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Since this paper is under journal submission, we publish only an extended abstract here. A full version can be found at https://arxiv.org/abs/2406.03938. 

Abstract Previous studies of the 70S ribosome from Flavobacterium johnsoniae revealed a novel ribosomal protein, bL38, which interacts with uL6 on the 50S subunit. This 5.6 kDa protein is conserved across the Bacteroidia and encoded downstream of bL28 and bL33 in a three-gene operon. Here, we show that bL38 is critical for the growth of F. johnsoniae, and depletion of bL38 leads to accumulation of immature 50S particles, which lack uL6 and retain precursor rRNA sequences. Cryo-EM analysis of these particles reveals several putative assembly intermediates, all showing an absence of electron density for uL6 and the entire uL12 stalk region and additional densities corresponding to the unprocessed ends of the pre-23S rRNA. Extra copies of the uL6 gene can rescue the phenotypes caused by bL38 depletion, suggesting that bL38 facilitates uL6 incorporation during 50S subunit biogenesis. Cryo-EM analysis of 50S particles from this rescued strain reveals nearly twice as many intermediates, suggesting a broader and more robust assembly landscape. Differential scanning fluorimetry shows that uL6 of F. johnsoniae is intrinsically unstable, and bL38 increases the melting temperature of uL6 by 12°C. Collectively, these data suggest that bL38 binds and stabilizes uL6, thereby promoting 50S biogenesis in the Bacteroidia. 

We consider the problem of \emph{identifying,} from statistics, a distribution of discrete random variables $$X_1 \ldots,X_n$$ that is a mixture of $$k$$ product distributions. The best previous sample complexity for $$n \in O(k)$$ was $$(1/\zeta)^{O(k^2 \log k)}$$ (under a mild separation assumption parameterized by $$\zeta$$). The best known lower bound was $$\exp(\Omega(k))$$. It is known that $$n\geq 2k-1$$ is necessary and sufficient for identification. We show, for any $$n\geq 2k-1$$, how to achieve sample complexity and run-time complexity $$(1/\zeta)^{O(k)}$$. We also extend the known lower bound of $$e^{\Omega(k)}$$ to match our upper bound across a broad range of $$\zeta$$. Our results are obtained by combining (a) a classic method for robust tensor decomposition, (b) a novel way of bounding the condition number of key matrices called Hadamard extensions, by studying their action only on flattened rank-1 tensors. 

Product of experts (PoE) are layered networks in which the value at each node is an AND (or product) of the values (possibly negated) at its inputs. These were introduced as a neural network architecture that can efficiently learn to generate high-dimensional data which satisfy many low-dimensional constraints---thereby allowing each individual expert to perform a simple task. PoEs have found a variety of applications in learning. We study the problem of identifiability of a product of experts model having a layer of binary latent variables, and a layer of binary observables that are iid conditional on the latents. The previous best upper bound on the number of observables needed to identify the model was exponential in the number of parameters. We show: (a) When the latents are uniformly distributed, the model is identifiable with a number of observables equal to the number of parameters (and hence best possible). (b) In the more general case of arbitrarily distributed latents, the model is identifiable for a number of observables that is still linear in the number of parameters (and within a factor of two of best-possible). The proofs rely on root interlacing phenomena for some special three-term recurrences. 

Ab initio chemical shift prediction plays a central role in nuclear magnetic resonance (NMR) crystallography, and the accuracy with which chemical shifts can be predicted relative to experiment impacts the... 

The queen caste plays a central role in colony success in eusocial insects, as queens lay eggs and regulate colony behavior and development. Queen failure can cause colonies to collapse, which is one of the major concerns of beekeepers. Thus, understanding the biology behind the queen’s health is a pressing issue. Previous studies have shown that the bee microbiome plays an important role in worker bee health, but little is known about the queen microbiome and its functionin vivo. Here, we characterized the queen microbiome, identifying for the first time the present species and their putative functions. We show that the queen microbiome has predicted nutritional and protective roles in queen association and comprises only four consistently present bacterial species. Additionally, we bring to attention the spread of phages in the queen microbiome, which increased in abundance in failing queens and may impact the fate of the colony. 

Abstract Aim and QuestionsSea‐level rise has been responsible for extensive vegetation changes in coastal areas worldwide. The intent of our study was to analyze vegetation dynamics of a South Florida coastal watershed within an explicit spatiotemporal framework that might aid in projecting the landscape's future response to restoration efforts. We also asked whether recent transgression by mangroves and other halophytes has resulted in reduced plant diversity at local or subregional scales. LocationFlorida’'s Southeast Saline Everglades, USA. MethodsWe selected 26 locations, representing a transition zone between sawgrass marsh and mangrove swamp, that was last sampled floristically in 1995. Within this transition zone, leading‐ and trailing‐edge subzones were defined based on plant composition in 1995. Fifty‐two site × time combinations were classified and then ordinated to examine vegetation–environment relationships using 2016 environmental data. We calculated alpha‐diversity using Hill numbers or Shannon–Weiner index species equivalents and compared these across the two surveys. We used a multiplicative diversity partition to determine beta‐diversity from landscape‐scale (gamma) diversity in the entire dataset or in each subzone. ResultsMangrove and mangrove associates became more important in both subzones: through colonization and establishment in the leading edge, and through population growth combined with the decline of freshwater species in the trailing edge. Alpha‐diversity increased significantly in the leading edge and decreased nominally in the trailing edge, while beta‐diversity declined slightly in both subzones as well as across the study area. ConclusionsRecent halophyte encroachment in the Southeast Saline Everglades continues a trend evident for almost a century. While salinity is an important environmental driver, species’ responses suggest that restoration efforts based on supplementing freshwater delivery will not reverse a trend that depends on multiple interacting factors. Sea‐level‐rise‐driven taxonomic homogenization in coastal wetland communities develops slowly, lagging niche‐based changes in community structure and composition.