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Afzal M.,National Institute for Biotechnology and Genetic Engineering NIBGE | Khan Q.M.,National Institute for Biotechnology and Genetic Engineering NIBGE | Sessitsch A.,AIT Austrian Institute of Technology
Chemosphere | Year: 2014

Recently, there has been an increased effort to enhance the efficacy of phytoremediation of contaminated environments by exploiting plant-microbe interactions. The combined use of plants and endophytic bacteria is an emerging approach for the clean-up of soil and water polluted with organic compounds. In plant-endophyte partnerships, plants provide the habitat as well as nutrients to their associated endophytic bacteria. In response, endophytic bacteria with appropriate degradation pathways and metabolic activities enhance degradation of organic pollutants, and diminish phytotoxicity and evapotranspiration of organic pollutants. Moreover, endophytic bacteria possessing plant growth-promoting activities enhance the plant's adaptation and growth in soil and water contaminated with organic pollutants. Overall, the application of endophytic bacteria gives new insights into novel protocols to improve phytoremediation efficiency. However, successful application of plant-endophyte partnerships for the clean-up of an environment contaminated with organic compounds depends on the abundance and activity of the degrading endophyte in different plant compartments. Although many endophytic bacteria have the potential to degrade organic pollutants and improve plant growth, their contribution to enhance phytoremediation efficiency is still underestimated. A better knowledge of plant-endophyte interactions could be utilized to increase the remediation of polluted soil environments and to protect the foodstuff by decreasing agrochemical residues in food crops. © 2014 Elsevier Ltd.


Rivera-Gil P.,University of Marburg | Nazarenus M.,University of Marburg | Ashraf S.,University of Marburg | Ashraf S.,National Institute for Biotechnology and Genetic Engineering NIBGE | Parak W.J.,University of Marburg
Small | Year: 2012

The concept of a long-term sensor for ion changes in the lysosome is presented. The sensor is made by layer-by-layer assembly of oppositely charged polyelectrolytes around ion-sensitive fluorophores, in this case for protons. The sensor is spontaneously incorporated by cells and resides over days in the lysosome. Intracellular changes of the concentration of protons upon cellular stimulation with pH-active agents are monitored by read-out of the sensor fluorescence at real time. With help of this sensor concept it is demonstrated that the different agents used (Monensin, Chloroquine, Bafilomycin A1, Amiloride) possessed different kinetics and mechanisms of action in affecting the intracellular pH values. The concept of a long-term sensor for ion changes in the lysosome is presented. The sensor is made by layer-by-layer assembly of oppositely charged polyelectrolytes around ion-sensitive fluorophores, in this case for protons. The sensor is spontaneously incorporated by cells and resides over days in the lysosome. Intracellular changes of the concentration of protons upon cellular stimulation with pH-active agents are monitored by read-out of the sensor fluorescence at real time. With help of this sensor concept it is demonstrated that the different agents used possess different kinetics and mechanisms of action in affecting the intracellular pH values. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Umer M.,International Agency for Research on Cancer IARC | Umer M.,National Institute for Biotechnology and Genetic Engineering NIBGE | Herceg Z.,International Agency for Research on Cancer IARC
Antioxidants and Redox Signaling | Year: 2013

Significance: Methylation of cytosine in DNA is linked with gene regulation, and this has profound implications in development, normal biology, and disease conditions in many eukaryotic organisms. A wide range of methods and approaches exist for its identification, quantification, and mapping within the genome. While the earliest approaches were nonspecific and were at best useful for quantification of total methylated cytosines in the chunk of DNA, this field has seen considerable progress and development over the past decades. Recent Advances: Methods for DNA methylation analysis differ in their coverage and sensitivity, and the method of choice depends on the intended application and desired level of information. Potential results include global methyl cytosine content, degree of methylation at specific loci, or genome-wide methylation maps. Introduction of more advanced approaches to DNA methylation analysis, such as microarray platforms and massively parallel sequencing, has brought us closer to unveiling the whole methylome. Critical Issues: Sensitive quantification of DNA methylation from degraded and minute quantities of DNA and high-throughput DNA methylation mapping of single cells still remain a challenge. Future Directions: Developments in DNA sequencing technologies as well as the methods for identification and mapping of 5-hydroxymethylcytosine are expected to augment our current understanding of epigenomics. Here we present an overview of methodologies available for DNA methylation analysis with special focus on recent developments in genome-wide and high-throughput methods. While the application focus relates to cancer research, the methods are equally relevant to broader issues of epigenetics and redox science in this special forum. Antioxid. Redox Signal. 18, 1972-1986. © 2013, Mary Ann Liebert, Inc.


Rafique B.,Government College University at Faisalabad | Khalid A.M.,University of Sargodha | Akhtar K.,National Institute for Biotechnology and Genetic Engineering NIBGE | Jabbar A.,Government College University at Faisalabad
Biosensors and Bioelectronics | Year: 2013

Electrochemical DNA biosensor was used to study the interaction of methotrexate (MTX) with DNA immobilized on the bare surface of glassy carbon electrode (GCE). The binding mechanism of MTX with DNA was elucidated by using constant current potentiometric technique further supported by UV-Visible and FT-IR studies. The decrease in guanine peak area was used as an analytical signal for the interaction of drug with DNA in acetate buffer solution at pH 4.2 (20% ethanol). The binding constant (K) value calculated for MTX was 3.821×105M-1. UV-Visible studies indicated hyperchromic and hypsochromic shifts in the maximum absorption bands of MTX after interaction with DNA. FT-IR investigations of MTX-DNA interaction revealed significant changes in the characteristic IR absorption bands of all the bases and phosphate groups of DNA. Furthermore, the shift of characteristics bands of C=O, N-H, C-H and O-H groups of MTX endow evidence for the interaction of MTX with DNA supporting the intercalative binding between them. © 2012 Elsevier B.V.


Ahmad N.,Imperial College London | Ahmad N.,National Institute for Biotechnology and Genetic Engineering NIBGE | Michoux F.,Imperial College London | Nixon P.J.,Imperial College London
PLoS ONE | Year: 2012

Chloroplast transformation provides an inexpensive, easily scalable production platform for expression of recombinant proteins in plants. However, this technology has been largely limited to the production of soluble proteins. Here we have tested the ability of tobacco chloroplasts to express a membrane protein, namely plastid terminal oxidase 1 from the green alga Chlamydomonas reinhardtii (Cr-PTOX1), which is predicted to function as a plastoquinol oxidase. A homoplastomic plant containing a codon-optimised version of the nuclear gene encoding PTOX1, driven by the 16S rRNA promoter and 5′UTR of gene 10 from phage T7, was generated using a particle delivery system. Accumulation of Cr-PTOX1 was shown by immunoblotting and expression in an enzymatically active form was confirmed by using chlorophyll fluorescence to measure changes in the redox state of the plastoquinone pool in leaves. Growth of Cr-PTOX1 expressing plants was, however, more sensitive to high light than WT. Overall our results confirm the feasibility of using plastid transformation as a means of expressing foreign membrane proteins in the chloroplast. © 2012 Ahmad et al.


Tahir M.N.,National Institute for Biotechnology and Genetic Engineering NIBGE | Amin I.,National Institute for Biotechnology and Genetic Engineering NIBGE | Briddon R.W.,National Institute for Biotechnology and Genetic Engineering NIBGE | Mansoor S.,National Institute for Biotechnology and Genetic Engineering NIBGE
PLoS ONE | Year: 2011

Cotton leaf curl disease (CLCuD) is a severe disease of cotton that occurs in Africa and Pakistan/northwestern India. The disease is caused by begomoviruses in association with specific betasatellites that differ between Africa and Asia. During survey of symptomatic cotton in Sindh (southern Pakistan) Cotton leaf curl Gezira virus (CLCuGV), the begomovirus associated with CLCuD in Africa, was identified. However, the cognate African betasatellite (Cotton leaf curl Gezira betasatellite) was not found. Instead, two Asian betasatellites, the CLCuD-associated Cotton leaf curl Multan betasatellite (CLCuMB) and Chilli leaf curl betasatellite (ChLCB) were identified. Inoculation of the experimental plant species Nicotiana benthamiana showed that CLCuGV was competent to maintain both CLCuMB and ChLCB. Interestingly, the enations typical of CLCuD were only induced by CLCuGV in the presence of CLCuMB. Also in infections involving both CLCuMB and ChLCB the enations typical of CLCuMB were less evident. This is the first time an African begomovirus has been identified on the Indian sub-continent, highlight the growing threat of begomoviruses and particularly the threat of CLCuD causing viruses to cotton cultivation in the rest of the world. © 2011 Tahir et al.


Khan S.,National Institute for Biotechnology and Genetic Engineering NIBGE | Afzal M.,National Institute for Biotechnology and Genetic Engineering NIBGE | Iqbal S.,National Institute for Biotechnology and Genetic Engineering NIBGE | Khan Q.M.,National Institute for Biotechnology and Genetic Engineering NIBGE
Chemosphere | Year: 2013

Plant-bacteria partnerships have been extensively studied and applied to improve crop yield. In addition to their application in agriculture, a promising field to exploit plant-bacteria partnerships is the remediation of soil and water polluted with hydrocarbons. Application of effective plant-bacteria partnerships for the remediation of hydrocarbons depend mainly on the presence and metabolic activities of plant associated rhizo- and endophytic bacteria possessing specific genes required for the degradation of hydrocarbon pollutants. Plants and their associated bacteria interact with each other whereby plant supplies the bacteria with a special carbon source that stimulates the bacteria to degrade organic contaminants in the soil. In return, plant associated-bacteria can support their host plant to overcome contaminated-induced stress responses, and improve plant growth and development. In addition, plants further get benefits from their associated-bacteria possessing hydrocarbon-degradation potential, leading to enhanced hydrocarbon mineralization and lowering of both phytotoxicity and evapotranspiration of volatile hydrocarbons. A better understanding of plant-bacteria partnerships could be exploited to enhance the remediation of hydrocarbon contaminated soils in conjunction with sustainable production of non-food crops for biomass and biofuel production. © 2012 Elsevier Ltd.


Tariq A.,National Institute for Biotechnology and Genetic Engineering NIBGE
Canadian journal of microbiology | Year: 2012

Bacillary dysentery, common in developing countries, is usually caused by Shigella species. A major problem in shigellosis is the rapid emergence of multidrug-resistant strains. This is the first detailed molecular study on drug resistance of Shigella isolates from the Faisalabad region of Pakistan. Ninety-five Shigella isolates obtained after screening of 2500 stool samples were evaluated for in vitro resistance to commonly used antimicrobial agents; the presence or absence of 20 of the most relevant drug resistance genes; and the prevalence of integrons 1, 2, and 3. Shigella flexneri was found to be the most prevalent and most resistant species. Collectively, high resistance was found towards ampicillin (96.84%), tetracycline (93.68%), streptomycin (77.89%), and chloramphenicol (72.63%). Significant emerging resistance was detected towards the modern frontline drugs ciprofloxacin (12.63%), cefradine (17.89%), ceftriaxone (20.00%), cefoperazone (22.10%), and cefixime (28.42%). Prevalence rates for bla(TEM), bla(CTX-M), gyrA, gyrB, qnrS, aadA1, strAB, tetA, tetB, catA, and catP were 78.94%, 12.63%, 20.00%, 21.05%, 21.05%, 67.36%, 42.10%, 12.63%, 53.68%, 33.68%, and 25.26%, respectively. Class 2 integrons (42.10%) were more common in the local isolates. Simultaneous detection of class 1 and 2 integrons in some isolates and a rapidly emerging resistance to modern frontline drugs are the major findings of this study.


Saeed M.,National Institute for Biotechnology and Genetic Engineering NIBGE
Australasian Plant Disease Notes | Year: 2010

Tomato leaf curl virus (ToLCV) from Australia is a monopartite begomovirus which is naturally associated with a DNA satellite, a vestigial betasatellite. Cotton leaf curl disease is caused by a complex consisting of one or more begomoviruses (eight species have been identified so far) associated with a single DNA β satellite named as Cotton leaf curl Multan betasatellite (CLCuMB). ToLCV and CLCuMB caused mild symptoms in cotton plants 1821 days post-inoculation. The mild symptoms caused by ToLCV and CLCuMB in cotton plants began to diminish 6 weeks post-inoculation and completely disappeared 810 weeks post-inoculation, raising the possibility that ToLCV may lack some factor(s) essential for persistent systemic infection of cotton. © Australasian Plant Pathology ociety 2010.


Ahmad N.,National Institute for Biotechnology and Genetic Engineering NIBGE | Mukhtar Z.,National Institute for Biotechnology and Genetic Engineering NIBGE
Gene Therapy and Molecular Biology | Year: 2013

The soaring costs along with the increasing demand of recombinant proteins in different walks of life have fuelled the quest to find out alternate modes for their production, which are cheaper, safer and can deliver the modern safety standards. In this context, plants are emerging as an alternative production platform for foreign proteins. Chloroplasts - the green plastids with an in-built remarkable capacity to express foreign proteins at high levels - offer several attractive features, which make plants an exceptionally useful system for low-cost production of highvalue targets at large scale. Transformation of chloroplasts, therefore, holds a great potential to meet the challenges in the areas of food, feed and medicine posed by a population on the rise. Numerous developments have been made in the field, all of which set plastids to become a centrepoint of future plant engineering efforts. The present review briefly describes 'the state of the art' of the technology along with its salient features whilst highlighting the latest trends in the area of chloroplast transformation.

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