An integrated network visualization framework towards metabolic engineering applications

Background

Over the last years, several methods for the phenotype simulation of microorganisms, under specified genetic and environmental conditions have been proposed, in the context of Metabolic Engineering (ME). These methods provided insight on the functioning of microbial metabolism and played a key role in the design of genetic modifications that can lead to strains of industrial interest. On the other hand, in the context of Systems Biology research, biological network visualization has reinforced its role as a core tool in understanding biological processes. However, it has been scarcely used to foster ME related methods, in spite of the acknowledged potential.

Results

In this work, an open-source software that aims to fill the gap between ME and metabolic network visualization is proposed, in the form of a plugin to the OptFlux ME platform. The framework is based on an abstract layer, where the network is represented as a bipartite graph containing minimal information about the underlying entities and their desired relative placement. The framework provides input/output support for networks specified in standard formats, such as XGMML, SBGN or SBML, providing a connection to genome-scale metabolic models. An user-interface makes it possible to edit, manipulate and query nodes in the network, providing tools to visualize diverse effects, including visual filters and aspect changing (e.g. colors, shapes and sizes). These tools are particularly interesting for ME, since they allow overlaying phenotype simulation results or elementary flux modes over the networks.

Conclusions

The framework and its source code are freely available, together with documentation and other resources, being illustrated with well documented case studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0420-0) contains supplementary material, which is available to authorized users.     

Association of TNF-α promoter gene G-308A polymorphism with metabolic syndrome, insulin resistance, serum TNF-α and leptin levels in Indian adult women

Background

Tumour necrosis factor alpha is a multifunctional proinflammatory cytokine involved in the pathogenesis of metabolic syndrome, insulin resistance, and obesity. Aim of this study is to investigate in a North Indian female population the impact of the G-308A TNF-α variant on various components of the metabolic syndrome, Insulin Resistance, serum TNF-α and Leptin levels.

Methods

The G-308A TNF-α polymorphism has been studied in 269 females with metabolic syndrome (NCEP ATP III criteria) (age 31.91 ± 6.05) and 272 healthy females without metabolic syndrome (age 30.96 ± 7.01). The G-308A variant was detected by PCR amplification and Nco-1 digestion.

Results

Homozygous mutant genotype (AA) (p = <0.001: OR = 3.24: 95% CI = 2.15-4.89) and mutant allele (A) (p = <0.001: OR = 3.04: 95% CI = 2.08-4.43) of TNF-α was significantly less frequently observed in the control population as compared to study group. Furthermore, on dividing the subjects into two groups according to the absence (TNF-1 allele) or presence of the mutant A (TNF-2) allele, significant results were obtained in most of the metabolic risk factors.

Conclusions

Our results suggest that the G-308A polymorphism of the TNF-α gene may be independently associated with hypertension, leptin level and hypercholesterolemia leading to metabolic syndrome independent of Insulin resistance and hyperglycemia.     

Effects of resveratrol on HepG2 cells as revealed by H-NMR based metabolic profiling

Background

Resveratrol, a polyphenol found in plant products, has been shown to regulate many cellular processes and to display multiple protective and therapeutic effects. Several in vitro and in vivo studies have demonstrated the influence of resveratrol on multiple intracellular targets that may regulate metabolic homeostasis.

Methods

We analysed the metabolic modifications induced by resveratrol treatment in a human hepatoblastoma line, HepG2 cells, using a ¹H-NMR spectroscopy-based metabolomics approach that allows the simultaneous screening of multiple metabolic pathways.

Results

Results demonstrated that cells cultured in the presence or absence of resveratrol displayed different metabolic profiles: the treatment induced a decreased utilisation of glucose and amino acids for purposes of energy production and synthesis associated to a decreased release of lactate in the culture medium and an increase in succinate utilisation. At the same time, resveratrol treatment slowed the cell cycle in the S phase without inducing apoptosis, and increased Sirt1 expression, also affecting its intracellular localisation.

Conclusions

Our results show that the metabolomic analysis of the exometabolome of resveratrol-treated HepG2 cells indicates a metabolic switch from glucose and amino acid utilisation to fat utilisation for the production of energy, and seem in agreement with an effect mediated via AMPK- and Sirt1-activation.

General significance

NMR-based metabolomics has been applied in a hepatocyte cell culture model in relation to resveratrol treatment; such an approach could be transferred to evaluate the effects of nutritional compounds with health impact.     

Apport de l’imagerie hybride TEMP/TDM dans la détection des ganglions sentinelles : à propos de 32 cas

Objectives

Retrospective evaluation of the SPECT/CT role in the Sentinel Lymph Node identification.

Patients and methods

Thirty-two patients underwent a lymphoscintigraphy with SPECT/CT imaging. Those patients presented several cancer types (16 melanoma, one squamous cell carcinoma, three breast cancers, eight vulvar cancers, three cervical cancers).

Results

The scintigraphic detection rate was 81% with planar imaging while this rate was 89% with SPECT/CT. The SPECT/CT provided an additional quantitative information in 66% cases. Moreover, the quality of the interpretation was better in two different conditions (planar interpretation followed by routine and blinded SPECT/CT interpretation) with SPECT/CT. In our study, the false negative rate is 4.5%.

Conclusions

SPECT/CT provides quantitative and qualitative informations in the sentinel lymph node detection. Therefore, it can be a valuable tool for the surgeon to find and harvest the sentinel lymph node especially where the lymphatic drainage pattern can be unusual or hard to predict (cervical or trunk localisation). It's a new tool for preoperative detection and it can decrease the false negative rate.     

Paraneoplastic syndrome in mice bearing high-angiogenic variant of Lewis lung carcinoma: relations with tumor derived VEGF

Background

It is well-known that tumor exerts nonmetastatic systemic effect on organism caused the development of paraneoplastic syndrome (PNS). Recent findings point to relationships between development of PNS and tumor-derived vascular endothelial growth factor (VEGF).

Aim

Comparative study of PNS manifestations in mice with transplanted two variants of Lewis lung carcinoma with different angiogenic potential.

Methods

Plasma VEGF level was determined by immunoenzyme method, hematological indices were estimated with the use of hematological analyzer, the weight and cellularity of spleen and thymus were registered and histological analysis of tissue section of these organs was performed.

Results

Manifestations of anemia, extramedullary hemopoiesis and tumor-associated inflammatory disease was observed in animals with high angiogenic LLC/R9 variant and was not registered in low angiogenic LLC. The emergence of PNS symptoms correlated with elevated level of circulating VEGF at the early stages of LLC/R9 growth.

Conclusion

Manifestation of the paraneoplastic hematological syndrome most likely is conditioned on the ability of cancer cell to secrete VEGF in a high rate.     

Hepatitis B in a high prevalence New Zealand population: a mathematical model applied to infection control policy

Background

Chronic hepatitis B (CHB) is a vaccine preventable disease of global public health importance. The prevalence of CHB in New Zealand's Tongan population is over 10%, a level consistent with endemic infection, which contrasts to the low overall New Zealand prevalence (<0.5%). Despite the introduction of infant vaccination in 1988, coverage among Tongan children is estimated to be only 53%.

Aims

To estimate the population benefit of additional public health control measures besides ‘business as usual’ infant vaccination for hepatitis B in high prevalence populations.

Methods

A mathematical model of hepatitis B virus (HBV) transmission was used to predict future CHB prevalence in the New Zealand Tongan population under different infection control strategies.

Results

Prevalence of CHB is predicted to plateau at 2% in the New Zealand Tongan population if coverage remains at current levels, which are therefore insufficient to achieve long-term elimination of HBV. The critical proportion of immunisation coverage for elimination of the virus is estimated to be 73%. The effect of screening for HBV carriage and early disease management was unable to be quantified, but is likely to reduce the population burden of HBV infection and thus contribute to accelerating elimination.

Conclusions and recommendations

Mathematical models are a useful tool to forecast the future burden of CHB under a range of control strategy scenarios in high prevalence populations. Serosurveillance and targeted vaccination has similarly arrested HBV transmission in time-series prevalence studies from Taiwan and Alaska. Such a policy may demonstrate similar efficacy in New Zealand ethnic groups with endemic HBV infection.     

Chemical composition and therapeutic effects of Lippia alba (Mill.) N. E. Brown leaves hydro-alcoholic extract in patients with migraine

Background

There is no universally accepted and effective prophylaxis of migraine headache episodes. Thus we aimed to investigate the effects of Lippia alba (Mill.) N. E. Brown, an herb with many effects on central nervous system, on pain frequency and intensity of migraine patients.

Methods

Patients were enrolled in a prospective, phase 2, non-controlled cohort study to orally receive hydro-alcoholic extract of L. alba leaves. Headache intensity and frequency of episodes were recorded before and after 30-60 days of treatment. We also studied the chemical composition of its essential oil by gas chromatography-mass spectrometry.

Results

We described for the first time a particular L. alba chemotype with geranial and carvenone as major compounds. With treatment, both frequency and intensity of pain episodes significantly decreased from baseline to first reassessment date. More than 80% of patients experienced a minimum 50% reduction on pain intensity and frequency. No side effects were reported.

Conclusions

Treatment with a geranial plus carvenone chemotype of L. alba hydro-alcoholic extract is a cheap, widely available, highly effective therapy to reduce both the intensity and the frequency of headache episodes of migraine patients with no side effects.     

Glutathione-S-transferase M1 and T1 genes and gastric cancer: a case control study in North Indian population

Background

Difference in the capacity of xenobiotic metabolising enzymes might be an important factor in genetic susceptibility to cancer.

Methods

A case control study involving forty one gastric cancer patients and one hundred and thirty controls was carried out to determine the frequency of GSTM1 and GSTT1 null genotypes. The frequency of GSTM1 and GSTT1 null genotype was observed by carrying out multiplex PCR.

Results

There was no difference in the frequencies of the GSTM1 and GSTT1 null and the combined GSTM1 and GSTT1 null genotype between patients and control.

Conclusions

Our data suggest that GSTM1 and GSTT1 status may not influence the risk of developing gastric cancer.     

Haplotype frequency distribution for 7 microsatellites in chromosome 8 and 11 in relation to the metabolic syndrome in four ethnic groups: Tehran Lipid and Glucose Study

Introduction

Different variants of haplotype frequencies may lead to various frequencies of the same variants in individuals with drug resistance and disease susceptibility at the population level.

Materials and methods

In this study, the haplotype frequencies of 4 STR loci including the D8S1132, D8S1779, D8S514 and D8S1743, and 3 STR loci including D11S1304, D11S1998 and D11S934 were investigated in 563 individuals of four Iranian ethnic groups in the capital city of Iran, Tehran. One hundred thirty subjects had the metabolic syndrome. Haplotype frequencies of all markers were calculated.

Results

There were significant differences in the haplotype frequencies in short and long alleles between the metabolic affected subjects and controls. In addition, haplotype frequencies were significant in the four ethnic groups in both chromosomes 8 and 11.

Conclusion

Our findings show a relation between the short allele of D8S1743 in all related haplotype frequencies of subjects with metabolic syndrome. These findings may require more studies of some candidate genes, including the lipoprotein lipase gene, in this chromosomal region.     

Medida de la capacidad funcional y la calidad de vida relacionada con la salud de un grupo de personas mayores que llevan a cabo un programa de caminatas: estudio piloto

Introduction

This pre-experimental study analyses the Functional Capacity (FC), Body Mass Index (BMI), Health Related Quality of Life (HRQoL) and Health Capital Stock (HCS) of elderly people participating in a Walking program in Granollers (Barcelona).

Material and methods

One hundred and seventy-three participants were invited to participate. One hundred and one of them were users of the Municipal Program for Elderly People, and 72 received information by the communication media. One hundred and thirty-one (76.3%) of the participants completed the Program.The intervention consisted of a 6-month program, supervised by a specialist instructor once a week and controlled daily by a pedometer.The 6-minute walk test (6MWT) was analysed for the FC, and the EuroQoL for the HRQoL. The preferences derived from the EuroQoL scores and the Life Expectancy were used to calculate the FC. The monetary data were obtained using a fixed value.

Results

An increase in the average number of steps was observed after the program, especially in men. The results also showed a decrease in the BMI. The participants showed a improvement in overall health perception at the end of the program. The HCS scores confirmed the improvement in the HRQoL in men.

Conclusions

The Program was positive for increasing the number of steps and improving physical condition and health. The usefulness of the pedometer as a motivational tool of physical exercise is discussed.     

Localization of nerve growth factor (NGF) receptors in the mitochondrial compartment: Characterization and putative role

Background

The neurotrophin NGF receptors trkA and p75NTR are expressed in the central and peripheral nervous system as well as in non-neuronal tissues; originally described to localize to the plasma membrane, recent studies have suggested other intracellular localizations for both NGF receptors.

Scope of review

In order to determine whether NGF receptors localize to the mitochondrial compartment mitochondria isolated from human kidney, rat tissues and a human podocyte as cell line before and after differentiation were used.

Major conclusions

Our results demonstrate that NGF receptors are localized in the mitochondrial compartment of undifferentiated human podocytes and in all tissues analyzed including rat central nervous system. In mitochondria p75NTR, but not trkA, co-immunoprecipitates with the adenine nucleotide translocator (ANT) and the phosphodiesterase 4 isoform A5 (PDE4A5). Moreover, NGF, via trkA, protects isolated mitochondria of rat brain cortex from mitochondrial permeability transition induced by Ca²⁺.

General significance

Although NGF receptors have been described as mainly citoplasmatic so far, we proved evidence of their expression at the mitochondrial level and their interaction with specific proteins. Our results demonstrating the expression of NGF receptors in the mitochondria provide new insights into the role of NGF at subcellular level, in different areas of the organism, including CNS.     

Study of the initial phase of biofilm formation using a biofomic approach

Aims

The purpose of this work was to study the initial steps of formation of a biofilm using the BioFilm Ring Test® and the Crystal violet staining technique.

Methods and results

Eight strains of Pseudomonas aeruginosa were studied. The two methods revealed that four strains formed a rapid biofilm. The biofilm formed by these strains was detected after only 45 min with the BioFilm Ring Test® and after 6 h with the Crystal violet method. The enumeration of bacteria of the PA01 strain confirmed that, after 30 min, a significant amount of bacteria had attached on the bottom of the culture wells. After 48 h the Crystal violet method detected a biofilm with all strains. The four strains which rapidly formed a biofilm did not differ from the slow-forming strains by their mucoid character or their swarming motility or their synthesis of rhamnose. They showed higher swimming mobility.

Conclusions

Our results show that the BioFilm Ring Test® is a method specially suited for the study of the initial phase of the formation of a biofilm.

Significance and impact of study

The BioFilm Ring Test® is an easy and rapid alternative to the Crystal violet staining and the enumeration methods.     

Evaluation of nitrate reduction assay, resazurin microtiter assay and microscopic observation drug susceptibility assay for first line antitubercular drug susceptibility testing of clinical isolates of M. tuberculosis

Background

Drug resistant tuberculosis (TB) is a growing concern worldwide. Early detection of multidrug-resistant Mycobacterium tuberculosis is of primary importance for both patient management and infection control. Optimal method for identifying drug-resistant M. tuberculosis in a timely and affordable way in resource-limited settings is not yet available.

Aim

This study evaluated; nitrate reductase assay (NRA), resazurin microtiter assay (REMA) and microscopic observation drug susceptibility assay (MODS) against the conventional 1% proportion method (PM) for the detection of resistance to first line antitubercular drugs, in M. tuberculosis clinical isolates.

Methods

A total of one hundred and five clinical isolates of M. tuberculosis; 50 pan sensitive and 55 pan resistant were tested with NRA, REMA and MODS. The 1% proportion method on Lowenstein-Jensen medium was used as reference test.

Results

Of all three methods which were tested NRA was found to be most sensitive and specific. Sensitivity for rifampicin resistance detection was 100%, 94.55% and 92.73% by NRA, REMA and MODS respectively. NRA and REMA were found to be 100% specific, while the MODS was 98% specific for detection of rifampicin resistance. Test results with all these methods were obtained within 8-14 days.

Conclusion

Rapid non-conventional and inexpensive methods may serve as a replacement for 1% proportion method in resource limited settings.     

Localization of the Sodium-Taurocholate cotransporting polypeptide in membrane rafts and modulation of its activity by cholesterol in vitro

Background

The relevance of discrete localization of hepatobiliary transporters in specific membrane microdomains is not well known.

Aim

To determine whether the Na⁺/taurocholate cotransporting polypeptide (Ntcp), the main hepatic sinusoidal bile salt transporter, is localized in specific membrane microdomains.

Methods

Presence of Ntcp in membrane rafts obtained from mouse liver was studied by immunoblotting and immunofluorescence. HEK-293 cells stably transfected with rat Ntcp were used for in vitro studies. Expression, localization and function of Ntcp in these cells were assessed by immunoblotting, immunofluorescence and biotinylation studies and Na⁺-dependent taurocholate uptake assays, respectively. The effect of cholesterol depletion/repletion assays on Ntcp function was also investigated.

Results

Ntcp localized primarily to membrane rafts in in vivo studies and localized partially in membrane rafts in transfected HEK-293 cells. In these cells, membrane cholesterol depletion resulted in a shift of Ntcp localization into non-membrane rafts, which correlated with a 2.5-fold increase in taurocholate transport. Cholesterol repletion shifted back part of Ntcp into membrane rafts, and normalized taurocholate transport to values similar to control cells.

Conclusion

Ntcp localizes in membrane rafts and its localization and function are regulated by membrane cholesterol content. This may serve as a novel regulatory mechanism of bile salt transport in liver.     

Consumption of green tea or green tea products: Is there an evidence for antioxidant effects from controlled interventional studies?

Purpose

Epidemiological data suggest that green tea (GT) consumption may protect against cardiovascular diseases (CVDs) and different types of cancer. This effect is attributed primarily to the antioxidant properties of flavanols from GT. This review provides an overview of controlled intervention studies investigating the effect of GT consumption on antioxidant effects ex vivo and in vivo.

Methods

The Medline and Cochrane databases were searched independently by two investigators for controlled intervention studies (English) on GT consumption and antioxidant effects published up to June 2010. Thirty-one studies investigating antioxidant effects ex vivo [plasma antioxidant capacity (AC), DNA's resistance against oxidative induced damage) or in vivo (lipid and protein oxidation, DNA damage] met the criteria. Results were compared by considering the participants, the dose of GT, the amount of ingested flavanols, the duration of supplementation and the investigated biomarkers.

Results

The comparison between the studies was difficult as relevant data, e.g., on flavanol concentration in plasma (10 of 31 studies) or on major antioxidants contributing to AC, were often missing. Lipid peroxidation and DNA damage were commonly investigated. Data on protein oxidation are scarce. An antioxidant effect of at least one parameter (increase in AC or reduction of oxidative stress marker) was observed in 15 out of 22 studies by daily consumption of GT, primarily in participants exposed to oxidative stress (smokers or mixed collectives of smokers and non-smokers and physical activity) and in 6 out of 9 studies investigating the bolus consumption of GT.

Conclusion

There is limited evidence that regular consumption of GT in amounts of at least 0.6-1.5 l/day may increase AC and reduce lipid peroxidation (especially oxidation of LDL). This may contribute to the protection against CVDs and different types of cancer. Beneficial effects seem to be more likely in participants exposed to oxidative challenge.