Ancient DNA Resolves Identity and Phylogeny of New Zealand's Extinct and Living Quail (Coturnix sp.)

BACKGROUND: The New Zealand quail, Coturnix novaezealandiae, was widespread throughout New Zealand until its rapid extinction in the 1870's. To date, confusion continues to exist concerning the identity of C. novaezealandiae and its phylogenetic relationship to Coturnix species in neighbouring Australia, two of which, C. ypsilophora and C. pectoralis, were introduced into New Zealand as game birds. The Australian brown quail, C. ypsilophora, was the only species thought to establish with current populations distributed mainly in the northern part of the North Island of New Zealand. Owing to the similarities between C. ypsilophora, C. pectoralis, and C. novaezealandiae, uncertainty has arisen over whether the New Zealand quail is indeed extinct, with suggestions that remnant populations of C. novaezealandiae may have survived on offshore islands. METHODOLOGY/PRINCIPAL FINDINGS: Using fresh and historical samples of Coturnix sp. from New Zealand and Australia, DNA analysis of selected mitochondrial regions was carried out to determine phylogenetic relationships and species status. Results show that Coturnix sp. specimens from the New Zealand mainland and offshore island Tiritiri Matangi are not the New Zealand quail but are genetically identical to C. ypsilophora from Australia and can be classified as the same species. Furthermore, cytochrome b and COI barcoding analysis of the New Zealand quail and Australia's C. pectoralis, often confused in museum collections, show that they are indeed separate species that diverged approximately 5 million years ago (mya). Gross morphological analysis of these birds suggests a parallel loss of sustained flight with very little change in other phenotypic characters such as plumage or skeletal structure. CONCLUSION/SIGNIFICANCE: Ancient DNA has proved invaluable for the detailed analysis and identification of extinct and morphologically cryptic taxa such as that of quail and can provide insights into the timing of evolutionary changes that influence morphology

Relating industrial symbiosis and circular economy to the sustainable development debate

Industrial Symbiosis (IS) is a business-focused collaborative approach oriented towards resource efficiency that has been theorised and studied mainly over the last twenty-five years. Recently, IS seems to have found a renewed impetus in the framework of the Circular Economy (CE), a novel approach to sustainability and Sustainable Development (SD) that has been rapidly gaining momentum world-wide. This opening chapter of the book provides an introduction to the concepts of IS, CE and SD, and summarizes their complex evolutionary paths, recalling the rel-evant developments and implementation challenges. In addition, the authors point out the divergences and interrelations of these concepts, both among themselves and with other related concepts and research fields, such as industrial ecology, eco-logical modernization and the green economy. Furthermore, the potential contribu-tion of IS and the CE to SD is briefly discussed, also highlighting critical issues and trade-offs, as well as gaps in research and application, especially relating to the so-cial component of sustainability. Particular attention is given to the potential role of IS in the achievement of targets connected to the Sustainable Development Goals set in the UN Agenda 2030. The recent advances in the IS and CE discussion in the context of the SD research community are further explored, with particular empha-sis on the contribution of the International Sustainable Development Research So-ciety (ISDRS) and its 24th annual conference organised in Messina, Italy, in 2018. The programme of that conference, indeed, included specific tracks on the above-mentioned themes, the contents of which are briefly commented on here, after an overview on the whole conference and the main cross-cutting concepts emerged. In the last part of the chapter, a brief description of the chapters collected in the book is presented. These contributions describe and discuss theoretical frameworks, methodological approaches and/or experiences and case studies where IS and the principles of CE are applied in different geographical context and at different scales to ultimately improve the sustainability of the current production patterns

Gene Ontology annotations and resources.

The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources

Carbon Dioxide Utilisation -The Formate Route

UIDB/50006/2020 CEEC-Individual 2017 Program Contract.The relentless rise of atmospheric CO2 is causing large and unpredictable impacts on the Earth climate, due to the CO2 significant greenhouse effect, besides being responsible for the ocean acidification, with consequent huge impacts in our daily lives and in all forms of life. To stop spiral of destruction, we must actively reduce the CO2 emissions and develop new and more efficient “CO2 sinks”. We should be focused on the opportunities provided by exploiting this novel and huge carbon feedstock to produce de novo fuels and added-value compounds. The conversion of CO2 into formate offers key advantages for carbon recycling, and formate dehydrogenase (FDH) enzymes are at the centre of intense research, due to the “green” advantages the bioconversion can offer, namely substrate and product selectivity and specificity, in reactions run at ambient temperature and pressure and neutral pH. In this chapter, we describe the remarkable recent progress towards efficient and selective FDH-catalysed CO2 reduction to formate. We focus on the enzymes, discussing their structure and mechanism of action. Selected promising studies and successful proof of concepts of FDH-dependent CO2 reduction to formate and beyond are discussed, to highlight the power of FDHs and the challenges this CO2 bioconversion still faces.publishersversionpublishe

Gene Ontology Consortium: going forward

The Gene Ontology (GO; http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community. The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes. We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions. The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data. Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser. We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology

Estimation of glucose uptake by ovarian follicular cells

In vitro maturation (IVM) of mammalian oocytes provides an alternative to traditional in vitro fertilization techniques for clinical treatment of infertility or animal breeding. IVM involves the collection of oocytes from the ovary prior to ovulation, with maturation occurring in a laboratory environment. The success of IVM is highly sensitive to the in vitro nutrient environment. The nurse cells surrounding the oocyte, known as cumulus cells, regulate this environment and removal of these cells reduces the ability of the oocyte to develop following insemination. Determining the nature of the interaction between the oocyte and cumulus cells, collectively called the cumulus–oocyte complex (COC), is a difficult task experimentally. Here we use a combination of experimental and mathematical techniques to investigate glucose transport within bovine COCs and find quantitative estimates of the glucose uptake rates of the oocyte and cumulus cells. Surprisingly, our modeling shows the rate of uptake of glucose by the oocyte to increase and then decrease with concentration, a result that needs further experimental investigation but which supports the expectation that high and low glucose concentrations are detrimental to oocyte development. The methodology described is suitable for use across species and for investigating the transport of other important nutrients within the COC.A. R. Clark, Y. M. Stokes, and J. G. Thompso