Recon3D enables a three-dimensional view of gene variation in human metabolism.

Genome-scale network reconstructions have helped uncover the molecular basis of metabolism. Here we present Recon3D, a computational resource that includes three-dimensional (3D) metabolite and protein structure data and enables integrated analyses of metabolic functions in humans. We use Recon3D to functionally characterize mutations associated with disease, and identify metabolic response signatures that are caused by exposure to certain drugs. Recon3D represents the most comprehensive human metabolic network model to date, accounting for 3,288 open reading frames (representing 17% of functionally annotated human genes), 13,543 metabolic reactions involving 4,140 unique metabolites, and 12,890 protein structures. These data provide a unique resource for investigating molecular mechanisms of human metabolism. Recon3D is available at http://vmh.life.

Somatic embryogenesis and plant regeneration capacity in Argentinean maize (Zea mays L. ) inbred lines

Somatic embryogenesis, which is still the method of choice for tissue culture, regeneration and transformation of maize, is largely considered highly genotype-dependent. The Hi II, a highly embryogenic genotype, has been extensively used in transformation protocols. However, this is not an inbred line; instead, it has a proportion of the undesirable A-188 background, and the progeny segregates for phenotypic characteristics and shows poor agronomic performance. In an effort to identify genotypes that combine a high somatic embryogenic response and good agronomic performance, we evaluated 48 advanced inbred lines developed at INTA. Callus development and somatic embryogenesis capacity were measured in 200 immature embryos per line. Embryogenic capacity [EC (mature somatic embryos/callus evaluated) x 100], Regeneration Capacity (RC) and Fertile Plant Recovery in greenhouse (FPR, fertile plants/regenerated plants) were recorded. A total of 17 lines reached an EC > 50 percent, and 14 out of those 17 lines regenerated seedlings. The FPR ranged between 50 and 100 percent. Also, we selected three promising lines with high agronomic performance, as alternatives to Hi II, in order to be included in a maize transformation scheme via somatic embryogenesis. In addition, we report the usefulness of Single Sequences Repeat (SSRs) in the determination of genetic diversity among 14 divergent lines for somatic embryogenesis response. The seven lines displaying good in vitro behaviour can be crossed to obtain hybrids combining desirable alleles for somatic embryogenesis response and different genetic backgrounds.