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Volume 5, Issue 2
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1 Visible Evolution

Imagine finding components of a human eye in a worm.  What would this tell us about eye evolution? Opponents of natural selection have frequently claimed the eye is too complex for Darwinian evolution to explain. However, current research on eyes casts new light on how they evolved. In the September 29th issue of Science, Professor Russell Fernald in Stanford’s Department of Biological Sciences reviews how genetics is helping scientists illuminate the evolution of eyes. 		Stephanie Le 144
2 The Ticking of Internal Clocks

Many organisms have circadian rhythms, internal clocks that are closely linked to the light-dark cycle of a day. Generally, if an organism’s internal clock is unsynchronized, it continues to live a normal life with no serious physical consequences. If these clocks seem so inconsequential, why has Mother Nature preserved them throughout evolutionary history? Recent research by Dr. Norman Ruby, a senior research scientist in Stanford’s Department of Biology, suggests that circadian rhythms are closely linked to the ability to learn new tasks. 		Michelle Meyer and Nishma Sachedina 143
3 The Cost of TB Resistance

For most people, coughing and sneezing may rarely be acknowledged beyond a perfunctory “bless you”, but these symptoms are very serious for patients suffering from tuberculosis. Often thought of as a disease of the past, tuberculosis is actually a major health problem in the world today. A Stanford research project recently made progress toward a better understanding of tuberculosis (TB) and multi-drug resistant tuberculosis (MDR-TB). Led by Stanford epidemiologists Gary K. Schoolnik and Peter M. Small (now at the Bill and Melinda Gates Foundation), Associate Professor of Biological Sciences Brendan J. M. Bohannan, former postdoctoral fellow Sebastien Gagneux and graduate student Clara Davis Long, the study examined a long-held belief that bacteria with drug-resistant mutations are at a competitive disadvantage compared to drug-susceptible bacteria. Results of the study, however, revealed that some types of mutations carry no competitive cost. 		Kathleen Jia 137
4 The Protein Switch

Recent advances made at Stanford University’s Departments of Chemistry and Chemical and Systems Biology will now allow scientists to control the function of a protein more rapidly through the administration of small molecules. In a paper published in the September 8th issue of Cell, Dr. Thomas Wandless and his team describe a revolutionary technique that allows researchers to control the stability of specific proteins in mammalian cells. This breakthrough has the potential to make the study of proteins dramatically better, faster, and more efficient. 		Quyna Anh Nguyen 169
5 The Invisible Polluter

The next time you reach for that bottle of Advil or that cup of coffee as you try to fend off an on-setting headache and to gain a few more hours for that problem set, consider this: you may be contributing to the presence of ibuprofen and caffeine in coastal oceans and inadvertently affecting coral reefs and other coastal ecosystems. In a study conducted by Dr. Adina Paytan, assistant professor of Geological and Environmental Sciences at Stanford, and her team of Stanford University researchers, Dr. Alexandria Boehm and students in Civil and Environmental Engineering, found that groundwater discharge is a source of pollution for coastal waters. 		Misha Tran 156
6 Pitx1 Mutations

Manatees gently paddling on the surface of warm waters have revealed a startling connection with fish and mice. These aquatic herbivores are mammals that evolved from four-legged ancestors into legless swimmers. Stanford Professor David Kingsley of the Developmental Biology Department has recently unraveled one of the secrets behind their evolutionary development, demonstrating that a single gene known as Pitx1 can affect highly divergent species.Discovery of the Pitx1 Gene Through research at the Stanford School of Medicine, Kingsley determined that manatees had asymmetrical pelvic bones - the left pelvic bones are larger than their right pelvic bones. Though initially this trait may not appear important, Kingsley had found a similar trend in distinct populations of threespine stickleback, a species of fish that once had pelvic fins. Larger left pelvic bones also pervade in these populations of fish now lacking pelvic fins.  		Erika Williams 163
7 A New Method to Monitor Proteins in vivo

Bioluminescent imaging is one of the most important tools available to scientists trying to understand how cells and proteins function. This technique has been revolutionized following a new discovery by Dr. Thomas Wehrman and Dr. Georges von Degenfeld, two postdoctoral fellows working with Dr. Helen Blau, Stanford professor in the department of Microbiology and Immunology. Their work will allow researchers to monitor protein transport in living cells in a new way.  Until now, those studying how cells work have been frustrated by the shortcomings of the available technology. By combining older methods into a single new technique, Wehrman and von Degenfeld have created a powerful tool for future research in molecular biology. 		Adrienne Sussman 169
8 Mitochondrial Disease

Two billion years ago, a hungry protoeukaryote engulfed an aerobic bacterium, but instead of digesting it, the protoeukaryote formed a symbiotic relationship with its helpful snack, feeding o the energy the bacterium produced by metabolizing undigested food particles. With time, natural selection morphed the bacterium into what has now become an essential organelle called the mitochondrion, the energy-producer of every eukaryotic cell. 		Julie Boiko 150
9 Controlling Metastatic Cancer

The majority of cancer deaths occur when cancer cells spread from a localized tumor to other parts of the body during a process called metastasis. Investigations into the mechanisms of metastasis have revealed that a low-oxygen micro-environment - hypoxia - within the tumor can contribute to this lethal process. Dr. Janine Erler and Dr. Amato Giaccia at the Stanford University School of Medicine found that a protein called lysyl oxidase (Lox) is related to high metastasis rates and low-oxygen micro-environments in breast, head and neck cancers. 		Jennifer Huang 148
10 Just What the Doctor Ordered

Research findings from a bioengineer’s lab bench have an exciting new application: wound healing. In collaboration with the Department of Surgery at the Stanford University School of Medicine, Jennifer Cochran, Assistant Professor of Bioengineering, is working on expediting the process that the body uses to heal skin wounds by delivering a mutated version of a naturally occurring protein. 		Elizabeth Burstein 153
11 Spying on the Grim Reaper

Apoptosis is a normal physiological process of programmed cell death or “cell suicide” that eliminates damaged or stressed cells. Errors in apoptosis are involved in approximately 70% of human diseases including cancer, Parkinson’s, Alzheimer’s, and the massive cell death that occurs after a heart attack or stroke. The caspases, a family of enzymes that break down proteins, are key players in the apoptosis program, but few tools are available to study caspase activity. However, in the August 18, 2006 issue of Molecular Cell, a team of researchers, including the author of this article, from the lab of Dr. Matthew Bogyo in the Pathology Department of the School of Medicine described the synthesis of novel tools called Activity Based Inhibitors and Probes (ABIs and ABPs) that can be used to inhibit and track caspase activity. ABIs and ABPs are helping researchers understand apoptosis, and may help to diagnose and develop therapeutics to treat diseases that result from aberrant apoptosis. 		Alicia B. Berger 136
12 Diabetes and Calcineurin

“The cause of diabetes continues to be a mystery,” states the American Diabetes Association (ADA) on its website. However, Stanford Medical School Professors Seung Kim and Gerald Crabtree, along with MD/PhD graduate student Jeremy Heit, are closer to solving this mystery. They recently singled out a specific protein that controls the disease’s symptoms -- a finding that could potentially lead to an effective cure for 20.8 million Americans - 7% of the U.S. population.
An Insulin Disease
After eating a meal, a person’s blood sugar level rises. Beta cells, located in the pancreas, sense this increase in glucose and release insulin into the body. Insulin is a hormone that induces cells in the muscles and liver to absorb and store the glucose as the body’s energy source. 		Chelsea Young 185