MetaboNexus: an interactive platform for integrated metabolomics analysis

MetaboNexus is an interactive metabolomics data analysis platform that integrates pre-processing of raw peak data with in-depth statistical analysis and metabolite identity search. It is designed to work as a desktop application hence uploading large files to web servers is not required. This could speed up the data analysis process because server queries or queues are avoided, while ensuring security of confidential clinical data on a local computer. With MetaboNexus, users can progressively start from data pre-processing, multi- and univariate analysis to metabolite identity search of significant molecular features, thereby seamlessly integrating critical steps for metabolite biomarker discovery. Data exploration can be first performed using principal components analysis, while prediction and variable importance can be calculated using partial least squares-discriminant analysis and Random Forest. After identifying putative features from multi- and univariate analyses (e.g. t test, ANOVA, Mann–Whitney U test and Kruskal–Wallis test), users can seamlessly determine the molecular identity of these putative features. To assist users in data interpretation, MetaboNexus also automatically generates graphical outputs, such as score plots, diagnostic plots, boxplots, receiver operating characteristic plots and heatmaps. The metabolite search function will match the mass spectrometric peak data to three major metabolite repositories, namely HMDB, MassBank and METLIN, using a comprehensive range of molecular adducts. Biological pathways can also be searched within MetaboNexus. MetaboNexus is available with installation guide and tutorial at http://www.sph.nus.edu.sg/index.php/research-services/research-centres/ceohr/metabonexus, and is meant for the Windows Operating System, XP and onwards (preferably on 64-bit). In summary, MetaboNexus is a desktop-based platform that seamlessly integrates the entire data analytical workflow and further provides the putative identities of mass spectrometric data peaks by matching them to databases.     

Genetic Variants in MicroRNA Machinery Genes Are Associate with Idiopathic Recurrent Pregnancy Loss Risk

Objective

Key molecules involved in microRNA (miRNA) biogenesis, such as DROSHA, XPO5, and DICER, have been identified in trophoblast cells, confirming that the miRNA biogenesis pathway is active in human placenta. In addition, miRNAs regulate uterine gene expression associated with inflammatory responses during the peri-implantation period and participate in maternal-fetal immune tolerance. The purpose of this study was to demonstrate whether genetic polymorphisms in miRNA machinery genes show an association with idiopathic recurrent pregnancy loss (RPL) in Korean women.

Study design

We performed a case-control study with 238 controls and 338 women who had experienced at least two consecutive pregnancy losses between 1999 and 2010. Genotypes of miRNA machinery genes, including DICER rs3742330, DROSHA rs10719, RAN GTPase (RAN) rs14035, and exportin-5 (XPO5) rs11077 were analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. The logistic odds ratios (ORs) of RPL were estimated with a 95% confidence interval (CI) in multivariate analysis after maternal age adjustment. Gene-gene interactions among the loci of the four gene polymorphisms were evaluated using the multifactor dimensionality reduction (MDR) method.

Results

The RAN rs14035 CC genotype and DICER rs3742330/DROSHA rs10719 GG/TC+CC, rs3742330/RAN rs14035 GG/CC, and DICER rs3742330/XPO5 rs11077 GG/AC+CC combinations were significantly associated with increased RPL risk, whereas the RAN rs14035 CT, DICER rs3742330/RAN rs14035 AA+AG/CT+TT, DROSHA rs10719/RAN rs14035 TC+CC/CT+TT, and RAN rs14035/XPO5 rs11077 CT+TT/AA combinations reduced RPL risk. The A-T-T-C and G-C-T-A allele combinations (DICER/DROSHA/RAN/XPO5) were 20 times more frequent in the RPL group than in the control group.

Conclusion

Our study demonstrates the relationship between RPL development and the polymorphism of the miRNA machinery gene RAN and combined genotype of DROSHA/DICER.     

Genetic Control of Obesity and Gut Microbiota Composition in Response to High-Fat,High-Sucrose Diet in Mice

1. Download : Download high-res image (253KB)
2. Download : Download full-size image

Highlights? Detailed analysis of diet-induced obesity in more than 100 inbred mouse strains ? Identification of 11 genetic loci associated with obesity and dietary responsiveness ? Significant overlap between mouse loci with human GWAS loci for obesity ? Strain-specific shifts in gut microbiota composition in response to dietary intervention     

Isolation and functional characterization of a delta 6-desaturase gene from the pike eel (Muraenesox cinereus)

Stearidonic acid (STA; 18:4n-3) and γ-linolenic acid (GLA; 18:3n-6) are significant intermediates in the biosynthetic pathway for the very-long-chain polyunsaturated fatty acids of eicosapentaenoic acid (EPA; 20:5n-3) and arachidonic acid (ARA; 20:4n-6), respectively. To develop a sustainable system for the production of dietary polyunsaturated fatty acids, we focused on the action of the enzyme delta 6-desaturase (D6DES) on the essential acids, linoleic acid (LA; 18:2n-6) and α-linolenic acid (ALA; 18:3n-3). A 1,335-bp full-length cDNA encoding D6DES (McD6DES) was cloned from Muraenesox cinereus using degenerate PCR and RACE-PCR methods. To investigate the enzymatic activity of McD6DES in the production of n-6 and n-3 fatty acids, a recombinant plasmid expressing McD6DES (pYES-McD6DES) was transformed into and expressed in Saccharomyces cerevisiae. The exogenously expressed McD6DES produced GLA and STA at conversion rates of 14.2% and 45.9%, respectively, from the exogenous LA and ALA substrates. These results indicate that McD6DES is essentially a delta 6-desaturase involved in very-long-chain polyunsaturated fatty acid synthesis.     

Vitamin D-binding protein interacts with Aβ and suppresses Aβ-mediated pathology

The level of vitamin D-binding protein (DBP) is increased in the cerebrospinal fluid of patients with Alzheimer''s disease (AD), suggesting a relationship with its pathogenesis. In this study, we investigated whether and how DBP is related to AD using several different approaches. A pull-down assay and a surface plasmon resonance binding assay indicated direct interactions between purified DBP and amyloid beta (Aβ), which was confirmed in the brain of AD patients and transgenic AD model mice by immunoprecipitation assay and immunohistochemical double-staining method. Moreover, atomic force microscopic examination revealed that DBP reduced Aβ aggregation in vitro. DBP also prevented Aβ-mediated death in cultured mouse hippocampal HT22 cell line. Finally, DBP decreased Aβ-induced synaptic loss in the hippocampus and rescued memory deficits in mice after injection of Aβ into the lateral ventricle. These results provide converging evidence that DBP attenuates the harmful effects of Aβ by a direct interaction, and suggest that DBP is a promising therapeutic agent for the treatment of AD.     

Next-generation sequencing-based transcriptome analysis of l-lysine-producing Corynebacterium glutamicum ATCC 21300 strain

In the present study, 151 genes showed a significant change in their expression levels in Corynebacterium glutamicum ATCC 21300 compared with those of C. glutamicum ATCC 13032. Of these 151 genes, 56 genes (2%) were up-regulated and 95 genes (3%) were down-regulated. RNA sequencing analysis also revealed that 11 genes, involved in the L-lysine biosynthetic pathway of C. glutamicum, were up- or down-regulated compared with those of C. glutamicum ATCC 13032. Of the 151 genes, 10 genes were identified to have mutations including SNP (9 genes) and InDel (1 gene). This information will be useful for genome breeding of C. glutamicum to develop an industrial amino acid-producing strain with minimal mutation.     

Volatile fatty acid production from lignocellulosic biomass by lime pretreatment and its applications to industrial biotechnology

Lignocellulosic biomass was pretreated with lime, and used for the production of VFA (volatile fatty acid) through batch anaerobic digestion. About 0.34 g VFA yield was obtained using 10 g/L reed, after 3 days of fermentation with lime treatment; however, a higher VFA yield (more than 0.5 g/g biomass) was achieved with a modified lime treatment. Overall, our study showed that that the modified lime treatment is better suited for VFA production. VFAs can be widely used in platforms for fuels and chemicals from biomass.