Regulation of autophagy by cytoplasmic p53

Multiple cellular stressors, including activation of the tumour suppressor p53, can stimulate autophagy. Here we show that deletion, depletion or inhibition of p53 can induce autophagy in human, mouse and nematode cells subjected to knockout, knockdown or pharmacological inhibition of p53. Enhanced autophagy improved the survival of p53-deficient cancer cells under conditions of hypoxia and nutrient depletion, allowing them to maintain high ATP levels. Inhibition of p53 led to autophagy in enucleated cells, and cytoplasmic, not nuclear, p53 was able to repress the enhanced autophagy of p53(-/-) cells. Many different inducers of autophagy (for example, starvation, rapamycin and toxins affecting the endoplasmic reticulum) stimulated proteasome-mediated degradation of p53 through a pathway relying on the E3 ubiquitin ligase HDM2. Inhibition of p53 degradation prevented the activation of autophagy in several cell lines, in response to several distinct stimuli. These results provide evidence of a key signalling pathway that links autophagy to the cancer-associated dysregulation of p53.     

Succinic acid production by <Emphasis Type="Italic">Actinobacillus succinogenes</Emphasis> from batch fermentation of mixed sugars

Succinic acid production from the monosaccharides xylose, arabinose, glucose, mannose and galactose was studied using the bacterium Actinobacillus succinogenes. In Duran bottle cultures, containing 10 g/L of each of sugar, succinic acid was produced from all sugars except for galactose. The highest succinate yield, 0.56 g/g, was obtained with glucose, whereas the succinate yield was 0.42, 0.38 and 0.44 g/g for xylose, mannose and arabinose, respectively. The specific succinate productivity was 0.7 g/g h for glucose, but below 0.2 g/g h for the other sugars. Batch bioreactor fermentations were carried out using a sugar mixture of the five sugars giving a total concentration of 50 g/L, mimicking the distribution of sugars in spent sulfite liquor (SSL) from Eucalyptus which is rich in xylose. In this mixture, an almost complete conversion of all sugars (except galactose) was achieved resulting in a final succinate concentration of 21.8–26.8 g/L and a total yield of 0.59–0.68 g/g. There was evidence of co-consumption of glucose and xylose, whereas mannose was consumed after glucose. The main by-products were acetate 0.14–0.20 g/g and formate 0.08–0.13 g/g. NADH balance calculations suggested that NADH required for succinate production was not met solely from formate and acetate production, but other means of NADH production was necessary. Results from mixed sugar fermentations were verified using SSL as substrate resulting in a succinate yield of 0.60 g/g. In addition, it was found that CO₂ sparging could replace carbonate supply in the form of MgCO₃ without affecting the succinate yield.     

Pathway activity inference for multiclass disease classification through a mathematical programming optimisation framework

Background

Applying machine learning methods on microarray gene expression profiles for disease classification problems is a popular method to derive biomarkers, i.e. sets of genes that can predict disease state or outcome. Traditional approaches where expression of genes were treated independently suffer from low prediction accuracy and difficulty of biological interpretation. Current research efforts focus on integrating information on protein interactions through biochemical pathway datasets with expression profiles to propose pathway-based classifiers that can enhance disease diagnosis and prognosis. As most of the pathway activity inference methods in literature are either unsupervised or applied on two-class datasets, there is good scope to address such limitations by proposing novel methodologies.

Results

A supervised multiclass pathway activity inference method using optimisation techniques is reported. For each pathway expression dataset, patterns of its constituent genes are summarised into one composite feature, termed pathway activity, and a novel mathematical programming model is proposed to infer this feature as a weighted linear summation of expression of its constituent genes. Gene weights are determined by the optimisation model, in a way that the resulting pathway activity has the optimal discriminative power with regards to disease phenotypes. Classification is then performed on the resulting low-dimensional pathway activity profile.

Conclusions

The model was evaluated through a variety of published gene expression profiles that cover different types of disease. We show that not only does it improve classification accuracy, but it can also perform well in multiclass disease datasets, a limitation of other approaches from the literature. Desirable features of the model include the ability to control the maximum number of genes that may participate in determining pathway activity, which may be pre-specified by the user. Overall, this work highlights the potential of building pathway-based multi-phenotype classifiers for accurate disease diagnosis and prognosis problems.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0390-2) contains supplementary material, which is available to authorized users.     

The vacuolar H+ -ATPase mediates intracellular acidification required for neurodegeneration in C. elegans

Numerous studies implicate necrotic cell death in devastating human pathologies such as stroke and neurodegenerative diseases. Investigations in both nematodes and mammals converge to implicate specific calpain and aspartyl proteases in the execution of necrotic cell death. It is believed that these proteases become activated under conditions that inflict necrotic cell death. However, the factors that modulate necrosis and govern the erroneous activation of these otherwise benign enzymes are largely unknown. Here we show that the function of the vacuolar H(+)-ATPase, a pump that acidifies lysosomes and other intracellular organelles, is essential for necrotic cell death in C. elegans. Cytoplasmic pH drops in dying cells. Intracellular acidification requires the vacuolar H(+)-ATPase, whereas alkalization of endosomal and lysosomal compartments by weak bases protects against necrosis. In addition, we show that vacuolar H(+)-ATPase activity is required downstream of cytoplasmic calcium overload during necrosis. Thus, intracellular pH is an important modulator of necrosis in C. elegans. We propose that vacuolar H(+)-ATPase activity is required to establish necrosis-promoting, acidic intracellular conditions that augment the function of executioner aspartyl proteases in dying cells. Similar mechanisms may contribute to necrotic cell death that follows extreme acidosis-for example, during stroke-in humans.     

The diagnostic role of glycosaminoglycans in pleural effusions: A pilot study

Background

While modulation of the serotonin transporter (5HTT) has shown to be a risk factor for pulmonary arterial hypertension for almost 40 years, there is a lack of in vivo data about the broad molecular effects of pulmonary inhibition of 5HTT. Previous studies have suggested effects on inflammation, proliferation, and vasoconstriction. The goal of this study was to determine which of these were supported by alterations in gene expression in serotonin transporter knockout mice.

Methods

Eight week old normoxic mice with a 5-HTT knock-out (5HTT-/-) and their heterozygote(5HTT+/-) or wild-type(5HTT+/+) littermates had right ventricular systolic pressure(RVSP) assessed, lungs collected for RNA, pooled, and used in duplicate in Affymetrix array analysis. Representative genes were confirmed by quantitative RT-PCR and western blot.

Results

RVSP was normal in all groups. Only 124 genes were reliably changed between 5HTT-/- and 5HTT+/+ mice. More than half of these were either involved in inflammatory response or muscle function and organization; in addition, some matrix, heme oxygenase, developmental, and energy metabolism genes showed altered expression. Quantitative RT-PCR for examples from each major group confirmed changes seen by array, with an intermediate level in 5HTT +/- mice.

Conclusion

These results for the first time show the in vivo effects of 5HTT knockout in lungs, and show that many of the downstream mechanisms suggested by cell culture and ex vivo experiments are also operational in vivo. This suggests that the effect of 5HTT on pulmonary vascular function arises from its impact on several systems, including vasoreactivity, proliferation, and immune function.     

Global metabolomics analysis reveals distinctive tolerance mechanisms in different plant organs of lentil (Lens culinaris) upon salinity stress

Plant and Soil - A major limitation to plant growth in acid soils is the prevalence of toxic Al3+. Most genotypic variation for acid soil-tolerance in wheat is linked with the Al3+-activated efflux...     

Leaf surface characteristics and wetting in Ceratonia siliqua L.

Compound leaves of Ceratonia siliqua L. (carob tree) exhibit a long life span and are exposed to environmental stimuli for approximately twenty months. The micromorphology of the adaxial and the abaxial leaflet surfaces was studied, in comparison with treated waxless epidermises (after the removal of cuticle and epicuticular waxes) and corresponding replicas, respectively. The microstructural surface features are evaluated as possible consistent parameters related to the wetness of leaves. The abaxial leaflet surface is more hydrophobic than the adaxial leaflet surface in C. siliqua, which may be particularly important for the ecophysiological status of its hypostomatic leaves.     

Short-term climate changes in the southern Aegean Sea over the last 48,000 years

High-resolution palaeoenvironmental changes, corresponding to a mean time interval of 450 years covering the last 48,000 years, were examined in a core from the Cretan Basin in the southern Aegean Sea. The intensity and duration of the climatic and oceanographic events were determined by examining the compositional changes in the planktonic foraminifera and pollen assemblages, along with the δ¹⁸O signal of Globigerinoides ruber. A reconstruction of sea-surface temperatures was attempted using the Modern Analogue Technique (MAT). In total, 10 stadials and 6 interstadials occurred over the last 48,000 years. These fluctuations in climatic conditions coincide with fluctuations documented in the western and central Mediterranean and seem to be associated with Dansgaard–Oeschger events. Some of these climatic fluctuations are correlated with changes in the vegetation in the surrounding land.

Between 48 and 10 cal kyr BP the most pronounced stadials occurred at 41 cal kyr BP (C69-ST10) and at 13 cal kyr BP (C69-ST4). These events are characterized by: (i) high positive δ¹⁸O values of Globigerinoides ruber, (ii) drops in SST and (iii) increases in aridity. These events may be correlated with the Heinrich H4 event and the Younger Dryas event, respectively. Two other stadials at 23 cal kyr BP (C69-ST6) and at 16 cal kyr BP (C69-ST5) which are characterized by increases in the abundance of the cold plaktonic foraminifera species and increases in aridity may be correlated with the H2 and H1 events, respectively. The dominant planktonic foraminiferal species during the stadials witch are correlated with the Heinrich events were Turborotalita quinqueloba and Globorotalia scitula. The most pronounced interstadials occurred between 39.5 and 38.5 cal kyr BP (C69-IST6) and between 25 and 24 cal kyr BP (C69-IST3) and are characterized by depletion in δ¹⁸O values, increases in SST and increases in humidity. The former event coincides with the formation of the sapropelitic layer S2.

In the Holocene the most pronounced stadial occurred between 8 and 6.5 cal kyr BP (C69-ST2), during the interruption of S1 and is characterized by a reduction in SST and an increase in aridity. The most pronounced interstadials of Holocene occurred during the formation of S1a and S1b between 9 and 8 cal kyr BP (C69-IST1) and between 6.5 and 5.5 cal kyr BP (C69-IST2), respectively. These events are characterized by depletion in δ¹⁸O values, increased SST and an increase in humidity as is indicated by the expansion of temperate evergreen and Mediterranean taxa in the pollen record.