For many undergraduates, getting their names on an academic paper is only the stuff of dreams.
But for a certain outstanding group of students from the School of Biological Sciences (SBS), the dream has become a reality. Working under Assistant Professor Marek Mutwil, a group of 23 students have built and launched a new informational resource, www.fungi.guru, for the purpose of studying and collating information based on gene expression and gene function in the fungi kingdom.
Assistant Professor Marek Mutwil helmed the www.fungi.guru project, hoping to expand the resources available to fungi researchers.
The bioinformatics project, the results of which were compiled and published in a paper in Computational and Structural Biotechnology, was conceived by Asst Prof Mutwil with the initial goal of rectifying an ongoing problem in the scientific community – the fact that there were no existing centralized resources to study gene expression in fungi.
But as the project began, the goals expanded with it.
Typically, high-level research activities have remained the domain of postgraduates and postdoctoral researchers. And so for Asst Prof Mutwil, the project also turned into an informal pedagogical experiment.
“I wanted to see how undergraduate students would do when exposed to a real scientific project, comprising data collection, analysis, paper writing, and publication,” he explained.
To do this, Asst Prof Mutwil raised the idea of a new project to the students of his introductory computational thinking course BS1009, offering up the opportunity of a post-semester internship – an idea that proved to be very popular.
23 students were ultimately selected to join the team. One of them, Lim Jia Jia, Jolyn, a second year Biological Sciences student (with a Second Major in Medicinal Chemistry and Pharmacology), was especially enthusiastic about embarking an “exciting learning opportunity”.
One of the 23 students involved in the project, Lim Jia Jia, Jolyn, was especially enthusiastic about embarking an “exciting learning opportunity”.
“I think being able to extract and interpret from large amounts of data is an extremely important and exciting skill to have,” Jolyn said. “Furthermore, mycology holds a huge potential in deriving key insights in biotechnology, drug discovery, and much more.”
For Erielle Villanueva, who is another member of the team and also a second-year Biological Sciences student, wanting to join the project was only par for the course in pursuing her passion for science.
“Biology has always been my favourite subject,” Erielle said. “I was excited by the prospect of finding something new and potentially beneficial to society.
And indeed, both Jolyn and Erielle have managed it.
For all that fungi are most well-known for the role as decomposers in Earth’s ecosystems, they are also highly essential sources of industrial enzymes, and more importantly, antibiotics. Penicillin, for example, is derived from the fungal mold Penicillium notatum.
But as it is, knowledge and research on fungi-related genomics has been relatively scarce, in comparison with other research subjects, which is where the project has come in.
Over the course of two months, with Asst Prof Mutwil’s guidance and with help of the Mutwil Lab members Dr. Irene Julca, Dr. Riccardo Delli-Ponti and PhD student Ng Jonathan Wei Xiong, the students worked to gather genomic and gene expression data of the 19 most-widely researched fungi, information that was then used to build www.fungi.guru.
“Our online database will allow for biologists with no bioinformatics background to make complex analyses,” Asst Prof Mutwil said. “We hope that it will become a go-to place for fungal researchers.”
The database contains tools for cross-species identification of conserved pathways, functional gene modules, and gene families. With the use of such tools, it becomes possible to identify yet unknown biosynthetic pathways more easily – in a more specific instance, the database can even identify which genes can produce a metabolite with potentially antibiotic properties and provide information on how such fungi can be treated to enhance the production of said metabolite.
Of course, what makes the project’s success all the more impressive are the circumstances behind it. Working mostly from home and with virtually no face-to-face contact, seminars and “lab” sessions were held over Zoom, with almost all communications taking place over WhatsApp.
The project was conducted virtually, for the most part, with seminars and “lab” sessions held over Zoom, and communications facilitated by WhatsApp.
“It went very smoothly, despite everything,” Asst Prof Mutwil said. “We managed to go from raw data to a publication-ready manuscript in two months, which is not a small feat for even an experienced research group.”
Nevertheless, the project had its setbacks. None of the students on the team, all of whom were only undergraduates, had ever been involved in a high-level research project before, meaning there was a steep learning curve to overcome.
“At first, I struggled with writing and understanding the codes in initial phases of the project,” Jolyn said. “But I grew to like the process of problem solving and the eureka moment when the codes finally worked.”
Then there was the process of actually analysing the raw data, writing the paper as a team and then sending it out – a process that was almost derailed when the paper’s first submission to a journal was rejected.
“I think the rejection was an unnerving experience for some of the students,” Asst Prof Mutwil said.
“But I also think it was a great lesson on how the publishing process can be like in academia,” he added, matter-of-factly, “You submit your paper, and you might be rejected. You can mope and grumble for a day, but then you have to go back to it – listen to the reviewer’s comments, amend the manuscript, and keep trying.”
The lesson had clearly stuck, especially for Erielle, who found the process of returning to and refining the work one of the more rewarding aspects about participating in the project.
Erielle Villanueva, a second year Biological Sciences major, joined the project to pursue her passion in science.
“I was able to practice writing more Python scripts and learned how to troubleshoot my own code when something wasn’t working properly,” she said. “I now have more confidence in my ability to code, and I am still learning how to improve in my spare time.”
For Asst Prof Mutwil, it was not just that the project’s goal had been successfully met, with www.fungi.guru providing crucial cover for a gap in the knowledge base of fungi-related research, but also that the students did as well as they have.
“I am quite impressed with them,” Asst Prof Mutwil said. “I was initially unsure what they were capable of, and I am happy to have discovered that they can complete complex projects, even as inexperienced undergraduates.”
Given the success of www.fungi.guru, it only stands to reason that more success may be found with building other similar databases.
“We have so much data that we could even build two new databases: bacteria.guru and protist.guru,” Asst Prof Mutwil said, on the topic of upcoming plans. “And of course, I would like to involve future cohorts of BS1009 – it’s a win-win opportunity, since the students get to experience being part of a real bioinformatics project, and can then put the published paper on their CVs, which is undoubtedly a good thing!”