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Computational cell biology

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https://www.readbyqxmd.com/read/28102262/scaling-single-cell-genomics-from-phenomenology-to-mechanism
#1
Amos Tanay, Aviv Regev
Three of the most fundamental questions in biology are how individual cells differentiate to form tissues, how tissues function in a coordinated and flexible fashion and which gene regulatory mechanisms support these processes. Single-cell genomics is opening up new ways to tackle these questions by combining the comprehensive nature of genomics with the microscopic resolution that is required to describe complex multicellular systems. Initial single-cell genomic studies provided a remarkably rich phenomenology of heterogeneous cellular states, but transforming observational studies into models of dynamics and causal mechanisms in tissues poses fresh challenges and requires stronger integration of theoretical, computational and experimental frameworks...
January 18, 2017: Nature
https://www.readbyqxmd.com/read/28098992/mechanistic-insights-into-tunable-metal-mediated-hydrolysis-of-amyloid-%C3%AE-peptides
#2
Jeffrey S Derrick, Jiwan Lee, Shin Jung C Lee, Yujeong Kim, Eunju Nam, Hyeonwoo Tak, Juhye Kang, Misun Lee, Sun Hee Kim, Kiyoung Park, Jaeheung Cho, Mi Hee Lim
An amyloidogenic peptide, amyloid-β (Aβ), has been implicated as a contributor to the neurotoxicity of Alzheimer's disease (AD) that continues to present a major socioeconomic burden for our society. Recently, the use of metal complexes capable of cleaving peptides has arisen as an efficient tactic for amyloid management; unfortunately, little has been reported to pursue this strategy. Herein, we report a novel approach to validate the hydrolytic cleavage of divalent metal complexes toward two major isoforms of Aβ (Aβ40 and Aβ42) and tune their proteolytic activity based on the choice of metal centers (M = Co, Ni, Cu, and Zn) which could be correlated to their anti-amyloidogenic properties...
January 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28098984/red-emitting-ruthenium-ii-and-iridium-iii-complexes-as-phosphorescent-probes-for-methylglyoxal-in-vitro-and-in-vivo
#3
Wenzhu Zhang, Feiyue Zhang, Yong-Lei Wang, Bo Song, Run Zhang, Jingli Yuan
Transition-metal complexes, ruthenium(II) and iridium(III) complexes in particular, with fascinating triplet emissions are rapidly emerging as important phosphorescent dyes for application in the sensing and imaging of biological makers in live cells and organisms. In this contribution, two red-emitting transition-metal complexes, [Ru(bpy)2(DA-phen)](PF6)2 and [Ir(ppy)2(DA-phen)](PF6) (bpy = 2,2'-bipyridine, DA-phen = 4,5-diamino-1,10-phenanthroline, and ppy = 2-phenylpyridine), were designed and synthesized as phosphorescent probes for the highly sensitive and selective detection of methylglyoxal (MGO), an essential biomarker in the etiopathogenesis of several diseases...
January 18, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28098449/targeting-type-2-diabetes-with-c-glucosyl-dihydrochalcones-as-selective-sodium-glucose-co-transporter-2-sglt2-inhibitors-synthesis-and-biological-evaluation
#4
Ana R Jesus, Diogo Vila-Viçosa, Miguel Machuqueiro, Ana P Marques, Timothy M Dore, Amélia P Rauter
Inhibiting glucose reabsorption by sodium glucose co-transporter proteins (SGLTs) in the kidneys is a relatively new strategy for treating type 2 diabetes. Selective inhibition of SGLT2 over SGLT1 is critical for minimizing adverse side effects associated with SGLT1 inhibition. A library of C-glucosyl dihydrochalcones and their dihydrochalcone and chalcone precursors was synthesized and tested as SGLT1/SGLT2 inhibitors using a cell-based fluorescence assay of glucose uptake. The most potent inhibitors of SGLT2 (IC50 = 9-23 nM) were considerably weaker inhibitors of SGLT1 (IC50 = 10-19 μM)...
January 18, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28098310/a-computational-model-predicts-genetic-nodes-that-allow-switching-between-species-specific-responses-in-a-conserved-signaling-network
#5
Adriana T Dawes, David Wu, Karley K Mahalak, Edward M Zitnik, Natalia Kravtsova, Haiwei Su, Helen M Chamberlin
Cell signaling networks regulate a variety of developmental and physiological processes, and changes in their response to external stimuli are often implicated in disease initiation and progression. To elucidate how different responses can arise from conserved signaling networks, we have developed a mathematical model of the well-characterized Caenorhabditis vulval development network involving EGF, Wnt and Notch signaling that recapitulates biologically observed behaviors. We experimentally block a specific element of the EGF pathway (MEK), and find different behaviors in vulval development in two Caenorhabditis species, C...
January 18, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28094442/identifying-niche-mediated-regulatory-factors-of-stem-cell-phenotypic-state-a-systems-biology-approach
#6
Srikanth Ravichandran, Antonio Del Sol
Understanding how the cellular niche controls the stem cell phenotype is often hampered due to the complexity of variegated niche composition, its dynamics, and non-linear stem cell-niche interactions. Here, we propose a systems biology view that considers stem cell-niche interactions as a many-body problem amenable to simplification by the concept of mean field approximation. This enables approximation of the niche effect on stem cells as a constant field that induces sustained activation/inhibition of specific stem cell signaling pathways in all stem cells within heterogeneous populations exhibiting the same phenotype (niche determinants)...
January 17, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28093295/in-silico-enhancement-of-the-stability-and-activity-of-keratinocyte-growth-factor
#7
Mansour Poorebrahim, Solmaz Sadeghi, Raziyeh Ghorbani, Matin Asghari, Mohammad Foad Abazari, Hourieh Kalhor, Hamzeh Rahimi
Keratinocyte growth factor (KGF), a member of the fibroblast growth factor (FGF) family, has been implicated in some biological processes such as cell proliferation, development and differentiation. High mitogenic activity of this protein has made it very suitable for repairing radiation-and chemotherapy-induced damages. KGF, which has been developed from human KGF, is clinically applied to reduce the incidence and duration of cancer therapeutic agents. However, the activity of KGF is limited during treatment due to its poor stability...
January 13, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28092960/mathematical-analysis-and-dynamic-active-subspaces-for-a-long-term-model-of-hiv
#8
Tyson Loudon, Stephen Pankavich
a long-term model of HIV infection dynamics [8] was developed to describe the entire time course of the disease. It consists of a large system of ODEs with many parameters, and is expensive to simulate. In the current paper, this model is analyzed by determining all infection-free steady states and studying the local stability properties of the unique biologically-relevant equilibrium. Active subspace methods are then used to perform a global sensitivity analysis and study the dependence of an infected individual's T-cell count on the parameter space...
June 1, 2017: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/28092826/synthesis-ph-dependent-photometric-and-electrochemical-investigation-redox-mechanism-and-biological-applications-of-novel-schiff-base-and-its-metallic-derivatives
#9
Abdur Rauf, Afzal Shah, Abdul Aziz Khan, Aamir Hassan Shah, Rashda Abbasi, Irfan Zia Qureshi, Saqib Ali
A novel Schiff base, 1-((2, 4-dimethylphenylimino)methyl)naphthalen-2-ol abbreviated as (HL) and its four metallic complexes were synthesized and confirmed by (1)H and (13)C NMR, FTIR, TGA and UV-Visible spectroscopy. Schiff base was also characterized by X-ray analysis. The photometric and electrochemical responses of all the synthesized compounds were investigated in a wide pH range. Structures of the compounds were optimized computationally for the evaluation of different physico-chemical parameters. On the basis of electrochemical results the redox mechanistic pathways of the compounds were proposed...
January 9, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28089542/parallelization-and-high-performance-computing-enables-automated-statistical-inference-of-multi-scale-models
#10
Nick Jagiella, Dennis Rickert, Fabian J Theis, Jan Hasenauer
Mechanistic understanding of multi-scale biological processes, such as cell proliferation in a changing biological tissue, is readily facilitated by computational models. While tools exist to construct and simulate multi-scale models, the statistical inference of the unknown model parameters remains an open problem. Here, we present and benchmark a parallel approximate Bayesian computation sequential Monte Carlo (pABC SMC) algorithm, tailored for high-performance computing clusters. pABC SMC is fully automated and returns reliable parameter estimates and confidence intervals...
January 10, 2017: Cell Systems
https://www.readbyqxmd.com/read/28089326/mechanical-response-of-common-millet-panicum-miliaceum-seeds-under-quasi-static-compression-experiments-and-modeling
#11
Benjamin P J Hasseldine, Chao Gao, Joseph M Collins, Hyun-Do Jung, Tae-Sik Jang, Juha Song, Yaning Li
The common millet (Panicum miliaceum) seedcoat has a fascinating complex microstructure, with jigsaw puzzle-like epidermis cells articulated via wavy intercellular sutures to form a compact layer to protect the kernel inside. However, little research has been conducted on linking the microstructure details with the overall mechanical response of this interesting biological composite. To this end, an integrated experimental-numerical-analytical investigation was conducted to both characterize the microstructure and ascertain the microscale mechanical properties and to test the overall response of kernels and full seeds under macroscale quasi-static compression...
January 6, 2017: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/28088216/immunohistochemical-features-of-giant-cell-ependymoma-of-the-filum-terminale-with-unusual-clinical-and-radiological-presentation
#12
Fernando Candanedo-Gonzalez, Cindy Sharon Ortiz-Arce, Samuel Rosales-Perez, Ana Lilia Remirez-Castellanos, Candelaria Cordova-Uscanga, Armando Gamboa-Dominguez
BACKGROUND: Giant cell ependymoma of the filum terminale is a rare variant, generally manifested as a well-circunscribed intradural mass with an indolent biological behavior. CASE PRESENTATION: We describe the case of a 48-year-old Mexican female who non-relevant past medical history, that developed a GCE of the filum terminale. Magnetic resonance imaging and computed tomography revealed the presence of an intra-axial tumor extending from L3 to L5 with extra-medullary invasion...
January 14, 2017: Diagnostic Pathology
https://www.readbyqxmd.com/read/28081212/correction-a-stochastic-model-of-the-yeast-cell-cycle-reveals-roles-for-feedback-regulation-in-limiting-cellular-variability
#13
(no author information available yet)
[This corrects the article DOI: 10.1371/journal.pcbi.1005230.].
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28080059/a-computational-approach-for-modeling-neutron-scattering-data-from-lipid-bilayers
#14
Jan-Michael Y Carrillo, John Katsaras, Bobby G Sumpter, Rana Ashkar
Biological cell membranes are responsible for a range of structural and dynamical phenomena crucial to a cell's well-being and its associated functions. Due to the complexity of cell membranes, lipid bilayer systems are often used as biomimetic models. These systems have led to significant insights into vital membrane phenomena such as domain formation, passive permeation and protein insertion. Experimental observations of membrane structure and dynamics are, however, limited in resolution, both spatially and temporally...
January 12, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28079126/detecting-n-6-methyladenosine-sites-from-rna-transcriptomes-using-ensemble-support-vector-machines
#15
Wei Chen, Pengwei Xing, Quan Zou
As one of the most abundant RNA post-transcriptional modifications, N(6)-methyladenosine (m(6)A) involves in a broad spectrum of biological and physiological processes ranging from mRNA splicing and stability to cell differentiation and reprogramming. However, experimental identification of m(6)A sites is expensive and laborious. Therefore, it is urgent to develop computational methods for reliable prediction of m(6)A sites from primary RNA sequences. In the current study, a new method called RAM-ESVM was developed for detecting m(6)A sites from Saccharomyces cerevisiae transcriptome, which employed ensemble support vector machine classifiers and novel sequence features...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28077404/high-throughput-sequencing-of-the-t-cell-receptor-repertoire-pitfalls-and-opportunities
#16
James M Heather, Mazlina Ismail, Theres Oakes, Benny Chain
T-cell specificity is determined by the T-cell receptor, a heterodimeric protein coded for by an extremely diverse set of genes produced by imprecise somatic gene recombination. Massively parallel high-throughput sequencing allows millions of different T-cell receptor genes to be characterized from a single sample of blood or tissue. However, the extraordinary heterogeneity of the immune repertoire poses significant challenges for subsequent analysis of the data. We outline the major steps in processing of repertoire data, considering low-level processing of raw sequence files and high-level algorithms, which seek to extract biological or pathological information...
January 10, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28069340/integrating-computational-methods-and-experimental-data-for-understanding-the-recognition-mechanism-and-binding-affinity-of-protein-protein-complexes
#17
REVIEW
M Michael Gromiha, K Yugandhar
Protein-protein interactions perform several functions inside the cell. Understanding the recognition mechanism and binding affinity of protein-protein complexes is a challenging problem in experimental and computational biology. In this review, we focus on two aspects (i) understanding the recognition mechanism and (ii) predicting the binding affinity. The first part deals with computational techniques for identifying the binding site residues and the contribution of important interactions for understanding the recognition mechanism of protein-protein complexes in comparison with experimental observations...
January 7, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28067293/drug-response-prediction-as-a-link-prediction-problem
#18
Zachary Stanfield, Mustafa Coşkun, Mehmet Koyutürk
Drug response prediction is a well-studied problem in which the molecular profile of a given sample is used to predict the effect of a given drug on that sample. Effective solutions to this problem hold the key for precision medicine. In cancer research, genomic data from cell lines are often utilized as features to develop machine learning models predictive of drug response. Molecular networks provide a functional context for the integration of genomic features, thereby resulting in robust and reproducible predictive models...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28065881/an-integrated-transcriptomics-guided-genome-wide-promoter-analysis-and-next-generation-proteomics-approach-to-mine-factor-s-regulating-cellular-differentiation
#19
Kamal Mandal, Samuel L Bader, Pankaj Kumar, Dipankar Malakar, David S Campbell, Bhola Shankar Pradhan, Rajesh K Sarkar, Neerja Wadhwa, Souvik Sensharma, Vaibhav Jain, Robert L Moritz, Subeer S Majumdar
Differential next-generation-omics approaches aid in the visualization of biological processes and pave the way for divulging important events and/or interactions leading to a functional output at cellular or systems level. To this end, we undertook an integrated Nextgen transcriptomics and proteomics approach to divulge differential gene expression of infant and pubertal rat Sertoli cells (Sc).Unlike, pubertal Sc, infant Sc are immature and fail to support spermatogenesis. We found exclusive association of 14 and 19 transcription factor binding sites to infantile and pubertal states of Sc, respectively, using differential transcriptomics-guided genome-wide computational analysis of relevant promoters employing 220 Positional Weight Matrices from the TRANSFAC database...
January 8, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28060821/customized-regulation-of-diverse-stress-response-genes-by-the-multiple-antibiotic-resistance-activator-mara
#20
Nicholas A Rossi, Mary J Dunlop
Stress response networks frequently have a single upstream regulator that controls many downstream genes. However, the downstream targets are often diverse, therefore it remains unclear how their expression is specialized when under the command of a common regulator. To address this, we focused on a stress response network where the multiple antibiotic resistance activator MarA from Escherichia coli regulates diverse targets ranging from small RNAs to efflux pumps. Using single-cell experiments and computational modeling, we showed that each downstream gene studied has distinct activation, noise, and information transmission properties...
January 6, 2017: PLoS Computational Biology
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