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https://www.readbyqxmd.com/read/29786967/developmental-chromatin-restriction-of-pro-growth-gene-networks-acts-as-an-epigenetic-barrier-to-axon-regeneration-in-cortical-neurons
#1
Ishwariya Venkatesh, Vatsal Mehra, Zimei Wang, Ben Califf, Murray G Blackmore
Axon regeneration in the central nervous system is prevented in part by a developmental decline in the intrinsic regenerative ability of maturing neurons. This loss of axon growth ability likely reflects widespread changes in gene expression, but the mechanisms that drive this shift remain unclear. Chromatin accessibility has emerged as a key regulatory mechanism in other cellular contexts, raising the possibility that chromatin structure may contribute to the age-dependent loss of regenerative potential. Here we establish an integrated bioinformatic pipeline that combines analysis of developmentally dynamic gene networks with transcription factor regulation and genome-wide maps of chromatin accessibility...
May 22, 2018: Developmental Neurobiology
https://www.readbyqxmd.com/read/29786795/protocols-for-studies-on-stromal-cells-in-prostate-cancer
#2
Damien A Leach, Grant Buchanan
Interactions between tumor cells and fibroblasts play a pivotal role in cancer development and progression. Indeed, the paracrine communication between these two cell types is known to have physiological effects that alter carcinogenic and metastatic potential. An often overlooked player in these interactions is the involvement of the extracellular matrix (ECM). The network of ECM proteins secreted from fibroblasts is reportedly altered with cancer initiation and progression, and in several cases has been associated with patient outcome...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29786167/neuroplasticity-in-stroke-recovery-the-role-of-microglia-in-engaging-and-modifying-synapses-and-networks
#3
REVIEW
Ioanna Sandvig, Ingrid Lovise Augestad, Asta Kristine Håberg, Axel Sandvig
Neuroplasticity after ischemic injury involves both spontaneous rewiring of neural networks and circuits as well as functional responses in neurogenic niches. These events involve complex interactions with activated microglia, which evolve in a dynamic manner over time. Although the exact mechanisms underlying these interactions remain poorly understood, increasing experimental evidence suggests a determining role of pro- and anti-inflammatory microglial activation profiles in shaping both synaptogenesis and neurogenesis...
May 22, 2018: European Journal of Neuroscience
https://www.readbyqxmd.com/read/29785835/predicting-the-ecological-impacts-of-large-dam-removals-on-a-river-network-based-on-habitat-network-structure-and-flow-regimes
#4
Nobuo Ishiyama, Masahiro Ryo, Taiga Kataoka, Shigeya Nagayama, Masanao Sueyoshi, Akira Terui, Terutaka Mori, Takumi Akasaka, Futoshi Nakamura
Large dams have provided vital protection and services to human life and the economy. However, an increasing number of large dams worldwide have aged considerably and have thus become hazardous due to impaired functions. The removal of large dams has excellent potential to restore habitat connectivity and flow regimes; therefore, projecting the related ecological consequences is a key emerging need for water resource and ecosystem management. However, no modeling methods are currently available for such projections at the basin scale...
May 22, 2018: Conservation Biology: the Journal of the Society for Conservation Biology
https://www.readbyqxmd.com/read/29785139/blockage-of-store-operated-ca-2-entry-antagonizes-epstein-barr-virus-promoted-angiogenesis-by-inhibiting-ca-2-signaling-regulated-vegf-production-in-nasopharyngeal-carcinoma
#5
Jiaxiang Ye, Junqi Huang, Qian He, Weilin Zhao, Xiaoying Zhou, Zhe Zhang, Yongqiang Li, Jiazhang Wei, Jinyan Zhang
Background: Epstein-Barr virus (EBV) actively contributes to the pathological process of nasopharyngeal carcinoma (NPC) by enabling NPC cells to acquire various capacities required for their malignant biological actions. Our earlier works demonstrated that EBV-encoded latent membrane protein 1 (LMP1) enhanced vascular endothelial growth factor (VEGF)-mediated angiogenesis by boosting store-operated Ca2+ entry (SOCE) upon extracellular epidermal growth factor (EGF) stimulation. However, the antagonistic effects of SOCE blockage on EBV-promoted angiogenesis must be appropriately evaluated in vivo, and the global effect of EBV infection on the EGF-elicited cytosolic Ca2+ signaling, which regulates VEGF-mediated angiogenesis remains to be further clarified...
2018: Cancer Management and Research
https://www.readbyqxmd.com/read/29785071/identification-of-cis-regulatory-elements-associated-with-salinity-and-drought-stress-tolerance-in-rice-from-co-expressed-gene-interaction-networks
#6
Pragya Mishra, Nisha Singh, Ajay Jain, Neha Jain, Vagish Mishra, Pushplatha G, Kiran P Sandhya, Nagendra Kumar Singh, Vandna Rai
Rice, a staple food crop, is often subjected to drought and salinity stresses thereby limiting its yield potential. Since there is a cross talk between these abiotic stresses, identification of common and/or overlapping regulatory elements is pivotal for generating rice cultivars that showed tolerance towards them. Analysis of the gene interaction network (GIN) facilitates identifying the role of individual genes and their interactions with others that constitute important molecular determinants in sensing and signaling cascade governing drought and/or salinity stresses...
2018: Bioinformation
https://www.readbyqxmd.com/read/29785028/the-reference-epigenome-and-regulatory-chromatin-landscape-of-chronic-lymphocytic-leukemia
#7
Renée Beekman, Vicente Chapaprieta, Núria Russiñol, Roser Vilarrasa-Blasi, Núria Verdaguer-Dot, Joost H A Martens, Martí Duran-Ferrer, Marta Kulis, François Serra, Biola M Javierre, Steven W Wingett, Guillem Clot, Ana C Queirós, Giancarlo Castellano, Julie Blanc, Marta Gut, Angelika Merkel, Simon Heath, Anna Vlasova, Sebastian Ullrich, Emilio Palumbo, Anna Enjuanes, David Martín-García, Sílvia Beà, Magda Pinyol, Marta Aymerich, Romina Royo, Montserrat Puiggros, David Torrents, Avik Datta, Ernesto Lowy, Myrto Kostadima, Maša Roller, Laura Clarke, Paul Flicek, Xabier Agirre, Felipe Prosper, Tycho Baumann, Julio Delgado, Armando López-Guillermo, Peter Fraser, Marie-Laure Yaspo, Roderic Guigó, Reiner Siebert, Marc A Martí-Renom, Xose S Puente, Carlos López-Otín, Ivo Gut, Hendrik G Stunnenberg, Elias Campo, Jose I Martin-Subero
Chronic lymphocytic leukemia (CLL) is a frequent hematological neoplasm in which underlying epigenetic alterations are only partially understood. Here, we analyze the reference epigenome of seven primary CLLs and the regulatory chromatin landscape of 107 primary cases in the context of normal B cell differentiation. We identify that the CLL chromatin landscape is largely influenced by distinct dynamics during normal B cell maturation. Beyond this, we define extensive catalogues of regulatory elements de novo reprogrammed in CLL as a whole and in its major clinico-biological subtypes classified by IGHV somatic hypermutation levels...
May 21, 2018: Nature Medicine
https://www.readbyqxmd.com/read/29782993/generalized-recurrent-neural-network-accommodating-dynamic-causal-modeling-for-functional-mri-analysis
#8
Yuan Wang, Yao Wang, Yvonne W Lui
Dynamic Causal Modeling (DCM) is an advanced biophysical model which explicitly describes the entire process from experimental stimuli to functional magnetic resonance imaging (fMRI) signals via neural activity and cerebral hemodynamics. To conduct a DCM study, one needs to represent the experimental stimuli as a compact vector-valued function of time, which is hard in complex tasks such as book reading and natural movie watching. Deep learning provides the state-of-the-art signal representation solution, encoding complex signals into compact dense vectors while preserving the essence of the original signals...
May 18, 2018: NeuroImage
https://www.readbyqxmd.com/read/29782831/mapping-cellular-polarity-networks-using-mass-spectrometry-based-strategies
#9
REVIEW
Avais M Daulat, Tania M Puvirajesinghe, Luc Camoin, Jean-Paul Borg
Cell polarity is a vital biological process involved in the building, maintenance and normal functioning of tissues in invertebrates and vertebrates. Unsurprisingly, molecular defects affecting polarity organization and functions have a strong impact on tissue homeostasis, embryonic development and adult life, and may directly or indirectly lead to diseases. Genetic studies have demonstrated the causative effect of several polarity genes in diseases, however much remains to be clarified before a comprehensive view of the molecular organization and regulation of the protein networks associated with polarity proteins is obtained...
May 18, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29782555/langerin-dcs-regulate-innate-il-17-production-in-the-oral-mucosa-during-candida-albicans-mediated-infection
#10
Florian Sparber, Tamas Dolowschiak, Sarah Mertens, Laura Lauener, Björn E Clausen, Nicole Joller, Patrizia Stoitzner, Roxane Tussiwand, Salomé LeibundGut-Landmann
The opportunistic fungal pathogen Candida albicans frequently causes diseases such as oropharyngeal candidiasis (OPC) in immunocompromised individuals. Although it is well appreciated that the cytokine IL-17 is crucial for protective immunity against OPC, the cellular source and the regulation of this cytokine during infection are still a matter of debate. Here, we directly visualized IL-17 production in the infected tongue of experimentally infected mice, thereby demonstrating that this key cytokine is expressed by three complementary subsets of CD90+ leukocytes: RAG-dependent αβ and γδ T cells, as well as RAG-independent ILCs...
May 21, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29782491/community-based-benchmarking-improves-spike-rate-inference-from-two-photon-calcium-imaging-data
#11
Philipp Berens, Jeremy Freeman, Thomas Deneux, Nicolay Chenkov, Thomas McColgan, Artur Speiser, Jakob H Macke, Srinivas C Turaga, Patrick Mineault, Peter Rupprecht, Stephan Gerhard, Rainer W Friedrich, Johannes Friedrich, Liam Paninski, Marius Pachitariu, Kenneth D Harris, Ben Bolte, Timothy A Machado, Dario Ringach, Jasmine Stone, Luke E Rogerson, Nicolas J Sofroniew, Jacob Reimer, Emmanouil Froudarakis, Thomas Euler, Miroslav Román Rosón, Lucas Theis, Andreas S Tolias, Matthias Bethge
In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations. However, the acquired signal is only an indirect measurement of neural activity due to the comparatively slow dynamics of fluorescent calcium indicators. Different algorithms for estimating spike rates from noisy calcium measurements have been proposed in the past, but it is an open question how far performance can be improved. Here, we report the results of the spikefinder challenge, launched to catalyze the development of new spike rate inference algorithms through crowd-sourcing...
May 21, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29782156/combining-high-throughput-sequencing-of-sedadna-and-traditional-palaeolimnological-techniques-to-infer-historical-trends-in-cyanobacterial-communities
#12
Timothy J Tse, Lorne E Doig, Song Tang, Xiaohui Zhang, Weimin Sun, Steve B Wiseman, Cindy Xin Feng, Hongling Liu, John P Giesy, Markus Hecker, Paul D Jones
Freshwaters worldwide are under increasing pressure from anthropogenic activities and changing climate. Unfortunately, many inland waters lack sufficient long-term monitoring to assess environmental trends. Analysis of sedimentary ancient DNA (sedaDNA) is emerging as a means to reconstruct the past occurrence of microbial communities of inland waters. The purpose of this study was to assess a combination of high-throughput sequencing (16S rRNA) of sedaDNA and traditional palaeolimnological analyses to explore multidecadal relationships among cyanobacterial community composition, the potential for cyanotoxin production and palaeoenvironmental proxies...
May 21, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29781488/electrohydrodynamic-fibrillation-governed-enhanced-thermal-transport-in-dielectric-colloids-under-a-field-stimulus
#13
Purbarun Dhar, Lakshmi Sirisha Maganti, A R Harikrishnan
Electrorheological (ER) fluids are known to exhibit enhanced viscous effects under an electric field stimulus. The present article reports the hitherto unreported phenomenon of greatly enhanced thermal conductivity in such electro-active colloidal dispersions in the presence of an externally applied electric field. Typical ER fluids are synthesized employing dielectric fluids and nanoparticles and experiments are performed employing an in-house designed setup. Greatly augmented thermal conductivity under a field's influence was observed...
May 21, 2018: Soft Matter
https://www.readbyqxmd.com/read/29781413/drivers-potentially-influencing-host-bat-fly-interactions-in-anthropogenic-neotropical-landscapes-at-different-spatial-scales
#14
Jacqueline Hernández-Martínez, Juan B Morales-Malacara, Mariana Yolotl Alvarez-Añorve, Sergio Amador-Hernández, Ken Oyama, Luis Daniel Avila-Cabadilla
The anthropogenic modification of natural landscapes, and the consequent changes in the environmental conditions and resources availability at multiple spatial scales can affect complex species interactions involving key-stone species such as bat-parasite interactions. In this study, we aimed to identify the drivers potentially influencing host-bat fly interactions at different spatial scales (at the host, vegetation stand and landscape level), in a tropical anthropogenic landscape. For this purpose, we mist-netted phyllostomid and moormopid bats and collected the bat flies (streblids) parasitizing them in 10 sites representing secondary and old growth forest...
May 21, 2018: Parasitology
https://www.readbyqxmd.com/read/29781389/tracking-neuronal-connectivity-from-electric-brain-signals-to-predict-performance
#15
Fabrizio Vecchio, Francesca Miraglia, Paolo Maria Rossini
The human brain is a complex container of interconnected networks. Network neuroscience is a recent venture aiming to explore the connection matrix built from the human brain or human "Connectome." Network-based algorithms provide parameters that define global organization of the brain; when they are applied to electroencephalographic (EEG) signals network, configuration and excitability can be monitored in millisecond time frames, providing remarkable information on their instantaneous efficacy also for a given task's performance via online evaluation of the underlying instantaneous networks before, during, and after the task...
May 1, 2018: Neuroscientist: a Review Journal Bringing Neurobiology, Neurology and Psychiatry
https://www.readbyqxmd.com/read/29781376/immediate-early-gene-activation-throughout-the-brain-is-associated-with-dynamic-changes-in-social-context
#16
Cait M Williamson, Inbal S Klein, Won Lee, James P Curley
Social competence is dependent on successful processing of social context information. The social opportunity paradigm is a methodology in which dynamic shifts in social context are induced through removal of the alpha male in a dominance hierarchy, leading to rapid ascent in the hierarchy of the beta male and of other subordinate males in the social group. In the current study, we use the social opportunity paradigm to determine what brain regions respond to this dynamic change in social context, allowing an individual to recognize the absence of the alpha male and subsequently perform status-appropriate social behaviors...
May 21, 2018: Social Neuroscience
https://www.readbyqxmd.com/read/29780993/ideal-reversible-polymer-networks
#17
German Alberto Parada, Xuanhe Zhao
In this article we introduce the concept of ideal reversible polymer networks, which have well-controlled polymer network structures similar to ideal covalent polymer networks but exhibit viscoelastic behaviors due to the presence of reversible crosslinks. We first present a theory to describe the mechanical properties of ideal reversible polymer networks. Because short polymer chains of equal length are used to construct the network, there are no chain entanglements and the chains' Rouse relaxation time is much shorter than the reversible crosslinks' characteristic time...
May 21, 2018: Soft Matter
https://www.readbyqxmd.com/read/29780992/electrostatic-interactions-in-soft-particle-systems-mesoscale-simulations-of-ionic-liquids
#18
Yong-Lei Wang, You-Liang Zhu, Zhong-Yuan Lu, Aatto Laaksonen
Computer simulations provide a unique insight into the microscopic details, molecular interactions and dynamic behavior responsible for many distinct physicochemical properties of ionic liquids. Due to the sluggish and heterogeneous dynamics and the long-ranged nanostructured nature of ionic liquids, coarse-grained meso-scale simulations provide an indispensable complement to detailed first-principles calculations and atomistic simulations allowing studies over extended length and time scales with a modest computational cost...
May 21, 2018: Soft Matter
https://www.readbyqxmd.com/read/29780536/thermoreversible-crystallization-driven-aggregation-of-diblock-copolymer-nanoparticles-in-mineral-oil
#19
Matthew J Derry, Oleksandr O Mykhaylyk, Anthony J Ryan, Steven P Armes
A poly(behenyl methacrylate)37 (PBeMA37 ) macromolecular chain transfer agent is utilized for the reversible addition-fragmentation chain transfer (RAFT) dispersion polymerization of benzyl methacrylate (BzMA) directly in mineral oil at 90 °C. Polymerization-induced self-assembly (PISA) occurs under these conditions, yielding a series of sterically-stabilized PBeMA37 -PBzMA x diblock copolymer spheres of tunable diameter as confirmed by dynamic light scattering (DLS) and transmission electron microscopy (TEM) studies...
May 7, 2018: Chemical Science
https://www.readbyqxmd.com/read/29780313/network-dynamics-of-attention-during-a-naturalistic-behavioral-paradigm
#20
René Weber, Bradly Alicea, Richard Huskey, Klaus Mathiak
This study investigates the dynamics of attention during continuous, naturalistic interactions in a video game. Specifically, the effect of repeated distraction on a continuous primary task is related to a functional model of network connectivity. We introduce the Non-linear Attentional Saturation Hypothesis (NASH), which predicts that effective connectivity within attentional networks increases non-linearly with decreasing distraction over time, and exhibits dampening at critical parameter values. Functional magnetic resonance imaging (fMRI) data collected using a naturalistic behavioral paradigm coupled with an interactive video game is used to test the hypothesis...
2018: Frontiers in Human Neuroscience
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