bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeting the mTORC2 signaling complex in B cell malignancies
Authors: Liao Wei , Jordaan Gwen , Benavides-Serrato Angelica , Holmes Brent , Gera Joseph , Sharma Sanjai 
Published: March 2019

AbstractHyperactive PI3 kinase-Akt (PI3K-Akt) signaling has an important role in cell growth and resistance to apoptosis in B cell malignancies. Inhibition of this pathway by blocking PI3K activity, and or inhibiting mTORC1/2 signaling complexes is an active area of research in B cell leukemia/lymphoma such as chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL). With a tissue-scan array, the expression of Rictor is a component of the mTORC2 complex was determined by quantitative PCR in a number of B cell malignancies. Rictor was found to be over-expressed in CLL and MCL cells as compared to normal B cells with no over-expression in Hodgkins and non-Hodgkins lymphomas. Inactivation of Rictor was performed by shRNA in two Mantle cell lines and these stable Rictor knockdown cell lines demonstrated a slower growth of cells as compared to scrambled shRNA control. In addition, there was a decrease of mTORC2 signaling and B cell receptor (BCR) cross-linking mediated Akt (Ser473) and NDRG1 (Thr 346) phosphorylation. To specifically disrupt the mTORC2 signaling complex and target Rictor overexpression, previously identified inhibitors that block Rictor and MTOR interaction in a yeast two-hybrid system were analyzed. Treatment of primary CLL specimens with these inhibitors followed by immunoprecipitation experiments confirmed the disruption of the mTORC2 complex. These inhibitors also induced apoptosis in CLL specimens and were more effective than rapamycin, an MTOR inhibitor and pp242, an mTORC1 and 2 inhibitors, at equimolar concentrations. Treatment of CLL specimens with the lead inhibitor, compound#6, resulted in inhibition of p-Akt, p-GSK 3 beta, p-PKC alpha, p-Foxo1, and p-Foxo3, with minimal effect on the phosphorylation of an mTORC1 target gene, S6 kinase. In comparison with Idelalisib (CAL-101), a clinically approved PI3Kinase p110 delta inhibitor in CLL, comp#6 is more effective in inducing apoptosis in primary CLL specimens at equimolar concentrations (mean 51.2, SD 21.7 as compared to mean 26.9, SD 17.2). The data support the effectiveness of these novel inhibitors that specifically disrupt the mTORC2 complex in primary CLL specimens.
Polychromatic solar energy conversion in pigment-protein chimeras that unite the two kingdoms of (bacterio)chlorophyll-based photosynthesis
Authors: Liu Juntai , Friebe Vincent M. , Frese Raoul N. , Jones Michael R. 
Published: March 2019

Natural photosynthesis can be divided between the chlorophyll-containing plants, algae and cyanobacteria that make up the oxygenic phototrophs and a diversity of bacteriochlorophyll-containing bacteria that make up the anoxygenic phototrophs. Photosynthetic light harvesting and reaction centre proteins from both groups of organisms have been exploited in a wide range of biohybrid devices for solar energy conversion, solar fuel synthesis and a variety of sensing technologies, but the energy harvesting abilities of these devices are limited by each protein’s individual palette of (bacterio)chlorophyll, carotenoid and bilin pigments. In this work we demonstrate a range of genetically-encoded, self-assembling photosystems in which recombinant plant light harvesting complexes are covalently locked with reaction centres from a purple photosynthetic bacterium, producing macromolecular chimeras that display mechanisms of polychromatic solar energy harvesting and conversion not present in natural systems. Our findings illustrate the power of a synthetic biology approach in which bottom-up construction of a novel photosystem using naturally disparate but mechanistically complementary components is achieved in a predictable fashion through the genetic encoding of adaptable, plug-and-play covalent interfaces.ToC image
Enduring and sex-specific changes in hippocampal gene expression after a subchronic immune challenge
Authors: Tchessalova Daria , Tronson Natalie C. 
Published: March 2019

AbstractMajor illnesses, including heart attack and sepsis, can cause cognitive impairments, depression, and progressive memory decline that persist long after recovery from the original illness. In rodent models of sepsis or subchronic immune challenge, memory deficits also persist for weeks or months, even in the absence of ongoing neuroimmune activation. This raises the question of what mechanisms in the brain mediate such persistent changes in neural function. Here, we used RNA-sequencing as a large-scale, unbiased approach to identify changes in hippocampal gene expression long after a subchronic immune challenge previously established to cause persistent memory impairments in both males and females. We observed enduring dysregulation of gene expression three months after the end of a subchronic immune challenge, Surprisingly, we also found striking sex differences in both the magnitude of changes and the specific genes and pathways altered, where males showed persistent changes in both immune- and plasticity-related genes three months after immune challenge, whereas females showed few such changes. In contrast, females showed striking differential gene expression in response to a subsequent immune challenge. Thus, immune activation has enduring and sex-specific consequences for hippocampal gene expression and the transcriptional response to subsequent stimuli. Together with findings of long-lasting memory impairments after immune challenge, these data suggest that illnesses can cause enduring vulnerability to, cognitive decline, affective disorders, and memory impairments via dysregulation of transcriptional processes in the brain.
Neural circuits mediating visual stabilization during active motion in zebrafish
Authors: Sun Sha , Zuo Zhentao , Ma Michelle Manxiu , Qian Chencan , Chen Lin , Zhou Wu , Drasbek Kim Ryun , Zuxiang Liu 
Published: March 2019

ABSTRACTVisual stabilization is an inevitable requirement for animals during active motion interaction with the environment. Visual motion cues of the surroundings or induced by self-generated behaviors are perceived then trigger proper motor responses mediated by neural representations conceptualized as the internal model: one part of it predicts the consequences of sensory dynamics as a forward model, another part generates proper motor control as a reverse model. However, the neural circuits between the two models remain mostly unknown. Here, we demonstrate that an internal component, the efference copy, coordinated the two models in a push-pull manner by generating extra reset saccades during active motion processing in larval zebrafish. Calcium imaging indicated that the saccade preparation circuit is enhanced while the velocity integration circuit is inhibited during the interaction, balancing the internal representations from both directions. This is the first model of efference copy on visual stabilization beyond the sensorimotor stage.
Analysis of miRNA inhibitors Efficacy using Capillary Electrophoresis with Laser-Induced Fluorescence
Authors: Chae Dong-Kyu , Ban Eunmi 
Published: March 2019

ABSTRACTIn the recent years, microRNAs (miRNAs) have been discovered to play a very important role in biological processes such as development, differentiation, and apoptosis. The miRNA expression levels in cells are associated with diverse diseases including cancers. MiRNA inhibitors have been widely employed for studying the functions and targets of miRNAs by transfecting the inhibitors into cells. The concentrations of miRNA inhibitors used for such studies can vary depending on the types of miRNAs being tested, the cell lines under study, and the analysis methods. Therefore, in order to obtain accurate results, appropriate amounts of miRNA inhibitors have to be used in the experiments. Apart from amounts, the evaluation of inhibitors may also have to be conducted for functional studies.Here we developed capillary electrophoresis with laser-induced fluorescence (CE-LIF) method for evaluating miRNA inhibitor and for optimizing miRNA inhibitor concentrations, in the A549 lung cancer cell line. The target miRNAs, miRNA-23a and miRNA-24 are biomarker candidates in lung cancer cell lines. Our results showed that miRNA-23a and miRNA-24 were effectively inhibited upon transfection with 20 nM miRNA inhibitors using CE-LIF method. Furthermore, these results demonstrated the potential of CE for fast, specific, sensitive and specific analyses for the evaluation and determination of the optimal concentration of miRNA inhibitors for functional studies.Abstract Graphics
Chromatin activity at GWAS loci identifies T cell states driving complex immune diseases
Authors: Soskic Blagoje , Cano-Gamez Eddie , Smyth Deborah J. , Rowan Wendy C. , Nakic Nikolina , Esparza-Gordillo Jorge , Bossini-Castillo Lara , Tough David F. , Larminie Christopher G. C. , Bronson Paola G. , Wille David , Trynka Gosia 
Published: March 2019

AbstractComplex immune disease variants are enriched in active chromatin regions of T cells and macrophages. However, whether these variants function in specific cell states or stages of cell activation is unknown. We stimulated T cells and macrophages in the presence of thirteen different cytokine cocktails linked to immune diseases and profiled active enhancers and promoters together with regions of open chromatin. We observed that T cell activation induced major chromatin remodelling, while additional exposure to cytokines fine-tuned the magnitude of these changes. Therefore, we developed a new statistical method that accounts for subtle changes in chromatin landscape to identify SNP enrichment across cell states. Our results point towards the role of immune disease variants in early rather than late activation of memory CD4+ T cells, and with limited differences across polarizing cytokines. Furthermore, we demonstrate that inflammatory bowel disease variants are enriched in chromatin regions active in Th1 cells, while asthma variants overlap regions active in Th2 cells. We also show that Alzheimer’s disease variants are enriched in different macrophage cell states. Our results represent the first in-depth analysis of immune disease variants across a comprehensive panel of activation states of T cells and macrophages.
Shared neural underpinnings of multisensory integration and trial-by-trial perceptual recalibration
Authors: Park Hame , Kayser Christoph 
Published: March 2019

AbstractMultisensory stimuli create behavioral flexibility, e.g. by allowing us to derive a weighted combination of the information received by different senses. They also allow perception to adapt to discrepancies in the sensory world, e.g. by biasing the judgement of unisensory cues based on preceding multisensory evidence. While both facets of multisensory perception are central for behavior, it remains unknown whether they arise from a common neural substrate. In fact, very little is known about the neural mechanisms underlying multisensory perceptual recalibration. To reveal these, we measured whole-brain activity using MEG while human participants performed an audio-visual ventriloquist paradigm designed to reveal multisensory integration within a trial, and the (trial-by-trial) recalibration of subsequent unisensory judgements. Using single trial classification and behavioral modelling, we localized the encoding of sensory information within and between trials, and determined the behavioral relevance of candidate neural representations. While we found neural signatures of perceptual integration within temporal and parietal regions, of these, only medial superior parietal activity retained multisensory information between trials and combined this with current evidence to mediate perceptual recalibration. These results suggest a common neural substrate of sensory integration and trial-by-trial perceptual recalibration, and expose the medial superior parietal cortex as a flexible hub that links present and previous evidence within and between senses to guide behavior.
Single-cell RNA-sequencing of Herpes simplex virus 1-infected cells identifies NRF2 activation as an antiviral program
Authors: Wyler Emanuel , Franke Vedran , Menegatti Jennifer , Christine Kocks , Boltengagen Anastasiya , Praktiknjo Samantha , Walch-Rückheim Barbara , Rajewsky Nikolaus , Grässer Friedrich , Akalin Altuna , Markus Landthaler 
Published: March 2019

AbstractHerpesvirus infection initiates a range of perturbations in the host cell, which remain poorly understood at the level of individual cells. Here, we quantified the transcrips of single human primary fibroblasts during the first hours of lytic infection with HSV-1. By applying a generalizable analysis scheme, we defined a precise temporal order of early viral gene expression and found unexpected bifurcations and bottlenecks. We identified individual host cell genes and pathways relevant in early infection by combining three different computational approaches: gene and pathway overdispersion analysis, prediction of cell-state transition probabilities as well as future cell states. One transcriptional program, which was turned on in infected cells and correlated with increased resistance to infection, implicated the transcription factor NRF2. Consequently, Bardoxolone methyl, a known NRF2 agonist, impaired virus production, suggesting that NRF2 activation restricts the progression of viral infection. Our study provides novel insights into early stages of HSV-1 infection and serves as a general blueprint for the investigation of heterogenous cell states in virus infection.
A high-density genetic map and molecular sex-typing assay for gerbils
Authors: Brekke Thomas D. , Supriya Sushmita , Denver Megan , Thom Angharad , Steele Katherine A. , Mulley John F. 
Published: March 2019

AbstractWe constructed a high-density genetic map in Mongolian gerbils (Meriones unguiculatus). We genotyped 137 F2 individuals with a genotype-by-sequencing (GBS) approach at over 10,000 loci and built the genetic map using a two-step approach. First, we chose the highest-quality set of 485 markers to construct a high-quality framework map of 1,239cM with 22 linkage groups as expected from the published karyotype. Second, we added an additional 5,449 markers onto the map based on their genotype similarity with the original markers. We used the final marker set to assemble 1,140 genomic scaffolds (containing ∼20% of annotated genes) into a chromosome-level framework. We used both genetic linkage and relative sequencing coverage in males and females to identify X- and Y-chromosome scaffolds and from these we designed a robust and internally-controlled PCR assay to determine sex. This assay will facilitate early stage sex-typing of embryonic and young gerbils which is not possible using current visual methods.
Impacts of climate change on high priority fruit fly species in Australia
Authors: Sultana Sabira , Baumgartner John B. , Dominiak Bernard C. , Royer Jane E. , Beaumont Linda J. 
Published: March 2019

AbstractTephritid fruit flies are among the most destructive horticultural pests and pose risks to Australia’s multi-billion-dollar horticulture industry. Currently, there are 11 pest fruit fly species of economic concern present in various regions of Australia. Of these, nine are native to this continent (Bactrocera aquilonis, B. bryoniae, B. halfordiae, B. jarvisi, B. kraussi, B. musae, B. neohumeralis, B. tryoniandZeugodacus cucumis), whileB. frauenfeldiandCeratitis capitataare introduced. To varying degrees these species are costly to Australia’s horticulture through in-farm management, monitoring to demonstrate pest freedom, quarantine and trade restrictions, and crop losses. Here, we used a common species distribution modelling approach, Maxent, to assess habitat suitability for these 11 species under current and future climate scenarios. These projections indicate that the Wet Tropics is likely to be vulnerable to all 11 species. The east coast of Australia will likely remain vulnerable to multiple species until at least 2070. Both the Cape York Peninsula and Northern Territory are also likely to be vulnerable, however, extrapolation to novel climates in these areas decrease confidence in model projections. The climate suitability of current major horticulture regions in north-western Australia, the Northern Territory, southern-central regions of New South Wales and southern Victoria to these pests is projected to increase as climate changes. Our study highlights areas at risk of pest range expansion in the future, to guide Australia’s horticulture industry in developing effective monitoring and management strategies.
Simulation of calcium signaling in fine astrocytic processes: effect of spatial properties on spontaneous activity
Authors: Audrey Denizot , Misa Arizono , Valentin Nägerl U. , Hédi Soula , Hugues Berry 
Published: March 2019

AbstractAstrocytes, a glial cell type of the central nervous system, have emerged as detectors and regulators of neuronal information processing. Astrocyte excitability resides in transient variations of free cytosolic calcium concentration over a range of temporal and spatial scales, from sub-microdomains to waves propagating throughout the cell. Despite extensive experimental approaches, it is not clear how these signals are transmitted to and integrated within an astrocyte. The localization of the main molecular actors and the geometry of the system, including calcium channels IP3R spatial organization, are deemed essential. However, as most calcium signals occur in astrocytic ramifications that are too fine to be resolved by conventional light microscopy, most of those spatial data are unknown and computational modeling remains the only methodology to study this issue. Here, we propose an IP3R-mediated calcium signaling model for dynamics in such small sub-cellular volumes. To account for the expected stochasticity and low copy numbers, our model is both spatially explicit and particle-based. Extensive simulations show that spontaneous calcium signals arise in the model via the interplay between excitability and stochasticity. The model reproduces the main forms of calcium signals and indicates that their frequency crucially depends on the spatial organization of the IP3R channels. Importantly, we show that two processes expressing exactly the same calcium channels can display different types of calcium signals depending on channels spatial organization. Our model with realistic process volume and calcium concentrations successfully reproduces spontaneous calcium signals that we measured in calcium micro-domains with confocal microscopy. To our knowledge, this model is the first model suited to investigate calcium dynamics in fine astrocytic processes and to propose plausible mechanisms responsible for their variability.
Analysis of factor V in zebrafish demonstrates minimal levels needed for hemostasis and risk stratifies human variants
Authors: Weyand Angela C. , Grzegorski Steve. J. , Rost Megan. S. , Lavik Kari. I. , Ferguson Allison C. , Menegatti Marzia , Richter Catherine E. , Asselta Rosanna , Duga Stefano , Peyvandi Flora , Shavit Jordan A. 
Published: March 2019

ABSTRACTIn humans, coagulation factor V (F5) deficiency is a rare, clinically heterogeneous bleeding disorder, suggesting that genetic modifiers may contribute to disease expressivity. Complete loss of mouse F5 results in early lethality. Zebrafish possess many distinct advantages including high fecundity, optical clarity, external development, and homology with the mammalian hemostatic system, features that make it ideal for genetic studies. Our aim was to study the role of F5 in zebrafish through targeted mutagenesis, and apply the model to the study of humanF5variants. CRISPR-mediated genome editing of the zebrafishf5locus was performed, generating mutants homozygous for a 49 base pair deletion in exon 4. Thrombus formation secondary to vascular endothelial injury was absent inf5-/-mutant embryos and larvae. Despite this severe hemostatic defect, homozygous mutants survived before succumbing to severe hemorrhage in adulthood. HumanF5variants of uncertain significance from patients with F5 deficiency were evaluated, and the causative mutations identified and stratified by their ability to restore thrombus formation in larvae. Analysis of these novel mutations demonstrates variable residual F5 function, with minimal activity being required to restore hemostasis. Thisin vivoevaluation may be beneficial for patients whose factor activity levels lack correlation with bleeding symptomatology. Furthermore, homozygous mutant embryos tolerate what is a severe and lethal defect in mammals, suggesting the possibility of species-specific factors enabling survival, and allowing further study not possible in the mouse. Identification of these factors or other genetic modifiers could lead to novel therapeutic modalities.Key PointsF5 mutant fish embryos tolerate symptoms lethal in mammals but succumb to bleeding in adulthoodAnalysis of human variants demonstrate that all have some residual function and that minimal F5 activity is required to restore hemostasis