Search for: All records

Abstract RNA-driven phase separation is emerging as a promising approach for engineering biomolecular condensates with diverse functionalities. Condensates form thanks to weak yet specific RNA–RNA interactions established by design via complementary sequence domains. Here, we demonstrate how RNA condensates formed by star-shaped RNA motifs, or nanostars, can be dynamically controlled when the motifs include additional linear or branch-loop domains that facilitate access of regulatory RNA molecules to the nanostar interaction domains. We show that condensates dissolve in the presence of RNA “invaders” that occlude selected nanostar bonds and reduce the valency of the nanostars, preventing phase separation. We further demonstrate that the introduction of “anti-invader” strands, complementary to the invaders, makes it possible to restore condensate formation. An important aspect of our experiments is that we demonstrate these behaviors in one-pot reactions, where RNA nanostars, invaders, and anti-invaders are simultaneously transcribed in vitro using short DNA templates. Our results lay the groundwork for engineering RNA-based assemblies with tunable, reversible condensation, providing a promising toolkit for synthetic biology applications requiring responsive, self-organizing biomolecular materials. 

Recent discoveries in biology have highlighted the importance of protein and RNA-based condensates as an alternative to classical membrane-bound organelles. Here, we demonstrate the design of pure RNA condensates from nanostructured, star-shaped RNA motifs. We generate condensates using two different RNA nanostar architectures: multi-stranded nanostars whose binding interactions are programmed via linear overhangs, and single-stranded nanostars whose interactions are programmed via kissing loops. Through systematic sequence design, we demonstrate that both architectures can produce orthogonal (distinct and immiscible) condensates, which can be individually tracked via fluorogenic aptamers. We also show that aptamers make it possible to recruit peptides and proteins to the condensates with high specificity. Successful co-transcriptional formation of condensates from single-stranded nanostars suggests that they may be genetically encoded and produced in living cells. We provide a library of orthogonal RNA condensates that can be modularly customized and offer a route toward creating systems of functional artificial organelles for the task of compartmentalizing molecules and biochemical reactions. 

Abstract When participants share data to a central entity, those who have taken on the responsibility of accepting the data and handling its management may also have control of decisions about the data, including its use, re‐use, accessibility, and more. Such concentrated control of data is often a default practice across many forms of participatory sciences, which can be extractive in some contexts and a way to protect participants in other contexts. To avoid extractive practices and related harms, projects can adopt structures so that those who make decisions about the data set and/or each datum are different from those responsible forexecutingthe subsequent decisions about data management. We propose two alternative models for improving equity in data governance, each model representing a spectrum of options. With an individualized control model, each participant can place their data in a central repository while still retaining control of it, such as through simple opt‐in or opt‐out features or through blockchain technology. With a shared control model, representatives of salient participant groups, such as through participant advisory boards, collectively make decisions on behalf of their constituents. These equitable models are relevant to all participatory science systems, and particularly necessary in contexts where dominant‐culture institutions engage marginalized peoples. 

Recent waste rock pile designs have been proposed to incorporate a fine-grained layer to create a capillary barrier to prevent surface water from draining into the pile interior. This study analyses active fibre optic distributed temperature sensing (FO-DTS) as a tool to measure the effectiveness a capillary barrier system following an infiltration test. A laboratory waste rock column was built with anorthosite waste rock overlain by sand. Volumetric water content is calculated during heat cycles lasting 15 min powered at 15 W/m in the column. A new algorithm is employed to circumvent several requirements for soil specific calibration. The inferred moisture contents were verified by soil moisture probes located adjacent to the cable. The FO-DTS data indicate, at vertical resolutions up to 2 cm, that water is retained in the sand and does not drain into the anorthosite following the infiltration test. The coefficient of determination, R 2 , between the inferred and measured volumetric water content in the fine cover sand layer is 0.90, while the screened anorthosite maintained an R 2 of 0.94 with constant moisture content throughout the test. This study will ultimately help guide future waste rock storage design initiatives incorporating fibre optic sensors, leading to improved environmental mine waste management. 

Abstract The design and construction of a waste rock pile influences water infiltration and may promote the production of contaminated mine drainage. The objective of this project is to evaluate the use of an active fiber optic distributed temperature sensing (aFO‐DTS) protocol to measure infiltration and soil moisture within a flow control layer capping an experimental waste rock pile. Five hundred meters of fiber optic cable were installed in a waste rock pile that is 70 m long, 10 m wide, and was covered with 0.60 m of fine compacted sand and 0.25 m of non‐reactive crushed waste rock. Volumetric water content was assessed by heating the fiber optic cable with 15‐min heat pulses at 15 W/m every 30 min. To test the aFO‐DTS system 14 mm of recharge was applied to the top surface of the waste rock pile over 4 h, simulating a major rain event. The average volumetric water content in the FCL increased from 0.10 to 0.24 over the duration of the test. The volumetric water content measured with aFO‐DTS in the FCL and waste rock was within ±0.06 and ±0.03, respectively, compared with values measured using 96 dielectric soil moisture probes over the same time period. Additional results illustrate how water can be confined within the FCL and monitored through an aFO‐DTS protocol serving as a practical means to measure soil moisture at an industrial capacity.