National Institute for Biotechnology and Genetic Engineering NIBGE

Faisalabad, Pakistan

National Institute for Biotechnology and Genetic Engineering NIBGE

Faisalabad, Pakistan
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Zaidi S.S.E.A.,National Institute for Biotechnology and Genetic Engineering NIBGE | Mahfouz M.M.,King Abdullah University of Science and Technology | Mansoor S.,National Institute for Biotechnology and Genetic Engineering NIBGE
Trends in Plant Science | Year: 2017

Clustered regularly interspaced palindromic repeats (CRISPR)-CRISPR-associated proteins (CRISPR-Cas), a groundbreaking genome-engineering tool, has facilitated targeted trait improvement in plants. Recently, CRISPR-CRISPR from Prevotella and Francisella 1 (Cpf1) has emerged as a new tool for efficient genome editing, including DNA-free editing in plants, with higher efficiency, specificity, and potentially wider applications than CRISPR-Cas9. © 2017 Elsevier Ltd.


Shan-E-Ali Zaidi S.,National Institute for Biotechnology and Genetic Engineering NIBGE | Mansoor S.,National Institute for Biotechnology and Genetic Engineering NIBGE
Frontiers in Plant Science | Year: 2017

Recent advances in genome engineering (GE) has made it possible to precisely alter DNA sequences in plant cells, providing specifically engineered plants with traits of interest. Gene targeting efficiency depends on the delivery-method of both sequence-specific nucleases and repair templates, to plant cells. Typically, this is achieved using Agrobacterium mediated transformation or particle bombardment, both of which transform only a subset of cells in treated tissues. The alternate in planta approaches, stably integrating nuclease-encoding cassettes and repair templates into the plant genome, are time consuming, expensive and require extra regulations. More efficient GE reagents delivery methods are clearly needed if GE is to become routine, especially in economically important crops that are difficult to transform. Recently, autonomously replicating virus-based vectors have been demonstrated as efficient means of delivering GE reagents in plants. Both DNA viruses (Bean yellow dwarf virus, Wheat dwarf virus and Cabbage leaf curl virus) and RNA virus (Tobacco rattle virus) have demonstrated efficient gene targeting frequencies in model plants (Nicotiana benthamiana) and crops (potato, tomato, rice, and wheat). Here we discuss the recent advances using viral vectors for plant genome engineering, the current limitations and future directions. © 2017 Zaidi and Mansoor.


Ahmad N.,National Institute for Biotechnology and Genetic Engineering NIBGE | Mukhtar Z.,National Institute for Biotechnology and Genetic Engineering NIBGE
Genomics | Year: 2017

An alarming increase in the human population necessitates doubling the world food production in the next few decades. Although a number of possible biotechnological measures are under consideration, central to these efforts is the development of transgenic crops to produce more food, and the traits with which plants could better adapt to adverse environmental conditions in a changing climate. The emergence of new tools for the introduction of foreign genes into plants has increased both our knowledge and the capacity to develop transgenic plants. In addition, a better understanding of genetic modifications has allowed us to study the impact that genetically modified crop plants may have on the environment. This article discusses different techniques routinely used to carry out genetic modifications in plants while highlighting challenges with them, which future research must address to increase acceptance of GM crops for meeting food security challenges effectively. © 2017 Elsevier Inc.


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.


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.

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