Near‐genomewide RNAi screening for regulators of BRAFV600E‐induced senescence identifies RASEF,a gene epigenetically silenced in melanoma

The activation of oncogenes in primary cells blocks proliferation by inducing oncogene‐induced senescence (OIS), a highly potent in vivo tumor‐suppressing program. A prime example is mutant BRAF, which drives OIS in melanocytic nevi. Progression to melanoma occurs only in the context of additional alteration(s) like the suppression of PTEN, which abrogates OIS. Here, we performed a near‐genomewide short hairpin (sh)RNA screen for novel OIS regulators and identified by next generation sequencing and functional validation seven genes. While all but one were upregulated in OIS, depletion of each of them abrogated BRAF^V600E‐induced arrest. With genome‐wide DNA methylation analysis, we found one of these genes, RASEF, to be hypermethylated in primary cutaneous melanomas but not nevi. Bypass of OIS by depletion of RASEF was associated with suppression of several senescence biomarkers including senescence‐associated (SA)‐β‐galactosidase activity, interleukins, and tumor suppressor p15^INK4B. Restoration of RASEF expression inhibited proliferation. These results illustrate the power of shRNA OIS bypass screens and identify a potential novel melanoma suppressor gene.     

MC1R Genotype and Plumage Colouration in the Zebra Finch (Taeniopygia guttata): Population Structure Generates Artefactual Associations

Polymorphisms at the melanocortin-1 receptor (MC1R) gene have been linked to coloration in many vertebrate species. However, the potentially confounding influence of population structure has rarely been controlled for. We explored the role of the MC1R in a model avian system by sequencing the coding region in 162 zebra finches comprising 79 wild type and 83 white individuals from five stocks. Allelic counts differed significantly between the two plumage morphs at multiple segregating sites, but these were mostly synonymous. To provide a control, the birds were genotyped at eight microsatellites and subjected to Bayesian cluster analysis, revealing two distinct groups. We therefore crossed wild type with white individuals and backcrossed the F1s with white birds. No significant associations were detected in the resulting offspring, suggesting that our original findings were a byproduct of genome-wide divergence. Our results are consistent with a previous study that found no association between MC1R polymorphism and plumage coloration in leaf warblers. They also contribute towards a growing body of evidence suggesting that care should be taken to quantify, and where necessary control for, population structure in association studies.     

An improved screening method for microorganisms able to convert crude glycerol to 1,3-propanediol and to tolerate high product concentrations

A new screening method was developed and established to find high-performance bacteria for the conversion of crude glycerol to 1,3-propanediol. Three soil samples from palm oil-rich habitats were investigated using crude glycerol of a German biodiesel plant. Nine promising 1,3-propanediol producers could be found. Because of a special pH buffer system, a fast evaluation on microscale and high 1,3-propanediol concentrations up to 40 g L⁻¹ could be achieved. Three strains demonstrated very high product tolerance and were identified as Clostridium butyricum. Two strains, AKR91b and AKR102a, grew and produced 1,3-propanediol in the presence of 60 g L⁻¹ initial 1,3-propanediol, the strain AKR92a even in the presence of 77 g L⁻¹ 1,3-propanediol. The strains AKR91b and AKR102a tolerated up to 150 g L⁻¹ crude glycerol and produced 80% of the 1,3-propanediol attained from pure glycerol of the same concentration. Further criteria for the choice of a production strain were the pathogenicity (risk class), ability to grow on low-cost media, e.g., with less yeast extract, and robustness, e.g., process stability after several bioconversions. Overall, the strain C. butyricum AKR102a was chosen for further process optimization and scale-up due to its high productivity and high final concentration in a pH-regulated bioreactor.     

Checkpoint kinase 1 negatively regulates somatic hypermutation

Immunoglobulin (Ig) diversification by somatic hypermutation in germinal center B cells is instrumental for maturation of the humoral immune response, but also bears the risk of excessive or aberrant genetic changes. Thus, introduction of DNA damage by activation-induced cytidine deaminase as well as DNA repair by multiple pathways need to be tightly regulated during the germinal center response to prevent lymphomagenesis. In the present study, we show that DNA damage checkpoint signaling via checkpoint kinase 1 (Chk1) negatively regulates somatic hypermutation. Chk1 inhibition in human B cell lymphoma lines as well as inactivation of Chk1 alleles by gene targeting in DT40 B cells leads to increased somatic hypermutation. This is apparently due to changes in DNA repair pathways regulated by Chk1, such as a decreased homologous recombination efficiency that also leads to decreased Ig gene conversion in DT40. Our data show that Chk1 signaling plays a crucial role in regulation of Ig diversification and sheds unexpected light on potential origins of aberrant somatic hypermutation in B cell lymphomagenesis.     

Water in Photosystem II: Structural,functional and mechanistic considerations

Water is clearly important for the functioning of Photosystem II (PSII). Apart from being the very substrate that needs to be transported in this water oxidation enzyme, water is also vital for the transport of protons to and from the catalytic center as well as other important co-factors and key residues in the enzyme. The latest crystal structural data of PSII have enabled detailed analyses of the location and possible function of water molecules in the enzyme. Significant progress has also been made recently in the investigation of channels and pathways through the protein complex. Through these studies, the mechanistic significance of water for PSII is becoming increasingly clear. An overview and discussion of key aspects of the current research on water in PSII is presented here. The role of water in three other systems (aquaporin, bacteriorhodopsin and cytochrome P450) is also outlined to illustrate further points concerning the central significance that water can have, and potential applications of these ideas for continued research on PSII. It is advocated that water be seen as an integral part of the protein and far from a mere solvent.     

The length of discontinuous gas exchange cycles in lepidopteran pupae may serve as a mechanism for natural selection

Gas exchange is studied in diapausing pupae of Mamestra brassicae L., whose larvae are reared under identical conditions. The release of CO₂ gas is recorded with infrared gaseous analyzers. Oxygen convective uptake into the tracheae and oxygen consumption rates are recorded by means of a constant‐volume coulometric respirometer. Outputs from both of these respirometry systems are combined with infrared actographs. All 3‐month‐old pupae of M. brassicae display a pattern of discontinuous gas exchange (DGE) cycles of CO₂ gas release by bursts, although the lengths of these cycles varies between individuals. Some pupae exhibit long DGE cycles of at least 20 h in duration, with negligible CO₂ gas release during interburst periods, and there is presumed to be a convective gas exchange at this time. As a result of a partial vacuum inside the tracheae, a large oxygen convective uptake always occurs at the start of the spiracular opening phase. Other pupae have short DGE cycles of less than 3 h in duration, with elevated CO₂ gas release during the interburst period, when gas exchange is predominantly diffusive. The spiracular open phase in these pupae consists of frequent separate convective bursts of CO₂ gas release, with the opening–closing rhythms of the spiracles, which are considered as O phase fluttering. The pupae with long DGE cycles exhibit extremely low metabolic rates and very low total water loss rates, whereas those with short DGE cycles have higher metabolic and total water loss rates. The pupae with long DGE cycles live approximately twice as long as those with short cycles; thus, the present study demonstrates that long DGE cycles confer a fitness benefit on pupae as a result of a lower metabolic rate associated with water economy, conferring on them a longer life.     

An analysis of heat effects in different subpopulations of Bangladesh

A substantial number of epidemiological studies have demonstrated an association between atmospheric conditions and human all-cause as well as cause-specific mortality. However, most research has been performed in industrialised countries, whereas little is known about the atmosphere–mortality relationship in developing countries. Especially with regard to modifications from non-atmospheric conditions and intra-population differences, there is a substantial research deficit. Within the scope of this study, we aimed to investigate the effects of heat in a multi-stratified manner, distinguishing by the cause of death, age, gender, location and socio-economic status. We examined 22,840 death counts using semi-parametric Poisson regression models, adjusting for a multitude of potential confounders. Although Bangladesh is dominated by an increase of mortality with decreasing (equivalent) temperatures over a wide range of values, the findings demonstrated the existence of partly strong heat effects at the upper end of the temperature distribution. Moreover, the study demonstrated that the strength of these heat effects varied considerably over the investigated subgroups. The adverse effects of heat were particularly pronounced for males and the elderly above 65 years. Moreover, we found increased adverse effects of heat for urban areas and for areas with a high socio-economic status. The increase in, and acceleration of, urbanisation in Bangladesh, as well as the rapid aging of the population and the increase in non-communicable diseases, suggest that the relevance of heat-related mortality might increase further. Considering rising global temperatures, the adverse effects of heat might be further aggravated.