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https://www.readbyqxmd.com/read/28231453/siderophore-transport-by-mmpl5-mmps5-protein-complex-in-mycobacterium-tuberculosis
#1
Padmani Sandhu, Yusuf Akhter
Iron is an essential metal ion required for the various physiological activities of bacteria. The pathogenic bacteria remain dependent on the host cell for their iron requirements and evolved with specialized scavenging machinery in the form of iron chelating siderophores. Mycobacterium tuberculosis has two types of siderophore molecules, mycobactin and carboxymycobactin. These are synthesized inside bacterial cells and need to be transported outside by specialized membrane associated proteins. MmpL5-MmpS5 (mycobacterial membrane protein large5-mycobacterial membrane protein small5) complex has been linked to the export of non-ferrated siderophores to extracellular environment but the precise molecular mechanism involved was largely unknown...
February 14, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28231333/molecular-mechanisms-of-cooperative-binding-of-transcription-factors-runx1-cbf%C3%AE-ets1-on-the-tcr%C3%AE-gene-enhancer
#2
Kota Kasahara, Masaaki Shiina, Ikuo Fukuda, Kazuhiro Ogata, Haruki Nakamura
Ets1 is an essential transcription factor (TF) for several important physiological processes, including cell proliferation and differentiation. Its recognition of the enhancer region of the TCRα gene is enhanced by the cooperative binding of the Runx1-CBFβ heterodimer, with the cancelation of phosphorylation-dependent autoinhibition. The detailed mechanism of this interesting cooperativity between Ets1 and the Runx1-CBFβ heterodimer is still largely unclear. Here, we investigated the molecular mechanisms of this cooperativity, by using molecular dynamics simulations...
2017: PloS One
https://www.readbyqxmd.com/read/28230186/glycan-independent-binding-and-internalization-of-human-igm-to-fcmr-its-cognate-cellular-receptor
#3
Katy A Lloyd, Jiabin Wang, Britta C Urban, Daniel M Czajkowsky, Richard J Pleass
IgM is the first antibody to be produced in immune responses and plays an important role in the neutralization of bacteria and viruses. Human IgM is heavily glycosylated, featuring five N-linked glycan sites on the μ chain and one on the J-chain. Glycosylation of IgG is known to modulate the effector functions of Fcγ receptors. In contrast, little is known about the effect of glycosylation on IgM binding to the human Fcμ receptor (hFCMR). In this study, we identify the Cμ4 domain of IgM as the target of hFCMR, and show that binding and internalization of IgM by hFCMR is glycan-independent...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28230057/ensemble-and-single-molecule-dynamics-of-ift-dynein-in-caenorhabditis-elegans-cilia
#4
Jona Mijalkovic, Bram Prevo, Felix Oswald, Pierre Mangeol, Erwin J G Peterman
Cytoplasmic dyneins drive microtubule-based, minus-end directed transport in eukaryotic cells. Whereas cytoplasmic dynein 1 has been widely studied, IFT dynein has received far less attention. Here, we use fluorescence microscopy of labelled motors in living Caenorhabditis elegans to investigate IFT-dynein motility at the ensemble and single-molecule level. We find that while the kinesin composition of motor ensembles varies along the track, the amount of dynein remains relatively constant. Remarkably, this does not result in directionality changes of cargo along the track, as has been reported for other opposite-polarity, tug-of-war motility systems...
February 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28229954/nano-cone-resistive-memory-for-ultralow-power-operation
#5
Sungjun Kim, Sunghun Jung, Min-Hwi Kim, Tae-Hyeon Kim, Suhyung Bang, Seongjae Cho, Byung-Gook Park
SiN x -based nano-structure resistive memory is fabricated by fully silicon CMOS compatible process integration including particularly designed anisotropic etching for the construction of a nano-cone silicon bottom electrode (BE). Bipolar resistive switching characteristics have significantly reduced switching current and voltage and are demonstrated in a nano-cone BE structure, as compared with those in a flat BE one. We have verified by systematic device simulations that the main cause of reduction in the performance parameters is the high electric field being more effectively concentrated at the tip of the cone-shaped BE...
February 23, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28228690/human-cytomegalovirus-interleukin-10-enhances-matrigel-invasion-of-mda-mb-231-breast-cancer-cells
#6
Cendy A Valle Oseguera, Juliet V Spencer
BACKGROUND: While some risk factors for breast cancer are well-known, the influence of other factors, particularly virus infection, remains unclear. Human cytomegalovirus (HCMV) is widespread in the general population, and both molecular and epidemiological evidence has indicated links between HCMV and breast cancer. The HCMV protein cmvIL-10 is a potent suppressor of immune function that has also been shown to promote proliferation and migration of breast cancer cells. In this study, the impact of cmvIL-10 on tumor cell invasion through a simulated basement membrane was investigated...
2017: Cancer Cell International
https://www.readbyqxmd.com/read/28228537/morphoelasticity-in-the-development-of-brown-alga-ectocarpus-siliculosus-from-cell-rounding-to-branching
#7
Fei Jia, Martine Ben Amar, Bernard Billoud, Bénédicte Charrier
A biomechanical model is proposed for the growth of the brown alga Ectocarpus siliculosus Featuring ramified uniseriate filaments, this alga has two modes of growth: apical growth and intercalary growth with branching. Apical growth occurs upon the mitosis of a young cell at one extremity and leads to a new tip cell followed by a cylindrical cell, whereas branching mainly occurs when a cylindrical cell becomes rounded and swells, forming a spherical cell. Given the continuous interplay between cell growth and swelling, a poroelastic model combining osmotic pressure and volumetric growth is considered for the whole cell, cytoplasm and cell wall...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28228240/modeling-spreading-of-oil-slicks-based-on-random-walk-methods-and-voronoi-diagrams
#8
İsmail Durgut, Mark Reed
We introduce a methodology for representation of a surface oil slick using a Voronoi diagram updated at each time step. The Voronoi cells scale the Gaussian random walk procedure representing the spreading process by individual particle stepping. The step length of stochastically moving particles is based on a theoretical model of the spreading process, establishing a relationship between the step length of diffusive spreading and the thickness of the slick at the particle locations. The Voronoi tessellation provides the areal extent of the slick particles and in turn the thicknesses of the slick and the diffusive-type spreading length for all particles...
February 19, 2017: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/28228017/adsorption-mechanism-of-an-antimicrobial-peptide-on-carbonaceous-surfaces-a-molecular-dynamics-study
#9
Danilo Roccatano, Edita Sarukhanyan, Ronen Zangi
Peptides are versatile molecules with applications spanning from biotechnology to nanomedicine. They exhibit a good capability to unbundle carbon nanotubes (CNT) by improving their solubility in water. Furthermore, they are a powerful drug delivery system since they can easily be uptaken by living cells, and their high surface-to-volume ratio facilitates the adsorption of molecules of different natures. Therefore, understanding the interaction mechanism between peptides and CNT is important for designing novel therapeutical agents...
February 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28227911/an-implementation-for-the-simulation-of-cells-on-micro-post-arrays
#10
Duy T Truong, Christian Bahls, Barbara Nebe, Ursula van Rienen, Duy T Truong, Christian Bahls, Barbara Nebe, Ursula van Rienen, Duy T Truong, Christian Bahls, Ursula van Rienen, Barbara Nebe
The mechanical interaction between cells and their underlying substrates is important in understanding the processes that take place at an interface between biological tissue and the surface of implants. There have been numerous studies that examine these interactions both by experimental and numerical modeling. The bio-chemo-mechanical model for cell contractility by Deshpande et al. [1] has numerous applications and advantages. This work shows a way to implement this model in COMSOL MULTIPHYSICS® so it can be easily modified or extended...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227869/simea-a-framework-for-simulating-neurons-on-multi-electrode-array
#11
Vafa Andalibi, Timo Aaltonen, Francois Christophe, Tommi Mikkonen, Vafa Andalibi, Timo Aaltonen, Francois Christophe, Tommi Mikkonen, Timo Aaltonen, Vafa Andalibi, Tommi Mikkonen, Francois Christophe
A Multi-Electrode Array (MEA) is a practical device for recording the extracellular activity of in-vitro biological culture. Such culture - for instance neurons - is prone to mistakes leading to irrelevant recordings or no recording at all. Additionally, with the expenses generated by in-vitro culture, minimizing risks is a must. This paper proposes a framework designed and implemented for simulating the spatial positioning of neuronal cultures on a MEA. The framework serves as a sandbox for researchers to simulate the model of their MEA experiments before its eventual in-vitro implementation...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227865/a-dce-mri-imaging-based-model-for-simulation-of-vascular-tumour-growth
#12
Thais Roque, Veerle Kersemans, Sean Smart, Danny Allen, Julia A Schnabel, Michael Chappell, Thais Roque, Veerle Kersemans, Sean Smart, Danny Allen, Julia A Schnabel, Michael Chappell, Sean Smart, Michael Chappell, Veerle Kersemans, Danny Allen, Julia A Schnabel, Thais Roque
Imaging-based modelling of tumour growth can serve as a powerful tool to understand and predict tumour evolution and its response to therapy. The purpose of this study was to introduce, calibrate and evaluate a multi-scale model of vascular tumour growth. The model allows for proliferation, death and spatial spread of tumour cells as well as for new vessel creation. Both the calibration and the evaluation of the tumour growth model were performed using pre-clinical longitudinal time series of dynamic contrast-enhanced magnetic resonance imaging of colon carcinoma...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227795/simplified-realistic-human-head-model-for-simulating-tumor-treating-fields-ttfields
#13
Cornelia Wenger, Ze'ev Bomzon, Ricardo Salvador, Peter J Basser, Pedro C Miranda, Cornelia Wenger, Ze'ev Bomzon, Ricardo Salvador, Peter J Basser, Pedro C Miranda, Peter J Basser, Pedro C Miranda, Cornelia Wenger, Ricardo Salvador, Ze'ev Bomzon
Tumor Treating Fields (TTFields) are alternating electric fields in the intermediate frequency range (100-300 kHz) of low-intensity (1-3 V/cm). TTFields are an anti-mitotic treatment against solid tumors, which are approved for Glioblastoma Multiforme (GBM) patients. These electric fields are induced non-invasively by transducer arrays placed directly on the patient's scalp. Cell culture experiments showed that treatment efficacy is dependent on the induced field intensity. In clinical practice, a software called NovoTal(TM) uses head measurements to estimate the optimal array placement to maximize the electric field delivery to the tumor...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227773/whole-heart-modeling-spatiotemporal-dynamics-of-electrical-wave-conduction-and-propagation
#14
Hui Yang, Yun Chen, Fabio M Leonelli, Hui Yang, Yun Chen, Fabio M Leonelli, Hui Yang, Fabio M Leonelli, Yun Chen
Cardiac electrical activities are varying in both space and time. Human heart consists of a fractal network of muscle cells, Purkinje fibers, arteries and veins. Whole-heart modeling of electrical wave conduction and propagation involves a greater level of complexity. Our previous work developed a computer model of the anatomically realistic heart and simulated the electrical conduction with the use of cellular automata. However, simplistic assumptions and rules limit its ability to provide an accurate approximation of real-world dynamics on the complex heart surface, due to sensitive dependence of nonlinear dynamical systems on initial conditions...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227742/a-computational-model-of-orientation-dependent-activation-of-retinal-ganglion-cells
#15
Timothy Esler, Anthony N Burkitt, David B Grayden, Robert R Kerr, Bahman Tahayori, Hamish Meffin, Timothy Esler, Anthony N Burkitt, David B Grayden, Robert R Kerr, Bahman Tahayori, Hamish Meffin, Anthony N Burkitt, Timothy Esler, Hamish Meffin, David B Grayden, Robert R Kerr, Bahman Tahayori
Currently, a challenge in electrical stimulation for epiretinal prostheses is the avoidance of stimulation of axons of passage in the nerve fiber layer that originate from distant regions of the ganglion cell layer. A computational model of extracellular stimulation that captures the effect of neurite orientation in anisotropic tissue is developed using a modified version of the standard volume conductor model, known as the cellular composite model, embedded in a four layer model of the retina. Simulations are conducted to investigate the interaction of neural tissue orientation, electrode placement, and stimulation pulse duration and amplitude...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227675/investigating-an-alternative-ring-design-of-transducer-arrays-for-tumor-treating-fields-ttfields
#16
Mario Macedo, Cornelia Wenger, Ricardo Salvador, Sofia R Fernandes, Pedro C Miranda, Mario Macedo, Cornelia Wenger, Ricardo Salvador, Sofia R Fernandes, Pedro C Miranda, Sofia R Fernandes, Pedro C Miranda, Cornelia Wenger, Ricardo Salvador, Mario Macedo
Tumor treating fields (TTFields) is a therapy that inhibits cell proliferation and has been approved by the U.S Food and Drug Administration (FDA) for the treatment of Glioblastoma Multiforme. This anti-mitotic technique works non-invasively and regionally, and is associated with less toxicity and a better quality of life. Currently a device called Optune™ is clinically used which works with two perpendicular and alternating array pairs each consisting of 3×3 transducers. The aim of this study is to investigate a theoretical alternative array design which consists of two rings of 16 transducers and thus permits various field directions...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227166/modeling-distinct-sources-of-neural-variability-driving-neuroprosthetic-control
#17
Preeya Khanna, Vivek R Athalye, Suraj Gowda, Rui M Costa, Jose M Carmena, Preeya Khanna, Vivek R Athalye, Suraj Gowda, Rui M Costa, Jose M Carmena, Jose M Carmena, Vivek R Athalye, Rui M Costa, Preeya Khanna, Suraj Gowda
Many closed-loop, continuous-control brain-machine interface (BMI) architectures rely on decoding via a linear readout of noisy population neural activity. However, recent work has found that decomposing neural population activity into correlated and uncorrelated variability reveals that improvements in cursor control coincide with the emergence of correlated neural variability. In order to address how correlated and uncorrelated neural variability arises and contributes to BMI cursor control, we simulate a neural population receiving combinations of shared inputs affecting all cells and private inputs affecting only individual cells...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227099/a-large-scale-detailed-neuronal-model-of-electrical-stimulation-of-the-dentate-gyrus-and-perforant-path-as-a-platform-for-electrode-design-and-optimization
#18
Clayton S Bingham, Kyle Loizos, Gene Yu, Andrew Gilbert, Jean-Marie Bouteiller, Dong Song, Gianluca Lazzi, Theodore W Berger, Clayton S Bingham, Kyle Loizos, Gene Yu, Andrew Gilbert, Jean-Marie Bouteiller, Dong Song, Gianluca Lazzi, Theodore W Berger, Kyle Loizos, Gene Yu, Theodore W Berger, Gianluca Lazzi, Jean-Marie Bouteiller, Clayton S Bingham, Dong Song, Andrew Gilbert
Owing to the dramatic rise in treatment of neurological disorders with electrical micro-stimulation it has become apparent that the major technological limitation in deploying effective devices lies in the process of designing efficient, safe, and outcome specific electrode arrays. The time-consuming and low-fidelity nature of gathering test data using experimental means and the immense control and flexibility of computational models, has prompted us and others to build models of electrical stimulation of neural networks that can be simulated in a computer...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226993/first-steps-to-creating-a-platform-for-high-throughput-simulation-of-ttfields
#19
Hadas Sara Hershkovich, Zeev Bomzon, Cornelia Wenger, Noa Urman, Aafia Chaudhry, Dario Garcia-Carracedo, Eilon D Kirson, Uri Weinberg, Yoram Wassermann, Yoram Palti, Hadas Sara Hershkovich, Zeev Bomzon, Cornelia Wenger, Noa Urman, Aafia Chaudhry, Dario Garcia-Carracedo, Eilon D Kirson, Uri Weinberg, Yoram Wassermann, Yoram Palti, Yoram Wassermann, Cornelia Wenger, Uri Weinberg, Hadas Sara Hershkovich, Zeev Bomzon, Eilon D Kirson, Dario Garcia-Carracedo, Yoram Palti, Noa Urman, Aafia Chaudhry
Tumor Treating Fields (TTFields) are low intensity alternating electric fields in the 100-500 KHz frequency range that are known to have an anti-mitotic effect on cancerous cells. In the USA, TTFields are approved by the Food and Drug Administration (FDA) for the treatment of glioblastoma (GBM) in both the newly diagnosed and recurrent settings. Optimizing treatment with TTFields requires a deep understanding of how TTFields distribute within the brain. To address this issue, simulations using realistic head models have been performed...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226889/dual-mode-cmos-analog-front-end-afe-for-electrical-impedance-spectroscopy-eis-systems
#20
Virgilio Valente, Dai Jiang, Andreas Demosthenous, Virgilio Valente, Dai Jiang, Andreas Demosthenous, Dai Jiang, Andreas Demosthenous, Virgilio Valente
This paper presents the operation of a dual-mode wideband CMOS analog front-end (AFE) for electrical impedance spectroscopy. The chip combines two current-readout (CR) channels and four voltage-readout (VR) channels suitable for both bipolar and tetrapolar EIS analysis. The chip addresses the need for flexible readout units for real-time simultaneous single-cell and large scale tissue/organ analysis. Postlayout simulations show that the VR channel is capable of wideband operation up to 12 MHz with noise floor as low as 16...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
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