Sequencing and Reconstructing Helminth Mitochondrial Genomes Directly from Genomic Next-Generation Sequencing Data.

We present a detailed method for extraction of high-molecular weight genomic DNA suitable for numerous DNA sequencing applications, and a straightforward in silico approach for reconstructing novel mitochondrial (mt) genomes directly from total genomic DNA extracts derived from next-generation sequencing (NGS) data sets. The in silico post-sequencing pipeline described is fast, accurate, and highly efficient, with modest memory requirements that can be performed using a standard desktop computer. The approach is particularly effective for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information currently available and overcomes many of the limitations of traditional strategies. The described methodologies are also applicable for metagenomics sequencing from mixed or pooled samples containing multiple species and subsequent specific assembly of specific mitochondrial genomes.

Preliminary study on the characterization of Longissimus lumborum dark cutting meat in Angus × Nellore crossbreed cattle using NMR-based metabolomics.

The aim of this preliminary study was to evaluate meat quality properties, muscle metabolite profile and metabolic pathways associated with the occurrence of dark cutting meat in Angus x Nellore crossbreed cattle. After 14 days' ageing, dark cutting meat presented a higher pH, lower cooking loss and colour parameters, and greater tenderness compared with normal meat. Dark cutting meat had a higher ATP level and lower concentrations of glucose-6-phosphate, lactate, glucose, serine, threonine, creatine phosphate, inosine, leucine, methionine, succinate and glucose-1-phosphate compared to normal meat. In dark cutting samples, the ultimate pH was positively correlated with carnitine and negatively correlated with glucose-6-phosphate. However, in normal meat, the ultimate pH presented a positive correlation with arginine, leucine, methionine, proline, threonine, tyrosine and valine. Pathway analysis showed that differentiation of the groups was linked to energetic pathways such as starch and sucrose metabolism, the pentose phosphate pathway, amino sugar, nucleotide sugar metabolism, and glycolysis or gluconeogenesis. In conclusion, the occurrence of dark cutting meat has a notable impact on meat quality attributes and concentrations of post-mortem glycolytic metabolites, appears to be correlated with mitochondrial activity and affects energetic metabolic pathways.