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https://www.readbyqxmd.com/read/29458166/statistical-approach-for-selection-of-biologically-informative-genes
#1
Samarendra Das, Anil Rai, D C Mishra, S N Rai
Selection of informative genes from high dimensional gene expression data has emerged as an important research area in genomics. Many gene selection techniques have been proposed so far are either based on relevancy or redundancy measure. Further, the performance of these techniques has been adjudged through post selection classification accuracy computed through a classifier using the selected genes. This performance metric may be statistically sound but may not be biologically relevant. A statistical approach, i...
February 16, 2018: Gene
https://www.readbyqxmd.com/read/29458110/investigation-of-adhesive-interactions-in-the-specific-targeting-of-triptorelin-conjugated-peg-coated-magnetite-nanoparticles-to-breast-cancer-cells
#2
Jingjie Hu, Sina Youssefian, John Obayemi, Karen Malatesta, Nima Rahbar, Winston Soboyejo
The understanding of adhesive interaction at the nanoscale between functionalized nanoparticles and biological cells is of great importance to develop effective theranostic nanocarriers for targeted cancer therapy. Here, we report a combination of experimental and computational approaches to evaluate the adhesion between Triptorelin (a Luteinizing Hormone-Releasing Hormone (LHRH) agonist)-conjugated poly-(ethylene glycol) (PEG)-coated magnetite nanoparticles (Triptorelin-MNPs) and breast cells. The adhesion forces between Triptorelin-MNPs and normal/cancerous breast cells are obtained using atomic force microscopy...
February 16, 2018: Acta Biomaterialia
https://www.readbyqxmd.com/read/29457870/effect-of-the-flow-profile-on-separation-efficiency-in-pressure-assisted-reversed-polarity-capillary-zone-electrophoresis-of-anions-simulation-and-experimental-evaluation
#3
Gabor Jarvas, Marton Szigeti, Andras Guttman
Capillary electrophoresis connected to electrospray ionization mass spectrometry is a promising combination to analyze complex biological samples. The use of sheathless electrospray ionization interfaces, such as a porous nanoelectrospray capillary emitter, requires the application of forward flow (either by pressure or electroosmosis) to maintain the electrospray process. The analysis of solute molecules with strong negative charges (e.g., aminopyrenetrisulfonate labeled glycans) necessitates a reversed-polarity capillary electrophoresis separation mode, in which case the electroosmotic flow is counter current, thus pressure assistance is necessary...
February 19, 2018: Journal of Separation Science
https://www.readbyqxmd.com/read/29457457/programming-hierarchical-self-assembly-of-patchy-particles-into-colloidal-crystals-via-colloidal-molecules
#4
Daniel Morphew, James Shaw, Christopher Avins, Dwaipayan Chakrabarti
Colloidal self-assembly is a promising bottom-up route to a wide variety of three-dimensional structures, from clusters to crystals. Programming hierarchical self-assembly of colloidal building blocks, which can give rise to structures ordered at multiple levels to rival biological complexity, poses a multiscale design problem. Here we explore a generic design principle that exploits a hierarchy of interaction strengths and employ this design principle in computer simulations to demonstrate the hierarchical self-assembly of triblock patchy colloidal particles into two distinct colloidal crystals...
February 19, 2018: ACS Nano
https://www.readbyqxmd.com/read/29456513/stochastic-effects-in-autoimmune-dynamics
#5
Farzad Fatehi, Sergey N Kyrychko, Aleksandra Ross, Yuliya N Kyrychko, Konstantin B Blyuss
Among various possible causes of autoimmune disease, an important role is played by infections that can result in a breakdown of immune tolerance, primarily through the mechanism of "molecular mimicry". In this paper we propose and analyse a stochastic model of immune response to a viral infection and subsequent autoimmunity, with account for the populations of T cells with different activation thresholds, regulatory T cells, and cytokines. We show analytically and numerically how stochasticity can result in sustained oscillations around deterministically stable steady states, and we also investigate stochastic dynamics in the regime of bi-stability...
2018: Frontiers in Physiology
https://www.readbyqxmd.com/read/29456488/exploring-the-complexity-of-cortical-development-using-single-cell-transcriptomics
#6
REVIEW
Hyobin Jeong, Vijay K Tiwari
The developing neocortex in the mammalian brain is composed of multiple cell types including apical progenitors (AP), basal progenitors (BP), and neurons that populate three different layers, the ventricular zone (VZ), the subventricular zone (SVZ), and the cortical plate (CP). Despite recent advances, the diversity of the existing cell populations including those which are differentiating and mature, their biogenesis and the underlying gene regulatory mechanisms remain poorly known. Recent studies have taken advantage of the rapidly emerging single-cell technologies to decode the heterogeneity of cell populations at the transcriptome level during cortical development and their molecular details...
2018: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/29456262/mixed-analytical-stochastic-simulation-method-for-the-recovery-of-a-brownian-gradient-source-from-probability-fluxes-to-small-windows
#7
U Dobramysl, D Holcman
Is it possible to recover the position of a source from the steady-state fluxes of Brownian particles to small absorbing windows located on the boundary of a domain? To address this question, we develop a numerical procedure to avoid tracking Brownian trajectories in the entire infinite space. Instead, we generate particles near the absorbing windows, computed from the analytical expression of the exit probability. When the Brownian particles are generated by a steady-state gradient at a single point, we compute asymptotically the fluxes to small absorbing holes distributed on the boundary of half-space and on a disk in two dimensions, which agree with stochastic simulations...
February 15, 2018: Journal of Computational Physics
https://www.readbyqxmd.com/read/29455637/molecular-dynamics-of-interaction-of-sesamin-and-related-compounds-with-the-cancer-marker-%C3%AE-catenin-an-in-silico-study
#8
Bindu Madhuri Cavuturu, Vishwambar Vishnu Bhandare, Amutha Ramaswamy, Neelakantan Arumugam
By virtue of their regulatory role in the biological process, certain protein-protein complexes form potential targets for designing and discovery of drugs. Alteration set in the controlled formation of such complexes results in dysregulation of several metabolic processes, leading to diseased condition. β-catenin/Tcf4 complex is one such protein-protein complex found altered in colorectal epithelial cells resulting in activation of target genes leading to cancer. Recently certain lignans from seeds of the oil crop sesame were found inhibiting initiation and progression of this type of cancer...
February 18, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29455577/exploring-autophagy-with-gene-ontology
#9
Paul Denny, Marc Feuermann, David P Hill, Ruth C Lovering, Helene Plun-Favreau, Paola Roncaglia
Autophagy is a fundamental cellular process that is well conserved among eukaryotes. It is one of the strategies that cells use to catabolize substances in a controlled way. Autophagy is used for recycling cellular components, responding to cellular stresses and ridding cells of foreign material. Perturbations in autophagy have been implicated in a number of pathological conditions such as neurodegeneration, cardiac disease and cancer. The growing knowledge about autophagic mechanisms needs to be collected in a computable and shareable format to allow its use in data representation and interpretation...
February 17, 2018: Autophagy
https://www.readbyqxmd.com/read/29454849/escmid-study-group-for-infections-in-compromised-hosts-esgich-consensus-document-on-the-safety-of-targeted-and-biological-therapies-an-infectious-diseases-perspective-intracellular-signaling-pathways-tyrosine-kinase-and-mtor-inhibitors
#10
REVIEW
Mark Reinwald, Jose T Silva, Nicolas J Mueller, Jesús Fortún, Christian Garzoni, Johan W de Fijter, Mario Fernández-Ruiz, Paolo Grossi, Jose María Aguado
BACKGROUND: The present review is part of the ESCMID Study Group for Infections in Compromised Hosts (ESGICH) Consensus Document on the safety of targeted and biological therapies. AIMS: To review, from an Infectious Diseases perspective, the safety profile of therapies targeting different intracellular signaling pathways and to suggest preventive recommendations. SOURCES: Computer-based MEDLINE searches with MeSH terms pertaining to each agent or therapeutic family...
February 15, 2018: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/29454060/aop-db-a-database-resource-for-the-exploration-of-adverse-outcome-pathways-through-integrated-association-networks
#11
Maureen E Pittman, Stephen W Edwards, Cataia Ives, Holly M Mortensen
The Adverse Outcome Pathway (AOP) framework describes the progression of a toxicity pathway from molecular perturbation to population-level outcome in a series of measurable, mechanistic responses. The controlled, computer-readable vocabulary that defines an AOP has the ability to, automatically and on a large scale, integrate AOP knowledge with publically available sources of biological high-throughput data and its derived associations. To support the discovery and development of putative (existing) and potential AOPs, we introduce the AOP-DB, an exploratory database resource that aggregates association relationships between genes and their related chemicals, diseases, pathways, species orthology information, ontologies, and gene interactions...
February 14, 2018: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/29453175/solubilization-of-polycyclic-aromatic-hydrocarbons-pahs-with-phenol-in-coking-wastewater-treatment-system-interaction-and-engineering-significance
#12
Qiaoping Kong, Haizhen Wu, Lei Liu, Fengzhen Zhang, Sergei Preis, Shuang Zhu, Chaohai Wei
Polycyclic aromatic hydrocarbons (PAHs) are accumulated in the sludge collected from the coking wastewater treatment. Phenol with its efficient degradation observed in biological treatment promotes the solubility of PAHs in aqueous phase. The interaction mechanism of phenol and PAHs in aqueous and sludge phases was systematically studied in two full-scale engineering projects composed of anaerobic-oxic-oxic (A-O 1 -O 2 ) and anaerobic-oxic-hydrolytic-oxic (A-O 1 -H-O 2 ) sequences. The results showed that reasonable use of phenol facilitates solubilization of PAHs alleviating their emission problems...
February 13, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29452171/evolution-of-model-specific-relative-growth-rate-its-genesis-and-performance-over-fisher-s-growth-rates
#13
Arijit Pal, Amiya Ranjan Bhowmick, Farhana Yeasmin, Sabyasachi Bhattacharya
Growth curve models play an instrumental role to quantify the growth of biological processes and have immense practical applications across disciplines. In the modelling approach, the absolute growth rate and relative growth rate (RGR) are two most commonly used measures of growth rates. RGR is empirically estimated by Fisher (1921) assuming exponential growth between two consecutive time points and remains invariant under any choice of the underlying growth model. In this article, we propose a new measure of RGR, called modified RGR, which is sensitive to the choice of underlying growth law...
February 13, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29451873/in-silico-analysis-of-antibiotic-induced-clostridium-difficile-infection-remediation-techniques-and-biological-adaptations
#14
Eric W Jones, Jean M Carlson
In this paper we study antibiotic-induced C. difficile infection (CDI), caused by the toxin-producing C. difficile (CD), and implement clinically-inspired simulated treatments in a computational framework that synthesizes a generalized Lotka-Volterra (gLV) model with SIR modeling techniques. The gLV model uses parameters derived from an experimental mouse model, in which the mice are administered antibiotics and subsequently dosed with CD. We numerically identify which of the experimentally measured initial conditions are vulnerable to CD colonization, then formalize the notion of CD susceptibility analytically...
February 16, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29451794/-s-2-amino-3-5-methyl-3-hydroxyisoxazol-4-yl-propanoic-acid-ampa-and-kainate-receptor-ligands-further-exploration-of-bioisosteric-replacements-structural-and-biological-investigation
#15
Simone Brogi, Margherita Brindisi, Stefania Butini, Giridhar Uttam Kshirsagar, Samuele Maramai, Giulia Chemi, Sandra Gemma, Giuseppe Campiani, Ettore Novellino, Paolo Fiorenzani, Jessica Pinassi, Anna Maria Aloisi, Mikko Gynther, Raminta Venskutonyte, Liwei Han, Karla Frydenvang, Jette Sandholm Kastrup, Darryl S Pickering
Starting from 1-4 and 7 structural templates, analogues based on bioisosteric replacements (5a-c vs 1, 2 and 6 vs 7) were synthesized for completing the SAR analysis. Interesting binding properties at GluA2, GluK1 and GluK3 receptors were discovered. The requirements for GluK3 interaction were elucidated determining the X-ray structures of the GluK3-LBD with 2 and 5c and by computational studies. Antinociceptive potential was demonstrated for GluK1 partial agonist 3 and antagonist 7 (2 mg/kg ip).
February 16, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29451603/from-medicinal-chemistry-to-human-health-current-approaches-to-drug-discovery-for-cancer-and-neglected-tropical-diseases
#16
Leonardo G Ferreira, Glaucius Oliva, Adriano D Andricopulo
Scientific and technological breakthroughs have compelled the current players in drug discovery to increasingly incorporate knowledge-based approaches. This evolving paradigm, which has its roots attached to the recent advances in medicinal chemistry, molecular and structural biology, has unprecedentedly demanded the development of up-to-date computational approaches, such as bio- and chemo-informatics. These tools have been pivotal to catalyzing the ever-increasing amount of data generated by the molecular sciences, and to converting the data into insightful guidelines for use in the research pipeline...
February 15, 2018: Anais da Academia Brasileira de Ciências
https://www.readbyqxmd.com/read/29451298/micro-computed-tomography-visualization-of-the-vestigial-alimentary-canal-in-adult-oestrid-flies
#17
D Martín-Vega, A Garbout, F Ahmed, L M Ferrer, J Lucientes, D D Colwell, M J R Hall
Oestrid flies (Diptera: Oestridae) do not feed during the adult stage as they acquire all necessary nutrients during the parasitic larval stage. The adult mouthparts and digestive tract are therefore frequently vestigial; however, morphological data on the alimentary canal in adult oestrid flies are scarce and a proper visualization of this organ system within the adult body is lacking. The present work visualizes the morphology of the alimentary canal in adults of two oestrid species, Oestrus ovis L. and Hypoderma lineatum (de Villiers), with the use of non-invasive micro-computed tomography (micro-CT) and compares it with the highly developed alimentary canal of the blow fly Calliphora vicina Robineau-Desvoidy (Diptera: Calliphoridae)...
February 16, 2018: Medical and Veterinary Entomology
https://www.readbyqxmd.com/read/29450984/computational-studies-on-horseshoe-shape-pocket-of-human-orexin-receptor-type-2-and-boat-conformation-of-suvorexant-by-molecular-dynamics-simulations
#18
Qifeng Bai, Horacio Pérez-Sánchez, Zhuoyu Shi, Lanlan Li, Danfeng Shi, Huanxiang Liu, Xiaojun Yao
The FDA approved drug suvorexant binds to the horseshoe shape pocket of OX 2 R with the boat conformation. The horseshoe shape pocket plays an important role on the biological activity of OX 2 R in the cell membrane. To study the binding mechanism between the horseshoe shape pocket of OX 2 R and boat conformation of suvorexant, the crystal structures of wild type and N324A mutant of OX 2 R in complex with antagonist suvorexant are chosen to perform molecular dynamics (MD) simulations, QM/MM and MMGBSA calculations...
February 16, 2018: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/29450674/risk-assessment-of-pesticides-in-estuaries-a-review-addressing-the-persistence-of-an-old-problem-in-complex-environments
#19
Nagore Cuevas, Marta Martins, Pedro M Costa
Estuaries, coastal lagoons and other transition ecosystems tend to become the ultimate reservoirs of pollutants transported by continental runoff, among which pesticides constitute the class of most concern. High amounts of dissolved and particulated organic matter greatly contribute to the accumulation of pesticides that eventually become trapped in sediments or find their way along food chains. Perhaps not so surprisingly, it is common to find elevated levels of pesticides in estuarine sediments decades after their embargo...
February 15, 2018: Ecotoxicology
https://www.readbyqxmd.com/read/29449571/an-in-silico-argument-for-mitochondrial-microrna-as-a-determinant-of-primary-non-function-in-liver-transplantation
#20
Shirin Elizabeth Khorsandi, Siamak Salehi, Miriam Cortes, Hector Vilca-Melendez, Krishna Menon, Parthi Srinivasan, Andreas Prachalias, Wayel Jassem, Nigel Heaton
Mitochondria have their own genomic, transcriptomic and proteomic machinery but are unable to be autonomous, needing both nuclear and mitochondrial genomes. The aim of this work was to use computational biology to explore the involvement of Mitochondrial microRNAs (MitomiRs) and their interactions with the mitochondrial proteome in a clinical model of primary non function (PNF) of the donor after cardiac death (DCD) liver. Archival array data on the differential expression of miRNA in DCD PNF was re-analyzed using a number of publically available computational algorithms...
February 15, 2018: Scientific Reports
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