Blog
2021
Dr. Mauricio Losilla has earned his Ph.D!
Dr. Mauricio Losilla successfully defended his Ph.D. on July 8th, 2021. Congratulations to Mauricio!
Dr. Savvas Constantinou has earned his Ph.D!
Dr. Savvas Constantinou successfully defended his Ph.D. on May 6, 2021. Congratulations to Savvas!
Mauricio Losilla Wins MSU EEB Graduate Student Distinguished Speaker Award
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!
Mauricio Losilla selected for MSU Natural Sciences Barnett Rosenberg Fellowship
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 selected for MSU Cloud Computing Fellowship
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!! Check out the full release here!
Dr. Sophie Picq is recognized for excellence in undergraduate mentorship
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. Check out the full release here!
2020
Check out our collections on iNaturalist!
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… https://www.inaturalist.org/projects/msu-electric-fish-lab-gabon-2019
Our latest paper on the role of genetic drift in signal evolution now published in Evolution!
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 Communication signals serve crucial survival and reproductive functions. In Gabon, the widely distributed mormyrid fish Paramormyrops kingsleyae emits an electric organ d...
2019
A Protocol for CRISPR/Cas9 Gene Editing in Weakly Electric Fish
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 Check out the protocol and video here: https://www.jove.com/video/60253/silencing-the-spark-crisprcas9-genome-editing-in-weakly-electric-fish
2018
We are pleased to announce that David Luecke will be joining the lab in October as our new postdoc! He joins us from UC Davis, where he did his Ph.D. work on Drosophila prolongata. David will be working on a new project on the evolution and development of electric organs!
New Ph.D. Student Lauren Koenig!
We are pleased to announce that Lauren Koenig joined the lab on August 30th, 2018! Welcome Lauren!
New Undergraduate Angelina Sdao!
We are pleased to announce that Angelina Sdao joined the lab on March 1st, 2018! Welcome Angelina!
We are pleased to announce that Dr. Sophie Picq joined the lab on February 15th, 2018. Welcome Sophie! Sophie completed her Ph.D. in Biology in 2017 from The International Max Planck Research School for Evolutionary Biology, a studying sympatric speciation in coral reef fish. Sophie previously worked at McGill University/STRI (Panama) where she worked on the phylogeography of Brachyhypopomus electric fishes. Welcome back to the EFISH world!
New Technician Jared Thompson!
We are pleased to announce our new technician, Jared Thompson, joined the lab on January 1st, 2018. Welcome Jared!
2017
NSF Grant "Enabling Genotype-Phenotype Studies in Weakly Electric Fish" is Funded!
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...
Welcome Colin, Kat, Hope and Nikki
Since November, we’ve added many new faces to the lab! Welcome to team e-fish! Colin Diesh joins us from Missouri and will be working as a programmer/bioinformatician technician for the next year. Katherine (Kat) Shaw will be our new laboratory technician, and she just moved to East Lansing from Montreal, where she worked with Dr. Rudiger Krahe. Nicole (Nikki) Robichaud started as an undergraduate research assistant, working on some of our molecular cloning projects in September 201...
2015
Jason Gallant Returns to the Mid-Michigan Pet Show
Dr. Jason Gallant was a featured guest on the Mid-Michigan Pet Expert Talk Show, hosted by Lee Cohen and Rick Preuss. The show was broadcast on September 12th, 2015 on 1320 AM WILS Lansing, but the interview segments are also posted here. Thanks Rick and Lee for a great conversation! Be sure to “like” the Mid-Michigan Pet show on Facebook!
We are pleased to announce our new postdoctoral research associate, Will Pitchers, joined the lab on August 1st, 2015. Will comes from Ian Dworkin’s lab, where he worked on the evolutionary genomics of wing shape in Drosophila. He received his Ph.D. at the University of Exeter in 2010 working on crickets, with a thesis entitled “Trait Integration as a Constraint on Phenotypic Evolution”. Will has published many scientific papers regarding genetics and evolution, and will be a very valuab...
Jason's talk at the Michigan State University Genome Editing Reception
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.
Pollimyrus isidori are great fathers
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! To my surprise, the 50 or so individual fry we found yesterday afternoon all seemed to be hanging out near their dad– certainly not a random distribution. Watc...
Savvas Constantinou Joins the Lab!
Savvas Constantinou (BS Trinity College ‘12; MS Central Connecticut State University ‘14) will be joining the Ph.D. program in Integrative Biology at Michigan State University in Fall 2015. Savvas did his master’s thesis working on classical conditioning in planarian flatworms, and is currently a technician in the laboratory of Terri Williams at Trinity College. We are very excited to have him join our lab, where he will be working on some exciting projects on the evolution and developmen...
Running MAKER Genome Annotation on STARCLUSTER
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 ...
NSF Grant "The Genomic Basis of Electric Signal Diversity" is Funded!
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...
2014
Perhaps the nerdiest of all Christmas decorations I’ve ever put up, here is the official electric fish christmas tree! This christmas tree is not “powered” by electric fish, rather it is controlled by an electric fish. Weakly electric fish continuously produce pulses of electricity for communication and navigation in their environments– every time the fish produces a pulse, the tree lights up. This is done with a little RadioShack magic– an Arduino board with a relay shield is all you nee...
Nicole Thompson Joins The Lab!
Nicole Thompson (MSU Zoology, Class of 2015) has joined the lab. Welcome Nicole!
Welcome to Sophia, Justin, and Sarah!
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!
Dr. Gallant on the Mid-Michigan Pet Expert Talk Show
Dr. Gallant was the guest for the Mid-Michigan Pet Show on Saturday April 19th! We had a long conversation about the Gallant lab’s research on electric fish, as well as the genetics behind Glofish. Click “play” below to listen to the full interview, or go to this link to find it and other great interviews in the archives! Many thanks to Rick Preuss and Lee Cohen for a very enjoyable time on the Radio! Be sure to “like” the Mid-Michigan Pet show on Facebook!
Dr. Gallant lectures at the Belle Isle Aquarium in Detroit
Dr. Gallant will be talking about his research on Electric Fish genomics at the Belle Isle Aquarium this weekend– feel free to stop in! For more information please see: http://belleisleconservancy.org/ai1ec_event/science-saturday-electric-fish-era-genome-sequencing/?instance_id=759
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 pro...
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...
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…
Early Electric Fish Development
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. In fish, development is discoidal meaning that the entire egg doesn’t divide, rather a thin layer of cells on the “top” of the egg– this portion is called the blastodisc. The cells of the developing fish are located...
Brienomyrus brachyistius spawning
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. For...
Welcome to our new research technologist, Monica Lucas!
2013
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: ` set mouse=a set number ` Save the file and fire up vim. Now you have a mouse scrolling text editor, with line n...
UNIX Hint: Get Environment Variable Autocomplete Back
I have several nested folders that I need to switch between periodically. I tried making environment variables for these: directories, but for some silly reason I couldn’t tab autocomplete them. Apparently this is a new “feature” in bash 4.2. The way to get it back is to add the following line to your ~/.bash_profile file: complete -r cd http://ubuntuforums.org/showthread.php?t=1749286 http://stackoverflow.com/questions/103316/in-bash-environmental-variables-not-tab-expanding-correctly
2012
Workflow for Genome Resequencing and SNP Calling
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: https://gist.github.com/3528691
Extract Sequences from FASTA file.
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: https://gist.github.com/3519281
Count specific characters per line using AWK
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: http://sparky.rice.edu/awk.html http://awk.info/?awk1line One thing I couldn’t seem to google was how to extract specific characters on a per-line, per column basis. After some mashing together and trial and error, I came up with a code that will count th...