Measurement errors and regression to the mean cannot explain bias in average Ellenberg indicator values

Smart & Scott (2004, this is sue) criticized our paper (Wamelink et al. 2002) about the bias in average Ellenberg indicator values. Their main criticism concerns the method we used, regression analysis. They state the bias can be mimicked by the construction of an artificial data set and that regression analysis is not a suited tool to investigate underlying phenomena. Moreover they claim that the present bias is caused by the distribution of Ellenberg indicator values between syntaxa, instead of a bias in average Ellenberg indicator values per species. We show that their criticism of the use of regression analysis does not hold. We selected average Ellenberg values per vegetation group for several pH classes and applied an F‐test to determine whether or not the vegetation groups within each pH class differed significantly from each other. This was the case for all tested classes (P < 0.001). Moreover we simulated an artificial data set, of which the F‐test for varying measurement error could not explain the magnitude of the F‐value we found earlier. This indicates that the bias we found in average Ellenberg indicator values cannot be explained by measurement errors or by regression to the mean. In the end, Smart & Scott, as we did, come to the conclusion that there is a bias present and that separate regression lines per vegetation type are necessary, but the debate remains open on whether or not this is caused by the bias in Ellenberg indicator values per species.     

Can Plants Grow on Mars and the Moon: A Growth Experiment on Mars and Moon Soil Simulants

When humans will settle on the moon or Mars they will have to eat there. Food may be flown in. An alternative could be to cultivate plants at the site itself, preferably in native soils. We report on the first large-scale controlled experiment to investigate the possibility of growing plants in Mars and moon soil simulants. The results show that plants are able to germinate and grow on both Martian and moon soil simulant for a period of 50 days without any addition of nutrients. Growth and flowering on Mars regolith simulant was much better than on moon regolith simulant and even slightly better than on our control nutrient poor river soil. Reflexed stonecrop (a wild plant); the crops tomato, wheat, and cress; and the green manure species field mustard performed particularly well. The latter three flowered, and cress and field mustard also produced seeds. Our results show that in principle it is possible to grow crops and other plant species in Martian and Lunar soil simulants. However, many questions remain about the simulants'' water carrying capacity and other physical characteristics and also whether the simulants are representative of the real soils.     

Apparently we do need phytosociological classes to calibrate Ellenberg indicator values!

Abstract. We stated (Wamelink et al. 2002) that mean Ellenberg indicator values are biased towards expectations of phytosociologists. Witte & von Asmuth (2003; this volume) have two major points of criticism: (1) the data we used would be systematically biased; (2) in calibrating Ellenberg indicator values for moisture availability against mean spring groundwater level we should have assumed a sigmoid response instead of a linear one. As to (1), a bias in the data would require that wet vegetation types were visited in wet years and dry vegetation types in dry years. We do not see any evidence for this. As to (2), our data do not provide strong evidence for a sigmoid relation instead of a linear one. Neither is there any indication that the bias in the Ellenberg indicator values would disappear when a sigmoid function would be fitted. We do agree with Witte & von Asmuth that it is preferable to characterize the species’ response by those variables to which they most directly respond.     

Pyruvate kinase triggers a metabolic feedback loop that controls redox metabolism in respiring cells

In proliferating cells, a transition from aerobic to anaerobic metabolism is known as the Warburg effect, whose reversal inhibits cancer cell proliferation. Studying its regulator pyruvate kinase (PYK) in?yeast, we discovered that central metabolism is?self-adapting to synchronize redox metabolism when respiration is activated. Low PYK activity activated yeast respiration. However, levels of reactive oxygen species (ROS) did not increase, and cells gained resistance to oxidants. This adaptation was attributable to accumulation of the PYK substrate phosphoenolpyruvate (PEP). PEP acted as feedback inhibitor of the glycolytic enzyme triosephosphate isomerase (TPI). TPI inhibition stimulated the pentose phosphate pathway, increased antioxidative metabolism, and prevented ROS accumulation. Thus, a metabolic feedback loop, initiated by PYK, mediated by its substrate and acting on TPI, stimulates redox metabolism in respiring cells. Originating from a single catalytic step, this autonomous reconfiguration of central carbon metabolism prevents oxidative stress upon shifts between fermentation and respiration.     

Both sexes pay a cost of reproduction in a frog with biparental care

The assumption that reproduction is costly is central to life‐history theory. Good evidence supporting this premise comes from studies, mostly in short‐lived invertebrates, demonstrating a negative relationship between reproduction and longevity. Whether this trade‐off operates broadly, for example in males and females and in short‐ and long‐lived organisms, remains unresolved. We found a negative relationship between reproduction and days survived in captive, wild‐caught, individuals of a long‐lived poison frog with biparental care (Oophaga pumilio). The proportion of time that individuals spent paired and tadpole production rate were negatively associated with days survived in both sexes, and clutch production was negatively associated with days survived in females. These results broaden the taxonomic base upon which this tenet of life‐history theory is built, empirically confirm that females of this species should be choosy when selecting mates and caring for offspring, and suggest that the costs of ‘limited’ male care in this species deserve re‐evaluation. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 211–218.     

Quantification of sugar phosphate intermediates of the pentose phosphate pathway by LC-MS/MS: application to two new inherited defects of metabolism

We describe a liquid chromatography tandem mass spectrometry (LC-MS/MS) method to quantify pentose phosphate pathway intermediates (triose-3-phosphates, tetrose-4-phosphate, pentose-5-phosphate, pentulose-5-phosphates, hexose-6-phosphates and sedoheptulose-7-phosphate (sed-7P)) in bloodspots, fibroblasts and lymphoblasts. Liquid chromatography was performed using an ion pair loaded C(18) HPLC column and detection of the sugar phosphates was carried out by tandem mass spectrometry using an electron ion spray source operating in the negative mode and multiple reaction monitoring. Reference values for the pentose phosphate pathway intermediates in blood spots, fibroblasts and lymphoblasts were established. The method was applied to cells from patients affected with a deficiency of transaldolase. The transaldolase-deficient cells showed an increased concentration of sedoheptulose-7-phosphate. (Bloodspots: 5.19 and 5.43 micromol/L [0.49-3.33 micromol/L]; fibroblasts 7.43 and 26.46 micromol/mg protein [0.31-1.14 micromol/mg protein]; lymphoblasts 16.03 micromol/mg protein [0.61-2.09 micromol/mg protein].) The method was also applied to study enzymes of the pentose phosphate pathway by incubating fibroblasts or lymphoblasts homogenates with ribose-5-phosphate or 6-phosphogluconate and the subsequent analysis of the formed sugar phosphates.     

Mitochondrial involvement and erythronic acid as a novel biomarker in transaldolase deficiency

BackgroundSedoheptulose, arabitol, ribitol, and erythritol have been identified as key diagnostic metabolites in TALDO deficiency.MethodUrine from 6 TALDO-deficient patients and TALDO-deficient knock-out mice were analyzed using ¹H-NMR spectroscopy and GC–mass spectrometry.ResultsOur data confirm the known metabolic characteristics in TALDO-deficient patients. The β-furanose form was the major sedoheptulose anomer in TALDO-deficient patients. Erythronic acid was identified as a major abnormal metabolite in all patients and in knock-out TALDO mice implicating an as yet unknown biochemical pathway in this disease. A putative sequence of enzymatic reactions leading to the formation of erythronic acid is presented. The urinary concentration of the citric acid cycle intermediates 2-oxoglutaric acid and fumaric acid was increased in the majority of TALDO-deficient patients but not in the knock-out mice.ConclusionErythronic acid is a novel and major hallmark in TALDO deficiency. The pathway leading to its production may play a role in healthy humans as well. In TALDO-deficient patients, there is an increased flux through this pathway. The finding of increased citric acid cycle intermediates hints toward a disturbed mitochondrial metabolism in TALDO deficiency.