bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ibrutinib blocks YAP1 activation and reverses BRAFi resistance in melanoma cells
Authors: Misek SA , Newbury PA , Chekalin E , Paithankar S , Doseff AI , Chen B , Gallo KA , Neubig RR 
Published: March 2020

AbstractMost BRAF-mutant melanoma tumors respond initially to BRAFi/MEKi therapy, although few patients have durable long-term responses to these agents. The goal of this study was to utilize an unbiased computational approach to identify inhibitors which reverse an experimentally derived BRAFi resistance gene expression signature. Using this approach, we found that ibrutinib effectively reverses this signature and we demonstrate experimentally that ibrutinib re-sensitizes a subset of BRAFi-resistant melanoma cells to vemurafenib. Ibrutinib is used clinically as a BTK inhibitor; however, neither BTK deletion nor treatment with acalabrutinib, another BTK inhibitor with reduced off-target activity, re-sensitized cells to vemurafenib. These data suggest that ibrutinib acts through a BTK-independent mechanism in vemurafenib re-sensitization. To better understand this mechanism, we analyzed the transcriptional profile of ibrutinib-treated BRAFi-resistant melanoma cells and found that the transcriptional profile of ibrutinib was highly similar to that of multiple SRC kinase inhibitors. Since ibrutinib, but not acalabrutinib, has significant off-target activity against multiple SRC family kinases, it suggests that ibrutinib may be acting through this mechanism. Furthermore, genes either upregulated or downregulated by ibrutinib treatment are enriched in YAP1 target genes and we showed that ibrutinib, but not acalabrutinib, reduces YAP1 activity in BRAFi-resistant melanoma cells. Taken together, these data suggest that ibrutinib, or other SRC family kinase inhibitors, may be useful for treating some BRAFi/MEKi-refractory melanoma tumors.
MeSSII interplays the amylose and amylopectin biosynthesis by protein interactions in cassava storage root
Authors: He Shutao , Hao Xiaomeng , Wang Shanshan , Zhou Wenzhi , Ma Qiuxiang , Lu Xinlu , Chen Luonan , Zhang Peng 
Published: March 2020

AbstractStarch is a glucose polymer synthesized by green plants for energy storage, and is crucial for plant growth and reproduction. The biosynthesis of starch polysaccharides is mediated by members of the large starch synthase (SS) protein superfamily. Here, we showed that in cassava storage roots, soluble starch synthase II (MeSSII) plays an important role in starch biosynthesis via forming protein complexes with other starch biosynthetic enzymes by directly interacting with MeSSI, MeSBEII and MeISAII. TheMeSSII-RNAi cassava lines showed increased amylose content and reduced intermediate chain of amylopectin (B1 type) biosynthesis in their storage roots, leading to altered starch physico-chemical properties. Further gel permeation chromatography analysis of starch biosynthetic enzymes between the wild type andMeSSII-RNAi lines confirmed the key rule of MeSSII in the organization of heteromeric starch synthetic protein complexes, including the MeSSII-MeSSI-MeGBSSI and MeSBEII-MeSSI-MeSSII-MeISAII-MeISAI complexes. The lack of MeSSII in cassava also reduced the binding capacity of the MeSSI, MeSBEII, MeISAI, and MeISAII to starch granules. Our results show a close coordination between granule-bound starch synthase and amylopectin biosynthetic enzymes, which implies that the processes of amylose synthesis and amylopectin synthesis are directly interrelated. These findings shed light on the key components of the starch biosynthesis machinery in root crops.One Sentence SummaryHere, by focusing on cassava SSII, we elucidated its function and the molecular mechanism by which it chaperones the starch synthase complex to regulate starch biosynthesis in cassava storage roots.
Sorting and cultivation ofFaecalibacterium prausnitziifrom fecal samples using flow cytometry in anaerobic conditions
Authors: Bellais Samuel , Nehlich Mélanie , Duquenoy Aurore , Ania Maryne , van den Engh Ger , Baijer Jan , Belotserkovsky Ilia , Thomas Vincent 
Published: March 2020

AbstractBackgroundThere is a growing interest in using gut commensal bacteria as ‘next generation’ probiotics. However, this approach is still hampered by the fact that there are few or no strains available for specific species that are difficult to cultivate. Our objective was therefore to adapt flow cytometry and cell sorting to be able to detect, separate, isolate and cultivate new strains of Extremely Oxygen Sensitive (EOS) species from fecal material, focusing onFaecalibacterium prausnitziias a proof-of-concept.ResultsA BD Influx®cell sorter was equipped with a glovebox that covers the sorting area. This box is flushed with nitrogen to deplete oxygen in the enclosure. Several non-specific staining methods including Wheat Germ Agglutinin (WGA), Vancomycin BODIPY™ and LIVE/DEAD BacLight were evaluated with three different strains of the EOS speciesF. prausnitzii. In parallel, we generated polyclonal antibodies directed against this species by immunizing rabbits with heat-inactivated bacteria. Anaerobic conditions were maintained during the full process, resulting in only minor viability loss during sorting and culture of unstainedF. prausnitziireference strains. In addition, staining solutions did not severely impact bacterial viability while allowing discrimination between groups of strains. Efficient detection was achieved using polyclonal antibodies directed against heat-fixed bacteria. Finally, we were able to detect, isolate and cultivate a variety ofF. prausnitziistrains from healthy volunteer’s fecal samples using WGA staining and antibodies. These strains present markedly different phenotypes, thus confirming the heterogeneity of the species.ConclusionsCell-sorting in anaerobic conditions is a promising tool for the study of fecal microbiota. It gives the opportunity to quickly analyze microbial populations and to sort strains of interest using specific antibodies, thus opening new avenues for targeted culturomics experiments.
Controlling minimal and maximal hook-length of the bacterial flagellum
Authors: Guse Alina , Rohde Manfred , Erhardt Marc 
Published: March 2020

AbstractHook-length control is a central checkpoint during assembly of the bacterial flagellum. During hook growth, a 405 amino acids (aa) protein, FliK, is intermittently secreted and thought to function as a molecular measuring tape that, in Salmonella, controls hook-length to 55 nm ± 6 nm. The underlying mechanism involves interactions of both the α-helical, N-terminal domain of FliK (FliKN) with the hook and hook cap, and of its C-terminal domain with a component of the export apparatus. However, various deletion mutants of FliKN display uncontrolled hook-length, which is not consistent with a ruler mechanism. Here, we carried out an extensive deletion analysis of FliKN to investigate its contribution in the hook-length control mechanism. We identified FliKN mutants deleted for up to 80 aa that retained wildtype motility. However, the short FliK variants did not produce shorter hook-lengths as expected from a physical ruler. Rather, the minimal length of the hook depends on the level of hook protein production and secretion. Our results thus support a model in which FliK functions as a hook growth terminator protein that limits the maximal length of the hook, and not as a molecular ruler that physically measures hook-length.
Sensing of endogenous nucleic acids by ZBP1 induces keratinocyte necroptosis and skin inflammation
Authors: Devos Michael , Tanghe Giel , Gilbert Barbara , Dierick Evelien , Verheirstraeten Maud , Nemegeer Josephine , de Reuver Richard , Lefebvre Sylvie , De Munck Jolien , Rehwinkel Jan , Vandenabeele Peter , Declercq Wim , Maelfait Jonathan 
Published: March 2020

AbstractAberrant detection of endogenous nucleic acids by the immune system can cause inflammatory disease. The scaffold function of the signalling kinase RIPK1 limits spontaneous activation of the nucleic acid sensor ZBP1. Consequently, loss of RIPK1 in keratinocytes induces ZBP1-dependent necroptosis and skin inflammation. Whether nucleic acid sensing is required to activate ZBP1 in RIPK1 deficient conditions and which immune pathways are associated with skin disease remained open questions. Using knock-in mice with disrupted ZBP1 nucleic acid binding activity, we report that sensing of endogenous nucleic acids by ZBP1 is critical in driving skin pathology characterised by antiviral and IL-17 immune responses. Inducing ZBP1 expression by interferons triggers necroptosis in RIPK1-deficient keratinocytes and epidermis-specific deletion of MLKL prevents disease, demonstrating that cell-intrinsic events cause inflammation. These findings indicate that dysregulated sensing of endogenous nucleic acid by ZBP1 can drive inflammation and may contribute to the pathogenesis of IL-17-driven inflammatory skin conditions such as psoriasis.SummaryDevos, Tangheet al. find that the recognition of endogenous nucleic acids by the nucleic acid sensor ZBP1 causes necroptosis of RIPK1-deficient keratinocytes. This process drives the development of an inflammatory skin disease characterised by an IL-17 immune response.
TheEnterprise: A massive transposon carryingSpokmeiotic drive genes
Authors: Vogan Aaron A. , Ament-Velásquez S. Lorena , Bastiaans Eric , Wallerman Ola , Saupe Sven J. , Suh Alexander , Johannesson Hanna 
Published: March 2020

AbstractThe genomes of eukaryotes are full of parasitic sequences known as transposable elements (TEs). Most TEs studied to date are relatively small (50 – 12000 bp), but can contribute to very large proportions of genomes. Here we report the discovery of a giant tyrosine-recombinase-mobilized DNA transposon,Enterprise, from the model fungusPodospora anserina. Previously, we described a large genomic feature called theSpokblock which is notable due to the presence of meiotic drive genes of theSpokgene family. TheSpokblock ranges from 110 kb to 247 kb and can be present in at least four different genomic locations withinP. anserina, despite what is an otherwise highly conserved genome structure. We have determined that the reason for its varying positions is that theSpokblock is not only capable of meiotic drive, but is also capable of transposition. More precisely, theSpokblock represents a unique case where theEnterprisehas captured theSpoks, thereby parasitizing a resident genomic parasite to become a genomic hyperparasite. Furthermore, we demonstrate thatEnterprise(without theSpoks) is found in other fungal lineages, where it can be as large as 70 kb. Lastly, we provide experimental evidence that theSpokblock is deleterious, with detrimental effects on spore production in strains which carry it. In contrast to the selfish role of theEnterpriseinP. anserina, we hypothesize that the mobility of theEnterprisemay also play an adaptive role in fungi whenEnterpriseundergoes horizontal transfer while carrying metabolic genes. This union of meiotic drivers and a transposon has created a selfish element of impressive size inPodospora, challenging our perception of how TEs influence genome evolution and broadening the horizons in terms of what the upper limit of transposition may be.
In vitroandIn vivoGenetic Disease Modelling via NHEJ-precise deletions using CRISPR/Cas9
Authors: López-Manzaneda Sergio , Ojeda-Pérez Isabel , Zabaleta Nerea , Garcia-Torralba Aída , Alberquilla Omaira , Torres Raúl , Sanchez-Dominguez Rebeca , Torella Laura , Olivier Emmanuel , Mountford Joanne , Ramírez Juan C. , Bueren Juan A. , González-Aseguinolaza Gloria , Segovia Jose-Carlos 
Published: March 2020

ABSTRACTDevelopment of advanced gene and cell therapies for the treatment of genetic diseases requires confident animal and cellular models to test their efficacy and is crucial in the cases where no primary samples from patients are available. CRISPR/Cas9 technology, has become one of the most spread endonuclease tools for editing the genome at will. Moreover, it is known that the use of two guides tends to produce the precise deletion between the guides via NHEJ. Different distances between guides were tested (from 8 to 500 base pairs). We found that distances between the two cutting sites and orientation of Cas9 protein-DNA interaction are important for the efficiency within the optimal range (30-60 bp), we could obtain new genetically reproducible models for two rare disease, a Pyruvate Kinase Deficiency model, using human primary cells, and a (forin vivoprimary hyperoxaluria therapeutic mouse model. We demonstrate that the use of a 2-guideRNAs at the optimal distance and orientation is a powerful strategy for disease modelling in those diseases where the availability of primary cells is limited.
The bacterial community structure dynamics inMeloidogyne incognitainfected roots and its role in worm-microbiome interactions
Authors: Yergaliyev Timur , Alexander-Shani Rivka , Dimeretz Hanna , Pivonia Shimon , Bird David McK. , Rachmilevitch Shimon , Szitenberg Amir 
Published: March 2020

AbstractBackgroundPlant parasitic nematodes such asMeloidogyne incognitahave a complex life cycle, occurring sequentially in various niches of the root and rhizosphere. They are known to form a range of interactions with bacteria and other microorganisms, that can affect their densities and virulence. High throughput sequencing can reveal these interactions in high temporal, and geographic resolutions, although thus far we have only scratched the surface. We have carried out a longitudinal sampling scheme, repeatedly collecting rhizosphere soil, roots, galls and second stage juveniles from 20 plants to provide a high resolution view of bacterial succession in these niches, using 16S rRNA metabarcoding.ResultsWe find that a structured community develops in the root, in which gall communities diverge from root segments lacking a gall, and that this structure is maintained throughout the crop season. We detail the successional process leading toward this structure, which is driven by interactions with the nematode and later by an increase in bacteria often found in hypoxic and anaerobic environments. We show evidence that this structure may play a role in the nematode’s chemotaxis towards uninfected root segments. Finally, we describe the J2 epibiotic microenvironment as ecologically deterministic, in part, due to active bacterial attraction of second stage juveniles.ConclusionsHigh density sampling, both temporally and across adjacent microniches, coupled with the power and relative low cost of metabarcoding, has provided us with a high resolution description of our study system. Such an approach can advance our understanding of holobiont ecology.Meloidogynespp., with their relatively low genetic diversity, large geographic range and the simplified agricultural ecosystems they occupy, can serve as a model organism. Additionally, the perspective this approach provides could promote the efforts toward biological control efficacy.
Revisiting animal photo-identification using deep metric learning and network analysis
Authors: Miele Vincent , Dussert Gaspard , Spataro Bruno , Chamaillé-Jammes Simon , Allainé Dominique , Bonenfant Christophe 
Published: March 2020

AbstractAn increasing number of ecological monitoring programs rely on photographic capture-recapture of individuals to study distribution, demography and abundance of species. Photo-identification of individuals can sometimes be done using idiosyncratic coat or skin patterns, instead of using tags or loggers. However, when performed manually, the task of going through photographs is tedious and rapidly becomes too time consuming as the number of pictures grows.Computer vision techniques are an appealing and unavoidable help to tackle this apparently simple task in the big-data era. In this context, we propose to revisit animal re-identification using image similarity networks and metric learning with convolutional neural networks (CNNs), taking the giraffe as a working example.We first developed an end-to-end pipeline to retrieve a comprehensive set of re-identified giraffes from about 4, 000 raw photographs. To do so, we combined CNN-based object detection, SIFT pattern matching, and image similarity networks. We then quantified the performance of deep metric learning to retrieve the identity of known individuals and detect unknown individuals never seen in the previous years of monitoring.After a data augmentation procedure, the re-identification performance of the CNN reached a Top-1 accuracy of about 90%, despite the very small number of images per individual in the training data set. While the complete pipeline succeeded in re-identifying known individuals, it slightly under-performed with unknown individuals.Fully based on open-source software packages, our work paves the way for further attempts to build automatic pipelines for re-identification of individual animals, not only in giraffes but also in other species.
Inhibition of mTOR signaling by genetic removal of p70 S6 Kinase 1 leads to anxiety-like disorders
Authors: Koehl Muriel , Ladeveze Elodie , Catania Caterina , Cota Daniela , Abrous Djoher Nora 
Published: March 2020

ABSTRACTThe mechanistic target or rapamycin (mTOR) is a ubiquitously expressed kinase that acts through two complexes, mTORC1 and mTORC2, to regulate protein homeostasis as well as long lasting forms of synaptic and behavioral plasticity. Alteration of the mTOR pathway is classically involved in neurodegenerative disorders, and it has been linked to dysregulation of cognitive functions and affective states. However, information concerning the specific involvement of the p70 S6 kinase 1 (S6K1), a downstream target of the mTORC1 pathway, in learning and memory processes and in the regulation of affective states remains scant. To fill this gap, we exposed adult male mice lacking S6K1 to a battery of behavioral tests aimed at measuring their learning and memory capabilities by evaluating reference memory and flexibility with the Morris water maze, and associative memory using the contextual fear conditioning task. We also studied their anxiety- and depression-like behaviors by respectively performing elevated plus maze, open field, light-dark emergence tests, and sucrose preference and forced swim tests. We found that deleting S6K1 leads to a robust anxious phenotype concomitant with associative learning deficits; these symptoms are associated with a reduction of adult neurogenesis and neuronal atrophy in the hippocampus. Collectively, these results provide grounds for the understanding of anxiety reports after treatments with mTOR inhibitors and will be critical for the development of novel compounds targeting anxiety.
EASE: EM-Assisted Source Extraction from calcium imaging data
Authors: Zhou Pengcheng , Reimer Jacob , Zhou Ding , Pasarkar Amol , Kinsella Ian , Froudarakis Emmanouil , Yatsenko Dimitri V , Fahey Paul G , Bodor Agnes , Buchanan JoAnn , Bumbarger Dan , Mahalingam Gayathri , Torres Russel , Dorkenwald Sven , Ih Dodam , Lee Kisuk , Lu Ran , Macrina Thomas , Wu Jingpeng , da Costa Nuno , Reid R. Clay , Tolias Andreas S , Paninski Liam 
Published: March 2020

AbstractCombining two-photon calcium imaging (2PCI) and electron microscopy (EM) provides arguably the most powerful current approach for connecting function to structure in neural circuits. Recent years have seen dramatic advances in obtaining and processing CI and EM data separately. In addition, several joint CI-EM datasets (with CI performed in vivo, followed by EM reconstruction of the same volume) have been collected. However, no automated analysis tools yet exist that can match each signal extracted from the CI data to a cell segment extracted from EM; previous efforts have been largely manual and focused on analyzing calcium activity in cell bodies, neglecting potentially rich functional information from axons and dendrites. There are two major roadblocks to solving this matching problem: first, dense EM reconstruction extracts orders of magnitude more segments than are visible in the corresponding CI field of view, and second, due to optical constraints and non-uniform brightness of the calcium indicator in each cell, direct matching of EM and CI spatial components is nontrivial.In this work we develop a pipeline for fusing CI and densely-reconstructed EM data. We model the observed CI data using a constrained nonnegative matrix factorization (CNMF) framework, in which segments extracted from the EM reconstruction serve to initialize and constrain the spatial components of the matrix factorization. We develop an efficient iterative procedure for solving the resulting combined matching and matrix factorization problem and apply this procedure to joint CI-EM data from mouse visual cortex. The method recovers hundreds of dendritic components from the CI data, visible across multiple functional scans at different depths, matched with densely-reconstructed three-dimensional neural segments recovered from the EM volume. We publicly release the output of this analysis as a new gold standard dataset that can be used to score algorithms for demixing signals from 2PCI data. Finally, we show that this database can be exploited to (1) learn a mapping from 3d EM segmentations to predict the corresponding 2d spatial components estimated from CI data, and (2) train a neural network to denoise these estimated spatial components. This neural network denoiser is a stand-alone module that can be dropped in to enhance any existing 2PCI analysis pipeline.
In vivo analysis of the evolutionary conserved BTD-box domain of Sp1 and Btd during Drosophila development
Authors: Blom-Dahl David , Córdoba Sergio , Gabilondo Hugo , Carr-Baena Pablo , Díaz-Benjumea Fernando J. , Estella Carlos 
Published: March 2020

AbstractThe Sp family of transcription factors plays important functions during development and disease. An evolutionary conserved role for some Sp family members is the control of limb development. The family is characterized by the presence of three C2H2-type zinc fingers and an adjacent 10 aa region with an unknown function called the Buttonhead (BTD) box. The presence of this BTD-box in all Sp family members identified from arthropods to vertebrates, suggests that it plays an important role during development. However, despite its conservation, thein vivofunction of the BTD-box has never been studied. In this work, we have generated specific BTD-box deletion alleles for theDrosophilaSp family membersSp1andbuttonhead(btd) using gene editing tools and analyzed its role during development. Unexpectedly,btdandSp1mutant alleles that lack the BTD-box are viable and have almost normal appendages. However, in a sensitized background the requirement of this domain to fully regulate some of Sp1 and Btd target genes is revealed. Furthermore, we have also identified a novel Sp1 role promoting legvsantenna identity through the repression ofspineless(ss) expression in the leg, a function that also depends on the Sp1 BTD-box.