Poly (A)+ Transcriptome Assessment of ERBB2-Induced Alterations in Breast Cell Lines

We report the first quantitative and qualitative analysis of the poly (A)+ transcriptome of two human mammary cell lines, differentially expressing (human epidermal growth factor receptor) an oncogene over-expressed in approximately 25% of human breast tumors. Full-length cDNA populations from the two cell lines were digested enzymatically, individually tagged according to a customized method for library construction, and simultaneously sequenced by the use of the Titanium 454-Roche-platform. Comprehensive bioinformatics analysis followed by experimental validation confirmed novel genes, splicing variants, single nucleotide polymorphisms, and gene fusions indicated by RNA-seq data from both samples. Moreover, comparative analysis showed enrichment in alternative events, especially in the exon usage category, in ERBB2 over-expressing cells, data indicating regulation of alternative splicing mediated by the oncogene. Alterations in expression levels of genes, such as LOX, ATP5L, GALNT3, and MME revealed by large-scale sequencing were confirmed between cell lines as well as in tumor specimens with different ERBB2 backgrounds. This approach was shown to be suitable for structural, quantitative, and qualitative assessment of complex transcriptomes and revealed new events mediated by ERBB2 overexpression, in addition to potential molecular targets for breast cancer that are driven by this oncogene

Nitrogen rhizodeposition from soybean (Glycine max) and its impact on nutrient budgets in two contrasting environments of the Guinean savannah zone of Nigeria

Nitrogen (N) rhizodeposition by grain legumes such as soybean is potentially a large but neglected source of N in cropping systems of Sub-Saharan Africa. Field studies were conducted to measure soybean N rhizodeposition in two environments of the Guinean savannah of Nigeria using 15N leaf labelling techniques. The first site was located in Ibadan in the humid derived savannah. The second site was in Zaria in the drier Northern Guinean savannah. Soybean N rhizodeposition in the top 0.30 m of soil varied from 7.5 kg ha-1 on a diseased crop in Ibadan to 33 kg ha-1 in Zaria. More than two-thirds of soybean belowground N was contained in the rhizodeposits at crop physiological maturity, while the rest was found in the recoverable roots. Belowground plant-derived N was found to constitute 16–23% of the total soybean N. Taking rhizodeposited pools into account led to N budgets close to zero when all residues were removed. If residues were left in the field or recycled as manure after being fed to steers, soybean cultivation led to positive N budgets of up to +95 kg N ha-1. The role and potential of grain legumes as N purveyors have been underestimated in the past by neglecting the N contained in their rhizodeposits