bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large scalein vivorecording of sensory neuron activity with GCaMP6
Authors: Chisholm Kim I , Khovanov Nikita , Lopes Douglas M , La Russa Federica , McMahon Stephen B 
Published: July 2017

AbstractGreater emphasis on the study of intact cellular networks in their physiological environment has led to rapid advances in intravital imaging in the central nervous system, while the peripheral system remains largely unexplored. To assess large networks of sensory neurons we selectively label primary afferents with GCaMP6s and visualise their functional responsesin vivoto peripheral stimulation. We show that we are able to monitor simultaneously the activity of hundreds of sensory neurons with sensitivity sufficient to detect, in most cases, single action potentials with a typical rise time of around 200 milliseconds, and an exponential decay with a time constant of approximately 700 milliseconds. Using this sensitive technique we are able to show that large scale recordings demonstrate the recently disputed polymodality of nociceptive primary afferents with between 40-80% of thermally sensitive DRG neurons responding also to noxious mechanical stimulation. We also specifically assess the small population of peripheral cold fibres and demonstrate significant sensitisation to cooling after a model of sterile and persistent inflammation, with significantly increased sensitivity already at decreases of 5°C when compared to uninflamed responses. This not only reveals interesting new insights into the (patho)physiology of the peripheral nervous system but also demonstrates the sensitivity of this imaging technique to physiological changes in primary afferents.Significance StatementMost of our functional understanding of the peripheral nervous system has come from single unit recordings. However, the acquisition of such data is labour-intensive and usually ‘low yield’. Moreover, some questions are best addressed by studying populations of neurons. To this end we report on a system that monitors activity in hundreds of single sensory neurons simultaneously, with sufficient sensitivity to detect in most cases single action potentials. We use this technique to characterise nociceptor properties and demonstrate polymodality in the majority of neurons and their sensitization under inflammatory conditions. We therefore believe this approach will be very useful for the studies of the somatosensory system in general and pain in particular.
Modelling glioblastoma tumour-host cell interactions using adult brain organotypic slice co-culture
Authors: Marques-Torrejon Maria Angeles , Gangoso Ester , Pollard Steven M. 
Published: July 2017

AbstractGlioblastoma (GBM) is an aggressive incurable brain cancer. The cells that fuel the growth of tumours resemble neural stem cells found in the developing and adult mammalian forebrain. These are referred to as GBM stem cells (GSCs). Similar to neural stem cells, GSCs exhibit a variety of phenotypic states: dormant, quiescent, proliferative and differentiating. How environmental cues within the brain influence these distinct states is not well understood. Laboratory models of GBM tumours can be generated using either genetically engineered mouse models, or via intracranial transplantation of cultured tumour initiating cells (mouse or human). Unfortunately, these approaches are expensive, time-consuming, low-throughput and ill-suited for monitoring of live cell behaviours. Here we explored whole adult brain coronal organotypic slices as a complementary strategy to remove the experimental bottleneck. Mouse adult brain slices remain viable in a neural stem cell serum-free basal media for several weeks. GSCs can therefore be easily microinjected into specific anatomical sitesex vivo. We demonstrated distinct responses of engrafted GSCs to different microenvironments in the brain. Within the subependymal zone – one of the adult neural stem cell niches – a subset of injected tumour cells could effectively engraft and respond to endothelial niche signals. GSCs transplanted slices were treated with the anti-mitotic drug temozolomide as proof-of-principle of the utility in modelling responses to existing treatments. Thus, engraftment of mouse or human GSCs onto whole brain coronal organotypic brain slices provides a convenient experimental model for studies of GSC-host interactions and preclinical testing of candidate therapeutic agents.
EndophyteChaetomium globosumD38 and its elicitors promote tanshinones accumulation ofSalvia miltiorrhiza
Authors: Zhai Xin , Luo Dong , Li Xiuqing , Han Ting , Kong Zhouyang , Ji Jiachen , Qin Luping , Zheng Chengjian 
Published: July 2017

AbstractDue to the low yield of tanshinones and their analogues inSalvia miltiorrhiza, there are all kinds of stimulation strategies having been applied to improve tanshinones output in plant tissue cultures. Endophytic fungi have formed various different relationships with their host plants withstanding host and environmental factors, including symbiotic, mutualistic, commensalistic, and parasitic. Thus we take the assumption that endophytic fungi may be an emerging microbial tool used to promote secondary metabolism, which will promote the production of active compounds through endophyte-based biology method. Our study therefore aimed to examine the effects of live endophytic fungusChaetomium globosumD38 and its elicitors on the accumulation of tanshinones in hairy root cultures ofSalvia miltiorrhiza. C. globosumD38 mainly colonized in the intercellular gap of xylem parenchyma cells ofS. miltiorrhizahairy root, during long term co-existence without any toxicity againstS. miltiorrhizahairy root. Moreover, both of the live fungus and its mycelia extracts could induce the production of tanshinones, in special dihydrotanshinone I and cryptotanshinone. The effects of mycelia extracts were much stronger than that of the live fungus on tanshinones synthesis, which increased the transcriptional activity of genes with repect to tanshinone biosynthetic pathway obviously. Our results indicated that both of the liveC. globosumD38 and its mycelia extracts could be utilized for tanshinones accumulation inS. miltiorrhizahairy root. What’s more, D38 also could be made into biotic fertilizer applying intoS.miltiorrhizaseddlings, which not only promoted host growth but the tanshinones and phenylpropionic acid accumulation. In the soil environment, D38 had formed bitrophic and mutual beneficial relationship with the host and enhanced the primary metabolism on the whole so as to have facilitative effects on phenylpropionic acid accumulation. To sum up,Chaetomium globosumD38 was a highly effective endophytic fungus forS. miltiorrhiza.
Effective normalization for copy number variation in Hi-C data
Authors: Servant N. , Varoquaux N. , Heard E. , Vert JP. , Barillot E. 
Published: July 2017

AbstractNormalization is essential to ensure accurate analysis and proper interpretation of sequencing data. Chromosome conformation data, such as Hi-C, is not different. The most widely used type of normalization of Hi-C data casts estimations of unwanted effects as a matrix balancing problem, relying on the assumption that all genomic regions interact as much as any other. Here, we show that these approaches, while very effective on fully haploid or diploid genome, fail to correct for unwanted effects in the presence of copy number variations. We propose a simple extension to matrix balancing methods that properly models the copy-number variation effects. Our approach can either retain the copy-number variation effects or remove it. We show that this leads to better downstream analysis of the three-dimensional organization of rearranged genome.
Regulating the UAS/GAL4 system in adultDrosophilawith Tet-off GAL80 transgenes
Authors: Barwell Taylor , DeVeale Brian , Poirier Luc , Zheng Jie , Seroude Frederique , Seroude Laurent 
Published: July 2017

SummaryThe UAS/GAL4 system is the most used method InDrosophila melanogasterfor directing the expression of a gene of interest to a specific tissue. However, the ability to control the temporal activity of GAL4 with this system is very limited. This study constructed and characterized Tet-off GAL80 transgenes designed to allow temporal control of GAL4 activity in aging adults. By placing GAL80 under the control of a Tet-off promoter, GAL4 activity is regulated by the presence or absence of tetracycline in the diet. Almost complete inhibition of the expression of UAS transgenes during the pre-adult stages of the life cycle is obtained by using four copies and two types of Tet-off GAL80 transgenes. Upon treatment of newly emerged adults with tetracycline, induction of GAL4 activity is observed but the level of induction is influenced by the concentration of the inducer, the age, the sex and the anatomical location of the expression. The inhibition of GAL4 activity and the maintenance of induced expression is altered in old animals. This study reveals that the repressive ability of GAL80 is affected by the age and sex of the animal which is a major limitation to regulate gene expression with GAL80 in agedDrosophila.
Age-related changes in the neural networks supporting semantic cognition: A meta-analysis of 47 functional neuroimaging studies
Authors: Hoffman Paul , Morcom Alexa M. 
Published: July 2017

AbstractSemantic cognition is central to understanding of language and the world and, unlike many cognitive domains, is thought to show little age-related decline. We investigated age-related differences in the neural basis of this critical cognitive domain by performing an activation likelihood estimation (ALE) meta-analysis of functional neuroimaging studies comparing young and older people. On average, young people outperformed their older counterparts during semantic tasks. Overall, both age groups activated similar left-lateralised regions. However, older adults displayed less activation than young people in some elements of the typical left-hemisphere semantic network, including inferior prefrontal, posterior temporal and inferior parietal cortex. They also showed greater activation in right frontal and parietal regions, particularly those held to be involved in domain-general controlled processing, and principally when they performed more poorly than the young. Thus, semantic processing in later life is associated with a shift from semantic-specific to domain-general neural resources, consistent with the theory of neural dedifferentiation, and a performance-related reduction in prefrontal lateralisation, which may reflect a response to increased task demands.
Inter-subject phase synchronization and the dynamics of human cognition
Authors: Bolt Taylor , Nomi Jason S. , Vij Shruti G. , Chang Catie , Uddin Lucina Q. 
Published: July 2017

AbstractMassive whole-brain blood-oxygen-level dependent (BOLD) signal modulation (up to 95% of brain voxels) in response to task stimuli has recently been reported in functional MRI investigations. These findings have two implications. First, they highlight inability of a conventional ‘top-down’ general linear model approach to capture all forms of task-driven brain activity. Second, as opposed to a static ‘active’ or ‘non-active’ localization theory of the neural implementation of cognitive processes, functional neuroimaging should develop and pursuedynamicaltheories of cognition involving the dynamic interactions ofallbrain networks, in line with psychological constructionist theories of cognition. In this study, we describe a novel exploratory, bottom-up approach that directly estimates task-driven brain activity regardless of whether it follows ana priorireference function. Leveraging the property that task-driven brain activity is associated with reductions in BOLD signal variability, we combine the tools of instantaneous phase synchronization and independent component analysis to characterizewhole-braintask-driven activity in terms of group-wise similarity in temporal signal dynamics of brain networks. We applied this novel framework to task fMRI data from a motor, theory of mind and working memory task provided through the Human Connectome Project. We discovered a large number of brain networks that dynamically synchronized to various features of the task scan, some overlapping with areas identified as ‘active’ in the top-down GLM approach. Using the results provided through this novel approach, we provide a more comprehensive description of cognitive processes whereby task-related brain activity is not restricted to dichotomous ‘active’ or ‘non-active’ inferences, but is characterized by the temporal dynamics of brain networks across time.Significance StatementThis study describes the results of a novel exploratory methodological approach that allows for direct estimation of task-driven brain activity in terms of group-wise similarity in temporal signal dynamics, as opposed to the conventional approach of identifying task-driven brain activity with a hypothesized temporal pattern. This approach applied to three different task paradigms yielded novel insights into the brain activity associated with these tasks in terms of time-varying, low-frequency dynamics of replicable synchronization networks. We suggest that this exploratory methodological approach provides a framework in which the complexity and dynamics of the neural mechanisms underlying cognitive processes can be captured more comprehensively.
Conformational Dynamics and Energy Landscapes of Ligand Binding in RyR1
Authors: Dashti A. , Hail D. Ben , Mashayekhi G. , Schwander P. , des Georges A. , Frank J. , Ourmazd A. 
Published: July 2017

AbstractUsing experimental single-particle cryo-EM snapshots of ryanodine receptor (RyR1), a Ca2+-channel involved in skeletal muscle excitation/contraction coupling, we present quantitative free-energy landscapes, reaction coordinates, and three-dimensional movies of the continuous conformational changes associated with the binding of activating ligands. Our results show multiple routes to ligand binding with comparable branching ratios. All high-probability routes involve significant conformational changes before and after the binding of ligands. We also present new insights into the local structural changes along the ligand-binding route, including accommodations at the calcium, ATP, and caffeine binding sites. These observations shed new light on the mechanisms and conformational routes to ligand binding.
Switchable amplification of fluoresence from a photosynthetic microbe
Authors: Bose Anirban , Raja Sufi O , Chowdhury Rajdeep , Nandi Somen , Ray Sanhita , Bhattacharyya Kankan , Dasgupta Anjan Kr 
Published: July 2017

AbstractOne known attribute of the photosynthetic apparatus is photon capture and generation of metabolic energy. The thermodynamic implications of fluorescence, invariably associated with the photosynthetic components is however poorly understood. In this paper we report a density dependent amplification of such fluorescence which can be interpreted as a thermodynamic strategy of controlled energy release by the cell. We show in support of this hypothesis that prolonged photo-exitation of cell free extract ofRhodobacter capsulatusSB1003 at 395 nm, induces fluorescence emission amplifying with time as long as the fluorophore density is above a critical level. The fact that the amplification disappears at low temperature and at dilute condition, is in accordance with the thermodynamic interpretation that energy is released as per requirement. Live cell imaging is also validation of the phenomenon even at the cellular level. Single cells ofRhodobacter capsulatusSB1003 shows time dependent loss of fluorescence, the process being reversed for cellular clusters. To explain the mechanism of this bistable fluorescence (F) amplification, variation of the scale free kinetic constant k=1/F (dF/dt) is studied at varying temperatures in presence and absence of static magnetic field. The sign of k shifts from positive to negative if T is lowered or if the system is diluted. But at low T, k again switches from negative to positive value, if static magnetic field is applied. The chain of events can be explained by a simple model assuming excretion of a porphyrin by the microbe and possible photon dependent aggregation behavior of such porphyrin complex, differential temperature and magnetic field sensitivity of the monomeric or aggregated forms of porphyrin being reported earlier.
Probing tissue-scale deformation byin vivoforce application reveals a fast tissue softening during early embryogenesis
Authors: D’Angelo Arturo , Dierkes Kai , Carolis Carlo , Salbreux Guillaume , Solon Jérôme 
Published: July 2017

AbstractDuring development, cell-generated forces induce tissue-scale deformations to shape the organism. Here, we present a method that allows to quantitatively relate such tissue-scale deformations to spatially localized forces and measure mechanical properties of epitheliain vivo. Our approach is based on the application of controlled forces on microparticles embedded in individual cells of an embryo. Combining measurements of the bead displacement with the analysis of induced deformation fields in a continuum mechanics framework, we can quantify tissue material properties and follow their change over time. In particular, we uncover a rapid change in tissue response occurring duringDrosophilacellularization, resulting from a softening of the blastoderm and an increase of external friction. Pharmacological treatments reveal that in addition to actomyosin, the microtubule cytoskeleton is a major contributor to epithelial mechanics at that stage. Overall, our method allows for measuring essential mechanical parameters governing tissue-scale deformations and flows occurring during morphogenesis.
Printed Droplet Microfluidics for on demand dispensing of picoliter droplets and cells
Authors: Cole Russell H. , Tang Shi-yang , Siltanen Christian A. , Shahi Payam , Zhang Jesse Q. , Poust Sean , Gartner Zev J. , Abate Adam R. 
Published: July 2017

AbstractAlthough the elementary unit of biology is the cell, high throughput methods for the microscale manipulation of cells and reagents are limited. The existing options are either slow, lack single cell specificity, or utilize fluid volumes out of scale with those of cells. Here, we present Printed Droplet Microfluidics, a technology to dispense picoliter droplets and cells with deterministic control. The core technology is a fluorescence-activated droplet sorter coupled to a specialized substrate that together act as a picoliter droplet and single cell printer, enabling high throughput generation of intricate arrays of droplets, cells, and microparticles. Printed Droplet Microfluidics provides a programmable and robust technology to construct arrays of defined cell and reagent combinations and to integrate multiple measurement modalities together in a single assay.
Systems-level identification of transcription factors critical for mouse embryonic development
Authors: Zhang Kai , Wang Mengchi , Zhao Ying , Wang Wei 
Published: July 2017

AbstractDynamic changes in the transcriptional regulatory circuit can influence the specification of distinct cell types. Numerous transcription factors (TFs) have been shown to function through dynamic rewiring during embryonic development but a comprehensive survey on the global regulatory network is still lacking. Here, we performed an integrated analysis of epigenomic and transcriptomic data to reveal key regulators from 2 cells to postnatal day 0 in mouse embryogenesis. We predicted 3D chromatin interactions including enhancer-promoter interactions in 12 tissues across 8 developmental stages, which facilitates linking TFs to their target genes for constructing genetic networks. To identify driver TFs particularly those not necessarily differentially expressed ones, we developed a new algorithm, dubbed as Taiji, to assess the global importance of TFs in development. Through comparative analysis across tissues and developmental stages, we systematically uncovered TFs that are critical for lineage-specific and stage-dependent tissue specification. Most interestingly, we have identified TF combinations that function in spatiotemporal order to form transcriptional waves regulating developmental progress and differentiation. Not only does our analysis provide the first comprehensive map of transcriptional regulatory circuits during mouse embryonic development, the identified novel regulators and the predicted 3D chromatin interactions also provide a valuable resource to guide further mechanistic studies.
TruePaiR: Software for the Accurate Identification of Complementary piRNA Read Pairs in High-Throughput Sequencing Data
Authors: Schreiner Patrick , Atkinson Peter W. 
Published: July 2017

AbstractpiRNAs and their biogenesis pathways are well-conserved in Metazoans (Grimson et al. 2008). piRNAs have been implicated in transcriptional, post-transcriptional, and translational regulation (Grivna et al. 2006; Lin & Yin 2008; Brennecke et al. 2008; Brennecke et al. 2007; Aravin et al. 2007). We analyze the signatures of a critical process in the primary and secondary mechanism of piRNA biogenesis, referred to as the amplification loop.The presence of U-1 and A-10 bias within piRNA populations is an indicator, but not an absolute measure of piRNA amplification. By further considering imperfect and perfect sequence complementarity within the first ten base pairs of piRNAs, the active site promoting secondary piRNA biogenesis, we developed practical and statistically powerful metrics to observe relative piRNA amplification. TruePaiR is a fast and effective general software tool to assess the relative utilization of piRNA amplification in high throughput sRNA sequencing data.The results of TruePaiR runs in seven species and five tissues serve as a benchmark for meaningful context of piRNA amplification. The TruePaiR metrics provide foundational data regarding the in terms of species specificity, tissue specificity, as well as the relative participation based upon origin-based piRNA subsets regarding piRNA amplification. The low degree of variability of same sample TruePaiR runs allows for metric reliability, reproducibility, as well as the ability to detect subtle differences in piRNA amplification within and between species and tissues. Given that TruePaiR serves as an effective and consistent metric of piRNA amplification across species, it can represent a new, meaningful standard in the degree of piRNA amplification in a specific organism and tissue that is or is not expected to undergo piRNA amplification.