Blog

Congratulations to Jason Gallant, on receiving the 2025 Mentorship Award from the Undergraduate Senior Class Council!

Congratulations to Rita Gorsuch, on receiving first place in the Cell Biology, Genetics and Genomics category at the 2025 MSU UURAF!

Congratulations to Alyssa Saunders, PhD student in the MSU Electric Fish Lab, on receiving the 2025 Graduate Student Award for Science Communication and Outreach from MSU’s Office of Outreach and Engagement!

Dr. Mauricio Losilla successfully defended his Ph.D. on July 8th, 2021. Congratulations to Mauricio!

Dr. Savvas Constantinou successfully defended his Ph.D. on May 6, 2021. Congratulations to Savvas!

Mauricio Losilla was recognized by the MSU EEB Graduate program for his outstanding dissertation work which integrates gene expression, molecular evolution and the evolution of electric signal diversity in mormyrids! This award will allow Mauricio a spot to present his work to the EEB community, as well as a $500 honorarium! Congratulations Mau!

Graduate student Mauricio Losilla was awarded the prestigious MSU Natural Sciences Barnett Rosenberg Fellowship to finish his dissertation work in our lab. We are very proud of Mauricio and his accomplishments!!!

Dr. David Luecke was selected by the MSU Institute for Cyber-Enabled Research as a member of the 2020 MSU Cloud Computing Fellow cohort! Congratulations to David!!

Dr. Sophie Picq was recognized by MSU for her fantastic work as a research mentor in our laboratory over the past several years for graduate and undergraduate students. We’re all super proud of Sophie’s accomplishments.

iNaturalist is a really cool project sponsored by the California Academy of Sciences and National Geographic, where you can use your smartphone to help catalog biodiversity. We created a project for our collections in Gabon from last summer as a way of contributing to this amazing resource. Check out our fish– there’s only a few for now, but we’ll be updating it over time…

Pleased to report that our latest paper, which tests a hypothesis about the role of genetic drift in electric signal evolution was published in Evolution online. This terrific work was led by @SofishPicq and features behavior work by @BruceCarlson75 https://t.co/B1zmAiD96a— jasongallant (@jasongallant) April 13, 2020

I’m pleased to report that @3_thumbs_up_SJC has successfully developed a CRISPR/Cas9 gene editing protocol in weakly electric fish. This effort has resulted in sexually mature, sodium channel knockout #efish, which are electrically silenced: (1/7) https://t.co/qDAzEE3AVG. .— jasongallant (@jasongallant) September 18, 2019

Electric fish have served as a model system in biology since the 18th century, providing insight into the nature of bioelectrogenesis, the structure of the synapse, and brain circuitry underlying complex behavior. Electric fishes exhibit many interesting characteristics or phenotypes, but very little is known about how these phenotypes are encoded in the genetic material or genome. Understanding this relation is a broad goal in 21st century biology. Electric fish offer a singular advantage in trying to understand the link between the genome and the phenotype it produces: two groups of electric fish evolved independently in Africa and South America, providing a system where biologists of all stripes can attack genotype-phenotype questions with built-in replication. There is a growing amount of electric fish genomic data; however, there are no functional tools to investigate this connection. The purpose of this project is to develop a robust, accessible, and easily transferable genetic manipulation toolbox for the electric fish model system full range of questions under investigation, regardless of a researchers’ background. The first phase of the project is rapid parallel protocol development, and the second phase of the project will be to disseminate knowledge gained by developing web-based software for sharing protocols, data, and resources, and to train the next generation of electric fish biologists–undergraduate and graduate students from diverse backgrounds–in the use of these techniques in preparation for careers in science and technology.

Since November, we’ve added many new faces to the lab!  Welcome to team e-fish!

The format of the reception featured a discussion by Patrick Hsu,  from Editas Medicine, formerly of Harvard (a feature speaker at last year’s CRISPR Symposium) as well as shorter talks by David Arnosti, Kathy Meek, Eran Andrechek, Keith Latham and Jason Gallant.

We’ve been trying to breed Pollimyrus isidori in the lab for the last couple of months, which are well reputed good parents .  Withstanding some pH problems that we have been having over the past months, we’ve finally witnessed the fruits of our labor.  As of another big clutch of eggs this morning, we have more than 200 individuals!

I’ve been running an experiment trying to implement AWS in some of our bioinformatics projects.  After surveying some nice reviews (Yandell and Ence, 2012), I’ve decided on the MAKER pipeline to get things started.  The basic approach will be to take orthologous proteins from other organisms, together with existing transcriptome data (assembled by cufflinks), and use this as a means of pulling out putative coding regions to train an ab-inito gene predictor (such as SNAP or Augustus) to build gene models.  Given the numerous BLAST steps that are involved in aligning this data, as well as processing it, the folks in the Yandell lab made MAKER parallel, through the use of either OpenMPI or MPICH2.  Although we have an installation of the MAKER software on campus, it hasn’t been updated in a while, and there is something of a queue run very long jobs with lots of processors– I wondered if there were other options.

Jason Gallant, assistant professor of Zoology received a $699,000 grant from the National Science Foundation to investigate the genomic basis of electric signal diversity in mormyrid electric fish. Electric fish, such as mormyrids, produce weak electric fields for the purposes of communication and navigation through their environments. As part of this three-year research project starting in May 2015, Gallant will leverage his recent discovery of a ‘hybrid zone’ between populations of electric fish with distinct electric signals to identify genes responsible for differences in electric signals. The project will draw on next-generation genomic sequencing technologies, as well the development of new transgenic techniques in electric fish. This research is important because electric discharges are a critical component in the speciation of mormyrid electric fish. Identifying genes responsible for behavioral differences within species will ultimately help biologists understand how changes in behavior can facilitate, or perhaps cause, one species to become multiple species. In connection with the work, Gallant’s laboratory will bring a new educational outreach program, focusing on “forms of energy”, to middle school students in Olivet, MI.

Perhaps the nerdiest of all Christmas decorations I’ve ever put up, here is the official electric fish christmas tree!

Nicole Thompson (MSU Zoology, Class of 2015) has joined the lab. Welcome Nicole!

We are excited to have three wonderful undergraduates working with us this summer– Sophia Sdao, Justin Rucinski, and Sarah Sam.  We will be working together on developing much needed software programs and data analysis procedures for our many exciting projects.  Stay tuned!

As another day ticks by, we see that the larva has developed still further, hatching from its chorion. The eyes are now dark and pigmented and can be clearly made out along with the ears.  The dark mass in the center of the head is the brain, and you can follow the CNS through the entire body of the animal.   You may also notice that the embryo is noticeably “darker” than yesterday– the process of melanogenesis has begun.  The animals are a dark brown color normally, and this pigmentation process will continue for the next several days.  Tomorrow, we will see more definition in the fins and the body shape start to more closely resemble the adult fish.

Here we go! The eggs have developed another day, and now the body parts are in full definition. Viewing under the microscope, you can see blood pumping through the circulatory system in vivid detail, as well as lots of movement of the fish embryo as it gets ready to push its way through the eggshell (chorion) and into the world! Also notable are the otic vesicles, the ears of the fish, which show up as a pair of dark circles on the sides of the larval head. While the eye is formed, it is not pigmented yet. In about another day, the eye will be visible.

Here’s a nice image– after developing through the evening in our incubators, a much higher proportion of embryos have survived! You can clearly see many little spinal cords in our petri dishes now. Here is a close-up of what we are seeing…

It’s starting! We’ve got another batch of fertilized eggs, now here at the lab instead of our satellite facility– they are developing more comfortably at highly controlled temperatures in our new incubator. You can see one of our new eggs here, about 14 hours after fertilization.

Monica and I have been hard at work getting Brienomyrus brachyistius to breed again in the lab– we’ve been having great success with getting them spawning!  Over the past month, we’ve had hundreds of eggs.  Here is a video of the “main event” occurring several hours after nightfall, which occurs at 19:00 hours.  While this is a 30 second clip, preliminary analysis of our video shows that the pair spawns repeatedly over the ensuing 10-15 minutes, and likely many more times out of frame.

Welcome to our new research technologist, Monica Lucas!

I’ve now realized that the build in UNIX text editor nano just doesn’t cut the mustard, so I’m switching to VIM.  So far, I like it though it is a little hard for a fervent nano & sublime text editor to get used to.  But, there are some ways to tweak it to get it feeling a bit more familiar.  Create a text file in your home directory called “.vimrc” that reads as following:

I have several nested folders that I need to switch between periodically.  I tried making environment variables for these:

Here is my current workflow for genome resequencing and SNP calling, culled from various helpfiles, internet sources, and of course, some things I have figured out myself:

So, I was trying to figure out a way of extracting significantly up regulated Transcripts from my Trinity assemblies.  Low and behold, it’s possible with BioPython:

I just figured out to use the handy little UNIX utility AWK, which makes parsing text files a breeze, if you know how to speak its language. For the uninitated, there is a great list of little AWK one liners that you can check out here: