bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circulating levels of epirubicin cause endothelial senescence while compromising metabolic activity and vascular function
Authors: Eakin Amanda J , McErlain Tamara , Burke Aileen , Eaton Amy , Tipping Nuala , Allocca Gloria , Branco Cristina M. 
Published: June 2020

AbstractAnthracycline-based chemotherapy is a common treatment for cancer patients. Because it is delivered intravenously, endothelial cells are exposed first and to the highest concentrations, prior to diffusion to target cells. Not surprisingly, vascular dysfunction is a consequence of anthracycline therapy. While chemotherapy-induced endothelial damage at administration sites has been investigated, the effects of lower doses encountered by distant microvascular networks has not. The aim of this study was to investigate the impact of epirubicin, a widely used anthracycline, on healthy endothelial cells to elucidate its effects on microvascular physiology.Here, endothelial cells were briefly exposed to low doses of epirubicin to recapitulate levels in circulation following dilution in the blood and compound half-life in circulation. Both immediate and prolonged responses to treatment were assessed to determine changes in endothelial function.Epirubicin caused a decrease in proliferation and viability in hUVEC, with lower doses resulting in a senescent phenotype in a large proportion of cells, accompanied by a significant increase in pro-inflammatory cytokines and a significant decrease in metabolic activity. Epirubicin exposure also impaired endothelial function with delayed wound closure, reduced angiogenic potential and increased monolayer permeability downstream of VE-cadherin internalization. Primary lung endothelial cells obtained from epirubicin-treated mice similarly demonstrated reduced viability and functional impairment.In vivo, epirubicin treatment resulted in persistent reduction in lung vascular density and significantly increased infiltration of myeloid cells.Modulation of endothelial status and inflammatory tissue microenvironment observed in response to low doses of epirubicin may predict risk for long-term secondary pathologies associated with chemotherapy.
Phylogenetic position and taxonomic rearrangement ofDavidina(Lepidoptera, Nymphalidae), an enigmatic butterfly genus new for Europe and America
Authors: Lukhtanov Vladimir A. , Dubatolov Vladimir V. 
Published: June 2020

AbstractDavidina, an enigmatic butterfly genus described from China in the 19thcentury, has been long time considered a member of the family Pieridae due to its pierid-like wing pattern. In the 20th century, it was transferred to the family Satyridae (now subfamily Satyrinae of Nymphalidae) based on analysis of genitalia structure and placed next to the species-rich genusOeneis(subtribe Satyrina), being separated from the latter by supposed differences in wing venation. Here we conducted phylogenetic and taxonomic study of the subtribe Satyrina using analysis of molecular and morphological characters. We show that the genusOeneisis not monophyletic, and consists of two non-sister, genetically diverged and morphologically differentiated groups (Oeneiss.s. andProtoeneis). We also demonstrate thatDavidinais closely related toProtoeneis, not toOeneiss.s. To avoid the discovered non-monophyly and morphological heterogeneity, several species should be extracted fromOeneisand transferred to the genusDavidina. As a consequence, we conclude that the nameProtoeneisGorbunov, 2001 is congeneric withDavidinaOberthür, 1879. We also conclude thatDavidinais not a monotypic Chinese endemic genus as it has been previously supposed, but is composed of nine species and has a broad distribution area in the Holarctic region including Europe and America.
Changes in local mineral homeostasis facilitate the formation of benign and malignant testicular microcalcifications
Authors: Boisen Ida Marie , Knudsen Nadia Krarup , Nielsen John Erik , Kooij Ireen , Bagger Mathilde Louise , Kaludjerovic Jovana , O’ Shaughnessy Peter J. , Andrews Peter W. , Ide Noriko , Toft Birgitte Grønkær , Juul Anders , Mehmedbašić Arnela , Jørgensen Anne , Smith Lee B. , Norman Richard W. , Meyts Ewa Rajpert-De , Lanske Beate , Jensen Martin Blomberg 
Published: June 2020

AbstractTesticular microcalcifications consist of hydroxyapatite and have been associated with an increased risk of testicular germ cell tumors (TGCTs) but are also found in benign cases such as loss-of-function variants in the phosphate-transporterSLC34A2. Here, we show that fibroblast growth factor 23 (FGF23), a regulator of phosphate homeostasis, is expressed in testicular germ cell neoplasiain situ(GCNIS), embryonal carcinoma (EC), and human embryonic stem cells. FGF23 is not glycosylated in TGCTs and therefore cleaved into a C-terminal fragment which competitively antagonizes full-length FGF23. Here,Fgf23knockout mice presented with marked calcifications in the epididymis, spermatogenic arrest, and focally germ cells expressing the osteoblast marker Osteocalcin (gene name:BGLAP, protein name: Osteocalcin). Moreover, the frequent testicular microcalcifications in mice with no functional androgen receptor and lack of circulating gonadotropins are associated with lowerSlc34a2and higherBglap/Slc34a1(protein name: NPT2a) expression compared with wild-type mice. In accordance, human testicular specimens with microcalcifications also have lowerSLC34A2and a subpopulation of germ cells express phosphate-transporter NPT2a, Osteocalcin, and RUNX2 highlighting aberrant local phosphate handling and expression of bone-specific proteins. Mineral disturbancein vitrousing calcium or phosphate treatment induced deposition of calcium-phosphate in a spermatogonial cell line and this effect was fully rescued by the mineralization-inhibitor pyrophosphate. In conclusion, testicular microcalcifications arise secondary to local alterations in mineral homeostasis, which in combination with impaired Sertoli cell function and reduced levels of mineralization-inhibitors due to high alkaline phosphatase activity in GCNIS and TGCTs, facilitate osteogenic-like differentiation of testicular cells and deposition of hydroxyapatite.
Structural basis for peptide substrate specificities of glycosyltransferase GalNAc-T2
Authors: Mahajan Sai Pooja , Srinivasan Yashes , Labonte Jason W. , DeLisa Matthew P. , Gray Jeffrey J. 
Published: June 2020

AbstractThe polypeptide N-acetylgalactosaminyl transferase (GalNAc-T) enzyme family initiates O-linked mucin-type glycosylation. The family constitutes 20 isozymes in humans—an unusually large number—unique to O-glycosylation. GalNAc-Ts exhibit both redundancy and finely tuned specificity for a wide range of peptide substrates. In this work, we deciphered the sequence and structural motifs that determine the peptide substrate preferences for the GalNAc-T2 isoform. Our approach involved sampling and characterization of peptide–enzyme conformations obtained from Rosetta Monte Carlo-minimization–based flexible docking. We computationally scanned 19 amino acid residues at positions −1 and +1 of an eight-residue peptide substrate, which comprised a dataset of 361 (19×19) peptides with previously characterized experimental GalNAc-T2 glycosylation efficiencies. The calculations recapitulated experimental specificity data, successfully discriminating between glycosylatable and non-glycosylatable peptides with a probability of 96.5% (ROC-AUC score), a balanced accuracy of 85.5% and a false positive rate of 7.3%. The glycosylatable peptide substrates viz. peptides with proline, serine, threonine, and alanine at the −1 position of the peptide preferentially exhibited cognate sequon-like conformations. The preference for specific residues at the −1 position of the peptide was regulated by enzyme residues R362, K363, Q364, H365 and W331, which modulate the pocket size and specific enzyme-peptide interactions. For the +1 position of the peptide, enzyme residues K281 and K363 formed gating interactions with aromatics and glutamines at the +1 position of the peptide, leading to modes of peptide-binding sub-optimal for catalysis. Overall, our work revealed enzyme features that lead to the finely tuned specificity observed for a broad range of peptide substrates for the GalNAc-T2 enzyme. We anticipate that the key sequence and structural motifs can be extended to analyze specificities of other isoforms of the GalNAc-T family and can be used to guide design of variants with tailored specificity.
GDSL-domain containing proteins mediate suberin biosynthesis and degradation, enabling developmental plasticity of the endodermis during lateral root emergence
Authors: Ursache Robertas , Vieira-Teixeira Cristovao De Jesus , Tendon Valérie Dénervaud , Gully Kay , De Bellis Damien , Schmid-Siegert Emanuel , Andersen Tonni Grube , Shekhar Vinay , Calderon Sandra , Pradervand Sylvain , Nawrath Christiane , Geldner Niko , Vermeer Joop E.M. 
Published: June 2020

ABSTRACTRoots anchor plants and deliver water and nutrients from the soil. The root endodermis provides the crucial extracellular diffusion barrier by setting up a supracellular network of lignified cell walls, called Casparian strips, supported by a subsequent formation of suberin lamellae. Whereas lignification is thought to be irreversible, formation of suberin lamellae was demonstrated to be dynamic, facilitating adaptation to different soil conditions. Plants shape their root system through the regulated formation of lateral roots emerging from within the endodermis, requiring local breaking and re-sealing of the endodermal diffusion barriers. Here, we show that differentiated endodermal cells have a distinct auxin-mediated transcriptional response that regulates cell wall remodelling. Based on this data set we identify a set of GDSL-lipases that are essential for suberin formation. Moreover, we find that another set of GDSL-lipases mediates suberin degradation, which enables the developmental plasticity of the endodermis required for normal lateral root emergence.
Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling
Authors: Yao Jun , Wu Douglas C. , Nottingham Ryan M. , Lambowitz Alan M. 
Published: June 2020

SummaryHuman plasma contains >40,000 different coding and non-coding RNAs that are potential biomarkers for human diseases. Here, we used thermostable group II intron reverse transcriptase sequencing (TGIRT-seq) combined with peak calling to simultaneously profile all RNA biotypes in apheresis-prepared human plasma pooled from healthy individuals. Extending previous TGIRT-seq analysis, we found that human plasma contains largely fragmented mRNAs from >19,000 protein-coding genes, abundant full-length, mature tRNAs and other structured small non-coding RNAs, and less abundant tRNA fragments and mature and pre-miRNAs. Many of the mRNA fragments identified by peak calling correspond to annotated protein-binding sites and/or have stable predicted secondary structures that could afford protection from plasma nucleases. Peak calling also identified novel repeat RNAs, miRNA-sized RNAs, and putatively structured intron RNAs of potential biological, evolutionary, and biomarker significance, including a family of full-length excised introns RNAs, subsets of which correspond to mirtron pre-miRNAs or agotrons.
Sex-specific expression and DNA methylation in a species with extreme sexual dimorphism and paternal genome elimination
Authors: Bain Stevie A. , Marshall Hollie , Ross Laura 
Published: June 2020

AbstractSexual dimorphism is exhibited in many species across the tree of life with many phenotypic differences mediated by differential expression and alternative splicing of genes present in both sexes. However, the mechanisms that regulate these sex-specific expression and splicing patterns remain poorly understood. The mealybug, Planococcus citri, displays extreme sexual dimorphism and exhibits an unusual instance of sex-specific genomic imprinting, Paternal Genome Elimination (PGE), in which the paternal chromosomes in males are highly condensed and eliminated from the sperm. P. citri also has no sex chromosomes and as such both sexual dimorphism and PGE are predicted to be under epigenetic control. We recently showed that P. citri females display a highly unusual DNA methylation profile for an insect species, with the presence of promoter methylation associated with lower levels of gene expression. In this study we therefore decided to explore genome-wide differences in DNA methylation between male and female P. citri using whole genome bisulfite sequencing. We have identified extreme differences in genome-wide levels and patterns between the sexes. Males display overall higher levels of DNA methylation which manifests as more uniform low-levels across the genome. Whereas females display more targeted high levels of methylation. We suggest these unique sex-specific differences are due to chromosomal differences caused by PGE and may be linked to possible ploidy compensation. Using RNA-Seq we identified extensive sex-specific gene expression and alternative splicing. We found cis-acting DNA methylation is not directly associated with differentially expressed or differentially spliced genes, indicating a broader role for chromosome-wide trans-acting DNA methylation in this species.
Impact of vector control on effective population sizes; empirical evidence for a control-based genetic bottleneck in the tsetse flyGlossina fuscipes
Authors: Muhwezi Allan , Cunningham Lucas J. , Esterhuizen Johan , Tirados Inaki , Matovu Enock , Donnelly Martin J. , Torr Stephen J. 
Published: June 2020

AbstractWe investigated genetic variation at 37 newly-developed microsatellite loci in populations of the tsetse flyGlossina fuscipes fuscipescaptured from the upper and lower reaches of a single hydrographical network within an endemic Human African Trypanosomiasis focus. Our primary aim was to assess the impact of vector control using insecticide-treated baits (Tiny Targets) on genetic structure. We initially usedSTRUCTUREto delineate geographical boundaries of two stable ‘ancestral’ reference populations without any history of vector control but marked for either vector control (‘intervention’) or no control (‘non-intervention’). We then used theADMIXTUREmodel to assess genetic divergence in temporal populations collected after vector control implementation. We applied the Linkage Disequilibrium method to explicitly measure spatial and temporal changes in effective population size (Ne). We observed a significant reduction inNecoincident with vector control, whereasNeremained stable in the non-intervention area. Our empirical findings show how classical population genetics approaches detected within a short period of time, a significant genetic bottleneck associated with vector control, and opens up the possibility of using routine genomic surveillance. We have also generated a resource of new genetic markers for studies on the population genetics of tsetse at finer-scale resolution.FundingThis work was funded through a Wellcome Trust Master’s Fellowship in Public Health and Tropical Medicine awarded to Allan Muhwezi (103268/Z/13/Z).
Scale invariance during bacterial reductive division observed by an extensive microperfusion system
Authors: Shimaya Takuro , Okura Reiko , Wakamoto Yuichi , Takeuchi Kazumasa A. 
Published: June 2020

AbstractIn stable environments, cell size fluctuations are thought to be governed by simple physical principles, as suggested by recent finding of scaling properties. Here we show, using E. coli, that the scaling concept also rules cell size fluctuations under time-dependent conditions, even though the distribution changes with time. We develop a microfluidic device for observing dense and large bacterial populations, under uniform and switchable conditions. Triggering bacterial reductive division by switching to non-nutritious medium, we find that the cell size distribution changes in a specific manner that keeps its normalized form unchanged; in other words, scale invariance holds. This finding is underpinned by simulations of a model based on cell growth and intracellular replication. We also formulate the problem theoretically and propose a sufficient condition for the scale invariance. Our results emphasize the importance of intrinsic cellular replication processes in this problem, suggesting different distribution trends for bacteria and eukaryotes.
Cheetah: a computational toolkit for cybergenetic control
Authors: Pedone Elisa , de Cesare Irene , Zamora-Chimal Criseida G. , Haener David , Postiglione Lorena , La Regina Antonella , Shannon Barbara , Savery Nigel J. , Grierson Claire S. , di Bernardo Mario , Gorochowski Thomas E. , Marucci Lucia 
Published: June 2020

AbstractAdvances in microscopy, microfluidics and optogenetics enable single-cell monitoring and environmental regulation and offer the means to control cellular phenotypes. The development of such systems is challenging and often results in bespoke setups that hinder reproducibility. To address this, we introduce Cheetah – a flexible computational toolkit that simplifies the integration of real-time microscopy analysis with algorithms for cellular control. Central to the platform is an image segmentation system based on the versatile U-Net convolutional neural network. This is supplemented with functionality to robustly count, characterise and control cells over time. We demonstrate Cheetah’s core capabilities by analysing long-term bacterial and mammalian cell growth and by dynamically controlling protein expression in mammalian cells. In all cases, Cheetah’s segmentation accuracy exceeds that of a commonly used thresholding-based method, allowing for more accurate control signals to be generated. Availability of this easy-to-use platform will make control engineering techniques more accessible and offer new ways to probe and manipulate living cells.
Balance between promiscuity and specificity in phage λ host range
Authors: Andrews Bryan , Fields Stanley 
Published: June 2020

AbstractAs hosts acquire resistance to viruses, viruses must overcome that resistance to re-establish infectivity, or go extinct. Despite the significant hurdles associated with adapting to a resistant host, viruses are evolutionarily successful and maintain stable coevolutionary relationships with their hosts. To investigate the factors underlying how pathogens adapt to their hosts, we performed a deep mutational scan of the region of the λ tail fiber tip protein that mediates contact with the λ host,E. coli. Phages harboring amino acid substitutions were subjected to selection for infectivity on wild typeE. coli, revealing a highly restrictive fitness landscape, in which most substitutions completely abrogate function. By comparing this lack of mutational tolerance to evolutionary diversity, we highlight a set of mutationally intolerant and diverse positions associated with host range expansion. Imposing selection for infectivity on three λ-resistant hosts, each harboring a different missense mutation in the λ receptor, reveals hundreds of adaptive variants in λ. We distinguish λ variants that confer promiscuity, a general ability to overcome host resistance, from those that drive host-specific infectivity. Both processes may be important in driving adaptation to a novel host.
DeepGANnel: Synthesis of fully annotated single molecule patch-clamp data using generative adversarial networks
Authors: Ball Sam T. M. , Celik Numan , Sayari Elaheh , Kadir Lina Abdul , O’Brien Fiona , Barrett-Jolley Richard 
Published: June 2020

Development of automated analysis tools for “single ion channel” recording is hampered by the lack of available training data. For machine learning based tools, very large training sets are necessary with sample-by-sample point labelled data (e.g., 1 sample point every 100microsecond). In an experimental context, such data are labelled with human supervision, and whilst this is feasible for simple experimental analysis, it is infeasible to generate the enormous datasets that would be necessary for a big data approach using hand crafting. In this work we aimed to develop methods to generate simulated ion channel data that is free from assumptions and prior knowledge of noise and underlying hidden Markov models.We successfully leverage generative adversarial networks (GANs) to build an end-to-end pipeline for generating an unlimited amount of labelled training data from a small annotated ion channel “seed” record, and this needs no prior knowledge of theoretical dynamical ion channel properties. Our method utilises 2D CNNs to maintain the synchronised temporal relationship between the raw and idealised record. We demonstrate the applicability of the method with 5 different data sources and show authenticity with t-SNE and UMAP projection comparisons between real and synthetic data. The model would be easily extendable to other time series data requiring parallel labelling, such as labelled ECG signals or raw nanopore sequencing data.
Dramatic shape changes occur as Cytochrome c folds
Authors: Kirmizialtin Serdal , Pitici Felicia , Cardenas Alfredo E , Elber Ron , Thirumalai D. 
Published: June 2020

AbstractExtensive experimental studies on the folding of Cytochrome c (Cyt c) make this small protein an ideal target for atomic detailed simulations for the purposes of quantitatively characterizing the structural transitions and the associated time scales for folding to the native state from an ensemble of unfolded states. We use previously generated atomically detailed folding trajectories by the Stochastic Difference Equation in Length (SDEL) to calculate the time-dependent changes in the Small Angle X-ray scattering (SAXS) profiles. Excellent agreement is obtained between experiments and simulations for the time dependent SAXS spectra, allowing us to identify the structures of the folding intermediates, which shows that Cyt c reaches the native state by a sequential folding mechanism. Using the ensembles of structures along the folding pathways we show that compaction and the sphericity of Cyt c change dramatically from the prolate ellipsoid shape in the unfolded state to the spherical native state. Our data, which provides unprecedented quantitative agreement with all aspects of time-resolved SAXS experiments, shows that hydrophobic collapse and amide group protection coincide on the 100 microseconds time scale, which is in accord with ultrafast Hydrogen/Deuterium exchange studies. Based on these results we propose that compaction of polypeptide chains, accompanied by dramatic shape changes, is a universal characteristic of globular proteins, regardless of the underlying folding mechanism.