A method for predicting disease subtypes in presence of misclassification among training samples using gene expression: application to human breast cancer

MOTIVATION: An accurate diagnostic and prediction will not be achieved unless the disease subtype status for every training sample used in the supervised learning step is accurately known. Such an assumption requires the existence of a perfect tool for disease diagnostic and classification, which is seldom available in the majority of the cases. Thus, the supervised learning step has to be conducted with a statistical model that contemplates and handles potential mislabeling in the input data. RESULTS: A procedure for handling potential mislabeling among training samples in the prediction of disease subtypes using gene expression data was proposed. A real data-based simulation study about the estrogen receptor status (ER+/ER-) of breast cancer patients was conducted. The results demonstrated that when 1-4 training samples (N = 30) were artificially mislabeled, the proposed method was able not only in correcting the ER status of mislabeled training samples but also more importantly in predicting the ER status of validation samples as well as using 'true' training data.     

MIQE précis: Practical implementation of minimum standard guidelines for fluorescence-based quantitative real-time PCR experiments

The conclusions of thousands of peer-reviewed publications rely on data obtained using fluorescence-based quantitative real-time PCR technology. However, the inadequate reporting of experimental detail, combined with the frequent use of flawed protocols is leading to the publication of papers that may not be technically appropriate. We take the view that this problem requires the delineation of a more transparent and comprehensive reporting policy from scientific journals. This editorial aims to provide practical guidance for the incorporation of absolute minimum standards encompassing the key assay parameters for accurate design, documentation and reporting of qPCR experiments (MIQE précis) and guidance on the publication of pure 'reference gene' articles.     

New insights into the intraspecific cytoplasmic DNA diversity,maternal lineages classification and conservation issues of Tunisian pearl millet landraces

Tunisian pearl millet (Pennisetum glaucum L.) landraces are still growing in contrasting agro-ecological environments and are considered potentially useful for national and international breeders. Despite its genetic potential, the cropping areas of this species are still limited and scattered which increases the risk of genetic erosion. The chloroplast DNA polymorphism and maternal lineages classification of forty nine pearl millet landraces representing seven populations covering the main distribution area of this crop in Tunisia were undertaken based on informative cpSSR molecular markers. A total of 21 alleles combining to 9 haplotypes were detected with a mean value of 3.5 alleles per locus and a haplotype genetic diversity (Hd) of 0.82. The number of chloroplast haplotypes per population ranged from 1 to 4 with an average of 1.28. The haplotypes median-joining network and UPGMA analyses revealed two probable ancestral maternal lineages with a differential pearl millet seed-exchange rate between the investigated areas. Northern and Central populations presented unique genetic backgrounds while historical farmers’ practices in the South-East area resulted in the isolation of their own local landraces. The genetic evidences strongly support at least two introduction origins of pearl millet in Tunisia, one in the North and the other in the South followed by distinct local dispersal histories. Complementary in-situ and ex-situ conservation strategies taking into account the conservation of the maternal lineage cytoplasmic diversity are required. The investigated chloroplast SSRs provide useful molecular markers which could be used in further genetic studies and breeding surveys of pearl millet genetic resources.     

Incidence of amplification of the C-erb B2/Her-2/neu gene in human breast cancer]

Activation of cellular proto-oncogenes can be detected in several human cancers. In the current study, alterations of C-erb B2 gene in primary human breast cancers were investigated. It was found to be amplified from 2 to 30 fold in 25% of the tumors. Correlations of gene amplification with several disease parameters was evaluated.     

Phylogeny and biogeography of ratite birds inferred from DNA sequences of the mitochondrial ribosomal genes

The origin of the flightless ratite birds of the southern continents has been debated for over a century. Whether dispersal or vicariance (continental breakup) best explains their origin depends largely on their phylogenetic relationships. No consensus has been reached on this issue despite many morphological and molecular studies. To address this question further we sequenced a 2.8-kb region of mitochondrial DNA containing the ribosomal genes in representative ratites and a tinamou. Phylogenetic analyses indicate that Struthio (Africa) is basal and Rhea (South America) clusters with living Australasian ratites. This phylogeny agrees with transferrin and DNA hybridization studies but not with sequence analyses of some protein-coding genes. These results also require reevaluation of the phylogenetic position of the extinct moas of New Zealand. We propose a new hypothesis for the origin of ratites that combines elements of dispersal and vicariance.      

Sexual behavior,insemination and development of the freshwater leech Helobdella stagnalis (Annelida,Hirudinea, Glossiphoniidae)

The reproductive biology of the Glossiphoniidae leech Helobdella stagnalis, under laboratory conditions, the structure of its eggs and its developmental stages were studied. Sperm transfer and insemination are made by hypodermic injection: one or numerous spermatophores were attached to the skin of the partner during copulation and sperm is injected through it. The leeches can copulate repeatedly with several partners. Each leech produces 4–8 cocoons containing 20–60 eggs whose are attached to the ventral side of the parent and carried around. At 22 °C, the developmental duration is 24 days from the oviposition until the juveniles leave the parent leech. Three (3) major stages have been distinguished: Eggs cleavage, germinal band generation, and juveniles hatching. The sexual behavior of Hellobdella stagnalis was described with a special attention given to parental care.     

Experimental investigation of the scaphoid strain during wrist motion

The scaphoid is the most frequently fractured of the carpal bones [Taleisnik, J., The Wrist, Churchill Livingstone, New York (1985)]. This project was undertaken to qualitatively evaluate the strain in the scaphoid during wrist motion using a newly developed strain gage method. Strain gage resettes were mounted within the scaphoid and the range of motion of the hand was monitored using a custom designed electrogoniometer and data acquisition system. Ten specimens were utilized for this study. Results indicated that supination/pronation (S/P) of the forearm did not affect the strain in the scaphoid. A map of the strain in the waist of the scaphoid, as a function of flexion/extension (F/E) and radial/ulnar deviation (R/U), was generated. The contour plot of scaphoid strain vs range of motion (ROM) shows a valley where strains are low. Minimum scaphoid strain was found near neutral F/E and 15° of ulnar deviation.