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Computational cell biology

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https://www.readbyqxmd.com/read/29684914/serum-calcium-is-related-to-the-degree-of-artery-stenosis-in-acute-ischemic-stroke
#1
Jiayan Wu, Junchao Xie, Yanxin Zhao, Li Gong, Xueyuan Liu, Wangmi Liu
BACKGROUND/AIMS: Acute ischemic stroke is caused by stenosis of artery supplying to brain. We aimed to detect some metabolites in the serum that would be related to the degree of artery stenosis and to analyze potential mechanisms. METHODS: Patients diagnosed with acute ischemic stroke were divided into two groups according to their degree of artery stenosis (which was determined by computed tomographic angiography): a mild group (stenosis ≤ 30%) and a severe group (stenosis > 30%)...
2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29680255/phase-2-study-of-stereotactic-body-radiation-therapy-and-stereotactic-body-proton-therapy-for-high-risk-medically-inoperable-early-stage-non-small-cell-lung-cancer
#2
Chonnipa Nantavithya, Daniel R Gomez, Xiong Wei, Ritsuko Komaki, Zhongxing Liao, Steven H Lin, Melenda Jeter, Quynh-Nhu Nguyen, Heng Li, Xiaodong Zhang, Falk Poenisch, X Ronald Zhu, Peter A Balter, Lei Feng, Noah C Choi, Radhe Mohan, Joe Y Chang
PURPOSE: To report the feasibility of conducting a randomized study to compare the toxicity and efficacy of stereotactic body radiation therapy (SBRT) versus stereotactic body proton therapy (SBPT) for high-risk, medically inoperable, early-stage non-small cell lung cancer (NSCLC). PATIENTS AND METHODS: Patients with medically inoperable NSCLC with high-risk features (centrally located or <5 cm T3 tumor or isolated lung parenchymal recurrences) were randomly assigned to SBRT or SBPT...
March 2, 2018: International Journal of Radiation Oncology, Biology, Physics
https://www.readbyqxmd.com/read/29678692/nucpospred-predicting-species-specific-genomic-nucleosome-positionin-g-via-four-different-modes-of-general-pseknc
#3
Cangzhi Jia, Qing Yang, Quan Zou
The nucleosome is the basic structure of chromatin in eukaryotic cells, with essential roles in the regulation of many biological processes, such as DNA transcription, replication and repair, and RNA splicing. Because of the importance of nucleosomes, the factors that determine their positioning within genomes should be investigated. High-resolution nucleosome-positioning maps are now available for organisms including Saccharomyces cerevisiae, Drosophila melanogaster and Caenorhabditis elegans, enabling the identification of nucleosome positioning by application of computational tools...
April 17, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29676100/-synthesis-biological-activity-computer-aided-drug-design-of-alpha-pinene-derivatives
#4
Meng-Die Yang, Qiu-Xiang Xu, Lian-Bao Ye, Ming Li, Yu Feng, Wei-Qiang Chen
Based on the anticancer mechanism of biological alkylating agent, we designed and synthesized two alpha pinene derivatives:(1R,5S)-(6,6-dimethylbicyclo[3,1,1]hept-2-en-2-yl)methyl benzenesulfonate and (1R,5S)-(6,6-dimethylbicyclo[3,1,1]hept-2-en-2-yl)methyl 4-methylbenzenesulfonate, of which structures were confirmed by ¹H-NMR, HPLC and MS date. These two compounds showed a good inhibition of tumor cells' proliferation. Further, the computer siuulation of molecular docking and metabolic kinetics indicated that these two copounds may have stable molecular complexation with protein CDK2, which closely related to the cell cycle...
March 2018: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29674686/evolutionary-plasticity-of-the-nhl-domain-underlies-distinct-solutions-to-rna-recognition
#5
Pooja Kumari, Florian Aeschimann, Dimos Gaidatzis, Jeremy J Keusch, Pritha Ghosh, Anca Neagu, Katarzyna Pachulska-Wieczorek, Janusz M Bujnicki, Heinz Gut, Helge Großhans, Rafal Ciosk
RNA-binding proteins regulate all aspects of RNA metabolism. Their association with RNA is mediated by RNA-binding domains, of which many remain uncharacterized. A recently reported example is the NHL domain, found in prominent regulators of cellular plasticity like the C. elegans LIN-41. Here we employ an integrative approach to dissect the RNA specificity of LIN-41. Using computational analysis, structural biology, and in vivo studies in worms and human cells, we find that a positively charged pocket, specific to the NHL domain of LIN-41 and its homologs (collectively LIN41), recognizes a stem-loop RNA element, whose shape determines the binding specificity...
April 19, 2018: Nature Communications
https://www.readbyqxmd.com/read/29674432/cell-type-atlas-and-lineage-tree-of-a-whole-complex-animal-by-single-cell-transcriptomics
#6
Mireya Plass, Jordi Solana, F Alexander Wolf, Salah Ayoub, Aristotelis Misios, Petar Glažar, Benedikt Obermayer, Fabian J Theis, Christine Kocks, Nikolaus Rajewsky
Flatworms of the species Schmidtea mediterranea are immortal-adult animals contain a large pool of pluripotent stem cells that continuously differentiate to all adult cell types. Therefore, single-cell transcriptome profiling of adult animals should reveal mature and progenitor cells. By combining perturbation experiments, gene expression analysis, a computational method that predicts future cell states from the transcriptional changes, and a lineage reconstruction method, we placed all major cell types onto a single lineage tree that connects all cells to a single stem cell compartment...
April 19, 2018: Science
https://www.readbyqxmd.com/read/29673065/insight-into-tetrodotoxin-blockade-and-resistance-mechanisms-of-na-v-1-2-sodium-channel-by-theoretical-approaches
#7
Lei Xu, Dayu Li, Junjie Ding, Li Pan, Xiaoqin Ding
Nav 1.2, a member of voltage-gated sodium channels (Nav s) that are responsible for the generation and propagation of action potentials along the cell membrane, and play a vital role in the process of information transmission within the nervous system and muscle contraction, is preferentially expressed in the central nervous system. As a potent and selective blocker of Nav s, tetrodotoxin (TTX) has been extensively studied in biological and chemical sciences, whereas the detailed mechanism by which it blocks nine Nav 1 channel subtypes remain elusive...
April 19, 2018: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/29670517/computational-models-for-calcium-mediated-astrocyte-functions
#8
REVIEW
Tiina Manninen, Riikka Havela, Marja-Leena Linne
The computational neuroscience field has heavily concentrated on the modeling of neuronal functions, largely ignoring other brain cells, including one type of glial cell, the astrocytes. Despite the short history of modeling astrocytic functions, we were delighted about the hundreds of models developed so far to study the role of astrocytes, most often in calcium dynamics, synchronization, information transfer, and plasticity in vitro , but also in vascular events, hyperexcitability, and homeostasis. Our goal here is to present the state-of-the-art in computational modeling of astrocytes in order to facilitate better understanding of the functions and dynamics of astrocytes in the brain...
2018: Frontiers in Computational Neuroscience
https://www.readbyqxmd.com/read/29668304/a-method-for-predicting-protein-complexes-from-dynamic-weighted-protein-protein-interaction-networks
#9
Lizhen Liu, Xiaowu Sun, Wei Song, Chao Du
Predicting protein complexes from protein-protein interaction (PPI) network is of great significance to recognize the structure and function of cells. A protein may interact with different proteins under different time or conditions. Existing approaches only utilize static PPI network data that may lose much temporal biological information. First, this article proposed a novel method that combines gene expression data at different time points with traditional static PPI network to construct different dynamic subnetworks...
April 18, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29667836/molecular-dynamics-simulations-are-redefining-our-view-of-peptides-interacting-with-biological-membranes
#10
Jakob P Ulmschneider, Martin B Ulmschneider
Ever since the first molecular mechanics computer simulations of biological molecules became possible, there has been the dream to study all complex biological phenomena in silico, simply bypassing the enormous experimental challenges and their associated costs. For this, two inherent requirements need to be met: First, the time scales achievable in simulations must reach up to the millisecond range and even longer. Second, the computational model must accurately reproduce what is measured experimentally. Despite some recent successes, the general consensus in the field to date has been that neither of these conditions have yet been met and that the dream will be realized, if at all, only in the distant future...
April 18, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29665140/review-functional-and-hybrid-imaging-of-bone-metastases
#11
Gary J R Cook, Vicky Goh
Bone metastases are common, cause significant morbidity and impact on healthcare resources. While radiographs, computed tomography (CT), magnetic resonance imaging (MRI) and bone scintigraphy have frequently been used for staging the skeleton, it is recognized that these methods are insensitive and non-specific for monitoring treatment response in a clinically relevant time frame. We summarize several recent reports on new functional and hybrid imaging methods including single photon emission CT / CT, positron emission tomography / CT and whole-body MRI with diffusion-weighted imaging...
April 17, 2018: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/29664953/combined-experimental-and-computational-characterization-of-crosslinked-collagen-based-hydrogels
#12
Clara Valero, Hippolyte Amaveda, Mario Mora, Jose Manuel García-Aznar
Collagen hydrogels are widely used for in-vitro experiments and tissue engineering applications. Their use has been extended due to their biocompatibility with cells and their capacity to mimic biological tissues; nevertheless their mechanical properties are not always optimal for these purposes. Hydrogels are formed by a network of polymer filaments embedded on an aqueous substrate and their mechanical properties are mainly defined by the filament network architecture and the individual filament properties...
2018: PloS One
https://www.readbyqxmd.com/read/29664602/engineering-persistent-luminescence-nanoparticles-for-biological-applications-from-biosensing-bioimaging-to-theranostics
#13
Shao-Kai Sun, He-Fang Wang, Xiu-Ping Yan
Persistent luminescence nanoparticles (PLNPs) are unique optical materials emitting long-lasting luminescence after ceasing excitation. Such a unique optical feature allows luminescence detection without constant external illumination to avoid the interferences of autofluorescence and scattering light from biological fluids and tissues. Besides, near-infrared (NIR) PLNPs have advantages of deep penetration and the reactivation of the persistent luminescence (PL) by red or NIR light. These features make the application of NIR-emitting PLNPs in long-term bioimaging no longer limited by the lifetime of PL...
April 17, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29664161/affinity-driven-covalent-modulator-of-glyceraldehyde-3-phosphate-dehydrogenase-gapdh-cascade
#14
Jeffy Chern, Chun-Ping Lu, Zhanxiong Fang, Ching-Ming Chang, Kuo-Feng Hua, Yi-Ting Chen, Cheng Yang Ng, Yi-Lin Sophia Chen, Yulin Lam, Shih-Hsiung Wu
Traditional medicines provide a fertile ground to explore potent lead compounds; yet, their transformation into modern drugs is fraught with challenges in deciphering the target that is mechanistically valid for its biological activity. Herein we revealed Z-(+)-isochaihulactone 1 exhibited significant inhibition against MDR cancer cell lines and mice xenografts. By NMR spectroscopy, 1 was shown to resist to an off-targeting thiolate, thus giving 1 a target covalent inhibitor-like (TCI) property. By identifying the pharmacophore of 1 (α,β-unsaturated moiety), a 1-derived probe was designed and synthesized for TCI-oriented activity-based proteome profiling (TCI-ABPP)...
April 17, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29663856/computational-insights-into-the-interaction-of-small-molecule-inhibitors-with-hri-kinase-domain
#15
Sourabh Palrecha, Dushant Lakade, Abhijeet Kulkarni, Jayanta K Pal, Manali Joshi
The heme-regulated inhibitor (HRI) kinase regulates globin synthesis in a heme-dependent manner in reticulocytes and erythroid cells in bone marrow. Inhibitors of HRI have been proposed to lead to an increased amount of hemoglobin, benefitting anemia patients. A series of indeno[1,2-c]pyrazoles were discovered to be the first known in vitro inhibitors of HRI. However, the structural mechanism of inhibition is yet to be understood. The aim of this study was to unravel the binding mechanism of these inhibitors using molecular dynamic simulations and docking...
April 17, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29657302/mirnatools-advanced-training-using-the-mirna-web-of-knowledge
#16
Ewa Ł Stępień, Marina C Costa, Francisco J Enguita
Micro-RNAs (miRNAs) are small non-coding RNAs that act as negative regulators of the genomic output. Their intrinsic importance within cell biology and human disease is well known. Their mechanism of action based on the base pairing binding to their cognate targets have helped the development not only of many computer applications for the prediction of miRNA target recognition but also of specific applications for functional assessment and analysis. Learning about miRNA function requires practical training in the use of specific computer and web-based applications that are complementary to wet-lab studies...
February 16, 2018: Non-Coding RNA
https://www.readbyqxmd.com/read/29656897/in-silico-labeling-predicting-fluorescent-labels-in-unlabeled-images
#17
Eric M Christiansen, Samuel J Yang, D Michael Ando, Ashkan Javaherian, Gaia Skibinski, Scott Lipnick, Elliot Mount, Alison O'Neil, Kevan Shah, Alicia K Lee, Piyush Goyal, William Fedus, Ryan Poplin, Andre Esteva, Marc Berndl, Lee L Rubin, Philip Nelson, Steven Finkbeiner
Microscopy is a central method in life sciences. Many popular methods, such as antibody labeling, are used to add physical fluorescent labels to specific cellular constituents. However, these approaches have significant drawbacks, including inconsistency; limitations in the number of simultaneous labels because of spectral overlap; and necessary perturbations of the experiment, such as fixing the cells, to generate the measurement. Here, we show that a computational machine-learning approach, which we call "in silico labeling" (ISL), reliably predicts some fluorescent labels from transmitted-light images of unlabeled fixed or live biological samples...
April 9, 2018: Cell
https://www.readbyqxmd.com/read/29656236/advancing-systems-immunology-through-data-driven-statistical-analysis
#18
REVIEW
Linda E Fong, Andrés R Muñoz-Rojas, Kathryn Miller-Jensen
Systems biology provides an effective approach to decipher, predict, and ultimately manipulate the complex and inter-connected networks that regulate the immune system. Advances in high-throughput, multiplexed experimental techniques have increased the availability of proteomic and transcriptomic immunological datasets, and as a result, have also accelerated the development of new data-driven computational algorithms to extract biological insight from these data. This review highlights how data-driven statistical models have been used to characterize immune cell subsets and their functions, to map the signaling and intercellular networks that regulate immune responses, and to connect immune cell states to disease outcomes to generate hypotheses for novel therapeutic strategies...
April 12, 2018: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29650893/-towards-development-of-innovative-cancer-therapies-trans-omics-approach
#19
Reika Kawabata-Iwakawa, Masahiko Nishiyama
Comprehensive genomic and transcriptome analyses using next-generation sequencing(NGS)analysis has lead a discovery of a variety of novel driver gene mutations and new therapeutic targets for cancer patients, and has remarkably improved outcome of the patients through the development novel molecular targeting drugs. Even so, in so-called intractable or refractory cancers, those "druggable"alterations common to the diseases are rarely found due to the high diversity of the tumor. Furthermore, most of molecular target therapy is known to acquire the resistance to the drug by means of multiple factors such as up-regulation of the partially inhibited pathway, mutation of the target, activation of alternative pathways, histological translocation, and oncogene de-addiction...
March 2018: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/29650353/reprint-of-environmental-toxicology-and-omics-a-question-of-sex
#20
Xuefang Liang, April Feswick, Denina Simmons, Christopher J Martyniuk
Molecular initiating events and downstream transcriptional/proteomic responses provide valuable information for adverse outcome pathways, which can be used predict the effects of chemicals on physiological systems. There has been a paucity of research that addresses sex-specific expression profiling in toxicology and due to cost, time, and logistic considerations, sex as a variable has not been widely considered. In response to this deficiency, federal agencies in the United States, Canada, and Europe have highlighted the importance of including sex as a variable in scientific investigations...
April 10, 2018: Journal of Proteomics
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