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Integrative Biology: Quantitative Biosciences From Nano to Macro

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https://www.readbyqxmd.com/read/29349465/exploring-candidate-biomarkers-for-lung-and-prostate-cancers-using-gene-expression-and-flux-variability-analysis
#1
Yazdan Asgari, Pegah Khosravi, Zahra Zabihinpour, Mahnaz Habibi
Genome-scale metabolic models have provided valuable resources for exploring changes in metabolism under normal and cancer conditions. However, metabolism itself is strongly linked to gene expression, so integration of gene expression data into metabolic models might improve the detection of genes involved in the control of tumor progression. Herein, we considered gene expression data as extra constraints to enhance the predictive powers of metabolic models. We reconstructed genome-scale metabolic models for lung and prostate, under normal and cancer conditions to detect the major genes associated with critical subsystems during tumor development...
January 19, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29340409/dynamics-of-3d-carcinoma-cell-invasion-into-aligned-collagen
#2
Arja Ray, Rachel K Morford, Nima Ghaderi, David J Odde, Paolo P Provenzano
Carcinoma cells frequently expand and invade from a confined lesion, or multicellular clusters, into and through the stroma on the path to metastasis, often with an efficiency dictated by the architecture and composition of the microenvironment. Specifically, in desmoplastic carcinomas such as those of the breast, aligned collagen tracks provide contact guidance cues for directed cancer cell invasion. Yet, the evolving dynamics of this process of invasion remains poorly understood, in part due to difficulties in continuously capturing both spatial and temporal heterogeneity and progression to invasion in experimental systems...
January 17, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29340399/landscape-of-gene-networks-for-random-parameter-perturbation
#3
Chunhe Li
Landscape approaches have been exploited to study the stochastic dynamics of gene networks. However, how to calculate the landscape with a wide range of parameter variations and how to investigate the influence of the network topology on the global properties of gene networks remain to be elucidated. Here, I developed an approach for the landscape of random parameter perturbation (LRPP) to address this issue. Based on a self-consistent approximation approach, by making perturbations to parameters in a given range, I obtained the landscape for gene network systems...
January 17, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29334399/chondrocyte-burst-promotes-space-for-mineral-expansion
#4
Emilio Satoshi Hara, Masahiro Okada, Noriyuki Nagaoka, Takako Hattori, Letycia Mary Iida, Takuo Kuboki, Takayoshi Nakano, Takuya Matsumoto
Analysis of tissue development from multidisciplinary approaches can result in more integrative biological findings, and can eventually allow the development of more effective bioengineering methods. In this study, we analyzed the initial steps of mineral formation during secondary ossification of mouse femur based on biological and bioengineering approaches. We first found that some chondrocytes burst near the mineralized area. External factors that could trigger chondrocyte burst were then investigated. Chondrocyte burst was shown to be modulated by mechanical and osmotic pressure...
January 15, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29333560/a-design-of-experiment-approach-for-efficient-multi-parametric-drug-testing-using-a-caenorhabditis-elegans-model
#5
M C Letizia, M Cornaglia, G Tranchida, R Trouillon, M A M Gijs
When studying the drug effectiveness towards a target model, one should distinguish the effects of the drug itself and of all the other factors that could influence the screening outcome. This comprehensive knowledge is crucial, especially when model organisms are used to study the drug effect at a systemic level, as a higher number of factors can influence the drug-testing outcome. Covering the entire experimental domain and studying the effect of the simultaneous change in several factors would require numerous experiments, which are costly and time-consuming...
January 15, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29327758/a-computational-analysis-of-pro-angiogenic-therapies-for-peripheral-artery-disease
#6
Lindsay E Clegg, Feilim Mac Gabhann
Inducing therapeutic angiogenesis to effectively form hierarchical, non-leaky networks of perfused vessels in tissue engineering applications and ischemic disease remains an unmet challenge, despite extensive research and multiple clinical trials. Here, we use a previously-developed, multi-scale, computational systems pharmacology model of human peripheral artery disease to screen a diverse array of promising pro-angiogenic strategies, including gene therapy, biomaterials, and antibodies. Our previously-validated model explicitly accounts for VEGF immobilization, Neuropilin-1 binding, and weak activation of VEGF receptor 2 (VEGFR2) by the "VEGFxxxb" isoforms...
January 12, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29296987/generic-maps-of-optimality-reveal-two-chemomechanical-coupling-regimes-for-motor-proteins-from-f1-atpase-and-kinesin-to-myosin-and-cytoplasmic-dynein
#7
Zhisong Wang
Many motor proteins achieve high efficiency for chemomechanical conversion, and single-molecule force-resisting experiments are a major tool to detect the chemomechanical coupling of efficient motors. Here, we introduce several quantitative relations that involve only parameters extracted from force-resisting experiments and offer new benchmarks beyond mere efficiency to judge the chemomechanical optimality or deficit of evolutionary remote motors on the same footing. The relations are verified by the experimental data from F1-ATPase, kinesin-1, myosin V and cytoplasmic dynein, which are representative members of four motor protein families...
January 3, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29234768/3d-printed-seed-planter-and-well-array-for-high-throughput-seed-germination-screening
#8
Hui Hui Chai, Yao Lu, Can Fang, Ya Dan Li, Yue Jun Kang, Chang Ming Li, Ling Yu
Seed germination is an important means of evaluating seed quality. In the present study, a well array for a seed germination experiment was designed and fabricated by 3D printing for the first time. Each hollow cone-shaped well can hold one seed, which not only prevented the seed from falling out of the well but also ensured that part of the seed was fully exposed to the sublayer of wet filter paper, allowing it to receive water for germination. Coupled with a 3D-printed seed planter, single seeds can be quickly placed into arrayed wells...
December 13, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29230464/do-protocells-preferentially-retain-macromolecular-solutes-upon-division-fragmentation-a-study-based-on-the-extrusion-of-popc-giant-vesicles
#9
Alessio Fanti, Leandro Gammuto, Fabio Mavelli, Pasquale Stano, Roberto Marangoni
A key process of protocell behaviour is their recursive growth and division. In order to be sustainable, the latter must be characterized by an even and homogeneous partition of the solute molecules initially present in the parent protocell among the daughter ones. Here we have investigated, by means of an artificial division model (extrusion of giant lipid vesicles) and confocal microscopy, the fate of solutes when a large vesicle fragments into many smaller vesicles. Solutes of low- and high-molecular weight such as pyranine, calcein, albumin-FITC, dextran-FITC and carbonic anhydrase have been employed...
December 12, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29188843/effect-of-suberoylanilide-hydroxamic-acid-saha-on-breast-cancer-cells-within-a-tumor-stroma-microfluidic-model
#10
N Peela, E S Barrientos, D Truong, G Mouneimne, M Nikkhah
Metastatic cancer is regarded as one of the largest contributors to disease-related deaths worldwide. Poor patient prognosis and treatment outcome is tied to the lack of efficacious anti-cancer therapies, which is due in part to the lack of physiologically relevant in vitro screening systems that can mimic the native tumor microenvironment. Conventional drug-screening platforms, which are often used in the pharmaceutical industry, are either two-dimensional (2D) assays or three-dimensional (3D) hydrogel-based matrices that lack precise control over cell distribution, matrix architecture, and organization...
November 30, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29186222/high-frequency-irreversible-electroporation-targets-resilient-tumor-initiating-cells-in-ovarian-cancer
#11
A Rolong, E M Schmelz, R V Davalos
We explored the use of irreversible electroporation (IRE) and high-frequency irreversible electroporation (H-FIRE) to induce cell death of tumor-initiating cells using a mouse ovarian surface epithelial (MOSE) cancer model. Tumor-initiating cells (TICs) can be successfully destroyed using pulsed electric field parameters common to irreversible electroporation protocols. Additionally, high-frequency pulses seem to induce cell death of TICs at significantly lower electric fields suggesting H-FIRE can be used to selectively target TICs and malignant late-stage cells while sparing the non-malignant cells in the surrounding tissue...
November 29, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29168874/bioreactor-model-of-neuromuscular-junction-with-electrical-stimulation-for-pharmacological-potency-testing
#12
Surapon N Charoensook, Damian J Williams, Syandan Chakraborty, Kam W Leong, Gordana Vunjak-Novakovic
In vitro models of the neuromuscular junction (NMJ) are emerging as a valuable tool to study synaptogenesis, synaptic maintenance, and pathogenesis of neurodegenerative diseases. Many models have previously been developed using a variety of cell sources for skeletal muscle and motoneurons. These models can advanced by integrating beneficial features of the native developmental milieu of the NMJ. We created a functional in vitro model of NMJ by bioreactor cultivation of transdifferentiated myocytes and stem cell-derived motoneurons, in the presence of electrical stimulation...
November 23, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29168871/probing-impaired-neurogenesis-in-human-brain-organoids-exposed-to-alcohol
#13
Yujuan Zhu, Li Wang, Fangchao Yin, Yue Yu, Yaqing Wang, Matthew J Shepard, Zhengping Zhuang, Jianhua Qin
The fetal brain is highly vulnerable to ethanol exposure, which can trigger various long-term neuronal disabilities and cognitive dysfunctions. However, a comprehensive understanding of fetal brain development under ethanol exposure is challenging due to the limitations of animal models. Here, we propose a human induced pluripotent stem cell (hiPSC)-based 3D brain organoid model, and explore the mechanisms underlying neural dysfunctions in prenatal alcohol exposure (PAE) in vitro. Brain organoids were examined to resemble brain organogenesis in vivo at early stages during gestation, with specific features of neuronal differentiation, brain regionalization, and cortical organization...
November 23, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29159332/a-biomaterial-screening-approach-reveals-microenvironmental-mechanisms-of-drug-resistance
#14
Alyssa D Schwartz, Lauren E Barney, Lauren E Jansen, Thuy V Nguyen, Christopher L Hall, Aaron S Meyer, Shelly R Peyton
Traditional drug screening methods lack features of the tumor microenvironment that contribute to resistance. Most studies examine cell response in a single biomaterial platform in depth, leaving a gap in understanding how extracellular signals such as stiffness, dimensionality, and cell-cell contacts act independently or are integrated within a cell to affect either drug sensitivity or resistance. This is critically important, as adaptive resistance is mediated, at least in part, by the extracellular matrix (ECM) of the tumor microenvironment...
November 21, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29138780/biological-network-border-detection
#15
Paulo E P Burke, Cesar H Comin, Filipi N Silva, Luciano da F Costa
Complex networks have been widely used to model biological systems. The concept of accessibility has been proposed recently as a means to organize the nodes of complex networks as belonging to its border or center. Such an approach paves the way to investigating how the functional and structural properties of nodes vary with their respective position in the networks. In this work, we approach such a problem in a biological context applying border detection to Protein-Protein Interaction networks from four organisms of the Mycoplasma genus...
November 15, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29120470/modulation-of-cellular-polarization-and-migration-by-ephrin-eph-signal-mediated-boundary-formation
#16
Sahar Javaherian, Elisa D'Arcangelo, Benjamin Slater, Camila Londono, Bin Xu, Alison P McGuigan
Compartment boundaries are essential for ensuring proper cell organization during embryo development and in adult tissues, yet the mechanisms underlying boundary establishment are not completely understood. A number of mechanisms, including (i) differential adhesion, (ii) differential tension, and (iii) cell signaling-mediated cell repulsion, are known to contribute and likely a context-dependent balance of each of these dictates boundary implementation. The ephrin/Eph signaling pathway is known to impact boundary formation in higher animals...
November 9, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29114690/effect-of-amino-acid-mutations-on-intra-dimer-tubulin-tubulin-binding-strength-of-microtubules
#17
Ning Liu, Ramana Pidaparti, Xianqiao Wang
Energetic interactions inside αβ-tubulin dimers of a microtubule (MT) with atomic resolutions are of importance in determining the mechanical properties and structural stability of the MT as well as designing self-assembled functional structures from it. Here, we carry out several comprehensive atomistic simulations to investigate the interaction properties within αβ-tubulin dimers and effect of residue mutations on the intra-dimer tubulin-tubulin (IDTT) binding strength. Results indicate that the force-displacement responses of the dimer could be roughly divided into three stages involving increasing, decreasing, and fluctuating forces...
November 8, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29109999/enhanced-directional-cell-migration-induced-by-vaccinia-virus-on-a-microfluidic-based-multi-shear-cell-migration-assay-platform
#18
Cheng Wang, Na Xu, Yu-Jun Yang, Qiu-Mei Wu, Dai-Wen Pang, Zhi-Ling Zhang
Virus-induced cell migration plays important roles in the direct and rapid spread of virus particles. As cell migration is also regulated by shear stress, it is necessary to explore the cell migration behavior influenced by multiple factors including a virus and shear stress. In this report, a three-layer microfluidic chip with symmetric channels was designed and fabricated to investigate vaccinia virus-induced cell migration in different shear stress environments. Regular "exclusion zones" without cell damage were formed by microvalves...
November 7, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29228066/front-cover
#19
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No abstract text is available yet for this article.
December 11, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29228065/back-cover
#20
(no author information available yet)
No abstract text is available yet for this article.
December 11, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
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