Link between viral infection and autoimmunity in primary Sjögren’s syndrome: clues from lymphocytic profile and ebv antibodies

RESUMO: A Síndrome de Sjögren primária (pSS) é uma doença sistémica autoimune caracterizada pela presença de infiltrados linfocitários nas glândulas exócrinas, predominantemente nas glândulas salivares e lacrimais. Ocorre principalmente em mulheres, onde os rácios de incidência feminino/masculino estão entre 10:1 e 20:1. Mulheres com mais de 50 anos de idade são mais afetadas. Os sintomas principais desta condição são: xerostomia (boca seca), keratoconjuctivitis sicca (secura dos olhos com inflamação), e secura de outras superfícies mucosas (pele, vagina e epitélio do aparelho respiratório). Vários vírus têm sido associados à pSS. O vírus Epstein-Barr (EBV) tem sido um forte candidato para o despoletar da epitelite autoimune presente na pSS. No entanto, não existe um causador viral estabelecido da epitelite autoimune em pSS. O presente estudo demonstrou um perfil linfocítico que indica hiperatividade da célula B, limitação da célula Breg e alterações na célula T, nomeadamente nas células T circulantes que possuem um fenótipo caracteristicamente folicular. Estas alterações podem apontar para a existência de um agente viral subjacente causador de uma resposta imune desregulada, uma vez que alterações semelhantes estão presentes num contexto de infeção viral. De facto, pacientes com pSS apresentam uma percentagem aumentada de soros positivos de IgG anti-EBV EA-D, que poderá apontar para o envolvimento do EBV na pSS. Assim, é necessário mais trabalho para estabelecer um causador viral em pSS. Para acrescentar a este estudo, mais anticorpos para antivirais podem ser avaliados, nomeadamente, anti-citomegalovirus, anti-vírus T linfotrópico humano, antihepatite C entre outros. Chamamos a atenção para as células T foliculares para uma possível ligação entre infeção viral e pSS. Estudos adicionais com modelos animais podem ser cruciais na compreensão do papel destas células em ambos os contextos e identificação de mecanismos e padrões de diferenciação similares e a falha dos mecanismos de tolerância.ABSTRACT: Primary Sjögren’s Syndrome (pSS) is a chronic systemic autoimmune disease characterized by lymphocytic infiltration of the exocrine glands, predominantly the salivary and lachrymal glands, leading to damage and secretory impairment. It occurs mainly in women, with ratios of incidence female/male are between 10:1 and 20:1. Women over 50 years of age are the most affected. The main symptoms of this condition are xerostomia (dry mouth), keratoconjunctivitis sicca (ocular dryness with corneal damage), and dryness of other mucosal surfaces (skin, vagina and respiratory epithelium). Extraglandular manifestations frequently occur, especially inflammatory articular and cutaneous manifestations, as well as less common and more serious involvement such as neuropathy, nephritis, vasculitis or lymphoma. Several viruses have been associated with pSS. Epstein-Barr virus (EBV) has been a strong candidate for the triggering of autoimmune epithelitis occurring in pSS. There isn’t, however, an established viral trigger for SS autoimmune epithelitis. Our study revealed a lymphocytic profile indicating B cell hyperactivity, Breg impairment and T cell alterations, namely in circulating T cells with follicular-like phenotype. These changes can be attributed to an underlying viral agent triggering an unregulated response. Indeed, pSS patients presented a higher percentage of positive serum for anti-EBV EA-D IgG, which might point towards a role of EBV in pSS. Still, more work is required to establish a definite viral trigger for pSS. Adding to this study, more antiviral Abs can be assessed, namely, against CMV, human T-lymphotropic virus (HTLV), HCV and others. We call the attention towards follicular T cell subsets for a possible link between viral infection and pSS. More studies using animal models can be paramount in the understanding of follicular T cells roles in both contexts and identify similar mechanisms and differentiation patterns and a breakdown of tolerance mechanisms

Correção cirúrgica como tratamento definitivo em casos de Hérnia Diafragmática: uma revisão de literatura: Surgical correction as definitive treatment in cases of Diaphragmatic Hernia: a literature review

A hérnia diafragmática congênita (HDC) é uma doença embriológica com defeito derivado da fusão incompleta do septo transverso, pregas pleuroperitoneais, mesentério esofágico, e músculos da parede do corpo. Tal anomalia pode estar localizada em qualquer lugar do diafragma, mas geralmente está localizado na região posterolateral, mais conhecida como hérnia de Bochdalek (HB), que é caracterizada por um defeito congênito situado na porção posterolateral do diafragma por obliteração incompleta de forame situado nesta região. Esse tipo em específico corresponde a até para 95% dos casos. Segundo estudos abordados, foi observada a necessidade de intervenção cirúrgica definitiva para HDC, visto que essa doença resulta no deslocamento de órgãos abdominais, que pode corroborar em combinações de hérnia de intestino, estômago e/ou fígado. Assim, desenvolve-se um efeito de massa na cavidade torácica do neonato acometido, reduzindo seu crescimento pulmonar o que gera, em diferentes graus, uma provável hipoplasia pulmonar e concomitantemente hipertensão pulmonar, que são as principais causas de morbidade pós-natal grave e mortalidade. Através dos estudos  analisados  foi  possível  verificar  que a HDC continua a ser uma das anomalias congênitas mais temidas nas Unidades de Terapia Intensiva Neonatal (UTIN). E o tratamento efetivo baseia-se no reparo cirúrgico da hérnia diafragmática pela sua realização por meio do acesso abdominal, torácico ou por ambos. Aumentando assim a taxa de sobrevivência dos neonatos acometidos por essa má-formação fetal

MAMMALS IN PORTUGAL : A data set of terrestrial, volant, and marine mammal occurrences in P ortugal

Mammals are threatened worldwide, with 26% of all species being includedin the IUCN threatened categories. This overall pattern is primarily associatedwith habitat loss or degradation, and human persecution for terrestrial mam-mals, and pollution, open net fishing, climate change, and prey depletion formarine mammals. Mammals play a key role in maintaining ecosystems func-tionality and resilience, and therefore information on their distribution is cru-cial to delineate and support conservation actions. MAMMALS INPORTUGAL is a publicly available data set compiling unpublishedgeoreferenced occurrence records of 92 terrestrial, volant, and marine mam-mals in mainland Portugal and archipelagos of the Azores and Madeira thatincludes 105,026 data entries between 1873 and 2021 (72% of the data occur-ring in 2000 and 2021). The methods used to collect the data were: live obser-vations/captures (43%), sign surveys (35%), camera trapping (16%),bioacoustics surveys (4%) and radiotracking, and inquiries that represent lessthan 1% of the records. The data set includes 13 types of records: (1) burrowsjsoil moundsjtunnel, (2) capture, (3) colony, (4) dead animaljhairjskullsjjaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8),observation in shelters, (9) photo trappingjvideo, (10) predators dietjpelletsjpine cones/nuts, (11) scatjtrackjditch, (12) telemetry and (13) vocalizationjecholocation. The spatial uncertainty of most records ranges between 0 and100 m (76%). Rodentia (n=31,573) has the highest number of records followedby Chiroptera (n=18,857), Carnivora (n=18,594), Lagomorpha (n=17,496),Cetartiodactyla (n=11,568) and Eulipotyphla (n=7008). The data setincludes records of species classified by the IUCN as threatened(e.g.,Oryctolagus cuniculus[n=12,159],Monachus monachus[n=1,512],andLynx pardinus[n=197]). We believe that this data set may stimulate thepublication of other European countries data sets that would certainly contrib-ute to ecology and conservation-related research, and therefore assisting onthe development of more accurate and tailored conservation managementstrategies for each species. There are no copyright restrictions; please cite thisdata paper when the data are used in publications.info:eu-repo/semantics/publishedVersio

SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal

Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. Methods By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARSCoV-2 introductions and early dissemination in Portugal. Results We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. Conclusions Here we conclude that the earlier implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.We gratefully acknowledge to Sara Hill and Nuno Faria (University of Oxford) and Joshua Quick and Nick Loman (University of Birmingham) for kindly providing us with the initial sets of Artic Network primers for NGS; Rafael Mamede (MRamirez team, IMM, Lisbon) for developing and sharing a bioinformatics script for sequence curation (https://github.com/rfm-targa/BioinfUtils); Philippe Lemey (KU Leuven) for providing guidance on the implementation of the phylodynamic models; Joshua L. Cherry (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health) for providing guidance with the subsampling strategies; and all authors, originating and submitting laboratories who have contributed genome data on GISAID (https://www.gisaid.org/) on which part of this research is based. The opinions expressed in this article are those of the authors and do not reflect the view of the National Institutes of Health, the Department of Health and Human Services, or the United States government. This study is co-funded by Fundação para a Ciência e Tecnologia and Agência de Investigação Clínica e Inovação Biomédica (234_596874175) on behalf of the Research 4 COVID-19 call. Some infrastructural resources used in this study come from the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT).info:eu-repo/semantics/publishedVersio

Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio

Geographic patterns of tree dispersal modes in Amazonia and their ecological correlates

Aim: To investigate the geographic patterns and ecological correlates in the geographic distribution of the most common tree dispersal modes in Amazonia (endozoochory, synzoochory, anemochory and hydrochory). We examined if the proportional abundance of these dispersal modes could be explained by the availability of dispersal agents (disperser-availability hypothesis) and/or the availability of resources for constructing zoochorous fruits (resource-availability hypothesis). Time period: Tree-inventory plots established between 1934 and 2019. Major taxa studied: Trees with a diameter at breast height (DBH) ≥ 9.55 cm. Location: Amazonia, here defined as the lowland rain forests of the Amazon River basin and the Guiana Shield. Methods: We assigned dispersal modes to a total of 5433 species and morphospecies within 1877 tree-inventory plots across terra-firme, seasonally flooded, and permanently flooded forests. We investigated geographic patterns in the proportional abundance of dispersal modes. We performed an abundance-weighted mean pairwise distance (MPD) test and fit generalized linear models (GLMs) to explain the geographic distribution of dispersal modes. Results: Anemochory was significantly, positively associated with mean annual wind speed, and hydrochory was significantly higher in flooded forests. Dispersal modes did not consistently show significant associations with the availability of resources for constructing zoochorous fruits. A lower dissimilarity in dispersal modes, resulting from a higher dominance of endozoochory, occurred in terra-firme forests (excluding podzols) compared to flooded forests. Main conclusions: The disperser-availability hypothesis was well supported for abiotic dispersal modes (anemochory and hydrochory). The availability of resources for constructing zoochorous fruits seems an unlikely explanation for the distribution of dispersal modes in Amazonia. The association between frugivores and the proportional abundance of zoochory requires further research, as tree recruitment not only depends on dispersal vectors but also on conditions that favour or limit seedling recruitment across forest types

Geography and ecology shape the phylogenetic composition of Amazonian tree communities

AimAmazonia hosts more tree species from numerous evolutionary lineages, both young and ancient, than any other biogeographic region. Previous studies have shown that tree lineages colonized multiple edaphic environments and dispersed widely across Amazonia, leading to a hypothesis, which we test, that lineages should not be strongly associated with either geographic regions or edaphic forest types.LocationAmazonia.TaxonAngiosperms (Magnoliids; Monocots; Eudicots).MethodsData for the abundance of 5082 tree species in 1989 plots were combined with a mega-phylogeny. We applied evolutionary ordination to assess how phylogenetic composition varies across Amazonia. We used variation partitioning and Moran's eigenvector maps (MEM) to test and quantify the separate and joint contributions of spatial and environmental variables to explain the phylogenetic composition of plots. We tested the indicator value of lineages for geographic regions and edaphic forest types and mapped associations onto the phylogeny.ResultsIn the terra firme and várzea forest types, the phylogenetic composition varies by geographic region, but the igapó and white-sand forest types retain a unique evolutionary signature regardless of region. Overall, we find that soil chemistry, climate and topography explain 24% of the variation in phylogenetic composition, with 79% of that variation being spatially structured (R2 = 19% overall for combined spatial/environmental effects). The phylogenetic composition also shows substantial spatial patterns not related to the environmental variables we quantified (R2 = 28%). A greater number of lineages were significant indicators of geographic regions than forest types.Main ConclusionNumerous tree lineages, including some ancient ones (>66 Ma), show strong associations with geographic regions and edaphic forest types of Amazonia. This shows that specialization in specific edaphic environments has played a long-standing role in the evolutionary assembly of Amazonian forests. Furthermore, many lineages, even those that have dispersed across Amazonia, dominate within a specific region, likely because of phylogenetically conserved niches for environmental conditions that are prevalent within regions

Geography and ecology shape the phylogenetic composition of Amazonian tree communities

Aim: Amazonia hosts more tree species from numerous evolutionary lineages, both young and ancient, than any other biogeographic region. Previous studies have shown that tree lineages colonized multiple edaphic environments and dispersed widely across Amazonia, leading to a hypothesis, which we test, that lineages should not be strongly associated with either geographic regions or edaphic forest types. Location: Amazonia. Taxon: Angiosperms (Magnoliids; Monocots; Eudicots). Methods: Data for the abundance of 5082 tree species in 1989 plots were combined with a mega-phylogeny. We applied evolutionary ordination to assess how phylogenetic composition varies across Amazonia. We used variation partitioning and Moran\u27s eigenvector maps (MEM) to test and quantify the separate and joint contributions of spatial and environmental variables to explain the phylogenetic composition of plots. We tested the indicator value of lineages for geographic regions and edaphic forest types and mapped associations onto the phylogeny. Results: In the terra firme and várzea forest types, the phylogenetic composition varies by geographic region, but the igapó and white-sand forest types retain a unique evolutionary signature regardless of region. Overall, we find that soil chemistry, climate and topography explain 24% of the variation in phylogenetic composition, with 79% of that variation being spatially structured (R$^{2}$ = 19% overall for combined spatial/environmental effects). The phylogenetic composition also shows substantial spatial patterns not related to the environmental variables we quantified (R$^{2}$ = 28%). A greater number of lineages were significant indicators of geographic regions than forest types. Main Conclusion: Numerous tree lineages, including some ancient ones (>66 Ma), show strong associations with geographic regions and edaphic forest types of Amazonia. This shows that specialization in specific edaphic environments has played a long-standing role in the evolutionary assembly of Amazonian forests. Furthermore, many lineages, even those that have dispersed across Amazonia, dominate within a specific region, likely because of phylogenetically conserved niches for environmental conditions that are prevalent within regions