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Computational cell biology

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https://www.readbyqxmd.com/read/28819560/a-novel-peptide-blocking-cancer-cell-invasion-by-structure-based-drug-design
#1
Yuki Yamada, Seiji Kanayama, Fuminori Ito, Noriyuki Kurita, Hiroshi Kobayashi
The receptor for the urokinase-type plasminogen activator (uPA), uPAR, facilitates tumor cell invasion and metastasis by focusing on several ligands, including uPA, integrins and vitronectin. With computational prediction algorithms and structure-based drug design, we identified peptides containing the Gly-Lys-Gly-Glu-Gly-Glu-Gly-Lys-Gly sequence (peptide H1), which strongly interacts with uPAR. The aim of the present study was to investigate the effect of allosteric inhibition at the uPAR interface using a novel synthetic peptide and its function on ovarian cancer cell invasion...
September 2017: Biomedical Reports
https://www.readbyqxmd.com/read/28818579/developing-integrated-pbpk-pd-coupled-mechanistic-pathway-model-mirna-bdnf-an-approach-towards-system-toxicology
#2
Raju Prasad Sharma, Marta Schuhmacher, Vikas Kumar
Integration of a dynamic signal transduction pathway into the tissue dosimetry model is a major advancement in the area of computational toxicology. This paper illustrates the ways to incorporate the use of existing system biological model in the field of toxicology via its coupling to the Physiological based Pharmacokinetics and Pharmacodynamics (PBPK/PD) model.This expansion framework of integrated PBPK/PD coupled mechanistic system pathway model can be called as system toxicology that describes the kinetics of both -the chemicals and -biomolecules, help us to understand the dynamic and steady-state behaviors of molecular pathways under perturbed condition...
August 14, 2017: Toxicology Letters
https://www.readbyqxmd.com/read/28817585/selecting-targets-for-the-diagnosis-of-schistosoma-mansoni-infection-an-integrative-approach-using-multi-omic-and-immunoinformatics-data
#3
Gardenia B F Carvalho, Daniela M Resende, Liliane M V Siqueira, Marcelo D Lopes, Débora O Lopes, Paulo Marcos Z Coelho, Andréa Teixeira-Carvalho, Jeronimo C Ruiz, Cristina T Fonseca
In order to effectively control and monitor schistosomiasis, new diagnostic methods are essential. Taking advantage of computational approaches provided by immunoinformatics and considering the availability of Schistosoma mansoni predicted proteome information, candidate antigens of schistosomiasis were selected and used in immunodiagnosis tests based on Enzime-linked Immunosorbent Assay (ELISA). The computational selection strategy was based on signal peptide prediction; low similarity to human proteins; B- and T-cell epitope prediction; location and expression in different parasite life stages within definitive host...
2017: PloS One
https://www.readbyqxmd.com/read/28817244/key-developments-that-impacted-the-field-of-mechanobiology-and-mechanotransduction
#4
Michelle Wall, David Butler, Alicia El Haj, Josephine C Bodle, Elizabeth G Loboa, Albert J Banes
Advances in mechanobiology have evolved through insights from multiple disciplines including structural engineering, biomechanics, vascular biology, and orthopaedics. In this paper, we reviewed the impact of key reports related to the study of applied loads on tissues and cells and the resulting signal transduction pathways. We addressed how technology has helped advance the burgeoning field of mechanobiology (over 33,600 publications from 1970-2016). We analyzed the impact of critical ideas and then determined how these concepts influenced the mechanobiology field by looking at the citation frequency of these reports as well as tracking how the overall number of citations within the field changed over time...
August 17, 2017: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
https://www.readbyqxmd.com/read/28816826/tissue-engineered-bone-differentiated-from-human-adipose-derived-stem-cells-inhibit-posterolateral-fusion-in-an-athymic-rat-model
#5
Comron Saifi, Jonahtan Bernhard, Jamal N Shillingford, Petros Petridis, Samuel Robinson, X Edward Guo, Mark Weidenbaum, Ronald A Lehman, Howard S An, Lawrence G Lenke, Gordana Vunjak-Novakovic, Joseph L Laratta
STUDY DESIGN: Biological augmentation spinal arthrodesis trial in athymic rats OBJECTIVE.: To assess the efficacy of tissue-engineered bone to promote L4-L5 intertransverse process fusion in an athymic rat model. SUMMARY OF BACKGROUND DATA: Each year in the United States, over 400,000 spinal fusion surgeries are performed requiring bone graft. The current gold standard for posterolateral lumbar fusion is autogenous iliac crest bone graft (ICBG), but the harvesting of ICBG is associated with increased operative time and significant complications...
August 14, 2017: Spine
https://www.readbyqxmd.com/read/28815872/a-multimethod-computational-simulation-approach-for-investigating-mitochondrial-dynamics-and-dysfunction-in-degenerative-aging
#6
Timothy E Hoffman, Katherine J Barnett, Lyle Wallis, William H Hanneman
Research in biogerontology has largely focused on the complex relationship between mitochondrial dysfunction and biological aging. In particular, the mitochondrial free radical theory of aging (MFRTA) has been well accepted. However, this theory has been challenged by recent studies showing minimal increases in reactive oxygen species (ROS) as not entirely deleterious in nature, and even beneficial under the appropriate cellular circumstances. To assess these significant and nonintuitive observations in the context of a functional system, we have taken an in silico approach to expand the focus of the MFRTA by including other key mitochondrial stress response pathways, as they have been observed in the nematode Caenorhabditis elegans...
August 16, 2017: Aging Cell
https://www.readbyqxmd.com/read/28815536/long-noncoding-rna-genome-organization-and-mechanism-of-action
#7
Vijay Suresh Akhade, Debosree Pal, Chandrasekhar Kanduri
For the last four decades, we have known that noncoding RNAs maintain critical housekeeping functions such as transcription, RNA processing, and translation. However, in the late 1990s and early 2000s, the advent of high-throughput sequencing technologies and computational tools to analyze these large sequencing datasets facilitated the discovery of thousands of small and long noncoding RNAs (lncRNAs) and their functional role in diverse biological functions. For example, lncRNAs have been shown to regulate dosage compensation, genomic imprinting, pluripotency, cell differentiation and development, immune response, etc...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28814944/cell-counting-and-viability-assessment-of-2d-and-3d-cell-cultures-expected-reliability-of-the-trypan-blue-assay
#8
Filippo Piccinini, Anna Tesei, Chiara Arienti, Alessandro Bevilacqua
BACKGROUND: Whatever the target of an experiment in cell biology, cell counting and viability assessment are always computed. The Trypan Blue (TB) assay was proposed about a century ago and is still the most widely used method to perform cell viability analysis. Furthermore, the combined use of TB with a haemocytometer is also considered the standard approach to estimate cell population density. There are numerous research articles reporting the use of TB assays to compute cell number and viability of 2D and 3D cultures...
2017: Biological Procedures Online
https://www.readbyqxmd.com/read/28813442/a-parallel-metaheuristic-for-large-mixed-integer-dynamic-optimization-problems-with-applications-in-computational-biology
#9
David R Penas, David Henriques, Patricia González, Ramón Doallo, Julio Saez-Rodriguez, Julio R Banga
BACKGROUND: We consider a general class of global optimization problems dealing with nonlinear dynamic models. Although this class is relevant to many areas of science and engineering, here we are interested in applying this framework to the reverse engineering problem in computational systems biology, which yields very large mixed-integer dynamic optimization (MIDO) problems. In particular, we consider the framework of logic-based ordinary differential equations (ODEs). METHODS: We present saCeSS2, a parallel method for the solution of this class of problems...
2017: PloS One
https://www.readbyqxmd.com/read/28811337/first-person-dougall-norris
#10
(no author information available yet)
First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping early-career researchers promote themselves alongside their papers. Dougall Norris is co-first author on 'An improved Akt reporter reveals intra- and intercellular heterogeneity and oscillations in signal transduction', published in Journal of Cell Science. Dougall is a PhD student in the Metabolic Systems Biology Group at The University of Sydney Charles Perkins Centre in Australia, where his project focuses on live-cell imaging, multiplexing fluorescent constructs and imaging modalities, coupled with powerful computational analysis...
August 15, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28810752/rupturing-the-hemi-fission-intermediate-in-membrane-fission-under-tension-reaction-coordinates-kinetic-pathways-and-free-energy-barriers
#11
Guojie Zhang, Marcus Müller
Membrane fission is a fundamental process in cells, involved inter alia in endocytosis, intracellular trafficking, and virus infection. Its underlying molecular mechanism, however, is only incompletely understood. Recently, experiments and computer simulation studies have revealed that dynamin-mediated membrane fission is a two-step process that proceeds via a metastable hemi-fission intermediate (or wormlike micelle) formed by dynamin's constriction. Importantly, this hemi-fission intermediate is remarkably metastable, i...
August 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28809010/bioinformatics-resources-for-interpreting-proteomics-mass-spectrometry-data
#12
Iulia M Lazar
Developments in mass spectrometry (MS) instrumentation have supported the advance of a variety of proteomic technologies that have enabled scientists to assess differences between healthy and diseased states. In particular, the ability to identify altered biological processes in a cell has led to the identification of novel drug targets, the development of more effective therapeutic drugs, and the growth of new diagnostic approaches and tools for personalized medicine applications. Nevertheless, large-scale proteomic data generated by modern mass spectrometers are extremely complex and necessitate equally complex bioinformatics tools and computational algorithms for their interpretation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28806767/hydrodynamic-repulsion-of-spheroidal-microparticles-from-micro-rough-surfaces
#13
Aleksey V Belyaev
Isolation of microparticles and biological cells from mixtures and suspensions is a central problem in a variety of biomedical applications. This problem, for instance, is of an immense importance for microfluidic devices manipulating with whole blood samples. It is instructive to know how the mobility and dynamics of rigid microparticles is altered by the presence of micrometer-size roughness on walls. The presented theoretical study addresses this issue via computer simulations. The approach is based on a combination of the Lattice Boltzmann method for calculating hydrodynamics and the Lagrangian Particle dynamics method to describe the dynamics of cell membranes...
2017: PloS One
https://www.readbyqxmd.com/read/28806716/efficient-hardware-implementation-of-the-subthalamic-nucleus-external-globus-pallidus-oscillation-system-and-its-dynamics-investigation
#14
Shuangming Yang, Xile Wei, Jiang Wang, Bin Deng, Chen Liu, Haitao Yu, Huiyan Li
Modeling and implementation of the nonlinear neural system with physiologically plausible dynamic behaviors are considerably meaningful in the field of computational neuroscience. This study introduces a novel hardware platform to investigate the dynamical behaviors within the nonlinear subthalamic nucleus-external globus pallidus system. In order to reduce the implementation complexities, a hardware-oriented conductance-based subthalamic nucleus (STN) model is presented, which can reproduce accurately the dynamical characteristics of biological conductance-based STN cells...
July 26, 2017: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/28805306/bioprocess-scale-up-down-as-integrative-enabling-technology-from-fluid-mechanics-to-systems-biology-and-beyond
#15
Frank Delvigne, Ralf Takors, Rob Mudde, Walter van Gulik, Henk Noorman
Efficient optimization of microbial processes is a critical issue for achieving a number of sustainable development goals, considering the impact of microbial biotechnology in agrofood, environment, biopharmaceutical and chemical industries. Many of these applications require scale-up after proof of concept. However, the behaviour of microbial systems remains unpredictable (at least partially) when shifting from laboratory-scale to industrial conditions. The need for robust microbial systems is thus highly needed in this context, as well as a better understanding of the interactions between fluid mechanics and cell physiology...
August 14, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28800475/biological-immunological-and-functional-properties-of-two-novel-multi-variant-chimeric-recombinant-proteins-of-csp-antigens-for-vaccine-development-against-plasmodium-vivax-infection
#16
Samaneh H Shabani, Sedigheh Zakeri, Ali H Salmanian, Jafar Amani, Akram A Mehrizi, Georges Snounou, François Nosten, Chiara Andolina, Yousef Mourtazavi, Navid D Djadid
The circumsporozoite protein (CSP) of the malaria parasite Plasmodium vivax is a major pre-erythrocyte vaccine candidate. The protein has a central repeat region that belongs to one of repeat families (VK210, VK247, and the P. vivax-like). In the present study, computer modelling was employed to select chimeric proteins, comprising the conserved regions and different arrangements of the repeat elements (VK210 and VK247), whose structure is similar to that of the native counterparts. DNA encoding the selected chimeras (named CS127 and CS712) were synthetically constructed based on E...
August 8, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28800286/clinical-pet-imaging-in-prostate-cancer
#17
Kathryn L Wallitt, Sairah R Khan, Suraiya Dubash, Henry H Tam, Sameer Khan, Tara D Barwick
Prostate cancer is the second most common cancer in men worldwide, with a wide spectrum of biologic behavior ranging from indolent low-risk disease to highly aggressive castration-resistant prostate cancer. Conventional imaging with computed tomography, magnetic resonance imaging, and bone scintigraphy is limited for the detection of nodal disease and distant bone metastases. In addition, advances in the available therapeutic options, both localized and systemic, drive the requirement for precise diagnostic and prognostic tools to refine the individual therapeutic approach at various times in the management of patients with prostate cancer...
August 11, 2017: Radiographics: a Review Publication of the Radiological Society of North America, Inc
https://www.readbyqxmd.com/read/28797226/network-design-and-analysis-for-multi-enzyme-biocatalysis
#18
Lisa Katharina Blaß, Christian Weyler, Elmar Heinzle
BACKGROUND: As more and more biological reaction data become available, the full exploration of the enzymatic potential for the synthesis of valuable products opens up exciting new opportunities but is becoming increasingly complex. The manual design of multi-step biosynthesis routes involving enzymes from different organisms is very challenging. To harness the full enzymatic potential, we developed a computational tool for the directed design of biosynthetic production pathways for multi-step catalysis with in vitro enzyme cascades, cell hydrolysates and permeabilized cells...
August 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28797096/prediction-of-n-linked-glycosylation-sites-using-position-relative-features-and-statistical-moments
#19
Muhammad Aizaz Akmal, Nouman Rasool, Yaser Daanial Khan
Glycosylation is one of the most complex post translation modification in eukaryotic cells. Almost 50% of the human proteome is glycosylated as glycosylation plays a vital role in various biological functions such as antigen's recognition, cell-cell communication, expression of genes and protein folding. It is a significant challenge to identify glycosylation sites in protein sequences as experimental methods are time taking and expensive. A reliable computational method is desirable for the identification of glycosylation sites...
2017: PloS One
https://www.readbyqxmd.com/read/28794860/minion-analysis-and-reference-consortium-phase-2-data-release-and-analysis-of-r9-0-chemistry
#20
Miten Jain, John R Tyson, Matthew Loose, Camilla L C Ip, David A Eccles, Justin O'Grady, Sunir Malla, Richard M Leggett, Ola Wallerman, Hans J Jansen, Vadim Zalunin, Ewan Birney, Bonnie L Brown, Terrance P Snutch, Hugh E Olsen
BACKGROUND: Long-read sequencing is rapidly evolving and reshaping the suite of opportunities for genomic analysis. For the MinION in particular, as both the platform and chemistry develop, the user community requires reference data to set performance expectations and maximally exploit third-generation sequencing. We performed an analysis of MinION data derived from whole genome sequencing of Escherichiacoli K-12 using the R9.0 chemistry, comparing the results with the older R7.3 chemistry...
2017: F1000Research
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