Multi-membership gene regulation in pathway based microarray analysis

This article is available through the Brunel Open Access Publishing Fund. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: Gene expression analysis has been intensively researched for more than a decade. Recently, there has been elevated interest in the integration of microarray data analysis with other types of biological knowledge in a holistic analytical approach. We propose a methodology that can be facilitated for pathway based microarray data analysis, based on the observation that a substantial proportion of genes present in biochemical pathway databases are members of a number of distinct pathways. Our methodology aims towards establishing the state of individual pathways, by identifying those truly affected by the experimental conditions based on the behaviour of such genes. For that purpose it considers all the pathways in which a gene participates and the general census of gene expression per pathway. Results: We utilise hill climbing, simulated annealing and a genetic algorithm to analyse the consistency of the produced results, through the application of fuzzy adjusted rand indexes and hamming distance. All algorithms produce highly consistent genes to pathways allocations, revealing the contribution of genes to pathway functionality, in agreement with current pathway state visualisation techniques, with the simulated annealing search proving slightly superior in terms of efficiency. Conclusions: We show that the expression values of genes, which are members of a number of biochemical pathways or modules, are the net effect of the contribution of each gene to these biochemical processes. We show that by manipulating the pathway and module contribution of such genes to follow underlying trends we can interpret microarray results centred on the behaviour of these genes.The work was sponsored by the studentship scheme of the School of Information Systems, Computing and Mathematics, Brunel Universit

Adiponectin Deficiency Impairs Maternal Metabolic Adaptation to Pregnancy in Mice.

Hypoadiponectinemia has been widely observed in patients with gestational diabetes mellitus (GDM). To investigate the causal role of hypoadiponectinemia in GDM, adiponectin gene knockout (Adipoq-/- ) and wild-type (WT) mice were crossed to produce pregnant mouse models with or without adiponectin deficiency. Adenoviral vector-mediated in vivo transduction was used to reconstitute adiponectin during late pregnancy. Results showed that Adipoq-/- dams developed glucose intolerance and hyperlipidemia in late pregnancy. Increased fetal body weight was detected in Adipoq-/- dams. Adiponectin reconstitution abolished these metabolic defects in Adipoq-/- dams. Hepatic glucose and triglyceride production rates of Adipoq-/- dams were significantly higher than those of WT dams. Robustly enhanced lipolysis was found in gonadal fat of Adipoq-/- dams. Interestingly, similar levels of insulin-induced glucose disposal and insulin signaling in metabolically active tissues in Adipoq-/- and WT dams indicated that maternal adiponectin deficiency does not reduce insulin sensitivity. However, remarkably decreased serum insulin concentrations were observed in Adipoq-/- dams. Furthermore, β-cell mass, but not glucose-stimulated insulin release, in Adipoq-/- dams was significantly reduced compared with WT dams. Together, these results demonstrate that adiponectin plays an important role in controlling maternal metabolic adaptation to pregnancy

Doxycycline alters metabolism and proliferation of human cell lines.

The tetracycline antibiotics are widely used in biomedical research as mediators of inducible gene expression systems. Despite many known effects of tetracyclines on mammalian cells-including inhibition of the mitochondrial ribosome-there have been few reports on potential off-target effects at concentrations commonly used in inducible systems. Here, we report that in human cell lines, commonly used concentrations of doxycycline change gene expression patterns and concomitantly shift metabolism towards a more glycolytic phenotype, evidenced by increased lactate secretion and reduced oxygen consumption. We also show that these concentrations are sufficient to slow proliferation. These findings suggest that researchers using doxycycline in inducible expression systems should design appropriate controls to account for potential confounding effects of the drug on cellular metabolism

Effects of pre-exercise carbohydrate consumption on metabolism during exercise

It is well documented that consuming carbohydrates (CHO) prior to exercise has been shown to alter metabolism. There are many ways that CHO ingestion affects substrate utilization and blood glucose dynamics at the start of exercise. Changes in the concentrations of blood glucose, insulin, glucagon, free fatty acids (FFAs) as well as varying utilizations of different substrates have been observed. Each of these responses is reflective of the body’s capacity to maintain homeostasis through different physiological conditions and demands. PURPOSE: The aim is to deduce how varying amounts (approximately 0, 12.5, 25 and 50g for a 70 kg person) of pre-exercise sucrose ingestion effects metabolism including blood glucose concentration and fat oxidation during 30 minutes of moderate intense exercise. METHODS: This will be a randomized crossover study. After the initial assessment of baseline data (VO2peak), participants will be asked to perform four cycling trials at 50% of VO2peak for 30 minutes. Forty-five minutes before each exercise trial, participants will consume 0, 12.5, 25 and 50g (for a 70kg person) of sucrose. VO2 and VCO2 will be collected for 15 minutes prior to exercise and for the entire 30 minutes of cycling. Blood glucose will be obtained through the finger prick method and collected directly prior to exercise, 5, 15 and 30 minutes into cycling. Heart rate and rate of perceived exertion will be measured every 5 minutes of exercise. DISCUSSION: It is speculated that a small dose (12.5g for a 70kg person) of pre-exercise sucrose consumption will be able to demonstrate a decline in blood glucose concentration during exercise with a step-wise reduction in fat oxidation. This dose response curve will display the sensitivity of metabolism to ingested sucrose.Kinesiology and Health Educatio

The Hepatocellular Hypoxia Criteria:2’Nitroimidazole Effect on Hepatocyte Carbohydrate Metabolizing Enzymes

Aim: to understand the 2’-nitroimidazole induced hypoxia and liver cell interaction, we proposed a “Hapatocellular Hypoxia Criteria”. Hypothesis: The nitroimidazole induced metabolic energy loss and oxygen depletion (hypoxia) in liver cell mitochondria causes the phagocytosis. Based on it, ten control subjects with 2’-nitroimidazole therapy were studied for their carbohydrate metabolizing enzymes in serum and hepatocellular enzymes in liver biopsy tissues. Materials and Methods: Proven ten control subjects were studied for hypoxia by enzyme assays. The 2’nitroimidazole treated paired ten subjects were studied for hypoxia using enzyme assays and hepatocellular cytomorphology by electron microscopy. Results and Discussion: Out of ten subjects on 2’-nitroimidazole, nine showed elevated carbohydrate metabolizing and lysosomal enzyme levels in serum. The enzymes glucokinase (in 80% samples), aldolase (in 80% samples), phosphofructokinase (in 80% samples), malate dehydrogenase (in 75% samples), isocitrate dehydrogenase (ICDH) (in 60% patients) were elevated while succinate dehydrogenase and lactate dehydrogenase (LDH) levels remained unaltered. Lysosomal enzymes β-glucuronidase, alkaline phosphatase, acid phosphatase, showed enhanced levels in the serum samples. In control ten liver biopsies, the hepatocytes and Kupffer cell preparations showed altered enzyme levels. Hepatocytes showed lowered glucokinase (in 80%), LDH (in 80%), and higher content of aldolase (in 80%), pyruvate kinase (in 100%), malate dehydrogenase (in 80%), ICDH (in 80%), citrate dehydrogenase (in 70%), phosphogluconate dehydrogenase (in 80%). Kupffer cells showed higher enzyme levels of β-glucuroronidase (in 80%), leucine aminopeptidase (in 70%), acid phosphatase (in 80%) and aryl sulphatase (in 88%). In these 10 biopsy samples from subjects on 2’-nitronidazole clinical trial, the electron microscopy cytomorphology observations showed swollen bizarre mitochondria, proliferative endoplasmic reticulum, and anisonucleosis after 2’-Nitroimidazole effect in liver cell damage. Conclusion: The proposed “Hepatocellular Hypoxia Criteria” served to define origin of liver hypoxia and showed altered hepatic enzyme activities with active phagocytosis and cytotoxicity in subjects after 2’-nitroimidazole treatment. The study suggests the enzyme based evaluation of nitroimidazole induced hypoxia monitoring and treatment of hepatic tumors and infected liver