Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons

<p>Abstract</p> <p>Background</p> <p>Urine within the urinary tract is commonly regarded as "sterile" in cultivation terms. Here, we present a comprehensive in-depth study of bacterial 16S rDNA sequences associated with urine from healthy females by means of culture-independent high-throughput sequencing techniques.</p> <p>Results</p> <p>Sequencing of the V1V2 and V6 regions of the 16S ribosomal RNA gene using the 454 GS FLX system was performed to characterize the possible bacterial composition in 8 culture-negative (<100,000 CFU/ml) healthy female urine specimens. Sequences were compared to 16S rRNA databases and showed significant diversity, with the predominant genera detected being <it>Lactobacillus</it>, <it>Prevotella </it>and <it>Gardnerella</it>. The bacterial profiles in the female urine samples studied were complex; considerable variation between individuals was observed and a common microbial signature was not evident. Notably, a significant amount of sequences belonging to bacteria with a known pathogenic potential was observed. The number of operational taxonomic units (OTUs) for individual samples varied substantially and was in the range of 20 - 500.</p> <p>Conclusions</p> <p>Normal female urine displays a noticeable and variable bacterial 16S rDNA sequence richness, which includes fastidious and anaerobic bacteria previously shown to be associated with female urogenital pathology.</p

The Danish Shoulder Arthroplasty Registry: clinical outcome and short-term survival of 2,137 primary shoulder replacements

The Danish Shoulder Arthroplasty Registry (DSR) was established in 2004. Data are reported electronically by the surgeons. Patient-reported outcome is collected 10–14 months postoperatively using the Western Ontario osteoarthritis of the shoulder index (WOOS). 2,137 primary shoulder arthroplasties (70% women) were reported to the registry between January 2006 and December 2008. Mean age at surgery was 69 years (SD 12). The most common indications were a displaced proximal humeral fracture (54%) or osteoarthritis (30%). 61% were stemmed hemiarthroplasties, 28% resurfacing hemiarthroplasties, 8% reverse shoulder arthroplasties, and 3% total arthroplasties. Median WOOS was 59% (IQR: 37–82). 5% had been revised by the end of June 2010. The most frequent indications for revision were dislocation or glenoid attrition

Geologiske kort i Danmark - hvad viser de kvartærgeologiske kort

Denne artikel er et svar p&aring; foreg&aring;ende&nbsp;debatindl&aelig;g om &ldquo;det &aelig;rlige&nbsp;jordartskort&rdquo;, hvori forfatterne forklarer&nbsp;bagrunden for fremstillingen&nbsp;af geologiske kort i Danmark

Analysis of a sprint ski race and associated laboratory determinants of world-class performance

This investigation was designed to analyze the time-trial (STT) in an international cross-country skiing sprint skating competition for (1) overall STT performance and relative contributions of time spent in different sections of terrain, (2) work rate and kinematics on uphill terrain, and (3) relationships to physiological and kinematic parameters while treadmill roller ski skating. Total time and times in nine different sections of terrain by 12 world-class male sprint skiers were determined, along with work rate and kinematics for one specific uphill section. In addition, peak oxygen uptake (VO2peak), gross efficiency (GE), peak speed (Vpeak), and kinematics in skating were measured. Times on the last two uphill and two final flat sections were correlated to overall STT performance (r = ~−0.80, P < 0.001). For the selected uphill section, speed was correlated to cycle length (r = −0.75, P < 0.01) and the estimated work rate was approximately 160% of peak aerobic power. VO2peak, GE, Vpeak, and peak cycle length were all correlated to STT performance (r = ~−0.85, P < 0.001). More specifically, VO2peak and GE were correlated to the last two uphill and two final flat section times, whereas Vpeak and peak cycle length were correlated to times in all uphill, flat, and curved sections except for the initial section (r = ~−0.80, P < 0.01). Performances on uphill and flat terrain in the latter part were the most significant determinants of overall STT performance. Peak oxygen uptake, efficiency, peak speed, and peak cycle length were strongly correlated to overall STT performance, as well as to performance in different sections of the race

The Atlantic salmon genome provides insights into rediploidization

The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.publishedVersio

Development of Transgenic Cloned Pig Models of Skin Inflammation by DNA Transposon-Directed Ectopic Expression of Human β1 and α2 Integrin

Integrins constitute a superfamily of transmembrane signaling receptors that play pivotal roles in cutaneous homeostasis by modulating cell growth and differentiation as well as inflammatory responses in the skin. Subrabasal expression of integrins α2 and/or β1 entails hyperproliferation and aberrant differentiation of keratinocytes and leads to dermal and epidermal influx of activated T-cells. The anatomical and physiological similarities between porcine and human skin make the pig a suitable model for human skin diseases. In efforts to generate a porcine model of cutaneous inflammation, we employed the Sleeping Beauty DNA transposon system for production of transgenic cloned Göttingen minipigs expressing human β1 or α2 integrin under the control of a promoter specific for subrabasal keratinocytes. Using pools of transgenic donor fibroblasts, cloning by somatic cell nuclear transfer was utilized to produce reconstructed embryos that were subsequently transferred to surrogate sows. The resulting pigs were all transgenic and harbored from one to six transgene integrants. Molecular analyses on skin biopsies and cultured keratinocytes showed ectopic expression of the human integrins and localization within the keratinocyte plasma membrane. Markers of perturbed skin homeostasis, including activation of the MAPK pathway, increased expression of the pro-inflammatory cytokine IL-1α, and enhanced expression of the transcription factor c-Fos, were identified in keratinocytes from β1 and α2 integrin-transgenic minipigs, suggesting the induction of a chronic inflammatory phenotype in the skin. Notably, cellular dysregulation obtained by overexpression of either β1 or α2 integrin occurred through different cellular signaling pathways. Our findings mark the creation of the first cloned pig models with molecular markers of skin inflammation. Despite the absence of an overt psoriatic phenotype, these animals may possess increased susceptibility to severe skin damage-induced inflammation and should be of great potential in studies aiming at the development and refinement of topical therapies for cutaneous inflammation including psoriasis

Alterations of microbiota in urine from women with interstitial cystitis

Background Interstitial Cystitis (IC) is a chronic inflammatory condition of the bladder with unknown etiology. The aim of this study was to characterize the microbial community present in the urine from IC female patients by 454 high throughput sequencing of the 16S variable regions V1V2 and V6. The taxonomical composition, richness and diversity of the IC microbiota were determined and compared to the microbial profile of asymptomatic healthy female (HF) urine. Results The composition and distribution of bacterial sequences differed between the urine microbiota of IC patients and HFs. Reduced sequence richness and diversity were found in IC patient urine, and a significant difference in the community structure of IC urine in relation to HF urine was observed. More than 90% of the IC sequence reads were identified as belonging to the bacterial genus Lactobacillus, a marked increase compared to 60% in HF urine. Conclusion The 16S rDNA sequence data demonstrates a shift in the composition of the bacterial community in IC urine. The reduced microbial diversity and richness is accompanied by a higher abundance of the bacterial genus Lactobacillus, compared to HF urine. This study demonstrates that high throughput sequencing analysis of urine microbiota in IC patients is a powerful tool towards a better understanding of this enigmatic disease

Fracture valleys in central Jylland – a neotectonic feature

Geomorphological indications of tectonic activity in the Danish glacial landscape were pointed out already by Milthers (1916, 1948). He described a conspicuous system of N–S-trending, narrow valleys in central Jylland and interpreted them as fault-generated features (fracture valleys). The valleys occur in the area between Ulstrup and Hammel and in a smaller area near Skjød (Fig. 1). The most significant valley system is found near Hvorslev, and it is here referred to as the Hvorslev lineaments (Fig. 1)

Translation and validation of the Western Ontario Osteoarthritis of the Shoulder (WOOS) index – the Danish version

BACKGROUND AND PURPOSE: The Western Ontario Osteoarthritis of the Shoulder (WOOS) index is a patient-reported, disease-specific questionnaire for the measurement of the quality-of-life in patients with osteoarthritis. The purpose of this study was to describe the process used to translate the WOOS into Danish and to test the translation in a Danish population, in terms of validity, reliability, and responsiveness. MATERIAL AND METHODS: The translation of the WOOS was done according to international standardized guidelines. The psychometric properties were tested in 20 consecutive patients. The eligibility criteria were: a diagnosis of osteoarthritis without symptomatic rotator cuff pathology and treated with primary shoulder replacement. Patients were excluded only in the case of other pathology of the upper extremity or in the case of cognitive or linguistic impairment compromising the ability to complete the questionnaires. RESULTS: The Pearson’s correlation coefficient between the WOOS and the Constant-Murley score (CMS), preoperatively was 0.62 (P = 0.004) and the correlation between the changes of score for the WOOS and CMS was 0.73 (P < 0.001). The correlation coefficient between the WOOS and the CMS, SF-36, and the Oxford Shoulder Score postoperatively was 0.82 (P < 0.001), 0.48 (P = 0.03), and 0.82 (P < 0.001), respectively. There were no floor and ceiling effects. The Cronbach’s alpha was 0.98. The intraclass correlation coefficient between test and retest was 0.96. The standardized response mean was 1.41, and effect size was 2.32. CONCLUSION: We have shown that the Danish version of the WOOS, translated according to international standardized guidelines, has substantial statistical and clinical psychometric properties at the same level as was described for the original version