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High-throughput metabarcoding studies on fungi and other eukaryotic microorganisms are rapidly becoming more frequent and more complex, requiring researchers to handle ever increasing amounts of raw sequence data. Here, we provide a flexible pipeline for pruning and analyzing fungal barcode (ITS rDNA) data generated as paired-end reads on Illumina MiSeq sequencers. The pipeline presented includes specific steps fine-tuned for ITS, that are mostly missing from pipelines developed for prokaryotes. It (1) employs state of the art programs and follows best practices in fungal high-throughput metabarcoding; (2) consists of modules and scripts easily modifiable by the user to ensure maximum flexibility with regard to specific needs of a project or future methodological developments; and (3) is straightforward to use, also in classroom settings. We provide detailed descriptions and revision techniques for each step, thus giving the user maximum control over data treatment and avoiding a black-box approach. Employing this pipeline will improve and speed up the tedious and error-prone process of cleaning fungal Illumina metabarcoding data.
Background: Knee osteoarthritis is associated with higher kinetic friction in the knee joint, hence increased acoustic emissions during motion. Decreases in compressive load and improvements in movement quality might reduce this friction and, thus, sound amplitude. We investigated if an exercise treatment acutely affects knee joint sounds during different activities of daily life.
Methods: Eighteen participants with knee osteoarthritis (aged 51.8 ± 7.3 years; 14 females) were included in this randomized crossover trial. A neuromuscular exercise intervention and a placebo laser needle acupuncture treatment were performed. Before and after both interventions, knee joint sounds were measured during three different activities of daily living (standing up/sitting down, walking, descending stairs) by means of vibroarthrography. The mean amplitude (dB) and the median power frequency (MPF, Hz) were assessed at the medial tibial plateau and the patella. Differences in knee acoustic emissions between placebo and exercise interventions were calculated by analyses of covariance.
Results: Controlled for participant's age, knee demanding activity level and osteoarthritis stage, the conditions significantly differed in their impact on the MPF (mean(± SD) pre-post-differences standing up: placebo: 9.55(± 29.15) Hz/ exercise: 13.01(± 56.06) Hz, F = 4.9, p < 0.05) and the amplitude (standing up: placebo:0.75(± 1.43) dB/ exercise: 0.51(± 4.68) dB, F = 5.0, p < 0.05; sitting down: placebo: 0.07(± 1.21) dB/ exercise: -0.16(± .36) dB, F = 4.7, p < 0.05) at the tibia. There were no differences in the MPF and amplitude during walking and descending stairs (p > 0.05). At the patella, we found significant differences in the MPF during walking (placebo 0.08(± 1.42) Hz/ exercise: 15.76(± 64.25) Hz, F = 4.8, p < .05) and in the amplitude during descending stairs (placebo: 0.02 (± 2.72) dB/ exercise: -0.73(± 2.84) dB, F = 4.9, p < 0.05). There were no differences in standing up/ sitting down for both parameters, nor in descending stairs for the MPF and walking for the amplitude (p > 0.05).
Conclusion: The MPF pre-post differences of the exercise intervention were higher compared to the MPF pre-post differences of the placebo treatment. The amplitude pre-post differences were lower in the exercise intervention. In particular, the sound amplitude might be an indicator for therapy effects in persons with knee osteoarthritis.
Trial registration: The study was retrospectively registered in the German Clinical Trials Register (DRKS00022936, date of registry: 26/08/2020).
Background: In clinical practice range of motion (RoM) is usually assessed with low-cost devices such as a tape measure (TM) or a digital inclinometer (DI). However, the intra- and inter-rater reliability of typical RoM tests differ, which impairs the evaluation of therapy progress. More objective and reliable kinematic data can be obtained with the inertial motion capture system (IMC) by Xsens. The aim of this study was to obtain the intra- and inter-rater reliability of the TM, DI and IMC methods in five RoM tests: modified Thomas test (DI), shoulder test modified after Janda (DI), retroflexion of the trunk modified after Janda (DI), lateral inclination (TM) and fingertip-to-floor test (TM).
Methods: Two raters executed the RoM tests (TM or DI) in a randomized order on 22 healthy individuals while, simultaneously, the IMC data (Xsens MVN) was collected. After 15 warm-up repetitions, each rater recorded five measurements.
Findings: Intra-rater reliabilities were (almost) perfect for tests in all three devices (ICCs 0.886–0.996). Inter-rater reliability was substantial to (almost) perfect in the DI (ICCs 0.71–0.87) and the IMC methods (ICCs 0.61–0.993) and (almost) perfect in the TM methods (ICCs 0.923–0.961). The measurement error (ME) for the tests measured in degree (°) was 0.9–3.3° for the DI methods and 0.5–1.2° for the IMC approaches. In the tests measured in centimeters the ME was 0.5–1.3cm for the TM methods and 0.6–2.7cm for the IMC methods. Pearson correlations between the results of the DI or the TM respectively with the IMC results were significant in all tests except for the shoulder test on the right body side (r = 0.41–0.81).
Interpretation: Measurement repetitions of either one or multiple trained raters can be considered reliable in all three devices.
Background: Many fungal species occur across a variety of habitats. Particularly lichens, fungi forming symbioses with photosynthetic partners, have evolved remarkable tolerances for environmental extremes. Despite their ecological importance and ubiquity, little is known about the genetic basis of adaption in lichen populations. Here we studied patterns of genome-wide differentiation in the lichen-forming fungus Lasallia pustulata along an altitudinal gradient in the Mediterranean region. We resequenced six populations as pools and identified highly differentiated genomic regions. We then detected gene-environment correlations while controlling for shared population history and pooled sequencing bias, and performed ecophysiological experiments to assess fitness differences of individuals from different environments.
Results: We detected two strongly differentiated genetic clusters linked to Mediterranean and temperate-oceanic climate, and an admixture zone, which coincided with the transition between the two bioclimates. High altitude individuals showed ecophysiological adaptations to wetter and more shaded conditions. Highly differentiated genome regions contained a number of genes associated with stress response, local environmental adaptation, and sexual reproduction.
Conclusions: Taken together our results provide evidence for a complex interplay between demographic history and spatially varying selection acting on a number of key biological processes, suggesting a scenario of ecological speciation.