Model organisms or research organisms, as they are also known are living things that scientists, such as biologists, use to study human and other animal or plant life.
A model organism can be anything from single-celled bacteria to viruses and fungi. They can be more complex organisms, such as monkeys, mice, rats, frogs, elephants and a salamandercalled axolotl.
Monkeys and mice are considered incredibly important for the study of human disease and ageing, because they are genetically so similar to humans. And research on primates and rodents has led to some major scientific breakthroughs.
Illustration by Per Sander
The field is not without its opponents, though, and let's not mince our words its downsides.
One of the most basic scientific and ethical questions asks whether it's okay to subject non-human animals to experimental pain in a laboratory when we wouldn't do that with humans.
Think of vaccines and other medicines: Before they get tested on people, they are tested on non-human animals to look for dangerous side-effects.
Even further down the track, in human clinical trials, people can have extreme and adverse reactions to a drug in development. And that's when the drug has been somewhat refined to limit negative outcomes.
Illustration by Simone Hls
But with monkeys and rats, is it okay to just go ahead and test potentially lethal chemicals? Or what of psychological trials, like studying pain stimuli on mice? Is that okay? Does that mean that a monkey's life is worth less than a human life?
There are regulations to ensure the welfare of animals in research and, increasingly, some technical alternatives, such as computing models that use artificial intelligence and machine learning systems.
They can calculate what may happen if you put a medicinal compound in a body. But you can't avoid testing medicines on animals, including humans, in the end. How else would you know whether there are any benefits for human life?
Illustration by Simone Hls
There are less controversial model organisms than monkeys unexpected yet common things such as tomatoes, fruit flies, worms, and other vegetation. The axolotl is especially interesting because it keeps it's tadpole-like juvenile characteristics into adulthood. This includesexternalgills. But it is not a fish, it's a salamander.
One such plant is even celebrating the 200th anniversary of its naming, or to be precise, its renaming, and that's Arabidopsis thaliana.
A Swiss botanist called A.P. de Candolle coined the term Arabidopsis to describe a group of Brassicaceae plants in the mustard family in 1821.
In a paper published in the Journal of Plant Biochemistry and Biotechnology, Rajnish Khana and Ulrich Kutschera explain how a German botanist, Friedrich Laibach, then "established the mustard plant A. thaliana (L.) Heynh as a model organism in plant genetics []."
It has since become integral to stem cell research and is still delivering insights.
Illustration by Barbara Scheid
Khana and Kutschera write that A. thaliana is an ideal model organism for some very basic reasons: it's small and easy to grow, it has a short generation time the average time from the birth of one living thing to the birth of its offspring it produces up to 10,000 seeds per plant, and it's easy to manipulate and mutate.
Model organisms are categorized into various groups. The categories start with viruses, such as Phage lambda and the Tobacco mosaic virus.
Illustration by Christian Kuhn
The Lambda phage, for instance, is what's known as a temperate virus, which infects host bacteria, such as E.coli.
Being temperate, Phage lambda has different ways of infecting a cell, but it has to decide which it wants to use. And it's that decision-making process at such a fundamental level of life that has intrigued scientists. Studying the process allows them to learn about our own biological development.
Some researchers say it's important to continue studying viruses on the brink of global eradication, such as polio.
Even viruses such as Ebola, Zika and influenza can be used as model organisms to teach us about genetic and hereditary processes in RNA, the messengers of DNA the thing that makes living things unique individuals.
The next category is Prokaryotes. A prokaryote is any organism that lacks a distinct nucleus, the thing that controls the activity of a cell.
Illustration by Barbara Scheid
The most common prokaryotes are bacteria, such as E.coli (Escherichia coli), which is used to study molecular genetics. Synechocystis is a bacterium that is commonly used to research photosynthesis.
Next on the list and arguably the largest and best-known group involves eukaryotes. Eukaryotes are cells or organisms that are thought to have evolved about 2 billion years ago.
Compared to prokaryotes, eukaryotes have a clearly defined nucleus.
They include protists. Protists are often but not exclusively microscopic, single-celled organisms.
Illustration by Christian Kuhn
Eukaryotes also include fungi. There's Neurospora crassa, an orange bread mold, for instance, that's been used to study metabolic regulation and the circadian rhythm the latter being a field that won a Nobel Prize only a few years ago.
Baker's yeast is used in genetic research, as are Coprinus cinereus mushrooms. They have been useful in the study of meiosis, or cell-division, which is important for understanding reproduction.
Arabidopsis thaliana, mentioned above, is also a eukaryote. It belongs to a group of so-called higher plants.
Illustration by Peter Steinmetz
Then there are animals, both invertebrate and vertebrate.
Let's start with invertebrate animals. The US National Wildlife Federation describes invertebrates as the "most diverse and numerous group of animals on Earth."
Invertebrates have no spine. They can live on land or in water.
Illustration by Simone Hls
So, they include animals such as the common fruit fly and hydra, an aquatic animal.
Many have been used in molecular biology or biomedical experiments.
And last, but by no means least, we have the vertebrates arguably, the most controversial group of model organisms.
Vertebrates are defined by their having a spine.
Illustration by Olof Pock
Now, if you wanted to be cynical, you may like to suggest that some vertebrates have more of a spine than others. We humans, for instance, could be accused of being spineless for willingly subjecting other animals to pain that we would rather not endure ourselves. But that argument is up for grabs.
The usual suspects among the vertebrate model organisms are the aforementioned monkeys, rats and mice. But they also include dogs, frogs, chickens and cats, and birds used to study communication among songbirds and non-mammalian auditory systems.
Then there's the beautiful zebrafish, a freshwater tropical specimen.
Zebrafish are virtually transparent. That offers scientists with an almost unique view of an animal's internal anatomy.
Illustration by Simone Hls
But if that's not cool enough, Zebrafish are becoming more and more attractive as a model organism because about 70% of their genes are similar to human genes.
They also have similar bodily components or organs. Zebrafish have two eyes, a mouth, a brain, intestine, pancreas, liver, bile ducts, kidney, a heart, ears, nose, cartilage, and teeth just like humans.
Researchers says it's therefore possible to use zebrafish to model and study genetic changes, which in humans would lead to disease.
That's also one reason why some researchers say zebrafish are becoming more popular in the lab than mice.
Illustration by Simone Hls
Mice are not to be discounted, however. German scientists recently reported that they had cured mice of paralysis after the animals had suffered a spinal cord injury.
But the use of animals, especially those so genetically close to humans, with all the scientific benefits for human life, remains contentious for both scientists and observers of research that uses mammalian model organisms.
Germany's Max-Planck Society writes that "monkeys are used in animal research only if a particular phenomenon cannot be studied on any other species of animal, such as mice, fish or fruit flies. [] They are used primarily for the final drug safety tests on new medicines before they are used on humans."
That is one perspective. Elsewhere, scientists are moving from mice to monkeys.
Illustration by Benjamin St
A feature article in Nature has suggested that cynomolgus macaque monkeys (also known as long-tailed or crab-eating macaques) may be the focus of a "new era of animal models for autism and other brain and psychiatric diseases."
Macaques are already among the most commonly used non-human primates in biomedical research.
The RSPCA, an animal welfare charity in the UK, saysprimates are "highly intelligent animals [] that suffer in similar ways to us."
It goes on to say that "the capture of wild primates for use in breeding colonies and for experiments in some countries causes very significant suffering we believe this is completely unacceptable."I
llustrations by Simone Hls, Christian Kuhn, Olof Pock, Per Sander, Barbara Scheid, Peter Steinmetz, Benjamin St
At a depth of 3,700 meters (12,000 feet), dozens of natural chimneys stick up from the seafloor emitting hot fluid at 290 degrees Celsius (554 degrees Fahrenheit). Over thousands of years, towers of lime have piled up. This is the hydrothermal vent field of the Pescadero Basin, about 150 kilometers east of La Paz in Mexico in the Gulf of California. A marvelous place!
US researchers at the Monterey Bay Aquarium Research Institute discovered the deep-sea vent field at Pescadero Basin in 2015. A few months ago, a research team went back on board the Schmidt Ocean Institute ship Falkor to explore this special place. They mapped the seafloor, recorded high-resolution video and brought back rocks and animal samples.
Due to volcanic activity underground, hot water creeps out of the seafloor, containing chemicals such as hydrogen sulfide - a gas that smells like rotten eggs. It is extremely toxic to humans, but some bacteria can metabolize it and gain energy from it. Those bacteria thrive down here at Pescadero Basin and form these thick, fluffy looking bacterial mats.
The vents are buried in the sediment, so the hot liquid reacts with rocks before it escapes. Therefore, the liquid is clear (like you can see in this picture). At another type of vent called a 'black smoker', dark, metal-rich fluid leaves the chimneys instead. Pescadero harbors life quite different from that what was found at other vent fields explored previously.
The vents are densely covered with tubeworms (Oasisia alvinae). These sessile invertebrates live in chitin tubes just a bit wider than their body. Tubeworms like this one were discovered in the 1970s at a vent field near the Galapagos. The researchers were amazed by how many of these animals live at Pescadero. They are literally everywhere.
Oasisia tubeworms dont have a mouth or a digestive system. Instead, the animals take up hydrogen sulfide and oxygen from the water with their orange-red plumes. They feed the nutrients into a bag filled with bacteria. The bacteria then generate energy for them. It works similar to the bacteria in our guts digesting food for us.
In Pescadero Basin, researchers found species they hadnt seen anywhere else before. Like this iridescent blue scale worm, named Peinaleopolynoe orphanae. Across their back, they have thick discs that refract light - just like the wings of a butterfly. The researchers watched the creatures fighting with each other. They have big jaws which they can project during a fight.
This strange creature is called Xenoturbella profunda, but scientists often call it simply the sock worm. This turns out to be quite literal they are just a bag with a mouth underneath. Scientists saw these strange animals gliding very slowly over the seafloor. They seem to feed on clams, as researchers found clam DNA inside their bodies. How they catch and eat their prey? Nobody knows.
Some animals such as tubeworms, scale worms and Xenoturbella live directly on the hydrothermal vents. Others, though, just float by, like fish or octopuses. Or this guy here, a siphonophore. It resembles a jellyfish, but it's not one. Its more closely related to the venomous Portuguese man o' war.
Apart from animals and rocks, there is more to see in the Pescadero Basin. Underwater lakes like this one, for example. They develop when hot fluid gets trapped under rocks or within caves and cannot escape.
An underwater-robot pilot on the ship steers the remotely-operated vehicle from vent to vent. Via a tether, the robot sends back data and high-resolution video footage to the surface. The researchers can thus see in real-time whats going on down there. An awesome experience, for sure.
The underwater robot has an arm with which it can pick up rocks and animals and bring them back to the surface. But most animals lose their colors and shape pretty soon when conserved in alcohol in the researchers lab. This for a example is a sea cucumber from Pescadero Basin, beautifully colored in life not anymore.
Author: Brigitte Osterath
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Model organisms are more than just monkeys and mice - DW (English)