Microbial genomic taxonomy

A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes, 70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups

Diurnal variability of precipitable water in the Baltic region, impact on transmittance of the direct solar radiation

Diurnal variations in the Integrated Precipitable Water Vapour (IPWV) are studied from GPS observations acquired at 32 sites in the Baltic region during 1996-2005. The seasonal means for spring and summer show a diurnal sinusoidal pattern of the IPWV with the maximum value in the afternoon. The peak-to-peak (PtP) value of the average diurnal IPWV cycle was 0.5 mm in the spring and 0.6 mm in the summer. In the autumn and in the winter the diurnal variations in IPWV show no clear patterns and the average PtP values of the noise-like signal are only 0.2-0.3 mm. The diurnal IPWV cycle can only be estimated by averaging data from many years because the IPWV can show fast and large variations, reaching up to 5 mm/hour during several hours. These are explained exclusively by changes in the synoptic situation and substitution of airmasses above the location of observations; two case studies with analyses of the vertical humidity profiles are presented. The impact on the transmittance of the direct solar radiation is evaluated

Synthesis and photochromic properties of a bis(diarylethene)-naphthopyran hybrid

The synthesis and photochromic properties of a triphotochromic molecule consisting of one naphthopyran flanked by two diarylethene units investigated by UV-Visible and NMR spectroscopies are reported. Six different states resulting from the open/closed naphthopyran associated with one or two open/cyclized diarylethenes have been characterized. Switching of the naphthopyran group is possible, independently of the state of the diarylethene groups, permitting the controlled generation of electronically connected diarylethene groups. However, the diarylethene groups cannot be closed if the naphthopyran group is open

Origin of the reduced exchange bias in epitaxial FeNi(111)/CoO(111) bilayer

We have employed Soft and Hard X-ray Resonant Magnetic Scattering and Polarised Neutron Diffraction to study the magnetic interface and the bulk antiferromagnetic domain state of the archetypal epitaxial Ni$_{81}$Fe$_{19}$(111)/CoO(111) exchange biased bilayer. The combination of these scattering tools provides unprecedented detailed insights into the still incomplete understanding of some key manifestations of the exchange bias effect. We show that the several orders of magnitude difference between the expected and measured value of exchange bias field is caused by an almost anisotropic in-plane orientation of antiferromagnetic domains. Irreversible changes of their configuration lead to a training effect. This is directly seen as a change in the magnetic half order Bragg peaks after magnetization reversal. A 30 nm size of antiferromagnetic domains is extracted from the width the (1/2 1/2 1/2) antiferromagnetic magnetic peak measured both by neutron and x-ray scattering. A reduced blocking temperature as compared to the measured antiferromagnetic ordering temperature clearly corresponds to the blocking of antiferromagnetic domains. Moreover, an excellent correlation between the size of the antiferromagnetic domains, exchange bias field and frozen-in spin ratio is found, providing a comprehensive understanding of the origin of exchange bias in epitaxial systems.Comment: 8 pages, 5 figures, submitte

Structural motifs of pre-nucleation clusters

Structural motifs of pre-nucleation clusters prepared in single, optically levitated supersaturated aqueous aerosol microparticles containing CaBr2 as a model system are reported. Cluster formation is identified by means of X-ray absorption in the Br K-edge regime. The salt concentration beyond the saturation point is varied by controlling the humidity in the ambient atmosphere surrounding the 15–30 μm microdroplets. This leads to the formation of metastable supersaturated liquid particles. Distinct spectral shifts in near-edge spectra as a function of salt concentration are observed, in which the energy position of the Br K-edge is red-shifted by up to 7.1 ± 0.4 eV if the dilute solution is compared to the solid. The K-edge positions of supersaturated solutions are found between these limits. The changes in electronic structure are rationalized in terms of the formation of pre- nucleation clusters. This assumption is verified by spectral simulations using first-principle density functional theory and molecular dynamics calculations, in which structural motifs are considered, explaining the experimental results. These consist of solvated CaBr2 moieties, rather than building blocks forming calcium bromide hexahydrates, the crystal system that is formed by drying aqueous CaBr2 solutions

Culturable aerobic bacteria from the upstream region of a karst water rivulet

The composition of 681 aerobic and heterotrophic strains that were isolated on two different media was assessed at four sampling points along a ~300 m stretch of a karst water rivulet. Based on partial sequence analysis of 16S rRNA genes, members of 35 genera were identified; however, only a few species dominated as their representatives were repeatedly isolated at different sampling sites. Determination of the phylum affiliation showed that the isolates included members of Bacteriodetes (especially the genus Flavobacterium) and Proteobacteria (mainly Pseudomonas and Stenotrophomonas). MALDI-TOF analysis and/or similarities of partial sequences of flavobacterial strains resulted in the generation of almost complete 16S rRNA gene sequences for 100 isolates, about 60 of which may represent novel phylospecies. The number as well as the intra-phylum distribution of the isolates changed with distance from the discharge site. While phylogenetically restricted at the spring, diversity increased at downstream sampling sites

Predictors of compliance with community-directed treatment with ivermectin for onchocerciasis control in Kabo area, southwestern Ethiopia

BACKGROUND: Compliance with annual ivermectin treatment is a major challenge in community-directed treatment with ivermectin (CDTI) implementation. There are individuals who do not comply with the annual mass treatment, which contributes to the continuity for disease transmission. Hence, ensuring high treatment coverage and sustained compliance should be given due emphasis in the control of onchocerciasis. The aim of this study was to determine CDTI compliance rate and predictors of compliance where the CDTI was in its 9(th) round in Kabo area, southwestern Ethiopia. METHODS: Community-based cross-sectional study was conducted in Kabo area, three weeks after the 9th round of annual ivermectin distribution. Systematic random sampling was used to select head of households and structured, pre-tested questionnaire was used to interview the study participants. Data was analyzed using SPSS version 16. Descriptive statistics was used to compute mean and standard deviation of continuous variables and frequency for categorical variables, while bivariate and multivariate logistic regressions were used to assess the effects of independent variables on the outcome variable. Variables which showed association in multivariate analysis were considered as final predictors of compliance and strength of association was measured through adjusted odds ratio (AOR). RESULTS: A total of 308 respondents (age range 18-70, mean age ± SD, 32.21 ± 9.64) participated in the study. Of these, 249 (80.8%) reported that they took ivermectin during the 9(th) round annual treatment. Significantly higher rate of treatment compliance was reported by participants age ≥35 years (AOR = 5.48, 95% CI; 1.97 - 15.23), participants who stayed in the area for more than ten years (AOR = 3.86, 95% CI; 1.83- 8.11), participants who perceive that they are at risk of contracting the disease(AOR = 7.05, 2.70- 18.43), participants who perceive community drug distributors (CDDs) are doing their work well (AOR = 2.35 95% CI; 1.15- 4.83) and participants who know at least one CDD in their village (AOR = 2.83, 95% CI; 1.26- 6.40). CONCLUSION: The majority of the study participants in the present study area complied with ivermectin treatment. Nevertheless, intervention packages should consider factors such as age, residence duration and community’s perception of the disease to improve compliance and make drug distribution sustainable

Comparison of individual and pooled urine samples for estimating the presence and intensity of Schistosoma haematobium infections at the population level

Background There is a lack of cost-effective diagnostic strategies to evaluate whether mass drug administration (MDA) programmes to control Schistosoma haematobium progress as anticipated. The purpose of this study is to provide a proof-of-principle for examination of pooled urine samples as a strategy for rapid assessment of presence and intensity of Schistosoma haematobium infections at the population level. Methods A total of 640 urine samples were collected from 520 school-aged children (520 at baseline and 120 at follow-up) during a clinical trial that was designed to assess the efficacy of praziquantel against Schistosoma haematobium infections in Ethiopia. Individual and pooled urine samples were screened using the filtration technique (volume of 10 ml urine) to determine the number of S. haematobium eggs in 10 ml of urine. Samples were pooled into pools of 5 (n = 128), 10 (n = 64) and 20 (n = 32) individual samples. The sensitivity, the probability of finding at least one egg in a pooled sample when the mean urine egg count (UEC) of the corresponding individual urine samples was not zero, was calculated for each pool size. UECs of a pooled examination strategy were compared with the mean UECs of the corresponding individual samples. Results The sensitivity of a pooled examination strategy was 50.6 % for pools of 5, 68.6 % for pools of 10 and 63.3 % for pools of 20. The sensitivity of a pooled examination strategy increased as a function of increasing mean UEC of the corresponding individual urine samples. For each of the three pool sizes, there was a significant positive correlation between mean UECs of individual and those obtained in pooled samples (correlation coefficient: 0.81 – 0.93). Examination of pools of 5 provided significantly lower UECs compared to the individual examination strategy (3.9 eggs/10 ml urine versus 5.0 eggs/10 ml urine). For pools of 10 (4.4 eggs/10 ml) and 20 (4.2 eggs/10 ml), no significant difference in UECs was observed. Conclusions Examination of pooled urine samples applying urine filtration holds promise for rapid assessment of intensity of S. haematobium infections, but may fail to detect presence of infections when endemicity is low. Further investigation is required to determine when and how pooling can be optimally implemented in monitoring of mass drug administration programmes