bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptomic analysis reveals conserved transcriptional programs underpinning organogenesis and reproduction in land plants
Authors: Julca Irene , Ferrari Camilla , Flores-Tornero María , Proost Sebastian , Lindner Ann-Cathrin , Hackenberg Dieter , Steinbachová Lenka , Michaelidis Christos , Pereira Sónia Gomes , Misra Chandra Shekhar , Kawashima Tomokazu , Borg Michael , Berger Frédéric , Goldberg Jacob , Johnson Mark , Honys David , Twell David , Sprunck Stefanie , Dresselhaus Thomas , Becker Jörg D. , Mutwil Marek 
Published: October 2020

AbstractThe evolution of plant organs, including leaves, stems, roots, and flowers, mediated the explosive radiation of land plants, which shaped the biosphere and allowed the establishment of terrestrial animal life. Furthermore, the fertilization products of angiosperms, seeds serve as the basis for most of our food. The evolution of organs and immobile gametes required the coordinated acquisition of novel gene functions, the co-option of existing genes, and the development of novel regulatory programs. However, our knowledge of these events is limited, as no large-scale analyses of genomic and transcriptomic data have been performed for land plants. To remedy this, we have generated gene expression atlases for various organs and gametes of 10 plant species comprising bryophytes, vascular plants, gymnosperms, and flowering plants. Comparative analysis of the atlases identified hundreds of organ- and gamete-specific gene families and revealed that most of the specific transcriptomes are significantly conserved. Interestingly, the appearance of organ-specific gene families does not coincide with the corresponding organ’s appearance, suggesting that co-option of existing genes is the main mechanism for evolving new organs. In contrast to female gametes, male gametes showed a high number and conservation of specific genes, suggesting that male reproduction is highly specialized. The expression atlas capturing pollen development revealed numerous transcription factors and kinases essential for pollen biogenesis and function. To provide easy access to the expression atlases and these comparative analyses, we provide an online database,www.evorepro.plant.tools, that allows the exploration of expression profiles, organ-specific genes, phylogenetic trees, co-expression networks, and others.
Elevated temperatures drive the evolution of armor loss in the threespine sticklebackGasterosteus aculeatus
Authors: Smith Carl , Zięba Grzegorz , Przybylski Mirosław 
Published: October 2020

AbstractWhile there is evidence of genetic and phenotypic responses to climate change, few studies have demonstrated change in functional traits with a known genetic basis. Here we present evidence for an evolutionary adaptive response to elevated temperatures in freshwater populations of the threespine stickleback (Gasterosteus aculeatus). Using a unique set of historical data and museum specimens, in combination with contemporary samples, we fitted a Bayesian spatial model to identify a population-level decline in the number of lateral bony plates, comprising anti-predator armor, in multiple populations of sticklebacks over the last 90 years in Poland. Armor loss was predicted by elevated temperatures and is proposed to be a correlated response to selection for reduced body size. This study demonstrates a change in a functional trait of known genetic basis in response to elevated temperature, and illustrates the utility of the threespine stickleback as a model for measuring the evolutionary and ecological impacts of environmental change across the northern hemisphere.
Stromal Oncostatin M axis promotes breast cancer progression
Authors: Araujo Angela M. , Abaurrea Andrea , Azcoaga Peio , López-Velazco Joanna I. , Rezola Ricardo , Osorio-Querejeta Iñaki , Valdés-Mora Fátima , Flores Juana M. , Jenkins Liam , Fernández-Nogueira Patricia , Ferrari Nicola , Martín-Martín Natalia , Tzankov Alexandar , Eppenberger-Castori Serenella , Alvarez-Lopez Isabel , Urruticoechea Ander , Bragado Paloma , Coleman Nicholas , Carracedo Arkaitz , Gallego-Ortega David , Calvo Fernando , Isacke Clare M. , Caffarel Maria M. , Lawrie Charles H. 
Published: October 2020

AbstractCancer cells are constantly communicating with the surrounding tumour microenvironment (TME) and they hijack physiological cell interactions to overcome immune system surveillance and promote cancer progression1,2. However, the contribution of stromal cells to the reprogramming of the TME is not well understood. In this study we provide unprecedented evidence of the role of the cytokine Oncostatin M (OSM) as central node for multicellular interactions between immune and non-immune stroma and the epithelial compartment. We show that stromal expression of the OSM:Oncostatin M Receptor (OSMR) axis plays a key role in breast cancer progression. OSMR deletion in a multistage breast cancer model delays tumour onset, tumour growth and reduces metastatic burden. We ascribed causality to the stromal function of OSM axis by demonstrating reduced tumour burden of syngeneic tumours implanted in mice. Single-cell and bioinformatic analysis of murine and human breast tumours revealed that the expression of OSM signalling components is compartmentalized in the tumour stroma. OSM expression is restricted to myeloid cells, whereas OSMR expression is detected predominantly in fibroblasts and, to a lower extent, cancer cells. Myeloid-derived OSM reprograms fibroblasts to a more contractile and pro-tumorigenic phenotype, elicits the secretion of VEGF and pro-inflammatory chemokines (e.g. CXCL1 and CXCL16), leading to increased neutrophil and macrophage recruitment. In summary, our work sheds light on the mechanism of immune regulation by the tumour microenvironment, and supports that targeting OSM:OSMR interactions is a potential therapeutic strategy to inhibit tumour-promoting inflammation and breast cancer progression.
Metabarcoding faecal samples to investigate spatiotemporal variation in the diet of the endangered Westland petrel (Procellaria westlandica)
Authors: Querejeta Marina , Lefort Marie-Caroline , Bretagnolle Vincent , Boyer Stéphane 
Published: October 2020

ABSTRACTAs top predators, seabirds can be indirectly impacted by climate variability and commercial fishing activities through changes in marine communities. However, high mobility and foraging behaviour enables seabirds to exploit prey distributed patchily in time and space. This capacity to adapt to environmental change can be described through the study of their diet. Traditionally, the diet of seabirds is assessed through the morphological identification of prey remains in regurgitates. This sampling method is invasive for the bird and limited in terms of taxonomic resolution. However, the recent progress in DNA-based approaches is now providing a non-invasive means to more comprehensively and accurately characterize animal diets. Here, we used a non-invasive metabarcoding approach to characterize the diet of the Westland petrel (Procellaria westlandica), which is an endangered burrowing species, endemic to the South Island of New Zealand. We collected 99 fresh faecal samples at two different seasons and in two different sub-colonies. Our aims were to describe the diet of the Westland petrel, investigate seasonal and spatial variation in the petrels’ diet, and assess potential impacts of the New Zealand fishery industry. We found that amphipods were the most common prey, followed by cephalopods and fish. Our results could be the result of natural foraging behaviour, but also suggest a close link between the composition of prey items and New Zealand’s commercial fishing activities. In particular, the high abundance of amphipods could be the result of Westland petrels feeding on discarded fisheries waste (fish guts). Our results also showed significant differences in diet between seasons (before hatching vs chick-rearing season) and between sampling sites (two sub-colonies 1.5 km apart), indicating plasticity in the foraging strategy of the Westland petrel. Due to its non-invasive nature, metabarcoding of faecal samples can be applied to large numbers of samples to help describe dietary variation in seabirds and indicate their ecological requirements. In our example, dietary DNA (dDNA) provided valuable information regarding the dietary preferences of an iconic species in New Zealand’s unique biodiversity. dDNA can thus inform the conservation of endangered or at-risk species that have elusive foraging behaviours.
Determinants of different facets of beta diversity in Mediterranean marine amphipods
Authors: Bellisario Bruno , Camisa Federica , Abbattista Chiara , Cimmaruta Roberta 
Published: October 2020

AbstractRelying on a purely taxonomic view of diversity may ignore the fact that ecological communities can be constituted of species having both distinct evolutionary histories and functional characteristics. Thus, considering how the multiple facets of diversity vary along environmental and geographic gradients may provide insights into the role of historic processes and current environmental conditions in determining the distribution of species, lineages and functions across space. By using distributional, taxonomic-distance and traits information, we explore the role of spatial/environmental gradients and of biogeographic subdivision of Mediterranean Sea on the different facets of beta diversity components in seagrass amphipods. Beta diversity partitioning and correlation analyses showed a nearly equal contribution of the replacement and richness components on total beta diversity for all facets, although the influence of environmental and geographic distance differs among components. While the replacement was mainly related to a pure spatial gradient, both the environmental and geographic distance were correlated with the richness component of beta diversities. Our results are in line with the complex paleobiogeographic history of the Mediterranean Sea, with the replacement component likely to be related to the progressive substitution of species of Atlantic origin with Mediterranean endemics along the west-east geographic gradient, and the richness component to the marked environmental difference between different basins. Moreover, the influence of biogeographic partition on the richness components suggests the role of spatially structured gradients at biogeographic level in determining the net loss/gain of species, lineages and functions, possibly influencing the assembly processes of passive dispersal organisms.
Assessment of transparency indicators across the biomedical literature: how open is open?
Authors: Serghiou Stylianos , Contopoulos-Ioannidis Despina G. , Boyack Kevin W. , Riedel Nico , Wallach Joshua D. , Ioannidis John P. A. 
Published: October 2020

AbstractRecent concerns about the reproducibility of science have led to several calls for more open and transparent research practices and for the monitoring of potential improvements over time. However, with tens of thousands of new biomedical articles published per week, manually mapping and monitoring changes in transparency is unrealistic. We present an open-source, automated approach to identify five indicators of transparency (data sharing, code sharing, conflicts of interest disclosures, funding disclosures and protocol registration) and apply it across the entire open access biomedical literature of 2.75 million articles on PubMed Central. Our results indicate remarkable improvements in some (e.g. conflict of interest disclosures, funding disclosures), but not other (e.g. protocol registration, code sharing) areas of transparency over time, and map transparency across fields of science, countries, journals and publishers. This work has enabled the creation of a large, integrated, and openly available database to expedite further efforts to monitor, understand and promote transparency and reproducibility in science.
Transcriptome analysis in the maize-Ustilago maydisinteraction identifies maize-line-specific activity of fungal effectors
Authors: Schurack S , Depotter JRL , Gupta D , Thines M , Doehlemann G 
Published: October 2020

AbstractThe biotrophic pathogenUstilago maydiscauses smut disease on maize (Zea mays) and induces the formation of tumours on all aerial parts of the plant. Unlike in other biotrophic interactions, no gene-for-gene interactions have been identified in the maize-U. maydispathosystem. Thus, maize resistance toU. maydisis considered a polygenic, quantitative trait. Here, we study the molecular mechanisms of quantitative disease resistance (QDR) in maize, and howU. maydisinterferes with its components. Based on quantitative scoring of disease symptoms in 26 maize lines, we performed an RNA-Seq analysis of sixU. maydis-infected maize lines of highly distinct resistance levels. In accordance with the complex nature of QDR, the different maize lines showed specific responses of diverse cellular processes toU. maydisinfection. On the pathogen side, our analysis identified 406U. maydisgenes being differentially expressed between maize lines, of which 102 encode predicted effector proteins. Based on this analysis, we generatedU. maydisCRISPR/Cas9 knockout mutants for selected candidate effector sets. Infections of different maize lines with the fungal mutants and subsequent RNA-sequencing identified effectors with quantitative, maize-line-specific virulence functions, and revealed auxin-related processes as a possible target for one of them. Thus, we show that both transcriptional activity and virulence function of fungal effector genes are modified according to the infected maize line, providing new insights into the molecular mechanisms underlying QDR in the maize-U. maydisinteraction.
Impact of explicit area scaling on kinetic models involving multiple compartments
Authors: Holzheu Pascal , Großeholz Ruth , Kummer Ursula 
Published: October 2020

AbstractBackgroundComputational modelling of cell biological processes is a frequently used technique to analyse the underlying mechanisms and to generally understand the behaviour of these processes in the context of a pathway, network or even the whole cell. The most common technique in this context is the usage of ordinary differential equations (ODEs) that describe the kinetics of the relevant processes in mechanistic detail. Here, it is usually assumed that the content of the cell is well-stirred and thus homogeneous - which is of course an over-simplification, but often worked in the past. However, many processes happen at membranes and thus not in 3D, but in 2D. The scaling of the rates of these processes poses a special problem, if volumes of compartments are changed. They will typically scale with an area, but not with the volume of the involved compartment. However, commonly, this is neglected when setting up models and/or volume scaling also sometimes automatically happens when using modelling software in the field.ResultsHere, we investigate generic as well as specific, realistic cases to find out, how strong the impact of the wrong scaling is for the outcome of simulations. We show that the importance of correct area scaling depends on the architecture of the reaction site and its changes upon volume alterations and it is hard to foresee, if it has a significant impact or not just by looking at the original model set-up. Moreover, scaled rates might exhibit more or less control over the behaviour of the system and therefore, accordingly, incorrect scaling will have more or less influence.ConclusionsWorking with multi-compartment reactions requires a careful consideration of the correct scaling of the rates when changing the volumes of the involved compartments. The error following incorrect scaling - often done by scaling with the volume of the respective compartments can lead to significant aberrations of model behaviour.
Increasing Grain Yield in Bread Wheat (Triticum aestivumL.) by Selection for High Spike Fertility Index
Authors: Pontaroli Ana Clara , Alonso María Pía , Mirabella Nadia Estefania , Panelo Juan Sebastián , Franco María Fiorella , Sebastián Vanzetti Leonardo , Lorenzo Máximo 
Published: October 2020

ABSTRACTSpike fertility index (SF) has been proposed as a promising selection criterion for increasing grain yield (GY) in bread wheat. Here, changes in GY and related traits after simulated selection (10% intensity) for high SF or high GYper sewere assessed in two RIL populations: (I) Avalon/Glupro and (II) Baguette 10/Klein Chajá, and in (III) advanced lines from a breeding program. Grain yield, SF, grain number per unit area (GN), grain weight (GW), test weight (TW) and grain protein content (GPC) were determined. Regardless of the environmental conditions, simulated selection for high SF always resulted in GN increases (between 1.6 and 27.4%). Average GY increase observed after selection for high SF (11.5%; N=10; SEM=5.8) did not differ (p=0.92) from the average GY increase observed after selection for GYper se(11.8%; N=10; SEM=4.9). Grain weight, GPC and TW tended to decrease with selection for high SF; however, these trade-offs might be avoided by concurrent selection. Our findings validate the use of SF as a selection criterion for increasing grain yield in bread wheat.
Correlative all-optical quantification of mass density and mechanics of sub-cellular compartments with fluorescence specificity
Authors: Schlüßler Raimund , Kim Kyoohyun , Nötzel Martin , Taubenberger Anna , Abuhattum Shada , Beck Timon , Müller Paul , Maharana Shovamayee , Cojoc Gheorghe , Girardo Salvatore , Hermann Andreas , Alberti Simon , Guck Jochen 
Published: October 2020

AbstractQuantitative measurements of physical parameters become increasingly important for understanding biological processes. Brillouin microscopy (BM) has recently emerged as one technique providing the 3D distribution of viscoelastic properties inside biological samples — so far relying on the implicit assumption that refractive index (RI) and density can be neglected. Here, we present a novel method (FOB microscopy) combining BM with optical diffraction tomography and epi-fluorescence imaging for explicitly measuring the Brillouin shift, RI and absolute density with specificity to fuorescently labeled structures. We show that neglecting the RI and density might lead to erroneous conclusions. Investigating the nucleoplasm of wild-type HeLa cells, we find that it has lower density but higher longitudinal modulus than the cytoplasm. Thus, the longitudinal modulus is not merely sensitive to the water content of the sample — a postulate vividly discussed in the field. We demonstrate the further utility of FOB on various biological systems including adipocytes and intracellular membraneless compartments. FOB microscopy can provide unexpected scientific discoveries and shed quantitative light on processes such as phase separation and transition inside living cells.
Genome-Wide Architecture of Adaptation in Experimentally EvolvedDrosophila
Authors: Barter Thomas T. , Greenspan Zachary S. , Phillips Mark A. , Ranz José M. , Rose Michael R. , Mueller Laurence D. 
Published: October 2020

AbstractThe molecular basis of adaptation remains elusive even with the current ease of sequencing the genome and transcriptome. We used experimentally evolved populations ofDrosophilain conjunction with statistical learning tools to explore interactions between the genome, the transcriptome, and phenotypes. Our results indicate that transcriptomic measures from adult samples can predict phenotypic characters at many adult ages. Importantly, when comparing the genome and transcriptome in predicting phenotypic characters, we find that the two types of data are comparably useful. When using genome sites as predictors for the expression of the transcriptome, we find that gene expression is influenced by genomic regions across all large chromosome arms. Conversely, we found many genomic regions influencing the expression of numerous genes, which is consistent with widespread pleiotropy. Our results also highlight the power of the combination of experimental evolution, next-generation sequencing, and statistical learning tools in exploring the molecular basis of adaptation.
Macrophages orchestrate the expansion of a pro-angiogenic perivascular niche during cancer progression
Authors: Opzoomer James W. , Anstee Joanne E. , Dean Isaac , Hill Emily J. , Bouybayoune Ihssane , Caron Jonathan , Muliaditan Tamara , Gordon Peter , Sosnowska Dominika , Nuamah Rosamond , Pinder Sarah E. , Ng Tony , Dazzi Francesco , Kordasti Shahram , Withers David R. , Lawrence Toby , Arnold James N. 
Published: October 2020

AbstractTumor associated macrophages (TAMs) are a highly plastic stromal cell type which support cancer progression. Using single-cell RNA-sequencing of TAMs from a spontaneous murine model of mammary adenocarcinoma (MMTV-PyMT) we characterize a subset of these cells expressing lymphatic vessel endothelial hyaluronic acid receptor 1 (Lyve-1) which spatially reside proximal to blood vasculature. We demonstrate that Lyve-1+TAMs support tumor growth and identify a pivotal role for these cells in maintaining a population of perivascular mesenchymal cells which express alpha-smooth muscle actin and phenotypically resemble pericytes. Using photolabeling techniques show that mesenchymal cells maintain their prevalence in the growing tumor through proliferation and uncover a role for Lyve-1+TAMs in orchestrating a selective platelet-derived growth factor-CC-dependent expansion of the perivascular mesenchymal population, creating a pro-angiogenic niche. This study highlights the inter-reliance of the immune and non-immune stromal network which support cancer progression and provides therapeutic opportunities for tackling the disease.