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Integrative Biology: Quantitative Biosciences From Nano to Macro

Ismael Galván, Javier Cerezo, Alberto Jorge, Kazumasa Wakamatsu
Animal colouration is characterized by the concentration of pigments in integumentary structures and by the nanoscale arrangement of constitutive elements. However, the influence of molecular vibration on colour expression has been overlooked in biology. Molecular vibration occurs in the infrared spectral region, but vibrational and electronic properties can influence each other. Thus, the vibration of pigment molecules may also affect their absorption properties and the resulting colours. We calculated for the first time the relative contribution of molecular vibration (by means of Raman spectroscopy) and concentration (by means of HPLC) of melanin polymers, the most common animal pigments, to generate diversity in plumage colour in 47 species of birds...
June 28, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Kuihua Zhan, Lun Bai, Guangqian Wang, Baoqi Zuo, Liang Xie, Xinhong Wang
An in vivo experimental model based on implanting porous biomaterials to study angiogenesis was proposed. In the implanted porous polyvinyl alcohol, three major modes of angiogenesis, sprouting, intussusception and splitting, were found. By electron microscopy and three-dimensional simulation of the angiogenic vessels, we investigated the morphological characteristics of the three modes and paid special attention to the initial morphological difference between intussusception and splitting, and it was confirmed that the endothelial abluminal invagination and intraluminal protrusion are pre-representations of intussusception and splitting, respectively...
June 28, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Pauline Lefrançois, Bertrand Goudeau, Stéphane Arbault
Phospholipid Giant Unilamellar Vesicles (GUVs) are usually prepared by electroformation in water, that is in a low-conductivity solution. We developed a protocol allowing their electroformation in the most common physiological buffer, phosphate-buffered saline (PBS). This was achieved based on a specific sequence of increasing electrical fields and for the two usual electrode types for electroformation, namely Indium Tin oxide-coated glass slides and Pt electrodes. These GUVs are stable over time (hour time-scale) and they can be isolated or micro-injected...
June 26, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
M D Wiens, F Hoffmann, Y Chen, R E Campbell
Improving fluorescent proteins through the use of directed evolution requires robust techniques for screening large libraries of genetic variants. Here we describe an effective and relatively low-cost system for screening libraries of fluorescent protein variants for improved photostability in the context of colonies on a Petri dish. Application of this system to the yellow fluorescent protein mCitrine, led to the development of Citrine2 with improved photostability and similar high fluorescent brightness. The photobleaching robot was constructed using a Lego Mindstorms Ev3 set and a xenon arc lamp, which together create even and high irradiance over an entire Petri dish through patterned illumination...
June 13, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Yanan You, Raquel Cuevas-Diaz Duran, Lihua Jiang, Xiaomin Dong, Shan Zong, Michael Snyder, Jia Qian Wu
Systematic study of the regulatory mechanisms of Hematopoietic Stem Cell and Progenitor Cell (HSPC) self-renewal is fundamentally important for understanding hematopoiesis and for manipulating HSPCs for therapeutic purposes. Previously, we have characterized gene expression and identified important transcription factors (TFs) regulating the switch between self-renewal and differentiation in a multipotent Hematopoietic Progenitor Cell (HPC) line, EML (Erythroid, Myeloid, and Lymphoid) cells. Herein, we report binding maps for additional TFs (SOX4 and STAT3) by using chromatin immunoprecipitation (ChIP)-Sequencing, to address the underlying mechanisms regulating self-renewal properties of lineage-CD34+ subpopulation (Lin-CD34+ EML cells)...
June 12, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Yasmin Z Paterson, David Shorthouse, Markus W Pleijzier, Nir Piterman, Claus Bendtsen, Benjamin A Hall, Jasmin Fisher
In an age where the volume of data regarding biological systems exceeds our ability to analyse it, many researchers are looking towards systems biology and computational modelling to help unravel the complexities of gene and protein regulatory networks. In particular, the use of discrete modelling allows generation of signalling networks in the absence of full quantitative descriptions of systems, which are necessary for ordinary differential equation (ODE) models. In order to make such techniques more accessible to mainstream researchers, tools such as the BioModelAnalyzer (BMA) have been developed to provide a user-friendly graphical interface for discrete modelling of biological systems...
June 18, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Yanan Xu, Jiumei Hu, Qiangyuan Zhu, Qi Song, Ying Mu
Cancer stem-like cells (CSCs) displaying the properties of normal stem cells have become the main culprit associated with cancer transportation and recurrence. As of now, various CSC functions and marker genes have been identified due to the heterogeneity of cancer, such as aldehyde dehydrogenase (ALDH), the second member of the ABC transporter G-subfamily (ABCG2), activated leukocyte cell adhesion molecule (ALCAM) and CD133. To investigate these markers, most conventional approaches are bulk-based strategies, which may veil the disparity of single cells' gene expression...
June 18, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Christopher Walter, Joshua T Davis, Jairaj Mathur, Amit Pathak
In fibrosis and cancer, degradation of basement membrane (BM) and cell invasion are considered as key outcomes of a cellular transformation called epithelial-mesenchymal transition (EMT). Here, we pose a converse question - can preexisting physical defects in the BM matrix cause EMT in normal epithelial cells? On a BM-mimicking matrix of collagen-IV-coated polyacrylamide (PA) gel, we have discovered a reverse phenomenon in which preexisting defects trigger EMT in normal epithelial cells. Through spatiotemporal measurements and simulations in silico, we demonstrate that the EMT precedes cellular mechanoactivation on defective matrices, but they occur concurrently on stiff matrices...
June 18, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Stefano Fornasaro, Annalisa Vicario, Luigina De Leo, Alois Bonifacio, Tarcisio Not, Valter Sergo
Raman hyperspectral imaging is an emerging practice in biological and biomedical research for label free analysis of tissues and cells. Using this method, both spatial distribution and spectral information of analyzed samples can be obtained. The current study reports the first Raman microspectroscopic characterisation of colon tissues from patients with Coeliac Disease (CD). The aim was to assess if Raman imaging coupled with hyperspectral multivariate image analysis is capable of detecting the alterations in the biochemical composition of intestinal tissues associated with CD...
June 18, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Eleonora Grespan, Giovanni G Giobbe, Florent Badique, Karine Anselme, Jürgen Rühe, Nicola Elvassore
Mechanical stimuli and geometrical constraints transmitted across the cytoskeleton to the nucleus affect the nuclear morphology and cell function. Human pluripotent stem cells (hPSCs) represent an effective tool for evaluating transitions in nuclear deformability from the pluripotent to differentiated stage, and for deciphering the underlying mechanisms. We report the first study that investigates the nuclear deformability induced by geometrical constraints of hPSCs both in the pluripotent stage and during early germ layer specification...
May 21, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Emmanuel Luján, Daniela Soto, María S Rosito, Alejandro Soba, Liliana N Guerra, Juan C Calvo, Guillermo Marshall, Cecilia Suárez
Mathematical modelling approaches have become increasingly abundant in cancer research. Tumour infiltration extent and its spatial organization depend both on the tumour type and stage and on the bio-physicochemical characteristics of the microenvironment. This sets a complex scenario that often requires a multidisciplinary and individually adjusted approach. The ultimate goal of this work is to present an experimental/numerical combined method for the development of a three-dimensional mathematical model with the ability to reproduce the growth and infiltration patterns of a given avascular microtumour in response to different microenvironmental conditions...
May 21, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Sreelatha Sarangapani, Ajeetkumar Patil, Yoke Keng Ngeow, Rosmin Elsa Mohan, Anand Asundi, Matthew J Lang
Targeting the oxidative stress response has recently emerged as a promising strategy for the development of therapeutic drugs for a broad spectrum of diseases. Supporting this strategy, we have reported that chitosan nanoparticles synthesized with a controlled size had selective cytotoxicity in leukemia cells through the mechanism related to reactive oxygen species (ROS) generation. Herein, we found that the cellular uptake of chitosan nanoparticles was enhanced in a time dependent manner and inhibited the cellular proliferation of leukemia cells in a dose dependent manner with elevation of the reactive oxygen species (ROS) showing a stronger effect on apoptosis, associated with the upregulation of caspase activity and the depletion of reduced glutathione...
May 21, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Masaya Hagiwara, Rina Nobata, Tomohiro Kawahara
Three-dimensional (3D) cell and tissue cultures more closely mimic biological environments than two-dimensional (2D) cultures and are therefore highly desirable in culture experiments. However, 3D cultures often fail to yield repeatable experimental results because of variation in the initial culture conditions, such as cell density and distribution in the extracellular matrix, and therefore reducing such variation is a paramount concern. Here, we present a 3D culture platform that demonstrates highly repeatable experimental results, obtained by controlling the initial cell cluster shape in the gel cube culture device...
May 21, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Bianca K Stöcker, Johannes Köster, Eli Zamir, Sven Rahmann
Protein interactions are fundamental building blocks of biochemical reaction systems underlying cellular functions. The complexity and functionality of these systems emerge not only from the protein interactions themselves but also from the dependencies between these interactions, as generated by allosteric effects or mutual exclusion due to steric hindrance. Therefore, formal models for integrating and utilizing information about interaction dependencies are of high interest. Here, we describe an approach for endowing protein networks with interaction dependencies using propositional logic, thereby obtaining constrained protein interaction networks ("constrained networks")...
May 21, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
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No abstract text is available yet for this article.
April 23, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Marie-Elena Brett, Heather E Bomberger, Geneva R Doak, Matthew A Price, James B McCarthy, David K Wood
Numerous studies have demonstrated the importance of altered hyaluronan metabolism to malignant progression of multiple tumor types, including breast carcinomas. Increased hyaluronan (HA) metabolism in the stroma of primary tumors promotes activation of oncogenic signaling pathways that impact tumor initiation, growth, and invasion. Carcinoma cell synthesis and assembly of HA-rich pericellular matrices induces a stromal-independent phenotype, which is associated with cancer progression. Although the pro-tumorigenic role of stromal HA is well established, a novel but unexplored hypothesis is that carcinoma cell-associated HA pericellular matrices promote metastasis of circulating tumor cells...
April 23, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Ding Li, Stacey D Finley
Multiple promoters and inhibitors mediate angiogenesis, the formation of new blood vessels, and these factors represent potential targets for impeding vessel growth in tumors. Vascular endothelial growth factor (VEGF) is a potent angiogenic factor targeted in anti-angiogenic cancer therapies. In addition, thrombospondin-1 (TSP1) is a major endogenous inhibitor of angiogenesis, and TSP1 mimetics are being developed as an alternative type of anti-angiogenic agent. The combination of bevacizumab, an anti-VEGF agent, and ABT-510, a TSP1 mimetic, has been tested in clinical trials to treat advanced solid tumors...
April 23, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Jessica E Kim, Daniel S Reynolds, Muhammad H Zaman, Michael Mak
Cellular processes, such as cell migration, adhesion, and proliferation depend on the interaction between the intracellular environment and the extracellular matrix (ECM). While many studies have explored the role of the microenvironment on cell behavior, the influence of 3D matrix mechanics on intracellular activity is not completely understood. To characterize the relationship between the mechanical components of the microenvironment and intracellular behavior, we use particle-tracking microrheology of metastatic breast cancer cells embedded in 3D collagen gels to quantify the intracellular activity from which the molecular motor activity and stiffness can be determined...
April 23, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Kendra D Nyberg, Samuel L Bruce, Angelyn V Nguyen, Clara K Chan, Navjot K Gill, Tae-Hyung Kim, Erica K Sloan, Amy C Rowat
The physical properties of cells are promising biomarkers for cancer diagnosis and prognosis. Here we determine the physical phenotypes that best distinguish human cancer cell lines, and their relationship to cell invasion. We use the high throughput, single-cell microfluidic method, quantitative deformability cytometry (q-DC), to measure six physical phenotypes including elastic modulus, cell fluidity, transit time, entry time, cell size, and maximum strain at rates of 102 cells per second. By training a k-nearest neighbor machine learning algorithm, we demonstrate that multiparameter analysis of physical phenotypes enhances the accuracy of classifying cancer cell lines compared to single parameters alone...
April 23, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Ning Kang, Quan Guo, Emel Islamzada, Hongshen Ma, Mark D Scott
Despite the critical importance of mechanical (rheological + extrudability) deformability in the vascular flow of lymphocytes, it has been poorly investigated due to the limitations of existing technological tools. Microfluidics analysis of leukocyte deformability offers significant advantages in that it offers high throughput, large sample population and the ability to analyze a heterogeneous population. These advantages are in stark contrast to previous approaches that focused on single cell measurements...
April 23, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
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