A 58,000-generation experiment catches evolution in the act
(chosen for Oct 26 discussion)

30 years ago, Richard Lenski started an evolution experiment that is still running today. The Long-Term Evolution Experiment, or LTEE, began in 1988 when Lenski started 12 lines of E. coli with a single clonal cell in each. By maintaining these lines under identical conditions for tens of thousands of generations and freezing still-viable samples of each line every 500 generations, Lenski created the ability to examine the repeatability of evolution and to replay evolution from any 500-generation time-point in the past. And when one line evolved a novel resource-use phenotype approximately 30,000 generations later, Lenski and colleagues were able to leverage this ingeniously simple design, using genome sequencing to reveal the genetic origin of the novel phenotype — and shedding new light on the importance of historical contingency in adaptive evolution.
Additional reading:
The first paper reporting the novel phenotype
A bit of model-fitting at the 60K-gen. mark suggests there may not be an upper limit to adaptation in a constant environment
A much earlier paper describing the design of the LTEE in detail
Lenski's LTEE website with more papers, data, news, and info for the lay public
An AmNat meeting talk by Lenski about where the LTEE is now, 65K gens. later

A Superhero against Poliomyelitis

Poliomyelitis "infant paralysis" is a lethal disease, caused by an Enterovirus that mainly affected children, presenting a variety of symptoms that include temporary or permanent paralysis. Many of the infected people died and others were disabled for life. This serious illness, had no distinction in people and also affected the president Franklin D. Roosevelt. Virologist Dr. Jonas Salk was the first to develop a safe and effective polio vaccine. His approach was to imitate the immunizing effect developed by natural infection with a chemically treated virus. This vaccine is composed of the dead virus, which is injected into the patient so that the immune system attacks the virus and creates immunity. Dr. Salk is a vivid example of putting his profession ahead of his personal interests by not patenting his vaccine. One of his phrases during an interview was "There is no patent. Could you patent the sun?"
Additional information:

What is the genetic material for life?

Today, the concepts "DNA" and "genetic" are inseparable. But before 1952, there was no consensus among biologists about which macromolecule was responsible for encoding and passing along genetic information. In fact, the majority of biologists assumed the genetic material was protein, since proteins were fivefold more complex at the monomeric level. To test the DNA/protein hypotheses, Hershey and Chase devised a
image credit: BOGObiology
clever radiolabeling experiment in which they infected bacteria with radioactive phage viruses. The phages were labeled either with radioactive phosphorus (only in DNA) or with radioactive sulfur (only in protein). Hershey and Chase showed that the viral progeny contained radioactive phosphorus, but not radioactive sulfur. This experiment showed that the original viral DNA (containing radioactive phosphorus) was preserved and passed along to its progeny. Proteins (containing radioactive sulfur) were not passed along, however, suggesting that DNA encoded the genetic information necessary to make copies of the virus.

What do platform shoes and the overthrowing of the Berlin wall have in common?
(discussed Oct 12)

Early 1960s. Suzie is trying on platform shoes. "I really like them but people will think I look ridiculous. Well heck, I don't care what others think. I like them!"

Berlin, November 9th, 1989. Franz is standing in front of the wall hammer in hand. He heard the news on the radio, the border just opened. "Time to tear down that wall!" he thought. At first, it was only him chipping away at the wall, but the crowd soon grew bigger and bigger.

The spread of certain behaviors relies heavily on individual thresholds. How many people have to wear platform shoes or hammer away at the wall before I join them? Is my threshold low like Franz and Suzie's? In 1978, Granovetter shows how very similar crowds can react completely differently because of individual thresholds. The applications of his model are endless: from fashion crazes to riots and voting behavior.
Additional resource:
A great video explaining this model (from the Model Thinking course on Coursera, which I highly recommend).

Would you drink a broth of bacteria to prove the real case of an illness?
(discussed Oct 12)

By the 1970s, cases of people with gastric ulcers were recurrent. Stress, spicy food, and lifestyle were thought to provoke peptic ulcers because no one believed in the presence of bacteria in the stomach. In 1981, Barry Marshall and Warren performed biopsies on patients and were able to isolate an unknown bacterial species present in almost all patients with gastric infarction, duodenal ulcers or gastric ulcers. For this reason, they proposed that this unknown bacterium was the cause of the disease. Their experiments and discoveries were not immediately accepted. Due to prohibitions on human subjects and after trying different animal models with no success, Marshall underwent a gastric biopsy to demonstrate absence of that bacterium and then swallowed bacterial broth that possessed the bacteria of an infected patient. After several days, the disease developed and the second biopsy of his own intestine proved that in effect, the bacteria was the cause of the ulcer.

It's Raining Liquids!

Some great experiments lead to new and exciting discoveries and open doors to new areas of science. However, other experiments change the way a field is thinking about old problems. This was the case when it was discovered that P granules and other RNA-protein bodies can behave as liquid droplets. A simple experiment of imaging sheared P-granules dripping and fusing off of dissected germline nuclei from C. elegans embryos led to the transformative idea that cells could use a very simple phase transition—like water condensing into dew—to assemble and organize various molecules. This experiment led to the discovery of this liquid-like mechanism of intracellular organization in countless other organisms, not to mention the birth of a new way of thinking about about molecular biology.

Creating the Central Dogma from Bread Mold experiments

An old saying goes that “two heads are better than one”, and very often this holds true in great scientific discoveries. In 1941, a geneticist and biochemist joined forces to develop and test a hypothesis that would forever change molecular biology. In 1941, Beadle and Tatum provided the missing link between genetics and molecular biology with their “one-gene-one enzyme hypothesis” experiment. Using the simple bread mold, Neurospora crassa, they were able to perform random mutagenesis and then identify strains that had metabolic defects. They found that most mutants were unable to grow unless their media was supplemented with particular amino acids that they were no longer able to synthesize. They reasoned this was due to the synthesis pathway being interrupted by the mutations, suggesting that the mutations affected only a single metabolic pathway, and thus, the central dogma of one gene: one protein was born.

You can't have your marshmallow and eat it too…

Four-year-old Steve Jobs probably would not have eaten it. Neither would have toddler Bill Gates, or the little Elon Musk. Don the kid probably grabbed it the second he could and stuffed it in his mouth as fast as possible. Stanford psychologist Walter Mischel and his team designed what probably is the fastest and cheapest way to determine a kid's future success in life. Put the kid in a room, give it a marshmallow, and tell it that it can eat it now or wait 15 minutes and get a second marshmallow. Children who were able to delay gratification and wait for the reward turned out to be much more balanced, resilient, and successful teenagers and adults. Mischel's marshmallow test proved to be a very reliable predictor of future success and has been replicated several times with children from different backgrounds and nationalities.
And you? Would you have waited?
Additional resources:
A great Ted talk on this experiment (about 5 min long) 
An article from the New Yorker about Walter Mischel, written by his former graduate student

Using Frankenstein-like rats to study the hypothalamus
(discussed Oct 12)

Parabiosis is a technique that involves surgically joining two living organisms such that they share a circulatory system. In 1959, G. R. Hervey utilized parabiosis to study the role of the brain’s hypothalamus in obesity. Hervey combined pairs of rats in which one rat had a surgical lesion in the hypothalamus and the other rat was healthy. Hervey noticed that the lesioned rat became obese and experienced significant weight gain and excessive hunger, while the healthy rat experienced weight loss and decreased appetite. The results suggested that there exists a feedback control system in the hypothalamus involving physiological signals that are released in order to suppress appetite. The healthy rat had decreased its eating in response to the signals in the blood from the lesioned rat whose feedback control system was impaired. In addition to obesity, parabiotic experiments have been used to study age-related chronic diseases (e.g. Alzheimer’s and osteoarthritis), stem cells, tissue regeneration, diabetes, and cancer among others.

Transforming principle that changed our world

Streptococcus pneumoniae caused an epidemic disease that took the lives of many people during the 1920s. A bacteriologist by the name of Frederick Griffith, sought to study the virulence of this organism and the development of a vaccine against it. His research focused on why some strains of S. pneumoniae caused the disease (virulent) and other strains did not (non-virulent). For this reason, he began to carry out experiments with different combinations of virulent vs non virulent and live vs dead strains. In his experiments, he showed that a virulent strain was able to transfer information to a benign strain and transform it into a virulent strain through what he called a “transforming factor”. Although Griffith did not know about the chemical and biological processes that were involved in the transformation process, these results were the beginning of what would later be key for the discovery of the horizontal gene transfer.

How did the blind cavefish lose its eyes?

The Mexican tetra, Astyanax mexicanus, has been the subject of great curiosity for developmental and evolutionary biologists for decades, largely because it exists in two strikingly different forms: a surface stream-dwelling form with fully functional eyes and a cave-dwelling form that does not develop eyes and is completely blind.  The surface-dwelling eyed form is ancestral, and the lack of eyes in the cave-dwelling form has inspired much speculation regarding possible selective pressures, fitness costs, and altered developmental mechanisms that might have led to the evolution of eyeless-ness.  In 2013, experiments by Rohner and colleagues revealed an intriguing component of the origins of eyeless-ness in blind cavefish, serving up evidence that cryptic genetic variation masked from selection by a key developmental mechanism may have been expressed and exposed to selection upon introduction to novel stressors in the cave environment.   

The paper:

Two-headed Newts: The Spemann-Mangold Monster


-Image source: Veterian Key
When cells construct an embryo, context matters. The concept of cell fate induction, seemingly so obvious to us, would not be known without the dedicated work of German PhD student Hilde Mangold. As a female graduate student in the 1920s, Mangold was not destined for fame or glory. In fact, her originally-assigned thesis work was to repeat the already-proven, tedious work of Abraham Trembley on inverting Hydra polyps. However, after numerous failed attempts on this front, Mangold approached her advisor, experimental embryologist Hans Spemann, for a new project. 250 newt embryos later, her thesis was a masterpiece in the field of experimental embryology, a ground-breaking and Nobel-prize winning finding that has dictated our view of life at the cellular level almost a century later. Sadly, Mangold would die in a house fire before seeing the publication and impact of her thesis work, leaving Spemann a Nobel on a silver platter.
For your information:
A review of the history and development of the Spemann-Mangold experiment can be found here.
Here is a nice blog post by Ellen Elliott of the JAX lab.

Left-right patterning, situs inversus, and (artificial) nodal flow - oh my!
(discussed Oct 12)

Cilia whips its head back 'n forth to flip symmetry.
[Modified from Babu and Roy, 2013; linked below]
One of the most important events in animal development is the establishment of body axes, a process crucial for defining overall body plan. In many cases, the genes required to establish these axes are understood. For example, in Drosophila, establishment of the dorsoventral axis primarily requires the aptly named Dorsal gene. However, although many genes have been linked to left-right patterning, the exact origin of this asymmetry remained elusive for many years.

Studies beginning in the 1970s gave the first hint towards the solution: human patients with Kartagener syndrome had situs inversus (whereby their internal left-right axis was flipped) together with respiratory disorders linked to ciliary dysfunction. Further studies solidified the connection between ciliary motion and left-right axis specification, but it was not until the cleverly-designed experiments of Nonaka et al. in 2002 that cilia-induced nodal flow was shown to be sufficient for left-right patterning in developing mouse embryos.
And here's a wonderful review on L-R patterning, for those interested.

FrankenCells: how fusing cells together led to an understanding of cell cycle regulation
(discussed Oct 12)

image adapted from Rao & Johnson, 1970 (Nature)

In the 1970s and 80s, the cell cycle was HOT. Major outstanding questions remained unanswered: namely how do cells "know" when to duplicate their DNA and divide? The molecular answers to these questions would come later in the decade from mutational experiments, but Rao and Johnson (1970) used a more clever approach: fusing cells in different parts of the cell cycle together and observe the effects on each nucleus's chromatin. If each cell cycle phase (G1, S, G2, M) uses different signaling factors in its cytoplasm, then what happens when those signals mix? Rao and Johnson showed not only that multinucleate cells will synchronize their nuclear division cycles, but that certain phases in the cell cycle can "dominate" over other phases. The authors' ingenuity required no great advances in genetic or optical tools; rather, they used a well-known virus to simply fuse together large populations of cells.

Monkey See, Monkey Do - The Bobo Doll Experiments

In 1961, Albert Bandura conducted a series of tests to see if aggression can be learned through observation and imitation. In his study consisting of 72 preschool children, he found that if the children were exposed to an aggressive male or female adult model who made distinct physical and verbal attacks against an inflatable toy called a “Bobo Doll”, the children were likely to imitate the model's aggressive behavior. He also made a number of other interesting observations such as the effect of same-sex models on the children’s behaviors and the difference in physical and verbal aggression between boys and girls. He later conducted several variations of his Bobo Doll experiments to observe the effect of aggressive behavior in films and the effects of reward and punishment on the children’s learning and imitation. These studies illustrated Bandura’s theory of Observational Learning and have also raised questions about the influence of violent media on children.
Additional information:
Bandura’s 1963 Bobo Doll study on the effect of films that depict aggressive behavior on learning and imitation
Bandura’s 1965 Bobo Doll study on the effects of reward and punishment on learning and imitation

Primordial Soup
(chosen for Oct 5 discussion)


The origin of life is a hotly debated topic. Before the 1950s, scientists were split on the exact makeup of the Earth’s atmosphere. Some thought life originated on Earth from an environment made up of carbon dioxide, nitrogen, oxygen and water. Miller and Urey argued that life formed from the mixture of methane, ammonia, water, and hydrogen. In 1953, the pair developed a simple apparatus that could simulate their proposed hypothetical conditions, and they were able to observe that 10-15% of the carbon within the apparatus formed the building blocks of life providing evidence to their hypothesis. The results remain controversial but one cannot deny that this is a great experiment; Even Miller himself remarked once, “The fact that the experiment is so simple that a high school student can almost reproduce it is not a negative at all. The fact that it works and is so simple is what is so great about it.”

The Discovery of Taq Polymerase and the Invention of PCR

Structure of Taq polymerase
The polymerase chain reaction (PCR) is one of the foundational molecular techniques of modern biology. Making it possible to perform a huge range of standard techniques such as cloning, genotyping, and mRNA quantification.

Today, we often take PCR for granted. Thermocyclers are ubiquitous, various polymerases and kits are commercially available and relatively inexpensive.

But the first iteration of PCR used polymerase purified from E. coli, which couldn't tolerate the high temperature required for denaturation of DNA, and thus had to be added fresh to the reaction after each round of amplification.

The essential breakthrough came when an eccentric chemist named Kary Mullis came up with the idea to try using a polymerase from a thermophilic bacteria, Thermus aquaticus. The use of this Taq polymerase dramatically improved the accuracy and speed of PCR, and ended up winning him the 1993 Nobel Prize in Chemistry.
Additional reading: Mullis is perhaps as famous for his work on PCR as he is for his wild behavior and views.
A good portrait of which can be found here:
NOBEL CHEMIST KARY MULLIS, MAKING WAVES AS A MIND SURFER

Paper on the first purification of Taq polymerase:
Chien et al. 1976. Deoxyribonucleic acid polymerase from the extreme thermophile Thermus aquaticus. 

The First Chemotherapy

Aminopterin Attempting to Slay Cancer
In a centuries-old battle against a relentless enemy, cancer biologists have had no choice but to plunge-in head first, using whatever weaponry was in arm’s reach as they fell. Only the most gruesome of treatments worked: mutilating surgeries, radiation bombardment, and mustard gas (a literal weapon), among others. Researchers yearned for a cancer-killing drug, a “cure.” By the 1940s they had grown despondent, hopeless that a cure could be found. Then in the winter of 1947, Sidney Farber (a laboratory pathologist, desperate to leave his microscope and treat patients) took the first successful step in that direction. He performed an impromptu clinical trial of Aminopterin (a then newly-synthesized folate antagonist) with a two-year old boy 'on the verge of death.' The offender: lymphoid leukemia. The young boy’s subsequent remission was momentous and ignited the field of chemotherapy and hope for a cure.
Looking for more?
1. You may find a nice history of cancer chemotherapy here.
2. Interested in reading further? I am presently in the throngs of The Emperor of All Maladies by Siddhartha Mukherjee. This NY Times article describes it nicely.

Can fearful memories be passed down generations?
(discussed Oct 12)

In this paper, mice whose father or grandfather learned to associate the smell of cherry blossom with an electric shock became more jumpy when smelling the same scent. They even responded to lower concentrations of it than normal mice (whose fathers weren't exposed). Many studies hint that stress or other events can change the immune system, emotional response, or metabolic health of future generations through epigenetic inheritance.

Brian Dias and his lab at Emory University School of Medicine in Atlanta, provide some of the best evidence yet for the inheritance of memories or traits across generations, as well as providing potential biological mechanisms by which this phenomenon is happening.
(Image unrelated, I just thought it was cute. Please do not make your mice label tubes, or expect a call or visit from The University of North Carolina at Chapel Hill Institutional Animal Care and Use Committee (IACUC))

Exchange of actin subunits at the leading edge of living fibroblasts: possible role of treadmilling
(discussed Oct 12)

How do cells move? The ability of living cells to crawl around has interested scientists for generations, and it has been known for a long time that actin dynamics play a critical role in allowing cells to move. In vitro work showed that actin was capable of treadmilling, but a role for treadmilling in vivo was not shown until 1985, when Wang injected fluorescently labeled actin into living fibroblast cells and visualized the flow of subunits from the periphery of the lamellapodium to the cell center by photobleaching a region at the edge of the cell and watching the bleached region move backwards. From these simple FRAP experiments he was able to infer a great deal about the dynamics of actin filaments and how they could contribute to cell crawling.

Why the jellyfish glow

In the waters of Friday Harbor, numerous glowing Aequorea jellyfish drift through the waters. From these jellyfish, Dr. Osamu Shimomura purified the bioluminescent protein, aequorin, for biochemical studies. While running the extractions, a fluorescent protein named green fluorescent protein (GFP) was also purified. Little did Shimomura know this "other" protein would revolutionize bio-imaging. About 30 years later in 1994, Dr. Martin Chalfie successfully expressed active GFP in E. coli and C. elegans. Successful GFP-fusion proteins soon followed; however, the brightness was weak. To overcome this, Dr. Roger Tsien and a post-doc in his lab, Roger Heim, began to make mutations in GFP to both increase the brightness and to create different colors. Today we have a whole rainbow of fluorescent proteins (image), but the purpose of GFP in Aequorea remains a mystery.
Supplements:

Chainsaw massacre in the Florida Keys - the effects of island size on species immigration and extinction rates
(chosen for Sept 28 discussion)

From Wilson and Simberloff, 1969.
This day started like most days in this little piece of paradise. The sun rose over the calm waters, softly warming up the mangrove trees sticking out above the ocean surface. Dan and his crew slowly approached the island, anchored their boat, and waded through the water to the little heap of branches and leaves. They hunted for arthropods, counting them, identifying species. They looked in every little corner, under every leaf, broke hollow twigs to make sure no insect was hiding inside. Once all animals were accounted for, the men returned to the barge and got their tools. Armed with chainsaws and machetes, they cut away at the island, leaving only half of it intact. Then, they left. With his island colonization experiments, Daniel Simberloff pioneered the field of island biogeography, trying to understand how species colonize new habitat, and why some populations reach equilibrium while others go extinct.

Additional resources:
A song about the theory of island biogeography
Background information about island biogeography
Paper on the defaunation and monitoring techniques used by Wilson and Simberloff
Paper on the colonization experiments first carried out by Simberloff and Wilson
Paper on the colonization model developed by Simberloff

Genotype after phenotype? Waddington and the "Genetic Assimilation of an Acquired Character"
(discussed Oct 12)

Can an apparently "acquired" character, initially induced by environmental perturbation in the course of development, become a genetically induced trait in a population? Using a series of Drosophila selection experiments, Conrad Waddington answered this question in the affirmative.  By selecting for a heat-shock-induced aberrant wing phenotype, Waddington produced lines that continued to develop the aberrant phenotype in subsequent generations even in the absence of the once-necessary environmental stimulus.  The founding population did not express this phenotype without the heat-shock treatment, but after continuing to breed together only those adults that expressed the phenotype in the absence of heat shock, Waddington eventually produced some lines in which 100% of offspring expressed the phenotype without being exposed to heat shock.  This is the seminal work that inspired far greater understanding and greater interest in the origins of phenotypic novelty and variation and their importance to adaptive evolution.
Additional reading:
1. Another genetic assimilation paper, in which Waddington expresses his thoughts on the potential evolutionary importance of the phenomenon. 
2. Mary Jane West-Eberhard synthesizing her theory of plasticity-first evolution.
3. A recent TREE article by UNC researchers about plasticity-first evolution.

How to sequence DNA

The Sanger method is the technology that allowed us to sequence the first human genome, completed in 2003. We've come a long way since then, but when Frederick Sanger et al developed a chain-termination method for DNA sequencing back in 1977 it soon became the most popular method of choice for many many years. Sanger employed dideoxynucleic acids, ddNTPs, in addition to deoxynucleic acids together in the amplification of DNA during the Polymerase Chain Reaction (PCR). Instead of amplifying a section of DNA, the ddNTPS would cause amplification to terminate in a random number of amplified products. This new approach used fewer toxic chemicals and lower amounts of radioactivity than previously used techniques and because of its comparative ease, the Sanger method was soon automated and is still used to this day.

Split Brain Experiments: Two brains in one head?
(chosen for Sept 21 discussion)

In the 1960s, a treatment for epileptic patients involved the removal of the corpus callosum, a bundle of nerves that allow the two hemispheres of the brain to communicate with each other. Using these patients, Roger Sperry conducted a series of simple but ingenious experiments to demonstrate that the two hemispheres of the brain work independently to receive and react to information. For example, when an object was presented to the left hemisphere, subjects could name it. When the object was presented to the right hemisphere, subjects claimed not to have seen anything. However, they could use their left hand (which is controlled by the right brain) to draw the object. This suggested that the left brain is dominant for speech while the right brain is important for nonverbal communication. For the next 25 years Sperry further elucidated the unique functions of the left and right brains, and earned the Nobel Prize in 1981. 

Keep it in your genes! Alternative splicing determines sexual orientation in flies
(chosen for Sept 14 discussion)

Modified gene splicing can alter sexual orientation in fruit flies
[Image modified from Chapman and Wolfner (2017)]
Countless experiments have been conducted to elucidate the genes and mechanisms involved in specifying sex across the animal kingdom. From counting chromosomes to alternative splicing, various processes come together to determine physical sex. However, little is known about how “mental” sex – most simply, one’s courtship behaviors – is determined. Physical sex is often attributed to switch-like genes; sex-specific innate behaviors, on the other hand, could be attributed to switch-like genes, interacting gene networks, or both. 

Addressing this problem in higher-level organisms presents a monumental hurdle: courtship behaviors are influenced by social expectations. To circumvent these problems, Demir and Dickson used the beautifully simple and well-characterized Drosophila melanogaster to parse out the differential effects of alternative splicing on physical and behavioral sex. Their creative experiments showed that physical sex and courtship behaviors are independently determined and that splicing of a single gene is sufficient to manipulate the inner workings of the brain.
(And here's some background on physical sex determination in Drosophila)

Selection does not induce mutations: it reveals them
(discussed Oct 12)

In the early 1900s, scientists discovered the existence of bacteria-killing viruses and soon after, observed singularities of resistant bacteria within cultures. This led to the description of bacteriophage as “dissociating agents,” yet no one could present evidence as to the mechanism of acquired resistance, what characteristic of bacteria was “dissociated” by bacteriophage. In 1943, Salvador Luria and Max Delbruck used logical deduction to simplify the problem and formulated two hypotheses: either the bacteria acquired heritable resistance in the presence of virus (adaptive) or the bacteria accrued mutations conferring resistance prior to viral exposure (spontaneous). They developed the theoretical distributions of resistant bacteria expected for each hypothesis and then experimentally observed that the actual distribution supports the mutation hypothesis. This simple logic puzzle not only answered a question in the minds of bacterial biologists; it demonstrated that mutations (beneficial or not) occur in the absence of selection. Selection simply reveals them.
Extra tidbits:


1. In addition to demonstrating that random, selection-independent mutations were the source of resistance in the bacterial cells, Luria and Delbruck also went so far as to formulate a mathematical model for estimating the mutation rate in a given culture. Their archaic method is one of a few models still used today.

2. The molecular basis of bacterial resistance has since been attributed to mutations in the fhuA gene, which encodes for a protein FhuA that acts as a phage receptor, among other functions. Read more here.

3. In his 1984 autobiography entitled A Slot Machine, A Broken Test Tube: An Autobiography, Salvador Luria wrote:
Everyone knows that in research there are no final answers, only insights that allow one to formulate new questions.
This work initiated the field of "modern" bacterial research and with it an unending cycle of new insights and new questions.

4. Six years later, Howard Newcombe published similar results in Nature.

(image source: Wikipedia)

MEGA-plate: A Tool for Watching the Evolution of Antibiotic Resistance
(discussed Oct 12)

The spread of antibiotic resistance poses a very serious health threat, particularly in environments that have a high degree of antibiotic and antibacterial use, like hospitals. How bacteria evolve antibiotic resistance, particularly in spatially structured environments where we are likely to encounter them, is not well understood.

With a simple but elegant experiment, Baym et al. characterize how bacteria adapt to distinct changes in antibiotic concentration as they migrate across a massive agar plate. Their Microbial Evolution Growth Arena (MEGA)-plate provides a large enough space such that separate mutant lineages can progress without significantly impacting each other, and that spatially specific antibiotic concentrations can be maintained with minimal diffusion.

With their setup, Baym et al. were able to observe as unique mutants appeared with each progressive step in antibiotic concentration, capturing a jaw-dropping visualization of rapid evolution.
Video credit: The Evolution of Bacteria on a “Mega-Plate” Petri Dish (Kishony Lab)

The Method of DNA Replication
(discussed Oct 12)

Three models of DNA replication were popular when Watson and Crick discovered the structure of DNA in 1953: conservative, semi-conservative, and dispersive. The conservative model proposed an entirely new DNA double helix was synthesized during each round of replication, resulting in one "new" helix and one "old" helix. According to semi-conservative model, each round of replication results in hybrid helices with one new strand and one old strand. The dispersive model also suggested hybrid DNA molecules, but the pieces were randomly dispersed throughout the helices. It took until 1958 for Meselson and Stahl to identify the semi-conservative model as the correct model. They measured the density of DNA molecules after subsequent replications when E. coli was transferred from N15 containing media to N14 media. This elegantly simple experiment laid the foundation for the discovery of many of the enzymatic processes involving DNA.
image credit: Pray, Nature Education, 2008
 






Do "spindle fibers" really exist in living cells?
(chosen for Sept 7 discussion)

Before 1953, the cell biology field was deeply divided in debate over the existence of apparent "fibers" in the mitotic and meiotic spindles of organisms. The only evidence for these fibers, which we know today as microtubules, came from images of fixed and stained cells. Many biologists claimed these fibers were simply artifacts of fixation, since no one had been able to see any fibrous spindle structure in any living organism with any microscope available at the time. Undeterred by the limitations of currently available technology, Shinya Inoué combined high-resolution microscopy with polarized light illumination (thus innovating polarized light microscopy) to make the invisible visible for the first time in vivo: Inoué showed spindle fibers moving with chromosomes in dividing Chaetopterus (annelid) oocytes and Lilium (lily) pollen cells. For this and his subsequent studies into these fibers, Shinya Inoué has come to be known as the father of cytoskeletal dynamics.
Related information:
1. Tribute to Shinya Inoué
2. Shinya speaking about his discovery
3. Edward Salmon (student of Shinya) on the evolution of light microscopy in the biological sciences
(image credit: iBiology)

How the genetic code was cracked
(chosen for Aug 31 discussion)

possible 3-letter codes (image credit)
The structure of DNA, solved in 1953, set off a race to crack the genetic code. How do sequences of 4 nucleotides code for sequences of 20 amino acids? This coding problem lies at the heart of molecular biology. Physicist George Gamow of Big Bang fame contributed the first guess: Spaces between neighboring nucleotides might fit individual amino acids, directly templating protein assembly on the DNA. In Gamow's solution, each nucleotide must contribute to defining two amino acids–an overlapping code. The numerology looked good (there were exactly 20 possible combinations), but Gamow's solution turned out to be dead wrong: In 1957, Sydney Brenner devised a clever test that disproved this and all overlapping triplet codes. The true code was soon cracked based on beautiful frameshift experiments by Crick and colleagues (proving a triplet code), and by analysis of proteins synthesized from artificial RNAs (solving each codon).
Supplements: Gamow's guess, Brenner disproves Gamow and all overlapping triplet codes, the decisive artificial RNA experiments

How do growing nerve cells find their targets?

Credit: Nobel Foundation
In 1949, Rita Levi-Montalcini noticed something unexpected. Her colleague Elmer Bueker had implanted tumors into chick embryos and found that nerves would invade the tumors, but what attracted nerves to tumors? Levi-Montalcini had noticed that the nerves were not just invading tumors: They were also invading the tissues near the tumors, even invading blood vessels downstream of tumors — suggesting that the tumors might have been releasing a diffusible nerve growth factor (NGF), a postulated substance that could guide either nerve differentiation, growth or survival. Levi-Montalcini proved the existence of NGF by culturing just tumors and ganglia in the same dish, finding that the nerves from the ganglia would connect to tumors even in vitro. Later, she, Stanley Cohen, and colleagues purified NGF. NGF told us that the way nerves find even their normal targets is unexpectedly adaptive: nerves grow just about everywhere, and they die off where they fail to find targets. 
A short review: Aloe, L. (2004) Rita Levi-Montalcini: the discovery of nerve growth factor and modern neurobiology. Trends Cell Biol 14:395-9. 

Some amazing historical background: An excerpt about her pre-NGF work, which she did in a makeshift home lab that she set up hiding out from Nazis and fascists during WWII, from her autobiography, In Praise of Imperfection. Open the excerpt in Acrobat and you'll see some helpful notes in red.

How the widowbird got its absurdly long tail

Wikimedia Commons
One glaring difficulty for early evolutionary biologists was the evolution of exaggerated male secondary sexual traits that would hinder the survival of males. Darwin was the first to suggest that sexual selection favoring an exaggerated trait could 'override' natural selection opposing the same trait, as long as the reproductive benefits outweighed the survival costs associated with it. During the modern synthesis, Ronald Fisher proposed a mechanism of ornament evolution wherein female preferences for an initially advantageous male trait drove that trait to an extreme where it no longer conferred a survival advantage. But little empirical evidence existed even into the early 1980s.  Andersson's work on long-tailed widowbirds provided the first experimental evidence of female preference for an extreme male ornament. This beautifully designed manipulation study was able to control for the confounding influence of variation in male territory quality, the experimental manipulation, and male behavior.
And a later paper summarizing subsequent work on widowbirds