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Integrative Biology: Quantitative Biosciences From Nano to Macro

Mayank, Navneet Kaur, Narinder Singh
Mutations in the BRAF gene are well known for their oncogenic effects. Point mutations in V599 are particularly oncogenic and are considered important for therapeutic purposes. Along with wild type, other V599 mutated BRAF variants viz. V599E, V599D and V599R are reported and crystals of the former two with inhibitor (BAY43-9006) are further detailed. Both wild-type and mutated BRAF forms show similar interaction patterns with BAY43-9006, but the 599th residue did not show any involvement in the interactions...
September 19, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Ningwei Li, Tianfa Xie, Yubing Sun
Recently, researchers have been attempting to control pluripotent stem cell fate or generate self-organized tissues from stem cells. Advances in bioengineering enable generation of organotypic structures, which capture the cellular components, spatial cell organization and even some functions of tissues or organs in development. However, only a few engineering tools have been utilized to regulate the formation and organization of spatially complex tissues derived from stem cells. Here, we provide a review of recent progress in the culture of organotypic structures in vitro, focusing on how microengineering approaches including geometric confinement, extracellular matrix (ECM) property modulation, spatially controlled biochemical factors, and external forces, can be utilized to generate organotypic structures...
September 18, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Catarina Costa Moura, Stuart A Lanham, Tual Monfort, Konstantinos N Bourdakos, Rahul S Tare, Richard O C Oreffo, Sumeet Mahajan
The unique properties of skeletal stem cells have attracted significant attention in the development of strategies for skeletal regeneration. However, there remains a crucial unmet need to develop quantitative tools to elucidate skeletal cell development and monitor the formation of regenerated tissues using non-destructive techniques in 3D. Label-free methods such as coherent anti-Stokes Raman scattering (CARS), second harmonic generation (SHG) and two-photon excited auto-fluorescence (TPEAF) microscopy are minimally invasive, non-destructive, and present new powerful alternatives to conventional imaging techniques...
September 18, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Vivi Andasari, Dongyuan Lü, Maciej Swat, Shiliang Feng, Fabian Spill, Li Chen, Xiangdong Luo, Muhammad Zaman, Mian Long
It is widely agreed that keratinocyte migration plays a crucial role in wound re-epithelialization. Defects in this function contribute to wound reoccurrence causing significant clinical problems. Several in vitro studies have shown that the speed of migrating keratinocytes can be regulated by epidermal growth factor (EGF) which affects keratinocyte's integrin expression. The relationship between integrin expression (through cell-matrix adhesion) stimulated by EGF and keratinocyte migration speed is not linear since increased adhesion, due to increased integrin expression, has been experimentally shown to slow down cell migration due to the biphasic dependence of cell speed on adhesion...
September 12, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Dana Mackey, Eilís Kelly, Robert Nooney, Richard O'Kennedy
The orientation and activity of antibodies immobilized on solid surfaces are of direct relevance to many immunosensing applications. We therefore investigate a mathematical model which estimates the fraction of antibodies which are available for reaction in a randomly adsorbed sample. Numerical simulations are presented which highlight the separate effects of antibody orientation, accessibility and loss of binding ability on the amount of captured antigen. The assay response can then be expressed as a function of total antibody density and used for optimizing the surface coverage strategy under various conditions...
September 6, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Henrik S Thoke, Luis A Bagatolli, Lars F Olsen
Water is involved in all aspects of biological activity, both as a solvent and as a reactant. It is hypothesized that intracellular water is in a highly structured state due to the high concentrations of macromolecules in the cell and that this may change the activity of intracellular enzymes due to altered binding affinities and allosteric regulations. Here we first investigate the kinetics of two glycolytic enzymes in artificially crowded aqueous solutions and show that crowding does indeed change their kinetics...
September 3, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Y Onishi, Y Eshita, R-C Ji, T Kobayashi, M Onishi, M Mizuno, J Yoshida, N Kubota
A DEAE-dextran-MMA copolymer (DDMC)-paclitaxel (PTX) conjugate was prepared using PTX as the guest and DDMC as the host. The resistance of B16F10 melanoma cells to PTX was confirmed, while the DDMC-PTX conjugate showed excellent anticancer activity that followed the Hill equation. The robustness in the tumor microenvironment of the allosteric system was confirmed via BIBO stability. This feedback control system, explained via a transfer function, was very stable and showed the sustainability of the system via a loop, and it showed superior anti-cancer activity without drug resistance from cancer cells...
September 17, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Alexandra L Crampton, Katherine A Cummins, David K Wood
A critical role of vascular endothelium is as a semi-permeable barrier, dynamically regulating the flux of solutes between blood and the surrounding tissue. Existing platforms that quantify endothelial function in vitro are either significantly throughput limited or overlook physiologically relevant extracellular matrix (ECM) interactions and thus do not recapitulate in vivo function. Leveraging droplet microfluidics, we developed a scalable platform to measure endothelial function in nanoliter-volume, ECM-based microtissues...
September 17, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Ivan de Carlos Cáceres, Daniel A Porto, Ivan Gallotta, Pamela Santonicola, Josue Rodríguez-Cordero, Elia Di Schiavi, Hang Lu
Spinal muscular atrophy (SMA) is a degenerative disorder that selectively deteriorates motor neurons due to a deficiency of survival motor neuron protein (SMN). The illness is the leading genetic cause of death in infants and is difficult to study in complex biological systems such as humans. A simpler model system, such as the nematode C. elegans, can be used to study potential mechanisms underlying this disease; C. elegans expresses the smn-1 gene, a homologue of SMN; powerful genetic tools in C. elegans research can be used to discover novel genes whose effect on SMN remains unknown or uncharacterized...
September 17, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Laura Bernardi, Costanza Giampietro, Vita Marina, Martina Genta, Edoardo Mazza, Aldo Ferrari
Mature epithelial monolayers share the ability to coherently respond to external mechanical stimuli. Tissue remodeling requires cell shape changes and coordinated movements. Human endothelia provide an exquisite example of such emerging collective activities. As part of their function in maintaining body homeostasis under variable hemodynamic loadings, endothelial ensembles must dynamically adapt to wall shear stress and cyclic deformation. While the alignment of several types of cells, including fibroblasts, osteoblasts and epithelial tissues, in response to various flow conditions or wall shear stress levels has been described in detail, less is known about collective endothelial remodeling under pure wall deformation...
September 17, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Julian Michael Rocha, Charles Joseph Richardson, Mingxing Zhang, Caroline Maureen Darch, Eugene Cai, Andreas Diepold, Andreas Gahlmann
In bacterial type 3 secretion, substrate proteins are actively transported from the bacterial cytoplasm into the host cell cytoplasm by a large membrane-embedded machinery called the injectisome. Injectisomes transport secretion substrates in response to specific environmental signals, but the molecular details by which the cytosolic secretion substrates are selected and transported through the type 3 secretion pathway remain unclear. Secretion activity and substrate selectivity are thought to be controlled by a sorting platform consisting of the proteins SctK, SctQ, SctL, and SctN, which together localize to the cytoplasmic side of membrane-embedded injectisomes...
September 17, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Kathryn E Worley, Jennifer Rico-Varela, Dominic Ho, Leo Q Wan
Birth defects are a common occurrence in the United States and worldwide. Currently, evaluation of potential developmental toxicants (i.e., teratogens) relies heavily on animal-based models which do not always adequately mimic human development. In order to address this, researchers are developing in vitro human-based models which utilize human pluripotent stem cells (hPSCs) to assess the teratogenic potential of chemical substances. The field of human developmental toxicity assays includes a variety of platforms including monolayer, micropattern, embryoid body, and 3D organoid cultures...
September 17, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Premashis Manna, Sheng-Ting Hung, Srijit Mukherjee, Pia Friis, David M Simpson, Maria N Lo, Amy E Palmer, Ralph Jimenez
Green fluorescent proteins (GFP) and their blue, cyan and red counterparts offer unprecedented advantages as biological markers owing to their genetic encodability and straightforward expression in different organisms. Although significant advancements have been made towards engineering the key photo-physical properties of red fluorescent proteins (RFPs), they continue to perform sub-optimally relative to GFP variants. Advanced engineering strategies are needed for further evolution of RFPs in the pursuit of improving their photo-physics...
September 17, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Atsushi Saito, Tatsuya Terai, Kei Makino, Masayuki Takahashi, Sachiko Yoshie, Masateru Ikehata, Yasuhiko Jimbo, Keiji Wada, Yukihisa Suzuki, Satoshi Nakasono
Threshold values of neuronal stimulation and modulation associated with exposure to time-varying electromagnetic fields contribute to establishing human protection guidelines and standards. However, biological evidence of threshold values in the intermediate-frequency range is limited. Additionally, although it is known that dendrites, a type of unmyelinated neuronal fibre, play an important role in information processing in the central nervous system, the stimulus threshold in dendrites has not been sufficiently investigated...
August 1, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
Tingting Li, Yiming Dong, Xuanqi Zhang, Xiangyu Ji, Chunxiong Luo, Chunbo Lou, Haoqian M Zhang, Qi Ouyang
Synthetic biologists are dedicated to designing genetic systems from the bottom up to understand how living systems work. To date, a variety of genetic circuits exhibiting bistability have been designed, greatly expanding our understanding of the biological multistability in natural systems. However, the study of more complex forms of biological multistability using synthetic methods is still limited. In this report, we describe the engineering of a genetic circuit with regulatable multistability. A novel genetic toggle switch exhibiting inducible bistability and a self-activation circuit were individually designed and characterized, after which they were assembled to create a circuit that presents tristability...
August 1, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
E A Mazzochette, A L Nekimken, F Loizeau, J Whitworth, B Huynh, M B Goodman, B L Pruitt
Sensory neurons embedded in skin are responsible for the sense of touch. In humans and other mammals, touch sensation depends on thousands of diverse somatosensory neurons. By contrast, Caenorhabditis elegans nematodes have six gentle touch receptor neurons linked to simple behaviors. The classical touch assay uses an eyebrow hair to stimulate freely moving C. elegans, evoking evasive behavioral responses. This assay has led to the discovery of genes required for touch sensation, but does not provide control over stimulus strength or position...
August 1, 2018: 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...
August 1, 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...
July 16, 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...
July 16, 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...
July 16, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
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