Search

Parisot et al., [Background]: The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions., [Results]: We sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino acids required for insect development and cuticle biosynthesis., [Conclusions]: Here we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes., Funding for this project was provided by the Fondation de l’Institut National des Sciences Appliquées-Lyon (INSA-Lyon), the research direction of INSA-Lyon, the Santé des Plantes et Environnement (SPE) department at the Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), the French ANR-10-BLAN-1701 (ImmunSymbArt), the French ANR-13-BSV7-0016-01 (IMetSym), the French ANR-17_CE20_0031_01 (GREEN), and a grant from la Région Rhône-Alpes (France) to AH. RR received funding from the French ANR-17-CE20-0015 (UNLEASH) and the IDEX-Lyon PALSE IMPULSION initiative. The project was also funded by European Regional Development Fund (ERDF) and Ministerio de Ciencia, Innovación y Universidades (Spain) PGC2018-099344-B-I00 to AL, and PID2019-105969GB-I00 to AM and Conselleria d’Educació, Generalitat Valenciana (Spain), grant number PROMETEO/2018/133 to AM. CV-C was a recipient of a fellowship from the Ministerio de Economía y Competitividad (Spain) and a grant from la Région Rhône-Alpes (France).

We present a review of the state of the art of the techniques and algorithms most used in the selection and detection of characteristics of electroencephalographic signals of people when consciously performing activities. These features are numeric parameters that describe the behavior of the signal and are the basis of patterns. In addition, previous experiences in the acquisition of electroencephalographic signals using the Epoc brain-computer interface manufactured by Emotiv are presented. First, some techniques used to eliminate artifacts (disturbances) present in the signal generated by blinking, strong breathing or other movements that contaminate the signal are presented. Later, the algorithms most frequently used in the processing of electroencephalographic signals are shown for the extraction of characteristics that describe the behavior of these patterns and that can be used to detect and recognize patterns in other signals. Finally, we present the lessons that we have acquired as a work team in the recording of electroencephalographic signals in order to be helpful for beginners.

Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the available genomes of five other aphids, along with the transcriptomes of two species belonging to Adelgidae (a closely related clade to the aphids) and Coccoidea. We found that gene duplication has been pervasive throughout the evolution of aphids, including many parallel waves of recent, species-specific duplications. Most notably, we identified a consistent set of very ancestral duplications, originating from a large-scale gene duplication predating the diversification of Aphidomorpha (comprising aphids, phylloxerids, and adelgids). Genes duplicated in this ancestral wave are enriched in functions related to traits shared by Aphidomorpha, such as association with endosymbionts, and adaptation to plant defenses and phloem-sap-based diet. The ancestral nature of this duplication wave (106–227 Ma) and the lack of sufficiently conserved synteny make it difficult to conclude whether it originated from a whole-genome duplication event or, alternatively, from a burst of large-scale segmental duplications. Genome sequencing of other aphid species belonging to different Aphidomorpha and related lineages may clarify these findings., This research was funded by European Regional Development Fund (ERDF) and Ministerio de Economía y Competitividad (Spain) (Grant Nos. PGC2018-099344-B-100 and BFU2015-67107). T.G. group also acknowledges support from the Catalan Research Agency (AGAUR) SGR857, and grants from the European Union’s Horizon 2020 research and innovation program under the grant agreements ERC-2016-724173 and MSC-747607. T.G. also receives support from an INB (Grant No. PT17/0009/0023—ISCIII-SGEFI/ERDF).

Toxoplasmosis, caused by Toxoplasma gondii, is a major public concern owing to its neurotropic nature and high morbidity and mortality rates in immunocompromised patients and newborns. Current treatment for this disease is inefficient and produces side effects. Inflammatory mediators produced during T. gondii infection (e.g., cytokines and nitric oxide) are crucial in controlling parasite replication. In this context, Tityus serrulatus venom (TsV) induces the production of inflammatory mediators by immune cells. Thus, this study aimed to isolate and identify the components of TsV with potential anti-T. gondii activity. TsV was extracted from scorpions and lyophilized or loaded onto a column to obtain its fractions. TsV subfractions were obtained using chromatography, and its amino acid sequence was identified and applied to peptide design using bioinformatics tools. The C57BL/6 mice and their harvested macrophages were used to test the anti-Toxoplasma activity of TsV components and peptides. TsV and its fraction F6 attenuated the replication of tachyzoites in macrophages and induced nitric oxide and cytokine (IL-12, TNF, and IL-6) production by infected cells, without host cell toxicity. Moreover, Su6-B toxin, a subfraction of F6, demonstrated anti-T. gondii activity. The partially elucidated and characterized amino acid sequence of Sub6-B demonstrated 93% similarity with T. serrulatus 2 toxin (Ts2). Ts2 mimetic peptides (“Pep1,” “Pep2a,” and “Pep2b”) were designed and synthesized. Pep1 and Pep2a, but not Pep2b, reduced the replication of tachyzoites in macrophages. In vivo, treatment of T. gondii-infected mice with Pep1, Pep2a, or Pep2b decreased the number of cerebral cysts and did not induce hepatotoxicity in the animals. Taken together, our data show promising immunomodulatory and antiparasitic activity of TsV that could be explored and applied in future therapies for treating infectious parasitic diseases such as toxoplasmosis.

BackgroundThe rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions.ResultsWe sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 Kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino-acids required for insect development and cuticle biosynthesis.ConclusionsHere we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.

Background and Aims The use of intradialytic exercise has been associated with improved clearance, oxygen consumption, quality of life, and physical performance. The aim of this study was to describe the association between of intradialytic exercise and some outcomes in a Mexican maintenance hemodialysis (HD) population. Method Observational comparative study that included 84 maintenance HD patients from one HD center in Mexico City. The population was grouped according to the intradialytic exercise local record. The aerobic intradialytic exercise protocol includes cycling for 30-45 min during the first 2 hours of the HD according to each patient’s ability. A retrospective registry of clinical and biochemical parameters was realized. Also, the hemodynamic parameters of the last six HD sessions for each patient was included. Data analysis was carried out through descriptive and inferential statistics. Results Of the total population, 45.2% were men (n= 38) and the mean age was 53.6 + 17 years. Fifty one percent (n= 43) had diabetes mellitus (DM), which resulted more prevalent in the subgroup of patients without intradialytic exercise (p=0.03) No differences between groups were present in age, history of previous peritoneal dialysis or kidney transplant. The rest of baseline data are shown in Table 1. The subgroup of patients who underwent intradialytic exercise presented higher levels of serum albumin (p=0.03) and lower levels of parathormone (p=0.03). A total of 504 HD sessions were analysed and intradialytic exercise was performed in 64.3% (n=324). Patients in the intradialytic exercise program presented high levels of systolic and diastolic blood pressure (graphic 1). Intradialytic hypotension occurred in 5.2% (n=26) and no differences are shown between groups (p=0.78). No mayor side effects were reported. Conclusion The intradialytic exercise could improve nutritional and bone-mineral status markers. The patients in an intradialytic exercise program presented higher levels of blood pressure.

Urbanization affects the ecology of wildlife diseases and although it has been suggested that there are lower risks of infection in urban areas, there have been no experiments to support this conclusion. We assessed haemosporidian prevalence and intensity in House Sparrows Passer domesticus using field and experimental data under contrasting conditions (i.e. urban vs. non‐urban). For experimental data, we kept 32 male House Sparrows in captivity as a proxy of stress, and for field data we sampled 49 House Sparrows (17 females). We made use of microscopy to determine the relative intensity and used the polymerase chain reaction to estimate infection prevalence. We obtained total leucocyte counts, leucocyte differentials, heterophil/lymphocyte ratio (H/L) as a measure of stress, and the Polychromatic Index as a measure of physiological condition (erythropoiesis). We identified a total of 10 haemosporidian lineages. For field samples (both males and females), we found a significantly higher prevalence of infection in non‐urban House Sparrows than in urban ones. Under experimental conditions, non‐urban House Sparrows showed a higher prevalence than urban ones both before and after captivity, with a significant increase in parasite intensity. The number of infected birds increased after captivity for both urban (~ 32%) and non‐urban House Sparrows (~ 19%), indicating either a recrudescence of chronic and relapses of latent infections or the appearance of infections that had been acquired earlier. The H/L ratio was significantly higher for non‐urban than for urban male House Sparrows before captivity. No difference in H/L was found for urban House Sparrows before and after captivity, indicating tolerance to city stressors. Our results showed a significant decrease in H/L for non‐urban birds after captivity, suggesting higher stress in the non‐urban agricultural environment. Haemosporidian infections were not associated with the H/L ratio. Our study provides evidence that highly urbanized areas within cities represent lower haemosporidian infection risks than do non‐urban areas for House Sparrows.

The evolution of winged insects revolutionized terrestrial ecosystems and led to the largest animal radiation on Earth. However, we still have an incomplete picture of the genomic changes that underlay this diversification. Mayflies, as one of the sister groups of all other winged insects, are key to understanding this radiation. Here, we describe the genome of the mayfly Cloeon dipterum and its gene expression throughout its aquatic and aerial life cycle and specific organs. We discover an expansion of odorant-binding-protein genes, some expressed specifically in breathing gills of aquatic nymphs, suggesting a novel sensory role for this organ. In contrast, flying adults use an enlarged opsin set in a sexually dimorphic manner, with some expressed only in males. Finally, we identify a set of wing-associated genes deeply conserved in the pterygote insects and find transcriptomic similarities between gills and wings, suggesting a common genetic program. Globally, this comprehensive genomic and transcriptomic study uncovers the genetic basis of key evolutionary adaptations in mayflies and winged insects., This project was mainly funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement 657732 to I.A., Grant BFU2015-66040-P to F.Ca., institutional Grant MDM-2016-0687 (MINECO, Spain). Additional funding was provided by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (ERC-StG-LS2-637591 to M.I.), the Spanish Ministerio de Ciencia (BFU2017-89201-P to M.I., RYC-2016-20089 and PGC2018-099392-A-I00 to I.M.).

File name: Supplementary Table S1. Title: Differentially gene expression results. Caption: Sequencing statistics for all the strains analyzed in this work, and expression values for all differentially expressed genes in each strain. Genes previously reported as oxidative stress responsive genes are also listed.-- File name: Supplementary Table S2. Title: Gene ontology enrichment analysis. Caption: Significant gene ontology clusters according to DAVID functional annotation tool for pairs of strains and for individual strains.-- File name: Supplementary Table S3. Title: Identification of hub genes in the four strains analyzed in this work Caption: Cytohubba results for individual strains, and list of the unique hubs genes found across strains including those located nearby a TE.-- File name: Supplementary Table S4. Title: Genotyping and genome distribution of TEs for each analyzed strain. Caption: Presence/absence of the reference TE insertions and distribution of these TEs regarding nearby genes in the strains analyzed in this work. The expression level of the genes nearby candidate TEs are also given.-- File name: Supplementary Table S5. Title: ATAC-seq analysis. Caption: Sequencing statistics and peak analysis for all the strains analyzed in this work.-- File name: Supplementary Table S6. Title: TE family expression analysis. Caption: Differentially expressed TE families and their distribution regarding nearby differentially expressed genes. The analysis of differentially expressed TE families in response to DDT is also given., Most of the genotype-phenotype analyses to date have largely centered attention on single nucleotide polymorphisms. However, transposable element insertions have arisen as a plausible addition to the study of the genotypic-phenotypic link due to their role in genome function and evolution. In this work, we investigate the contribution of transposable element insertions to the regulation of gene expression in response to insecticides. We exposed four Drosophila melanogaster strains to malathion, a commonly used organophosphate insecticide. By combining information from different approaches, including RNA-seq and ATAC-seq, we found that transposable elements can contribute to the regulation of gene expression under insecticide exposure by rewiring cis-regulatory networks., This work was supported by the European Commission (H2020-ERC-2014-CoG-647900), by the Ministerio de Ciencia, Innovación y Universidades/AEI/FEDER (BFU2017-82937-P), and by the “Secretaria d’Universitats i Recerca. Departament d’Economia i Coneixement. Generalitat de Catalunya” (GRC 2017 SGR 880). JSO is funded by a Juan de la Cierva-Formación fellowship (FJCI-2016-28380).

Mosquitoes from the Anopheles genus have been extensively studied given their role as vectors of several human infectious diseases. While the genomes of 27 species are available, only a few of them have been studied from a population genomics perspective. Additionally, most of these studies have relied on single nucleotide polymorphisms while other genetic variants, including transposable element (TE) insertions have been neglected. TEs are important players in genome function, structure, and evolution. Indeed, given their capacity to generate mutations and to respond to environmental changes, TEs have been shown to play an important role in adaptation. However, given their repetitive nature they remain challenging to annotate. In this work, we aim at summarizing the current knowledge on TE content and TE diversity in anopheline genomes as the necessary first step to include these relevant genetic variants in population genomics studies. The comparison of the TE content obtained using different annotation strategies in three anopheline species suggests that combining strategies is essential to fully characterize the TE repertoire. As a first approach to the characterization of the TE repertoire in all 27 available anopheline genomes, we used TEfam, a database specialized in mosquitoes TEs, to annotate them. We found that the TE content, and its composition, varied among anopheline species, with some TE families restricted to specific phylogenetic groups. Furthermore, we showed that using all the available libraries allowed us to uncover the TE diversity to a larger extent. The ongoing efforts to improve the already available genome sequences together with the generation of new population genomic resources should allow us to assess in the near future the role of TE insertions in the evolution and function of anopheline genomes.

The Symbiotic Genomes Database (SymGenDB; http://symbiogenomesdb.uv.es/) is a public resource of manually curated associations between organisms involved in symbiotic relationships, maintaining a catalog of completely sequenced/finished bacterial genomes exclusively. It originally consisted of three modules where users could search for the bacteria involved in a specific symbiotic relationship, their genomes and their genes (including their orthologs). In this update, we present an additional module that includes a representation of the metabolic network of each organism included in the database, as Directed Acyclic Graphs (MetaDAGs). This module provides unique opportunities to explore the metabolism of each individual organism and/or to evaluate the shared and joint metabolic capabilities of the organisms of the same genera included in our listing, allowing users to construct predictive analyses of metabolic associations and complementation between systems. We also report a ~25% increase in manually curated content in the database, i.e. bacterial genomes and their associations, with a final count of 2328 bacterial genomes associated to 498 hosts. We describe new querying possibilities for all the modules, as well as new display features for the MetaDAGs module, providing a relevant range of content and utility. This update continues to improve SymGenDB and can help elucidate the mechanisms by which organisms depend on each other., National Board of Science and Technology of México (CONACYT) (538243 to M.R.P.); FPI fellowship from the Ministry of Economy and Competitiveness (BES-2013-063548 to C.V.C.); Spanish Ministry of Science, Innovation and Universities and the European Regional Development Fund through projects DPI2015-67082-P and PGC2018-096956-B-C43 (FEDER/MICINN/AEI) and the Spanish Ministry of Economy and Competitiveness (projects SAF2012-31187, SAF2013-49788-EXP, SAF2015-65878-R and BFU2015-64322-C2-1-R, co-financed by FEDER funds); Carlos III Institute of Health (projects PIE14/00045 and AC15/00022); Generalitat Valenciana (project Prometeo/2018/A/133); Asociación Española contra el Cáncer (project AECC 2017-1485) and co-financed by the European Regional Development Fund (ERDF).

The first winged insects underwent profound morphological and functional transformations leading to the most successful animal radiations in the history of earth. Despite this, we still have a very incomplete picture of the changes in their genomes that underlay this radiation. Mayflies (Ephemeroptera) are one of the extant sister groups of all other winged insects and therefore are at a key phylogenetic position to understand this radiation. Here, we describe the genome of the cosmopolitan mayfly Cloeon dipterum and study its expression along development and in specific organs. We discover an expansion of odorant-binding proteins, some expressed specifically in the breathing gills of aquatic nymphs, suggesting a novel sensory role for gills. In contrast, as flying adults, mayflies make use of an enlarged set of opsins and utilise these visual genes in a sexually dimorphic manner, with some opsins expressed only in males. Finally, to illuminate the origin of wings, we identify a core set of deeply conserved wing-specific genes at the root of the pterygote insects. Globally, this is the first comprehensive study of the structure and expression of the genome of a paleopteran insect and shows how its genome has kept a record of its functional adaptations.

Air pollution is a risk factor for cardiovascular and Alzheimer's disease (AD). Iron-rich, strongly magnetic, combustion- and friction-derived nanoparticles (CFDNPs) are abundant in particulate air pollution. Metropolitan Mexico City (MMC) young residents have abundant brain CFDNPs associated with AD pathology. We aimed to identify if magnetic CFDNPs are present in urbanites' hearts and associated with cell damage. We used magnetic analysis and transmission electron microscopy (TEM) to identify heart CFDNPs and measured oxidative stress (cellular prion protein, PrPC), and endoplasmic reticulum (ER) stress (glucose regulated protein, GRP78) in 72 subjects age 23.8 ± 9.4y: 63 MMC residents, with Alzheimer Continuum vs 9 controls. Magnetite/maghemite nanoparticles displaying the typical rounded crystal morphologies and fused surface textures of CFDNPs were more abundant in MMC residents' hearts. NPs, ∼2–10 × more abundant in exposed vs controls, were present inside mitochondria in ventricular cardiomyocytes, in ER, at mitochondria-ER contact sites (MERCs), intercalated disks, endothelial and mast cells. Erythrocytes were identified transferring ‘hitchhiking’ NPs to activated endothelium. Magnetic CFDNP concentrations and particle numbers ranged from 0.2 to 1.7 μg/g and ∼2 to 22 × 109/g, respectively. Co-occurring with cardiomyocyte NPs were abnormal mitochondria and MERCs, dilated ER, and lipofuscin. MMC residents had strong left ventricular PrPC and bi-ventricular GRP78 up-regulation. The health impact of up to ∼22 billion magnetic NPs/g of ventricular tissue are likely reflecting the combination of surface charge, ferrimagnetism, and redox activity, and includes their potential for disruption of the heart's electrical impulse pathways, hyperthermia and alignment and/or rotation in response to magnetic fields. Exposure to solid NPs appears to be directly associated with early and significant cardiac damage. Identification of strongly magnetic CFDNPs in the hearts of children and young adults provides an important novel layer of information for understanding CVD pathogenesis emphasizing the urgent need for prioritization of particulate air pollution control.

Plant survival depends on the optimal use of resources under variable environmental conditions. Among the mechanisms that mediate the balance between growth, differentiation, and stress responses, the regulation of transcriptional activity by DELLA proteins stands out. In angiosperms, DELLA accumulation promotes defense against biotic and abiotic stress and represses cell division and expansion, while the loss of DELLA function is associated with increased plant size and sensitivity toward stress.1 Given that DELLA protein stability is dependent on gibberellin (GA) levels2 and GA metabolism is influenced by the environment,3 this pathway is proposed to relay environmental information to the transcriptional programs that regulate growth and stress responses in angiosperms.4,5 However, DELLA genes are also found in bryophytes, whereas canonical GA receptors have been identified only in vascular plants.6, 7, 8, 9, 10 Thus, it is not clear whether these regulatory functions of DELLA predated or emerged with typical GA signaling. Here, we show that, as in vascular plants, the only DELLA in the liverwort Marchantia polymorpha also participates in the regulation of growth and key developmental processes and promotes oxidative stress tolerance. Moreover, part of these effects is likely caused by the conserved physical interaction with the MpPIF transcription factor. Therefore, we suggest that the role in the coordination of growth and stress responses was already encoded in the DELLA protein of the common ancestor of land plants, and the importance of this function is underscored by its conservation over the past 450 million years., Work in the authors’ laboratories has been funded by the Spanish Agencia Estatal de Investigación and FEDER (grants BFU2016-80621-P and PID2019-110717GB to M.A.B.) and JSPS/MEXT KAKENHI (JP17H07424 and JP19H05675 to T.K.; 20H04884 to R.N.). J.H.-G. and A.S.-M. were supported by a predoctoral fellowship from the Spanish Ministry of Education, Culture and Sport (FPU15/01756) and an MSCA Individual Fellowship (H2020-MSCA-IF-2016-746396), respectively. R.S. was supported by the Japanese Government (MEXT) Scholarship Program.

The role of badges as indicators of contest ability has been previously described. In hummingbirds, the exhibition of a badge is expected to save energy expenditure in agonistic interactions and to favor energy intake. Here, we investigate whether variable supercilium size in the white-eared hummingbird has a role in dominance status signaling. Firstly, 45 hummingbird males were captured and their superciliums were photographed to investigate variation in size and any possible allometric relationships. Secondly, 42 male birds were used to analyze whether the supercilium has a role in dominance status signaling in a dyadic contest. We found that supercilium size varied continuously but that despite variability between individuals, there was no relationship between supercilium size and body size. However, our dyad experiment indicated that birds with larger badges were able to make more visits to the feeders than individuals with smaller badges. We suggest a status signaling function of the supercilium.

Hermit crabs respond to predators by hiding in their shells. However, retraction may cause the crab to lose hold of the rock and fall through the water column, and the crab may land with the shell aperture in a different orientation. When the shell is aperture down, hermit crabs return to activity by moving their bodies forward and placing their legs on the ground. In contrast, when the shell is aperture up, crabs need to perform a righting maneuver by extending part of their bodies out of the shell, which makes them more vulnerable to predation. The main goal of this study was to examine the hiding time of the hermit crab Calcinus californiensis Bouvier, 1898 in different shell species under these two different situations to better understand the conflict between the cost of staying in hiding and the risk of predation. The study was conducted in rocky tide pools using seven different shell types that reflect different predator protection and resource value to the crab (based on previous studies). We measured the time required to perform the righting maneuver as a measure of the potential risk incurred when returning to activity. The hiding time with the shell aperture down was not affected by shell species. The requirement to carry out a righting maneuver lengthened the hiding time, which varied in the different shell species according to the time required to recover the natural position. The potential risks associated with the righting time, the protection offered by the shells, and the resource value played an important role in the hiding time of the crabs using different shells. This study shows that hermit crabs are aware of the attributes of the shell and use this information to make decisions about how long to stay hidden after being threatened.

International audience; Hemipteran insects are well-known in their ability to establish symbiotic relationships with bacteria. Among them, heteropteran insects present an array of symbiotic systems, ranging from the most common gut crypt symbiosis to the more restricted bacteriome-associated endosymbiosis, which have only been detected in members of the superfamily Lygaeoidea and the family Cimicidae so far. Genomic data of heteropteran endosymbionts are scarce and have merely been analyzed from the Wolbachia endosymbiont in bed bug and a few gut crypt-associated symbionts in pentatomoid bugs. In this study, we present the first detailed genomic analysis of a bacteriome-associated endosymbiont of a phytophagous heteropteran, present in the seed bug Henestaris halophilus (Hemiptera: Heteroptera: Lygaeoidea). Using phylogenomics and genomics approaches, we have assigned the newly characterized endosymbiont to the Sodalis genus, named as Candidatus Sodalis baculum sp. nov. strain kilmister. In addition, our findings support the reunification of the Sodalis genus, currently divided into six different genera. We have also conducted comparative analyses between 15 Sodalis species that present different genome sizes and symbiotic relationships. These analyses suggest that Ca. Sodalis baculum is a mutualistic endosymbiont capable of supplying the amino acids tyrosine, lysine, and some cofactors to its host. It has a small genome with pseudogenes but no mobile elements, which indicates middle-stage reductive evolution. Most of the genes in Ca. Sodalis baculum are likely to be evolving under purifying selection with several signals pointing to the retention of the lysine/tyrosine biosynthetic pathways compared with other Sodalis.

Many insects rely on bacterial endosymbionts to obtain nutrients that are scarce in their highly specialized diets. The most surprising example corresponds to the endosymbiotic system found in mealybugs from subfamily Pseudococcinae in which two bacteria, the betaproteobacterium 'Candidatus Tremblaya princeps' and a gammaproteobacterium, maintain a nested endosymbiotic consortium. In the sister subfamily Phenacoccinae, however, a single beta-endosymbiont, 'Candidatus Tremblaya phenacola', has been described. In a previous study, we detected a trpB gene of gammaproteobacterial origin in 'Ca. Tremblaya phenacola' from two Phenacoccus species, apparently indicating an unusual case of horizontal gene transfer (HGT) in a bacterial endosymbiont. What we found by sequencing the genome of 'Ca. Tremblaya phenacola' PPER, single endosymbiont of Phenacoccus peruvianus, goes beyond a HGT phenomenon. It rather represents a genome fusion between a beta and a gammaproteobacterium, followed by massive rearrangements and loss of redundant genes, leading to an unprecedented evolutionary collage. Mediated by the presence of several repeated sequences, there are many possible genome arrangements, and different subgenomic sequences might coexist within the same population.

Hermit crabs recognize different shell attributes and choose shell size, type, or species to maximize their individual fitness. Aquatic hermit crab species commonly prefer relatively heavy shells species in contrast to semi-terrestrial crabs which prefer lighter shells. Lighter shells favor rapid growth and increase individual fitness because larger individ- ual achieve higher success in intra- and inter-individ- ual competition. In this study, we experimentally measured the daily growth of hermit crabs Calcinus californiensis that were forced to occupy four different shell species with different internal volume to mass ratios (IV/M ratio), and whose sequence in preference is known from previous studies (Cantharus ( Stra- monita ( Columbella ( Nerita). The shell with the highest IV/M ratio (Nerita) favored body growth rate, while the relatively heaviest (lowest IV/M ratios) and most preferred shells (Stramonita and Cantharus) hindered body growth. Our results suggest that in this aquatic hermit crab, the benefits of carrying heavy shells that give better predatory protection exceeded the benefits of rapid growth that can be obtained using lighter, thinner, and less protective shells.

Although plumage coloration has been widely used as a model in studies of the evolution of signaling, the role of plumage in intrasexual communication has been less studied, especially in cases of the structural plumage color. The aim of our study was to use choice trials and plumage manipulation to test whether or not the structural blue color of the male Blue Grosbeak (Passerina caerulea) works as a signal of social status. Additionally, we tested whether or not females exploit signals used in aggression between males. If they do, it suggests that plumage coloration is also used in mate choice. In 2007, we captured males and females from two different populations. We performed two choice experiments by manipulating plumage color: (1) a status-signaling experiment, in which a male had to choose one of two other males, and (2) a mate-choice experiment, in which a female had to choose one of two males. Males clearly foraged near less blue birds during their first encounter and on the first day. H...

DELLA proteins are transcriptional regulators present in all land plants which have been shown to modulate the activity of over 100 transcription factors in Arabidopsis, involved in multiple physiological and developmental processes. It has been proposed that DELLAs transduce environmental information to pre-wired transcriptional circuits because their stability is regulated by gibberellins (GAs), whose homeostasis largely depends on environmental signals. The ability of GAs to promote DELLA degradation coincides with the origin of vascular plants, but the presence of DELLAs in other land plants poses at least two questions: what regulatory properties have DELLAs provided to the behavior of transcriptional networks in land plants, and how has the recruitment of DELLAs by GA signaling affected this regulation. To address these issues, we have constructed gene co-expression networks of four different organisms within the green lineage with different properties regarding DELLAs: Arabidopsis thaliana and Solanum lycopersicum (both with GA-regulated DELLA proteins), Physcomitrella patens (with GA-independent DELLA proteins) and Chlamydomonas reinhardtii (a green alga without DELLA), and we have examined the relative evolution of the subnetworks containing the potential DELLA-dependent transcriptomes. Network analysis indicates a relative increase in parameters associated with the degree of interconnectivity in the DELLA-associated subnetworks of land plants, with a stronger effect in species with GA-regulated DELLA proteins. These results suggest that DELLAs may have played a role in the coordination of multiple transcriptional programs along evolution, and the function of DELLAs as regulatory ‘hubs’ became further consolidated after their recruitment by GA signaling in higher plants, We acknowledge support of the publication fee by the CSIC Open Access Support Initiative through its Unit of Information Resources for Research (URICI), Work in the laboratories was funded by grants BFU2016-80621-P and BIO2014-52425-P of the Spanish Ministry of Economy, Industry and Competitiveness, and H2020-MSCA-RISE-2014-644435 of the European Union. AB-M and JH-G hold Fellowships of the Spanish Ministry of Education, Culture and Sport FPU14/01941 and FPU15/01756, respectively.

We report the genome sequence of Exiguobacterium chiriqhucha str. N139, isolated from a high-altitude Andean lake. Comparative genomic analyses of the Exiguobacterium genomes available suggest that our strain belongs to the same species as the previously reported E. pavilionensis str. RW-2 and Exiguobacterium str. GIC 31. We describe this species and propose the chiriqhucha name to group them. ‘Chiri qhucha’ in Quechua means ‘cold lake’, which is a common origin of these three cosmopolitan Exiguobacteria. The 2,952,588-bp E. chiriqhucha str. N139 genome contains one chromosome and three megaplasmids. The genome analysis of the Andean strain suggests the presence of enzymes that confer E. chiriqhucha str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals, high ultraviolet B radiation, scavenging for phosphorous and coping with high salinity. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina. Fil: Gutierrez, Ana. Universidad de Valencia; España Fil: Vargas Chaves, Carlos. Universidad de Valencia; España Fil: Reyes Prieto, Mariana. Universidad de Valencia; España Fil: Ordoñez, Omar Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Planta Piloto de Procesos Industriales Microbiologicos; Argentina Fil: Santos-García, Diego. Universidad de Valencia; España Fil: Rosas-Pérez, Tania. Universidad de Valencia; España Fil: Valdivia-Anistro, Jorge. Universidad de Valencia; España Fil: Rebollar, Eria A.. Universidad Nacional Autónoma de México; México Fil: Saralegui, Andrés. Universidad Nacional Autónoma de México; México Fil: Moya, Andrés. Universidad de Valencia; España Fil: Merino, Enrique. Universidad Nacional Autónoma de México; México Fil: Farias, Maria Eugenia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucuman. Planta Piloto de Procesos Industriales Microbiologicos; Argentina Fil: Latorre, Amparo. Universidad de Valencia; España Fil: Souza, Valeria. Universidad Nacional Autónoma de México; México

In this study we measured two physiological traits (levels of corticosterone and immunoglobulin) in two species of landbirds, the Canyon Towhee (Melozone fusca) and Inca Dove (Columbina inca), occupying three degrees of human alteration of a subtropical mountain landscape: forest edges, croplands, and urban sites. We found that both physiological variables differed by species and habitat condition. In both species, corticosterone concentration was significantly higher in croplands. But immunoglobulin concentration behaved differently, in C. inca being highest at urban sites, where in M. fusca it was lowest. Contrary to expectation, we only found one strong significant relationship between both physiological variables: M. fusca in urban areas. Our results suggest that 30% of the towhees captured in urban areas are under chronic stress. Results for body condition support this hypothesis, as the condition of towhees in urban areas was poorer, suggesting physiological vulnerability. Although we expe...

We report the genome sequence of Exiguobacterium pavilionensis str. N139, isolated from a high-altitude Andean lake. The 2,952,588-bp genome contains one chromosome and three megaplasmids. The genome analysis suggests the presence of enzymes that confer E. pavilionensis str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals and high ultraviolet B radiation. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina .

Urbanization generates human-made habitats with novel resources. Such change is not homegeneous, and includes different urban land uses characterized by specific habitat traits. In this study we explored the ecophysiologial response of an urban-exploiter species in three different urban land uses (urban, suburban, industrial). Our results show that corticosterone (obtained through fecal samples) and immunoglobulin (obtained through blood samples) concentrations did not differ significantly among the studied urban land uses. Corticosterone and immunoglobulin concentration showed both high and low values in urban and suburban areas, while industrial areas had low and high levels of corticosterone, and medium-to-low immunoglobulin concentration values. Also, we found a negative relationship between corticosterone and immunoglobulin concentrations in industrial areas. Based on corticosterone and immunoglobulin concentration thresholds established from previous studies, our results suggest that: (1) birds in the three studied urban conditions are both stressed and non-stressed; and (2) the immune system of industrial House Sparrows could not be responding successfully to pathogens. Not finding physiological relationships in urban and suburban areas underline that this species has a large capacity to respond to the different stress and immune challenges found in urban areas. However, our results suggest that the physiological condition of industrial House Sparrows could be compromised by differences in the frequency and intensity of the stressor agents faced by the birds in this land use category.

Symbiotic relationships occur naturally throughout the tree of life, either in a commensal, mutualistic or pathogenic manner. The genomes of multiple organisms involved in symbiosis are rapidly being sequenced and becoming available, especially those from the microbial world. Currently, there are numerous databases that offer information on specific organisms or models, but none offer a global understanding on relationships between organisms, their interactions and capabilities within their niche, as well as their role as part of a system, in this case, their role in symbiosis. We have developed the SymbioGenomesDB as a community database resource for laboratories which intend to investigate and use information on the genetics and the genomics of organisms involved in these relationships. The ultimate goal of SymbioGenomesDB is to host and support the growing and vast symbiotic-host relationship information, to uncover the genetic basis of such associations. SymbioGenomesDB maintains a comprehensive organization of information on genomes of symbionts from diverse hosts throughout the Tree of Life, including their sequences, their metadata and their genomic features. This catalog of relationships was generated using computational tools, custom R scripts and manual integration of data available in public literature. As a highly curated and comprehensive systems database, SymbioGenomesDB provides web access to all the information of symbiotic organisms, their features and links to the central database NCBI. Three different tools can be found within the database to explore symbiosis-related organisms, their genes and their genomes. Also, we offer an orthology search for one or multiple genes in one or multiple organisms within symbiotic relationships, and every table, graph and output file is downloadable and easy to parse for further analysis. The robust SymbioGenomesDB will be constantly updated to cope with all the data being generated and included in major databases, in order to serve as an important, useful and timesaving tool. Database URL: http://symbiogenomesdb.uv.es.

Background The diagnosis of leprosy is primarily based on clinical manifestations, and there is no widely available laboratory test for the early detection of this disease, which is caused by Mycobacterium leprae. In fact, early detection and treatment are the key elements to the successful control of leprosy. Methodology/Principal Findings Peptide ligands for antibodies from leprosy patients were selected from phage-displayed peptide libraries. Three peptide sequences expressed by reactive phage clones were chemically synthesized. Serological assays that used synthetic peptides were evaluated using serum samples from leprosy patients, household contacts (HC) of leprosy patients, tuberculosis patients and endemic controls (EC). A pool of three peptides identified 73.9% (17/23) of multibacillary (MB) leprosy patients using an enzyme-linked immunosorbent assay (ELISA). These peptides also showed some seroreactivities to the HC and EC individuals. The peptides were not reactive to rabbit polyclonal antisera against the different environmental mycobacteria. The same peptides that were conjugated to the carrier protein bovine serum albumin (BSA) induced the production of antibodies in the mice. The anti-peptide antibodies that were used in the Western blotting analysis of M. leprae crude extracts revealed a single band of approximately 30 kDa in one-dimensional electrophoresis and four 30 kDa isoforms in the two-dimensional gel. The Western blotting data indicated that the three peptides are derived from the same bacterial protein. Conclusions/Significance These new antigens may be useful in the diagnosis of MB leprosy patients. Their potentials as diagnostic reagents must be more extensively evaluated in future studies using a large panel of positive and negative sera. Furthermore, other test approaches using peptides should be assessed to increase their sensitivity and specificity in detecting leprosy patients. We have revealed evidence in support of phage-displayed peptides as promising biotechnological tools for the design of leprosy diagnostic serological assays.

The protozoan Trypanosoma cruzi is the etiologic agent of Chagas disease, an infection that afflicts approximately 8 million people in Latin America. Diagnosis of chronic Chagas disease is currently based on serological tests because this condition is usually characterized by high anti-T. cruzi IgG titers and low parasitemia. The antigens used in these assays may have low specificity due to cross reactivity with antigens from related parasite infections, such as leishmaniasis, and low sensitivity caused by the high polymorphism among T. cruzi strains. Therefore, the identification of new T. cruzi-specific antigens that are conserved among the various parasite discrete typing units (DTUs) is still required. In the present study, we have explored the hybrid nature of the T. cruzi CL Brener strain using a broad genome screening approach to select new T. cruzi antigens that are conserved among the different parasite DTUs and that are absent in other trypanosomatid species. Peptide arrays containing the conserved antigens with the highest epitope prediction scores were synthesized, and the reactivity of the peptides were tested by immunoblot using sera from C57BL/6 mice chronically infected with T. cruzi strains from the TcI, TcII or TcVI DTU. The two T. cruzi proteins that contained the most promising peptides were expressed as recombinant proteins and tested in ELISA experiments with sera from chagasic patients with distinct clinical manifestations: those infected with T. cruzi from different DTUs and those with cutaneous or visceral leishmaniasis. These proteins, named rTc_11623.20 and rTc_N_10421.310, exhibited 94.83 and 89.66% sensitivity, 98.2 and 94.6% specificity, respectively, and a pool of these 2 proteins exhibited 96.55% sensitivity and 98.18% specificity. This work led to the identification of two new antigens with great potential application in the diagnosis of chronic Chagas disease.

Apical membrane antigen 1 (AMA-1) is considered to be a major candidate antigen for a malaria vaccine. Previous immunoepidemiological studies of naturally acquired immunity to Plasmodium vivax AMA-1 (PvAMA-1) have shown a higher prevalence of specific antibodies to domain II (DII) of AMA-1. In the present study, we confirmed that specific antibody responses from naturally infected individuals were highly reactive to both full-length AMA-1 and DII. Also, we demonstrated a strong association between AMA-1 and DII IgG and IgG subclass responses. We analyzed the primary sequence of PvAMA-1 for B cell linear epitopes co-occurring with intrinsically unstructured/disordered regions (IURs). The B cell epitope comprising the amino acid sequence 290–307 of PvAMA-1 (SASDQPTQYEEEMTDYQK), with the highest prediction scores, was identified in domain II and further selected for chemical synthesis and immunological testing. The antigenicity of the synthetic peptide was identified by serological analysis using sera from P. vivax-infected individuals who were knowingly reactive to the PvAMA-1 ectodomain only, domain II only, or reactive to both antigens. Although the synthetic peptide was recognized by all serum samples specific to domain II, serum with reactivity only to the full-length protein presented 58.3% positivity. Moreover, IgG reactivity against PvAMA-1 and domain II after depletion of specific synthetic peptide antibodies was reduced by 18% and 33% (P = 0.0001 for both), respectively. These results suggest that the linear epitope SASDQPTQYEEEMTDYQK is highly antigenic during natural human infections and is an important antigenic region of the domain II of PvAMA-1, suggesting its possible future use in pre-clinical studies.