On the Metropolis-Hastings acceptance probability to add or drop a quantitative trait locus in Markov chain Monte Carlo-based Bayesian analyses

The Metropolis-Hastings algorithm used in analyses that estimate the number of QTL segregating in a mapping population requires the calculation of an acceptance probability to add or drop a QTL from the model. Expressions for this acceptance probability need to recognize that sets of QTL are unordered such that the number of equivalent sets increases with the factorial of the QTL number. Here, we show how accounting for this fact affects the acceptance probability and review expressions found in the literature.     

A Sri Lankan child with 49,XXXXY syndrome

Pentasomy 49,XXXXY is a rare sex chromosome disorder usually presenting with ambigous genitalia, facial dysmorphism, mental retardation and a combination of cardiac, skeletal and other malformations. The incidence of the condition is estimated to be 1 in 85,000 male births. Previously, this condition was identified as a Klinefelter variant. The condition is suspected in a patient, by a combination of characteristic clinical findings, and the diagnosis is confirmed by chromosome culture and karyotyping. In the case we report here, the main presentation of ambiguous genitalia led to a suspicion of a sex chromosome aneuploidy which was subsequently confirmed by chromosomal analysis.     

Sequence analysis and homology modeling of laccase from Pycnoporus cinnabarinus

Industrial effluents of textile, paper, and leather industries contain various toxic dyes as one of the waste material. It imparts major impact on human health as well as environment. The white rot fungus Pycnoporus cinnabarinus Laccase is generally used to degrade these toxic dyes. In order to decipher the mechanism of process by which Laccase degrade dyes, it is essential to know its 3D structure. Homology modeling was performed in presented work, by satisfying Spatial restrains using Modeller Program, which is considered as standard in this field, to generate 3D structure of Laccase in unison, SWISSMODEL web server was also utilized to generate and verify the alternative models. We observed that models created using Modeller stands better on structure evaluation tests. This study can further be used in molecular docking techniques, to understand the interaction of enzyme with its mediators like 2, 2-azinobis (3-ethylbenzthiazoline-6-sulfonate) (ABTS) and Vanillin that are known to enhance the Laccase activity.     

Phosphoinositide 3-kinase �� regulates membrane fission of Golgi carriers for selective cytokine secretion

Phosphoinositide 3-kinase (PI3K) p110 isoforms are membrane lipid kinases classically involved in signal transduction. Lipopolysaccharide (LPS)-activated macrophages constitutively and abundantly secrete proinflammatory cytokines including tumor necrosis factor-α (TNF). Loss of function of the p110δ isoform of PI3K using inhibitors, RNA-mediated knockdown, or genetic inactivation in mice abolishes TNF trafficking and secretion, trapping TNF in tubular carriers at the trans-Golgi network (TGN). Kinase-active p110δ localizes to the Golgi complex in LPS-activated macrophages, and TNF is loaded into p230-labeled tubules, which cannot undergo fission when p110δ is inactivated. Similar blocks in fission of these tubules and in TNF secretion result from inhibition of the guanosine triphosphatase dynamin 2. These findings demonstrate a new function for p110δ as part of the membrane fission machinery required at the TGN for the selective trafficking and secretion of cytokines in macrophages.     

Genetic dissection of gene regulation in multiple mouse tissues

The analysis of the influence of genetic variation on regulation of gene expression at a near-genome-wide level has become the focus of much recent interest. It is widely appreciated that many genes are expressed in a tissue-specific manner and that others are more ubiquitously expressed but relatively little is known about how genetic variation might influence these tissue patterns of gene expression. In this review we discuss what is known about the tissue specificity of the influence of genetic variation and review the challenges that we face in combining hugely parallel, microarray-based gene analysis with equally expensive genetic analysis. We conclude that the available data suggest that genetic variation is essentially tissue specific in its effects upon gene expression and this has important implications for experimental analysis.     

Improvement of N-glycan site occupancy of therapeutic glycoproteins produced in Pichia pastoris

Yeast is capable of performing posttranslational modifications, such as N- or O-glycosylation. It has been demonstrated that N-glycans play critical biological roles in therapeutic glycoproteins by modulating pharmacokinetics and pharmacodynamics. However, N-glycan sites on recombinant glycoproteins produced in yeast can be underglycosylated, and hence, not completely occupied. Genomic homology analysis indicates that the Pichia pastoris oligosaccharyltransferase (OST) complex consists of multiple subunits, including OST1, OST2, OST3, OST4, OST5, OST6, STT3, SWP1, and WBP1. Monoclonal antibodies produced in P. pastoris show that N-glycan site occupancy ranges from 75–85 % and is affected mainly by the OST function, and in part, by process conditions. In this study, we demonstrate that N-glycan site occupancy of antibodies can be improved to greater than 99 %, comparable to that of antibodies produced in mammalian cells (CHO), by overexpressing Leishmania major STT3D (LmSTT3D) under the control of an inducible alcohol oxidase 1 (AOX1) promoter. N-glycan site occupancy of non-antibody glycoproteins such as recombinant human granulocyte macrophage colony-stimulating factor (rhGM-CSF) was also significantly improved, suggesting that LmSTT3D has broad substrate specificity. These results suggest that the glycosylation status of recombinant proteins can be improved by heterologous STT3 expression, which will allow for the customization of therapeutic protein profiles.     

Insights into the PX (phox-homology) domain and SNX (sorting nexin) protein families: structures, functions and roles in disease

The mammalian genome encodes 49 proteins that possess a PX (phox-homology) domain, responsible for membrane attachment to organelles of the secretory and endocytic system via binding of phosphoinositide lipids. The PX domain proteins, most of which are classified as SNXs (sorting nexins), constitute an extremely diverse family of molecules that play varied roles in membrane trafficking, cell signalling, membrane remodelling and organelle motility. In the present review, we present an overview of the family, incorporating recent functional and structural insights, and propose an updated classification of the proteins into distinct subfamilies on the basis of these insights. Almost all PX domain proteins bind PtdIns3P and are recruited to early endosomal membranes. Although other specificities and localizations have been reported for a select few family members, the molecular basis for binding to other lipids is still not clear. The PX domain is also emerging as an important protein-protein interaction domain, binding endocytic and exocytic machinery, transmembrane proteins and many other molecules. A comprehensive survey of the molecular interactions governed by PX proteins highlights the functional diversity of the family as trafficking cargo adaptors and membrane-associated scaffolds regulating cell signalling. Finally, we examine the mounting evidence linking PX proteins to different disorders, in particular focusing on their emerging importance in both pathogen invasion and amyloid production in Alzheimer's disease.     

Liquid-liquid extraction for recovery of paclitaxel from plant cell culture: Solvent evaluation and use of extractants for partitioning and selectivity

A major challenge in the production of metabolites by plant cells is the separation and purification of a desired product from a number of impurities. An important application of plant cell culture is the biosynthesis of the anticancer agent paclitaxel. Liquid–liquid extraction plays a critical role in the recovery of paclitaxel and other valuable plant‐derived products from culture broth. In this study, the extraction of paclitaxel and a major unwanted by‐product, cephalomannine, from plant cell culture broth into organic solvents is quantified. Potential solvent mixtures show varying affinity and selectivity for paclitaxel over cephalomannine. The partition coefficient of paclitaxel is highest in ethyl acetate and dichloromethane, with measured values of 28 and 25, respectively; however, selectivity coefficients are less than 1 for paclitaxel over cephalomannine for both solvents. Selectivity coefficient increases to 1.7 with extraction in n‐hexane, but the partition coefficient decreases to 1.9. Altering the pH of the aqueous phase results in an increase in both recovery and selectivity using n‐hexane but does not change the results for other solvents significantly. The addition of extractants trioctylamine (TOA) or tributylphosphate (TBP) to n‐hexane gives significantly higher partition coefficients for paclitaxel (8.6 and 23.7, respectively) but no selectivity. Interestingly, when 20% hexafluorobenzene (HFB) is added to n‐hexane, the partition coefficient remains approximately constant, but the selectivity coefficient for paclitaxel over cephalomannine improves to 4.5. This significant increase in selectivity early in the purification process has the potential to simplify downstream processing steps and significantly reduce overall purification costs. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 28: 990–997, 2012     

Determinants of Childhood Adiposity: Evidence from the Australian LOOK Study

Background

To contribute to the current debate as to the relative influences of dietary intake and physical activity on the development of adiposity in community-based children.

Methods

Participants were 734 boys and girls measured at age 8, 10 and 12 years for percent body fat (dual emission x-ray absorptiometry), physical activity (pedometers, accelerometers); and dietary intake (1 and 2-day records), with assessments of pubertal development and socioeconomic status.

Results

Cross-sectional relationships revealed that boys and girls with higher percent body fat were less physically active, both in terms of steps per day and moderate and vigorous physical activity (both sexes p<0.001 for both measures). However, fatter children did not consume more energy, fat, carbohydrate or sugar; boys with higher percent body fat actually consumed less carbohydrate (p = 0.01) and energy (p = 0.05). Longitudinal analysis (combined data from both sexes) was weaker, but supported the cross-sectional findings, showing that children who reduced their PA over the four years increased their percent body fat (p = 0.04). Relationships in the 8 year-olds and also in the leanest quartile of all children, where adiposity-related underreporting was unlikely, were consistent with those of the whole group, indicating that underreporting did not influence our findings.

Conclusions

These data provide support for the premise that physical activity is the main source of variation in the percent body fat of healthy community-based Australian children. General community strategies involving dietary intake and physical activity to combat childhood obesity may benefit by making physical activity the foremost focus of attention.