Electric LAMP: Virtual Loop-Mediated Isothermal AMPlification

We present eLAMP, a PERL script, with Tk graphical interface, that electronically simulates Loop-mediated AMPlification (LAMP) allowing users to efficiently test putative LAMP primers on a set of target sequences. eLAMP can match primers to templates using either exact (via builtin PERL regular expressions) or approximate matching (via the tre-agrep library). Performance was tested on 40 whole genome sequences of Staphylococcus. eLAMP correctly predicted that the two tested primer sets would amplify from S. aureus genomes and not amplify from other Staphylococcus species. Open source (GNU Public License) PERL scripts are available for download from the New York Botanical Garden’s website

Las ericáceas de la vertiente pacífica de nariño, colombia

Se realizó el tratamiento taxonómico de la familia Ericaceae para la vertiente pacífica del departamento de Nariño, Colombia. El área de estudio abarca toda la llanura del pacífico y la vertiente pacífica de la cordillera de los Andes, hasta los 2.000 m de altitud, de dicho departamento. Los registros de las especies se obtuvieron mediante trabajo de campo, revisión de literatura y el estudio de las colecciones depositadas en los  herbarios CAUP, COL, HUA, PSO, QCA y QCNE. En el tratamiento taxonómico se incluyen descripciones morfológicas para la familia Ericaceae y para cada uno de los géneros y especies, acompañadas de comentarios sobre su distribución geográfica y altitudinal, y en algunos casos, de comentarios taxonómicos. También se incluye una clave sinóptica y una clave dicotómica para determinar especies, un glosario de los términos botánicos utilizados y un listado de los especímenes citados. Se encontraron 53 especies, agrupadas en 11 géneros, de las cuales una es una especie nueva de Vaccinium para la ciencia, tres son nuevos registros para Colombia (Cavendishia awa, Psammisia chionantha y P. oreogenes), antes registradas solo para el norte del Ecuador, y 15 son nuevos registros para el departamento de Nariño (Anthopterus oliganthus, Cavendishia awa, C. palustris, Diogenesia floribunda,  Disterigma humboldtii, D. pseudokillipiella, Psammisia chionantha, P. dolichopoda, P. oreogenes, P. ulbrichiana, Sphyrospermum buxifolium, S. dissimile, S. distichum, Themistoclesia alata y Thibaudia archeri). Los géneros con más especies fueron Cavendishia (15), Psammisia (10), Disterigma (6) y Sphyrospermum (7), seguidos por Thibaudia con cuatro especies, Anthopterus y Macleania con tres especies, Diogenesia con dos especies y Satyria, Themistoclesia y Vaccinium con una especie. Por otra parte, nueve especies tienen distribución geográfica muy restringida, de las cuales tres solo han sido registradas para el área de estudio (Cavendishia oligantha, Diogenesia alstoniana y Vaccinium sp. nov.) y las seis restantes son compartidas con la región  limítrofe del norte del Ecuador. Tres especies (Cavendishia callista, Disterigma pseudokillipiella y Macleania smithiana) fueron exclusivas de la llanura del Pacífico (por debajo de 500 m de altitud), 31 especies de la región Andina (por encima de 500 m de altitud) y 19 se compartieron entre ambas regiones.La mayor riqueza de especies y endemismos se presentó entre 1.000 y 1.600 m de altitud, con 45 especies. Los resultados obtenidos muestran que la vertiente pacífica del departamento de Nariño, Colombia, es la región de América con mayor número de especies de ericáceas por unidad de área

2MATRIX: A UTILITY FOR INDEL CODING AND PHYLOGENETIC MATRIX CONCATENATION

Premise of the study: Phylogenetic analysis of DNA and amino acid sequences requires the creation of files formatted specifically for each analysis package. Programs currently available cannot simultaneously code inferred insertion/deletion (indel) events in sequence alignments and concatenate data sets. Methods and Results: A novel Perl script, 2matrix, was created to concatenate matrices of non-molecular characters and/or aligned sequences and to code indels. 2matrix outputs a variety of formats compatible with popular phylogenetic programs. Conclusions: 2matrix efficiently codes indels and concatenates matrices of sequences and non-molecular data. It is available for free download under a GPL (General Public License) open source license (https://github.com/nrsalinas/2matrix/archive/master.zip)

El ocaso de pseudaechmea (bromeliaceae: bromelioideae)

Se propone y se discute la inclusión del género monotípico Pseudaechmea dentrode Billbergia (Bromeliaceae: Bromelioideae). Además, se presenta la combinaciónrespectiva, la ilustración y la redescripción morfológica de Billbergia ambigua(L. B. Sm. and amp; R. W. Read) Betancur and amp; N. R. Salinas, especie conocida sólo deldepartamento de Antioquia, Colombia

Dispersal of transgenes through maize seed systems in Mexico.

ObjectivesCurrent models of transgene dispersal focus on gene flow via pollen while neglecting seed, a vital vehicle for gene flow in centers of crop origin and diversity. We analyze the dispersal of maize transgenes via seeds in Mexico, the crop's cradle.MethodsWe use immunoassays (ELISA) to screen for the activity of recombinant proteins in a nationwide sample of farmer seed stocks. We estimate critical parameters of seed population dynamics using household survey data and combine these estimates with analytical results to examine presumed sources and mechanisms of dispersal.ResultsRecombinant proteins Cry1Ab/Ac and CP4/EPSPS were found in 3.1% and 1.8% of samples, respectively. They are most abundant in southeast Mexico but also present in the west-central region. Diffusion of seed and grain imported from the United States might explain the frequency and distribution of transgenes in west-central Mexico but not in the southeast.ConclusionsUnderstanding the potential for transgene survival and dispersal should help design methods to regulate the diffusion of germplasm into local seed stocks. Further research is needed on the interactions between formal and informal seed systems and grain markets in centers of crop origin and diversification

Una nueva especie de costus (costaceae) de la amazonia colombiana

Se describe e ilustra Costus fissicalyx N. R. Salinas, Clavijo and amp; Betancur, una especienueva del sudeste de la Amazonia colombiana; además, se presenta información sobresus relaciones taxonómicas, distribución y hábitat. Costus fissicalyx se diferencia delas otras especies del género principalmente por la forma y el tipo de crecimientodel cáli

Preliminary phylogenetic analysis of the Andean clade and the placement of new Colombian blueberries (Ericaceae, Vaccinieae)

The blueberry tribe Vaccinieae (Ericaceae) is particularly diverse in South America and underwent extensive radiation in Colombia where many endemics occur. Recent fi eldwork in Colombia has resulted in valuable additions to the phylogeny and as well in the discovery of morphologically noteworthy new species that need to be phylogenetically placed before being named. Th is is particularly important, as the monophyly of many of the studied genera have not been confi rmed. In order to advance our understanding of the relationships within neotropical Vaccinieae and advice the taxonomy of the new blueberry relatives, here we present the most comprehensive phylogenetic analysis for the Andean clade. Anthopterus, Demosthenesia, and Pellegrinia are among the putative Andean genera recovered as monophyletic, while other eight Andean genera were not. Th e analyses also showed that genera that have been traditionally widely defi ned are non-monophyletic and could be further split into more discrete groups. Four newly discovered Colombian Vaccinieae are placed in the monophyletic Satyria s.s. and the Psammisia I clade. Although these new species are endemic to the Colombian Western Cordillera and Chocó biogeographic region and three are not known outside of Las Orquídeas National Park, they do not form sister pairs

Preliminary phylogenetic analysis of the Andean clade and the placement of new Colombian blueberries (Ericaceae, Vaccinieae)

The blueberry tribe Vaccinieae (Ericaceae) is particularly diverse in South America and underwent extensive radiation in Colombia where many endemics occur. Recent fi eldwork in Colombia has resulted in valuable additions to the phylogeny and as well in the discovery of morphologically noteworthy new species that need to be phylogenetically placed before being named. Th is is particularly important, as the monophyly of many of the studied genera have not been confi rmed. In order to advance our understanding of the relationships within neotropical Vaccinieae and advice the taxonomy of the new blueberry relatives, here we present the most comprehensive phylogenetic analysis for the Andean clade. Anthopterus, Demosthenesia, and Pellegrinia are among the putative Andean genera recovered as monophyletic, while other eight Andean genera were not. Th e analyses also showed that genera that have been traditionally widely defi ned are non-monophyletic and could be further split into more discrete groups. Four newly discovered Colombian Vaccinieae are placed in the monophyletic Satyria s.s. and the Psammisia I clade. Although these new species are endemic to the Colombian Western Cordillera and Chocó biogeographic region and three are not known outside of Las Orquídeas National Park, they do not form sister pairs

Reducing model bias in a deep learning classifier using domain adversarial neural networks in the MINERvA experiment

We present a simulation-based study using deep convolutional neural networks (DCNNs) to identify neutrino interaction vertices in the MINERvA passive targets region, and illustrate the application of domain adversarial neural networks (DANNs) in this context. DANNs are designed to be trained in one domain (simulated data) but tested in a second domain (physics data) and utilize unlabeled data from the second domain so that during training only features which are unable to discriminate between the domains are promoted. MINERvA is a neutrino-nucleus scattering experiment using the NuMI beamline at Fermilab. $A$-dependent cross sections are an important part of the physics program, and these measurements require vertex finding in complicated events. To illustrate the impact of the DANN we used a modified set of simulation in place of physics data during the training of the DANN and then used the label of the modified simulation during the evaluation of the DANN. We find that deep learning based methods offer significant advantages over our prior track-based reconstruction for the task of vertex finding, and that DANNs are able to improve the performance of deep networks by leveraging available unlabeled data and by mitigating network performance degradation rooted in biases in the physics models used for training.Comment: 41 page

Direct Measurement of Nuclear Dependence of Charged Current Quasielastic-like Neutrino Interactions using MINERvA

Charged-current $\nu_{\mu}$ interactions on carbon, iron, and lead with a final state hadronic system of one or more protons with zero mesons are used to investigate the influence of the nuclear environment on quasielastic-like interactions. The transfered four-momentum squared to the target nucleus, $Q^2$, is reconstructed based on the kinematics of the leading proton, and differential cross sections versus $Q^2$ and the cross-section ratios of iron, lead and carbon to scintillator are measured for the first time in a single experiment. The measurements show a dependence on atomic number. While the quasielastic-like scattering on carbon is compatible with predictions, the trends exhibited by scattering on iron and lead favor a prediction with intranuclear rescattering of hadrons accounted for by a conventional particle cascade treatment. These measurements help discriminate between different models of both initial state nucleons and final state interactions used in the neutrino oscillation experiments