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| possible 3-letter codes (image credit) |
Supplements: Gamow's guess, Brenner disproves Gamow and all overlapping triplet codes, the decisive artificial RNA experiments
How the genetic code was cracked
(chosen for Aug 31 discussion)
Supplements: Gamow's guess, Brenner disproves Gamow and all overlapping triplet codes, the decisive artificial RNA experiments
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.
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.
- Baym et al. Spatiotemporal microbial evolution on antibiotic landscapes, Science 2016.
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
Chainsaw massacre in the Florida Keys - the effects of island size on species immigration and extinction rates
(chosen for Sept 28 discussion)
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| From Wilson and Simberloff, 1969. |
- Simberloff, D., 1976. Experimental zoogeography of islands: effects of island size. Ecology, 57 (4): 629-648.
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
How cats learn to see
When the cats were removed from these conditions, they continued to have developmental defects. For instance, cats raised in the horizontal condition would bump into table legs. When they examined the responses of these “complex cells” to lines of different orientations in the vertical and horizontal cats they found that the complex cells only responded to lines of a given orientation. This showed that visual experiences are developmentally dependent and was a major experiment showing that there are critical periods of brain development.
Background:
Hubel and Wiesel Original Experiments
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1363130/pdf/jphysiol01298-0128.pdf
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1359523/pdf/jphysiol01247-0121.pdf
A 58,000-generation experiment catches evolution in the act
(chosen for Oct 26 discussion)
- The paper: Blount et al. 2012. Nature 489.
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
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.Daddy, can I has a pet fox please?
"Njet! Now go clean up your room." For most kids in Russia, this would have been the standard answer to their
wishful request to own a pet fox. Unless their dad was the famous soviet geneticist Dmitry Belyaev. In 1959, Belyaev founded the Institute of
Cytology and Genetics in Siberia and started a lifelong experiment to
domesticate silver-black foxes. By selecting only for behavior, he
obtained a tame fox population that started to show morphological and
physiological changes not selected for but also present in many other
domesticated species. These changes, including instances of
pedomorphosis, suggest that behavioral traits favorable to domestication
are genetically linked to morphological and physiological traits. So
when his children asked him for a pet fox, Belyaev's answer might have
been "Why, yes, of course! Just give me a couple of decades. And you
must not forget: you become responsible, forever, for what you have
tamed."
- Trut, L. N., 1999. Early canid domestication: the farm-fox experiment. American Scientist, 87 (2): 160-169.
Prismatic coloration: how Newton showed different colors of light behave differently
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| Image credit: The Dark Side of the Moon, Pink Floyd, 1973 |
Other readings:
Morgan's Fly Room
The Fly Room at Columbia University - Restored to Its Original State from Imaginal Disc on Vimeo
Since this is my last post, and there won't be any more voting, I thought I'd share a very cool project that I recently came across that recreated Thomas Hunt Morgan's famous fly room at Columbia University. The fly room was a hot, cramped, putrid smelling room where Morgan and his colleagues unraveled some of the biggest mysteries of heredity and sex determination, work that earned them the Nobel Prize in 1933.
The room was recreated for a 2014 feature film aptly named "The Fly Room," and they do a remarkable job of recreating the details of the lab. The production company, Imaginal Disc, also put together a great website with some stories about the lab and interviews with Morgan's daughter Betsy. The video above is a short produced by Imaginal Disc showing off the room, and I've linked to the trailer for the full movie below.
Thanks everyone for a great seminar!
Imaginal Disc: http://www.imaginaldisc.com/
Trailer: https://www.youtube.com/watch?v=Cejz9HKRS-M
The Fly Room website: http://www.theflyroom.com/
Since this is my last post, and there won't be any more voting, I thought I'd share a very cool project that I recently came across that recreated Thomas Hunt Morgan's famous fly room at Columbia University. The fly room was a hot, cramped, putrid smelling room where Morgan and his colleagues unraveled some of the biggest mysteries of heredity and sex determination, work that earned them the Nobel Prize in 1933.
The room was recreated for a 2014 feature film aptly named "The Fly Room," and they do a remarkable job of recreating the details of the lab. The production company, Imaginal Disc, also put together a great website with some stories about the lab and interviews with Morgan's daughter Betsy. The video above is a short produced by Imaginal Disc showing off the room, and I've linked to the trailer for the full movie below.
Thanks everyone for a great seminar!
Imaginal Disc: http://www.imaginaldisc.com/
Trailer: https://www.youtube.com/watch?v=Cejz9HKRS-M
The Fly Room website: http://www.theflyroom.com/
The "Hunt" for Cyclin
In the early 1980s, much was known about hairspray, big hair, and questionable fashion. However, in the world of cell biology, little was know how exactly the process that allowed cells to divide was regulated. Enter Tim Hunt and a lab full of eager Physiology students that spent their summer radio labeling sea urchin eggs that they had collected from the nearby sea. They noticed something strange on their protein gels, a protein (later to be named cyclin) would accumulate and then disappear at the onset of cell division. This discovery would set into motion thousands of experiments and one Nobel Prize that led to the discovery of the fundamental mechanism of cell division. This discovery has had far reaching implications in the fields of developmental, cell, and cancer biology to name a few. This classic experiment, although simple, was cleverly designed and allowed the capture of one of the most studied processes in all of science.
Can exosomal microRNAs control insulin sensitivity in vivo?
In this paper, they use a mouse model to study obesity, insulin sensitivity and exosomal RNA. Basically, they inject extracellular vesicles, or exosomes, from a lean mouse into an obese mouse with insulin sensitivity problems and the impairments are reversed. Exosomes from the obese mice into the lean mice cause insulin resistance. Will this also work as a potential future therapeutic for humans?
- http://www.cell.com/cell/fulltext/S0092-8674(17)30993-5 <-- The paper
DNA Damage Checkpoint is Rad!!!
For example, how do cells ensure that DNA is accurately replicated before the cell goes through mitosis? In the 1980’s, Weinert and Hartwell reasoned there are two simple possibilities- first, successful mitosis could directly depend on having properly replicated chromosomes, rather like a car needing wheels in order to move. The other possibility is that the cell has a control system in place that halts the cell in S phase until it senses that the DNA is correctly replicated, similar to an inspector examining the car before it can leave the shop.
But how to distinguish between these two possibilities? The investigators looked specifically for mutant cells that did NOT arrest in response to radiation, indicating that this hypothetical control system was no longer functioning. These cells were missing their DNA damage checkpoint, and could no longer detect and repair damaged DNA- a critical step in ensuring faithful replication!
DYING GOATS, CANNIBALISM, And the central dogma
So if 18,000 sheep dying of the mystery illness, scrapie, isn’t weird enough, let’s add in a cannibalistic tribe on a small island in the Pacific. The Fore people were dying of a strikingly similar illness, and it appeared to be transmitted through consumption of human flesh. The brains of affected people bore the same hole-ridden, spongey texture seen in biopsies of scrapie-affected sheep. What agent could be responsible for two infectious, neurodegenerative diseases? How could it be resistant to formalin?
Many hypotheses were offered, ranging from “slow virus” to “replicating polysaccharide”. However, it was work by Stanley Prusiner that lead to the unravelling of this mystery. Through tried and true reductionist biochemistry, Prusiner achieved the purest preparation of the scrapie agent yet. After quantitatively determining the amount of infectivity present in his preparation, he sought to determine what treatments would eliminate that infectivity. Through simple biochemical experiments, such as treatments with proteases and nucleases, Prusiner demonstrated that the scrapie agent was predominantly proteinaceous in nature. Prusiner also calculated the size of the agent, less than 50,000 Daltons, and inferred that this size did not allow for the presence of a replicating nucleic acid within the structure. And thus the term prion, or proteinaceous infectious agent, was coined by Prusiner. For his ability to follow his data and think beyond the central dogma, Prusiner was awarded the Nobel Prize, only 15 years later.
The Unknown Vital Ingredient
At the turn of the 20th century, diseases such as scurvy and beri-beri were thought to be caused by microbial infections. However, experiments by Eijkman and others found dietary supplementation could cure these diseases. Eijkman then proposed that improperly prepared foods contained disease causing toxins. This theory was disproved by studies showing food contained an active factor vital for health, rather than a toxin. To try and identify the active factor, Gowland Hopkins fed rats a diet of purified protein, fat, and carbohydrates: the only known essential components of food. He found the rats ceased to grow unless their diet was supplemented with milk. Therefore, food must contain some other essential nutrient. Over the next few decades, other labs identified the essential nutrients we now know as vitamins. Although, the term vitamin was coined in 1910 when Casimir Funk falsely believed he had isolated a vital amine as the "active factor."
Other readings:
The Nobel Prize and the Discovery of Vitamins https://pdfs.semanticscholar.org/26b3/ac4d28c9bde1cbd840d5e1d17dea0a2116a3.pdf
Evolutionary family planning: life-history experiments in a natural population
What determines the timing and characteristics of major life events, such as sexual maturation, reproductive investment, and the onset of senescence? Because these types of traits, or life-history parameters, are key determinants of fitness, evolutionary theory has long proposed that, to the extent that these traits are heritable, they should manifest as adaptations to the particular environments and ecologies of natural populations. Further, changes in a natural population's environment should result in life-history evolution whenever altered timing or qualities of life-history parameters can increase fitness. Reznick et al. set out in the 1970s to test these predictions in a natural fish population by transplanting a subpopulation to a section of stream with a very different predation regime, one in which changes in the timing of maturation and reproduction should have been adaptive. Their 11-year field experiment provided the first solid experimental evidence of life-history evolution in nature. 
The paper:
More:
Another great story of evolution in this system: Endler 1982
Reznick lab website
Tumorless Tumor Transmission
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2124874/pdf/397.pdf
Other readings:
The History of Tumor Virology https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3501656/
If you can't see it... just make it bigger: The development of Expansion Microscopy
For hundreds of years, scientists have been developing ever better methods of microscopy for visualizing the molecular world. Turns out this has been a massive waste of time. Why bother making your microscope better when you can just make your sample bigger?
That's the idea behind Expansion Microscopy (ExM), which was developed by Ed Boyden's lab at MIT. ExM uses a polyelectrolyte polymer to physically anchor, and then expand the sample, causing minimal disruption of structure, while achieving superresolution with diffraction limited microscopes. In some cases ExM could achieve higher resolution with a confocal system than was possible with a superresolution approach like Structured Illumination Microscopy.
While the Boyden group’s 2015 paper describing ExM isn’t so much of an experiment, I think this lands squarely in the category of “I wish I’d thought of that,” and in my opinion is one of the great experiments of microscopy.
Supplements:
New York Times -- Expansion Microscopy Stretches Limits of Conventional Microscopes
Anfinsen's Dogma
Thanks to Christian Anfinsen, we now know that the instructions for the folding of small globular proteins all come from the primary sequence itself. Anfinsen demonstrated this idea in 1962 by using a protein called ribonuclease A, which contains four disulfide bridges that are vital to protein structure and function. First, Anfinsen unfolded RNase A with the denaturant urea and βME, a reducing agent that breaks disulfide bridges. When Anfinsen removed urea first and βME second, the protein refolded and regained 100% activity. However, when he switched the order and removed βME first and urea second, the protein only regained 1% of its original activity. This result is attributed to the fact that removing βME when the enzyme is still unfolded causes cysteine residues to randomly form bonds with each other. The idea that the amino acid sequence acts as the "blueprint" for protein folding was later referred to as Anfinsen's dogma.
Holey Moly! The history of digestion
(chosen for Nov 9 discussion)
In 1822, Alexis St. Martin was accidentally shot in the stomach and treated by Dr. Beaumont. He was expected to die from his wounds, but remarkably he survived - with a hole in his stomach.
Dr. Beaumont doing what any opportunistic scientist would do, used this strange case to study digestion in the human body. For the next 11 years, St. Martin and Beaumont conducted a series of experiments ranging from the simple observation of normal digestion to the effects that temperature, exercise and even emotions have on the digestive process.
Supplement: The whole 1833 book, Experiments and observations on the gastric juice, and the physiology of digestion, by William Beaumont. Flip through it for interesting pictures and descriptions.
Would you use a 8-year boy as guinea pig to test a theory for the treatment of a deadly infection disease?
For addition information:
https://www.cdc.gov/smallpox/about/index.html
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1200696/pdf/bumc0018-0021.pdf
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC495097/pdf/jclinpath00423-0016.pdf
https://biotech.law.lsu.edu/cphl/history/articles/jenner.htm#paperI
Even moderate attraction is blind?
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| Do "nice" people appear more attractive, smart, and kind? Apparently so! [Source] |
Phrases such as “love is blind” suggest that strong emotions can blind us to any negative attributes of that person. But the phrase is a hyperbole; human beings couldn’t possibly be so influenced by their feelings… or could they? The phrase “the halo effect” has been given to this phenomenon.
Simply, it is the idea that we assume that nice people have good qualities while mean people have bad qualities. This doesn’t seem to be an inconceivable idea, but it had not been shown experimentally in an unbiased way—having human beings assessing other human beings on both their appearance and several unrelated attributes. Then, in 1977, one clever experiment utilized college students and their assessment of a fake professor to confirm that not only does our general impression of a person influence how we assess their attributes, but also that we are even unaware of our own “blindness”.
The power of beads: FGF-4 beads can direct limb growth and patterning
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| Key experiments show factors required for limb development, and show the plasticity of this process! [Source] |
In 1993, Lee Niswander and colleagues demonstrated that one specific growth factor, FGF-4, was both necessary and sufficient for limb development and patterning. They soaked beads in FGF-4 and placed them at various locations on developing limb buds in chick embryos. Through these technically creative experiments, Niswander et al. showed that FGF-4 beads, placed specifically at the posterior edge of the limb bud, could direct normal development and patterning of limbs even in the absence of the apical ectodermal ridge! These experiments ultimately suggest that it is not the distal-most tissue that is required for the growth and patterning of the embryo, but instead, that this tissue uses one signaling molecule FGF-4 to direct a specifically-localized tissue to orchestrate proper limb development.
Darwin's Witnesses
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| The Grants measuring finch beaks in a cave on Daphne Major, an island in the Galapagos. Photo credit: Princeton Alumni Weekly |
Well, to Rosemary and Peter Grant, evolution acts quickly. To them evolution is incredibly familiar, for they witnessed it with their own eyes. Starting in 1973, the two set-out on a 40-year experiment to observe the forces of natural selection on the sizes and shapes of two species of Darwin’s finches on Daphne Major, a volcanic island in the Galapagos. This experiment has revealed how the environment (an unpredictable factor), together with the predictable forces of inheritance and selection for fitness, influence the selection of traits. Did I mention the Grants are married? Even after 40 years of measuring finch beaks in a cave on a volcanic rock with no people in sight, they have remained so for 55 years. Below are the results for their first 30 years of work.
- The paper: P. and B. R. Grant, 2002, Science 296.
A Princeton Alumni Weekly review of the Grants' book 40 Years of Evolution. Darwin’s Finches on Daphne Major Island.
The Grants wrote a perspectives piece for Science this year (that mentions the hidden genetic variation of Mexican cave fish eyes).
The First Chemotherapy
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| Aminopterin Attempting to Slay Cancer |
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.
How did the blind cavefish lose its eyes?
(chosen for Nov 2 discussion)
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:
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
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.
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| image credit: BOGObiology |
What do platform shoes and the overthrowing of the Berlin wall have in common?
(discussed Oct 12)
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.
- Granovetter, M. S., 1978. Threshold models of collective behavior. American Journal of Sociology, 83 (6): 1420-1443.
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.
For your information: https://www.youtube.com/watch?v=AO1T-NhcVoU&feature=youtu.be
It's Raining Liquids!
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.