Network modeling in systems biology

A key aim of current systems biology research is to understand biology at the system level, to systematically catalogue all molecules and their interactions within a living cell, rather than the characteristics of isolated parts of a cell or organism. Network modeling is characterized by viewing cells in terms of their underlying network structure at many different levels of detail is a cornerstone of systems biology. Two emerging methodologies in network modeling provide invaluable insights into biological systems: static large-scale biological network modeling and dynamic quantitative modeling. Static large-scale biological network modeling focuses on integrating, visualizing and topologically modeling To facilitate application of these methods in biological research and improve existing network modeling software, this work presents: i) OmicsViz and OmicsAnalyzer, software tools, dedicated to integrating and analyzing omics data sets in network context. ii) CytoModeler, software tool, dedicated to providing a bridge between static large-scale biological network modeling and dynamic quantitative modeling methods. It not only facilitates network design, model creation, and computational simulation but provides advanced visualization for simulation results. iii) Comparative network modeling application in the systems biology of the SM-SNARE protein regulation in exocytotic membrane fusion. This work presents applications of biological network modeling methods to understand regulation mechanisms in complex biological systems. all kinds of omics data sets which are produced by innovative high throughput screening biotechnologies. Dynamic quantitative modeling focuses on exploring dynamics of biological systems by applying computational simulation and mathematical modeling

Membrane protein production in Escherichia coli cell-free lysates

AbstractCell-free protein production has become a core technology in the rapidly spreading field of synthetic biology. In particular the synthesis of membrane proteins, highly problematic proteins in conventional cellular production systems, is an ideal application for cell-free expression. A large variety of artificial as well as natural environments for the optimal co-translational folding and stabilization of membrane proteins can rationally be designed. The high success rate of cell-free membrane protein production allows to focus on individually selected targets and to modulate their functional and structural properties with appropriate supplements. The efficiency and robustness of lysates from Escherichia coli strains allow a wide diversity of applications and we summarize current strategies for the successful production of high quality membrane protein samples

Systems biology of ion channels and transporters in tumor angiogenesis: An omics view

AbstractSolid tumors require the formation of new blood vessels to support their growth, invasiveness and metastatic potential. Tumor neovascularization is achieved by vasculogenesis from endothelial precursors and by sprouting angiogenesis from preexisting vessels. The complex sequence of events driving these processes, including endothelial activation, proliferation, migration and differentiation, is associated with fluxes of ions, water and other small molecules mediated by a great pool of ion channels and transporters (ICT). This ‘transportome’ is regulated by environmental factors as well as intracellular signaling molecules. In turn, ICT play a prominent role in the response to angiogenesis-related stimuli through canonical and ‘unconventional’ activities: indeed, there is an increasing recognition of the multifunctionality of several ion channels that could also be annotated as receptors, enzymes, scaffolding proteins, mechanical and chemical sensors.The investigation of ICT structure and function has been far from the experimental oncology for long time and these two domains converged only very recently. Furthermore, the systems biology viewpoint has not received much attention in the biology of cancer transportome. Modulating angiogenesis by interference with membrane transport has a great potential in cancer treatment and the application of an ‘omics’ logic will hopefully contribute to the overall advancement in the field.This review is an attempt to apply the systems biology approach to the analysis of ICT involved in tumor angiogenesis, with a particular focus on endothelial transportome diversity. This article is part of a Special Issue entitled: Membrane channels and transporters in cancers

A classroom deployment of a haptic system for learning cell biology

The use of haptic systems in the classroom for enhancing science education is an underexplored area. In the education literature, it has been reported that certain concepts in science education are difficult for students to grasp and, as a result, misconceptions can be formed in the students' knowledge. We conducted a study with 62 Year 8 (typically 12-13 years old) students who used a haptic application to study cell biology, specifically the concept of diffusion across a cell membrane. The preliminary analysis of the feedback from the students suggests opportunities for haptic applications to enhance their learning, and also highlights a number of points to consider in the design of the application, including the choice of haptic interface and the design of the virtual environment

Development of a cell surface display system in Chlamydomonas reinhardtii

Cell-surface display systems are biotechnological techniques used to express heterologous proteins on the cell surface. Their application depends directly on the cell system used, as well as on the anchoring point for the surface displayed protein. To meet most application demands an inexpensive, safe, and scalable production platform, that reduces the economic barriers for large scale use is needed. Toward this goal, we screened three possible cell surface anchoring points in the green algae Chlamydomonas by fusing mVenus to prospective anchors moieties. The vectors harboring mVenus:anchor were screened for mVenus fluorescence and tested for cellular localization by confocal laser scanning microscopy. This strategy allowed the identification of two functional anchors, one for the cytoplasmic membrane using the MAW8 GPI-anchor signal, and one for the cell wall using the GP1 protein. We also exploited GP1 chemical and biological traits to release the fused proteins efficiently during cell wall shedding. Our work provides a foundation for surface engineering of C reinhardtii supporting both cell biology studies and biotechnology applications

Fabrication of perforated polymer membranes using imprinting technology

The goal of the present study was to fabricate perforated membrane structures in polymers with the pore diameter ranging from 10 ìm down to the sub ìm scale. The perforated membrane structure plays an important role in many biological systems. Thus the ability to reproduce such architecture will help with the study of biological systems by mimicking biological cell membrane-like structures and open new vistas in the study of transport behavior in cell biology and the separation of biological vesicles. Such structures also have potential uses as components in polymer optics and modular micro/nanofluidic devices. Use of polymer substrates is desirable due to the variety of materials and properties available, their biocompatibility and low manufacturing cost. In order to realize low cost production of the membrane structures, a single step imprinting process was employed, which was combined with a sacrificial layer technology and semiconductor micromachining processes. The stamps with micrometer-scale features were fabricated using photolithography on a resist-coated Si wafer, followed by deep reactive ion etching into substrate Si. Prior to imprinting, the stamp surface was treated with a fluorinated silane in the vapor phase in an in house chemical vapor deposition (CVD) chamber to improve the demolding process. SU-8 was used as an imprint resist and either poly(methyl-methacrylate) (PMMA), or a lift off resist (LOR) as a sacrificial layer. Optimal imprinting conditions for SU-8 imprinting were found at 135°C and 4 MPa. Demolding performed at (60 ± 5)°C showed minimal or no damage to both stamps and imprinted structures. UV curing of SU-8 lead to sufficient mechanical strength of the resist to enable it to form free standing membrane after lift-off of the sacrificial layer. In order to demonstrate the application of the perforated membrane structures, selective formation of lipid vesicles was demonstrated in SU-8 membranes by using Poly(L-Lysine)-poly(ethylene glycol) (PLL-PEG) to selectively pattern the membrane surface providing a nonspecific adsorption of the lipid vesicles in the non-porous areas. The pores showed formation of lipid bi-layer as confirmed by optical micrographs of the membrane surface showing faint traces of Trypan-blue dye used to the stain the lipid solution

Optogenetics : past, present and future

The term ‘optogenetics’ was introduced into the scientific literature less than a decade ago by Karl Deisseroth, developer of pioneering optogenetic techniques, who defined optogenetics as “the combination of genetic and optical methods to achieve gain or loss of function of well-defined events in specific cells of living tissue”. Since then this new field of biology has become a very exciting and rapidly developing area producing hundreds of scientific publications. New methods and tools have been developed and long-sought answers found in these new experimental systems. Discussion and full elaboration of every optogenetic approach and application are beyond the scope of this review, instead, it gives a short insight to (i) how light can be used to manipulate the membrane potential of various cells; (ii) how light-sensitive proteins can be used to regulate targeted gene expression, and (iii) how controlled release or spatio-temporal targeting of certain molecules can be modulated by light. Besides, the most widely used light-sensor proteins, including their structure, working mechanism and their involvement in existing optogenetic applications are also discussed

Computing with cells: membrane systems - some complexity issues.

Membrane computing is a branch of natural computing which abstracts computing models from the structure and the functioning of the living cell. The main ingredients of membrane systems, called P systems, are (i) the membrane structure, which consists of a hierarchical arrangements of membranes which delimit compartments where (ii) multisets of symbols, called objects, evolve according to (iii) sets of rules which are localised and associated with compartments. By using the rules in a nondeterministic/deterministic maximally parallel manner, transitions between the system configurations can be obtained. A sequence of transitions is a computation of how the system is evolving. Various ways of controlling the transfer of objects from one membrane to another and applying the rules, as well as possibilities to dissolve, divide or create membranes have been studied. Membrane systems have a great potential for implementing massively concurrent systems in an efficient way that would allow us to solve currently intractable problems once future biotechnology gives way to a practical bio-realization. In this paper we survey some interesting and fundamental complexity issues such as universality vs. nonuniversality, determinism vs. nondeterminism, membrane and alphabet size hierarchies, characterizations of context-sensitive languages and other language classes and various notions of parallelism

Yeast Two-Hybrid, a Powerful Tool for Systems Biology

A key property of complex biological systems is the presence of interaction networks formed by its different components, primarily proteins. These are crucial for all levels of cellular function, including architecture, metabolism and signalling, as well as the availability of cellular energy. Very stable, but also rather transient and dynamic protein-protein interactions generate new system properties at the level of multiprotein complexes, cellular compartments or the entire cell. Thus, interactomics is expected to largely contribute to emerging fields like systems biology or systems bioenergetics. The more recent technological development of high-throughput methods for interactomics research will dramatically increase our knowledge of protein interaction networks. The two most frequently used methods are yeast two-hybrid (Y2H) screening, a well established genetic in vivo approach, and affinity purification of complexes followed by mass spectrometry analysis, an emerging biochemical in vitro technique. So far, a majority of published interactions have been detected using an Y2H screen. However, with the massive application of this method, also some limitations have become apparent. This review provides an overview on available yeast two-hybrid methods, in particular focusing on more recent approaches. These allow detection of protein interactions in their native environment, as e.g. in the cytosol or bound to a membrane, by using cytosolic signalling cascades or split protein constructs. Strengths and weaknesses of these genetic methods are discussed and some guidelines for verification of detected protein-protein interactions are provided