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Computational cell biology

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https://www.readbyqxmd.com/read/29220306/improving-spiking-dynamical-networks-accurate-delays-higher-order-synapses-and-time-cells
#1
Aaron R Voelker, Chris Eliasmith
Researchers building spiking neural networks face the challenge of improving the biological plausibility of their model networks while maintaining the ability to quantitatively characterize network behavior. In this work, we extend the theory behind the neural engineering framework (NEF), a method of building spiking dynamical networks, to permit the use of a broad class of synapse models while maintaining prescribed dynamics up to a given order. This theory improves our understanding of how low-level synaptic properties alter the accuracy of high-level computations in spiking dynamical networks...
December 8, 2017: Neural Computation
https://www.readbyqxmd.com/read/29218556/structural-characterization-of-highly-flexible-proteins-by-small-angle-scattering
#2
Tiago N Cordeiro, Fátima Herranz-Trillo, Annika Urbanek, Alejandro Estaña, Juan Cortés, Nathalie Sibille, Pau Bernadó
Intrinsically Disordered Proteins (IDPs) are fundamental actors of biological processes. Their inherent plasticity facilitates very specialized tasks in cell regulation and signalling, and their malfunction is linked to severe pathologies. Understanding the functional role of disorder requires the structural characterization of IDPs and the complexes they form. Small-angle Scattering of X-rays (SAXS) and Neutrons (SANS) have notably contributed to this structural understanding. In this review we summarize the most relevant developments in the field of SAS studies of disordered proteins...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29217484/the-impact-of-protein-interaction-networks-characteristics-on-computational-complex-detection-methods
#3
Xiaoxia Liu, Zhihao Yang, Ziwei Zhou, Yuanyuan Sun, Hongfei Lin, Jian Wang, Bo Xu
Protein complexes of physically interacting proteins play an important role in organizing various biological processes in the cell. Therefore, correctly identifying complexes is useful for deciphering the cellular mechanisms underlying many biological processes. Since the existing high-throughput techniques have produced a large amount of protein interactions, computational methods are useful complements to the experimental methods for detecting protein complexes. In this paper, we analyze six protein interaction networks widely used for protein complex detection, and compare the performance of six classic computational methods on them in order to find the impacts of network characteristics on the performances of these complex detection methods...
December 4, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29213288/microrna-214-suppresses-osteogenic-differentiation-of-human-periodontal-ligament-stem-cells-by-targeting-atf4
#4
Siqi Yao, Wei Zhao, Qianmin Ou, Lanchen Liang, Xuefeng Lin, Yan Wang
Periodontitis is the main cause of adult tooth loss. Stem cell-based tissue engineering has become a promising therapy for periodontitis treatment. To date, human periodontal ligament stem cells (hPDLSCs) have been shown to be a favorable source for tissue engineering, but modulatory mechanisms of hPDLSCs remain unclear. Approximately 60% of mammalian genes are the targets of over 2000 miRNAs in multiple human cell types, and miRNAs are able to influence various biological processes in the human body, including bone formation...
2017: Stem Cells International
https://www.readbyqxmd.com/read/29209065/cellular-automaton-models-for-time-correlated-random-walks-derivation-and-analysis
#5
J M Nava-Sedeño, H Hatzikirou, R Klages, A Deutsch
Many diffusion processes in nature and society were found to be anomalous, in the sense of being fundamentally different from conventional Brownian motion. An important example is the migration of biological cells, which exhibits non-trivial temporal decay of velocity autocorrelation functions. This means that the corresponding dynamics is characterized by memory effects that slowly decay in time. Motivated by this we construct non-Markovian lattice-gas cellular automata models for moving agents with memory...
December 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29207673/comparison-among-conventional-and-advanced-mri-18f-fdg-pet-ct-phenotype-and-genotype-in-glioblastoma
#6
Maria Consuelo Valentini, Marta Mellai, Laura Annovazzi, Antonio Melcarne, Tetyana Denysenko, Paola Cassoni, Cristina Casalone, Cristiana Maurella, Silvia Grifoni, Piercarlo Fania, Angelina Cistaro, Davide Schiffer
Glioblastoma (GB) is a highly heterogeneous tumor. In order to identify in vivo the most malignant tumor areas, the extent of tumor infiltration and the sites giving origin to GB stem cells (GSCs), we combined positron emission tomography/computed tomography (PET/CT) and conventional and advanced magnetic resonance imaging (MRI) with histology, immunohistochemistry and molecular genetics. Prior to dura opening and tumor resection, forty-eight biopsy specimens [23 of contrast-enhancing (CE) and 25 of non-contrast enhancing (NE) regions] from 12 GB patients were obtained by a frameless image-guided stereotactic biopsy technique...
October 31, 2017: Oncotarget
https://www.readbyqxmd.com/read/29203214/unravelling-the-differences-comparative-proteomic-analysis-of-a-clonal-virulent-and-an-attenuated-histomonas-meleagridis-strain
#7
Andreas Monoyios, Martina Patzl, Sarah Schlosser, Michael Hess, Ivana Bilic
The current study focused on Histomonas meleagridis, a unicellular protozoan, responsible for histomonosis in poultry. Recently, the occurrence of the disease increased due to the ban of effective chemotherapeutic drugs. Basic questions regarding the molecular biology, virulence mechanisms or even life cycle of the flagellate are still puzzling. In order to address some of these issues, we conducted a comparative proteomic analysis of a virulent and an attenuated H. meleagridis strain traced back to a single cell and propagated in vitro as monoxenic mono-eukaryotic cultures...
December 1, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/29202036/free-radicals-and-advanced-chemistries-involved-in-cell-membrane-organization-influence-oxygen-diffusion-and-pathology-treatment
#8
Richard C Petersen
A breakthrough has been discovered in pathology chemistry related to increasing molecular structure that can interfere with oxygen diffusion through cell membranes. Free radicals can crosslink unsaturated low-viscosity fatty acid oils by chain-growth polymerization into more viscous liquids and even solids. Free radicals are released by mitochondria in response to intermittent hypoxia that can increase membrane molecular organization to reduce fluidity and oxygen diffusion in a possible continuing vicious cycle toward pathological disease...
2017: AIMS Biophysics
https://www.readbyqxmd.com/read/29201868/the-scope-of-big-data-in-one-medicine-unprecedented-opportunities-and-challenges
#9
REVIEW
Molly E McCue, Annette M McCoy
Advances in high-throughput molecular biology and electronic health records (EHR), coupled with increasing computer capabilities have resulted in an increased interest in the use of big data in health care. Big data require collection and analysis of data at an unprecedented scale and represents a paradigm shift in health care, offering (1) the capacity to generate new knowledge more quickly than traditional scientific approaches; (2) unbiased collection and analysis of data; and (3) a holistic understanding of biology and pathophysiology...
2017: Frontiers in Veterinary Science
https://www.readbyqxmd.com/read/29200531/a-composite-smeared-finite-element-for-mass-transport-in-capillary-systems-and-biological-tissue
#10
M Kojic, M Milosevic, V Simic, E J Koay, J B Fleming, S Nizzero, N Kojic, A Ziemys, M Ferrari
One of the key processes in living organisms is mass transport occurring from blood vessels to tissues for supplying tissues with oxygen, nutrients, drugs, immune cells, and - in the reverse direction - transport of waste products of cell metabolism to blood vessels. The mass exchange from blood vessels to tissue and vice versa occurs through blood vessel walls. This vital process has been investigated experimentally over centuries, and also in the last decades by the use of computational methods. Due to geometrical and functional complexity and heterogeneity of capillary systems, it is however not feasible to model in silico individual capillaries (including transport through the walls and coupling to tissue) within whole organ models...
September 1, 2017: Computer Methods in Applied Mechanics and Engineering
https://www.readbyqxmd.com/read/29198012/successful-local-treatment-for-repeated-hepatic-recurrences-of-cholangiolocellular-carcinoma-a-report-on-a-long-term-survivor
#11
Kentaro Shinohara, Tomoki Ebata, Yukihiro Yokoyama, Tsuyoshi Igami, Gen Sugawara, Takashi Mizuno, Junpei Yamaguchi, Yoshie Shimoyama, Shuichiro Shiina, Ryosuke Tateishi, Toru Arano, Masato Nagino
BACKGROUND: Cholangiolocellular carcinoma (CoCC) is a rare liver tumor arising from the canals of Hering found between the cholangioles and interlobular bile ducts. Although morphologically CoCC mimics intrahepatic cholangiocarcinoma (ICC), CoCC exhibits a unique intermediate biologic behavior between hepatocellular carcinoma (HCC) and ICC. Curative resection is required for prolonged survival in patients with CoCC. However, effective therapy for postoperative hepatic recurrence has not yet been standardized...
December 2, 2017: Surgical Case Reports
https://www.readbyqxmd.com/read/29197000/proteomics-method-to-identification-of-protein-profiles-in-exosomes
#12
Andrew Lai, Vyjayanthi Kinhal, Zarin Nuzhat, Ramkumar Menon, Gregory E Rice, Carlos Salomon
Exosomes are membrane-bound nanovesicles that transport molecular signals (e.g., proteins) between cells and are released from a wide range of cells, including the human placenta. Interestingly, the levels of exosomes present in maternal circulation are higher in preeclamptic pregnancies and their protein content profile change in response to the microenvironment milieu. Through the discovery of candidate biomarkers, mass spectrometry (MS)-based proteomics may provide a better understanding of the pathophysiology underlying pregnancy-associated disorders...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29195008/consensus-predictive-model-for-the-prediction-of-human-k562-cell-growth-inhibition-through-enalos-cloud-platform
#13
Antreas Afantitis, Georgios Leonis, Roberto Gambari, Georgia Melagraki
Beta thalassemia is an inherited hematologic disorder caused by various mutations of the β-globin gene, thus resulting in a significant decrease of adult hemoglobin (HbA) production. Since no other specific treatment exists to date, apart from blood transfusion and chelation therapy, the increase of fetal hemoglobin (HbF) levels by drug molecules is considered of great potential in β-thalassemia treatment, being expected to counterbalance the impaired production of HbA. Within this context, we have worked towards the development of a predictive model that will allow the identification of new possible HbF inducers...
December 1, 2017: ChemMedChem
https://www.readbyqxmd.com/read/29193879/organ-bioprinting-are-we-there-yet
#14
REVIEW
Guifang Gao, Ying Huang, Arndt F Schilling, Karen Hubbell, Xiaofeng Cui
About 15 years ago, bioprinting was coined as one of the ultimate solutions to engineer vascularized tissues, which was impossible to accomplish using the conventional tissue fabrication approaches. With the advances of 3D-printing technology during the past decades, one may expect 3D bioprinting being developed as much as 3D printing. Unfortunately, this is not the case. The printing principles of bioprinting are dramatically different from those applied in industrialized 3D printing, as they have to take the living components into account...
November 29, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/29192556/bacterial-endotoxin-lipopolysaccharide-binds-to-the-surface-of-gold-nanoparticles-interferes-with-biocorona-formation-and-induces-human-monocyte-inflammatory-activation
#15
Yang Li, Zhenzhen Shi, Isabella Radauer-Preiml, Ancuela Andosch, Eudald Casals, Ursula Luetz-Meindl, Macarena Cobaleda, Zhoumeng Lin, Majid Jaberi-Douraki, Paola Italiani, Jutta Horejs-Hoeck, Martin Himly, Nancy A Monteiro-Riviere, Albert Duschl, Victor F Puntes, Diana Boraschi
Nanoparticles (NPs) are easily contaminated by bacterial endotoxin (lipopolysaccharide [LPS]). The presence of LPS can be responsible for many immune/inflammatory effects attributed to NPs. In this study, we examined the effects of LPS adsorption on the NP surface on the formation of a biocorona in biological fluids and on the subsequent inflammation-inducing activity of NPs. Different gold (Au) NPs with sizes ranging from 10 to 80 nm and with different surface functionalization (sodium citrate, lipoic acid, and branched polyethyleneimine (BPEI), or polyethylene glycol (PEG)) were exposed to E...
December 1, 2017: Nanotoxicology
https://www.readbyqxmd.com/read/29191553/amp-and-adenosine-are-both-ligands-for-adenosine-2b-receptor-signaling
#16
Jessica K Holien, Benjamin Seibt, Veena Roberts, Evelyn Salvaris, Michael W Parker, Peter J Cowan, Karen M Dwyer
Adenosine is considered the canonical ligand for the adenosine 2B receptor (A2BR). A2BR is upregulated following kidney ischemia augmenting post ischemic blood flow and limiting tubular injury. In this context the beneficial effect of A2BR signaling has been attributed to an increase in the pericellular concentration of adenosine. However, following renal ischemia both kidney adenosine monophosphate (AMP) and adenosine levels are substantially increased. Using computational modeling and calcium mobilization assays, we investigated whether AMP could also be a ligand for A2BR...
November 20, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/29190967/differential-prioritization-of-therapies-to-subtypes-of-triple-negative-breast-cancer-using-a-systems-medicine-method
#17
Henri Wathieu, Naiem T Issa, Aileen I Fernandez, Manisha Mohandoss, Deanna M Tiek, Jennifer L Franke, Stephen W Byers, Rebecca B Riggins, Sivanesan Dakshanamurthy
Triple negative breast cancer (TNBC) is a group of cancers whose heterogeneity and shortage of effective drug therapies has prompted efforts to divide these cancers into molecular subtypes. Our computational platform, entitled GenEx-TNBC, applies concepts in systems biology and polypharmacology to prioritize thousands of approved and experimental drugs for therapeutic potential against each molecular subtype of TNBC. Using patient-based and cell line-based gene expression data, we constructed networks to describe the biological perturbation associated with each TNBC subtype at multiple levels of biological action...
November 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/29190638/linking-gene-dynamics-to-vascular-hyperplasia-toward-a-predictive-model-of-vein-graft-adaptation
#18
Stefano Casarin, Scott A Berceli, Marc Garbey
Reductionist approaches, where individual pieces of a process are examined in isolation, have been the mainstay of biomedical research. While these methods are effective in highly compartmentalized systems, they fail to account for the inherent plasticity and non-linearity within the signaling structure. In the current manuscript, we present the computational architecture for tracking an acute perturbation in a biologic system through a multiscale model that links gene dynamics to cell kinetics, with the overall goal of predicting tissue adaptation...
2017: PloS One
https://www.readbyqxmd.com/read/29189124/overview-on-anticancer-drug-design-and-development
#19
Sureyya Olgen
Many impediments of current anti-cancer therapies have urged scientists to discover new agents. As a result of growing spectrums of new targets and strategies and recent biological and biotechnological progresses, many anti-cancer agents such as monoclonal antibodies, small molecule tyrosine kinase inhibitors and epigenetic drugs have been reached to clinical trials. Addition to the traditional targets (mitosis, DNA synthesis, repairing systems, tumor growth, apoptosis, tumor vasculature and cell signaling mechanisms), other targets such as proteasome, heat shock proteins (HSPs), and epigenetics (HDACs, HATs, DNMT, PAD4, AID, and Tet1) are used to design new anti-cancer agents...
November 29, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/29187729/inference-of-differentiation-time-for-single-cell-transcriptomes-using-cell-population-reference-data
#20
Na Sun, Xiaoming Yu, Fang Li, Denghui Liu, Shengbao Suo, Weiyang Chen, Shirui Chen, Lu Song, Christopher D Green, Joseph McDermott, Qin Shen, Naihe Jing, Jing-Dong J Han
Single-cell RNA sequencing (scRNA-seq) is a powerful method for dissecting intercellular heterogeneity during development. Conventional trajectory analysis provides only a pseudotime of development, and often discards cell-cycle events as confounding factors. Here using matched cell population RNA-seq (cpRNA-seq) as a reference, we developed an "iCpSc" package for integrative analysis of cpRNA-seq and scRNA-seq data. By generating a computational model for reference "biological differentiation time" using cell population data and applying it to single-cell data, we unbiasedly associated cell-cycle checkpoints to the internal molecular timer of single cells...
November 30, 2017: Nature Communications
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