Multiple invasions of Gypsy and Micropia retroelements in genus Zaprionus and melanogaster subgroup of the genus Drosophila

<p>Abstract</p> <p>Background</p> <p>The <it>Zaprionus </it>genus shares evolutionary features with the <it>melanogaster </it>subgroup, such as space and time of origin. Although little information about the transposable element content in the <it>Zaprionus </it>genus had been accumulated, some of their elements appear to be more closely related with those of the <it>melanogaster </it>subgroup, indicating that these two groups of species were involved in horizontal transfer events during their evolution. Among these elements, the <it>Gypsy </it>and the <it>Micropia </it>retroelements were chosen for screening in seven species of the two <it>Zaprionus </it>subgenera, <it>Anaprionus </it>and <it>Zaprionus</it>.</p> <p>Results</p> <p>Screening allowed the identification of diverse <it>Gypsy </it>and <it>Micropia </it>retroelements only in species of the <it>Zaprionus </it>subgenus, showing that they are transcriptionally active in the sampled species. The sequences of each retroelement were closely related to those of the <it>melanogaster </it>species subgroup, and the most parsimonious hypothesis would be that 15 horizontal transfer events shaped their evolution. The <it>Gypsy </it>retroelement of the <it>melanogaster </it>subgroup probably invaded the <it>Zaprionus </it>genomes about 11 MYA. In contrast, the <it>Micropia </it>retroelement may have been introduced into the <it>Zaprionus </it>subgenus and the <it>melanogaster </it>subgroup from an unknown donor more recently (~3 MYA).</p> <p>Conclusion</p> <p><it>Gypsy </it>and <it>Micropia </it>of <it>Zaprionus </it>and <it>melanogaster </it>species share similar evolutionary patterns. The sharing of evolutionary, ecological and ethological features probably allowed these species to pass through a permissive period of transposable element invasion, explaining the proposed waves of horizontal transfers.</p

Plant degreening: evolution and expression of tomato\ud (Solanum lycopersicum) dephytylation enzymes

Chlorophyll is the most abundant pigment on earth and even though it is known that its high photo-excitability necessitates a tight regulation of its degradation pathway, to date there are still several steps in chlorophyll breakdown that remain obscure. In order to better understand the ‘degreening’ processes that accompany leaf senescence and fruit ripening, we characterized the enzyme-encoding genes involved in dephytylation from tomato (Solanum lycopersicum). A single pheophytinase (PPH) gene and four chlorophyllase (CLH) genes were identified in the tomato genome. A phenetic analysis revealed two groups of CLHs in eudicot species and further evolutionary analysis indicated that these enzymes are under diverse selection pressures. A comprehensive expression profile analysis also suggested functional specificity for these dephytylating enzymes. The integrated analysis allows us to propose three general roles for chlorophyll dephytylation: i) PPH, which is under high selective constraint, is responsible for chlorophyll degradation during developmentally programed physiological processes; ii) Group I CLHs, which are under relaxed selection constraint, respond to environmental and hormonal stimuli and play a role in plant adaptation plasticity; and iii) Group II CLHs, which are also under high selective constraint, are mostly involved in chlorophyll recycling.BSL and JA were recipients of FAPESP fellowships and MR was funded by a fellowship from CNPq. This work was supported by FAPESP2012-12531-8 (Brazil). The authors thank Rohm and Haas Company for generous donation of the 1-methylcyclopropene (SmartFresh®) used for the experiments

Functional and comparative analysis of THI1 gene in grasses with a focus on sugarcane

De novo synthesis of thiamine (vitamin B1) in plants depends on the action of thiamine thiazole synthase, which synthesizes the thiazole ring, and is encoded by the THI1 gene. Here, we investigated the evolution and diversity of THI1 in Poaceae, where C4 and C3 photosynthetic plants co-evolved. An ancestral duplication of THI1 is observed in Panicoideae that remains in many modern monocots, including sugarcane. In addition to the two sugarcane copies (ScTHI1-1 and ScTHI1-2), we identified ScTHI1-2 alleles showing differences in their sequence, indicating divergence between ScTHI1-2a and ScTHI1-2b. Such variations are observed only in the Saccharum complex, corroborating the phylogeny. At least five THI1 genomic environments were found in Poaceae, two in sugarcane, M. sinensis, and S. bicolor. The THI1 promoter in Poaceae is highly conserved at 300 bp upstream of the start codon ATG and has cis-regulatory elements that putatively bind to transcription factors associated with development, growth, development and biological rhythms. An experiment set to compare gene expression levels in different tissues across the sugarcane R570 life cycle showed that ScTHI1-1 was expressed mainly in leaves regardless of age. Furthermore, ScTHI1 displayed relatively high expression levels in meristem and culm, which varied with the plant age. Finally, yeast complementation studies with THI4-defective strain demonstrate that only ScTHI1-1 and ScTHI1-2b isoforms can partially restore thiamine auxotrophy, albeit at a low frequency. Taken together, the present work supports the existence of multiple origins of THI1 harboring genomic regions in Poaceae with predicted functional redundancy. In addition, it questions the contribution of the levels of the thiazole ring in C4 photosynthetic plant tissues or potentially the relevance of the THI1 protein activity

Complication of acute Otitis media in pediatrics: a case report: Complicação de Otite média aguda em pediatria: um relato de caso

The acute otitis media (AOM) is a frequent bacterial infection in Pediatrics. Despite the advance of antibiotic therapy in the treatment of this infection, there is the possibility of a rare complication, Gradenigo Syndrome (GS). This is a serious complication that should be suspected in a patient with abducens nerve paralysis, pain in the trigeminal innervation area and AOM. The objective of this work was to describe a case report in pediatric regarding to Gradenigo’s Syndrome and reinforce the importance of early diagnosis in the treatment. In addition, a literature review of articles in journals indexed in the following databases was carried out: Pubmed, Lilacs and Scielo. The case report presented is a 7-year-old girl, presenting a typical clinical of GS that evolved satisfactorily with the management based on broad-spectrum antibiotic therapy, without the need for a subsequent surgical approach. Thus, it is clear that the identification of the classic triad of GS, in addition to performing imaging tests, allows for an early diagnosis of the disease, favoring a conservative approach with antibiotic therapy

Estimating genomic instability mediated by Alu retroelements in breast cancer

Alu-PCR is a relatively simple technique that can be used to investigate genomic instability in cancer. This technique allows identification of the loss, gain or amplification of gene sequences based on the analysis of segments between two Alu elements coupled with quantitative and qualitative analyses of the profiles obtained from tumor samples, surgical margins and blood. In this work, we used Alu-PCR to identify gene alterations in ten patients with invasive ductal breast cancer. Several deletions and insertions were identified, indicating genomic instability in the tumor and adjacent normal tissue. Although not associated with specific genes, the alterations, which involved chromosomal bands 1p36.23, 1q41, 11q14.3, 13q14.2, occurred in areas of well-known genomic instability in breast and other types of cancer. These results indicate the potential usefulness of Alu-PCR in identifying altered gene sequences in breast cancer. However, caution is required in its application since the Alu primer can produce non-specific amplification

Elementos de transposição no gênero Zaprionus (Diptera, Drosophilidae): estudos genômicos e evolutivos em ênfase nos retrotensposons copia, gypsy e micropia

O gênero Zaprionus tem sido eleito como um bom modelo biológico para estudos genéticocomparativos com as espécies do subgrupo melanogaster do gênero Drosophila, embora seu posicionamento filogenético dentro da família Drosophilidae ainda seja controverso. Na presente Tese foi investigada a presença de 10 elementos de transposição (TEs) em Zaprionus indianus e Drosophila malerkotliana, bem como a distribuição, a atividade transcricional e as relações evolutivas de três retrotransposons (copia, gypsy e micropia) em sete espécies do gênero Zaprionus. Para isso, foram empregadas as técnicas de Dot blot, PCR, RT-PCR e seqüenciamento. As seqüências obtidas foram comparadas às dos respectivos elementos das demais espécies de drosofilídeos disponíveis nas bases de dados genômicas. Os resultados indicam que Z. indianus e D. malerkotliana apresentam em seus genomas todos os TEs de D. melanogaster investigados. O retrotransposon copia foi seqüenciado e está transcricionalmente ativo nas sete espécies do gênero Zaprionus e constitui uma nova subfamília relacionada aos elementos do subgrupo melanogaster, que foi denominada subfamília GBFDouble-gap. Por outro lado, os retrotransposons gypsy e micropia foram identificados nas espécies do subgênero Zaprionus, onde também estão transcricionalmente ativos, e pertencem às subfamílias já descritas para as espécies do subgrupo melanogaster. As análises evolutivas sugeriram que esses três retrotransposons devem ter participado de eventos de transferência horizontal com as espécies do subgrupo melanogaster e com pelo menos um doador desconhecido, no caso do retrotransposon micropia. Além disso, o cálculo dos tempos de divergência dos elementos sugere que eles passaram por ondas de transferências horizontais, mais antigas para o retrotransposon copia, e mais recentes para gypsy e micropia. Esses resultados...The Zaprionus genus has been elected as a good biological model for comparative analyses with the melanogaster subgroup of Drosophila genus, though its phylogenetic positioning within the Drosophilidae family is still controversial. This study aiming at investigating the occurrence of 10 transposable elements (TEs) in Zaprionus indianus and Drosophila malerkotliana species, as well the distribution, transcriptional activity and evolutionary relationships of three retrotransposons (copy, gypsy and micropia) in seven species of Zaprionus genus. To do so, Dot blot, PCR, RT-PCR and sequencing methods were employed. The Zaprionus sequences obtained were compared with the drosophilid sequences available in genomic databases. The results indicated that Z. indianus and D. malerkotliana harbor all D. melanogaster TEs investigated. The copia retrotransposon is present and transcriptionally active in seven species of the Zaprionus genus and represents a new subfamily related to that of the melanogaster subgroup, named as GBFDouble-gap subfamily. Additionally, gypsy and micropia retrotransposons were identified in the Zaprionus species subgenus, which are transcriptionally active and belong to the melanogaster subgroup subfamilies. The evolutionary analysis showed the three retrotransposons could have been involved in horizontal transfer events with species of the melanogaster subgroup for the three retrotransposons and at least one unknown donor regarding to micropia retrotransposon. Moreover, the time of divergence seems to indicate that the retrotransposons experienced horizontal transfer waves, the oldest involving the copia element followed by the gypsy and micropia retrotransposons in more recent times. These results suggest that the horizontal transfer phenomenon has happened repeatedly during the Zaprionus genus and melanogaster subgroup evolution in the Afrotropical region.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Fitness components of a recently-established population of Zaprionus indianus (Diptera, Drosophilidae) in Brazil

Neste estudo foram avaliados componentes do valor adaptativo de Zaprionus indianus Gupta, 1970, uma espécie recentemente introduzida no Brasil e, atualmente, em processo de colonização de praticamente todas as regiões brasileiras. Foram avaliadas a longevidade, a produtividade, a velocidade de desenvolvimento e a viabilidade de indivíduos amostrados de uma população de Mirassol (estado de São Paulo, Brasil). A longevidade foi maior do que aquelas registradas em populações indianas, enquanto que a produtividade foi similar ou maior do que a observada em outros Drosophilidae. O tempo de desenvolvimento, um dos principais componentes relacionados à habilidade competitiva, foi muito similar aos valores registrados para Drosophila sturtevanti Duda, 1927, espécie que ocorre em alta freqüência na mesma área que Z. indianus. Esses dados podem contribuir para o entendimento do sucesso de colonização desta espécie recém-introduzida na América do Sul.This study aimed to evaluate fitness components of Zaprionus indianus Gupta, 1970, a species recently introduced in Brazil and currently in process of colonization. Longevity, productivity, developmental speed and viability of flies sampled from a population from Mirassol (state of São Paulo, Brazil) were evaluated. Longevity was higher than that of some Indian populations and productivity was similar or higher than in other Drosophilidae. Time of development, one of the main fitness components for competition, was very similar to the values scored in Drosophila sturtevanti Duda, 1927, a species that occurs in high frequencies in the same area as Z. indianus. These data might contribute further for understanding the colonization success of this newcomer species in South America.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Drought Responses in Poaceae: Exploring the Core Components of the ABA Signaling Pathway in <i>Setaria italica</i> and <i>Setaria viridis</i>

Drought severely impacts plant development and reproduction, reducing biomass and seed number, and altering flowering patterns. Drought-tolerant Setaria italica and Setaria viridis species have emerged as prominent model species for investigating water deficit responses in the Poaceae family, the most important source of food and biofuel biomass worldwide. In higher plants, abscisic acid (ABA) regulates environmental stress responses, and its signaling entails interactions between PYR/PYL/RCAR receptors and clade A PP2C phosphatases, which in turn modulate SnRK2 kinases via reversible phosphorylation to activate ABA-responsive genes. To compare the diversity of PYR/PYL/RCAR, PP2C, and SnRK2 between S. italica and S. viridis, and their involvement in water deficit responses, we examined gene and regulatory region structures, investigated orthology relationships, and analyzed their gene expression patterns under water stress via a meta-analysis approach. Results showed that coding and regulatory sequences of PYR/PYL/RCARs, PP2Cs, and SnRK2s are highly conserved between Setaria spp., allowing us to propose pairs of orthologous genes for all the loci identified. Phylogenetic relationships indicate which clades of Setaria spp. sequences are homologous to the functionally well-characterized Arabidopsis thaliana PYR/PYL/RCAR, PP2C, and SnRK2 genes. Gene expression analysis showed a general downregulation of PYL genes, contrasting with upregulation of PP2C genes, and variable expression modulation of SnRK2 genes under drought stress. This complex network implies that ABA core signaling is a diverse and multifaceted process. Through our analysis, we identified promising candidate genes for further functional characterization, with great potential as targets for drought resistance studies, ultimately leading to advances in Poaceae biology and crop-breeding strategies