The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl

The Sol Genomics Network (SGN; http://solgenomics.net/) is a clade-oriented database (COD) containing biological data for species in the Solanaceae and their close relatives, with data types ranging from chromosomes and genes to phenotypes and accessions. SGN hosts several genome maps and sequences, including a pre-release of the tomato (Solanum lycopersicum cv Heinz 1706) reference genome. A new transcriptome component has been added to store RNA-seq and microarray data. SGN is also an open source software project, continuously developing and improving a complex system for storing, integrating and analyzing data. All code and development work is publicly visible on GitHub (http://github.com). The database architecture combines SGN-specific schemas and the community-developed Chado schema (http://gmod.org/wiki/Chado) for compatibility with other genome databases. The SGN curation model is community-driven, allowing researchers to add and edit information using simple web tools. Currently, over a hundred community annotators help curate the database. SGN can be accessed at http://solgenomics.net/

Evaluation of a Bayesian inference network for ligand-based virtual screening

Background Bayesian inference networks enable the computation of the probability that an event will occur. They have been used previously to rank textual documents in order of decreasing relevance to a user-defined query. Here, we modify the approach to enable a Bayesian inference network to be used for chemical similarity searching, where a database is ranked in order of decreasing probability of bioactivity. Results Bayesian inference networks were implemented using two different types of network and four different types of belief function. Experiments with the MDDR and WOMBAT databases show that a Bayesian inference network can be used to provide effective ligand-based screening, especially when the active molecules being sought have a high degree of structural homogeneity; in such cases, the network substantially out-performs a conventional, Tanimoto-based similarity searching system. However, the effectiveness of the network is much less when structurally heterogeneous sets of actives are being sought. Conclusion A Bayesian inference network provides an interesting alternative to existing tools for ligand-based virtual screening

Densidad de fibras y densidad de conductos pilosos como criterios de selección para mejorar la calidad y el peso de vellones de alpacas

Improvements in the weight of greasy fleece (GFW) and mean fibre diameter (MED) can favour the income of alpaca producers; however, these variables are directly related, complicating the simultaneous improvement of both characteristics. Therefore, it is necessary to find new selection criteria for the simultaneous improvement of both characteristics. The purpose of the study was to characterize the fibre density (FibDen), density of hair ducts (DenDucts) and the fibre/duct ratio and No. of fibres/ducts (Fib/Duct_R) as possible selection criteria. Likewise, determine the type of relationship between them and with GFW and MFD, and construct and evaluate formal selection indices under scenarios with different available measurements, considering in all cases GFW and MFD duly weighted by their economic weights, as selection objectives. For this, fibre samples and skin images were taken, and the GFW of alpacas from four herds raised in Huancavelica and Caylloma, Arequipa, Perú, between 2018 and 2020 were recorded. The density characteristics were obtained through the procedure called Fiber Den, while the FMD was assessed using the FIBER EC, and GFW was recorded using a scale. In the construction of the selection indices for GFW and MFD Hazel's theory of selection indices was applied, considering the values indicated in the bibliography and in the present study. The FibDen, DenDucts and Fib/Ducts_R ranged from 8.8 to 60 fib/mm2, 3.8 to 21.2 ducts/mm2 and 2.0 to 4.3 fib/ducts, respectively. There are hair ducts with up to 8 fibres, the most frequent being ducts with 1, 2 or 3 fibres. It is concluded that FibDen and DenDcuts have a linear and direct relationship with the GFW and inversely with the MFD, and that the inclusion of the FibDen and DenDucts as selection criteria within a selection index would improve the accuracy from 0.53 to 0.63, being able to obtain further progress genetic between 15 and 18%, with better economic benefits than when only GFW and MFD are used.Mejoras en el peso de vellón de sucio (PVe) y diámetro medio de la fibra (DMF) favorece los ingresos de los productores de alpacas; sin embargo, estas variables están relacionadas directamente, complicando el mejoramiento simultáneo de ambas características. Por tanto, se requiere buscar nuevos criterios de selección para la mejora simultánea de ambas características. El propósito del estudio fue caracterizar la densidad de fibras (DenFib), densidad de conductos pilosos (DenCond) y la relación N.° de fibras/conductos (R_Fib/Cond) como posibles criterios de selección. Asimismo, determinar el tipo de relación entre ellas y con el PVe y DMF, y construir y evaluar índices de selección formales bajo escenarios con diferentes mediciones disponibles, considerando en todos los casos PVe y DMF debidamente ponderados por sus pesos económicos, como objetivos de selección. Para ello, se tomaron muestras de fibras, imágenes de piel y se registraron el PVe de alpacas de cuatro rebaños criadas en Huancavelica y Caylloma-Arequipa (Perú) entre 2018 y 2020. Las características de densidad fueron obtenidas mediante el procedimiento denominado Fiber Den, mientras que el DMF se evaluó mediante el FIBER EC, y el PVe se registró con una balanza. En la construcción de los índices de selección para PVe y DMF se aplicó la teoría de índices de selección de Hazel, considerando los valores indicados en la bibliografía y en el presente trabajo. La DenFib, DenCon y R_Fib/Cond varía entre 8.8 a 60 fib/mm2, 3.8 a 21.2 cond/mm2 y 2.0 a 4.3 fib/cond, respectivamente. Se encontraron conductos pilosos de hasta 8 fibras, siendo los más frecuentes los conductos con 1, 2 o 3 fibras. Se concluye que la DenFib y DenCond tienen relación lineal y directa con el PVe e inversa con el DMF, y que la inclusión de la DenFib y DenCond como criterios de selección dentro de un índice de selección mejorarían la exactitud de 0.53 a 0.63, pudiéndose obtener mayores progresos genéticos entre 15 y 18%, con mejores beneficios económicos, que cuando solo se utiliza el PVe y DMF

Analytical Plan for Roman Glasses

Roman glasses that have been in the sea or underground for about 1800 years can serve as the independent “experiment” that is needed for validation of codes and models that are used in performance assessment. Two sets of Roman-era glasses have been obtained for this purpose. One set comes from the sunken vessel the Iulia Felix; the second from recently excavated glasses from a Roman villa in Aquileia, Italy. The specimens contain glass artifacts and attached sediment or soil. In the case of the Iulia Felix glasses quite a lot of analytical work has been completed at the University of Padova, but from an archaeological perspective. The glasses from Aquileia have not been so carefully analyzed, but they are similar to other Roman glasses. Both glass and sediment or soil need to be analyzed and are the subject of this analytical plan. The glasses need to be analyzed with the goal of validating the model used to describe glass dissolution. The sediment and soil need to be analyzed to determine the profile of elements released from the glass. This latter need represents a significant analytical challenge because of the trace quantities that need to be analyzed. Both pieces of information will yield important information useful in the validation of the glass dissolution model and the chemical transport code(s) used to determine the migration of elements once released from the glass. In this plan, we outline the analytical techniques that should be useful in obtaining the needed information and suggest a useful starting point for this analytical effort

Avihepadnavirus diversity in parrots is comparable to that found amongst all other avian species

Avihepadna viruses have previously been isolated from various species of duck ,goose, stork, heron and crane. Recently the first parrot avihepadna virus was isolated from a Ring-necked Parakeet in Poland. In this study, 41 psittacineliver samples archived in Poland over the last nine years were tested for presence of Parrot hepatitis B virus(PHBV). We cloned and sequenced PHBVisolates from 18 birds including a Crimson Rosella, an African grey parrot and sixteen Ring-necked Parakeets. PHBVisolates display a degree of diversity (478% genome wide pair wise identity) that is comparable to that found amongst all other avihepadna viruses (479% genome wide pair wise identity). The PHBV viruses can be subdivided into seven genetically distinct groups (tentatively named A-G) of which the two isolated of PHBV-Gare the most divergent sharing 79% genome wide pair wise identity with all their PHBVs. All PHBV isolates display classical avihepadnavirus genome architecture.Department of HE and Training approved lis

Lost in diversity: the interactions between soil-borne fungi, biodiversity and plant productivity

There is consensus that plant species richness enhances plant productivity within natural grasslands, but the underlying drivers remain debated. Recently, differential accumulation of soil-borne fungal pathogens across the plant diversity gradient has been proposed as a cause of this pattern. However, the below-ground environment has generally been treated as a ‘black box’ in biodiversity experiments, leaving these fungi unidentified. * Using next generation sequencing and pathogenicity assays, we analysed the community composition of root-associated fungi from a biodiversity experiment to examine if evidence exists for host specificity and negative density dependence in the interplay between soil-borne fungi, plant diversity and productivity. * Plant species were colonised by distinct (pathogenic) fungal communities and isolated fungal species showed negative, species-specific effects on plant growth. Moreover, 57% of the pathogenic fungal operational taxonomic units (OTUs) recorded in plant monocultures were not detected in eight plant species plots, suggesting a loss of pathogenic OTUs with plant diversity. * Our work provides strong evidence for host specificity and negative density-dependent effects of root-associated fungi on plant species in grasslands. Our work substantiates the hypothesis that fungal root pathogens are an important driver of biodiversity-ecosystem functioning relationships

A surrogate method for comparison analysis of salivary concentrations of Xylitol-containing products

Background: Xylitol chewing gum has been shown to reduce Streptococcus mutans levels and decay. Two studies examined the presence and time course of salivary xylitol concentrations delivered via xylitol-containing pellet gum and compared them to other xylitol-containing products. Methods: A within-subjects design was used for both studies. Study 1, adults (N = 15) received three xylitol-containing products (pellet gum (2.6 g), gummy bears (2.6 g), and commercially available stick gum (Koolerz, 3.0 g)); Study 2, a second group of adults (N = 15) received three xylitol-containing products (pellet gum, gummy bears, and a 33% xylitol syrup (2.67 g). For both studies subjects consumed one xylitol product per visit with a 7-day washout between each product. A standardized protocol was followed for each product visit. Product order was randomly determined at the initial visit. Saliva samples (0.5 mL to 1.0 mL) were collected at baseline and up to 10 time points (~16 min in length) after product consumption initiated. Concentration of xylitol in saliva samples was analyzed using high-performance liquid chromatography. Area under the curve (AUC) for determining the average xylitol concentration in saliva over the total sampling period was calculated for each product. Results: In both studies all three xylitol products (Study 1: pellet gum, gummy bears, and stick gum; Study 2: pellet gum, gummy bears, and syrup) had similar time curves with two xylitol concentration peaks during the sampling period. Study 1 had its highest mean peaks at the 4 min sampling point while Study 2 had its highest mean peaks between 13 to 16 minutes. Salivary xylitol levels returned to baseline at about 18 minutes for all forms tested. Additionally, for both studies the total AUC for the xylitol products were similar compared to the pellet gum (Study 1: pellet gum - 51.3 [micro]g.min/mL, gummy bears - 59.6 [micro]g.min/mL, and stick gum - 46.4 [micro]g.min/mL; Study 2: pellet gum - 63.0 [micro]g.min/mL, gummy bears - 55.9 [micro]g.min/mL, and syrup - 59.0 [micro]g.min/mL). Conclusion: The comparison method demonstrated high reliability and validity. In both studies other xylitol-containing products had time curves and mean xylitol concentration peaks similar to xylitol pellet gum suggesting this test may be a surrogate for longer studies comparing various products.NIDCR-NIH U54 DE14254; Head Start, HRSA 90YD0188/03; and MCHB, HRSA R40MC03622-03

Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest

Understanding the interactions among microbial communities, plant communities and soil properties following deforestation could provide insights into the long-term effects of land-use change on ecosystem functions, and may help identify approaches that promote the recovery of degraded sites. We combined high-throughput sequencing of fungal rDNA and molecular barcoding of plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation. We found significant effects of land-use change on fungal community composition, which was more closely correlated to plant community composition than to changes in soil properties or geographic distance, providing evidence for strong links between above- and below-ground communities in tropical forests. © 2014 International Society for Microbial Ecology All rights reserved