Evaluation of reference genes for real-time RT-PCR expression studies in the plant pathogen Pectobacterium atrosepticum

Background

Translation initiation factors of the 4E and 4G protein families mediate resistance to several RNA plant viruses in the natural diversity of crops. Particularly, a single point mutation in melon eukaryotic translation initiation factor 4E (eIF4E) controls resistance to Melon necrotic spot virus (MNSV) in melon. Identification of allelic variants within natural populations by EcoTILLING has become a rapid genotype discovery method.

Results

A collection of Cucumis spp. was characterised for susceptibility to MNSV and Cucumber vein yellowing virus (CVYV) and used for the implementation of EcoTILLING to identify new allelic variants of eIF4E. A high conservation of eIF4E exonic regions was found, with six polymorphic sites identified out of EcoTILLING 113 accessions. Sequencing of regions surrounding polymorphisms revealed that all of them corresponded to silent nucleotide changes and just one to a non-silent change correlating with MNSV resistance. Except for the MNSV case, no correlation was found between variation of eIF4E and virus resistance, suggesting the implication of different and/or additional genes in previously identified resistance phenotypes. We have also characterized a new allele of eIF4E from Cucumis zeyheri, a wild relative of melon. Functional analyses suggested that this new eIF4E allele might be responsible for resistance to MNSV.

Conclusion

This study shows the applicability of EcoTILLING in Cucumis spp., but given the conservation of eIF4E, new candidate genes should probably be considered to identify new sources of resistance to plant viruses. Part of the methodology described here could alternatively be used in TILLING experiments that serve to generate new eIF4E alleles.     

Role of Cx43 Phosphorylation and MAP Kinase Activation in EGF Induced Enhancement of Cell Communication in Human Kidney Epithelial Cells

Epidermal growth factor (EGF) has been found to induce enhanced gap junctional intercellular communication (GJIC) in the human kidney epithelial cell line K7. This is in contrast to what is reported for other cell types, which all show decreased GJIC in response to EGF. In the present study it is shown that 12-O-tetradecanoylphorbol-13-acetate (TPA) and EGF induce similar phosphorylation pattern of the gap junction protein connexin43 (Cx43) in K7 cells, although their effects on GJIC are opposite. Tyrosine phosphorylation of a 42 kD protein was observed to be induced concomitantly with phosphorylation of Cx43. EGF was however found to induce only serine phosphorylation of Cx43, indicating that the tyrosine kinase activity of the EGF receptor was not directly affecting the gap junction protein. The 42 kD protein phosphorylated on tyrosine was identified to be a mitogen activated protein (MAP) kinase. Both EGF and TPA was found to activate MAP kinase in these cells. Phosphorylation of Cx43 and enhancement of GJIC in response to EGF occurred with difference in time course. Phosphorylation of Cx43 was completed within 15 min, while the enhanced GJIC appeared 2-3 h later. It is therefore possible that regulation of synthesis or transport of Cx43 is responsible for the increase in GJIC, rather than direct involvement of Cx43 phosphorylation. This is in support of our previous finding that protein synthesis is necessary for EGF induced upregulation of GJIC in K7 cells.     

Low support for separate species within the redpoll complex (Carduelis flammea-hornemanni-cabaret) from analyses of mtDNA and microsatellite markers

The redpoll complex, consisting of three currently recognized species (Carduelis flammea, C. hornemanni and C. cabaret), is polytypic in biometry, morphology, physiology and behaviour. However, previous genetic work has not revealed any indications of genetic differentiation. We analysed sequence variation in the mtDNA control region, and allele frequencies of supposedly faster evolving microsatellites (n=10), in an attempt to detect molecular genetic support for the three species, as well as two subspecies of C. flammea (ssp. flammea and rostrata), within this complex. We used samples from two subspecies of the twite (Carduelis flavirostris, ssp. flavirostris and rufostrigata) as outgroup. We found no structure among redpoll individuals in mtDNA haplotypes or microsatellite allele frequencies, and only marginal differences between redpoll taxa in analyses of molecular variance (AMOVAs) of predefined groups. In contrast, the two twite subspecies constituted two well-supported monophyletic groups. Our study thus strengthens previous indications of low genetic support for current redpoll taxa. Two major alternative interpretations exist. Either redpolls form a single gene pool with geographical polymorphisms possibly explained by Bergmann's and Gloger's rules, or there are separate gene pools of recent origin but with too little time elapsed for genetic differentiation to have evolved in the investigated markers. Future studies should therefore examine whether reproductive isolation mechanisms and barriers to gene flow exist in areas with sympatric breeding.     

ELF-magnetic flux densities measured in a city environment in summer and winter

Epidemiological studies have indicated a connection between extremely low frequency magnetic flux densities above 0.4 microT (time weighted average) and childhood leukemia risks. This conclusion is based mainly on indoor exposure measurements. We therefore regarded it important to map outdoor magnetic flux densities in public areas in Trondheim, Norway. Because of seasonal power consumption variations, the fields were measured during both summer and winter. Magnetic flux density was mapped 1.0 m above the ground along 17 km of pavements in downtown Trondheim. The spectrum was measured at some spots and the magnetic flux density emanated mainly from the power frequency of 50 Hz. In summer less than 4% of the streets showed values exceeding 0.4 microT, increasing to 29% and 34% on cold and on snowy winter days, respectively. The average levels were 0.13 microT (summer), 0.85 microT (winter, cold), and 0.90 microT (winter, snow), with the highest recorded value of 37 microT. High spot measurements were usually encountered above underground transformer substations. In winter electric heating of pavements also gave rise to relatively high flux densities. There was no indication that the ICNIRP basic restriction was exceeded. It would be of interest to map the flux density situation in other cities and towns with a cold climate.     

Genetic associations with temporal shifts in obesity and severe obesity during the obesity epidemic in Norway: A longitudinal population-based cohort (the HUNT Study)

BackgroundObesity has tripled worldwide since 1975 as environments are becoming more obesogenic. Our study investigates how changes in population weight and obesity over time are associated with genetic predisposition in the context of an obesogenic environment over 6 decades and examines the robustness of the findings using sibling design.Methods and findingsA total of 67,110 individuals aged 13–80 years in the Nord-Trøndelag region of Norway participated with repeated standardized body mass index (BMI) measurements from 1966 to 2019 and were genotyped in a longitudinal population-based health study, the Trøndelag Health Study (the HUNT Study). Genotyping required survival to and participation in the HUNT Study in the 1990s or 2000s. Linear mixed models with observations nested within individuals were used to model the association between a genome-wide polygenic score (GPS) for BMI and BMI, while generalized estimating equations were used for obesity (BMI ≥ 30 kg/m²) and severe obesity (BMI ≥ 35 kg/m²).The increase in the average BMI and prevalence of obesity was steeper among the genetically predisposed. Among 35-year-old men, the prevalence of obesity for the least predisposed tenth increased from 0.9% (95% confidence interval [CI] 0.6% to 1.2%) to 6.5% (95% CI 5.0% to 8.0%), while the most predisposed tenth increased from 14.2% (95% CI 12.6% to 15.7%) to 39.6% (95% CI 36.1% to 43.0%). Equivalently for women of the same age, the prevalence of obesity for the least predisposed tenth increased from 1.1% (95% CI 0.7% to1.5%) to 7.6% (95% CI 6.0% to 9.2%), while the most predisposed tenth increased from 15.4% (95% CI 13.7% to 17.2%) to 42.0% (95% CI 38.7% to 45.4%). Thus, for 35-year-old men and women, respectively, the absolute change in the prevalence of obesity from 1966 to 2019 was 19.8 percentage points (95% CI 16.2 to 23.5, p < 0.0001) and 20.0 percentage points (95% CI 16.4 to 23.7, p < 0.0001) greater for the most predisposed tenth compared with the least predisposed tenth, defined using the GPS for BMI. The corresponding absolute changes in the prevalence of severe obesity for men and women, respectively, were 8.5 percentage points (95% CI 6.3 to 10.7, p < 0.0001) and 12.6 percentage points (95% CI 9.6 to 15.6, p < 0.0001) greater for the most predisposed tenth. The greater increase in BMI in genetically predisposed individuals over time was apparent after adjustment for family-level confounding using a sibling design. Key limitations include a slightly lower survival to date of genetic testing for the older cohorts and that we apply a contemporary genetic score to past time periods. Future research should validate our findings using a polygenic risk score constructed from historical data.ConclusionsIn the context of increasingly obesogenic changes in our environment over 6 decades, our findings reveal a growing inequality in the risk for obesity and severe obesity across GPS tenths. Our results suggest that while obesity is a partially heritable trait, it is still modifiable by environmental factors. While it may be possible to identify those most susceptible to environmental change, who thus have the most to gain from preventive measures, efforts to reverse the obesogenic environment will benefit the whole population and help resolve the obesity epidemic.

In a longitudinal population-based cohort study in Norway, Maria Brandkvist and colleagues investigate how genetic predisposition relates to changes in BMI and obesity over the past six decades.     

Evaluating the terrestrial carbon dioxide removal potential of improved forest management and accelerated forest conversion in Norway

As a carbon dioxide removal measure, the Norwegian government is currently considering a policy of large‐scale planting of spruce (Picea abies (L) H. Karst) on lands in various states of natural transition to a forest dominated by deciduous broadleaved tree species. Given the aspiration to bring emissions on balance with removals in the latter half of the 21st century in effort to limit the global mean temperature rise to “well below” 2°C, the effectiveness of such a policy is unclear given relatively low spruce growth rates in the region. Further convoluting the picture is the magnitude and relevance of surface albedo changes linked to such projects, which typically counteract the benefits of an enhanced forest CO₂ sink in high‐latitude regions. Here, we carry out a rigorous empirically based assessment of the terrestrial carbon dioxide removal (tCDR) potential of large‐scale spruce planting in Norway, taking into account transient developments in both terrestrial carbon sinks and surface albedo over the 21st century and beyond. We find that surface albedo changes would likely play a negligible role in counteracting tCDR, yet given low forest growth rates in the region, notable tCDR benefits from such projects would not be realized until the second half of the 21st century, with maximum benefits occurring even later around 2150. We estimate Norway's total accumulated tCDR potential at 2100 and 2150 (including surface albedo changes) to be 447 (±240) and 852 (±295) Mt CO₂‐eq. at mean net present values of US$ 12 (±3) and US$ 13 (±2) per ton CDR, respectively. For perspective, the accumulated tCDR potential at 2100 represents around 8 years of Norway's total current annual production‐based (i.e., territorial) CO₂‐eq. emissions.