Comparing methods for metabolic network analysis and an application to metabolic engineering

Bioinformatics tools have facilitated the reconstruction and analysis of cellular metabolism of various organisms based on information encoded in their genomes. Characterization of cellular metabolism is useful to understand the phenotypic capabilities of these organisms. It has been done quantitatively through the analysis of pathway operations. There are several in silico approaches for analyzing metabolic networks, including structural and stoichiometric analysis, metabolic flux analysis, metabolic control analysis, and several kinetic modeling based analyses. They can serve as a virtual laboratory to give insights into basic principles of cellular functions. This article summarizes the progress and advances in software and algorithm development for metabolic network analysis, along with their applications relevant to cellular physiology, and metabolic engineering with an emphasis on microbial strain optimization. Moreover, it provides a detailed comparative analysis of existing approaches under different categories.     

Association of the I148M/PNPLA3 variant with elevated alanine transaminase levels in normal-weight and overweight/obese Mexican children

Background and aims

Non-alcoholic fatty liver disease (NAFLD) and elevated alanine transaminase (ALT) levels are common in obese Hispanic adults and children. Recently, a PNPLA3 gene variant (I148M) was strongly associated with NAFLD and higher ALT levels in obese adults, including Hispanics. The aims of this study were to estimate the frequency of elevated ALT levels, and to address the influence of obesity and PNPLA3/I148M on ALT levels in a general population sample of Mexican school-aged children.

Methods

A total of 1037 non-related Mexican children aged 6 to 12 years were genotyped for the I148M variant. Anthropometric, clinical and metabolic parameters were collected from all participants.

Results

Elevated ALT levels (> 35 U/L) were more frequent in obese (26.9%) and overweight (9.3%) than in normal weight children (2.2%). The M148M genotype was significantly associated with elevated ALT levels in this population (OR = 3.7, 95% CI 2.3–5.9; P = 3.7 × 10^− 8), and children carrying the M148M genotype showed significantly lower HDL cholesterol levels and BMI z-core (P = 0.036 and 0.015, respectively). On stratifying by BMI percentile, this genotype conferred a much greater risk of elevated ALT levels in normal weight (OR = 19.9, 95% CI 2.5–157.7; P = 0.005) than overweight and obese children (OR = 3.4, 95% CI 1.3–8.9; P = 0.014 and OR = 3.1, 95% CI 1.7–5.5; P = 1.4 x10^− 4, respectively).

Conclusions

The I148M PNPLA3 variant is strongly associated with elevated ALT levels in normal weight and overweight/obese Mexican children. Thus, the M148M genotype may be considered as an important risk factor for liver damage in this population.     

Association between interleukin-10 promoter polymorphisms and endometriosis: A meta-analysis

To investigate the influence of the interleukin-10 gene promoter polymorphisms on the susceptibility of endometriosis, we examined the association by performing a meta-analysis. The PubMed, Embase, HuGE Navigator and CNKI were searched to identify eligible studies. We then conducted a meta-analysis to examine the association between interleukin-10 gene promoter polymorphisms and endometriosis. Eight case–control studies which examined the association between the IL-10 gene promoter polymorphisms and the susceptibility to endometriosis were finally included in the meta-analysis. Meta-analysis of the IL-10 − 592 A/C polymorphisms showed a significant increased risk of endometriosis in the overall and Asian population in all genetic models and allele contrast. However, meta-analysis of the IL-10 − 1082 A/G and IL-10 − 819 T/C polymorphisms showed no association with endometriosis in all genetic models and allele contrast in the overall and Asian population samples. In addition, there was not a significant association between the IL-10 − 592 A/C gene promoter polymorphisms with the severity of endometriosis.     

THE PLACE OF GOD IN SYNTHETIC BIOLOGY: HOW WILL THE CATHOLIC CHURCH RESPOND?

Some religious believers may see synthetic biology as usurping God's creative role. The Catholic Church has yet to issue a formal teaching on the field (though it has issued some informal statements in response to Craig Venter's development of a 'synthetic' cell). In this paper I examine the likely reaction of the Catholic Magisterium to synthetic biology in its entirety. I begin by examining the Church's teaching role, from its own viewpoint, to set the necessary backround and context for the discussion that follows. I then describe the Church's attitude to science, and particularly to biotechnology. From this I derive a likely Catholic theology of synthetic biology. The Church's teachings on scientific and biotech research show that it is likely to have a generally positive disposition to synbio, if it and its products can be acceptably safe. Proper evaluation of, and protection against, risk will be a significant factor in determining the morality of the research. If the risks can be minimized through regulation or other means, then the Church is likely to be supportive. The Church will also critique the social and legal environment in which the research is done, evaluating issues such as the patenting of scientific discoveries and of life.     

The population ecology of Rattus exulans on Tiritiri Matangi Island,and a model of comparative population dynamics in New Zealand

Abstract

On Tiritiri, a small predator-free island in northern New Zealand, kiore (Rattus exulans) were live and snap trapped in grassland and forest. In both habitats, kiore abundance peaked in late summer/autumn. The increase followed a 3 month breeding season during which females produced two to three litters, each averaging 7 young. During the population decline in autumn and winter, animals lost weight. Few bred in the breeding season of their birth and none lived to breed in a second breeding season, so the population consisted of distinct age cohorts. These patterns may relate to a highly seasonal food supply.

Kiore elsewhere in New Zealand show seasonal breeding, but the length of breeding, sexual maturation, and litter size vary. Other studies of kiore in the Pacific show less marked seasonal fluctuations, longer breeding seasons, and smaller litters. We propose a model to explain the variation in rodent demography in New Zealand. The model is based on the seasonal availability of food, along with the modifying influences of predation and dispersal.     

Metformin increases liver accumulation of vitamin B12 – An experimental study in rats

Aims/hypothesis

Patients treated with metformin exhibit low levels of plasma vitamin B₁₂ (B₁₂), and are considered at risk for developing B₁₂ deficiency. In this study, we investigated the effect of metformin treatment on B₁₂ uptake and distribution in rats.

Methods

Sprague Dawley rats (n = 18) were divided into two groups and given daily subcutaneous injections with metformin or saline (control) for three weeks. Following this, the animals received an oral dose of radio-labeled B₁₂ (⁵⁷[Co]-B₁₂), and urine and feces were collected for 24 h. Plasma, bowel content, liver, and kidneys were collected and analyzed for B₁₂, unsaturated B₁₂-binding capacity, and ⁵⁷[Co]-B₁₂.

Results

Three weeks of metformin treatment reduced plasma B₁₂ by 22% or 289 [47-383] pmol/L (median and [range]) (p = 0.001), while no effect was observed on unsaturated B₁₂-binding capacity. Compared with controls, the amount of B₁₂ in the liver was 36% (p = 0.007) higher in metformin-treated rats, while the B₁₂ content in the kidney was 34% (p = 0.013) lower. No difference in the total amount of absorbed ⁵⁷[Co]-B₁₂ present in the tissues and organs studied was found, suggesting that metformin has no decreasing effect on the B₁₂ absorption.

Conclusions/interpretation

These results show that metformin treatment increases liver accumulation of B₁₂, thereby resulting in decreases in circulating B₁₂ and kidney accumulation of the vitamin. Our data questions whether the low plasma B₁₂ observed in patients treated with metformin reflects impaired B₁₂ status, and rather suggests altered tissue distribution and metabolism of the vitamin.     

The hMLH1 promoter polymorphisms and cancer susceptibility in Asian populations: A meta-analysis

Background

A variety of studies have evaluated the associations between polymorphisms in the promoter regions of the hMLH1 and cancer risk. However, the results remain inconclusive. To better understand the roles of the hMLH1 polymorphisms and cancer risk, we conducted a comprehensive meta-analysis to investigate the association between the hMLH1 − 93G/A and 1151T/A (Val384Asp) polymorphisms and cancer risk in Asian population.

Methods

We performed a meta-analysis by conducting searches of the published studies in Pub Med, CNKI, CBM, ISI web of knowledge and Google scholar search databases. Finally, 12 studies were included into our meta-analysis. Overall and subgroup analyses were performed. Odds ratio (OR) and 95% confidence interval (CI) were used to evaluate the associations between hMLH1 polymorphisms and cancer risk. Statistical analysis was performed with Review Manager 5.0.

Results

Twelve studies addressing two hMLH1 polymorphisms were analyzed among a total of 4128 cancer cases and 4678 controls. For hMLH1 − 93G/A, there was no evidence that the hMLH1 − 93G/A polymorphism was significantly associated with an increased cancer risk (P > 0.05) in Asian populations (heterozygote comparison: OR = 0.89 [95% CI (0.75, 1.060)] P = 0.20; dominant model comparison: OR = 0.98 [95% CI (0.83, 1.15)] P = 0.79). In subgroup analysis based on cancer types and the sources of control, no associations were found in colorectal cancer, gastric cancer and “other cancers” under the any gene model except for lung cancer (recessive model comparison: OR = 1.69 [95% CI (1.30, 2.19)] P < 0.0001). For hMLH1 1151T/A, the polymorphism significantly associated with an increased cancer risk in Asians: OR = 1.88 [95% CI (1.49, 2.25)], P < 0.0001, and OR = 1.87 [95% CI (1.49, 2.25)], P < 0.0001.

Conclusions

Our investigations demonstrated that the hMLH1 − 93G/A polymorphism is not a candidate for susceptibility to overall cancers, and that the hMLH1 1151T/A polymorphism is significantly associated with higher cancer risk in Asian populations. Further studies with large sample size for hMLH1 should be conducted.     

Evaluation of glutathione S-transferase genetic variants affecting type 2 diabetes susceptibility: A meta-analysis

Genetic polymorphisms of glutathione S-transferases (GSTs) and type 2 diabetes mellitus (T2DM) risk have been widely studied, however, the results were somewhat conflicting. To evaluate the association of GSTs (GSTM1, GSTT1 and GSTP1) gene polymorphisms with T2DM, a meta-analysis was performed before October, 2012. ORs were pooled according to random-effects model. There were a total of 1354/1666 (n = 9) cases/controls (studies) for GSTM1, 1271/1470 (n = 8) for GSTT1, and 1205/1250 (n = 7) for GSTM1. There were significant associations between GSTM1 polymorphism, GSTT1 polymorphism and T2DM in the contrast of present genotype vs. null genotype, with pooled OR = 1.99 (95%CI = 1.46–2.71) and OR = 1.61 (95%CI = 1.19–2.17), respectively. Yet no significant association of GSTP1 polymorphism and T2DM was showed. When stratified by ethnicity, the significant associations were also existed in Asians for GSTM1 and GSTT1, but not GSTP1. No publication bias but some extent of heterogeneity was observed. Finally, the accumulated evidence proved the obvious associations of GSTM1 and GSTT1 polymorphisms with an increased risk of T2DM.     

Hemocyanin gene family evolution in spiders (Araneae), with implications for phylogenetic relationships and divergence times in the infraorder Mygalomorphae

Hemocyanins are multimeric copper-containing hemolymph proteins involved in oxygen binding and transport in all major arthropod lineages. Most arachnids have seven primary subunits (encoded by paralogous genes a–g), which combine to form a 24-mer (4 × 6) quaternary structure. Within some spider lineages, however, hemocyanin evolution has been a dynamic process with extensive paralog duplication and loss. We have obtained hemocyanin gene sequences from numerous representatives of the spider infraorders Mygalomorphae and Araneomorphae in order to infer the evolution of the hemocyanin gene family and estimate spider relationships using these conserved loci. Our hemocyanin gene tree is largely consistent with the previous hypotheses of paralog relationships based on immunological studies, but reveals some discrepancies in which paralog types have been lost or duplicated in specific spider lineages. Analyses of concatenated hemocyanin sequences resolved deep nodes in the spider phylogeny and recovered a number of clades that are supported by other molecular studies, particularly for mygalomorph taxa. The concatenated data set is also used to estimate dates of higher-level spider divergences and suggests that the diversification of extant mygalomorphs preceded that of extant araneomorphs. Spiders are diverse in behavior and respiratory morphology, and our results are beneficial for comparative analyses of spider respiration. Lastly, the conserved hemocyanin sequences allow for the inference of spider relationships and ancient divergence dates.