell fate decisions and, in somatic lineages, transcription control is a major determinant of fateful biomolecular transitions. By contrast, early germline fate specification in numerous vertebrate and invertebrate species relies extensively on RNA-level regulation, exerted on asymmetrically inherited maternal supplies, with little-to-no zygotic transcription. However delayed, a maternal-to-zygotic transition is nevertheless poised to complete the deployment of pre-gametic programs in the germline. Here, we focused on early germline specification in the tunicateCionato study zygotic genome activation. We first demonstrate that a peculiar cellular remodeling event excludes localized postplasmic mRNAs, includingPem-1, which encodes the general inhibitor of transcription. Subsequently, zygotic transcription begins inPem-1-negative primordial germ cells (PGCs), as revealed by histochemical detection of elongating RNA Polymerase II (RNAPII), and nascent transcripts from theMef2locus. Using PGC-specificMef2transcription as a read-out, we uncovered a provisional antagonism between JAK and MEK/BMPRI/GSK3 signaling, which controls the onset of zygotic gene expression, following cellular remodeling of PGCs. We propose a 2-step model for the onset of zygotic transcription in theCionagermline, which relies on successive cellular remodeling and JAK inhibition, and discuss the significance of germ plasm dislocation and remodeling in the context of developmental fate specification.
Proteome-wide quantitative RNA interactome capture (qRIC) identifies phosphorylation sites with regulatory potential in RBM20
Authors: Vieira-Vieira Carlos Henrique , Dauksaite Vita , Gotthardt Michael , Selbach Matthias 
Published: July 2021

SummaryRNA-binding proteins (RBPs) are major regulators of gene expression at the post-transcriptional level. While many posttranslational modification sites in RBPs have been identified, little is known about how these modifications regulate RBP function. Here, we developed quantitative RNA-interactome capture (qRIC) to quantify the fraction of cellular RBPs pulled down with polyadenylated mRNAs. Applying qRIC to HEK293T cells quantified pull-down efficiencies of over 300 RBPs. Combining qRIC with phosphoproteomics allowed us to systematically compare pull-down efficiencies of phosphorylated and non-phosphorylated forms of RBPs. Over hundred phosphorylation events increased or decreased pull-down efficiency compared to the unmodified RBPs and thus have regulatory potential. Our data captures known regulatory phosphorylation sites in ELAVL1, SF3B1 and UPF1 and identifies new potentially regulatory sites. Follow-up experiments on the cardiac splicing regulator RBM20 revealed that multiple phosphorylation sites in the C-terminal disordered region affect nucleo-cytoplasmic localization, association with cytosolic RNA granules and alternative splicing. Together, we show that qRIC is a scalable method to identify functional posttranslational modification sites in RBPs.HighlightsqRIC globally quantifies the fraction of RNA-binding proteins pulled down with mRNACombining qRIC with phosphoproteomics identifies sites that affect RNA bindingPhosphorylation sites in RBM20 regulate its function in splicing
How fragile we are. Influence of STimulator of INterferon Genes, STING, variants on pathogen recognition and immune response efficiency
Authors: Morere Jeremy , Hognon Cécilia , Miclot Tom , Jiang Tao , Dumont Elise , Barone Giampaolo , Bignon Emmanuelle , Monari Antonio 
Published: July 2021

AbstractThe STimulator of INterferon Genes (STING) protein is a cornerstone of the human immune response. Its activation by cGAMP upon the presence of cytosolic DNA stimulates the production of type I interferons and inflammatory cytokines which are crucial for protecting cells from infections. STING signaling pathway can also influence both tumor-suppressive and tumor-promoting mechanisms, rendering it an appealing target for drug design. In the human population, several STING variants exist and exhibit dramatic differences in their activity, impacting the efficiency of the host defense against infections. Understanding the differential molecular mechanisms exhibited by these variants is of utmost importance notably towards personalized medicine treatments against diseases such as viral infections (COVID-19, Dengue…), cancers, or auto-inflammatory diseases. Owing to micro-seconds scale molecular modeling simulations and post-processing by contacts analysis and Machine Learning techniques, we reveal the dynamical behavior of four STING variants (wild type, G230A, R293Q, and G230A-R293Q) and we rationalize the variability of efficiency observed experimentally. Our results show that the decrease of STING activity is linked to a stiffening of key-structural features of the binding cavity, together with changes of the interaction patterns within the protein.
Single-nucleus sequencing reveals enriched expression of genetic risk factors in Extratelencephalic Neurons sensitive to degeneration in ALS
Authors: Limone Francesco , Mordes Daniel A. , Couto Alexander , Joseph Brian J. , Mitchell Jana M. , Therrien Martine , Ghosh Sulagna Dia , Meyer Daniel , Zhang Yingying , Goldman Melissa , Bortolin Laura , Cobos Inma , Kadiu Irena , McCarroll Steven A. , Stevens Beth , Pietiläinen Olli , Burberry Aaron , Eggan Kevin 
Published: July 2021

Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disorder characterised by a progressive loss of motor function. The eponymous spinal sclerosis observed at autopsy is the result of the degeneration of extratelencephalic neurons, Betz cells (ETNs, Cortico-Spinal Motor Neuron). It remains unclear why this neuronal subtype is selectively affected. To understand the unique molecular properties that sensitise these cells to ALS, we performed RNA sequencing of 79,169 single nuclei from cortices of patients and controls. In unaffected individuals, we found that expression of ALS risk genes was significantly enriched inTHY1+-ETNs and not in other cell types. In patients, these genetic risk factors, as well as genes involved in protein homeostasis and stress responses, were significantly induced in a wide collection of ETNs, but not in neurons with more superficial identities. Examination of oligodendroglial and microglial nuclei revealed patient-specific changes that were at least in part a response to alterations in neurons: downregulation of myelinating genes in oligodendrocytes and upregulation of a reactive state connected to endo-lysosomal pathways in microglia. Our findings suggest that the selective vulnerability of extratelencephalic neurons is partly connected to their intrinsic molecular properties sensitising them to genetics and mechanisms of degeneration.Graphical abstract and working modelOur study highlights cell type specific changes in premotor/motor cortex of sporadic ALS patients. Specifically, we identify upregulation of synaptic molecules in excitatory neurons of upper cortical layers, interestingly correlating to hyperexcitability phenotypes seen in patients. Moreover, excitatory neurons of the deeper layers of the cortex, that project to the spinal cord and are most affected by the disease, show higher levels of cellular stresses than other neuronal types. Correspondently, oligodendrocytes transition from a highly myelinating state to a more neuronally engaged state, probably to counteract stressed phenotypes seen in excitatory neurons. At the same time, microglia show a reactive state with specific upregulation of endo-lysosomal pathways.
Zic1 advances epaxial myotome morphogenesis to cover the neural tube via Wnt11r
Authors: Heilig Ann Kathrin , Nakamura Ryohei , Shimada Atsuko , Hashimoto Yuka , Nakamura Yuta , Wittbrodt Joachim , Takeda Hiroyuki , Kawanishi Toru 
Published: July 2021

AbstractThe dorsal axial muscles, or epaxial muscles, are a fundamental structure covering the spinal cord and vertebrae, as well as mobilizing the vertebrate trunk. To date, mechanisms underlying the morphogenetic process shaping the epaxial myotome are largely unknown. To address this, we used the medaka zic1/zic4-enhancer mutant Double anal fin (Da), which exhibits ventralized dorsal trunk structures resulting in impaired epaxial myotome morphology and incomplete coverage over the neural tube. In wild type, dorsal dermomyotome (DM) cells, progenitors of myotomal cells, reduce their proliferative activity after somitogenesis and subsequently form unique large protrusions extending dorsally, potentially guiding the epaxial myotome dorsally. In Da, by contrast, DM cells maintain the high proliferative activity and form mainly small protrusions. By combining RNA- and ChIP-sequencing analyses, we revealed direct targets of Zic1 which are specifically expressed in dorsal somites and involved in various aspects of development, such as cell migration, extracellular matrix organization and cell-cell communication. Among these, we identified wnt11r as a crucial factor regulating both cell proliferation and protrusive activity of DM cells. We propose that the dorsal movement of the epaxial myotome is guided by DM cells and that Zic1 empowers this activity via Wnt11r to achieve the neural tube coverage.
A comparison of wild and captive Comal Springs riffle beetle (Heterelmis comalensis) microbiomes
Authors: Mays Zachary , Hunter Amelia , Campbell Lindsay Glass , Carlos-Shanley Camila 
Published: July 2021

AbstractThe gut microbiome is affected by host intrinsic factors, diet, environment, and strongly linked to host’s health. Although fluctuations of microbiome composition are normal, some are due to changes in host environmental conditions. When species are moved into captive environments for conservation, education, or rehabilitation, these new conditions can influence a change in gut microbiome composition. Here, we compared the microbiomes of wild and captive Comal Springs riffle beetles (Heterelmis comalensis) by using amplicon sequencing of the 16S rRNA gene. We found that the microbiome of captive beetles was more diverse than wild beetle microbiomes. We identified 24 Amplicon Sequence Variants (ASVs) with relative abundances significantly different between the wild and captive beetles. Many of the ASVs overrepresented in captive beetle microbiomes belong to taxa linked to nitrogen-rich environments. This is one of the first studies comparing the effects of captivity on the microbiome of an endangered insect species. Our findings provide valuable information for future applications in the management of captive populations of H. comalensis.
The autonomous side of EO and firm performance: the role of professional experience and entrepreneurial engagement
Authors: Tufa Tesfaye Leta , Belete Aselefech Hailgiorgis , Patel Ashwinkumar A. 
Published: July 2021

PurposeThe purpose of this study is to investigate the direct and indirect role of autonomy on firm performance. It also determines the role of professional experience in the relationship.Design/methodology/approachThe authors analyzed data collected from 124 small firms in Addis Ababa city using the ordinary least square (OLS) regression and hierarchical regression analysis.FindingsThe result of the OLS regression revealed that autonomy directly and indirectly (through entrepreneurial engagement) influences the firm's performance. Besides, professional experience moderates the relationship between autonomy and performance, as well as the relationship between autonomy and entrepreneurial engagement.Practical implicationsEntrepreneurs should tend to engage in the works that they have professional experience than involving in jobs that they have no experience.Originality/valueThis study examines the relationship between autonomy and firm performance in established firms. It is among the first studies that tested the moderation influence in the relationship. That is, determining the role of professional experience is a novel contribution of this study, which is forgotten previously.
Some fixed-point theorems for a general class of mappings in modular G-metric spaces
Authors: Okeke Godwin Amechi , Francis Daniel 
Published: July 2021

PurposeThis paper aims to prove some fixed-point theorems for a general class of mappings in modular G-metric spaces. The results of this paper generalize and extend several known results to modular G-metric spaces, including the results of Mutluet al.[1]. Furthermore, the authors produce an example to demonstrate the applicability of the results.Design/methodology/approachThe results of this paper are theoretical and analytical in nature.FindingsThe authors established some fixed-point theorems for a general class of mappings in modular G-metric spaces. The results generalize and extend several known results to modular G-metric spaces, including the results of Mutluet al. [1]. An example was constructed to demonstrate the applicability of the results.Research limitations/implicationsAnalytical and theoretical results.Practical implicationsThe results of this paper can be applied in science and engineering.Social implicationsThe results of this paper is applicable in certain social sciences.Originality/valueThe results of this paper are new and will open up new areas of research in mathematical sciences.
Surface wave scattering analysis in an initially stressed stratified media
Authors: Mandi Anand , Kundu Santimoy , Pal Prakash Chandra 
Published: July 2021

Design/methodology/approach
The present discussed problem deals with the torsional surface wave scattering in an initially stressed inhomogeneous medium. The assumed model consists of tri-mediums resting over a viscoelastic semi-infinite medium and the considered tri-mediums are transversely isotropic, porous, and heterogeneous respectively under the impression of initial stress.

Design/methodology/approach
Heterogeneities are associated with density and rigidity in the intermediate layer and considered heterogeneities are of the trigonometric form. Displacement components are derived for mediums by applying separable variables.

Findings
Frequency equation is deduced by using suitable boundary conditions, defined at the free surface of the uppermost medium, and on the interfaces between mediums. The derived equation is of the complex form, real and imaginary parts direct the phase/damped velocities respectively. Additional results are considered in particular cases. Numerical examples are adopted for computing frequency equation and drawn consequences are demonstrated graphically to analyze the significant impact of various parameters on the phase velocity as well as on damped velocity of the surface wave sketched against the wavenumber.

Originality/Value
This presented research work provides a different view over the analysis of torsional surface waves than the earlier investigations. Previously studied problems on the wave generation were conducted in different models under the various affecting parameters. Study on torsional wave generation in the present model is not carried out till now. This study may find its virtue in the theoretical aspect as well as in the possible practical implications. The outcomes are relevant to geology and allied areas; moreover, the concern applications may be implicated in geological exploration, civil engineering, and prediction of Earthquake etc.