MetFrag relaunched: incorporating strategies beyond in silico fragmentation

Background: The in silico fragmenter MetFrag, launched in 2010, was one of the first approaches combining compound database searching and fragmentation prediction for small molecule identification from tandem mass spectrometry data. Since then many new approaches have evolved, as has MetFrag itself. This article details the latest developments to MetFrag and its use in small molecule identification since the original publication.Results: MetFrag has gone through algorithmic and scoring refinements. New features include the retrieval of reference, data source and patent information via ChemSpider and PubChem web services, as well as InChIKey filtering to reduce candidate redundancy due to stereoisomerism. Candidates can be filtered or scored differently based on criteria like occurence of certain elements and/or substructures prior to fragmentation, or presence in so-called “suspect lists”. Retention time information can now be calculated either within MetFrag with a sufficient amount of user-provided retention times, or incorporated separately as “user-defined scores” to be included in candidate ranking. The changes to MetFrag were evaluated on the original dataset as well as a dataset of 473 merged high resolution tandem mass spectra (HR-MS/MS) and compared with another open source in silico fragmenter, CFM-ID. Using HR-MS/MS information only, MetFrag2.2 and CFM-ID had 30 and 43 Top 1 ranks, respectively, using PubChem as a database. Including reference and retention information in MetFrag2.2 improved this to 420 and 336 Top 1 ranks with ChemSpider and PubChem (89 and 71 %), respectively, and even up to 343 Top 1 ranks (PubChem) when combining with CFM-ID. The optimal parameters and weights were verified using three additional datasets of 824 merged HR-MS/MS spectra in total. Further examples are given to demonstrate flexibility of the enhanced features.Conclusions: In many cases additional information is available from the experimental context to add to small molecule identification, which is especially useful where the mass spectrum alone is not sufficient for candidate selection from a large number of candidates. The results achieved with MetFrag2.2 clearly show the benefit of considering this additional information. The new functions greatly enhance the chance of identification success and have been incorporated into a command line interface in a flexible way designed to be integrated into high throughput workflows. Feedback on the command line version of MetFrag2.2 available at http://c-ruttkies.github.io/MetFrag/ is welcome

Rock and stiff-Soil site amplification: Dependency on VS30 and Kappa (κ0)

A ground‐motion prediction equation (GMPE) specific to rock and stiff‐soil sites is derived using seismic motion recorded on high VS30 sites in Japan. This GMPE applies to events with 4.5≤Mw≤6.9 and VS30 ranging from 500 to 1500  m/s (stiff‐soil to rock sites). The empirical site coefficients obtained and the comparison with the simulated site functions show that seismic motion on rock and stiff‐soil sites does not depend only on VS30, but also on the high‐frequency attenuation site properties (κ0). The effects of the site‐specific κ0 on site amplification are analyzed using stochastic simulations, with the need to take into account both of these parameters for rock‐site adjustments. Adding the site‐specific κ0 into the GMPEs thus appears to be essential in future work. The rock‐site stochastic ground‐motion simulations show that the site‐specific κ0 controls the frequency corresponding to the maximum response spectral acceleration (famp1). This observation is used to link the peak of the response spectral shape to κ0 in this specific Japanese dataset and then to add the effects of high‐frequency attenuation into the previous GMPE from the peak ground acceleration and up to periods of 0.2 s. The inclusion of κ0 allows the observed bias to be corrected for the intraevent residuals and thus reduces sigma. However, this κ0 determination is limited to a minimum number of rock‐site records with Mw≥4.5 and to distances of less than 50 km

Serological diagnosis of brucellosis in goats: comparison of techniques

Goat production is an important item in the agricultural system of Argentina and brucellosis caused by Brucella melitensis is considered the main cause reproductive problems in this species. Although definitive diagnosis for this disease is made by isolation of the etiologic agent, but in practice the health status of a herd was evaluated by serological techniques indirect testing. To evaluate and compare the performance of different serological tests for diagnosis of brucellosis in goats, serum samples were analyzed. The following tests were performed: buffered plate antigen (BPA), rose bengal (RB RB 3% and 8%), fluorescence polarization (FPA) and the test tube and 2-mercaptoethanol (SAT/2ME). The validity of each test was determined in a relative manner by combination of indirect ELISA (IELISA) and complement fixation (CF). BPA was the most sensitive test, followed by SAT/2ME, 3% RB, FPA and, finally, RB 8%. FPA test, when used in series with BPA, significantly improved overall specificity. Based on these results it was proposed for brucellosis diagnosis in goats, BPA as a screening test, FPA as complementary test, and FC and IELISA as confirmatory tests. SAT/2ME is recommended only when it is not possible to perform other tests, due to the toxic effects of SAT/2ME reagents.Fil: Cisterna, C. Comisión de Investigaciones Científicas (CIC). Buenos Aires, ArgentinaFil: Conde, S. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Patobiología. Buenos Aires, ArgentinaFil: Hollender, D. CONICET. ArgentinaFil: Martino, P.E. Comisión de Investigaciones Científicas (CIC). Buenos Aires, ArgentinaFil: Samartino L. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Patobiología. Buenos Aires, ArgentinaLa producción caprina representa un rubro importante dentro del sistema agropecuario de la República Argentina y la brucelosis causada por Brucella melitensis es considerada el motivo principal de los problemas reproductivos en esta especie. El diagnóstico de certeza se realiza aislando el agente etiológico, aunque en la práctica se evalúa el estado sanitario de un hato mediante pruebas serológicas. El objetivo de este trabajo fue evaluar y comparar el desempeño de las distintas pruebas serológicas tamíz y complementarias para el diagnóstico de la brucelosis caprina. Para ello, se analizaron muestras de suero de animales sin vacunación, realizando antígeno buferado en placa (BPA), rosa de bengala (RB 3 % y RB 8 %), polarización fluorescente (FPA) y pruebas de tubo y 2 mercaptoetanol (SAT/2ME). La validez de cada prueba se determinó por combinación de ELISA Indirecto (IELISA) y Fijación de Complemento (FC). BPA resultó ser más sensible, seguido de SAT/2ME, RB 3%, FPA y por último RB 8%. Al realizar FPA en serie con BPA mejoró significativamente la especificidad global. Se propone BPA como prueba tamíz, FPA como complementaria y FC e IELISA como confirmatorias. Se recomienda SAT/2ME sólo en los casos en que no sea posible la realización de las otras pruebas debido a los efectos tóxicos de los reactivos empleados para su realización

Diagnóstico serológico de brucelosis en caprinos: comparación de técnicas

La producción caprina representa un rubro importante dentro del sistema agropecuario de la República Argentina y la brucelosis causada por Brucella melitensis es considerada el motivo principal de los problemas reproductivos en esta especie. El diagnóstico de certeza se realiza aislando el agente etiológico, aunque en la práctica se evalúa el estado sanitario de un hato mediante pruebas serológicas. El objetivo de este trabajo fue evaluar y comparar el desempeño de las distintas pruebas serológicas tamíz y complementarias para el diagnóstico de la brucelosis caprina. Para ello, se analizaron muestras de suero de animales sin vacunación, realizando antígeno buferado en placa (BPA), rosa de bengala (RB 3 % y RB 8 %), polarización fluorescente (FPA) y pruebas de tubo y 2 mercaptoetanol (SAT/2ME). La validez de cada prueba se determinó por combinación de ELISA Indirecto (IELISA) y Fijación de Complemento (FC). BPA resultó ser más sensible, seguido de SAT/2ME, RB 3%, FPA y por último RB 8%. Al realizar FPA en serie con BPA mejoró significativamente la especificidad global. Se propone BPA como prueba tamíz, FPA como complementaria y FC e IELISA como confirmatorias. Se recomienda SAT/2ME sólo en los casos en que no sea posible la realización de las otras pruebas debido a los efectos tóxicos de los reactivos empleados para su realización.Goat production is an important item in the agricultural system of Argentina and brucellosis caused by Brucella melitensis is considered the main cause reproductive problems in this species. Although definitive diagnosis for this disease is made by isolation of the etiologic agent, but in practice the health status of a herd was evaluated by serological techniques indirect testing. To evaluate and compare the performance of different serological tests for diagnosis of brucellosis in goats, serum samples were analyzed. The following tests were performed: buffered plate antigen (BPA), rose bengal (RB RB 3% and 8%), fluorescence polarization (FPA) and the test tube and 2-mercaptoethanol (SAT/2ME). The validity of each test was determined in a relative manner by combination of indirect ELISA (IELISA) and complement fixation (CF). BPA was the most sensitive test, followed by SAT/2ME, 3% RB, FPA and, finally, RB 8%. FPA test, when used in series with BPA, significantly improved overall specificity. Based on these results it was proposed for brucellosis diagnosis in goats, BPA as a screening test, FPA as complementary test, and FC and IELISA as confirmatory tests. SAT/2ME is recommended only when it is not possible to perform other tests, due to the toxic effects of SAT/2ME reagents

Topological representations of matroid maps

The Topological Representation Theorem for (oriented) matroids states that every (oriented) matroid can be realized as the intersection lattice of an arrangement of codimension one homotopy spheres on a homotopy sphere. In this paper, we use a construction of Engstr\"om to show that structure-preserving maps between matroids induce topological mappings between their representations; a result previously known only in the oriented case. Specifically, we show that weak maps induce continuous maps and that the process is a functor from the category of matroids with weak maps to the homotopy category of topological spaces. We also give a new and conceptual proof of a result regarding the Whitney numbers of the first kind of a matroid.Comment: Final version, 21 pages, 8 figures; Journal of Algebraic Combinatorics, 201

Extended suspect and non-target strategies to characterize emerging polar organic contaminants in raw wastewater with LC-HRMS/MS

An integrated workflow based on liquid chromatography coupled to a quadrupole-time-of-flight mass spectrometer (LC-QTOF-MS) was developed and applied to detect and identify suspect and unknown contaminants in Greek wastewater. Tentative identifications were initially based on mass accuracy, isotopic pattern, plausibility of the chromatographic retention time and MS/MS spectral interpretation (comparison with spectral libraries, in silico fragmentation). Moreover, new specific strategies for the identification of metabolites were applied to obtain extra confidence including the comparison of diurnal and/or weekly concentration trends of the metabolite and parent compounds and the complementary use of HILIC. Thirteen of 284 predicted and literature metabolites of selected pharmaceuticals and nicotine were tentatively identified in influent samples from Athens and seven were finally confirmed with reference standards. Thirty four nontarget compounds were tentatively identified, four were also confirmed. The sulfonated surfactant diglycol ether sulfate was identified along with others in the homologous series (SO4C2H4(OC2H4)xOH), which have not been previously reported in wastewater. As many surfactants were originally found as nontargets, these compounds were studied in detail through retrospective analysi

Matrix and serine protease expression during leukemic cell differentiation induced by aclacinomycin and all-trans-retinoic acid

In myeloid leukemia, immature leukemic cells are able to egress into peripheral blood to infiltrate extra-medullary organs. We therefore analyzed the migrating and invasive potential of human HL-60 and NB4 cell lines, representative of acute myelogenous leukemia, their ability to express matrix metalloproteases (MMPs), tissue inhibitors of metalloproteases (TIMPs) and urokinase plasminogen activator (uPA) in response to differentiating agents. Granulocytic differentiation by all-trans-retinoic acid (ATRA) and aclacinomycin (ACLA) strongly increased HL-60 and NB4 cell migration and invasion. At mRNA and protein levels, these cell lines produced significant amounts of MMP-9 (HL-60 < NB4). Granulocytic differentiation by ACLA increased both pro and active forms of MMP-9 whereas ATRA decreased them and stimulated uPA mRNAs. TIMP-1, the physiological MMP inhibitor, increased during granulocytic differentiation whereas TIMP-2 did not significantly vary. Use of Batimastat and aprotinin suggests that ATRA was active by modulating the uPA system while ACLA interfered with MMP expression. In conclusion, our data demonstrate that HL-60 and NB4 cells express MMPs and uPA which are differentially regulated by the differentiating agents ATRA and ACLA and suggest the clinical usefulness of MMPs and serine protease inhibitors in the prophylaxis and treatment of the ATRA syndrome. (C) 2002 Elsevier Science Inc. All rights reserved

Egg and clutch sizes of western chicken turtles (Deirochelys reticularia miaria)

Chicken turtles (Deirochelys reticularia) are generally characterized as having atypical reproductive characteristics relative to other sympatric emydids. However, the comparatively understudied western chicken turtle (D. r. miaria) has been shown to exhibit some reproductive characteristics that differ from the other subspecies. Therefore, we examined clutch and egg sizes from six D. r. miaria (13 clutches) in Oklahoma and compared the results to values that have been reported for the other two subspecies. Females nested up to three times per year, with clutches ranging from 8-13 eggs per clutch (mean = 10.9). The eggs were 19.4-25.3 mm wide (mean = 22.2 mm). These values are greater than the means reported for the other subspecies, but the differences were not statistically significant

Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa)

RNA-seq has been used to perform global expression analysis of the achene and the receptacle at four stages of fruit ripening, and of the roots and leaves of strawberry (Fragaria × ananassa). About 967 million reads and 191 Gb of sequence were produced, using Illumina sequencing. Mapping the reads in the related genome of the wild diploid Fragaria vesca revealed differences between the achene and receptacle development program, and reinforced the role played by ethylene in the ripening receptacle. For the strawberry transcriptome assembly, a de novo strategy was followed, generating separate assemblies for each of the ten tissues and stages sampled. The Trinity program was used for these assemblies, resulting in over 1.4 M isoforms. Filtering by a threshold of 0.3 FPKM, and doing Blastx (E-value < 1 e-30) against the UniProt database of plants reduced the number to 472,476 isoforms. Their assembly with the MIRA program (90% homology) resulted in 26,087 contigs. From these, 91.34 percent showed high homology to Fragaria vesca genes and 87.30 percent Fragaria iinumae (BlastN E-value < 1 e-100). Mapping back the reads on the MIRA contigs identified polymorphisms at nucleotide level, using FREEBAYES, as well as estimate their relative abundance in each sample