Efficient CRISPR-mediated base editing in Agrobacterium spp.

Agrobacterium spp. are important plant pathogens that are the causative agents of crown gall or hairy root disease. Their unique infection strategy depends on the delivery of part of their DNA to plant cells. Thanks to this capacity, these phytopathogens became a powerful and indispensable tool for plant genetic engineering and agricultural biotechnology. Although Agrobacterium spp. are standard tools for plant molecular biologists, current laboratory strains have remained unchanged for decades and functional gene analysis of Agrobacterium has been hampered by time-consuming mutation strategies. Here, we developed clustered regularly inter-spaced short palindromic repeats (CRISPR)-mediated base editing to enable the efficient introduction of targeted point mutations into the genomes of both Agrobacterium tumefaciens and Agro-bacterium rhizogenes. As an example, we generated EHA105 strains with loss-of-function mutations in recA, which were fully functional for maize (Zea mays) transformation and confirmed the importance of RolB and RolC for hairy root development by A. rhizogenes K599. Our method is highly effective in 9 of 10 colonies after transformation, with edits in at least 80% of the cells. The genomes of EHA105 and K599 were resequenced, and genome-wide off-target analysis was applied to investigate the edited strains after curing of the base editor plasmid. The off-targets present were characteristic of Cas9-independent off-targeting and point to TC motifs as activity hotspots of the cytidine deaminase used. We anticipate that CRISPR-mediated base editing is the start of "engineering the engineer," leading to improved Agrobacterium strains for more efficient plant transformation and gene editing

Occurrence of halogenated flame retardants in commercial seafood species available in European markets

PBDEs (congeners 28, 47, 99, 100, 153, 154, 183, 209), HBCD (α, β, γ), emerging brominated flame retardants (PBEB, HBB and DBDPE), dechloranes (Dec 602, 603, 604, syn- and anti-DP), TBBPA, 2,4,6-TBP and MeO-PBDEs (8 congeners) were analysed in commercial seafood samples from European countries. Levels were similar to literature and above the environmental quality standards (EQS) limit of the Directive 2013/39/EU for PBDEs. Contaminants were found in 90.5% of the seafood samples at n. d.-356 ng/g lw (n. d.-41.1 ng/g ww). DBDPE was not detected and 2,4,6-TBP was detected only in mussels, but at levels comparable to those of PBDEs. Mussel and seabream were the most contaminated species and the Mediterranean Sea (FAO Fishing Area 37) was the most contaminated location. The risk assessment revealed that there was no health risk related to the exposure to brominated flame retardants via seafood consumption. However, a refined risk assessment for BDE-99 is of interest in the future. Moreover, the cooking process concentrated PBDEs and HB

Concurrent Assessment of Phthalates/HEXAMOLL® DINCH Exposure and Wechsler Intelligence Scale for Children Performance in Three European Cohorts of the HBM4EU Aligned Studies

Information about the effects of phthalates and non-phthalate substitute cyclohexane-1,2-dicarboxylic acid diisononyl ester (HEXAMOLL® DINCH) on children's neurodevelopment is limited. The aim of the present research is to evaluate the association between phthalate/HEXAMOLL® DINCH exposure and child neurodevelopment in three European cohorts involved in HBM4EU Aligned Studies. Participating subjects were school-aged children belonging to the Northern Adriatic cohort II (NAC-II), Italy, Odense Child Cohort (OCC), Denmark, and PCB cohort, Slovakia. In each cohort, children's neurodevelopment was assessed through the Full-Scale Intelligence Quotient score (FSIQ) of the Wechsler Intelligence Scale of Children test using three different editions. The children's urine samples, collected for one point in time concurrently with the neurodevelopmental evaluation, were analyzed for several phthalates/HEXAMOLL® DINCH biomarkers. The relation between phthalates/HEXAMOLL® DINCH and FSIQ was explored by applying separate multiple linear regressions in each cohort. The means and standard deviations of FSIQ were 109 ± 11 (NAC-II), 98 ± 12 (OCC), and 81 ± 15 (PCB cohort). In NAC-II, direct associations between FSIQ and DEHP's biomarkers were found: 5OH-MEHP+5oxo-MEHP (β = 2.56; 95% CI 0.58-4.55; N = 270), 5OH-MEHP+5cx-MEPP (β = 2.48; 95% CI 0.47-4.49; N = 270) and 5OH-MEHP (β = 2.58; 95% CI 0.65-4.51; N = 270). On the contrary, in the OCC the relation between DEHP's biomarkers and FSIQ tended to be inverse but imprecise (p-value ≥ 0.10). No associations were found in the PCB cohort. FSIQ was not associated with HEXAMOLL® DINCH in any cohort. In conclusion, these results do not provide evidence of an association between concurrent phthalate/DINCHHEXAMOLLR DINCH exposure and IQ in children.This work received external funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 733032 [“European Human Biomonitoring Initiative” (HBM4EU)] and received co-funding from the author’s organizations. NAC-II: This research was funded by: the European Union through its Sixth Framework Program for RTD (contract “PHIME” No. FOOD-CT-2006-016253); the Institute for Maternal and Child Health IRCCS “Burlo Garofolo”, Trieste, Italy (RC 12/12 funded by Ministry of Health—Italy); CROME LIFE Project “Cross-Mediterranean Environment and Health Network” (LIFE12 ENV/GR/001040). OCC: The cohort was funded by the Odense University Hospital, Denmark; the Region of Southern Denmark, The Municipality of Odense, Denmark; The University of Southern Denmark; the Mental Health Service of the Region of Southern Denmark; Odense Patient data Exploratory Network (OPEN), Den mark; The Danish Center for Hormone Disrupting Chemicals (MST-611-00012); The Danish Research Council (4004-00352B_FSS); Novo Nordisk Foundation, Denmark (grant no. NNF19OC0058266 and NNF17OC0029404); Sygeforsikring Danmark (journalnr. 2021-0173); The Collaborative foundation between Odense University Hospital and Rigshospitalet, Helsefonden, Beckettfonden, the Danish Mental Health Fund, Health Insurance Denmark. The LS-MS/MS equipment was financially supported by the Velux Foundation. PCB: PCB cohort was funded by the Slovak Research and Development Agency, project no. APVV-0571-12 and the Ministry of Health of the Slovak Republic, project no. 2014/47-SZU-11. The APC was funded by the European Union’s Horizon 2020 research and innovation program under grant agreement No. 733032.S

Inter-laboratory mass spectrometry dataset based on passive sampling of drinking water for non-target analysis

Non-target analysis (NTA) employing high-resolution mass spectrometry is a commonly applied approach for the detection of novel chemicals of emerging concern in complex environmental samples. NTA typically results in large and information-rich datasets that require computer aided (ideally automated) strategies for their processing and interpretation. Such strategies do however raise the challenge of reproducibility between and within different processing workflows. An effective strategy to mitigate such problems is the implementation of inter-laboratory studies (ILS) with the aim to evaluate different workflows and agree on harmonized/standardized quality control procedures. Here we present the data generated during such an ILS. This study was organized through the Norman Network and included 21 participants from 11 countries. A set of samples based on the passive sampling of drinking water pre and post treatment was shipped to all the participating laboratories for analysis, using one pre-defined method and one locally (i.e. in-house) developed method. The data generated represents a valuable resource (i.e. benchmark) for future developments of algorithms and workflows for NTA experiments

On the Relation between a Nonlinear Elliptic Equation and Its Uniform Approximation

AbstractThe qualitative behavior of the solution set of nonlinear elliptic boundary value problems has in some instances been studied by reducing the partial differential equation to a related algebraic equation. Although this procedure often gives a good picture of the bifurcation diagram, it can be quite wrong. In this paper some relationships between the solutions of the two problems are investigated

The role of TRPM4 in cardiac contractility and arrhythmias

TRPM4 is a Ca2+-activated non-selective cation channel that belongs to the family of the Transient Receptor Potential (TRP) ion channels. TRPM4 is a monovalent-selective cation channel, which is activated by an increase of the intracellular Ca2+ concentration. Trpm4 is highly expressed in the heart and was recently suggested as a novel regulator of ventricular contractility. Additionally, it was hypothesized before that TRPM4-like channels might play a role in the development of Ca2+-dependent triggered arrhythmias. Therefore, we investigated the role of TRPM4 in cardiac contractility and arrhythmias in living animals.nrpages: 126status: publishe

Interleukin/cytokine profiles in haemodialysis and in continuous peritoneal dialysis

The uraemic syndrome is a complex condition that results from the retention of 'waste' compounds that normally would be excreted into the urine or catabolized by the kidneys. In addition, inflammation has been implicated in symptoms associated with uraemia, including its role in the malnutrition-inflammation-atherosclerosis syndrome. Regarding vascular disease, traditional risk factors such as hypertension and gender do not seem to have the same significance in the uraemic population compared with patients without renal failure, and so the possibility has been raised that the uraemic toxins that result in the uraemic syndrome could play a role in this process. In this review, various questions are addressed regarding the involvement of cytokines in uraemia and the effects of dialysis membranes and fluids in patients receiving haemodialysis or peritoneal dialysis on cytokine levels. The effects of non-dialysis-related factors on levels of cytokines, mortality rates and other uraemic disorders are also discussed. It is concluded that cytokines are undoubtedly retained in uraemia, and that the loss of renal excretion almost certainly plays a key role in this process. Many cytokines have a pro-inflammatory role, probably resulting in a number of clinical events that are related to the increased morbidity and mortality of uraemic and haemodialysis patients. Any adjustment of the subtle balance between pro- and anti-inflammation by medical interventions should be conducted carefully because of an enhanced risk of serious infectious episodes. Bioincompatibility of dialysis techniques probably enhances the generation of cytokines as well as other uraemic toxins