GraphCrunch 2: Software tool for network modeling,alignment and clustering

Background  

Recent advancements in experimental biotechnology have produced large amounts of protein-protein interaction (PPI) data. The topology of PPI networks is believed to have a strong link to their function. Hence, the abundance of PPI data for many organisms stimulates the development of computational techniques for the modeling, comparison, alignment, and clustering of networks. In addition, finding representative models for PPI networks will improve our understanding of the cell just as a model of gravity has helped us understand planetary motion. To decide if a model is representative, we need quantitative comparisons of model networks to real ones. However, exact network comparison is computationally intractable and therefore several heuristics have been used instead. Some of these heuristics are easily computable "network properties," such as the degree distribution, or the clustering coefficient. An important special case of network comparison is the network alignment problem. Analogous to sequence alignment, this problem asks to find the "best" mapping between regions in two networks. It is expected that network alignment might have as strong an impact on our understanding of biology as sequence alignment has had. Topology-based clustering of nodes in PPI networks is another example of an important network analysis problem that can uncover relationships between interaction patterns and phenotype.     

Extracting message inter-departure time distributions from the human electroencephalogram

The complex connectivity of the cerebral cortex is a topic of much study, yet the link between structure and function is still unclear. The processing capacity and throughput of information at individual brain regions remains an open question and one that could potentially bridge these two aspects of neural organization. The rate at which information is emitted from different nodes in the network and how this output process changes under different external conditions are general questions that are not unique to neuroscience, but are of interest in multiple classes of telecommunication networks. In the present study we show how some of these questions may be addressed using tools from telecommunications research. An important system statistic for modeling and performance evaluation of distributed communication systems is the time between successive departures of units of information at each node in the network. We describe a method to extract and fully characterize the distribution of such inter-departure times from the resting-state electroencephalogram (EEG). We show that inter-departure times are well fitted by the two-parameter Gamma distribution. Moreover, they are not spatially or neurophysiologically trivial and instead are regionally specific and sensitive to the presence of sensory input. In both the eyes-closed and eyes-open conditions, inter-departure time distributions were more dispersed over posterior parietal channels, close to regions which are known to have the most dense structural connectivity. The biggest differences between the two conditions were observed at occipital sites, where inter-departure times were significantly more variable in the eyes-open condition. Together, these results suggest that message departure times are indicative of network traffic and capture a novel facet of neural activity.     

Associations between Family-Related Factors,Breakfast Consumption and BMI among 10- to 12-Year-Old European Children: The Cross-Sectional ENERGY-Study

Objective

To investigate associations of family-related factors with children’s breakfast consumption and BMI-z-score and to examine whether children’s breakfast consumption mediates associations between family-related factors and children’s BMI-z-score.

Subjects

Ten- to twelve-year-old children (n = 6374; mean age = 11.6±0.7 years, 53.2% girls, mean BMI-z-score = 0.4±1.2) and one of their parents (n = 6374; mean age = 41.4±5.3 years, 82.7% female, mean BMI = 24.5±4.2 kg/m²) were recruited from schools in eight European countries (Belgium, Greece, Hungary, the Netherlands, Norway, Slovenia, Spain, and Switzerland). The children self-reported their breakfast frequency per week. The body weight and height of the children were objectively measured. The parents responded to items on family factors related to breakfast (automaticity, availability, encouragement, paying attention, permissiveness, negotiating, communicating health beliefs, parental self-efficacy to address children’s nagging, praising, and family breakfast frequency). Mediation analyses were performed using multi-level regression analyses (child-school-country).

Results

Three of the eleven family-related variables were significantly associated with children’s BMI-z-score. The family breakfast frequency was negatively associated with the BMI-z-score; permissiveness concerning skipping breakfast and negotiating about breakfast were positively associated with the BMI-z-score. Children’s breakfast consumption was found to be a mediator of the two associations. All family-related variables except for negotiating, praising and communicating health beliefs, were significantly associated with children’s breakfast consumption.

Conclusions

Future breakfast promotion and obesity prevention interventions should focus on family-related factors including the physical home environment and parenting practices. Nevertheless, more longitudinal research and intervention studies to support these findings between family-related factors and both children’s breakfast consumption and BMI-z-score are needed.     

Predicting disease associations via biological network analysis

Background

Understanding the relationship between diseases based on the underlying biological mechanisms is one of the greatest challenges in modern biology and medicine. Exploring disease-disease associations by using system-level biological data is expected to improve our current knowledge of disease relationships, which may lead to further improvements in disease diagnosis, prognosis and treatment.

Results

We took advantage of diverse biological data including disease-gene associations and a large-scale molecular network to gain novel insights into disease relationships. We analysed and compared four publicly available disease-gene association datasets, then applied three disease similarity measures, namely annotation-based measure, function-based measure and topology-based measure, to estimate the similarity scores between diseases. We systematically evaluated disease associations obtained by these measures against a statistical measure of comorbidity which was derived from a large number of medical patient records. Our results show that the correlation between our similarity measures and comorbidity scores is substantially higher than expected at random, confirming that our similarity measures are able to recover comorbidity associations. We also demonstrated that our predicted disease associations correlated with disease associations generated from genome-wide association studies significantly higher than expected at random. Furthermore, we evaluated our predicted disease associations via mining the literature on PubMed, and presented case studies to demonstrate how these novel disease associations can be used to enhance our current knowledge of disease relationships.

Conclusions

We present three similarity measures for predicting disease associations. The strong correlation between our predictions and known disease associations demonstrates the ability of our measures to provide novel insights into disease relationships.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-304) contains supplementary material, which is available to authorized users.     

Mouse knockout of the cholesterogenic cytochrome P450 lanosterol 14alpha-demethylase (Cyp51) resembles Antley-Bixler syndrome

Antley-Bixler syndrome (ABS) represents a group of heterogeneous disorders characterized by skeletal, cardiac, and urogenital abnormalities that have frequently been associated with mutations in fibroblast growth factor receptor 2 or cytochrome P450 reductase genes. In some ABS patients, reduced activity of the cholesterogenic cytochrome P450 CYP51A1, an ortholog of the mouse CYP51, and accumulation of lanosterol and 24,25-dihydrolanosterol has been reported, but the role of CYP51A1 in the ABS etiology has remained obscure. To test whether Cyp51 could be involved in generating an ABS-like phenotype, a mouse knock-out model was developed that exhibited several prenatal ABS-like features leading to lethality at embryonic day 15. Cyp51(-/-) mice had no functional Cyp51 mRNA and no immunodetectable CYP51 protein. The two CYP51 enzyme substrates (lanosterol and 24,25-dihydrolanosterol) were markedly accumulated. Cholesterol precursors downstream of the CYP51 enzymatic step were not detected, indicating that the targeting in this study blocked de novo cholesterol synthesis. This was reflected in the up-regulation of 10 cholesterol synthesis genes, with the exception of 7-dehydrocholesterol reductase. Lethality was ascribed to heart failure due to hypoplasia, ventricle septum, and epicardial and vasculogenesis defects, suggesting that Cyp51 deficiency was involved in heart development and coronary vessel formation. As the most likely downstream molecular mechanisms, alterations were identified in the sonic hedgehog and retinoic acid signaling pathways. Cyp51 knock-out mice provide evidence that Cyp51 is essential for embryogenesis and present a potential animal model for studying ABS syndrome in humans.     

Water-restraint stress enhances methamphetamine-induced cardiotoxicity

Methamphetamine (MAP) and stress both cause a variety of cardiovascular problems. Stress also increases stimulant drug-seeking or drug-taking behavior by both humans and animals. In addition to the physiological effects on circulation, metabolism, and excretion, stress affects subject's responses to stimulant drugs such as MAP. However, the mechanisms underlying the drug–stress interactions remain unknown. In the present study, we assessed the effects of stress on myocardial responses to MAP in mice. Mice were injected with MAP (30 mg/kg) immediately before exposure to water-restraint stress (WRS), which has often been used as a stressor in animal experiments. The combination of MAP with WRS produced a significant increase (p < 0.01) in the leakage of proteins specific to myocardial damage and the levels of cytokines IL-6, TNF-α, and IL-10. The histological findings indicated the possibility that a combination of MAP with WRS induced cardiac myocytolysis. We also examined the expression of heat shock proteins (Hsps), which have cardioprotective effects. Administration of MAP alone significantly stimulated the RNA expressions of Hsp32, 60, 70, and 90 and the protein Hsp70 in cardiac muscles, whereas the expressions due to WRS or MAP plus WRS were not increased. These results reveal the fact that exposure to WRS depresses the induction of Hsps, in particular Hsp70, due to MAP injection, following to enhance MAP-induced myocardial damage. We believe that interactions between MAP and severe stress, including environmental temperature, affect the induction of Hsps, following to susceptibility of hosts to cardiotoxicity due to the stimulant drug.     

Liposomal Encapsulation of Oleuropein and an Olive Leaf Extract: Molecular Interactions,Antioxidant Effects and Applications in Model Food Systems

The influence of actively/passively encapsulated oleuropein on DPPC liposomes thermal and structural properties, and its antioxidant capacity against lipid peroxidation were investigated. Also, an oleuropein-rich olive leaf extract was encapsulated in soy phosphatidylcholine (PL-90 g) and incorporated in model and commercial drinks. Oleuropein induced a concentration-dependent broadening and splitting of the gel-to-liquid phase transition temperature. Fluorescence measurements revealed a fluidizing effect on liposomes below their gel-to-liquid phase transition temperature, and a higher lipid ordering above, especially to active encapsulation. Oleuropein also showed an antioxidant effect against lipid peroxidation in PL-90 g liposomes. PL-90 g Liposomes with olive leaf extract showed a mean diameter of 405 ± 4 nm and oleuropein encapsulation efficiency of 34% and delayed oleuropein degradation at pH 2.0 and 2.8 model drinks. In conclusion, greater effects were observed on the structure and fluidity of DPPC liposomes when oleuropein was actively encapsulated, while its incorporation into acidic foods in encapsulated form could enhance its stability.

     

Fructose consumption enhances glucocorticoid action in rat visceral adipose tissue

The rise in consumption of refined sugars high in fructose appears to be an important factor for the development of obesity and metabolic syndrome. Fructose has been shown to be involved in genesis and progression of the syndrome through deregulation of metabolic pathways in adipose tissue. There is evidence that enhanced glucocorticoid regeneration within adipose tissue, mediated by the enzyme 11beta-hydroxysteroid dehydrogenase Type 1 (11βHSD1), may contribute to adiposity and metabolic disease. 11βHSD1 reductase activity is dependent on NADPH, a cofactor generated by hexose-6-phosphate dehydrogenase (H6PDH). We hypothesized that harmful effects of long-term high fructose consumption could be mediated by alterations in prereceptor glucocorticoid metabolism and glucocorticoid signaling in the adipose tissue of male Wistar rats. We analyzed the effects of 9-week drinking of 10% fructose solution on dyslipidemia, adipose tissue histology and both plasma and tissue corticosterone level. Prereceptor metabolism of glucocorticoids was characterized by determining 11βHSD1 and H6PDH mRNA and protein levels. Glucocorticoid signaling was examined at the level of glucocorticoid receptor (GR) expression and compartmental redistribution, as well as at the level of expression of its target genes (GR, phosphoenolpyruvate carboxyl kinase and hormone-sensitive lipase). Fructose diet led to increased 11βHSD1 and H6PDH expression and elevated corticosterone level within the adipose tissue, which was paralleled with enhanced GR nuclear accumulation. Although the animals did not develop obesity, nonesterified fatty acid and plasma triglyceride levels were elevated, indicating that fructose, through enhanced prereceptor metabolism of glucocorticoids, could set the environment for possible later onset of obesity.     

Autophagic activity in the mouse urinary bladder urothelium as a response to starvation

The urinary bladder urothelium is subjected to mechanical forces during cycles of distension and contraction, and its superficial cells are constantly flushed by toxic urine. Yet, the urothelium shows a very slow turnover of cells and superficial cells are extremely long lived. Autophagy has a well-known role in tissue homeostasis and serves as a protective mechanism against cellular stress. Therefore, the presence of autophagy as one of possible processes of survival in an unpleasant environment and during long lifetime of superficial cells was examined in mouse urothelium. We detected and evaluated autophagic activity of superficial urothelial cells under normal and stress conditions, caused by short-term starvation of newborn and 24-h-starved adult mice. Immunolabeling and Western blotting of essential effectors of autophagy, LC3 and Beclin 1, showed a weak signal in superficial urothelial cells. On the other hand, ultrastructural analysis, which proved to be the most reliable method in our study, revealed the presence of autophagic vacuoles, some of them containing specific urothelial structures, fusiform vesicles. Quantitative analysis showed increased autophagy in newborn and starved mice in comparison to a low basic level of autophagy in the urothelium of normal mice. Interestingly, some superficial cells of adults and neonates exhibit intense immunoreactions against LC3 and Beclin 1 and the typical ultrastructural characteristics of autophagy-dependent cell death. We conclude that autophagy, despite low basic activity under physiological conditions, plays an important role in urothelial homeostasis and stability under stress.