Milsee Mol

Immune signal transduction in leishmaniasis from natural to artificial systems: role of feedback loop insertion.

BACKGROUND Modulated immune signal (CD14-TLR and TNF) in leishmaniasis can be linked to EGFR pathway involved in wound healing, through crosstalk points. This signaling network can be further linked to a synthetic gene circuit acting as a positive feedback loop to elicit a synchronized intercellular communication among the immune cells which may contribute to a better understanding of signaling dynamics in leishmaniasis. METHODS Network reconstruction with positive feedback loop, simulation (ODE 15s solver) and sensitivity analysis of CD14-TLR, TNF and EGFR was done in SimBiology (MATLAB 7.11.1). Cytoscape and adjacency matrix were used to calculate network topology. PCA was extracted by using sensitivity coefficient in MATLAB. Model reduction was done using time, flux and sensitivity score. RESULTS Network has five crosstalk points: NIK, IκB-NFκB and MKK (4/7, 3/6, 1/2) which show high flux and sensitivity. PI3K in EGFR pathway shows high flux and sensitivity. PCA score was high for cytoplasmic ERK1/2, PI3K, Atk, STAT1/3 and nuclear JNK. Of the 125 parameters, 20% are crucial as deduced by model reduction. CONCLUSIONS EGFR can be linked to CD14-TLR and TNF through the MAPK crosstalk points. These pathways may be controlled through Ras and Raf that lie upstream of signaling components ERK ½ (c) and JNK (n) that have a high PCA score via a synthetic gene circuit for activating cell-cell communication to elicit an inflammatory response. Also a disease resolving effect may be achieved through PI3K in the EGFR pathway. GENERAL SIGNIFICANCE The reconstructed signaling network can be linked to a gene circuit with a positive feedback loop, for cell-cell communication resulting in synchronized response in the immune cell population, for disease resolving effect in leishmaniasis.

Synthetic circuit of inositol phosphorylceramide synthase in Leishmania: a chemical biology approach

Building circuits and studying their behavior in cells is a major goal of systems and synthetic biology. Synthetic biology enables the precise control of cellular states for systems studies, the discovery of novel parts, control strategies, and interactions for the design of robust synthetic systems. To the best of our knowledge, there are no literature reports for the synthetic circuit construction for protozoan parasites. This paper describes the construction of genetic circuit for the targeted enzyme inositol phosphorylceramide synthase belonging to the protozoan parasite Leishmania. To explore the dynamic nature of the circuit designed, simulation was done followed by circuit validation by qualitative and quantitative approaches. The genetic circuit designed for inositol phosphorylceramide synthase (Biomodels Database—MODEL1208030000) shows responsiveness, oscillatory and bistable behavior, together with intrinsic robustness.

Genome modularity and synthetic biology: Engineering systems

Whole genome sequencing projects running in various laboratories around the world has generated immense data. A systematic phylogenetic analysis of this data shows that genome complexity goes on decreasing as it evolves, due to its modular nature. This modularity can be harnessed to minimize the genome further to reduce it with the bare minimum essential genes. A reduced modular genome, can fuel progress in the area of synthetic biology by providing a ready to use plug and play chassis. Advances in gene editing technology such as the use of tailor made synthetic transcription factors will further enhance the availability of synthetic devices to be applied in the fields of environment, agriculture and health.

Nano-Synthetic Devices in Leishmaniasis: A Bioinformatics Approach.

Synthetic biology is an investigative and constructive means of understanding the complexities of biology. Substantial progress in the fields has resulted in the creation of synthetic gene circuits, which when uploaded into the appropriate nanoliposomal vehicle, can be used for a tunable response in a cell. These tunable elements can be applied to treat diseased condition for a transition to a healthy state. Though in its nascent stage of development synthetic biology is beginning to use its constructs to bring engineering approaches into biomedicine for treatment of infectious disease leishmaniasis.

Transcription Factor Target Gene Network governs the Logical Abstraction Analysis of the Synthetic Circuit in Leishmaniasis

With the advent of synthetic biology in medicine many synthetic or engineered proteins have made their way to therapeutics and diagnostics. In this paper, the downstream gene network of CD14-TNF-EGFR pathway in leishmaniasis, a tropical disease, is reconstructed. Network analysis showed that NFkB links the signaling and gene network, used as a point of intervention through a synthetic circuit embedded within the negative autoregulatory feedback loop. A chimeric protein kinase C (PKC) is incorporated in the synthetic circuit, under the transcriptional regulation of Lac repressor and IPTG, as an inducer. The chimeric PKC_ζα via IκKb phosphorylation activates NFκB, and modulates the gene expression from an anti-inflammatory to a pro-inflammatory phenotype in in vitro L. major infected macrophage model. This is the first ever report of a synthetic device construction in leishmania.

Systems-synthetic biology in understanding the complexities and simple devices in immunology

Systems and synthetic biology in the coming era has the ability to manipulate, stimulate and engineer cells to counteract the pathogenic immune response. The inherent biological complexities associated with the creation of a device allow capitalizing the biotechnological resources either by simply administering a recombinant cytokine or just reprogramming the immune cells. The strategy outlined, adopted and discussed may mark the beginning with promising therapeutics based on the principles of synthetic immunology.

Microbial Chassis Assisting Retrosynthesis

Synthetic biology has come a long way from constructing simple regulatory element to de novo pathway construction in heterologous host chassis. This is achieved by the transfer of the desired pathway from a rare organism to an organism that can be readily genetically engineered. These developments have great potential for application in biosynthesis of drugs, biofuels and bulk chemicals from simple and inexpensive starting material. As the complexity within a re-engineered system increases, there is an increasing need for efficient computational tools that can support them. Myriad of algorithms are available and are being developed that aid the re-engineering of pathways that help select and prioritize pathways, optimize enzyme performance, select parts for constructing the pathway, metabolic modelling and flux analysis and final integration into the chassis. This chapter gives a gist into the development of de novo pathway, the bioinformatics tools available, future challenges and research efforts needed for the implementation of synthetic biology for the production of key metabolites.

Computational Design of Biological Systems: From Systems to Synthetic Biology

Abstract: Today biology is overwhelmed with ‘big data’, amassed from genomic projects carried out in various laboratories around the world using efficient high throughput technologies. Biologists are co-opting mathematical and computational techniques developed to address these data and derive meaningful interpretations. These developments have led to new disciplines: systems and synthetic biology. To explore these two evolving branches of biology one needs to be familiar with technologies such as genomics, bioinformatics and proteomics, mathematical and computational modeling techniques that help predict the dynamic behavior of the biological system, ruling out the trial-and-error methods of traditional genetic engineering. Systems and synthetic biology have developed hand-in-hand towards building artificial biological devices using engineered biological units as basic building blocks. Systems biology is an integrated approach for studying the dynamic and complex behaviors of biological components, which may be difficult to interpret and predict from properties of individual constituents making up the biological systems. While, synthetic biology aims to engineer biologically inspired devices, such as cellular regulatory circuits that do not exist in nature but are designed using well characterized genes, proteins and other biological components in appropriate combinations to perform a desired function. This is analogous to an electronic circuit board design that is fabricated using well characterized electrical components such as resistors, capacitors and so on. The in silico abstractions and predictions should be tightly linked to experimentation to be proved in vitro and in vivo systems for their successful applications in biotechnology. This chapter focuses on mathematical approaches and computational tools available to engineer biological regulatory circuits and how they can be implemented as next generation therapeutics in infectious disease.