Frisch team studies a tiny plant with a big impact

Frisch team studies a tiny plant with a big impact

The science of sequencing: Decoding duckweed genes

Every living thing has a genetic blueprint, called a genome, that determines how the organism is structured and how it works. The genomes of plants and animals are made up of billions of chemical subunits called base pairs, strung together in a sequence unique to each creature. Base pairs are the letters of the genetic alphabet, arranged differently for each gene, like the chapters of a book.

The Human Genome Project has led to the decoding of more than 3 billion base pairs found in human beings. The genomes of other animals, plants, and microorganisms have also been decoded. But the Wolffia australiana (duckweed) genome is still largely unknown, hence the goal of this project is to sequence and analyze, gene by gene, the base pairs of the tiny plant. Some of those genes are similar to those found in other plants and animals and some are used by the plant for its unique functions.

For the Waksman Student Scholars Program, Rutgers scientists have taken DNA from the plant and used special enzymes to connect it to DNA from bacterial cells. The hybrid DNA can be carried by bacteria, which can be grown in large amounts. The bacteria are grown on petri dishes, and the colonies carrying plant DNA are called clones.

These clones are provided to the WSSP high schools for further study. The Frisch School’s science department chair, Mindy Furman, and her students began to study the clones by making many copies of the duckweed DNA inserts using PCR (a procedure commonly used in forensic labs to make millions of copies of DNA). The students measured the plant DNA pieces with gel electrophoresis. Any clones found to have a big enough piece of duckweed DNA are sent back to Rutgers for decoding the genetic letters, that is, DNA sequencing.

“You insert your DNA into a well and you run electrical current through it and it pulls down the DNA,” explained Jennifer Ledner of Paramus. “We compare it to a ladder of identified DNA fragments, where you know the size. If it’s too small you won’t be able to learn anything from it.”

“We deal with the actual base pairs of the DNA,” said Ben Sultan of West Orange. “My clone had an insert of 790 base pairs. It’s interesting that we are studying the building blocks of the duckweed.”

At Rutgers, DNA sequencing is performed to read the genetic alphabet of each student’s clones. Since plants and animals can have billions of genetic letters, the information is catalogued, organized, and processed using computer programs. The genetic sequences, in the form of graphs called waveforms, are sent back to the students for further study.

DNA base pairs are strung together in each gene like letters in a language. And like most languages there are also punctuation marks, which can be found in the genetic narrative. When the students receive the sequence data for the clones, they can use a computer program called DSAP (DNA Sequence Analysis Program) to find these punctuation marks, showing the beginnings and ends of the genes. They can also use computer analysis to determine what the proteins, produced by genetic instruction, might look like.

In addition, students will compare the sequence of their clones to other genetic sequences in a vast database, maintained by the National Center for Biotechnology Information, or NCBI. According to NCBI’s website, the database contains the genetic sequences from more than 800 organisms, including plants, animals, and microorganisms, from bees and bacteria to zebrafish. Using very powerful computer programs they will be able to answer questions such as: “Is your sequence similar to sequences found in any other organism?” and “What is the function of your gene?”

Hannah Lebovics and Ariana Schanzer, both 16-year-olds from Englewood, accompanied Furman to the WSSP training institute in July.

“We sequenced four clones each and analyzed what proteins they code for, how it can improve our knowledge and understanding of duckweed, and how it can help us,” said Hannah.

“We had noncoding regions and we had coding regions,” said Ariana, referring to types of DNA they studied. “A seemingly negative result [that did not match the database] … could mean you found a new gene,” she added. The students working on this project could discover duckweed genes that look and act like genes found in other plants and animals, or genes that were novel, i.e., brand-new discoveries.

One example of a gene the two girls studied in the summer workshop was one that works in mitochondria, the cell structures found in all plants and animals that provide energy for the cell. “We found proteins that were also found in humans and other organisms, that were important for mitochondrial transport and removal of copper,” Ariana reported.

“It’s a necessity for all living organisms, so it should be important,” she concluded.

Ariana, Hannah, and their classmates are now studying a new set of clones, a process that can take months from start to finish. They are patiently pursuing the project, step-by-step, hoping to contribute to the understanding of the duckweed genome and how it can be used to help humankind.

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