Today I am going to tell you the story about the superpower of bioinformaticians in the research world!

Once upon a time………. NO! not all stories are starting with this line. 

 

 

 

 

 

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So, before I start my storytelling mode, I’d like to give a quick introduction about myself and my host institution in the Netherlands. My official name is Kah Yen, but people call me Claire in Europe, my family calls me Yan Yan or some others call me 家欣 (Jia Xin). This is because I come from a multinational and multilingual country – MALAYSIA, where a lot of people have more than two names :P. I have resided 3 years in Bonn, Germany for my BSc. in Applied Biology and 2 years in Göttingen, Germany for my MSc. in Microbiology and Biochemistry. Now, I have just moved to the Netherlands for my P.h.D and I am glad that I am on board with 12 other P.h.D students in the Boeing 017-020 PATHSENSE! Together, we work for the ambitious pathogen sensing research project.

My host institution is NIZO, a contract-based research company located in Ede, the Netherlands. For more information about the company read more… Despite the weather, I must say that there is no more complain in this country! Friendly colleagues and nice working environments 🙂

 

In my Ph.D. project, the main goal is to investigate how Bacteria (to be specific the big Bacillus family) can sense and adapt to the changes in environments. In decades of research, scientists have found out many key players that assist the bacteria to overcome environmental stresses (no food, high pressure, extreme temperature etc.) and help them to survive in these harsh conditions.  However, no one knows how they actually detect the alarming signals when they encounter stresses in their surroundings and how they integrate those signals into their cells. They have perhaps receptors like the human, but how does it work exactly? What about the mechanism behind? 

In order to find out how bacteria can adapt to environmental changes rapidly, we have to do a post-mortem and examine them at the DNA level. This is because DNA in cells carries the genetic instructions to command cells to grow, to develop and to function properly. DNA will make RNA in the process known as transcription, and RNA will make proteins in the subsequent process – translation. Each of the protein is made to carry out a distinct role in the cells, thus, we can compare the type of proteins that are produced when cells are under stress, therefrom, understand how certain proteins function to help the bacteria to sense and to integrate signals in harsh surroundings. NOW! LETS GETS BACKS TO THE STORY.

So, how do we compare the occurrence of a specific gene/protein or similar proteins (homologous proteins) in different bacteria? For instance in the Bacillus family and their close relative: Geobacillus. The answer is ………………………………………………………to do an in silico (in computer) comparison with the advanced and combined bioinformatic tools. In this case, we will make use of all the genome and proteome databases on the internet, and combined all of them to reconstruct a phylogenetic tree. The advantage is that we can directly analyze our genes/proteins of interest in a large number of organisms. The generated phylogenetic tree will consist of two axes. The Y-axis will show the phylogenetic relationships between different microorganisms (could be bacteria from different genus or in the same genus) and the X-axis will show the presence or absence of genes of interest.The final phylogenetic tree thus gives a glance of all the genes/proteins that found in different bacteria species. Therefore, one could easily identify and analyze the most interesting genes/proteins, and design experiments accordingly. With the NIZO- developed program, one does not need to go to different databases and check the information one by one, for example, BLAST, reconstruct orthology group (explanation of orthology), find relevant orthology groups, create reference genome sets….. etc.  Bioinformatician can perform almost all of the procedures by simple commands, and whenever something goes wrong, a window will pop up and notify you the errors that you have to fix in order to continue the analysis. Each new click on the ” enter” represents one new experiment for a bioinformatician, this is a huge difference when compared to real-life experiments in the lab, in which, a single experiment could take up weeks or months or even years. The automated program can thus be a lot more time efficient and this marks the crucial role (the superpower) of bioinformaticians in research today. Especially in large datasets analysis, multiple sequence alignment, and others. 

In the first deliverable of my project, I perform genome mining on more than 100 Bacillus and Geobacillus strains that were isolated either from food products or from extreme environments during food production process (e.g vacuum, high temperature). I am fortunate to be able to work on this analysis with the NIZO-developed bioinformatic tools together with a senior bioinformatician Jos Boekhorst at NIZO. Now, the Y-axis of the phylogenetic tree of the Bacillus genus has been successfully reconstructed and the next step is to identify the most-similar organism, define clades with desire function (X- axis) and look at the presence or absence of impact genes.  In this project, the gene of interests are genes that play a role in the general stress response in Bacillus species including B. subtilis, B. cereus, B. licheniformis, B. vallimortis, B. amyloliquefaciens and more…. Following the final analysis, we will design specific experiments to further examine the impact genes and hopefully, we will obtain further insight into the sensory and signaling mechanisms that function in the genus Bacillus, as well as to better understand the evolution of stress response in bacteria.

 

Further information on this project will be updated in the next post. 

 

” KEEP CHANCES BY KEEP TRYING”

—–Claire 

 

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Kah Yen Claire Yeak
PhD student


T: +31 318 659 639

F: +31 318 650 400

E: 
KahYen.Yeak@nizo.com

P.O. Box 20, 6710 BA EDE, The Netherlands

Kernhemseweg 2, 6718 ZB EDE, The Netherlands
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