From Microbial Communities to Distributed Computing Systems

A distributed biological system can be defined as a system whose components are located in different subpopulations, which communicate and coordinate their actions through interpopulation messages and interactions. We see that distributed systems are pervasive in nature, performing computation across all scales, from microbial communities to a flock of birds. We often observe that information processing within communities exhibits a complexity far greater than any single organism. Synthetic biology is an area of research which aims to design and build synthetic biological machines from biological parts to perform a defined function, in a manner similar to the engineering disciplines. However, the field has reached a bottleneck in the complexity of the genetic networks that we can implement using monocultures, facing constraints from metabolic burden and genetic interference. This makes building distributed biological systems an attractive prospect for synthetic biology that would alleviate these constraints and allow us to expand the applications of our systems into areas including complex biosensing and diagnostic tools, bioprocess control and the monitoring of industrial processes. In this review we will discuss the fundamental limitations we face when engineering functionality with a monoculture, and the key areas where distributed systems can provide an advantage. We cite evidence from natural systems that support arguments in favor of distributed systems to overcome the limitations of monocultures. Following this we conduct a comprehensive overview of the synthetic communities that have been built to date, and the components that have been used. The potential computational capabilities of communities are discussed, along with some of the applications that these will be useful for. We discuss some of the challenges with building co-cultures, including the problem of competitive exclusion and maintenance of desired community composition. Finally, we assess computational frameworks currently available to aide in the design of microbial communities and identify areas where we lack the necessary tool

Characterization of cooperators in Quorum sensing with 2D molecular signal analysis

In quorum sensing (QS), bacteria exchange molecular signals to work together. An analytically-tractable model is presented for characterizing QS signal propagation within a population of bacteria and the number of responsive cooperative bacteria (i.e., cooperators) in a two-dimensional (2D) environment. Unlike prior works with a deterministic topology and a simplified molecular propagation channel, this work considers continuous emission, diffusion, degradation, and reception among randomly-distributed bacteria. Using stochastic geometry, the 2D channel response and the corresponding probability of cooperation at a bacterium are derived. Based on this probability, new expressions are derived for the moment generating function and different orders of moments of the number of cooperators. The analytical results agree with the simulation results obtained by a particle-based method. In addition, the Poisson and Gaussian distributions are compared to approximate the distribution of the number of cooperators and the Poisson distribution provides the best overall approximation. The derived channel response can be generally applied to any molecular communication model where single or multiple transmitters continuously release molecules into a 2D environment. The derived statistics of the number of cooperators can be used to predict and control the QS process, e.g., predicting and decreasing the likelihood of biofilm formation

Development of Solution Blow Spun Nanofibers as Electrical and Whole Cell Biosensing Interfaces

Infectious pathogens place a huge burden on the US economy with more than $120 billion spent annually for direct and indirect costs for the treatment of infectious diseases. Rapid detection schemes continue to evolve in order to meet the demand of early diagnosis. In chronic wound infections, bacterial load is capable of impeding the healing process. Additionally, bacterial virulence production works coherently with bacterial load to produce toxins and molecules that prolongs the healing cycle. This work examines the use of nonwoven polymeric conductive and non-conductive nanofiber mats as synthetic biosensor scaffolds, drug delivery and biosensor interface constructs. A custom-made nanofiber platform was built to produce solution blow spun nanofibers of various polymer loading. Antimicrobial nanofiber mats were made with the use of an in-situ silver chemical reduction method. Ceria nanoparticles were incorporated to provide an additional antioxidative property. Conductivity properties were examined by using silver and multi-walled carbon nanotubes (MWCNT) as a filler material. SBS parameters were adjusted to analyze electrical conductivity properties. Nanofiber mats were used to detect bacteria concentrations in vitro. Protein adhesion to conductive nanofibers was studied using fluorescent antibodies and BCA assay. Anti-rabbit and streptavidin Alexa Flour 594 was used to examine the adsorption properties of SBS nanofiber mats. Enhancements were made to further improve interface design for specificity. SBS nanofiber electrodes were fabricated to serve as scaffold and detection site for spike protein detection. Bacteria virulence production was examined by the detection of pyocyanin and quorum sensing molecules. The opportunistic pathogen, Pseudomonas aeruginosa is a nosocomial iii pathogen found in immunocompromised patients with such as those with chronic wounds and cystic fibrosis. Pyocyanin is one of four quorum sensing molecules that the pathogen produces which can be detected electrochemically due to its inherent redox-active activity. SBS has been used to develop a sensing scheme to detect pyocyanin. This work also examines the use of a synthetic biosensor with a LasR based system capable of detecting homoserine lactone produced by P. aeruginosa and other common gram-negative pathogens. Genetic modifications were made to biosensor in order to replace a green, fluorescent reporter with a chromoprotein based reporter system for visual readout. Additionally, work related to community service and outreach regarding the encouragement of middle school students to pursue Science, Technology, Engineering and Math (STEM) was conducted. Results from outreach program showed an increase in the STEM interest among a group of middle school students. There was a general trend with STEM career knowledge, STEM self-efficacy and the level of interest in STEM careers and activities. Military research was also done with the United States Army Medical Research Institute of Infectious Diseases (USAMRIID) to develop several assays for the detection of several highly infectious viruses and bacteria. Due to confidentiality, the work cannot be published in this manuscript