Ask A Biologist

Why do I wake up at the same time on weekends as on weekdays...

Written by Anna Cacciaglia

...even when I haven't set an alarm?

It seems reasonable to assume that the time we wake up each day is based on environmental clues (such as the amount of light in the sky) or individual conditions (e.g., how much sleep we need on a particular day.) While both of these things can play a role, it is a clock in your brain that tells your body when to wake up, whether you want to or not.

The hypothalamus, a marble-sized structure sitting over the roof of your mouth, is the location of this clock. The hypothalamus mediates hormone release, influencing when we sleep and wake. Experiments in which participants are isolated from any time-cues show the power of this clock. Even without external clues, your body can assume and maintain a predictable sleep-wake schedule. The Shafer lab utilizes the fly Drosophila melanogaster as a model to study how the brain's clock controls rhythmic behavior. Using anatomical, genetic, and live-imaging techniques, the lab seeks to understand how clock neurons influence behavioral changes on a daily and seasonal scale.

Under conditions when your body's clock must regularly be overruled, such as the case of a shift worker or doctor on call, the medical consequences can be serious. People whose sleep-wake schedules are regularly unpredictable face higher rates of several diseases, including metabolic syndrome and cancer. Researchers hope that an improved understanding of our natural rhythms can prevent these consequences in a society in which obeying an internal clock has become a luxury.

As frustrating as it may be on a Saturday morning, our hypothalmus's agenda is crucial to our wellbeing. So the next time you find yourself staring at the ceiling hours before you were planning on rising, remember how essential timekeeping is to the health of your whole body and have confidence that your brain is taking good care of the rest of you.

How can we study evolution if the process takes thousands of years?

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.

Can bacteria make you lose weight?

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 Assistant Professor Blaise Boles

Understanding how DNA is repaired when damaged

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 Assistant Professor Lyle Simmons
Photo: C. elegans embryo under the microscope

Are the genes in my eye the same as the genes in my liver?

The cells are different, but they have the same genes. A copy of your DNA is contained in every cell, holding the genetic instructions to generating all your specialized cells. Your DNA has roughly 25,000 genes to choose from to create the cells your body needs to live. The Csankovszki lab is learning how cells decide which genes to turn on which genes to turn off.

Research in the lab is done on the one-millimeter long round worm, C. elegans. This model organism is dissected and has its nuclei studied under a microscope. Several C. elegans are studied at one time, with normal cells being compared to mutant cells.

The need to understand how cells regulate their genes is important. Without this cell regulation, a cell's controls can go awry. Cancerous cells have lost their internal controls and do not mature into a specialized cell. With a better understanding of gene regulation, when something goes wrong in a cell, we will be better equipped to learn how to fix it.

Answer courtesy of Assistant Professor Gyorgyi Csankovszki

You are what your mother ate

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 Robert Denver

Why do plants have a fragrant scent?

Scents have a way of jolting us into recalling deeply seated memories.The whiff of a plant's fragrance might bring to mind childhood experiences, evoking a sense of time and place more powerfully than any other stimulus. Our ancestors knew the emotional power of particular smells, which are mentioned in ancient religious texts such as the Egyptian Book of the Dead, the Hindu Vedas and the Judeo-Christian Bible.

What we perceive as a fragrant perfume is actually a sophisticated tool used by plants to entice pollinators,discourage microbes and fend off predators.

Although we generally think of plant aromas as pleasant, many plant volatiles are toxic when eaten. These compounds may be used by plants to protect vulnerable organs (such as sugar-laden fruits) from microbial assault. Humans have recognized and taken advantage of these antimicrobials since antiquity, when they were used to retard spoilage.

Right: The contest between insect herbivores and their leafy meals is merciless. This tobacco hornworm (Manduca sexta) is at the end of its life after being eaten from the inside out by braconid wasp larvae. These parasitic wasps respond to volatile compounds emitted by the plant as it is being eaten. Homing in on the plant's distress call as a chemical invitation to dine, the tiny wasp lays its eggs in the grazing caterpillar.

What is plant biotechnology and how can it help feed the world?

A growing world population, increased demand for food and the constant reduction in farm land used for agriculture can pose a great risk to food-production stability and supply.

While efficient distribution and better access to food sources is currently required to solve hunger and malnutrition in about 20% of the world's population, it is obvious that significant improvements in agriculture are required if we wish to maintain and, in fact, improve our ability to feed the world.

Basic plant research, which helps us understand how plants develop, grow and interact with the environment and their pathogens, can help us design new ways of improving and controlling their growth not only for further research, but also for improving their agricultural traits. Plant biotechnology is one of the special niches in plant biology research which is typically aimed at improving and using plants for various applications by means of molecular biology and the production of genetically modified (also known as transgenic) plants.

Answers courtesy of Assistant Professor Tzvi Tzfira.

Why should you avoid looking directly at the sun, even during an eclipse?

Because sunlight is so bright—even the few rays of light that escape from the edges of the sun during an eclipse—that the photoreceptors in your eye can be destroyed by over-stimulation. And, if you lose too many of your photoreceptors, you will go blind.

Photoreceptors in fishes can be destroyed by mimicking what happens when you look into the sun; a high-intensity metal halide light source produces a bright spot of light that is shined into the fishes' eyes through an optic fiber cable. The bright light destroys both cone and rod photoreceptors, and the fish is temporarily blinded, but the photoreceptors regenerate within a few weeks.

Photoreceptors are specialized neurons in the retina that respond to photons of light by generating neural signals. These signals are processed by other neurons in the retinal network and then sent via the optic nerve to the brain, to produce visual perception.

The human neural retina, like the other parts of the central nervous system (i.e., the brain and the spinal cord), is unable to replace neurons that are lost through disease or damage. However, fishes have a robust ability to regenerate neurons and nerve fibers in the brain, spinal cord and retina, and are able to repair neuronal damage and restore function.

Cone photoreceptors regenerating in a zebrafish (Zebra Danio) retina. The green, finger-like, feathery cells are cones. A region of undamaged retina with intact, normal cones is at the upper right side of the figure. The magenta dots mark regenerated neurons. In the boxed areas, shown at higher magnification at the bottom, are small, immature regenerating cones.

The retina in fishes contains neural stem cells that regenerate neurons, including rod and cone photoreceptors, and recent research has identified these neural stem cells as a type of support cell called Müller glial cells.

The human retina also has Müller glial cells, which proliferate and generate cells when the retina is damaged, but in humans the Müller cells generate a glial scar, rather than new neurons. Research on fish retinas may lead us to discover how we can coax Müller glia in the human retina to generate neurons, so that we can better treat retinal diseases and injuries that lead to blindness.

Answer courtesy of Professor Pamela Raymond.

What are transgenic plants and why do we need them?

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.

How do we create transgenic plants?

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.