Genotyping of clinically relevant human adenoviruses by array-in-well hybridization assay

AbstractA robust oligonucleotide array-in-well hybridization assay using novel up-converting phosphor reporter technology was applied for genotyping clinically relevant human adenovirus types. A total of 231 adenovirus-positive respiratory, ocular swab, stool and other specimens from 219 patients collected between April 2010 and April 2011 were included in the study. After a real-time PCR amplification targeting the adenovirus hexon gene, the array-in-well assay identified the presence of B03 (n = 122; 57.5% of patients), E04 (29; 13.7%), C02 (21; 9.9%), D37 (14; 6.6%), C01 (12; 5.7%), C05 (5; 2.4%), D19 (4; 1.9%), C06 (2; 0.9%), D08 (1; 0.5%), A31 (1; 0.5%) and F41 (1; 0.5%) genotypes among the clinical sample panel. The typing result was obtained for all specimens that could be amplified (n = 223; 97%), and specificity of the typing was confirmed by sequencing specimens representing each of the different genotypes. No hybridization signal was obtained in adenovirus-negative specimens or specimens with other viruses (n = 30). The array-in-well hybridization assay has great potential as a rapid and multiplex platform for the typing of clinically relevant human adenovirus genotypes in different specimen types

Isotopic insights into the early Medieval (600-1100 CE) diet in the Luistari cemetery at Eura, Finland

In this article, we present the results of an isotopic study of diet for the early medieval (Merovingian, Viking, Early Christian) humans buried in the unique Luistari cemetery at Eura (ca. 600-1400 CE), southwestern Finland, the largest cemetery of the region. Isotope analysis was conducted on 37 humans for dentine and bone collagen (delta C-13, delta N-15, and delta S-34), and five of them were also studied using compound-specific nitrogen isotope analysis. Dental enamel and/or bone carbonate delta C-13 values were studied from altogether 65 humans, five cattle, and five sheep/goats. The bone and dentine collagen and carbonate data show that throughout the centuries, freshwater fish was a stable part of the diet for the population. Our results do not show systematic dietary differences between estimated males and females, but differences can be large on the individual level. We also discovered a possible temporal change in the enamel carbonate delta C-13 values that could be related to the increasing role of carbohydrates (e.g., crops) in the diet. Luistari burials are well comparable to contemporary Swedish Viking trading communities like Birka in their higher protein intake. But contrary to the wider Viking network, they do not show the same marine signal.Peer reviewe

The dIANA database - Resource for isotopic paleodietary research in the Baltic Sea area

Paleodietary research is a complex field, which requires large sets of background information. Owing to increasing interest and activity in the field, a substantial amount of archaeological isotope baseline data exist for Northern Europe, consisting mainly of animal bone collagen delta C-13, delta N-15, and delta S-34 values. However, the data are scattered into dozens of publications written in multiple languages and less-accessible formats, making the data laborious to use. This article presents the first compilation work of this data, the open access dIANA database (Dietary Isotopic baseline for the Ancient North; https://www.oasisnorth.org/diana.html), aimed to support (paleo)dietary research in the Baltic Sea area. The database work is complemented with new analyses of archaeological and (pre-)modern domestic and wild fauna from Finland and Russia broadening the selection of analysed species in the database. We present and discuss data examples, which on one hand show existing spatiotemporal isotope patterns related to diet and differences in the environmental carbon sources and on the other, also visualize the current status of baseline research and the need for further analyses in the circum-Baltic area

Tree height strongly affects estimates of water-use efficiency responses to climate and CO2 using isotopes

Various studies report substantial increases in intrinsic water-use efficiency (Wi), estimated using carbon isotopes in tree rings, suggesting trees are gaining increasingly more carbon per unit water lost due to increases in atmospheric CO2. Usually, reconstructions do not, however, correct for the effect of intrinsic developmental changes in Wi as trees grow larger. Here we show, by comparingWi across varying tree sizes at one CO2 level, that ignoring such developmental effects can severely affect inferences of trees' Wi. Wi doubled or even tripled over a trees' lifespan in three broadleaf species due to changes in tree height and light availability alone, and there are also weak trends for Pine trees. Developmental trends in broadleaf species are as large as the trends previously assigned to CO2 and climate. Credible future tree ring isotope studies require explicit accounting for species-specific developmental effects before CO2 and climate effects are inferred.Peer reviewe

Holistic corpus-based dialectology

This paper is concerned with sketching future directions for corpus-based dialectology. We advocate a holistic approach to the study of geographically conditioned linguistic variability, and we present a suitable methodology, 'corpusbased dialectometry', in exactly this spirit. Specifically, we argue that in order to live up to the potential of the corpus-based method, practitioners need to (i) abandon their exclusive focus on individual linguistic features in favor of the study of feature aggregates, (ii) draw on computationally advanced multivariate analysis techniques (such as multidimensional scaling, cluster analysis, and principal component analysis), and (iii) aid interpretation of empirical results by marshalling state-of-the-art data visualization techniques. To exemplify this line of analysis, we present a case study which explores joint frequency variability of 57 morphosyntax features in 34 dialects all over Great Britain

A 1500-year multiproxy record of coastal hypoxia from the northern Baltic Sea indicates unprecedented deoxygenation over the 20th century

The anthropogenically forced expansion of coastal hypoxia is a major environmental problem affecting coastal ecosystems and biogeochemical cycles throughout the world. The Baltic Sea is a semi-enclosed shelf sea whose central deep basins have been highly prone to deoxygenation during its Holocene history, as shown previously by numerous paleoenvironmental studies. However, long-term data on past fluctuations in the intensity of hypoxia in the coastal zone of the Baltic Sea are largely lacking, despite the significant role of these areas in retaining nutrients derived from the catchment. Here we present a 1500-year multiproxy record of near-bottom water redox changes from the coastal zone of the northern Baltic Sea, encompassing the climatic phases of the Medieval Climate Anomaly (MCA), the Little Ice Age (LIA), and the Modern Warm Period (MoWP). Our reconstruction shows that although multicentennial climate variability has modulated the depositional conditions and delivery of organic matter (OM) to the basin the modern aggravation of coastal hypoxia is unprecedented and, in addition to gradual changes in the basin configuration, it must have been forced by excess human-induced nutrient loading. Alongside the anthropogenic nutrient input, the progressive deoxygenation since the beginning of the 1900s was fueled by the combined effects of gradual shoaling of the basin and warming climate, which amplified sediment focusing and increased the vulnerability to hypoxia. Importantly, the eutrophication of coastal waters in our study area began decades earlier than previously thought, leading to a marked aggravation of hypoxia in the 1950s. We find no evidence of similar anthropogenic forcing during the MCA. These results have implications for the assessment of reference conditions for coastal water quality. Furthermore, this study highlights the need for combined use of sedimentological, ichnological, and geochemical proxies in order to robustly reconstruct subtle redox shifts especially in dynamic, non-euxinic coastal settings with strong seasonal contrasts in the bottom water quality.</p

Human mitochondrial DNA lineages in Iron-Age Fennoscandia suggest incipient admixture and eastern introduction of farming-related maternal ancestry

Human ancient DNA studies have revealed high mobility in Europe's past, and have helped to decode the human history on the Eurasian continent. Northeastern Europe, especially north of the Baltic Sea, however, remains less well understood largely due to the lack of preserved human remains. Finland, with a divergent population history from most of Europe, offers a unique perspective to hunter-gatherer way of life, but thus far genetic information on prehistoric human groups in Finland is nearly absent. Here we report 103 complete ancient mitochondrial genomes from human remains dated to AD 300-1800, and explore mtDNA diversity associated with hunter-gatherers and Neolithic farmers. The results indicate largely unadmixed mtDNA pools of differing ancestries from Iron-Age on, suggesting a rather late genetic shift from hunter-gatherers towards farmers in North-East Europe. Furthermore, the data suggest eastern introduction of farmer-related haplogroups into Finland, contradicting contemporary genetic patterns in Finns

The population history of northeastern Siberia since the Pleistocene

FGW – Publications without University Leiden contractDescriptive and Comparative Linguistic