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Integrative Biology: Quantitative Biosciences From Nano to Macro

Kevin A Janes, Preethi L Chandran, Roseanne M Ford, Matthew J Lazzara, Jason A Papin, Shayn M Peirce, Jeffrey J Saucerman, Douglas A Lauffenburger
Measuring and modeling the integrated behavior of biomolecular-cellular networks is central to systems biology. Over several decades, systems biology has been shaped by quantitative biologists, physicists, mathematicians, and engineers in different ways. However, the basic and applied versions of systems biology are not typically distinguished, which blurs the separate aspirations of the field and its potential for real-world impact. Here, we articulate an engineering approach to systems biology, which applies educational philosophy, engineering design, and predictive models to solve contemporary problems in an age of biomedical Big Data...
June 7, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
Koji Sakai, Kenta Shimba, Kiyoshi Kotani, Yasuhiko Jimbo
Schwann cells (SCs) contribute to the regulation of axonal conduction in a myelin-dependent and -independent manner. However, due to the lack of investigative techniques that are able to record axonal conduction under conditions that control the proliferation of specific SC types, little is known about the extent to which myelinated SCs (mSCs) and unmyelinated SCs (umSCs) modulate axonal conduction. In this study, a microtunnel-electrode approach was applied to a neuron/SC co-culture technique. Rat dorsal root ganglion neurons and SCs were co-cultured in a microtunnel-electrode device, which enabled recording of the conduction delay in multiple axons passing through microtunnels...
June 5, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
Yuji Nashimoto, Tomoya Hayashi, Itsuki Kunita, Akiko Nakamasu, Yu-Suke Torisawa, Masamune Nakayama, Hisako Takigawa-Imamura, Hidetoshi Kotera, Koichi Nishiyama, Takashi Miura, Ryuji Yokokawa
Creating vascular networks in tissues is crucial for tissue engineering. Although recent studies have demonstrated the formation of vessel-like structures in a tissue model, long-term culture is still challenging due to the lack of active perfusion in vascular networks. Here, we present a method to create a three-dimensional cellular spheroid with a perfusable vascular network in a microfluidic device. By the definition of the cellular interaction between human lung fibroblasts (hLFs) in a spheroid and human umbilical vein endothelial cells (HUVECs) in microchannels, angiogenic sprouts were induced from microchannels toward the spheroid; the sprouts reached the vessel-like structures in a spheroid to form a continuous lumen...
May 31, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
Yves Dehouck, Ugo Bastolla
Tikhonov regularization, or ridge regression, is a popular technique to deal with collinearity in multivariate regression. We unveil a formal analogy between ridge regression and statistical mechanics, where the objective function is comparable to a free energy, and the ridge parameter plays the role of temperature. This analogy suggests two novel criteria for selecting a suitable ridge parameter: specific-heat (Cv) and maximum penalty (MP). We apply these fits to evaluate the relative contributions of rigid-body and internal fluctuations, which are typically highly collinear, to crystallographic B-factors...
May 30, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
Yuanyuan Zhang, Jine Wang, Hui Cheng, Na Sun, Min Liu, Zhengyan Wu, Renjun Pei
The regulation of RNA interference (RNAi) could be a powerful method for the study of temporal and dose dependent effects of gene expression. In this study, we designed the hepatitis delta virus (HDV) ribozyme with an embedded theophylline aptamer as the sensor domain and the pri-miRNA of endogenous gene Bcl-2 as the effector domain to engineer an RNAi-regulatory device in MCF-7 cells. The system allowed us to control gene expression by adding theophylline into the culture media in a dose dependent fashion...
May 26, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
Daisuke Yoshino, Naoya Sakamoto, Masaaki Sato
High shear stress (SS) causes local changes around arterial bifurcations, which are common sites for cerebral aneurysms. High SS and SS spatial gradient (SSG) are thought to play important roles in the pathology of cerebral aneurysms. However, whether SS and SSG independently affect the function and morphology of vascular endothelial cells (ECs) exposed to fluid flow remains unclear. This study evaluated the morphology of ECs exposed to various SS and SSG combinations. Confluent ECs were exposed to a SS of 2-60 Pa and a uniform SSG of 0, 5, 10, or 15 Pa mm(-1) for 24 h...
May 26, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
Sophie Chagnon-Lessard, Hubert Jean-Ruel, Michel Godin, Andrew E Pelling
The strain-induced reorientation response of cyclically stretched cells has been well characterized in uniform strain fields. In the present study, we comprehensively analyse the behaviour of human fibroblasts subjected to a highly non-uniform strain field within a polymethylsiloxane microdevice. Our results indicate that the strain gradient amplitude and direction regulate cell reorientation through a coordinated gradient avoidance response. We provide critical evidence that strain gradient is a key physical cue that can guide cell organization...
May 23, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
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May 23, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
Kerryn Matthews, Simon P Duffy, Marie-Eve Myrand-Lapierre, Richard R Ang, Li Li, Mark D Scott, Hongshen Ma
Hemolytic anemia is one of the hallmarks of malaria and leads to an increase in oxidized heme (hemin) within the plasma of infected individuals. While scavenger proteins sequester much of the circulating heme, it has been hypothesized that extracellular heme may play a central role in malaria pathogenesis. We have previously developed the multiplex fluidic plunger (MFP) device for the measurement of red blood cell (RBC) deformability. Here, we demonstrate that the measurement of changes in RBC deformability is a sensitive method for inferring heme-induced oxidative stress...
May 19, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
Suyu Mei, Erik K Flemington, Kun Zhang
Recognition of indirect interactions is instrumental to in silico reconstruction of signaling pathways and sheds light on the exploration of unknown physical paths between two indirectly interacting genes. However, very limited computational methods have explicitly exploited the indirect interactions with experimental evidence thus far. In this work, we attempt to distinguish direct versus indirect interactions in human functional protein-protein interaction (PPI) networks via a predictive l2-regularized logistic regression model built on the experimental data...
May 19, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
Yuan Ma, Xin Han, Oscar Quintana Bustamante, Ricardo Bessa de Castro, Kai Zhang, Pengchao Zhang, Ying Li, Zongbin Liu, Xuewu Liu, Mauro Ferrari, Zhongbo Hu, José Carlos Segovia, Lidong Qin
Recently, the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 bacterial immunity system has opened a promising avenue to treat genetic diseases that affect the human hematopoietic stem cells (HSCs). Therefore, finding a highly efficient delivery method capable of modifying the genome in the hard-to-transfect HSCs, combined with the advanced CRISPR-Cas9 system, may meet the challenges for dissecting the hematologic disease mechanisms and facilitate future clinical applications. Here, we developed an effective HSC-specified delivery microfluidic chip to disrupt the cell membrane transiently by inducing rapid mechanical deformation that allowed the delivery of biomaterials into the cytoplasm from the surrounding matrix...
May 17, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
Manashjit Gogoi, Manish K Jaiswal, Haladhar Dev Sarma, Dhirendra Bahadur, Rinti Banerjee
Magnetic liposome-mediated combined chemotherapy and hyperthermia is gaining importance as an effective therapeutic modality for cancer. However, control and maintenance of optimum hyperthermia are major challenges in clinical settings due to the overheating of tissues. To overcome this problem, we developed a novel magnetic liposomes formulation co-entrapping a dextran coated biphasic suspension of La0.75Sr0.25MnO3 (LSMO) and iron oxide (Fe3O4) nanoparticles for self-controlled hyperthermia and chemotherapy...
May 17, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
Katherine E Schaberg, Venktesh S Shirure, Elizabeth A Worley, Steven C George, Kristen M Naegle
Overexpression of HER2, a receptor tyrosine kinase of the ERBB family, in breast cancer is related to increased cancer progression and aggressiveness. A breast epithelial cell model with the single perturbation of HER2 overexpression is capable of replicating the increased aggressiveness of HER2 overexpressing cancers. In previous work, Wolf-Yadlin and colleagues (Wolf-Yadlin et al., Mol. Syst. Biol., 2006, 2) measured the proximal tyrosine phosphorylation dynamics of the parental and HER2 overexpressing cells (24H) in response to EGF...
May 11, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
Kenichi Funamoto, Daisuke Yoshino, Kento Matsubara, Ioannis K Zervantonakis, Kiyoe Funamoto, Masafumi Nakayama, Jun Masamune, Yoshitaka Kimura, Roger D Kamm
Endothelial permeability has been extensively investigated in the context of pathologies such as cancer and also in studies of drug delivery from the circulation. Hypoxia is a critical regulator of endothelial cell (EC) behavior and affects the barrier function of endothelial linings, yet its role has been little studied. This paper reveals the effect of hypoxia on the permeability of an EC monolayer by cellular experiments using a microfluidic device and a conventional cell culture dish. Human umbilical vein endothelial cells (HUVECs) were seeded into one microfluidic channel, creating an EC monolayer on each vertical surface of a collagen gel confined to a central chamber...
May 10, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
Guangsheng Pei, Xiangfeng Niu, Yuqing Zhou, Lei Chen, Weiwen Zhang
Unicellular model cyanobacterium Synechocystis sp. PCC 6803 has received considerable attention as a sustainable energy resource because of its photosynthetic machinery. However, two-component signal transduction systems (TCSTSs) in regulating central carbohydrate and energy metabolism of cyanobacteria are still poorly understood due to their diversity and functional complication. In this study, by comparing the growth of knockout mutants of 44 response regulators (RRs) of TCSTSs in Synechocystis, several RR mutants demonstrating differential growth patterns were identified under auto- or photomixotrophic conditions...
May 22, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
Naifu Jin, Dayi Zhang, Francis L Martin
There is an increasing need to investigate microbiomes in their entirety in a variety of contexts ranging from environmental to human health scenarios. This requirement is becoming increasingly important with the emergence of antibiotic resistance. In general, more conventional approaches are too expensive and/or time-consuming and often predicated on prior knowledge of the microorganisms one wishes to study. Herein, we propose the use of biospectroscopy tools as relatively high-throughput, non-destructive approaches to profile microbiomes under study...
May 22, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
Jared C Weddell, Princess I Imoukhuede
Recently, intracellular receptor signaling has been identified as a key component mediating cell responses for various receptor tyrosine kinases (RTKs). However, the extent each endocytic compartment (endocytic vesicle, early endosome, recycling endosome, late endosome, lysosome and nucleus) contributes to receptor signaling has not been quantified. Furthermore, our understanding of endocytosis and receptor signaling is complicated by cell- or receptor-specific endocytosis mechanisms. Therefore, towards understanding the differential endocytic compartment signaling roles, and identifying how to achieve signal transduction control for RTKs, we delineate how endocytosis regulates RTK signaling...
May 22, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
Heidi Haibei Hu, Huayun Deng, Shizhang Ling, Haiyan Sun, Terry Kenakin, Xinmiao Liang, Ye Fang
GPR35, a family A orphan G protein-coupled receptor, has been implicated in inflammatory, neurological, and cardiovascular diseases. However, not much is known about the signaling and functions of GPR35. We performed a label-free kinome short hairpin RNA screen and identified a putative signaling network of GPR35 in HT-29 cells, some of which was validated using gene expression, biochemical and cellular assays. The results showed that GPR35 induced hypoxia-inducible factor 1α, and was involved in synaptic transmission, sensory perception, the immune system, and morphogenetic processes...
May 22, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
R Joshi, J C Buchanan, H Tavana
Embryonic stem cells (ESCs), due to their intrinsic capability to generate somatic cells of all three germ layers, are potential sources of neural cells for cell replacement therapies. However, the empirical differentiation protocols and the lack of mechanistic understanding of the neural differentiation of ESCs have limited the utility of ESCs as a developmental model or as a cell source for neural cell populations for replacement therapies. Co-culturing ESCs with stromal cells is one of the extensively used methods to induce neural differentiation...
May 22, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
Urszula M Migas, Michelle K Quinn, Jennifer J McManus
The self-assembly of proteins has been widely studied in controlled in vitro conditions, and more recently in biological environments. The self-assembly of proteins in biology can be a feature of the pathogenesis of protein condensation disease, or can occur during normal physiological function, for example during the formation of intracellular non-membrane bound organelles. To determine the mechanisms for the assembly process fully, controlled in vitro experiments using purified protein solutions are often required...
May 22, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
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