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Computational cell biology

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https://www.readbyqxmd.com/read/28646471/decoding-early-myelopoiesis-from-dynamics-of-core-endogenous-network
#1
Hang Su, Gaowei Wang, Ruoshi Yuan, Junqiang Wang, Ying Tang, Ping Ao, Xiaomei Zhu
A decade ago mainstream molecular biologists regarded it impossible or biologically ill-motivated to understand the dynamics of complex biological phenomena, such as cancer genesis and progression, from a network perspective. Indeed, there are numerical difficulties even for those who were determined to explore along this direction. Undeterred, seven years ago a group of Chinese scientists started a program aiming to obtain quantitative connections between tumors and network dynamics. Many interesting results have been obtained...
May 29, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28643868/the-potassium-battery-a-mobile-energy-source-for-transport-processes-in-plant-vascular-tissues
#2
REVIEW
Ingo Dreyer, Judith Lucia Gomez-Porras, Janin Riedelsberger
Contents I. II. III. IV. V. VI. VII. VIII. References SUMMARY: Plant roots absorb potassium ions from the soil and transport them in the xylem via the transpiration stream to the shoots. There, in source tissues where sufficient chemical energy (ATP) is available, K(+) is loaded into the phloem and then transported with the phloem stream to other parts of the plant; in part, transport is also back to the roots. This, at first sight, futile cycling of K(+) has been uncovered to be part of a sophisticated mechanism that (1) enables the shoot to communicate its nutrient demand to the root, (2) contributes to the K(+) nutrition of transport phloem tissues and (3) transports energy stored in the K(+) gradient between phloem cytosol and the apoplast...
June 23, 2017: New Phytologist
https://www.readbyqxmd.com/read/28640862/a-biosystems-approach-to-identify-the-molecular-signaling-mechanisms-of-tmem30a-during-tumor-migration
#3
Jiao Wang, Qian Wang, Dongfang Lu, Fangfang Zhou, Dong Wang, Ruili Feng, Kai Wang, Robert Molday, Jiang Xie, Tieqiao Wen
Understanding the molecular mechanisms underlying cell migration, which plays an important role in tumor growth and progression, is critical for the development of novel tumor therapeutics. Overexpression of transmembrane protein 30A (TMEM30A) has been shown to initiate tumor cell migration, however, the molecular mechanisms through which this takes place have not yet been reported. Thus, we propose the integration of computational and experimental approaches by first predicting potential signaling networks regulated by TMEM30A using a) computational biology methods, b) our previous mass spectrometry results of the TMEM30A complex in mouse tissue, and c) a number of migration-related genes manually collected from the literature, and subsequently performing molecular biology experiments including the in vitro scratch assay and real-time quantitative polymerase chain reaction (qPCR) to validate the reliability of the predicted network...
2017: PloS One
https://www.readbyqxmd.com/read/28640810/lassim-a-network-inference-toolbox-for-genome-wide-mechanistic-modeling
#4
Rasmus Magnusson, Guido Pio Mariotti, Mattias Köpsén, William Lövfors, Danuta R Gawel, Rebecka Jörnsten, Jörg Linde, Torbjörn Nordling, Elin Nyman, Sylvie Schulze, Colm E Nestor, Huan Zhang, Gunnar Cedersund, Mikael Benson, Andreas Tjärnberg, Mika Gustafsson
Recent technological advancements have made time-resolved, quantitative, multi-omics data available for many model systems, which could be integrated for systems pharmacokinetic use. Here, we present large-scale simulation modeling (LASSIM), which is a novel mathematical tool for performing large-scale inference using mechanistically defined ordinary differential equations (ODE) for gene regulatory networks (GRNs). LASSIM integrates structural knowledge about regulatory interactions and non-linear equations with multiple steady state and dynamic response expression datasets...
June 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28640080/immature-enteric-ganglion-cells-were-observed-in-a-13-year-old-colon-signet-ring-cell-carcinoma-patient-a-case-report-and-literature-review
#5
Huili Li, Kun Huang, Hui Wang, Lin Wang, Ming Yang, Lixia Wang, Rong Lin, Hongli Liu, Jinbo Gao, Xiaoming Shuai, Xinghua Liu, Kaixiong Tao, Guobin Wang, Zheng Wang
RATIONALE: All the enteric ganglion cells are fully mature by 2 to 5 years of age in human. No one had reported the presentation of immature enteric ganglion cells in elder ones. Colorectal carcinoma is also rare in the adolescent population. The coincidence of these 2 rare events in a 13-year-old boy has never been reported elsewhere, which may suggest some linkage between them. PATIENT CONCERN: A 13-year-old boy presented with progressive abdominal pain and melena for 3 months...
June 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28639943/bioprintable-form-of-chitosan-hydrogel-for-bone-tissue-engineering
#6
T Tolga Demirtas, Gülseren Irmak, Menemse Gumusderelioglu
Bioprinting can be defined as the 3D patterning of living cells and other biologics by using a computer-aided layer-by-layer deposition approach. Presence of cells within the ink to usage of a "bio-ink" presents the potential to print of living tissues and organ analogs that can be implanted into damaged/diseased tissue to promote highly controlled cell-based regeneration. In this study, it was shown for the first time that chitosan solution and its composite with nanostructured bone-like hydroxyapatite (HA) can be mixed with cells and printed successfully...
June 22, 2017: Biofabrication
https://www.readbyqxmd.com/read/28638442/computational-dynamic-approaches-for-temporal-omics-data-with-applications-to-systems-medicine
#7
REVIEW
Yulan Liang, Arpad Kelemen
Modeling and predicting biological dynamic systems and simultaneously estimating the kinetic structural and functional parameters are extremely important in systems and computational biology. This is key for understanding the complexity of the human health, drug response, disease susceptibility and pathogenesis for systems medicine. Temporal omics data used to measure the dynamic biological systems are essentials to discover complex biological interactions and clinical mechanism and causations. However, the delineation of the possible associations and causalities of genes, proteins, metabolites, cells and other biological entities from high throughput time course omics data is challenging for which conventional experimental techniques are not suited in the big omics era...
2017: BioData Mining
https://www.readbyqxmd.com/read/28637405/molecular-dynamics-simulations-challenges-and-opportunities-a-biologist-s-prospective
#8
Indu Kumari, Padmani Sandhu, Mushtaq Ahmed, Yusuf Akhter
Molecular dynamics (MD) is a computational technique which is used to study biomolecules in virtual environment. Each of the constituent atoms represents a particle and hence the biomolecule embodies a multi-particle mechanical system analyzed within a simulation box during MD analysis. The potential energies of the atoms are explained by a mathematical expression consisting of different forces and space parameters. There are various software and force fields that have been developed for MD studies of the biomolecules...
June 21, 2017: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/28636349/water-dynamics-from-the-surface-to-the-interior-of-a-supramolecular-nanostructure
#9
Julia H Ortony, Baofu Qiao, Christina J Newcomb, Timothy J Keller, Liam C Palmer, Elad Deiss-Yehiely, Monica Olvera de la Cruz, Songi Han, Samuel I Stupp
Water within and surrounding the structure of a biological system adopts context-specific dynamics that mediate virtually all of the events involved in the inner workings of a cell. These events range from protein folding and molecular recognition to the formation of hierarchical structures. Water dynamics are mediated by the chemistry and geometry of interfaces where water and biomolecules meet. Here we investigate experimentally and computationally the translational dynamics of vicinal water molecules within the volume of a supramolecular peptide nanofiber measuring 6...
June 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28634040/1-2-4-triazole-and-1-3-4-oxadiazole-analogues-synthesis-mo-studies-in-silico-molecular-docking-studies-antimalarial-as-dhfr-inhibitor-and-antimicrobial-activities
#10
Sampark S Thakkar, Parth Thakor, Hiren Doshi, Arabinda Ray
1,2,4-Triazole and 1,3,4-oxadiazole analogues are of interest due to their potential activity against microbial and malarial infections. In search of suitable antimicrobial and antimalarial compounds, we report here the synthesis, characterization and biological activities of 1,2,4-triazole and 1,3,4-oxadiazole analogues (SS 1-SS 10). The molecules were characterized by IR, mass, (1)H NMR, (13)C NMR and elemental analysis. The in vitro antimicrobial activity was investigated against pathogenic strains, the results were explained with the help of DFT and PM6 molecular orbital calculations...
May 27, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28632415/synthesis-and-biological-evaluation-of-tanshinone-iia-derivatives-as-novel-endothelial-protective-agents
#11
Xiaoling Bi, Kuojun Zhang, Long He, Biao Gao, Qinlan Gu, Xueyan Li, Jun Chen, Jinxin Wang
AIM: Oxidative stress-induced endothelial injury is a main risk factor in the pathogenesis of cardiovascular diseases. Tanshinone IIA (Tan IIA) exerts protective functions on endothelial cells in response to oxidative stress. To exploit new bioactive compounds from this natural product, 12 derivatives were first synthesized and evaluated for endothelial protective activities. MATERIALS & METHODS: Title compounds were prepared according to high-yielded synthetic routes, and their protective effects on human endothelial EA...
June 20, 2017: Future Medicinal Chemistry
https://www.readbyqxmd.com/read/28631574/microrna-125a-5p-plays-a-role-as-a-tumor-suppressor-in-lung-carcinoma-cells-by-directly-targeting-stat3
#12
Lou Zhong, Siyuan Sun, Jiahai Shi, Fei Cao, Xiao Han, Zhong Chen
Increasing evidence supports that the dysregulation of microRNA expression plays an important role in the process of tumor occurrence and development. Studies have found that mir-125a-5p expression was downregulated in a variety of tumors, but the effects and mechanism of mir-125a-5p in lung cancer are still unclear. The aim of this study is to detect the expression of mir-125a-5p in lung cancer tissues and lung cancer cell lines and to explore the effects of mir-125a-5p on the biological characteristics of lung cancer cells; thus, this study aims to provide new methods and new strategies for the treatment of lung cancer...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28631251/regulation-of-cardiac-myocyte-cell-death-and-differentiation-by-myocardin
#13
REVIEW
Joseph W Gordon
Myocardin is a cardiac- and smooth muscle-enriched transcriptional co-activator that was originally described as an interacting partner of the serum response factor. Shortly after myocardin's discovery, a wealth of published literature described the role of myocardin as a regulator of smooth muscle differentiation and phenotype modulation, while gene-targeting studies confirmed the essential role of myocardin in vascular development. More recently, myocardin has been implicated as an important regulator of cardiac myocyte differentiation in studies demonstrating direct programming of fibroblasts towards the cardiac lineage...
June 19, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28629368/identification-and-characterization-of-long-intergenic-noncoding-rnas-in-bovine-mammary-glands
#14
Chao Tong, Qiaoling Chen, Lili Zhao, Junfei Ma, Eveline M Ibeagha-Awemu, Xin Zhao
BACKGROUND: Mammary glands of dairy cattle produce milk for the newborn offspring and for human consumption. Long intergenic noncoding RNAs (lincRNAs) play various functions in eukaryotic cells. However, types and roles of lincRNAs in bovine mammary glands are still poorly understood. RESULTS: Using computational methods, 886 unknown intergenic transcripts (UITs) were identified from five RNA-seq datasets from bovine mammary glands. Their non-coding potentials were predicted by using the combination of four software programs (CPAT, CNCI, CPC and hmmscan), with 184 lincRNAs identified...
June 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28628118/oncoppi-informed-discovery-of-mitogen-activated-protein-kinase-kinase-3-as-a-novel-binding-partner-of-c-myc
#15
A A Ivanov, V Gonzalez-Pecchi, L F Khuri, Q Niu, Y Wang, Y Xu, Y Bai, X Mo, E V Prochownik, M A Johns, Y Du, F R Khuri, H Fu
Mitogen-activated protein kinase kinase 3 (MKK3) is a dual threonine/tyrosine protein kinase that regulates inflammation, proliferation and apoptosis through specific phosphorylation and activation of the p38 mitogen-activated protein kinase. However, the role of MKK3 beyond p38-signaling remains elusive. Recently, we reported a protein-protein interaction (PPI) network of cancer-associated genes, termed OncoPPi, as a resource for the scientific community to generate new biological models. Analysis of the OncoPPi connectivity identified MKK3 as one of the major hub proteins in the network...
June 19, 2017: Oncogene
https://www.readbyqxmd.com/read/28627761/biological-effects-of-hydrogen-peroxide-administered-intratumorally-with-or-without-irradiation-in-murine-tumors
#16
Taiki Takaoka, Yuta Shibamoto, Masayuki Matsuo, Chikao Sugie, Taro Murai, Yasutaka Ogawa, Akifumi Miyakawa, Yoshihiko Manabe, Takuhito Kondo, Koichiro Nakajima, Dai Okazaki, Takahiro Tsuchiya
Despite insufficient laboratory data, radiotherapy after intratumoral injection of hydrogen peroxide (H2 O2 ) is increasingly being used clinically for radioresistant tumors. Especially, this treatment might become an alternative definitive treatment for early and advanced breast cancer in patients who refuse any type of surgery. The purpose of this study was to investigate the biological effects and appropriate combination methods of irradiation and H2 O2 in vivo. SCCVII tumor cells transplanted into the legs of C3H/HeN mice were used...
June 19, 2017: Cancer Science
https://www.readbyqxmd.com/read/28623512/phosphatidylethanolamine-targeting-for-cell-death-imaging-in-early-treatment-response-evaluation-and-disease-diagnosis
#17
REVIEW
Filipe Elvas, Sigrid Stroobants, Leonie Wyffels
Phosphatidylethanolamine (PE) is one of the most abundant phospholipids in mammalian plasma membranes. In healthy cells, PE resides predominantly in the inner leaflet of the cell membrane. In dead or dying cells on the other hand, PE is externalized to the outer leaflet of the plasma membrane. The exposure of PE on the cell surface has therefore become an attractive target for the molecular imaging of cell death using single-photon emission computed tomography (SPECT) and positron emission tomography (PET)...
June 16, 2017: Apoptosis: An International Journal on Programmed Cell Death
https://www.readbyqxmd.com/read/28620761/medicinal-chemistry-of-%C3%AF-1-receptor-ligands-pharmacophore-models-synthesis-structure-affinity-relationships-and-pharmacological-applications
#18
Frauke Weber, Bernhard Wünsch
In the first part of this chapter, we summarize the various pharmacophore models for σ1 receptor ligands. Common to all of them is a basic amine flanked by two hydrophobic regions, representing the pharmacophoric elements. The development of computer-based models like the 3D homology model is described as well as the first crystal structure of the σ1 receptor. The second part focuses on the synthesis and biological properties of different σ1 receptor ligands, identified as 1-9. Monocyclic piperazines 1 and bicyclic piperazines 2 and 3 were developed as cytotoxic compounds, thus the IC50 values of cell growth and survival inhibition studies are given for all derivatives...
June 16, 2017: Handbook of Experimental Pharmacology
https://www.readbyqxmd.com/read/28620181/hair-bundles-of-cochlear-outer-hair-cells-are-shaped-to-minimize-their-fluid-dynamic-resistance
#19
Nikola Ciganović, Amanuel Wolde-Kidan, Tobias Reichenbach
The mammalian sense of hearing relies on two types of sensory cells: inner hair cells transmit the auditory stimulus to the brain, while outer hair cells mechanically modulate the stimulus through active feedback. Stimulation of a hair cell is mediated by displacements of its mechanosensitive hair bundle which protrudes from the apical surface of the cell into a narrow fluid-filled space between reticular lamina and tectorial membrane. While hair bundles of inner hair cells are of linear shape, those of outer hair cells exhibit a distinctive V-shape...
June 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28619968/breast-cancer-neoantigens-can-induce-cd8-t-cell-responses-and-antitumor-immunity
#20
Xiuli Zhang, Samuel Kim, Jasreet Hundal, John M Herndon, Shunqiang Li, Allegra A Petti, Savas D Soysal, Lijin Li, Michael D McLellan, Jeremy Hoog, Tina Primeau, Nancy Myers, Tammi L Vickery, Mark Sturmoski, Ian S Hagemann, Christopher A Miller, Matthew J Ellis, Elaine R Mardis, Ted Hansen, Timothy P Fleming, Peter Goedegebuure, William E Gillanders
Next-generation sequencing technologies have provided insights into the biology and mutational landscape of cancer. Here we evaluate the relevance of cancer neoantigens in human breast cancers. Using patient-derived xenografts from three patients with advanced breast cancer (xenografts were designated as WHIM30, WHIM35, and WHIM37), we sequenced exomes of tumor and patient-matched normal cells. We identified 2091 (WHIM30), 354 (WHIM35), and 235 (WHIM37) nonsynonymous somatic mutations. A computational analysis identified and prioritized HLA class I-restricted candidate neoantigens expressed in the dominant tumor clone...
June 15, 2017: Cancer Immunology Research
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