- Biosecurity, pest and disease, invasion biology, Insect pest modelling
- Large-scale analysis of Next Generation Sequencing (NGS) data, metagenomics and microbial ecology
- Developing biological databases, bioinformatics software/tools and website development
- Antibiotic, biocide and metal resistance; and co- and cross-resistance (co-selection) of antibiotic resistance
- Bacterial virulence and pathogenesis
- Plasmids and other mobile genetic elements (e.g. transposons and integrons), Horizontal gene transfer (HGT)
- Potential role of human microbiome in health and disease
- Fecal microbiota transplant (FMT) and its long-term consequences
- Understanding evolution of prokaryotic genomes
- Understanding of host-parasite interactions using genomic approaches, specifically comparative genomics to identify candidate genes involved in the pathogenesis, understand the evolutionary process in adaptive lifestyle.
- Understanding how individual microorganisms differ or species have diverged; how genes, genomes and gene products have changed over time and the mechanisms in which these changes took place.
Current research work
Project 1. Application of eDNA metabarcoding for rapid screening of exotic mosquotoes and biting midges
Project 2. Developing an effective method for tracing the geographic origin of brown marmorated stink bug (BMSB)
Project 3. Investigation of Rickettsia-like Organisms (RLOs) in New Zealand wild shellfish
Project 4. Investigation of cattle disease caused by Mycoplasma bovis
Project 5. Investigation of Tail fan necrosis in lobster
Project 6. Disease investigation in New Zealand wild bird Kaka.
Project 7. Novel virus detection using Hidden Markov models and k-mer approach
Project 8. Phytophthora hybrid genome sequencing
Project 9. Application of eDNA metabarcoding in marine biosecurity
Project 10. Gut microbiota of Indian trial community
Previous Research work
As part of the Centre for Antibiotic Resistance Research (CARe) at the University of Gothenburg, I was involved in a range of different research projects. My PhD project was primarily funded by the Gothenburg Centre for Sea and Society and Swedish Research Council FORMAS ( 'INTERACT' project) to investigate the contributions of antibacterial biocides (such as disinfectants, antiseptic) and metals (such as copper, zinc) in the selection of antibiotic resistant bacteria using genomic and metagenomic approaches.
Title: Evolution of genes in the tsetse endosymbiont Sodalis glossinidius with a particular focus on pseudogenes in the genome.
Centre for Genomic Research, University of Liverpool, United Kingdom
October 2011-September 2012 (under the supervision of Dr. Alistair Darby)
It is believed that the evolutionary secondary endosymbiotic relationship between bacteria and insect have led to several heterogeneous genomic features. Many non-essential genes are inactivated and their DNA is lost in a stepwise process (e.g indel mutations). In the genome sequence of Sodalis glossinidius, an endosymbiont of tsetse flies (vector of Trypanosomiasis, African sleeping sickness disease) revealed genomic features closer to free-living gammaproteobacteria like E. coli than obligatory symbionts. In a recent study, it was found that approximately one-third of Sodalis CDS-region is inactive (1501 pseudogenes, higher than any other bacterial species) and most of these pseudogenes are homologs of the known proteins that function either in defence or transport or metabolisms in carbohydrates. These pseudogenes originated by multiple frameshift mutations and premature stop codons. Therefore, a complete re-analysis of complete Sodalis genome can reveal novel insights into the evolutionary history of its genes and the clear picture of the roles of the pseudogenes in all CDS-regions of the genome.
The aims of the project:
- Culturing the tsetse endosymbiont bacteria Sodalis glossinidius in vitro with a special focus on growth dynamics.
- Sequencing 2 different bacterial strains of the same species in Illumina high-throughput sequencing platform,
- annotating the produced next generation sequencing genome dataset and assembling the genome through bioinformatics analyses.
- Comparing experimentally sequenced strains of Sodalis to newly sequenced strains from previous works available in the public database and see whether they are same or not.
- Characterising the sequence differences and understanding how the bacterial genome (gene products) has changed over time to draw a clear picture of the evolution of its genome.
- Annotating all pseudogenes in the genome and investigating the role of pseudogenes in the functional part of the genome (all CDS-regions) of Sodalis.
(THE MSc THESIS IS AVAILABLE ON REQUEST)
Title: Investigation of methylglyoxal in New Zealand manuka honeys through HPLC and UV detection.
Auckland University of Technology (AUT), New Zealand (Research was conducted at the Environmental Science and Research Limited (ESR), Christchurch, New Zealand)
April 2011 - July 2011 (under the supervision of Mr. Darren Saunders, ESR and Dr. Michael Edmonds, CPIT)
Naturally-occurring methylglyoxal (MGO) is the aldehyde or ketone form of pyruvic acid which is produced the during the conversion of glucose. MGO is the dominant constituent in Manuka honey that is almost exclusively responsible for its reliable anti-bacterial properties.
The aims of this study were to validate a method to quantify methylglyoxal in a range of New Zealand manuka honey, study on derivatization reaction time and check the stability of derivatization product. These were achieved through the following objectives:
- Validating a method statistically based on the used literature methods.
- After validating the new method in our laboratory conditions, running a trial on few New Zealand manuka honeys to evaluate the proposed validated method and quantify the methylglyoxal level in all of these honey.
- Determining the exact time the derivatization reaction takes.
- Checking the stability of quinoxaline product after derivatization through a short-term study over few days to
weeks in different storage conditions of derivatization product and choose the best condition to allow
derivatization reaction to occur.
Lab technician (molecular-biology):
Project title: Genetic variations in KRT1.2, KRT2.13, B2A (KAP1.1) and other KRTAP (Keratin Associated Proteins) for sheep wool quality determination.
Lincoln University, New Zealand
July 2008-January 2009 (at prof. Jon Hickford's lab)
Gene markers: KRT 2.13 and B2A (KAP1.1), KRT 1.2 etc. of sheep (Ovis sp.) genome.
We are aware that wool has some unique properties (does not burn/melt, can absorb 30% of its weight in water before it feels wet). It is thought that these unique properties and the differences in the wool quality attributes between different breeds and between animals of the same breed (in the same flock) are caused by variation in these genes.
We were trying to determine if genetic variation at these and other keratin genes is associated with trait variation (differences in the wool that we can observe). As a research technician in the FRST-funded research project of Hickford group, I was responsible to do wet-lab experiment part of the project with another senior research technician and report to project supervisor and project leader time to time about research progression. As a technician, I have been asked to perform different wet-lab experiments to meet project supervisor‟s requirements.
- Extracting and purifying DNA from FTA cards (sent to laboratory by farmers) of sheep blood samples and ear tissue samples using phenol-chlorophorm extraction.
- Amplifying extracted DNA samples and standards using PCR with a variety of primer sets designed by Post-doctoral research staff.
- Preparing and running agarose submarine electrophoresis gels for the purpose of checking the quality and size of PCR amplicons and for genotyping.
- SSCP (Single-Stranded Conformational Polymorphism) gel preparation and running, sample analysis and genotyping.
- Data entry and record keeping of each procedure used and obtained results; reporting to the project supervisor and project leader about research progression and results occasionally.
- Ordering necessary chemicals, reagents and equipments for the project as required time to time.
The project work demonstrated the presence of genetic variation in the ovine KRT2.13 promoter region. Nine variant sequences were identified for this gene from 100 animals originating from different sheep breeds that were subjected to PCR-SSCP analysis. The power of SSCP analysis in identifying genetic variation is therefore emphasised in this study. The results revealed that sheep breeds of various utility types (i.e. wool, meat or dual purpose breeds) have considerable variability in the 5′ UTR of ovine KRT2.13. Based on these results we can suggest that KRT2.13 is highly variable and could therefore rightfully be called 'polymorphic'.