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| 2. |
- Ginja, Catarina, et al.
(författare)
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Iron age genomic data from Althiburos - Tunisia renew the debate on the origins of African taurine cattle
- 2023
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Ingår i: iScience. - : Cell Press. - 2589-0042. ; 26:7
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Tidskriftsartikel (refereegranskat)abstract
- The Maghreb is a key region for understanding the dynamics of cattle dispersal and admixture with local aurochs following their earliest domestication in the Fertile Crescent more than 10,000 years ago. Here, we present data on autosomal genomes and mitogenomes obtained for four archaeological specimens of Iron Age (∼2,800 cal BP–2,000 cal BP) domestic cattle from the Eastern Maghreb, i.e. Althiburos (El Kef, Tunisia). D-loop sequences were obtained for an additional eight cattle specimens from this site. Maternal lineages were assigned to the elusive R and ubiquitous African-T1 haplogroups found in two and ten Althiburos specimens, respectively. Our results can be explained by post-domestication hybridization of Althiburos cattle with local aurochs. However, we cannot rule out an independent domestication in North Africa considering the shared ancestry of Althiburos cattle with the pre-domestic Moroccan aurochs and present-day African taurine cattle.
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| 3. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 4. |
- Yu, He, et al.
(författare)
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Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history
- 2022
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we first generate a de novo genome assembly of the black rat. We then sequence 67 ancient and three modern black rat mitogenomes, and 36 ancient and three modern nuclear genomes from archaeological sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of our newly reported sequences, together with published mitochondrial DNA sequences, confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling. 'Archaeogenetic analysis of black rat remains reveals that this species was introduced into temperate Europe twice, in the Roman and medieval periods. This population turnover was likely associated with multiple historical and environmental factors.'
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| 5. |
- Antoniou, Antonis C., et al.
(författare)
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Common alleles at 6q25.1 and 1p11.2 are associated with breast cancer risk for BRCA1 and BRCA2 mutation carriers
- 2011
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 20:16, s. 3304-3321
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Tidskriftsartikel (refereegranskat)abstract
- Two single nucleotide polymorphisms (SNPs) at 6q25.1, near the ESR1 gene, have been implicated in the susceptibility to breast cancer for Asian (rs2046210) and European women (rs9397435). A genome-wide association study in Europeans identified two further breast cancer susceptibility variants: rs11249433 at 1p11.2 and rs999737 in RAD51L1 at 14q24.1. Although previously identified breast cancer susceptibility variants have been shown to be associated with breast cancer risk for BRCA1 and BRCA2 mutation carriers, the involvement of these SNPs to breast cancer susceptibility in mutation carriers is currently unknown. To address this, we genotyped these SNPs in BRCA1 and BRCA2 mutation carriers from 42 studies from the Consortium of Investigators of Modifiers of BRCA1/2. In the analysis of 14 123 BRCA1 and 8053 BRCA2 mutation carriers of European ancestry, the 6q25.1 SNPs (r(2) = 0.14) were independently associated with the risk of breast cancer for BRCA1 mutation carriers [ hazard ratio (HR) = 1.17, 95% confidence interval (CI): 1.11-1.23, P-trend = 4.5 x 10(-9) for rs2046210; HR = 1.28, 95% CI: 1.18-1.40, P-trend = 1.3 x 10(-8) for rs9397435], but only rs9397435 was associated with the risk for BRCA2 carriers (HR = 1.14, 95% CI: 1.01-1.28, P-trend = 0.031). SNP rs11249433 (1p11.2) was associated with the risk of breast cancer for BRCA2 mutation carriers (HR = 1.09, 95% CI: 1.02-1.17, P-trend = 0.015), but was not associated with breast cancer risk for BRCA1 mutation carriers (HR = 0.97, 95% CI: 0.92-1.02, P-trend = 0.20). SNP rs999737 (RAD51L1) was not associated with breast cancer risk for either BRCA1 or BRCA2 mutation carriers (P-trend = 0.27 and 0.30, respectively). The identification of SNPs at 6q25.1 associated with breast cancer risk for BRCA1 mutation carriers will lead to a better understanding of the biology of tumour development in these women.
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| 6. |
- Brantner, Cornelia, et al.
(författare)
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Gauging the Google gaze : A digital visual analysis of images of a semi-peripheral town
- 2024
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Ingår i: Culture Unbound. - : Linköping University Electronic Press. - 2000-1525. ; 16:1, s. 86-116
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Tidskriftsartikel (refereegranskat)abstract
- This study explores the visual representation of Great Yarmouth, a British coastal town caught between the urban and the rural, as seen through the quasi-monopolistic image search engine Google Images. The research examines levels of pluralistic or biased place representations to consider how rankings employed by Google Images algorithms represent Great Yarmouth’s identity. The study adopts a visual culture perspective that recognises the role of images in place making and combines digital methods with an image type analysis to investigate how online representations reflect and create the town’s identities. The data shows that Google Images’ preference for representing Yarmouth as a sunny seaside town indicates that the search engine prioritises marketable assets above its connections with its hinterland, its diversity of people, and the cultural activities it has to offer. This, the authors state, is a place far away from Tuan’s (1979) idea of a place that is given meaning and identity from the perspective of people. Instead, Google Images’ representations of Great Yarmouth are an example of a created form of place making as commodification. The article concludes that the inscribed bias and unbalanced search priority criteria employed by the search engine impact upon the diversity of the semi-peripheral town.
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| 7. |
- Brantner, Cornelia, et al.
(författare)
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It’s always sunny in Yarmouth (according to Google Images) : Visual representations of a semi-peripheral town.
- 2023
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Konferensbidrag (refereegranskat)abstract
- This study explores the visual representation of Great Yarmouth, a British coastal town caught between the urban and the rural, as seen through the quasi-monopolistic image search engine Google Images. The research examines levels of pluralistic or biased place representations to consider how rankings employed by Google Images algorithms represent Great Yarmouth’s identity. The study adopts a visual culture perspective that recognises the role of images in place making and combines digital methods with an image type analysis to investigate how online representations reflect and create the town’s identities. The data shows that Google Images’ preference for representing Yarmouth as a sunny seaside town indicates that the search engine prioritises marketable assets above its connections with its hinterland, its diversity of people, and the cultural activities it has to offer. This, the authors state, is a place far away from Tuan’s (1979) idea of a place that is given meaning and identity from the perspective of people. Instead, Google Images’ representations of Great Yarmouth are an example of a created form of place making as commodification. The article concludes that the inscribed bias and unbalanced search priority criteria employed by the search engine impact upon the diversity of the semi-peripheral town.
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| 8. |
- Brantner, Cornelia, et al.
(författare)
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Structures of the Public Sphere : Contested Spaces as Assembled Interfaces
- 2021
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Ingår i: Media and Communication. - : COGITATIO PRESS. - 2183-2439. ; 9:3, s. 16-27
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Tidskriftsartikel (refereegranskat)abstract
- This article updates certain aspects of the normative notions of the public sphere. The complex ecosystem of social communications enhanced by mobile media platform activity has changed our perception of space. If the public sphere has to normatively assess the expected conditions for public debate and for democracy, the assemblage of devices, discourses, infrastructures, locations, and regulations must be considered together. The literature reviewed about the public sphere, spaces, and geographically-enabled mobile media leads this article to the formulation of a concept of the public sphere that considers such assemblage as an interface. As an empirically applicable update to the definition of the public sphere the text offers a model that helps analyze those factors considering how they shape the communicative space in four modes: representations, structures, textures, and connections. These modes consider the roles played by assemblages of devices, infrastructures, and content in delimiting the circulation of information. The second part of the article illustrates the model with examples from previous research, paying particular attention to the structures' mode. The dissection of qualitative, quantitative, and geodata generated by digital and (visual) (n)ethnographic tools reveals three subcategories for the analysis of structures of space: barriers, shifts, and flows. The structures effectively enable/disable communication and define centers and peripheries in the activity flows. The contribution of this article is, thus, conceptual-it challenges and updates the notion of the public sphere; and methodological-it offers tools and outputs that align with the previously developed theoretical framework.
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| 9. |
- Bru, Samuel, et al.
(författare)
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Polyphosphate is involved in cell cycle progression and genomic stability in Saccharomyces cerevisiae
- 2016
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Ingår i: Molecular Microbiology. - : Wiley. - 0950-382X .- 1365-2958. ; 101:3, s. 367-380
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Tidskriftsartikel (refereegranskat)abstract
- Polyphosphate (polyP) is a linear chain of up to hundreds of inorganic phosphate residues that is necessary for many physiological functions in all living organisms. In some bacteria, polyP supplies material to molecules such as DNA, thus playing an important role in biosynthetic processes in prokaryotes. In the present study, we set out to gain further insight into the role of polyP in eukaryotic cells. We observed that polyP amounts are cyclically regulated in Saccharomyces cerevisiae, and those mutants that cannot synthesise (vtc4 Delta) or hydrolyse polyP (ppn1 Delta, ppx1 Delta) present impaired cell cycle progression. Further analysis revealed that polyP mutants show delayed nucleotide production and increased genomic instability. Based on these findings, we concluded that polyP not only maintains intracellular phosphate concentrations in response to fluctuations in extracellular phosphate levels, but also muffles internal cyclic phosphate fluctuations, such as those produced by the sudden demand of phosphate to synthetize deoxynucleotides just before and during DNA duplication. We propose that the presence of polyP in eukaryotic cells is required for the timely and accurate duplication of DNA.
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| 10. |
- Casas, Joan Ramon, et al.
(författare)
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Assessment methods for elderly rail infrastructure : MAINLINE, Deliverable D1.2, EU FP7
- 2013
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Rapport (refereegranskat)abstract
- An accurate and advanced assessment will allow keeping in service many assets that otherwise will be condemned to repair, strengthening and/or replacement. Because interventions in many bridges at the same time is not economically feasible, their advanced assessment could help prioritize the repair/strengthening works in the coming years. The main objective of this deliverable is to present the existing possibilities for an accurate assessment of railway assets condition. The two specific objectives of this report are:1. - To describe a set of proposed advanced assessment methods that may be incorporated in the life-cycle management of railway infrastructures2. - To see how the costs and benefits of the proposed advanced assessment methods may be incorporated within a LCA framework.The scope of this report is limited to the assessment of relevant railway infrastructure assets. The assessment methods considered will be those applicable to the following asset types: Cuttings Metallic Bridges Lined Tunnels Track (including rails, sleepers, ballast, switches and crossings).The most appropriate assessment method for every specific infrastructure asset strongly depends on many variables. This deliverable seeks to help the assessing engineer, first showing the available alternatives and, after that, in the decision making for the best method and technique to be used within a Life-Cycle Assessment framework, where the optimization of cost in a wide sense (including environmental costs) is the final objective.
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