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Antonie Van Leeuwenhoek May 2024Despite being one of the most abundant elements in soil, phosphorus (P) often becomes a limiting macronutrient for plants due to its low bioavailability, primarily... (Comparative Study)
Comparative Study
Despite being one of the most abundant elements in soil, phosphorus (P) often becomes a limiting macronutrient for plants due to its low bioavailability, primarily locked away in insoluble organic and inorganic forms. Phosphate solubilizing and mineralizing bacteria, also called phosphobacteria, isolated from P-deficient soils have emerged as a promising biofertilizer alternative, capable of converting these recalcitrant P forms into plant-available phosphates. Three such phosphobacteria strains-Serratia sp. RJAL6, Klebsiella sp. RCJ4, and Enterobacter sp. 198-previously demonstrated their particular strength as plant growth promoters for wheat, ryegrass, or avocado under abiotic stresses and P deficiency. Comparative genomic analysis of their draft genomes revealed several genes encoding key functionalities, including alkaline phosphatases, isonitrile secondary metabolites, enterobactin biosynthesis and genes associated to the production of indole-3-acetic acid (IAA) and gluconic acid. Moreover, overall genome relatedness indexes (OGRIs) revealed substantial divergence between Serratia sp. RJAL6 and its closest phylogenetic neighbours, Serratia nematodiphila and Serratia bockelmanii. This compelling evidence suggests that RJAL6 merits classification as a novel species. This in silico genomic analysis provides vital insights into the plant growth-promoting capabilities and provenance of these promising PSRB strains. Notably, it paves the way for further characterization and potential application of the newly identified Serratia species as a powerful bioinoculant in future agricultural settings.
Topics: Soil Microbiology; Genomics; Genome, Bacterial; Phylogeny; Indoleacetic Acids; Serratia; Enterobacter; Klebsiella; Plant Development; Soil; Plant Growth Regulators
PubMed: 38705910
DOI: 10.1007/s10482-024-01961-1 -
SLAS Technology Jun 2024Laboratory management automation is essential for achieving interoperability in the domain of experimental research and accelerating scientific discovery. The...
Laboratory management automation is essential for achieving interoperability in the domain of experimental research and accelerating scientific discovery. The integration of resources and the sharing of knowledge across organisations enable scientific discoveries to be accelerated by increasing the productivity of laboratories, optimising funding efficiency, and addressing emerging global challenges. This paper presents a novel framework for digitalising and automating the administration of research laboratories through The World Avatar, an all-encompassing dynamic knowledge graph. This Digital Laboratory Framework serves as a flexible tool, enabling users to efficiently leverage data from diverse systems and formats without being confined to a specific software or protocol. Establishing dedicated ontologies and agents and combining them with technologies such as QR codes, RFID tags, and mobile apps, enabled us to develop modular applications that tackle some key challenges related to lab management. Here, we showcase an automated tracking and intervention system for explosive chemicals as well as an easy-to-use mobile application for asset management and information retrieval. Implementing these, we have achieved semantic linking of BIM and BMS data with laboratory inventory and chemical knowledge. Our approach can capture the crucial data points and reduce inventory processing time. All data provenance is recorded following the FAIR principles, ensuring its accessibility and interoperability.
Topics: Automation, Laboratory; Laboratories; Information Storage and Retrieval
PubMed: 38703999
DOI: 10.1016/j.slast.2024.100135 -
BMJ (Clinical Research Ed.) May 2024
Topics: Humans; Child; Environmental Exposure; Air Pollution, Indoor; Child, Preschool
PubMed: 38702067
DOI: 10.1136/bmj-2023-077046 -
BMJ (Clinical Research Ed.) May 2024
Topics: Humans; Food Insecurity; United Kingdom; Child; Family Characteristics; Child, Preschool
PubMed: 38702058
DOI: 10.1136/bmj.q997 -
Food Chemistry: X Jun 2024With the proliferation of the consumer's awareness of wine provenance, wines with unique origin characteristics are increasingly in demand. This study aimed to...
With the proliferation of the consumer's awareness of wine provenance, wines with unique origin characteristics are increasingly in demand. This study aimed to investigate the influence of geographical origins and climatological characteristics on grapes and wines. A total of 94 anthocyanins and 78 non-anthocyanin phenolic compounds in grapes and wines from five Chinese viticultural vineyards (CJ, WH, QTX, WW, and XY) were identified by UHPLC-QqQ-MS/MS. Chemometric methods PCA and OPLS-DA were established to select candidate differential metabolites, including flavonols, stilbenes, hydroxycinnamic acids, peonidin derivatives, and malvidin derivatives. CCA showed that malvidin-3--glucoside had a positive correlation with mean temperature, and quercetin-3--glucoside had a negative correlation with precipitation. In addition, enrichment analysis elucidated that the metabolic diversity in different origins mainly occurred in flavonoid biosynthesis. This study would provide some new insights to understand the effect of geographical origins and climatological characteristics on phenolic compounds in grapes and wines.
PubMed: 38699585
DOI: 10.1016/j.fochx.2024.101396 -
IEEE Transactions on Visualization and... May 2024Visualizing event timelines for collaborative text writing is an important application for navigating and understanding such data, as time passes and the size and...
Visualizing event timelines for collaborative text writing is an important application for navigating and understanding such data, as time passes and the size and complexity of both text and timeline increase. They are often employed by applications such as code repositories and collaborative text editors. In this paper, we present a visualization tool to explore historical records of writing of legislative texts, which were discussed and voted on by an assembly of representatives. Our visualization focuses on event timelines from text documents that involve multiple people and different topics, allowing for observation of different proposed versions of said text or tracking data provenance of given text sections, while highlighting the connections between all elements involved. We also describe the process of designing such a tool alongside domain experts, with three steps of evaluation being conducted to verify the effectiveness of our design.
PubMed: 38696299
DOI: 10.1109/TVCG.2024.3376406 -
The Journal of Allergy and Clinical... Apr 2024Autoimmune cytopenias (AICs) regularly occur in profoundly IgG-deficient patients with common variable immunodeficiency (CVID). The isotypes, antigenic targets, and...
BACKGROUND
Autoimmune cytopenias (AICs) regularly occur in profoundly IgG-deficient patients with common variable immunodeficiency (CVID). The isotypes, antigenic targets, and origin(s) of their disease-causing autoantibodies are unclear.
OBJECTIVE
We sought to determine reactivity, clonality, and provenance of AIC-associated IgM autoantibodies in patients with CVID.
METHODS
We used glycan arrays, patient erythrocytes, and platelets to determine targets of CVID IgM autoantibodies. Glycan-binding profiles were used to identify autoreactive clones across B-cell subsets, specifically circulating marginal zone (MZ) B cells, for sorting and IGH sequencing. The locations, transcriptomes, and responses of tonsillar MZ B cells to different T- cell subsets were determined by confocal microscopy, RNA-sequencing, and cocultures, respectively.
RESULTS
Autoreactive IgM coated erythrocytes and platelets from many CVID patients with AICs (CVID+AIC). On glycan arrays, CVID+AIC plasma IgM narrowly recognized erythrocytic i antigens and platelet i-related antigens and failed to bind hundreds of pathogen- and tumor-associated carbohydrates. Polyclonal i antigen-recognizing B-cell receptors were highly enriched among CVID+AIC circulating MZ B cells. Within tonsillar tissues, MZ B cells secreted copious IgM when activated by the combination of IL-10 and IL-21 or when cultured with IL-10/IL-21-secreting FOXP3CD25 T follicular helper (Tfh) cells. In lymph nodes from immunocompetent controls, MZ B cells, plentiful FOXP3 regulatory T cells, and rare FOXP3CD25 cells that represented likely CD25 Tfh cells all localized outside of germinal centers. In CVID+AIC lymph nodes, cellular positions were similar but CD25 Tfh cells greatly outnumbered regulatory cells.
CONCLUSIONS
Our findings indicate that glycan-reactive IgM autoantibodies produced outside of germinal centers may contribute to the autoimmune pathogenesis of CVID.
PubMed: 38692308
DOI: 10.1016/j.jaci.2024.04.018 -
Analytical Chemistry May 2024Uranium isotopic composition can provide valuable information about the history and provenance of a nuclear material; therefore, uranium isotopic analyses are frequently...
Uranium isotopic composition can provide valuable information about the history and provenance of a nuclear material; therefore, uranium isotopic analyses are frequently made in the nuclear forensics, safeguards, and environmental monitoring communities. These measurements have always presented challenges due to the extreme variability in the relative abundance between the major (U, U) and minor (U, U, U) isotopes of uranium. The recently developed ATONA (Atto- to Nano-Amp) amplification system paired with Faraday cup detectors has a large dynamic range and low noise floor making it ideal for measuring uranium isotopic ratios in materials of both natural and anthropogenic origin. A wide variety of certified reference materials were analyzed to investigate the utility of the ATONA amplification system for determining uranium isotopic composition in samples ranging from depleted to highly enriched. The ATONA amplifiers provide nearly an order of magnitude improvement in external reproducibility over 10 Ω amplifiers when measuring the minor U/U ratio in isotopically natural and depleted samples and when paired with a secondary electron multiplier can measure very low relative abundance uranium isotopes (i.e., U).
PubMed: 38687593
DOI: 10.1021/acs.analchem.4c00471 -
Heritage Science 2024This paper presents the results of the first X-ray fluorescence (XRF) investigation conducted on three late medieval chalices associated with Ireland: the Ó Learghusa...
UNLABELLED
This paper presents the results of the first X-ray fluorescence (XRF) investigation conducted on three late medieval chalices associated with Ireland: the Ó Learghusa chalice, auctioned as medieval Irish in 2021, does not have a confirmed provenance; the de Burgo-O'Malley chalice, dated 1494, and the TP-IEP chalice, dated 1589, both of Irish provenance. This study effectively addressed the knowledge gap concerning Irish medieval silver chalices composition. The analysis revealed that both the Ó Learghusa and de Burgo-O'Malley chalices were crafted from a silver-copper alloy and adorned using a fire-gilding technique. The blue and green enamels on the de Burgo-O'Malley chalice were found to be constituted by cobalt and iron/copper glasses, respectively. In contrast, the TP-IEP chalice exhibited a more intricate structure, being a composite object with partial silver gilt and with the bowl and base possibly made of a ternary silver-copper-gold alloy. The TP-IEP chalice's knop displayed glass, simulating gems with transparent, blue, and purple colorations. XRF analysis allowed identification of lead-potash glass, while the red glass displayed a rich iron content and was identified as soda-lime glass. The analysis allowed concluding that the de Burgo-O'Malley chalice had retained its original condition, including its original gilding and enamels, while the Ó Learghusa and TP-IEP chalices appeared to have undergone refurbishment. These significant discoveries contribute to a deeper understanding of the historical context and artistic craftsmanship behind these late medieval chalices, shedding light on their unique stories within Irish art and history.
SUPPLEMENTARY INFORMATION
The online version contains supplementary material available at 10.1186/s40494-024-01240-2.
PubMed: 38682009
DOI: 10.1186/s40494-024-01240-2 -
Heliyon Apr 2024The Pisha Sandstone is widely exposed in the northeastern margin of the Ordos basin. Since the Mesozoic the basin was subjected to uneven uplift several times, strong...
The Pisha Sandstone is widely exposed in the northeastern margin of the Ordos basin. Since the Mesozoic the basin was subjected to uneven uplift several times, strong weathering and erosion have been occurring and a large amount of sediments derived from these erosional strata are input into the lower Yellow River, posing a fragile ecological environment along the river. However, the geochemical characteristics of the Pisha Sandstone have remained poorly understood. In this study, we focus on the Pisha Sandstone from Early-Middle Triassic Liujiagou, Heshanggou and Ermaying Formation, present a very first petrographic and geochemical data together with detailed field geological characteristics, aiming to place geochemical indicators on weathering, provenance and tectonic setting of the Pisha Sandstone. The results show that sandstones in Pisha Sandstone are classified as arkose, litharenite and wacke. The geochemical proxies including Chemical Index of Alteration (CIA = 67.2), Chemical Index of Weathering (CIW = 80.1), Plagioclase Index of Alteration (PIA = 75.6) and Index of Compositional Variability (ICV = 1.6) indicate Pisha Sandstone experienced first-cycle deposit and moderate to strong chemical weathering. Trace element and rare earth element concentrations together with their ratios (La/Sc, La/Co, Th/Sc, Th/Co, Cr/Th) reveal a felsic provenance, and source rock compositions are predominantly granodiorite and granite from the north margin of the Inner Mongolia Paleo-Uplift (IMPU), with a small amount of mafic or intermediate components. The geochemical signatures and tectonic discrimination diagrams display a collision setting for the Pisha Sandstone and further reveal the sediments had been deposited in a continental island arc setting. The results of this work may provide new theoretical basis for environmental protection in the Pisha Sandstone area.
PubMed: 38681579
DOI: 10.1016/j.heliyon.2024.e29120