bluuebunny/crossref_metadata_2025_split huggingface dataset:
Etv6/Runx1 Fusion Gene Abrogation Decreases The Oncogenic Potencial Of Tumour Cells In A Preclinical Model Of Acute Lymphoblastic Leukaemia
Authors: Montaño Adrián , Ordoñez Jose Luis , Alonso-Pérez Verónica , Hernández-Sánchez Jesús , González Teresa , Benito Rocío , García-Tuñón Ignacio , Hernández-Rivas Jesús María 
Published: October 2019

ABSTRACTBackgroundThe t(12;21)(p13;q22), which fuses ETV6 and RUNX1 genes, is the most common genetic abnormality in children with B-cell precursor acute lymphoblastic leukaemia. The implication of the fusion protein in leukaemogenesis seems to be clear. However, its role in the maintenance of the disease continues to be controversial.AimTo eliminate the expression of the ETV6/RUNX1 fusion gene, in order to elucidate the effect in the leukaemic cells.MethodsGeneration of an in vitro ETV6/RUNX1 knock out model using the genetic modification system CRISPR/Cas9. Functional studies and generation of edited-cell xenograft model were carried out.ResultsFor the first time, the expression of ETV6/RUNX1 fusion gene was completely eliminated, thus generating a powerful model on which to study the role of the fusion gene in leukaemic cells. ETV6/RUNX1 inactivation caused the deregulation of cellular processes that could be participating in the maintenance of the leukaemic phenotype, such as differentiation and lymphoid activation, apoptosis, cell signaling and cell migration. Tumour cells showed higher levels of apoptosis, lower proliferation rate and a greater sensitivity to PI3K inhibitors in vitro along as a decrease in tumour growth in xenografts models after ETV6/RUNX1 fusion gene abrogation.ConclusionsETV6/RUNX1 fusion protein plays a fundamental role in the maintenance of the leukaemic phenotype, thereby being making the fusion protein a potential therapeutic target.
Building customizable auto-luminescent luciferase-based reporters in plants
Authors: Khakhar Arjun , Starker Colby , Chamness James , Lee Nayoung , Stokke Sydney , Wang Cecily , Swanson Ryan , Rizvi Furva , Imaizumi Takato , Voytas Dan 
Published: October 2019

AbstractBioluminescence is a powerful biological signal that scientists have repurposed to design reporters for gene expression in plants and animals. However, there are some downsides associated with the need to provide a substrate to these reporters, such as its high cost and non-uniform tissue penetration. In this work we reconstitute a fungal bioluminescence pathway (FBP) in planta using an easily composable toolbox of parts. We demonstrate that the FBP can create luminescence across various tissues in a broad range of plants without external substrate addition. We also show how our toolbox can be used to deploy the FBP in planta to build auto-luminescent reporters for the study of gene-expression and hormone fluxes. A low-cost imaging platform for gene expression profiling is also described. These experiments lay the groundwork for the future construction of programmable auto-luminescent plant traits, such as creating light driven plant-pollinator interactions or light emitting plant-based sensors.
Awake reactivation and suppression after brief task exposure depend on task novelty
Authors: Bang Ji Won , Rahnev Dobromir 
Published: October 2019

AbstractPreviously learned information is known to be reactivated during periods of quiet wakefulness and such awake reactivation is considered to be a key mechanism for memory consolidation. We recently demonstrated that feature-specific awake reactivation occurs in early visual cortex immediately after extensive visual training on a novel task. To understand the exact role of awake reactivation, here we investigated whether such reactivation depends specifically on the task novelty. Subjects completed a brief visual task that was either novel or extensively trained on previous days. Replicating our previous results, we found that awake reactivation occurs for the novel task even after a brief learning period. Surprisingly, however, brief exposure to the extensively trained task led to “awake suppression” such that neural activity immediately after the exposure diverged from the pattern for the trained task. Further, subjects who had greater performance improvement showed stronger awake suppression. These results suggest that the brain operates different post-task processing depending on prior visual training.
Plasma-derived exosomal analysis and deconvolution enables prediction and tracking of melanoma checkpoint blockade response
Authors: Shi Alvin , Kasumova Gyulnara G. , Michaud William A. , Cintolo-Gonzales Jessica , Martínez Marta Díaz , Ohmura Jacqueline , Mehta Arnav , Chien Isabel , Frederick Dennie T. , Cohen Sonia , Plana Deborah , Johnson Douglas , Flaherty Keith T. , Sullivan Ryan J. , Kellis Manolis , Boland Genevieve M. 
Published: October 2019

AbstractPurposeImmune checkpoint inhibitors (ICI) have demonstrated promising therapeutic benefit although a majority will not respond. Here we identify and validate predictive biomarkers from plasma-derived exosomes that allow non-invasive monitoring of tumor intrinsic and host immune status and prediction of ICI success.Experimental DesignTranscriptomic profiling of peripheral blood bulk exosomes and tumors from a discovery cohort of 50 patients with metastatic melanoma treated with ICI was undertaken; a further validation cohort of 30 patients was utilized to validate findings from the discovery cohort. We designed a Bayesian probabilistic model to partition bulk exosomes into tumor-specific and non-tumor-specific proportions.ResultsExosomal RNA signatures exhibit significant correlations with tumor transcriptomes. Exosomal profiles reflect several key biological drivers of ICI resistance or melanoma progression, exhibit significantly differentially expressed genes and pathways, and correlate with and are predictive of clinical response to therapy. Our deconvolution model estimates contributions from tumor and non-tumor sources, enabling more precise interpretation of differentially-expressed genes and pathways. Exosomal RNA-seq mutational information can be used to segregate responders and non-responders.ConclusionsPeripheral blood-derived exosomes can serve as a non-invasive biomarker to jointly probe tumor-intrinsic and immune changes to ICI, and can potentially function as predictive markers of ICI responsiveness and a monitoring tool for tumor persistence and immune activation.Statement of SignificanceWe use transcriptomic analysis of bulk, non-selected, peripheral blood derived exosomes to reveal both tumor-intrinsic and immune-derived signatures predictive of early response to immune checkpoint inhibitor therapy. We develop a novel computational model to classify exosomal transcripts into tumor and non-tumor components and establish relevance in immune checkpoint blockade therapy. We show that tumor driver load from RNA-seq mutational calls are significantly different between responders and non-responders.
High-quality chromosome-scale assembly of the walnut (Juglans regiaL) reference genome
Authors: Marrano Annarita , Britton Monica , Zaini Paulo A. , Zimin Aleksey V. , Workman Rachael E. , Puiu Daniela , Bianco Luca , Di Pierro Erica Adele , Allen Brian J. , Chakraborty Sandeep , Troggio Michela , Leslie Charles A. , Timp Winston , Dandekar Abhaya , Salzberg Steven L. , Neale David B. 
Published: October 2019

ABSTRACTThe release of the first reference genome of walnut (Juglans regiaL.) enabled many achievements in the characterization of walnut genetic and functional variation. However, it is highly fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to fully elucidate walnut biological processes. Here we report the new chromosome-scale assembly of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the previous reference genome, the new assembly features an 84.4-fold increase in N50 size, and the full sequence of all 16 chromosomal pseudomolecules, nine of which present telomere sequences at both ends. Using full-length transcripts from single-molecule real-time sequencing, we predicted 40,491 gene models, with a mean gene length higher than the previous gene annotations. Most of the new protein-coding genes (90%) are full-length, which represents a significant improvement compared to Chandler v1.0 (only 48%). We then tested the potential impact of the new chromosome-level genome on different areas of walnut research. By studying the proteome changes occurring during catkin development, we observed that the virtual proteome obtained from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic regions highly differentiated between Western and Eastern walnut cultivars. Overall, Chandler v2.0 is a valuable resource to understand and explore walnut biology better.
Drug-tolerant idling melanoma cells exhibit theory-predicted metabolic low-low phenotype
Authors: Jia Dongya , Paudel B. Bishal , Hayford Corey E. , Hardeman Keisha N. , Levine Herbert , Onuchic José N. , Quaranta Vito 
Published: October 2019

AbstractCancer cells adjust their metabolic profiles to evade treatment. Metabolic adaptation is complex and hence better understood by an integrated theoretical-experimental approach. Using a minimal kinetic model, we predicted a previously undescribed Low/Low (L/L) phenotype, characterized by low oxidative phosphorylation (OXPHOS) and low glycolysis. Here, we report that L/L metabolism is observed in BRAF-mutated melanoma cells that enter a drug-tolerant “idling state” upon long-term MAPK inhibition (MAPKi). Consistently, using publicly available RNA-sequencing data of both cell lines and patient samples, we show that melanoma cells decrease their glycolysis and/or OXPHOS activity upon MAPKi and converge toward the L/L phenotype. L/L metabolism is unfavorable for tumor growth, yet supports successful cell division at ~50% rate. Thus, L/L drug-tolerant idling cells are a reservoir for accumulating mutations responsible for relapse, and it should be considered as a target subpopulation for improving MAPKi outcomes in melanoma treatment.
Quasi-periodic migration of single cells on short microlanes
Authors: Zhou Fang , Schaffer Sophia A. , Schreiber Christoph , Segerer Felix J. , Goychuk Andriy , Frey Erwin , Rädler Joachim O. 
Published: October 2019

AbstractCell migration on microlanes represents a suitable and simple platform for the exploration of the molecular mechanisms underlying cell cytoskeleton dynamics. Here, we report on the quasi-periodic movement of cells confined in stripe-shaped microlanes. We observe persistent polarized cell shapes and directed pole-to-pole motion within the microlanes. Cells depolarize at one end of a given microlane, followed by delayed repolarization towards the opposite end. We analyze cell motility via the spatial velocity distribution, the velocity frequency spectrum and the reversal time as a measure for depolarization and spontaneous repolarization of cells at the microlane ends. The frequent encounters of a boundary in the stripe geometry provides a robust framework for quantitative investigations of the cytoskeleton protrusion and repolarization dynamics. In a first advance to rigorously test physical models of cell migration, we find that the statistics of the cell migration is recapitulated by a Cellular Potts model with a minimal description of cytoskeleton dynamics. Using LifeAct-GFP transfected cells and microlanes with differently shaped ends, we show that the local deformation of the leading cell edge in response to the tip geometry can locally either amplify or quench actin polymerization, while leaving the average reversal times unaffected.
Gene Ontology Meta Annotator for Plants (GOMAP)
Authors: Wimalanathan Kokulapalan , Lawrence-Dill Carolyn J. 
Published: October 2019

AbstractAnnotating gene structures and functions to genome assemblies is necessary to make assembly resources useful for biological inference. Gene Ontology (GO) term assignment is the most used functional annotation system, and new methods for GO assignment have improved the quality of GO-based function predictions. The Gene Ontology Meta Annotator for Plants (GOMAP) is an optimized, high-throughput, and reproducible pipeline for genome-scale GO annotation of plants. We containerized GOMAP to increase portability and reproducibility and also optimized its performance for HPC environments. Here we report on the pipeline’s availability and performance for annotating large, repetitive plant genomes and describe how GOMAP was used to annotate multiple maize genomes as a test case. Assessment shows that GOMAP expands and improves the number of genes annotated and annotations assigned per gene as well as the quality (based on Fmax) of GO assignments in maize. GOMAP has been deployed to annotate other species including wheat, rice, barley, cotton, and soy. Instructions and access to the GOMAP Singularity container are freely available online at https://bioinformapping.com/gomap/. A list of annotated genomes and links to data is maintained at https://dill-picl.org/projects/gomap/.
Partial metal ion saturation of C2 domains primes Syt1-membrane interactions
Authors: Katti Sachin , Nyenhuis Sarah B. , Her Bin , Cafiso David S. , Igumenova Tatyana I. 
Published: October 2019

AbstractSynaptotagmin 1 (Syt1) is an integral membrane protein that acts as a Ca2+sensor of neurotransmitter release. How the Ca2+-sensing function of Syt1 is coupled to its interactions with anionic membranes and synaptic fusion machinery is not well understood. Here, we investigated the dynamics and membrane-binding properties of Syt1 under conditions where its highest affinity Ca2+sites, which are thought to drive the initial membrane recruitment, are selectively populated by divalent metal ions. To create such protein states for the Ca2+-sensing C2 domains of Syt1, we exploited the unique chemistry of Pb2+, a xenobiotic metal ion that is isostructural and isofunctional to Ca2+. NMR experiments revealed that binding of a single metal ion results in the loss of conformational plasticity of the C2 domain loop regions that are involved in both coordinating metal ions and membrane interactions. In the C2A domain, a single metal ion is sufficient to drive its weak association with PtdSer-containing membranes; in C2B, it enhances the interactions with the signaling lipid PtdIns(4,5)P2. In full-length Syt1, both C2 domains associate with PtdSer-containing membranes, with the depth of insertion modulated by the occupancy of the metal ion sites. Our data suggest that Syt1 adopts a shallow membrane-bound state upon initial recruitment of its C2 domains to the membranes. The properties of this state, such as conformationally restricted loop regions and positioning of C2 domains in close proximity to anionic lipid headgroups, “prime” Syt1 for binding a full complement of metal ions required for activation of protein function.
Integrative analysis of 10,000 epigenomic maps across 800 samples for regulatory genomics and disease dissection
Authors: Adsera Carles B. , Park Yongjin P. , Meuleman Wouter , Kellis Manolis 
Published: October 2019

AbstractTo help elucidate genetic variants underlying complex traits, we develop EpiMap, a compendium of 833 reference epigenomes across 18 uniformly-processed and computationally-completed assays. We define chromatin states, high-resolution enhancers, activity patterns, enhancer modules, upstream regulators, and downstream target gene functions. We annotate 30,247 genetic variants associated with 534 traits, recognize principal and partner tissues underlying each trait, infer trait-tissue, tissue-tissue and trait-trait relationships, and partition multifactorial traits into their tissue-specific contributing factors. Our results demonstrate the importance of dense, rich, and high-resolution epigenomic annotations for complex trait dissection, and yield numerous new insights for understanding the molecular basis of human disease.
Analysis the Detailed Process of Glomerular Capillary Formation Using Immunofluorescence Perform With Ultrathick Section
Authors: Yu Ting , Liu Chi 
Published: October 2019

AbstractBackgroundGlomerular capillary formation is one of the fundamental mysteries in renal developmental biology. However, there are still debates on this issue, and its detailed formation process has not been clarified.ResultsTo resolve this problem, we performed antibody staining with ultra-thick section on embryonic and postnatal mouse kidneys to detect and analyze the development of glomerular capillaries. We found that blood vessel of the fetal kidneys expanded through proliferation and sprouting. During the comma-stage and S-shaped stages, 3-4 capillaries began to bud and migrate into the glomerular cleft, forming a capillary bed in the Bowman’s capsule. Then, the capillary bed expanded into mature glomerular capillary by intussusceptive angiogenesis. The afferent and efferent arterioles were formed through pruning. The distribution of VEGFA in the nephron epithelial cells but not only in podocytes, induced multiple capillaries sprouted into the glomerular cleft. And CXCR4 played an important role in the differentiation and expansion of capillary bed into glomerular capillary.ConclusionsImmunofluorescence performed with ultra-thick section allowed us to investigate the development of complex structure tissues systematically and comprehensively.
Pseudo-data generation allows the statistical re-evaluation of toxicological bioassays based on summary statistics
Authors: Hothorn Ludwig A. , Kluxen Felix M. , Hasler Mario 
Published: October 2019

AbstractSometimes a re-analysis of toxicological data is useful. However, this usually requires the availability of the original data and in many cases only summary data are available in the publications. Here the generation of pseudo-data under certain assumptions using extension packages in the open-source project R on statistical computing is shown. Several case studies are used to illustrate the applicability in regulatory toxicology.
Prototypic SNARE proteins are encoded in the genomes of Heimdallarchaeota, potentially bridging the gap between the prokaryotes and eukaryotes
Authors: Neveu Emilie , Khalifeh Dany , Salamin Nicolas , Fasshauer Dirk 
Published: October 2019

AbstractA defining feature of eukaryotic cells is the presence of numerous membrane-bound organelles that subdivide the intracellular space into distinct compartments. How the eukaryotic cell acquired its internal complexity is still poorly understood. Material exchange among most organelles occurs via vesicles that bud off from a source and specifically fuse with a target compartment. Central players in the vesicle fusion process are the Soluble N-ethylmaleimide-sensitive factor Attachment protein REceptor (SNARE) proteins. These small tail-anchored (TA) membrane proteins zipper into elongated four-helix bundles that pull membranes together1–3. SNARE proteins are highly conserved among eukaryotes but are thought to be absent in prokaryotes. Here, we identified SNARE-like factors in the genomes of uncultured organisms of Asgard archaea of the Heimdallarchaeota clade4,5, which are thought to be the closest living relatives of eukaryotes. Biochemical experiments show that the archaeal SNARE-like proteins can interact with eukaryotic SNARE proteins. We did not detect SNAREs in α-proteobacteria, the closest relatives of mitochondria, but identified several genes encoding for SNARE proteins in γ-proteobacteria of the order Legionellales, pathogens that live inside eukaryotic cells. Very probably, their SNAREs stem from lateral gene transfer from eukaryotes. Together, this suggests that the diverse set of eukaryotic SNAREs evolved from an archaeal precursor. However, whether Heimdallarchaeota actually have a simplified endomembrane system will only be seen when we succeed studying these organisms under the microscope.
The M-phase regulatory phosphatase PP2A-B55δ opposes protein kinase A on Arpp19 to initiate meiotic division
Authors: Lemonnier Tom , Daldello Enrico Maria , Poulhe Robert , Le Tran , Miot Marika , Jessus Catherine , Dupré Aude 
Published: October 2019

ABSTRACTOocytes are held in meiotic prophase for prolonged periods until hormonal signals trigger meiotic divisions. Key players of M-phase entry are the opposing Cdk1 kinase and PP2A-B55δ phosphatase. InXenopus, the protein Arpp19, phosphorylated at serine 67 by Greatwall, plays an essential role in inhibiting PP2A-B55δ, promoting Cdk1 activation. Furthermore Arpp19 has an earlier role in maintaining the prophase arrest through a second serine (S109) phosphorylated by PKA. Prophase release, induced by progesterone, relies on Arpp19 dephosphorylation at S109, owing to an unknown phosphatase. Here we identified this phosphatase as PP2A-B55δ. In prophase, PKA and PP2A-B55δ are simultaneously active, suggesting the presence of other important targets for both enzymes. The drop in PKA activity induced by progesterone decreases S109 phosphorylation, unlocking the prophase block. Hence, PP2A-B55δ acts critically on Arpp19 on two distinct sites, opposing PKA and Greatwall to orchestrate the prophase release and M-phase entry.
Nanopore sequencing for the detection and the identification of Xylella fastidiosa subspecies and sequence types from naturally infected plant material
Authors: Faino Luigi , Scala Valeria , Albanese Alessio , Modesti Vanessa , Grottoli Alessandro , Pucci Nicoletta , L’Aurora Alessia , Reverberi Massimo , Loreti Stefania 
Published: October 2019

SummaryXylella fastidiosa (Xf) is a polyphagous gram-negative bacterial plant pathogen that can infect more than 300 plant species. It is endemic in America while, in 2013, Xf subsp. pauca was for the first time reported in Europe on olive tree in the Southern Italy. The availability of fast and reliable diagnostic tools is indispensable for managing current and future outbreaks of Xf.In this work, we used the Oxford Nanopore Technologies (ONT) device MinION platform for detecting and identifying Xf at species, subspecies and Sequence Type (ST) level straight from infected plant material. The study showed the possibility to detect Xf by direct DNA sequencing and identify the subspecies in highly infected samples. In order to improve sensitivity, Nanopore amplicon sequencing was assessed. Using primers within the set of the seven MLST officially adopted for identifying Xf at type strain level, we developed a workflow consisting in a multiple PCR and an ad hoc pipeline to generate MLST consensus after Nanopore-sequencing of the amplicons. The here-developed combined approach achieved a sensitivity higher than real-time PCR allowing within few hours, the detection and identification of Xf at ST level in infected plant material, also at low level of contamination.Originality Significance StatementIn this work we developed a methodology that allows the detection and identification of Xylella fastidiosa in plant using the Nanopore technology portable device MinION. The approach that we develop resulted more sensitive than methods currently used for detecting X. fastidiosa, like real-time PCR. This approach can be extensively used for X. fastidiosa detection and it may pave the road for the detection of other tedious vascular pathogens.