bluuebunny/crossref_metadata_2025_split huggingface dataset:
A spatially explicit and mechanistic model for exploring coral reef dynamics
Authors: Carturan Bruno S. , Maréchal Jean-Philippe , Bradshaw Corey J. A. , Pither Jason , Parrott Lael 
Published: April 2020

AbstractThe complexity of coral-reef ecosystems makes it challenging to predict their dynamics and resilience under future disturbance regimes. Models for coral-reef dynamics do not adequately accounts for the high functional diversity exhibited by corals. Models that are ecologically and mechanistically detailed are therefore required to simulate the ecological processes driving coral reef dynamics. Here we describe a novel model that includes processes at different spatial scales, and the contribution of species’ functional diversity to benthic-community dynamics. We calibrated and validated the model to reproduce observed dynamics using empirical data from Caribbean reefs. The model exhibits realistic community dynamics, and individual population dynamics are ecologically plausible. A global sensitivity analysis revealed that the number of larvae produced locally, and interaction-induced reductions in growth rate are the parameters with the largest influence on community dynamics. The model provides a platform for virtual experiments to explore diversity-functioning relationships in coral reefs.
Comprehensive transcriptome data of normal andAscosphaera apis-infected western honeybee larval guts
Authors: Du Yu , Wang Jie , Zhu Zhiwei , Jiang Haibin , Fan Xiaoxue , Fan Yuanchan , Zheng Yanzhen , Xiong Cuiling , Chen Dafu , Guo Rui 
Published: April 2020

ABSTRAmTApis mellifera ligusticais a well-known subspecies of western honeybee,Apis mellifera. Ascosphaera apisis a common fungal pathogen of honeybee larvae, resulting in Chalkbrood disease. In this article, deep sequencing of un-treated 4-, 5-, and 6-day-old larval guts (AmCK1, AmCK2, AmCK3) andA. apis-treated 4-, 5- and 6-day-old larval guts (AmT1, AmT2, AmT3) ofApis mellifera ligusticawere conducted using Illumina HiSeq™ 4000 platform. In total, 85811046, 81962296, 85636572, 79267686, 82889882, and 100211796 raw reads were respectively yielded from above-mentioned six groups. The result of sequencing satuation analysis suggested that the sequencing depth in this work was enough to detect nearly all expressed genes. After quality control, 85739414, 81896402, 85573798, 79202304, 82828926, and 100128692 clean reads were obtained. Additionally, the GC content of each group was above 45.26%. Furthermore, 47035852, 65612676, 71803878, 62560904, 65018360, and 56278272 clean reads were mapped to theApis melliferagenome, including 41221479, 61172916, 66724233, 57531335, 60245732, and 52638986 unique mapped clean reads, and 2078427, 986825, 915375, 1082925, 1097130, and 716436 multiple mapped clean reads. In addition, exons were the most abundant regions mapped by clean reads, follow by intergenic regions and introns. The strand-specific cDNA library-based RNA sequencing data documented here will faciliate study on molecualr mechanisms underlying host immune response and host-pathogen interaction during chalkbrood disease, and benefit understanding of non-coding RNA-mediated cross-kingdom regulation betweenA. m. ligusticalarvae andA. apis.Value of the DataThis data reported here could be used to explore circRNAs, lncRNAs, mRNAs and their competing endogenous RNA networks involved in response of western honeybee larvae toAscosphaera apisinfection.The current data contributes to better understanding mechanisms regulating host-pathogen interaction during chalkbrood disease.Our data can provide novel insights into understanding non-coding RNA-mediated cross-kingdom regulation betweenApis mellifera ligusticaandA. apis.
Anosmia and dysgeusia in patients with mild SARS-CoV-2 infection
Authors: Levinson Ruth , Elbaz Meital , Ben-Ami Ronen , Shasha David , levinson Tal , Choshen Guy , Petrov Ksenia , Gadoth Avi , Paran Yael 
Published: April 2020

AbstractIn this cohort of 42 patients with mild COVID19 we found a unique clinical feature of acute anosmia and dysgeusia in more than third of patients. Median onset of these features was 3.3 days after onset of illness (range 0-7) with rapid recovery in most patients.Article Summary LineAnosmia and dysgeusia appeared early in third of our patients with mild SARS-CoV-2 infection and were short-lived in most patients.
Western Ghats Myrtaceae are not Gondwana elements but likely dispersed from south-east Asia
Authors: Ray Rajasri , Chattopadhyay Balaji , Garg Kritika M , Ramachandra TV , Ray Avik 
Published: April 2020

AbstractGondwana break-up is one of the key sculptors of the global biogeographic pattern including Indian subcontinent. Myrtaceae, a Gondwana family, demonstrates a high diversity across Indian Western Ghats. A rich paleo-records in Deccan Intertrappean bed in India strive to reconcile two contending hypothesis of origin and diversification of Myrtaceae in India, namely Gondwana elements floated on peninsular India or lineages invading from south-east Asia. In this study, we have reconstructed the biogeographic history of Myrtaceae of Western Ghats of India combining fossil-calibrated phylogeny, ancestral area reconstruction, and comparing various dispersal models.Phylogenetic reconstructions divided lineages into multiple clades at the tribal level that mostly is in agreement with previous descriptions. Dated tree indicated a presumable Gondwanan origin of Myrtaceae (95.7 Ma). The Western Ghats taxa are relatively younger and seem to have arrived either through long-distance oceanic dispersal in middle Eocene (Rhodomyrtus tomentosa), and Miocene (Eugenia) or through major overland dispersals throughout Miocene (Syzygium). However, late Cretaceous fossilsin India lends support to the existence of proto-Myrtaceae on floating peninsular India. Taken together, we conclude that Myrtaceae lineages on the biotic ferry were perhaps extirpated by Deccan volcanism leaving a little or no trace of living Gondwanan link, while the Western Ghats was likely enriched by dispersed elements either from south-east Asia or from South America.
Environment-dependent behavioral traits and experiential factors shape addiction vulnerability
Authors: Fouyssac Maxime , Puaud Mickaël , Ducret Eric , Marti-Prats Lucia , Vanhille Nathalie , Ansquer Solène , Zhang Xinxuan , Belin-Rauscent Aude , Giuliano Chiara , Houeto Jean-Luc , Everitt Barry. J , Belin David 
Published: April 2020

AbstractThe transition from controlled drug use to drug addiction depends on an interaction between a vulnerable individual, their environment and a drug. Here we tested the hypothesis that conditions under which individuals live influence behavioral vulnerability traits and experiential factors operating in the drug taking environment to determine the vulnerability to addiction. The role of behavioural vulnerability traits in mediating the influence of housing conditions on the tendency to acquire cocaine self-administration was characterised in 48 rats housed in either an enriched (EE) or a standard (SE) environment. Then, the influence of these housing conditions on the individual vulnerability to develop addiction-like behaviour for cocaine or alcohol was measured in 72 EE or SE rats after several months of cocaine self-administration or intermittent alcohol drinking, respectively. The determining role of negative experiential factors in the drug taking context was further investigated in 48 SE rats that acquired alcohol drinking as a self-medication strategy. The environment influenced the acquisition of drug intake through its effect on behavioral markers of resilience to addiction. In contrast, the initiation of drug taking as a coping strategy or in a negative state occasioned by the contrast between enriched housing conditions and a relatively impoverished drug taking setting, facilitated the development of compulsive cocaine and alcohol intake. These data demonstrate that addiction vulnerability depends on environmentally determined experiential factors, suggesting that initiating drug use through negative reinforcement-based self-medication facilitates the development of addiction in vulnerable individuals.Significance StatementThe factors that underlie an individual’s vulnerability to switch from controlled, recreational drug use to addiction are not well understood. We showed that in individuals housed in enriched conditions, the experience of drugs in the relative social and sensory impoverishment of the drug taking context, and the associated change in behavioural traits of resilience to addiction, exacerbate the vulnerability to develop compulsive drug intake. We further demonstrated that the acquisition of alcohol drinking as a mechanism to cope with distress increases the vulnerability to develop compulsive alcohol intake. Together these results demonstrate that experiential factors in the drug taking context shape the vulnerability to addiction.
Cyclopamine sensitizes Glioblastoma cells to Temozolomide treatment through Sonic Hedgehog pathway
Authors: Carballo Gabriela Basile , Matias Diana , Honorato Jessica , Pessoa Luciana Santos , Arrais Neto Ananias Matos , de Sampaio e Spohr Tania Cristina Leite 
Published: April 2020

AbstractAimGlioblastoma is an extremely aggressive glioma, resistant to radio and chemotherapy usually performed with temozolomide. One of the main reasons for glioblastoma resistance to conventional therapies is due to the presence of cancer stem-like cells. These cells could recapitulate some signaling pathways important for embryonic development, such as Sonic hedgehog. Here, we investigated if the inhibitor of the Sonic hedgehog pathway, cyclopamine, could potentiate the temozolomide effect in cancer stem-like cells and glioblastoma cell linesin vitro.Main methodsThe viability of glioblastoma cells exposed to cyclopamine and temozolomide treatment was evaluated by using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay while the induction of apoptosis was assessed by western blot. The stemness properties of glioma cells were verified by clonogenic and differentiation assay and the expression of stem cell markers were measured by fluorescence microscopy and western blot.Key findingsThe glioblastoma viability was reduced by cyclopamine treatment. Cyclopamine potentiated temozolomide treatment in glioblastoma cell lines by inducing apoptosis through activation of caspase-3 cleaved. Conversely, the combined treatment of cyclopamine and temozolomide potentiated the stemness properties of glioblastoma cells by inducing the expression of SOX-2 and OCT-4.SignificanceCyclopamine plays an effect on glioblastoma cell lines but also sensibilize them to temozolomide treatment. Thus, first-line treatment with Sonic hedgehog inhibitor followed by temozolomide could be used as a new therapeutic strategy for glioblastoma patients.
A single dose of ChAdOx1 MERS provides broad protective immunity against a variety of MERS-CoV strains
Authors: van Doremalen Neeltje , Haddock Elaine , Feldmann Friederike , Meade-White Kimberly , Bushmaker Trenton , Fischer Robert J. , Okumura Atsushi , Hanley Patrick W. , Saturday Greg , Edwards Nick J. , Clark Madeleine H.A. , Lambe Teresa , Gilbert Sarah C. , Munster Vincent J. 
Published: April 2020

AbstractMiddle East respiratory syndrome coronavirus (MERS-CoV) continues to infect humans via the dromedary camel reservoir and can transmit between humans, most commonly via nosocomial transmission. Currently, no licensed vaccine is available. Previously we showed that vaccination of transgenic mice with ChAdOx1 MERS, encoding the MERS S protein, prevented disease upon lethal challenge. In the current study we show that rhesus macaques seroconverted rapidly after a single intramuscular vaccination with ChAdOx1 MERS. Upon MERS-CoV challenge vaccinated animals were protected against respiratory injury and pneumonia and had a reduction in viral load in lung tissue of several logs. Furthermore, we did not detect MERS-CoV replication in type I and II pneumocytes of ChAdOx1 MERS vaccinated animals. A prime-boost regimen of ChAdOx1 MERS boosted antibody titers, and viral replication was completely absent from the respiratory tract tissue of these rhesus macaques. Finally, we investigated the ability of ChAdOx1 MERS to protect against six different MERS-CoV strains, isolated between 2012 to 2018, from dromedary camels and humans in the Middle East and Africa. Antibodies elicited by ChAdOx1 MERS in rhesus macaques were able to neutralize all MERS-CoV strains. Vaccination of transgenic hDPP4 mice with ChAdOx1 MERS completely protected the animals against disease and lethality for all different MERS-CoV strains. The data support further clinical development of ChAdOx1 MERS supported by CEPI.One Sentence SummaryPrime-only vaccination with ChAdOx1 MERS provides protective immunity against HCoV-EMC/2012 replication in rhesus macaques, and a wide variety of MERS-CoV strains in mice.
FingerprintContacts: Predicting Alternative Conformations of Proteins from Coevolution
Authors: Feng Jiangyan , Shukla Diwakar 
Published: April 2020

AbstractProteins are dynamic molecules which perform diverse molecular functions by adopting different three-dimensional structures. Recent progress in residue-residue contacts prediction opens up new avenues for thede novoprotein structure prediction from sequence information. However, it is still difficult to predict more than one conformation from residue-residue contacts alone. This is due to the inability to deconvolve the complex signals of residue-residue contacts, i.e. spatial contacts relevant for protein folding, conformational diversity, and ligand binding. Here, we introduce a machine learning based method, called FingerprintContacts, for extending the capabilities of residue-residue contacts. This algorithm leverages the features of residue-residue contacts, that is, (1) a single conformation outperforms the others in the structural prediction using all the top ranking residue-residue contacts as structural constraints, and (2) conformation specific contacts rank lower and constitute a small fraction of residue-residue contacts. We demonstrate the capabilities of FingerprintContacts on eight ligand binding proteins with varying conformational motions. Furthermore, FingerprintContacts identifies small clusters of residue-residue contacts which are preferentially located in the dynamically fluctuating regions. With the rapid growth in protein sequence information, we expect FingerprintContacts to be a powerful first step in structural understanding of protein functional mechanisms.
Histone variants in archaea and the evolution of combinatorial chromatin complexity
Authors: Stevens Kathryn M , Swadling Jacob B , Hocher Antoine , Bang Corinna , Gribaldo Simonetta , Schmitz Ruth A , Warnecke Tobias 
Published: April 2020

ABSTRACTNucleosomes in eukaryotes act as platforms for the dynamic integration of epigenetic information. Post-translational modifications are reversibly added or removed and core histones exchanged for paralogous variants, in concert with changing demands on transcription and genome accessibility. Histones are also common in archaea. Their role in genome regulation, however, and the capacity of individual paralogs to assemble into histone-DNA complexes with distinct properties remain poorly understood. Here, we combine structural modelling with phylogenetic analysis to shed light on archaeal histone paralogs, their evolutionary history and capacity to generate complex combinatorial chromatin states through hetero-oligomeric assembly. Focusing on the human commensal Methanosphaera stadtmanae as a model archaeal system, we show that the heteromeric complexes that can be assembled from its seven histone paralogs vary substantially in DNA binding affinity and tetramer stability, occupying a large but densely populated chromatin state space. Using molecular dynamics simulations, we go on to identify unique paralogs in M. stadtmanae and Methanobrevibacter smithii that are characterized by unstable dimer:dimer interfaces. We propose that these paralogs act as capstones that prevent stable tetramer formation and extension into longer oligomers characteristic of model archaeal histones. Importantly, we provide evidence from phylogeny and genome architecture that these capstones, as well as other paralogs in the Methanobacteriales, have been maintained for hundreds of millions of years following ancient duplication events. Taken together, our findings indicate that at least some archaeal histone paralogs have evolved to play distinct and conserved functional roles, reminiscent of eukaryotic histone variants. We conclude that combinatorially complex histone-based chromatin is not restricted to eukaryotes and likely predates their emergence.
Intragenic conflict in phylogenomic datasets
Authors: Smith Stephen A. , Walker-Hale Nathanael , Walker Joseph F. 
Published: April 2020

AbstractMost phylogenetic analyses assume that a single evolutionary history underlies one gene. However, both biological processes and errors in dataset assembly can violate this assumption causing intragenic conflict. The extent to which this conflict is present in empirical datasets is not well documented. However, if common, it would have far-reaching implications for phylogenetic analyses. Here, we examined several large phylogenomic datasets from diverse taxa using a fast and simple method to identify well supported intragenic conflict. We found conflict to be highly variable between datasets, from 1% to more than 92% of genes investigated. To better characterize patterns of conflict, we analyzed four genes with no obvious data assembly errors in more detail. Analyses on simulated data highlighted that alignment error may be one major source of conflict. Whether as part of data analysis pipelines or in order to explore potential biologically compelling intragenic processes, analyses of within gene signal should become common. The method presented here provides a relatively fast means for identifying conflicts that is agnostic to the generating process. Datasets identified with high intragenic conflict may either have significant errors in dataset assembly or represent conflict generated by biological processes. Conflicts that are the result of error should be identified and discarded or corrected. For those conflicts that are the result of biological processes, these analyses contribute to the growing consensus that, similar to genomes, genes themselves may exhibit multiple conflicting evolutionary histories across the tree of life.
Zirconium(IV)-IMAC for phosphopeptide enrichment in phosphoproteomics
Authors: Diez Ignacio Arribas , Govender Ireshyn , Naicker Previn , Stoychev Stoyan , Jordaan Justin , Jensen Ole N. 
Published: April 2020

ABSTRACTPhosphopeptide enrichment is an essential step in large-scale, quantitative phosphoproteomics studies by mass spectrometry. Several phosphopeptide affinity enrichment techniques exist, such as Immobilized Metal ion Affinity Chromatography (IMAC) and Metal Oxide Affinity Chromatography (MOAC). We compared Zirconium (IV) IMAC (Zr-IMAC) magnetic microparticles to more commonly used Titanium (IV) IMAC (Ti-IMAC) and TiO2magnetic microparticles for phosphopeptide enrichment from simple and complex protein samples prior phosphopeptide sequencing and characterization by mass spectrometry (LC-MS/MS). We optimized sample-loading conditions to increase phosphopeptide recovery for Zr-IMAC, Ti-IMAC and TiO2based workflows. The performance of Zr-IMAC was enhanced by 19-22% to recover up to 5173 phosphopeptides from 200 µg of protein extract from HepG2/C3A cells, making Zr-IMAC the preferred method for phosphopeptide enrichment in this study. Ti-IMAC and TiO2performance were also optimized to improve phosphopeptide numbers by 28% and 35%, respectively. Furthermore, Zr-IMAC based phosphoproteomics in the magnetic microsphere format identified 23% more phosphopeptides than HPLC-based Fe(III)-IMAC for same sample amount (200 µg), thereby adding 37% more uniquely identified phosphopeptides. We conclude that Zr-IMAC improves phosphoproteome coverage and recommend that this affinity enrichment method should be more widely used in biological and biomedical studies of cell signalling and in the search for disease-biomarkers.
Reflux of Endoplasmic Reticulum proteins to the cytosol yields inactivation of tumor suppressors
Authors: Sicari Daria , Pineau Raphael , Reste Pierre-Jean Le , Negroni Luc , Chat Sophie , Mohtar Aiman , Thomas Daniel , Gillet Reynald , Hupp M. Ted , Chevet Eric , Igbaria Aeid 
Published: April 2020

ABSTRACTIn the past decades many studies reported Endoplasmic Reticulum (ER) resident proteins to localize to the cytosol but the mechanisms by which this occurs and whether these proteins exert cytosolic functions remain unknown. We found that select ER luminal proteins accumulate in the cytosol of glioblastoma cells isolated from mouse and human tumors. In cultured cells ER protein reflux to the cytosol occurs upon proteostasis perturbation. As such we investigated whether refluxed proteins gain new functions in the cytosol thus providing advantage to tumor cells. Using the ER luminal protein AGR2 as a model, we showed that it is refluxed to the cytosol where it binds and inhibits the tumor suppressor p53. We named this phenomenon ER to Cytosol Signaling (ERCYS) as an ER surveillance mechanism conserved in Eukaryotes to relieve the ER from its contents upon stress and to provide selective advantage to tumor cells through gain-of-cytosolic functions.
Water and nutrient cycling regulation functions in forest ecosystems: a comparison between native forests and exotic fast-growing tree species plantations in tropical highlands
Authors: León-Peláez Juan Diego , Villegas Juan Camilo , Amador-Pérez Jorge Alejandro 
Published: April 2020

AbstractAn improved understanding of ecosystem functions is increasingly needed as ecosystem management moves towards optimizing their capacity to provide services to society. Such a task requires the characterization of ecosystem functions in strategic systems such as tropical mountain forests, which are also subject to pressure due to both global and local environmental changes. In particular, transformation of native forests into pastures or agriculture, has been regarded as the type of transformation with the largest effects in ecosystem regulating and provision functions. However, the effects of other transformations such as those associated with replacement of native with planted forests, have been less studied. To evaluate the effect of forest type on key-ecosystem functions related to water resources, we studied the dynamics of rainfall partitioning and nutrient circulation on a suite of representative forest types in neotropical mountain systems: two plantations of exotic fast-growing species and two types of native forests. Our results illustrate that, when considered in a per-basal unit area, water transmission to the forest floor is significantly higher in both native forests. Similarly, native forests are more effective on circulating nutrients on the ecosystem as they are better adapted to oligotrophic soils such as those occurring in tropical mountains. These results suggest that the replacement of native forests with exotic tree plantations can potentially impact hydrological regulation and the nutrient cycling in these high Andean lands, affecting both directly and indirectly the capacity of ecosystems to produce services to society.