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63 results for “Agrobacterium”
Glycerol Trinitrate Reductase XdpB from Agrobacterium sp. R89-1 (FMN-free form) - Diffraction Data
<p>Glycerol Trinitrate Reductase XdpB from Agrobacterium sp. R89-1 (FMN-free form) - Diffraction Data</p> <p>PDB code: 5EPD<br> http://www.rcsb.org/pdb/explore/explore.do?structureId=5EPD</p> <p>Funding:<br> The study was supported by grant No. 720414 of the Grant Agency of Charles University, the project RVO 61388971 to the Institute of Microbiology CAS, v. v. i. and 86 652 036 to the Institute of Biotechnology CAS, v. v. i. and to project<br> BIOCEV CZ.1.05/2.1.00/19.0390 from the ERDF and MEYS and in part by the Grant Agency of the Czech Technical University in Prague, grant No. SGS16/246/OHK4/3T/14.</p> <p> </p>
Agrobacterium phylogeny analysis
<p>Complete dataset for phylogeny analysis of new Agrobacterium species proposed as <em>Agrobacterium bohemicum </em>sp. nov.. </p>
Agrobacterium sp014851585 BIGb0125
This is one of the Wormbiome database archive files.<br>This entry includes all the genome annotation files related to Agrobacterium sp014851585 BIGb0125, a\(n\) Alphaproteobacteria.<br>The Wormbiome collection is an online database dedicated to centralizing all the information related to bacteria associated with C. elegans. More information on <a href="https://bitbucket.org/the-samuel-lab/wbm_scripts/src/master/DOCS/Annotations_output.md" target="_blank" rel="noopener noreferrer">the documentation page</a>.<br><br>
Rhizogenic Agrobacterium-specific bacteriophages
<p>Raw fastq sequences (Illumina) of the phages isolated in the VIROPLANT project to control hairy roots disease in tomato.</p> <p>ST40-104 = OLIVR1</p> <p>125 = OLIVR2</p> <p>128g = OLIVR3</p> <p>128k = OLIVR4</p> <p>ST57-123 = OLIVR6</p> <p>ST95-126 = OLIVR5</p> <p> </p> <p>Finalised genbank files that were submitted in NCBI are also part of this dataset.</p> <p> </p>
Efficient Agrobacterium-mediated transformation and genome editing of Fagopyrum tataricum
<p><em>Fagopyrum tataricum</em> (L.) Gaertn. is an exceptional crop known for its remarkable health benefits, high levels of beneficial polyphenols and gluten-free properties, making it highly sought-after as a functional food. Its self-fertilisation capability and adaptability to challenging environments further contribute to its potential as a sustainable agricultural option. To harness its unique traits, genetic transformation in <em>F. tataricum</em> is crucial. In this study, we optimised the Agrobacterium-mediated transformation protocol for <em>F. tataricum</em> callus, resulting in a transformation rate of regenerated plants of approximately 20%. The protocol’s effectiveness was confirmed through successful GUS staining, GFP expression, and the generation of albino plants via <em>FtPDS</em> gene inactivation. These results validate the feasibility of genetic manipulation and highlight the potential for trait enhancement in <em>F. tataricum</em>.</p>
Rhizogenic Agrobacterium strains assemblies
<p>Illumina assemblies of 25 rhizogenic Agrobacterium strains, isolated from hairy roots disease in tomato in Belgium for the VLAIO-LA project HBC.2017.0816 <a href="https://research.kuleuven.be/portal/en/project/3E181081" target="_blank" rel="noopener">BARATOM</a> (also see Kim et al., 2023; doi: <span><a href="https://doi.org/10.1128/mra.00124-23" target="_blank" rel="noopener">10.1128/mra.00124-23</a>)</span>. Sequencing data here was generated in the framework of the H2020 project VIROPLANT. Assemblies made with SPAdes.</p>
Dataset for "Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4"
<p>Please read the README.txt file in each folder prior to doing any analysis.</p> <p>1. Agro_CDHIT.tar.gz contains files and a script to generate the input files that can be submitted to http://bioinfogp.cnb.csic.es/tools/venny/ for Venn Diagram generation.</p> <p>2. Agro_Roary.tar.gz contains files (gff) and a script to perform identification and alignment of core and accessory genes using the Roary software.</p> <p> </p>
Raw diffraction images of the type VI amidase immunity (Tai4) and the effector-immunity complex (Tae4-Tai4) from Agrobacterium tumefaciens
<p>X-ray diffraction images of the type VI amidase immunity (Tai4) and the effector-immunity complex (Tae4-Tai4) crystals from Agrobacterium tumefaciens.<br> <br> This upload includes:</p> <ul> <li>AtTai4 (PDB code: 6IJE) collected on BL41XU, SPring-8 using PILATUS3 6M detector. <ul> <li>0.5°/frame × 360 frames (helical data collection)</li> <li>P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub>, a=53.92, b=57.76, c=71.47 Å</li> </ul> </li> <li>AtTae4-AtTai4 complex (PDB code: 6IJF) collected on BL32XU, SPring-8 using MX225-HS CCD detector. <ul> <li>0.5°/frame × 360 frames (helical data collection)</li> <li>P6<sub>1</sub>, a=b=72.03, c=194.35 Å</li> </ul> </li> </ul> <p> </p>
Highly Efficient Agrobacterium rhizogenes-mediated Genetic Transformation Technology Bypassing Tissue Culture in Citrus
<p>Highly efficient genetic transformation technology is of great significance for the gene function analysis and precision breeding of crops. However, the most commonly used genetic transformation technology mediated by <em>Agrobacterium tumefaciens</em> in plants especially xylophyta is time-consuming and inefficient, which seriously hinders the progress of gene function analysis. In this study, a simple and highly efficient genetic transformation technology mediated by <em>Agrobacterium rhizogenes</em> bypassing tissue culture is described. Only 2~8 weeks were required for the whole workflow, with an average successful transformation ratio of 57% in shoots from adult plants. By using this technology, we successfully transferred plasmids containing gRNA, Cas9, and other exogenous genes into citrus, and achieved genome editing on target loci and overexpressed multiple foreign genes at the same time. In this method, a student could simultaneously conduct genome editing experiment using 10 plasmids targeting different genome positions and finally obtained all the corresponding transformants with target DNA knocked out, indicating that <em>A. rhizogenes</em>-mediated genome editing technology is highly efficient. In addition, <em>A. rhizogenes</em> can be used for direct viral vector inoculation on citrus bypassing the step of viron enrichment in tobacco, which facilitates the experiment operation of virus-induced gene silence (VIGS) and foreign gene expression. In summary, we established a highly efficient genetic transformation technology bypassing tissue culture in citrus, which can be used for genome editing, gene overexpression, and virus-mediated gene function analysis. We anticipate that by removing high cost, heavy workload, long experiment period and other technical obstacles, this genetic transformation technology will be a valuable tool for routine investigation of endogenous and exogenous genes in citrus.</p>
Figure 4 in Agrobacterium-mediated gene delivery and transient expression in the red macroalga Chondrus crispus
Figure 4: Effect of cultivation medium, wounding method and acetosyringone on Agrobacterium transformation efficiency. The transformation efficiencies of Chondrus thalli segments co-cultivated with pCAMBIA 1301-transformed Agrobacterium in seawater and Induction Medium (IM) were compared. Using seawater as co-cultivation medium, the wound-related treatments, namely biolistics wounding, wounding using pin-pricks and no wounding, were compared. The effect of acetosyringone (100 µM) was also studied. Data are expressed as means ± SE (n = 4). The Mann-Whitney non-parametric test was conducted to compare between two groups.
Figure 2 in Agrobacterium-mediated gene delivery and transient expression in the red macroalga Chondrus crispus
Figure 2: Intimate contact and adhesion of bacteria to wound sites of Chondrus thalli. Thalli co-cultivated for 48 h in induction medium were fixed and viewed under a scanning electron microscope: (A) control thallus incubated without bacteria showing a clean bacterium-free surface; (B) close up view of rod-shaped bacteria attached to thallus surface at wound site; (C) bacterial film at wound sites on thallus surface.
Figure 1 in Agrobacterium-mediated gene delivery and transient expression in the red macroalga Chondrus crispus
Figure 1: Features of binary vectors for Agrobacterium-mediated transformation. (A) Chondrus-specific expression cassette. Salient features: 1.812 kbp GUS gene modified to match the favoured codon usage of Chondrus, promoter region of the Chondrus actin gene, nopaline synthase (NOS) gene terminator from Genbank accession AF502128.1; (B) Binary vector pCAMBIA 1301. Salient features: GUS gene with castor bean catalase intron driven by a CAMV 35 S promoter and terminated by NOS.
Figure 5 in Agrobacterium-mediated gene delivery and transient expression in the red macroalga Chondrus crispus
Figure 5: GUS expression in Chondrus thallus segments transformed with LBA 4404/pRI 910 (Ac-GUS). (A) Surface view of control thallus not co-cultivated with Agrobacterium, (B) surface view of transformed thallus showing GUS expression at wound sites, (C) section through untransformed thallus, (D) thallus section within wounded area showing blue medullary cells at wound spots, (E) cortical cells from untransformed control thallus, (F) GUS-expressing cortical cells in transformed thallus, (G) medullary filaments from untransformed control thallus, (H) medullary filaments from transformed thallus.
Figure 3 in Agrobacterium-mediated gene delivery and transient expression in the red macroalga Chondrus crispus
Figure 3: Histochemical staining and low-power microscopic analysis of Chondrus thallus segments for transient expression of GUS 7 days after co-cultivation. (A) Pin-pricked thalli co-cultivated without bacteria, (B) pin-pricked thalli co-cultivated with untransformed LBA4404 bacteria, (C) unwounded and untransformed thalli, (D) pin-pricked thalli co-cultivated with LBA4404/pRI 910 (no GUS gene), (E) thalli transformed with LBA4404 (pCAMBIA 1301), scale bar: 1 cm.
Agrobacterium-mediated cassava transformation for the Asian-elite variety KU50
GEO Series GSE169685. Manihot esculenta. 8 samples. Type: Expression profiling by array.
Linear dicentric bacterial chromosomes in Agrobacterium tumefaciens natural isolates reveal common constraints for replicon fusion
GEO Series GSE285100. Agrobacterium tumefaciens. 6 samples. Type: Other.
Gene expression profiling of rice embryogenic calli after Agrobacterium infection
GEO Series GSE32426. Oryza sativa Indica Group; Oryza sativa Japonica Group; Oryza sativa. 36 samples. Type: Expression profiling by array.
Centromere interactions promote the maintenance of the multipartite genome in Agrobacterium tumefaciens
GEO Series GSE196319. Agrobacterium tumefaciens; Bacillus subtilis PY79. 29 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
Chromosome Architecture Impacts Virulence and Competitiveness in Agrobacterium tumefaciens C58
GEO Series GSE293397. Agrobacterium tumefaciens. 20 samples. Type: Other.
The effect of expression of the Agrobacterium tumefaciens virulence protein VirE3 on gene expression in Arabidopsis thaliana.
GEO Series GSE68130. Arabidopsis thaliana. 4 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.