School of Agriculture, Food and Ecosystem Sciences - Research Publications
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ItemPhylogenetic and functional diversity of metagenomic libraries of phenol degrading sludge from petroleum refinery wastewater treatment system(SPRINGER, 2012)In petrochemical refinery wastewater treatment plants (WWTP), different concentrations of pollutant compounds are received daily in the influent stream, including significant amounts of phenolic compounds, creating propitious conditions for the development of particular microorganisms that can rapidly adapt to such environment. In the present work, the microbial sludge from a refinery WWTP was enriched for phenol, cloned into fosmid vectors and pyrosequenced. The fosmid libraries yielded 13,200 clones and a comprehensive bioinformatic analysis of the sequence data set revealed a complex and diverse bacterial community in the phenol degrading sludge. The phylogenetic analyses using MEGAN in combination with RDP classifier showed a massive predominance of Proteobacteria, represented mostly by the genera Diaphorobacter, Pseudomonas, Thauera and Comamonas. The functional classification of phenol degrading sludge sequence data set generated by MG-RAST showed the wide metabolic diversity of the microbial sludge, with a high percentage of genes involved in the aerobic and anaerobic degradation of phenol and derivatives. In addition, genes related to the metabolism of many other organic and xenobiotic compounds, such as toluene, biphenyl, naphthalene and benzoate, were found. Results gathered herein demonstrated that the phenol degrading sludge has complex phylogenetic and functional diversities, showing the potential of such community to degrade several pollutant compounds. This microbiota is likely to represent a rich resource of versatile and unknown enzymes which may be exploited for biotechnological processes such as bioremediation.
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ItemPlant homeostasis of foliar manganese sinks: specific variation in hyperaccumulators(SPRINGER, 2012-11)Plant manganese (Mn) hyperaccumulation provides unusual insight into homeostasis of this essential micronutrient, in particular its excessive storage in shoot tissues. The compartmentation of hyperaccumulated foliar Mn appears exceptional among metal hyperaccumulators, since it occurs via specific microdistribution patterns. Here, three associated Mn hyperaccumulators, Virotia neurophylla, Maytenus fournieri, and Garcinia amplexicaulis exhibiting distinctly different Mn detoxification strategies were examined. Non-invasive sample preparation in conjunction with cryo scanning electron microscopy (SEM) was used to obtain in vivo quantitative microprobe X-ray and anatomical data from fully hydrated cells. Highly vacuolated large palisade mesophyll cells in V. neurophylla leaves were found to contain around 650 mM Mn. The large non-photosynthetic hypodermal cells of M. fournieri leaves, also with high vacuolar content, and the main site for Mn disposal, had an estimated mean vacuolar Mn concentration of around 600 mM. Previous qualitative X-ray mapping had shown Mn to be almost evenly sequestered across the entire leaf cross section of G. amplexicaulis. However, quantitative data obtained here showed a marked variation in localised concentrations that ranged between ~15 and >800 mM. Notable among these were mean values of >600 mM in spongy mesophyll cells, and ~800 mM within cells of a narrow sub epidermal layer preceding the palisade mesophyll. This study demonstrated the extraordinary Mn carrying capacities of different types of leaf cell vacuoles.
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ItemNo Preview AvailableGenetic Diversity of Cultivated Barley Landraces in Iran Measured Using Microsatellites(IACSIT Press, 2012)The cultivated barley (Hordeum vulgare subsp. vulgare) is one of the major crops in the world. In this study the genetic diversity of 32 individuals of two-rowed and six-rowed Iranian landraces barley evaluated using 17 microsatellite markers. A high level of polymorphism information content (PIC; average = 0.651) and an average of 8.117 allele per locus were observed. In dendrograms constructed based on the SSR data, the two group of cultivars (var. distichon and var. hexastichon) were separated. Based on the results of this study, it can be concluded that there is a high level of genetic diversity between the barely landraces in Iran and that the barely Iranian gene pool is valuable source to search for new useful alleles for crop improvement.
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ItemEfficacy and Safety of a Chinese Herbal Medicine Formula (RCM-104) in the Management of Simple Obesity: A Randomized, Placebo-Controlled Clinical Trial.(Hindawi Limited, 2012)Objective. This study was to evaluate the efficacy and safety of a Chinese herbal medicine formula (RCM-104) for the management of simple obesity. Method. Obese subjects aged between 18 and 60 years were selected for 12-week, double-blind, randomized, placebo-controlled trial. Subjects were randomly assigned to take 4 capsules of either the RCM-104 formula (n = 59) or placebo (n = 58), 3 times daily for 12 weeks. Measures of BW, BMI and WC, HC, WHR and BF composition were assessed at baseline and once every four weeks during the 12 week treatment period. Results. Of the 117 subjects randomised, 92 were included in the ITT analysis. The weight, BMI and BF in RCM-104 group were reduced by 1.5 kg, 0.6 kg/m(2) and 0.9% and those in the placebo group were increased by 0.5 kg, 0.2 kg/m(2) and 0.1% respectively. There were significant differences in BW and BMI (P < 0.05) between the two groups. Eleven items of the WLQOQ were significantly improved in the RCM-104 group while only 2 items were significantly improved in the placebo group. Adverse events were minor in both groups. Conclusion. RCM-104 treatment appears to be well tolerated and beneficial in reducing BW and BMI in obese subjects.
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ItemA Two-Staged Model of Na+ Exclusion in Rice Explained by 3D Modeling of HKT Transporters and Alternative Splicing(PUBLIC LIBRARY SCIENCE, 2012-07-11)The HKT family of Na(+) and Na(+)/K(+) transporters is implicated in plant salinity tolerance. Amongst these transporters, the cereal HKT1;4 and HKT1;5 are responsible for Na(+) exclusion from photosynthetic tissues, a key mechanism for plant salinity tolerance. It has been suggested that Na(+) is retrieved from the xylem transpiration stream either in the root or the leaf sheath, protecting the leaf blades from excessive Na(+) accumulation. However, direct evidence for this scenario is scarce. Comparative modeling and evaluation of rice (Oryza sativa) HKT-transporters based on the recent crystal structure of the bacterial TrkH K(+) transporter allowed to reconcile transcriptomic and physiological data. For OsHKT1;5, both transcript abundance and protein structural features within the selectivity filter could control shoot Na(+) accumulation in a range of rice varieties. For OsHKT1;4, alternative splicing of transcript and the anatomical complexity of the sheath needed to be taken into account. Thus, Na(+) accumulation in a specific leaf blade seems to be regulated by abundance of a correctly spliced OsHKT1;4 transcript in a corresponding sheath. Overall, allelic variation of leaf blade Na(+) accumulation can be explained by a complex interplay of gene transcription, alternative splicing and protein structure.
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