bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fish functional diversity as an indicator of resilience to industrial fishing in Patagonia Argentina
Authors: Rincón-Díaz Martha Patricia , Bovcon Nelson D. , Cochia Pablo D. , Góngora María Eva , Galván David E. 
Published: April 2021

AbstractThe relationship between fish functional diversity and fishing levels at which its baselines shift is important to identify the consequences of fishing in ecosystem functioning. For the first time, we implemented a trait-based approach in the Argentine Patagonian sea to identify the vulnerability and spatiotemporal changes in functional diversity of fish assemblages bycatch by a trawling fleet targeting the Argentine red shrimpPleoticus muelleri(Spence Bate, 1888) between 2003 and 2014. We coupled seven fish trophic traits to a reconstructed fish assemblage for the study area and bycatch and evaluated changes in fish species richness and four complementary functional diversity metrics [functional richness, redundancy, dispersion, and community trait values] along with fishing intensity, temporal use, latitudinal location, and depth of fishing grounds. Resident fishes larger than 30 cm in TL, with depressed and fusiform bodies, intermediate to high trophic levels, and feeding in shallow benthic, benthodemersal, and benthopelagic areas were vulnerable to bycatch. Fish assemblages exhibited a low functional trait redundancy, likely related to species influxes in a biogeographic ecotone with tropicalisation signs. Significantly increases in fish trait richness and dispersion polewards and with depth suggested new functional roles in these grounds, matching trends in community body size, reproductive load, maximum depth, trophic level, and diet breadth. Finally, a temporal increase in fish species and functional trait removal in fishing grounds led to trait homogenisation since the first year of trawling. The identified tipping points in temperate fish functional trait diversity highlight trait-based approaches within ecosystem-based fisheries management.
Structural variants contribute to pangenome evolution of a plant pathogenic fungus
Authors: Guo Li , Dong Quanbin , Wang Bo , Guo Mengyao , Ye Kai 
Published: April 2021

ABSTRACTGenetic variation is the driving force of plant-pathogen co-evolution. Large-scale genetic variations such as structural variations (SVs) often alter genome stability and organismal fitness. However, the pangenomic landscape and functional implications of SVs remain largely unexplored in plant pathogens. Here, we characterized the pangenomic and SV landscape in wheat head blight fungusFusarium graminearumby producing and comparing chromosome-level (average contig N50 of 8.9 Mb) genome assemblies of 98 accessions using a reference-guided approach. Accounting for 29.05% and 19.01% ofF. graminearumpangenome, respectively, accessory and private genomes are enriched with functions related to membrane trafficking, metabolism of fatty acids and tryptophans, with the private also enriched with putative effectors. Furthermore, using chromosome-level assemblies, we detected 52,420 SVs, 69.51% of which are inaccessible using read-mapping based approach. Over a half (55.65%) of 52,645 merged SVs affected 1,660 protein-coding genes, the most variable of which are involved in fungal virulence, cellular contact and communications. Interestingly, highly variable effectors and secondary metabolic enzymes are co-localized with SVs at subtelomeric and centromeric regions. Collectively, this landmark study shows the prevalence and functional relevance of SVs inF. graminearum, providing a valuable resource for future pangenomic studies in this cosmopolitan pathogen of cereal crops.
Fine-tuning heat stress algorithms to optimise global predictions of mass coral bleaching
Authors: Lachs Liam , Bythell John C. , East Holly K. , Edwards Alastair J. , Mumby Peter J. , Skirving William J. , Spady Blake L. , Guest James R. 
Published: April 2021

AbstractIncreasingly severe marine heatwaves under climate change threaten the persistence of many marine ecosystems. Mass coral bleaching events, caused by periods of anomalously warm sea surface temperatures (SST), have led to catastrophic levels of coral mortality globally. Remotely monitoring and forecasting such biotic responses to heat stress is key for effective marine ecosystem management. The Degree Heating Week (DHW) metric, designed to monitor coral bleaching risk, reflects the duration and intensity of heat stress events, and is computed by accumulating SST anomalies (HotSpot) relative to a stress threshold over a 12-week moving window. Despite significant improvements in the underlying SST datasets, corresponding revisions of the HotSpot threshold and accumulation window are still lacking. Here, we fine-tune the operational DHW algorithm to optimise coral bleaching predictions using the 5km satellite-based SSTs (CoralTemp v3.1) and a global coral bleaching dataset (37,871 observations, National Oceanic and Atmospheric Administration). After developing 234 test DHW algorithms with different combinations of HotSpot threshold and accumulation window, we compared their bleaching-prediction ability using spatiotemporal Bayesian hierarchical models and sensitivity-specificity analyses. Peak DHW performance was reached using HotSpot thresholds less than or equal to Maximum Monthly Mean SST and accumulation windows of 4 – 8 weeks. This new configuration correctly predicted up to an additional 310 bleaching observations compared to the operational DHW algorithm, an improved hit rate of 7.9 %. Given the detrimental impacts of marine heatwaves across ecosystems, heat stress algorithms could also be fine-tuned for other biological systems, improving scientific accuracy, and enabling ecosystem governance.
In vivodissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation
Authors: Anania Chiara , Acemel Rafael D. , Jedamzick Johanna , Bolondi Adriano , Cova Giulia , Brieske Norbert , Kühn Ralf , Wittler Lars , Real Francisca M. , Lupiáñez Darío G. 
Published: April 2021

ABSTRACTVertebrate genomes organize into topologically associating domains (TADs), delimited by boundaries that insulate regulatory elements from non-target genes. However, how boundary function is established is not well understood. Here, we combine genome-wide analyses and transgenic mouse assays to dissect the regulatory logic of clustered-CTCF boundariesin vivo, interrogating their function at multiple levels: chromatin interactions, transcription and phenotypes. Individual CTCF binding sites (CBS) deletions revealed that the characteristics of specific sites can outweigh other factors like CBS number and orientation. Combined deletions demonstrated that CBS cooperate redundantly and provide boundary robustness. We show that divergent CBS signatures are not strictly required for effective insulation and that chromatin loops formed by non-convergently oriented sites could be mediated by a loop interference mechanism. Further, we observe that insulation strength constitutes a quantitative modulator of gene expression and phenotypes. Our results highlight the modular nature of boundaries and their control over developmental processes.
Evaluation of different concentrations antibiotics on gut bacteria and growth ofEctropis obliquaProut (Lepidoptera: Geometridae)
Authors: Gao Tian , Zhou Xiaomin , Jiang Rui , Zhang Chen , Liu Song , Zhao Tianyu , Li Xiayu , Long Yanhua , Yang Yunqiu 
Published: April 2021

AbstractThe use of antibiotics to remove gut bacteria is a commonly used method to study gut function of insects. We assessed the impact of the artificial diet made from tea powder with different concentrations of antibiotics mixture (containing tetracycline, gentamicin, penicillin, and rifampicin) onEctropis obliquaProut (Lepidoptera: Geometridae) survival, growth, and reproduction. Antibiotic-induced bacterial clearance was monitored by Polymerase Chain Reaction (PCR) and by Colony-counting Methods. The results indicated that administration of the antibiotic mixture at a concentration of 200μg/ml caused the increase of gut bacteria, while a concentration of 300μg/ml was more effective in clearing gut bacteria but the concentration of 400μg/ml caused a large number of larval deaths. The concentration of 300μg/ml had no significant effect on the growth and development ofE. obliqua, but had impact on fecundity. Therefore, we could use 300μg/ml concentrations of the antibiotic mixture to obtain sterileE. obliquato study the function of intestinal microbes.
Evolution of Nuclear Receptors in Platyhelminths
Authors: Wu Wenjie , LoVerde Philip T. 
Published: April 2021

ABSTRACTSince the first complete set of Platyhelminth nuclear receptors (NRs) fromSchistosoma mansoniwere identified a decade ago, more flatworm genome data is available to identify their NR complement and to analyze the evolutionary relationship of Platyhelminth NRs. NRs are important transcriptional modulators that regulate development, differentiation and reproduction of animals. In this study, NRs are identified in genome databases of thirty-three species including in all Platyhelminth classes (Rhabditophora, Monogenea, Cestoda and Trematoda). Phylogenetic analysis shows that NRs in Platyhelminths follow two different evolutionary lineages: 1) NRs in a free-living freshwater flatworm (Schmidtea mediterranea) and all parasitic flatworms share the same evolutionary lineage with extensive gene loss. 2) NRs in a free-living intertidal zone flatworm (Macrostomum lignano) follow a different evolutionary lineage with a feature of multiple gene duplication and gene divergence. The DNA binding domain (DBD) is the most conserved region in NRs which contains two C4-type zinc finger motifs. A novel zinc finger motif is identified in parasitic flatworm NRs: the second zinc finger of parasitic Platyhelminth HR96b possesses a CHC2 motif which is not found in NRs of all other animals. In this study, novel NRs (members of NR subfamily 3 and 6) are identified in flatworms, this result demonstrates that members of all six classical NR subfamilies are present in the Platyhelminth phylum. NR gene duplication, loss and divergence in Platyhelminths are analyzed along with the evolutionary relationship of Platyhelminth NRs.
Phenotypic divergence between the cultivated apple (Malus domestica) and its primary wild progenitor (Malus sieversii)
Authors: Davies Thomas , Watts Sophie , McClure Kendra , Migicovsky Zoë , Myles Sean 
Published: April 2021

ABSTRACTAn understanding of the relationship between the cultivated apple (Malus domestica) and its primary wild progenitor species (M. sieversii) not only provides an understanding of how apples have been improved in the past, but may be useful for apple improvement in the future. We measured 10 phenotypes in over 1000 unique apple accessions belonging toM. domesticaandM. sieversiifrom Canada’s Apple Biodiversity Collection. Using principal components analysis (PCA), we determined thatM. domesticaandM. sieversiidiffer significantly in phenotypic space and are nearly completely distinguishable as two separate groups. We found thatM. domesticahad a shorter juvenile phase thanM. sieversiiand that cultivated trees produced flowers and ripe fruit later than their wild progenitors. Cultivated apples were also 3.6 times heavier, 43% less acidic, and had 68% less phenolic content than wild apples. Using historical records, we found that apple breeding over the past 200 years has resulted in a trend towards apples that have higher soluble solids, are less bitter, and soften less during storage. Our results quantify the significant changes in phenotype that have taken place since apple domestication, and provide evidence that apple breeding has led to continued phenotypic divergence of the cultivated apple from its wild progenitor species.
A secreted proteomic footprint for stem cell pluripotency
Authors: Lewis Philip , Silajzick Edina , Smith Helen , Bates Nicola , Smith Christopher A , Knight David , Denning Chris , Brison Daniel R , Kimber Susan J 
Published: April 2021

AbstractWith a view to developing a much-needed non-invasive method for monitoring the healthy pluripotent state of human stem cells in culture, we undertook proteomic analysis of the spent medium from cultured embryonic (Man-13) and induced (Rebl.PAT) human pluripotent stem cells (hPSCs). Cells were grown in E8 medium to maintain pluripotency, and then transferred to FGF2 and TGFβ deficient media for 48 hours to replicate an early, undirected dissolution of pluripotency.We identified a distinct proteomic footprint associated with early loss of pluripotency in both hPSC lines, and a strong correlation with changes in the transcriptome. We demonstrate that multiplexing of 4 E8- against 4 E6- enriched biomarkers provides 16 ratio abundances which are each robustly diagnostic for pluripotent state. These biomarkers were further confirmed by Western blotting which demonstrated consistent correlation with the pluripotent state across cell lines, and in response to recovery assays.
Investigating the Effect of Flow Compensation and Quantitative Susceptibility Mapping Method on the Accuracy of Venous Susceptibility Measurement
Authors: Berg Ronja C. , Preibisch Christine , Thomas David L. , Shmueli Karin , Biondetti Emma 
Published: April 2021

AbstractQuantitative susceptibility mapping (QSM) is a promising non-invasive method for obtaining information relating to the oxygen metabolism. However, the optimal acquisition sequence and QSM reconstruction method for reliable venous susceptibility measurements are unknown. Full flow compensation is generally recommended to correct for the influence of venous blood flow, although the effect of flow compensation on the accuracy of venous susceptibility values has not been systematically evaluated. In this study, we investigated the effect of different acquisition sequences, including different flow compensation schemes, and different QSM reconstruction methods on venous susceptibilities.Ten healthy subjects were scanned with five or six distinct QSM sequence designs implementing different flow compensation schemes. All data sets were processed using six different QSM pipelines and venous blood susceptibility was evaluated in whole-brain segmentations of the venous vasculature and single veins. The quality of vein segmentations and the accuracy of venous susceptibility values were analyzed and compared between all combinations of sequences and QSM methods.The influence of the QSM method on average venous susceptibility values was found to be 2.7 - 11.6 times greater than the influence of the acquisition sequence, including flow compensation. The majority of the investigated QSM reconstruction methods tended to underestimate venous susceptibility values in the vein segmentations that were obtained.Using multi-echo gradient-echo acquisitions with monopolar readout gradients, we found that sequences without full flow compensation yielded venous susceptibility values comparable to sequences with full flow compensation. However, the QSM method had a great influence on susceptibility values and thus needs to be considered carefully for accurate venous QSM.
Resolving Between Novelty and Homology in the Rapidly Evolving Phallus of Drosophila
Authors: Rice Gavin R. , David Jean R. , Gompel Nicolas , Yassin Amir , Rebeiz Mark 
Published: April 2021

AbstractThe genitalia present some of the most rapidly evolving anatomical structures in the animal kingdom, possessing a variety of parts that can distinguish recently diverged species. In theDrosophila melanogastergroup, the phallus is adorned with several processes, pointed outgrowths, that are similar in size and shape between species. However, the complex three-dimensional nature of the phallus can obscure the exact connection points of each process. Previous descriptions based upon adult morphology have primarily assigned phallic processes by their approximate positions in the phallus and have remained largely agnostic regarding their homology relationships. In the absence of clearly identified homology, it can be challenging to model when each structure first evolved. Here, we employ a comparative developmental analysis of these processes in eight members of themelanogasterspecies group to precisely identify the tissue from which each process forms. Our results indicate that adult phallic processes arise from three pupal primordia in all species. We found that in some cases the same primordia generate homologous structures whereas in other cases, different primordia produce phenotypically similar but remarkably non-homologous structures. This suggests that the same gene regulatory network may have been redeployed to different primordia to induce phenotypically similar traits. Our results highlight how traits diversify and can be redeployed, even at short evolutionary scales.Research HighlightBy incorporating developmental analysis, we find that genital structures previously identified as homologs are novel structures. This highlights how developmental analysis can help resolve contentious claims of homology.
Analysis of gene expression and mutation data points on contribution of transcription to the mutagenesis by APOBEC enzymes
Authors: Chervova Almira , Fatykhov Bulat , Koblov Alexander , Shvarov Evgeny , Preobrazhenskaya Julia , Vinogradov Dmitry , Ponomarev Gennady V. , Gelfand Mikhail S. , Kazanov Marat D. 
Published: April 2021

AbstractSince the discovery of the role of the APOBEC enzymes in human cancers, the mechanisms of this type of mutagenesis remain little understood. Theoretically, targeting of single-stranded DNA by the APOBEC enzymes could occur during cellular processes leading to the unwinding of DNA double-stranded structure. Some evidence points to the importance of replication in the APOBEC mutagenesis, while the role of transcription is still underexplored. Here, we analyzed gene expression and whole genome sequencing data from five types of human cancers with substantial APOBEC activity to estimate the involvement of transcription in the APOBEC mutagenesis and compare its impact with that of replication. Using the TCN motif as the mutation signature of the APOBEC enzymes, we observed a correlation of active APOBEC mutagenesis with gene expression, confirmed the increase of APOBEC-induced mutations in early-replicating regions, and estimated the relative impact of transcription and replication on the APOBEC mutagenesis, which turned out to be approximately equal in transcribed regions. We also found that the known effect of higher density of APOBEC-induced mutations on the lagging strand was highest in middle-replicating regions, and observed higher APOBEC mutation density on the sense strand, the latter bias positively correlated with the gene expression level.Bullet points–The APOBEC mutagenesis rate is higher in actively expressed genes–The APOBEC mutation density is higher on the sense strand–The lagging/leading strand ratio of the APOBEC mutational density is highest in middle-replicating regions
An automated workflow for multiplexed single-cell proteomics sample preparation at unprecedented sensitivity
Authors: Ctortecka Claudia , Hartlmayr David , Seth Anjali , Mendjan Sasha , Tourniaire Guilhem , Mechtler Karl 
Published: April 2021

AbstractThe analysis of single-cell proteomes has recently become a viable complement to transcriptomics and genomics studies. Proteins are the primary driver of cellular functionality and mRNA levels are often an unreliable proxy of such. Therefore, the global analysis of the proteome is essential to study cellular identities. Multiplexed and label-free mass spectrometry-based approaches with single-cell resolution have lately attributed surprising heterogeneity to presumed homogenous cell populations. Even though specialized experimental designs and instrumentation have demonstrated remarkable advances, the efficient sample preparation of single cells still lag. Here, we introduce the proteoCHIP, a universal option for single-cell proteomics sample preparation at surprising sensitivity and throughput. The automated processing using a commercial system combining single-cell isolation and picoliter dispensing, the cellenONE®, reduces final sample volumes to low nanoliters submerged in a hexadecane layer simultaneously eliminating error-prone manual sample handling and overcoming evaporation. The specialized proteoCHIP design allows direct injection of single cells via a standard autosampler resulting in around 1,500 protein groups per analytical run at remarkable reporter ion signal to noise while reducing or eliminating the carrier proteome. We identified close to 2,600 proteins across 170 multiplexed single cells from two highly similar human cell types. This dedicated loss-less workflow allows distinguishingin vitroco-differentiated cell types of self-organizing cardiac organoids based on indicative markers across 150 single cells. In-depth characterization revealed enhanced cellular motility of cardiac endothelial cells and sarcomere organization in cardiomyocytes. Our versatile and automated sample preparation has not only proven to be easily adaptable but is also sufficiently sensitive to drive biological applications of single-cell proteomics.
The SARS-CoV-2 mRNA-1273 vaccine elicits more RBD-focused neutralization, but with broader antibody binding within the RBD
Authors: Greaney Allison J. , Loes Andrea N. , Gentles Lauren E. , Crawford Katharine H.D. , Starr Tyler N. , Malone Keara D. , Chu Helen Y. , Bloom Jesse D. 
Published: April 2021

AbstractThe emergence of SARS-CoV-2 variants with mutations in key antibody epitopes has raised concerns that antigenic evolution will erode immunity. The susceptibility of immunity to viral evolution is shaped in part by the breadth of epitopes targeted. Here we compare the specificity of antibodies elicited by the mRNA-1273 vaccine versus natural infection. The neutralizing activity of vaccine-elicited antibodies is even more focused on the spike receptor-binding domain (RBD) than for infection-elicited antibodies. However, within the RBD, binding of vaccine-elicited antibodies is more broadly distributed across epitopes than for infection-elicited antibodies. This greater binding breadth means single RBD mutations have less impact on neutralization by vaccine sera than convalescent sera. Therefore, antibody immunity acquired by different means may have differing susceptibility to erosion by viral evolution.One Sentence SummaryDeep mutational scanning shows the mRNA-1273 RBD-binding antibody response is less affected by single viral mutations than the infection response.