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Ammonia is a morphogen in Dictyostelium and is known to arise from the catabolism of proteins and RNA. However, we show that extracellular adenosine deamination catalysed by 'adenosine deaminase-related growth factor' (ADGF) is a major source of ammonia and demonstrate a direct role of ammonia in tip organizer development. The tip formed during early development in Dictyostelium functions analogously to the embryonic organizer of higher vertebrates. Dictyostelium strains carrying mutations in the gene adgf fail to establish an organizer, and this could be reversed by exposing the mutants to volatile ammonia. Interestingly, Klebsiella pneumoniae physically separated from the Dictyostelium adgf mutants in a partitioned dish also rescues the mound arrest phenotype. Both the substrate, adenosine and the product, ammonia, regulate adgf expression, and ADGF acts downstream of the histidine kinase DhkD in regulating tip formation. Thus, the consecutive transformation of extracellular cAMP to adenosine, and adenosine to ammonia is integral steps during Dictyostelium development. Remarkably, in higher vertebrates, adgf expression is elevated during gastrulation and thus adenosine deamination may be a conserved process driving organizer development in different organisms.
Pubmed ID: 41406008
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Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB.
View all literature mentionsA portal to biomedical and genomic information. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information for the better understanding of molecular processes affecting human health and disease.
View all literature mentionsModel organism database for the social amoeba Dictyostelium discoideum that provides the biomedical research community with integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase houses the complete genome sequence, ESTs, and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome to provide a ''''reference genome'''' in the Amoebozoa clade. They highlight several new features in the present update: (i) new annotations; (ii) improved interface with web 2.0 functionality; (iii) the initial steps towards a genome portal for the Amoebozoa; (iv) ortholog display; and (v) the complete integration of the Dicty Stock Center with dictyBase. The Dicty Stock Center currently holds over 1500 strains targeting over 930 different genes. There are over 100 different distinct amoebozoan species. In addition, the collection contains nearly 600 plasmids and other materials such as antibodies and cDNA libraries. The strain collection includes: * strain catalog * natural isolates * MNNG chemical mutants * tester strains for parasexual genetics * auxotroph strains * null mutants * GFP-labeled strains for cell biology * plasmid catalog The Dicty Stock Center can accept Dictyostelium strains, plasmids, and other materials relevant for research using Dictyostelium such as antibodies and cDNA or genomic libraries.
View all literature mentionsDatabase of protein structure predictions by AlphaFold that are freely and openly available to global scientific community. Included are nearly all catalogued proteins known to science. Provides programmatic access to and interactive visualization of predicted atomic coordinates, per residue and pairwise model confidence estimates and predicted aligned errors.
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View all literature mentionsTE2000 was developed as full system with 3 models, the S, the U and the E. TE2000E is high precision Z-focus automated model that features 5 output ports and 5-way motorized light path changer. Used for advanced research that requires image capture in 3D, including confocal microscopy and deconvolution processing.TE2000U is universal model that comes with 4 output ports as standard, plus optional fifth user defined position, thereby providing unprecedented 5-way light path.The U model also features integrated magnification changer module providing 1x or 1.5x magnification to all ports.
View all literature mentionsStatistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.
View all literature mentionsA user-sponsored molecular visualization software system on an open-source foundation. The software has the capabilities to view, render, animate, export, present and develop three dimensional molecular structures.
View all literature mentionsSoftware integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny.
View all literature mentionsOpen source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.
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