Insights from the GC content analysis of 76genome survey sequences (GSS) from Elaeisoleifera

South American oil-palm (Elaeis oleifera) is not cultivated in tropical countries like Malaysia on large scale due to low yield of palm oil derived from its fruit mesocarp. However, its fruit mesocarp oil contains about 68.6 % oleic acid (C_18:1) which is more than double in comparison to commercially cultivated oilpalm, E. guineensis Jacq Tenera (hybrid of Dura (♀) x Pisifera (♂)). It is also known that E. oleifera is a good source of tocotrienols and carotenoids. Therefore, it is of interest to know the genome sequence of E. oleifera. The objective of this study is to generate genome survey sequences (GSS) to get GC content insight in the E. oleifera genome. The nuclear genomic DNA isolated from young leaf‐tissues was digested with EcoRI and NdeI/DraI restriction enzymes; and three genomic DNA libraries were constructed using Lambda ZAP‐II, pGEM®‐T Easy, and pDONR 222™ as cloning vectors. Generated 76 GSSs were analyzed by using Bioinformatics tools. The analysis result indicates that the adenine, cytosine, guanine and thymine content in generated GSSs are 30%, 20%, 20%, and 30% respectively. In conclusion, based on the precise GC content analysis of the randomly isolated 76 GSSs by using Bioinformatics tools we hypothesize that GC content in E. oleifera genome is 40%. The hypothesized 40% GC content in E. oleifera genome is expected to remain close to the GC content based on the whole genome analysis.^ψThe nucleotide sequence data reported in this paper have been submitted to dbGSS division of the international DNA database (GenBank/DDBJ/EMBL) under accession numbers: {"type":"entrez-nucleotide-range","attrs":{"text":"DX575945- DX575972","start_term":"DX575945","end_term":"DX575972","start_term_id":"94323534","end_term_id":"94323561"}}DX575945- DX575972 and {"type":"entrez-nucleotide-range","attrs":{"text":"EI798032-EI798079","start_term":"EI798032","end_term":"EI798079","start_term_id":"146199019","end_term_id":"146199066"}}EI798032-EI798079.

Abbreviations

gDNA - Nuclear genomic DNA, GSSs - Genome survey sequences K12, SAOP - South American oil‐palm Db1     

Microwave‐assisted extraction of total bioactive saponin fraction from Gymnema sylvestre with reference to gymnemagenin: a potential biomarker

Objective – To develop a fast and ecofriendly microwave assisted extraction (MAE) technique for the effective and exhaustive extraction of gymnemagenin as an indicative biomarker for the quality control of Gymnema sylvestre. Methodology – Several extraction parameters such as microwave power, extraction time, solvent composition, pre‐leaching time, loading ratio and extraction cycle were studied for the determination of the optimum extraction condition. Scanning electron micrographs were obtained to elucidate the mechanism of extraction Results – The final optimum extraction conditions as obtained from the study were: 40% microwave power, 6 min irradiation time, 85% v/v methanol as the extraction solvent, 15 min pre‐leaching time and 25 : 1 (mL/g) as the solvent‐to‐material loading ratio. The proposed extraction technique produced a maximum yield of 4.3% w/w gymnemagenin in 6 min which was 1.3, 2.5 and 1.95 times more efficient than 6 h of heat reflux, 24 h of maceration and stirring extraction, respectively. A synergistic heat and mass transfer theory was also proposed to support the extraction mechanism Conclusion – Comparison with conventional extraction methods revealed that MAE could save considerable amounts of time and energy, whilst the reduction of volume of organic solvent consumed provides an ecofriendly feature. Copyright © 2009 John Wiley & Sons, Ltd.     

Putrescine overproduction negatively impacts the oxidative state of poplar cells in culture

While polyamines (PAs) have been suggested to protect cells against Reactive Oxygen Species (ROS), their catabolism is known to generate ROS. We compared the activities of several enzymes and cellular metabolites involved in the ROS scavenging pathways in two isogenic cell lines of poplar (Populus nigra × maximowiczii) differing in their PA contents. Whereas the control cell line was transformed with β-glucuronidase (GUS), the other, called HP (High Putrescine), was transformed with a mouse ornithine decarboxylase (mODC) gene. The expression of mODC resulted in several-fold increased production of putrescine as well its enhanced catabolism. The two cell lines followed a similar trend of growth over the seven-day culture cycle, but the HP cells had elevated levels of soluble proteins. Accumulation of H₂O₂ was higher in the HP cells than the control cells, and so were the activities of glutathione reductase and monodehydroascorbate reductase; the activity of ascorbate peroxidase was lower in the former. The contents of reduced glutathione and glutamate were significantly lower in the HP cells but proline was higher on some days of analysis. There was a small difference in mitochondrial activity between the two cell lines, and the HP cells showed increased membrane damage. In the HP cells, increased accumulation of Ca was concomitant with lower accumulation of K. We conclude that, while increased putrescine accumulation may have a protective role against ROS in plants, enhanced turnover of putrescine actually can make them vulnerable to increased oxidative damage.     

Deglycosylated milin unfolds via inactive monomeric intermediates

The effect of deglycosylation on the physiological and functional organization of milin was studied under different denaturizing conditions. Trifluoromethanesulfonic acid mediated deglycosylation resulted in insoluble milin, which was found to be soluble only in 1.5 M GuHCl with native-like folded structure. Kinetic stability, proteolytic activity, and dimeric association were lost in deglycosylated milin. Urea-induced unfolding revealed two inactive, highly stable equilibrium intermediates at pH 7.0 and pH 2.0. These intermediates were stable between 5.5–6.5 and 5.0–6.0 M total chaotropes (urea + 1.5 M GuHCl) at pH 7.0 and pH 2.0, respectively. GuHCl-induced unfolding was cooperative and noncoincidental with a broad transition range (2.0–5.0 M) at pH 7.0 and pH 2.0. Equilibrium unfolding of deglycosylated milin by urea and GuHCl substantiates the involvement of various inactive monomeric intermediates. This study provides a way to understand the role of glycosylation in the unfolding mechanism, stability, and functional activity of the serine protease milin.     

Pharmacokinetics and biodistribution of genetically engineered antibodies

The engineering of monoclonal antibodies has created a new generation of pharmaceuticals with the desired pharmacokinetics and biodistribution properties. For radioimmunotherapy and radioscintigraphy, optimum tumor targeting can be achieved using engineered constructs that provide high antigen affinity and specificity, effective tumor penetration, circulation properties that allow high tumor uptake with acceptable doses to the normal tissues, and fast clearance allowing low background. Recent advances have made possible the development of antibodies with these properties.     

Endophytic colonization ability of two deep-water rice endophytes, Pantoea sp. and Ochrobactrum sp. using green fluorescent protein reporter

Colonization ability of the two endophytic bacteria, isolated from surface sterilized seeds of Jaisurya variety of deep-water rice viz., Pantoea sp. and Ochrobactrum sp., was compared after genetically tagging them with a constitutively expressing green fluorescent protein gene (gfp). Confocal laser scanning microscopy (CLSM) of hydroponically grown seedlings of Jaisurya rice, inoculated with gfp-tagged endophytes, revealed that both Pantoea sp. and Ochrobactrum sp. colonized the intercellular spaces in the root cortex when inoculated separately. Colonization by gfp-tagged Ochrobactrum sp. was severely inhibited when co-inoculated with an equal number (10(5) c.f.u. ml(-1)) of wild type Pantoea sp., but the converse was not true. Pantoea sp. was a more aggressive endophytic colonizer of its host than Ochrobactrum sp. The potential of using GFP reporter and CLSM as tools in evaluating competitive ability of colonization among endophytes is herewith demonstrated.     

The annotation and analysis of complex 3D plant organs using 3DCoordX

A fundamental question in biology concerns how molecular and cellular processes become integrated during morphogenesis. In plants, characterization of 3D digital representations of organs at single-cell resolution represents a promising approach to addressing this problem. A major challenge is to provide organ-centric spatial context to cells of an organ. We developed several general rules for the annotation of cell position and embodied them in 3DCoordX, a user-interactive computer toolbox implemented in the open-source software MorphoGraphX. 3DCoordX enables rapid spatial annotation of cells even in highly curved biological shapes. Using 3DCoordX, we analyzed cellular growth patterns in organs of several species. For example, the data indicated the presence of a basal cell proliferation zone in the ovule primordium of Arabidopsis (Arabidopsis thaliana). Proof-of-concept analyses suggested a preferential increase in cell length associated with neck elongation in the archegonium of Marchantia (Marchantia polymorpha) and variations in cell volume linked to central morphogenetic features of a trap of the carnivorous plant Utricularia (Utricularia gibba). Our work demonstrates the broad applicability of the developed strategies as they provide organ-centric spatial context to cellular features in plant organs of diverse shape complexity.

Spatial context is essential to draw biological insight from 3D image data, and 3DCoordX is an intuitive, open-source computational tool that provides this context for plant organs with complex shapes.     

Gingivitis resolution followed by optical coherence tomography and fluorescence imaging: A case study

Gingivitis is highly prevalent in adults, and if left untreated, can progress to periodontitis. In this article, we present an interesting case study where the resolution of gingivitis was followed over a period of 10 days using optical coherence tomography (OCT) and light-induced autofluorescence (LIAF). We demonstrate that OCT and its functional angiography can distinctively capture the changes during the resolution of gingivitis; while LIAF can detect red-fluorescent signals associated with mature plaque present at the inflamed site. The acute inflammatory region showed evidence of angiogenesis based on the quantification of vessel density and number; while no angiogenesis was detected within the less inflamed region. Gingival thickness showed a reduction of 140 ± 26 μm on average, measured between the peak gingivitis event and the period wherein the inflammation was resolved. Vessels in the angiogenesis site was found to reduce exponentially. The mildly inflamed site showed a decreasing trend in the vessel size, which however was within the error of the measurement.