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Abstract Formalin-fixed paraffin-embedded (FFPE) samples are valuable but underutilized in single-cell omics research due to their low RNA quality. In this study, leveraging a recent advance in single-cell genomic technology, we introduce snPATHO-seq, a versatile method to derive high-quality single-nucleus transcriptomic data from FFPE samples. We benchmarked the performance of the snPATHO-seq workflow against existing 10x 3’ and Flex assays designed for frozen or fresh samples and highlighted the consistency in snRNA-seq data produced by all workflows. The snPATHO-seq workflow also demonstrated high robustness when tested across a wide range of healthy and diseased FFPE tissue samples. When combined with FFPE spatial transcriptomic technologies such as FFPE Visium, the snPATHO-seq provides a multi-modal sampling approach for FFPE samples, allowing more comprehensive transcriptomic characterization.

Endangered sharks and rays usually often lack basic information specific to conservation, such as population size. Previous studies have reconstructed shark and ray catch statistics between 1950 and 2019 for the southeast = south of Brazil, but lacking detail at the species level, because the catches were grouped by family, genus or even common name (e.g., skates and rays, Dasyatidae, Rhinobatos, Sphyrnidae, Squatinidae). In this study, we used proportions between species from scientific observer fishing trips and Dirichlet regression modelling to reclassify these categories. This model is a multivariate extension of beta regression and enables the modeling of asymmetric and heteroscedastic compositional data, allowing multinomial data to be obtained in a more informative way. The reconstruction of catches for unclassified data showed a massive dominance of the Squatinidae family until the late 1970s, when catches showed signs of decline. At the same time, the rays of the “emplastro” family showed a progressive increase from 2006 onwards. However, this scenario changed after the reclassification. The category Squatinidae was maintained almost exclusively by S. guggenheim, while 16 categories of species were observed within “emplastro” rays, many of which fall into “endangered”, “vulnerable” and “critically endangered” criteria. These reconstructed series provide a more reliable scenario of the catches of thirty elasmobranch species in the southeast and south of Brazil and serve as baseline information for understanding the conservation status of these species.

Both maternal and paternal supportive parenting (i.e., sensitivity, warmth, stimulation, and engagement) across early childhood have been found to be associated with multiple domains of children's positive socioemotional functioning. However, few studies have considered how maternal and paternal supportive parenting may interact to impact child development. Thus, the present study assessed direct and moderated longitudinal relations between maternal and paternal supportive parenting in toddlerhood (24 and 36 months, respectively) and fathers' and teachers' reports of children's socioemotional and behavioral adjustment in first grade. Data were drawn from a large, sample of Norwegian parents and children (N = 455, 51% female, 49% male, 10% endorsed financial strain, 75% of fathers and 86% of mothers born in Norway). After controlling for child temperamental activity level and soothability in infancy, path analysis revealed that higher paternal supportive parenting was associated with fewer symptoms of father-reported child hyperactivity/impulsivity in first grade. In addition, a significant interaction between maternal and paternal supportive parenting was evident for three out of the four assessed outcomes (per both father- and teacher-reports): externalizing problems, hyperactivity/impulsivity symptoms, and social skills. Simple slope analyses revealed a negative relation between parental supportive parenting and children's externalizing (father-reported) and hyperactivity/impulsivity problems (father- and teacher-reported) when the child's other parent engaged in low levels of supportive parenting. Similarly, paternal supportive parenting was positively associated with children's social skills (father-report) when mothers engaged in low levels of supportive parenting. Results are discussed with implications for including both mothers and fathers in early childhood research, intervention, and social policy.

Abstract The use of single-cell technologies for clinical applications requires disconnecting sampling from downstream processing steps. Early sample preservation can further increase robustness and reproducibility by avoiding artifacts introduced during specimen handling. We present FixNCut, a methodology for the reversible fixation of tissue followed by dissociation that overcomes current limitations. We applied FixNCut to human and mouse tissues to demonstrate the preservation of RNA integrity, sequencing library complexity, and cellular composition, while diminishing stress-related artifacts. Besides single-cell RNA sequencing, FixNCut is compatible with multiple single-cell and spatial technologies, making it a versatile tool for robust and flexible study designs.

Conventional type 1 dendritic cells (cDC1) are critical regulators of anti-tumoral T-cell responses. The structure and abundance of intercellular contacts between cDC1 and CD8 T cells in cancer tissues is important to determine the outcome of the T-cell response. However, the molecular determinants controlling the stability of cDC1–CD8 interactions during cancer progression remain poorly investigated. Here, we generated a genetic model of non-small cell lung cancer crossed to a fluorescent cDC1 reporter (KP-XCR1venus) to allow the detection of cDC1-CD8T cell clusters in tumor tissues across tumor stages. We found that cDC1-CD8 clusters are abundant and productive at the early stages of tumor development but progressively diminish in advanced tumors. Transcriptional profiling and flow cytometry identified the adhesion molecule ALCAM/CD166 (Activated Leukocyte Cell Adhesion Molecule, ligand of CD6) as highly expressed by lung cDC1 and significantly downregulated in advanced tumors. Analysis of human datasets indicated that ALCAM is downregulated in non-small cell lung cancer and its expression correlates to better prognosis. Mechanistically, triggering ALCAM on lung cDC1 induces cytoskeletal remodeling and contact formation whereas its blockade prevents T-cell activation. Together, our results indicate that ALCAM is important to stabilize cDC1–CD8 interactions at early tumor stages, while its loss in advanced tumors contributes to immune evasion.

Summary: An altered gut microbiota is associated with type 1 diabetes (T1D), affecting the production of short-chain fatty acids (SCFA) and glucose homeostasis. We previously demonstrated that enhancing serum acetate and butyrate using a dietary supplement (HAMSAB) improved glycemia in non-obese diabetic (NOD) mice and patients with established T1D. The effects of SCFA on immune-infiltrated islet cells remain to be clarified. Here, we performed single-cell RNA sequencing on islet cells from NOD mice fed an HAMSAB or control diet. HAMSAB induced a regulatory gene expression profile in pancreas-infiltrated immune cells. Moreover, HAMSAB maintained the expression of β-cell functional genes and decreased cellular stress. HAMSAB-fed mice showed preserved pancreatic endocrine cell identity, evaluated by decreased numbers of poly-hormonal cells. Finally, SCFA increased insulin levels in human β-like cells and improved transplantation outcome in NOD/SCID mice. Our findings support the use of metabolite-based diet as attractive approach to improve glucose control in T1D.

Otoliths are acellular apposition structures composed of approximately 90% of calcium carbonate and other inorganic salts, which develop over a protein matrix located in the inner ear of bony fishes playing an essential role in the senses of balance and hearing. These structures grow throughout a fish’s lifetime. Owing to their species-specific shape, otoliths are an important tool for the identification of fish species in the diet of predators when collected from stomachs and, due to their low water content, are helpful for archaeological, paleontological and anthropological studies for its presence in fossilized remains. This atlas is aimed at the identification of abundant or frequent bony fishes otoliths in the diet of predators and in fossilized remains from the continental shelf and upper continental slope of southern Brazil between Santa Marta Grande cape (28° S) and Chuí (34° S) on the border with Uruguay. It includes the otolith description of 136 bony fishes species, including most of the abundant and frequent species in the region. Easy to use graphics are provided to infer fish size based on otolith measurements. Vouchers of different sizes of otolith of all species included in this atlas are deposited and available for consultation at the Demersal Fisheries Resources and Cephalopods Laboratory (IO-FURG).

The deamination of all adenosines in the wobble base position is essential to empower the individual tRNA to decode several codons. Here, the authors present the cryo-EM structure of the tRNA-bound ADAT2/3 deaminase, revealing how the geometry-specific enzyme acquiesces sequence-divergent tRNAs to its active site.

Asian soybean rust, caused by the fungus Phakopsora pachyrhizi, is one of the most important diseases affecting soybean production in tropical areas. During infection, P. pachyrhizi secretes proteins from haustoria that are transferred into plant cells to promote virulence. To date, only one candidate P. pachyrhizi effector protein has been characterized in detail to understand the mechanism by which it suppresses plant defenses to enhance infection. Here, we aimed to extend understanding of the pathogenic mechanisms of P. pachyrhizi based on the discovery of host proteins that interact with the effector candidate Phapa-7431740. We demonstrated that Phapa-7431740 suppresses pathogen-associated molecular pattern-triggered immunity (PTI) and that it interacts with a soybean glucan endo-1,3-β-glucosidase (GmβGLU), a pathogenesis-related (PR) protein belonging to the PR-2 family. Structural and phylogenetic characterization of the PR-2 protein family predicted in the soybean genome and comparison to PR-2 family members in Arabidopsis thaliana and cotton, demonstrated that GmβGLU is a type IV β-1,3-glucanase. Transcriptional profiling during an infection time course showed that the GmβGLU mRNA is highly induced during the initial hours after infection, coinciding with peak of expression of Phapa-7431740. The effector was able to interfere with the activity of GmβGLU in vitro, with a dose-dependent inhibition. Our results suggest that Phapa-7431740 may suppress PTI by interfering with glucan endo-1,3-β-glucosidase activity. [Graphic: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.

Four new species of the scaleless black dragonfish genus Eustomias are described based on specimens collected during the ABRACOS (Acoustics along the BRAzilian COaSt) expeditions along the Fernando de Noronha Ridge, off northeastern Brazil, western tropical Atlantic. Eustomias (Haploclonus) antea sp. nov. differs from its congeners by having a long chin barbel without appendages, ending in a very small terminal bulb without terminal filaments. Eustomias (Haploclonus) lucenae sp. nov. has the lowest count of photophores in the lateral series (56) and a simple, short barbel, ending in a small and asymmetrical terminal bulb. Eustomias (Nominostomias) ophioglossa sp. nov. differs from its congeners by the long chin barbel with two terminal bulbs and long terminal filament with bifurcated axis along its length and with bulblets of different sizes and arrangements inside. Eustomias (Nominostomias) bertrandi sp. nov. can be distinguished by the long chin barbel with two terminal bulbs, the distal bulb more than twice as long as the proximal one, and a short terminal filament. Morphological description of a specimen identified as Eustomias (Dinematochirus) cf. minimus is provided, and an overview of the species of Eustomias reported in Brazilian waters is presented and discussed. [ABSTRACT FROM AUTHOR]

Endangered sharks and rays usually often lack basic information specific to conservation, such as population size. Previous studies have reconstructed shark and ray catch statistics between 1950 and 2019 for the southeast = south of Brazil, but lacking detail at the species level, because the catches were grouped by family, genus or even common name (e.g., skates and rays, Dasyatidae, Rhinobatos, Sphyrnidae, Squatinidae). In this study, we used proportions between species from scientific observer fishing trips and Dirichlet regression modelling to reclassify these categories. This model is a multivariate extension of beta regression and enables the modeling of asymmetric and heteroscedastic compositional data, allowing multinomial data to be obtained in a more informative way. The reconstruction of catches for unclassified data showed a massive dominance of the Squatinidae family until the late 1970s, when catches showed signs of decline. At the same time, the rays of the "emplastro" family showed a progressive increase from 2006 onwards. However, this scenario changed after the reclassification. The category Squatinidae was maintained almost exclusively by S. guggenheim, while 16 categories of species were observed within "emplastro" rays, many of which fall into "endangered", "vulnerable" and "critically endangered" criteria. These reconstructed series provide a more reliable scenario of the catches of thirty elasmobranch species in the southeast and south of Brazil and serve as baseline information for understanding the conservation status of these species. [ABSTRACT FROM AUTHOR]