bluuebunny/crossref_metadata_2025_split huggingface dataset:
Forest condition in the Congo Basin for the assessment of ecosystem conservation status
Authors: Shapiro Aurélie , Grantham Hedley S. , Aguilar-Amuchastegui Naikoa , Murray Nicholas J. , Gond Valery , Bonfils Djoan , Rickenbach Olivia 
Published: March 2020

AbstractMeasuring forest degradation is important for understanding and designing measures to protect biodiversity and the capacity of forests to deliver ecosystem services. Conservation planning, particularly the prioritization of management interventions for forests, is often lacking spatial data on ecological condition, and it is often overlooked within decision-making processes. Existing methods for assessing forest degradation via proxies or binary measures (i.e. intact or not) cannot adequately consider the important variations of ecological condition. Direct methods to measure degradation (e.g. through remote sensing) require extensive training data, calibration and validation, and may be too sensitive to small-scale or short-term changes which may not be related to degradation. We developed a metric termed Forest Condition (FC) which aims to measure the degree of forest degradation, incorporating temporal history of forest change over a large spatial extent. We parameterized this metric based on estimated changes in above ground biomass in the context of forest fragmentation over time to estimate a continuous measure of forest degradation for Congo Basin countries. We estimate that just less than 70% of Congo Basin forests remain fully intact. FC was validated by direct remote sensing measurements from Landsat imagery for DRC. Results showed that FC was significantly positively correlated with forest canopy cover, gap area per hectare, and magnitude of temporal change in Normalized Burn Ratio. We tested the ability of FC to distinguish primary and secondary degradation and deforestation and found significant differences in gap area and spectral anomalies to validate our theoretical model. We used the IUCN Red List of Ecosystems criteria to demonstrate the value of applying forest degradation to assess the risk of ecosystem collapse. Based on this assessment, we found that without including FC in the assessment of biotic disruption, 12 ecosystems could not have a threat status assigned, and a further 9 ecosystems would have a lower threat status. Our overall assessment of ecosystems found approximately half of forest of Congo Basin ecosystem types which cover over 20% of all forest area are threatened including 4 ecosystems (<1% of total area) which are critically engendered. FC is a transferrable and scalable assessment to support forest monitoring, planning, and management.
Ape cultures do not require behaviour copying
Authors: Acerbi Alberto , Snyder William Daniel , Tennie Claudio 
Published: March 2020

AbstractWhile culture is widespread in the animal kingdom, human culture has been claimed to be special due to being cumulative. It is currently debated which cognitive abilities support cumulative culture, but behavioural form copying is one of the main abilities proposed. One important source of contention is the presence or absence of behaviour copying in our closest living relatives, non-human great apes (apes) – especially given that their behaviour does not show clear signs of cumulation. Those who claim that apes copy behaviour often base this claim on the existence of stable ape cultures in the wild. We developed an individual-based model to test whether ape cultural patterns can emerge in absence of any behaviour copying, when only allowing for a well-supported alternative social learning mechanism, socially mediated reinnovation, where only the frequency of reinnovation is under social influence, but the form of the behaviour is not. Our model reflects wild ape life conditions, including physiological and behavioural needs, demographic and spatial features, and possible genetic and ecological variation between populations. Our results show that, under a wide range of values of parameters, we can reproduce the defining features of wild ape cultural patterns. Overall, our results show that ape cultures can emerge and stabilise without behaviour copying. Ape cultures do not show the signatures of behaviour copying abilities, lending support to the notion that behaviour copying is, among apes, unique in the human lineage. It therefore remains an open question when and why behaviour copying evolved in hominins.
TMS alters multivoxel patterns in the absence of overall activity changes
Authors: Rafiei Farshad , Safrin Martin , Wokke Martijn E. , Lau Hakwan , Rahnev Dobromir 
Published: March 2020

AbstractTranscranial magnetic stimulation (TMS) has become one of the major tools for establishing the causal role of specific brain regions in perceptual, motor, and cognitive processes. Nevertheless, a persistent limitation of the technique is the lack of clarity regarding its precise effects on neural activity. Here, we examined the effects of TMS intensity and frequency on concurrently recorded blood-oxygen level-dependent (BOLD) signals at the site of stimulation. In two experiments, we delivered TMS to the dorsolateral prefrontal cortex in human subjects of both sexes. In Experiment 1, we delivered a series of pulses at high (100% of motor threshold) or low (50% of motor threshold) intensity, whereas in Experiment 2, we always used high intensity but delivered stimulation at four different frequencies (5, 8.33, 12.5, and 25 Hz). We found that the TMS intensity and frequency could be reliably decoded using multivariate analysis techniques even though TMS had no effect on overall BOLD activity at the site of stimulation in either experiment. These results provide important insight into the mechanisms through which TMS influences neural activity.SignificanceTranscranial magnetic stimulation (TMS) is a promising tool for the treatment of a number of neuropsychiatric disorders. However, its effectiveness is still impeded by an incomplete understanding of its neural effects. One fundamental unresolved issue is whether TMS leads to local changes in overall neural activity in the absence of a task. Here we performed two experiments where TMS was delivered inside an MRI scanner while brain activity was continuously monitored. We found converging evidence for the notion that TMS affects the pattern of local activity changes but does not lead to an overall increase in activity. These results help clarify the mechanisms of how TMS affects local neural activity.
Maximizing Quantitative Phosphoproteomics of Kinase Signaling Expands the Mec1 and Tel1 Networks
Authors: Faca Vitor Marcel , Sanford Ethan , Tieu Jennifer , Marshall Shannon , Comstock William , Smolka Marcus 
Published: March 2020

ABSTRACTGlobal phosphoproteome analysis is crucial for comprehensive and unbiased investigation of kinase-mediated signaling. However, since each phosphopeptide represents a unique entity for defining identity, site-localization, and quantitative changes, phosphoproteomics often suffers from lack of redundancy and statistical power for generating high confidence datasets. Here we developed a phosphoproteomic approach in which data consistency among experiments using reciprocal stable isotope labeling defines a central filtering rule for achieving reliability in phosphopeptide identification and quantitation. We find that most experimental error or biological variation in phosphopeptide quantitation does not revert in quantitation once light and heavy media are swapped between two experimental conditions. Exclusion of non-reverting data-points from the dataset not only reduces quantitation error and variation, but also drastically reduces false positive identifications. Application of our approach in combination with extensive fractionation of phosphopeptides by HILIC identifies new substrates of the Mec1 and Tel1 kinases, expanding our understanding of the DNA damage signaling network regulated by these kinases. Overall, the proposed quantitative phosphoproteomic approach should be generally applicable for investigating kinase signaling networks with high confidence and depth.
Conservation and discreteness of the atromentin gene cluster in fungi
Authors: Tauber James P. , Hintze John 
Published: March 2020

AbstractThe atromentin synthetase gene cluster is responsible for catalyzing the precursor pigment atromentin, which is further catalyzed into hundreds of different pigments that span different taxa in the Basidiomycota and is a distinguished feature of Boletales. Previous work identified co-transcription of the two essential clustered atromentin genes (the atromentin synthetase (NPS) and the aminotransferase) by inducible pigment conditions and also conserved genetic elements in the promoter regions (motifs). For this work, we found that theNPSand its promoter motif appeared to follow the same evolutionary path as the mushrooms’. TheNPSappears to predate Boletales and originate in Agaricomycetes, and with convergent/parallel evolution that allowed ascomycetes to produce atromentin. Additionally, a consensus of the intron-exon gene structure for basidiomycetous, atromentin-catalyzingNPSswas identified whereby a significant deviation occurred in the paraphyletic group, Paxillaceae. This gene structure was not present inNPSsin Aspergilli. Lastly, we found a putative TATA box adjacent to the palindromic motif ofNPS, indicating (co-)transcriptional control by a TATA(-like) binding transcription factor. Combined with previous decades’ worth of research, our results support that not only can atromentin derivatives be used for chemo-taxonomy, but also atromentin’s genetic basis. Future work using the putative promoter motif will provide new insight into which (co-)transcription factor may be responsible for the transcriptional control of atromentin synthetases.
Age-dependent selection on MHC class 2 variation in a free-living ruminant
Authors: Huang Wei , Dicks Kara L , Hadfield Jarrod D , Johnston Susan E , Ballingall Keith T , Pemberton Josephine M 
Published: March 2020

AbstractGenes within the major histocompatibility complex (MHC) are the most variable identified in vertebrates. Pathogen-mediated selection (PMS) is believed to be the main force maintaining diversity at MHC class I and II genes, but it has proven hard to demonstrate the exact PMS regime that is acting in natural populations. Demonstrating contemporary selection on MHC alleles is not trivial, and previous work has been constrained by limited genetic tools, low sample sizes and short time scales and has sometimes involved anticonservative statistical approaches. Here, we use appropriate statistical approaches to examine associations between MHC variation and several fitness measurements including total fitness (lifetime breeding success) and five fitness components, in 3400 wild Soay sheep (Ovis aries) monitored over their lifetimes between 1989 and 2012. We found haplotypes C and D were associated with decreased and increased male total fitness respectively. In terms of fitness components, juvenile survival was positively associated with haplotype divergence. Of the eight MHC haplotypes (A-H), haplotypes C and F were associated with decreased adult male breeding success and decreased adult female life span respectively. Consistent with the increased male total fitness, haplotype D, which is the rarest, has increased in frequency throughout the study period. Our results suggest that contemporary balancing selection is acting on MHC class II genes in Soay sheep and that different selection mechanisms are acting between juveniles and adults.
First report of ‘CandidatusLiberibacter asiaticus’ affecting sour orange in urban areas of Mayabeque, Cuba
Authors: Pérez-López Edel , Dumonceaux Tim J. 
Published: March 2020

Abstract‘CandidatusLiberibacter asiaticus’ (CLas) is an unculturable, Gram-negative, phloem restricted plant pathogenic bacterium associated with a very serious disease of citrus worldwide known as Citrus Huanglongbing (HLB). CLas is widely spread in the Americas. In Cuba, CLas has been associated with HLB symptoms and has seriously affected the Cuban citrus industry. In this short communication we discuss the identification of CLas-infected sour orange in urban areas of Mayabeque Province in Cuba, an area previously unexplored for the presence of HLB, and a host widely cultivated in gardens and yards along Cuba. We used for the first time the bacteria molecular barcode chaperonin-60 universal target (cpn60UT) to identify and to detect CLas in HLB-symptomatic host plants.
Evaluation of theEscherichia colipopulation in the intestinal microbiota of rattus wistar submitted to secondhand smoke and supplemented with prebiotics
Authors: Silva Bruna Rafaela dos Santos , Perez Paula Marioto , Bremer Neto Hermann , Keller Rogeria 
Published: March 2020

AbstractMany chronic conditions, including smoking, have been shown to be associated with modifications in the gut microbiota and to remedy the effects of these changes, functional foods such as prebiotics have shown beneficial effects. The aim of this work was to evaluate changes in the bacterial population ofEscherichia coliin the intestinal microbiota of rats submitted to passive smoke and to the supplementation of prebiotics incorporated into the basal diet. The animals were divided into: Control Group (CG) = basal diet; Smoking Control Group (GCT) = basal diet with exposure to smoking; Prebiotic Group (GP) = basal diet incorporated with 1g of Immunowall® per kg of diet; Prebiotic Tobacco Group (GPT) = basal diet incorporated with 1g of ImmunowallTM per kg of diet with exposure to smoking. The animals were exposed to the smoke twice a day for 180 days. The obtained data were analyzed through the nonparametric Kruklla-Wallis test. Bacterial populations were amplified by real-time PCR. The results of this study revealed a significant decrease (p = 0.04 and p = 0.01) inEscherichia colipopulation in the group of animals supplemented with prebiotics in the intestinal microbiota of rats exposed and not exposed to cigarette smoke reinforcing the modulating effect of potential pathogens on the intestinal microbiota by functional foods.
Updated population viability analysis, population trends and PBRs for Hector’s and Maui dolphin
Authors: Slooten Elisabeth , Dawson Stephen Michael 
Published: March 2020

EXECUTIVE SUMMARYUpdated population viability analyses, incorporating the latest abundance and bycatch data indicate that:The estimated population decline for Maui dolphin is 2% per yearThere is a 68% probability that the population is continuing to declineAfter 30 years (6 more surveys) statistical power of detecting this rate of decline would be < 15%Only very large declines (37%) and recovery (45%) would be detectable with 80% statistical power after 30 years (6 more surveys)The level of conservation threat for Hector’s dolphin remains high despite a recent, larger population estimate off the east coast of the South IslandIncreased overlap between dolphins and fisheries, due to more extensive offshore distribution of dolphins off the South Island east coast, more than offsets the apparently higher population sizeThe Hector’s dolphin population has declined 70% over the last 3 generations, exceeding the 50% threshold for EndangeredPopulation declines are predicted to continue under current protection levelsThe results of this research are consistent with:◯ NOAA proposal to list Hector’s and Maui dolphins under the US Endangered Species Act◯ IWC recommendation to ban gillnets and trawling throughout Maui dolphin habitat◯ IUCN recommendation to ban gillnets and trawling throughout Hector’s and Maui dolphin habitat
Pinpointing of cysteine oxidation sites in vivo by high-resolution proteomics reveals mechanism of redox-dependent inhibition of STING
Authors: Cuervo Natalia Zamorano , Fortin Audray , Caron Elise , Chartier Stéfany , Grandvaux Nathalie 
Published: March 2020

AbstractProtein function is regulated by post-translational modifications, among which reversible oxidation of Cys (Cys ox-PTM) emerged as a key regulatory mechanism of cellular responses. The redox regulation of virus-host interactions is well documented, but in most cases, proteins subjected to Cys ox-PTM remain unknown. The identification of Cys ox-PTM sites in vivo is essential to underpin our understanding of the mechanisms of the redox regulation. In this study, we present a proteome-wide identification of reversible Cys ox-PTM sites in vivo during stimulation by oxidants using a maleimide-based bioswitch method coupled to mass spectrometry. We identified 2720 unique Cys ox-PTM sites encompassing 1473 proteins with distinct abundance, location and functions. Label-free quantification (LFQ)-based analysis revealed the enrichment of ox-PTM in numerous pathways, many relevant to virus-host interaction. Here, we focused on the oxidation of STING, the central adaptor of the innate immune type I interferon pathway induced upon detection of cytosolic DNA. We provide the first in vivo demonstration of reversible oxidation of Cys148and Cys206of STING. Molecular analyses led us to establish a new model in which Cys148oxidation is constitutive, while Cys206oxidation is inducible by oxidative stress or by the natural ligand 2’3’-cGAMP. We show that oxidation of Cys206has an inhibitory function to prevent STING hyperactivation through the constraint of a conformational change associated with the formation of inactive polymers containing intermolecular disulfide bonds. This provides new ground for the design of therapies targeting STING relevant to autoinflammatory disorders, immunotherapies and vaccines.Brief summary of the main resultsThe function of proteins is regulated by post-translational modifications, among which reversible oxidation of Cys recently emerged as a key component. Comprehension of redox regulation of cellular responses requires identification of specific oxidation sites in vivo. Using a bioswitch method to specifically label Cys subjected to reversible oxidation coupled to mass spectrometry, we identified thousands of novel oxidation sites. Many are relevant to virus-host interaction pathways. Here, we focused on the oxidation of STING, an adaptor critical for activating the innate immune type I interferon pathway engaged upon cytosolic DNA sensing. Molecular studies led us to establish a new model in which STING Cys148is oxidized at basal levels, while Cys206oxidation is induced by oxidative stress and ligand binding. We show that oxidation of Cys206has an inhibitory function to prevent STING hyperactivation. This study provides ground for novel research avenues aimed at designing therapeutics that target this pathway.
An ectosymbiosis-based mechanism of eukaryogenesis
Authors: Wong Tze-Fei , Chan Chung-Kwon , Long Xi , Xue Hong 
Published: March 2020

ABSTRACTThe mechanisms proposed for eukaryogenesis are divisible into mitochondria-early and mitochondria-late ones, where the mitochondriate-eukaryotes (MTEs) were evolutionary precursors or products of the amitochondriate-eukaryotes (AMIs) respectively. Analysis of prokaryote-to-eukaryote gene transfers in eukaryogenesis showed two tranches of high-intensity transfers from prokaryotes to eukaryotes mediated by endosymbioses that gave rise to mitochondria and chloroplasts, and hundreds of medium-intensity transfers which included the transfer of hydrogenase and pyruvate: ferredoxin oxidoreductase genes from theThermoanaerobacter-Hungateiclostridium-Sporanaerobactergroup to the AMIs. Since 94.5% of these medium-intensity transfers generated more than 100 inter-proteome similarity hits between each donor-recipient pair, they were not readily explicable by horizontal gene transfers (HGTs) or endosymbioses, pointing instead to the participation of a large number of ectosymbiotic transfers. The euryarchaeonAciduliprofundum boonei(Abo) and the gammaproteobacteriumEscherichia coli(Eco) were the foremost contributors of archaeal and bacterial genes for the eukaryotic DNA-apparatus respectively, and the Abo/Eco ratios for the prokaryote-derived genes in eukaryotes decreased from Microsporidia to other AMIs, and even more so in the MTEs. These findings supported an ectosymbiosis-based mechanism of eukaryogenesis with Abo as the Archaeal Parent of Eukarya, and Microsporidia as the eukaryotes phylogenetically closest to the Last Eukaryotic Common Ancestor (LECA).
A potent antibiofilm agent inhibits and eradicates mono- and multi-species biofilms
Authors: Long Lexin , Wang Ruojun , Chiang Ho Yin , Li Yong-Xin , Chen Feng , Qian Pei-Yuan 
Published: March 2020

AbstractBiofilms are surface-attached multicellular communities that create many problems in human health and various industries. Given the prominence of biofilms in biofouling and infectious diseases, antibiofilm control approaches are highly sought after. In the present study, we identified elasnin as a potent antibiofilm agent through a bioassay-guided approach. Elasnin specifically inhibited the biofilm formation of bacterial mono-species and eradicated the mature biofilm of Gram-positive bacteria at concentrations below 2.5 μg/mL with a low toxic effect on cells and a low resistance risk. Confocal observations illustrated that elasnin decreased cell aggregations and destroyed the biofilm matrix. Furthermore, elasnin-based antibiofilm coatings were prepared and inhibited the formation of multi-species biofilms and the attachment of large biofouling organisms in the field test. These findings suggest that elasnin is a promising antibiofilm agent for future applications in biofilm control.ImportanceDue to the increased diversity of biofilm-associated infections and the failure of conventional antimicrobial treatment, new and effective biofilm-specific pharmacologic strategies are urgently needed. Elasnin is a new antibiofilm natural product produced by Streptomyces with high efficiency and low toxicity. Elasnin effectively destroyed the biofilm matrix of Gram-positive bacteria, thus making them more susceptible to antibiotics. Unlike currently deployed antibiotic vancomycin, which exclusively targets essential life processes and kills the pathogen, elasnin did not exhibit bactericidal effect and thus held great potential in delaying resistance. With high yield, elasnin-based coatings were easily prepared with low expenditures and exhibited favorable performance in field test. Collectively, the antibiofilm properties of elasnin, combined with the low cost of supply and the low risk of resistance, could provide the basis for the development of a novel antibiofilm agent that could help fight to antibiotics resistance.