bluuebunny/crossref_metadata_2025_split huggingface dataset:
Staufen 1 amplifies pro-apoptotic activation of the unfolded protein response
Authors: Gandelman Mandi , Dansithong Warunee , Figueroa Karla P , Paul Sharan , Scoles Daniel R , Pulst Stefan M 
Published: October 2019

AbstractStaufen-1 (STAU1) is an RNA binding protein that becomes highly overabundant in numerous neurodegenerative disease models, including those carrying mutations in presenilin1 (PSEN1), microtubule associated protein tau (MAPT), huntingtin (HTT), TAR DNA-binding protein-43 gene (TARDBP) or C9orf72. We previously reported that elevations in STAU1 determine autophagy defects. Additional functional consequences of STAU1 overabundance, however, have not been investigated. We studied the role of STAU1 in the chronic activation of the Unfolded Protein Response (UPR), a common feature among the neurodegenerative diseases where STAU1 is increased, and is directly associated with neuronal death. Here we report that STAU1 is a novel modulator of the UPR, and is required for apoptosis induced by activation of the PERK-CHOP pathway. STAU1 levels increased in response to multiple ER stressors and exogenous expression of STAU1 was sufficient to cause apoptosis through the PERK-CHOP pathway of the UPR. Cortical neurons and skin fibroblasts derived from Stau1−/− mice showed reduced UPR and apoptosis when challenged with thapsigargin. In fibroblasts from SCA2 patients or with ALS-causing TDP-43 and C9ORF72 mutations we found highly increased STAU1 and CHOP levels in basal conditions. STAU1 knockdown restored CHOP levels to normal. Taken together, these results show STAU1 overabundance reduces cellular resistance to ER stress and precipitates apoptosis.
C-terminal binding proteins 1 and 2 in traumatic brain injury-induced inflammation and their inhibition as an approach for anti-inflammatory treatment
Authors: Li Hong , Zhang Caiguo , Yang Chunxia , Blevins Melanie , Norris David , Zhao Rui , Huang Mingxia 
Published: October 2019

AbstractTraumatic brain injury (TBI) induces an acute inflammatory response in the central nervous system that involves both resident and peripheral immune cells. The ensuing chronic neuroinflammation causes cell death and tissue damage and may contribute to neurodegeneration. The molecular mechanisms involved in the maintenance of this chronic inflammation state remain underexplored. C-terminal binding protein (CtBP) 1 and 2 are transcriptional coregulators that repress diverse cellular processes. Unexpectedly, we find that the CtBPs can transactivate a common set of proinflammatory genes both in lipopolysaccharide-activated microglia, astrocytes and macrophages, and in a mouse model of the mild form of TBI. We also find that the expression of these genes is markedly enhanced by a single mild injury in both brain and peripheral blood leukocytes in a severity- and time-dependent manner. Moreover, we were able to demonstrate that specific inhibitors of the CtBPs effectively suppress the expression of the CtBP target genes and thus improve neurological outcome in mice receiving single and repeated mild TBIs. This discovery suggests new avenues for therapeutic modulation of the inflammatory response to brain injury.
Integration of ethnobotany and population genetics uncovers the agrobiodiversity of date palms of Siwa Oasis (Egypt) and their importance to the evolutionary history of the species
Authors: Gros-Balthazard Muriel , Battesti Vincent , Ivorra Sarah , Paradis Laure , Aberlenc Frédérique , Zango Oumarou , Zehdi Salwa , Moussouni Souhila , Naqvi Summar Abbas , Newton Claire , Terral Jean-Frédéric 
Published: October 2019

AbstractCrop diversity is shaped by biological and social processes interacting at different spatiotemporal scales. Here we combined population genetics and ethnobotany to investigate date palm (Phoenix dactyliferaL.) diversity in Siwa Oasis, Egypt. Based on interviews with farmers and observation of practices in the field, we collected 149 date palms from Siwa Oasis and 27 uncultivated date palms from abandoned oases in the surrounding desert. Using genotyping data from 18 nuclear and plastid microsatellite loci, we confirmed that some named types each constitute a clonal line, i.e. a true-to-type cultivar. We also found that others are collections of clonal lines, i.e. ethnovarieties, or even unrelated samples, i.e. local categories. This alters current assessments of agrobiodiversity, which are visibly underestimated, and uncovers the impact of low-intensity, but highly effective, farming practices on biodiversity. These hardly observable practices, hypothesized by ethnographic survey and confirmed by genetic analysis, are enabled by the way Isiwans conceive and classify living beings in their oasis, which do not quite match the way biologists do: a classic disparity ofeticvs.emiccategorizations. In addition, we established that Siwa date palms represent a unique and highly diverse genetic cluster, rather than a subset of North African and Middle Eastern palm diversity. As previously shown, North African date palms display evidence of introgression by the wild relativePhoenix theophrasti, and we found that the uncultivated date palms from the abandoned oases share even more alleles with this species than cultivated palms in this region. The study of Siwa date palms could hence be a key to the understanding of date palm diversification in North Africa. Integration of ethnography and population genetics promoted the understanding of the interplay between diversity management in the oasis (short-time scale), and the origins and dynamic of diversity through domestication and diversification (long-time scale).
annonex2embl: automatic preparation of annotated DNA sequences for bulk submissions to ENA
Authors: Gruenstaeudl Michael 
Published: October 2019

ABSTRACTMotivationThe submission of annotated sequence data to public sequence databases constitutes a central pillar in biological research. The surge of novel DNA sequences awaiting database submission due to the application of next-generation sequencing has increased the need for software tools that facilitate bulk submissions. This need has yet to be met with a concurrent development of tools to automate the preparatory work preceding such submissions.ResultsI introduceannonex2embl, a Python package that automates the preparation of complete sequence flatfiles for large-scale sequence submissions to the European Nucleotide Archive. The tool enables the conversion of DNA sequence alignments that are co-supplied with sequence annotations and metadata to submission-ready flatfiles. Among other features, the software automatically accounts for length differences among the input sequences while maintaining correct annotations, automatically interlaces metadata to each record, and displays a design suitable for easy integration into bioinformatic workflows. As proof of its utility,annonex2emblis employed in preparing a dataset of more than 1,500 fungal DNA sequences for database submission.
Low atmospheric CO2 levels induce nocturnal carbon accumulation in the lycophyte genus Isoëtes
Authors: Suissa Jacob S. , Green Walton A. 
Published: October 2019

Background and AimsCrassulacean Acid Metabolism (CAM) is an adaptation to increase water use efficiency in dry environments. Oddly, similar biochemical patterns occur in the submerged aquatic lycophyte genus Isoëtes. It has long been assumed that CAM-like nocturnal carbon accumulation in aquatic plants is an adaptation to low daytime carbon levels in aquatic ecosystems, but this has never been directly tested.MethodsTo test this hypothesis, populations of terrestrial Isoëtes engelmannii and I. tuckermanii were grown in climate-controlled chambers and starved of atmospheric CO2 during the day while pH was measured for 24-hours.Key resultsWe demonstrate that terrestrial plants exposed to low atmospheric CO2 display diel acidity cycles similar to those in both xerophytic CAM plants and submerged Isoëtes.ConclusionsCO2 starvation induces CAM-like nocturnal carbon accumulation in terrestrial Isoëtes, substantiating the hypothesis that carbon starvation is a selective pressure for nocturnal carbon accumulation in Isoëtes. Furthermore, while aquatic carbon levels undoubtedly promote nocturnal carbon accumulation in extant Isoëtes, the induction of this behavior in terrestrial plants suggests a possible earlier terrestrial evolution of this metabolism in Isoetalean ancestors in response to low atmospheric CO2 levels. We both provide support for a long-standing assumption about nocturnal carbon accumulation Isoëtes as well as suggest an earlier evolution of this behavior.
High-resolution in vivo identification of miRNA targets by Halo-Enhanced Ago2 Pulldown
Authors: Li Xiaoyi , Pritykin Yuri , Concepcion Carla P. , Lu Yuheng , Rocca Gaspare La , Zhang Minsi , Cook Peter J. , Au Yu Wah , Popow Olesja , Paulo Joao A. , Otis Hannah G. , Mastroleo Chiara , Ogrodowski Paul , Schreiner Ryan , Haigis Kevin M. , Betel Doron , Leslie Christina S. , Ventura Andrea 
Published: October 2019

SUMMARYThe identification of miRNA targets by Ago2 crosslinking-immunoprecipitation (CLIP) methods has provided major insights into the biology of this important class of non-coding RNAs. However, these methods are technically challenging and not easily translated to an in vivo setting. To overcome these limitations and to facilitate the investigation of miRNA functions in mice, we have developed a method (HEAP: for Halo-Enhanced Ago2 Pulldown) to map miRNA-mRNA binding sites. This method is based on a novel genetically engineered mouse harboring a conditional, Cre-regulated, Halo-Ago2 allele expressed from the endogenous Ago2 locus. By using a resin conjugated to the HaloTag ligand, Ago2-miRNA-mRNA complexes can be efficiently purified from cells and tissues expressing the endogenous Halo-Ago2 allele. We demonstrate the reproducibility and sensitivity of this method in mouse embryonic stem cells, in developing embryos, in adult tissues and in autochthonous mouse models of human brain and lung cancers.The tools and the datasets we have generated will serve as a valuable resource to the scientific community and will facilitate the characterization of miRNA functions under physiological and pathological conditions.
Adaptive Spike-Artifact Removal from Local Field Potentials Uncovers Prominent Beta and Gamma Band Neuronal Synchronization
Authors: Boroujeni Kianoush Banaie , Tiesinga Paul , Womelsdorf Thilo 
Published: October 2019

AbstractBackgroundMany neurons synchronize their action potentials to the phase of local field potential (LFP) fluctuations in one or more frequency bands. Analyzing this spike-to-LFP synchronization is challenging, however, when neural spikes and LFP are generated in the same local circuit, because the spike’s action potential waveform leak into the LFP and distort phase synchrony estimates. Existing approaches to address this spike bleed-through artifact relied on removing the average action potential waveforms of neurons, but this leaves artifacts in the LFP and distorts synchrony estimates.New MethodWe describe a spike-removal method that surpasses these limitations by decomposing individual action potentials into their frequency components before their removal from the LFP. The adaptively estimated frequency components allow for variable spread, strength and temporal variation of the spike artifact.ResultsThis adaptive approach effectively removes spike bleed-through artifacts in synthetic data with known ground truth, and in single neuron and LFP recordings in nonhuman primate striatum. For a large population of neurons with both narrow and broad action potential waveforms, the use of adaptive artifact removal uncovered 20-35 Hz beta and 35-45 Hz gamma band spike-LFP synchronization that would have remained contaminated otherwise.Comparison with Existing MethodsWe demonstrate that adaptive spike-artifact removal cleans LFP data that remained contaminated when applying existing Bayesian and non-Bayesian methods of average spike-artifact removal.ConclusionsApplying adaptive spike-removal from field potentials allows to estimate the phase at which neurons synchronize and the consistency of their phase-locked firing for both beta and low gamma frequencies. These metrics may prove essential to understand cell-to-circuit neuronal interactions in multiple brain systems.
A comprehensive conceptual and computational dynamics framework for Autonomous Regeneration Systems
Authors: Minh-Thai Tran Nguyen , Samarasinghe Sandhya , Levin Michael 
Published: October 2019

AbstractThis paper presents a new conceptual and computational dynamics framework for damage detection and regeneration in multicellular structures similar to living animals. The model uniquely achieves complete and accurate regeneration from any damage anywhere in the system. We demonstrated the efficacy of the proposed framework on an artificial organism consisting of three tissue structures corresponding to the head, body and tail of a worm. Each structure consists of a stem cell surrounded by a tissue of differentiated cells. We represent a tissue as an Auto-Associative Neural Network (AANN) with local interactions and stem cells as a self-repair network with long-range interactions. We also propose another new concept, Information Field which is a mathematical abstraction over traditional components of tissues, to keep minimum pattern information of the tissue structures to be accessed by stem cells in extreme cases of damage. Through entropy, a measure of communication between a stem cell and differentiated cells, stem cells monitor the tissue pattern integrity, violation of which triggers damage detection and tissue repair. Stem cell network monitors its state and invokes stem cell repair in the case of stem cell damage. The model accomplishes regeneration at two levels: In the first level, damaged tissues with intact stem cells regenerate themselves. Here, stem cell identifies entropy change and finds the damage and regenerates the tissue in collaboration with the AANN. In the second level, involving missing whole tissues and stem cells, the remaining stem cell(s) access the information field to restore the stem cell network and regenerate missing tissues. In the case of partial tissue damage with missing stem cells, the two levels collaborate to accurately restore the stem cell network and tissues. This comprehensive hypothetical framework offers a new way to conceptualise regeneration for better understanding the regeneration processes in living systems. It could also be useful in biology for regenerative medicine and in engineering for building self-repairing biobots.
Sea foams are ephemeral hotspots for distinctive bacterial communities contrasting sea-surface microlayer and underlying surface water
Authors: Rahlff Janina , Stolle Christian , Giebel Helge-Ansgar , Mustaffa Nur Ili Hamizah , Wurl Oliver , Herlemann Daniel P. R. 
Published: October 2019

AbstractThe occurrence of foams at oceans’ surfaces is patchy and generally short-lived but a detailed understanding of bacterial communities inhabiting sea foams is lacking. Here we investigated how marine foams differ from the sea-surface microlayer (SML), a <1 mm thick layer at the air-sea interface and underlying water from 1 m depth. Samples of sea foams, SML and underlying water collected from the North Sea and Timor Sea indicated that foams were often characterized by a high abundance of small eukaryotic phototrophic and prokaryotic cells as well as a high concentration of surface-active substances (SAS). Amplicon sequencing of 16S rRNA (gene) revealed a distinctive foam bacterial community compared to SML and underlying water, with high abundance of Gammaproteobacteria. Especially Pseudoalteromonas and Vibrio, typical SML dwellers, were highly abundant, active foam inhabitants and thus might enhance foam formation and stability by producing SAS. Despite a clear difference in the overall bacterial community composition between foam and SML, the presence of SML bacteria in foams supports previous assumptions that foam is strongly influenced by the SML. We conclude that active and abundant bacteria from interfacial habitats potentially contribute to foam formation and stability, carbon cycling and air-sea exchange processes in the ocean.One-sentence summaryFloating foams at the oceans’ surface have a unique bacterial community signature in contrast to sea-surface microlayer and underlying water but receive and select for bacterial inhabitants from surface habitats.
Heliconiusbutterflies host characteristic and phylogenetically structured adult-stage microbiomes
Authors: Hammer Tobin J. , Dickerson Jacob C. , McMillan W. Owen , Fierer Noah 
Published: October 2019

AbstractLepidoptera (butterflies and moths) are diverse and ecologically important, yet we know little about how they interact with microbes as adults. Due to metamorphosis, the form and function of their adult-stage microbiomes might be very different from microbiomes in the larval stage (caterpillars). We studied adult-stage microbiomes ofHeliconiusand closely related passion-vine butterflies (Heliconiini), which are an important model system in evolutionary biology. To characterize the structure and dynamics of heliconiine microbiomes, we used field collections of wild butterflies, 16S rRNA gene sequencing, quantitative PCR, and shotgun metagenomics. We found thatHeliconiusharbor simple and abundant bacterial communities that are moderately consistent among conspecific individuals and over time. Heliconiine microbiomes also exhibited a strong signal of host phylogeny, with a major distinction betweenHeliconiusand other butterflies. These patterns were largely driven by differing relative abundances of bacterial phylotypes shared among host species and genera, as opposed to the presence or absence of host-specific phylotypes. We suggest that phylogenetic structure in heliconiine microbiomes arises from conserved host traits that differentially filter microbes from the environment. While the relative importance of different traits remains unclear, our data indicate that pollen-feeding (unique toHeliconius) is not a primary driver. Using shotgun metagenomics, we also discovered trypanosomatids and microsporidia to be prevalent in butterfly guts, raising the possibility of antagonistic interactions between eukaryotic parasites and co-localized gut bacteria. Our discovery of characteristic and phylogenetically structured microbiomes provides a foundation for tests of adult-stage microbiome function, a poorly understood aspect of lepidopteran biology.ImportanceMany insects host microbiomes with important ecological functions. However, the prevalence of this phenomenon is unclear, because in many insect taxa microbiomes have only been studied in part of the life cycle, if at all. A prominent example is the butterflies and moths, in which the composition and functional role of adult-stage microbiomes are largely unknown. We comprehensively characterized microbiomes in adult passion-vine butterflies. Butterfly-associated bacterial communities are generally abundant in guts, consistent within populations, and composed of taxa widely shared among hosts. More closely related butterflies harbor more similar microbiomes, with the most dramatic shift in microbiome composition occurring in tandem with a suite of ecological and life history traits unique to the genusHeliconius. Butterflies are also frequently infected with previously undescribed eukaryotic parasites, which may interact with bacteria in important ways. These findings advance our understanding of butterfly biology and of insect-microbe interactions generally.
N-linked surface glycan biosynthesis, composition, inhibition, and function in cnidarian-dinoflagellate symbiosis
Authors: Tivey Trevor R. , Parkinson John Everett , Mandelare Paige E. , Adpressa Donovon A. , Peng Wenjing , Dong Xue , Mechref Yehia , Weis Virginia M. , Loesgen Sandra 
Published: October 2019

AbstractThe success of symbioses between cnidarian hosts (e.g. corals and sea anemones) and micro-algal symbionts hinges on the molecular interactions that govern the establishment and maintenance of intracellular mutualisms. As a fundamental component of innate immunity, glycan-lectin interactions impact the onset of marine endosymbioses, but our understanding of the effects of cell surface glycome composition on symbiosis establishment remains limited. In this study, we examined the canonical N-glycan biosynthesis pathway in the genome of the dinoflagellate symbiontBreviolum minutum(family Symbiodiniaceae) and found it to be conserved with the exception of the transferase GlcNAc-TII (MGAT2). Using coupled liquid chromatography-mass spectrometry (LC-MS/MS), we characterized the cell surface N-glycan content ofB. minutum, providing the first insight into the molecular composition of surface glycans in dinoflagellates. We then used the biosynthesis inhibitors kifunensine and swainsonine to alter the glycan composition ofB. minutum. Successful high-mannose enrichment via kifunensine treatment resulted in a significant decrease in colonization of the model sea anemone Aiptasia (Exaiptasia pallida) byB. minutum. Hybrid glycan enrichment via swainsonine treatment, however, could not be confirmed and did not impact colonization. We conclude that functional Golgi processing of N-glycans is critical for maintaining appropriate cell surface glycan composition and for ensuring colonization success byB. minutum.
Genome wide association study reveals novel candidate genes associated with productivity and disease resistance to Moniliophthora spp. in cacao (Theobroma cacao L.)
Authors: Osorio-Guarín Jaime A. , Berdugo-Cely Jhon A. , Coronado-Silva Roberto A. , Baez Eliana , Jaimes Yeirme , Yockteng Roxana 
Published: October 2019

ABSTRACTCacao (Theobroma cacao L.), the source of chocolate, is one the most important commodity products for farmers to improve their economic benefits. However, diseases such as frosty pod rot (FPRD) caused by Moniliophthora roreri and witches’ broom (WBD) caused by Moniliophthora perniciosa, limits the increase in yields. Molecular tools can help to develop more rapidly cacao varieties with disease resistance. In the present study, we sequenced by genotyping-by-sequencing (GBS), 229 cacao accessions to examine their genetic diversity and population structure. From those accessions, 102 have been evaluated for disease resistance and productivity to conduct a genome-wide association study (GWAS) based on 9,003 and 8,131 SNPs recovered by mapping against to the annotated cacao genomes (Criollo and Matina). Three promissory accessions for productivity and 10 accessions showing good tolerance to the evaluated diseases were found in the phenotypic evaluation. The work presented herein provides the first association mapping study in cacao using SNP markers based on GBS data. The GWAS identified two genes associated to productivity and seven to disease resistance. The results enriched the knowledge of the genetic regions associated to important traits in cacao that can have significant implications for conservation and breeding strategies such as marker-assisted selection (MAS).