Methods and Tools for Studying Cell Organization

Although cells have been around as long as life has existed, their small size made them impossible to study for most of human history. In the 17th century, advances in optics made possible the first lenses capable of magnifying cells to a visible size. This led to a science called microscopy, the use of a microscope.

The first person to observe cells was English scientist Robert Hooke. Hooke used an ornate, handmade microscope to observe slices of cork. He saw many small chambers, which he equated to the cells of a monastery. Thus the word cell was coined to describe these basic biological units of life. Hooke published his observations in a book titled Micrographia, which was published in 1665. Soon after, Dutch scientist Antonie van Leeuwenhoek built his own microscope using lenses he ground himself. He used this microscope to magnify drops of pond water, among other samples, and thus observed single-celled organisms for the first time. He first saw protists (also called protozoa), or single-celled eukaryotes, and later saw bacteria. An example of a protist is from the genus Euglena, which contains around 800 species. Euglena are single-celled flagellates, which means they propel themselves by means of a long tail, a flagellum. Antonie van Leeuwenhoek reported his findings to the Royal Society, an English organization dedicated to the advancement of knowledge. The Royal Society published van Leeuwenhoek's findings in several editions in the 1670s, ushering in the golden age of microbiology, a time when many great advancements in microbiology were made.

When Hooke first looked at cells using a handmade microscope with a candle as a light source, he used a light microscope. A light microscope is a microscope that uses light passing through optical lenses to magnify objects. For many years this was the only type of microscope used, and it allowed many advancements to be made.

Light microscopes are still very common and widely used today. A major advantage of light microscopes is that they are relatively inexpensive and simple to use. They require little maintenance and very little power to operate. Light microscopes have a useful magnifying power up to about $1{,}000\times$. In order to distinguish between cellular structures, many scientists will often use dyes, which give particular target structures a certain color. Light microscopes can also be used to view living cells and tissues, which can then be used in further research. A variation on the light microscope is a fluorescence microscope, which is the use of specific wavelengths of light to excite dyes or naturally occurring compounds in specimens in order to view them with a microscope. Fluorescence microscopy often uses ultraviolet wavelengths for excitation, which necessitates a separate bulb from the visible light bulb. A filter allows only a small range of wavelengths to pass through, which excite the fluorescent dye. Light microscopes have many applications, but they do not resolve the structures within cells well. To see these structures, a higher magnification power is needed. A transmission electron microscope (TEM) is a microscope that passes a beam of electrons through a sample and onto a sensor. This sensor can be a screen, film, or charge-coupled device that amplifies low-resolution images. TEMs have a magnification power of 1,000,000$\times$, with a resolution of 0.2 nm. A scanning electron microscope (SEM) is a microscope that scans the surface of a sample with a beam of electrons, which are then scattered and reflected to form an image. SEMs provide information about the appearance of the outside of an object. Because SEM images appear similar to photographic images, they are often falsely colored to give the appearance of photos. The magnification and resolution of an SEM are slightly lower than those of a TEM; however, the SEM requires less power to operate because the electrons do not have to pass through the sample. The techniques used by the TEM and SEM can be combined, the result being the scanning transmission electron microscope (STEM), which gives the greatest resolution, below 50 picometers (pm), $1\times10^{-12}$ meters. However, electron microscopes are very expensive and require careful and regular maintenance, and their use to visualize cells results in the death of the organism or cells studied because the specimen is mounted in a vacuum chamber.

Cells can be grown in culture in the laboratory. When living cells are taken from living tissue and grown in artificial media, this process is referred to as tissue culture. This is true even if the cultured cells do not form tissues in the laboratory. When the cultured cells are derived from a single cell, it is known as a cell line. Because of this derivation, all the cells are considered to be genetically identical.

Many kinds of cells are maintained in cultures, but due to the fact that a great deal of research is concerned with humans, human-derived tissue culture lines are of the highest importance. The most common and thus most widely used human cell culture line is called HeLa. These cells were obtained from the cervical tumor of Henrietta Lacks in 1951. Ms. Lacks was a young mother who visited the Johns Hopkins Hospital when she noted vaginal bleeding, and was subsequently diagnosed with cervical cancer. The cells taken from Ms. Lacks were given her name—Henrietta (He) and Lacks (La), hence the name HeLa cell. A great deal of controversy surrounds the methods by which the cells were obtained, because the doctors who took them did not have permission to do so. However, HeLa cells have proved vital to much of the biological and medical research of the 20th and 21st centuries.

To grow the cells, researchers place a single cell in a nutrient-rich growth medium and place that medium in a glass flask incubated at 37°C, human body temperature. The cells divide and divide again, continuing until the flask is filled. At that point some cells can be removed and placed in a new flask, and the process can be repeated. In this way, HeLa cells have been maintained continuously since 1951.

Although organisms such as human beings, flies, and bacteria appear very different from each other, the cells that make them up have many things in common. Some cells are easier to study than others, and scientists can learn a great deal about the functions of all cells by examining only a few. For this reason, some species are studied as model organisms. A model organism is a species that is studied because of specific characteristics that make it easy to understand, with an expectation that much of what is learned about the species applies to other species as well.

The reasons some species are chosen as model organisms vary. Some species are transparent, making the structures of their bodies easy to see even while they are alive, such as zebrafish. Some have short generation times, so that the heritance of information can easily be studied by humans, such as E. coli. Others are susceptible to genetic manipulation, so that new genes can easily be introduced or existing genes can be turned on or off at will, such as fruit flies. Some have organs and organ systems that behave in ways very similar to those of humans, such as mice.

A few of these model organisms have been instrumental in modern understanding of biology. The most famous of these is Escherichia coli, or E. coli. This bacterium readily grows in artificial media, and its genetic material can easily be manipulated. Much of modern knowledge about DNA, proteins, and the ways in which cells carry out life processes comes from studying E. coli. A major drawback of using E. coli as a model organism is that it is a prokaryote and humans are eukaryotes. Saccharomyces cerevisiae, also known as brewer's yeast, offers many of the advantages of E. coli, such as short generation times and ability to be grown in artificial media, but is eukaryotic, thus offering insights into the workings of eukaryotic cells.

A common model plant is Arabidopsis thaliana, the common wall cress. It can easily be grown indoors and has very short generation times.

Animal models make up many of the common model organisms. Drosophila melanogaster, the fruit fly, is a useful animal model because of its short generation times and the insights it offers into genetics and heredity. The nematode worm Caenorhabditis elegans gives a great deal of information about organism growth and development. The zebrafish, Danio rerio, offers insights about the development of vertebrates, namely because zebrafish are transparent during the first few weeks of their lives. Finally, the mouse, usually species Mus musculus, is the most common mammal model, with entire model lines having been bred over several decades. These lines have been bred to have certain characteristics that make them ideal for specific studies. For example, the BALB/c line is especially susceptible to tumor growth when tumor cells are introduced, making them instrumental in the study of cancer.

There has been recent debate regarding the importance of model organism study. Recent technological advances appear to be superseding the use of model organisms. One such advance is CRISPR, which stands for clustered, regularly interspaced, short palindromic repeats. CRISPR is a group of bacterial DNA sequences that are used to defend against viruses. CRISPR can be altered and used to target and modify specific gene sequences.