Towards a unified paradigm for sequence‐based identification of fungi

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database ( http://unite.ut.ee ) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third‐party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released ( http://unite.ut.ee/repository.php ) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web‐based sequence management system in UNITE.     

β₁-Adrenergic receptors increase UCP1 in human MADS brown adipocytes and rescue cold-acclimated β₃-adrenergic receptor-knockout mice via nonshivering thermogenesis

With the finding that brown adipose tissue is present and negatively correlated to obesity in adult man, finding the mechanism(s) of how to activate brown adipose tissue in humans could be important in combating obesity, type 2 diabetes, and their complications. In mice, the main regulator of nonshivering thermogenesis in brown adipose tissue is norepinephrine acting predominantly via β(3)-adrenergic receptors. However, vast majorities of β(3)-adrenergic agonists have so far not been able to stimulate human β(3)-adrenergic receptors or brown adipose tissue activity, and it was postulated that human brown adipose tissue could be regulated instead by β(1)-adrenergic receptors. Therefore, we have investigated the signaling pathways, specifically pathways to nonshivering thermogenesis, in mice lacking β(3)-adrenergic receptors. Wild-type and β(3)-knockout mice were either exposed to acute cold (up to 12 h) or acclimated for 7 wk to cold, and parameters related to metabolism and brown adipose tissue function were investigated. β(3)-knockout mice were able to survive both acute and prolonged cold exposure due to activation of β(1)-adrenergic receptors. Thus, in the absence of β(3)-adrenergic receptors, β(1)-adrenergic receptors are effectively able to signal via cAMP to elicit cAMP-mediated responses and to recruit and activate brown adipose tissue. In addition, we found that in human multipotent adipose-derived stem cells differentiated into functional brown adipocytes, activation of either β(1)-adrenergic receptors or β(3)-adrenergic receptors was able to increase UCP1 mRNA and protein levels. Thus, in humans, β(1)-adrenergic receptors could play an important role in regulating nonshivering thermogenesis.     

Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA

DNA sequencing technology has proven very valuable for analysing the microbiota of poorly accessible ecosystems such as hydrothermal vents. Using a combination of amplicon and shotgun sequencing of small-subunit rRNA and its gene, we examined the composition and diversity of microbial communities from the recently discovered Jan Mayen vent field, located on Mohn's Ridge in the Norwegian-Greenland Sea. The communities were dominated by the epsilonproteobacterial genera Sulfurimonas and Sulfurovum. These are mesophiles involved in sulphur metabolism and typically found in vent fluid mixing zones. Composition and diversity predictions differed systematically between extracted DNA and RNA samples as well as between amplicon and shotgun sequencing. These differences were more substantial than those between two biological replicates. Amplicon vs. shotgun sequencing differences could be explained to a large extent by bias introduced during PCR, caused by preferential primer-template annealing, while DNA vs. RNA differences were thought to be caused by differences between the activity levels of taxa. Further, predicted diversity from RNA samples was consistently lower than that from DNA. In summary, this study illustrates how different methods can provide complementary ecological insights.     

Cytochrome p450‐dependent disposition of the enantiomers of citalopram and its metabolites: In vivo studies in Sprague‐Dawley and Dark Agouti rats

The female Sprague‐Dawley (SD) and Dark Agouti (DA) rats are considered the animal counterparts of the human extensive and poor metabolizer cytochrome P450 (CYP) 2D6 phenotypes, respectively. The aim of this work was to study possible rat strain differences in the steady‐state pharmacokinetics of the (+)‐(S)‐ and (−)‐(R)‐enantiomers of citalopram and its demethylated metabolites. A chronic drug treatment regimen (15 mg/kg daily) was implemented for 13 days in separate groups of SD (n = 9) and DA (n = 9) rats by using osmotic pumps. The concentrations of citalopram and two major metabolites in serum and two brain regions were analyzed by an enantioselective high‐performance liquid chromatography assay. Higher serum and brain levels of citalopram and demethylcitalopram, but lower levels of didemethylcitalopram, were observed in DA rats when compared with SD rats. The enantiomeric (S/R) concentrations ratios of citalopram were lower in the DA rats when compared with the SD rats (0.53 ± 0.05 vs. 0.80 ± 0.03, P < 0.001), indicating a possibly decreased capacity in the metabolism of the (−)‐(R)‐enantiomer in the DA rats. This study shows that CYP2D deficiency results in steady‐state pharmacokinetic differences of the enantiomers of citalopram and its metabolites. Chirality, 2011. © 2010 Wiley‐Liss, Inc.     

Unexpected evidence for active brown adipose tissue in adult humans

The contention that brown adipose tissue is absent in adult man has meant that processes attributed to active brown adipose tissue in experimental animals (mainly rodents), i.e., classical nonshivering thermogenesis, adaptive adrenergic thermogenesis, diet-induced thermogenesis, and antiobesity, should be either absent or attributed to alternative (unknown) mechanisms in man. However, serendipidously, as a consequence of the use of fluorodeoxyglucose positron emission tomography (FDG PET) to trace tumor metastasis, observations that may change that notion have recently been made. These tomography scans have visualized symmetrical areas of increased tracer uptake in the upper parts of the human body; these areas of uptake correspond to brown adipose tissue. We examine here the published observations from a viewpoint of human physiology. The human depots are somewhat differently located from those in rodents, the main depots being found in the supraclavicular and the neck regions with some additional paravertebral, mediastinal, para-aortic, and suprarenal localizations (but no interscapular). Brown adipose tissue activity in man is acutely cold induced and is stimulated via the sympathetic nervous system. The prevalence of active brown adipose tissue in normal adult man can be only indirectly estimated, but it would seem that the prevalence of active brown adipose tissue in the population may be at least in the range of some tens of percent. We conclude that a substantial fraction of adult humans possess active brown adipose tissue that thus has the potential to be of metabolic significance for normal human physiology as well as to become pharmaceutically activated in efforts to combat obesity.     

Online Respondent-Driven Sampling for Studying Contact Patterns Relevant for the Spread of Close-Contact Pathogens: A Pilot Study in Thailand

Background

Information on social interactions is needed to understand the spread of airborne infections through a population. Previous studies mostly collected egocentric information of independent respondents with self-reported information about contacts. Respondent-driven sampling (RDS) is a sampling technique allowing respondents to recruit contacts from their social network. We explored the feasibility of webRDS for studying contact patterns relevant for the spread of respiratory pathogens.

Materials and Methods

We developed a webRDS system for facilitating and tracking recruitment by Facebook and email. One-day diary surveys were conducted by applying webRDS among a convenience sample of Thai students. Students were asked to record numbers of contacts at different settings and self-reported influenza-like-illness symptoms, and to recruit four contacts whom they had met in the previous week. Contacts were asked to do the same to create a network tree of socially connected individuals. Correlations between linked individuals were analysed to investigate assortativity within networks.

Results

We reached up to 6 waves of contacts of initial respondents, using only non-material incentives. Forty-four (23.0%) of the initially approached students recruited one or more contacts. In total 257 persons participated, of which 168 (65.4%) were recruited by others. Facebook was the most popular recruitment option (45.1%). Strong assortative mixing was seen by age, gender and education, indicating a tendency of respondents to connect to contacts with similar characteristics. Random mixing was seen by reported number of daily contacts.

Conclusions

Despite methodological challenges (e.g. clustering among respondents and their contacts), applying RDS provides new insights in mixing patterns relevant for close-contact infections in real-world networks. Such information increases our knowledge of the transmission of respiratory infections within populations and can be used to improve existing modelling approaches. It is worthwhile to further develop and explore webRDS for the detection of clusters of respiratory symptoms in social networks.     

Soil moisture variations affect short‐term plant‐microbial competition for ammonium,glycine, and glutamate

We tested whether the presence of plant roots would impair the uptake of ammonium (), glycine, and glutamate by microorganisms in a deciduous forest soil exposed to constant or variable moisture in a short‐term (24‐h) experiment. The uptake of ¹⁵NH₄ and dual labeled amino acids by the grass Festuca gigantea L. and soil microorganisms was determined in planted and unplanted soils maintained at 60% WHC (water holding capacity) or subject to drying and rewetting. The experiment used a design by which competition was tested in soils that were primed by plant roots to the same extent in the planted and unplanted treatments. Festuca gigantea had no effect on microbial N uptake in the constant moist soil, but its presence doubled the microbial uptake in the dried and rewetted soil compared with the constant moist. The drying and rewetting reduced by half or more the uptake by F. gigantea, despite more than 60% increase in the soil concentration of . At the same time, the amino acid and ‐ N became equally valued in the plant uptake, suggesting that plants used amino acids to compensate for the lower acquisition. Our results demonstrate the flexibility in plant‐microbial use of different N sources in response to soil moisture fluctuations and emphasize the importance of including transient soil conditions in experiments on resource competition between plants and soil microorganisms. Competition between plants and microorganisms for N is demonstrated by a combination of removal of one of the potential competitors, the plant, and subsequent observations of the uptake of N in the organisms in soils that differ only in the physical presence and absence of the plant during a short assay. Those conditions are necessary to unequivocally test for competition.     

Implementation of Web-Based Respondent-Driven Sampling among Men Who Have Sex with Men in Vietnam

Objective

Lack of representative data about hidden groups, like men who have sex with men (MSM), hinders an evidence-based response to the HIV epidemics. Respondent-driven sampling (RDS) was developed to overcome sampling challenges in studies of populations like MSM for which sampling frames are absent. Internet-based RDS (webRDS) can potentially circumvent limitations of the original RDS method. We aimed to implement and evaluate webRDS among a hidden population.

Methods and Design

This cross-sectional study took place 18 February to 12 April, 2011 among MSM in Vietnam. Inclusion criteria were men, aged 18 and above, who had ever had sex with another man and were living in Vietnam. Participants were invited by an MSM friend, logged in, and answered a survey. Participants could recruit up to four MSM friends. We evaluated the system by its success in generating sustained recruitment and the degree to which the sample compositions stabilized with increasing sample size.

Results

Twenty starting participants generated 676 participants over 24 recruitment waves. Analyses did not show evidence of bias due to ineligible participation. Estimated mean age was 22 years and 82% came from the two large metropolitan areas. 32 out of 63 provinces were represented. The median number of sexual partners during the last six months was two. The sample composition stabilized well for 16 out of 17 variables.

Conclusion

Results indicate that webRDS could be implemented at a low cost among Internet-using MSM in Vietnam. WebRDS may be a promising method for sampling of Internet-using MSM and other hidden groups.     

Genetic diversity among VRE isolates from Swedish broilers with the coincidental finding of transferrable decreased susceptibility to narasin

Aims: In this study, the molecular diversity among clones of vancomycin resistant Enterococcus faecium with vanA gene (VRE) is investigated. The aims were to better understand why one clone is predominant in Swedish broiler production and to better assess the potential for zoonotic gene transfer from the different clones. Methods and Results: Twenty‐six isolates were separated into 11 clones. Vancomycin resistance was transferrable from the predominant and five minority clones. Decreased susceptibility to narasin was co‐transferred with vancomycin resistance in four clones, including the predominant. The plasmid addiction system axe‐txe was not detected, and the ω‐ε‐ζ system was detected in one of the minority clones but was not co‐transferred with vancomycin resistance. Conclusions: The results do not explain why one clone is predominant among VRE in Swedish broiler production but confirms the potential for zoonotic spread of vancomycin resistance genes. The near absence of investigated plasmid addiction systems indicates that they do not play an important role in the epidemiology of VRE in Swedish broiler production. The finding that decreased susceptibility to narasin can be co‐transferred with the vanA gene indicates that the use of narasin might play a role in the persistence of vancomycin resistance in enterococci colonizing Swedish broilers. Significance and Impact of the Study: This is, to our knowledge, the first report of transferrable decreased susceptibility to narasin.