Work History

Work History
Jul 2010 - Present

Research associate

Texas Tech University-HSC
Pseudomonas aeruginosa is an opportunist bacterial pathogen causing both chronic and systemic infections in immune-compromised patients. P. aeruginosa develop biofilm at various infection sites including burn-wound and lungs of cystic fibrosis patients which are very resistant to antibiotics. Biofilms occasionally occur on clinical instruments and catheters which pose a big challenge in the treatment of infections in the clinical environments. I am working on the investigation of mechanism, structure and formation of biofilm along with the therapies to eradicate them. P. aeruginosa causes systemic infections by release of various virulence factors including toxins, pyocyanin and siderophores in the external environment and by excreting quorum sensing molecules which regulate these virulence factors. The aim of this NIH funded research is to understand the mechanism of quorum sensing and bacterial virulence in vivo using burn mouse model and to find methods or therapies to eliminate the infections caused by P. aeruginosa in particular. Alzheimer's is an old age disease caused in humans involving neural degeneration and gradual memory loss. There are no known therapies for this disease partly due to the narrow research focus. In order to understand this complex disease in broader spectrum, we employed the global gene expression profiling technique to compare brain microvessel samples of diseased and normal human beings. For this study, I provided my skill to Garrison institute of aging, Texas Tech University Health Science Center, Lubbock, TX. in checking integrity of RNA, cDNA synthesis, labeling of cDNA, hybridization, Scanning, data acquisition and microarray data analysis. Moreover I did pathway analysis and gene regulation analysis of the differentially expressed genes in Alzheimer's Disease microvessel.
Jul 2008 - Jul 2010

Post-doctoral research associate

Texas Tech University

Worked as a lab menager in cotton functional genomics core facility which provides microarray processing and data analysis services to the Texas Tech University and health science centre. During my stay in this lab I worked on following two different projects with the common goal of improvement of cotton fiber quality and yield through genetic engineering.

1. Development of high throughput method for screening of a wide variety of cultivars of cotton on the basis of resistance to verticillium wilt, a disease caused by Verticillium dahliae and to investigate the molecular mechanism involved in resistance.

2. Investigation of suberin biosynthetic pathway in green fiber mutant of cotton to better understand the mechanism of suberin biosynthesis and using microarrays studies associate the novel genes to this pathway. This research is not only helpful in understanding basic science behind suberine biosyntesis but has advanced applications in Cotton fiber quality improvement.

Dec 2007 - Jul 2008

Research associate

University of Arizona

Worked on heterologous CGH microarray to investigate the homology between Gossypium arboreum and model organisms of Arabidopsis thaliana and Oryza sativa genomes. Developed a method for labeling the genomic DNA using T7 RNA plymerase and used custom oligo microarray platforms and optimized hybridization, scanning, and data analysis for above study. This study culminated in the functional characterization of Gossypium arboreum genome.

Education

Education

Skills

Skills

Protein profiling

Isolation of bacterial proteins and analysis using bioanalyzer (Agilent) to compare protein profiles of multiple samples under study.

DNA binding experiments

Training and experience of working with radioactivity in order to label probe to study the binding of a specific protein to the promoter of an operon or a gene

Animal experiments

Experience and training for working with burn mouse model to study virulence and systemic spread in various strains of P. aeruginosa.

Thin Layer Chromatography (TLC)

Silica gel thin layer chromatography to analyse various molecules eg PQS and paerucumarin in the bacterial cultures.

Scanning Electron Microscopy

Scanning electron microscopy of bacterial biofilms formed on plastic cover slips.

Confocal Laser Scanning Electron Microscopy

Confocal :aser Scanning Electron Microscopy of bacterial biofilm along with the image processing tools and quantification using comstat, metamorph or flouview.

bio-chemical analysis

Measurment of chlorophyll, nitrate reductase activity and epi-cuticular wax.

Verticillium dahliae detection assay in cotton

Verticillium dahliae is a soil born fungus causing verticillium wilt in over 200 plant species including cotton. A sensitive method was developed for the detection of pathogen in the plant before the symptoms appear and this method was used for the selection of Verticillium wilt resistant cultivars.

Bioinformatics

I have been working on GO ontology, pathway analysis, clustering and phylogeny. Moreover have worked with earray, genomic workbench, genespring, bioconductor, perl, limma, blast2go , mapman, ingenuity and other bioinformatics tools. 

Genome walker

Making of DNA libraries and Genome walking to identify and sequence promoter regions of various genes.

Gene Cloning

Gene cloning for making constructs, bacterial transformations and working with bacterial cultures.

RACE PCR

Using Rapid Amplification of cDNA Ends (RACE) identified and sequenced novel full length genes in Cotton. Making of cDNA libraries and screening them by PCR for the selection of specific clones.

CGH microarrays

Comparative genome hybridization (CGH) microarrays wity Both single and Double Channel experiments comparing wild type with the mutant to investigate the genetic basis of mutation and locate the mutation in the genome. Analysis of CGH data analysis using genomic workbench (Agilent).

Expression Microarrays

worked with both custom printed oligo arrays and agilent platforms for human, mouse, arabidopsis, rice and cotton arrays. Microarray chip designing, RNA extraction, dye incorporation, hybridization, scanning, feature extraction and data analysis is my strength.

Expression analysis by Real Time PCR

Absolute and relative Quantification of DNA and RNA in complex studies. Developed a sensitive, realtime PCR-based diagnostic method for the detection and quantification of a fungal pathogen in infected cotton with the potential use of selecting the resistant breeding lines. 

EST's Reported

Gossypium arboreum (cotton) cDNA libraries were constructed and sequenced. 1411 novel  Expressed Sequence Tags (ESTs) were identified and deposited to the NCBI genbank. The IDs of these ESTs range from cembMI0001-cembMI1401 and cembu01-cembu11.

Membership of Scientific Societies

1. International Cotton genome Initiative (ICGI) society since January 2009.

2. Editorial board of Pure and Applied Biology (PAB) journal.

Abstracts and Poster presentations

Uzma Qaisar, Terry Wheeler and Thea A. Wilkins. 2009. Approach to Identify Sources of Verticillium-resistance in Cotton. Beltwide cotton conference 2009. San antonio, TX.

Thea Wilkins, Ingrid E. Lindquist. Uzma Qaisar, Arvind K. Bharti, Terry Wheeler, Gregory D. May and Joann Mudge. 2010. Early Molecular Events in Conferring Resistance to Verticillium Wilt Disease in Pima Cotton Revealed by Next-Generation Sequencing. Beltwide cotton conference.

Thea A Wilkins , Ingrid E Lindquist , Uzma Qaisar , Arvind K Bharti , Terry Wheeler , Gregory D May and Joann Mudge. 2010. Early Molecular Events In Resistance To Verticillium Wilt Disease Revealed By Solexa Transcriptomics In Pima Cotton. Plant & Animal Genomes XVIII Conference. San Diego, CA.January 9-13, 2010

Trainings and Workshops

1. Advance bioinformatics training held by Agilent. 2009 in Houston, TX

2. International Microarray Workshop 2008, Tucson, Arizona

3. Training on methods ofteaching of science in class room environment. Allama Iqbal Open University, Islamabad, Pakistan.

4. Data entry and basic computer skills Training, University of COMSATS, Ministry of Science and Technology, Govt of Pakistan.

Full Length Gene Sequences Reproted

1. Qaisar,U., Majeed,A., Husnain,T. and Riazuddin,S. 2008. Gossypium arboreum plastid fructose 1,6 bisphosphate aldolase (Aldp) gene, complete cds; nuclear gene for plastid product. gi|166203460|gb|EU107768.1|[166203460]

2. Qaisar,U., Majeed,A., Husnain,T. and Riazuddin,S. 2007. Gossypium arboreum plastid fructose 1,6 bisphosphate aldolase class 1 (ALDP) mRNA, complete cds; nuclear gene for plastid product. gi|126571483|gb|EF105116.1|[126571483]

Publications (Articles and books)

1.  Uzma Qaisar, Shu Wang, Xiangling Yin, Paula Grammas. 2012. Gene Expression Profiling in Microvessels Isolated from Human Alzheimer’s disease Brains. JAD. 31(1):193-205 Impact Factor 3.745

2.  Uzma Qaisar. 2012. Drought Tolerance. Lambert Academic Publishing AG & Co. KG. ISBN-13: 9783848404636 (http://www.barnesandnoble.com/w/drought-tolerance-uzma-qaisar/1108828331?ean=9783848404636)

3.  Uzma Qaisar, Liming Luo and Abdul Hamood. 2012. Regulation of cup fimbriae by pvc operon in Pseudomonas aeruginosa. Submitted to Molecular Microbiology journal. Impact factor 5.01

4.  Uzma Qaisar, Muhammad Irfan, Asma Meqbool, Muzna Zahoor, Muhammad Younas Khan, Bushra Rashid, Sheikh Riazuddin, and Tayyab Husnain. 2010. Identification, sequencing and characterization of a stress induced homologue of fructose bisphosphate aldolase from cotton. Can. J Plant Sci. 90 (1), 41-48. Impact factor 0.613

5.  Roger A. Barthelson. Uzma Qaisar and David W. Galbraith. 2009. Functional Analysis of the Gossypium arboreum Genome. Plant Mol Biol Rep. DOI 10.1007/s11105-009-0157-5 Impact factor 2.453

6.    Muzna Zahur, Asma Maqbool, Muhammad Irfan, Muhammad Younas Khan Barozai, Uzma Qaisar, Bushra Rashid, Tayyab Husnain and Shiekh Riazuddin. 2009. Functional analysis of cotton small heat shock protein promoter region in response to abiotic stresses in tobacco using Agrobacterium-mediated transient assay. Mol Biol Rep 36:1915–1921. Impact factor 2.929

7.    Muhammad Younas Khan Barozai, Muhammad Irfan, Rizwan Yousaf, Imran Ali , Uzma Qaisar, Asma Maqbool, Muzna Zahoor, Bushra Rashid, Tayyab Hussnain and Sheikh Riazuddin. 2008. Identification of micro-RNAs in cotton. Plant Physi and Biochem. 46:739-751 Impact factor 3.023

8.    Asma Maqbool, Muzna Zahur, Muhammad Irfan, Uzma Qaisar, Bushra Rashid, Tayyab Husnain and Shiekh Riazuddin. 2007. Identification,Characterization and Expression of Drought Related alpha-Crystalline Heat Shock Protein Gene (GHSP26)from Desi Cotton. Crop Sci 47:2437-2444. Impact factor 1.641

MANUSCRIPT REVIEW

    Articles reviewed for the following peer review journals

1. Molecular Biology Reports

2. African Journal of Biotechnology

3. Pure and applied biology journalhttps