Microbial community
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA742479 | ENA |
REPOSITORIES: ENA
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Project description:CD47 is a transmembrane glycoprotein that is ubiquitously expressed in different organs and tissues (Barclay and Van den Berg 2014; Liu, et al. 2017). In the human immune system, CD47 interacts with some integrins, two counter-receptor signal regulator protein (SIRP) family members, and the secreted thrombospondin-1 (TSP1) (Barclay and Van den Berg 2014; Gao, et al. 2016; Kaur, et al. 2013; Oldenborg, et al. 2000). CD47 has two established roles in the immune system. The CD47-SIRPα interaction was identified as a critical innate immune checkpoint, which delivers an antiphagocytic signal to macrophages and inhibits neutrophil cytotoxicity (Martínez- Sanz, et al. 2021). Its interaction with inhibitory SIRPα is a physiological anti-phagocytic “don’t eat me” signal on circulating red blood cells that is co-opted by cancer cells (Matlung, et al. 2017). Many malignant cells overexpress CD47 (Betancur, et al. 2017; Chao, et al. 2011; Jaiswal, et al. 2009; Majeti, et al. 2009; Oronsky, et al. 2020; Petrova, et al. 2017). CD47/SIRPα-targeted therapeutics have been developed to overcome this immune checkpoint for cancer treatment (Kaur, et al. 2020; Matlung, et al. 2017). Secondly, engagement of CD47 on T cells by TSP1 regulates their differentiation and survival (Grimbert, et al. 2006; Lamy, et al. 2007) and inhibits T cell receptor signaling and antigen presentation by dendritic cells (DCs) (Kaur, et al. 2014; Li, et al. 2002; Liu, et al. 2015; Miller, et al. 2013; Soto-Pantoja, et al. 2014; Weng, et al. 2014). TSP1/CD47 signaling has similar inhibitory functions to limit NK cell activation (Kim, et al. 2008; Nath, et al. 2018; Nath, et al. 2019; Schwartz, et al. 2019) and IL1β production by macrophages (Stein, et al. 2016). CD47 is therefore a checkpoint that regulates both innate and adaptive immunity. The recent understanding of CD47 antagonism associated with increased antigen presentation by DCs (Liu, et al. 2016) and natural killer cell cytotoxicity (Nath, et al. 2019) contributes to the heightened interest in CD47 as a therapeutic target (Kaur, et al. 2020).
2022-09-21 | GSE198820 | GEO
Project description:Canonical auxin signalling starts with auxin binding to the receptor complex, followed by modulation of gene transcription and protein abundance (Tan et al., 2007; Chapman and Estelle, 2009; Slade et al., 2017). However, recent studies also showed an alternative mechanism in roots involving intra-cellular auxin perception, but not transcriptional reprogramming (Fendrych et al., 2018). Despite knowledge on effects of auxin on Arabidopsis root growth at the protein and phosphorylation level is increasing (Zhang et al., 2013; Mattei et al., 2013; Slade et al., 2017), it still remains incomplete. To address this gap in our knowledge, we explored the impact of auxin on the root tip proteome and phosphoproteome.
2021-09-09 | PXD021267 | Pride
Project description:The endophytic fungus Piriformospora indica is a member of Sebacinales. It colonizes the roots of many plant species including the model plant Arabidospis thaliana (Peskan-Berghofer et al. 2004). P. indica promotes plant growth (Peskan-Berghofer et al. 2004), seed production (Shahollari et al. 2007) and confers resistance to biotic (Camehl et al. 2011) and abiotic stresses (Sherameti et al., 2008, Matsuo et al., 2015). Vadassery et al. (2009) have shown that a cell wall extract from P. indica induces cytoplasmic calcium elevation in Arabidopsis Col-0 roots. Johnson et al. (2017) isolated an ethylmethane-induced mutant cycam (cytoplasmic calcium elevation mutant) which fails to induce cytoplasmic calcium elevation in response to the cell wall preparation. The active compound was identified as cellotriose (CT) (Johnson et al., 2017). The cycam mutant shows a wild-type response to treatment with chitin. The expression profiles compare the response of WT and cycam roots to treatments with CT and chitin. References: Camehl I, Drzewiecki C, Vadassery J, Shahollari B, Sherameti I, Forzani C, Munnik T, Hirt H, Oelmüller R. (2011) The OXI1 kinase pathway mediates Piriformospora indica-induced growth promotion in Arabidopsis. PLoS Pathog. 7(5):e1002051. Johnson JM, Thürich J, Petutschnig EK, Altschmied L, Meichsner D, Sherameti I, Dindas J, Mrozinska A, Paetz C, Scholz S, Furch A, Lipka V, Hedrich R, Schneider B, Svatoš S, Oelmüller R. (2017) Cellotriose-induced cytoplasmic calcium elevation is controlled by a poly(A) ribonuclease in Arabidopsis root. (submitted to elife). Matsuo M, Johnson JM, Hieno A, Tokizawa M, Nomoto M, Tada Y, Godfrey R, Obokata J, Sherameti I, Yamamoto YY, Böhmer FD, Oelmüller R. (2015) High REDOX RESPONSIVE TRANSCRIPTION FACTOR1 Levels Result in Accumulation of Reactive Oxygen Species in Arabidopsis thaliana Shoots and Roots. Mol Plant. 8(8):1253-73. Peškan-Berghöfer T, Shahollari B, Giang PH, Hehl S, Markert C, Blanke V, Varma AK, Oelmüller R. (2004) Association of Piriformospora indica with Arabidopsis thaliana roots represents a novel system to study beneficial plant–microbe interactions and involves early plant protein modifications in the endoplasmatic reticulum and at the plasma membrane. Physiol. Plant. 122: 465–477. Shahollari B, Vadassery J, Varma A, Oelmüller R. (2007) A leucine-rich repeat protein is required for growth promotion and enhanced seed production mediated by the endophytic fungus Piriformospora indica in Arabidopsis thaliana. Plant J. 50(1):1-13. Sherameti, I., Tripathi, S., Varma, A., and Oelmüller, R. (2008). The root-colonizing endophyte Pirifomospora indica confers drought tolerance in Arabidopsis by stimulating the expression of drought stress-related genes in leaves. Mol. Plant Microbe Interact. 21: 799-807. Vadassery, J., Ranf, S., Drzewiecki, C., Mithöfer, A., Mazars, C., Scheel, D., Lee, J., and Oelmüller, R. (2009) A cell wall extract from the endophytic fungus Piriformospora indica promotes growth of Arabidopsis seedlings and induces intracellular calcium elevation in roots. Plant J. 59: 193-206.
2018-02-09 | GSE98880 | GEO
Project description:Soil microbial community is a complex blackbox that requires a multi-conceptual approach (Hultman et al., 2015; Bastida et al., 2016). Most methods focus on evaluating total microbial community and fail to determine its active fraction (Blagodatskaya & Kuzyakov 2013). This issue has ecological consequences since the behavior of the active community is more important (or even essential) and can be different to that of the total community. The sensitivity of the active microbial community can be considered as a biological mechanism that regulates the functional responses of soil against direct (i.e. forest management) and indirect (i.e. climate change) human-induced alterations. Indeed, it has been highglihted that the diversity of the active community (analyzed by metaproteomics) is more connected to soil functionality than the that of the total community (analyzed by 16S rRNA gene and ITS sequencing) (Bastida et al., 2016). Recently, the increasing application of soil metaproteomics is providing unprecedented, in-depth characterisation of the composition and functionality of active microbial communities and overall, allowing deeper insights into terrestrial microbial ecology (Chourey et al., 2012; Bastida et al., 2015, 2016; Keiblinger et al., 2016). Here, we predict the responsiveness of the soil microbial community to forest management in a climate change scenario. Particularly, we aim: i) to evaluate the impacts of 6-years of induced drought on the diversity, biomass and activity of the microbial community in a semiarid forest ecocosystem; and ii) to discriminate if forest management (thinning) influences the resistance of the microbial community against induced drought. Furthermore, we aim to ascertain if the functional diversity of each phylum is a trait that can be used to predict changes in microbial abundance and ecosystem functioning.
2021-02-02 | PXD005447 | Pride
Project description:ATAC-seq samples from 2 species and 2 cell types were generated to study cis-regulatory element evolution. Briefly, previously generated urinary stem cell derived iPS-cells (Homo sapiens) of 2 human individuals and fibroblast derived cynomolgus macaque iPSCs (Macaca fascicularis) of 2 individuals (Geuder et al. 2021) were differentiated to neural progenitor cells via dual-SMAD inhibition as three-dimensional aggregation culture (Chambers et al. 2009; Ohnuki et al. 2014). The NPC lines were cultured in NPC proliferation medium and passaged 2 - 4 times until they were dissociated and subjected to ATAC-seq together with the respective iPSC clones. ATAC-seq libraries were generated using the Omni-ATAC protocol (Corces et al. 2017) with minor modifications.
2023-10-25 | E-MTAB-13373 | biostudies-arrayexpress
Project description:The goal of this study was to optimize protein extraction methods to study root-associated bacteria in maize. For this we inoculated sterile maize plants with a synthetic community composed of seven different bacteria (Ben Niu et al. PNAS 2017, vol 114, n 12). Then, we extracted proteins from maize roots using eight different protein extraction methods in triplicates. These methods were a combination of different extraction buffers (SDS or Triton-based) and mechanical disruption methods (bead-beating, N2 grinding, glass homogenizer and freeze-thaw cycles). We found that vortexing maize roots with glass beads in PBS yielded the highest numbers of microbial protein identification.
2022-09-08 | PXD026369 | Pride
Project description:The TNF superfamily is large, including TNF ligands (n = 19) and TNF receptors (n = 29),as determined following the completion of large-scale sequencing of the human and mouse genomes. These members not only function in immune cells but are also involved in respiratory and intestinal diseases, and some members may act as a double-edged sword. Tumor necrosis factor-like cytokine 1A (TL1A, also known as TNFSF15) is the only known death receptor 3 (DR3, also known as TNFRSF25) ligand (Meylan et al., 2011). The TL1A/DR3 axis plays a role in the regulation of intestinal immunity and fibrosis (Valatas et al., 2019), asthma airway remodeling (Zhang et al., 2022; Herro et al., 2010), and other autoimmune and inflammatory diseases (Herro et al., 2021), exacerbating disease progression. However, some researchers have proposed that the TL1A/DR3 axis has a protective role in some disease models. A novel role for TL1A/DR3 in protection against intestinal injury was reported by Jia et al (Jia et al., 2016). Yang et al. revealed a protective effect of TL1A against intracerebral hemorrhage-induced secondary brain injury and infection (Yang et al., 2021). In addition, TL1A maintains the blood–retinal barrier by modulating SHP-1-Src-VE-cadherin signaling in diabetic retinopathy, as verified by Li et al (Li et al., 2021). However, the role of TL1A/DR3 in ARDS has not been explored.
2023-02-07 | PXD039909 | iProX