bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phospholipid peroxidation fuels ExoU phospholipase-dependent cell necrosis and supportsPseudomonas aeruginosa-driven pathology
Authors: Bagayoko Salimata , Icaza Stephen Leon , Pinilla Miriam , Hessel Audrey , Santoni Karin , Bordignon Pierre-Jean , Moreau Flavie , Eren Elif , Boyancé Aurélien , Naser Emmanuelle , Lefèvre Lise , Berrone Céline , Iakobachvili Nino , Metais Arnaud , Rombouts Yoann , Coste Agnès , Attrée Ina , Frank Dara W. , Clevers Hans , Peters Peter J. , Cougoule Céline , Planès Rémi , Meunier Etienne 
Published: February 2021

SummaryRegulated cell necrosis supports immune and anti-infectious strategies of the body; however, dysregulation of these processes drives pathological organ damage.Pseudomonas aeruginosaexpresses a phospholipase, ExoU that triggers pathological host cell necrosis through a poorly characterized pathway. Here, we investigated the molecular and cellular mechanisms of ExoU-mediated necrosis. We show that cellular peroxidised phospholipids enhance ExoU phospholipase activity, which drives necrosis of immune and non-immune cells. Conversely, both the endogenous lipid peroxidation regulator GPX4 and the pharmacological inhibition of lipid peroxidation delay ExoU-dependent cell necrosis and improve bacterial eliminationin vitroandin vivo. Our findings also pertain to the ExoU-related phospholipase from the bacterial pathogenBurkholderia thailandensis, suggesting that exploitation of peroxidised phospholipids might be a conserved virulence mechanism among various microbial phospholipases. Overall, our results identify an original lipid peroxidation-based virulence mechanism as a strong contributor of microbial phospholipase-driven pathology.
Skillful prediction of tropical Pacific fisheries provided by Atlantic Niños
Authors: Gómara Iñigo , Rodríguez-Fonseca Belén , Mohino Elsa , Losada Teresa , Polo Irene , Coll Marta 
Published: February 2021

AbstractTropical Pacific upwelling-dependent ecosystems are the most productive and variable worldwide, mainly due to the influence of El Niño Southern Oscillation (ENSO). ENSO can be forecasted seasons ahead thanks to assorted climate precursors (local-Pacific processes, pantropical interactions). However, owing to observational data scarcity and bias-related issues in earth system models, little is known about the importance of these precursors for marine ecosystem prediction. With recently released reanalysis-nudged global marine ecosystem simulations, these constraints can be sidestepped, allowing full examination of tropical Pacific ecosystem predictability. By complementing historical fishing records with marine ecosystem model data, we show herein that equatorial Atlantic Sea Surface Temperatures (SSTs) constitute a superlative predictability source for tropical Pacific marine yields, which can be forecasted over large-scale areas up to 2 years in advance. A detailed physical-biological mechanism is proposed whereby Atlantic SSTs modulate upwelling of nutrient-rich waters in the tropical Pacific, leading to a bottom-up propagation of the climate-related signal across the marine food web. Our results represent historical and near-future climate conditions and provide a useful springboard for implementing a marine ecosystem prediction system in the tropical Pacific.
Evidences for functional trans-acting eRNA-promoter R-loops at Alu sequences
Authors: Bai Xue , Li Feifei , Zhang Zhihua 
Published: February 2021

AbstractEnhancers modulate gene expression by interacting with promoters. Models of enhancer-promoter interactions (EPIs) in the literature involve the activity of many components, including transcription factors and nucleic acid. However, the role that sequence similarity plays in EPIs, remains largely unexplored. Herein, we report that Alu-derived sequences dominate sequence similarity between enhancers and promoters. After rejecting the alternative DNA:DNA and DNA:RNA triplex models, we proposed that enhancer-associated RNAs, or eRNAs, may directly contact their targeted promoters by forming trans-acting R-loops at those Alu sequences. We showed how the characteristic distribution of functional genomic data, such as RNA-DNA proximate ligation reads, binding of transcription factors, and RNA-binding proteins, align with the Alu sequences of EPIs. We also showed that these aligned Alu sequences may be subject to the constraint of coevolution, further implying the functional significance of these R-loop hybrids. Finally, our results showed that eRNA and Alu elements associate in a manner previously unrecognized in the EPIs and the evolution of gene regulation networks in mammals.
Gene expression profiling of skeletal muscles
Authors: Alto Sarah I. , Chang Chih-Ning , Brown Kevin , Kioussi Chrissa , Filtz Theresa M. 
Published: February 2021

AbstractSoleus and tibialis anterior are two well-characterized skeletal muscles commonly utilized in skeletal muscle-related studies. Next-generation sequencing provides an opportunity for an in-depth biocomputational analysis to identify the gene expression patterns between soleus and tibialis anterior and analyze those genes’ functions based on past literature. This study acquired the gene expression profiles from soleus and tibialis anterior murine skeletal muscle biopsies via RNA-sequencing. Read counts were processed through edgeR’s differential gene expression analysis. Differentially expressed genes were filtered down using a false discovery rate less than 0.05c, a fold-change value larger than twenty, and an association with overrepresented pathways based on the Reactome pathway over-representation analysis tool. Most of the differentially expressed genes associated with soleus encoded for components of lipid metabolism and unique contractile elements. Differentially expressed genes associated with tibialis anterior encoded mostly for glucose and glycogen metabolic pathways’ regulatory enzymes and calcium-sensitive contractile components. These gene expression distinctions partly explain the genetic basis for muscle specialization and may help to explain skeletal muscle susceptibility to disease and drugs and refine tissue engineering approaches.
Soil respiration variation along an altitudinal gradient in Italian Alps: Disentangling forest structure and temperature effects
Authors: Badraghi Aysan , Ventura Maurizio , Polo Andrea , Borruso Luigimaria , Montagnani Leonardo 
Published: February 2021

AbstractTo understand the main determinants of soil respiration (SR), we investigated the changes of soil respiration and soil physicochemical properties, including soil carbon (C) and nitrogen (N), root C and N, litter C and N, soil bulk densities and soil pH at five forest sites, along an elevation/temperature gradient (404 to 2101 m a.s.l) in Northern Italy, where confounding factors such as aspect and soil parent material are minimized, but an ample variation in forest structure and composition is present. Our result indicated that SR rates increased with temperature in all sites, and about 55% - 76% of SR was explained by temperature. Annual cumulative SR, ranging between 0.65 and 1.40 kg C m-2yr-1, declined along the elevation gradient, while temperature sensitivity (Q10) of SR increased with elevation. However, a high SR rate (1.27 kg C m-2yr-1) and low Q10 were recorded in the old conifer forest stand at 1731 m a.s.l., characterized by a complex structure and high productivity, introducing nonlinearity in the relations with elevation and temperature. Reference SR at the temperature of 10°C (SRref) was not related to elevation. A significant linear negative relationship was found for bulk density with elevation. On the contrary, soil C, soil N, root C, root N, pH and litter mass were better fitted by nonlinear relations with elevation. However, it was not possible to confirm a significant correlation of SR with these parameters once the effect of temperature has been removed (SRref). These results show how the main factor affecting SR in forest ecosystems along this Alpine elevation gradient is temperature, but its regulating role can be strongly influenced by site biological characteristics, particularly vegetation type and structure. This study also confirms that high elevation sites are rich in C stored in the soil and also more sensitive to climate change, being prone to high carbon losses as CO2. Conversely, forest ecosystems with a complex structure, with high SRrefand moderate Q10, can be more resilient.
Stink bugAgonoscelisspp. (Heteroptera: Pentatomidae)-An Emerging Threat for Seed Production in Alfalfa Crop (Medicago sativaL.) and Their Successful Management
Authors: Karar Haider , Bashir Muhammad Amjad , Khaliq Abdul , Ali Muhammad Jaffar , Alajmi Reem Atalla , Metwally Dina M. 
Published: February 2021

AbstractForages are vital constituent for sustainable agriculture because they provide feed for animals that ultimately converted into human food. Alfalfa is one of the most important forages that has highest feeding value for livestock, and seed production of alfalfa seriously affected by several factors, but seed yield loss due to stink bug attack is more as compared to other factors. Studies were conducted to control stink bug by different insecticides at Fodder Research Institute, Sargodha, Punjab-Pakistan during 2016-17. The efficacy of ten insecticides viz., acephate, dimethoate, malathion, chlorpyriphos, bifenthrin, lambdacyhalothrin, deltamethrin, acetamiprid, imidacloprid and carbosulfan were tested against stink bug,Agonoscelisspp. (Heteroptera Pentatomidae) on alfalfa,Medicago sativaL. variety SGD-2002. The mortality of stink bug was recorded one, three, five, seven, ten and fifteen days after spray. Similarly the population of pollinators was recorded before and one, three and five days after spray. From this study it had been observed that acetamiprid (81.14 %) and acephate (80.65%) had the higest mortality of stink bug and proved to be the most effective insecticides against stink bug. By spray of insecticides the population of pollinators declined one day after spray, but it had been rehabilitated three days after spray. By chemical treatment against stink bug, seed yield increased from 28.05 Kg/acre (during last four year without chemical control of stink bug) to 116 Kg/acre in 2016-17 (with chemical control). From this study it has been concluded that chemicals can be used in integrated management program of alfalfa seed production.
Time Trend, Social Vulnerability, and Identification of Risk Areas for Tuberculosis in Brazil: an Ecological Study
Authors: de Paiva João Paulo Silva , Magalhães Mônica Avelar Figueiredo Mafra , Leal Thiago Cavalcanti , da Silva Leonardo Feitosa , da Silva Lucas Gomes , do Carmo Rodrigo Feliciano , de Souza Carlos Dornels Freire 
Published: February 2021

ABSTRACTINTRODUCTIONTuberculosis is one of the ten leading causes of death and the leading infectious cause worldwide. The disease represents a challenge to health systems around the world. In 2018, it is estimated that 10 million people were affected by tuberculosis, and approximately 1.5 million people died due to the disease worldwide, including 251,000 patients coinfected with HIV. In Brazil, the disease caused 4,490 deaths, with rate of 2.2 deaths per 100,000 inhabitants. The objective of this study was to analyze the time behavior, spatial distribution, and the effects of social vulnerability on the incidence of TB in Brazil during the period from 2001 to 2017.METHODSA spatial-temporal ecological study was conducted, including all new cases of tuberculosis registered in Brazil during the period from 2001 to 2017. The following variables were analyzed: incidence rate of tuberculosis, the Social Vulnerability Index, its subindices, its 16 indicators, and an additional 14 variables available on the Atlas of Social Vulnerability. The statistical treatment of the data consisted of the following three stages: a) time trend analysis with a joinpoint regression model; b) spatial analysis and identification of risk areas based on smoothing of the incidence rate by local empirical Bayesian model, application of global and local Moran statistics, and, finally, spatial-temporal scan statistics; and c) analysis of association between the incidence rate and the indicators of social vulnerability.RESULTSBrazil reduced the incidence of tuberculosis from 42.8 per 100,000 to 35.2 per 100,000 between 2001 and 2017. Only the state of Minas Gerais showed an increasing trend, whereas nine other states showed a stationary trend. A total of 326 Brazilian municipalities were classified as high priority, and 22 high-risk spatial clusters were identified. The overall Social Vulnerability Index and the subindices of Human Capital and Income and Work were associated with the incidence of tuberculosis. It was also observed that the incidence rates were greater in municipalities with greater social vulnerability.CONCLUSIONSThis study identified spatial clusters with high risk of TB in Brazil. A significant association was observed between the incidence rate of TB and the indices of social vulnerability.
A parasite’s paradise: Biotrophic species prevail oomycete community composition in tree canopies
Authors: Jauss Robin-Tobias , Walden Susanne , Fiore-Donno Anna Maria , Schaffer Stefan , Wolf Ronny , Feng Kai , Bonkowski Michael , Schlegel Martin 
Published: February 2021

AbstractOomycetes (Stramenopiles, Protista) are among the most severe plant pathogens, comprising species with a high economic and ecologic impact on forest ecosystems. Their diversity and community structures are well studied in terrestrial habitats, but tree canopies as huge and diverse habitats have been widely neglected. A recent study highlighted distinct oomycete communities in the canopy region compared to forest soils when taking oomycete abundances into account, in contrast to the homogeneity at the incidence level. It remains however unknown if this homogeneity also leads to a functional homogenisation among microhabitats. In this study, we supplemented functional traits to oomycete canopy and ground communities, which were determined over a time period of two years with a metabarcoding approach. Our results showed that even though most oomycetes occurred in all habitats, a strong discrepancy between the strata and correspondingly the distribution of oomycete lifestyles could be observed, which was constant over time. Obligate biotrophic species, exclusively feeding on living host tissue, dominated the canopy region, implying tree canopies to be a hitherto neglected reservoir for parasitic protists. Parasites highly specialised on hosts that were not sampled could be determined in high abundances in the canopy and the surrounding air, challenging the strict host dependencies ruled for some oomycetes. Our findings further contribute to the understanding of oomycete ecosystem functioning in forest ecosystems.
Stony Coral Tissue Loss Disease biomarker bacteria identified in corals and overlying waters using a rapid field-based sequencing approach
Authors: Becker Cynthia C. , Brandt Marilyn , Miller Carolyn A. , Apprill Amy 
Published: February 2021

AbstractStony Coral Tissue Loss Disease (SCTLD) is a devastating disease. Since 2014, it has spread along the entire Florida Reef Tract, presumably via a water-borne vector, and into the greater Caribbean. It was first detected in the United States Virgin Islands (USVI) in January 2019. To more quickly identify disease biomarker microbes, we developed a rapid pipeline for microbiome sequencing. Over a span of 10 days we collected, processed, and sequenced coral tissue and near-coral seawater microbiomes from diseased and apparently healthyColpophyllia natans,Montastraea cavernosa,Meandrina meandritesandOrbicella franksi. Analysis of the resulting bacterial and archaeal 16S ribosomal RNA sequences revealed 25 biomarker amplicon sequence variants (ASVs) enriched in diseased tissue. These biomarker ASVs were additionally recovered in near-coral seawater (within 5 cm of coral surface), a potential recruitment zone for pathogens. Phylogenetic analysis of the biomarker ASVs belonging toVibrio, Arcobacter,Rhizobiaceae, and Rhodobacteraceae revealed relatedness to other coral disease-associated bacteria and lineages novel to corals. Additionally, four ASVs (Algicola,Cohaesibacter,ThalassobiusandVibrio) were exact sequence matches to microbes previously associated with SCTLD. This work represents the first rapid coral disease sequencing effort and identifies biomarkers of SCTLD that could be targets for future SCTLD research.
Multiple Sites on SARS-CoV-2 Spike Protein are Susceptible to Proteolysis by Cathepsins B, K, L, S, and V
Authors: Bollavaram Keval , Leeman Tiffanie H. , Lee Maggie W. , Kulkarni Akhil , Upshaw Sophia G. , Yang Jiabei , Song Hannah , Platt Manu O. 
Published: February 2021

AbstractSARS-CoV-2 is the coronavirus responsible for the COVID-19 pandemic. Proteases are central to the infection process of SARS-CoV-2. Cleavage of the spike protein on the virus’s capsid causes the conformational change that leads to membrane fusion and viral entry into the target cell. Since inhibition of one protease, even the dominant protease like TMPRSS2, may not be sufficient to block SARS-CoV-2 entry into cells, other proteases that may play an activating role and hydrolyze the spike protein must be identified. We identified amino acid sequences in all regions of spike protein, including the S1/S2 region critical for activation and viral entry, that are susceptible to cleavage by furin and cathepsins B, K, L, S, and V using PACMANS, a computational platform that identifies and ranks preferred sites of proteolytic cleavage on substrates, and verified with molecular docking analysis and immunoblotting to determine if binding of these proteases can occur on the spike protein that were identified as possible cleavage sites. Together, this study highlights cathepsins B, K, L, S, and V for consideration in SARS-CoV-2 infection and presents methodologies by which other proteases can be screened to determine a role in viral entry. This highlights additional proteases to be considered in COVID-19 studies, particularly regarding exacerbated damage in inflammatory preconditions where these proteases are generally upregulated.
A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features
Authors: Fatihi Saman , Rathore Surabhi , Pathak Ankit K. , Gahlot Deepanshi , Mukerji Mitali , Jatana Nidhi , Thukral Lipi 
Published: February 2021

AbstractThe recent release of SARS-CoV-2 genomic data from several countries has provided clues into the potential antigenic drift of the coronavirus population. In particular, the genomic instability observed in the spike protein necessitates immediate action and further exploration in the context of viralhost interactions. By temporally tracking 527,988 SARS-CoV-2 genomes, we identified invariant and hypervariable regions within the spike protein. We evaluated combination of mutations from SARS-CoV-2 lineages and found that maximum number of lineage-defining mutations were present in the N-terminal domain (NTD). Based on mutant 3D-structural models of known Variants of Concern (VOCs), we found that structural properties such as accessibility, secondary structural type, and intra-protein interactions at local mutation sites are greatly altered. Further, we observed significant differences between intra-protein networks of wild-type and Delta mutant, with the latter showing dense intra-protein contacts. Extensive molecular dynamics simulations of D614G mutant spike structure with hACE2 further revealed dynamic features with 47.7% of mutations mapping on flexible regions of spike protein. Thus, we propose that significant changes within spike protein structure have occurred that may impact SARS-CoV-2 pathogenesis, and repositioning of vaccine candidates is required to contain the spread of COVID-19 pathogen.
Climate change shifts abiotic niche of temperate skates towards deeper zones in the Southwestern Atlantic Ocean
Authors: Coelho Jéssica Fernanda Ramos , Lima Sergio Maia Queiroz , Petean Flávia de Figueiredo 
Published: February 2021

ABSTRACTClimatic changes are disrupting distribution patterns of populations through shifts in species abiotic niches and habitat loss. The abiotic niche of marine benthic taxa such as skates, however, may be more climatically stable compared to upper layers of the water column, in which aquatic organisms are more exposed to immediate impacts of warming. Here, we estimate climate change impacts in Riorajini, a tribe of four skates, as a proxy to (1) evaluate the vulnerability of a temperate coastal zone in the Atlantic Southwest, and (2) study niche dynamics in a scenario of environmental changes on this group of threatened species. We modelled each species abiotic niche under present (2000–2014) and future (2100, Representative Concentration Pathway 8.5) climatic scenarios, then measured niche overlap, stability, expansion, and unfilling. Our results reveal an expansion of suitable environment for the occurrence of the tribe in up to 20% towards deeper areas (longitudinal shift), although still within the limits of the continental shelf. We discussed the downfalls of such shift to the species and to the local biota in newly invaded areas, and suggest that even deeper layers of marine temperate zones are vulnerable to dramatic environmental changes as a consequence of global warming.
Pak1 kinase controls cell shape through ribonucleoprotein granules
Authors: Magliozzi Joseph O. , Moseley James B. 
Published: February 2021

ABSTRACTFission yeast cells maintain a rod shape due to conserved signaling pathways that organize the cytoskeleton for polarized growth. We discovered a mechanism linking the conserved protein kinase Pak1 with cell shape through the RNA-binding protein Sts5. Pak1 (also called Shk1 and Orb2) prevents Sts5 association with P bodies by directly phosphorylating its intrinsically disordered region (IDR). Pak1 and the cell polarity kinase Orb6 both phosphorylate the Sts5 IDR but at distinct residues. Mutations preventing phosphorylation in the Sts5 IDR cause increased P body formation and defects in cell shape and polarity. Unexpectedly, when cells encounter glucose starvation, PKA signaling triggers Pak1 recruitment to stress granules with Sts5. Through retargeting experiments, we reveal that Pak1 localizes to stress granules to promote rapid dissolution of Sts5 upon glucose addition. Our work reveals a new role for Pak1 in regulating cell shape through ribonucleoprotein granules during normal and stressed growth conditions.
Association between land use and composition of amphibian species in temperate Brazilian forest remnants
Authors: dos Santos Roseli Coelho , Dalmolin Diego Anderson , Brum Diego , Veronez Mauricio Roberto , Lucas Elaine Maria , Tozetti Alexandro Marques 
Published: February 2021

AbstractWe evaluated the influence of landscape configuration on the diversity of anurans in Atlantic Forest remnants in southern Brazil. As natural habits provide better conditions for the survival of amphibians, we expected to find more diverse communities in areas with more forest cover. We sampled tadpoles in 28 breeding sites distributed in seven forest remnants. We recorded 22 anuran species and richness varied from 6 to 12 species between sites. Most of the recorded species were not forest specialists, except forBoana curupiandCrossodactylus schmidti. There was a significant overlap in the species composition between all remnants, and the Generalized Linear Mixed Model indicated that landscape use did not affect species richness. The PERMANOVA showed that forest and livestock farming explained the dissimilarity in the composition of the communities. One possible explanation for this is that the remnants are surrounded by a relatively well-preserved landscape, which offers favorable conditions for the maintenance of local populations and homogenizes species composition across the sampling sites. The lack of any strong association between tadpole species richness and land use suggests that anurans are primally affected by habitat characteristics that are detected only on a fine-scale analysis.