The underestimated role of pest pentatomid parasitoids in Southern South America.

Stink bugs are pests of economic importance of extensive crops (commodities) in the Neotropics, particularly in Southern South America. They are abundant, have a broad geographical distribution, and cause severe damage. Main species include the Neotropical brown-stink bug, Euschistus heros (F.), the red-banded stink bug, Piezodorus guildinii (Westwood), the Southern green stink bug, Nezara viridula (L.), the green-belly stink bugs, Dichelops furcatus (F.), and D. melacanthus (Dallas), and the brown-winged stink bug, Edessa meditabunda (F.). The management of these pest species on crops is complex because they can cause economic damage in low numbers, and it is difficult to control by the commonly used insecticides. Therefore, biological control appears as the most important tactic to be implemented in stink bug management programs. Among the many natural enemies present on the various agroecosystems, egg parasitoids (Hymenoptera) and parasitoids of adult stink bugs (Diptera and Hymenoptera) are the most promising groups to be exploited as biological control agents of pest species. Despite attempts in the past, implementation of biological control of stink bugs on major commodities in Southern South America still remains at a low level of adoption, and its high potential is, generally, underestimated. In this review article, we present extensive data from the literature on the two main groups of biological control agents referred above. Moreover, we discuss ways to promote biological control as the most important tactic to manage stink bugs in Southern South America. Keywords Heteroptera · Pentatomidae · Adult parasitoids · Egg parasitoids · Southern South Americ

Overwintering of Piezodorus guildinii (Heteroptera, Pentatomidae) populations.

Piezodorus guildinii (Westwood) is a soybean pest that causes significant economic losses in the Americas. The variability of overwintering (diapause) traits was evaluated in populations of the Southwest (SW) (33°55′?34°17′S, 57°13′?57°46′W) during 2-year period (2011?2013) and of the Northwest (NW) (32°01′?33°02′S, 57°50′?57°24′W) during 1-year period (2014?2015) Regions of Uruguay. Samples were taken from different plant species (cultivated legumes, wild shrubs, and trees) and from overwintering sites (leaf litter and bark). Alfalfa, Medicago sativa L. was the main host, with a collection period of 10?11 months in the SW and 12 months in the NW. Cluster analysis for each sex was carried out to group the months according to the similarity in diapause traits of populations (body size, body lipid content, immature reproductive organs, and clear type of pronotum band and connexivum in females). Female diapause in the SWwas longer (beginning of autumn to end of winter) than that in the NW (mid-autumn to mid-winter). Male diapause was longer (mid-autumn o mid-winter) in SW1 (1st year) than in SW2 (2nd year) and NW (lateautumn to mid-winter). In both regions, male diapause was shorter than female. Differences were associated with maximum temperature at daylight hours ≤ 12.1, being necessary maximum temperatures below 23.8 °C for females and 19.2 °C for males to initiate diapause

Cerulean: A hybrid assembly using high throughput short and long reads

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking regions. The emergence of third generation sequencing (Pacific Biosciences) with long reads enables the opportunity to resolve complicated repeats that could not be resolved by the short read data. However, these long reads have high error rate and it is an uphill task to assemble the genome without using additional high quality short reads. Recently, Koren et al. 2012 proposed an approach to use high quality short reads data to correct these long reads and, thus, make the assembly from long reads possible. However, due to the large size of both dataset (short and long reads), error-correction of these long reads requires excessively high computational resources, even on small bacterial genomes. In this work, instead of error correction of long reads, we first assemble the short reads and later map these long reads on the assembly graph to resolve repeats. Contribution: We present a hybrid assembly approach that is both computationally effective and produces high quality assemblies. Our algorithm first operates with a simplified version of the assembly graph consisting only of long contigs and gradually improves the assembly by adding smaller contigs in each iteration. In contrast to the state-of-the-art long reads error correction technique, which requires high computational resources and long running time on a supercomputer even for bacterial genome datasets, our software can produce comparable assembly using only a standard desktop in a short running time.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Sequence Ontology terminology for gene regulation

The Sequence Ontology (SO) is a structured, controlled vocabulary that provides terms and definitions for genomic annotation. The Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC) initiative has gathered input from many groups of researchers, including the SO, the Gene Ontology (GO), and gene regulation experts, with the goal of curating information about how gene expression is regulated at the molecular level. Here we discuss recent updates to the SO reflecting current knowledge. We have developed more accurate human-readable terms (also known as classes), including new definitions, and relationships related to the expression of genes. New findings continue to give us insight into the biology of gene regulation, including the order of events, and participants in those events. These updates to the SO support logical reasoning with the current understanding of gene expression regulation at the molecular level

Gold oxide films grown in the confined aqueous layer between gold and organic solvents

The properties of anodic passive films potentiostatically formed on polycrystalline gold in aqueous phosphate solutions were studied using voltammetry, electrochemical impedance spectroscopy, and contact angle measurements. The nature of the gold oxide layer was analyzed as a function of a potential holding in the aqueous double layer charge region at the interface between gold and the aqueous layer confined by insoluble organic solvents (hexane, chloroform, anisole, butyl acetate, xylene, and isopropyl ether). Different growth conditions change the homogeneity of the oxide layer leading to different passive properties. A synergetic effect on the gold oxidation of hydrogen dissolved in both the bulk metal and the confined aqueous layer is discussed.Instituto de Investigaciones Fisicoquímicas Teóricas y AplicadasInstituto de Física de Líquidos y Sistemas Biológico

Ellipsometry of iron hydrous oxide layers formed by potentiodynamic techniques

Hydrous iron oxide layers electrochemically formed on iron electrodes in different electrolytes (8.9 < pH < 12.6) have been investigated by ellipsometry. Data have been interpreted on the basis of a duplex oxide layer structure consisting of an inner barrier layer and an outer hydrous layer. The optical response of the hydrous oxide layer depends on the solution composition and in particular on the presence of carbonate ions and the applied potential.Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicada

Genome Sequence of Stenotrophomonas maltophilia PML168, Which Displays Baeyer-Villiger Monooxygenase Activity

Stenotrophomonas maltophilia PML168 was isolated from Wembury Beach on the English Coast from a rock pool following growth and selection on agar plates. Here we present the permanent draft genome sequence, which has allowed prediction of function for several genes encoding enzymes relevant to industrial biotechnology, including a novel flavoprotein monooxygenase

Simultaneous genome sequencing of symbionts and their hosts

Second-generation sequencing has made possible the sequencing of genomes of interest for even small research groups. However, obtaining separate clean cultures and clonal or inbred samples of metazoan hosts and their bacterial symbionts is often difficult. We present a computational pipeline for separating metazoan and bacterial DNA in silico rather than at the bench. The method relies on the generation of deep coverage of all the genomes in a mixed sample using Illumina short-read sequencing technology, and using aggregate properties of the different genomes to identify read sets belonging to each. This inexpensive and rapid approach has been used to sequence several nematode genomes and their bacterial endosymbionts in the last year in our laboratory and can also be used to visualize and identify unexpected contaminants (or possible symbionts) in genomic DNA samples. We hope that this method will enable researchers studying symbiotic systems to move from gene-centric to genome-centric approaches

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

Strain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Several systems have been proposed to classify MTBC strains into distinct lineages and families. Here, we investigate single-nucleotide polymorphisms (SNPs) as robust (stable) markers of genetic variation for phylogenetic analysis. We identify ~92k SNP across a global collection of 1,601 genomes. The SNP-based phylogeny is consistent with the gold-standard regions of difference (RD) classification system. Of the ~7k strain-specific SNPs identified, 62 markers are proposed to discriminate known circulating strains. This SNP-based barcode is the first to cover all main lineages, and classifies a greater number of sublineages than current alternatives. It may be used to classify clinical isolates to evaluate tools to control the disease, including therapeutics and vaccines whose effectiveness may vary by strain type

A Unifying Model of Genome Evolution Under Parsimony

We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double cut and join (DCJ) rearrangements in the presence of duplications. The problem of constructing parsimonious history graphs thus subsumes related maximum parsimony problems in the fields of phylogenetic reconstruction and genome rearrangement. We show that tractable functions can be used to define upper and lower bounds on the minimum number of substitutions and DCJ rearrangements needed to explain any history graph. These bounds become tight for a special type of unambiguous history graph called an ancestral variation graph (AVG), which constrains in its combinatorial structure the number of operations required. We finally demonstrate that for a given history graph $G$, a finite set of AVGs describe all parsimonious interpretations of $G$, and this set can be explored with a few sampling moves.Comment: 52 pages, 24 figure