Ask A Biologist

Written by Anna Cacciaglia

We may be used to thinking of evolution as the cause of big changes, such as the emergence of a brand new trait or species. But evolution really takes place on a much smaller scale, from the compounding of slight changes to individual genomes. While the evolution of novel traits like opposable thumbs or feathers doesn't usually take place on a timescale practical for observation, these huge developments result from many small changes; changes which can be possible to examine in the lab. Using DNA analysis as their guide, researchers have developed ways to study both short and long term changes in the genome, and more completely understand what might be the most important theory in biology.

For example, the field of "experimental evolution" makes short term changes visible in the lab. Using organisms like bacteria, viruses, and yeast, which evolve quickly by virtue of short generation times, researchers can track the changes in DNA sequence between generations and observe those changes' effects, giving them a window to watch a population of living things adapting to an environment in real time.

Researchers interested in changes that took place long ago must use a different approach: looking at biology forensically. The study of prehistoric changes draws on a wide range of scientific fields, from molecular biology and chemistry, to ecology, geology, and paleontology. Keen observations of present inheritance patterns, like the influence of mutation, natural selection, and chance, when combined with physical clues like fossils, can provide some insight into the evolutionary process. However, much of the investigation relies on DNA evidence. Because DNA is passed faithfully from parent to offspring, every change that has occurred in the sequence is preserved and can be accounted for today. Sequence comparison between different species can tell us about the genomic differences between them, and those disparities can be narrowed down to a single gene, hinting at the specific modifications that may have prompted staggering evolutionary shifts.

The Wittkopp lab uses techniques like these to study the evolutionary process. Their studies involve investigating mutations as the raw material for evolution, finding the genetic differences that make individuals of the same and different species unique, and determining the molecular and developmental consequences of these genetic changes. The lab studies the regulation and evolution of gene expression in both fruit flies and yeast, with a special interest in pigmentation differences within and among fruit fly species.

Every cell in your body encounters roughly 50,000 DNA lesions per day. This high number doesn't include events that expose your body to more damage, such as sun tanning. The Simmons Lab uses a common soil bacterium to learn how DNA abnormalities are identified in the cell and how DNA damage is repaired.

To study DNA repair, the bacteria are exposed to chemicals that cause DNA damage. A variety of techniques are then used to study the repair process, one of which is watching the proteins work through a microscope in live cells. Within minutes, the bacteria has identified the damage, and begun the repair process. The Simmons Lab studies this process imaging thousands of bacteria daily.

The Simmons lab also studies DNA mispairing events. DNA is copied quickly at roughly 1,000 bases per second. As the bacteria's DNA is copied, mistakes can be made, caused by mispairing in the DNA. While mispairing is rare in cells, with the human body consisting of 100 trillion cells, mispairing in the human body is not uncommon. Sometimes mispairing in humans can have serious health consequences resulting in mutations that can lead to cancer. Through using biochemistry and genetics to study how the mispairs are identified and corrected in bacteria, the Simmons lab relates this information to human cells in an effort to improve our understanding of mutation-associated diseases.

Answer courtesy of Professor Lyle Simmons

In 1944 the Nazis cut off the Netherlands from its food supply, leading to the Dutch famine ("Hunger Winter.") The children of the stressed and malnourished pregnant women were smaller at birth, but when the war ended and food was plentiful they appeared to grow to a normal size for their age. However, as adults they had a greater incidence of cardiovascular disease and diabetes. These adverse health effects may be attributed to exposure of the offspring to elevated stress hormones while in the womb caused by the maternal malnutrition and psychological stress.

Elevations in stress hormones during early development caused by exposure to stressors may predispose individuals to disease and psychosocial disorders later in life. Stress hormones may cause modifications to DNA (DNA methylation) and the proteins that surround the DNA (the histones). These changes are called "epigenetic" in that they do not involve mutations in the DNA, but lead to altered levels of gene expression. There is a growing body of evidence that epigenetic mechanisms of gene regulation play central roles in mediating the relationship between the early environment and later life physiology and behavior.

Answer courtesy of Professor Emeritus Robert Denver

Transgenic plants, also known as genetically modified plants, are plants that have been modified to carry genes from various sources. While some genes can simply come from other non related plant species, plants can be engineered to carry genes from bacteria, animals and even human cells.

Carrying and expressing foreign genes does not necessarily mean that transgenic plants pose a risk to humans, animals or their environments, but rather that these plants now carry new and sometimes unique traits that are useful for research and agriculture.

Such genes, for example, can make crop plants resistant to herbicides or insects, which enables a reduction in the use of herbicides and pesticides in the field, while others enhance the crop plants' nutritional value, making them more beneficial for human consumption. Future crop plants may also carry genes for salt and drought tolerance, allowing them to grow in arid and salty soils, and even genes that encode pharmaceuticals, for the production of edible vaccines.

Agrobacterium is a unique bacterium that is capable of transferring part of its own genome into plant cells. Extensive studies of its unique life cycle have allowed researchers to engineer the bacterium such that it will no longer transfer its own DNA but will transfer other fragments of DNA carrying genes that are useful for plant research and biotechnology.

Transformed cells, carrying the new and transformed DNA, can be selected and regenerated into full-grown transgenic plants. Because the bacterium is eliminated after delivering the DNA into the plant cells, the new transgenic plants are essentially identical to their parent plants except that now they contain a new gene; they do not, however, contain any bacterial residues or genes.

While Agrobacterium is the most widely used vehicle for the production of transgenic plants, other methods make use of mechanical means and physical pressure to deliver foreign DNA into plant cells which can then be regenerated into full-grown, genetically modified plants.

When it comes to things like bacteria and parasites, you probably think, "Yuck, I don't want them on or in me." But there are tons of good guys in the microbial world – many bacteria that live in and on our bodies have profound effects on keeping us healthy.

New research is showing that microbes living inside our digestive track help improve metabolism and spur weight loss. Evidence suggests a person's ability to extract energy and store fat from food changes depending on which combination of bacteria are living in the person's gut. Those who are morbidly obese tend to nurture bacteria that promote the fat-storage process, which is likely a factor in their excessive weight.

The composition of your microflora, (or bacteria living in and on your body), helps to establish how many calories you absorb from the food you eat. This might explain why two individuals can consume the same amount of calories, but one will gain weight and the other won't.In the future, we may be able to manipulate the microbes of obese individuals to look like those of normal-weight people which would likely aid in weight loss.

Answer courtesy of former Assistant Professor Blaise Boles