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https://www.readbyqxmd.com/read/28227910/development-of-a-three-dimensional-lattice-free-multiscale-model-of-the-mammary-terminal-end-bud
#1
Joseph D Butner, Vittorio Cristini, Zhihui Wang, Joseph D Butner, Vittorio Cristini, Zhihui Wang, Vittorio Cristini, Joseph D Butner, Zhihui Wang
The terminal end bud (TEB) is a bulbous structure composed of highly proliferative cells that is responsible for mammary gland development during the pubertal stage. This is a highly organized process, involving cellular differentiation hierarchies regulated by endocrine and paracrine signaling. Here, we present development of a lattice-free, three dimensional multiscale agent based model of the TEB to study the effects of cellular phenotypic hierarchies, endocrine and paracrine signaling, and proliferation demographics on pubertal mammary gland development...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226725/a-chicken-embryo-cardiac-outflow-tract-atlas-for-registering-changes-due-to-abnormal-blood-flow
#2
James P Carson, Monique Y Rennie, Michael Danilchik, Kent Thornburg, Sandra Rugonyi, James P Carson, Monique Y Rennie, Michael Danilchik, Kent Thornburg, Sandra Rugonyi, Kent Thornburg, Michael Danilchik, James P Carson, Monique Y Rennie, Sandra Rugonyi
Subdivision-based image registration has previously been applied to co-localize digital information extracted from rigid structures in biological specimens, such as the brain. Here, we describe and demonstrate the creation and application of a two-dimensional subdivision-based atlas representing a dynamic structure: the outflow tract of the developing chicken heart. The atlas is designed to segment three different anatomical layers of the outflow tract, and is demonstrated on the characterization of collagen XIV in both control and induced abnormal flow specimens...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226271/thermal-buckling-behavior-of-defective-cnts-under-pre-load-a-molecular-dynamics-study
#3
Fahimeh Mehralian, Yaghoub Tadi Beni, Yaser Kiani
Current study is concentrated on the extraordinary properties of defective carbon nanotubes (CNTs). The role of vacancy defects in thermal buckling response of precompressed CNTs is explored via molecular dynamics (MD) simulations. Defective CNTs are initially compressed at a certain ratio of their critical buckling strain and then undergo a uniform temperature rise. Comprehensive study is implemented on both armchair and zigzag CNTs with different vacancy defects including monovacancy, symmetric bivacancy and asymmetric bivacancy...
January 25, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28226233/chemical-genetic-dissection-of-membrane-trafficking
#4
Lorena Norambuena, Ricardo Tejos
The plant endomembrane system is an extensively connected functional unit for exchanging material between compartments. Secretory and endocytic pathways allow dynamic trafficking of proteins, lipids, and other molecules, regulating a myriad of biological processes. Chemical genetics-the use of compounds to perturb biological processes in a fast, tunable, and transient manner-provides elegant tools for investigating this system. Here, we review how chemical genetics has helped to elucidate different aspects of membrane trafficking...
February 13, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28226232/the-epigenome-and-transcriptional-dynamics-of-fruit-ripening
#5
James Giovannoni, Cuong Nguyen, Betsy Ampofo, Silin Zhong, Zhangjun Fei
Fruit has evolved myriad forms that facilitate seed dispersal in varied environmental and ecological contexts. Because fleshy fruits become attractive and nutritious to seed-dispersing animals, the transition from unripe to ripe fruit represents a dramatic shift in survival strategy-from protecting unripe fruit against damaging animals to making it appealing to those same animals once ripened. For optimal fitness, ripening therefore must be tightly controlled and coordinated with seed development. Fruits, like many vegetative tissues of plants that contribute to human diets, are also subject to decay, which is enhanced as a consequence of the ripening transition...
February 22, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28226222/computer-simulations-of-intrinsically-disordered-proteins
#6
Song-Ho Chong, Prathit Chatterjee, Sihyun Ham
The investigation of intrinsically disordered proteins (IDPs) is a new frontier in structural and molecular biology that requires a new paradigm to connect structural disorder to function. Molecular dynamics simulations and statistical thermodynamics potentially offer ideal tools for atomic-level characterizations and thermodynamic descriptions of this fascinating class of proteins that will complement experimental studies. However, IDPs display sensitivity to inaccuracies in the underlying molecular mechanics force fields...
February 6, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28226220/water-oxidation-mechanisms-of-metal-oxide-catalysts-by-vibrational-spectroscopy-of-transient-intermediates
#7
Miao Zhang, Heinz Frei
Water oxidation is an essential reaction of an artificial photosystem for solar fuel generation because it provides electrons needed to reduce carbon dioxide or protons to a fuel. Earth-abundant metal oxides are among the most attractive catalytic materials for this reaction because of their robustness and scalability, but their efficiency poses a challenge. Knowledge of catalytic surface intermediates gained by vibrational spectroscopy under reaction conditions plays a key role in uncovering kinetic bottlenecks and provides a basis for catalyst design improvements...
February 22, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/28225613/dehydrogenation-free-energy-of-co-2-aq-from-density-functional-theory-based-molecular-dynamics
#8
Florian H Hodel, Sandra Luber
Electron and proton transfers are important steps occurring in nature and in artificial (catalytic) reaction mechanisms. The often employed approach of calculating the energy differences of those steps using methods involving geometry optimizations neglects the influence of dynamic effects such as solvent rearrangement. To further investigate this issue and inspired by recent research in water oxidation, we calculate in the present study the dehydrogenation free energy of aqueous Co(2+), which is the free energy change associated with the first step of the reaction mechanism of model Co(II)-based water oxidation catalysts...
February 22, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28225608/time-dependent-markov-state-models-for-single-molecule-force-spectroscopy
#9
Susmita Ghosh, Abhijit Chatterjee, Swati Bhattacharya
This Letter demonstrates that using time-dependent Markov state models (TD-MSMs) one can obtain molecular-scale insights into force-extension curves for a variety of stretching experiments. A master-MSM constructed at a reference extension using a handful of molecular dynamics calculations forms the basis for generating the required TD-MSM. Changes in the network topology upon stretching is related through a thermodynamic quantity termed the mechanical disposition. Proof-of-principle is provided using a stretched alanine decapeptide under a time-varying pulling force...
February 22, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28225593/programmed-self-assembly-of-hierarchical-nanostructures-through-protein-nanoparticle-co-engineering
#10
Rubul Mout, Gulen Yesilbag Tonga, Li-Sheng Wang, Moumita Ray, Trinava Roy, Vincent M Rotello
Hierarchical organization of macromolecules through self-assembly is a prominent feature in biological systems. Synthetic fabrication of such structures provides materials with emergent functions. Here we report the fabrication of self-assembled superstructures through co-engineering of recombinant proteins and nanoparticles. These structures feature a highly-sophisticated level of multi-layered hierarchical organization of the components: individual proteins and nanoparticles co-assemble to form discrete assemblies that collapse to form granules, which then further self-organize to generate superstructures of hundreds of nanometer size...
February 22, 2017: ACS Nano
https://www.readbyqxmd.com/read/28225578/detection-of-volume-alterations-in-hippocampal-subfields-of-rats-under-chronic-unpredictable-mild-stress-using-7t-mri-a-follow-up-study
#11
Yuefeng Li, Xiaolan Zhu, Shenghong Ju, Jinchuan Yan, Dongqing Wang, Yan Zhu, Fengchao Zang
PURPOSE: To determine hippocampal subfields volume loss in depression, which was simulated by a rat chronic unpredictable mild stress (CUMS) model. As different cellular and molecular characteristics in hippocampal subfields, these subfields are regarded as differentially vulnerable to processes associated with stress. MATERIALS AND METHODS: Twenty male Wistar rats were exposed to various stressors until the model was successfully established. The effects of physical exercise on recovery of hippocampal volume in depressed rats were simulated using the wheel running test (WRT)...
February 22, 2017: Journal of Magnetic Resonance Imaging: JMRI
https://www.readbyqxmd.com/read/28225561/flotillins-control-zebrafish-epiboly-through-their-role-in-cadherin-mediated-cell-cell-adhesion
#12
Eduardo A Rios Morris, Stéphane Bodin, Bénédicte Delaval, Franck Comunale, Virginie Georget, Manoel L Costa, Georges Lutfalla, Cécile Gauthier-Rouvière
Zebrafish gastrulation and particularly epiboly that involves coordinated movements of several cell layers is a dynamic process for which regulators remain to be identified. We show here that Flotillin 1 and 2, ubiquitous and highly conserved proteins, are required for epiboly. Flotillins knockdown compromised embryo survival, strongly delayed epiboly and impaired deep cell radial intercalation and directed collective migration without affecting enveloping layer cell movement. At the molecular level, we identified that Flotillins are required for the formation of E-cadherin-mediated cell-cell junctions...
February 22, 2017: Biology of the Cell
https://www.readbyqxmd.com/read/28225285/multi-scale-modeling-of-the-effects-of-salt-and-perfume-raw-materials-on-the-rheological-properties-of-commercial-thread-like-micellar-solutions
#13
Xueming Tang, Weizhong Zou, Peter H Koenig, Shawn D McConaughy, Michael R Weaver, David Michael Eike, Michael J Schmidt, Ronald G Larson
We link micellar structures to rheological properties for two surfactant body-wash formulations at various concentrations of salts and perfume raw materials (PRMs) using molecular simulations and micellar-scale modeling as well as traditional surfactant packing arguments. The two body washes, named BW-1EO and BW-3EO, are composed of sodium lauryl ethylene glycol ether sulfate (SLEnS, where n is the average number of ethylene glycol repeat units), cocamidopropyl betaine (CAPB), ACCORD (which is a mixture of six PRMs), and NaCl salt...
February 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28225107/chirality-in-curved-polyaromatic-systems
#14
Michel Rickhaus, Marcel Mayor, Michal Juríček
Carbon allotropes constituted of sp(2)-hybridised carbon atoms display a variety of properties that arise from their delocalised π-conjugated electronic structure. Apart from carbon's planar allotropic form graphene, bent or curved structures, such as carbon nanotubes or fullerenes, respectively, have been discovered. In this Tutorial Review, we analyse and conceptually categorise chiral synthetic molecular fragments of non-planar sp(2)-carbon allotropes, including hypothetical forms of carbon that have been proposed to exist as stable entities...
February 22, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/28225102/stability-of-reverse-micelles-in-rare-earth-separation-a-chemical-model-based-on-a-molecular-approach
#15
Yushu Chen, Magali Duvail, Philippe Guilbaud, Jean-François Dufrêche
Molecular complexes formed in the organic phase during solvent extraction may self-assemble as reverse micelles, and therefore induce a supramolecular organization of this phase. In most of the cases, water molecules play an essential role in the organization of this non polar medium. The aim of this work is to investigate the speciation of the aggregates formed in the organic phase during solvent extraction, and especially to assess their stability as a function of the number of water molecules included in their polar core...
February 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28225092/controlled-propulsion-and-separation-of-helical-particles-at-the-nanoscale
#16
Maria Michiko T Alcanzare, Vaibhav Thakore, Santtu T T Ollila, Mikko Karttunen, Tapio Ala-Nissila
Controlling the motion of nano and microscale objects in a fluid environment is a key factor in designing optimized tiny machines that perform mechanical tasks such as transport of drugs or genetic material in cells, fluid mixing to accelerate chemical reactions, and cargo transport in microfluidic chips. Directed motion is made possible by the coupled translational and rotational motion of asymmetric particles. A current challenge in achieving directed and controlled motion at the nanoscale lies in overcoming random Brownian motion due to thermal fluctuations in the fluid...
February 22, 2017: Soft Matter
https://www.readbyqxmd.com/read/28225090/proton-transfer-dynamics-dictate-quinone-speciation-at-lipid-modified-electrodes
#17
Edmund C M Tse, Christopher J Barile, Ying Li, Steven C Zimmerman, Ali Hosseini, Andrew A Gewirth
Proton-coupled electron transfer (PCET) reactions are ubiquitous in biochemistry and alternative energy schemes. Natural enzymes utilize quinones in proton transfer chains and energy conversion processes. Here, we utilize a bio-inspired hybrid bilayer membrane system to control the reaction mechanism of a quinone molecule covalently bound to an electrode surface. In particular, by impeding proton access to the quinone moiety, we change the reaction pathway from a PCET process to a pure electron transfer step...
February 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28225056/comparative-rna-seq-analysis-of-transcriptome-dynamics-during-petal-development-in-rosa-chinensis
#18
Yu Han, Huihua Wan, Tangren Cheng, Jia Wang, Weiru Yang, Huitang Pan, Qixiang Zhang
The developmental process that produces the ornate petals of the China rose (Rosa chinensis) is complex and is thought to depend on the balanced expression of a functionally diverse array of genes; however, the molecular basis of rose petal development is largely unknown. Here, petal growth of the R. chinensis cultivar 'Old Blush' was divided into four developmental stages, and RNA-seq technology was used to analyse the dynamic changes in transcription that occur as development progresses. In total, 598 million clean reads and 61,456 successfully annotated unigenes were obtained...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28224788/coarse-grained-molecular-modeling-of-solution-structure-ensemble-of-dengue-virus-non-structural-protein-5-with-small-angle-x-ray-scattering-intensity
#19
Guanhua Zhu, Wuan Geok Saw, Anjaiah Nalaparaju, Gerhard Grüber, Lanyuan Lu
An ensemble modeling scheme incorporating coarse-grained simulations with experimental small-angle X-ray scattering (SAXS) data is applied to the dengue virus 2 (DENV2) non-structural protein 5 (NS5). NS5 serves a key role in viral replication through its two domains that are connected by a ten-residue polypeptide segment. A set of representative structures are generated from a simulated structure pool using SAXS data fitting by the non-negativity least squares (NNLS) or the standard Ensemble Optimization Method (EOM) based on a genetic algorithm (GA)...
February 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28224677/dynamic-nanoparticle-assemblies-for-biomedical-applications
#20
REVIEW
Fangyuan Li, Jingxiong Lu, Xueqian Kong, Taeghwan Hyeon, Daishun Ling
Designed synthesis and assembly of nanoparticles assisted by their surface ligands can create "smart" materials with programmed responses to external stimuli for biomedical applications. These assemblies can be designed to respond either exogenously (for example, to magnetic field, temperature, ultrasound, light, or electric pulses) or endogenously (to pH, enzymatic activity, or redox gradients) and play an increasingly important role in a diverse range of biomedical applications, such as biosensors, drug delivery, molecular imaging, and novel theranostic systems...
February 22, 2017: Advanced Materials
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