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  1. Abstract

    Artificially Expanded Genetic Information Systems (AEGIS) add independently replicable unnatural nucleotide pairs to the natural G:C and A:T/U pairs found in native DNA, joining the unnatural pairs through alternative modes of hydrogen bonding. Whether and how AEGIS pairs are recognized and processed by multi-subunit cellular RNA polymerases (RNAPs) remains unknown. Here, we show thatE. coliRNAP selectively recognizes unnatural nucleobases in a six-letter expanded genetic system. High-resolution cryo-EM structures of three RNAP elongation complexes containing template-substrate UBPs reveal the shared principles behind the recognition of AEGIS and natural base pairs. In these structures, RNAPs are captured in an active state, poised to perform the chemistry step. At this point, the unnatural base pair adopts a Watson-Crick geometry, and the trigger loop is folded into an active conformation, indicating that the mechanistic principles underlying recognition and incorporation of natural base pairs also apply to AEGIS unnatural base pairs. These data validate the design philosophy of AEGIS unnatural basepairs. Further, we provide structural evidence supporting a long-standing hypothesis that pair mismatch during transcription occurs via tautomerization. Together, our work highlights the importance of Watson-Crick complementarity underlying the design principles of AEGIS base pair recognition.

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  2. Anion exchange is a facile, post-synthetic method to tune the emission wavelength of colloidal cesium lead halide (CsPbX3, X = Cl, Br, I) perovskite nanocrystals. While colloidal nanocrystals can exhibit size-dependent phase stability and chemical reactivity, the role of size in the mechanism of anion exchange in CsPbX3 nanocrystals has not been elucidated. We used single-particle fluorescence microscopy to monitor the transformation of individual CsPbBr3 nanocrystals to CsPbI3. By systematically varying the size of the nanocrystals and the concentration of substitutional iodide, we observed that smaller nanocrystals exhibit longer transition times in their fluorescence trajectories, while larger nanocrystals undergo a more abrupt transition during anion exchange. Monte Carlo simulations were used to rationalize the size-dependent reactivity, in which we varied how each exchange event affects the probability for further exchange. Greater cooperativity for simulated ion exchange leads to shorter transition times to complete the exchange. We propose that size-dependent miscibility between CsPbBr3 and CsPbI3 at the nanoscale controls the reaction kinetics. Smaller nanocrystals maintain a homogeneous composition during anion exchange. As the nanocrystal size increases, variations in the octahedral tilting patterns of the perovskite crystals lead to different structures for CsPbBr3 and CsPbI3. Thus, an iodide-rich region must first nucleate within larger CsPbBr3 nanocrystals, which is followed by rapid transformation to CsPbI3. While higher concentrations of substitutional anions can suppress this size-dependent reactivity, the inherent differences in reactivity between nanocrystals of different sizes are important to consider when scaling up this reaction for applications in solid-state lighting and biological imaging. 
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    Free, publicly-accessible full text available July 7, 2024
  3. Free, publicly-accessible full text available September 1, 2024
  4. Free, publicly-accessible full text available September 1, 2024
  5. Abstract Background

    A considerable amount of various types of data have been collected during the COVID-19 pandemic, the analysis and understanding of which have been indispensable for curbing the spread of the disease. As the pandemic moves to an endemic state, the data collected during the pandemic will continue to be rich sources for further studying and understanding the impacts of the pandemic on various aspects of our society. On the other hand, naïve release and sharing of the information can be associated with serious privacy concerns.


    We use three common but distinct data types collected during the pandemic (case surveillance tabular data, case location data, and contact tracing networks) to illustrate the publication and sharing of granular information and individual-level pandemic data in a privacy-preserving manner. We leverage and build upon the concept of differential privacy to generate and release privacy-preserving data for each data type. We investigate the inferential utility of privacy-preserving information through simulation studies at different levels of privacy guarantees and demonstrate the approaches in real-life data. All the approaches employed in the study are straightforward to apply.


    The empirical studies in all three data cases suggest that privacy-preserving results based on the differentially privately sanitized data can be similar to the original results at a reasonably small privacy loss ($$\epsilon \approx 1$$ϵ1). Statistical inferences based on sanitized data using the multiple synthesis technique also appear valid, with nominal coverage of 95% confidence intervals when there is no noticeable bias in point estimation. When$$\epsilon <1$$ϵ<1 and the sample size is not large enough, some privacy-preserving results are subject to bias, partially due to the bounding applied to sanitized data as a post-processing step to satisfy practical data constraints.


    Our study generates statistical evidence on the practical feasibility of sharing pandemic data with privacy guarantees and on how to balance the statistical utility of released information during this process.

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  6. Free, publicly-accessible full text available September 1, 2024
  7. Abstract

    Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting “preferred orientations” on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen stage during data collection is a generalizable solution but has historically led to substantial resolution attenuation. Here, we develop updated data collection and image processing workflows and demonstrate, using multiple specimens, that resolution attenuation is negligible or significantly reduced across tilt angles. Reconstructions with and without the stage tilted as high as 60° are virtually indistinguishable. These strategies allowed the reconstruction to 3 Å resolution of a bacterial RNA polymerase with preferred orientation, containing an unnatural nucleotide for studying novel base pair recognition. Furthermore, we present a quantitative framework that allows cryo-EM practitioners to define an optimal tilt angle during data acquisition. These results reinforce the utility of employing stage tilt for data collection and provide quantitative metrics to obtain isotropic maps.

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