High‐Throughput DNA sequencing of ancient wood

Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high‐throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long‐term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human‐induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro‐evolutionary response of trees to climate change and human forest management.     

Morphological and Spatio‐Temporal Mismatches Shape a Neotropical Savanna Plant‐Hummingbird Network

Complex networks of species interactions might be determined by species traits but also by simple chance meetings governed by species abundances. Although the idea that species traits structure mutualistic networks is appealing, most studies have found abundance to be a major structuring mechanism underlying interaction frequencies. With a well‐resolved plant–hummingbird interaction network from the Neotropical savanna in Brazil, we asked whether species morphology, phenology, nectar availability and habitat occupancy and/or abundance best predicted the frequency of interactions. For this, we constructed interaction probability matrices and compared them to the observed plant‐hummingbird matrix through a likelihood approach. Furthermore, a recently proposed modularity algorithm for weighted bipartite networks was employed to evaluate whether these factors also scale‐up to the formation of modules in the network. Interaction frequencies were best predicted by species morphology, phenology and habitat occupancy, while species abundances and nectar availability performed poorly. The plant–hummingbird network was modular, and modules were associated to morphological specialization and habitat occupancy. Our findings highlight the importance of traits as determinants of interaction frequencies and network structure, corroborating the results of a previous study on a plant–hummingbird network from the Brazilian Atlantic Forest. Thus, we propose that traits matter more in tropical plant–hummingbird networks than in less specialized systems. To test the generality of this hypothesis, future research could employ geographic or taxonomic cross‐system comparisons contrasting networks with known differences in level of specialization.     

Genetic Variations in the Vitamin D Receptor Predict Type 2 Diabetes and Myocardial Infarction in a Community-Based Population: The Troms? Study

BackgroundThough the associations between low serum 25-hydroxyvitamin D (25(OH)D) levels and health outcomes such as type 2 diabetes (T2D), myocardial infarction (MI), cancer, and mortality are well-studied, the effect of supplementation with vitamin D is uncertain. This may be related to genetic differences. Thus, rs7968585, a single nucleotide polymorphism (SNP) of the vitamin D receptor (VDR), has recently been reported as a predictor of composite health outcome. We therefore aimed to evaluate whether rs7968585 predicts separate clinical outcomes such as T2D, MI, cancer, and mortality in a community-based Norwegian population.ConclusionsThe VDR-related SNP rs7968585 minor allele is a significant and positive predictor for T2D and possibly for MI. Since the functional mechanism of this SNP is not yet understood, and the association with T2D is reported for the first time, confirmatory studies are needed.     

Evaluation of Petrifilm™ Select <Emphasis Type="Italic">E. coli</Emphasis> Count Plate medium to discriminate antimicrobial resistant <Emphasis Type="Italic">Escherichia coli</Emphasis>

Background  

Screening and enumeration of antimicrobial resistant Escherichia coli directly from samples is needed to identify emerging resistant clones and obtain quantitative data for risk assessment. Aim of this study was to evaluate the performance of 3M™ Petrifilm™ Select E. coli Count Plate (SEC plate) supplemented with antimicrobials to discriminate antimicrobial-resistant and non-resistant E. coli.     

Biochemical fingerprinting for typing of Aeromonas strains from food and water

The PhenePlate (PhP) system for biochemical fingerprinting is based on analysis of the kinetics of biochemical tests in microplates. This was evaluated for typing Aeromonas spp. isolates from drinking water and food and 78 Aeromonas strains isolated on different occasions over 6 months from three public drinking water systems. The system was highly discriminating and the diversity index, as calculated from 65 unrelated isolates, was 0.993, and 53 different biochemical phenotypes (BPTs) were found. Food isolates were more homogeneous than random Aeromonas strains and identical isolates were sometimes found in food of different origin. Each public drinking water system contained several BPTs but some of these were dominant at several sampling sites and on several sampling occasions in a system. The PhP system is suitable for typing Aeromonas strains from food and water. It is simple to handle and can be used with large numbers of isolates.     

Digital Unbounding of the Polling Booth: Ethnography in Small Places

This article discusses how a small place – the polling booth – can be bounded as an ethnographic site with reference to the political and democratic event that it is supposed to facilitate. Concerns about the socio-material bounding of the booth form the main empirical case – a debate, which recently occurred in Denmark when the government proposed to digitalise voting. Digitalisation here became a controversy because of the potential illicit influences that computer experts argued would enter the polling booth and challenge the secrecy and the privacy of the vote, the transparency of the electoral process, and thus the electoral enactment of democracy itself. In this way the polling booth potentially works as an ethnographic entry point for following shifts in contemporary debates.     

The Swedish version of the Normalization Process Theory Measure S-NoMAD: translation,adaptation, and pilot testing

Background

The original British instrument the Normalization Process Theory Measure (NoMAD) is based on the four core constructs of the Normalization Process Theory: Coherence, Cognitive Participation, Collective Action, and Reflexive Monitoring. They represent ways of thinking about implementation and are focused on how interventions can become part of everyday practice.

Aim

To translate and adapt the original NoMAD into the Swedish version S-NoMAD and to evaluate its psychometric properties based on a pilot test in a health care context including in-hospital, primary, and community care contexts.

Methods

A systematic approach with a four-step process was utilized, including forward and backward translation and expert reviews for the test and improvement of content validity of the S-NoMAD in different stages of development. The final S-NoMAD version was then used for process evaluation in a pilot study aimed at the implementation of a new working method for individualized care planning. The pilot was executed in two hospitals, four health care centres, and two municipalities in a region in northern Sweden. The S-NoMAD pilot results were analysed for validity using confirmatory factor analysis, i.e. a one-factor model fitted for each of the four constructs of the S-NoMAD. Cronbach’s alpha was used to ascertain the internal consistency reliability.

Results

In the pilot, S-NoMAD data were collected from 144 individuals who were different health care professionals or managers. The initial factor analysis model showed good fit for two of the constructs (Coherence and Cognitive Participation) and unsatisfactory fit for the remaining two (Collective Action and Reflexive Monitoring) based on three items. Deleting those items from the model yielded a good fit and good internal consistency (alphas between 0.78 and 0.83). However, the estimation of correlations between the factors showed that the factor Reflexive Monitoring was highly correlated (around 0.9) with the factors Coherence and Collective Action.

Conclusions

The results show initial satisfactory psychometric properties for the translation and first validation of the S-NoMAD. However, development of a highly valid and reliable instrument is an iterative process, requiring more extensive validation in various settings and populations. Thus, in order to establish the validity and reliability of the S-NoMAD, additional psychometric testing is needed.

     

Microbial biomass C,N and P in two arctic soils and responses to addition of NPK fertilizer and sugar: implications for plant nutrient uptake

The soil microbial carbon (C), nitrogen (N) and phosphorus (P) pools were quantified in the organic horizon of soils from an arctic/alpine low-altitude heath and a high-altitude fellfield by the fumigation-extraction method before and after factorial addition of sugar, NPK fertilizer and benomyl, a fungicide. In unamended soil, microbial C, N and P made up 3.3–3.6%, 6.1–7.3% and 34.7% of the total soil C, N and P content, respectively. The inorganic extractable N pool was below 0.1% and the inorganic extractable P content slightly less than 1% of the total soil pool sizes. Benomyl addition in spring and summer did not affect microbial C or nutrient content analysed in the autumn. Sugar amendments increased microbial C by 15 and 37% in the two soils, respectively, but did not affect the microbial nutrient content, whereas inorganic N and P either declined significantly or tended to decline. The increased microbial C indicates that the microbial biomass also increased but without a proportional enhancement of N and P uptake. NPK addition did not affect the amount of microbial C but almost doubled the microbial N pool and more than doubled the P pool. A separate study has shown that CO₂ evolution increased by more than 50% after sugar amendment and by about 30% after NPK and NK additions to one of the soils. Hence, the microbial biomass did not increase in response to NPK addition, but the microbes immobilized large amounts of the added nutrients and, judging by the increased CO₂ evolution, their activity increased. We conclude: (1) that microbial biomass production in these soils is stimulated by labile carbon and that the microbial activity is stimulated by both labile C and by nutrients (N); (2) that the microbial biomass is a strong sink for nutrients and that the microbial community probably can withdraw substantial amounts of nutrients from the inorganic, plant-available pool, at least periodically; (3) that temporary declines in microbial populations are likely to release a flush of inorganic nutrients to the soil, particularly P of which the microbial biomass contained more than one third of the total soil pool; and (4) that the mobilization-immobilization cycles of nutrients coupled to the population dynamics of soil organisms can be a significant regulating factor for the nutrient supply to the primary producers, which are usually strongly nutrient-limited in arctic ecosystems.     

Structure and organization of pigMHC class IIDRB genes: evidence for genetic exchange between loci

The pig major histocompatibility complexDRB genes were studied by polymerase chain reaction (PCR) amplification of exon 2 from eight domestic pigs and two European wild boars. Sequence comparisons together with a phylogenetic analysis showed the existence of at least threeDRB genes of which only one appears to be expressed. The two putativeDRB pseudogenes contained delections in exon 2, making it possible to confirm the presence of three non-allelicDRB genes by analyzing the length polymorphism of the amplified PCR products. The expressed gene shows allelic polymorphism at the same positions as in the humanDRB1 gene. In addition this pig gene shows extensive allelic polymorphism at positions 84–88, whereas, e.g., humanDRB genes do not. Surprisingly, the the two putativeDRB pseudogenes also display a considerable amount of allelic polymorphism, albeit of a different character as compared with the expressedDRB gene. Short stretches of sequences are shared between individual alleles at different loci. These sequence similarities cannot be due to natural selection, since two of the threeDRB genes involved are polymorphic pseudogenes constituting allelic series that have diverged after the inactivation event. Instead, the results indicate that the sequences have been exchanged between theDRB genes by intergenic recombination. The nucleotide sequence data reported in this paper have been submitted to the EMBL/GenBank nucleotide sequence databases and have been assigned the accession numbers L36567 (DRB1 ^* 1) L36568 (DRB1 ^* 2), L36569 (DRB1 ^* 3), L36570 (DRB1 ^* 4), L36571 (DRB1 ^* 5), L36572 (DRB1 ^* 6), L36573 (DRB1 ^* 7), L36574 (DRB1 ^* 8), L36575 (DRB2 ^* 1), L36576 (DRB2 ^* 2A), L36577 (DRB2 ^* 2B), L36578 (DRB2 ^* 2C), L36579 (DRB1 ^* 2D), L36580 (DRB2 ^* 3), L36581 (DRB2 ^* 4), L36582 (DRB3 ^* 1A), L36583 (DRB3 ^* 1B), L36584 (DRB3 ^* 1C), L36585 (DRB3 ^* 1D)