QTLs for oil yield components in an elite oil palm (Elaeis guineensis) cross

Increased modern farming of superior types of the oil palm, Elaeis guineensis Jacq., which has naturally efficient oil biosynthesis, has made it the world’s foremost edible oil crop. Breeding improvement is, however, circumscribed by time and costs associated with the tree’s long reproductive cycle, large size and 10–15 years of field testing. Marker-assisted breeding has considerable potential for improving this crop. Towards this, quantitative trait loci (QTL) linked to oil yield component traits were mapped in a high-yield population. In total, 164 QTLs associated with 21 oil yield component traits were discovered, with cumulative QTL effects increasing in tandem with the number of QTL markers and matching the QT+ alleles for each trait. The QTLs confirmed all traits to be polygenic, with many genes of individual small effects on independent loci, but epistatic interactions are not ruled out. Furthermore, several QTLs maybe pleiotropic as suggested by QTL clustering of inter-related traits on almost all linkage groups. Certain regions of the chromosomes seem richer in the genes affecting a particular yield component trait and likely encompass pleiotropic, epistatic and heterotic effects. A large proportion of the identified additive effects from QTLs may actually arise from genic interactions between loci. Comparisons with previous mapping studies show that most of the QTLs were for similar traits and shared similar marker intervals on the same linkage groups. Practical applications for such QTLs in marker-assisted breeding will require seeking them out in different genetic backgrounds and environments

An integrative approach for a network based meta-analysis of viral RNAi screens.

BACKGROUND: Big data is becoming ubiquitous in biology, and poses significant challenges in data analysis and interpretation. RNAi screening has become a workhorse of functional genomics, and has been applied, for example, to identify host factors involved in infection for a panel of different viruses. However, the analysis of data resulting from such screens is difficult, with often low overlap between hit lists, even when comparing screens targeting the same virus. This makes it a major challenge to select interesting candidates for further detailed, mechanistic experimental characterization. RESULTS: To address this problem we propose an integrative bioinformatics pipeline that allows for a network based meta-analysis of viral high-throughput RNAi screens. Initially, we collate a human protein interaction network from various public repositories, which is then subjected to unsupervised clustering to determine functional modules. Modules that are significantly enriched with host dependency factors (HDFs) and/or host restriction factors (HRFs) are then filtered based on network topology and semantic similarity measures. Modules passing all these criteria are finally interpreted for their biological significance using enrichment analysis, and interesting candidate genes can be selected from the modules. CONCLUSIONS: We apply our approach to seven screens targeting three different viruses, and compare results with other published meta-analyses of viral RNAi screens. We recover key hit genes, and identify additional candidates from the screens. While we demonstrate the application of the approach using viral RNAi data, the method is generally applicable to identify underlying mechanisms from hit lists derived from high-throughput experimental data, and to select a small number of most promising genes for further mechanistic studies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13015-015-0035-7) contains supplementary material, which is available to authorized users

Sound Practices for Consistent Human Visual Inspection

Numerous presentations and articles on manual inspection of pharmaceutical drug products have been released, since the pioneering articles on inspection by Knapp and associates Knapp and Kushner (J Parenter Drug Assoc 34:14, 1980); Knapp and Kushner (Bull Parenter Drug Assoc 34:369, 1980); Knapp and Kushner (J Parenter Sci Technol 35:176, 1981); Knapp and Kushner (J Parenter Sci Technol 37:170, 1983). This original work by Knapp and associates provided the industry with a statistical means of evaluating inspection performance. This methodology enabled measurement of individual inspector performance, performance of the entire inspector pool and provided basic suggestions for the conduct of manual inspection. Since that time, numerous subject matter experts (SMEs) have presented additional valuable information for the conduct of manual inspection Borchert et al. (J Parenter Sci Technol 40:212, 1986); Knapp and Abramson (J Parenter Sci Technol 44:74, 1990); Shabushnig et al. (1994); Knapp (1999); Knapp (2005); Cherris (2005); Budd (2005); Barber and Thomas (2005); Knapp (2005); Melchore (2007); Leversee and Ronald (2007); Melchore (2009); Budd (2007); Borchert et al. (1986); Berdovich (2005); Berdovich (2007); Knapp (2007); Leversee and Shabushing (2009); Budd (2009). Despite this abundance of knowledge, neither government regulations nor the multiple compendia provide more than minimal guidance or agreement for the conduct of manual inspection. One has to search the literature for useful information that has been published by SMEs in the field of Inspection. The purpose of this article is to restate the sound principles proclaimed by SMEs with the hope that they serve as a useful guideline to bring greater consistency to the conduct of manual inspection