M.Sc. Research Experience:
Literature review: Title “Introduction to Reporter Genes”, describing CAT, β-Gal, Lux, Luc, Aequorin, GFP, Urogen reporter genes focusing Lux Operon regulation. Quorum sensing, autoinduction and bioassays associated with it. Envi-ronmental and ecological significance of bioluminescence and bacterial biosensing systems.
Research project: Title “Study of Stress on Luminescent and Metal Resistant Bacteria”. Extensive experimental studies were carried on bioluminescent bacteria focusing on lux operon and luciferase enzyme and metal resistant bacteria. This experimental work was part of Higher Education Commission Research project entitled:” Construction of Multiplex Biosensor for Monitoring Heavy Metal Contaminants in the Polluted Environments of Industrial Effluent” awarded to Dr Uzma Badar.
Name of supervisor: Dr. Uzma Badar (Ph.D).
Name of department & university: Department of Genetics, University of Karachi.
Duration: Literature review Jan’2009-June’2009, Research project July’2009-Dec’2009.
My research was part of Higher Education Commission project, awarded to Dr. Uzma Badar. I was appointed merito-riously on scoring second highest marks in microbial genetics course. Basic aim of one year research course was to introduce potential scientist to research field to practice experimental design. My work was purely related to bacteria and its genetics referring future research related to marker and reporter gene.
Marker and reporter genes are tools for quantization or in situ detection of specific cell populations and/or gene activi-ties in complex samples such as soil or plant material. Marker genes have constitutive promoters while reporter genes have inducible promoter expressing a detectable phenotype. Aseptic techniques were used for isolation. Characteriza-tion of metal resistant and bioluminescent bacteria was done on the basis of cellular and colonial morphology using enriched and minimal media. Maximum tolerance concentrations (MTC) were determined for different metal salts and antibiotics. Effect of temperature, metal salt and antibiotics were observed on bacterial growth. Culture growth and luminescence of bioluminescent bacteria were compared in control and stress medium.
To carry out genetics studies, genomic DNA and plasmid DNA were isolated after culturing isolates in different stress and control medium to examine its effect through agarose gel electrophoresis. Restriction digestion and plasmid DNA transformation was carried out by EcoR1. The marine and industrial waste water carry large amounts of heavy metals enabling bacteria to get adapted to such environment. Therefore, significant difference observed in MTC’s of resistance while cellular and colonial morphology was almost similar. The MTC’s suggested that resistance was probably due to presence of R plasmid or resistance genes on the chromosomal DNA as it had been reported that heavy metal resistance genes are often found on plasmids and transposons. It was observed that plasmid copy number vary among salt treated and untreated cultures. Treatment affect was compared and interpreted as direct relation between luminescent and growth. Treatment was definitely affecting plasmid copy number, hence inducing quorum sensing. Further 16S RNA amplification of luminescent strain was done and sequencing data were submitted.
Concluding the results, I assert that the evolution is adaptation to ambience. Effects of enviromental factors ultimately alter gene regulation, plasmid copy number, gene expression, growth etc. These affects could be lethal or beneficial and reversible or irreversible depending on the balance between interior and exterior of living system such as bacteria in the above mentioned research. For one bacterial strain tested factors were noxious while innocuous to other bacterial specie. It left the question to inspect the differences in the two systems. Through transformation I learned that set of genes can work in similar system depending on the expression prerequisites to have an active output.
• Graduate Record Examination:
GRE molecular medicine: 67 percentile
GRE ETS: Verbal score: 135, Quantitative score: 145
GRE subjective Molecular Medicine: 67 percentile
To seek a challenging position in a dynamic and research oriented environment where I can fully utilize my knowledge and skills to achieve personal & organizational objectives effectively and efficiently, to develop professional skills in my career. Future objective is to research in area of genetics and system biology in order to develop economical therapeu-tics and diagnostics.
• Date of Birth : March 23rd, 1986.
• Place of Birth: Pakistan.
• Marital Status: Single.
• Nationality: Pakistani
EXPERIMENTAL AND TECHNICAL SKILLS:
Genetics / genetics screening skills: Experience of agarose gel electrophoresis, PCR, restriction enzyme digestion for DNA analysis, transformation, transfection, cloning and expression of DNA, DNA isolation and purification by crude me-thod as well as by commercial kits and karyotyping.
Southern blotting, DNA sequencing and microarray technique through on-line lectures and course work are well understood.
Microbiology skills: Advance level experience of aseptic techniques for collection, isolation, purification and preserva-tion of microbial sample (bacteria and fungi) using different enriched and minimal agar media. Examination of cellular and colonial morphology of isolates. Biochemical characterization of isolates. Metal and antibiotic resistance analysis for characterization of microbial isolates. Replica plating and growth curve determination. Streak plate procedure, quantification through colony forming units (CFU) method, dilution plating to quantify and isolate single colonies, Experience of microscopy (worked on bright field, dark field, inverted, upright light microscope) and related staining techniques.
Phage quantification through plaque forming units (PFU), flourescent microscopy and electron microscopy are well understood through on-line lectures and course work lectures.
Other experimental skills: Experience of chromatography, ELISA, spectrophotometery, nanodrop use, luminometer use, flow cytometery and western blotting. Protein isolation from bacteria and other cell type using ultra sonicator. And study of extracted and isolated proteins in different buffer systems to analyze its structural and functional characteris-tics. Command on SDS-PAGE.
There are other techniques which are well understood for example cell culturing, slide preparation for histology using microscopy and NMR through on-line lectures and course work.
Language skills: Fluent English and Urdu
PARTICIPATION IN SYMPOSIA:
• Poster presentation: Participated in 12th International Symposium on Natural Product Chemistry. Title of poster, “Characterization of Luminescent Bacterial Strain Isolated from Karachi Coastal Area, Clifton”.
• Poster presentation: 14TH ASIAN SYMPOSIUM ON MEDICINAL PLANTS,SPICES AND OTHER NATURAL PRODUCTS (ASOMPS-XIV). Title: “Cloning, Expression, Purification and Structural Studiesof MRSA252 trxA gene”.
• Poster presentation: MMDR-5 Conference, poster title “Cloning, Expression, Purification and Structural Stu-dies of MRSA252 rsbV Gene”.
• Oral presentation: Participated in 10th Biennial Conference of Pakistan Society for Biochemistry and Molecu-lar Biology, “Biomolecular Sciences in Development”. Title of oral presentation, “Characterization of Lumines-cent Bacterial Strain Isolated from Karachi Coastal Area, Clifton”.
• 3rd International Symposium-cum-Training Course on Molecular Medicine and Drug Research.
• Participation in “Press conference / Launch of ISAAA Brief 42 and One Day Seminar on Application of Modern Biotechnology” held on 21st May, 2011 organized by the Pakistan Biotechnology Information Center.
• 3rd Prize in Poster Competition: MMDR-5 Conference, poster title “Cloning, Expression, Purification and Structural Studies of MRSA252 rsbV Gene”.
• 2nd Prize in Poster Competition: 14TH ASIAN SYMPOSIUM ON MEDICINAL PLANTS,SPICES AND OTHER NATURAL PRODUCTS (ASOMPS-XIV). Title: “Cloning, Expression, Purification and Structural Studiesof MRSA252 trxA gene”.
• Award of Scholarship: ” Mitsubishi Corporation International Scholarship” 2008. On August 25, 2009 scholarship cheque was distributed. An official letter is uploaded.
• Research Accomplishments: “Screening and Characterization of Luminescent Bacterial Strain.“ Uzma Ba-dar1,*, Erum Shoeb1, Komal Daredia1, Durr-e-Shawar1, Jameela Akhtar2 and Maqsood A. Ansari1. 1Department of Genetics University of Karachi, 75270-Karachi, Pakistan. 2Centre for Molecular Genetics University of Karachi, 75270-Karachi. Pakistan Journal of Basic & Applied Sciences, 2012, 8, 602-606.