Rules extraction from neural networks applied to the prediction and recognition of prokaryotic promoters

Promoters are DNA sequences located upstream of the gene region and play a central role in gene expression. Computational techniques show good accuracy in gene prediction but are less successful in predicting promoters, primarily because of the high number of false positives that reflect characteristics of the promoter sequences. Many machine learning methods have been used to address this issue. Neural Networks (NN) have been successfully used in this field because of their ability to recognize imprecise and incomplete patterns characteristic of promoter sequences. In this paper, NN was used to predict and recognize promoter sequences in two data sets: (i) one based on nucleotide sequence information and (ii) another based on stability sequence information. The accuracy was approximately 80% for simulation (i) and 68% for simulation (ii). In the rules extracted, biological consensus motifs were important parts of the NN learning process in both simulations

Yield gains in extra-early maize cultivars of three breeding eras under multiple environments

Open Access JournalAvailability of extra-early maize cultivars has facilitated the expansion of maize production into savannas of West and Central Africa (WCA). Fifty-six extra-early maize cultivars of three breeding eras;1995 to 2000, 2001 to 2006, and 2007 to 2012 were evaluated for 2 yr under 24 multiple-stress and 28 non-stress environments in WCA. Objectives of the study were to determine genetic improvement in grain yield of cultivars developed during the breeding eras, and identify high-yielding and s multiple-stress and non-stress environments. Yield gains from era 1 to era 3 under multiple stresses was associated with increased days to anthesis, reduced stalk lodging, and improved husk cover. Cultivars 2004 TZEE-Y Pop STR C4, TZEE-W Pop STR QPM C0, and TZEE-W Pop STR BC2 C0 of era 2; and TZEE-W STR 107 BC1, TZEE-W Pop STR C5, and 2012 TZEE-Y DT STR C5 of era 3 were high-yielding and stable across multiple-stress environments while 98 Syn EE-W from era 1, FERKE TZEE-W STR, TZEE-W Pop STR C3, and TZEE-Y Pop STR QPM C0 from era 2, and TZEE-W Pop STR C5, 2009 TZEE-OR2 STR QPM, 2009 TZEE-W STR, TZEE-Y STR 106, and TZEE-W DT C0 STR C5 from era 3 were outstanding across non-stress environments and should be tested extensively and commercialized. Considerable improvement has been made in breeding for multiple-stress tolerant extra-early maize cultivars

TAT-Mediated Transduction of MafA Protein In Utero Results in Enhanced Pancreatic Insulin Expression and Changes in Islet Morphology

Alongside Pdx1 and Beta2/NeuroD, the transcription factor MafA has been shown to be instrumental in the maintenance of the beta cell phenotype. Indeed, a combination of MafA, Pdx1 and Ngn3 (an upstream regulator of Beta2/NeuroD) was recently reported to lead to the effective reprogramming of acinar cells into insulin-producing beta cells. These experiments set the stage for the development of new strategies to address the impairment of glycemic control in diabetic patients. However, the clinical applicability of reprogramming in this context is deemed to be poor due to the need to use viral vehicles for the delivery of the above factors. Here we describe a recombinant transducible version of the MafA protein (TAT-MafA) that penetrates across cell membranes with an efficiency of 100% and binds to the insulin promoter in vitro. When injected in utero into living mouse embryos, TAT-MafA significantly up-regulates target genes and induces enhanced insulin production as well as cytoarchitectural changes consistent with faster islet maturation. As the latest addition to our armamentarium of transducible proteins (which already includes Pdx1 and Ngn3), the purification and characterization of a functional TAT-MafA protein opens the door to prospective therapeutic uses that circumvent the use of viral delivery. To our knowledge, this is also the first report on the use of protein transduction in utero