Find research datasets worth reusing

opencc-zeroFeb 2024View details →

Dataset: T-DNA characterization of genetically modified 3-R-gene late blight resistant potato events with a novel procedure utilizing the Samplix Xdrop® Enrichment Technology

Before commercialization of genetically modified crops, the events carrying the novel DNA must be thoroughly evaluated for agronomic, nutritional, and molecular characteristics. Over the years, Polymerase Chain Reaction-based methods, Southern blot, and short-read sequencing techniques have been utilized for collecting molecular characterization data. Multiple genomic applications are necessary to determine the insert location, flanking sequence analysis, characterization of the inserted DNA, and determination of any interruption of native genes. These techniques are time-consuming and labor-intensive, making it difficult to characterize multiple events. Current advances in sequencing technologies are enabling whole genomic sequencing of modified crops to obtain full molecular characterization. However, in polyploids, such as the tetraploid potato, it is a challenge to obtain whole genomic sequencing coverage that meets regulatory approval of the genetic modification. Here we describe an alternative to labor-intensive applications with a novel procedure using Samplix Xdrop® enrichment technology and next-generation Nanopore sequencing technology to more efficiently characterize the T-DNA insertions of four genetically modified potato events developed by the Feed the Future Global Biotech Potato Partnership: DIA_MSU_UB015, DIA_MSU_UB255, GRA_MSU_UG234 and GRA_MSU_UG265 (derived from regionally important varieties Diamant and Granola). Using the Xdrop® /Nanopore technique, we obtained a very high sequence read coverage within the T-DNA and junction regions. In three of the four events, we were able to use the data to confirm single T-DNA insertions, identify insert locations, identify flanking sequences, and characterize the inserted T-DNA. We further used the characterization data to identify native gene interruption and confirm the stability of the T-DNA across clonal cycles. These results demonstrate the functionality of using the Xdrop® /Nanopore technique for T-DNA characterization. This research will contribute to meeting regulatory safety and regulatory approval requirements for commercialization with small shareholder farmers in target countries within our partnership.

opencc-zeroDec 2022View details →

Assessing potential hybridization between a hypothetical gene drive-modified Drosophila suzukii and non-target Drosophila species

Genetically engineered gene drives (geGD) are potentially powerful tools for suppressing or even eradicating populations of pest insects. Before living geGD insects can be released into the environment, they must pass an environmental risk assessment (ERA) to ensure that their release will not harm valued and protected entities of the environment. A key research question concerns the likelihood that non-target species will acquire the functional GD elements; such acquisition could lead to the loss of those species and to a disruption of the ecosystem services they provide. The main route for gene flow is through hybridization between the GD insect strain and closely related species that co-occur in the area of release. Using the invasive spotted-wing drosophila, Drosophila suzukii, as a case study, we demonstrate how a combination of interspecific hybridization experiments, behavioral observations, and molecular genetic analyses can be used to assess the potential for hybridization.

zenodo36/100

Summary statistics for "Variants in the TERT gene increase the occurrence of solar lentigines by modifying telomerase expression exclusively in the skin"

Publication: Deecke et al., Variants in the TERT gene increase the occurrence of solar lentigines by modifying telomerase expression exclusively in the skin, manuscript under revision Brief summary: Solar lentigines (SL) are a characteristic of the aging skin. Their occurrence is likely determined by a combination of genetic variants and environmental factors such as chronic sun exposure. However, the genetic factors underlying SL formation remain largely unknown. A recently performed genome-wide association study (GWAS) of SL in two Chinese cohorts reported TERT and OCA2 as novel genome-wide significant genetic loci for SL, while only the TERT locus could be validated in a cohort of European descent (Peng et al, 2023). The telomerase reverse transcriptase TERT is known to be involved in the process of maintenance of telomere lengths, but interestingly no causal relationship between telomere length and the SL GWAS results was observed by the investigators. In this study, we quantified the heritability of SL located on the back of the hands and performed a de novo GWAS in 1,137 elderly participants (aged 60 and more) of European descent from the Berlin Aging Study II. We confirmed TERT as the only genome-wide significant locus for SL (top SNP: rs2735940, p= 1.35E-16). In line with the previous Mendelian Randomization (MR) results by Peng et al., our updated MR using substantially larger datasets did not show a causal relationship between the occurrence of SL and telomere lengths measured in blood leukocytes. Importantly, rs2735940 modifies TERT expression in skin tissue (based on GTEx data), but not in any of the other GTEx tissues including blood. Furthermore, colocalization analyses suggested a shared causal effect of rs2735940 on SL occurrence and on TERT expression in skin but not in blood. Thus, we could show that variants in the TERT gene increase the occurrence of SL by modifying TERT expression exclusively in the skin, based on currently available GTEx data. This skin-specific effect was not reported previously and may provide the hitherto missing functional link for the occurrence of SLs via TERT expression and telomere length alterations.

opencc-by-4.0Sep 2023View details →

ClinicalTrials.gov36/100

Study of Gene Modified Immune Cells in Patients With Advanced Melanoma

ClinicalTrials.gov study NCT00910650. IPD Sharing: Not stated. Countries: 1. Publications: 3.

publicFeb 2024View details →

Dataset: T-DNA characterization of genetically modified 3-R-gene late blight resistant potato events with a novel procedure utilizing the Samplix Xdrop® Enrichment Technology

Open the record for dataset details and reuse information.

publicDec 2022View details →

Assessing potential hybridization between a hypothetical gene drive-modified Drosophila suzukii and non-target Drosophila species

Open the record for dataset details and reuse information.

dryad32/100

Data from: Local selection modifies phenotypic divergence among Rana temporaria populations in the presence of gene flow

In ectotherms, variation in life-history traits among populations is common and suggests local adaptation. However, geographic variation itself is not a proof for local adaptation, since genetic drift and gene flow may also shape patterns of quantitative variation. We studied local and regional variation in means and phenotypic plasticity of larval life history traits in the common frog Rana temporaria using six populations from central Sweden, breeding in either open canopy or partially closed canopy ponds. To separate local adaptation from genetic drift we compared differentiation in quantitative genetic traits (QST) obtained from a common garden experiment with differentiation in presumably neutral microsatellite markers (FST). We found that R. temporaria populations differ in means and plasticities of life-history traits in different temperatures at local, and in Fst at regional scale. Comparisons of differentiation in quantitative traits and in molecular markers suggested that natural selection was responsible for the divergence in growth and development rates as well as in temperature-induced plasticity, indicating local adaptation. However, at low temperature the role of genetic drift could not be separated from selection. Phenotypes were correlated with forest canopy closure but not with geographical or genetic distance. These results indicate that local adaptation can evolve in the presence of ongoing gene flow among populations, and that natural selection is strong in this system.

opencc-zeroDec 2009View details →

opencc-by-4.0Apr 2023View details →

Modifying the expression of cysteine protease gene PCP affects pollen develop-ment, germination and plant drought tolerance in maize

Figure S1: The sequencing results of pollen grains of T2 mutants. Figure S2: The relative expression levels of PCP were analyzed via RT-qPCR in pcp mutant lines. Data represent means ± SD of three replicates. Significant differences were indicated with different letters (P < 0.05, one-way ANOVA). Figure S3: Pictures of pollen germination and growth in vitro between wild type and transgenic lines after 4 h and 6 h incubation. Scale bar: 100 μm; Figure S4: Phenotypic observation of wild-type and transgenic maize at flowering stage. Scale bar: 10 cm. Figure S5. DAB staining detection of ROS in WT, KO and OE plants under drought stress. Table S1: PCR primers used in this study.

Fig. 4. A in Hairy root transformation of Brassica rapa with bacterial halogenase genes and regeneration to adult plants to modify production of indolic compounds

Fig. 4. A. Growth of wild type root cultures on different Trp derivatives as compared to growth on MS medium only. B. Correlation of the relative growth and the production of different Cl-Trp compounds.

Fig. 3. A in Hairy root transformation of Brassica rapa with bacterial halogenase genes and regeneration to adult plants to modify production of indolic compounds

Fig. 3. A. All transgenic root lines were analyzed by the following experiments and the data are presented for selected lines transformed with the pMDC32+2xCaMV35S:pyrH:nosT construct (pyrH = 5-Cl-Trp-forming). Transformation of roots with A. rhizogenes was verified using gDNA and cDNA for a successful insertion and expression, respectively. A. Upper panel: Amplified rolB (423 bp) and rolC (626 bp) for three different lines (lanes 1–3) using gDNA. The virG gene (350 bp) was only detectable in the positive control (Ri-plasmid of A. rhizogenes) (lane +) "-" denotes a negative PCR control. Lower panel: Integration of full length hal gene (ca. 1.5 kb) using gDNA. Expression of full length hal gene (ca. 1.5 kb) using cDNA. "+": positive control (plasmid containing pyrH or the other hal genes), "-": negative PCR control, g: gDNA wild type, c: cDNA wild type, 1–3: three independent transgenic root culture lines with the pMDC32+2xCaMV35S:pyrH:nosT construct, "1-"-"3-": RT negative controls (containing no DNA). B. Western blot with the purified His-tagged proteins: 1: PyrH, 2: ThaI, 3: PrnA, a: PyrH synthesized in E. coli, b: positive control ThaI synthesized in E. coli, c: positive control PrnA synthesized in E. coli. Wild type protein as control did not show any signal (data not shown). C. Enzyme assay with the purified halogenase PyrH. The positive control is PyrH protein synthesized in bacteria. The negative control is purified protein from wild type root cultures. Since only for PyrH enzyme activity could be detected, the data for the other halogenases are shown in the supplement (Fig. S1). D. Production of chlorinated tryptophan (Cl-Trp) and indole-3-acetonitrile (ClIAN) in transgenic root lines. For each halogenase construct five independent lines were tested. Results for 5 lines per halogenase type with and without Histag are indicated by the numbers of lines with the respective metabolites. The detailed results for all individual lines are shown in the supplement (Fig. S2).

Fig. 6. A in Hairy root transformation of Brassica rapa with bacterial halogenase genes and regeneration to adult plants to modify production of indolic compounds

Fig. 6. A. Confirmation of i) that the regenerated plants contain still the rol genes and ii) the integration of the hal gene into the genome and its transcription into cDNA (1: regenerated plants from wild type root cultures; 2: BrRP-pyrHHIS.6; 3: A. rhizogenes plasmid; 4: negative PCR control; 5: positive control - hal amplification from plasmid; a: cDNA, b: cDNA "no template control; genomic DNA. B. Western blot of His-tagged halogenase (PyrH, Thal, PrnA: purified enzymes from overexpressing E. coli strain as positive controls; BrRP-HR = WT, regenerated plants from wild type root cultures; BrRP-S: regenerated plants from Chinese cabbage seedlings; BrRP-pyrH, -thal, -prnA: regenerated plants from transgenic roots.). Always two different dilutions were applied. The gel strips were from the same gel, but due to large parts with samples without an immunosignal, the respective areas were cut out and are presented here. C. Relative amounts of chlorinated metabolites in the regenerated plants.

Fig. 2 in Hairy root transformation of Brassica rapa with bacterial halogenase genes and regeneration to adult plants to modify production of indolic compounds

Fig. 2. Expected indole metabolites and their interconversion (in black) that could be derived from tryptophan via the indole glucosinolate/indole phytoalexin pathway. It is indicated (in grey) that there are alternative pathways to IAA. The possible induction (dashed arrows) of chlorinated metabolites by abiotic and biotic stress factors, the latter also via the signaling molecules salicylic acid and jasmonic acid, is shown.

Fig. 1 in Hairy root transformation of Brassica rapa with bacterial halogenase genes and regeneration to adult plants to modify production of indolic compounds

Fig. 1. Experimental scheme showing the different types of plant materials generated. A. Mature wild type plants/seedlings; B. Wild type and transgenic root cultures; C. Regenerated sterile plants from wild type seedlings; D. Regenerated sterile plants from wild type and transgenic root cultures; E. Adult plants in soil from wild type cultures; F. Adult plants in soil from transgenic root cultures.

Fig. 5 in Hairy root transformation of Brassica rapa with bacterial halogenase genes and regeneration to adult plants to modify production of indolic compounds

Fig. 5. Left: Average number of regenerated shoots for 25 Brassica rapa "hairy root" lines (denoted therefore as BrHR ….) on 3 media compositions (n = 24). Medium A: GB5 medium containing 8 g l−1 phytoagar, 20 g l−1 sucrose and 10 mg l−1 6-BAP. Medium B: MS medium containing 8 g l−1 phytoagar, 30 g l−1 sucrose, 4 mg l−1 6-BAP, 4 mg l−1 AgNO3 and 3 mg l−1 NAA. Medium C: MS medium containing 8 g l−1 phytoagar, 30 g l−1 sucrose, 4 mg l−1 6-BAP, 4 mg l−1 AgNO3 and 0.5 mg l−1 NAA. Right: Shoot regeneration from B. rapa root cultures. Pieces from these root cultures were cut into pieces of approximately 1 cm2 and placed on semisolid agar (A). Regeneration of shoots was visible after 4 weeks of cultivation (B). Regenerated shoots were separated and transferred to fresh media (C). Shoot growth was often accompanied by growth of transformed/transgenic roots (D). Shoots of adequate biomass quality were subcultivated (E). Some B. rapa lines displayed a shortened life cycle after regeneration and began flowering (F).

Fig. 7 in Hairy root transformation of Brassica rapa with bacterial halogenase genes and regeneration to adult plants to modify production of indolic compounds

Fig. 7. Comparison of phenotypic traits for three groups of Brassica rapa grown in the greenhouse. WT – shoots from wild type plants grown from seeds (photo A); REG – regenerated shoots originated from transformed root cultures (photo B); HLR – regenerated shoots originated from transgenic roots transfected with bacterial hal genes (photo C). Significant differences between treatments are labeled as follows: 0 '***' 0.001 '**' 0.01 '*' 0.05 (with n = minimum of 20 individually potted plants). Leaves of in vitro shoots originated from seeds (left) or regenerated from root cultures (right) are shown.

closedIPD-NOFeb 2026View details →

Gene Therapy with Modified Autologous Hematopoietic Stem Cells for Patients with Mucopolysaccharidosis Type IIIA

ClinicalTrials.gov study NCT04201405. IPD Sharing: NO. Countries: 1. Publications: 5.

Phase II Study of a B7-1 Gene-Modified Autologous Tumor Cell Vaccine and Systemic IL-2

ClinicalTrials.gov study NCT00031564. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Disease Modifying Genes in Severe Asthma

ClinicalTrials.gov study NCT00212537. IPD Sharing: Not stated. Countries: 1. Publications: 3.

Gene-Modified T Cells, Vaccine Therapy, and Ipilimumab in Treating Patients With Locally Advanced or Metastatic Malignancies

ClinicalTrials.gov study NCT02070406. IPD Sharing: Not stated. Countries: 1. Publications: 1.