My name is Danang Crysnanto and I am now pursuing master’s study in quantitative genetics and genome analysis (QGGA) at the University of Edinburgh. You can view my complete CV here.

I am generally interested in dissecting information from genome for elucidating immune system, host-pathogen interactions and lately I also found my interest in the quantitative genetics for livestock genetic improvement. Well, field of genomic is full of new things to explore.

In the area of research, I have strong interest in quantitative genetics  and bioinformatics particularly its application on comprehending the pathogen and host co-evolution as well as on how selection shapes the genomic profile of the organism. To achieve this, I am keen to apply computational approach coupled with the laboratory works. I believe that narrowed gap between both approach will enhance the discovery and better reveal the life sciences phenomenon, reflected the famous quote “mathematics is the next microscope of biology” (Cohen, 2004).

My prospective research for master’s study is about RNAi pathway duplication in Drosophila. Immune system has been proved to evolve faster than other gene due to arm-race with pathogen. For example, Argounate has been duplicated several times in Drosophila psudoobscura but still retains ancestral state in Drosophila melanogaster. Interestingly, other’s immune genes such as Teja, Vret also duplicated in the former species. I will test whether the timing of gene duplication is consistent each other and also to test the gene expression specificity. The hypothesis explaining of gene duplication is that usually the recent gene duplication is evolved in testis, and then undergo rapid evolution and evolve to a new function (neofunctionalization). This termed as a ‘out of testis’ hypothesis and the evidences remain inconsistent. If the timing of duplication is similar probably the RNAi-related gene duplication evolve to a new unknown RNAi pathway (for function other than antiviral such as TE suppresion) that missed because of research mostly focus on Drosophila melanogaster. I will work with Dr Darren Obbard in Institute of Evolutionary Biology (IEB) at Asworth Lab, University of Edinburgh.

These are several research I have done in the past:

  1. Application of RNA interference in aquatic ecosystem

RNA interference technology offers innovative way to silence the particular gene of interest and potentially is able to be used for overcoming the problem in aquaculture. My research with Dr. Adi Pancoro in Genetic’s Group SITH ITB (Institut Teknologi Bandung) emphasizes the usage of RNA interefence for accelerating the reproduction cycle in Indonesia native shrimp (Penaeus monodon) by silencing the expression of Gonad Inhibiting Hormone. In order to improve the delivery efficiency of RNAi, we try to implement nanotechnology  by encapsulating the dsRNA (RNAi inducer) inside of the chitosan nanoparticle. We also look for the opportunity of technology to be implemented in tackling never-ending shrimp viral disease particularly Whitespot virus.


2. Regional Genetic Diversification and Genomic Profile  of IMN (Infectious Myonecrosis) Virus

This research was completely done computationally using available sequence data of IMN Virus in Gene Bank. IMN Virus is a type of dsRNA virus attacking shrimp with genome size approximately 8000 bp. I compared the virus phylogenetically by employing Bayesian approach. Based on the result, It has been predicted, that IMN virus in Indonesia and Brazil underwent regional genetic diversification from its unknown earliest sources. Although the genome was only in order of thousands, I was impressed with the IMN Virus genomic organisation which is able enhance the gene density, such as overlapping ORF and ribosomal frameshifting. This work was collaboration with Dr. Sidrotun Naim (Surya University, Indonesia).

Genomic structure of IMN Virus

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