Modelled ocean changes at the Plio-Pleistocene transition driven by Antarctic ice advance

The Earth underwent a major transition from the warm climates of the Pliocene to the Pleistocene ice ages between 3.2 and 2.6 million years ago. The intensification of Northern Hemisphere Glaciation is the most obvious result of the Plio-Pleistocene transition. However, recent data show that the ocean also underwent a significant change, with the convergence of deep water mass properties in the North Pacific and North Atlantic Ocean. Here we show that the lack of coastal ice in the Pacific sector of Antarctica leads to major reductions in Pacific Ocean overturning and the loss of the modern North Pacific Deep Water (NPDW) mass in climate models of the warmest periods of the Pliocene. These results potentially explain the convergence of global deep water mass properties at the Plio-Pleistocene transition, as Circumpolar Deep Water (CDW) became the common source

Considering Transposable Element Diversification in De Novo Annotation Approaches

Transposable elements (TEs) are mobile, repetitive DNA sequences that are almost ubiquitous in prokaryotic and eukaryotic genomes. They have a large impact on genome structure, function and evolution. With the recent development of high-throughput sequencing methods, many genome sequences have become available, making possible comparative studies of TE dynamics at an unprecedented scale. Several methods have been proposed for the de novo identification of TEs in sequenced genomes. Most begin with the detection of genomic repeats, but the subsequent steps for defining TE families differ. High-quality TE annotations are available for the Drosophila melanogaster and Arabidopsis thaliana genome sequences, providing a solid basis for the benchmarking of such methods. We compared the performance of specific algorithms for the clustering of interspersed repeats and found that only a particular combination of algorithms detected TE families with good recovery of the reference sequences. We then applied a new procedure for reconciling the different clustering results and classifying TE sequences. The whole approach was implemented in a pipeline using the REPET package. Finally, we show that our combined approach highlights the dynamics of well defined TE families by making it possible to identify structural variations among their copies. This approach makes it possible to annotate TE families and to study their diversification in a single analysis, improving our understanding of TE dynamics at the whole-genome scale and for diverse species

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio

Nevo displásico (nevo atípico) Dysplastic nevus (atypical nevus)

O nevo atípico (displásico) é considerado um fator importante associado com o risco aumentado de desenvolvimento do melanoma cutâneo. Acredita-se que nevos atípicos sejam lesões precursoras do melanoma cutâneo. Podem estar presentes em pacientes com múltiplos nevos melanocíticos (síndrome do nevo atípico) ou isolados e em poucas quantidades em um contexto não familial. Aparecem, geralmente, na puberdade e prevalecem em indivíduos jovens. Têm predileção por áreas expostas ao sol, especialmente, o tronco. O grande desafio em relação ao nevo atípico reside na controvérsia em se definir sua nomenclatura, diagnóstico clínico, critérios dermatoscópicos, diagnóstico histopatológico e aspectos moleculares. Esta revisão tem por objetivo trazer o conhecimento, facilitar o entendimento e responder às questões duvidosas concernentes ao nevo atípico.<br>Atypical nevum (dysplastic) is considered an important factor associated with increased risk of developing cutaneous melanoma. It is believed that atypical nevi are precursor lesions of cutaneous melanoma. They may be present in patients with multiple melanocytic nevi (atypical nevus syndrome) or isolated and in small numbers in a non-familial context. The disease usually begins at puberty and predominates in young people. It has a predilection for sun-exposed areas, especially the trunk. The major challenge in relation to atypical nevi lies in the controversy of defining its nomenclature, clinical diagnosis, dermoscopic criteria, histopathological diagnosis and molecular aspects. This review aims at bringing knowledge, facilitating comprehension and clarifying doubts about atypical nevus