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The emergence of COVID-19 and its variants has dramatically shifted the way that societies respond to a pandemic crisis and postpandemic plans. One of the response needs is the ability to track potential transmissions within population movements effectively, which can exploit the means of pervasive computing by collecting and processing ubiquitously acquired anonymously aggregated data, as well as long-term data that constitute prior but limited contextual knowledge. This article presents a practical method for the assessment of the risk profiles of communities by acquiring, fusing, and analyzing data from public transportation, district population distribution, passenger interactions, and cross-locality travel data while still preserving individual user privacy. The proposed framework fuses these data sources into a realistic simulation of a transit network for a given time span to report on the risk of the public transit system as whole, as well as problematic wards and routes. By shedding credible insights into the impact of public transit on pandemic spread, the article findings will help to set the groundwork for aggregate transmission simulation tools that could provide pandemic response teams with a robust framework for the evaluations of city districts most at risk, and how to adjust municipal services accordingly.

One challenge in engineering organisms is taking responsibility for their behavior over many generations. Spontaneous mutations arising before or during use can impact heterologous genetic functions, disrupt system integration, or change organism phenotype. Here, we propose restructuring the genetic code itself such that point mutations in protein-coding sequences are selected against. Synthetic genetic systems so-encoded should fail more safely in response to most spontaneous mutations. We designed fail-safe codes and simulated their expected effects on the evolution of so-encoded proteins. We predict fail-safe codes supporting expression of 20 or 15 amino acids could slow protein evolution to ∼30% or 0% the rate of standard-encoded proteins, respectively. We also designed quadruplet-codon codes that should ensure all single point mutations in protein-coding sequences are selected against while maintaining expression of 20 or more amino acids. We demonstrate experimentally that a reduced set of 21 tRNAs is capable of expressing a protein encoded by only 20 sense codons, whereas a standard 64-codon encoding is not expressed. Our work suggests that biological systems using rationally depleted but otherwise natural translation systems should evolve more slowly and that such hypoevolvable organisms may be less likely to invade new niches or outcompete native populations.

One challenge in engineering organisms is guaranteeing system behavior over many generations. Spontaneous mutations that arise before or during use can impact heterologous genetic functions, disrupt system integration, or change organism phenotype. Here, we propose restructuring the genetic code itself such that all point mutations in protein-coding sequences are selected against. Synthetic genetic systems so-encoded should “fail safely” in response to many individual spontaneous mutations. We designed a family of such fail-safe codes and analyzed their expected effect on the evolution of engineered organisms via simulation. We predict that fail-safe codes supporting expression of 20 or 15 amino acids could slow the evolution of proteins in so-encoded organisms to 30% or 0% the rate of standard-code organisms, respectively. We also designed quadruplet-codon codes that should be capable of encoding at least 20 amino acids while ensuring all single point mutations in protein-coding sequences are selected against. We show by in vitro experiments that a reduced set of 21 tRNA is capable of expressing a protein whose coding sequence is recoded to use a fail-safe code, whereas a standard-code encoding is not expressed. Our work suggests that a rationally depleted but otherwise natural translation system should yield biological systems with intrinsically reduced evolutionary capacity, and that so-encoded hypoevolvable organisms might be less likely to invade new niches or outcompete native populations.

The self-assembly in aqueous solution of the well-known cyclophane, cyclobis(paraquat-p-phenylene) (BB(4+) ), and two cucurbit[7]uril (CB7) hosts around a simple hydroquinol-based, diamine guest (GH2 (2+) ) was investigated by (1) H NMR and electronic absorption spectroscopies, electrospray mass spectrometry and DFT computations. The formation of a quaternary supramolecular assembly [GH2 (2+) ⋅BB(4+) ⋅ (CB7)2 ] was shown to be a very efficient process, which takes place not only because of the attractive forces between each of the hosts and the guest, but also because of the lateral interactions between the hosts in the final assembly. This complementary set of attractive interactions results in clear cooperative binding effects that help overcome the entropic barriers for multiple component assembly.