keyword
MENU ▼
Read by QxMD icon Read
search

Cell simulation

keyword
https://www.readbyqxmd.com/read/29667836/molecular-dynamics-simulations-are-redefining-our-view-of-peptides-interacting-with-biological-membranes
#1
Jakob P Ulmschneider, Martin B Ulmschneider
Ever since the first molecular mechanics computer simulations of biological molecules became possible, there has been the dream to study all complex biological phenomena in silico, simply bypassing the enormous experimental challenges and their associated costs. For this, two inherent requirements need to be met: First, the time scales achievable in simulations must reach up to the millisecond range and even longer. Second, the computational model must accurately reproduce what is measured experimentally. Despite some recent successes, the general consensus in the field to date has been that neither of these conditions have yet been met and that the dream will be realized, if at all, only in the distant future...
April 18, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29667689/no-unjamming-transition-in-a-voronoi-model-of-biological-tissue
#2
Daniel M Sussman, Matthias Merkel
Vertex models are a popular approach to simulating the mechanical and dynamical properties of dense biological tissues, describing the tissue as a network of polygons. Recently a class of two-dimensional vertex models was shown to exhibit a disordered rigidity transition controlled by the preferred cellular geometry, which was subsequently echoed by experimental findings. An attractive variant of these models uses a Voronoi tessellation to describe the cells, which reduces the number of degrees of freedom as compared the original vertex model...
April 18, 2018: Soft Matter
https://www.readbyqxmd.com/read/29667579/intracellular-antibody-signalling-is-regulated-by-phosphorylation-of-the-fc-receptor-trim21
#3
Claire Dickson, Adam J Fletcher, Marina Vaysburd, Ji-Chun Yang, Donna L Mallery, Jingwei Zeng, Christopher M Johnson, Stephen H McLaughlin, Mark Skehel, Sarah Maslen, James Cruickshank, Nicolas Huguenin-Dezot, Jason W Chin, David Neuhaus, Leo C James
Cell surface Fc receptors activate inflammation and are tightly controlled to prevent autoimmunity. Antibodies also simulate potent immune signalling from inside the cell via the cytosolic antibody receptor TRIM21, but how this is regulated is unknown. Here we show that TRIM21 signalling is constitutively repressed by its B-Box domain and activated by phosphorylation. The B-Box occupies an E2 binding site on the catalytic RING domain by mimicking E2-E3 interactions, inhibiting TRIM21 ubiquitination and preventing immune activation...
April 18, 2018: ELife
https://www.readbyqxmd.com/read/29667549/dentification-and-quantification-of-quercetin-a-major-consitituent-of-artocarpus-altilis-by-targeting-related-genes-of-apoptosis-and-cell-cycle-in-vitro-cytotoxic-activity-against-human-lung-carcinoma-cell-lines-a549
#4
Silvana Russo, Walter Filgueira De Azevedo
BACKGROUND: Cannabinoid Receptor 1 (CB1) is a membrane protein prevalent in the central nervous system, whose crystallographic structure has recently been solved. Studies will be needed to investigate CB1 complexes with its ligands and its role in the development of new drugs. OBJECTIVE: Our goal here is to review the studies on CB1, starting with general aspects and focusing on the recent structural studies, with emphasis on the inverse agonists bound structures...
April 17, 2018: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/29667410/controlling-cargo-trafficking-in-multicomponent-membranes
#5
Tine Curk, Peter Wirnsberger, Jure Dobnikar, Daan Frenkel, Andela Saric
Biological membranes typically contain a large number of different components dispersed in small concentrations in the main membrane phase, including proteins, sugars, and lipids of varying geometrical properties. Most of these components do not bind the cargo. Here, we show that such `inert' components can be crucial for precise control of cross-membrane trafficking. Using a statistical mechanics model and molecular dynamics simulations, we demonstrate that the presence of inert membrane components of small isotropic curvatures dramatically influences cargo endocytosis, even if the total spontaneous curvature of such a membrane remains unchanged...
April 18, 2018: Nano Letters
https://www.readbyqxmd.com/read/29667066/population-exposure-response-analysis-of-cabozantinib-efficacy-and-safety-endpoints-in-patients-with-renal-cell-carcinoma
#6
Steven Lacy, Jace Nielsen, Bei Yang, Dale Miles, Linh Nguyen, Matt Hutmacher
BACKGROUND: In the phase III METEOR trial, tyrosine kinase inhibitor cabozantinib significantly improved progression-free survival (PFS), objective response rate (ORR), and overall survival compared to everolimus in patients with advanced renal cell carcinoma (RCC) who had received prior VEGFR inhibitor therapy. In METEOR, RCC patients started at a daily 60-mg cabozantinib tablet (Cabometyx™) dose but could reduce to 40- or 20-mg to achieve a tolerated exposure. OBJECTIVES AND METHODS: Exposure-response (ER) models were developed to characterize the relationship between cabozantinib at clinically relevant exposures in RCC patients enrolled in METEOR and efficacy (PFS and tumor response) and safety endpoints...
April 17, 2018: Cancer Chemotherapy and Pharmacology
https://www.readbyqxmd.com/read/29666865/preparation-of-lactic-acid-and-glucose-responsive-poly-%C3%AE%C2%B5-caprolactone-b-poly-ethylene-oxide-block-copolymer-micelles-using-phenylboronic-ester-as-a-sensitive-block-linkage
#7
David Vrbata, Mariusz Uchman
The present study describes the synthesis, self-assembly and responsiveness to glucose and lactic acid of biocompatible and biodegradable block copolymer micelles using phenylboronic ester as the linkage between hydrophobic poly(ε-caprolactone) (PCL) and hydrophilic poly(ethylene oxide) (PEO). The PCL block with pendant phenylboronic acid (PCLBA) was synthesized by combining ε-caprolactone (ε-CL) ring-opening polymerisation (ROP), using 4-hydroxymethyl(phenylboronic) acid pinacolate as the initiator, and pinacol deprotection...
April 18, 2018: Nanoscale
https://www.readbyqxmd.com/read/29666762/coccolith-arrangement-follows-eulerian-mathematics-in-the-coccolithophore-emiliania-huxleyi
#8
Kai Xu, David Hutchins, Kunshan Gao
Background: The globally abundant coccolithophore, Emiliania huxleyi , plays an important ecological role in oceanic carbon biogeochemistry by forming a cellular covering of plate-like CaCO3 crystals (coccoliths) and fixing CO2 . It is unknown how the cells arrange different-sized coccoliths to maintain full coverage, as the cell surface area of the cell changes during daily cycle. Methods: We used Euler's polyhedron formula and CaGe simulation software, validated with the geometries of coccoliths, to analyze and simulate the coccolith topology of the coccosphere and to explore the arrangement mechanisms...
2018: PeerJ
https://www.readbyqxmd.com/read/29666154/prediction-and-quantification-of-hepatic-transporter-mediated-uptake-of-pitavastatin-utilizing-a-combination-of-the-relative-activity-factor-approach-and-mechanistic-modeling
#9
Pallabi Mitra, Samantha Weinheimer, Meeghan Michalewicz, Mitchell E Taub
Quantification of the fraction transported (ft) by a particular transporter will facilitate more robust estimations of transporter interactions. Using pitavastatin as a model uptake transporter substrate, we investigated the utility of the relative activity factor (RAF) approach and mechanistic modeling, to estimate ft in hepatocytes. Transporters evaluated were OATP1B1, OATP1B3, and NTCP. Transporter expressing HEK293 cells and human hepatocytes were used for determining RAF values, which were then incorporated into the mechanistic model to simulate hepatocyte uptake of pitavastatin over time...
April 17, 2018: Drug Metabolism and Disposition: the Biological Fate of Chemicals
https://www.readbyqxmd.com/read/29665686/autofluorescent-polymers-1h-1h-2h-2h-perfluoro-1-decanol-grafted-poly-styrene-b-acrylic-acid-block-copolymers-without-conventional-fluorophore
#10
Wenting Li, Chaoyue Che, Juanjuan Pang, Zhenhao Cao, Yapei Jiao, Jingjing Xu, Yufang Ren, Xue Li
Recently, although several unconventional luminescent polymers have been synthesized, it still remains a significant challenge to prepare various new fluorescent polymers by functionalization of nonflurescent polymers. In the present study, a nonfluorescent 1H,1H,2H,2H-perfluoro-1-decanol grafted to nonflurescent polystyrene-b-poly(acrylic acid) block copolymers through simply esterification reaction can exhibit strong blue emission. Based on control experiments and theoretical simulation, we have proposed that the luminescence stems from interchain n→π* interaction between the lone pair (n) of hydroxyl O atoms of carboxyl units and empty π* orbital of ester carbonyl unit...
April 17, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29665173/a-novel-gjb2-compound-heterozygous-mutation-c-257c-g-p-t86r-c-176del16-p-g59a-fs-18-causes-sensorineural-hearing-loss-in-a-chinese-family
#11
Xi Shi, Yan Zhang, Shiwei Qiu, Wei Zhuang, Na Yuan, Tiantian Sun, Jian Gao, Yuehua Qiao, Ke Liu
OBJECTIVE: To investigate whether a novel compound heterozygous mutations c.257C>G (p.T86R)/c.176del16 (p.G59A fs*18) in GJB2 result in hearing loss. METHODS: Allele-specific PCR-based universal array (ASPUA) screening and sequence analysis were applied to identify these mutations. 3D model was built to perform molecular dynamics (MD) simulation to verify the susceptibility of the mutations. Furthermore, WT- and Mut-GJB2 DNA fragments, containing the mutation of c...
April 17, 2018: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/29664978/high-reliability-of-cone-cell-measurements-with-adaptive-optics-scanning-laser-ophthalmoscopy-in-a-simulated-real-life-clinical-setting
#12
Samaneh Davoudi, Damla Duriye Sevgi, Cagla Yasa, Inês Laíns, Nazanin Ebrahimiadib, Ramak Roohipoor, Evangelia Papavasilieou, Jason Comander, Lucia Sobrin
BACKGROUND AND OBJECTIVE: The authors evaluated adaptive optics scanning laser ophthalmoscopy (AO-SLO) in a simulated real-life clinical setting to identify factors that impact its reliability in this setting. PATIENTS AND METHODS: For this prospective study, macular cones were imaged in five healthy eyes using an AO-SLO prototype machine. Multilevel mixed-effect regression was used to compare the cone densities across different analysis parameters. Intergrader, intragrader, interphotographer, and intersession reliabilities were determined with intraclass correlation coefficients (ICCs)...
April 1, 2018: Ophthalmic Surgery, Lasers & Imaging Retina
https://www.readbyqxmd.com/read/29664599/bioinspired-materials-for-controlling-ice-nucleation-growth-and-recrystallization
#13
Zhiyuan He, Kai Liu, Jianjun Wang
Ice formation, mainly consisting of ice nucleation, ice growth, and ice recrystallization, is ubiquitous and crucial in wide-ranging fields from cryobiology to atmospheric physics. Despite active research for more than a century, the mechanism of ice formation is still far from satisfactory. Meanwhile, nature has unique ways of controlling ice formation and can provide resourceful avenues to unravel the mechanism of ice formation. For instance, antifreeze proteins (AFPs) protect living organisms from freezing damage via controlling ice formation, for example, tuning ice nucleation, shaping ice crystals, and inhibiting ice growth and recrystallization...
April 17, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29664344/how-criticality-of-gene-regulatory-networks-affects-the-resulting-morphogenesis-under-genetic-perturbations
#14
Hyobin Kim, Hiroki Sayama
Whereas the relationship between criticality of gene regulatory networks (GRNs) and dynamics of GRNs at a single-cell level has been vigorously studied, the relationship between the criticality of GRNs and system properties at a higher level has not been fully explored. Here we aim at revealing a potential role of criticality of GRNs in morphogenesis, which is hard to uncover through the single-cell-level studies, especially from an evolutionary viewpoint. Our model simulated the growth of a cell population from a single seed cell...
April 17, 2018: Artificial Life
https://www.readbyqxmd.com/read/29663856/computational-insights-into-the-interaction-of-small-molecule-inhibitors-with-hri-kinase-domain
#15
Sourabh Palrecha, Dushant Lakade, Abhijeet Kulkarni, Jayanta K Pal, Manali Joshi
The heme-regulated inhibitor (HRI) kinase regulates globin synthesis in a heme-dependent manner in reticulocytes and erythroid cells in bone marrow. Inhibitors of HRI have been proposed to lead to an increased amount of hemoglobin, benefitting anemia patients. A series of indeno[1,2-c]pyrazoles were discovered to be the first known in vitro inhibitors of HRI. However, the structural mechanism of inhibition is yet to be understood. The aim of this study was to unravel the binding mechanism of these inhibitors using molecular dynamic simulations and docking...
April 17, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29663740/mirna-223-regulates-ischemic-neuronal-injury-by-targeting-the-type-1-insulin-like-growth-factor-receptor-igf1r
#16
She-Jun Feng, Xue-Qiang Zhang, Jun-Tao Li, Xiao-Min Dai, Fei Zhao
Cerebral ischemia injury seriously endangers human health and its molecular mechanism is still not fully understood. microRNA-223 (miR-223) has been reported to be involved in many physiological functions but the specific role of miRNA-223 in ischemic neuronal injury is still unclear. An oxygen-glucose deprivation and simulated reperfusion (OGD/R) model was constructed here to investigate the possible role miR-223 played in ischemic neuronal injury. The expression of miRNA-223 in the OGD/R model and its effect on cell proliferation were studied by qPCR and CCK8 assay...
2018: Folia Neuropathologica
https://www.readbyqxmd.com/read/29663421/population-pharmacokinetic-analysis-of-busulfan-in-japanese-pediatric-and-adult-hct-patients
#17
Atsuko Kawazoe, Tomoo Funaki, Seongryul Kim
Busulfan is the most common chemotherapy agent used in allogeneic hematopoietic cell transplant (HCT) conditioning regimens. As narrow therapeutic index and interpatient variability exists in the effectiveness and toxicity of conditioning regimens, personalizing intravenous busulfan therapy is desirable. Population pharmacokinetic-based approaches have been applied to therapeutic drug monitoring for the purpose of personalizing therapy. A population pharmacokinetic analysis with the objective of personalizing therapy in Japanese patients was conducted by integrating pediatric patient data with adult patient data...
April 17, 2018: Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/29661935/the-labile-iron-pool-attenuates-peroxynitrite-dependent-damage-and-can-no-longer-be-considered-solely-a-pro-oxidative-cellular-iron-source
#18
Fernando Cruvinel Damasceno, André Luis Condeles, Angélica Kodama Bueno Lopes, Rômulo Rodrigues Facci, Edlaine Linares, Daniela Ramos Truzzi, Ohara Augusto, Jose Carlos Toledo
The ubiquitous cellular labile iron pool (LIP) is often associated with the production of the highly reactive hydroxyl radical, which forms through a redox reaction with hydrogen peroxide. Peroxynitrite is a biologically relevant peroxide produced by the recombination of nitric oxide and superoxide. It is a strong oxidant that may be involved in multiple pathological conditions, but whether and how it interacts with the LIP is unclear. Here, using fluorescence spectroscopy, we investigated the interaction between the LIP and peroxynitrite by monitoring peroxynitrite-dependent accumulation of nitrosated and oxidized fluorescent intracellular indicators...
April 16, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29660842/kinetic-models-of-hematopoietic-differentiation
#19
REVIEW
Victor Olariu, Carsten Peterson
As cell and molecular biology is becoming increasingly quantitative, there is an upsurge of interest in mechanistic modeling at different levels of resolution. Such models mostly concern kinetics and include gene and protein interactions as well as cell population dynamics. The final goal of these models is to provide experimental predictions, which is now taking on. However, even without matured predictions, kinetic models serve the purpose of compressing a plurality of experimental results into something that can empower the data interpretation, and importantly, suggesting new experiments by turning "knobs" in silico...
April 16, 2018: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/29660699/a-new-model-for-simulating-microbial-cyanide-production-and-optimizing-the-medium-parameters-for-recovering-precious-metals-from-waste-printed-circuit-boards
#20
Zhihui Yuan, Jujun Ruan, Yaying Li, Rongliang Qiu
Bioleaching is a green recycling technology for recovering precious metals from waste printed circuit boards (WPCBs). However, this technology requires increasing cyanide production to obtain desirable recovery efficiency. Luria-Bertani medium (LB medium, containing tryptone 10 g/L, yeast extract 5 g/L, NaCl 10 g/L) was commonly used in bioleaching of precious metal. In this study, results showed that LB medium did not produce highest yield of cyanide. Under optimal culture conditions (25 °C, pH 7...
April 10, 2018: Journal of Hazardous Materials
keyword
keyword
23904
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"