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Gene expression analyses of the calmodulin binding protein 60 family under water stress conditions in rice
STANCE: a unified statistical model to detect cell-type-specific spatially variable genes in spatial transcriptomics
Abstract One of the major challenges in spatial transcriptomics is to detect spatially variable genes (SVGs), whose expression patterns are non-random across tissue locations. Many SVGs correlate with cell type compositions, introducing the concept of cell type-specific SVGs (ctSVGs). Existing ctSVG detection methods treat cell type-specific spatial effects as fixed effects, leading to tissue spatial rotation-dependent results. Moreover, SVGs may exhibit random spatial patterns within cell types, meaning an SVG is not always a ctSVG, and vice versa, further complicating detection. We propose STANCE, a unified statistical model for both SVGs and ctSVGs detection under a linear mixed-effect model framework that integrates gene expression, spatial location, and cell type composition information. STANCE ensures tissue rotation-invariant results, with a two-stage approach: initial SVG/ctSVG detection followed by ctSVG-specific testing. We demonstrate its performance through extensive simulations and analyses of public datasets. Downstream analyses reveal STANCE’s potential in spatial transcriptomics analysis.
New insights into the range and transmission dynamics of a koala gammaherpesvirus, phascolarctid gammaherpesvirus 2
High throughput analysis of rare nanoparticles with deep-enhanced sensitivity via unsupervised denoising
Author Correction: Optimal planning and sizing of microgrid cluster for performance enhancement
A μGal MOEMS gravimeter designed with free-form anti-springs
The relationship between body mass index and pathological complete response in Brazilian breast cancer patients
Calcium levels in ASER neurons determine behavioral valence by engaging distinct neuronal circuits in C. elegans
Secondary Hemophagocytic Lymphohistiocytosis in severe COVID-19 - a retrospective cohort study
Molecular basis of foreign DNA recognition by BREX anti-phage immunity system
Abstract Anti-phage systems of the BREX (BacteRiophage EXclusion) superfamily rely on site-specific epigenetic DNA methylation to discriminate between the host and invading DNA. We demonstrate that in Type I BREX systems, defense and methylation require BREX site DNA binding by the BrxX (PglX) methyltransferase employing S-adenosyl methionine as a cofactor. We determined 2.2-Å cryoEM structure of Escherichia coli BrxX bound to target dsDNA revealing molecular details of BREX DNA recognition. Structure-guided engineering of BrxX expands its DNA specificity and dramatically enhances phage defense. We show that BrxX alone does not methylate DNA, and BREX activity requires an assembly of a supramolecular BrxBCXZ immune complex. Finally, we present a cryoEM structure of BrxX bound to a phage-encoded inhibitor Ocr that sequesters BrxX in an inactive dimeric form. We propose that BrxX-mediated foreign DNA sensing is a necessary first step in activation of BREX defense.
Changing ecosystems promote generalism and enhanced heterogeneity in diet composition in the endangered St. Lawrence Estuary beluga
Abstract Changes in trophodynamics may affect trophic niche both at the individual and population levels. Using stable isotope ratios, we showed how contrasting oceanographic and trophic conditions in 1997–2003 and 2015–2020 have altered the diet and degree of individual specialization of St. Lawrence Estuary beluga (Delphinapterus leucas). The trophic niche of all sex and age classes changed over time, with beluga consuming more small pelagic prey during the first than the second period. Adult male diets differed from that of adult females and juveniles during the first period due to the other prey that were consumed. In 2015–2020, diet contributions by small pelagic prey decreased in all segments of the population and led to marginally significant differences in diet between adult males and females. These dietary changes were concomitant to a diversification of diet at the individual level and to an increase in diet heterogeneity among conspecifics and years within the 2015–2020 period. Whether these patterns emerged from an environment-driven reduction in prey biomass or from an increase in intra- and/or interspecific competition is unknown. Our findings illustrate the importance of considering individuals and not just the population when studying the foraging ecology of endangered species.
Ameba-inspired strategy enhances probiotic efficacy via prebound nutrient supply
Nutritional quality profiles of six microgreens
Abstract Globally, one in every four individuals faces a deficiency in essential micronutrients. Harvested early from various vegetables, grains, and herbs, microgreens have rich nutritional profiles that can mitigate nutrient deficiencies. Here, we analyzed six microgreens’ nutritional profiles for broccoli, black radish, red beet, pea, sunflower, and bean. Ascorbic acid content varied widely, from 32.72 mg/100 g fresh weight (FW) in red beet to 80.45 mg/100 g FW in beans. All microgreens exhibited high macro elements (mg/100 g FW), with potassium ranging from 187.07 to 416.05, magnesium from 45.96 to 86.83, calcium from 67.18 to 148.63, and phosphorus from 2.57 to 4.88. They also contained significant microelements (µg/100 g FW), including iron from 524 to 2610, manganese from 176.32 to 350.56, zinc from 31.92 to 129.78, and copper from 458.84 to 956.34. Glucose content surpassed sucrose and fructose, ranging from 0.114 to 0.580 mg/100 g FW. Among organic acids, citric acid was highest in red beet, succinic acid in beans, and fumaric acid in sunflower. Broccoli microgreens had the highest total phenolic content (825.53 mg GA/100 g FW), while beans had the highest total flavonoid content (758.0 mg RU/100 g FW). Black radish microgreens demonstrated the highest antioxidant capacity. Additionally, volatile aromatic compounds were analyzed across the six microgreen species. These findings highlight the nutritional potential of microgreens, advocating for their inclusion in diets to enhance human health. Red beet microgreens were the richest in organic acids, particularly citric acid, and flavonoids, supporting antioxidant activity, while black radish microgreens exhibited the highest DPPH antioxidant capacity and phenolic content. Bean microgreens stood out for their high ascorbic acid content. Sunflower microgreens had the highest levels of calcium and fumaric acid. Broccoli microgreens were abundant in phenolic compounds and contained high concentrations of iron and manganese. Finally, pea microgreens excelled in phosphorus and copper content.
Explainable artificial intelligence of DNA methylation-based brain tumor diagnostics
In vivo and in vitro investigations of schisandrin B against angiotensin II induced ferroptosis and atrial fibrosis by regulation of the SIRT1 pathway
Method for detecting cracks in retaining walls based on improved YOLOv5s
The beneficial effects of a probiotic mix on bone and lean mass are dependent on the diet in female mice
Abstract Bone mass and lean mass decrease with age and these changes are associated with increased fracture risk and sarcopenia. Previous studies demonstrated that a probiotic mixture of Lacticaseibacillus paracasei DSM13434, Lactiplantibacillus plantarum DSM 15312 and DSM 15313 (L. Mix) prevents bone loss in ovariectomized (ovx) female mice. The purpose of the present study is to test if the beneficial effect of L. Mix is modified by the diet. Female mice were fed either a high-fat (HFD, 60% kcal from fat) or a low-fat (LFD, 10% kcal from fat) diet and subjected to either sham or ovx surgery and treated with L. Mix for 12 weeks. L. Mix treatment increased total body bone mineral density (p ≤ 0.01), by increasing cortical bone area, and total body lean mass (p = 0.035) in mice on LFD but not in mice on HFD. Metagenome sequencing of cecal content showed that L. Mix treatment increased the relative abundance of Lacticaseibacillus paracasei and, Lactiplantibacillus plantarum, demonstrating successful treatment. In addition, the probiotic treatment affected the overall gut microbiota composition and functionality. These findings demonstrate that the L. Mix in combination with a healthy diet is beneficial for musculoskeletal health in female mice.