CCAR1 promotes DNA repair via alternative splicing.

DNA repair is directly performed by hundreds of core factors and indirectly regulated by thousands of others. We massively expanded a CRISPR inhibition and Cas9-editing screening system to discover factors indirectly modulating homology-directed repair (HDR) in the context of ∼18,000 individual gene knockdowns. We focused on CCAR1, a poorly understood gene that we found the depletion of reduced both HDR and interstrand crosslink repair, phenocopying the loss of the Fanconi anemia pathway. CCAR1 loss abrogated FANCA protein without substantial reduction in the level of its mRNA or that of other FA genes. We instead found that CCAR1 prevents inclusion of a poison exon in FANCA. Transcriptomic analysis revealed that the CCAR1 splicing modulatory activity is not limited to FANCA, and it instead regulates widespread changes in alternative splicing that would damage coding sequences in mouse and human cells. CCAR1 therefore has an unanticipated function as a splicing fidelity factor.

Compact sum-of-products form of the molecular electronic Hamiltonian based on canonical polyadic decomposition.

We propose an approach to represent the second-quantized electronic Hamiltonian in a compact sum-of-products (SOP) form. The approach is based on the canonical polyadic decomposition of the original Hamiltonian projected onto the sub-Fock spaces formed by groups of spin-orbitals. The algorithm for obtaining the canonical polyadic form starts from an exact sum-of-products, which is then optimally compactified using an alternating least squares procedure. We discuss the relation of this specific SOP with related forms, namely the Tucker format and the matrix product operator often used in conjunction with matrix product states. We benchmark the method on the electronic dynamics of an excited water molecule, trans-polyenes, and the charge migration in glycine upon inner-valence ionization. The quantum dynamics are performed with the multilayer multiconfiguration time-dependent Hartree method in second quantization representation. Other methods based on tree-tensor Ansätze may profit from this general approach.

Quantum and classical molecular dynamics for H atom scattering from graphene.

This work presents systematic comparisons between classical molecular dynamics (cMD) and quantum dynamics (QD) simulations of 15-dimensional and 75-dimensional models in their description of H atom scattering from graphene. We use an experimentally validated full-dimensional neural network potential energy surface of a hydrogen atom interacting with a large cell of graphene containing 24 carbon atoms. For quantum dynamics simulations, we apply Monte Carlo canonical polyadic decomposition to transform the original potential energy surface (PES) into a sum of products form and use the multi-layer multi-configuration time-dependent Hartree method to simulate the quantum scattering of a hydrogen or deuterium atom with an initial kinetic energy of 1.96 or 0.96 eV and an incident angle of 0°, i.e., perpendicular to the graphene surface. The cMD and QD initial conditions have been carefully chosen in order to be as close as possible. Our results show little differences between cMD and QD simulations when the incident energy of the H atom is equal to 1.96 eV. However, a large difference in sticking probability is observed when the incident energy of the H atom is equal to 0.96 eV, indicating the predominance of quantum effects. To the best of our knowledge, our work provides the first benchmark of quantum against classical simulations for a system of this size with a realistic PES. Additionally, new projectors are implemented in the Heidelberg multi-configuration time-dependent Hartree package for the calculation of the atom scattering energy transfer distribution as a function of outgoing angles.

Simultaneous bilateral TKA in the context of fast track surgery - Do patients meet discharge criteria as anticipated?

BACKGROUND: The efficacy and safety of enhanced recovery after surgery (ERAS) protocols for patients undergoing total knee arthroplasty (TKA) have been generally proven. Previous studies investigating patients undergoing simultaneous bilateral TKA (SBTKA) focused on complications, mortality, and pain and did not examine patients' functional limitations. Therefore, the aim of this study was to investigate to what extent patients undergoing SBTKA are able to meet functional discharge criteria originally designed for their counterparts undergoing unilateral TKA (UTKA) in an ERAS setting. MATERIALS AND METHODS: All patients who received primary SBTKA between June 2015 and December 2018 were included in this retrospective analysis. For comparison, UTKA patients were matched 1:1 to SBTKA patients using Propensity Score Matching based on age, gender, and BMI. The times to achieving the rehabilitation checkpoints of walking 150 m, walking a flight of stairs, and 90° knee flexion were evaluated. RESULTS: 63 (SBTKA group) and 64 (UTKA group) patients were included. Due to the Propensity-Score-Matching there were no differences regarding age, gender, and BMI. The mean length of stay (LOS) was 9.1 days in the SBTKA and 7.6 days in the UTKA group (p = 0.003). On average, it took SBTKA patients 5.4 days to achieve an uninterrupted walking distance of at least 150 m, while it took UTKA patients 4.1 days (p < 0.001). Mean time to walking a flight of stairs was 6.3 days for SBTKA patients and 4.7 days for UTKA patients (p < 0.001). 90° flexion was achieved after 4.1 days by SBTKA patients and 3.5 days by UTKA patients (p = 0.241). CONCLUSION: The vast majority of SBTKA patients were able to achieve functional discharge criteria within their inpatient stay when allowed about 30% extra time. Therefore, functional discharge criteria in ERAS protocols designed for UTKA can be considered appropriate for SBTKA patients. LEVEL OF EVIDENCE: Therapeutic Level III.

PnB Designer: a web application to design prime and base editor guide RNAs for animals and plants.

BACKGROUND: The rapid expansion of the CRISPR toolbox through tagging effector domains to either enzymatically inactive Cas9 (dCas9) or Cas9 nickase (nCas9) has led to several promising new gene editing strategies. Recent additions include CRISPR cytosine or adenine base editors (CBEs and ABEs) and the CRISPR prime editors (PEs), in which a deaminase or reverse transcriptase are fused to nCas9, respectively. These tools hold great promise to model and correct disease-causing mutations in animal and plant models. But so far, no widely-available tools exist to automate the design of both BE and PE reagents. RESULTS: We developed PnB Designer, a web-based application for the design of pegRNAs for PEs and guide RNAs for BEs. PnB Designer makes it easy to design targeting guide RNAs for single or multiple targets on a variant or reference genome from organisms spanning multiple kingdoms. With PnB Designer, we designed pegRNAs to model all known disease causing mutations available in ClinVar. Additionally, PnB Designer can be used to design guide RNAs to install or revert a SNV, scanning the genome with one CBE and seven different ABE PAM variants and returning the best BE to use. PnB Designer is publicly accessible at http://fgcz-shiny.uzh.ch/PnBDesigner/ CONCLUSION: With PnB Designer we created a user-friendly design tool for CRISPR PE and BE reagents, which should simplify choosing editing strategy and avoiding design complications.

Effect of progesterone on Candida albicans biofilm formation under acidic conditions: A transcriptomic analysis.

Vulvovaginal candidiasis (VVC) caused by Candida albicans is a common disease worldwide. A very important C. albicans virulence factor is its ability to form biofilms on epithelium and/or on intrauterine devices promoting VVC. It has been shown that VVC has a hormonal dependency and that progesterone affects virulence traits of C. albicans cells. To understand how the acidic environment (pH 4) and progesterone (either alone and in combination) modulate C. albicans response during formation of biofilm, a transcriptomic analysis was performed together with characterization of the biofilm properties. Compared to planktonic cells, acidic biofilm-cells exhibited major changes in their transcriptome, including modifications in the expression of 286 genes that were not previously associated with biofilm formation in C. albicans. The vast majority of the genes up-regulated in the acidic biofilm cells (including those uniquely identified in our study) are known targets of Sfl1, and consistently, Sfl1 deletion is herein shown to impair the formation of acidic biofilms (pH 4). Under the acidic conditions used, the presence of progesterone reduced C. albicans biofilm biomass and structural cohesion. Transcriptomic analysis of biofilms developed in the presence of progesterone led to the identification of 65 down-regulated genes including, among others, the regulator Tec1 and several of its target genes, suggesting that the function of this transcription factor is inhibited by the presence of the hormone. Additionally, progesterone reduced the susceptibility of biofilm cells to fluconazole, consistent with an up-regulation of efflux pumps. Overall, the results of this study show that progesterone modulates C. albicans biofilm formation and genomic expression under acidic conditions, which may have implications for C. albicans pathogenicity in the vaginal environment.

Transforming high-dimensional potential energy surfaces into a canonical polyadic decomposition using Monte Carlo methods.

A Monte Carlo method is proposed for transforming high-dimensional potential energy surfaces evaluated on discrete grid points into a sum-of-products form, more precisely into a Canonical Polyadic Decomposition form. To this end, a modified existing ansatz based on the alternating least squares method is used, in which numerically exact integrals are replaced with Monte Carlo integrals. This largely reduces the numerical cost by avoiding the evaluation of the potential on all grid points and allows the treatment of surfaces with many degrees of freedom. Calculations on the 15D potential of the protonated water dimer (Zundel cation) in a sum-of-products form are presented and compared to the results obtained in a previous work [M. Schröder and H.-D. Meyer, J. Chem. Phys. 147, 064105 (2017)], where a sum-of-products form of the potential was obtained in the Tucker format.

Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis.

Complete and accurate genome assembly and annotation is a crucial foundation for comparative and functional genomics. Despite this, few complete eukaryotic genomes are available, and genome annotation remains a major challenge. Here, we present a complete genome assembly of the skin commensal yeast Malassezia sympodialis and demonstrate how proteogenomics can substantially improve gene annotation. Through long-read DNA sequencing, we obtained a gap-free genome assembly for M. sympodialis (ATCC 42132), comprising eight nuclear and one mitochondrial chromosome. We also sequenced and assembled four M. sympodialis clinical isolates, and showed their value for understanding Malassezia reproduction by confirming four alternative allele combinations at the two mating-type loci. Importantly, we demonstrated how proteomics data could be readily integrated with transcriptomics data in standard annotation tools. This increased the number of annotated protein-coding genes by 14% (from 3612 to 4113), compared to using transcriptomics evidence alone. Manual curation further increased the number of protein-coding genes by 9% (to 4493). All of these genes have RNA-seq evidence and 87% were confirmed by proteomics. The M. sympodialis genome assembly and annotation presented here is at a quality yet achieved only for a few eukaryotic organisms, and constitutes an important reference for future host-microbe interaction studies.

Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species.

Mating between different species produces hybrids that are usually asexual and stuck as diploids, but can also lead to the formation of new species. Here, we report the genome sequences of 27 isolates of the pathogenic yeast Candida orthopsilosis. We find that most isolates are diploid hybrids, products of mating between two unknown parental species (A and B) that are 5% divergent in sequence. Isolates vary greatly in the extent of homogenization between A and B, making their genomes a mosaic of highly heterozygous regions interspersed with homozygous regions. Separate phylogenetic analyses of SNPs in the A- and B-derived portions of the genome produces almost identical trees of the isolates with four major clades. However, the presence of two mutually exclusive genotype combinations at the mating type locus, and recombinant mitochondrial genomes diagnostic of inter-clade mating, shows that the species C. orthopsilosis does not have a single evolutionary origin but was created at least four times by separate interspecies hybridizations between parents A and B. Older hybrids have lost more heterozygosity. We also identify two isolates with homozygous genomes derived exclusively from parent A, which are pure non-hybrid strains. The parallel emergence of the same hybrid species from multiple independent hybridization events is common in plant evolution, but is much less documented in pathogenic fungi.

Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin.

Malassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina, (Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens. Malassezia are typically isolated from warm-blooded animals, are dominant members of the human skin mycobiome and are associated with common skin disorders. To characterize the genetic basis of the unique phenotypes of Malassezia spp., we sequenced the genomes of all 14 accepted species and used comparative genomics against a broad panel of fungal genomes to comprehensively identify distinct features that define the Malassezia gene repertoire: gene gain and loss; selection signatures; and lineage-specific gene family expansions. Our analysis revealed key gene gain events (64) with a single gene conserved across all Malassezia but absent in all other sequenced Basidiomycota. These likely horizontally transferred genes provide intriguing gain-of-function events and prime candidates to explain the emergence of Malassezia. A larger set of genes (741) were lost, with enrichment for glycosyl hydrolases and carbohydrate metabolism, concordant with adaptation to skin's carbohydrate-deficient environment. Gene family analysis revealed extensive turnover and underlined the importance of secretory lipases, phospholipases, aspartyl proteases, and other peptidases. Combining genomic analysis with a re-evaluation of culture characteristics, we establish the likely lipid-dependence of all Malassezia. Our phylogenetic analysis sheds new light on the relationship between Malassezia and other members of Ustilaginomycotina, as well as phylogenetic lineages within the genus. Overall, our study provides a unique genomic resource for understanding Malassezia niche-specificity and potential virulence, as well as their abundance and distribution in the environment and on human skin.

Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer.

UNLABELLED: Breast cancer is one of the most frequent cancers among women. Extensive studies into the molecular heterogeneity of breast cancer have produced a plethora of molecular subtype classification and prognosis prediction algorithms, as well as numerous gene expression signatures. However, reimplementation of these algorithms is a tedious but important task to enable comparison of existing signatures and classification models between each other and with new models. Here, we present the genefu R/Bioconductor package, a multi-tiered compendium of bioinformatics algorithms and gene signatures for molecular subtyping and prognostication in breast cancer. AVAILABILITY AND IMPLEMENTATION: The genefu package is available from Bioconductor. http://www.bioconductor.org/packages/devel/bioc/html/genefu.html Source code is also available on Github https://github.com/bhklab/genefu CONTACT: bhaibeka@uhnresearch.ca SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Transforming high-dimensional potential energy surfaces into sum-of-products form using Monte Carlo methods.

We propose a Monte Carlo method, "Monte Carlo Potfit," for transforming high-dimensional potential energy surfaces evaluated on discrete grid points into a sum-of-products form, more precisely into a Tucker form. To this end we use a variational ansatz in which we replace numerically exact integrals with Monte Carlo integrals. This largely reduces the numerical cost by avoiding the evaluation of the potential on all grid points and allows a treatment of surfaces up to 15-18 degrees of freedom. We furthermore show that the error made with this ansatz can be controlled and vanishes in certain limits. We present calculations on the potential of HFCO to demonstrate the features of the algorithm. To demonstrate the power of the method, we transformed a 15D potential of the protonated water dimer (Zundel cation) in a sum-of-products form and calculated the ground and lowest 26 vibrationally excited states of the Zundel cation with the multi-configuration time-dependent Hartree method.

Comparative phenotypic analysis of the major fungal pathogens Candida parapsilosis and Candida albicans.

Candida parapsilosis and Candida albicans are human fungal pathogens that belong to the CTG clade in the Saccharomycotina. In contrast to C. albicans, relatively little is known about the virulence properties of C. parapsilosis, a pathogen particularly associated with infections of premature neonates. We describe here the construction of C. parapsilosis strains carrying double allele deletions of 100 transcription factors, protein kinases and species-specific genes. Two independent deletions were constructed for each target gene. Growth in >40 conditions was tested, including carbon source, temperature, and the presence of antifungal drugs. The phenotypes were compared to C. albicans strains with deletions of orthologous transcription factors. We found that many phenotypes are shared between the two species, such as the role of Upc2 as a regulator of azole resistance, and of CAP1 in the oxidative stress response. Others are unique to one species. For example, Cph2 plays a role in the hypoxic response in C. parapsilosis but not in C. albicans. We found extensive divergence between the biofilm regulators of the two species. We identified seven transcription factors and one protein kinase that are required for biofilm development in C. parapsilosis. Only three (Efg1, Bcr1 and Ace2) have similar effects on C. albicans biofilms, whereas Cph2, Czf1, Gzf3 and Ume6 have major roles in C. parapsilosis only. Two transcription factors (Brg1 and Tec1) with well-characterized roles in biofilm formation in C. albicans do not have the same function in C. parapsilosis. We also compared the transcription profile of C. parapsilosis and C. albicans biofilms. Our analysis suggests the processes shared between the two species are predominantly metabolic, and that Cph2 and Bcr1 are major biofilm regulators in C. parapsilosis.

Sodium butyrate protects mice from the development of the early signs of non-alcoholic fatty liver disease: role of melatonin and lipid peroxidation.

Non-alcoholic fatty liver disease (NAFLD) is one of the most common liver diseases worldwide with universally accepted treatments still lacking. Oral supplementation of sodium butyrate (SoB) has been suggested to attenuate liver damage of various aetiologies. Our study aimed to further delineate mechanisms involved in the SoB-dependent hepatic protection using a mouse model of fructose-induced NAFLD and in in vitro models. C57BL/6J mice were either pair-fed a fructose-enriched liquid diet ±0·6 g/kg body weight per d SoB or standard chow for 6 weeks. Markers of liver damage, intestinal barrier function, glucose metabolism, toll-like receptor-4 (TLR-4) and melatonin signalling were determined in mice. Differentiated human carcinoma colon-2 (Caco-2) and J774A.1 cells were used to determine molecular mechanisms involved in the effects of SoB. Despite having no effects on markers of intestinal barrier function and glucose metabolism or body weight gain, SoB supplementation significantly attenuated fructose-induced hepatic TAG accumulation and inflammation. The protective effects of SoB were associated with significantly lower expression of markers of the TLR-4-dependent signalling cascade, concentrations of inducible nitric oxide synthase (iNOS) protein and 4-hydroxynonenal protein adducts in liver. Treatment with SoB increased melatonin levels and expression of enzymes involved in melatonin synthesis in duodenal tissue and Caco-2 cells. Moreover, treatment with melatonin significantly attenuated lipopolysaccharide-induced expression of iNOS and nitrate levels in J774A.1 cells. Taken together, our results indicated that the protective effects of SoB on the development of fructose-induced NAFLD in mice are associated with an increased duodenal melatonin synthesis and attenuation of iNOS induction in liver.

Comparative genome analysis and gene finding in Candida species using CGOB.

The Candida Gene Order Browser (CGOB) was developed as a tool to visualize and analyze synteny relationships in multiple Candida species, and to provide an accurate, manually curated set of orthologous Candida genes for evolutionary analyses. Here, we describe major improvements to CGOB. The underlying structure of the database has been changed significantly. Genomic features are now based directly on genome annotations rather than on protein sequences, which allows non-protein features such as centromere locations in Candida albicans and tRNA genes in all species to be included. The data set has been expanded to 13 species, including genomes of pathogens (C. albicans, C. parapsilosis, C. tropicalis, and C. orthopsilosis), and those of xylose-degrading species with important biotechnological applications (C. tenuis, Scheffersomyces stipitis, and Spathaspora passalidarum). Updated annotations of C. parapsilosis, C. dubliniensis, and Debaryomyces hansenii have been incorporated. We discovered more than 1,500 previously unannotated genes among the 13 genomes, ranging in size from 29 to 3,850 amino acids. Poorly conserved and rapidly evolving genes were also identified. Re-analysis of the mating type loci of the xylose degraders suggests that C. tenuis is heterothallic, whereas both Spa. passalidarum and S. stipitis are homothallic. As well as hosting the browser, the CGOB website (http://cgob.ucd.ie) gives direct access to all the underlying genome annotations, sequences, and curated orthology data.

RamiGO: an R/Bioconductor package providing an AmiGO visualize interface.

SUMMARY: The R/Bioconductor package RamiGO is an R interface to AmiGO that enables visualization of Gene Ontology (GO) trees. Given a list of GO terms, RamiGO uses the AmiGO visualize API to import Graphviz-DOT format files into R, and export these either as images (SVG, PNG) or into Cytoscape for extended network analyses. RamiGO provides easy customization of annotation, highlighting of specific GO terms, colouring of terms by P-value or export of a simplified summary GO tree. We illustrate RamiGO functionalities in a genome-wide gene set analysis of prognostic genes in breast cancer. AVAILABILITY AND IMPLEMENTATION: RamiGO is provided in R/Bioconductor, is open source under the Artistic-2.0 License and is available with a user manual containing installation, operating instructions and tutorials. It requires R version 2.15.0 or higher. URL: http://bioconductor.org/packages/release/bioc/html/RamiGO.html

Calculation of the vibrational excited states of malonaldehyde and their tunneling splittings with the multi-configuration time-dependent Hartree method.

We report energies and tunneling splittings of vibrational excited states of malonaldehyde which have been obtained using full dimensional quantum mechanical calculations. To this end we employed the multi configuration time-dependent Hartree method. The results have been obtained using a recently published potential energy surface [Y. Wang, B. J. Braams, J. M. Bowman, S. Carter, and D. P. Tew, J. Chem. Phys. 128, 224314 (2008)] which has been brought into a suitable form by a modified version of the n-mode representation which was used with two different arrangements of coordinates. The relevant terms of the expansion have been identified with a Metropolis algorithm and a diffusion Monte-Carlo technique, respectively.

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures.

GeneSigDB (http://www.genesigdb.org or http://compbio.dfci.harvard.edu/genesigdb/) is a database of gene signatures that have been extracted and manually curated from the published literature. It provides a standardized resource of published prognostic, diagnostic and other gene signatures of cancer and related disease to the community so they can compare the predictive power of gene signatures or use these in gene set enrichment analysis. Since GeneSigDB release 1.0, we have expanded from 575 to 3515 gene signatures, which were collected and transcribed from 1604 published articles largely focused on gene expression in cancer, stem cells, immune cells, development and lung disease. We have made substantial upgrades to the GeneSigDB website to improve accessibility and usability, including adding a tag cloud browse function, facetted navigation and a 'basket' feature to store genes or gene signatures of interest. Users can analyze GeneSigDB gene signatures, or upload their own gene list, to identify gene signatures with significant gene overlap and results can be viewed on a dynamic editable heatmap that can be downloaded as a publication quality image. All data in GeneSigDB can be downloaded in numerous formats including .gmt file format for gene set enrichment analysis or as a R/Bioconductor data file. GeneSigDB is available from http://www.genesigdb.org.

Ab initio potential energy and dipole moment surfaces for CS2: determination of molecular vibrational energies.

The ground state potential energy and dipole moment surfaces for CS2 have been determined at the CASPT2/C:cc-pVTZ,S:aug-cc-pV(T+d)Z level of theory. The potential energy surface has been fit to a sum-of-products form using the neural network method with exponential neurons. A generic interface between neural network potential energy surface fitting and the Heidelberg MCTDH software package is demonstrated. The potential energy surface has also been fit using the potfit procedure in MCTDH. For fits to the low-energy regions of the potential, the neural network method requires fewer parameters than potfit to achieve high accuracy; global fits are comparable between the two methods. Using these potential energy surfaces, the vibrational energies have been computed for the four most abundant CS2 isotopomers. These results are compared to experimental and previous theoretical data. The current potential energy surfaces are shown to accurately reproduce the low-lying vibrational energies within a few wavenumbers. Hence, the potential energy and dipole moments surfaces will be useful for future study on the control of quantum dynamics in CS2.

Direct determination of glyphosate, aminomethylphosphonic acid and glufosinate in food samples with ion chromatography coupled to electrospray ionization tandem mass spectrometry.

A fast and reliable method for the direct determination of the herbicide glyphosate, its major degradation product aminomethylphosphonic acid (AMPA) and glufosinate is presented for a variety of food matrices. The Quick Polar Pesticides in food of Plant Origin method (QuPPe-PO-Method) was used for extraction without further preconcentration or clean-up steps involving e.g. solid phase extraction (SPE). The method makes use of a commercially available high performance liquid chromatograph coupled to a tandem mass spectrometer with electrospray ionization (LC-ESI-MS/MS) - as present in many laboratories - equipped with an ion chromatography (IC)-column using an MS-compatible eluent made of 0.8% formic acid in water. Due to the absence of time-consuming clean-up procedures, strong matrix effects (ME) of up to 91% for AMPA in grapefruit can be observed, when comparing its sensitivity to that obtained for solvent-based standards. The limits of detection (LODs) were determined for the sample matrices apple, mushrooms, grapefruit, linseed, red lentils and wheat and they were found to be in the range of 0.09 to 0.8, 0.04 to 1 and 0.2 to 2 µg/kg for glyphosate, AMPA and glufosinate, respectively. For the same matrices the validation was carried out according to SANTE guidelines for different commodity groups by spiking them up prior to extraction to concentrations ranging from 10 to 400 µg/kg for matrices with high water content and from 10 to 800 µg/kg for matrices with low water content. When using solvent-based calibration under the use of isotopically labelled internal standards (ILIS) the recoveries were found to range from 84% to 120% and the relative standard deviations (RSD) range between 1% and 19% for glyphosate, AMPA and glufosinate at all fortification levels for all matrices investigated. Accordingly, the method was successfully introduced in our laboratory with limits of quantification (LOQs) of 10 µg/kg for glyphosate, AMPA and glufosinate in samples from SANTE commodity groups 1, 2, 4a and 5. The reliability and robustness of the method are demonstrated by showing a recovery control chart obtained for glyphosate in randomly selected samples from different commodity groups. Therefore, the samples were spiked up with 10 µg/kg of glyphosate during routine analysis, whereby all recoveries were found to be in the range between 70 and 120%.