0000000000802746
AUTHOR
Pedro Dorado-morales
Unveiling Bacterial Interactions through Multidimensional Scaling and Dynamics Modeling
AbstractWe propose a new strategy to identify and visualize bacterial consortia by conducting replicated culturing of environmental samples coupled with high-throughput sequencing and multidimensional scaling analysis, followed by identification of bacteria-bacteria correlations and interactions. We conducted a proof of concept assay with pine-tree resin-based media in ten replicates, which allowed detecting and visualizing dynamical bacterial associations in the form of statistically significant and yet biologically relevant bacterial consortia.
Responsibility and intellectual property in synthetic biology: A proposal for using Responsible Research and Innovation as a basic framework for intellectual property decisions in synthetic biology
Synthetic biology (SynBio) is an engineering view of biotechnology that has the potential to increase the number and industrial utility of biotechnological applications by implementing engineering principles such as standardization and modularity. The boundaries between SynBio, biotechnology, and metabolic engineering are not always clear, but assessing SynBio in a wider sense—that of modeling‐based biotechnology and/or “sophisticated” metabolic engineering—we find that a significant number of applications and research articles have been generated in the past few years [1]. One of the best‐known examples is that of a synthetic pathway for producing artemisinic acid, a precursor to the antim…
Additional file 1: Table S1. of Standards not that standard
Biobrick parts (Bb1 to Bb6) included in the different DNA constructions tested in this work. Table S2. Proteins displaying statistically significant alterations in their expression levels, as detected by iTRAQ analysis (DOCX 18 kb).
Standards not that standard
There is a general assent on the key role of standards in Synthetic Biology. In two consecutive letters to this journal, suggestions on the assembly methods for the Registry of standard biological parts have been described. We fully agree with those authors on the need of a more flexible building strategy and we highlight in the present work two major functional challenges standardization efforts have to deal with: the need of both universal and orthogonal behaviors. We provide experimental data that clearly indicate that such engineering requirements should not be taken for granted in Synthetic Biology. Electronic supplementary material The online version of this article (doi:10.1186/s1303…
A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city
AbstractMicroorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the …
Engineering Bacteria to Form a Biofilm and Induce Clumping in Caenorhabditis elegans
Bacteria are needed for a vast range of biotechnological processes, which they carry out either as pure cultures or in association with other bacteria and/or fungi. The potential of bacteria as biofactories is hampered, though, by their limited mobility in solid or semisolid media such as agricultural or domestic waste. This work represents an attempt toward overcoming this limitation by associating bacterial biotechnological properties with the transport ability of the nematode Caenorhabditis elegans. We report here biofilm formation on C. elegans by engineered Escherichia coli expressing a Xhenorhabdus nematophila adhesion operon and induction of nematode social feeding behavior (clumping…
Towards light-mediated sensing of bacterial comfort
Abstract Bacterial comfort is central to biotechnological applications. Here, we report the characterization of different sensoring systems, the first step within a broader synthetic biology-inspired light-mediated strategy to determine Escherichia coli perception of environmental factors critical to bacterial performance. We did so by directly ‘asking’ bacterial cultures with light-encoded questions corresponding to the excitation wavelength of fluorescent proteins placed under the control of environment-sensitive promoters. We built four genetic constructions with fluorescent proteins responding to glucose, temperature, oxygen and nitrogen; and a fifth construction allowing UV-induced exp…