Literature and Bioinformatics Analyses of Wheat-specific Detection Methods

In view of the recent necessity to perform testing for the detection of genetically modified common wheat (Triticum aestivum), the need arises for a taxon-specific method for this organism. However, no such method has yet been officially validated. Multiple species of wheat exist on the market, such as common wheat, durum wheat, emmer wheat, etc. These plants have complex genomes, composed of different combinations (from diploid to hexaploid) of common sets of chromosomes. The specificity of a method then depends on which set of chromosome the targeted region is located, which increases the complexity of identifying methods specific to Triticum aestivum. Often, such methods were developed for the specific regulatory need of differentiating durum and common wheat (for example, in alimentary pasta labeling), with minimal concerns for non-specific detection of other plants. This document summarises the review performed by the EU-RL GMFF, complemented with in-house bioinformatics analyses, in order to identify and characterise Triticum aestivum-specific detection methods that have been described in the scientific literature. Methods with apparent specificity (based on results shown and bioinformatics analyses) and promising performance (based on results shown) are highlighted and their primers and probe sequences reported. Those methods are the 'SS II-D' and ' SS II ex7' methods described in Matsuoka et al. (2012) and the 'wx012' method described in Iida et al. (2005), and they represent good candidates to uniquely identify common wheat in complex food samples.JRC.I.3-Molecular Biology and Genomic

Reminiscence of classical chaos in driven transmons

Transmon qubits are ubiquitously used in quantum information processing architectures based on superconducting circuits. Because of their lifetime, strong drives are required to realize fast, high-fidelity, gates and measurements, including parametrically activated processes. Here, we show that even off-resonant drives, in regimes routinely used in experiments, can cause strong modifications to the structure of the transmon spectrum rendering a large part of it chaotic. Accounting for the full nonlinear dynamics in a Floquet-Markov formalism, we find that the coherence time of the computational states of transmons can be significantly altered in the presence of a chaotic layer. In particular, chaos-assisted quantum phase slips greatly enhance band dispersions. In the presence of a measurement resonator, we find that approaching chaotic behavior correlates with strong transmon-resonator hybridization, and an average resonator response centered on the bare resonator frequency. The phenomena described here should be present in all circuits based on low-impedance Josephson-junctions

Report on the Verification of the Performance of a Method for the Detection of Event MON71800 in Wheat Using Real-Time PCR

Following the United States Department of Agriculture's (USDA) Animal and Plant Health Inspection Service (APHIS) announcement that test results confirmed the finding of unauthorised GM glyphosate-resistant wheat "volunteer" plants harbouring the event MON71800 on a farm in Oregon, the European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) was requested to provide as soon as possible a method to test wheat consignments for the presence of this genetically modified organism (GMO) to the National Reference Laboratories (NRLs) for GMOs of the EU Member States. In response, the EU-RL put together a testing strategy, based on readily available screening tests which was published here (http://gmo-crl.jrc.ec.europa.eu/GM_wheat.htm). Upon request, Monsanto provided in May 2013 the EU-RL with the procedure “Roundup Ready® Wheat MON71800 Event Specific Endpoint TaqMan® PCR with acc Internal Control for Seed Pools of 1:15” that had previously been made available to, and was used by USDA. The EU-RL GMFF tested this protocol on positive control samples consisting of MON71800 crude lysate, also provided by Monsanto. Our results can be summarised as follow: The method is apparently event-specific. Our specificity-tests did not show cross-reactivity on genomic DNA from a wide selection of similar GMO. The sensitivity of the method was found to be in agreement with previous findings of USDA, i.e. the relative limit of detection lies at 0.5% in a background of 301 ng of total wheat genomic DNA. The absolute limit of detection (LODabs) was determined between 5 and 10 copies of MON71800 target. The latter was not indicated by the USDA. For seed/grains the application of a sub-sampling strategy could allow detection below 0.5% but would require significant additional efforts, including the analysis of numerous sub-samples. Our tests also indicated that the duplex PCR system at the tested stage of optimisation is characterised by poor efficiency at increasing background DNA concentration in reaction. Based on the scientific evidence described in the present report, the EU-RL suggest that its testing strategy (http://gmo-crl.jrc.ec.europa.eu/GM_wheat.htm), making use of validated element and construct-specific methods and found to be more sensitive, is used to test for presence of MON71800 GM-wheat. The verified event specific method of Monsanto could be used to confirm positive findings at GM-target concentration equal or above 0.5% or it could be used for detection of GM-event MON71800 below 0.5% but it would require a costly sub-sampling strategy, which, in addition, is only possible in seeds/grains.JRC.I.3-Molecular Biology and Genomic

Report on the Verification of the Performance of a Testing Strategy for the Detection of Wheat MON71800 Event Using Real-Time PCR

In response to a request of DG SANCO to provide National Reference Laboratories (NRLs) as soon as possible with a method to test soft white wheat consignments for the presence of unauthorised GM glyphosate-resistant wheat harbouring the event MON71800, the European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) developed, in collaboration with the European Network of GMO Laboratories (ENGL), a testing strategy intended to be immediately implementable by EU NRLs. The testing strategy is based on a combination of three validated screening methods that allow excluding (detectable) presence of Monsanto’s GM glyphosate-resistant wheat (MON71800) in wheat grain or food/feed products and confirming its presence whenever other GMOs can be excluded. The present report describes the results of the tests carried out by the EU-RL GMFF to verify the testing strategy proposed; the tests were conducted using the positive control sample represented by a crude DNA lysate of MON71800 provided by Monsanto and genomic DNA samples of genetically modified organisms harbouring the CTP2-CP4epsps element for which a validated event-specific method is available. The sensitivity of the three methods was assessed by verifying the relative limit of detection (LODrel) on MON71800 wheat DNA. The LODrel is approximately 0.03% for the P-35S and for T-nos methods and 0.06% for the CTP2-CP4epsps method in 300 nanograms of wheat genomic DNA. Further experimental evidence confirmed that the three methods react against genomic DNA extracted from GM events containing the CTP2-CP4epsps element for which a validated event-specific method is available. The experimental verification hereby reported confirmed the validity of the EU-RL GMFF guidance on testing for GM glyphosate-resistant wheat (MON71800) in wheat grain or in food/feed products containing wheat flour originating or consigned from the US, provided that DNA of acceptable quality can be obtained.JRC.I.3-Molecular Biology and Genomic

Crustal Evolution of the Northeast Laurentian Margin and the Peri-Gondwanan Microcontinent Ganderia Prior to and During Closure of the Iapetus Ocean: Detrital Zircon U–Pb and Hf Isotope Evidence from Newfoundland

Detrital zircon populations in sedimentary rocks from the Laurentian margin and the accreted microcontinent Ganderia on both sides of the main Iapetus suture (Red Indian Line) in central Newfoundland have been studied by combined U–Pb and Lu–Hf isotope analyses. Variation in εHf(t) values with age of zircon populations of distal provenance (>900 Ma) reflect the crustal evolution within the source continents: in zircon derived from Laurentia, episodes of juvenile magma production in the source could be detected at 1.00 – 1.65 and 2.55 – 3.00 Ga, and mixing of juvenile and recycled crust in continental magmatic arcs occurred at 0.95 – 1.40, 1.45 – 1.60, 1.65 – 2.05 and 2.55 – 2.75 Ga. These ages are consistent with the crustal history of northeastern Laurentia. Similarly, zircon of distal provenance from Ganderia reveals times of juvenile magma production in the source at 0.70 – 0.90, 1.40 – 1.75, 1.85 – 2.40 and 2.7 – 3.5 Ga, and episodes of mixing juvenile and recycled crust at 0.95 – 1.35, 1.45 – 1.60, 1.70 – 2.15 and 2.6 – 2.8 Ga. These data reflect the crustal evolution in the present northern part of Amazonia, its likely source craton.      The evolution of magmatic arcs at the margins of both continents can be studied in a similar way using detrital zircon having a proximal provenance (<900 Ma). In contrast to the Laurentian margin, Ganderia is characterized by development of Neoproterozoic – Cambrian continental arcs (ca. 500 – 670 Ma) that were built on the margin of Gondwana. εHf(t) values indicate recycling of Neo- and Mesoproterozoic crust. During and following accretion of the various elements of Ganderia to Laurentia, the syn-tectonic Late Ordovician to Silurian sedimentary rocks deposited on the upper plate (composite Laurentia) continued showing only detritus derived from Laurentia. These sedimentary rocks contain detrital zircon from Iapetan juvenile, continental and successor arcs that were active between ca. 440 and 550 Ma, and from continuing magmatic activity until 423 Ma. Arrival of the first Laurentian detritus at the outermost part of Ganderia indicates that the Iapetus ocean was closed at ca. 452 Ma. The magmatic arcs along the former Laurentian margin in Newfoundland evolved differently. In the northwestern part, εHf(t) values point to recycling of Mesoproterozoic and Paleoproterozoic crust. In the southwest, εHf(t) values indicate addition of juvenile crust, recycling of Mesoproterozoic crust and mixing with juvenile magma. SOMMAIRELes populations de zircons détritiques des roches sédimentaires issus de la marge laurentienne et du microcontinent d’accrétion de Ganderia, des deux côtés de la principale suture Iapetus (linéation de Red Indian) dans le centre de Terre-Neuve, ont été étudiés par analyses combinées U–Pb et Lu–Hf.  Les variations des valeurs εHf(t) en fonction de l’âge des populations de zircons distaux (>900 Ma) reflètent l’évolution de la croûte des continents sources : les zircons de Laurentie ont permis de détecter des épisodes magmatiques juvéniles dans la source entre 1,00 - 1,5, et 2,55 - 3,00 Ga, ainsi que des épisodes de mélange de croûte juvénile avec des croûtes d’arcs magmatiques continentaux recyclés entre 0,95 – 1,40, 1,45 – 1,60, 1,65 – 2,05, et 2,55 – 2,75 Ga.  Ces datations correspondent bien à l’histoire de la croûte de la portion nord-est de la Laurentie.  De même, le zircon distal de Ganderia révèle des épisodes de production de magmas juvéniles dans la source entre 0,70 - 0,90, 1,40 - 1,75, 1,85 - 2,40, et 2,7 - 3,5 Ga, ainsi que des épisodes de mélanges de matériaux juvéniles et de croûtes recyclés entre 0,95 - 1,35, 1,45 - 1,60, 1,70 - 2,15, et 2,6 - 2,8 Ga.  Ces données reflètent l’évolution de la croûte dans la portion nord actuelle de l’Amazonie, son craton source probable.     L’évolution des arcs magmatiques à la marge de ces deux continents peuvent être étudiées de la même manière en utilisant le zircon détritique proximal (<900 Ma).  Contrairement à la marge laurentienne, celle de Ganderia est caractérisée par le développement d’arcs continentaux Néoprotéozoïque-Cambrien (env. 500 – 670 Ma) qui se sont constitués à la marge du Gondvana.  Les valeurs de εHf(t) indiquent un recyclage de la croûte au Néoprotérozoïque et au Mésoprotérozoïque.  Durant et après l’accrétion des divers éléments de Ganderia et de la Laurentie, les roches sédimentaires syntectoniques de la fin de l’Ordovicien et du Silurien qui se sont déposées sur la portion supérieure de la plaque (Laurentie composite) ne montrent toujours que des débris provenant de la Laurentie.  Ces roches sédimentaires renferment des zircons détritiques juvéniles iapétiques, et d’arcs continentaux et d’arcs subséquents, qui ont été actifs entreentre (env. 440 et 550 Ma) et  d’une activité magmatique continue jusqu’à 423 Ma.  L’apport des premiers débris à la marge extrême de Ganderia indique que l’océan s’est fermée il y a env. 452 Ma.  Les arcs magmatiques le long de l'ancienne marge laurentienne à Terre-Neuve ont évolué différemment.  Dans la portion nord-ouest, les valeurs de εHf(t) indiquent un recyclage de la croûte au Mésoprotérozoïque et au Paléoprotérozoïque.  Dans la portion sud-ouest, les valeurs de εHf(t) indiquent l’ajout d’une croûte juvénile, un recyclage de la croûte mésoprotérozoïque et un mélange avec un magma juvénile

An Interactive Interface for Novel Class Discovery in Tabular Data

Novel Class Discovery (NCD) is the problem of trying to discover novel classes in an unlabeled set, given a labeled set of different but related classes. The majority of NCD methods proposed so far only deal with image data, despite tabular data being among the most widely used type of data in practical applications. To interpret the results of clustering or NCD algorithms, data scientists need to understand the domain- and application-specific attributes of tabular data. This task is difficult and can often only be performed by a domain expert. Therefore, this interface allows a domain expert to easily run state-of-the-art algorithms for NCD in tabular data. With minimal knowledge in data science, interpretable results can be generated.Comment: 5 page

Towards plant species identification in complex samples: a bioinformatics pipeline for the identification of novel nuclear barcode candidates

Monitoring of the food chain to fight fraud and protect consumer health relies on the availability of methods to correctly identify the species present in samples, for which DNA barcoding is a promising candidate. The nuclear genome is a rich potential source of barcode targets, but has been relatively unexploited until now. Here, we show the development and use of a bioinformatics pipeline that processes available genome sequences to automatically screen large numbers of input candidates, identifies novel nuclear barcode targets and designs associated primer pairs, according to a specific set of requirements. We applied this pipeline to identify novel barcodes for plant species, a kingdom for which the currently available solutions are known to be insufficient. We tested one of the identified primer pairs and show its capability to correctly identify the plant species in simple and complex samples, validating the output of our approach.JRC.I.3-Molecular Biology and Genomic

Baryonic effects for weak lensing. Part I. Power spectrum and covariance matrix

Baryonic feedback effects lead to a suppression of the weak lensing angular power spectrum on small scales. The poorly constrained shape and amplitude of this suppression is an important source of uncertainties for upcoming cosmological weak lensing surveys such as Euclid or LSST. In this first paper in a series of two, we use simulations to build a Euclid-like tomographic mock data-set for the cosmic shear power spectrum and the corresponding covariance matrix, which are both corrected for baryonic effects following the baryonification method of Schneider et al. (2019). In addition, we develop an emulator to obtain fast predictions of the baryonic power suppression, allowing us to perform a likelihood inference analysis for a standard $\Lambda$CDM cosmology with both cosmological and astrophysical parameters. Our main findings are the following: (i) ignoring baryonic effects leads to a greater than 5$\sigma$ bias on the cosmological parameters $\Omega_m$ and $\sigma_8$; (ii) restricting the analysis to the largest scales, that are mostly unaffected by baryons, makes the bias disappear, but results in a blow-up of the $\Omega_m$-$\sigma_8$ contour area by more than a factor of 10; (iii) ignoring baryonic effects on the covariance matrix does not significantly affect cosmological parameter estimates; (iv) while the baryonic suppression is mildly cosmology dependent, this effect does not noticeably modify the posterior contours. Overall, we conclude that including baryonic uncertainties in terms of nuisance parameters results in unbiased and surprisingly tight constraints on cosmology.Comment: Accepted version (JCAP