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Computational cell biology

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https://www.readbyqxmd.com/read/28212192/genetic-control-of-erythropoiesis
#1
Laxminath Tumburu, Swee Lay Thein
PURPOSE OF REVIEW: The discovery of several genetic variants associated with erythroid traits and subsequent elucidation of their functional mechanisms are exemplars of the power of the new genetic and genomic technology. The present review highlights findings from recent genetic studies related to the control of erythropoiesis and dyserythropoiesis, and fetal hemoglobin, an erythroid-related trait. RECENT FINDINGS: Identification of the genetic modulators of erythropoiesis involved two approaches: genome-wide association studies (GWASs) using single nucleotide polymorphism (SNP) arrays that revealed the common genetic variants associated with erythroid phenotypes (hemoglobin, red cell count, MCV, MCH) and fetal hemoglobin; and massive parallel sequencing such as whole genome sequencing (WGS) and whole exome sequencing (WES) that led to the discovery of the rarer variants (GFI1B, SBDS, RPS19, PKLR, EPO, EPOR, KLF1, GATA1)...
February 15, 2017: Current Opinion in Hematology
https://www.readbyqxmd.com/read/28211907/identification-of-extracellular-segments-by-mass-spectrometry-improves-topology-prediction-of-transmembrane-proteins
#2
Tamás Langó, Gergely Róna, Éva Hunyadi-Gulyás, Lilla Turiák, Julia Varga, László Dobson, György Várady, László Drahos, Beáta G Vértessy, Katalin F Medzihradszky, Gergely Szakács, Gábor E Tusnády
Transmembrane proteins play crucial role in signaling, ion transport, nutrient uptake, as well as in maintaining the dynamic equilibrium between the internal and external environment of cells. Despite their important biological functions and abundance, less than 2% of all determined structures are transmembrane proteins. Given the persisting technical difficulties associated with high resolution structure determination of transmembrane proteins, additional methods, including computational and experimental techniques remain vital in promoting our understanding of their topologies, 3D structures, functions and interactions...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28210916/a-multiscale-mathematical-model-of-tumour-invasive-growth
#3
Lu Peng, Dumitru Trucu, Ping Lin, Alastair Thompson, Mark A J Chaplain
Known as one of the hallmarks of cancer (Hanahan and Weinberg in Cell 100:57-70, 2000) cancer cell invasion of human body tissue is a complicated spatio-temporal multiscale process which enables a localised solid tumour to transform into a systemic, metastatic and fatal disease. This process explores and takes advantage of the reciprocal relation that solid tumours establish with the extracellular matrix (ECM) components and other multiple distinct cell types from the surrounding microenvironment. Through the secretion of various proteolytic enzymes such as matrix metalloproteinases or the urokinase plasminogen activator (uPA), the cancer cell population alters the configuration of the surrounding ECM composition and overcomes the physical barriers to ultimately achieve local cancer spread into the surrounding tissue...
February 16, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28205527/an-end-to-end-software-solution-for-the-analysis-of-high-throughput-single-cell-migration-data
#4
Paola Masuzzo, Lynn Huyck, Aleksandra Simiczyjew, Christophe Ampe, Lennart Martens, Marleen Van Troys
The systematic study of single-cell migration requires the availability of software for assisting data inspection, quality control and analysis. This is especially important for high-throughput experiments, where multiple biological conditions are tested in parallel. Although the field of cell migration can count on different computational tools for cell segmentation and tracking, downstream data visualization, parameter extraction and statistical analysis are still left to the user and are currently not possible within a single tool...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28203679/biomaterials-and-computation-a-strategic-alliance-to-investigate-emergent-responses-of-neural-cells
#5
Pier Nicola Sergi, Elisabetta Ada Cavalcanti-Adam
Topographical and chemical cues drive migration, outgrowth and regeneration of neurons in different and crucial biological conditions. In the natural extracellular matrix, their influences are so closely coupled that they result in complex cellular responses. As a consequence, engineered biomaterials are widely used to simplify in vitro conditions, disentangling intricate in vivo behaviours, and narrowing the investigation on particular emergent responses. Nevertheless, how topographical and chemical cues affect the emergent response of neural cells is still unclear, thus in silico models are used as additional tools to reproduce and investigate the interactions between cells and engineered biomaterials...
February 16, 2017: Biomaterials Science
https://www.readbyqxmd.com/read/28201981/identification-of-effector-like-proteins-in-trichoderma-spp-and-role-of-a-hydrophobin-in-the-plant-fungus-interaction-and-mycoparasitism
#6
Paulina Guzmán-Guzmán, Mario Iván Alemán-Duarte, Luis Delaye, Alfredo Herrera-Estrella, Vianey Olmedo-Monfil
BACKGROUND: Trichoderma spp. can establish beneficial interactions with plants by promoting plant growth and defense systems, as well as, antagonizing fungal phytopathogens in mycoparasitic interactions. Such interactions depend on signal exchange between both participants and can be mediated by effector proteins that alter the host cell structure and function, allowing the establishment of the relationship. The main purpose of this work was to identify, using computational methods, candidates of effector proteins from T...
February 15, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28198519/correlation-of-hypoxia-inducible-transcription-factor-in-breast-cancer-and-suvmax-of-f-18-fdg-pet-ct
#7
Young-Ju Jeong, Jae-Won Jung, Yoon-Young Cho, Sung-Hwan Park, Hoon-Kyu Oh, Sungmin Kang
BACKGROUND: Tumor hypoxia induces the expression of several genes via the hypoxia-inducible transcription factor-1 alpha (HIF-1a). It is associated with the prognosis of several cancers. We studied the immunohistochemical expression of HIF-1a in patients with invasive ductal cancer (IDC) of the breast and the possible correlation with the maximum standardized uptake value of the primary tumor (pSUVmax) as well as other biological parameters. Prognostic significance of pSUVmax and expression of HIF-1a for the prediction of progression-free survival (PFS) was also assessed...
2017: Nuclear Medicine Review. Central & Eastern Europe
https://www.readbyqxmd.com/read/28194627/fragment-based-in-silico-modeling-of-multi-target-inhibitors-against-breast-cancer-related-proteins
#8
Alejandro Speck-Planche, M Natália D S Cordeiro
Breast cancer is the most frequent cancer reported in women, being responsible for hundreds of thousands of deaths. Chemotherapy has proven to be effective against this malignant neoplasm depending on different biological factors such as the histopathology, grade, and stage, among others. However, breast cancer cells have become resistant to current chemotherapeutic regimens, urging the discovery of new anti-breast cancer drugs. Computational approaches have the potential to offer promising alternatives to accelerate the search for potent and versatile anti-breast cancer agents...
February 13, 2017: Molecular Diversity
https://www.readbyqxmd.com/read/28192937/amplification-and-quantification-of-an-antisense-oligonucleotide-from-target-microrna-using-programmable-dna-and-a-biological-nanopore
#9
Moe Hiratani, Masayuki Ohara, Ryuji Kawano
This paper describes a strategy for autonomous diagnoses of cancers using microRNA (miRNA) and therapy for tumor cells by DNA computing techniques and nanopore measurement. Theranostics, which involves the combination of diagnosis and therapy, has emerged as an approach for personalized medicine or point-of-care cancer diagnostics. DNA computing will become a potent tool for theranostics because it functions completely autonomously without the need for external regulations. However, conventional theranostics using DNA computing involves a one-to-one reaction in which a single input molecule generates a single output molecule; the concentration of the antisense drug is insufficient for the therapy in this type of reaction...
February 9, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28192427/comparing-individual-based-approaches-to-modelling-the-self-organization-of-multicellular-tissues
#10
James M Osborne, Alexander G Fletcher, Joe M Pitt-Francis, Philip K Maini, David J Gavaghan
The coordinated behaviour of populations of cells plays a central role in tissue growth and renewal. Cells react to their microenvironment by modulating processes such as movement, growth and proliferation, and signalling. Alongside experimental studies, computational models offer a useful means by which to investigate these processes. To this end a variety of cell-based modelling approaches have been developed, ranging from lattice-based cellular automata to lattice-free models that treat cells as point-like particles or extended shapes...
February 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28191459/epidermal-growth-factor-signaling-towards-proliferation-modeling-and-logic-inference-using-forward-and-backward-search
#11
Adrián Riesco, Beatriz Santos-Buitrago, Javier De Las Rivas, Merrill Knapp, Gustavo Santos-García, Carolyn Talcott
In biological systems, pathways define complex interaction networks where multiple molecular elements are involved in a series of controlled reactions producing responses to specific biomolecular signals. These biosystems are dynamic and there is a need for mathematical and computational methods able to analyze the symbolic elements and the interactions between them and produce adequate readouts of such systems. In this work, we use rewriting logic to analyze the cellular signaling of epidermal growth factor (EGF) and its cell surface receptor (EGFR) in order to induce cellular proliferation...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28185541/kaos-a-new-automated-computational-method-for-the-identification-of-overexpressed-genes
#12
Angelo Nuzzo, Giovanni Carapezza, Sebastiano Di Bella, Alfredo Pulvirenti, Antonella Isacchi, Roberta Bosotti
BACKGROUND: Kinase over-expression and activation as a consequence of gene amplification or gene fusion events is a well-known mechanism of tumorigenesis. The search for novel rearrangements of kinases or other druggable genes may contribute to understanding the biology of cancerogenesis, as well as lead to the identification of new candidate targets for drug discovery. However this requires the ability to query large datasets to identify rare events occurring in very small fractions (1-3 %) of different tumor subtypes...
November 8, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28182018/genome-wide-base-resolution-mapping-of-dna-methylation-in-single-cells-using-single-cell-bisulfite-sequencing-scbs-seq
#13
Stephen J Clark, Sébastien A Smallwood, Heather J Lee, Felix Krueger, Wolf Reik, Gavin Kelsey
DNA methylation (DNAme) is an important epigenetic mark in diverse species. Our current understanding of DNAme is based on measurements from bulk cell samples, which obscures intercellular differences and prevents analyses of rare cell types. Thus, the ability to measure DNAme in single cells has the potential to make important contributions to the understanding of several key biological processes, such as embryonic development, disease progression and aging. We have recently reported a method for generating genome-wide DNAme maps from single cells, using single-cell bisulfite sequencing (scBS-seq), allowing the quantitative measurement of DNAme at up to 50% of CpG dinucleotides throughout the mouse genome...
March 2017: Nature Protocols
https://www.readbyqxmd.com/read/28181481/dpath-software-reveals-hierarchical-haemato-endothelial-lineages-of-etv2-progenitors-based-on-single-cell-transcriptome-analysis
#14
Wuming Gong, Tara L Rasmussen, Bhairab N Singh, Naoko Koyano-Nakagawa, Wei Pan, Daniel J Garry
Developmental, stem cell and cancer biologists are interested in the molecular definition of cellular differentiation. Although single-cell RNA sequencing represents a transformational advance for global gene analyses, novel obstacles have emerged, including the computational management of dropout events, the reconstruction of biological pathways and the isolation of target cell populations. We develop an algorithm named dpath that applies the concept of metagene entropy and allows the ranking of cells based on their differentiation potential...
February 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28176001/multilayer-gyroid-cubic-membrane-organization-in-green-alga-zygnema
#15
Ting Zhan, Wenhua Lv, Yuru Deng
Biological cubic membranes (CM), which are fluid membranes draped onto the 3D periodic parallel surface geometries with cubic symmetry, have been observed within subcellular organelles, including mitochondria, endoplasmic reticulum, and thylakoids. CM transition tends to occur under various stress conditions; however, multilayer CM organizations often appear associated with light stress conditions. This report is about the characterization of a projected gyroid CM in a transmission electron microscopy study of the chloroplast membranes within green alga Zygnema (LB923) whose lamellar form of thylakoid membrane started to fold into multilayer gyroid CM in the culture at the end of log phase of cell growth...
February 7, 2017: Protoplasma
https://www.readbyqxmd.com/read/28166845/let-s-get-fissical-fast-in-silico-synchronization-as-a-new-tool-for-cell-division-cycle-analysis
#16
Brooke Morriswood, Markus Engstler
Cell cycle progression is a question of fundamental biological interest. The coordinated duplication and segregation of all cellular structures and organelles is however an extremely complex process, and one which remains only partially understood even in the most intensively researched model organisms. Trypanosomes are in an unusual position in this respect - they are both outstanding model systems for fundamental questions in eukaryotic cell biology, and pathogens that are the causative agents of three of the neglected tropical diseases...
February 7, 2017: Parasitology
https://www.readbyqxmd.com/read/28166542/expectation-propagation-for-large-scale-bayesian-inference-of-non-linear-molecular-networks-from-perturbation-data
#17
Zahra Narimani, Hamid Beigy, Ashar Ahmad, Ali Masoudi-Nejad, Holger Fröhlich
Inferring the structure of molecular networks from time series protein or gene expression data provides valuable information about the complex biological processes of the cell. Causal network structure inference has been approached using different methods in the past. Most causal network inference techniques, such as Dynamic Bayesian Networks and ordinary differential equations, are limited by their computational complexity and thus make large scale inference infeasible. This is specifically true if a Bayesian framework is applied in order to deal with the unavoidable uncertainty about the correct model...
2017: PloS One
https://www.readbyqxmd.com/read/28161684/silk-based-anisotropical-3d-biotextiles-for-bone-regeneration
#18
Viviana P Ribeiro, Joana Silva-Correia, Ana I Nascimento, Alain da Silva Morais, Alexandra P Marques, Ana S Ribeiro, Carla J Silva, Graça Bonifácio, Rui A Sousa, Joaquim M Oliveira, Ana L Oliveira, Rui L Reis
Bone loss in the craniofacial complex can been treated using several conventional therapeutic strategies that face many obstacles and limitations. In this work, novel three-dimensional (3D) biotextile architectures were developed as a possible strategy for flat bone regeneration applications. As a fully automated processing route, this strategy as potential to be easily industrialized. Silk fibroin (SF) yarns were processed into weft-knitted fabrics spaced by a monofilament of polyethylene terephthalate (PET)...
January 26, 2017: Biomaterials
https://www.readbyqxmd.com/read/28158307/aspasia-a-toolkit-for-evaluating-the-effects-of-biological-interventions-on-sbml-model-behaviour
#19
Stephanie Evans, Kieran Alden, Lourdes Cucurull-Sanchez, Christopher Larminie, Mark C Coles, Marika C Kullberg, Jon Timmis
A calibrated computational model reflects behaviours that are expected or observed in a complex system, providing a baseline upon which sensitivity analysis techniques can be used to analyse pathways that may impact model responses. However, calibration of a model where a behaviour depends on an intervention introduced after a defined time point is difficult, as model responses may be dependent on the conditions at the time the intervention is applied. We present ASPASIA (Automated Simulation Parameter Alteration and SensItivity Analysis), a cross-platform, open-source Java toolkit that addresses a key deficiency in software tools for understanding the impact an intervention has on system behaviour for models specified in Systems Biology Markup Language (SBML)...
February 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28156095/optimized-translocator-protein-ligand-for-optical-molecular-imaging-and-screening
#20
Jun Li, Jarrod A Smith, Eric S Dawson, Allie Fu, Michael L Nickels, Michael L Schulte, H Charles Manning
Translocator protein (TSPO) is a validated target for molecular imaging of a variety of human diseases and disorders. Given its involvement in cholesterol metabolism, TSPO expression is commonly elevated in solid tumors, including glioma, colorectal cancer, and breast cancer. TSPO ligands capable of detection by optical imaging are useful molecular tracers for a variety of purposes that range from quantitative biology to drug discovery. Leveraging our prior optimization of the pyrazolopyrimidine TSPO ligand scaffold for cancer imaging, we report herein a new generation of TSPO tracers with superior binding affinity and suitability for optical imaging and screening...
February 13, 2017: Bioconjugate Chemistry
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