More Like this

1. Metaphors as design tools for microbial consortia: An analysis of recent peer‐reviewed literature

   https://doi.org/10.1111/1751-7915.14366  

   Szymanski, Erika_Amethyst; Turner, Marie (November 2023, Microbial Biotechnology)

   Abstract Single engineered microbial species cannot always conduct complex transformations, while complex, incompletely defined microbial consortia have heretofore been suited to a limited range of tasks. As biodesigners bridge this gap with intentionally designed microbial communities, they will, intentionally or otherwise, build communities that embody particular ideas about what microbial communities can and should be. Here, we suggest that metaphors—ideas about what microbial communities arelike—are therefore important tools for designing synthetic consortia‐based bioreactors. We identify a range of metaphors currently employed in peer‐reviewed microbiome research articles, characterizing each through its potential structural implications and distinctive imagery. We present this metaphor catalogue in the interest of, first, making metaphors visible as design choices, second, enabling deliberate experimentation with them towards expanding the potential design space of the field, and third, encouraging reflection on the goals and values they embed. 

   more » « less
2. Spatial Metaphor and the Development of Cross-Domain Mappings in Early Childhood

   Starr, Ariel; Srinivasan, Mahesh (April 2018, Developmental psychology)

   Spatial language is often used metaphorically to describe other domains, including time (long sound) and pitch (high sound). How does experience with these metaphors shape the ability to associate space with other domains? Here, we tested 3- to 6-year-old English-speaking children and adults with a cross-domain matching task. We probed cross-domain relations that are expressed in English metaphors for time and pitch (length-time and height-pitch), as well as relations that are unconventional in English but expressed in other languages (size-time and thickness-pitch). Participants were tested with a perceptual matching task, in which they matched between spatial stimuli and sounds of different durations or pitches, and a linguistic matching task, in which they matched between a label denoting a spatial attribute, duration, or pitch, and a picture or sound representing another dimension. Contrary to previous claims that experience with linguistic metaphors is necessary for children to make cross-domain mappings, children performed above chance for both familiar and unfamiliar relations in both tasks, as did adults. Children’s performance was also better when a label was provided for one of the dimensions, but only when making length-time, size-time, and height-pitch mappings (not thickness-pitch mappings). These findings suggest that, although experience with metaphorical language is not necessary to make cross-domain mappings, labels can promote these mappings, both when they have familiar metaphorical uses (e.g., English ‘long’ denotes both length and duration), and when they describe dimensions that share a common ordinal reference frame (e.g., size and duration, but not thickness and pitch). 

   more » « less
3. Reconfiguring the Challenge of Biological Complexity as a Resource for Biodesign

   https://doi.org/10.1128/msphere.00547-22  

   Szymanski, Erika Amethyst; Henriksen, James (December 2022, mSphere)

   Tringe, Susannah Green (Ed.)

   ABSTRACT Biological complexity is widely seen as the central, intractable challenge of engineering biology. Yet this challenge has been constructed through the field’s dominant metaphors. Alternative ways of thinking—latent in progressive experimental approaches, but rarely articulated as such—could instead position complexity as engineering biology’s greatest resource. We outline how assumptions about engineered microorganisms have been built into the field, carried by entrenched metaphors, even as contemporary methods move beyond them. We suggest that alternative metaphors would better align engineering biology’s conceptual infrastructure with the field’s move away from conventionally engineering-inspired methods toward biology-centric ones. Innovating new conceptual frameworks would also enable better aligning scientific work with higher-level conversations about that work. Such innovation—thinking about how engineering microbes might be more like user-centered design than like programming a computer or building a car—could highlight complexity as a resource to leverage, not a problem to erase or negate. 

   more » « less
4. A modular plasmid toolkit applied in marine bacteria reveals functional insights during bacteria-stimulated metamorphosis

   https://doi.org/10.1128/mbio.01502-23  

   Alker, Amanda T.; Farrell, Morgan V.; Aspiras, Alpher E.; Dunbar, Tiffany L.; Fedoriouk, Andriy; Jones, Jeffrey E.; Mikhail, Sama R.; Salcedo, Gabriella Y.; Moore, Bradley S.; Shikuma, Nicholas J. (August 2023, mBio)

   Ruby, Edward G. (Ed.)

   ABSTRACT A conspicuous roadblock to studying marine bacteria for fundamental research and biotechnology is a lack of modular synthetic biology tools for their genetic manipulation. Here, we applied, and generated new parts for, a modular plasmid toolkit to study marine bacteria in the context of symbioses and host-microbe interactions. To demonstrate the utility of this plasmid system, we genetically manipulated the marine bacteriumPseudoalteromonas luteoviolacea, which stimulates the metamorphosis of the model tubeworm,Hydroides elegans. Using these tools, we quantified constitutive and native promoter expression, developed reporter strains that enable the imaging of host-bacteria interactions, and used CRISPR interference (CRISPRi) to knock down a secondary metabolite and a host-associated gene. We demonstrate the broader utility of this modular system for testing the genetic tractability of marine bacteria that are known to be associated with diverse host-microbe symbioses. These efforts resulted in the successful conjugation of 12 marine strains from the Alphaproteobacteria and Gammaproteobacteria classes. Altogether, the present study demonstrates how synthetic biology strategies enable the investigation of marine microbes and marine host-microbe symbioses with potential implications for environmental restoration and biotechnology. IMPORTANCEMarine Proteobacteria are attractive targets for genetic engineering due to their ability to produce a diversity of bioactive metabolites and their involvement in host-microbe symbioses. Modular cloning toolkits have become a standard for engineering model microbes, such asEscherichia coli, because they enable innumerable mix-and-match DNA assembly and engineering options. However, such modular tools have not yet been applied to most marine bacterial species. In this work, we adapt a modular plasmid toolkit for use in a set of 12 marine bacteria from the Gammaproteobacteria and Alphaproteobacteria classes. We demonstrate the utility of this genetic toolkit by engineering a marinePseudoalteromonasbacterium to study their association with its host animalHydroides elegans. This work provides a proof of concept that modular genetic tools can be applied to diverse marine bacteria to address basic science questions and for biotechnology innovations. 

   more » « less
5. Caenorhabditis elegans processes sensory information to choose between freeloading and self-defense strategies

   https://doi.org/10.7554/eLife.56186  

   Schiffer, Jodie A; Servello, Francesco A; Heath, William R; Amrit, Francis Raj; Stumbur, Stephanie V; Eder, Matthias; Martin, Olivier MF; Johnsen, Sean B; Stanley, Julian A; Tam, Hannah; et al (May 2020, eLife)

   null (Ed.)

   Cells of all kinds often wage chemical warfare against each other. Hydrogen peroxide is often the weapon of choice on the microscopic battlefield, where it is used to incapacitate opponents or to defend against attackers. For example, some plants produce hydrogen peroxide in response to infection to fight off disease-causing microbes. Individual cells have also evolved defenses to prevent or repair ‘injuries’ caused by hydrogen peroxide. These are similar across many different species. They include enzymes called catalases, which break down hydrogen peroxide, and others to repair damage. However, scientists still do not fully understand how animals and other multicellular organisms might coordinate these defenses across their cells. Caenorhabditis elegans is a microscopic species of worm that lives in rotting fruits. It often encounters the threat of cellular warfare: many types of bacteria in its environment generate hydrogen peroxide, and some can make enough to kill the worms outright. Like other organisms, C. elegans also produces catalases to defend itself against hydrogen peroxide attacks. However, it must activate its defenses at the right time; if it did so when they were not needed, this would result in a detrimental energy ‘cost’ to the worm. Although C. elegans is a small organism containing only a defined number of cells, exactly why and how it switches its chemical defenses on or off remains unknown. Schiffer et al. therefore set out to determine how C. elegans controls these defenses, focusing on the role of the brain in detecting and processing information from its environment. Experiments looking at the brains of genetically manipulated worms revealed a circuit of sensory nerve cells whose job is to tell the rest of the worm’s tissues that they no longer need to produce defense enzymes. Crucially, the circuit became active when the worms sensed E. coli bacteria nearby. Bacteria in the same family as E. coli are normally found in in the same habitat as C. elegans and these bacteria are also known to make enzymes of their own to eliminate hydrogen peroxide around them. These results indicate that C. elegans can effectively decide, based on the activity of its circuit, when to use its own defenses and when to ‘freeload’ off those of neighboring bacteria. This work is an important step towards understanding how sensory circuits in the brain can control hydrogen peroxide defenses in multicellular organisms. In the future, it could help researchers work out how more complex animals, like humans, coordinate their cellular defenses, and therefore potentially yield new strategies for improving health and longevity. 

   more » « less