Biology subjects

Berg, L.

Publications and source records attributed to Berg, L..

5 recordsLinked to original sources

bioRxiv2026

A single-cell transcriptome atlas of the barley root apical meristem uncovers conserved and divergent roles of HvWOX5

Single-cell approaches have transformed plant developmental biology; however, cell-type-resolved resources for cereals remain limited. Here, we present a single-cell transcriptome atlas of the barley root apical meristem (RAM), which resolves 24 transcriptionally distinct cell populations. We assigned major root cell identities by integrating marker gene validation using Hybridization Chain Reaction (HCR) RNA fluorescence in situ hybridization and spatial transcriptomics with cross-species comparisons of published root atlases. Pseudotime analysis reconstructed developmental trajectories from the quiescent center to differentiating tissues, supporting the spatial and developmental organization of the atlas. We further demonstrated the utility of this resource by identifying HvWOX5 expression in the quiescent center and metaxylem and showing that HvWOX5 loss-of-function mutants displayed reduced root and meristem lengths, altered stem cell niche homeostasis, and disrupted metaxylem organization. Taken together, this atlas provides a framework for dissecting barley root development and identifies HvWOX5 as a key regulator of RAM organization and metaxylem patterning.

Plant Biology↗

bioRxiv2024

Strong pairwise Interactions do not Drive Interactions in a Plant Leaf Associated Microbial Community

Microbial communities that promote plant growth show promise in reducing the impacts of climate change on plant health and productivity. Understanding microbe-microbe interactions in a community context is paramount for designing effective microbial consortia that enhance plant resilience. In this study, we investigated the dynamics of a synthetic microbial community (SynCom) assembled from Arabidopsis thaliana leaves to elucidate factors shaping community composition and stability. We found notable disparities between in vitro pairwise interactions and those inferred from correlation networks in planta. Our findings suggested that secondary metabolites, particularly antimicrobials, might mediate interactions in vitro, but fade into the background in the community context. Through co-cultivation experiments, we identified the siderophore pseudobactin as a potent antimicrobial agent against several SynCom members, but its impact on community composition in planta was negligible. Notably, dominant SynCom members, such as Pseudomonas koreensis, Flavobacterium pectinovorum, and Sporobolomyces roseus, exhibited only positive correlations, suggesting synergism based on for example exopolysaccharides and biotransformation might drive community dynamics rather than competition. Two correlations between SynCom members in the co-abundance network corresponded with their pairwise in vitro interactions, highlighting the potential for further research, and demonstrating the usefulness of correlation networks in identifying key microbe-microbe interactions. Our findings highlight the importance of considering microbiome-wide interaction studies and synthetic communities in understanding and manipulating plant microbiomes.

microbiology↗

bioRxiv2022

Temporal Extracellular Vesicle Protein Changes following Intraarticular Treatment with Integrin α10β1-selected Mesenchymal Stem Cells in Equine Osteoarthritis

Equine osteoarthritis is a heterogeneous, degenerative disease of the musculoskeletal system with multifactorial causation, characterised by a joint metabolic imbalance. Extracellular vesicles are nanoparticles involved in intracellular communication. Mesenchymal stem cell (MSC) therapy is a form of regenerative medicine that utilises their properties to repair damaged tissues. Despite its wide use in veterinary practice, the exact mechanism of action of MSCs is not fully understood. The aim of this study was to determine the synovial fluid extracellular vesicle protein cargo following integrin 10{beta}1-selected mesenchymal stem cell treatment in an experimental model of equine osteoarthritis with longitudinal sampling. Adipose tissue derived, integrin 10-MSCs were injected into the osteoarthritis afflicted joint after 18 days post surgery. Sixty-nine synovial fluid samples were collected via aseptic arthrocentesis at day 0, 18, 21, 28, 35, and 70. Synovial fluid was hyaluronidase treated and extracellular vesicles isolated using differential ultracentrifugation. Extracellular vesicles were characterised using the Exoview human tetraspanin chip. Extracellular vesicle concentration, surface marker identification, fluorescent microscopy and tetraspanin colocalization analysis was undertaken, in conjunction with nanoparticle tracking analysis. For proteomics, extracellular vesicle pellets were suspended in urea lysis buffer. Samples were reduced, alkylated and digested on SP3 beads with trypsin/LysC. A data independent acquisition mode was utilised for nano liquid chromatography tandem mass spectrometry analysis on a Triple TOF 6600 mass spectrometer. A total of 442 proteins were identified across all samples, with 48 proteins differentially expressed (FDR[≤] 0.05) between control and osteoarthritis treated with MSCs.. The most significant pathways following functional enrichment analysis of the differentially abundant protein dataset were serine endopeptidase activity (p=0.023), complement activation (classical pathway) (p=0.023), and collagen containing extracellular matrix (p=0.034). To date this is the first study to quantify the global extracellular vesicle proteome in synovial fluid following MSC treatment of osteoarthritis. Changes in the proteome of the synovial fluid-derived EVs following MSC injection suggest EVs may play a role in mediating the effect of cell therapy through altered joint homeostasis and an improved phenotype.

molecular biology↗

bioRxiv2020

Identifying novel B-cell targets for chronic inflammatory autoimmune disease by screening of chemical probes in a patient-derived cell assay

B-cell secretion of autoantibodies drives autoimmune diseases, including systemic lupus erythematosus and idiopathic inflammatory myositis. Few therapies are presently available for treatment of these patients, often resulting in unsatisfactory effects and helping only some of patients. We developed a screening assay for evaluation of novel targets suspending B-cell maturation into antibody secreting cells, which could contribute to future drug development. The assay was employed for testing 43 high quality chemical probes and compounds inhibiting under-explored protein targets, using primary cells from patients with autoimmune disease. Probes inhibiting bromodomain family proteins and histone methyl transferases demonstrated abrogation of B-cell functions to a degree comparable to a positive control, the JAK inhibitor tofacitinib. Inhibition of each target rendered a specific functional cell and potential disease modifying effect, indicating specific epigenetic protein targets as potential new intervention points for future drug discovery and development efforts.

immunology↗

bioRxiv2019

Anti-inflammatory properties of chemical probes in human whole blood: focus on prostaglandin E2 production

We screened 57 chemical probes, high-quality tool compounds, and relevant clinically used drugs to investigate their effect on pro-inflammatory prostaglandin E2 (PGE2) production and interleukin-8 (IL-8) secretion in human whole blood. Freshly drawn blood from healthy volunteers and patients with systemic lupus erythematosus (SLE) or dermatomyositis was incubated with compounds at 0.1 or 1 M and treated with lipopolysaccharide (LPS, 10 g/mL) to induce a pro-inflammatory condition. Plasma was collected after 24 hours for lipid profiling using liquid chromatography tandem mass spectrometry (LC-MS/MS) and IL-8 quantification using enzyme-linked immunosorbent assay (ELISA). Each compound was tested in at least four donors at one concentration based on prior knowledge of binding affinities and in vitro activity. Our screening suggested that PD0325901 (MEK-1/2 inhibitor), trametinib (MEK-1/2 inhibitor), and selumetinib (MEK-1 inhibitor) decreased while tofacitinib (JAK inhibitor) increased PGE2 production. These findings were validated by concentration-response experiment in two donors. Moreover, the tested MEK inhibitors decreased thromboxane B2 (TXB2) production and IL-8 secretion. We also investigated the lysophophatidylcholine (LPC) profile in plasma from treated whole blood as these lipids are potentially important mediators in inflammation, and we did not observe any changes in LPC profiles. Collectively, we deployed a semi-high throughput and robust methodology to investigate anti-inflammatory properties of new chemical probes. HighlightsO_LIInhibitors for MEK decreased PGE2 and TXB2 production C_LIO_LIInhibitors for MEK and ERK decreased IL-8 secretion C_LIO_LIJAK inhibitor tofacitinib increased PGE2 and TXB2 production C_LI

immunology↗