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  1. Abstract Background

    RNA sequencing is a powerful approach to quantify the genome-wide distribution of mRNA molecules in a population to gain deeper understanding of cellular functions and phenotypes. However, unlike eukaryotic cells, mRNA sequencing of bacterial samples is more challenging due to the absence of a poly-A tail that typically enables efficient capture and enrichment of mRNA from the abundant rRNA molecules in a cell. Moreover, bacterial cells frequently contain 100-fold lower quantities of RNA compared to mammalian cells, which further complicates mRNA sequencing from non-cultivable and non-model bacterial species. To overcome these limitations, we report EMBR-seq (Enrichment of mRNA by Blocked rRNA), a method that efficiently depletes 5S, 16S and 23S rRNA using blocking primers to prevent their amplification.

    Results

    EMBR-seq results in 90% of the sequenced RNA molecules from anE. coliculture deriving from mRNA. We demonstrate that this increased efficiency provides a deeper view of the transcriptome without introducing technical amplification-induced biases. Moreover, compared to recent methods that employ a large array of oligonucleotides to deplete rRNA, EMBR-seq uses a single or a few oligonucleotides per rRNA, thereby making this new technology significantly more cost-effective, especially when applied to varied bacterial species. Finally, compared to existing commercial kits for bacterial rRNA depletion, we show that EMBR-seq can be used to successfully quantify the transcriptome from more than 500-fold lower starting total RNA.

    Conclusions

    EMBR-seq provides an efficient and cost-effective approach to quantify global gene expression profiles from low input bacterial samples.

     
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  2. Abstract

    Since doped polymers require a charge‐neutralizing counter‐ion to maintain charge neutrality, tailored and high degrees of doping in organic semiconductors requires an understanding of the coupling between ionic and electronic carrier motion. A method of counter‐ion exchange is utilized using the polymeric semiconductor poly[2,5‐bis(3‐tetradecylthiophen‐2‐yl)thieno[3,2‐b]thiophene] ‐C14to deconvolute the effects of ionic/polaronic interactions with the electrical properties of doped semiconducting polymers. In particular, exchanging the counter‐ions of the dopant nitrosonium hexafluorophosphate enables investigation into the role of counter‐ion size from 5.2 to 8.2 Å in diameter. The orientational order of the polymeric crystallites is not affected with this exchange process while effectively modifying the counter‐ion distance to the charge carrier. Doped films have electrical conductivities of 320 S cm−1and are not sensitive to an increased ion‐polaron distance. It is posited that other factors dominate the electrical properties at a device scale, such as the morphology and presence of domain boundaries. Interestingly, the temperature stability of the doped film can be drastically improved with the use of counter‐ions containing less labile bonds. This platform serves as a unique way to retain the morphology of polymeric thin films while studying charge interactions at the local scale.

     
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  3. Summary

    Foliar fungal endophytes are one of the most diverse guilds of symbiotic fungi found in the photosynthetic tissues of every plant lineage, but it is unclear how plant environments and leaf resource availability shape their diversity.

    We explored correlations between leaf nutrient availability and endophyte diversity amongPinus muricataandVaccinium ovatumplants growing across a soil nutrient gradient spanning a series of coastal terraces in Mendocino, California.

    Endophyte richness decreased in plants with higher leaf nitrogen‐to‐phosphorus ratios for both host species, but increased with sodium, which may be toxic to fungi at high concentrations. Isolation frequency, a proxy of fungal biomass, was not significantly predicted by any of the same leaf constituents in the two plant species.

    We propose that stressed plants can exhibit both low foliar nutrients or high levels of toxic compounds, and that both of these stress responses predict endophyte species richness. Stressful conditions that limit growth of fungi may increase their diversity due to the suppression of otherwise dominating species. Differences between the host species in their endophyte communities may be explained by host specificity, leaf phenology, or microclimates.

     
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  4. Abstract

    Different modes of non‐genetic inheritance are expected to affect population persistence in fluctuating environments. We here analyseCaenorhabditis elegansdensity‐independent per capita growth rate time series on 36 populations experiencing six controlled sequences of challenging oxygen level fluctuations across 60 generations, and parameterise competing models of non‐genetic inheritance in order to explain observed dynamics. Our analysis shows that phenotypic plasticity and anticipatory maternal effects are sufficient to explain growth rate dynamics, but that a carryover model where ‘epigenetic’ memory is imperfectly transmitted and might be reset at each generation is a better fit to the data. We further find that this epigenetic memory is asymmetric since it is kept for longer when populations are exposed to the more challenging environment. Our analysis suggests that population persistence in fluctuating environments depends on the non‐genetic inheritance of phenotypes whose expression is regulated across multiple generations.

     
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  5. Recent single-molecule measurements [Schoch et al., Proc. Natl. Acad. Sci. U. S. A. 118, e2113202118 (2021)] have observed dynamic lipid–lipid correlations in membranes with submicrometer spatial resolution and submillisecond temporal resolution. While short from an instrumentation standpoint, these length and time scales remain long compared to microscopic molecular motions. Theoretical expressions are derived to infer experimentally measurable correlations from the two-body diffusion matrix appropriate for membrane-bound bodies coupled by hydrodynamic interactions. The temporal (and associated spatial) averaging resulting from finite acquisition times has the effect of washing out correlations as compared to naive predictions (i.e., the bare elements of the diffusion matrix), which would be expected to hold for instantaneous measurements. The theoretical predictions are shown to be in excellent agreement with Brownian dynamics simulations of experimental measurements. Numerical results suggest that the experimental measurement of membrane protein diffusion, in complement to lipid diffusion measurements, might help to resolve the experimental ambiguities encountered for certain black lipid membranes. 
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