Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays

We present a genotyping method for simultaneously scoring 116,204 SNPs using oligonucleotide arrays. At call rates >99%, reproducibility is >99.97% and accuracy, as measured by inheritance in trios and concordance with the HapMap Project, is >99.7%. Average intermarker distance is 23.6 kb, and 92% of the genome is within 100 kb of a SNP marker. Average heterozygosity is 0.30, with 105,511 SNPs having minor allele frequencies >5%.     

HPV E6/E7 mRNA testing is more specific than cytology in post-colposcopy follow-up of women with negative cervical biopsy

Background

In Norway, women with negative or low-grade cervical biopsies (normal/CIN1) are followed up after six months in order to decide on further follow-up or recall for screening at three-year intervals. A high specificity and positive predictive value (PPV) of the triage test is important to avoid unnecessary diagnostic and therapeutic procedures whereas a low risk of high-grade disease among triage negative women assures safety.

Materials and Methods

At the University Hospital of North Norway, cytology and the HPV mRNA test PreTect HPV-Proofer, detecting E6/E7 mRNA from HPV types 16, 18, 31, 33 and 45, are used in post-colposcopy follow-up of women with negative or low-grade biopsy. In this study, women with negative biopsy after high grade cytology (ASC-H/HSIL) and/or positive HPV mRNA test in the period 2005–2009 were included (n = 520). Histologically confirmed cervical intraepithelial neoplasia of grade 2 or worse (CIN2+) was used as study endpoint.

Results

Of 520 women with negative or low-grade biopsy, 124 women (23.8%) had CIN2+ in follow-up biopsy. The sensitivity and specificity of the HPV mRNA test were 89.1% (95% CI, 80.1–98.1) and 92.5% (95% CI, 88.2–96.7), respectively. The ratios of sensitivity, specificity and PPV of HPV mRNA testing compared to repeat cytology for finding CIN2+ was 1.05 (95% CI: 0.92–1.21), 1.21 (95% CI: 1.12–1.32), and 1.49 (95% CI: 1.20–1.86), respectively. The PPV of mRNA was 77.3% (95% CI, 59.8–94.8) in women aged 40 or older.

Conclusion

Women with negative cervical biopsy require follow-up before resumption of routine screening. Post-colposcopy HPV mRNA testing was as sensitive but more specific than post-colposcopy cytology. In addition, the HPV mRNA test showed higher PPV. A positive mRNA test post-colposcopy could justify treatment in women above 40 years.     

Incubation temperature influences survival in a small passerine bird

In birds parental incubation behaviour is an important factor shaping the environmental conditions under which the embryos develop, and sub‐optimal incubation temperatures are known to negatively affect early growth and development. It is less well known if variation in incubation temperature can impose life‐long differences in individual performance and survival. In the present study we investigated the effects of incubation temperature on long‐term survival in a small passerine bird. Using our captive population of the zebra finch Taeniopygia guttata we artificially incubated eggs at three biologically relevant temperatures (35.9, 37.0 and 37.9°C) for two‐thirds of the incubation period and then monitored individual lifespan of the hatched chicks for two and a half years. We found that individuals from eggs incubated under the lowest temperature exhibited significantly lower long‐term survival compared to those which had been incubated at the highest temperature. Our results show that incubation temperature in birds, and thus parental incubation behaviour, play an important role in shaping the life‐history trajectories of offspring.     

Biodegradation of oily sludge in Norwegian soils

Summary The degradation rate of oily sludge in soil under Norwegian conditions has been studied in field experiments during a 32 months' period. The experimental plots were added 0, 200, 400, and 600 kg N per ha. In uncultivated soil the oil content was reduced by respectively 4, 9, 22, and 26% during the first 9 months. In the same period the corresponding biodegradation in cultivated soil were 10, 15, 39, and 45%. At the end of the experiment only minor differences between the two different soil types were found. The mean degradation in percent was now 35, 50, 74, and 83, respectively. The optimum temperature for oil degradation in soil was found to be about 18°C. About 2/3 of the optimum activity was retained at 12°C. No leaching of oil or lead through soil columns infiltrated with oily sludge could be observed. A close relationship between oil content of the soil and the rate of water infiltration was found. Due to the extremely high content of lead in this oily sludge, a second application of sludge could not be recommended.     

Triage of Women with Minor Cervical Lesions: Data Suggesting a “Test and Treat” Approach for HPV E6/E7 mRNA Testing

Background

Human papillomavirus (HPV) testing is included in the cervical cancer screening program in the triage of women with equivocal (ASC-US) or low-grade (LSIL) cytological lesions. These women have an increased risk for developing high grade dysplasia and cancer (CIN2+) compared to women with normal cytology. However, in order to avoid unnecessary follow-up, as well as overtreatment, a high positive predictive value (PPV) of the triage test is important.

Methodology/Principal Findings

The HPV test PreTect HPV-Proofer, detecting E6/E7 mRNA from the HPV types 16, 18, 31, 33 and 45, is used as triage test together with repeat cytology. PPV data for HPV E6/E7 mRNA testing during the period from January 2006 up to June 2009 are reported. In total, 406 of 2099 women (19.3%) had a positive HPV test result. Of the women with a positive test result and with a histological diagnosis (n = 347), 243 women had histological high-grade dysplasia or cancer (CIN2+), giving a PPV of 70.0% (95% confidence interval [CI], 65.2%–74.8%). For HPV 16 or HPV 33 positive women above 40 years of age, the PPV was 83.7% (95% CI, 73.3%–94.0%) and 84.6% (95% CI, 65.0%–100.0%) respectively. The PPV of test positive women with HSIL cytology was 94.2% (95% CI, 88.7%–99.7%).

Conclusions

When the result in triage is HPV mRNA positive, our data suggest direct treatment for women above 40 years of age or for women with a concurrent cytological HSIL diagnosis, contributing to better clinical safety for these women. In addition, by decreasing the time to treatment, thereby reducing the number of recalls, the patient management algorithm will be considerably improved, in turn reducing follow-up costs as well as unnecessary psychological stress among patients.     

Factors influencing return rate and marine residence duration in sea trout populations in Central Norway

Brown trout (Salmo trutta) display extensive plasticity in marine migratory behaviours, with marine migrations considered to be an adaptive strategy which enables sea trout to maximize growth and reproductive potential. However, marine migrations are not without associated costs, including threats posed by ever-increasing salmon lice (Lepeophtheirus salmonis) infestations. In the present study, we used passive integrated transponder technology to characterize variability in sea trout migration behaviour amongst three catchments situated in a region of intensive salmon farming in central Norway. Specifically, we investigate how lice infestation, out-migration date and body size alter sea trout return rate and marine residence duration during the first out-migration to sea from each catchment. Distinct catchment-specific differences in sea trout out-migration size and the number of cohorts were observed, but larger body size did not guarantee the successful return of migrating trout. The marine residence duration of individuals that successfully returned to freshwater was positively correlated with lice infestation risk, suggesting for these individuals the lethal infestation threshold had not been reached. Our results also suggest that sea trout populations from lotic-dominated catchments are potentially at greater risk from size-related threats to their survival encountered during their marine migrations than sea trout from lentic-dominated catchments. The variability in sea trout migratory behaviour amongst catchments observed here emphasizes the challenges fisheries managers face when deciding the best actions to take to protect the anadromous portion of brown trout populations.     

Elevated mRNA-Levels of Gonadotropin-Releasing Hormone and Its Receptor in Plaque-Bearing Alzheimer's Disease Transgenic Mice

Research on Alzheimer''s disease (AD) has indicated an association between hormones of the hypothalamic–pituitary–gonadal (HPG) axis and cognitive senescence, indicating that post meno-/andropausal changes in HPG axis hormones are implicated in the neuropathology of AD. Studies of transgenic mice with AD pathologies have led to improved understanding of the pathophysiological processes underlying AD. The aims of this study were to explore whether mRNA-levels of gonadotropin-releasing hormone (Gnrh) and its receptor (Gnrhr) were changed in plaque-bearing Alzheimer''s disease transgenic mice and to investigate whether these levels and amyloid plaque deposition were downregulated by treatment with a gonadotropin-releasing hormone analog (Gnrh-a; Leuprorelin acetate). The study was performed on mice carrying the Arctic and Swedish amyloid-β precursor protein (AβPP) mutations (tgArcSwe). At 12 months of age, female tgArcSwe mice showed a twofold higher level of Gnrh mRNA and more than 1.5 higher level of Gnrhr mRNA than age matched controls. Male tgArcSwe mice showed the same pattern of changes, albeit more pronounced. In both sexes, Gnrh-a treatment caused significant down-regulation of Gnrh and Gnrhr mRNA expression. Immunohistochemistry combined with quantitative image analysis revealed no significant changes in the plaque load after Gnrh-a treatment in hippocampus and thalamus. However, plaque load in the cerebral cortex of treated females tended to be lower than in female vehicle-treated mice. The present study points to the involvement of hormonal changes in AD mice models and demonstrates that these changes can be effectively counteracted by pharmacological treatment. Although known to increase in normal aging, our study shows that Gnrh/Gnrhr mRNA expression increases much more dramatically in tgArcSwe mice. Treatment with Leuprorelin acetate successfully abolished the transgene specific effects on Gnrh/Gnrhr mRNA expression. The present experimental approach should serve as a platform for further studies on the usefulness of Gnrh-a treatment in suppressing plaque development in AD.