scholarly journals T-DNA integration is rapid and influenced by the chromatin state of the host genome

2017 ◽  
Author(s):  
Shay Shilo ◽  
Pooja Tripathi ◽  
Cathy Melamed-Bessudo ◽  
Oren Tzfadia ◽  
Theodore R. Muth ◽  
...  
Keyword(s):  
Agrobacterium Tumefaciens ◽  
High Throughput ◽  
Post Infection ◽  
Nucleosome Occupancy ◽  
Plant Genome ◽  
Epigenetic Landscape ◽  
Dna Integration ◽  
Time Points ◽  
Genome Manipulation ◽  
Border Sequence

AbstractAgrobacterium tumefaciens mediated T-DNA integration is a common tool for plant genome manipulation. However, there is controversy regarding whether T-DNA integration is biased towards genes or randomly distributed throughout the genome. In order to address this question, we performed high-throughput mapping of T-DNA-genome junctions obtained in the absence of selection at several time points after infection. T-DNA-genome junctions were detected as early as 6 hours post-infection. T-DNA distribution was apparently uniform throughout the chromosomes, yet local biases toward AT-rich motifs and T-DNA border sequence micro-homology were detected. Analysis of the epigenetic landscape of integration showed that selected events reported on previously were associated with extremely low methylation and nucleosome occupancy. Conversely, non-selected events from this study showed chromatin marks, such as high nucleosome occupancy and high H3K27me3 that correspond to 3D-interacting heterochromatin islands embedded within euchromatin. Such structures might play a role in capturing and silencing invading T-DNA.

T-DNA integration patterns in transgenic plants mediated by Agrobacterium tumefaciens

2011 ◽  
Vol 33 (12) ◽  
pp. 1327-1334 ◽  
Author(s):  
Lin YANG ◽  
Feng-Ling FU ◽  
Wan-Chen LI
Keyword(s):  
Agrobacterium Tumefaciens ◽  
Transgenic Plants ◽  
Dna Integration

scholarly journals Strategies to produce T-DNA free CRISPRed fruit trees via Agrobacterium tumefaciens stable gene transfer

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Lorenza Dalla Costa ◽  
Stefano Piazza ◽  
Valerio Pompili ◽  
Umberto Salvagnin ◽  
Alessandro Cestaro ◽  
...  
Keyword(s):  
Agrobacterium Tumefaciens ◽  
Gene Transfer ◽  
Genomic Dna ◽  
Fruit Trees ◽  
Plant Genome ◽  
Stable Gene ◽  
Binary Vectors ◽  
Exogenous Dna ◽  
Left Behind ◽  
Dicotyledonous Plants

AbstractGenome editing via CRISPR/Cas9 is a powerful technology, which has been widely applied to improve traits in cereals, vegetables and even fruit trees. For the delivery of CRISPR/Cas9 components into dicotyledonous plants, Agrobacterium tumefaciens mediated gene transfer is still the prevalent method, although editing is often accompanied by the integration of the bacterial T-DNA into the host genome. We assessed two approaches in order to achieve T-DNA excision from the plant genome, minimizing the extent of foreign DNA left behind. The first is based on the Flp/FRT system and the second on Cas9 and synthetic cleavage target sites (CTS) close to T-DNA borders, which are recognized by the sgRNA. Several grapevine and apple lines, transformed with a panel of CRISPR/SpCas9 binary vectors, were regenerated and characterized for T-DNA copy number and for the rate of targeted editing. As detected by an optimized NGS-based sequencing method, trimming at T-DNA borders occurred in 100% of the lines, impairing in most cases the excision. Another observation was the leakage activity of Cas9 which produced pierced and therefore non-functional CTS. Deletions of genomic DNA and presence of filler DNA were also noticed at the junctions between T-DNA and genomic DNA. This study proved that many factors must be considered for designing efficient binary vectors capable of minimizing the presence of exogenous DNA in CRISPRed fruit trees.

scholarly journals 230 Genome editing applications in plants: high-throughput CRISPR/Cas editing for crop improvement

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 56-56
Author(s):  
Michael Thomson
Keyword(s):  
Genome Editing ◽  
High Throughput ◽  
Positional Cloning ◽  
Gene Editing ◽  
Crop Improvement ◽  
Cost Effective ◽  
Gene Families ◽  
Ease Of Use ◽  
Plant Genome ◽  
Wide Range

Abstract The precision and ease of use of CRISPR nucleases, such as Cas9 and Cpf1, for plant genome editing has the potential to accelerate a wide range of applications for crop improvement. For upstream research on gene discovery and validation, rapid gene knock-outs can enable testing of single genes and multi-gene families for functional effects. Large chromosomal deletions can test the function of tandem gene arrays and assist with positional cloning of QTLs by helping to narrow down the target region. Nuclease-deactivated Cas9 fusion proteins with transcriptional activators and repressors can be used to up and down-regulate gene expression. Even more promising, gene insertions and allele replacements can provide the opportunity to rapidly test the effects of different alleles at key loci in the same genetic background, providing a more precise alternative to marker-assisted backcrossing. Recently, Texas A&M AgriLife Research has supported the development of a Crop Genome Editing Lab at Texas A&M working towards optimizing a high-throughput gene editing pipeline and providing an efficient and cost-effective gene editing service for research and breeding groups. The lab is using rice as a model to test and optimize new approaches aimed towards overcoming current bottlenecks. For example, a wealth of genomics data from the rice community enables the development of novel approaches to predict which genes and target modifications may be most beneficial for crop improvement, taking advantage of known major genes, high-resolution GWAS data, multiple high-quality reference genomes, transcriptomics data, and resequencing data from the 3,000 Rice Genomes Project. Current projects have now expanded to work across multiple crops to provide breeding and research groups with a rapid gene editing pipeline to test candidate genes in their programs, with the ultimate goal of developing nutritious, high-yielding, stress-tolerant crops for the future.

scholarly journals Riemerella anatipestifer infection in ducks induces IL-17A production, but not IL-23p19

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Rochelle A. Flores ◽  
Cherry P. Fernandez-Colorado ◽  
Fahmida Afrin ◽  
Paula Leona T. Cammayo ◽  
Suk Kim ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Proinflammatory Cytokines ◽  
Post Infection ◽  
Proinflammatory Cytokine ◽  
Th17 Cells ◽  
Critical Role ◽  
Splenic Lymphocytes ◽  
Expression Levels ◽  
Time Points ◽  
Mrna Expression Analysis

Abstract R. anatipestifer (RA) is one of the most harmful bacterial pathogens affecting the duck industry, and infection is associated with the production of proinflammatory cytokines, including IL-17A. Another proinflammatory cytokine, IL-23, is critical for the development of Th17 cells, which produce IL-17. However, IL-23 roles have not been studied in this infection. Here, we describe the identification and mRNA expression analysis of duck IL-23p19 (duIL-23p19) in splenic lymphocytes and macrophages stimulated with killed RA and in spleens of RA-infected ducks. Expression of duIL-23p19 transcript identified in this study was relatively high in livers of healthy ducks and was upregulated in mitogen-activated splenic lymphocytes as well as in splenic lymphocytes and macrophages stimulated with killed RA. In spleens of RA-infected ducks, expression levels of duIL-23p19 transcript were unchanged at all time points except on days 4 and 7 post-infection; however, duIL-17A and IL-17F expression levels were upregulated in both spleens of RA-infected ducks and splenic lymphocytes and macrophages stimulated with killed RA. In sera collected at 24 h after this infection, duIL-23p19 expression levels were unchanged, whereas IL-17A significantly upregulated. These results suggest that IL-23p19 does not play a critical role in the IL-17A response in early stages of RA-infected ducks.

scholarly journals Agrobacterium tumefaciens Transformation of the Radiation Hypersensitive Arabidopsis thaliana Mutants uvh1 and rad5

1998 ◽  
Vol 11 (11) ◽  
pp. 1136-1141 ◽  
Author(s):  
Jaesung Nam ◽  
Kirankumar S. Mysore ◽  
Stanton B. Gelvin
Keyword(s):  
Arabidopsis Thaliana ◽  
Agrobacterium Tumefaciens ◽  
Transformation Process ◽  
Stable Transformation ◽  
Wild Type ◽  
Dna Integration ◽  
Agrobacterium Tumefaciens Transformation ◽  
Inoculation Assay

The Arabidopsis thaliana mutants uvh1 and rad5, originally identified as radiation hypersensitive, were reported to be deficient in T-DNA integration based on the relative efficiencies of stable transformation and T-DNA transfer. We reassessed these mutants for susceptibility to transformation by Agrobacterium tumefaciens. The mutant rad5 showed a significant reduction in the efficiency of transient as well as stable transformation, compared with its wild-type progenitor. These data indicate that rad5 is blocked at a step in the transformation process prior to T-DNA integration. We additionally found, using both an in vitro root inoculation and an in vivo flower bolt inoculation assay, that the mutant uvh1 is as susceptible to A. tumefaciens-mediated transformation as is its wild-type progenitor, C10.

Comparison of parasitological, immunological and molecular methods for evaluation of fecal samples of immunosuppressed rats experimentally infected with Strongyloides venezuelensis

Parasitology ◽  
2015 ◽  
Vol 142 (14) ◽  
pp. 1715-1721 ◽  
Author(s):  
LEILANE A. CHAVES ◽  
ANA LÚCIA R. GONÇALVES ◽  
FABIANA M. PAULA ◽  
NEIDE. M. SILVA ◽  
CLÁUDIO V. SILVA ◽  
...  
Keyword(s):  
Post Infection ◽  
Pcr Amplification ◽  
Conventional Polymerase Chain Reaction ◽  
Diagnostic Value ◽  
Diagnostic Methods ◽  
Enzyme Linked Immunosorbent Assay ◽  
Fecal Samples ◽  
Infection Time ◽  
Time Points ◽  
Strongyloides Venezuelensis

SUMMARYDefinitive diagnosis of strongyloidiasis in humans is typically achieved by detection of larvae in fecal samples. However, limitations on sensitivity of parasitological methods emphasize the need for more robust diagnostic methods. The aim of this study was to compare the diagnostic value of three methods: eggs per gram of feces (EPG), coproantigen detection by enzyme linked immunosorbent assay (ELISA), and DNA detection by conventional polymerase chain reaction (PCR). The assays were performed at 0 and 5, 8, 13, 21 and 39 days post-infection (dpi) using fecal samples from experimentally infected immunocompetent and immunosuppressed rats. In immunocompetent rats, eggs were detected in feces on days 5, 8 and 13 dpi; coproantigen detection and PCR amplification were successful at all post-infection time points (5, 8, 13, 21 and 39 dpi). In immunosuppressed rats, eggs were detected at 5, 8, 13 and 21; coproantigen detection and PCR amplification were successful at all post-infection time points. In conclusion, these results suggest that coproantigen detection and PCR may be more sensitive alternatives to traditional methods such as EPG for diagnosis of Strongyloides venezuelensis infection.

scholarly journals Identification of Pathogenesis-Associated Genes by T-DNA–Mediated Insertional Mutagenesis in Botrytis cinerea: A Type 2A Phosphoprotein Phosphatase and an SPT3 Transcription Factor Have Significant Impact on Virulence

2012 ◽  
Vol 25 (4) ◽  
pp. 481-495 ◽  
Author(s):  
S. Giesbert ◽  
J. Schumacher ◽  
V. Kupas ◽  
J. Espino ◽  
N. Segmüller ◽  
...  
Keyword(s):  
Botrytis Cinerea ◽  
Protein Phosphatase ◽  
Insertional Mutagenesis ◽  
Single Copy ◽  
Gene Replacement ◽  
Gray Mold ◽  
Dna Integration ◽  
Bean Plants ◽  
Mold Fungus ◽  
Border Sequence

Agrobacterium tumefaciens–mediated transformation (ATMT) was used to generate an insertional mutant library of the gray mold fungus Botrytis cinerea. From a total of 2,367 transformants, 68 mutants showing significant reduction in virulence on tomato and bean plants were analyzed in detail. As reported for other fungal ATMT libraries, integrations were mostly single copy, occurred preferentially in noncoding (regulatory) regions, and were frequently accompanied by small deletions of the target sequences and loss of parts of the border sequence. Two T-DNA integration events that were found to be linked to virulence were characterized in more detail: a catalytic subunit of a PP2A serine/threonine protein phosphatase (BcPP2Ac) and the SPT3 subunit of a Spt-Ada-Gcn5-acetyltransferase (SAGA-like) transcriptional regulator complex. Gene replacement and silencing approaches revealed that both Bcpp2Ac and SPT3 are crucial for virulence, growth, and differentiation as well as for resistance to H2O2 in B. cinerea.

scholarly journals High-throughput glycomic analyses reveal unique oligosaccharide profiles of canine and feline milk samples

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243323
Author(s):  
David J. Wrigglesworth ◽  
Elisha Goonatilleke ◽  
Richard Haydock ◽  
Kevin R. Hughes ◽  
Carlito B. Lebrilla ◽  
...  
Keyword(s):  
High Throughput ◽  
Maternal Diet ◽  
Labrador Retriever ◽  
Diverse Range ◽  
Maternal Milk ◽  
Time Points ◽  
Milk Samples ◽  
Fundamental Understanding ◽  
Nutritional Needs ◽  
Pathogen Colonization

Oligosaccharides are important components of milk, serving as substrates for the intestinal microbiota, acting as antimicrobials that prevent pathogen colonization, and supporting the developing gastrointestinal immune system of neonates. Nutrient composition of canine and feline milk samples has been described previously, but little is known about the oligosaccharide content. Therefore, the objective of this study was to characterize canine and feline milk samples using a high-throughput glycomics approach. 23 dogs (9 Labrador retriever and 14 Labrador retriever x golden retriever crossbreed) and 6 domestic shorthair cats were recruited to the study. Milk samples were collected by manual expression at time points after parturition. Samples were collected across 2 phases per species, differentiated by maternal diet. Following extraction, oligosaccharide content was determined by liquid chromatography-mass spectrometry (LC-MS). In canine milk samples, 3 structures accounted for over 90% of all oligosaccharides detected across two diet groups. These were 3’-sialyllactose, 6’-sialyllactose, and 2’-fucosyllactose. In feline samples, a more diverse range of oligosaccharides was detected, with up to 16 structures present at relative abundance >1% of the total. Difucosyllactose-N-hexaose b, 3’-sialyllactose and lacto-N-neohexaose were all detected at abundances >10% in feline milk samples. Statistically significant differences (p<0.05) in oligosaccharide abundances were observed between collection time points and between diet groups within species. These data explore the oligosaccharide content of canine and feline maternal milk, representing an opportunity to generate a fundamental understanding of the nutritional needs of new-born puppies and kittens.

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