bluuebunny/crossref_metadata_2025_split huggingface dataset:
The microRNA miR-132 is a key regulator of lymphatic vascular remodelling
Authors: Arcucci Valeria , Ishaq Musarat , Roufail Sally , Dredge B. Kate , Bert Andrew G. , Hackett-Jones Emily , Liu Ruofei , Pillman Katherine A. , Fox Stephen B. , Stacker Steven A. , Goodall Gregory J. , Achen Marc G. 
Published: December 2021

ABSTRACTLymphangiogenesis (growth of new lymphatic vessels), and lymphatic remodelling more broadly, are important for disease progression in cancer, lymphedema and the pulmonary disease lymphangioleiomyomatosis. Multiple molecular pathways which signal for aspects of lymphangiogenesis are known but little is understood about their co-ordinate regulation in lymphatic endothelial cells (LECs). Small RNA molecules co-ordinately regulate complex biological processes, but knowledge about their involvement in lymphangiogenesis is limited. Here we used high-throughput small RNA sequencing of LECs to identify microRNAs (miRs) regulating lymphatic remodelling driven by the lymphangiogenic growth factors VEGF-C and VEGF-D. We identified miR-132 as up-regulated by both growth factors, and demonstrated that inhibiting miR-132 in LECs in vitro blocked cell proliferation and tube formation, key steps in lymphangiogenesis. We showed that miR-132 is expressed in human LECs in vivo in the lymphatics of human breast tumours expressing VEGF-D. Importantly, we demonstrated that inhibiting miR-132 in vivo blocked many aspects of lymphangiogenesis in mice. Finally, we identified mRNAs regulated by miR-132 in LECs, by sequencing after RNA-protein cross-linking and Argonaute immunoprecipitation, which demonstrated how miR-132 co-ordinately regulates signalling pathways in lymphangiogenesis. This study shows miR-132 is a critical regulator of lymphangiogenesis and a potential target for therapeutically manipulating lymphatic remodelling in disease.
Blue and green food webs respond differently to elevation and land use
Authors: Ho Hsi-Cheng , Brodersen Jakob , Gossner Martin M. , Graham Catherine H. , Kaeser Silvana , Chacko Merin Reji , Seehausen Ole , Zimmermann Niklaus E. , Pellissier Loïc , Altermatt Florian 
Published: December 2021

AbstractWhile aquatic (blue) and terrestrial (green) food webs are parts of the same landscape, it remains unclear whether they respond similarly to shared environmental gradients. We use empirical community data from hundreds of sites across Switzerland, and show that blue and green food webs have different structural and ecological properties along elevation as a temperature proxy, and among various land-use types. Specifically, in green food webs, their modular structure increases with elevation and the overlap of consumers’ diet niche decreases, while the opposite pattern is observed in blue food webs. Such differences between blue and green food webs are particularly pronounced in farmland-dominated habitats, indicating that anthropogenic habitat modification moderates the climatic effects on food webs but differently in blue versus green systems. These findings indicate general structural differences between blue and green food webs and suggest their potential divergent future alterations through land use or climatic changes.
Dead infant carrying by chimpanzee mothers in the Budongo Forest
Authors: Soldati Adrian , Fedurek Pawel , Crockford Catherine , Adue Sam , Akankwasa John Walter , Asiimwe Caroline , Asua Jackson , Atayo Gideon , Chandia Boscou , Freymann Elodie , Fryns Caroline , Muhumuza Geresomu , Taylor Derry , Zuberbühler Klaus , Hobaiter Catherine 
Published: December 2021

ABSTRACTIt has been suggested that non-human primates can respond to deceased conspecifics in ways that suggest they experience psychological states not unlike humans, some of which could indicate they exhibit a notion of death. Here, we report long-term demographic data from two East African chimpanzee groups. During a combined 40-year observation period we recorded 191 births of which 68 died in infancy, mostly within the first year. We documented the post-mortem behaviour of the mothers and describe nine occasions where Budongo chimpanzee mothers carried infants for 1-3 days after their death, usually until the body started to decompose. We also observed three additional cases of extended carrying lasting for more than two weeks, one of which was followed by the unusual extended carrying of an object and another which lasted three months. In each case, the corpses mummified. In addition, we report four instances of recurring dead infant carrying by mothers, three of whom carried the corpse for longer during the second instance. We discuss these observations in view of functional hypotheses of dead infant carrying in primates and the potential proximate mechanisms involved in this behaviour.
binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets
Authors: Hickl Oskar , Queirós Pedro , Wilmes Paul , May Patrick , Heintz-Buschart Anna 
Published: December 2021

AbstractThe reconstruction of genomes is a critical step in genome-resolved metagenomics and for multi-omic data integration from microbial communities. Here, we presentbinny, a binning tool that produces complete and pure metagenome-assembled genomes (MAG) from both contiguous and highly fragmented genomes. Based on established metrics,binnyoutperforms or is highly competitive with commonly-used and state- of-the-art binning methods and finds unique genomes that could not be detected by other methods.binnyuses k-mer-composition and coverage by metagenomic reads for iterative, non-linear dimension reduction of genomic signatures, as well as subsequent automated contig clustering with cluster assessment using lineage-specific marker gene sets. When compared to seven widely used binning algorithms,binnyprovides substantial amounts of uniquely identified MAGs and almost always recovers the most near-complete (>95% pure, >90% complete) and high-quality (>90% pure, >70% complete) genomes from simulated data sets from the Critical Assessment of Metagenome Interpretation (CAMI) initiative, as well as substantially more high-quality draft genomes, as defined by the Minimum Information about a Metagenome-Assembled Genome (MIMAG) standard, from a real-world benchmark comprised of metagenomes from various environments than any other tested method.
Image-based taxonomic classification of bulk biodiversity samples using deep learning and domain adaptation
Authors: Fujisawa Tomochika , Noguerales Víctor , Meramveliotakis Emmanouil , Papadopoulou Anna , Vogler Alfried P. 
Published: December 2021

ABSTRACTComplex bulk samples of invertebrates from biodiversity surveys present a great challenge for taxonomic identification, especially if obtained from unexplored ecosystems. High-throughput imaging combined with machine learning for rapid classification could overcome this bottleneck. Developing such procedures requires that taxonomic labels from an existing source data set are used for model training and prediction of an unknown target sample. Yet the feasibility of transfer learning for the classification of unknown samples remains to be tested. Here, we assess the efficiency of deep learning and domain transfer algorithms for family-level classification of below-ground bulk samples of Coleoptera from understudied forests of Cyprus. We trained neural network models with images from local surveys versus global databases of above-ground samples from tropical forests and evaluated how prediction accuracy was affected by: (a) the quality and resolution of images, (b) the size and complexity of the training set and (c) the transferability of identifications across very disparate source-target pairs that do not share any species or genera. Within-dataset classification accuracy reached 98% and depended on the number and quality of training images and on dataset complexity. The accuracy of between-datasets predictions was reduced to a maximum of 82% and depended greatly on the standardisation of the imaging procedure. When the source and target images were of similar quality and resolution, albeit from different faunas, the reduction of accuracy was minimal. Application of algorithms for domain adaptation significantly improved the prediction performance of models trained by non-standardised, low-quality images. Our findings demonstrate that existing databases can be used to train models and successfully classify images from unexplored biota, when the imaging conditions and classification algorithms are carefully considered. Also, our results provide guidelines for data acquisition and algorithmic development for high-throughput image-based biodiversity surveys.
Frequency transfer of the ventriloquism aftereffect
Authors: Ege Rachel , van Opstal A. John , van Wanrooij Marc M. 
Published: December 2021

AbstractThe ventriloquism aftereffect (VAE) describes the persistent shift of perceived sound location after having been adapted to a ventriloquism condition, in which the sound was repeatedly paired with a displaced visual stimulus. In the latter case, participants consistently mislocalize the sound in the direction of the visual stimulus (ventriloquism effect, VE). Previous studies provide conflicting reports regarding the strength of the VAE, ranging from 0 to nearly 100%. Moreover, there is controversy about its generalization to different sounds than the one inducing the VE, ranging from no transfer at all, to full transfer across different sound spectra. Here, we imposed the VE for three different sounds: a low-frequency and a high-frequency narrow-band noise, and a broadband Gaussian white noise (GWN). In the adaptation phase, listeners generated fast goal-directed head movements to localize the sound, presented across a 70 deg range in the horizontal plane, while ignoring a visual distracter that was consistently displaced 10 deg to the right of the sound. In the post-adaptation phase, participants localized narrow-band sounds with center frequencies from 0.5 to 8 kHz, as well as GWN, without the visual distracter. Our results show that the VAE amounted to approximately 40% of the VE and generalized well across the entire frequency domain. We also found that the strength of the VAE correlated with the pre-adaptation sound-localization performance. We compare our results with previous reports and discuss different hypotheses regarding optimal audio-visual cue integration.Significance statementWhere we believe sounds to emanate from is heavily influenced by what we see. We experience this illusion - the ventriloquism effect - regularly. For example, when watching movies, we perceive the voices of actors to originate from the actors’ lips rather than from the speakers. Long exposure to a spatial mismatch between what we hear and what we see, leads to a recalibration of our localization of sounds - the ventriloquism aftereffect. Unclear was whether exposure to an audiovisual mismatch for one sound type would also lead to adaptive changes for other sounds. The present study shows that the ventriloquism aftereffect generalizes, implying that it does not act at an early auditory stage, but at a late multisensory stage.
Opto-Katanin: An Optogenetic Tool for Localized Microtubule Disassembly
Authors: Meiring Joyce C. M. , Grigoriev Ilya , Nijenhuis Wilco , Kapitein Lukas C. , Akhmanova Anna 
Published: December 2021

AbstractMicrotubules are major cytoskeletal filaments that drive chromosome separation during cell division, serve as rails for intracellular transport and as a scaffold for organelle positioning. Experimental manipulation of microtubules is widely used in cell and developmental biology, but tools for precise subcellular spatiotemporal control of microtubule integrity are currently lacking. Here, we exploit the dependence of the mammalian microtubule-severing protein katanin on microtubule-targeting co-factors to generate a light-activated system for localized microtubule disassembly that we named opto-katanin. Targeted illumination with blue light induces rapid and localized opto-katanin recruitment and local microtubule depolymerization, which is quickly reversible after stopping light-induced activation. Opto-katanin can be employed to locally perturb microtubule-based transport and organelle morphology in dividing cells and differentiated neurons with high spatiotemporal precision. We show that different microtubule-associated proteins can be used to recruit opto-katanin to microtubules and induce severing, paving the way for spatiotemporally precise manipulation of specific microtubule subpopulations.
What do zebrafish prefer? Directional and color preferences in maze tasks
Authors: Marcon Matheus , Benvenutti Radharani , Gallas-Lopes Matheus , Herrmann Ana Paula , Piato Angelo 
Published: December 2021

ABSTRACTStudies regarding the animals’ innate preferences help elucidate and avoid probable sources of bias and serve as a reference to improve and develop new behavioral tasks. In zebrafish research, the results of innate directional and color preferences are often not replicated between research groups or even inside the same laboratory raising huge concerns on the replicability and reproducibility. Thus, this study aimed to investigate the male and female zebrafish innate directional and color preferences in the plus-maze and T-maze behavioral tasks. As revealed by the percentage of time spent in each zone of the maze, our results showed that males and females zebrafish demonstrated no difference in directional preference in the plus-maze task. Surprisingly, male and female zebrafish showed color preference differences in the plus-maze task; males did not show any color preference, while female zebrafish demonstrated a red preference compared to white, blue, and yellow colors. Moreover, both male and female zebrafish demonstrated a strong black color preference compared to the white color in the T-maze task. Thus, our results demonstrate the importance of innate preference assays involved with the directionality of the apparatus or the application of colors as a screening process conducting behavioral tests (e.g., anxiety, learning and memory assessment, locomotion, and preference) and highlight the need to analyze sex differences.
Transcriptome features of trained immunity in Drosophila
Authors: Fuse Naoyuki , Okamori Chisaki , Tang Chang , Hirai Kikuko , Okaji Ryoma , Kurata Shoichiro 
Published: December 2021

SummaryImmune memory is an ability of organisms to potentiate immune responses at secondary infection. Current studies have revealed that innate immunity, as well as adaptive immunity, exhibits the memory character called “trained immunity”. Although it is suggested that epigenetic reprogramming plays important roles in trained immunity, its underlying mechanism is not fully understood, especially on the individual level.Here we established experimental systems for detecting trained immunity in Drosophila melanogaster. Namely, training infection with low-pathogenic bacteria enhanced the survival rate of the flies at subsequent challenge infection with high-pathogenic bacteria. We found that among low-pathogenic bacteria, Micrococcus luteus (Ml) and Salmonella typhimurium (St) mediated apparent training effects in fly, but seemed to act through different ways. Ml left training effects even after its removal from flies, while living St persisted inside flies for a long time. Our RNA-Seq analysis revealed that Ml-training enhanced the expression of immune-related genes during the challenge infection, but did not do so without challenge infection. In contrast, St-training maintained high expression of the immune-related genes with or without challenge. These results suggest that training effects with Ml and St were due to memory and persistence of immune responses, respectively. Furthermore, we searched the factor involved in Ml-training and identified a candidate, Ada2b, which is a component of the histone modification complex. We found that the Ada2b RNAi and mutant flies showed dampened enhancement of survival rates after Ml-training. These results suggest that Ada2b is involved in the Drosophila trained immunity.
The ‘squalene route’ to carotenoid biosynthesis is widespread in Bacteria
Authors: Santana-Molina Carlos , Henriques Valentina , Hornero-Méndez Damaso , Devos Damien P. , Rivas-Marin Elena 
Published: December 2021

AbstractSqualene is mostly associated with the biosynthesis of polycyclic triterpenes. Although there have been suggestions that squalene could be involved in the biosynthesis of carotenoids, functionally and evolutionarily related to polycyclic triterpenes, evidence of this ‘squalene route’ in nature was lacking. We demonstrate that planctomycetes synthesize C30 carotenoids via squalene and that this ‘squalene route’ is widely distributed in Bacteria. We also investigated the functional roles of hopanoids and carotenoids in Planctomycetes and show that their protective functions under stress conditions are complementary. Our evolutionary analyses suggest that the C30 carotenoid biosynthetic pathway is the most ancestral, with a potential origin in Firmicutes or Planctomycetes. In addition, we propose an evolutionary scenario to explain the diversification of the different carotenoid and squalene pathways. Together, these results improve the evolutionary contextualization of these molecules. Likewise, the widespread occurrence of the squalene route in bacteria increases the functional repertoire of squalene.
The transcription factor Zic4 acts as a transdifferentiation switch
Authors: Vogg Matthias Christian , Ferenc Jaroslav , Buzgariu Wanda Christa , Perruchoud Chrystelle , Papasaikas Panagiotis , Sanchez Paul Gerald Layague , Nuninger Clara , Delucinge-Vivier Céline , Rampon Christine , Beccari Leonardo , Vriz Sophie , Vincent Stéphane , Galliot Brigitte , Tsiairis Charisios D. 
Published: December 2021

AbstractThe molecular mechanisms that maintain cell identities and prevent transdifferentiation remain mysterious. Interestingly, both dedifferentiation and transdifferentiation are transiently reshuffled during regeneration. Therefore, organisms that regenerate readily offer a fruitful paradigm to investigate the regulation of cell fate stability. Here, we used Hydra as a model system and show that Zic4 silencing is sufficient to induce transdifferentiation of tentacle into foot cells. We identified a Wnt-controlled Gene Regulatory Network that controls a transcriptional switch of cell identity. Furthermore, we show that this switch also controls the re-entry into the cell cycle. Our data indicate that maintenance of cell fate by a Wnt-controlled GRN is a key mechanism during both homeostasis and regeneration.One-Sentence SummaryA Wnt-controlled GRN controls fate maintenance in Hydra.
Transport receptor occupancy in Nuclear Pore Complex mimics
Authors: Fragasso Alessio , de Vries Hendrik W. , Andersson John , van der Sluis Eli O. , van der Giessen Erik , Onck Patrick R. , Dekker Cees 
Published: December 2021

AbstractNuclear Pore Complexes (NPCs) regulate all molecular transport between the nucleus and the cytoplasm in eukaryotic cells. Intrinsically disordered Phe-Gly nucleoporins (FG Nups) line the central conduit of NPCs to impart a selective barrier where large proteins are excluded unless bound to a transport receptor (karyopherin; Kap). Here, we assess ‘Kap-centric’ NPC models, which postulate that Kaps participate in establishing the selective barrier. We combine biomimetic nanopores, formed by tethering Nsp1 to the inner wall of a solid-state nanopore, with coarse-grained modeling to show that yeast Kap95 exhibits two populations in Nsp1-coated pores: one population that is transported across the pore in milliseconds, and a second population that is stably assembled within the FG mesh of the pore. Ionic current measurements show a conductance decrease for increasing Kap concentrations and noise data indicate an increase in rigidity of the FG-mesh. Modeling reveals an accumulation of Kap95 near the pore wall, yielding a conductance decrease. We find that Kaps only mildly affect the conformation of the Nsp1 mesh and that, even at high concentrations, Kaps only bind at most 8% of the FG-motifs in the nanopore, indicating that Kap95 occupancy is limited by steric constraints rather than by depletion of available FG-motifs. Our data provide an alternative explanation of the origin of bimodal NPC binding of Kaps, where a stable population of Kaps binds avidly to the NPC periphery, while fast transport proceeds via a central FG-rich channel through lower affinity interactions between Kaps and the cohesive domains of Nsp1.
The impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip
Authors: Watkins Sarah Holmes , Ho Karen , Testa Christian , Falk Louise , Soule Patrice , Nguyen Linda V. , FitzGibbon Sophie , Slack Catherine , Chen Jarvis T. , Smith George Davey , De Vivo Immaculata , Simpkin Andrew J. , Tilling Kate , Waterman Pamela D. , Krieger Nancy , Suderman Matthew , Relton Caroline 
Published: December 2021

AbstractBackgroundDNA methylation (DNAm) is commonly assayed using the Illumina Infinium MethylationEPIC BeadChip, but there is currently little published evidence to define the lower limits of the amount of DNA that can be used whilst preserving data quality. Such evidence is valuable for analyses utilising precious or limited DNA sources.Materials and methodsWe use a single pooled sample of DNA in quadruplicate at three dilutions to define replicability and noise, and an independent population dataset of 328 individuals (from a community-based study including US-born non-Hispanic Black and white persons) to assess the impact of total DNA input on the quality of data generated using the Illumina Infinium MethylationEPIC BeadChip.ResultsData are less reliable and more noisy as DNA input decreases to 40ng, with clear reductions in data quality; however samples with a total input as low as 40ng pass standard quality control tests, and we observe little evidence that low input DNA obscures the associations between DNAm and two phenotypes, age and smoking status.ConclusionsDNA input as low as 40ng can be used with the Illumina Infinium MethylationEPIC BeadChip, provided quality checks and sensitivity analyses are undertaken.
Photosynthetic light harvesting and thylakoid organization in a CRISPR/Cas9 Arabidopsis thaliana LHCB1 knockout mutant
Authors: Sattari Vayghan Hamed , Nawrocki Wojciech J. , Schiphorst Christo , Tolleter Dimitri , Hu Chen , Douet Veronique , Glauser Gaëtan , Giovanni Finazzi , Croce Roberta , Wientjes Emilie , Longoni Fiamma 
Published: December 2021

AbstractLight absorbed by chlorophylls of photosystem II and I drives oxygenic photosynthesis. Light-harvesting complexes increase the absorption cross-section of these photosystems. Furthermore, these complexes play a central role in photoprotection by dissipating the excess of absorbed light energy in an inducible and regulated fashion. In higher plants, the main light-harvesting complex is the trimeric LHCII.In this work, we used CRISPR/Cas9 to knockout the five genes encoding LHCB1, which is the major component of the trimeric LHCII. In absence of LHCB1 the accumulation of the other LHCII isoforms was only slightly increased, thereby resulting in chlorophyll loss leading to a pale green phenotype and growth delay. Photosystem II absorption cross-section was smaller while photosystem I absorption cross-section was unaffected. This altered the chlorophyll repartition between the two photosystems, favoring photosystem I excitation. The equilibrium of the photosynthetic electron transport was partially maintained by a lower photosystem I over photosystem II reaction center ratio and by the dephosphorylation of LHCII and photosystem II. Loss of LHCB1 altered the thylakoid structure, with less membrane layers per grana stack and reduced grana width. Stable LHCB1 knock out lines allow characterizing the role of this protein in light harvesting and acclimation and pave the way for future in vivo mutational analyses of LHCII.