Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Alginate metabolic pathways of the strain C42 associated with Sargassum

ABSTRACT: Based on the genome sequencing and gene annotation, we analyzed the alginate lyases and other genes related to alginate metabolism of strain Vibrio sp. C42, with the highest alginate-degrading activity. Combined with proteome measurement, we proposed its alginate metabolic pathways.

INSTRUMENT(S):

ORGANISM(S): Vibrio Atlanticus

SUBMITTER: Sun Xiaomeng

LAB HEAD: Xiaomeng Sun

PROVIDER: PXD037554 | Pride | 2026-06-04

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	P20211205791_C42_G_1.raw	Raw
	P20211205791_C42_G_3.raw	Raw
	P20211205791_C42_SA_2.raw	Raw
	P20211205791_C42_SA_3.raw	Raw
	txt.zip	Other

Items per page:

1 - 5 of 5

Similar Datasets

Cultivable Alginate Lyase-Excreting Bacteria Associated with Sargassum and their alginate metabolic pathways

Project description:Based on the genome sequencing and gene annotation, we analyzed the alginate lyases and other genes related to alginate metabolism of strain Vibrio sp. C42, with the highest alginate-degrading activity. Combined with secretome measurement, we proposed its alginate metabolic pathways.

2026-06-04 | PXD029037 | Pride

Gene expression in cells encapsulated within different types of alginate microcapsules

Project description:D1 multipotent mesenchymal stromal cells (D1‐MSCs,ATCC® CRL 12424TM) and genetically modified with the lentiviral vector pSIN‐EF2‐Epo‐Pur to express erythropoietin (EPO). D1‐MSCs genetically modified to release EPO were immobilized into 3D alginatepoly‐ L‐lysine‐alginate (APA) microcapsules. Since different formulations of alginate 1.5%, poly‐L‐lysine 0.05%, alginate 0.1% and washings were designed, two types of APA microcapsules were obtained: Biological microcapsules (made of Biological formulations) and Technological microcapsules (made of Technological formulations). The expression of the cells under different conditions of these two types of microcapsules have been analyzed. The present analysis proved that the mechanical properties of the matrix in which cells are enclosed influences drastically gene expression

2017-10-30 | E-MTAB-5786 | biostudies-arrayexpress

Dynamic study of In vitro murine follicle maturation in 3% alginate gels

Project description:Multilayer murine follicles were grown in 3% alginate and follicles were isolated for transcriptomics analysis at day 0, 2, 4,5,6,and 8 after encapsulation. This data complements to the GSE42795, where follicles were grown in vitro in 0.5% alginate gels A total of 8 samples were analyzed, each of them repeted in triplicate

2014-06-01 | E-GEOD-55969 | biostudies-arrayexpress

Identification of adsorbing human plasma proteins on alginate gel beads

Project description:The biocompatibility of immunoisolation devices is a major challenge for their use in cellular therapies. Utilisation of alginate for the encapsulation of pancreatic islets as a potential cellular therapy for type 1 diabetes has shown to be limited in terms of long-term graft survival, due to pericapsular fibrotic overgrowth. Fibrotic overgrowth is a complex process that involves several factors, including protein adsorption. This work investigates the protein adsorption profiles of plasma incubated alginate beads for the identification of key proteins that may play a role in the biocompatibility of this biomaterial.

2023-03-10 | PXD009135 | Pride

Microbial alginate foraging is conserved in geographically and taxonomically distinct ruminant microbiomes

Project description:Saccharina latissima is a brown alga commonly found in the North Atlantic, Arctic and Pacific oceans. Alginate constitutes a substantial portion of the cell wall of S. latissima, and its digestion requires a specific set of enzymes, alginate lyases. We investigated if and how S. latissima is metabolized in geographically distinct rumen ecosystems through in vivo lamb feeding experiments (2.5 and 5% inclusion, DM basis) and in vitro cattle-based rumen simulation technique, RUSITEC, experiments (up to 50% inclusion). Evidence supporting ruminal degradation of alginate was explored using a combination of 16S rRNA sequencing, metagenomics and metaproteomics, physiology (fluorescently labelled S. latissima hot water extracts (FLA-SLAT)) and biochemical characterization of PL6 alginate lyases.

2026-04-16 | PXD059090 | Pride

Expression analysis of Sphingomonas. sp A1 AlgO-deficient mutant grown in 0.5% alginate medium or 0.5% yeast extract medium

Project description:Investigation of whole genome gene expression level changes in Sphingomonas. sp A1 AlgO-deficient mutant grown on alginate compared with that on yeast extract AlgO is a possble transcriptional factor described in J. Bacteriol. (2000) 182(14):3998-4004 by Momma K, Okamoto M, Mishima Y, Mori S, Hashimoto W, and Murata K. A two chip study using total RNA recovered from two cultures of Sphingomonas. sp A1 AlgO-deficient mutant grown in 0.5% alginate medium and 0.5% yeast extract medium. Each chip measures the expression level of genes from Sphingomonas. sp A1.

2014-01-28 | E-GEOD-54410 | biostudies-arrayexpress

Towards optimized tissue regeneration: A new 3D printable bioink of alginate/cellulose hydrogel loaded with thrombocyte concentrate

Project description:Introduction: Autologous platelet concentrates (APC) are pro-angiogenic and can promote wound healing and tissue repair, also in combination with other biomaterials. However, challenging defect situations remain demanding. 3D bioprinting of an APC based bioink encapsulated in a hydrogel could overcome this limitation with enhanced physio-mechanical interface, growth factor retention/secretion and defect-personalized shape to ultimately enhance regeneration. Methods: This study used extrusion-based bioprinting to create a novel bioink of alginate/cellulose hydrogel loaded with thrombocyte concentrate. Chemico-physical testing exhibited an amorphous structure characterized by high shape fidelity. Cytotoxicity assay and incubation of human osteogenic sarcoma cells (SaOs2) exposed excellent biocompatibility. ELISA analysis confirmed pro-angiogenic growth factor release of the printed constructs, and co-incubation with HUVECS displayed proper cell viability and proliferation. Chorioallantoic membrane (CAM) assay explored the pro-angiogenic potential of the prints in vivo. Detailed proteome and secretome analysis revealed a substantial amount and homologous presence of pro-angiogenic proteins in the 3D construct. Results: This study demonstrated a 3D bioprinting approach to fabricate a novel bioink of alginate/cellulose hydrogel loaded with thrombocyte concentrate with high shape fidelity, biocompatibility, and substantial pro-angiogenic properties. Conclusion: This approach may be suitable for challenging physiological and anatomical defect situations when translated into clinical use.

2024-06-23 | PXD050629 | Pride

Epithelium-only cultured stem cells isolated from human pluripotent stem cell derived intestinal organoids grown in matrigel and alginate

Project description:Human intestinal organoids were grown in a typical 3D matrigel culture environment, or in an alginate gel, then a subset from each condition were xenotransplanted to vascularized and mature in vivo. Epithelium was isolated and epithelial only organoids (enteroids) were then grown from each condition prior to sequencing bulk RNA-sequencing.

2019-06-27 | E-MTAB-7000 | biostudies-arrayexpress

Chondrogenic differentiation of human bone marrow-derived mesenchymal stem cells in self-gelling alginate discs reveals novel chondrogenic signature gene clusters

Project description:We have used a disc-shaped self-gelling alginate hydrogel as a scaffold for in vitro chondrogenic differentiation of human bone marrow-derived mesenchymal stem cells. The comparison of monolayer cells and alginate embedded cells with or without differentiation medium allowed us to perform a detailed kinetic study of the expression of a range of genes and proteins known to be involved in chondrogenesis, using real-time polymerase chain reaction, fluorescence immunohistochemistry, and glycosaminoglycan measurement in the supernatant. mRNA encoding type II collagen (COL2), COL10, aggrecan, and SOX5, 6, and 9 were greatly elevated already at day 7, whereas COL1 and versican mRNA were gradually reduced. COL2 and aggrecan were dispersed throughout the extracellular matrix at day 21, whereas COL10 distribution was mainly intra/pericellular. COL1 seemed to be produced by only some of the cells. SOX proteins were predominantly localized in the nuclei. Then, using microarray analysis, we identified a signature cluster of extracellular matrix and transcription factor genes upregulated during chondrogenesis similar to COL2A1, and clusters of genes involved in immune responses, blood vessel development, and cell adhesion downregulated similar to the chemokine CXCL12. Analysis of the signature chondrogenic clusters, including novel potential marker genes identified here, may provide a better understanding of how the stem cell fate could be directed to produce perfect hyaline cartilage implants Comparison of gene expression patterns in 4 BM-MSC donors, before and after chondrogenic differentiation in alginate (BM-MSCs and DIF)

2012-08-17 | E-GEOD-40175 | biostudies-arrayexpress

Green production of alginate oligosaccharides from Laminaria japonica root by fermentation of a Laminaria japonica-degrading strain Pseudoaltermonas sp. A3

Project description:To identify carbohydrate-active enzymes in the secretome of strain A3 when L. japonica was the sole carbon source and key alginate lyases in the supernatant of fermentation broth.

2022-11-30 | PXD037880 |