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DNA sequences were obtained from 32 blade-formingUlvaspecimens collected in 2018 and 2019 from four islands in the Galápagos Archipelago: Fernandina, Floreana, Isabela and San Cristóbal. The loci sequenced were nuclear encoded ITS and plastid encodedrbcL andtufA, all recognized as barcode markers for green algae. Four species were found,Ulva adhaerens,U. lactuca,U. ohnoiandU. tanneri, all of which have had their type specimens sequenced, ensuring the correct application of these names. Only one of these,U. lactuca, was reported historically from the archipelago.Ulva adhaerenswas the species most commonly collected and widely distributed, occurring on all four islands. Previously known only from Japan and Korea, this is the first report ofU. adhaerensfrom the southeast Pacific Ocean.Ulva ohnoiwas collected on three islands, Isabela, Floreana, and San Cristóbal, andU. lactucaonly on the last two.Ulva tanneriis a diminutive, 1–2 cm tall, high intertidal species that is easily overlooked, but likely far more common than the one specimen that was collected. This study of blade-formingUlvaspecies confirms that a concerted effort, using DNA sequencing, is needed to document the seaweed flora of the Galápagos Archipelago.

 

We present the optical photometric variability of 32 planet-hosting M dwarfs within 25 pc over timescales of months to decades. The primary goal of this project—A Trail to Life Around Stars (ATLAS)—is to follow the trail to life by revealing nearby M dwarfs with planets that are also “quiet,” which may make them more amiable to habitability. There are 69 reported exoplanets orbiting the 32 stars discussed here, providing a rich sample of worlds for which environmental evaluations are needed. We examine the optical flux environments of these planets over month-long timescales for 23 stars observed by TESS, and find that 17 vary by less than 1% (∼11 mmag). All 32 stars are being observed at the CTIO/SMARTS 0.9 m telescope, with a median duration of 19.1 yr of optical photometric data in theVRIbands. We find over these extended timescales that six stars show optical flux variations less than 2%, 25 vary from 2% to 6% (∼22–67 mmag), and only one, Proxima Centauri, varies by more than 6%. Overall, LHS 1678 exhibits the lowest optical variability levels measured over all timescales examined, thereby providing one of the most stable photometric environments among the planets reported around M dwarfs within 25 pc. More than 600 of the nearest M dwarfs are being observed at the 0.9 m telescope in the RECONS program that began in 1999, and many more planet hosts will undoubtedly be revealed, providing more destinations to be added to the ATLAS sample in the future.

 

Controlling excited-state reactivity is a long-standing challenge in photochemistry, as a desired pathway may be inaccessible or compete with other unwanted channels. An important example is internal conversion of the anionic green fluorescent protein (GFP) chromophore where non-selective progress along two competing torsional modes (P: phenolate and I: imidazolinone) impairs and enablesZ-to-Ephotoisomerization, respectively. Developing strategies to promote photoisomerization could drive new areas of applications of GFP-like proteins. Motivated by the charge-transfer dichotomy of the torsional modes, we explore chemical substitution on the P-ring of the chromophore as a way to control excited-state pathways and improve photoisomerization. As demonstrated by methoxylation, selective P-twisting appears difficult to achieve because the electron-donating potential effects of the substituents are counteracted by inertial effects that directly retard the motion. Conversely, these effects act in concert to promote I-twisting when introducing electron-withdrawing groups. Specifically, 2,3,5-trifluorination leads to both pathway selectivity and a more direct approach to the I-twisted intersection which, in turn, doubles the photoisomerization quantum yield. Our results suggest P-ring engineering as an effective approach to boost photoisomerization of the anionic GFP chromophore.

 

Abstract As clinical testing declines, wastewater monitoring can provide crucial surveillance on the emergence of SARS-CoV-2 variant of concerns (VoCs) in communities. In this paper we present QuaID, a novel bioinformatics tool for VoC detection based on quasi-unique mutations. The benefits of QuaID are three-fold: (i) provides up to 3-week earlier VoC detection, (ii) accurate VoC detection (>95% precision on simulated benchmarks), and (iii) leverages all mutational signatures (including insertions & deletions). 

The Jaccard similarity on k-mer sets has shown to be a convenient proxy for sequence identity. By avoiding expensive base-level alignments and comparing reduced sequence representations, tools such as MashMap can scale to massive numbers of pairwise comparisons while still providing useful similarity estimates. However, due to their reliance on minimizer winnowing, previous versions of MashMap were shown to be biased and inconsistent estimators of Jaccard similarity. This directly impacts downstream tools that rely on the accuracy of these estimates.

To address this, we propose the minmer winnowing scheme, which generalizes the minimizer scheme by use of a rolling minhash with multiple sampled k-mers per window. We show both theoretically and empirically that minmers yield an unbiased estimator of local Jaccard similarity, and we implement this scheme in an updated version of MashMap. The minmer-based implementation is over 10 times faster than the minimizer-based version under the default ANI threshold, making it well-suited for large-scale comparative genomics applications.

MashMap3 is available at https://github.com/marbl/MashMap.

 

Interactions among microbes within microbial communities have been shown to play crucial roles in human health. In spite of recent progress, low-level knowledge of bacteria driving microbial interactions within microbiomes remains unknown, limiting our ability to fully decipher and control microbial communities.

We present a novel approach for identifying species driving interactions within microbiomes. Bakdrive infers ecological networks of given metagenomic sequencing samples and identifies minimum sets of driver species (MDS) using control theory. Bakdrive has three key innovations in this space: (i) it leverages inherent information from metagenomic sequencing samples to identify driver species, (ii) it explicitly takes host-specific variation into consideration, and (iii) it does not require a known ecological network. In extensive simulated data, we demonstrate identifying driver species identified from healthy donor samples and introducing them to the disease samples, we can restore the gut microbiome in recurrent Clostridioides difficile (rCDI) infection patients to a healthy state. We also applied Bakdrive to two real datasets, rCDI and Crohn's disease patients, uncovering driver species consistent with previous work. Bakdrive represents a novel approach for capturing microbial interactions.

Bakdrive is open-source and available at: https://gitlab.com/treangenlab/bakdrive.