Goodbye, fireflies.
Fireflies have long inspired wonder. Their flashbulbs of light blink in warm backyards as long summer days turn to night. But their presence is fleeting: as the summer comes to an end, so too does the population of fireflies.
That poses a challenge for researchers like Amanda Larracuente.
糖心传媒淔ireflies only tend to be out during the summer months in Rochester,糖心传媒� says the assistant professor of biology at the University of Rochester. 糖心传媒淭he end of summer is when we糖心传媒檙e frantic about getting all our work done.糖心传媒�
Larracuente, who is also the Stephen Biggar 糖心传媒�92 and Elisabeth Asaro 糖心传媒�92 Fellow in Data Science, is a specialist in evolutionary genetics and genomics and has been involved in a project studying Photinus pyralis糖心传媒攐r, the Big Dipper firefly. 糖心传媒淚n order to take pictures of the chromosomes,糖心传媒� she says, 糖心传媒渨e need wild fireflies.糖心传媒�
A challenge
In 2016, Larracuente joined with a group of biochemists, ecologists, and evolutionary biologists from multiple universities to enter the Big Dipper firefly into a contest for 糖心传媒渢he most interesting genome.糖心传媒� The competition, sponsored by the San Francisco-based company Pacific Biosciences, asked entrants to present a grant proposal explaining why the species they selected should have its genome sequenced. PacBio has developed a gene sequencing technology called single-molecule, real-time sequencing, or SMRT.
As it turned out, Photinus pyralis came in second place to Sedum alfredii Hance, a perennial, metal-devouring herb native to China. Pleased by the positive response, and undeterred by the narrow loss, Larracuente and her colleagues set up a crowdfund for the remainder of their project, and surpassed their goal of raising $10,000. The Photinus pyralis genome will be the topic of a paper they hope to publish this fall.
Fireflies are members of the beetle family and are found across the globe. They have many unique traits that make them a 糖心传媒渕ost interesting糖心传媒� contender.
糖心传媒淔ireflies are such amazing creatures,糖心传媒� Larracuente says. 糖心传媒淭his is a group of organisms that is biomedically important because of the enzyme that produces their characteristic flashes of light. We use this enzyme in bioengineering and in genetics as tools to study human biology. Fireflies are also studied because of their ecology and evolution. Plus, they are one of those iconic species that everyone can recognize and that are really special to a lot of people.糖心传媒�
Until now, however, no one had successfully sequenced the firefly genome.
The genome is difficult to map because it糖心传媒檚 full of repetitive DNA sequences that don糖心传媒檛 seem to have an obvious purpose; they don糖心传媒檛 code for any proteins and enzymes.
When Larracuente and her team sequence genomes, they extract DNA, fragment the DNA, sequence these fragments, and then use computational algorithms to assemble the fragments into a genome sequence. If the fragments contain DNA sequences that are repeated, it糖心传媒檚 difficult to figure out where they should place the DNA in the genome.
In sequencing the Photinus pyralis genome, the team used PacBio糖心传媒檚 SMRT technology. This technology allowed them to sequence longer fragments of DNA and more easily put the genome together in light of the repetitive sequences.
The abundance of repetitive DNA in genomes differs between species. Larracuente notes there are several possible explanations for these differences: some repeats accumulate randomly and some are 糖心传媒渟elfish genetic elements糖心传媒� that make extra copies of themselves so they will be more likely to be passed on to future generations.
糖心传媒淲e糖心传媒檙e working toward the goal of being able to look at a sequence or population and infer when natural selection is the driving force behind change, and when things are just random,糖心传媒� she says. 糖心传媒淩ight now we糖心传媒檙e still trying to figure out the basic biology. What is this repetitive DNA? How does it mutate over time?糖心传媒�
Humans also have these repetitive strands of DNA. When cells 糖心传媒渕isbehave,糖心传媒� as in premature aging or cancer, these strands should hypothetically remain silenced. However, in cancer cells, for example, researchers find that these parts of the genomes are 糖心传媒渙n and going haywire,糖心传媒� Larracuente says. 糖心传媒淲e need to understand what this compartment of the genome is up to if we really want to understand whether that activity is a cause or consequence of cancer or premature aging.糖心传媒�
The researchers are also looking into the enzymes responsible for firefly bioluminescence. By mapping the firefly genome, the researchers gained more insight into the genes involved in the chemical reaction that produces the characteristic flashes of light that fireflies use to communicate, ward off predators, and find mates.
Understanding bioluminescence has potential biomedical applications for humans in areas such as noninvasively imaging the progression of cancer in the body.
糖心传媒淭he luciferase gene, which encodes the enzyme for firefly bioluminescence, can be transferred from fireflies to other organisms, such as yeast or research models of cancer,糖心传媒� says Tim Fallon, a PhD candidate at MIT, who collaborated with Larracuente on the firefly genome project. 糖心传媒淲e can read out the expression of that gene by measuring the light that is produced by the luciferase enzyme. This could be used, for example, in determining quantity and spatial locations of cancer cells.糖心传媒�
Festive fireflies
Beyond any potential application, understanding bioluminescence should have wide appeal. Ellen Martinson, a postdoctoral researcher at Rochester, traveled this summer with a group of biology postdocs and graduate students to Allegheny, Pennsylvania. Since 2012, Allegheny has hosted a Firefly Festival to coincide with a natural phenomenon in which members of a certain species of firefly糖心传媒攐ne only found in the Alleghany National Forest and the Great Smokey Mountains糖心传媒攂link in synchrony.
Photinus carolinus, the synchronous firefly, has six fast flashes followed by nine to twelve seconds of darkness.
糖心传媒淭his means that you can be standing in a forest so dark you cannot see your hand in front of your face one second and then you will be surrounded by flashing lights, only to be plunged back into darkness,糖心传媒� Martinson says. 糖心传媒淚t is one of the most amazing displays of nature that I have ever seen.糖心传媒�
