By Indiana State University
Oct 28, 2019
When Hugo Gante headed back to his home country of Portugal last summer the Indiana State University assistant professor of biology didn’t go alone – or without a mission.
Gante and two State undergraduate biology majors traveled overseas in June to complete one component of Gante’s research in population genomics, using the latest molecular methods in terms of sequencing to do “nature CSI” and detect what species are in the river.
“In particular, we’re focusing on fish but in theory it could be used to look at anything that crosses paths with or lives in the river – animals, plants or fungi that live in there or bacteria, viruses,” Gante said. “Anything that crosses paths with the river will shed cells or DNA that we’re essentially collecting from the environment and then ID’ing a species based on that.”
To do that, they will need to build databases for what’s what.
“It’s like having blueprints and then trying to see on the database what matches,” Gante said. “If it’s not on the database, we’re not going to find a match but we might find something similar.”
Though this aspect of Gante’s research is just getting underway, he’s been working with fish since his time as a student.
“I’ve always liked fish and there are a lot of them,” he said. “Being interested in nature and diversity, fish are kind of a window into the natural world that you can keep indoors if you have an aquarium, which I did as a kid.”
One aspect of trying to gauge the health of the environment is determining what is in the river.
“We can have very common species and then there are a few that will be rare and those are going to be difficult to catch,” he said. “Traditionally, we would just catch the fish that are there but quite often we would miss those species that are valuable for different reasons. There are native species that might be endangered and we want to know if they’re there and how well they’re doing. Then, we have introduced species, until they actually reach a certain population size threshold, we don’t know they’re there. The idea is that we’d catch this invasion earlier enough to be able to do something before it gets out of control.”
Despite 15 years working abroad, Gante has stayed connected to collaborators and friends in his home country, which is helpful as he enters the second year of the research project, which is being funded with a three-year grant from the Portuguese Science Foundation.
Gante’s research has also been an opportunity for Indiana State students Daniel Licari and Benjamin Prindle to get hands-on experience in everything from organizational aspects to getting their hands dirty collecting and measuring fish or getting and filtering water as part of a team of five to six people, depending on the day.
“The days were long, very long. We would get up and get breakfast about 7 a.m., then go out to one collection site and do our thing,” Gante said. “If we were lucky, we might have lunch by 2 p.m. If we were not lucky, maybe it would be 4 p.m. then we’d move on to the next place and eat dinner about 10 p.m. and then start again the next day.”
The research opportunity was an irreplaceable experience for the students.
“You cannot get this type of experience just sitting and watching. You have to actually do it,” Gante said. “In a way, this is also how I started in this field and I would say 9 out of 10 people start this way, going out and seeing if they actually like to do it. It’s translating what you learned in the classroom and seeing if you can really do it.
Licari and Prindle started working with Gante last school year getting their hands dirty with research questions in the lab.
“We’d meet and go through research questions and as they were interested in the topic and the opportunity was there, it made sense that they would join me for the month of June in central Portugal, traveling for two weeks doing research in the countryside,” Gante said.
The next step will be getting the genetic sequencing data from the environment and contrasting it with what they think they know lives there.
“The idea is to calibrate this method using environmental DNA and see if it matches with what we expect from the sites we collected from,” Gante said. “We have long-term data from the fishes that live there, but we also collected to make sure that the species would still be there. We’re not just going to determine what’s there, but try and quantify how much of each species is there. That’s why we collected, measured and weighed them. We want to try and get the genetic variability from the environment because that would be less intrusive.”
Now in his second year on faculty at State, Gante is juggling the Portugal research along with other faculty collaborations within the biology department, looking at cardiac development. He’s teamed up with Shaad Ahmad, an assistant professor who uses fruit flies, and Kristopher Schwab, an assistant professor who uses mice in his research.
“Fish are in between in the way of complexity and they’re still vertebrates, so they’re perhaps more comparable to humans than some other organisms and they have relatively simple hearts,” Gante said. “We’ll use zebrafish from the Indian subcontinent because that is one of the officially recognized biomedical model systems, so we are in the process of establishing a colony of zebrafish in-house. We’re going to be playing with their genes and trying to dissect the genetic basis of their heart development.”