Computational Models for Trapping Ebola Virus Using Engineered Bacteria

Synthetic biology-inspired cell engineering in diagnosis, treatment, and drug development

The fast-developing synthetic biology (SB) has provided many genetic tools to reprogram and engineer cells for improved performance, novel functions, and diverse applications. Such cell engineering resources can play a critical role in the research and development of novel therapeutics. However, there are certain limitations and challenges in applying genetically engineered cells in clinical practice. This literature review updates the recent advances in biomedical applications, including diagnosis, treatment, and drug development, of SB-inspired cell engineering. It describes technologies and relevant examples in a clinical and experimental setup that may significantly impact the biomedicine field. At last, this review concludes the results with future directions to optimize the performances of synthetic gene circuits to regulate the therapeutic activities of cell-based tools in specific diseases.

Molecular Communications in Viral Infections Research: Modeling, Experimental Data, and Future Directions

Hundreds of millions of people worldwide are affected by viral infections each year, and yet, several of them neither have vaccines nor effective treatment during and post-infection. This challenge has been highlighted by the COVID-19 pandemic, showing how viruses can quickly spread and impact society as a whole. Novel interdisciplinary techniques must emerge to provide forward-looking strategies to combat viral infections, as well as possible future pandemics. In the past decade, an interdisciplinary area involving bioengineering, nanotechnology and information and communication technology (ICT) has been developed, known as Molecular Communications. This new emerging area uses elements of classical communication systems to molecular signalling and communication found inside and outside biological systems, characterizing the signalling processes between cells and viruses. In this paper, we provide an extensive and detailed discussion on how molecular communications can be integrated into the viral infectious diseases research, and how possible treatment and vaccines can be developed considering molecules as information carriers. We provide a literature review on molecular communications models for viral infection (intra-body and extra-body), a deep analysis on their effects on immune response, how experimental can be used by the molecular communications community, as well as open issues and future directions.

An In Vivo Proposal of Cell Computing Inspired by Membrane Computing

Intractable problems are challenging and not uncommon in Computer Science. The computing generation we are living in forces us to look for an alternative way of computing, as current computers are facing limitations when dealing with complex problems and bigger input data. Physics and Biology offer great alternatives to solve these problems that traditional computers cannot. Models like Quantum Computing and cell computing are emerging as possible solutions to the current problems the conventional computers are facing. This proposal describes an in vivo framework inspired by membrane computing and based on alternative computational frameworks that have been proven to be theoretically correct such as chemical reaction series. The abilities of a cell as a computational unit make this proposal a starting point in the creation of feasible potential frameworks to enhance the performance of applications in different disciplines such as Biology, BioMedicine, Computer networks, and Social Sciences, by accelerating drastically the way information is processed by conventional architectures and possibly achieving results that presently are not possible due to the limitations of the current computing paradigm. This paper introduces an in vivo solution that uses the principles of membrane computing and it can produce non-deterministic outputs.

Quality and Capacity Analysis of Molecular Communications in Bacterial Synthetic Logic Circuits

Synthetic logic circuits have been proposed as potential solutions for theranostics of biotechnological problems. One proposed model is the engineering of bacteria cells to create logic gates, and the communication between the bacteria populations will enable the circuit operation. In this paper, we analyze the quality of bacteria-based synthetic logic circuit through molecular communications that represent communication along a bus between three gates. In the bacteria-based synthetic logic circuit, the system receives environmental signals as molecular inputs and will process this information through a cascade of synthetic logic gates and free diffusion channels. We analyze the performance of this circuit by evaluating its quality and its relationship to the channel capacity of the molecular communications links that interconnect the bacteria populations. Our results show the effect of the molecular environmental delay and molecular amplitude differences over both the channel capacity and circuit quality. Furthermore, based on these metrics, we also obtain an optimum region for the circuit operation resulting in an accuracy of 80% for specific conditions. These results show that the performance of synthetic biology circuits can be evaluated through molecular communications, and lays the groundwork for combined systems that can contribute to future biomedical and biotechnology applications.