Design Approaches to Expand the Toolkit for Building Cotranscriptionally Encoded RNA Strand Displacement Circuits.

Cotranscriptionally encoded RNA strand displacement (ctRSD) circuits are an emerging tool for programmable molecular computation, with potential applications spanning in vitro diagnostics to continuous computation inside living cells. In ctRSD circuits, RNA strand displacement components are continuously produced together via transcription. These RNA components can be rationally programmed through base pairing interactions to execute logic and signaling cascades. However, the small number of ctRSD components characterized to date limits circuit size and capabilities. Here, we characterize over 200 ctRSD gate sequences, exploring different input, output, and toehold sequences and changes to other design parameters, including domain lengths, ribozyme sequences, and the order in which gate strands are transcribed. This characterization provides a library of sequence domains for engineering ctRSD components, i.e., a toolkit, enabling circuits with up to 4-fold more inputs than previously possible. We also identify specific failure modes and systematically develop design approaches that reduce the likelihood of failure across different gate sequences. Lastly, we show the ctRSD gate design is robust to changes in transcriptional encoding, opening a broad design space for applications in more complex environments. Together, these results deliver an expanded toolkit and design approaches for building ctRSD circuits that will dramatically extend capabilities and potential applications.

Global Transcriptional Response of Escherichia coli Exposed In Situ to Different Low-Dose Ionizing Radiation Sources.

Characterization of biological and chemical responses to ionizing radiation by various organisms is essential for potential applications in bioremediation, alternative modes of detecting nuclear material, and national security. Escherichia coli DH10ß is an optimal system to study the microbial response to low-dose ionizing radiation at the transcriptional level because it is a well-characterized model bacterium and its responses to other environmental stressors, including those to higher radiation doses, have been elucidated in prior studies. In this study, RNA sequencing with downstream transcriptomic analysis (RNA-seq) was employed to characterize the global transcriptional response of stationary-phase E. coli subjected to 239Pu, 3H (tritium), and 55Fe, at an approximate absorbed dose rate of 10 mGy day-1 for 1 day and 15 days. Differential expression analysis identified significant changes in gene expression of E. coli for both short- and long-term exposures. Radionuclide source exposure induced differential expression in E. coli of genes involved in biosynthesis pathways of nuclear envelope components, amino acids, and siderophores, transport systems such as ABC transporters and type II secretion proteins, and initiation of stress response and regulatory systems of temperature stress, the RpoS regulon, and oxidative stress. These findings provide a basic understanding of the relationship between low-dose exposure and biological effect of a model bacterium that is critical for applications in alternative nuclear material detection and bioremediation. IMPORTANCE Escherichia coli strain DH10ß, a well-characterized model bacterium, was subjected to short-term (1-day) and long-term (15-day) exposures to three different in situ radiation sources comprised of radionuclides relevant to nuclear activities to induce a measurable and identifiable genetic response. We found E. coli had both common and unique responses to the three exposures studied, suggesting both dose rate- and radionuclide-specific effects. This study is the first to provide insights into the transcriptional response of a microorganism in short- and long-term exposure to continuous low-dose ionizing radiation with multiple in situ radionuclide sources and the first to examine microbial transcriptional response in stationary phase. Moreover, this work provides a basis for the development of biosensors and informing more robust dose-response relationships to support ecological risk assessment.

Flowthrough of239PU and55FE during RNA extraction.

Analysis of gene expression has become an important tool in understanding low-dose effect mechanisms of ionizing radiation at the cellular level. Metal binding to nucleic acids needs to be considered when interpreting these results, as some radioactive metals, particularly actinides, may produce free radicals and cause oxidative stress damage via chemical means at rates much higher than free radical formation related to their radiological properties. Bacteria exposedin situto low dose rates of plutonium-239 (239Pu) and iron-55 (55Fe) were previously analysed for gene expression. The work herein was motivated by an interest in more precisely identifying the distribution of radionuclides in these bacteria as well as the practical need to ensure appropriate transport and handling of the associated ribonucleic acid (RNA) extractions. RNA extractions were performed on bacteria growth media with and without bacteria cells (i.e. with and without RNA) at several different concentrations of239Pu and55Fe to inform the level of specificity of the extraction membrane as well as provide insight into internal (uptake) vs external (sorption) accumulation of these radionuclides in bacteria cells. Results of the study suggest that239Pu and55Fe detected in RNA extraction samples during long term cell studies is the result of binding to RNA prior to the time of extraction, as opposed to flow through or binding after cell lysis, and it highlights the practical importance of nucleic acid sample characterization to radiation protection more generally.

Accumulation of radio-iron and plutonium, alone and in combination, inPseudomonas putidagrown in liquid cultures.

The impact of low doses of ionising radiation on biological and environmental systems have been historically difficult to study. Modern biological tools have provided new methods for studying these mechanisms but applying these tools to a dose-response relationship may require refinement of dosimetric techniques that incorporate a detailed understand of radionuclide accumulation in biological cells, particularly when assessing the impact of low doses of ionising radiation. In this workPseudomonas putida (KT2440) grown in liquid culture was exposed to low dose rates (10-20 mGy d-1) of239Pu and55Fe, both alone and in combination, for a period of 20 days, and the accumulation of239Pu and55Fe in cell pellets was analysed via liquid scintillation counting. The study also considered of cells grown with239Pu and stable Fe (primarily56Fe). In addition to the analysis of cell pellet and media samples, this work includes analysis of the radiological content of ribonucleic acid extraction samples to examine uptake of radionuclides. Results indicate that239Pu inhibited the uptake of55Fe, and that the presence of stable and radioactive isotopes of Fe in cultures may promote pathways for Fe accumulation that are used by239Pu. The work herein provides foundational insight into future dosimetric models for our work with environmental bacteria.

Pu-239 Accumulation in E. Coli and P. Putida Grown in Liquid Cultures.

ABSTRACT: Understanding of the behavior and effects of plutonium (Pu) in the environment is an important aspect of developing responsible and effective strategies for remediation and environmental stewardship. This work studies the sorption and uptake of 239Pu by common environmental bacteria, Escherichia coli DH10ß and Pseudomonas putida KT-2440. Plutonium was directly incorporated into growth media prior to inoculation (0.12 kBq mL-1), and samples from the liquid cultures of E. coli and P. putida were analyzed over a 15-d growth period through liquid scintillation counting (LSC) of plutonium in cell pellets and cell culture media following centrifugation. To improve its solubility in the liquid cultures, Pu was complexed with citrate prior to inoculation. P. putida cultures were also grown without citrate to examine potential impact of P. putida's ability to use citrate as a food source. The accumulation of Pu in P. putida cells was found to increase both with and without citrate complexation for the first 5 d and then plateau until the end of the study period (15 d). A higher activity concentration of Pu was found in P. putida cells grown with citrate complexation than without. The activity concentration of plutonium in E. coli cells was greater than that in P. putida cells, which may be the result of a stronger complexing agent made by E. coli for the purpose of iron uptake. There are a variety of factors that influence Pu behavior in bacterial systems, and results confirm that even in a simple system, multiple mechanisms are at play.

Indirect, Non-Thermal Atmospheric Plasma Promotes Bacterial Killing in vitro and Wound Disinfection in vivo Using Monogenic and Polygenic Models of Type 2 Diabetes (Without Adverse Metabolic Complications).

A novel atmospheric plasma device that uses indirect, non-thermal plasma generated from room air is being studied for its effects on wound disinfection in animal wounds of monogenic and polygenic murine models of type 2 diabetes. As a proof-of-concept report, the goal of this study was to demonstrate the efficacy and safety of the indirect non-thermal plasma (INTP) device in disinfecting polycarbonate filters established with Pseudomonas aeruginosa (PAO1) biofilms as well as wound disinfection in diabetic murine wounds. Dorsal excisional wounds in BALB/c, polygenic TALLYHO, and monogenic db/db mice established with PAO1 infection all demonstrated a 3-log colony-forming unit (CFU) reduction when subjected to a course of 20-min INTP treatments. Importantly, blood glucose and body weights in these animals were not significantly impacted by plasma treatment over the study period. Plasma safety was also analyzed via complete blood count and comprehensive metabolic panels, showing no deleterious systemic effects after 3 consecutive days of 20-min plasma applications. Therefore, the results obtained demonstrated the Pseudomonas aeruginosa isolates were highly sensitive to INTP in vitro, CFU reduction of infectious Pseudomonas in wounds of diabetic mice after INTP treatment is far superior to that of non-treated infected wounds, and the application of INTP shows no indication of toxic effects. Our results are consistent with indirect non-thermal atmospheric plasma as a promising adjunct to disinfecting wounds.