Comparative transcriptomic response of two Pinus species to infection with the pine wood nematode Bursaphelenchus xylophilus

Pine wilt disease (PWD) caused by pine wood nematode (PWN), Bursaphelenchus xylophilus, is a serious threat to global forest populations of conifers, in particular Pinus spp. Recently, the presence of PWN was reported in dead Yunnan pine (Pinus yunnanensis) trees under natural conditions. To further understand the potential impact caused by PWN in Yunnan pine populations, a transcriptional profiling analysis was performed over di erent time points (0 hours (h), 6 h, 24 h, 48 h, and 7 days) after PWN inoculation. A total of 9961 di erentially expressed genes were identified after inoculation, which suggested a dynamic response against the pathogen, with a more intense pattern at 48 h after inoculation. The results also highlighted a set of biological mechanisms triggered after inoculation that provide valuable information regarding the response of Yunnan pine to PWN infection. When compared with maritime pine (Pinus pinaster), the Yunnan pine response was less complex and involved a smaller number of di erentially expressed genes, which may be associated with the increased degree of resistance to PWN displayed by Yunnan pine. These results revealed di erent strategies to cope with PWN infection by these two pine species, which display contrasting degrees of susceptibility, especially in the timely perception of the infection and response magnitudeinfo:eu-repo/semantics/publishedVersio

Kinship Analysis and Pedigree Reconstruction of a Natural Regenerated Cork Oak (Quercus suber) Population

Cork oak (Quercus suber L.) is a valuable forest species in the western Mediterranean Basin due to its ecological value and the production of cork (a renewable natural material). Cork quality depends on the genetic background and cork oak environment, which has long been recognized. As no cork oak genetic trials with pedigree information were available, the inference of the genetic relatedness between individuals from molecular markers can potentially be applied to natural populations. This work aimed to investigate the potential of performing kinship prediction and pedigree reconstruction by SNP genotyping a natural cork oak population. A total of 494 trees located in Portugal were genotyped with 8K SNPs. The raw SNP set was filtered differently, producing four SNP sets that were further filtered by missing data, genotype frequency, and minor allele frequency. For each set, an identity by descent (IBD) matrix was generated to perform the relationship prediction, revealing from 22,114 to 23,859 relationships. Familial categories from the first to the third degree were able to be assigned. The feasibility of SNP genotyping for future studies on the kinship analysis and pedigree reconstruction of cork oak populations was demonstrated. The information produced may be used in further breeding and conservation programs for cork oakinfo:eu-repo/semantics/publishedVersio

Automatic verification of design rules in PCB manufacturing

Nowadays, electronics can be found in almost every available device. At the core of electronic devices there are Printed Circuit Boards (PCB). To create a suitable PCB there is the need of complying with several constraints, both concerning electrical and layout design. Thus, the design rules related to the PCB manufacturing and assembly are very important since these restrictions are fundamental to ensure the creation of a viable physical PCB. Electrical Computer Aided Design (ECAD) tools are able to automatically verify such rules, but they only consider a subset of the total required rules. The remaining rules are currently manually checked, which may increase the occurrence of errors and, consequently, increase the overall costs in designing and in the manufacturing process of a PCB. Being the design a crucial phase in the manufacturing procedure, a software system that automatically verifies all design rules and produce the corresponding assessment report is fundamental. Such software system is addressed in this paper.This work was funded by the project “iFACTORY: Novas Capacidades de Industrialização”, with reference 002814 supported by FEDER trough “Portugal2020 Programa Operacional Competitividade e Internacionalização” (COMPETE2020). This work has been supported by COMPETE: POCI-01-0145-FEDER-007043and FCT - Fundação para a Ciência e a Tecnologia within the Project Scope: UID/CEC/00319/201

A metagenomics approach to characterize the footrot microbiome in Merino sheep

In the Portuguese Alentejo region, Merino sheep breed is the most common breed, reared for the production of meat, dairy, and wool. Footrot is responsible for lameness, decreased animal welfare, and higher production losses, generating a negative economic impact. The disease is caused by Dichelobacter nodosus that interacts with the sheep foot microbiome, to date largely uncharacterized. In fact, Dichelobacter nodosus is not able to induce footrot by itself being required the presence of a second pathogen known as Fusobacterium necrophorum. To understand and characterize the footrot microbiome dynamics of different footrot lesion scores, a whole metagenome sequencing (WMGS) approach was used. Foot tissue samples were collected from 212 animals with different degrees of footrot lesion scores, ranging from 0 to 5. Distinct bacterial communities were associated with feet with different footrot scores identifying a total of 63 phyla and 504 families. As the severity of footrot infection increases the microorganisms’ diversity decreases triggering a shift in the composition of the microbiome from a dominant gram-positive in mild stages to a dominant gram-negative in the severe stages. Several species previously associated with footrot and other polymicrobial diseases affecting the epidermis and provoking inflammatory responses such as Treponema spp., Staphylococcus spp., Streptococcus spp. and Campylobacter spp. were identified proliferating along with the lesions’ severity. Although these bacteria are not able to initiate footrot, several evidences have been described supporting their association with the severity and incidence increase of footrot lesions caused by Dichelobacter nodosus and Fusobacterium necrophorum. Further investigation is required to establish the roles of particular taxa and identify which of them play a role in the disease process and which are opportunistic pathogens

The crown pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

Since historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially in Europe. This mussel presents a myriad of rare biological features, e.g. high longevity coupled with low senescence and Doubly Uniparental Inheritance of mitochondrial DNA, for which the underlying molecular mechanisms are poorly known. Here, the first draft genome assembly of M. margaritifera was produced using a combination of Illumina Paired-end and Mate-pair approaches. The genome assembly was 2.4 Gb long, possessing 105,185 scaffolds and a scaffold N50 length of 288,726 bp. The ab initio gene prediction allowed the identification of 35,119 protein-coding genes. This genome represents an essential resource for studying this species' unique biological and evolutionary features and ultimately will help to develop new tools to promote its conservation.A.G.-d.-S. was funded by the Portuguese Foundation for Science and Technology (FCT) under the grants SFRH/BD/137935/2018, EF (CEECIND/00627/2017) and MLL (2020.03608.CEECIND). This research was developed under ConBiomics: the missing approach for the Conservation of freshwater Bivalves Project No. NORTE-01-0145-FEDER- 030286, co-financed by COMPETE 2020, Portugal 2020 and the European Union through the ERDF, and by FCT through national funds. Additional strategic funding was provided by FCT UIDB/04423/2020 and UIDP/04423/2020. Authors’ interaction and writing of the article was promoted and facilitated by the COST Action CA18239: CONFREMU—Conservation of freshwater mussels: a pan- European approach.info:eu-repo/semantics/publishedVersio

Parâmetros genéticos da peeira em ovinos das raças Merina Branca e Merina Preta em Portugal

A peeira influencia negativamente diversos aspetos da ovinicultura e tem grande impacto económico e social em diversos países produtores de ovinos de ambos os hemisférios, particularmente na indústria da lã fina, amplamente dominada pelas raças Merinas. Com este trabalho pretendeu-se estimar componentes de variância associados à peeira em ovinos das raças Merina Branca (MB) e Merina Preta (MP), tendo sido realizado no âmbito das atividades previstas no Projeto GEN-RES-Alentejo, que tem como objetivo principal, contribuir para a melhoria da produtividade das explorações de ovinos no Alentejo, através da identificação, por metodologias genómicas de última geração, de marcadores genéticos associados à resistência à peeira e ao parasitismo gastrointestinal por nematodos. Utilizaram-se 745 registos de scores de peeira (positivo vs negativo) de 437 fêmeas inscritas nos Livros de Adultos (239♀MB e 198♀MP), recolhidos entre 2016 e 2018 em 3 criadores. A partir dos 437 animais com registos de score de peeira, construiu-se de forma ascendente um ficheiro de pedigrees, que incluiu toda a informação genealógica destes animais, obtendo-se no final um ficheiro com 1229 indivíduos (136♂ e 1093♀). Os registos disponíveis foram analisados segundo uma abordagem frequentista e depois bayesiana. Assim, inicialmente foram analisados por máxima verosimilhança restrita, com o software MTDFREML e com um critério de convergência de 10-9, através de um modelo animal com registos repetidos, que incluiu os efeitos fixos do criador*ano de avaliação do score, estação, raça e idade à avaliação (covariável linear e quadrática); como efeitos aleatórios foram considerados o valor genético do animal, o efeito ambiental permanente e o erro residual. Posteriormente, exatamente com mesmo tipo de modelo animal, efeitos fixos e aleatórios, os dados foram submetidos a análise com o software TM e por amostragem de Gibbs. As estimativas dos parâmetros genéticos e ambientais foram semelhantes segundo as duas metodologias, respetivamente, frequentista e bayesiana: variância genética, 0.12595 e 0.12781; variância ambiental permanente, 0.00000 e 0.00000; variância residual, 0.86336 e 0.85372; variância fenotípica, 0.98931 e 0.98153; heritabilidade, 0.127 e 0.130 e repetibilidade, 0.127 e 0.130. Os resultados obtidos neste trabalho, ainda que preliminares e baseados em pouca informação, permitiram demonstrar que existe algum determinismo genético associado à suscetibilidade/resistência à peeira. Consequentemente, é possível encarar com otimismo as ações a desenvolver no âmbito do projeto GEN-RES-Alentejo, designadamente, na identificação de marcadores genéticos relacionados com esta doença infeciosa de tão grande impacto nos ovinos e, num futuro próximo, a possibilidade das raças Merinas portuguesas poderem integrar novas metodologias de seleção nos respetivos programas de melhoramento genético

Artistas sobre outras obras

Este número da Revista Estúdio assinala a crescente maturação de um espaço de comunicação algo alternativo, onde artistas falam de artistas, dão a conhecer obras menos conhecidas, e ocupam uma área de curadoria expontânea e paralela aos centros do arte world. Dá-se a palavra aos próprios criadores, e há seis anos que o seu olhar vem enriquecendo um património crescente, com especiais ligações aos países onde se fala as línguas ibéricas. A presença de obras de Portugal, Espanha, Brasil, Angola, Argentina, Perú, Venezuela, Bolívia e muitos outros países tornou-se habitual, fazendo da Estúdio uma instância da semiosfera (Lotman). Mais do que a presença, é a dimensão do conhecimento transmitido, a que se segue, naturalmente, o estabelecimento de novas teias de referência entre os artistas destes países: há novos grupos, novas cumplicidades, novas realizações dentro deste Estúdio, que completa seis anos de publicação persistente. A Revista Estúdio é também mais uma via disponível para o exercício da interpretação, através de descodificações mais informadas, mais negociadas, dos textos artísticos, pois são efectuadas por outros artistas. Reuniram-se nesta edição 24 artigos originais, mantendo a sua linha editorial inicial. O projecto mantém a sua componente de resistência, de plataforma de conhecimento para os pares, não abdicando também da validação externa, ou seja, do uso de protocolos de produção e transmissão de conhecimento. Falamos pois das normas de redação, de referenciação, de estruturação de textos e de articulação de argumentos, visuais ou verbais. Estabelece-se neste volume uma articulação entre cinema, vídeo, redes, escultura, instalação, fotografia, performance, banda desenhada, pintura, cerâmica, poesia concreta, livros de artista, sendo este conjunto não exaustivo testemunha do grau de hibridação que hoje o discurso artístico convoca. Apanhando-lhe o pulso, a Estúdio acompanha a arte desde os seus produtores, dos seus procedimentos, dos seus recursos, dos seus resultados. A Estúdio permite visitar muitos estúdios.info:eu-repo/semantics/publishedVersio

"Effect of diflubenzuron on the development of Pinus pinaster seedlings inoculated with ectomycorrhizal fungi".

Contaminação e Toxicologia AmbientaisMaster of Environmental Contamination and Toxicolog

Transcriptome Characterization of Different Tissues of Stone Pine (Pinus pinea L.): De Novo Assembly

Stone pine (Pinus pinea L.) is an emblematic tree distributed around the whole Mediterranean basin. The species is well known for the economics of its timber, resins and edible seeds, the stone pine nuts commercialized in the food industry. Despite its relevance, the genomic information available for the species is scarce, and until now no reference genome has been available. The main purpose of this study was to characterize the stone pine transcriptome of seven different tissues, by performing a de novo transcriptome assembly. A total of 55,328 genes were predicted and functionally annotated based on the SWISS-PROT and nr-NCBI databases and InterProScan signatures

Draft genome sequence of a rare pigmented mycobacterium avium subsp. paratuberculosis type C strain

Mycobacterium avium subsp. paratuberculosis is the causative agent of paratuberculosis. We report here the draft genome sequence of a rare pigmented M. avium subsp. paratuberculosis type C strain, comprising 58 contigs and having a genome size of 4,851,414 bp. The genome will assist in the execution of pigmentation and virulence studies on this mycobacterium.publishersversionpublishe