Utilization of a New Hundred-Genomes Pipeline to Design a Rapid Duplex LAMP Detection Assay for Xanthomonas euvesicatoria and X. vesicatoria in Tomato.

Xanthomonas euvesicatoria and X. vesicatoria are two economically important causal agents of bacterial spot (BS) of tomato and pepper. Management of BS in the field requires rapid and accurate detection. Therefore, this work aimed to develop a pipeline to design a simple, fast, and reliable assay for the detection of X. euvesicatoria and X. vesicatoria by loop-mediated isothermal amplification. In total, 109 publicly available whole genomic sequences of 24 different species of bacterial pathogens were used to design primers that would amplify the DNA of the two target species. Laboratory testing of the assay was performed on pure bacterial cultures and artificially infected plants, and amplification was conducted with both a sophisticated laboratory instrument and a simple mobile platform. The testing of the assay confirmed its specificity with a sensitivity reaching 1 pg µl-1 for both pathogens with an assay duration of 40 min on a mobile detection platform. Our diagnostics development pipeline enables the easy and fast design of a reliable detection assay in the genomics age. By validating the pipeline with X. euvesicatoria and X. vesicatoria pathogens, we have simultaneously developed an assay with high specificity, sensitivity, and speed, which will allow it to be deployed, contributing to successful management of BS.

KEC: unique sequence search by K-mer exclusion.

SUMMARY: Searching for amino acid or nucleic acid sequences unique to one organism may be challenging depending on size of the available datasets. K-mer elimination by cross-reference (KEC) allows users to quickly and easily find unique sequences by providing target and non-target sequences. Due to its speed, it can be used for datasets of genomic size and can be run on desktop or laptop computers with modest specifications. AVAILABILITY AND IMPLEMENTATION: KEC is freely available for non-commercial purposes. Source code and executable binary files compiled for Linux, Mac and Windows can be downloaded from https://github.com/berybox/KEC. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

ABIF Manager: simple reading and editing of ABIF formatted files.

UNLABELLED: ABIF Manager is simple application for low-level access to ABIF formatted files. Those are produced by Data Collection software based on the data, collected from capillary sequencing machine. The application shows all the data as readable text, which can be easily edited. AVAILABILITY AND IMPLEMENTATION: The program source code and compiled executable is freely available at: https://sourceforge.net/projects/abifmanager/.

Covalent dimers of 1,3-diphenylisobenzofuran for singlet fission: synthesis and electrochemistry.

The synthesis of covalent dimers in which two 1,3-diphenylisobenzofuran units are connected through one phenyl substituent on each is reported. In three of the dimers, the subunits are linked directly, and in three others, they are linked via an alkane chain. A seventh new compound in which two 1,3-diphenylisobenzofuran units share a phenyl substituent is also described. These materials are needed for investigations of the singlet fission process, which promises to increase the efficiency of solar cells. The electrochemical oxidation and reduction of the monomer, two previously known dimers, and the seven new compounds have been examined, and reversible redox potentials have been compared with results obtained from density functional theory. Although the overall agreement is satisfactory, some discrepancies are noted and discussed.

Diethyl fluoronitromethylphosphonate: synthesis and application in nucleophilic fluoroalkyl additions.

Diethyl fluoronitromethylphosphonate (3), a previously unknown compound, was synthesized by electrophilic fluorination of diethyl nitromethylphosphonate with Selectfluor. Base-induced decomposition of 3 was studied by NMR spectroscopy, which identified diethyl fluorophosphate and fluoronitromethane as the main decomposition products. C-H acidities [pK(a) values in dimethyl sulfoxide (DMSO)] of 3, 1-fluoro-1-phenylsulfonylmethanephosphonate (1; McCarthy's reagent), tetraethyl fluoromethylenebisphosphonate (2), and some nonfluorinated phosphonates were computed, and a good correlation between calculated and experimental pK(a) values was found. The calculated C-H acidities increased in the sequence 2<1<3. Diethyl fluoronitromethylphosphonate (3) was applied in the Horner-Wadsworth-Emmons reaction with aldehydes and trifluoromethyl ketones to provide new 1-fluoro-1-nitroalkenes with good to high stereoselectivities. Alkylation of 3 was successful only with iodomethane, however, conjugate additions of 3 to Michael acceptors such as α,ß-unsaturated carbonyl compounds, sulfones, and nitro compounds allowed access to variously modified diethyl 1-fluoro-1-nitrophosphonates.

On the mechanism of dihydrogen activation by frustrated Lewis pairs. Insights from the analysis of domain averaged Fermi holes and generalized population analysis.

The electron reorganization responsible for the facilitation of heterolytic splitting of H-H bond by frustrated Lewis pair (FLP) catalysts has been studied using the analysis of domain averaged Fermi holes and generalized population analysis. The analysis of electron structures of the species along the reaction path has revealed that the anticipated synchronicity of previously considered electron shifts of electron pair of the σHH bond to a vacant orbital on B and from the lone pair on the basic N site to an antibonding σHH* orbital is associated with the build up of extensive delocalized bonding that can conveniently be characterized in terms of multicenter bond indices. In addition, the detailed scrutiny of the IRC-dependence of the 2-center bond indices of the disappearing H-H bond resulted in the proposal of a simple heuristic measure of the efficiency of the FLP catalysts. Attention was also paid to the evaluation of the presumed facilitating effect on the dissociation of the H-H bond of the electric field in the cavity of FLP catalyst. It has been shown that the strength of this field does not reach the critical values required for the efficient facilitation of the splitting of the H-H bond.

Projection-Based Density Matrix Renormalization Group in Density Functional Theory Embedding.

The density matrix renormalization group (DMRG) method has already proved itself as a very efficient and accurate computational method, which can treat large active spaces and capture the major part of strong correlation. Its application on larger molecules is, however, limited by its own computational scaling as well as demands of methods for treatment of the missing dynamical electron correlation. In this work, we present the first step in the direction of combining DMRG with density functional theory (DFT), one of the most employed quantum chemical methods with favorable scaling, by means of the projection-based wave function (WF)-in-DFT embedding. On two proof-of-concept but important molecular examples, we demonstrate that the developed DMRG-in-DFT approach provides a very accurate description of molecules with a strongly correlated fragment.

Microsatellite Markers: A Tool to Assess the Genetic Diversity of Yellow Mustard (Sinapis alba L.).

Microsatellite markers were used for the assessment of genetic diversity and genetic structure in a germplasm collection of yellow mustard, Sinapis alba L. The comprehensive collection of genetic resources represented 187 registered varieties, landraces, and breeding materials. Microsatellites generated 44 polymorphic alleles in 15 loci. Eleven of them were medium to highly polymorphic, and the high levels of observed heterozygosity (0.12-0.83) and Nei's gene diversity index (0.11-0.68) indicated a high level of polymorphism. Based on PCoA and neighbor joining analyses, the genetic resources were divided into two groups. The range of genetic dissimilarity in the analysed collection was in the range of 0.00-1.00. The high level of dissimilarity between the accessions was documented by the high WAM value (33.82%). Bayesian clustering algorithms were performed in the STRUCTURE 2.3.4 software. The number of clusters was estimated at K = 2. The accessions were classified according to Q1/Q2 values. The low average values of the parameters Fst_1 (0.3482), Fst_2 (0.1916), and parameter alpha (0.0602) indicated substantial mating barriers between varieties and reproductive isolation due to the limited exchange of genetic resources between breeders. These results demonstrated the importance of extensive collections of genetic resources for the maintenance of genetic diversity and indicated considerable genetic differentiation among accessions.

Efficient Adiabatic Connection Approach for Strongly Correlated Systems: Application to Singlet-Triplet Gaps of Biradicals.

Strong electron correlation can be captured with multireference wave function methods, but an accurate description of the electronic structure requires accounting for the dynamic correlation, which they miss. In this work, a new approach for the correlation energy based on the adiabatic connection (AC) is proposed. The ACn method accounts for terms up to order n in the coupling constant, and it is size-consistent and free from instabilities. It employs the multireference random phase approximation and the Cholesky decomposition technique, leading to a computational cost growing with the fifth power of the system size. Because of the dependence on only one- and two-electron reduced density matrices, ACn is more efficient than existing ab initio multireference dynamic correlation methods. ACn affords excellent results for singlet-triplet gaps of challenging organic biradicals. The development presented in this work opens new perspectives for accurate calculations of systems with dozens of strongly correlated electrons.

Density Matrix Renormalization Group with Dynamical Correlation via Adiabatic Connection.

The quantum chemical version of the density matrix renormalization group (DMRG) method has established itself as one of the methods of choice for calculations of strongly correlated molecular systems. Despite its great ability to capture strong electronic correlation in large active spaces, it is not suitable for computations of dynamical electron correlation. In this work, we present a new approach to the electronic structure problem of strongly correlated molecules, in which DMRG is responsible for a proper description of the strong correlation, whereas dynamical correlation is computed via the recently developed adiabatic connection (AC) technique which requires only up to two-body active space reduced density matrices. We report the encouraging results of this approach on typical candidates for DMRG computations, namely, n-acenes (n = 2 → 7), Fe(II)-porphyrin, and the Fe3S4 cluster.

Unravelling the Open-Shell Character of Peripentacene on Au(111).

Polycyclic aromatic hydrocarbons (PAHs) are a family of organic compounds comprising two or more fused aromatic rings which feature manifold applications in modern technology. Among these species, those presenting an open-shell magnetic ground state are of particular interest for organic electronic, spintronic, and non-linear optics and energy storage devices. Within PAHs, special attention has been devoted in recent years to the synthesis and study of the acene and fused acene (periacene) families, steered by their decreasing HOMO-LUMO gap with length and predicted open-shell character above some size. However, an experimental fingerprint of such magnetic ground state has remained elusive. Here, we report on the in-depth electronic characterization of isolated peripentacene molecules on a Au(111) surface. Scanning tunnelling spectroscopy, complemented by computational investigations, reveals an antiferromagnetic singlet ground state, characterized by singlet-triplet inelastic excitations with an experimental effective exchange coupling (Jeff) of 40.5 meV. Our results deepen the fundamental understanding of organic compounds with magnetic ground states, featuring perspectives in carbon-based spintronic devices.

Development of Real-Time and Colorimetric Loop Mediated Isothermal Amplification Assay for Detection of Xanthomonas gardneri.

Xanthomonas gardneri is one of the causal agents of bacterial spot (BS), an economically important bacterial disease of tomato and pepper. Field-deployable and portable loop-mediated isothermal amplification (LAMP)-based instruments provide rapid and sensitive detection of plant pathogens. In order to rapidly and accurately identify and differentiate X. gardneri from other BS-causing Xanthomonas spp., we optimized a new real-time monitoring LAMP-based method targeting the X. gardneri-specific hrpB gene. Specificity and sensitivity of real-time and colorimetric LAMP assays were tested on the complex of bacterial strains pathogenic to tomato and pepper and on plants infected by the pathogen. The assay detection limit was 1 pg/µL of genomic DNA with an assay duration of only 30 min. The use of portable and handheld instruments allows for fast analysis, reducing the diagnosis time, and can contribute to proper disease management and control of X. gardneri. Due to the high efficiency of this method, we suggest its use as a standard diagnostic tool during phytosanitary controls.