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https://www.readbyqxmd.com/read/28645179/system-wide-analysis-of-short-term-response-to-high-temperature-in-pinus-radiata
#1
Mónica Escandón, Luis Valledor, Jesús Pascual, Gloria Pinto, María Jesús Cañal, Mónica Meijón
Pinus radiata seedlings, the most widely planted pine species in the world, were exposed to temperatures within a range mimicking future scenarios based on current models of heat increase. The short-term heat response in P. radiata was studied in detail by exploring the metabolome, proteome and targeted transcriptome. The use of complementary mass spectrometry techniques, GC-MS and LC-Orbitrap-MS, together with novel bioinformatics tools allowed the reliable quantification of 2,075 metabolites and 901 protein groups...
June 22, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28644902/sirt6-alters-adult-hippocampal-neurogenesis
#2
Eitan Okun, Daniel Marton, Daniel Cohen, Kathleen Griffioen, Yariv Kanfi, Tomer Illouz, Ravit Madar, Haim Y Cohen
Sirtuins are pleiotropic NAD+ dependent histone deacetylases involved in metabolism, DNA damage repair, inflammation and stress resistance. SIRT6, a member of the sirtuin family, regulates the process of normal aging and increases the lifespan of male mice over-expressing Sirt6 by 15%. Neurogenesis, the formation of new neurons within the hippocampus of adult mammals, involves several complex stages including stem cell proliferation, differentiation, migration and network integration. During aging, the number of newly generated neurons continuously declines, and this is correlated with a decline in neuronal plasticity and cognitive behavior...
2017: PloS One
https://www.readbyqxmd.com/read/28644841/low-dimensional-spike-rate-models-derived-from-networks-of-adaptive-integrate-and-fire-neurons-comparison-and-implementation
#3
Moritz Augustin, Josef Ladenbauer, Fabian Baumann, Klaus Obermayer
The spiking activity of single neurons can be well described by a nonlinear integrate-and-fire model that includes somatic adaptation. When exposed to fluctuating inputs sparsely coupled populations of these model neurons exhibit stochastic collective dynamics that can be effectively characterized using the Fokker-Planck equation. This approach, however, leads to a model with an infinite-dimensional state space and non-standard boundary conditions. Here we derive from that description four simple models for the spike rate dynamics in terms of low-dimensional ordinary differential equations using two different reduction techniques: one uses the spectral decomposition of the Fokker-Planck operator, the other is based on a cascade of two linear filters and a nonlinearity, which are determined from the Fokker-Planck equation and semi-analytically approximated...
June 23, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28644436/the-lats1-and-lats2-tumor-suppressors-beyond-the-hippo-pathway
#4
REVIEW
Noa Furth, Yael Aylon
Proper cellular functionality and homeostasis are maintained by the convergent integration of various signaling cascades, which enable cells to respond to internal and external changes. The Dbf2-related kinases LATS1 and LATS2 (LATS) have emerged as central regulators of cell fate, by modulating the functions of numerous oncogenic or tumor suppressive effectors, including the canonical Hippo effectors YAP/TAZ, the Aurora mitotic kinase family, estrogen signaling and the tumor suppressive transcription factor p53...
June 23, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28644419/context-relevant-prediction-model-for-copd-domain-using-bayesian-belief-network
#5
Hamid Mcheick, Lokman Saleh, Hicham Ajami, Hafedh Mili
In the last three decades, researchers have examined extensively how context-aware systems can assist people, specifically those suffering from incurable diseases, to help them cope with their medical illness. Over the years, a huge number of studies on Chronic Obstructive Pulmonary Disease (COPD) have been published. However, how to derive relevant attributes and early detection of COPD exacerbations remains a challenge. In this research work, we will use an efficient algorithm to select relevant attributes where there is no proper approach in this domain...
June 23, 2017: Sensors
https://www.readbyqxmd.com/read/28644387/rna-binding-proteins-and-genome-integrity
#6
REVIEW
Kensei Nishida, Yuki Kuwano, Tatsuya Nishikawa, Kiyoshi Masuda, Kazuhito Rokutan
Genome integrity can be threatened by various endogenous or exogenous events. To counteract these stressors, the DNA damage response network contributes to the prevention and/or repair of genomic DNA damage and serves an essential function in cellular survival. DNA binding proteins are involved in this network. Recently, several RNA-binding proteins (RBPs) that are recruited to DNA damage sites have been shown to be direct players in the prevention or repair of DNA damage. In addition, non-coding RNAs, themselves, are involved in the RNA-mediated DNA repair system...
June 23, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28643924/exosomes-novel-regulators-of-bone-remodelling-and-potential-therapeutic-agents-for-orthodontics
#7
REVIEW
L S Holliday, K P McHugh, J Zuo, J I Aguirre, J K Neubert, W J Rody
Recent studies suggest that exosomes are involved in intercellular communication required for the maintenance of healthy bone. Exosomes are small (30-150 nm in diameter) extracellular vesicles that are formed in multivesicular bodies and are released from cells as the multivesicular bodies fuse with the plasma membrane. Regulatory exosomes have the capacity to exert profound control over target cells. They can stimulate plasma membrane receptors and are also internalized by the target cell delivering proteins, lipids, small molecules and functional RNAs from the cell of origin...
June 2017: Orthodontics & Craniofacial Research
https://www.readbyqxmd.com/read/28643618/heat-stabilised-rice-bran-consumption-by-colorectal-cancer-survivors-modulates-stool-metabolite-profiles-and-metabolic-networks-a-randomised-controlled-trial
#8
Dustin G Brown, Erica C Borresen, Regina J Brown, Elizabeth P Ryan
Rice bran (RB) consumption has been shown to reduce colorectal cancer (CRC) growth in mice and modify the human stool microbiome. Changes in host and microbial metabolism induced by RB consumption was hypothesised to modulate the stool metabolite profile in favour of promoting gut health and inhibiting CRC growth. The objective was to integrate gut microbial metabolite profiles and identify metabolic pathway networks for CRC chemoprevention using non-targeted metabolomics. In all, nineteen CRC survivors participated in a parallel randomised controlled dietary intervention trial that included daily consumption of study-provided foods with heat-stabilised RB (30 g/d) or no additional ingredient (control)...
May 2017: British Journal of Nutrition
https://www.readbyqxmd.com/read/28643167/microbiome-probiotics-and-neurodegenerative-diseases-deciphering-the-gut-brain-axis
#9
REVIEW
Susan Westfall, Nikita Lomis, Imen Kahouli, Si Yuan Dia, Surya Pratap Singh, Satya Prakash
The gut microbiota is essential to health and has recently become a target for live bacterial cell biotherapies for various chronic diseases including metabolic syndrome, diabetes, obesity and neurodegenerative disease. Probiotic biotherapies are known to create a healthy gut environment by balancing bacterial populations and promoting their favorable metabolic action. The microbiota and its respective metabolites communicate to the host through a series of biochemical and functional links thereby affecting host homeostasis and health...
June 22, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28643166/structural-disorder-in-plant-proteins-where-plasticity-meets-sessility
#10
REVIEW
Alejandra A Covarrubias, Cesar L Cuevas-Velazquez, Paulette S Romero-Pérez, David F Rendón-Luna, Caspar C C Chater
Plants are sessile organisms. This intriguing nature provokes the question of how they survive despite the continual perturbations caused by their constantly changing environment. The large amount of knowledge accumulated to date demonstrates the fascinating dynamic and plastic mechanisms, which underpin the diverse strategies selected in plants in response to the fluctuating environment. This phenotypic plasticity requires an efficient integration of external cues to their growth and developmental programs that can only be achieved through the dynamic and interactive coordination of various signaling networks...
June 22, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28642938/correlation-weighted-sparse-group-representation-for-brain-network-construction-in-mci-classification
#11
Renping Yu, Han Zhang, Le An, Xiaobo Chen, Zhihui Wei, Dinggang Shen
Analysis of brain functional connectivity network (BFCN) has shown great potential in understanding brain functions and identifying biomarkers for neurological and psychiatric disorders, such as Alzheimer's disease and its early stage, mild cognitive impairment (MCI). In all these applications, the accurate construction of biologically meaningful brain network is critical. Due to the sparse nature of the brain network, sparse learning has been widely used for complex BFCN construction. However, the conventional l1-norm penalty in the sparse learning equally penalizes each edge (or link) of the brain network, which ignores the link strength and could remove strong links in the brain network...
October 2016: Medical Image Computing and Computer-assisted Intervention: MICCAI ..
https://www.readbyqxmd.com/read/28642740/multigenerational-influences-of-the-fut2-gene-on-the-dynamics-of-the-gut-microbiota-in-mice
#12
Philipp Rausch, Sven Künzel, Abdulhadi Suwandi, Guntram A Grassl, Philip Rosenstiel, John F Baines
The FUT2 gene encodes an α-1,2-fucosyltransferase responsible for the expression of ABO histo-blood-group antigens on mucosal surfaces and bodily secretions. Individuals who carry at least one functional allele are known as "secretors," whereas those homozygous for loss-of-function mutations are known as "non-secretors." Non-secretor individuals are more susceptible to chronic inflammatory disorders such as Crohn's Disease, which may be mediated by alterations in the microbiota. Here, we investigated the dynamics of microbial community assembly with respect to genotype using a Fut2-deficient mouse model, taking the genotype of the maternal lineage over two generations into account...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28642593/transforming-growth-factor-%C3%AE-1-regulates-the-nascent-hematopoietic-stem-cell-niche-by-promoting-gluconeogenesis
#13
C-Y Zhang, H-M Yin, H Wang, D Su, Y Xia, L-F Yan, B Fang, W Liu, Y-M Wang, A-H Gu, Y Zhou
The understanding of hematopoietic stem cell (HSC) emergence is important to generate HSCs from pluripotent precursors. However, integrated signaling network that regulates the niche of nascent HSCs remains unclear. Herein, we uncovered a novel role of TGF-β1 in the metabolic niche of HSC emergence using the tgf-β1b(-/-) zebrafish. Our findings first showed that Tgf-β1 transcripts were enriched in the nascent HSCs. Loss of tgf-β1b caused a decrease of nascent HSCs within the aorta-gonad-mesonephros. Moreover, tgf-β1b(+) cells were runx1(+) HSCs and underwent an endothelial-to-hematopoietic-transition process...
June 23, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28642592/integrative-network-analysis-identifies-novel-drivers-of-pathogenesis-and-progression-in-newly-diagnosed-multiple-myeloma
#14
A Laganà, D Perumal, D Melnekoff, B Readhead, B A Kidd, V Leshchenko, P-Y Kuo, J Keats, M DeRome, J Yesil, D Auclair, S Lonial, A Chari, H J Cho, B Barlogie, S Jagannath, J T Dudley, S Parekh
Multiple Myeloma (MM) is an incurable malignancy of bone marrow plasma cells characterized by wide clinical and molecular heterogeneity. In this study we applied an integrative network biology approach to molecular and clinical data measured from 450 patients with newly diagnosed MM from the MMRF CoMMpass study. A novel network model of myeloma (MMNet) was constructed, revealing complex molecular disease patterns and novel associations between clinical traits and genomic markers. Genomic alterations and groups of co-expressed genes correlate with disease stage, tumor clonality, and early progression...
June 23, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28642548/hemodynamics-of-speech-production-an-fnirs-investigation-of-children-who-stutter
#15
B Walsh, F Tian, J A Tourville, M A Yücel, T Kuczek, A J Bostian
Stuttering affects nearly 1% of the population worldwide and often has life-altering negative consequences, including poorer mental health and emotional well-being, and reduced educational and employment achievements. Over two decades of neuroimaging research reveals clear anatomical and physiological differences in the speech neural networks of adults who stutter. However, there have been few neurophysiological investigations of speech production in children who stutter. Using functional near-infrared spectroscopy (fNIRS), we examined hemodynamic responses over neural regions integral to fluent speech production including inferior frontal gyrus, premotor cortex, and superior temporal gyrus during a picture description task...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28641502/ordering-theories-typologies-and-conceptual-frameworks-for-sociotechnical-change
#16
Benjamin K Sovacool, David J Hess
What theories or concepts are most useful at explaining socio technical change? How can - or cannot - these be integrated? To provide an answer, this study presents the results from 35 semi-structured research interviews with social science experts who also shared more than two hundred articles, reports and books on the topic of the acceptance, adoption, use, or diffusion of technology. This material led to the identification of 96 theories and conceptual approaches spanning 22 identified disciplines. The article begins by explaining its research terms and methods before honing in on a combination of fourteen theories deemed most relevant and useful by the material...
June 1, 2017: Social Studies of Science
https://www.readbyqxmd.com/read/28641124/neural-repair-by-nt3-chitosan-via-enhancement-of-endogenous-neurogenesis-after-adult-focal-aspiration-brain-injury
#17
Peng Hao, Hongmei Duan, Fei Hao, Lan Chen, Min Sun, Kevin S Fan, Yi Eve Sun, David Williams, Zhaoyang Yang, Xiaoguang Li
The latent regenerative potential of endogenous neural stem/progenitor cells (NSCs) in the adult mammalian brain has been postulated as a likely source for neural repair. However, the inflammatory and inhibitory microenvironment after traumatic brain injury (TBI) prohibits NSCs from generating new functional neurons to restore brain function. Here we report a biodegradable material, chitosan, which, when loaded with neurotrophin-3 (NT3) and injected into the lesion site after TBI, effectively engaged endogenous NSCs to proliferate and migrate to the injury area...
April 26, 2017: Biomaterials
https://www.readbyqxmd.com/read/28640862/a-biosystems-approach-to-identify-the-molecular-signaling-mechanisms-of-tmem30a-during-tumor-migration
#18
Jiao Wang, Qian Wang, Dongfang Lu, Fangfang Zhou, Dong Wang, Ruili Feng, Kai Wang, Robert Molday, Jiang Xie, Tieqiao Wen
Understanding the molecular mechanisms underlying cell migration, which plays an important role in tumor growth and progression, is critical for the development of novel tumor therapeutics. Overexpression of transmembrane protein 30A (TMEM30A) has been shown to initiate tumor cell migration, however, the molecular mechanisms through which this takes place have not yet been reported. Thus, we propose the integration of computational and experimental approaches by first predicting potential signaling networks regulated by TMEM30A using a) computational biology methods, b) our previous mass spectrometry results of the TMEM30A complex in mouse tissue, and c) a number of migration-related genes manually collected from the literature, and subsequently performing molecular biology experiments including the in vitro scratch assay and real-time quantitative polymerase chain reaction (qPCR) to validate the reliability of the predicted network...
2017: PloS One
https://www.readbyqxmd.com/read/28640810/lassim-a-network-inference-toolbox-for-genome-wide-mechanistic-modeling
#19
Rasmus Magnusson, Guido Pio Mariotti, Mattias Köpsén, William Lövfors, Danuta R Gawel, Rebecka Jörnsten, Jörg Linde, Torbjörn Nordling, Elin Nyman, Sylvie Schulze, Colm E Nestor, Huan Zhang, Gunnar Cedersund, Mikael Benson, Andreas Tjärnberg, Mika Gustafsson
Recent technological advancements have made time-resolved, quantitative, multi-omics data available for many model systems, which could be integrated for systems pharmacokinetic use. Here, we present large-scale simulation modeling (LASSIM), which is a novel mathematical tool for performing large-scale inference using mechanistically defined ordinary differential equations (ODE) for gene regulatory networks (GRNs). LASSIM integrates structural knowledge about regulatory interactions and non-linear equations with multiple steady state and dynamic response expression datasets...
June 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28640508/intraglomerular-gap-junctions-enhance-interglomerular-synchrony-in-a-sparsely-connected-olfactory-bulb-network
#20
Frederic Pouille, Thomas S McTavish, Lawrence E Hunter, Diego Restrepo, Nathan E Schoppa
A dominant feature of the olfactory bulb response to odour is fast synchronized oscillations at beta (15-40 Hz) or gamma (40-90 Hz) frequencies, thought to be involved in integration of olfactory signals. Mechanistically, the bulb presents an interesting case study for understanding how beta/gamma oscillations arise. Fast oscillatory synchrony in the activity of output mitral cells (MCs) appears to result from interactions with GABAergic granule cells (GCs), yet the incidence of MC-GC connections is very low, around 4%...
June 22, 2017: Journal of Physiology
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