Comparison of three ternary lipid bilayer mixtures: FRET and ESR reveal nanodomains

Phase diagrams of ternary lipid mixtures containing cholesterol have provided valuable insight into cell membrane behaviors, especially by describing regions of coexisting liquid-disordered (Ld) and liquid-ordered (Lo) phases. Fluorescence microscopy imaging of giant unilamellar vesicles has greatly assisted the determination of phase behavior in these systems. However, the requirement for optically resolved Ld + Lo domains can lead to the incorrect inference that in lipid-only mixtures, Ld + Lo domain coexistence generally shows macroscopic domains. Here we show this inference is incorrect for the low melting temperature phosphatidylcholines abundant in mammalian plasma membranes. By use of high compositional resolution Förster resonance energy transfer measurements, together with electron spin resonance data and spectral simulation, we find that ternary mixtures of DSPC and cholesterol together with either POPC or SOPC, do indeed have regions of Ld + Lo coexistence. However, phase domains are much smaller than the optical resolution limit, likely on the order of the Förster distance for energy transfer (R₀, ∼2-8 nm).     

Genetic variation of growth and tree quality traits among 42 diverse genetic origins of Tectona grandis planted under humid tropical conditions in Sabah, East Malaysia

Forty-two different genetic origins of teak (Tectona grandis) comprising 26 open-pollinated families from a clonal seed orchard (CSO) were planted in a replicated trial under 2,500 mm of annual rainfall and no distinct dry season, in 1997, in Sabah, East Malaysia. The trees were measured or scored for various traits at 13, 35, 49, 61, 72, 85, 96, and 106 months after planting. Mortality rate, height (H), diameter at breast height (DBH), volume (V), and fork height (FH) varied strongly among populations and origins. The best population means after 106 months for growth H (21.1 m), DBH (21.1 cm), and V (278 dm³) were for the CSO families. Narrow sense heritabilities for the CSO families increased gradually with age but remained lower after 106 months for DBH (h ² = 0.24) and V (h ² = 0.34) than for H (h ² = 0.51) and FH (h ² = 0.56). Overall, the CSO families were also straighter, less forked, and grew more vertically than the native provenance and seed-derived sources. Such differences did not exist for flowering ability, and at 106 months, the great majority of the trees of the various origins had not yet entered the flowering stage. Overall, at 106 months, the phenotypic correlations between the various quantitative and qualitative traits were weak, except between straightness and bending with values higher than 0.50. These findings confirm the usefulness of CSO for teak improvement and demonstrate the beneficial influence of wet tropical conditions on traits of major economical importance for this species.     

Dual perfluorocarbon method to noninvasively monitor dissolved oxygen concentration in tissue engineered constructs in vitro and in vivo

Noninvasive in vivo monitoring of tissue implants provides important correlations between construct function and the observed physiologic effects. As oxygen is a key parameter affecting cell and tissue function, we established a monitoring method that utilizes ¹⁹F nuclear magnetic resonance (NMR) spectroscopy, with perfluorocarbons (PFCs) as oxygen concentration markers, to noninvasively monitor dissolved oxygen concentration (DO) in tissue engineered implants. Specifically, we developed a dual PFC method capable of simultaneously measuring DO within a tissue construct and its surrounding environment, as the latter varies among animals and with physiologic conditions. In vitro studies using an NMR‐compatible bioreactor demonstrated the feasibility of this method to monitor the DO within alginate beads containing metabolically active murine insulinoma βTC‐tet cells, relative to the DO in the culture medium, under perfusion and static conditions. The DO profiles obtained under static conditions were supported by mathematical simulations of the system. In vivo, the dual PFC method was successful in tracking the oxygenation state of entrapped βTC‐tet cells and the surrounding peritoneal DO over 16 days in normal mice. DO measurements correlated well with the extent of cell growth and host cell attachment examined postexplantation. The peritoneal oxygen environment was found to be variable and hypoxic, and significantly lower in the presence of metabolically active cells. The significance of the dual PFC system in providing critical DO measurements for entrapped cells and other tissue constructs, in vitro and in vivo, is discussed. © 2011 American Institute of Chemical Engineers Biotechnol. Prog., 2011     

Life expectancy of oil palm (Elaeis guineensis) infected by Ganoderma boninense in coastal soils,Malaysia: a case study

Ganoderma boninense basal stem rot poses a serious threat to the oil palm industry. The effects of external disease symptoms and coastal soils (Briah – Typic Endoaquepts, Jawa – Typic Sulfaquepts, and Selangor – Typic Humaquepts) on the life expectancy of the infected palms, from disease detection to death, were studied. Six-monthly censuses on disease classes for each palm were recorded between 2004 and 2012. Survival curves of disease symptoms and soil types were compared using Kaplan–Meier and log-rank methods, respectively. Ganoderma-infected palms in acid-sulphate (AS) and potential AS soils recorded lower life expectancy. Survival duration of infected palms with foliar symptoms was 12-months shorter. External factors, such as soil type may influence the survival of infected palms and soil types may pre-dispose oil palm to higher risk of Ganoderma infection. More effective Ganoderma management for palms planted on Coastal soils (with and without AS layer) have been proposed.     

An integrated feature selection and classification method to select minimum number of variables on the case study of gene expression data

This paper introduces a novel generic approach for classification problems with the objective of achieving maximum classification accuracy with minimum number of features selected. The method is illustrated with several case studies of gene expression data. Our approach integrates filter and wrapper gene selection methods with an added objective of selecting a small set of non-redundant genes that are most relevant for classification with the provision of bins for genes to be swapped in the search for their biological relevance. It is capable of selecting relatively few marker genes while giving comparable or better leave-one-out cross-validation accuracy when compared with gene ranking selection approaches. Additionally, gene profiles can be extracted from the evolving connectionist system, which provides a set of rules that can be further developed into expert systems. The approach uses an integration of Pearson correlation coefficient and signal-to-noise ratio methods with an adaptive evolving classifier applied through the leave-one-out method for validation. Datasets of gene expression from four case studies are used to illustrate the method. The results show the proposed approach leads to an improved feature selection process in terms of reducing the number of variables required and an increased in classification accuracy.     

Multicenter evaluation of mycobacteria identification by PCR restriction enzyme analysis in laboratories from Latin America and the Caribbean

The identification of mycobacterial species in clinical isolates is essential for making patient care decisions. Polymerase chain reaction (PCR) restriction enzyme analysis (PRA) is a simple and rapid identification method, based on amplification of 441 bp of the hsp65 gene and restriction with BstEII and HaeIII. As a contribution to the validation of PRA, a multicenter study was performed in eight laboratories located in Argentina, Brazil, Colombia, Chile, and Guadeloupe. Each laboratory received 18 coded isolates from the collection of the Institute of Tropical Medicine (Antwerp, Belgium), representing duplicates of nine laboratory strains: Mycobacterium terrae CIPT 140320001, Mycobacterium scrofulaceum CIPT 140220031, Mycobacterium flavescens ATCC 14474, Mycobacterium triviale ATCC 23292, Mycobacterium nonchromogenicum ATCC 19530, Mycobacterium chitae ATCC 19627, Mycobacterium abscessus ATCC 19977, Mycobacterium kansasii ATCC 12478, and Mycobacterium peregrinum ATCC 14467. A detailed protocol including amplification, enzymatic digestion, and gel preparation was provided to each laboratory. Two laboratories identified correctly all 18 (100%) isolates, one identified correctly 17 (94.5%), two identified 14 (77.7%), one identified 11 (61%), and two identified 8 (44.4%) isolates. Errors detected in laboratories with more than 77% accuracy were associated with electrophoresis running conditions and an unspecific amplicon produced by a single strain. Lower accuracy was mainly related to inappropriate use of DNA markers and insufficient training in interpretation of patterns. In conclusion, the PRA method was readily implemented in some Latin American and Caribbean laboratories of mycobacteria, but improvements in critical points, as gel running conditions and training in interpretiation of patterns, are needed in order to improve accuracy. In others, improvement in critical points is still necessary.