When researching the effects medicine has on a living organism or when trying to track how a disease is contracted and spreads throughout the body or when just simply wanting to test an observation in nature within a controlled and reliable setting, the scientific community has the greatest thanks to offer to the model organisms. While it was a collective decision on which organisms should be given such a title, their innate capabilities more than make them stand out. They act as the perfect representations for broader species beyond themselves or as active and responsive partners in chemical testing. Regardless of how they are ultimately used, these models have proven to be the best of the best for one field of study or perhaps many.

In this sequel to the prior article, we will be covering yet another set of critical model organisms, their history, and how they have contributed to the progression of science and the world as a whole. In some cases, they may manage to overlap, but model organisms almost always have unique niches that only they can fill due to their biology. Let us start with one of the most well known of the models throughout the past several centuries.

Mus musculus: The Human Disease Model Organism

The humble mouse has much to brag about. While its original inclusion among model organisms may have been a product of fickle chance, it has proven its viability in the races over the decades since. But we should start at the beginning, the beginning of genetics in particular.

Though Gregor Mendel’s groundbreaking research was lost for quite a long time after its completion, two full decades after his own death, its resurfacing in 1900 would create a revolution. The process of Mendelian inheritance would undermine many of the long-standing beliefs about biology at the time and would usher in an age that led directly to the discovery of DNA half a century later. Those early papers though, especially in the years up through 1905, were a rush, as multiple famous scientists tried to be the first to find new insights into the world around them and to be the first to find a stable model organism to represent genetic change.

The most famous outcome of this time period were a series of papers by Lucien Cuénot, who chose mice to be the first example of such inheritance. At the same time, William E. Castle started looking into coat color inheritance in the same species, even though he had been prior and would be after a mainstay in Drosophila genetic research. Those same teams would discover up through 1910 that if they wanted to have a pure and expressive example of visual phenotypic inheritance, then they needed to make homozygous strains for only the one set of dominant or recessive genes, to remove the possibility of heterozygous combinations occurring. The only way they found to ensure this was the method of inbreeding.

The first inbred strain of mice was produced by C.C. Little in 1909, where he managed to create a population of mice with homozygous traits for brown fur. There was no color invariance in the line, proving he had successfully stabilized the inheritability of the trait. This DBA line would be the first of many to follow and with more complicated traits to boot, but this was the starting point of the mouse genetics period of history. C.C. Little himself would prove the foundation for something much bigger than he likely realized in his early days working with mice at Harvard University.

Characteristics of Mice

There are several factors that play into the usefulness of mice as model organisms and that also act as barriers to the results of experiments being perfectly transferable to human beings. The first and most obvious of these is the difference in size between our two species. Humans stand, on average, at about 2500 times the mass of your common house mouse. This results in a change in metabolic rate and of our ingrained techniques for obtaining food, so studies that focus on metabolic changes have to be careful when generalizing impacts.

Thermoregulation and heat loss at different sizes also comes into play, along with nutrient demand for keeping up the energy of mice bodies versus human bodies. It is well known that mice have higher metabolic functionality, causing increased liver and kidney breakdown of toxins, along with requiring higher amounts of food in relation to body mass. This, in turn, also causes changes on the cellular level. Mice feature higher amounts of mitochondria and also have a higher amount of certain fatty acids that make up the plasma membrane of their cell walls and their organelle membranes.

Their differing speed of maturation and subsequent reproductive cycle also inhibits certain kinds of reproductive studies, while also making mice incredibly convenient for studies involving rapid production of new generations and the effect of compounds over generations. It is common for lab strains of mice to be bred for higher fertility to benefit from this as well. They also are set to consume a different diet, usually high in grains, which alters their gut microbiomes as compared to humans.

Complicated disparities involving unknown chemical metabolism and immune system cells in mice means that toxicology results can be misleading when compared to humans, which is why multiple model organisms are suggested in order to ensure toxicology testing has the same impact on multiple species. Being closer to the ground also means having a higher exposure to inhalation of pathogens, which is why mice have higher densities of lymphoid tissues leading to their lungs, in order to block out harmful microorganisms.

Mice As A Microbiome Model

As was just mentioned, the utility of the mouse model organism in the field of gut microbiota research is a heavily debated topic. The similarities we share in overall physiology, genetics, and even simple anatomy is a significant boon to the field, especially the short generational time period. Since mice are also one of the most heavily studied organisms with deep knowledge on their genomic makeup, along with the already created numerous knockout and genetically modified lines of mice for every desired purpose, they seem like they should be perfect for studies on this and other topics. And, indeed, that has proven to be the case and has brought much scientific and medical benefit.

Even if their personal gut microbiome differs from our own, they can still act as a model for how microbiomes function in a general sense and how they respond to induced perturbations. Disorders like obesity and type 2 diabetes are particularly beneficial, as we can use mice to study how the onset of these issues begins and what the symptoms and characteristics are that lead up to them. Autoimmune disorders and allergies as well serve as a good starting point in mice, even if precise cellular types may not be comparatively relative to humans.

Some of the important research being done includes creating gene knockout lines for genes that match up with the human genome and seeing how that alters the population of gut microbes, Tests in germ-free mice or those requiring antibiotic treatment or fecal transplants can also help explain the long term impact of these medical options. The kinds of interventions possible in mice wouldn’t be realistic in humans due to them requiring a large portion of the organism’s lifespan to see any results, whether they are positive or negative.

So, it’s easy to tell that there are good and bad parts to using mouse models to study health-related issues in humans. If they are appropriately generalized, then the results can be considered reliable enough to the effects seen in humans. It’s when specificity is being dealt with that mice may diverge in the effects seen, especially when it comes to early development. There are other areas, however, where mice can be particularly helpful.

Mice and Immunology

When searching for a translational model to humans, mammals are often the only option. If possible, our close cousins in chimpanzees are heavily desired, but often impractical for certain kinds of research, even within biomedical areas. But, close phylogenetic relation doesn’t guarantee success regardless. There are certain parts of human physiology that a model other than a chimp turns out to be more translationally accurate.

In the case of single-celled parasites like protozoa and other parasitic infections, mice have commonly been viewed as superior options for testing immune system responses and as antibody producers. The usage of rodents as models in these cases has often topped 90% of all species utilized and mice will likely become even more dominant with the advent of CRISPR technologies allowing easier gene knockout strains to be made without the need of inbred lines.

The ability to control their surroundings and access to food, water, bedding, and even light and dark cycles means that pathogenic infection can be monitored and processed from every angle. Anxiety and depression has been shown in such experiments to play a role in infectivity and risk of lowered immune system response. But, even with all these benefits, there remains plenty of cases where mice models alone can prove significantly harmful when taken straight into human trials.

The CD28 antibody test was just such a case. This was where a humanized version of an antibody, originally tested in mice, against the human T cell receptor CD28 was used in an attempt to alleviate the effects of the autoimmune disorder known as rheumatoid arthritis. It did quite the opposite of what was expected. All six of the human patients were hospitalized, several of whom had multiple organ failure due to a cytokine storm, where a huge amount of immune cells were produced and began to attack the body itself.

Even the tests in closely related monkeys that were done as a secondary model organism didn’t show this result. It turned out that this was due to our close relatives not expressing CD28. Humans are, apparently, specifically unique in that function among primates, while being similar enough with rodents that can themselves express it. But why did the results not match up between humans and mice, when we both share the expression of CD28?

It turns out that because the mice had been kept in a sterile lab their entire lives, they were never exposed to microbes that would have activated CD4+ memory T cells. Thus, their exposure to the antibody only caused a first time immune response and memory storage. When the treatment was tested on wild “dirty” mice, their immune systems went haywire much like it did in the human patients and caused a huge overproduction of immune cells.

This oversight has, thankfully, resulted in a change of procedure since, where medical testing in mice is done on both lab and wild mice in order to ensure the result is the same. With every mistake, we learn more and can take steps to improve and prevent that same issue from arising again. The primary hope in the medical community is that such testing won’t require the cost of lives in the process, but time wasted is equally more people lost.

Mice have their upsides that has cemented them as prime real estate for medical and genetic testing in science, but we are discovering over time the areas where they fall short and have to be backed up by subsequent model organisms. Whether lab mice will continue to be in their dominant position in the lab is hard to determine and only the future will tell.

Danio rerio: The Developmental Model Organism

On a similar competitive scale, but filling in its own region of the scientific space lies the zebrafish, Danio rerio. This small and innocuous fish has only come to specialized scientific attention in the past several decades. It is easily grown and controlled, along with having a perfect setup for genetic manipulation and the study of embryology and body plan development. The transparent eggs it lays are a ready bonus to its other traits.

The history of zebrafish in science is both longer and shorter than one would expect and is filled with the love that certain researchers had for the little fish and what it brought to their experiments. To discuss all that though, we have to go back to the start.

A Globe Away, Filled With Zebrafish

The first classification and description of the zebrafish happened under somewhat strange circumstances, conducted by a physician as a member of the British East India Company in 1822. This original classification has undergone several revisions in the period since due to phylogenetic rearrangements and discoveries of true relatives of the species. Later investigations found populations of the fish across the Indian subcontinent and in many forms of water conditions, including up through rivers near the Himalayas.

Due to only simple tasks being needed to care for and grow the fish, their early use as an object of study for vertebrate anatomy and some development goes back to the 1930’s. It was a scientist by the name of Charles Creaser at Wayne University that became one of the first advocates for more widespread usage of zebrafish, believing they should be used both by students in college and by experimental researchers themselves. The next several decades saw several isolated, though prolific, groups of scientists use zebrafish in studies ranging from toxicology to animal behavior to neurobiology.

But the application of zebrafish was quite haphazard and followed no designated system by the scientific community, who had yet to fully embrace the lowly fish as a true model organism. It was finally thanks to George Streisinger, a famed Drosophila researcher, that this all changed. He spent over ten years looking into optimized ways of breeding and making use of zebrafish, including in mutation studies, genetic engineering, and clonal cell development, all of which he published about throughout the 1980’s.

Streisinger started an early genetic screening test of zebrafish using gamma rays to look for genetic variants and unique phenotypic expressions. Alterations in pigmentation were some of the more common forms of changes that were observed during this experimentation. Unfortunately, the famed scientist ended up dying in 1984 after a horrific accident and it was his colleagues in his lab that finished up and published in his name the research he had been conducting. The University of Oregon itself, his place of residence, took up the fight to turn the zebrafish into a recognized model organism for vertebrate science.

At the same time as this was going on, another team led by Christiane Nüsslein‐Volhard at the Max Planck Institute began working on conducting a “Big Screen” focused on vertebrates. Her group had already completed such a screening on Drosophila in the 70’s and 80’s, but they wanted to find biological pathways with greater relation to human development and a vertebrate was their best bet. And the zebrafish was what they chose to go with. In 1993, they began using the mutagenic agent ethylnitrosourea in order to mutate sperm from zebrafish and created highly mutated offspring to see how this affected their development. Over 4000 mutant lines of the fish were made in this manner.

The final “Big Screen” published in 1996 made use of 1163 of these lines and comprised an entire special edition of the journal Development with multiple papers coming out from her team. The rest of Nüsslein‐Volhard’s students went off to form their own independent research labs and continued using zebrafish as their focus. In 2001, the Sanger Institute began sequencing the genome of the zebrafish and finished in 2013, causing a huge boom in the vertebrate being seen in research experiments, especially due to it coinciding with the rising tide of CRISPR science. Things have only gotten crazier since.

Zebrafish Traits and Secrets

The omnivorous nature of the zebrafish is one part of their physiology that makes them amenable to containment in a lab, while also making it perfect to study both sides of its eating habits as a vertebrate. Study into how diets of only meat or only plant material affected the gut of these fish was revealing, as a 2011 study found that there appears to be a so-called “core” set of gut microbiota in the species that are kept no matter the eating habits and environmental conditions that may alter it. These microbes likely play a role in early growth and development of the fish and raise questions on whether the same is true for other vertebrate species, including humans.

A downside of such early use of zebrafish starting from the 1800’s and their remote settings in the wild is that very little is known about their behaviors in nature and whether how they are observed in a laboratory setting coincides with their actual activity. But the opening up of the zebrafish genome has at least enabled us to figure out the parts of their genetic makeup that facilitates certain behaviors. Originally, they did not stack up well against mice as a model organism due to the inability to easily insert transgenic changes into their genes.

This all was blown away in the early 2000’s when work on transposons revealed methods to randomly insert transgenes and allow for the creation of transgenic lines involving fluorescent protein markers. Early developmental changes turned out to be easier in the fish this way too, due to their fertilized eggs being outside of their body, rather than developing inside a mother’s uterus like in mice. As transgenic and knockout techniques have improved, zebrafish have become more and more the organism of choice for single gene research, though many scientists still stick to their old reliable standby of the mouse.

This deeper understanding of the zebrafish genome has also revealed just how genetically diverse the species is. When two zebrafish from different lab strains were compared, they were found to have more than 7 million single nucleotide variations between them. When a wild zebrafish was then put through the same test, 5 million more such nucleotide mutations were found. This amount of diversity was astounding to find in a vertebrate species. In comparison, when 1000 human genomes were compared, they found a total of 38 million differences. For only 3 zebrafish to reach nearly a third of that was bizarre.

Why the species has this complexity is unknown and there certainly doesn’t appear to be higher amounts of lethal phenotypes being expressed in the wild. But it does pose a challenge to experimentation, as it means genetic testing has to be able to control for these differences or it could throw off the results when contrasting experimental groups. And it also factors into another strange result that lab domestication appears to have caused in zebrafish strains.

For the longest time, it was unclear what the sex-determining genes in zebrafish were and it was a puzzling absence that troubled many scientists. Among those studies that had been able to successfully identify such regions differed on where the regions were and for no clear reason. Then, in 2014, a researcher was finally able to show that in wild zebrafish, they have a very distinct sex-determining region on their chromosome 4, but that all lab strains appear to have lost this region, instead distributing their sex-determining genes across their genome. Which explains the varying answers that were being found.

The domestication of zebrafish for work in the lab appears to have forcibly evolved them into no longer having distinct, recognizable sex chromosomes and instead having those same genes be all over the place. While it has served as an incredibly beneficial look into how sex determination may have initially evolved, it has made comparative studies between wild type and lab strains even more difficult. The impact this has had on their reproductive capabilities and internal physiology has yet to be looked into.

This short look into one of the primary vertebrate model organisms has hopefully proven their distinctiveness and also the challenges that arise for every model and how it is hard to say that one is truly better than another. They all have their good points and they all have their crippling downsides, but its how they are employed that matters the most. As a final overview, let’s move onto a model organism that has less weaknesses than most and shows broad applications in industrial production.

Saccharomyces cerevisiae: The Productive Model Organism

Of all model organisms, it can be argued that the simple budding and brewer’s yeast, Saccharomyces cerevisiae is the oldest of them all, with the longest extended history into the lives of humans past. We used it for the fermenting of our bread and our alcohol and it has been needed for staple foods around the world for thousands of years. Though its usage did not coincide with real understanding of its properties until just over a century ago when Louis Pasteur was able to directly break down the fermentation process of alcohol in 1857.

Research into how to make better alcohol coincided with ideas about genetics and selective breeding around the turn of the century. Emil Christian Hansen was the first to find a way to obtain a purified strain of yeast from a mixed starter culture. By the 1930’s, crossbred strains of high quality were being pumped out by breweries around the world. At the same time, the first work on having yeast be a scientific tool began when two researchers started creating genetic crosses as the initial step toward unraveling the yeast genome. Desired traits were isolated and strain lines focused around individual genes produced.

The 1950’s saw the S288C strain, thereafter the commonly procured lab line of yeast, being applied by Robert Mortimer with mutagenic chemicals to start large scale mutant lines of yeast with variable traits. Though yeast lines being featured in the lab continued to grow through the 60’s and 70’s, it was still considered yet another microbial model organism with no defining characteristics to have it stand out from the pack. The biotechnology age would take care of that problem though.

In 1978, the first reports of yeast being transformed thanks to a plasmid from E. coli changed everything. It began being chosen for gene modification experiments left and right and that has defined its utility to the sciences ever since, the simplicity of which genes can be added and taken out from the tiny yeast cell. Not only does this make it incredibly easy to divulge the secrets of the yeast genome, but it also means that yeast is one of the optimal candidates for producing complex molecules for which there is no chemical alternative to make. The way that plasmids or the yeast chromosomes themselves can be manipulated with little effort opened an innumerable amount of doors.

The high amount of focus on S. cerevisiae resulted in it being the first eukaryotic organism to have its genome completely sequenced, as was shown in 1996. The homology that this tiny little fungal-esque organism had with humans shocked the scientific community, confirming the profound and innate relationships living organisms hold, even those with distant relations going back hundreds of millions of years. Many molecular functions that were expected to only be a part of higher, complex creatures was found to be just as present and functional in yeast, all of the same entangled chemical pathways being conserved.

It is this steady accumulation of insights that had led to baker’s yeast being one of the most unveiled organisms that have ever walked the planet, in regards to humanity’s knowledge about them. Let’s go over some of its mechanisms, lifestyles, and character traits.

The Lives of Yeast

There is an inherent paradox in our study of yeast. They are arguably the most mechanically understood organism on the planet, yet we’ve only managed to find out that information within a laboratory system. There is little to no knowledge on yeast activity in the wild, which is itself due to how incredibly rare it is to find a wild population and that they are often undernourished when they are found. So, its true natural life cycle may forever be a mystery. Or perhaps it is the same as in the lab and we already know all about it anyways.

For the places they are found, such as on oak bark, they are often subjected to inclement conditions like flowing tree sap that force them into a hibernation-like state in order to survive. But, given favorable atmosphere and food in a container and they will happily grow hog wild on a fair amount of media, so long as it has fermentable sugars. Their twin sexual cycles of both mitosis and meiosis reproduction additionally serve as a perfect testing hub for the effects of clonal versus sexual reproduction on genetic outcomes. Haploid spore production can also be manipulated to test single parent and one-sided chromosome differentiation and the effects on development this has.

The growth media that yeast can be placed in bely the types of fermentation that they can undertake. The type of alcohol (or more recently agar plates) that they were grown in over the centuries inherently morphed the strains toward more efficient utilization of the fermentable sugars. This adaptation also steadily led to higher alcohol levels in their contents over time. Though there are plenty of non-fermentation based strains used in labs for other purposes.

In addition to the discoveries presented involving eukaryotic function and the processes of cell division, other famous scientists have put forward yeast inventions related to the creation of industrial and medically important molecules. The work pioneered by researcher Randy Schekman on vesicle trafficking and the secretion system in eukaryotes was a direct foreshadowing of the eventual use of yeast as molecule secretors from insulin to phenols, alkaloids, and other molecules that would be at too small an abundance if gathered in any other way.

The options for yeast in science cross nearly every field and touch every discipline in some manner, showing just how relevant this small microorganism continues to be, as it has been for all of human history.

A Drop In The Bucket

That’s three more model organisms considered and yet we’ve barely even looked at what is out there. Even among the most popular specimens, there are several that will have to be left out for now. We will have to find them again next time.

Hopefully this dive into other aspects of model organisms, the roles they’ve played in our lives, and how they continue to serve as the basis for all our knowledge today about the natural world helps inspire further interest into what else is out there. No model organism is perfect and no model can tell us everything we want to know. The search continues not only with those we have and know so little about, but also for the organisms out there yet to uncover and the properties that might further revolutionize our growing world.


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Photo CCs: Zebrafish (26436913602) from Wikimedia Commons

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