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https://www.readbyqxmd.com/read/27918583/the-gene-regulatory-network-of-lens-induction-is-wired-through-meis-dependent-shadow-enhancers-of-pax6
#1
Barbora Antosova, Jana Smolikova, Lucie Klimova, Jitka Lachova, Michaela Bendova, Iryna Kozmikova, Ondrej Machon, Zbynek Kozmik
Lens induction is a classical developmental model allowing investigation of cell specification, spatiotemporal control of gene expression, as well as how transcription factors are integrated into highly complex gene regulatory networks (GRNs). Pax6 represents a key node in the gene regulatory network governing mammalian lens induction. Meis1 and Meis2 homeoproteins are considered as essential upstream regulators of Pax6 during lens morphogenesis based on their interaction with the ectoderm enhancer (EE) located upstream of Pax6 transcription start site...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27908049/fast-computation-of-time-dependent-acoustic-fields
#2
Michael Carley, Ghader Ghorbaniasl
A method for the fast evaluation of time-dependent acoustic fields from complex sources is presented. The technique is based on a fast integration method for the boundary integral arising in a Kirchhoff formulation and requires a small, and roughly constant, computation time to compute a transient signal, at the expense of a pre-processing stage. In the calculations in this paper, based on test cases for a single rotor, a counter-rotating open rotor, and a broadband volume source, it is found that transient field calculations require an order of magnitude less computational time for the field from an array of 16 384 sources, a computational advantage that increases with source number...
November 2016: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/27903652/prepore-stability-controls-productive-folding-of-the-bam-independent-multimeric-outer-membrane-secretin-puld
#3
Ingrid Guilvout, Sébastien Brier, Mohamed Chami, Véronique Hourdel, Olivera Francetic, Anthony P Pugsley, Julia Chamot-Rooke, Gerard H M Huysmans
Members of a group of multimeric secretion pores that assemble independently of any known membrane-embedded insertase in Gram-negative bacteria fold into a prepore before membrane-insertion occurs. The mechanisms and the energetics that drive the folding of these proteins are poorly understood. Here, equilibrium unfolding and hydrogen/deuterium exchange monitored by mass spectrometry indicated that a loss of 4-5 kJ/mol/protomer in the N3-domain that is peripheral to the membrane-spanning C-domain in the dodecameric secretin PulD, the founding member of this class, prevents pore formation by destabilizing the prepore into a poorly structured dodecamer as visualized by electron microscopy...
November 30, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27899609/enabling-the-democratization-of-the-genomics-revolution-with-a-fully-integrated-web-based-bioinformatics-platform
#4
Po-E Li, Chien-Chi Lo, Joseph J Anderson, Karen W Davenport, Kimberly A Bishop-Lilly, Yan Xu, Sanaa Ahmed, Shihai Feng, Vishwesh P Mokashi, Patrick S G Chain
Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27895917/validation-of-biomarkers-to-predict-response-to-immunotherapy-in-cancer-volume-i-pre-analytical-and-analytical-validation
#5
REVIEW
Giuseppe V Masucci, Alessandra Cesano, Rachael Hawtin, Sylvia Janetzki, Jenny Zhang, Ilan Kirsch, Kevin K Dobbin, John Alvarez, Paul B Robbins, Senthamil R Selvan, Howard Z Streicher, Lisa H Butterfield, Magdalena Thurin
Immunotherapies have emerged as one of the most promising approaches to treat patients with cancer. Recently, there have been many clinical successes using checkpoint receptor blockade, including T cell inhibitory receptors such as cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and programmed cell death-1 (PD-1). Despite demonstrated successes in a variety of malignancies, responses only typically occur in a minority of patients in any given histology. Additionally, treatment is associated with inflammatory toxicity and high cost...
2016: Journal for Immunotherapy of Cancer
https://www.readbyqxmd.com/read/27891308/comparative-evaluation-of-the-efficacy-of-fluoride-varnish-and-casein-phosphopeptide-amorphous-calcium-phosphate-in-reducing-streptococcus-mutans-counts-in-dental-plaque-of-children-an-in-vivo-study
#6
Shweta Chandak, Ashish Bhondey, Amit Bhardwaj, Jitesh Pimpale, Manisha Chandwani
AIM: To assess the comparative efficacy of fluoride varnish and casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) complex visa viz. Streptococcus mutans in plaque, and thereby the role that these two agents could play in the prevention of dental caries. MATERIALS AND METHODS: A cluster sample of 120 caries inactive individuals belonging to moderate and high caries risk group were selected from 3-5-year-old age group based on the criteria given by Krassee and were randomized to four groups, namely, fluoride varnish - Group I, CPP-ACP complex - Group II, mixture of CPP-ACP complex -Gourp III, and fluoride and routine oral hygiene procedures as control - Group IV...
September 2016: Journal of International Society of Preventive & Community Dentistry
https://www.readbyqxmd.com/read/27891090/disrupted-nodal-and-hub-organization-account-for-brain-network-abnormalities-in-parkinson-s-disease
#7
Yuko Koshimori, Sang-Soo Cho, Marion Criaud, Leigh Christopher, Mark Jacobs, Christine Ghadery, Sarah Coakeley, Madeleine Harris, Romina Mizrahi, Clement Hamani, Anthony E Lang, Sylvain Houle, Antonio P Strafella
The recent application of graph theory to brain networks promises to shed light on complex diseases such as Parkinson's disease (PD). This study aimed to investigate functional changes in sensorimotor and cognitive networks in Parkinsonian patients, with a focus on inter- and intra-connectivity organization in the disease-associated nodal and hub regions using the graph theoretical analyses. Resting-state functional MRI data of a total of 65 participants, including 23 healthy controls (HCs) and 42 patients, were investigated in 120 nodes for local efficiency, betweenness centrality, and degree...
2016: Frontiers in Aging Neuroscience
https://www.readbyqxmd.com/read/27890600/folate-status-and-colorectal-cancer-risk-a-2016-update
#8
REVIEW
Joel B Mason, San Yuan Tang
The consensus of epidemiologic evidence indicates that an abundant intake of foodstuffs rich in folate conveys protection against the development of colorectal cancer, and perhaps some other common cancers as well. Pre-clinical models substantiate that the relationship is a genuinely causal one. Pre-clinical models have also lent mechanistic insights into the biochemical and molecular pathways by which adequate folate exposure conveys these protective effects, although human studies are beginning to establish the relevance of our mechanistic understanding to human cancer biology...
November 24, 2016: Molecular Aspects of Medicine
https://www.readbyqxmd.com/read/27867830/niche-construction-social-cognition-and-language-hypothesizing-the-human-as-the-production-of-place
#9
Oliver Davies
New data is emerging from evolutionary anthropology and the neuroscience of social cognition on our species-specific hyper-cooperation (HC). This paper attempts an integration of third-person archaeological and second-person, neuroscientific perspectives on the structure of HC, through a post-Ricoeurian development in hermeneutical phenomenology. We argue for the relatively late evolution of advanced linguistic consciousness (ALC) (Hiscock in Biological Theory 9:27-41, 2014), as a reflexive system based on the 'in-between' or 'cognitive system' as reported by Vogeley et al...
2016: Culture and Brain
https://www.readbyqxmd.com/read/27855964/interventions-to-reduce-emergency-department-utilisation-a-review-of-reviews
#10
Koen Van den Heede, Carine Van de Voorde
OBJECTIVE: To describe policy interventions that have the objective to reduce ED use and to estimate their effectiveness. METHODS: Narrative review by searching three electronic databases for scientific literature review papers published between 2010 and October 2015. The quality of the included studies was assessed with AMSTAR, and a narrative synthesis of the retrieved papers was applied. RESULTS: Twenty-three included publications described six types of interventions: (1) cost sharing; (2) strengthening primary care; (3) pre-hospital diversion (including telephone triage); (4) coordination; (5) education and self-management support; (6) barriers to access emergency departments...
December 2016: Health Policy
https://www.readbyqxmd.com/read/27853269/unraveling-the-association-between-genetic-integrity-and-metabolic-activity-in-pre-implantation-stage-embryos
#11
Fiona D'Souza, Shivanand M Pudakalakatti, Shubhashree Uppangala, Sachin Honguntikar, Sujith Raj Salian, Guruprasad Kalthur, Renu Pasricha, Divya Appajigowda, Hanudatta S Atreya, Satish Kumar Adiga
Early development of certain mammalian embryos is protected by complex checkpoint systems to maintain the genomic integrity. Several metabolic pathways are modulated in response to genetic insults in mammalian cells. The present study investigated the relationship between the genetic integrity, embryo metabolites and developmental competence in preimplantation stage mouse embryos with the aim to identify early biomarkers which can predict embryonic genetic integrity using spent medium profiling by NMR spectroscopy...
November 17, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27852861/pre-mrna-processing-factor-prp18-is-a-stimulatory-factor-of-influenza-virus-rna-synthesis-and-possesses-the-np-chaperone-activity
#12
M Minakuchi, K Sugiyama, Y Kato, T Naito, M Okuwaki, A Kawaguchi, K Nagata
: The genome of influenza virus (vRNA) is associated with nucleoprotein (NP) and viral RNA-dependent RNA polymerases, and forms helical viral ribonucleoprotein (vRNP) complexes. NP-vRNA complex is the biologically active template for RNA synthesis by the viral polymerase. Previously, we identified human pre-mRNA processing factor 18 (Prp18) as a stimulatory factor for viral RNA synthesis using an yeast replicon system and single-gene deletion library of yeast (Naito T, Kiyasu Y, Sugiyama K, Kimura A, Nakano R, Matsukage A, Nagata K...
November 16, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27852738/contributions-of-rapid-neuromuscular-transmission-to-the-fine-control-of-acoustic-parameters-of-birdsong
#13
Caitlin Mencio, Balagurunathan Kuberan, Franz Goller
Neural control of complex vocal behaviors, such as birdsong and speech, requires integration of biomechanical nonlinearities through muscular output. Although control of airflow and tension of vibrating tissues are known functions of vocal muscles, it remains unclear how specific muscle characteristics contribute to specific acoustic parameters. To address this gap, we removed heparan sulfate chains using heparitinases to subtly perturb neuromuscular transmission in the syrinx of adult male zebra finches (Taeniopygia guttata)...
November 16, 2016: Journal of Neurophysiology
https://www.readbyqxmd.com/read/27846884/future-perspectives-in-melanoma-research-meeting-report-from-the-melanoma-bridge-napoli-december-1st-4th-2015
#14
Paolo A Ascierto, Sanjiv Agarwala, Gerardo Botti, Alessandra Cesano, Gennaro Ciliberto, Michael A Davies, Sandra Demaria, Reinhard Dummer, Alexander M Eggermont, Soldano Ferrone, Yang Xin Fu, Thomas F Gajewski, Claus Garbe, Veronica Huber, Samir Khleif, Michael Krauthammer, Roger S Lo, Giuseppe Masucci, Giuseppe Palmieri, Michael Postow, Igor Puzanov, Ann Silk, Stefani Spranger, David F Stroncek, Ahmad Tarhini, Janis M Taube, Alessandro Testori, Ena Wang, Jennifer A Wargo, Cassian Yee, Hassane Zarour, Laurence Zitvogel, Bernard A Fox, Nicola Mozzillo, Francesco M Marincola, Magdalena Thurin
The sixth "Melanoma Bridge Meeting" took place in Naples, Italy, December 1st-4th, 2015. The four sessions at this meeting were focused on: (1) molecular and immune advances; (2) combination therapies; (3) news in immunotherapy; and 4) tumor microenvironment and biomarkers. Recent advances in tumor biology and immunology has led to the development of new targeted and immunotherapeutic agents that prolong progression-free survival (PFS) and overall survival (OS) of cancer patients. Immunotherapies in particular have emerged as highly successful approaches to treat patients with cancer including melanoma, non-small cell lung cancer (NSCLC), renal cell carcinoma (RCC), bladder cancer, and Hodgkin's disease...
November 15, 2016: Journal of Translational Medicine
https://www.readbyqxmd.com/read/27833619/translating-the-banana-genome-to-delineate-stress-resistance-dwarfing-parthenocarpy-and-mechanisms-of-fruit-ripening
#15
REVIEW
Prasanta K Dash, Rhitu Rai
Evolutionary frozen, genetically sterile and globally iconic fruit "Banana" remained untouched by the green revolution and, as of today, researchers face intrinsic impediments for its varietal improvement. Recently, this wonder crop entered the genomics era with decoding of structural genome of double haploid Pahang (AA genome constitution) genotype of Musa acuminata. Its complex genome decoded by hybrid sequencing strategies revealed panoply of genes and transcription factors involved in the process of sucrose conversion that imparts sweetness to its fruit...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27830755/dynamic-oligomerization-of-integrase-orchestrates-hiv-nuclear-entry
#16
Doortje Borrenberghs, Lieve Dirix, Flore De Wit, Susana Rocha, Jolien Blokken, Stéphanie De Houwer, Rik Gijsbers, Frauke Christ, Johan Hofkens, Jelle Hendrix, Zeger Debyser
Nuclear entry is a selective, dynamic process granting the HIV-1 pre-integration complex (PIC) access to the chromatin. Classical analysis of nuclear entry of heterogeneous viral particles only yields averaged information. We now have employed single-virus fluorescence methods to follow the fate of single viral pre-integration complexes (PICs) during infection by visualizing HIV-1 integrase (IN). Nuclear entry is associated with a reduction in the number of IN molecules in the complexes while the interaction with LEDGF/p75 enhances IN oligomerization in the nucleus...
November 10, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27824034/akap95-regulates-splicing-through-scaffolding-rnas-and-rna-processing-factors
#17
Jing Hu, Alireza Khodadadi-Jamayran, Miaowei Mao, Kushani Shah, Zhenhua Yang, Md Talat Nasim, Zefeng Wang, Hao Jiang
Alternative splicing of pre-mRNAs significantly contributes to the complexity of gene expression in higher organisms, but the regulation of the splice site selection remains incompletely understood. We have previously demonstrated that a chromatin-associated protein, AKAP95, has a remarkable activity in enhancing chromatin transcription. In this study, we show that AKAP95 interacts with many factors involved in transcription and RNA processing, including selective groups of hnRNP proteins, through its N-terminal region, and directly regulates pre-mRNA splicing...
November 8, 2016: Nature Communications
https://www.readbyqxmd.com/read/27814521/the-central-nervous-system-and-the-gut-microbiome
#18
REVIEW
Gil Sharon, Timothy R Sampson, Daniel H Geschwind, Sarkis K Mazmanian
Neurodevelopment is a complex process governed by both intrinsic and extrinsic signals. While historically studied by researching the brain, inputs from the periphery impact many neurological conditions. Indeed, emerging data suggest communication between the gut and the brain in anxiety, depression, cognition, and autism spectrum disorder (ASD). The development of a healthy, functional brain depends on key pre- and post-natal events that integrate environmental cues, such as molecular signals from the gut...
November 3, 2016: Cell
https://www.readbyqxmd.com/read/27804896/investigating-cholesterol-metabolism-and-ageing-using-a-systems-biology-approach
#19
A E Morgan, K M Mooney, S J Wilkinson, N A Pickles, M T Mc Auley
CVD accounted for 27 % of all deaths in the UK in 2014, and was responsible for 1·7 million hospital admissions in 2013/2014. This condition becomes increasingly prevalent with age, affecting 34·1 and 29·8 % of males and females over 75 years of age respectively in 2011. The dysregulation of cholesterol metabolism with age, often observed as a rise in LDL-cholesterol, has been associated with the pathogenesis of CVD. To compound this problem, it is estimated by 2050, 22 % of the world's population will be over 60 years of age, in culmination with a growing resistance and intolerance to pre-existing cholesterol regulating drugs such as statins...
November 2, 2016: Proceedings of the Nutrition Society
https://www.readbyqxmd.com/read/27802424/dual-role-of-the-integrated-stress-response-in-medulloblastoma-tumorigenesis
#20
Sarrabeth Stone, Yeung Ho, Xiting Li, Stephanie Jamison, Heather P Harding, David Ron, Wensheng Lin
In response to endoplasmic reticulum (ER) stress, activation of pancreatic ER kinase (PERK) coordinates an adaptive program known as the integrated stress response (ISR) by phosphorylating translation initiation factor 2α (eIF2α). Phosphorylated eIF2α is quickly dephosphorylated by the protein phosphatase 1 and growth arrest and DNA damage 34 (GADD34) complex. Data indicate that the ISR can either promote or suppress tumor development. Our previous studies showed that the ISR is activated in medulloblastoma in both human patients and animal models, and that the decreased ISR via PERK heterozygous deficiency attenuates medulloblastoma formation in Patched1 heterozygous deficient (Ptch1+/-) mice by enhancing apoptosis of pre-malignant granule cell precursors (GCPs) during cell transformation...
September 6, 2016: Oncotarget
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