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133 results for “Genetic Engineering”
Genome report: Genome sequence of 1S1, a transformable and highly regenerable diploid potato for use as a model for gene editing and genetic engineering
<p>Generation of a genomic resource for a readily transformable diploid potato would provide a resource for high throughput functional analysis in potato. The heterozygous <em>Solanum tuberosum</em> Group Phureja clone 1S1 has a high regeneration rate, self-fertility, desirable tuber traits and is amenable to <em>Agrobacterium</em>-mediated transformation. To create a contiguous genome assembly, a homozygous doubled monoploid of 1S1 (DM1S1) was sequenced using 44 Gbp of long reads generated from Oxford Nanopore Technologies (ONT), yielding a 736 Mb assembly that encoded 31,145 protein-coding genes. The final assembly for DM1S1 represents a nearly complete genic space, shown by the presence of 99.6% (C:99.5%[S:97.8%, D:1.7%],F:0.1%,M:0.4%,n:1614) of the Benchmarking Universal Single Copy Orthologs. Variant analysis with Illumina reads from 1S1 was used to deduce its alternate haplotype using the variant calling tools Strelka2 (v2.9.10), GATK's Haplotypecaller (v4.1.4.1), and Freebayes (v1.3.2). These variants were used to create consensus fasta sequences with the DM1S1 assembly using bcftools (v1.9.64).</p>
Genome report: Genome sequence of 1S1, a transformable and highly regenerable diploid potato for use as a model for gene editing and genetic engineering
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Scripts from: Controlling evolution in genetically engineered systems through repeated introduction
<p>Genetically engineered transgenes evolve in the same way as other genetic material. However, evolution in engineered genes is often undesirable and can negatively affect their stability, frequency, and efficacy over time. Methods that maintain the stability of engineered genomes are therefore critical to the successful design and use of genetically engineered organisms. One potential method to limit unwanted evolution is by taking advantage of the ability of gene-flow to counter local adaption, a process of supplementation. Here we investigate the feasibility of supplementation as a mechanism to offset the evolutionary degradation of a transgene in three model systems: a bioreactor, a gene drive, and a transmissible vaccine. In each model, continual introduction from a stock is used to balance mutation and selection against the transgene. Each system has its unique features. The bioreactor system is especially tractable and has a simple answer: the level of supplementation required to maintain the transgene at a frequency is approximately , where <i>s</i> is the selective disadvantage of the transgene. Supplementation is also feasible in the transmissible vaccine case but is probably not practical to prevent the evolution of resistance against a gene drive. We note, however, that the continual replacement of even a small fraction of a large population can be challenging, limiting the usefulness of supplementation as a means of controlling unwanted evolution.</p>
Database of non-target invertebrates recorded in field experiments of genetically engineered Bt maize and corresponding non-Bt maize: data files
<p><span>This database represents a comprehensive collection of experimental field data from all over the world on non-target invertebrates recorded in genetically engineered/modified Bt and non-Bt maize. The three data files deposited here are described by Meissle et al. (2022), BMC Research Notes, <span><a href="https://doi.org/10.1186/s13104-022-06021-3"><span>https://doi.org/10.1186/s13104-022-06021-3</span></a></span><span> </span>.</span></p> <p><span>The database was created for a systematic review with the question if growing Bt maize changes abundance or ecological function of non-target animals compared to growing of non-GM maize, published by Meissle et al. (2022), Environmental Evidence, <a href="https://doi.org/10.1186/s13750-022-00272-0"><span>https://doi.org/10.1186/s13750-022-00272-0</span></a></span>.</p> <p>Data file 1 contains the database with 7279 records of non-target invertebrate abundance, activity density, or predation or parasitism in Bt and non-Bt maize, extracted from 120 publications. Data file 2 includes the list and definitions of variables in the database, and data file 3 represents the critical appraisal questions and answer options.</p>
Engineering gene overlaps to sustain genetic constructs in vivo
<p>Experimental data, simulation data, and code for data analysis and figure production for the paper "Engineering gene overlaps to sustain genetic constructs in vivo" (Decrulle, Frenoy, et al, PloS Computational Biology)</p>
Millions of lung tumors harboring KRAS, BRAF, EGFR, and tumor suppressor alterations from genetically engineered mouse models
<p><span>Tumors acquire alterations in oncogenes and tumor suppressor genes in an adaptive walk through the fitness landscape of tumorigenesis. However, the <a>interactions </a></span><span>between oncogenes and tumor suppressor genes that shape this landscape remain poorly resolved and cannot be revealed by human cancer genomics alone. Here, we use a multiplexed, autochthonous mouse platform to model and quantify the initiation and growth of more than one hundred genotypes of lung tumors across four oncogenic contexts: KRAS G12D, KRAS G12C, BRAF V600E, and EGFR L858R. We show that the fitness landscape is rugged—the effect of tumor suppressor inactivation often switches between beneficial and deleterious depending on the oncogenic context—and shows no evidence of diminishing-returns epistasis within variants of the same oncogene. These findings argue against a simple linear signaling relationship amongst these three oncogenes and imply a critical role for off-axis signaling in determining the fitness effects of inactivating tumor suppressors.</span></p>
Genetically Engineered Cells (MAGE-A1-specific T Cell Receptor-transduced Autologous T-cells) and Atezolizumab for the Treatment of Metastatic Triple Negative Breast Cancer, Urothelial Cancer, or Non-
ClinicalTrials.gov study NCT04639245. IPD Sharing: NO. Countries: 1. Publications: 1.
A Pilot Study of Genetically Engineered NY-ESO-1 Specific NY-ESO-1ᶜ²⁵⁹T in HLA-A2+ Patients With Synovial Sarcoma
ClinicalTrials.gov study NCT01343043. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Genetically Engineered Lymphocyte Therapy After Peripheral Blood Stem Cell Transplant in Treating Patients With High-Risk, Intermediate-Grade, B-cell Non-Hodgkin Lymphoma
ClinicalTrials.gov study NCT01318317. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Scripts from: Controlling evolution in genetically engineered systems through repeated introduction
Open the record for dataset details and reuse information.
Database of non-target invertebrates recorded in field experiments of genetically engineered Bt maize and corresponding non-Bt maize: data files
Open the record for dataset details and reuse information.
Millions of lung tumors harboring KRAS, BRAF, EGFR, and tumor suppressor alterations from genetically engineered mouse models
Open the record for dataset details and reuse information.
Supplementary Table S1 and Supplementary Table S2 - Part of "Next generation leishmanization: revisiting molecular targets for selecting genetically engineered live-attenuated Leishmania"
<p>Supplementary Table S1 and Supplementary Table S2 -</p> <p>Part of "Next generation leishmanization: revisiting molecular targets for selecting genetically engineered live-attenuated Leishmania"</p>
Malignant Pleural Disease Treated With Autologous T Cells Genetically Engineered to Target the Cancer-Cell Surface Antigen Mesothelin
ClinicalTrials.gov study NCT02414269. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Genetically Engineered Natural Killer (NK) Cells With or Without Atezolizumab for the Treatment of Non-small Cell Lung Cancer Previously Treated With PD-1 and/or PD-L1 Immune Checkpoint Inhibitors
ClinicalTrials.gov study NCT05334329. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Genetically Engineered PBMC and PBSC Expressing NY-ESO-1 TCR After a Myeloablative Conditioning Regimen to Treat Patients With Advanced Cancer
ClinicalTrials.gov study NCT03240861. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Genetically Engineered Lymphocyte Therapy in Treating Patients With Lymphoma That is Resistant or Refractory to Chemotherapy
ClinicalTrials.gov study NCT01735604. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Administration of Autologous T-Cells Genetically Engineered to Express T-Cell Receptors Reactive Against Neoantigens in People With Metastatic Cancer
ClinicalTrials.gov study NCT03412877. IPD Sharing: YES. Countries: 1. Publications: 7.
Genetically Engineered Lymphocytes, Cyclophosphamide, and Aldesleukin in Treating Patients With Relapsed or Refractory Mantle Cell Lymphoma or Indolent B-Cell Non-Hodgkin Lymphoma
ClinicalTrials.gov study NCT00621452. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Research on key generic technology prediction based on graph neural networks under the perspective of patent citation - An example from the field of genetic engineering
<p>In this research, we adopted graph neural network models for key generic prediction based on cited patent data. Through the construction of the patent citation network and the design of a key generic evaluation system, 20879 relevant patents and 51,610 irrelevant patents were screened out. Further, we utilized the LDA topic model to interpret technical topics at a finer granularity. Finally, to test the effectiveness of this method, we took the field of genetic engineering as an example for key generic technology prediction, with an accuracy rate of 95%.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.