Examining Ancient Inter-domain Horizontal Gene Transfer

Details of the genomic changes that occurred in the ancestors of Eukarya, Archaea and Bacteria are elusive. Ancient interdomain horizontal gene transfer (IDHGT) amongst the ancestors of these three domains has been difficult to detect and analyze because of the extreme degree of divergence of genes in these three domains and because most evidence for such events are poorly supported. In addition, many researchers have suggested that the prevalence of IDHGT events early in the evolution of life would most likely obscure the patterns of divergence of major groups of organisms let alone allow the tracking of horizontal transfer at this level. In order to approach this problem, we mined the E. coli genome for genes with distinct paralogs. Using the 1,268 E. coli K-12 genes with 40% or higher similarity level to a paralog elsewhere in the E. coli genome we detected 95 genes found exclusively in Bacteria and Archaea and 86 genes found in Bacteria and Eukarya. These genes form the basis for our analysis of IDHGT. We also applied a newly developed statistical test (the node height test), to examine the robustness of these inferences and to corroborate the phylogenetically identified cases of ancient IDHGT. Our results suggest that ancient inter domain HGT is restricted to special cases, mostly involving symbiosis in eukaryotes and specific adaptations in prokaryotes. Only three genes in the Bacteria + Eukarya class (Deoxyxylulose-5-phosphate synthase (DXPS), fructose 1,6-phosphate aldolase class II protein and glucosamine-6-phosphate deaminase) and three genes–in the Bacteria + Archaea class (ABC-type FE3+-siderophore transport system, ferrous iron transport protein B, and dipeptide transport protein) showed evidence of ancient IDHGT. However, we conclude that robust estimates of IDHGT will be very difficult to obtain due to the methodological limitations and the extreme sequence saturation of the genes suspected of being involved in IDHGT

Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta

Manduca sexta, known as the tobacco hornworm or Carolina sphinx moth, is a lepidopteran insect that is used extensively as a model system for research in insect biochemistry, physiology, neurobiology, development, and immunity. One important benefit of this species as an experimental model is its extremely large size, reaching more than 10 g in the larval stage. M. sexta larvae feed on solanaceous plants and thus must tolerate a substantial challenge from plant allelochemicals, including nicotine. We report the sequence and annotation of the M. sexta genome, and a survey of gene expression in various tissues and developmental stages. The Msex_1.0 genome assembly resulted in a total genome size of 419.4 Mbp. Repetitive sequences accounted for 25.8% of the assembled genome. The official gene set is comprised of 15,451 protein-coding genes, of which 2498 were manually curated. Extensive RNA-seq data from many tissues and developmental stages were used to improve gene models and for insights into gene expression patterns. Genome wide synteny analysis indicated a high level of macrosynteny in the Lepidoptera. Annotation and analyses were carried out for gene families involved in a wide spectrum of biological processes, including apoptosis, vacuole sorting, growth and development, structures of exoskeleton, egg shells, and muscle, vision, chemosensation, ion channels, signal transduction, neuropeptide signaling, neurotransmitter synthesis and transport, nicotine tolerance, lipid metabolism, and immunity. This genome sequence, annotation, and analysis provide an important new resource from a well-studied model insect species and will facilitate further biochemical and mechanistic experimental studies of many biological systems in insect

Insights into the 3D In Vitro Permeability and In Vivo Antioxidant Protective Effects of Kiwiberry Leaf Extract: A Step Forward to Human Nutraceutical Use

Actinidia arguta (Siebold & Zucc.) Planch. ex Miq. (kiwiberry) leaves are a source of phenolic compounds with pro-health biological effects, such as antioxidant and anti-inflammatory activities. Despite the huge number of studies reporting the composition of A. arguta leaves, no in vitro or in vivo studies explore its potential use as nutraceutical ingredient based on these activities. Therefore, this study aims to characterize the safety profile of kiwiberry leaf extracts using in vitro and in vivo approaches through the assessment of intestinal cell viability (Caco-2 and HT29-MTX), 3D intestinal permeation, and, most important, the redox markers, biochemical profile and liver and kidney function effects after the animal assays. Briefly, wistar rats were orally treated for 7 days with kiwiberry leaf extracts (50 and 75 mg/kg bw), water (negative control), or vitamin C (positive control). The cell viability was above 90% at 1000 μg/mL for both cells. Coumaroyl quinic acid and rutin achieved a permeation higher than 25% in the 3D intestinal model. The animal studies confirmed the extracts’ ability to increase superoxide dismutase, glutathione peroxidase, and catalase content in animals’ livers and kidneys while simultaneously decreasing the triglycerides content. This study highlighted the antioxidant capacity of kiwiberry leaf extracts, ensuring their efficacy and safety as a nutraceutical ingredientThis research was funded by project EXPL/BAA-GR/0663/2021—Kiwi4Health—Exploring the Eco-Innovative Re-Use of Kiwiberry, supported by national funds by FCT/MCTES and by the projects UIDB/50006/2020 and UIDP/50006/2020 through national funds. This work was also financed by national funds from FCT—Fundação para a Ciência e a Tecnologia, I.P., in the scope of the project UIDP/04378/2020 and UIDB/04378/2020 of the Research Unit on Applied Molecular Biosciences—UCIBIO and the project LA/P/0140/2020 of the Associate Laboratory Institute for Health and Bioeconomy—i4HB. The authors are thankful to Minikiwi Land for the samples and all availability during this work. Ana Margarida Silva is thankful for the Ph.D. grant (SFRH/BD/144994/2019) financed by POPH-QREN and subsidized by the European Science Foundation and Ministério da Ciência, Tecnologia e Ensino Superior. Francisca Rodrigues (CEECIND/01886/2020) is thankful for her contract financed by FCT/MCTES—CEEC Individual Program Contract.info:eu-repo/semantics/publishedVersio

Comparative analysis of tissue-specific transcriptomes in the funnel-web spider Macrothele calpeiana (Araneae, Hexathelidae)

Altres ajuts: Beatriu de Pinós (Generalitat de Catalunya, 2010BP-A 00438 i 2010BP-B 00175)The funnel-web spider Macrothele calpeiana is a charismatic Mygalomorph with a great interest in basic, applied and translational research. Nevertheless, current scarcity of genomic and transcriptomic data of this species clearly limits the research in this non-model organism. To overcome this limitation, we launched the first tissue-specific enriched RNA-seq analysis in this species using a subtractive hybridization approach, with two main objectives, to characterize the specific transcriptome of the putative chemosensory appendages (palps and first pair of legs), and to provide a new set of DNA markers for further phylogenetic studies. We have characterized the set of transcripts specifically expressed in putative chemosensory tissues of this species, much of them showing features shared by chemosensory system genes. Among specific candidates, we have identified some members of the iGluR and NPC2 families. Moreover, we have demonstrated the utility of these newly generated data as molecular markers by inferring the phylogenetic position M. calpeina in the phylogenetic tree of Mygalomorphs. Our results provide novel resources for researchers interested in spider molecular biology and systematics, which can help to expand our knowledge on the evolutionary processes underlying fundamental biological questions, as species invasion or biodiversity origin and maintenance

Caracterização experimental do desempenho térmico de escolas antes e após a reabilitação

A grande maioria das escolas portuguesas caracteriza-se por um desconforto higrotérmico assinalável, em condições de serviço, resultante das características construtivas da envolvente, do perfil de ocupação das salas de aula e da falta de recursos financeiros para a gestão das escolas. Existem também muitos edifícios escolares degradados que irão exigir intervenções num futuro próximo. Nesse sentido, é necessário encontrar tecnologias construtivas que, atendendo à realidade climática, económica e cultural, conduzam a soluções com desempenho higrotérmico e conforto adequados. Existem em Portugal cerca de 100 escolas do modelo Brandão não reabilitadas. Atualmente, estão a ser efetuadas medições in situ de temperatura, humidade relativa, concentração de CO2 e consumos energéticos numa sala de aula de um edifício escolar Brandão localizado no Porto (sala protótipo). Esta monitorização tem como objetivo avaliar as condições destas escolas em serviço. No âmbito deste estudo, implementaram-se algumas medidas de reabilitação na sala de aula protótipo, nomeadamente na envolvente (isolamento da cobertura e proteções solares) e nos sistemas técnicos (ventilação e aquecimento), com o objetivo de encontrar um modelo otimizado que possa ser replicado em futuras intervenções. Nesta comunicação apresentam-se os resultados experimentais do desempenho térmico de uma sala tipo, antes da introdução de medidas de reabilitação, que caracterizam as escolas Brandão não reabilitadas, em serviço, e que permitem quantificar o desconforto durante o período de ocupação. Apresentam-se igualmente os resultados após a introdução das medidas de reabilitação e as correspondentes alterações no comportamento térmico do espaço e no conforto térmico dos utilizadores. Desenvolveram-se ainda indicadores de desconforto que facilitam o estudo comparativo de diferentes soluções de reabilitação.Este trabalho foi financiado por: Projeto POCI-01-0145-FEDER-007457 - CONSTRUCT - Instituto de I&D em Estruturas e Construções - financiado pelo Fundo Europeu de Desenvolvimento Regional (FEDER), através do COMPETE2020 – Programa Operacional Competitividade e Internacionalização (POCI) e por fundos nacionais através da Fundação para a Ciência e a Tecnologia I.P.; Bolsa FCT PD/BD/52658/2014.info:eu-repo/semantics/publishedVersio

Non-canonical Wnt signaling regulates junctional mechanocoupling during angiogenic collective cell migration

© 2019, Carvalho et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.Morphogenesis of hierarchical vascular networks depends on the integration of multiple biomechanical signals by endothelial cells, the cells lining the interior of blood vessels. Expansion of vascular networks arises through sprouting angiogenesis, a process involving extensive cell rearrangements and collective cell migration. Yet, the mechanisms controlling angiogenic collective behavior remain poorly understood. Here, we show this collective cell behavior is regulated by non-canonical Wnt signaling. We identify that Wnt5a specifically activates Cdc42 at cell junctions downstream of ROR2 to reinforce coupling between adherens junctions and the actin cytoskeleton. We show that Wnt5a signaling stabilizes vinculin binding to alpha-catenin, and abrogation of vinculin in vivo and in vitro leads to uncoordinated polarity and deficient sprouting angiogenesis in Mus musculus. Our findings highlight how non-canonical Wnt signaling coordinates collective cell behavior during vascular morphogenesis by fine-tuning junctional mechanocoupling between endothelial cells.Research was supported by European Research Council starting grant (679368), the H2020-Twinning grant (692322), the Fundação para a Ciência e a Tecnologia funding (grants: IF/00412/2012; EXPL-BEX-BCM-2258–2013; PRECISE-LISBOA-01–0145-FEDER-016394; UID/BIM/50005/2019, a project funded by Fundação para a Ciência e a Tecnologia (FCT)/ Ministério da Ciência,Tecnologia e Ensino Superior (MCTES) through Fundos do Orçamento de Estado; and a grant from the Fondation Leducq (17CVD03); and personal fellowships: BD/52224/2013​​ to JRC, BD/105856/2014 to PB, and BD/128375/2017 to CF) and LISBOA-01–0145-FEDER-007391, project cofunded by FEDER, through POR Lisboa 2020 - Programa Operacional Regional de Lisboa, PORTUGAL 2020, and Fundação para a Ciência e a Tecnologia.info:eu-repo/semantics/publishedVersio

Comparative genomics uncovers unique gene turnover and evolutionary rates in a gene family involved in the detection of insect cuticular pheromones

Chemoreception is an essential process for the survival and reproduction of animals. Many of the proteins responsible for recognizing and transmitting chemical stimuli in insects are encoded by genes that are members of moderately sized multigene families. The members of the CheB family are specialized in gustatory-mediated detection of long-chain hydrocarbon pheromones in Drosophila melanogaster and play a central role in triggering and modulating mating behavior in this species. Here, we present a comprehensive comparative genomic analysis of the CheB family across 12 species of the Drosophila genus. We have identified a total of 102 new CheB genes in the genomes of these species, including a functionally divergent member previously uncharacterized in D. melanogaster. We found that, despite its relatively small repertory size, the CheB family has undergone multiple gain and loss events and various episodes of diversifying selection during the divergence of the surveyed species. Present estimates of gene turnover and coding sequence substitution rates show that this family is evolving faster than any known Drosophila chemosensory family. To date, only other insect gustatory-related genes among these families had shown evolutionary dynamics close to those observed in CheBs. Our findings reveal the high adaptive potential of molecular components of the gustatory system in insects and anticipate a key role of genes involved in this sensory modality in species adaptation and diversification

Multi-biologic group analysis for an ecosystem response to longitudinal river regulation gradients

This work assesses the effects of river regulation on the diversity of different instream and riparian biological communities along a relieve gradient of disturbance in regulated rivers. Two case studies in Portugal were used, with different river regulation typology (downstream of run-of-river and reservoir dams), where regulated and free-flowing river stretches were surveyed for riparian vegetation, macrophytes, bryophytes, macroalgae, diatoms and macroinvertebrates. The assessment of the regulation effects on biological communities was approached by both biological and functional diversity analysis. Results of this investigation endorse river regulation as a major factor differentiating fluvial biological communities through an artificial environmental filtering that governs species assemblages by accentuating species traits related to river regulation tolerance. Communities' response to regulation gradient seem to be similar and insensitive to river regulation typology. Biological communities respond to this regulation gradient with different sensibilities and rates of response, with riparian vegetation and macroinvertebrates being the most responsive to river regulation and its gradient. Richness appears to be the best indicator for general fluvial ecological quality facing river regulation. Nevertheless, there are high correlations between the biological and functional diversity indices of different biological groups, which denotes biological connections indicative of a cascade of effects leading to an indirect influence of river regulation even on non-responsive facets of communities' biological and functional diversities. These results highlight the necessary holistic perspective of the fluvial system when assessing the effects of river regulation and the proposal of restoration measures.publishe

Positive selection in extra cellular domains in the diversification of Strigamia maritima chemoreceptors

The recent publication of a centipede (Strigamia maritima) genome has revealed that most members of the chemosensory gene families of ionotropic (IR) and gustatory (GR) receptors do not have identifiable orthologs in insect species. In other words, the diversity of these chemoreceptors in centipedes appears to have evolved after its split from other arthropod lineages. Here we investigate the role of adaptive evolution in S. maritima chemoreceptor diversification using an approach that allows us to discuss functional aspects of such diversification. We applied codon substitution models in a phylogenetic framework to obtain the distribution of selective constraints across the different domains in the IR and GR proteins, and to assess the impact of positive selection in the evolution of these chemoreceptors. We found low selective constraints in most IR and GR duplicates and significant evidence for the presence of positively selected amino acids in 2 of the 4 IR, and in 6 of the GR recent specific expansions. Mapping the sites with high posterior probability of positive selection in protein structure revealed a remarkable uneven distribution of fast-evolving sites across protein domains. Most of these sites are located in extracellular fragments of these receptors, which likely participate in ligand recognition. We hypothesize that adaptive evolution in ligand-binding domains was a major force driving the functional diversification of centipede chemoreceptors

Family Size Evolution in Drosophila Chemosensory Gene Families: A Comparative Analysis with a Critical Appraisal of Methods

Gene turnover rates and the evolution of gene family sizes are important aspects of genome evolution. Here, we use curated sequence data of the major chemosensory gene families from Drosophila-the gustatory receptor, odorant receptor, ionotropic receptor, and odorant-binding protein families-to conduct a comparative analysis among families, exploring different methods to estimate gene birth and death rates, including an ad hoc simulation study. Remarkably, we found that the state-of-the-art methods may produce very different rate estimates, which may lead to disparate conclusions regarding the evolution of chemosensory gene family sizes in Drosophila. Among biological factors, we found that a peculiarity of D. sechellia's gene turnover rates was a major source of bias in global estimates, whereas gene conversion had negligible effects for the families analyzed herein. Turnover rates vary considerably among families, subfamilies, and ortholog groups although all analyzed families were quite dynamic in terms of gene turnover. Computer simulations showed that the methods that use ortholog group information appear to be the most accurate for the Drosophila chemosensory families. Most importantly, these results reveal the potential of rate heterogeneity among lineages to severely bias some turnover rate estimation methods and the need of further evaluating the performance of these methods in a more diverse sampling of gene families and phylogenetic contexts. Using branch-specific codon substitution models, we find further evidence of positive selection in recently duplicated genes, which attests to a nonneutral aspect of the gene birth-and-death process