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Datasets for "Targeted insertion and reporter transgene activity at a gene safe harbor of the human blood fluke, Schistosoma mansoni"
<p>To identify sites that could serve as potential genomic safe harbours (GSHs) for transgene integration, we conducted a genome-wide bioinformatic search based on established, widely accepted criteria, along with newly introduced criteria (below), that would satisfy benign and stable gene expression. </p> <p>At the outset, we identified <strong>euchromatic</strong> regions in all developmental stages of <em>S. mansoni </em>to avoid silencing genes to be integrated upon CRISPR/Cas manipulation. With these criteria, we enriched for regions that were, (i) close to peaks of H3K4me3, a histone modification that is associated with euchromatin and transcription start sites, (ii) regions that did not include H3K27me3, a histone modification that is associated with heterochromatin, (iii) regions of open euchromatin accessible to Tn5 integration, in an Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) providing a positive display of integration events, and (iv) given that HIV-1 integrates preferentially into euchromatin in human cell lines, we used sites of HIV proviral integration known from <em>S. mansoni</em> to likewise support predictions of euchromatic regions.</p> <p>Examination of the draft genome of <em>S. mansoni</em> in Worm Base Parasite, version 7 (WormBase Parasite) identified 6,884 regions with enrichment of H3K4me3 in the absence of H3K27me3 in available developmental stages (H3K4me3 not K3K27me3). In mature, adult schistosomes, we found consistently 10,533 ATAC positive regions. There were 4,027 ATAC regions that overlapped with H3K4me3 but not K3K27me3, and 2,915 genes overlapped with (ATAC and H3K4me3 not H3K27me3). Forty-two unambiguous HIV integration sites were identified, and eight genes were ≤ 11 kb upstream or downstream from these integration sites. Repeats were masked with RepeatMasker V4.1.0 using a specific repeat library produced with RepeatModeler2 V2.0.1 and stored as a GFF file.</p> <p>To identify intergenic GSH, we located 10,149 intergenic regions. There were 9,985 regions beyond 2 kb upstream and 8,837 regions outside long non-coding-RNA (lncRNA), which were intersected to 95,587 unique intergenic regions outside 2 kb and lncRNA of ≥100 bp. Two hundred regions were identified intersecting with merged ATAC H3K4me3 signal. Four of these were situated ≤ 11 kb distance from HIV integration sites. </p> <p>Made at George Washington University, Justus Liebig University Giessen, Khon Kaen University, Naresuan University, Aberystwyth University, Schistosomiasis Resource Center, IHPE. </p>
Data from: field evaluation: the effect of two transgenic Bt maize events on predatory arthropods in the Huang-Huai-Hai summer maize-growing region of China
<p>To illustrate the impact of genetically modified (GM) Bt maize on the natural enemy communities in the Huang-Huai-Hai summer maize-growing region in China, the abundance of seven common predator groups (<em>Geocoris pallidipennis</em>, <em>Harmonia axyridis</em>, lacewings, <em>Orius sauteri</em>, <em>Propylea japonica</em>, spiders, Staphylinidae) was quantitatively evaluated by planting Bt-Cry1Ab DBN9936 and Bt-Cry1Ab/Cry2Aj Ruifeng 125 events during the growing season from 2016 to 2019. A total of 11,172- 13,739 predators were observed in each varieties during four years, and the abundance of each groups on Bt maize varied between sample dates and among those enemy taxons. The shannon-Wiener diversity index from seven groups showed very similar temporal dynamics and there were not significant differences in Bt and non-Bt maize, showing that Bt maize did not disrupt the stability of predator enemy aggregation in the field. Spiders, <em>H. axyridis</em>, <em>P. japonica</em>, Lacewing, <em>O. sauteri</em> with positive taxon weights after using principal response curve (PRC) method, indicated that Bt maize had a positive effect on the abundances of individual taxa. All this indicating that the two Bt maize hybrids did not adversely affect predator community in the Huang-Huai-Hai summer maize-growing region of China.</p>
Figure 9 in Evaluation of the Chilli veinal mottle virus CP gene expressing transgenic Nicotiana benthamiana plants for disease resistance against the virus
Figure 9. ELISA plate readings (O.D at 405nm) of leaf samples of transgenic lines (T1-T8) and control plants after 15 dpi.
Figure 7 in Evaluation of the Chilli veinal mottle virus CP gene expressing transgenic Nicotiana benthamiana plants for disease resistance against the virus
Figure 7. PCR Products of the hpt gene from T0 transgenic plants. Lane 1-9 are transgenic. Lane 10, +ve control. Lane 11, control (untransformed) plant.
Figure 6. DNA bands from T0 in Evaluation of the Chilli veinal mottle virus CP gene expressing transgenic Nicotiana benthamiana plants for disease resistance against the virus
Figure 6. DNA bands from T0 transgenic and Agro-infilterated plants. Lane 1-10, transgenic plants. Lane 11-13, agro-infilterated plants.
Figure 3 in Evaluation of the Chilli veinal mottle virus CP gene expressing transgenic Nicotiana benthamiana plants for disease resistance against the virus
Figure 3. Symptoms development on propagative host plants after mechanical inoculation with ChiVMV isolate ATIPK. (a) N. tabacum showing mosaic, mottling and vein clearing (b) C. annum (cv. Loungi) displays the symptoms of mottling, mosaic, leaf deformation and vein clearing.
Figure 2 in Evaluation of the Chilli veinal mottle virus CP gene expressing transgenic Nicotiana benthamiana plants for disease resistance against the virus
Figure 2. Symptoms of ChiVMV on chilli leaves collected from Islamabad. (a) Shows mottling and severe vein clearing and distortion. (b) Shows reduced leaf size with mottling and distortion.
Figure 2 in A 6-year field monitoring of fall armyworm, Spodoptera frugiperda, in transgenic Bt maize in Brazil
Figure 2 Average number of fall armyworm larvae, Spodoptera frugiperda, collected in Bt hybrids, non-Bt hybrids and non-Bt hybrids sprayed with methomyl in 2015 and 2016 (period II), in Sete Lagoas and Nova Porteirinha. Average followed by the same upper-case letter between municipalities and same lower-case letter in each municipality do not differ statistically (Scott-Knott test at p ≤ 0.05).
Figure 1 in A 6-year field monitoring of fall armyworm, Spodoptera frugiperda, in transgenic Bt maize in Brazil
Figure 1 Average number of fall armyworm larvae, Spodoptera frugiperda collected in Bt hybrids, non-Bt hybrids and non-Bt hybrids sprayed with methomyl from 2011 to 2014 (period I), in Sete Lagoas and Nova Porteirinha. Average followed by the same upper-case letter between municipalities and same lower-case letter in each municipality do not differ statistically (Scott-Knott test at p ≤ 0.05).
Fig. 1 in First record of Peridroma saucia Hübner (Lepidoptera: Noctuidae) in transgenic soybeans
Fig. 1. Developmental stages of Peridroma saucia collected in genetically modified soybeans: (A) eggs, (B) larvae and (C) adult emerged in laboratory (scale = 1 cm).
Fig. 1 in Comparison of Bemisia tabaci infestation, virus infection, and yield in conventional and transgenic Bean golden mosaic virus-resistant common bean elite lines
Fig. 1. Symptoms of virus infection on common bean plants under field situation: (A) Bean golden mosaic virus; (B) Cowpea mild mottle virus on old transgenic plants and (C) young transgenic plant; (D) symptoms of mixed infection caused by Bean golden mosaic virus and Cowpea mild mottle virus.
Transgenic A53T mice have astrocytic a-synuclein aggregates in dopamine and striatal regions
<p>Quantification of astrocyte expression, co-expression of astrocytes with a-syn, and astrocyte morphological data (soma size and number of processes) from 6 month transgenic A53T PD mice.</p>
Comparison of tetracycline and temperature sensitive GAL80 transgenes with UAS-lacZ
<p>ß-galactosidase specific activity was measured during development and aging (Experimental workflow) as described in <a href="https://star-protocols.cell.com/protocols/2150">STAR Protocols 3, 101843, 2022</a>. Two different muscle-specific GAL4 drivers, Mef2-Gal4 (BDSC:27390) and DJ694 (BDSC: 8176), were each crossed with a second chromosome insertion of UAS-lacZ (Bg2) (BDSC: 1776), Bg2 recombined with third chromosome insertions of TetOFF-GAL80 (3.3+1077, <a href="https://peerj.com/articles/4167/">PeerJ 5:e4167</a>), and Bg2 recombined with third chromosome insertions of GAL80ts (BDSC:7017). Flies were raised at 20˚C and 29℃. Two independent sets of parents were used for each cross (biological replicates 1 and 2). After 2-3 days, parents were flipped into a new bottles (technical replicates 1 and 2 reported as replicate 3 and 4 in the dataset). CPRG and Bradford assays were performed on whole animal for the third instar larvae (L3), early pupae (EP) and late pupae (LP) stages, and on dissected thoraces for adult stages. Five extracts (1 individual in each) were measured per experimental replicate. Raw microplate readings are available upon request.</p>
Comparison of tetracycline and temperature sensitive GAL80 transgenes with UAS-grim
<p>In order to assess the ability of GAL80 to repress the expression of a UAS transgene, lethality tests were performed in presence of a UAS-grim reporter (<a href="http://doi.org/10.1002/gene.10128"><em>Genesis</em> 34:34, 2002</a>, <a href="https://peerj.com/articles/4167/"><em>PeerJ</em> 5:e4167, 2017</a>). The Grim reporter gene encodes a strong pro-apoptotic factor, thus the lethality across development (embryonic, larval, pupal) can be scored to assess the repression ability of GAL80. The UAS-grim lethality test facilitates the determination of the developmental period during which GAL4 activity is not inhibited.</p> <p>Two different muscle-specific GAL4 drivers, Mef2-Gal4 (BDSC:27390) and DJ694 (BDSC: 8176), were each crossed with a second chromosome insertion of UAS-grim (<a href="https://doi.org/10.1038/sj.cdd.4400423">Cell Death Differ 5:930,1998</a>), UAS-grim recombined with third chromosome insertions of GAL80TET (3.3+1077, <a href="https://peerj.com/articles/4167/">PeerJ 5:e4167</a>), and UAS-grim recombined with third chromosome insertions of GAL80ts (BDSC:7017). Negative control (no lethality) was generated by crossing the UAS-grim strain with a strain without any GAL4 transgene (w<sup>1118</sup>,<a href="https://www.cell.com/cell/pdf/0092-8674(84)90240-X.pdf?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2F009286748490240X%3Fshowall%3Dtrue">Cell 36:469, 1984</a> ). Crosses were maintained, and eggs were collected at 20˚C (Experimental workflow). Parents were obtained from multiple independent cultures to set-up independent crosses (biological replicates, Set indicates parents from the same culture). Crosses were kept 24 to 48h in culture tubes to allow mating before transferring them to egg collectors. Multiple egg collections were done for each parental set (technical replicates, Date indicates dates of collection). Parents were allowed to lay eggs for 12h to 16h. Up to 25 eggs were aligned on a slice of food and up to 4 slices were used for a given collection from a set. Slices of food are then transferred to culture vials and incubated at the indicated temperature. The scoring of the number of first-instar larvae (L1) was done by scoring the number of empty eggs 25-30h (29˚C) or 43-48h (20˚C) after egg alignment. The number of pupae and adults was scored 5-6 days (29˚C) or 8-10 days (20˚C) after the scoring of the previous stage.</p>
Set of Data from "Selective targeting of striatal parvalbumin-expressing interneurons for transgene delivery" https://doi.org/10.1016/j.jneumeth.2021.109105
<p>PV<sup>Cre</sup> (+/+) mice were injected in the right striatum with AAV2/1-hsyn-FLEX-eGFP AAV2/9-CBA-FLEX-eGFP or AAV2/9-hsyn-FLEX-eGFP vectors. Two weeks after, cells were manually counted by a blind observer on 2D maximal intensity projections of confocal images transformed into the tiff format using the Multi-point tool in ImageJ. The GraphPad .pzfx files show the quantitative anaylsis of the proportion of GFP+ cells which were PV+ (specificty) , the proportion of PV+ cells which were GFP+ (efficiency), the proportion of PV+ cells in the injected striatum relative to to the injected striatum of PV<sup>Cre</sup> (+/+) mice (absence of vector toxicity) and the proportion of PV+ cells in the striatum of PV<sup>Cre</sup> (+/+) mice versus wt mice.</p> <p> </p>
Data from: field evaluation: the effect of two transgenic Bt maize events on predatory arthropods in the Huang-Huai-Hai summer maize-growing region of China
Open the record for dataset details and reuse information.
Data from: Detecting the population dynamics of an autosomal sex-ratio distorter transgene in malaria vector mosquitoes
<p>1. The development of genetically modified mosquitoes and their subsequent field release offers innovative and cost-effective approaches to reduce mosquito-borne diseases, such as malaria. A sex-distorting autosomal transgene has been developed recently in G3 mosquitoes, a lab strain of the malaria vector Anopheles gambiae s.l. The transgene expresses an endonuclease called I-PpoI during spermatogenesis, which selectively cleaves the X chromosome to result in ~95% male progeny. Following the World Health Organization Guidance Framework for the testing of genetically modified mosquitoes, we assessed the dynamics of this transgene in large cages using a joint experimental-modelling approach.</p> <p>2. We performed a four-month experiment in indoor large cages to study the population genetics of the transgene. The cages were set up to mimic a simple tropical environment with a diurnal light-cycle, constant temperature, and constant humidity. We allowed the generations to overlap to engender a stable age structure in the populations. We constructed a model to mimic the experiments, and used the experimental data to infer the key model parameters.</p> <p>3. We identified two fitness costs associated to the transgene. First, transgenic adult males have reduced fertility and, second, their female progeny have reduced pupal survival rates. Our results demonstrate that the transgene is likely to disappear in less than three years under our confined conditions. Model predictions suggest this will be true over a wide range of background population sizes and transgene introduction rates.</p> <p>4. Synthesis and applications: Our semi-field indoor cage experiments are in line with WHO guidance recommendations in regards to the development and testing of self-limiting technologies. Since the transgenic strain (Ag(PMB)1) has been considered for genetic vector control of malaria, our results are fundamentally important for determining expectations on the persistence of the transgene post-release. Our results provide a demonstration of the self-limiting nature of the transgene, and indicate that longevity will be further reduced by fitness costs that were not previously identified. Finally, our study has showcased an alternative and effective method for characterising the phenotypic expression of a transgene in an insect pest population.</p>
Data for: Phytochemical shift from condensed tannins to flavonoids in transgenic Betula pendula decreases consumption and growth but improves growth efficiency of Epirrita autumnata larvae
<p>Despite active research, antiherbivore activity of specific plant phenolics remains largely unresolved. We constructed silver birch (<em>Betula pendula</em>) lines with modified phenolic metabolism to study the effects of foliar flavonoids and condensed tannins on consumption and growth of larvae of a generalist herbivore, the autumnal moth (<em>Epirrita autumnata</em>). We conducted a feeding experiment using birch lines in which expression of dihydroflavonol reductase (<em>DFR</em>), anthocyanidin synthase (<em>ANS</em>) or anthocyanidin reductase (<em>ANR</em>) had been decreased by RNA interference. Modification-specific effects on plant phenolics, nutrients and phenotype, and on larval consumption and growth were analyzed using uni- and multivariate methods. Inhibiting <em>DFR</em> expression increased the concentration of flavonoids at the expense of condensed tannins, and silencing <em>DFR </em>and <em>ANR </em>decreased leaf and plant size. <em>E. autumnata </em>larvae consumed on average 82% less of DFRi plants than of unmodified controls, suggesting that flavonoids or glandular trichomes deter larval feeding. However, larval growth efficiency was highest on low-tannin DFRi plants, indicating that condensed tannins (or their monomers) are physiologically more harmful than non-tannin flavonoids for <em>E. autumnata </em>larvae. Our results show that genetic manipulation of the flavonoid pathway in plants can effectively be used to produce altered phenolic profiles required for elucidating the roles of low-molecular weight phenolics and condensed tannins in plant–herbivore relationships, and suggest that phenolic secondary metabolites participate in regulation of plant growth.</p>
Confocal stacks of Cii_beta gamma crystalin_hM4D(Gi)_mCherry transgenic Ciona Larvae
<p>Confocal stacks of Cii_beta gamma crystalin_hM4D(Gi)_mCherry transgenic Ciona Larvae used to generate the panels of Hoyer et al.</p>
Improved production of HIV-1 subtype C protease from transgenic E coli
<p>The data set belongs to study carried out by Uraisha Ramlucken at Department of Biochemistry, University of KwaZulu-Natal, Durban, South Africa. This study was made possible through financial support from the National Research Foundation.</p>
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