Roux-En Y Gastric Bypass Surgery Induces Genome-Wide Promoter-Specific Changes in DNA Methylation in Whole Blood of Obese Patients

Context DNA methylation has been proposed to play a critical role in many cellular and biological processes. Objective To examine the influence of Roux-en-Y gastric bypass (RYGB) surgery on genome-wide promoter-specific DNA methylation in obese patients. Promoters are involved in the initiation and regulation of gene transcription. Methods Promoter-specific DNA methylation in whole blood was measured in 11 obese patients (presurgery BMI >35 kg/m2, 4 females), both before and 6 months after RYGB surgery, as well as once only in a control group of 16 normal-weight men. In addition, body weight and fasting plasma glucose were measured after an overnight fast. Results The mean genome-wide distance between promoter-specific DNA methylation of obese patients at six months after RYGB surgery and controls was shorter, as compared to that at baseline (p<0.001). Moreover, postsurgically, the DNA methylation of 51 promoters was significantly different from corresponding values that had been measured at baseline (28 upregulated and 23 downregulated, P<0.05 for all promoters, Bonferroni corrected). Among these promoters, an enrichment for genes involved in metabolic processes was found (n = 36, P<0.05). In addition, the mean DNA methylation of these 51 promoters was more similar after surgery to that of controls, than it had been at baseline (P<0.0001). When controlling for the RYGB surgery-induced drop in weight (-24% of respective baseline value) and fasting plasma glucose concentration (-16% of respective baseline value), the DNA methylation of only one out of 51 promoters (~2%) remained significantly different between the pre-and postsurgery time points. Conclusions Epigenetic modifications are proposed to play an important role in the development of and predisposition to metabolic diseases, including type II diabetes and obesity. Thus, our findings may form the basis for further investigations to unravel the molecular effects of gastric bypass surgery. Clinical Trial ClinicalTrials.gov NCT0173074

The Drosophila ETV5 Homologue Ets96B: Molecular Link between Obesity and Bipolar Disorder

Several reports suggest obesity and bipolar disorder (BD) share some physiological and behavioural similarities. For instance, obese individuals are more impulsive and have heightened reward responsiveness, phenotypes associated with BD, while bipolar patients become obese at a higher rate and earlier age than people without BD; however, the molecular mechanisms of such an association remain obscure. Here we demonstrate, using whole transcriptome analysis, that Drosophila Ets96B, homologue of obesity-linked gene ETV5, regulates cellular systems associated with obesity and BD. Consistent with a role in obesity and BD, loss of nervous system Ets96B during development increases triacylglyceride concentration, while inducing a heightened startle-response, as well as increasing hyperactivity and reducing sleep. Of notable interest, mouse Etv5 and Drosophila Ets96B are expressed in dopaminergic-rich regions, and loss of Ets96B specifically in dopaminergic neurons recapitulates the metabolic and behavioural phenotypes. Moreover, our data indicate Ets96B inhibits dopaminergic-specific neuroprotective systems. Additionally, we reveal that multiple SNPs in human ETV5 link to body mass index (BMI) and BD, providing further evidence for ETV5 as an important and novel molecular intermediate between obesity and BD. We identify a novel molecular link between obesity and bipolar disorder. The Drosophila ETV5 homologue Ets96B regulates the expression of cellular systems with links to obesity and behaviour, including the expression of a conserved endoplasmic reticulum molecular chaperone complex known to be neuroprotective. Finally, a connection between the obesity-linked gene ETV5 and bipolar disorder emphasizes a functional relationship between obesity and BD at the molecular level

Aptamer-based multiplexed proteomic technology for biomarker discovery

Interrogation of the human proteome in a highly multiplexed and efficient manner remains a coveted and challenging goal in biology. We present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes (15 [mu]L of serum or plasma). Our current assay allows us to measure ~800 proteins with very low limits of detection (1 pM average), 7 logs of overall dynamic range, and 5% average coefficient of variation. This technology is enabled by a new generation of aptamers that contain chemically modified nucleotides, which greatly expand the physicochemical diversity of the large randomized nucleic acid libraries from which the aptamers are selected. Proteins in complex matrices such as plasma are measured with a process that transforms a signature of protein concentrations into a corresponding DNA aptamer concentration signature, which is then quantified with a DNA microarray. In essence, our assay takes advantage of the dual nature of aptamers as both folded binding entities with defined shapes and unique sequences recognizable by specific hybridization probes. To demonstrate the utility of our proteomics biomarker discovery technology, we applied it to a clinical study of chronic kidney disease (CKD). We identified two well known CKD biomarkers as well as an additional 58 potential CKD biomarkers. These results demonstrate the potential utility of our technology to discover unique protein signatures characteristic of various disease states. More generally, we describe a versatile and powerful tool that allows large-scale comparison of proteome profiles among discrete populations. This unbiased and highly multiplexed search engine will enable the discovery of novel biomarkers in a manner that is unencumbered by our incomplete knowledge of biology, thereby helping to advance the next generation of evidence-based medicine

S.I.Lex, le blog revisité

Très fourni, avec plus de 600 billets denses et documentés, ce blog méritait de disposer de passeurs prêts à partager leurs parcours de lecture, depuis 10 ans, pour rendre visibles les éclats d’une pensée investie et engagée dans la défense des droits numériques des usagers. Ce sont près de 15 très fins connaisseurs du blog qui présentent « leur » S.I.Lex à travers une sélection de billets éditorialisés : une manière de faire circuler autrement les analyses de Lionel Maurel notamment dans le domaine des bibliothèques numériques, des modèles économiques et des biens communs

Involvement of EphB1 Receptors Signalling in Models of Inflammatory and Neuropathic Pain

EphB receptors tyrosine kinases and ephrinB ligands were first identified as guidance molecules involved in the establishment of topographical mapping and connectivity in the nervous system during development. Later in development and into adulthood their primary role would switch from guidance to activity-dependent modulation of synaptic efficacy. In sensory systems, they play a role in both the onset of inflammatory and neuropathic pain, and in the establishment of central sensitisation, an NMDA-mediated form of synaptic plasticity thought to underlie most forms of chronic pain. We studied wild type and EphB1 knockout mice in a range of inflammatory and neuropathic pain models to determine 1), whether EphB1 expression is necessary for the onset and/or maintenance of persistent pain, regardless of origin; 2), whether in these models cellular and molecular changes, e.g. phosphorylation of the NR2B subunit of the NMDA receptor, increased c-fos expression or microglial activation, associated with the onset of pain, are affected by the lack of functional EphB1 receptors. Differences in phenotype were examined behaviourally, anatomically, biochemically and electrophysiologically. Our results establish firstly, that functional EphB1 receptors are not essential for the development of normal nociception, thermal or mechanical sensitivity. Secondly, they demonstrate a widespread involvement of EphB1 receptors in chronic pain. NR2B phosphorylation, c-fos expression and microglial activation are all reduced in EphB1 knockout mice. This last finding is intriguing, since microglial activation is supposedly triggered directly by primary afferents, therefore it was not expected to be affected. Interestingly, in some models of long-term pain (days), mechanical and thermal hyperalgesia develop both in wild type and EphB1 knockout mice, but recovery is faster in the latter, indicating that in particular models these receptors are required for the maintenance, rather than the onset of, thermal and mechanical hypersensitivity. This potentially makes them an attractive target for analgesic strategies

Management of Hazardous Waste and Contaminated Land

Regulation of hazardous waste and cleanup of contaminated sites are two major components of modern public policy for environmental protection. We review the literature on these related areas, with emphasis on empirical analyses. Researchers have identified many behavioral responses to regulation of hazardous waste, including changes in the location of economic activity. However, the drivers behind compliance with these costly regulations remain a puzzle, as most research suggests a limited role for conventional enforcement. Increasingly sophisticated research examines the benefits of cleanup of contaminated sites, yet controversy remains about whether the benefits of cleanup in the U.S. exceed its costs. Finally, research focusing on the imposition of legal liability for damages from hazardous waste finds advantages and disadvantages of the U.S. reliance on legal liability to pay for cleanup, as opposed to the government-financed approaches more common in Europe

Two-locus genome-wide linkage scan for prostate cancer susceptibility genes with an interaction effect

Prostate cancer represents a significant worldwide public health burden. Epidemiological and genetic epidemiological studies have consistently provided data supporting the existence of inherited prostate cancer susceptibility genes. Segregation analyses of prostate cancer suggest that a multigene model may best explain familial clustering of this disease. Therefore, modeling gene–gene interactions in linkage analysis may improve the power to detect chromosomal regions harboring these disease susceptibility genes. In this study, we systematically screened for prostate cancer linkage by modeling two-locus gene–gene interactions for all possible pairs of loci across the genome in 426 prostate cancer families from Johns Hopkins Hospital, University of Michigan, University of Umeå, and University of Tampere. We found suggestive evidence for an epistatic interaction for six sets of loci (target chromosome-wide/reference marker-specific P ≤0.0001). Evidence for these interactions was found in two independent subsets from within the 426 families. While the validity of these results requires confirmation from independent studies and the identification of the specific genes underlying this linkage evidence, our approach of systematically assessing gene–gene interactions across the entire genome represents a promising alternative approach for gene identification for prostate cancer.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47598/1/439_2005_Article_99.pd

Gene fusion in protein engineering : design of novel peptides and bifunctional enzymes

The gene fusion technique is widely used in protein engineering and in this thesis it constitutes the basis of both the construction of artificial bifunctional enzymes and the display of two novel peptides. Artificial bifunctional enzymes have been used as model systems in the studies of native multifunctional enzymes and proximity effects within these complexes. Two various constructs are described. First, the structural genes of lactate dehydrogenase and galactose dehydrogenase were fused in-frame and expressed in Escherichia coli. In vitro observations showed that the chimeric enzyme was able to recycle the coenzyme NAD(H) with a continuos production of lactate without any externally added NADH. Furthermore, proximity effects were pronounced when diffusion hindrance was applied during the recycling reaction. Secondly, the design of the linker region within the bifunctional construct ß-galactosidase/galactose dehydrogenase was examined. The specific activity of the galactose dehydrogenase part of the complex was increased when longer linkers (9 and 13 amino acids) were used within the connecting region. The sequential reaction was carried out more efficiently when enzymes with longer linkers were used as demonstrated both in vivo and in vitro. The co-expression of the genetically engineered bifunctional enzymes and a corresponding native protein subunit was investigated as a method to influence the association pattern of oligomeric proteins and to improve the stability of the artificial bifunctional proteins. Native galactose dehydrogenase was utilised together with both the ß-galactosidase/galactose dehydrogenase and the lactate dehydrogenase/galactose dehydrogenase constructs. Altered associations patterns were observed in both cases. The peptide, Phe-Glu-Ala-His-Ala-Ser, mimicking the catalytic triad in the active site of many serine proteases was expressed as a fusion within the structural gene of the major coat protein of bacteriophage f1. Hydrolytic activity was detectable whit p-nitrophenol activated esters as substrates and it was further possible to elucidate that serine contributed the most to the catalytic activity and the relative position of serine and histidine had a significant influence on the observed activities. A cadmium binding peptide was selected using the phage display technique using a hexapeptide library and cadmium ions immobilised on a metal chelating sepharose. The selected peptide, His-Ser-Gln-Lys-Val-Phe, was cloned as a fusion to the outer cell membrane protein OmpA. Escherichia coli cells harbouring this construct showed a higher degree of survival in growth media supplemented with up to 1.2 mM CdCl2 when compared with cells not expressing this peptide

Dricka lagom - Tillit och normer i applikationer för att reglera alkoholkonsumtion

To drink moderately can be hard for many people and there is a lot of norms that will amp up the temptation to drink more. In this essay the focus is to see what effect technology has when it comes to regulate alcohol consumption. The technology reviewed was the application Promillekoll, created by Systembolaget. This application gives the user an estimated value on what blood alcohol level the user had after consuming alcohol. By using different methods to collect data it helped to locate what kinds of norms there was when alcohol was being consumed and how they are playing a part in the regulation of alcohol. This essay also helped to figure out what kind of trust the user has for this type of application and what the application need so that the user will continue to use the application. The result indicate that the user can achieving a change in their behavior but they need the right attitude to achieve it. Many wanted an update of the features in the application to make it more appealing for them to use it, because the interaction in the application is not perfect. The main thing that hindering the application was the social norms that comes with drinking alcohol. Att dricka lagom mycket kan vara svårt för många och det finns flera normer som ökar påfrestelsen att dricka mera. I denna studie ligger fokus på att ta reda på vilken effekt tekniken har när det kommer till att reglera alkoholkonsumtion. Den teknik som granskades är applikationen Promillekoll, som är en applikation framtagen av Systembolaget. Den ger  användaren ett uppskattat värde av ens promillehalt när de dricker. Men hjälp av olika metoder samlades data in för att ta reda på över vilka typer av normer som finns när det kommer till alkoholkonsumtion och hur de spelar in för regleringen av alkohol samt ta reda på hur stor tillit användarna hade till applikationen och vad som krävdes för att de skulle fortsätta användningen av applikationen. Resultatet tyder på att det går att uppnå en förändring med hjälp av applikationen men då krävs det att användaren har rätt attityd från början. Många respondenter ville däremot ha en uppdatering av applikationen då interaktionen inte var så effektiv som den skulle kunnat vara. Dock stod flera sociala normer i vägen för att tekniken skulle kunna vara effektiv.

Dricka lagom - Tillit och normer i applikationer för att reglera alkoholkonsumtion

To drink moderately can be hard for many people and there is a lot of norms that will amp up the temptation to drink more. In this essay the focus is to see what effect technology has when it comes to regulate alcohol consumption. The technology reviewed was the application Promillekoll, created by Systembolaget. This application gives the user an estimated value on what blood alcohol level the user had after consuming alcohol. By using different methods to collect data it helped to locate what kinds of norms there was when alcohol was being consumed and how they are playing a part in the regulation of alcohol. This essay also helped to figure out what kind of trust the user has for this type of application and what the application need so that the user will continue to use the application. The result indicate that the user can achieving a change in their behavior but they need the right attitude to achieve it. Many wanted an update of the features in the application to make it more appealing for them to use it, because the interaction in the application is not perfect. The main thing that hindering the application was the social norms that comes with drinking alcohol. Att dricka lagom mycket kan vara svårt för många och det finns flera normer som ökar påfrestelsen att dricka mera. I denna studie ligger fokus på att ta reda på vilken effekt tekniken har när det kommer till att reglera alkoholkonsumtion. Den teknik som granskades är applikationen Promillekoll, som är en applikation framtagen av Systembolaget. Den ger  användaren ett uppskattat värde av ens promillehalt när de dricker. Men hjälp av olika metoder samlades data in för att ta reda på över vilka typer av normer som finns när det kommer till alkoholkonsumtion och hur de spelar in för regleringen av alkohol samt ta reda på hur stor tillit användarna hade till applikationen och vad som krävdes för att de skulle fortsätta användningen av applikationen. Resultatet tyder på att det går att uppnå en förändring med hjälp av applikationen men då krävs det att användaren har rätt attityd från början. Många respondenter ville däremot ha en uppdatering av applikationen då interaktionen inte var så effektiv som den skulle kunnat vara. Dock stod flera sociala normer i vägen för att tekniken skulle kunna vara effektiv.