Explainer: DNA hunters | Science News for Students

Explainer: DNA hunters

Genetic clues can tell scientists which organisms have been moving through the environment
Mar 13, 2018 — 6:30 am EST
DNA display

Scientists can extract DNA (parts of which are displayed on screen) from samples they picked up in the environment. They then look for patterns in this genetic material to identify which species had left it. In this way, biologists can “detect” what organisms had been around.

Wavebreakmedia/iStockphoto

“Traces of DNA are left behind by every species everywhere,” says Ryan Kelly. He is an ecologist with the University of Washington at Seattle. He also works at the Center for Ocean Solutions at Stanford University in Palo Alto, Calif. Scratch an itch, he says, and you shed skin cells containing your DNA. Pets and other animals leave behind bits of dead skin known as dander. Reptiles shed skin as they grow. There’s even DNA in poop.

“Just like forensic scientists do at a crime scene every day, we are detecting that trail of DNA that’s left behind,” explains David Lodge. He’s a biologist at the University of Notre Dame in South Bend, Ind. And he hunts for signs an animal has been around by scouting for bits of the DNA it had shed. Scientists refer to this genetic litter as e-DNA. Here, the “e” stands for environmental.

DNA strand
DNA is shaped like a twisted ladder. Its rungs are made of what are known as base pairs. There are four types.
FORLUVOFT/WIKIMEDIA COMMONS

DNA is the genetic material found in the cells of all living organisms. It looks like a long, twisting ladder. Each rung on that ladder is a pair of chemicals called nucleotides. There are four of these chemicals: adenine, thymine, cytosine and guanine. Scientists refer to them as A, T, C and G, for short. Each nucleotide on one long side of the ladder must pair with a specific one on the other side. A’s only pair with T’s. Any C’s must pair with G’s.

Humans have about 3 billion rungs, or base pairs, in their DNA. Other species have more or fewer. The order of base pairs in every individual’s DNA is unique, but its pattern will be very similar to that of other members of its species. Scientists can use that code to identify a species.

Scientists prowl for eDNA throughout the environment, in water, soil, ice cores — even the guts of leeches.

Researchers in the lab start with some environmental sample. It might be a leaf, a vial of water, some animal tissue or dust. The first step is to isolate cells of one or more living organisms in the sample. Then they add these to some hard-working chemicals. One chemical breaks down cell walls to release their DNA. Another chemical grabs onto proteins and other materials that are not DNA. A machine then spins the mix at high speed. DNA-filled liquid floats to the top. Everything else sinks to the bottom. More steps get rid of extra liquid from that top layer.

Additional work might be needed along the way to “clean up” samples even more, explains Margaret Hunter. She’s a geneticist with the U.S. Geological Survey in Gainesville, Fla. For example, her lab had to remove certain compounds produced by local trees. She was looking for DNA from invasive Burmese pythons. Those tree chemicals could have stopped reactions that should take place in the next set of steps in her search for python eDNA.

In projects focused on some particular species, such as the python, those next steps search through the sample for a particular span of rungs from the DNA’s ladder-like structure. This specific span of the DNA molecule is known as a sequence. And it will be unique to its species.

If it’s found, the method will then make many, many copies of that DNA fragment. This copying process is called the polymerase (Puh-LIM-er-ase) chain reaction, or PCR. In effect, it works like a photocopier for DNA.

Using PCR will boost that DNA signal, explains Eva Egelyng Sigsgaard. She’s a biologist with the Natural History Museum of Denmark in Copenhagen. Think of turning up the volume on your cell phone. After you amplify the sound, you can hear the ring over any background noise in a room. Similarly, she says, “When we amplify the DNA, we make large amounts of the specific DNA that we’re looking for.” That makes this DNA stand out against the “noise” of other species’ genetic debris.

Hunter at USGS tailored her work to find and copy a part of the Burmese python’s DNA that is different from that in all other species. In 2015, that let her team show for the first time that the big snakes could be detected through eDNA. If eDNA sampling becomes more routine, it could help scientists track — or scout for — evidence of rare or camouflaged species at relatively low cost.

Power Words

(for more about Power Words, click here)

amplify     To increase in number, volume or other measure of responsiveness.

base     (in genetics) A shortened version of the term nucleobase. These bases are building blocks of DNA and RNA molecules.

base pairs     (in genetics) Sets of nucleotides that match up with each other on DNA or RNA. For DNA, adenine (A) matches up with thymine (T), and cytosine (C) matches up with guanine (G).

biology     The study of living things. The scientists who study them are known as biologists.

Burmese     An adjective that describes something of, from, or related to the Southeast Asian nation formerly known as Burma (such as the Burmese python and Burmese cat, for example). Burma is now known as Myanmar.

cell     The smallest structural and functional unit of an organism. Typically too small to see with the unaided eye, it consists of a watery fluid surrounded by a membrane or wall. Depending on their size, animals are made of anywhere from thousands to trillions of cells. Most organisms, such as yeasts, molds, bacteria and some algae, are composed of only one cell.

chemical     A substance formed from two or more atoms that unite (bond) in a fixed proportion and structure. For example, water is a chemical made when two hydrogen atoms bond to one oxygen atom. Its chemical formula is H2O. Chemical also can be an adjective to describe properties of materials that are the result of various reactions between different compounds.

compound     (often used as a synonym for chemical) A compound is a substance formed when two or more chemical elements unite (bond) in fixed proportions. For example, water is a compound made of two hydrogen atoms bonded to one oxygen atom. Its chemical symbol is H2O.

core     Something — usually round-shaped — in the center of an object.

dander     Flakes of skin in an animal’s fur or hair.

debris     Scattered fragments, typically of trash or of something that has been destroyed. Space debris, for instance, includes the wreckage of defunct satellites and spacecraft.

DNA     (short for deoxyribonucleic acid) A long, double-stranded and spiral-shaped molecule inside most living cells that carries genetic instructions. It is built on a backbone of phosphorus, oxygen, and carbon atoms. In all living things, from plants and animals to microbes, these instructions tell cells which molecules to make.

ecology      A branch of biology that deals with the relations of organisms to one another and to their physical surroundings. A scientist who works in this field is called an ecologist.

eDNA     Short for environmental DNA. A tool for detecting the presence of a species solely from the genetic material (DNA) it has left in the environment.

environment     The sum of all of the things that exist around some organism or the process and the condition those things create. Environment may refer to the weather and ecosystem in which some animal lives, or, perhaps, the temperature and humidity (or even the placement of components in some electronics system or product).

forensics     The use of science and technology to investigate and solve crimes.

genetic     Having to do with chromosomes, DNA and the genes contained within DNA. The field of science dealing with these biological instructions is known as genetics. People who work in this field are geneticists.

geological     Adjective to describe things related to Earth’s physical structure and substance, its history and the processes that act on it. People who work in this field are known as geologists.

guanine     One of four substances that organisms need to produce DNA.

gut     An informal term for the gastrointestinal tract, especially the intestines.

litter     Material that lies around in the open, having been discarded or left to fall where it may. (in biology) Decaying leaves and other plant matter on the surface of a forest floor.

molecule     An electrically neutral group of atoms that represents the smallest possible amount of a chemical compound. Molecules can be made of single types of atoms or of different types. For example, the oxygen in the air is made of two oxygen atoms (O2), but water is made of two hydrogen atoms and one oxygen atom (H2O).

nucleotides     The four chemicals that, like rungs on a ladder, link up the two strands that make up DNA. They are: A (adenine), T (thymine), C (cytosine) and G (guanine). A links with T, and C links with G, to form DNA. In RNA, uracil takes the place of thymine.

organism     Any living thing, from elephants and plants to bacteria and other types of single-celled life.

polymerase chain reaction (PCR)     A biochemical process that repeatedly copies a particular sequence of DNA. A related, but somewhat different technique, copies genes expressed by the DNA in a cell. This technique is called reverse transcriptase PCR. Like regular PCR, it copies genetic material so that other techniques can identify aspects of the genes or match them to known genes.

protein     A compound made from one or more long chains of amino acids. Proteins are an essential part of all living organisms. They form the basis of living cells, muscle and tissues; they also do the work inside of cells. Among the better-known, stand-alone proteins are the hemoglobin (in blood) and the antibodies (also in blood) that attempt to fight infections. Medicines frequently work by latching onto proteins.

python     A large, heavy-bodied, nonpoisonous constrictor snake.

species     A group of similar organisms capable of producing offspring that can survive and reproduce.

survey     (v.) To ask questions that glean data on the opinions, practices (such as dining or sleeping habits), knowledge or skills of a broad range of people. Researchers select the number and types of people questioned in hopes that the answers these individuals give will be representative of others who are their age, belong to the same ethnic group or live in the same region. (n.) The list of questions that will be offered to glean those data.

tissue     Made of cells, any of the distinct types of materials that make up animals, plants or fungi. Cells within a tissue work as a unit to perform a particular function in living organisms. Different organs of the human body, for instance, often are made from many different types of tissues.

U.S. Geological Survey (or USGS)     This is the largest nonmilitary U.S. agency charged with mapping water, Earth and biological resources. It collects information to help monitor the health of ecosystems, natural resources and natural hazards. It also studies the impacts of climate and land-use changes. A part of the U.S. Department of the Interior, USGS is headquartered in Reston, Va.

unique     Something that is unlike anything else; the only one of its kind.