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Dr Shajahan Anver
Research Associate
Genetics, Evolution & Environment
Div of Biosciences
- Joined UCL
- 1st Apr 2016
Research summary
More than 80% of the genomes of many organisms are transcribed whereas only 2% comprises of protein coding transcripts. Some of the transcribed non-coding RNAs may be mere biological noise whereas some were shown to be biologically important. Since many basic biological pathways are well conserved from yeast to human it is convenient to use a simple unicellular model system such as Schizosaccharomyces pombe to answer complex biological questions. We take omics based approaches to identify intergenic long non-coding RNA (lincRNA) candidates with potential biological significance. Many lncRNAs are differentially expressed under special conditions, especially during chronological ageing in S. pombe. I am particularly interested in the Influence of lincRNA on cellular ageing. I identified a couple of lincRNAs with potential biological significance during ageing and currently functionally characterizing them.
On the side, I am also interested in the eco-bio question:
How do yeasts/ single celled organisms live so long in the wild? Do nutrient deficiencies affect complete communities or some members sacrifice (to generate "the" signal) for the survival of the community? How do the microorganisms like it? Shaken vigorously like we do in laboratories? Is this a good system to assess cellular longevity? Is it advantageous to grow and divide faster? May be! If you are a pathogen, then you would like to infect, find the nutrient sources, grow faster. and colonise faster If you are a saprophyte, is that the same? Don't you settle/survive and wait for the next wave, at least few cells of the colony at the expense of others? We hope to find "the" above signal if there is one!
Teaching summary
Teaching in life sciences at the university level comes in different flavours! It involves both lecturing, laboratory demonstrations (lectures and practicals) and research mentoring in the laboratory. It also may involve working with general public and young school age children. I enjoyed and gained valuable experience in all forms of these teaching in different institutions. Although, my journey as a teacher started as a young kid with my peers, I chose to start the story after my graduation with a BSc degree in 2002.
LECTURING / CURRICULUM DESIGN / and the sort
Soon after graduation I joined the staff of the Department of Biology of the University of Peradeniya (UoP) as a temporary assistant lecturer (April 2002 - October 2003) and in October 2003 I was appointed as a lecturer (probationary). There I taught and coordinated courses in Plant physiology. Environmental Physiology, Post-harvest Biology and Scientific Writing. The responsibilities involved designing (or upgrading and restructuring) the course, planning and delivering lectures and practical sessions, and evaluating students. The mandatory certificate course in Teaching Methodologies by the UoP was very instrumental in gaining the required knowledge, confidence, and hands-on experiences to accomplish these tasks successfully along with valuable mentoring from Profs. D.C. Bandara and J.M.R.S. Bandara. A major curriculum revision in undergraduate education funded by World Bank (IRQUE) happened during this time. The aim was to restructure the BSc Agriculture curriculum of the UoP to suit the changing needs of the century. I played an active role in evaluating courses, designing new courses, or restructuring the existing ones for the Department of Biology under this project. During my MS and PhD at UC Davis (2007-2013) I worked as a Teaching Assistant (TA) for Profs. J.J. Harada and S.L. Harmer to teach Molecular Biology courses for senior undergraduates (3rd year undergraduates and graduate [MS/PhD] students). The responsibilities involved preparing and leading discussion classes, holding office hours to help students and assess student evaluations.
MENTORING in research
At UoP I also supervised final year undergraduate students’ thesis research. In the Harmer laboratory at UC Davis, I mentored several senior undergraduates and a high school student. During my time as a postdoctoral researcher at Max Plant Institute I mentored a PhD student (Germany) and two Erasmus senior undergraduate students from Poland. I mentored several undergraduate students and a MS student at UCL in the Bahler lab as well.
Other Mentoring and Public Engagement
During my time as a PhD student at UC Davis and later I served as a mentor and a mentor liaison in the Planting Science Program (https://plantingscience.org/), an online mentoring program that works with teachers and students in selected public schools in USA to mentor and encourage students into science. At UCL, I also mentored several school students under the In2ScienceUK (https://in2scienceuk.org/) program which aims to promote social mobility and diversity in STEM.
Education
- Other Postgraduate qualification (including professional), ATQ10 - Overseas accreditation or qualification for any level of teaching |
- University of California, Davis
- Doctorate, Doctorat | 2013
- University of California, Davis
- Other higher degree, Master of Science | 2009
- University of Peradeniya
- Other higher degree, Master of Science | 2005
- University of Peradeniya
- First Degree, Bachelor of Science | 2002
Biography
During my BSc I developed a greater interest in genetics and microbiology along with biotechnology. This drove me to pursue MS and PhD in molecular biology. My PhD training exposed me to the wonderful world of omics and bioinformatics. I learnt to appreciate the power of omics approaches to answer some basic questions that the living systems put forward. Now, I strongly believe omics approacahes could be wisely used to decode the complex language of life along with the associated data analyses tools.
During my PhD at UC Davis, I used both Arabidopsis thaliana and Schizosaccharomyces pombe model systems to functionally characterize a functionally unknown protein initially identified in a screen designed to capture mutants with defects in the plant circadian rhythms. We took genome-wide genetic, transcriptomic, and proteomic approaches along with other basic physiological experiments in both model systems to show that X-chromosome associated protein 5 (Xap5) binds chromatin and repress cryptic transcripts including transposable elements and long terminal repeats.
Soon after my PhD, I joined Max Plank Institute for Plant Breeding Research as a MaxPlank Research Fellow. There, I explored conservation and diversification of innatee immune system in Brassicaceae using omics approaches. We took transcriptomics, hormonomics, and biochemical approaches along with other basic physiology to answer the question. Comparative genomics analysis of available genome sequences of different Brassicaceae species revealed interesting phylogenetic relationships among prominent defence-associated genes compared to A. thaliana genome. Some genes are highly conserved at sequence level whereas some gene sequences have evolved considerably to include new motifs(?). Genes with paralogous partners in Arabidopsis have lost them in some other species. On the contrary, some genes have acquired paralogs due to whole genome duplications in certain other species. These are all interesting changes at the sequence level. However, are these orthologs transcriptionally regulated similarly upon pathogen challenge? Our time-course RNAseq at different times after challenging with flg22 suggests: some modules are conserved and yet some are not at transcriptional level. The transcriptional landscapes during PTI is interestingly very different in different Brassicaceae species tested.
Going back to work with fission yeast! Use omics in S. pombe to answer interesting biological questions! Joined Jürg Bähler group at UCL in 2016 as a Research Associate. Yet another question to find answers with omics approaches! More than 80% of the genomes of many organisms are transcribed whereas only 2% comprises of protein coding transcripts. Many of these are long non-coding RNAs (lncRNAs). Many lncRNAs are differentially expressed especially during ageing and cancers. What is their biological significance? We tried to answer some of these questions as stated in Research Summary.