Stakeholder analysis in the portuguese artificial reef context: winners and losers

Nesta análise de intervenientes relativa ao programa de recifes artificiais (RAs) localizado na costa do Algarve (Sul de Portugal continental) foram identificados 21 grupos de atores distintos. Os intervenientes foram classificados em 3 grupos: primários, secundários e externos. Verificou-se que o interesse dos intervenientes face às estruturas recifais (interação) pode ser do tipo privado, público ou cooperativo. Na análise foram identificados os impactos do projeto sobre os intervenientes e o poder destes para influenciar os resultados do programa recifal. Foram definidas quais as interações e possíveis atitudes e comportamento dos intervenientes em relação aos RAs. Finalmente, todos os grupos de intervenientes foram classificados de acordo com o grau de envolvimento esperado ao longo das diferentes fases do programa recifal. O propósito desta análise de intervenientes foi identificar ganhadores e perdedores relacionados com a criação dos recifes artificiais. Verificou-se que a maioria dos grupos de intervenientes pode ser afetado positivamente, mas existem quatro grupos supostamente afetados negativamente. Contudo, acredita-se que estes últimos não constituem um risco sério ao desenvolvimento do programa recifal no decurso do seu tempo de vida.In this stakeholder analysis related to the artificial reef (AR) program located in the Algarve (Southern Portugal mainland) 21 different stakeholder clusters were identified. Stakeholders were classified as primary, secondary and external. It was found that stakeholder interaction with the structures can be of private, public or cooperative interest. In the analysis there were also identified and mapped the impact of the program on stakeholders and their power to influence the ARs' outcomes. Stakeholders' interactions with the ARs were studied, along with their likely attitudes and behavior towards the man-made structures. Finally, all stakeholder clusters were classified according to their expected degree of involvement throughout the different AR stages. The purpose of this stakeholder analysis was to find out winners and losers connected with the reef deployment. It was found that most stakeholder clusters were affected positively, but also four clusters affected negatively. However, it is believed that those that may be affected negatively do not pose a serious threat to the expected AR development along its lifetime

Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris)

Supplementary information is available for this paper at https://doi.org/10.1038/s41598-020-76012-6.The first genome of Vitis vinifera vinifera (PN40024), published in 2007, boosted grapevine related studies. While this reference genome is a suitable tool for the overall studies in the field, it lacks the ability to unveil changes accumulated during V. v. vinifera domestication. The subspecies V. v. sylvestris preserves wild characteristics, making it a good material to provide insights into V. v. vinifera domestication. The difference in the reproductive strategy between both subspecies is one of the characteristics that set them apart. While V. v. vinifera flowers are hermaphrodite, V. v. sylvestris is mostly dioecious. In this paper, we compare the re-sequencing of the genomes from a male and a female individual of the wild sylvestris, against the reference vinifera genome (PN40024). Variant analysis reveals a low number but with high impact modifications in coding regions, essentially non-synonymous single nucleotide polymorphisms and frame shifts caused by insertions and deletions. The sex-locus was manually inspected, and the results obtained are in line with the most recent works related with wild grapevine sex. In this paper we also describe for the first time RNA editing in transcripts of 14 genes in the sex-determining region, including VviYABBY and VviPLATZ.Tis work was supported by Fundação para a Ciência e Tecnologia (FCT) through the Research Center LEAF (UIDP/04129/2020). Authors JLCoito, MJNRamos, MRocheta, were funded by FCT fellowships SFRH/ BD/85824/2012 and CEECIND2017, SFRH/BD/110274/2015, SFRH/BPD/64905/2009, respectively

Registering the evolutionary history in individual-based models of speciation

Understanding the emergence of biodiversity patterns in nature is a central problem in biology. Theoretical models of speciation have addressed this question in the macroecological scale, but little has been done to connect microevolutionary processes with macroevolutionary patterns. Knowledge of the evolutionary history allows the study of patterns underlying the processes being modeled, revealing their signatures and the role of speciation and extinction in shaping macroevolutionary patterns. In this paper we introduce two algorithms to record the evolutionary history of populations and species in individual-based models of speciation, from which genealogies and phylogenies can be constructed. The first algorithm relies on saving ancestor–descendant relationships, generating a matrix that contains the times to the most recent common ancestor between all pairs of individuals at every generation (the Most Recent Common Ancestor Time matrix, MRCAT). The second algorithm directly records all speciation and extinction events throughout the evolutionary process, generating a matrix with the true phylogeny of species (the Sequential Speciation and Extinction Events, SSEE). We illustrate the use of these algorithms in a spatially explicit individual-based model of speciation. We compare the trees generated via MRCAT and SSEE algorithms with trees inferred by methods that use only genetic distance between individuals of extant species, commonly used in empirical studies and applied here to simulated genetic data. Comparisons between trees are performed with metrics describing the overall topology, branch length distribution and imbalance degree. We observe that both MRCAT and distance-based trees differ from the true phylogeny, with the first being closer to the true tree than the second.Facultad de Ciencias Naturales y Muse

Cadernos escolares como patrimônio da educação brasileira

Disponível em: http://acervo.ghemat.com.br/index.php/ACERVO-GHEMAT/article/view/13Os cadernos escolares se constituem como produto de uma cultura escolar, raramente catalogados e inventariados, mas carregam vestígios do ensino brasileiro. Este artigo tem como objetivo elucidar os cadernos escolares como um patrimônio da educação brasileira, assim como divulgar um acervo digital e público para pesquisas históricas. Como referencial teórico metodológico, adotam-se os estudos de Viñao (2008), Peres (2017), Chartier (2002) e Mignot (2008) para tratar dos cadernos escolares, e de Julia (2001) acerca da cultura escolar. Apresentam-se resultados de duas pesquisas desenvolvidas no âmbito do Grupo de Pesquisa de História da Educação Matemática (GHEMAT) que tomaram como universo de amostras, presentes no Repositório de Conteúdo Digital (RCD), 371 cadernos, produzidos entre 1915 e 2009. A partir de estudos e análises realizadas em um caderno de aluno (1968) e um caderno de normalista (1950), infere-se que os cadernos sejam considerados como um patrimônio da educação brasileira

Husbandry or Hunting? Prospects for Co-managed Fisheries Based on Artificial Reefs in the Algarve (Portugal)

Fisheries exploited under open-access conditions create externalities, resulting in a range of problems associated with over-capitalisation and stock depletion. One answer to this is to shift the mode of production away from hunting and towards husbandry, an approach which becomes feasible where some control can be exercised over the resource and the harvesting pressure to which it is subject. Physical structures in the form of artificial reefs make such control a practical possibility, but the way these might be managed so as to support a sustainable fishery is by no means obvious. To investigate this further, the views of commercial fishermen who use the artificial reefs in the Algarve region of Portugal were canvassed and their opinions sought specifically on the prospects for co-management. In general, it was found that for each of the three different geographical areas where the ARs were deployed, there were different views on the establishment of management measures. The reasons for this may be related to the fact that each skipper had different incentives, once they were subjected to different fishing conditions (e.g. target species, fishing area and hauls, gear, vessel, crew, etc). Different fishing incentives reflect no consensual agreements in terms of possible management measures to adopt. However, a trade-off solution could be obtained for both area closure and users, and the use of scientific expertise consultancy (e.g. weight-length studies for the target species found in each reef area) could help managers in the establishment of an adequate measure to be adopted for the season closure option

RNA editing in inflorescences of wild grapevine unveils association to sex and development

RNA editing challenges the central dogma of molecular biology, by modifying the genetic information at the transcription level. Recent reports, suggesting increased levels of RNA editing in plants, raised questions on the nature and dynamics of such events during development. We here report the occurrence of distinct RNA editing patterns in wild Vitis flowers during development, with twelve possible RNA editing modifications observed for the first time in plants. RNA editing events are gender and developmental stage specific, identical in subsequent years of this perennial species and with distinct nucleotide frequencies neighboring editing sites on the 5' and 3' flanks. The transcriptome dynamics unveils a new regulatory layer responsible for gender plasticity enhancement or underling dioecy evolution in Vitis

RBCS1 expression in coffee: Coffea orthologs, Coffea arabica homeologs, and expression variability between genotypes and under drought stress

Background: In higher plants, the inhibition of photosynthetic capacity under drought is attributable to stomatal and non-stomatal (i.e., photochemical and biochemical) effects. In particular, a disruption of photosynthetic metabolism and Rubisco regulation can be observed. Several studies reported reduced expression of the RBCS genes, which encode the Rubisco small subunit, under water stress. Results: Expression of the RBCS1 gene was analysed in the allopolyploid context of C. arabica, which originates from a natural cross between the C. canephora and C. eugenioides species. Our study revealed the existence of two homeologous RBCS1 genes in C. arabica: one carried by the C. canephora sub-genome (called CaCc) and the other carried by the C. eugenioides sub-genome (called CaCe). Using specific primer pairs for each homeolog, expression studies revealed that CaCe was expressed in C. eugenioides and C. arabica but was undetectable in C. canephora. On the other hand, CaCc was expressed in C. canephora but almost completely silenced in non-introgressed ("pure") genotypes of C. arabica. However, enhanced CaCc expression was observed in most C. arabica cultivars with introgressed C. canephora genome. In addition, total RBCS1 expression was higher for C. arabica cultivars that had recently introgressed C. canephora genome than for "pure" cultivars. For both species, water stress led to an important decrease in the abundance of RBCS1 transcripts. This was observed for plants grown in either greenhouse or field conditions under severe or moderate drought. However, this reduction of RBCS1 gene expression was not accompanied by a decrease in the corresponding protein in the leaves of C. canephora subjected to water withdrawal. In that case, the amount of RBCS1 was even higher under drought than under unstressed (irrigated) conditions, which suggests great stability of RBCS1 under adverse water conditions. On the other hand, for C. arabica, high nocturnal expression of RBCS1 could also explain the accumulation of the RBCS1 protein under water stress. Altogether, the results presented here suggest that the content of RBCS was not responsible for the loss of photosynthetic capacity that is commonly observed in water-stressed coffee plants. Conclusion: We showed that the CaCe homeolog was expressed in C. eugenioides and non-introgressed ("pure") genotypes of C. arabica but that it was undetectable in C. canephora. On the other hand, the CaCc homeolog was expressed in C. canephora but highly repressed in C. arabica. Expression of the CaCc homeolog was enhanced in C. arabica cultivars that experienced recent introgression with C. canephora. For both C. canephora and C. arabica species, total RBCS1 gene expression was highly reduced with WS. Unexpectedly, the accumulation of RBCS1 protein was observed in the leaves of C. canephora under WS, possibly coming from nocturnal RBCS1 expression. These results suggest that the increase in the amount of RBCS1 protein could contribute to the antioxidative function of photorespiration in water-stressed coffee plants. (Résumé d'auteur

Airway hyperresponsiveness, inflammation, and pulmonary emphysema in rodent models designed to mimic exposure to fuel oil-derived volatile organic compounds encountered during an experimental oil spill

Fuel oil-derived volatile organic compounds (VOCs) inhalation is associated with accidental marine spills. After the Prestige petroleum tanker sank off northern Spain in 2002 and the Deepwater Horizon oil rig catastrophe in 2009, subjects involved in environmental decontamination showed signs of ongoing or residual lung disease up to 5 y after the exposure. We aimed at investigating mechanisms driving persistent respiratory disease by developing an animal model of inhalational exposure to fuel oil-derived VOCs. Female Wistar and Brown Norway (BN) rats and C57BL mice were exposed to VOCs produced from fuel oil mimicking the Prestige spill. Exposed animals inhaled the VOCs 2 h daily, 5 d per week, for 3 wk. Airway responsiveness to methacholine (MCh) was assessed, and bron-choalveolar lavage (BAL) and lung tissues were analyzed after the exposure and following a 2-wk washout. Consistent with data from human studies, both strains of rats that inhaled fuel oil-derived VOCs developed airway hyperresponsiveness that persisted after the washout period, in the absence of detectable inflammation in any lung compartment. Histopathology and quantitative morphology revealed the development of peripherally distributed pulmonary emphysema, which persisted after the washout period, associated with increased alveolar septal cell apoptosis, microvascular endothelial damage of the lung parenchyma, and inhibited expression of vascular endothelial growth factor (VEGF). In this rat model, fuel oil VOCs inhalation elicited alveolar septal cell apoptosis, likely due to DNA damage. In turn, the development of a peculiar pulmonary emphysema pattern altered lung mechanics and caused persistent noninflammatory airway hyperresponsiveness. Such findings suggest to us that humans might also respond to VOCs through physiopathological pathways different from those chiefly involved in typical cigarette smoke-driven emphysema in chronic obstructive pulmonary disease (COPD). If so, this study could form the basis for a novel disease mechanism for lasting respiratory disease following inhalational exposure to catastrophic fuel oil spills

Ameliorating Systematic Uncertainties in the Angular Clustering of Galaxies: A Study using SDSS-III

We investigate the effects of potential sources of systematic error on the angular and photometric redshift, z_phot, distributions of a sample of redshift 0.4 < z < 0.7 massive galaxies whose selection matches that of the Baryon Oscillation Spectroscopic Survey (BOSS) constant mass sample. Utilizing over 112,778 BOSS spectra as a training sample, we produce a photometric redshift catalog for the galaxies in the SDSS DR8 imaging area that, after masking, covers nearly one quarter of the sky (9,913 square degrees). We investigate fluctuations in the number density of objects in this sample as a function of Galactic extinction, seeing, stellar density, sky background, airmass, photometric offset, and North/South Galactic hemisphere. We find that the presence of stars of comparable magnitudes to our galaxies (which are not traditionally masked) effectively remove area. Failing to correct for such stars can produce systematic errors on the measured angular auto-correlation function, w, that are larger than its statistical uncertainty. We describe how one can effectively mask for the presence of the stars, without removing any galaxies from the sample, and minimize the systematic error. Additionally, we apply two separate methods that can be used to correct the systematic errors imparted by any parameter that can be turned into a map on the sky. We find that failing to properly account for varying sky background introduces a systematic error on w. We measure w, in four z_phot slices of width 0.05 between 0.45 < z_phot < 0.65 and find that the measurements, after correcting for the systematic effects of stars and sky background, are generally consistent with a generic LambdaCDM model, at scales up to 60 degrees. At scales greater than 3 degrees and z_phot > 0.5, the magnitude of the corrections we apply are greater than the statistical uncertainty in w.Comment: Accepted by MNRA