STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse

Multi-omics approaches use a diversity of high-throughput technologies to profile the different molecular layers of living cells. Ideally, the integration of this information should result in comprehensive systems models of cellular physiology and regulation. However, most multi-omics projects still include a limited number of molecular assays and there have been very few multi-omic studies that evaluate dynamic processes such as cellular growth, development and adaptation. Hence, we lack formal analysis methods and comprehensive multi-omics datasets that can be leveraged to develop true multi-layered models for dynamic cellular systems. Here we present the STATegra multi-omics dataset that combines measurements from up to 10 different omics technologies applied to the same biological system, namely the well-studied mouse pre-B-cell differentiation. STATegra includes high-throughput measurements of chromatin structure, gene expression, proteomics and metabolomics, and it is complemented with single-cell data. To our knowledge, the STATegra collection is the most diverse multi-omics dataset describing a dynamic biological system

Enhanced Botrytis cinerea resistance of Arabidopsis plants grown in compost may be explained by increased expression of defense-related genes, as revealed by microarray analysis

Composts are the products obtained after the aerobic degradation of different types of organic matter waste and can be used as substrates or substrate/soil amendments for plant cultivation. There is a small but increasing number of reports that suggest that foliar diseases may be reduced when using compost, rather than standard substrates, as growing medium. The purpose of this study was to examine the gene expression alteration produced by the compost to gain knowledge of the mechanisms involved in compost-induced systemic resistance. A compost from olive marc and olive tree leaves was able to induce resistance against Botrytis cinerea in Arabidopsis, unlike the standard substrate, perlite. Microarray analyses revealed that 178 genes were differently expressed, with a fold change cut-off of 1, of which 155 were up-regulated and 23 were down-regulated in compost-grown, as against perlite-grown plants. A functional enrichment study of up-regulated genes revealed that 38 Gene Ontology terms were significantly enriched. Response to stress, biotic stimulus, other organism, bacterium, fungus, chemical and abiotic stimulus, SA and ABA stimulus, oxidative stress, water, temperature and cold were significantly enriched, as were immune and defense responses, systemic acquired resistance, secondary metabolic process and oxireductase activity. Interestingly, PR1 expression, which was equally enhanced by growing the plants in compost and by B. cinerea inoculation, was further boosted in compost-grown pathogen-inoculated plants. Compost triggered a plant response that shares similarities with both systemic acquired resistance and ABA-dependent/independent abiotic stress responses

Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches

Extracellular vesicles (EVs), through their complex cargo, can reflect the state of their cell of origin and change the functions and phenotypes of other cells. These features indicate strong biomarker and therapeutic potential and have generated broad interest, as evidenced by the steady year-on-year increase in the numbers of scientific publications about EVs. Important advances have been made in EV metrology and in understanding and applying EV biology. However, hurdles remain to realising the potential of EVs in domains ranging from basic biology to clinical applications due to challenges in EV nomenclature, separation from non-vesicular extracellular particles, characterisation and functional studies. To address the challenges and opportunities in this rapidly evolving field, the International Society for Extracellular Vesicles (ISEV) updates its 'Minimal Information for Studies of Extracellular Vesicles', which was first published in 2014 and then in 2018 as MISEV2014 and MISEV2018, respectively. The goal of the current document, MISEV2023, is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues. In addition to presenting the latest state of the art in basic principles of EV research, this document also covers advanced techniques and approaches that are currently expanding the boundaries of the field. MISEV2023 also includes new sections on EV release and uptake and a brief discussion of in vivo approaches to study EVs. Compiling feedback from ISEV expert task forces and more than 1000 researchers, this document conveys the current state of EV research to facilitate robust scientific discoveries and move the field forward even more rapidly

Stress inducible glycosyltransferases in <em>Arabidopsis thaliana</em> and their impact on plant metabolism and defense mechanisms.

Small molecule glycosylation in plants is crucial for the biosynthesis of secondary metabolites and the regulation of the activity of several signaling molecules and defense compounds. One hundred and twenty-two different UDP-dependent glycosyltransferases (UGTs) catalyzing these conjugations exist in the model plant Arabidopsis thaliana. Despite major advances in plant biology due to genome annotations and &lsquo;omics&rsquo; approaches, the vast majority are still uncharacterized enzymes without known specific substrates and physiological roles. In this project, the role of UGTs in plant stress response was investigated focusing on top stress responsive candidate genes. Transcriptional responsiveness of all UGT members of Arabidopsis was analyzed using publicly available expression data of plants exposed to several abiotic and biotic stress cues. A clear clustering of stress-dependent inductions was observed highlighting several highly responsive UGT genes with yet unknown function. The two top-ranking stress-induced and previously uncharacterized glucosyltransferases UGT76B1 and UGT87A2 were selected for further functional characterization. Both are broadly up-regulated by abiotic as well as biotic cues, suggesting an important stress related role. Using a reverse genetics approach (knockout and overexpression lines) metabolic and phenotypic changes correlating with the expression of the corresponding UGT gene were analyzed. In the case of UGT87A2, plants with altered UGT expression did not reveal any obvious phenotypes even when several stress cues were applied. Non-targeted FT-ICR-MS analyses in the negative mode of two knockout lines did not reveal significant metabolic changes, whereas independent overexpression lines showed several m/z peaks indicating up-regulated metabolites. Further characterization of these compounds led to the identification of a new metabolite in Arabidopsis, ascorbic acid 2-O-&szlig;-glucoside. Together with the upregulation of other putative compounds, the results suggest potential roles for UGT87A2 in ascorbic acid homeostasis or cell wall biosynthesis. UGT76B1 was identified as a novel player in plant defense affecting the antagonistic salicylic acid and jasmonate-dependent signaling pathways. Loss of the UGT76B1 function led to enhanced resistance to hemibiotrophic pathogens and accelerated senescence. This was accompanied by constitutively elevated SA levels and SA-related marker gene expression and repression of JA-dependent marker genes. The overexpression caused the opposite phenotypes. UGT76B1 therefore attenuates SA-dependent plant defense in the absence of infection, promotes JA response and suppresses the onset of senescence. Non-targeted metabolomic analyses of ugt76b1 knockout and UGT76B1-OE lines using ultra-high resolution Fourier-transform ion cyclotron mass spectrometry led to an unprecedented ab initio substrate identification. In vitro assays employing the recombinant enzyme confirmed isoleucic acid (2-hydroxy-3-methyl-pentanoic acid) as the UGT76B1 substrate. The findings indicate a novel link of amino acid-related molecules to plant pathogen defense pathways via small-molecule glucosylation. Together these findings emphasize the importance of plant secondary metabolite UGTs in plant defense mechanisms and provide a foundation for a detailed understanding of their role in plant stress response. Further, the results presented highlight the great potential of using high resolution metabolomic analysis for non-targeted screening plant mutants to identify new metabolites and reveal novel gene functions without any other prior knowledge

Mass spectrometric stereoisomeric differentiation between &alpha;- and &beta;-ascorbic acid 2-O-glucosides. Experimental and density functional theory study.

L-Ascorbic acid and two distinct anomers, namely the &alpha;-D-glucopyranosyl and &beta;-D-glucopyranosyl-(1&rarr;2)-L-ascorbic acid (stereoisomers), were studied within the scope of collision-induced dissociation (CID) experiments, performed by linear ion acceleration and collision with argon atoms inside a hexapole quadrupole hexapole ion beam guide, which is coupled to an ion cyclotron resonance (ICR) cell with a 12 Tesla magnet for high-resolution measurements. Loss of C(2)H(4)O(2) neutral from the [M-H](-) anion of L-ascorbic acid was observed. Density functional theory (DFT) calculations on the 6-311+G(2d,p)//6-31+G(d) level of theory reveal a new concerted mechanism for an intramolecular gas-phase rearrangement, through which the observed ejected neutral C(2)H(4)O(2) can take place. A similar rearrangement also occurs in the case of &alpha;- and &beta;-D-glucopyranosyl-(1&rarr;2)-L-ascorbic acid. For the &alpha; isomer, only homolytic glycoside fragmentation was observed. For the &beta; isomer, both homolytic and heterolytic glycoside cleavages were possible. The mechanisms behind all observed fragmentation pathways were fully understood by the implementation of accurate DFT calculations. Stereoisomeric differentiation between &alpha; and &beta; isomers of the L-ascorbic acid-2-O-glucoside could be revealed by tandem mass spectrometry (MS/MS) experiments and were explained theoretically

The defense-related isoleucic acid differentially accumulates in <em>Arabidopsis</em> among branched-chain amino acid-related 2-hydroxy carboxylic acids. (vol 9, 766, 2018).

FIGURE LEGEND In the original article, there was a mistake in the legend for Figure 6 and Figure 7 as published. The numbering for Figure 6 was mixed with Figure 7 and not in agreement with the text: this mistake was introduced during proof stage, since the editing changed both legend and figure number. In addition, DC3000 should not be in italics. The correct numbering of Figures 6 and 7 appear below. FIGURE 6BCAA levels after exogenous application of 2-HAs to A. thaliana plants FIGURE 7ILA and LA abundance in response to P. syringae virulent strain infection. ERROR IN FIGURE In the original article, there was a mistake in Figures 2–4, and 6 as published. Due to the incorrect calculation of 2-HA level (a factor 50 was missed), all figures showing such measurements have to be replaced with the corrected y axis and limit of detection. The corrected Figures 2–4, and 7 appear below. (Figure presented.)

The defense-related isoleucic acid differentially accumulates in arabidopsis among branched-chain amino acid-related 2-hydroxy carboxylic acids.

The branched-chain amino acid (BCAA) related 2-hydroxy carboxylic acid isoleucic acid (ILA) enhances salicylic acid-mediated pathogen defense in Arabidopsis thaliana. ILA has been identified in A. thaliana as its glucose conjugate correlated with the activity of the small-molecule glucosyltransferase UGT76B1, which can glucosylate both salicylic acid and ILA in vitro. However, endogenous levels of the ILA aglycon have not yet been determined in planta. To quantify ILA as well as the related leucic acid (LA) and valic acid (VA) in plant extracts, a sensitive method based on the derivatization of small carboxylic acids by silylation and gas chromatography&ndash;mass spectrometric analysis was developed. ILA was present in all species tested including several monocotyledonous and dicotyledonous plants as well as broadleaf and coniferous trees, whereas LA and VA were only detectable in a few species. In A. thaliana both ILA and LA were found. However, their levels varied during plant growth and in root vs. leaves. ILA levels were higher in 2-week-old leaves and decreased in older plants, whereas LA exhibited a reverted accumulation pattern. Roots displayed higher ILA and LA levels compared to leaves. ILA was inversely related to UGT76B1 expression level indicating that UGT76B1 glucosylates ILA in planta. In contrast, LA was not affected by the expression of UGT76B1. To address the relation of both 2-hydroxy acids to plant defense, we studied ILA and LA levels upon infection by Pseudomonas syringae. LA abundance remained unaffected, whereas ILA was reduced. This change suggests an ILA-related attenuation of the salicylic acid response. Collectively, the BCAA-related ILA and LA differentially accumulated in Arabidopsis, supporting a specific role and regulation of the defense-modulating small-molecule ILA among these 2-hydroxy acids. The new sensitive method will pave the way to further unravel their role in plants