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1.  Cadmium Phytoremediation by Arundo donax L. from Contaminated Soil and Water 
BioMed Research International  2013;2013:324830.
The potential of Arundo donax L. for phytoextraction of cadmium (Cd) from contaminated soil and water was probed. The plants were grown under greenhouse conditions in pots containing a nutrient solution or soil with increasing doses of Cd (0, 50, 100, 250, 500, 750, and 1000 μg L−1) for 21 days. The growth and physiology of plants were evaluated at the end of the experiment. The maximum Cd content in root was 300 μg g−1 during hydroponics experiments over 230 μg g−1 in soil experiment. Cd concentration in stem was 262 μg g−1 at 750 μg L−1 supplied Cd in hydroponics over 191.2 μg g−1 at 1000 in soil experiment. The maximum Cd concentration in leaves from hydroponics was 187 μg g−1. Relatively low Cd uptake occurred during soil experiment with low translocation factor (TF) values. Both Bioaccumulation Factor (BF) and TF values for hydroponics were greater than 1. The IC50 values of ABTS and DPPH showed that both time and increasing Cd concentrations affected the production of antioxidants with lower half maximal inhibitory concentration (IC50) value on the 21st days. A. donax showed better potential for Cd remediation of aquatic environments.
doi:10.1155/2013/324830
PMCID: PMC3888719  PMID: 24459667
2.  Combined Industrial Wastewater Treatment in Anaerobic Bioreactor Posttreated in Constructed Wetland 
BioMed Research International  2013;2013:957853.
Constructed wetland (CW) with monoculture of Arundo donax L. was investigated for the posttreatment of anaerobic bioreactor (ABR) treating combined industrial wastewater. Different dilutions of combined industrial wastewater (20, 40, 60, and 80) and original wastewater were fed into the ABR and then posttreated by the laboratory scale CW. The respective removal efficiencies of COD, BOD, TSS, nitrates, and ammonia were 80%, 78–82%, 91.7%, 88–92%, and 100% for original industrial wastewater treated in ABR. ABR was efficient in the removal of Ni, Pb, and Cd with removal efficiencies in the order of Cd (2.7%) > Ni (79%) > Pb (85%). Posttreatment of the ABR treated effluent was carried out in lab scale CW containing A. donax L. CW was effective in the removal of COD and various heavy metals present in ABR effluents. The posttreatment in CW resulted in reducing the metal concentrations to 1.95 mg/L, 0 mg/L, and 0.004 mg/L for Ni, Pb, and Cd which were within the permissible water quality standards for industrial effluents. The treatment strategy was effective and sustainable for the treatment of combined industrial wastewater.
doi:10.1155/2013/957853
PMCID: PMC3876802  PMID: 24396832
3.  Characterization of purified and Xerogel immobilized Novel Lignin Peroxidase produced from Trametes versicolor IBL-04 using solid state medium of Corncobs 
BMC Biotechnology  2012;12:46.
Background
Cost-effective production of industrially important enzymes is a key for their successful exploitation on industrial scale. Keeping in view the extensive industrial applications of lignin peroxidase (LiP), this study was performed to purify and characterize the LiP from an indigenous strain of Trametes versicolor IBL-04. Xerogel matrix enzyme immobilization technique was applied to improve the kinetic and thermo-stability characteristics of LiP to fulfil the requirements of the modern enzyme consumer sector of biotechnology.
Results
A novel LiP was isolated from an indigenous T. versicolor IBL-04 strain. T. versicolor IBL-04 was cultured in solid state fermentation (SSF) medium of corn cobs and maximum LiP activity of 592 ± 6 U/mL was recorded after five days of incubation under optimum culture conditions. The crude LiP was 3.3-fold purified with specific activity of 553 U/mg after passing through the DEAE-cellulose and Sephadex-G-100 chromatography columns. The purified LiP exhibited a relatively low molecular weight (30 kDa) homogenous single band on native and SDS-PAGE. The LiP was immobilized by entrapping in xerogel matrix of trimethoxysilane (TMOS) and proplytetramethoxysilane (PTMS) and maximum immobilization efficiency of 88.6% was achieved. The free and immobilized LiPs were characterized and the results showed that the free and immobilized LiPs had optimum pH 6 and 5 while optimum temperatures were 60°C and 80°C, respectively. Immobilization was found to enhance the activity and thermo-stability potential of LiP significantly and immobilized LiP remained stable over broad pH and temperature range as compare to free enzyme. Kinetic constants Km and Vmax were 70 and 56 μM and 588 and 417 U/mg for the free and immobilized LiPs, respectively. Activity of this novel extra thermo-stable LiP was stimulated to variable extents by Cu2+, Mn2+ and Fe2+ whereas, Cystein, EDTA and Ag+ showed inhibitory effects.
Conclusions
The indigenously isolated white rot fungal strain T. versicolor IBL-04 showed tremendous potential for LiP synthesis in SSF of corncobs in high titters (592 U/mL) than other reported Trametes (Coriolus, Polyporus) species. The results obtained after dual phase characterization suggested xerogel matrix entrapment a promising tool for enzyme immobilization, hyper-activation and stabilization against high temperature and inactivating agents. The pH and temperature optima, extra thermo-stability features and kinetic characteristics of this novel LiP of T. versicolor IBL-04 make it a versatile enzyme for various industrial and biotechnological applications.
doi:10.1186/1472-6750-12-46
PMCID: PMC3442999  PMID: 22862820
T. versicolor IBL-04; LiP; Immobilization; Xerogel; Characterization; Hyper-activation; Thermo-stabilization; Inactivation tolerance
4.  Cell wall biogenesis of Arabidopsis thaliana elongating cells: transcriptomics complements proteomics 
BMC Genomics  2009;10:505.
Background
Plant growth is a complex process involving cell division and elongation. Arabidopsis thaliana hypocotyls undergo a 100-fold length increase mainly by cell elongation. Cell enlargement implicates significant changes in the composition and structure of the cell wall. In order to understand cell wall biogenesis during cell elongation, mRNA profiling was made on half- (active elongation) and fully-grown (after growth arrest) etiolated hypocotyls.
Results
Transcriptomic analysis was focused on two sets of genes. The first set of 856 genes named cell wall genes (CWGs) included genes known to be involved in cell wall biogenesis. A significant proportion of them has detectable levels of transcripts (55.5%), suggesting that these processes are important throughout hypocotyl elongation and after growth arrest. Genes encoding proteins involved in substrate generation or in synthesis of polysaccharides, and extracellular proteins were found to have high transcript levels. A second set of 2927 genes labeled secretory pathway genes (SPGs) was studied to search for new genes encoding secreted proteins possibly involved in wall expansion. Based on transcript level, 433 genes were selected. Genes not known to be involved in cell elongation were found to have high levels of transcripts. Encoded proteins were proteases, protease inhibitors, proteins with interacting domains, and proteins involved in lipid metabolism. In addition, 125 of them encoded proteins with yet unknown function. Finally, comparison with results of a cell wall proteomic study on the same material revealed that 48 out of the 137 identified proteins were products of the genes having high or moderate level of transcripts. About 15% of the genes encoding proteins identified by proteomics showed levels of transcripts below background.
Conclusion
Members of known multigenic families involved in cell wall biogenesis, and new genes that might participate in cell elongation were identified. Significant differences were shown in the expression of such genes in half- and fully-grown hypocotyls. No clear correlation was found between the abundance of transcripts (transcriptomic data) and the presence of the proteins (proteomic data) demonstrating (i) the importance of post-transcriptional events for the regulation of genes during cell elongation and (ii) that transcriptomic and proteomic data are complementary.
doi:10.1186/1471-2164-10-505
PMCID: PMC2774874  PMID: 19878582
5.  A new picture of cell wall protein dynamics in elongating cells of Arabidopsis thaliana: Confirmed actors and newcomers 
BMC Plant Biology  2008;8:94.
Background
Cell elongation in plants requires addition and re-arrangements of cell wall components. Even if some protein families have been shown to play roles in these events, a global picture of proteins present in cell walls of elongating cells is still missing. A proteomic study was performed on etiolated hypocotyls of Arabidopsis used as model of cells undergoing elongation followed by growth arrest within a short time.
Results
Two developmental stages (active growth and after growth arrest) were compared. A new strategy consisting of high performance cation exchange chromatography and mono-dimensional electrophoresis was established for separation of cell wall proteins. This work allowed identification of 137 predicted secreted proteins, among which 51 had not been identified previously. Apart from expected proteins known to be involved in cell wall extension such as xyloglucan endotransglucosylase-hydrolases, expansins, polygalacturonases, pectin methylesterases and peroxidases, new proteins were identified such as proteases, proteins related to lipid metabolism and proteins of unknown function.
Conclusion
This work highlights the CWP dynamics that takes place between the two developmental stages. The presence of proteins known to be related to cell wall extension after growth arrest showed that these proteins may play other roles in cell walls. Finally, putative regulatory mechanisms of protein biological activity are discussed from this global view of cell wall proteins.
doi:10.1186/1471-2229-8-94
PMCID: PMC2551616  PMID: 18796151
6.  Evaluation of cell wall preparations for proteomics: a new procedure for purifying cell walls from Arabidopsis hypocotyls 
Plant Methods  2006;2:10.
Background
The ultimate goal of proteomic analysis of a cell compartment should be the exhaustive identification of resident proteins; excluding proteins from other cell compartments. Reaching such a goal closely depends on the reliability of the isolation procedure for the cell compartment of interest. Plant cell walls possess specific difficulties: (i) the lack of a surrounding membrane may result in the loss of cell wall proteins (CWP) during the isolation procedure, (ii) polysaccharide networks of cellulose, hemicelluloses and pectins form potential traps for contaminants such as intracellular proteins. Several reported procedures to isolate cell walls for proteomic analyses led to the isolation of a high proportion (more than 50%) of predicted intracellular proteins. Since isolated cell walls should hold secreted proteins, one can imagine alternative procedures to prepare cell walls containing a lower proportion of contaminant proteins.
Results
The rationales of several published procedures to isolate cell walls for proteomics were analyzed, with regard to the bioinformatic-predicted subcellular localization of the identified proteins. Critical steps were revealed: (i) homogenization in low ionic strength acid buffer to retain CWP, (ii) purification through increasing density cushions, (iii) extensive washes with a low ionic strength acid buffer to retain CWP while removing as many cytosolic proteins as possible, and (iv) absence of detergents. A new procedure was developed to prepare cell walls from etiolated hypocotyls of Arabidopsis thaliana. After salt extraction, a high proportion of proteins predicted to be secreted was released (73%), belonging to the same functional classes as proteins identified using previously described protocols. Finally, removal of intracellular proteins was obtained using detergents, but their amount represented less than 3% in mass of the total protein extract, based on protein quantification.
Conclusion
The new cell wall preparation described in this paper gives the lowest proportion of proteins predicted to be intracellular when compared to available protocols. The application of its principles should lead to a more realistic view of the cell wall proteome, at least for the weakly bound CWP extractable by salts. In addition, it offers a clean cell wall preparation for subsequent extraction of strongly bound CWP.
doi:10.1186/1746-4811-2-10
PMCID: PMC1524762  PMID: 16729891

Results 1-6 (6)