Bacterial computing: A form of natural computing and its applications

The capability to establish adaptive relationships with the environment is an essential characteristic of living cells. Both bacterial computing and bacterial intelligence are two general traits manifested along adaptive behaviors that respond to surrounding environmental conditions. These two traits have generated a variety of theoretical and applied approaches. Since the different systems of bacterial signaling and the different ways of genetic change are better known and more carefully explored, the whole adaptive possibilities of bacteria may be studied under new angles. For instance, there appear instances of molecular "learning" along the mechanisms of evolution. More in concrete, and looking specifically at the time dimension, the bacterial mechanisms of learning and evolution appear as two different and related mechanisms for adaptation to the environment; in somatic time the former and in evolutionary time the latter. In the present chapter it will be reviewed the possible application of both kinds of mechanisms to prokaryotic molecular computing schemes as well as to the solution of real world problems

Bacterial computing with engineered populations

We describe strategies for the construction of bacterial computing platforms by describing a number of results from the recently completed bacterial computing with engineered populations project. In general, the implementation of such systems requires a framework containing various components such as intracellular circuits, single cell input/output and cell–cell interfacing, as well as extensive analysis. In this overview paper, we describe our approach to each of these, and suggest possible areas for future research

Bacteria as computers making computers

Various efforts to integrate biological knowledge into networks of interactions have produced a lively microbial systems biology. Putting molecular biology and computer sciences in perspective, we review another trend in systems biology, in which recursivity and information replace the usual concepts of differential equations, feedback and feedforward loops and the like. Noting that the processes of gene expression separate the genome from the cell machinery, we analyse the role of the separation between machine and program in computers. However, computers do not make computers. For cells to make cells requires a specific organization of the genetic program, which we investigate using available knowledge. Microbial genomes are organized into a paleome (the name emphasizes the role of the corresponding functions from the time of the origin of life), comprising a constructor and a replicator, and a cenome (emphasizing community-relevant genes), made up of genes that permit life in a particular context. The cell duplication process supposes rejuvenation of the machine and replication of the program. The paleome also possesses genes that enable information to accumulate in a ratchet-like process down the generations. The systems biology must include the dynamics of information creation in its future developments

Biological Peer-to-Peer Networks: From Bacterial Communication to the Development of Synthetic Distributed Systems

Poster presented at the ESC-EBSCO Conference: Biology of plastids: Towards a blueprint for synthetic organelles which took place in 2014 June 21-23, in Pultusk (POLAND). The Web Site of the event: http://bioplastids.esf.org/This communication was supported by a European Science Foundation gran

Construction of the publication and patent clusters produced by the arbitrary terms with the use of the specialized Google tools

There has been developed the analytical technique of construction of the publication and patent clusters produced by the arbitrary terms with the use of the specialized Google tools. Different names of types of the computer calculations and devices were selected as the scienfific terms for testing with the use of Google Scholar, Google Books and Google Patents beginning with the words: Quantum, Bacterial, Cognitive, Cellular, Cloud, Ubiquitou

Modelización de Sistemas de Computación Distribuida con Bacterias Sintéticas mediante Autómatas Celulares

La conjugación es un sistema de comunicación distribuido que permite los intercambios de información genética entre bacterias. Este mecanismo peer-to-peer permite a las bacterias compartir estrategias de supervivencia implementadas en plásmidos de ADN. El presente trabajo se centra en la modelización de las dinámicas de conjugación mediante el uso de un autómata celular asíncrono y pretende servir como una aproximación formal y una herramienta de validación conceptual dentro del ámbito de la biología sintética. Este modelo se ha centrado en un caso de uso específico, una colonia heterogénea de bacterias modificadas genéticamente para discriminar plásmidos en base a la afinidad de los promotores y factores de transcripción de dos conjuntos de partida.Conjugation is a distributed communication system which allows exchanges of genetic information among bacteria. This peer-to-peer mechanism allows bacteria to share survival strategies implemented in DNA plasmids. This paper focuses on the modeling of conjugation dynamics by using asynchronous cellular automata. It intends to serve in the field of synthetic biology as a formal approach and a conceptual validation tool. This model has been focused on a specific use case, a heterogeneous colony of engineered bacteria that discriminate plasmids by evaluating affinity among pairs of promoters and transcription factors