bluuebunny/crossref_metadata_2025_split huggingface dataset:
UV-B exposure and exogenous hydrogen peroxide application leads to cross-tolerance toward drought in Nicotiana tabacum L
Authors: Diana Sáenz-de la O , Morales Luis O. , Strid Åke , Torres-Pacheco Irineo , Guevara-González Ramón G. 
Published: February 2021

AbstractAcclimation of plants to water deficit involves biochemical and physiological adjustments. Here, we studied how UV-B exposure and exogenously applied hydrogen peroxide (H2O2) potentiates drought tolerance in tobacco (Nicotiana tabacum L.). Separate and combined applications for 14 days of 1.75 kJ m−2 day−1 UV-B radiation and 0.2 mM H2O2 were assessed. Both factors, individually and combined, resulted in inhibition of growth. Furthermore, the combined treatment led to the most compacted plants. UV-B- and UV-B+H2O2-treated plants increased total antioxidant capacity and foliar epidermal flavonol content. H2O2- and UV-B+H2O2-pre-treated plants showed cross-tolerance to a subsequent 7-day drought treatment. Plant responses to the pre-treatment were notably different: i) H2O2 increased the activity of catalase, phenylalanine ammonia lyase and peroxidase activities, and ii) the combined treatment induced epidermal flavonols which were key to drought tolerance. We report synergistic effects of UV-B and H2O2 on transcription accumulation of UV RESISTANCE LOCUS 8, NAC DOMAIN PROTEIN 13 (NAC13), and BRI1-EMS-SUPPRESSOR 1 (BES1). Our data demonstrate a pre-treatment-dependent response to drought for NAC13, BES1 and CHALCONE SYNTHASE transcript accumulation. This study highlights the potential of combining UV-B and H2O2 to improve drought tolerance which could become a useful tool to reduce water use.
DENTIST – using long reads for closing assembly gaps at high accuracy
Authors: Ludwig Arne , Pippel Martin , Myers Gene , Hiller Michael 
Published: February 2021

AbstractBackgroundLong sequencing reads allow increasing contiguity and completeness of fragmented, short-read based genome assemblies by closing assembly gaps, ideally at high accuracy. While several gap closing methods have been developed, these methods often close an assembly gap with sequence that does not accurately represent the true sequence.FindingsHere, we present DENTIST, a sensitive, highly accurate and automated pipeline method to close gaps in short-read assemblies with long error-prone reads. DENTIST comprehensively determines repetitive assembly regions to identify reliable and unambiguous alignments of long reads to the correct loci, integrates a consensus sequence computation step to obtain a high base accuracy for the inserted sequence, and validates the accuracy of closed gaps. Unlike previous benchmarks, we generated test assemblies that have gaps at the exact positions where real short-read assemblies have gaps. Generating such realistic benchmarks forDrosophila(134 Mb genome),Arabidopsis(119 Mb), hummingbird (1 Gb) and human (3 Gb) and using simulated or real PacBio continuous long reads, we show that DENTIST consistently achieves a substantially higher accuracy compared to previous methods, while having a similar sensitivity.ConclusionDENTIST provides an accurate approach to improve the contiguity and completeness of fragmented assemblies with long reads. DENTIST’s source code including a Snakemake workflow, conda package and Docker container is available athttps://github.com/a-ludi/dentist. All test assemblies as a resource for future benchmarking are athttps://bds.mpi-cbg.de/hillerlab/DENTIST/.
Phylogenomic Analyses Of 2,786 Genes In 158 Lineages Support a Root of The Eukaryotic Tree of Life Between Opisthokonts (Animals, Fungi and Their Microbial Relatives) and All Other Lineages
Authors: Cerón-Romero Mario A. , Fonseca Miguel M. , de Oliveira Martins Leonardo , Posada David , Katz Laura A. 
Published: February 2021

AbstractAdvances in phylogenetics and high-throughput sequencing have allowed the reconstruction of deep phylogenetic relationships in the evolution of eukaryotes. Yet, the root of the eukaryotic tree of life remains elusive. The most popular hypothesis in textbooks and reviews is a root between Unikonta (Opisthokonta + Amoebozoa) and Bikonta (all other eukaryotes), which emerged from analyses of a single gene fusion. Subsequent highly-cited studies based on concatenation of genes supported this hypothesis with some variations or proposed a root within Excavata. However, concatenation of genes neither considers phylogenetically-informative events (i.e. gene duplications and losses), nor provides an estimate of the root. A more recent study using gene tree-species tree reconciliation methods suggested the root lies between Opisthokonta and all other eukaryotes, but only including 59 taxa and 20 genes. Here we apply a gene tree – species tree reconciliation approach to a gene-rich and taxon-rich dataset (i.e. 2,786 gene families from two sets of ~158 diverse eukaryotic lineages) to assess the root, and we iterate each analysis 100 times to quantify tree space uncertainty. We estimate a root between Fungi and all other eukaryotes, or between Opisthokonta and all other eukaryotes, and reject alternative roots from the literature. Based on further analysis of genome size we propose Opisthokonta + others as the most likely root.Impact summaryFinding the root of the eukaryotic tree of life is critical for the field of comparative biology as it allows us to understand the timing and mode of evolution of characters across the evolutionary history of eukaryotes. But this is one of the most challenging questions in evolutionary biology because the age (~1.8 billion years), diversity and complexity of eukaryotes challenge phylogenomic methods. This study evaluates the root using reconciliation of gene trees and species trees instead of the more common approach of analyzing concatenated genes. The dataset used in this study is bigger and more taxonomically inclusive than the dataset of any previous study about the eukaryotic root, and supports a root at or within Opisthokonta (e.g. animals and fungi). Finally, we explicitly test alternative hypotheses from the literature, and again find support for an Opisthokonta root.
Sequence-unrelated long noncoding RNAs converged to modulate the activity of conserved epigenetic machineries across kingdoms
Authors: Fonouni-Farde Camille , Christ Aurélie , Blein Thomas , Ramírez-Prado Juan Sebastián , Legascue María Florencia , Latrasse David , Moison Michaël , Lucero Leandro , Ferrero Lucía , Gonzalez Daniel , Benhamed Moussa , Quadrana Leandro , Crespi Martin , Ariel Federico 
Published: February 2021

SUMMARYRNA-DNA hybrid (R-loop)-associated long noncoding RNAs (lncRNAs), including the Arabidopsis lncRNAAUXIN-REGULATED PROMOTER LOOP(APOLO), are emerging as important regulators of three-dimensional chromatin conformation and gene transcriptional activity. Here, we showed that in addition to the PRC1-component LIKE-HETEROCHROMATIN PROTEIN 1 (LHP1),APOLOinteracts with the methylcytosine-binding protein VARIANT IN METHYLATION 1 (VIM1), a conserved homolog of the mammalian DNA methylation regulator UBIQUITIN-LIKE CONTAINING PHD AND RING FINGER DOMAINS 1 (UHRF1). TheAPOLO-VIM1-LHP1 complex directly regulates the transcription of the auxin biosynthesis geneYUCCA2by dynamically determining DNA methylation and H3K27me3 deposition over its promoter during the plant thermomorphogenic response. Strikingly, we demonstrated that the lncRNAUHRF1 Protein Associated Transcript(UPAT), a direct interactor of UHRF1 in humans, can be recognized by VIM1 and LHP1 in plant cells, despite the lack of sequence homology betweenUPATandAPOLO. In addition, we showed that increased levels ofAPOLOorUPAThamper VIM1 and LHP1 binding toYUCCA2promoter. Collectively, our results uncover a new mechanism in which a plant lncRNA coordinates Polycomb action and DNA methylation, and reveal that evolutionary unrelated lncRNAs may exert similar functions across kingdoms.
A cytofluorimetric analysis of aSaccharomyces cerevisiaepopulation cultured in a fed-batch bioreactor
Authors: Palomba Emanuela , Tirelli Valentina , de Alteriis Elisabetta , Landi Carmine , Mazzoleni Stefano , Sanchez Massimo 
Published: February 2021

AbstractThe yeastSaccharomyces cerevisiaeis a reference model system and one of the widely used microorganisms in many biotechnological processes. In industrial yeast applications, combined strategies aim to maximize biomass/product yield, with the fed-batch culture being one of the most frequently used. Flow cytometry (FCM) is widely applied in biotechnological processes and represents a key methodology to monitor cell population dynamics. We propose here an application of FCM in the analysis of yeast cell cycle along the time course of a typical S.cerevisiaefed-batch culture. We used two different dyes, SYTOX Green and SYBR Green, with the aim to better define each stage of cell cycle during S.cerevisiaefed-batch culture. The results provide novel insights in the use of FCM cell cycle analysis for the real-time monitoring ofS. cerevisiaebioprocesses.
Seasonal dynamics are the major driver of microbial diversity and composition in intensive freshwater aquaculture
Authors: Marmen Sophi , Fadeev Eduard , Al Ashhab Ashraf , Benet-Perelberg Ayana , Naor Alon , Patil Hemant J. , Cytryn Eddie , Viner-Mozzini Diti , Sukenik Assaf , Lalzar Maya , Sher Daniel 
Published: February 2021

AbstractAquaculture facilities such as fishponds are one of the most anthropogenically impacted freshwater ecosystems. The high fish biomass reared in aquaculture is associated with an intensive input into the water of fish-feed and fish excrements. This nutrients load may affect the microbial community in the water, which in turn can impact the fish health. To determine to what extent aquaculture practices and natural seasonal cycles affect the microbial populations, we characterized the microbiome of an inter-connected aquaculture system at monthly resolution, over three years. The system comprised two fishponds, where fish are grown, and a “control” operational water reservoir in which fish are not actively stocked. Clear natural seasonal cycles of temperature and inorganic nutrients concentration, as well as recurring cyanobacterial blooms during summer, were observed in both the fishponds and the reservoir. The structure of the aquatic bacterial communities in the system, characterized using 16S rRNA sequencing, was explained primarily by the natural seasonality, whereas aquaculture-related parameters had only a minor explanatory power. However, the cyanobacterial blooms were characterized by different cyanobacterial clades dominating at each fishpond, possibly in response to distinct nitrogen and phosphate ratios. In turn, nutrient ratios may have been by the magnitude of fish feed input. Taken together, our results show that, even in strongly anthropogenically impacted aquatic ecosystems, the structure of bacterial communities is mainly driven by the natural seasonality, with more subtle effects if aquaculture-related factors.HighlightsWe present three years of monthly microbiome data from an aquaculture facility.The microbiome changes seasonally, likely driven by temperature and rainwater runoff.Summer blooms of toxin-producing cyanobacteria are repeatedly observed.Fish food may impact microbiome through changes in nutrient ratios.
Big fish, little fish: N-terminal acetyltransferase Naa40p proteoforms caught in the act
Authors: Jonckheere Veronique , Van Damme Petra 
Published: February 2021

AbstractNatD consist of the evolutionary conserved N-alpha acetyltransferase catalytic subunit Naa40p and is among the most selective N-terminal acetyltransferase (NAT) complexes identified to date. Here we identified a conserved 22 amino acid N-terminally truncated Naa40 proteoform named Naa40p25 or short Naa40 (Naa40S). Intriguingly, while upon ectopic expression in yeast, both Naa40p proteoforms were capable of restoring N-terminal acetylation of the well characterized yeast histone H2A Naa40p substrate, the Naa40p histone H4 substrate remained N-terminally free in human haploid cells specifically deleted for canonical Naa40p27 or 237 amino acid long Naa40 (Naa40L), but expressing Naa40S. Interestingly, human Naa40Land Naa40Sdisplayed differential expression and subcellular localization patterns by exhibiting a principal nuclear and cytoplasmic localization, respectively. Further, since Naa40Lwas identified as being N-terminally myristoylated and shown to interact with N-myristoyltransferase 1 (NMT1), NMT1 may steer Naa40Lnuclear import. Differential interactomics data obtained by biotin-dependent proximity labeling (BioID) further hints to context dependent roles of Naa40p proteoforms. More specifically, with Naa40Srepresenting the main co-translationally acting actor, the interactome of Naa40Lwas enriched for nucleolar proteins implicated in ribosome biogenesis and the assembly of ribonucleoprotein particles, overall indicating a proteoform-specific segregation of previously reported Naa40p activities. Finally, the yeast histone variant H2A.Z and the transcriptionally regulatory protein Lge1 were identified as novel Naa40p substrates, expanding the restricted substrate repertoire of Naa40p with two additional members and further confirming Lge1 as being the first redundant yNatA and yNatD substrate identified to date.
PI3K Signaling Specifies Proximal-Distal Fate by Driving a Developmental Gene Regulatory Network in Sox9+ Lung Progenitors
Authors: Khattar Divya , Fernandes Sharlene , Snowball John , Guo Minzhe , Gillen Matthew C. , Sinner Deborah , Zacharias William , Swarr Daniel T. 
Published: February 2021

AbstractThe tips of the developing respiratory buds are home to important progenitor cells marked by the expression of SOX9 and ID2. Early in embryonic development (prior to E13.5), SOX9+ progenitors are multipotent, generating both airway and alveolar epithelium, but are selective progenitors of alveolar epithelial cells later in development. Transcription factors, includingSox9, Etv5,Irx,Mycn, andFoxp1/2interact in complex gene regulatory networks to control proliferation and differentiation of SOX9+ progenitors. Molecular mechanisms by which these transcription factors and other signaling pathways control chromatin state to establish and maintain cell-type identity are not well-defined. Herein, we analyze paired gene expression (RNA-Seq) and chromatin accessibility (ATAC-Seq) data from SOX9+ epithelial progenitor cells (EPCs) during embryonic development. Widespread changes in chromatin accessibility were observed between E11.5 and E16.5, particularly at distal cis-regulatory elements (e.g. enhancers). Gene regulatory network (GRN) inference identified a common SOX9+ progenitor GRN, implicating phosphoinositide 3-kinase (PI3K) signaling in the developmental regulation of SOX9+ progenitor cells. Consistent with this model, conditional ablation of PI3K signaling in the developing lung epitheliumin vivoand in lung explantsin vitroresulted in an expansion of the SOX9+ EPC population and impaired epithelial cell differentiation. These data demonstrate that PI3K signaling is required for epithelial patterning during lung organogenesis, and emphasize the combinatorial power of paired RNA-Seq and ATAC-Seq in defining regulatory networks in development.
Microtubule-based Transport is Essential to Distribute RNA and Nascent Protein in Skeletal Muscle
Authors: Denes Lance T. , Kelley Chase P. , Wang Eric T. 
Published: February 2021

SUMMARYWhile the importance of RNA localization in highly differentiated cells is well appreciated, basic principles of RNA localization in skeletal muscle remain poorly characterized. Here, we develop a method to detect single RNA molecules and quantify localization patterns in skeletal myofibers, and we uncover a critical and general role for directed transport of RNPs in muscle. We find that RNAs are localized and translated along cytoskeletal filaments, and we identify the Z-disk as a biological hub for RNA localization and protein synthesis. We show that muscle development triggers complete reliance on the lattice-like microtubule network to transport RNAs and that disruption of microtubules leads to striking accumulation of RNPs and nascent protein around myonuclei. Our observations suggest that active transport may be globally required to distribute RNAs in highly differentiated cells and reveal fundamental mechanisms relevant to myopathies caused by perturbations to RNPs, microtubules, and the nuclear envelope.Abstract Figure
A novel reticular oscillator in the brainstem synchronizes neonatal crying with breathing
Authors: Wei Xin Paul , Collie Matthew , Dempsey Bowen , Fortin Gilles , Yackle Kevin 
Published: February 2021

AbstractHuman speech can be divided into short, rhythmically-timed elements, similar to syllables within words. Even our cries and laughs, as well as the vocalizations of other species, are periodic. However, the cellular and molecular mechanisms underlying the tempo of mammalian vocalizations remain unknown. Here we describe rhythmically-timed neonatal mouse vocalizations that occur within single breaths, and identify a brainstem node that structures these cries, which we name the intermediate reticular oscillator (iRO). We show that the iRO acts autonomously and sends direct inputs to key muscles in order to coordinate neonatal vocalizations with breathing, as well as paces and patterns these cries. These results reveal that a novel mammalian brainstem oscillator embedded within the conserved breathing circuitry plays a central role in the production of neonatal vocalizations.
Improved correspondence of fMRI visual field localizer data after cortex-based macroanatomical alignment
Authors: Qubad Mishal , Barnes-Scheufler Catherine V. , Schaum Michael , Raspor Eva , Rösler Lara , Peters Benjamin , Schiweck Carmen , Goebel Rainer , Reif Andreas , Bittner Robert A. 
Published: February 2021

ABSTRACTStudying the visual system with fMRI often requires using localizer paradigms to define regions of interest (ROIs). However, the considerable interindividual variability of the cerebral cortex represents a crucial confound for group-level analyses. Cortex-based alignment (CBA) techniques reliably reduce interindividual macroanatomical variability. Yet, their utility has not been assessed for visual field localizer paradigms, which map specific parts of the visual field within retinotopically organized visual areas. We evaluated CBA for an attention-enhanced visual field localizer mapping homologous parts of each visual quadrant in 50 participants. We compared CBA with volume-based alignment and a surface-based analysis, which did not include macroanatomical alignment. CBA led to the strongest increase in the probability of activation overlap (up to 40 percent). On the group level, CBA led to the most consistent increase in ROI size while preserving vertical ROI symmetry. Overall, our results indicate, that in addition to the increased signal-to-noise ratio of a surface-based analysis macroanatomical alignment considerably improves statistical power. These findings confirm and extend the utility of CBA for the study of the visual system in the context of group analyses. CBA should be particularly relevant when studying neuropsychiatric disorders with abnormally increased interindividual macroanatomical variability.
Transcriptional regulation ofHSFA7and post-transcriptional modulation ofHSFB4aby miRNA4200 govern general and varietal thermotolerance in tomato
Authors: Rao Sombir , Balyan Sonia , Das Jaishri Rubina , Verma Radhika , Mathur Saloni 
Published: February 2021

AbstractHeat shock factors (HSFs) are at the core of heat stress (HS) response in plants. However, the contribution of HSFs governing the inherent thermotolerance mechanism in tomato from sub-tropical hot climates is poorly understood. With the above aim, comparative expression profiles of theHSFfamily in a HS tolerant (CLN1621L) and a sensitive cultivar (CA4) of tomato under HS revealed cultivar-biased regulation of an activator (HSFA7a) and repressor (HSFB4a) class HSF. Functional characterization ofHSFA7athat was strongly up-regulated in the tolerant cultivar by VIGS-based silencing and overexpression established it as a positive regulator of HS-tolerance. While knock-down and overexpression analyses ofHSFB4athat was down-regulated in CLN1621L in HS, showed it as a negative regulator of thermotolerance. Promoter:GUSreporter assays and promoter sequence analyses suggest heat-mediated transcriptional control of both theHSFgenes in the contrasting cultivars. Moreover, we showHSFB4ais also regulated post-transcriptionally by microRNA Sly-miR4200 using degradome, short-tandem-target-mimic of Sly-miR4200 and transientin-plantaSly-miR4200-effector:HSFB4a-reporter assays. This miRNA is induced several folds upon HS in the tolerant variety thereby reducingHSFB4alevels. We thus propose that the alleviation of HSFB4a repressor governs thermotolerance in the tolerant cultivar by regulating downstream heat stress responsive genes.
Discovering differential genome sequence activity with interpretable and efficient deep learning
Authors: Hammelman Jennifer , Gifford David K. 
Published: February 2021

AbstractDiscovering sequence features that differentially direct cells to alternate fates is key to understanding both cellular development and the consequences of disease related mutations. We introduce Expected Pattern Effect and Differential Expected Pattern Effect, two black-box methods that can interpret genome regulatory sequences for cell type-specific or condition specific patterns. We show that these methods identify relevant transcription factor motifs and spacings that are predictive of cell state-specific chromatin accessibility. Finally, we integrate these methods into framework that is readily accessible to non-experts and available for download as a binary or installed via PyPI or bioconda athttps://cgs.csail.mit.edu/deepaccess-package/.Author SummaryWithin the genome are the instructions to build all the cell types that make up the human body. However, understanding these instructions and how and when these instructions go wrong in cancer or genetically inherited disease is an open problem. Deep neural networks provide powerful models to learn the relationship between DNA sequence and functional consequence across many different cell types, such as whether a particular stretch of DNA is accessible and genes in that region can be expressed or is inaccessible and therefore genes are inactive. Despite these advances, a major setback in deep learning is that it is challenging to understand what patterns of DNA sequences a deep learning model has learned to associate with a particular genomic function, whether these patterns are significant, and how to determine whether these patterns are specific to a particular cell type or are general “housekeeping” patterns that function across many cell types. We introduce Expected Pattern Effect and Differential Expected Pattern Effect, two methods which allow us to evaluate the significance of particular patterns of DNA sequence features on models trained to predict function across multiple cell types, and apply this to problems of transcription factor binding and DNA accessibility across multiple cell types.