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| 2. |
- Nilsson, R. Henrik, 1976, et al.
(author)
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How, not if, is the question mycologists should be asking about DNA-based typification
- 2023
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In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; :96, s. 143-157
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Journal article (peer-reviewed)abstract
- Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings chal-lenge the present stance of some in the mycological community - that the current situation is satisfactory and that no change is needed to "the code" - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants.
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| 3. |
- Buckland, Philip I., 1973-
(author)
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SEAD - The Strategic Environmental Archaeology Database Inter-linking Multiproxy Environmental Data with Archaeological Investigations and Ecology
- 2013
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In: Archaeology in the Digital Era. - : Amsterdam University Press. - 9789089646637 - 9789048519590 - 9789048519606 ; , s. 320-331
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Conference paper (peer-reviewed)abstract
- The volume of data on past environmental and climate changes, as well as human interactions with these, has long since passed the level where it is manageable outside of large scale database systems. The Strategic Environmental Archaeology Database project aims to not only store and disseminate such data, but also provide tools for querying and analysing them, whilst maintaining a close connection with the archaeological and ecological data that are essential for their comprehensive interpretation. Large scale, geographically and chronologically unrestricted databases provide us with essentially unlimited scope for putting individual sites into a broader context and applying locally collated data to the investigation of earth system level changes. By providing integrated access to data from a variety of proxies, including plant macrofossils, pollen, insects and geochemistry, along with dating evidence, more complex questions can be answered where any single proxy would not be able to provide comprehensive answers.
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| 4. |
- Kõljalg, Urmas, et al.
(author)
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Digital identifiers for fungal species
- 2016
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 352:6290, s. 1182-1183
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Journal article (peer-reviewed)
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| 5. |
- Liljenström, Hans
(author)
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Multi-scale Causation in Brain Dynamics
- 2016
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In: Cognitive Phase Transitions in the Cerebral Cortex - Enhancing the Neuron Doctrine by Modeling Neural Fields. - Cham : Springer International Publishing. - 9783319244044 ; 39:39, s. 177-186
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Book chapter (other academic/artistic)abstract
- For any complex system, consisting of several organizational levels, the problem of causation is profound. Usually, science considers upward causation as funda-mental, paying less or no attention to any downward causation. This is also true for the nervous system, where cortical neurodynamics, or even higher mental functions of the brain are normally considered causally dependent on the nerve cell activity, or even the activity at the ion channel level. This study presents both upward and downward causation in cortical neural systems, using computational methods with focus on cortical fluctuations. We have developed models of paleo- and neocortical structures, in order to study their mesoscopic neurodynamics, as a link between the microscopic neuronal and macroscopic mental events and pro-cesses. We demonstrate how both noise and chaos may play a role for the func-tions of cortical structures. While microscopic random noise may trigger meso- or macroscopic states, the nonlinear dynamics at these levels may also affect the ac-tivity at the microscopic level.
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| 6. |
- Bergfeldt, Nora, et al.
(author)
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Identification of microbial pathogens in Neolithic Scandinavian humans
- 2024
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In: Scientific Reports. - : NATURE PORTFOLIO. - 2045-2322. ; 14
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Journal article (peer-reviewed)abstract
- With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.
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| 7. |
- Buckland, Philip I., et al.
(author)
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BugsCEP : Coleopteran Ecology Package (software)
- 2006
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Other publication (pop. science, debate, etc.)abstract
- BugsCEP is a research and teaching aid for palaeoentomology, entomology and ecology. As well as habitat and distribution data, it includes tools for climate and environmental reconstruction, and facilities for storing site based abundance/collection data. A variety of searching and reporting functions greatly augment the efficiency of beetle based research. Bugs is built around a comprehensive database of beetle ecology and European fossil records which has been accumulated over the past 20 years.
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| 8. |
- Howard, Heidi Carmen, et al.
(author)
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One small edit for humans, one giant edit for humankind? Points and questions to consider for a responsible way forward for gene editing in humans
- 2018
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In: European Journal of Human Genetics. - : Springer Science and Business Media LLC. - 1018-4813 .- 1476-5438. ; 26:1, s. 1-11
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Journal article (peer-reviewed)abstract
- Gene editing, which allows for specific location(s) in the genome to be targeted and altered by deleting, adding or substituting nucleotides, is currently the subject of important academic and policy discussions. With the advent of efficient tools, such as CRISPR-Cas9, the plausibility of using gene editing safely in humans for either somatic or germ line gene editing is being considered seriously. Beyond safety issues, somatic gene editing in humans does raise ethical, legal and social issues (ELSI), however, it is suggested to be less challenging to existing ethical and legal frameworks; indeed somatic gene editing is already applied in (pre-) clinical trials. In contrast, the notion of altering the germ line or embryo such that alterations could be heritable in humans raises a large number of ELSI; it is currently debated whether it should even be allowed in the context of basic research. Even greater ELSI debates address the potential use of germ line or embryo gene editing for clinical purposes, which, at the moment is not being conducted and is prohibited in several jurisdictions. In the context of these ongoing debates surrounding gene editing, we present herein guidance to further discussion and investigation by highlighting three crucial areas that merit the most attention, time and resources at this stage in the responsible development and use of gene editing technologies: (1) conducting careful scientific research and disseminating results to build a solid evidence base; (2) conducting ethical, legal and social issues research; and (3) conducting meaningful stakeholder engagement, education and dialogue.
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| 9. |
- Kirdok, Emrah, et al.
(author)
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Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals
- 2024
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In: Scientific Reports. - : Springer Nature. - 2045-2322. ; 13:1
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Journal article (peer-reviewed)abstract
- Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890-9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70-80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.
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| 10. |
- Uhen, Mark D., et al.
(author)
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The EarthLife Consortium API: an extensible, open-source service foraccessing fossil data and taxonomies from multiple communitypaleodata resources
- 2021
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In: Frontiers of Biogeography. - : International Biogeography Society. ; 13:2
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Journal article (peer-reviewed)abstract
- Paleobiologists and paleoecologists interested in studying biodiversity dynamics over broadspatial and temporal scales have built multiple community-curated data resources, eachemphasizing a particular spatial domain, timescale, or taxonomic group(s). This multiplicity ofdata resources is understandable, given the enormous diversity of life across Earth's history,but creates a barrier to achieving a truly global understanding of the diversity and distributionof life across time. Here we present the Earth Life Consortium Application ProgrammingInterface (ELC API), a lightweight data service designed to search and retrieve fossil occurrenceand taxonomic information from across multiple paleobiological resources. Key endpointsinclude Occurrences (returns spatiotemporal locations of fossils for selected taxa), Locales(returns information about sites with fossil data), References (returns bibliographicinformation), and Taxonomy (returns names of subtaxa associated with selected taxa). Dataobjects are returned as JSON or CSV format. The ELC API supports tectonic-driven shifts ingeographic position back to 580 Ma using services from Macrostrat and GPlates. The ELC APIhas been implemented first for the Paleobiology Database and Neotoma PaleoecologyDatabase, with a test extension to the Strategic Environmental Archaeology Database. The ELCAPI is designed to be readily extensible to other paleobiological data resources, with allendpoints fully documented and following open-source standards (e.g., Swagger, OGC). Thebroader goal is to help build an interlinked and federated ecosystem of paleobiological andpaleoenvironmental data resources, which together provide paleobiologists, macroecologists,biogeographers, and other interested scientists with full coverage of the diversity anddistribution of life across time.
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