Models for Cell-Free Synthetic Biology: Make Prototyping Easier, Better, and Faster

Cell-free TX-TL is an increasingly mature and useful platform for prototyping, testing, and engineering biological parts and systems. However, to fully accomplish the promises of synthetic biology, mathematical models are required to facilitate the design and predict the behavior of biological components in cell-free extracts. We review here the latest models accounting for transcription, translation, competition, and depletion of resources as well as genome scale models for lysate-based cell-free TX-TL systems, including their current limitations. These models will have to find ways to account for batch-to-batch variability before being quantitatively predictive in cell-free lysate-based platforms

Noise-induced oscillatory shuttling of NF-{\kappa}B in a two compartment IKK-NF-{\kappa}B-I{\kappa}B-A20 signaling model

NF-{\kappa}B is a pleiotropic protein whose nucleo-cytoplasmic trafficking is tightly regulated by multiple negative feedback loops embedded in the NF-{\kappa}B signaling network and contributes to diverse gene expression profiles important in immune cell differentiation, cell apoptosis, and innate immunity. The intracellular signaling processes and their control mechanisms, however, are susceptible to both extrinsic and intrinsic noise. In this article, we present numerical evidence for a universal dynamic behavior of NF-{\kappa}B, namely oscillatory nucleo-cytoplasmic shuttling, due to the fundamentally stochastic nature of the NF-{\kappa}B signaling network. We simulated the effect of extrinsic noise with a deterministic ODE model, using a statistical ensemble approach, generating many copies of the signaling network with different kinetic rates sampled from a biologically feasible parameter space. We modeled the effect of intrinsic noise by simulating the same networks stochastically using the Gillespie algorithm. The results demonstrate that extrinsic noise diversifies the shuttling patterns of NF-{\kappa}B response, whereas intrinsic noise induces oscillatory behavior in many of the otherwise non-oscillatory patterns. We identify two key model parameters which significantly affect the NF-{\kappa}B dynamic response and deduce a two-dimensional phase-diagram of the NF-{\kappa}B response as a function of these parameters. We conclude that if single-cell experiments are performed, a rich variety of NF-{\kappa}B response will be observed, even if population-level experiments, which average response over large numbers of cells, do not evidence oscillatory behavior.Comment: 49 pages, 12 figure

A retrosynthetic biology approach to metabolic pathway design for therapeutic production

<p>Abstract</p> <p>Background</p> <p>Synthetic biology is used to develop cell factories for production of chemicals by constructively importing heterologous pathways into industrial microorganisms. In this work we present a retrosynthetic approach to the production of therapeutics with the goal of developing an <it>in situ </it>drug delivery device in host cells. Retrosynthesis, a concept originally proposed for synthetic chemistry, iteratively applies reversed chemical transformations (reversed enzyme-catalyzed reactions in the metabolic space) starting from a target product to reach precursors that are endogenous to the chassis. So far, a wider adoption of retrosynthesis into the manufacturing pipeline has been hindered by the complexity of enumerating all feasible biosynthetic pathways for a given compound.</p> <p>Results</p> <p>In our method, we efficiently address the complexity problem by coding substrates, products and reactions into molecular signatures. Metabolic maps are represented using hypergraphs and the complexity is controlled by varying the specificity of the molecular signature. Furthermore, our method enables candidate pathways to be ranked to determine which ones are best to engineer. The proposed ranking function can integrate data from different sources such as host compatibility for inserted genes, the estimation of steady-state fluxes from the genome-wide reconstruction of the organism's metabolism, or the estimation of metabolite toxicity from experimental assays. We use several machine-learning tools in order to estimate enzyme activity and reaction efficiency at each step of the identified pathways. Examples of production in bacteria and yeast for two antibiotics and for one antitumor agent, as well as for several essential metabolites are outlined.</p> <p>Conclusions</p> <p>We present here a unified framework that integrates diverse techniques involved in the design of heterologous biosynthetic pathways through a retrosynthetic approach in the reaction signature space. Our engineering methodology enables the flexible design of industrial microorganisms for the efficient on-demand production of chemical compounds with therapeutic applications.</p

Connecting Protein Structure and Dynamics on Biomaterials with the Foreign Body Response

The harsh environment of the foreign body response (FBR) has the potential to negatively impact the implantations of biomaterials in the body. The FBR is initiated by inflammatory cells that recognize the material as foreign through surface-adsorbed proteins. When proteins interact with surfaces, they can unfold and expose epitopes that may be recognized by immune cells and trigger a series of reactions. Importantly, the presentation of unfolded proteins is directly influenced by the highly dynamic and heterogeneous behavior of proteins in near-surface environments, as well as by the physicochemical features of the underlying surface. Such behavior is the result of transient unfolding and refolding, rapid exchange of folded and unfolded protein molecules between the surface and the bulk solution, intermittent interfacial diffusion, and protein-protein associations. While these interfacial processes are likely involved in the FBR, both their characterization and respective roles in the FBR have been ignored due to the lack of experimental techniques to directly observe individual molecular processes. The work presented here aims to address this lack of fundamental understanding by applying novel single-molecule (SM) methods, which are uniquely sensitive to interfacial dynamics as well as protein and surface heterogeneities, to investigate the mechanisms that lead to the FBR. Specifically, we focused on tuning surface functionalization to reveal the connection between material properties, protein adsorption and stabilization, and ultimately cell response. Total internal reflection fluorescence microscopy (TIRFM) was combined with Förster resonance energy transfer (FRET) to independently dissect individual molecular processes, such as adsorption, desorption, diffusion, folding, unfolding, and binding. The studies were performed using recombinant fibronectin (FN) as a model protein, which was site-specifically labeled to undergo FRET. First, the effect of poly(ethylene glycol) (PEG) grafting density on protein adsorption and stabilization was studied. Furthermore, mapping accumulated probe trajectories (MAPT) with an environmentally sensitive molecule was used as a tool to identify local changes in brush hydrophobicity. Secondly, in order to understand the connection between surface properties, FN conformation (ligand), and integrins (cell receptors), a three-color FRET method was developed to track both protein conformation and ligand-receptor binding as a function of surface chemistry. Finally, the extent to which the addition of a zwitterionic polymer (poly(sulfobetaine)) to PEG can improve the stability of FN was explored. Altogether, the results obtained from these studies will shed light on the rational design of materials to mediate cell signaling in physiological and synthetic environments

Integrated predictive genome-scale models to improve the metabolic re-engineering efficiency

One of the most common applications of metabolic circuits is to produce a desired chemical in a chassis organism, such as the Escherichia coli (E. coli), by importing heterologous genes encoding for the enzymes that participate in the biosynthetic pathway. Recently, an automated pipeline named RetroPath was developed to synthesise embedded metabolic circuits [1]. These circuits are to be embedded in E. coli for a wide range of applications such as regulating biomass productions, sensing specifc molecules, processing specific molecules, and releasing specific molecules. In this paper, we improve the efficiency of RetroPath via quadratic programming

Random forests with random projections of the output space for high dimensional multi-label classification

We adapt the idea of random projections applied to the output space, so as to enhance tree-based ensemble methods in the context of multi-label classification. We show how learning time complexity can be reduced without affecting computational complexity and accuracy of predictions. We also show that random output space projections may be used in order to reach different bias-variance tradeoffs, over a broad panel of benchmark problems, and that this may lead to improved accuracy while reducing significantly the computational burden of the learning stage

Sensitivity analysis of a computational model of the IKK-NF-{\kappa}B-I{\kappa}B{\alpha}-A20 signal transduction network

The NF-{\kappa}B signaling network plays an important role in many different compartments of the immune system during immune activation. Using a computational model of the NF-{\kappa}B signaling network involving two negative regulators, I{\kappa}B{\alpha} and A20, we performed sensitivity analyses with three different sampling methods and present a ranking of the kinetic rate variables by the strength of their influence on the NF-{\kappa}B signaling response. We also present a classification of temporal response profiles of nuclear NF-{\kappa}B concentration into six clusters, which can be regrouped to three biologically relevant clusters. Lastly, based upon the ranking, we constructed a reduced network of the IKK-NF-{\kappa}B-I{\kappa}B{\alpha}-A20 signal transduction.Comment: 32 pages, 8 figure

Shotgun protein sequencing.

A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins

3-D Structural Modeling of Humic Acids through Experimental Characterization, Computer Assisted Structure Elucidation and Atomistic Simulations. 1. Chelsea Soil Humic Acid

This paper describes an integrated experimental and computational framework for developing 3-D structural models for humic acids (HAs). This approach combines experimental characterization, computer assisted structure elucidation (CASE), and atomistic simulations to generate all 3-D structural models or a representative sample of these models consistent with the analytical data and bulk thermodynamic/structural properties of HAs. To illustrate this methodology, structural data derived from elemental analysis, diffuse reflectance FT-IR spectroscopy, 1-D/2-D ^1H and ^(13)C solution NMR spectroscopy, and electrospray ionization quadrupole time-of-flight mass spectrometry (ESI QqTOF MS) are employed as input to the CASE program SIGNATURE to generate all 3-D structural models for Chelsea soil humic acid (HA). These models are subsequently used as starting 3-D structures to carry out constant temperature-constant pressure molecular dynamics simulations to estimate their bulk densities and Hildebrand solubility parameters. Surprisingly, only a few model isomers are found to exhibit molecular compositions and bulk thermodynamic properties consistent with the experimental data. The simulated ^(13)C NMR spectrum of an equimolar mixture of these model isomers compares favorably with the measured spectrum of Chelsea soil HA