Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

The combined application of next-generation sequencing platforms has provided an economical approach to unlocking the potential of the turkey genome

Heesterveld gone green

After doing a collective research in Heesterveld, positive and negative aspects were mentioned by the government, residents, makers and owners. The goal of this design is to embrace the valuable aspects of Heesterveld and improve the problems. The problems in the neighbourhood mainly arose on the social level, more specifically in the public space. The unique identity of Heesterveld was also mentioned during the research, this will also be preserved and emphasized in the design. From literature research, two other challenges in Heesterveld came up, which were also mentioned by the residents. According to the municipality, there were also many socio-economic issues, which needed to be resolved. Lastly, the global problem of climate change also has a big impact on a small scale, so this issue was also addressed in the design. Heesterveld had to improve on social, economic and environmental aspects, which is done in the design. This is done by adding a blue green infrastructure, adding various new functions on the ground floor and by future-proofing the building. The blue green infrastructure tackles the social and environmental issues and by creating diversity on the ground floor, the social and economic problems will be solved. The existing building itself is also made future proof by adding insulation on the inside, solar panels and a thermal energy storage. So in conclusion, Heesterveld is ready for the future with this sustainable design, which solves the social, economic and environmental issues

Early and late feathering in Turkey and chicken : Same gene but different mutations

Background: Sex-linked slow (SF) and fast (FF) feathering rates at hatch have been widely used in poultry breeding for autosexing at hatch. In chicken, the sex-linked K (SF) and k+ (FF) alleles are responsible for the feathering rate phenotype. Allele K is dominant and a partial duplication of the prolactin receptor gene has been identified as the causal mutation. Interestingly, some domesticated Turkey lines exhibit similar slow- and fast-feathering phenotypes, but the underlying genetic components and causal mutation have never been investigated. In this study, our aim was to investigate the molecular basis of feathering rate at hatch in domestic Turkey. Results: We performed a sequence-based case-control association study and detected a genomic region on chromosome Z, which is statistically associated with rate of feathering at hatch in Turkey. We identified a 5-bp frameshift deletion in the prolactin receptor (PRLR) gene that is responsible for slow feathering at hatch. All female cases (SF Turkeys) were hemizygous for this deletion, while 188 controls (FF Turkeys) were hemizygous or homozygous for the reference allele. This frameshift mutation introduces a premature stop codon and six novel amino acids (AA), which results in a truncated PRLR protein that lacks 98 C-terminal AA. Conclusions: We present the causal mutation for feathering rate in Turkey that causes a partial C-terminal loss of the prolactin receptor, and this truncated PRLR protein is strikingly similar to the protein encoded by the slow feathering K allele in chicken

Whole Genome SNP Discovery and Analysis of Genetic Diversity in Turkey (Meleagris gallopavo)

Alignment of next generation sequencing data of 32 individual turkeys from different populations was used for the discovery of 5.49 million SNPs, and subsequent analysis of genetic diversity among the different populations. All of the commercial lines branched from a single node relative to the heritage varieties and the South Mexican turkey population. Heterozygosity of all individuals from the different turkey populations ranged from 0.17-2.73 SNPs/Kb, while heterozygosity of populations ranged from 0.73-1.64 SNPs/Kb. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/Kb. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that showed state of fixation towards alleles different than wild alleles

MOESM1 of Early and late feathering in turkey and chicken: same gene but different mutations

Additional file 1: Table S1. Line, animal ID, phenotype, sex and mean sequence coverage for slow feathering (SF) and fast feathering (FF) turkey samples. Table S2. Number of variants per type. Table S3. Effects of variants per type and region. Table S4. Effects of coding SNPs. Table S5. List of top 100 significant polymorphisms on chromosome Z

MOESM2 of Early and late feathering in turkey and chicken: same gene but different mutations

Additional file 2: Figure S1. Population PCA for fast feathering (red) and slow-feathering samples (green). Figure S2: GWAS results for feathering rate at hatch on chromosome Z. Figure S3. Chicken (Galgal) and turkey (Melgal) PRLR protein alignment. PRLR sequences share 90.24% identity. The red (turkey) and blue (chicken) arrows indicate the starting point of the C-terminal loss in PRLR for both species

MOESM3 of Early and late feathering in turkey and chicken: same gene but different mutations

Additional file 3: CNV-seq results within the associated region on ChrZ:7.9-10.0 Mb for all SF and FF Turkey samples. Each figure shows the log2 ratio between case and control samples in each window across the region

Ambulance Work : Relationships between occupational demands, individual characteristics and health-related outcomes

Although musculoskeletal disorders (MSDs) and other health complaints are an occupational problem for ambulance personnel, there is a lack of knowledge regarding work-related factors associated with MSDs and other health complaints. The overall aim of this thesis was to investigate the relationships between occupational demands, individual characteristics and health-related outcomes among ambulance personnel. A random sample of 234 female and 953 male ambulance personnel participated in a national questionnaire survey on work-related factors, and musculoskeletal and other health complaints. Physical demands was associated with activity limitation due to neck-shoulder and low-back complaints among the female personnel. Among the male personnel, physical demands was associated with low-back complaints and activity limitation due to low-back complaints. Psychological demands was significantly associated with neck-shoulder complaints, sleeping problems, headache and stomach symptoms among both female and male ambulance personnel. Worry about work conditions was associated with musculoskeletal disorders and sleeping problems, headache and stomach symptoms. A local sample of 26 ambulance personnel was followed during a 24-hour work shift and for the next two work-free days. Subjective stress- and energy levels, and cortisol levels were measured at regular intervals, and heart rate was registered continuously by electrocardiogram (ECG). Autonomic reactivity to standardized tests before (pre-work) and at the end of the work shift (post-work) was also investigated. For the whole group, baseline values of heart rate were higher pre-work than post-work, but autonomic reactivity did not differ. Increased reactivity to the mental test, modest deviation in heart rate variability (HRV) pattern during the late night hours at work and higher morning cortisol values during work than during leisure time were observed in personnel with many health complaints, but not among their co-workers without or with few complaints. Ambulance personnel with many health complaints also reported higher psychological demands and tended to be more worried about work conditions. Heart rate (HR), lactate level (LL) and perceived exertion (RPE) were investigated in 17 female and 48 male ambulance personnel during a simulated standardized work task “carry a loaded stretcher”. The ambulance personnel had to carry the loaded stretcher (920 N) up and down three flights of stairs twice. The high physiological strain (HR, LL, RPE) for the male, and near or at maximal strain for the female ambulance personnel, implied the importance to identify what kind of physical capacity is most important for ambulance personnel. Therefore, the explained variance of developed fatigue by tests of cardiorespiratory capacity, muscular strength and endurance, and coordination was investigated. The results showed that VO2max and isometric back endurance were important predictors for development of fatigue when carrying a loaded stretcher. The influence of body size on the relationships between maximal strength and functional performance was investigated in a methodological study. The results confirm that the assessment of physical performance could be confounded by the body weight. Therefore, the models for explaining development of fatigue when carrying the loaded stretcher were adjusted for height and weight. Including height in the models significantly increased the explained variance of accumulated lactate among female, but not among male personnel. Lactate levels were higher among short compared to tall female personnel. Weight had no effect on any of the models. In conclusion, the national survey showed that self-reported physical demands was a risk factor of having MSDs, and that self-reported psychological demands and worry about work were important risk factors of having MSDs and other health complaints. Stress monitoring of ambulance personnel during work and leisure time showed that physiological and subjective stress markers did not show any differences between the 24-hour ambulance work shift and leisure time afterwards. However, ambulance personnel with many health complaints had certain physiological changes during the work shift in comparison with the next two work-free days. The physiological and subjective responses during carrying a loaded stretcher, especially among the female ambulance personnel, showed that female and male ambulance personnel could be exposed to internal exposures at different levels when performing the same work task. A better understanding of the relationships between occupational demands and health-related outcomes require further studies on age- and gender matched groups in long-term perspective studies

Whole genome SNP discovery and analysis of genetic diversity in Turkey (<it>Meleagris gallopavo</it>)

Abstract Background The turkey (Meleagris gallopavo) is an important agricultural species and the second largest contributor to the world’s poultry meat production. Genetic improvement is attributed largely to selective breeding programs that rely on highly heritable phenotypic traits, such as body size and breast muscle development. Commercial breeding with small effective population sizes and epistasis can result in loss of genetic diversity, which in turn can lead to reduced individual fitness and reduced response to selection. The presence of genomic diversity in domestic livestock species therefore, is of great importance and a prerequisite for rapid and accurate genetic improvement of selected breeds in various environments, as well as to facilitate rapid adaptation to potential changes in breeding goals. Genomic selection requires a large number of genetic markers such as e.g. single nucleotide polymorphisms (SNPs) the most abundant source of genetic variation within the genome. Results Alignment of next generation sequencing data of 32 individual turkeys from different populations was used for the discovery of 5.49 million SNPs, which subsequently were used for the analysis of genetic diversity among the different populations. All of the commercial lines branched from a single node relative to the heritage varieties and the South Mexican turkey population. Heterozygosity of all individuals from the different turkey populations ranged from 0.17-2.73 SNPs/Kb, while heterozygosity of populations ranged from 0.73-1.64 SNPs/Kb. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/Kb. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that showed state of fixation towards alleles different than wild alleles. Conclusion The turkey genome is much less diverse with a relatively low frequency of heterozygous SNPs as compared to other livestock species like chicken and pig. The whole genome SNP discovery study in turkey resulted in the detection of 5.49 million putative SNPs compared to the reference genome. All commercial lines appear to share a common origin. Presence of different alleles/haplotypes in the SM population highlights that specific haplotypes have been selected in the modern domesticated turkey.</p