Assembling the Tree of Life in Europe (AToLE)

A network of scientists under the umbrella of 'Assembling the Tree of Life in Europe (AToLE)' seeks funding under the FP7-Theme: Cooperation - Environment (including Climate Change and Biodiversity Conservation) programme of the European Commission.
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Global Genome Biodiversity Network:saving a blueprint of the Tree of Life - a botanical perspective

Background Genomic research depends upon access to DNA or tissue collected and preserved according to high-quality standards. At present, the collections in most natural history museums do not sufficiently address these standards, making them often hard or impossible to use for whole-genome sequencing or transcriptomics. In response to these challenges, natural history museums, herbaria, botanical gardens and other stakeholders have started to build high-quality biodiversity biobanks. Unfortunately, information about these collections remains fragmented, scattered and largely inaccessible. Without a central registry or even an overview of relevant institutions, it is difficult and time-consuming to locate the needed samples. Scope The Global Genome Biodiversity Network (GGBN) was created to fill this vacuum by establishing a one-stop access point for locating samples meeting quality standards for genome-scale applications, while complying with national and international legislations and conventions. Increased accessibility to genomic samples will further genomic research and development, conserve genetic resources, help train the next generation of genome researchers and raise the visibility of biodiversity collections. Additionally, the availability of a data-sharing platform will facilitate identification of gaps in the collections, thereby empowering targeted sampling efforts, increasing the breadth and depth of preservation of genetic diversity. The GGBN is rapidly growing and currently has 41 members. The GGBN covers all branches of the Tree of Life, except humans, but here the focus is on a pilot project with emphasis on ‘harvesting’ the Tree of Life for vascular plant taxa to enable genome-level studies. Conclusion While current efforts are centred on getting the existing samples of all GGBN members online, a pilot project, GGI-Gardens, has been launched as proof of concept. Over the next 6 years GGI-Gardens aims to add to the GGBN high-quality genetic material from at least one species from each of the approx. 460 vascular plant families and one species from half of the approx. 15 000 vascular plant genera

The plasma level of soluble urokinase receptor is elevated in patients with Streptococcus pneumoniae bacteraemia and predicts mortality

ABSTRACTThis multicentre prospective study was conducted to investigate whether the level of the soluble form of urokinase-type plasminogen activator receptor (suPAR) is elevated during pneumococcal bacteraemia and is of predictive value in the early stage of the disease. Plasma levels of suPAR were increased significantly (median 5.5; range 2.4–21.0 ng/mL) in 141 patients with pneumococcal bacteraemia, compared to 31 healthy controls (median 2.6, range 1.5–4.0 ng/mL, p 0.001). Furthermore, suPAR levels were elevated significantly in patients who died from the infection (n = 24) compared to survivors (n = 117; p < 0.001). No correlation was found between suPAR levels and C-reactive protein. In univariate logistic regression analysis, hypotension, renal failure, cerebral symptoms and high serum concentrations of protein YKL-40 and suPAR were associated significantly with mortality (p < 0.05). In multivariate analysis, only suPAR remained a significant predictor of death (mortality rate of 13 for suPAR levels of > 10 ng/mL; 95% CI: 1.1–158). The increase in suPAR levels may reflect increased expression by vascular or inflammatory cells in the setting of pneumococcal sepsis. This plasma protein may be used to identify patients who are severely ill with pneumococcal bacteraemia

Pre-treatment of blood samples reveal normal blood hypocretin/orexin signal in narcolepsy type 1

The hypocretin/orexin system regulates arousal through central nervous system mechanisms and plays an important role in sleep, wakefulness and energy homeostasis. It is unclear whether hypocretin peptides are also present in blood due to difficulties in measuring reliable and reproducible levels of the peptides in blood samples. Lack of hypocretin signalling causes the sleep disorder narcolepsy type 1, and low concentration of cerebrospinal fluid hypocretin-l/oreadn-A peptide is a hallmark of the disease. This measurement has high diagnostic value, but performing a lumbar puncture is not without discomfort and possible complications for the patient. A blood-based test to assess hypocretin-1 deficiency would therefore be of obvious benefit. We here demonstrate that heating plasma or scrum samples to 65 degrees C for 30 min at pH 8 significantly increases hypocretin-1 immunoreactivity enabling stable and reproducible measurement of hypocretin-1 in blood samples. Specificity of the signal was verified by high-performance liquid chromatography and by measuring blood samples from mice lacking hypocretin. Unspecific background signal in the assay was high. Using our method, we show that hypocretin-1 immunoreactivity in blood samples from narcolepsy type 1 patients does not differ from the levels detected in control samples. The data presented here suggest that hypocretin-1 is present in the blood stream in the low picograms per millilitres range and that peripheral hypocretin-1 concentrations are unchanged in narcolepsy type 1

Different partial volume correction methods lead to different conclusions: An 18F-FDG-PET study of aging.

A cross-sectional group study of the effects of aging on brain metabolism as measured with 18F-FDG-PET was performed using several different partial volume correction (PVC) methods: no correction (NoPVC), Meltzer (MZ), Müller-Gärtner (MG), and the symmetric geometric transfer matrix (SGTM) using 99 subjects aged 65-87years from the Harvard Aging Brain study. Sensitivity to parameter selection was tested for MZ and MG. The various methods and parameter settings resulted in an extremely wide range of conclusions as to the effects of age on metabolism, from almost no changes to virtually all of cortical regions showing a decrease with age. Simulations showed that NoPVC had significant bias that made the age effect on metabolism appear to be much larger and more significant than it is. MZ was found to be the same as NoPVC for liberal brain masks; for conservative brain masks, MZ showed few areas correlated with age. MG and SGTM were found to be similar; however, MG was sensitive to a thresholding parameter that can result in data loss. CSF uptake was surprisingly high at about 15% of that in gray matter. The exclusion of CSF from SGTM and MG models, which is almost universally done, caused a substantial loss in the power to detect age-related changes. This diversity of results reflects the literature on the metabolism of aging and suggests that extreme care should be taken when applying PVC or interpreting results that have been corrected for partial volume effects. Using the SGTM, significant age-related changes of about 7% per decade were found in frontal and cingulate cortices as well as primary visual and insular cortices

Cow Farmers’ Homes Host More Diverse Airborne Bacterial Communities Than Pig Farmers’ Homes and Suburban Homes

Living on a farm has been linked to a lower risk of immunoregulatory disorders, such as asthma, allergy, and inflammatory bowel disease. It is hypothesized that a decrease in the diversity and composition of indoor microbial communities is a sensible explanation for the upsurge in immunoregulatory diseases, with airborne bacteria contributing to this protective effect. However, the composition of this potentially beneficial microbial community in various farm and suburban indoor environments is still to be characterized. We collected settled airborne dust from stables and the associated farmers’ homes and from suburban homes using electrostatic dust collectors (EDCs) over a period of 14 days. Then, quantitative PCR (qPCR) was used to assess bacterial abundance. The V3–V4 region of the bacterial 16S rRNA gene was amplified and sequenced using Ilumina MiSeq in order to assess microbial diversity. The Divisive Amplicon Denoising Algorithm (DADA2) algorithm was used for the inference of amplicon sequence variants from amplicon data. Airborne bacteria were significantly more abundant in farmers’ indoor environments than in suburban homes (p < 0.001). Cow farmers’ homes had significantly higher bacterial diversity than pig farmers’ and suburban homes (p < 0.001). Bacterial taxa, such as Firmicutes, Prevotellaceae, Lachnospiraceae, and Lactobacillus were significantly more abundant in farmers’ homes than suburban homes, and the same was true for beneficial intestinal bacterial species, such as Lactobacillus amylovorus, Eubacterium hallii, and Faecalibacterium prausnitzii. Furthermore, we found a higher similarity between bacterial communities in individual farmers’ homes and their associated cow stables than for pig stables. Our findings contribute with important knowledge on bacterial composition, abundance, and diversity in different environments, which is highly valuable in the discussion on how microbial exposure may contribute to the development of immune-mediated diseases in both children and adults.publishedVersio

A comparative analysis of European press coverage of children and the internet

This article reports a content analysis of press coverage of children and the internet in order to examine cross-cultural similarities and differences in the news values framing accounts of the benefits from and risks facing children online. By comparing media reporting in 14 European countries, the study found greater coverage of online risks than opportunities across Europe, which appears to be due to the high position of crime stories on the news agenda.. Thus readers, including parents, are exposed to media representations that often show the online world as being risky for children, which may affect perceptions of the prevalence of risk. However, there is national variation in terms of which risks receive more press attention, meaning that parents in different countries are potentially sensitised to different risks

Lung cancer in HIV patients and their parents: A Danish cohort study

<p>Abstract</p> <p>Background</p> <p>HIV patients are known to be at increased risk of lung cancer but the risk factors behind this are unclear.</p> <p>Methods</p> <p>We estimated the cumulative incidence and relative risk of lung cancer in 1) a population of all Danish HIV patients identified from the Danish HIV Cohort Study (n = 5,053) and a cohort of population controls matched on age and gender (n = 50,530) (study period; 1995 - 2009) and 2) their parents (study period; 1969 - 2009). Mortality and relative risk of death after a diagnosis of lung cancer was estimated in both populations.</p> <p>Results</p> <p>29 (0.6%) HIV patients vs. 183 (0.4%) population controls were diagnosed with lung cancer in the observation period. HIV patients had an increased risk of lung cancer (adjusted incidence rate ratio (IRR); 2.38 (95% CI; 1.61 - 3.53)). The IRR was considerably increased in HIV patients who were smokers or former smokers (adjusted IRR; 4.06 (95% CI; 2.66 - 6.21)), male HIV patients with heterosexual route of infection (adjusted IRR; 4.19 (2.20 - 7.96)) and HIV patients with immunosuppression (adjusted IRR; 3.25 (2.01 - 5.24)). Both fathers and mothers of HIV patients had an increased risk of lung cancer (adjusted IRR for fathers; 1.31 (95% CI: 1.09 - 1.58), adjusted IRR for mothers 1.35 (95% CI: 1.07 - 1.70)). Mortality after lung cancer diagnose was increased in HIV patients (adjusted mortality rate ratio 2.33 (95%CI; 1.51 - 3.61), but not in the parents. All HIV patients diagnosed with lung cancer were smokers or former smokers.</p> <p>Conclusion</p> <p>The risk was especially increased in HIV patients who were smokers or former smokers, heterosexually infected men or immunosuppressed. HIV appears to be a marker of behavioural or family related risk factors that affect the incidence of lung cancer in HIV patients.</p

Mitochondrial Data in Monocot Phylologenetics

Mitochondrial sequences are an important source of data in animal phylogenetics, equivalent in importance to plastid sequences in plants. However, in recent years plant systematists have begun exploring the mitochondrial genome as a source of phylogenetically useful characters. The plant mitochondrial genome is renowned for its variability in size, structure, and gene organization, but this need not be of concern for the application of sequence data in phylogenetics. However, the incorporation of reverse transcribed mitochondrial genes ( processed paralogs ) and the recurring transfer of genes from the mitochondrion to the nucleus are evolutionary events that must be taken into account. RNA editing of mitochondrial genes is sometimes considered a problem in phylogenetic reconstruction, but we regard it only as a mechanism that may increase variability at edited sites and change the codon position bias accordingly. Additionally, edited sites may prove a valuable tool in identifying processed paralogs. An overview of genes and sequences used in phylogenetic studies of angiosperms is presented. In the monocots, a large amount of mitochondrial sequence data is being collected together with sequence data from plastid and nuclear genes, thus offering an opportunity to compare data from different genomic compartments. The mitochondrial and plastid data are incongruent when organelle gene trees are reconstructed. Possible reasons for the observed incongruence involve sampling of paralogous sequences and highly divergent substitution rates, potentially leading to longbranch attraction. The above problems are addressed in Acorales, Alismatales, Poales, Liliaceae, the Anthericum clade (in Agavaceae), and in some achlorophyllous taxa