Authoritative subspecies diagnosis tool for European honey bees based on ancestry informative SNPs.

BACKGROUND: With numerous endemic subspecies representing four of its five evolutionary lineages, Europe holds a large fraction of Apis mellifera genetic diversity. This diversity and the natural distribution range have been altered by anthropogenic factors. The conservation of this natural heritage relies on the availability of accurate tools for subspecies diagnosis. Based on pool-sequence data from 2145 worker bees representing 22 populations sampled across Europe, we employed two highly discriminative approaches (PCA and FST) to select the most informative SNPs for ancestry inference. RESULTS: Using a supervised machine learning (ML) approach and a set of 3896 genotyped individuals, we could show that the 4094 selected single nucleotide polymorphisms (SNPs) provide an accurate prediction of ancestry inference in European honey bees. The best ML model was Linear Support Vector Classifier (Linear SVC) which correctly assigned most individuals to one of the 14 subspecies or different genetic origins with a mean accuracy of 96.2% ± 0.8 SD. A total of 3.8% of test individuals were misclassified, most probably due to limited differentiation between the subspecies caused by close geographical proximity, or human interference of genetic integrity of reference subspecies, or a combination thereof. CONCLUSIONS: The diagnostic tool presented here will contribute to a sustainable conservation and support breeding activities in order to preserve the genetic heritage of European honey bees.

Validity of Self-Reported Running Distance.

It is unclear whether there is a difference between subjective evaluation and objective global positioning systems (GPS) measurement of running distance. The purpose of this study was to investigate if such difference exists. A total of 100 participants (51% men; median age, 41.5; body mass, 78.1 kg ±13.8 SD) completed a run of free choice, then subjectively reported the distance in kilometer (km). This information was subsequently compared with the distance derived from a nondifferential GPS watch using paired t-tests and Bland-Altman's 95% limits of agreement. No significant difference was found between the mean paired differences between subjective evaluations and GPS measurements (1.86%, 95% confidence interval = -1.53%; 5.25%, p = 0.96). The Bland-Altman 95% limits of agreement revealed considerable variation (lower limit = -28% and upper limit = 40%). Such variation exceeds the clinical error range of 10%. In conclusion, the mean running distance (km) is similar between self-reporting and GPS measurements. However, researchers should consider using GPS measurements in favor of subjective reporting of running distance because of considerable variation on an individual level.

Structured RNAs and synteny regions in the pig genome.

BACKGROUND: Annotating mammalian genomes for noncoding RNAs (ncRNAs) is nontrivial since far from all ncRNAs are known and the computational models are resource demanding. Currently, the human genome holds the best mammalian ncRNA annotation, a result of numerous efforts by several groups. However, a more direct strategy is desired for the increasing number of sequenced mammalian genomes of which some, such as the pig, are relevant as disease models and production animals. RESULTS: We present a comprehensive annotation of structured RNAs in the pig genome. Combining sequence and structure similarity search as well as class specific methods, we obtained a conservative set with a total of 3,391 structured RNA loci of which 1,011 and 2,314, respectively, hold strong sequence and structure similarity to structured RNAs in existing databases. The RNA loci cover 139 cis-regulatory element loci, 58 lncRNA loci, 11 conflicts of annotation, and 3,183 ncRNA genes. The ncRNA genes comprise 359 miRNAs, 8 ribozymes, 185 rRNAs, 638 snoRNAs, 1,030 snRNAs, 810 tRNAs and 153 ncRNA genes not belonging to the here fore mentioned classes. When running the pipeline on a local shuffled version of the genome, we obtained no matches at the highest confidence level. Additional analysis of RNA-seq data from a pooled library from 10 different pig tissues added another 165 miRNA loci, yielding an overall annotation of 3,556 structured RNA loci. This annotation represents our best effort at making an automated annotation. To further enhance the reliability, 571 of the 3,556 structured RNAs were manually curated by methods depending on the RNA class while 1,581 were declared as pseudogenes. We further created a multiple alignment of pig against 20 representative vertebrates, from which RNAz predicted 83,859 de novo RNA loci with conserved RNA structures. 528 of the RNAz predictions overlapped with the homology based annotation or novel miRNAs. We further present a substantial synteny analysis which includes 1,004 lineage specific de novo RNA loci and 4 ncRNA loci in the known annotation specific for Laurasiatheria (pig, cow, dolphin, horse, cat, dog, hedgehog). CONCLUSIONS: We have obtained one of the most comprehensive annotations for structured ncRNAs of a mammalian genome, which is likely to play central roles in both health modelling and production. The core annotation is available in Ensembl 70 and the complete annotation is available at http://rth.dk/resources/rnannotator/susscr102/version1.02.

Can GPS be used to detect deleterious progression in training volume among runners?

There is a need to ascertain if an association exists between excessive progression in weekly volume and development of running-related injuries (RRI). The purpose of this study was to investigate if GPS can be used to detect deleterious progression in weekly training volume among 60 novice runners included in a 10-week prospective study. All participants used GPS to quantify training volume while running. In case of injury, participants attended a clinical examination. The 13 runners who sustained injuries during follow-up had a significantly higher weekly progression in total training volume in the week before the injury origin (86% [95% confidence interval: 12.9-159.9], p = 0.026) compared with other weeks. Although not significant, participants with injuries had an increase in weekly training volume of 31.6% compared with a 22.1% increase among the healthy participants. The error of the GPS measurements in open landscape, forest, and urban area of volume was ≤6.2%. To conclude, no clinically relevant measurement errors of the GPS devices were found for training volume. Based on this, GPS has a potential to detect errors in training volume, which may be associated with development of RRI. Based on the results from the current study, increases in weekly training progression may become deleterious at a weekly increase above 30%, which is more than the 10% rule currently used as a guideline for correct progression in weekly volume by runners and coaches. Still, no clear evidence for safe progression of weekly volume exists. But it seems likely that some individuals may tolerate weekly progressions around 20-25%, at least for a short period of time.

A transcriptome map of perennial ryegrass (Lolium perenne L.).

BACKGROUND: Single nucleotide polymorphisms (SNPs) are increasingly becoming the DNA marker system of choice due to their prevalence in the genome and their ability to be used in highly multiplexed genotyping assays. Although needed in high numbers for genome-wide marker profiles and genomics-assisted breeding, a surprisingly low number of validated SNPs are currently available for perennial ryegrass. RESULTS: A perennial ryegrass unigene set representing 9,399 genes was used as a reference for the assembly of 802,156 high quality reads generated by 454 transcriptome sequencing and for in silico SNP discovery. Out of more than 15,433 SNPs in 1,778 unigenes fulfilling highly stringent assembly and detection parameters, a total of 768 SNP markers were selected for GoldenGate genotyping in 184 individuals of the perennial ryegrass mapping population VrnA, a population being previously evaluated for important agronomic traits. A total of 592 (77%) of the SNPs tested were successfully called with a cluster separation above 0.9. Of these, 509 (86%) genic SNP markers segregated in the VrnA mapping population, out of which 495 were assigned to map positions. The genetic linkage map presented here comprises a total of 838 DNA markers (767 gene-derived markers) and spans 750 centi Mogan (cM) with an average marker interval distance of less than 0.9 cM. Moreover, it locates 732 expressed genes involved in a broad range of molecular functions of different biological processes in the perennial ryegrass genome. CONCLUSIONS: Here, we present an efficient approach of using next generation sequencing (NGS) data for SNP discovery, and the successful design of a 768-plex Illumina GoldenGate genotyping assay in a complex genome. The ryegrass SNPs along with the corresponding transcribed sequences represent a milestone in the establishment of genetic and genomics resources available for this species and constitute a further step towards molecular breeding strategies. Moreover, the high density genetic linkage map predominantly based on gene-associated DNA markers provides an important tool for the assignment of candidate genes to quantitative trait loci (QTL), functional genomics and the integration of genetic and physical maps in perennial ryegrass, one of the most important temperate grassland species.

Physical activity through social prescribing: An interview-based study of Danish general practitioners' opinions.

Previous research suggested that regular physical activity (PA) is beneficial in both prevention and treatment of physical and mental conditions. Danish general practitioners' (GPs) have an ideal position to motivate inactive patients to increase their PA. Social prescribing (SP) enables GPs and other healthcare professionals in primary care to link patients to community-based activities of support provided by the community and the voluntary sector. This interview-based study aimed to explore viewpoints among Danish GPs regarding the advantages and disadvantages of applying SP to promote PA. The GPs were recruited through snowball sampling. Semi-structured interviews with nine Danish GPs were held via telephone or via Skype video conference. All interviews were audio-recorded and transcribed. Data were managed using the program NVivo 12 and analysed using the Framework Method procedure for analysis. The findings highlighted the need for tools to support GPs in providing an overview of patient-tailored options for PA in the local community. Advantages of applying SP to promote PA were related to the social aspect, the non-medical approach to a healthier lifestyle and the GPs' opportunity to signpost patients to PA in their local community. A supporting link-worker facilitating a bridge between general practice and community-based activities was identified as a pivotal component, specifically among patients with complex needs. Disadvantages of applying SP to promote PA were related to patients' expectations to general practice, stigmatising attitudes of society and lack of financial resources in patients. This study is the first to explore SP to promote PA in a Danish context. There is a need for an easy-to-use tool to support GPs in providing specific PA counselling. On this basis, SP appears as a promising tool for GPs to promote PA.

Population Structure and Diversity in European Honey Bees (Apismellifera L.)-An Empirical Comparison of Pool and Individual Whole-Genome Sequencing.

BACKGROUND: Whole-genome sequencing has become routine for population genetic studies. Sequencing of individuals provides maximal data but is rather expensive and fewer samples can be studied. In contrast, sequencing a pool of samples (pool-seq) can provide sufficient data, while presenting less of an economic challenge. Few studies have compared the two approaches to infer population genetic structure and diversity in real datasets. Here, we apply individual sequencing (ind-seq) and pool-seq to the study of Western honey bees (Apis mellifera). METHODS: We collected honey bee workers that belonged to 14 populations, including 13 subspecies, totaling 1347 colonies, who were individually (139 individuals) and pool-sequenced (14 pools). We compared allele frequencies, genetic diversity estimates, and population structure as inferred by the two approaches. RESULTS: Pool-seq and ind-seq revealed near identical population structure and genetic diversities, albeit at different costs. While pool-seq provides genome-wide polymorphism data at considerably lower costs, ind-seq can provide additional information, including the identification of population substructures, hybridization, or individual outliers. CONCLUSIONS: If costs are not the limiting factor, we recommend using ind-seq, as population genetic structure can be inferred similarly well, with the advantage gained from individual genetic information. Not least, it also significantly reduces the effort required for the collection of numerous samples and their further processing in the laboratory.

Feasibility and acceptability of a six-month exercise and patient education intervention for patients with hip dysplasia: A mixed methods study.

BACKGROUND AND OBJECTIVES: To evaluate the feasibility and acceptability of exercise and patient education for patients with hip dysplasia not receiving surgery. DESIGN: Feasibility study. METHODS: The participants received exercise instruction and patient education over six months. Feasibility covered recruitment, retention, and mechanisms of change (MC). MC were measured with Hip and Groin Outcome Score (HAGOS), muscle strength tests, Y-balance test, and hop for distance test (HDT) over six months. Acceptability covered adherence, expectations, perceptions, benefits, and harms. RESULTS: Thirty of 32 were recruited (median age: 30 years); six were lost to follow-up. Twenty-four participants improved by a mean of 11 (95%CI: 5-17) HAGOS pain points, improvements in all subscales were 1-11 points. Mean hip abduction strength improved 0.2 (95%CI: 0.04-0.4) Nm/kg, similar to flexion and extension. Median Y-balance test improvements: anterior: 70 (IQR: 64-74) to 75 (IQR: 72-80) centimetres; posteromedial: 104 (IQR: 94-112) to 119 (IQR: 112-122) centimetres and posterolateral: 98 (IQR: 89-109) to 116 (IQR: 108-121) centimetres (p < .001). Median improvement in HDT was: 37 (IQR: 30-44) to 52 (IQR: 45-58) centimetres (p < .001). Participants adhered to 84% of scheduled sessions (1,581:1,872), expectations were met, and perceptions were characterized by high self-efficacy for exercise. Benefits were reported with no serious harms. CONCLUSION: Patients with hip dysplasia are willing to be recruited for exercise and patient education, with acceptable retention. MC were observed through improvements in pain, strength and function with high acceptance of the exercise and patient education intervention. Thus, it seems feasible to conduct a full-scale randomised controlled trial.

Medial shoe-ground pressure and specific running injuries: A 1-year prospective cohort study.

OBJECTIVES: Achilles tendinitis, plantar fasciopathy and medial tibial stress syndrome injuries (APM-injuries) account for approximately 25% of the total number of running injuries amongst recreational runners. Reports on the association between static foot pronation and APM-injuries are contradictory. Possibly, dynamic measures of pronation may display a stronger relationship with the risk of APM-injuries. Therefore, the purpose of the present study was to investigate if running distance until the first APM-injury was dependent on the foot balance during stance phase in recreational male runners. DESIGN: Prospective cohort study. METHODS: Foot balance for both feet was measured during treadmill running at the fastest possible 5000-m running pace in 79 healthy recreational male runners. Foot balance was calculated by dividing the average of medial pressure with the average of lateral pressure. Foot balance was categorized into those which presented a higher lateral shod pressure (LP) than medial pressure, and those which presented a higher medial shod pressure (MP) than lateral pressure during the stance phase. A time-to-event model was used to compare differences in incidence between foot balance groups. RESULTS: Compared with the LP-group (n=59), the proportion of APM-injuries was greater in the MP-group (n=99) after 1500km of running, resulting in a cumulative risk difference of 16%-points (95% CI=3%-point; 28%-point, p=0.011). CONCLUSIONS: Runners displaying a more medial pressure during stance phase at baseline sustained a greater amount of APM-injuries compared to those displaying a lateral shod pressure during stance phase. Prospective studies including a greater amount of runners are needed to confirm this relationship.

Does running with or without diet changes reduce fat mass in novice runners? A 1-year prospective study.

BACKGROUND: The aim of this study was to explore how average weekly running distance, combined with changes in diet habits and reasons to take up running, influence fat mass. METHODS: Fat mass was assessed by bioelectrical impedance at baseline and after 12 months in 538 novice runners included in a 1-year observational prospective follow-up study. During follow-up, running distance for each participant was continuously measured by GPS while reasons to take up running and diet changes were assessed trough web-based questionnaires. Loss of fat mass was compared between runners covering an average of 5 km or more per week and those running shorter distances. RESULTS: Runners who took up running to lose weight and ran over 5 km per week in average over a one-year period combined with a diet change reduced fat mass by -5.58 kg (95% CI: -8.69; -2.46; P<0.001). Compared with subjects also running over 5 km per week but without diet changes, the mean difference in fat mass between groups was 3.81 kg (95% CI: -5.96; -1.66; P<0.001). A difference of -3.55 kg (95% CI: -5.69; -1.41; P<0.001) was found when comparing with those running less than 5 km per week and making changes to their own diet. CONCLUSIONS: An average running distance of more than 5 km per week in runners who took up running to lose weight combined with a targeted diet change seems effective in reducing fat mass over a one-year period among novice runners. Still, randomized controlled trials are needed to better document the effects of self-selected diet changes.

High eccentric hip abduction strength reduces the risk of developing patellofemoral pain among novice runners initiating a self-structured running program: a 1-year observational study.

STUDY DESIGN: Observational prospective cohort study with 1-year follow-up. OBJECTIVES: To investigate the relationship between eccentric hip abduction strength and the development of patellofemoral pain (PFP) in novice runners during a self-structured running regime. BACKGROUND: Recent research indicates that gluteal muscle weakness exists in individuals with PFP. However, current prospective research has been limited to the evaluation of isometric strength, producing inconsistent findings. Considering that hip muscles, including the gluteus maximus and medius, activate eccentrically to control hip and pelvic motion during weight-bearing activities such as running, the potential link between eccentric strength and PFP risk should be evaluated. METHODS: Eight hundred thirty-two novice runners were included at baseline, and 629 participants were included in the final analysis. Maximal eccentric hip abduction strength was measured using a handheld dynamometer prior to initiating a self-structured running program. The diagnostic criteria to classify knee pain as PFP were based on a thorough clinical examination. Participants were followed for 12 months and training characteristics were gathered with a global positioning system. RESULTS: Results from the unadjusted generalized linear regression model for cumulative risk at 25 and 50 km indicated differences in cumulative risk of PFP between high strength, normal strength, and low strength (P<.05), with higher strength associated with reduced risk. CONCLUSION: Findings from this study indicate that, among novice runners, a level of peak eccentric hip abduction strength that is higher than normal may reduce the risk of PFP during the first 50 km of a self-structured running program.

Head-to-head comparison of intensive lifestyle intervention (U-TURN) versus conventional multifactorial care in patients with type 2 diabetes: protocol and rationale for an assessor-blinded, parallel group and randomised trial.

INTRODUCTION: Current pharmacological therapies in patients with type 2 diabetes (T2D) are challenged by lack of sustainability and borderline firm evidence of real long-term health benefits. Accordingly, lifestyle intervention remains the corner stone in the management of T2D. However, there is a lack of knowledge regarding the optimal intervention programmes in T2D ensuring both compliance as well as long-term health outcomes. Our objective is to assess the effects of an intensive lifestyle intervention (the U-TURN intervention) on glycaemic control in patients with T2D. Our hypothesis is that intensive lifestyle changes are equally effective as standard diabetes care, including pharmacological treatment in maintaining glycaemic control (ie, glycated haemoglobin (HbA1c)) in patients with T2D. Furthermore, we expect that intensive lifestyle changes will decrease the need for antidiabetic medications. METHODS AND ANALYSIS: The study is an assessor-blinded, parallel group and a 1-year randomised trial. The primary outcome is change in glycaemic control (HbA1c), with the key secondary outcome being reductions in antidiabetic medication. Participants will be patients with T2D (T2D duration <10 years) without complications who are randomised into an intensive lifestyle intervention (U-TURN) or a standard care intervention in a 2:1 fashion. Both groups will be exposed to the same standardised, blinded, target-driven pharmacological treatment and can thus maintain, increase, reduce or discontinue the pharmacological treatment. The decision is based on the standardised algorithm. The U-TURN intervention consists of increased training and basal physical activity level, and an antidiabetic diet including an intended weight loss. The standard care group as well as the U-TURN group is offered individual diabetes management counselling on top of the pharmacological treatment. ETHICS AND DISSEMINATION: This study has been approved by the Scientific Ethical Committee at the Capital Region of Denmark (H-1-2014-114). Positive, negative or inconclusive findings will be disseminated in peer-reviewed journals, at national and international conferences. TRIAL REGISTRATION NUMBER: NCT02417012.

Genomic resources notes accepted 1 October 2014-30 November 2014.

This article documents the public availability of (i) RAD sequencing data and validated SNPs for the American mink Neovison vison and (ii) Transcriptome resources for two nonmodel freshwater crustacean species, the copepod Eucyclops serrulatus and the amphipod Echinogammarus veneris.

Comparisons of increases in knee and ankle joint moments following an increase in running speed from 8 to 12 to 16km·h(-1.).

BACKGROUND: Knowledge regarding knee and ankle joint load across a range of running speeds is important, if running related injuries are to be prevented. The purpose of the present study was to test the hypothesis that peak plantar flexion moment increases relatively more than peak knee extension moment when running speed is increased. METHODS: Kinematic and ground reaction force data were collected from 33 recreational runners during steady-state running at three different speeds: 7.96km·h(-1) (SD 0.18), 11.92km·h(-1) (SD 0.25) and 15.91km·h(-1) (SD 0.36). Peak plantar flexion moment and peak knee extension moment were calculated using a standard three-dimensional inverse dynamics approach. FINDINGS: There was a significant interaction between the joint location and the running speed (P=0.03): When running speed increased from 7.96 to 15.91km·h(-1), mean peak plantar flexion moment increased by 0.74N·m·kg(-1) (95% CI: 0.64; 0.85) which was more than the 0.52N·m·kg(-1) (95% CI: 0.42; 0.63) increase in mean peak knee extension moment. INTERPRETATION: A greater increase in biomechanical load occurs for the plantar flexors of the ankle joint than for the extensors of the knee joint when running speed increases. This may indicate that at an excessive running speed, the structures at the posterior part of the lower leg and underneath the foot are relatively more vulnerable to injury compared with the structures at the anterior part of the knee. As a considerable load reduction is achieved, a decrease in running speed may benefit rearfoot striking recreational runners experiencing pain in the posterior lower leg or underneath the foot.

Footstrike patterns among novice runners wearing a conventional, neutral running shoe.

INTRODUCTION: It has been suggested that striking on the midfoot or forefoot, rather than the rearfoot, may lessen injury risk in the feet and lower limb. In previous studies, a disparity in distribution in footstrike patterns was found among elite-, sub-elite, and recreational runners. PURPOSE: The purpose of this study was to investigate the footstrike patterns among novice runners. METHODS: All runners were equipped with the same conventional running shoe. Participants were video filmed at 300 frames per second and the footstrike patterns were evaluated by two observers. The footstrike was classified as rearfoot, midfoot, forefoot, or asymmetrical. RESULTS: A total of 903 persons were evaluated. The percentages of rearfoot-, midfoot-, forefoot-, and asymmetrical footstrike among men were 96.9%, 0.4%, 0.9%, and 1.8%, respectively. Among women the percentages were 99.3%, 0%, 0%, and 0.7%, respectively. CONCLUSION: Nearly all novice runners utilize a rearfoot strike when taking up running in a conventional running shoe. Hereby, the footstrike patterns among novice runners deviate from footstrike patterns among elite and sub-elite runners.

SNP discovery using Next Generation Transcriptomic Sequencing in Atlantic herring (Clupea harengus).

The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, providing studies of non-model species with unprecedented genomic coverage, allowing evolutionary biologists to address questions previously far beyond the reach of available resources. Furthermore, the simple mutation model of Single Nucleotide Polymorphisms (SNPs) permits cost-effective high-throughput genotyping in thousands of individuals simultaneously. Genomic resources are scarce for the Atlantic herring (Clupea harengus), a small pelagic species that sustains high revenue fisheries. This paper details the development of 578 SNPs using a combined NGS and high-throughput genotyping approach. Eight individuals covering the species distribution in the eastern Atlantic were bar-coded and multiplexed into a single cDNA library and sequenced using the 454 GS FLX platform. SNP discovery was performed by de novo sequence clustering and contig assembly, followed by the mapping of reads against consensus contig sequences. Selection of candidate SNPs for genotyping was conducted using an in silico approach. SNP validation and genotyping were performed simultaneously using an Illumina 1,536 GoldenGate assay. Although the conversion rate of candidate SNPs in the genotyping assay cannot be predicted in advance, this approach has the potential to maximise cost and time efficiencies by avoiding expensive and time-consuming laboratory stages of SNP validation. Additionally, the in silico approach leads to lower ascertainment bias in the resulting SNP panel as marker selection is based only on the ability to design primers and the predicted presence of intron-exon boundaries. Consequently SNPs with a wider spectrum of minor allele frequencies (MAFs) will be genotyped in the final panel. The genomic resources presented here represent a valuable multi-purpose resource for developing informative marker panels for population discrimination, microarray development and for population genomic studies in the wild.

Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake.

The growing accessibility to genomic resources using next-generation sequencing (NGS) technologies has revolutionized the application of molecular genetic tools to ecology and evolutionary studies in non-model organisms. Here we present the case study of the European hake (Merluccius merluccius), one of the most important demersal resources of European fisheries. Two sequencing platforms, the Roche 454 FLX (454) and the Illumina Genome Analyzer (GAII), were used for Single Nucleotide Polymorphisms (SNPs) discovery in the hake muscle transcriptome. De novo transcriptome assembly into unique contigs, annotation, and in silico SNP detection were carried out in parallel for 454 and GAII sequence data. High-throughput genotyping using the Illumina GoldenGate assay was performed for validating 1,536 putative SNPs. Validation results were analysed to compare the performances of 454 and GAII methods and to evaluate the role of several variables (e.g. sequencing depth, intron-exon structure, sequence quality and annotation). Despite well-known differences in sequence length and throughput, the two approaches showed similar assay conversion rates (approximately 43%) and percentages of polymorphic loci (67.5% and 63.3% for GAII and 454, respectively). Both NGS platforms therefore demonstrated to be suitable for large scale identification of SNPs in transcribed regions of non-model species, although the lack of a reference genome profoundly affects the genotyping success rate. The overall efficiency, however, can be improved using strict quality and filtering criteria for SNP selection (sequence quality, intron-exon structure, target region score).