Page 1

Vol. 3 Issue 2

BREVIA Fall 2016

ORIGINS A HARVARD COLLEGE UNDERGRADUATE RESEARCH ASSOCIATION PUBLICATION


Brevia Fall 2016 Masthead Editor-in-Chief Jessi Glueck

Publisher

Nathan Williams

Design Editor

Erica Newman-Corre

Designers Reece Akana Jeongmin Lee

Cathy Wang Alan Yang

Staff Writers Reece Akana Teddy Chappell Erin Hollander Jennifer Kizza

Rubini Naidu Lizzy Thomas Nathan Williams Alan Yang

Primary Research Editor Atrin Toussi

Features Editor Alan Yang

Sponsors

Brevia would like to thank the Harvard Undergraduate Council and the Harvard College Office of Undergraduate Research and Fellowships for their generous support of our publication.

2

BREVIA Fall 2016

Acknowledgements Thank you to Gregory Lacer for his extensive support of Brevia and HCURA.

Notes The views expressed in Brevia articles are solely those of the authors. They do not represent the official stance of the magazine or any of its sponsers and affiliates

brevia.hcura.org


On The Cover: The photo was taken...right at the start of spring. I just... happened to catch a moment when the sun slipped through the space of the window. -Daniel Chen ’17, the photographer

Table of Contents If you can look into the seeds of time, and say which grain will grow and which will not, speak then unto me. - Macbeth, William Shakespeare “Seeds.” Image by the US Department of Agriculture via Flickr. Creative Commons Attribution.

brevia.hcura.org

BREVIA Fall 2016

3


EDITOR’S NOTE

The word “origins” derives from the Latin word oriri, meaning “to rise”--the same verb the Romans used to refer to the sun’s rising. This etymology makes the image on our cover particularly fitting. For us, this photograph represents the dawn, a reminder that each new day brings an opportunity to start afresh. But this image also represents another concept central to the theme of “origins”: the contingency that accompanies new beginnings. We glimpse the rays of the sun through a tiny opening in the window’s shutters; they are nearly hidden from our gaze. If a draft of wind had blown the window shut, or if the photographer had poised his camera a moment earlier or a moment later, this image would have been lost. So, too, most important beginnings are dependent partly on chance, haunted by the possibility of failure. Life as we know it might never have existed if asteroids containing the necessary elements had not pummeled our nascent planet. The processes of evolution began because of random mutations. The conception of each individual life requires a dizzying number of favorable probabilities. Often, we think of origins as inevitable. We imagine that these processes had to start and develop the way they did. But when we attend to the myriad chances that have shaped us, when we acknowledge how close we came to never existing at all, we can embrace existence with fresh wonder. Whether you are a researcher or simply a lover of ideas, we hope this wonder inspires you to explore our complex, contingent world.

Jessi Glueck

4

BREVIA Fall 2016

brevia.hcura.org


EDITOR’S NOTE

“Origins” is about beginnings and discoveries. It’s a word that asks us to gaze over our shoulders at the inception of undertakings currently in motion. But in addition to its retrospective connotations, the word “origins” can also evoke a prospective sensation: it draws our attention to nascent ideas that are just starting to take shape. I hope through this edition of Brevia you gain not only an understanding of the origins of ideas that already exist but also a feeling of excitement at the research that is just starting to blossom. Many of the stories in this issue deal with the origins of existing technologies and phenomena. For instance, Erin Hollander’s piece “Clarifying CRISPR” describes her research probing the properties and mechanisms of the now famous CRISPR-Cas system that has revolutionized genetics research. Similarly, in “The Diagnosis of Difference,” Jennifer Kizza describes her research about the clinical origins of autism spectrum disorder and specific language impairment, two cognitive disorders that often display similar symptoms in a child’s earliest years. But our stories also invite you to think ahead toward novel, exciting ideas. In “Of Copies and Cures,” for instance, Lizzy Thomas writes about her efforts in developing a cure for type I diabetes by regenerating the cells that malfunction in type I diabetics from stem cells. These and many other stories in this issue illuminate the ways in which research both digs deep at our fundamental understanding of the world around us and raises new possibilities through groundbreaking, innovative discoveries.

Alan Yang

brevia.hcura.org

BREVIA Fall 2016

5


Origins

Endless Forms Alan Yang 8 Evolution As A Force that Never Stops

When the Trimmers Go Wild

Nathan Williams

10

Synaptic Pruning and the Roots of Schizophrenia

Diagnosis of Difference

Jennifer Kizza 12 Comparing the Origins of Autism Spectrum Disorder and Specific Language Impairment

Gazing at Gravity

Features

Reece Akana 14

Gravitational Waves Explained

Images of India Rubini Naidu 16 A Photo Story

Racing Evolution Alan Yang 20 A New Strategy for Antibiotic Synthesis

Primary Research

Clarifying CRISPR Erin Hollander 22 The Bacterial Immune System That Could Change the World

The Harmonies of Nature and Knowledge Antonio Nardi’s Selva

Teddy Chappell

24

Of Copies and Cures Lizzy Thomas 26 The Drug War Alan Yang 28 A New Weapon in the Fight Against Antibiotic Resistance 6

BREVIA Fall 2016

brevia.hcura.org


brevia.hcura.org

Origins

Fall2016

BREVIA Fall 2016

7


COVERS

Endless Forms

Evolution As A Force that Never Stops By Alan Yang “[F]rom so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.� - Charles Darwin, On the Origin of Species Evolution is responsible for the remarkable diversity of life forms that inhabit our planet, from angler fish and venus fly traps to sea sponges, pterodactyls, and humans. Over a century ago, Charles Darwin famously set forth his theory of evolution via natural selection in his book On the Origin of Species; the theory is still widely applied and accepted today. Drawing on the works of other great minds, Darwin argued that those organisms best suited to their environment are more likely to survive and reproduce than those less well-adapted to their environment. As a result, the frequency of the genes of the better-adapted organisms will increase in the overall gene pool, and these changes in gene

8

BREVIA Fall 2016

frequencies over time lead to species differentiation and evolution. Moreover, evolution happens most rapidly when there is significant selection pressure-that is, when organisms live in an environment where poorly-adapted creatures quickly die out. Scarcity of food, for example, exerts such selection pressure and forces populations to evolve faster. Although Darwin set forth this general framework for thinking about evolution long ago, there are still aspects of evolution that we do not understand today. One unanswered question is whether evolution ever stops: whether natural selection can create an species that is perfectly adapted to its environment and will not change further. Professor Richard Lenski from the University of Michigan thinks he has the answer after a 27-year-long (and counting!) experiment.1 Although the evolution of humans and other slowly-reproducing animals often takes hundreds of thousands of years, Professor Lenski wanted to be able to observe evolution taking place in real time. Thus in 1988, Professor Lenski set in motion a long-term experiment with E. coli bacteria that would allow

brevia.hcura.org


COVERS him to track the course of evolution in his lab in a ding the nature of evolution: given a set of unchanmatter of decades. This experiment is still ongoing, ging conditions (in this case, the growth medium), and it represents the longest continuous study of a does evolution ever reach a stopping point? In other population of organisms in a fixed environment.2 words, is there such a thing as an ideal organism that The design of Lenski’s experiment is quite simple. no longer continues to evolve? In the beginning, twelve cultures of genetically idenIn mathematical terms, Lenski was trying to figure tical E. coli bacteria were cultivated in a growth out whether or not evolution follows a hyperbolic tramedium consisting mainly of glucose, a sugar that jectory, in which the rate of genetic change decreases nourishes the bacteria. E. coli’s quick reproduction over time as the population gene pool approaches a rate--once every 20-30 milimit that it cannot surpass. This nutes--allowed Lenski to ...the rate of evolution slows “limit” can be thought of as the track evolution across many, over time, but there is no ideal population gene pool, one many generations.3 Every that includes only organisms upper bound — evolution which are ideally adapted to their day, one percent of each population was transferred does not stop, and there is environments. Under the hyperto a new flask containing no such thing as an ideally bolic model, therefore, as gene the growth medium. The pools approach this ideal, evoluadapted organism. amount of glucose in the tion becomes slower and slower medium was carefully meaand eventually stops. sured so that by the next day, the bacteria would be However, in December 2015 Lenski announced growing under conditions of glucose scarcity. By that his data exhibit not a hyperbolic trajectory, but growing each day’s bacteria in the same glucose- a power law trajectory.1 Under a power law, the rate scarce medium, Lenski was able to subject the bacte- of evolution slows over time, but there is no upper ria to a continual selection pressure that would drive bound — evolution does not stop, and there is no evolution. Every 75 days, a sample of the bacteria such thing as an ideally adapted organism. population was frozen as a record, a time capsule of Lenski’s work demonstrates just how powerful a sorts. This procedure has been replicated every day force evolution is. Even in the context of an unchansince 1988, and today roughly 60,000 generations of ging environment, there seems to be no limit for a bacteria have been grown since the experiment’s in- species’ capacity to evolve. His work reveals evoluception. To put things in perspective, this is approxi- tion as a powerful force that endlessly shapes and mately the same number of generations that humans refashions life on earth. have undergone since the beginning of our species.2 In recent years, Lenski’s long-term project has Images by NiAID via Flickr. Creative Commons enabled him to tackle an important question regar- Attribution.

brevia.hcura.org

BREVIA Fall 2016

9


COVERS

When the Trimmers Go Wild Synaptic Pruning and the Roots of Schizophrenia By Nathan Williams

Since Biblical times, the origins of madness have been mysterious and misunderstood. Some attributed it to bad spirits or witchcraft, others to an imbalance in the body, and still others to divine punishment. In the book of Mark, Jesus himself healed a man said to be “possessed” by evil demons — a man who was probably suffering from mental illness.1 Since then, our understanding of psychosis has changed drastically as neuroscience and psychology made huge advances. Scientists have now explored the causes and treatment of multiple psychotic disorders, including the condition known as schizophrenia. Schizophrenia is an incredibly complex disease marked by hallucinations, paranoia, cognitive impairment, characteristic changes in brain structure, and numerous other symptoms.2 It is also one of the most complex brain disorders: scientists hypothesize that its causes could include brain development, genetics, prenatal infection, environmental factors, and irregularities in neurotransmitters.2 It remains unclear which of these factors is most important or

10

BREVIA Fall 2016

if there are other factors that contribute to the disease, but scientists made an important step in understanding the origins of schizophrenia this February. Their study,3 published in Nature, involved researchers at Harvard Medical School, the Broad Institute, and Boston Children’s Hospital. It highlighted one of the critical features of normal brain development — synaptic pruning. As a toddler, you had many more neural connections, or synapses, than you do now. Like a gardener pruning hedges, your brain prunes some of its extra synapses, eliminating the underused connections and leaving the more frequently used ones alone.4 This process of neural trimming begins in adolescence and lasts into the late 20s, a period that roughly aligns with the time that schizophrenia typically develops.5 Scientists had previously hypothesized that synaptic pruning might be one of schizophrenia’s underlying causes, but this study is the first to provide experimental evidence for this claim. The researchers began in a surprising place — not the nervous system, but the immune system.

brevia.hcura.org


COVERS

For years, scientists have known that several of the main genes linked to schizophrenia risk coded for proteins involved in the immune system, but they weren’t sure why. The researchers decided to study the gene C4, which codes for the protein known as “complement complement 4” and is linked to schizophrenia. C4 is part of the complement system, a defense system that is always protecting the body from bacteria, viruses, and other pathogens. The researchers found that the protein was expressed 40% more in those with schizophrenia.3 But why would variations in this immune system protein be linked to schizophrenia? To find out, the scientists turned to mice without a functional C4 gene. These mice experienced markedly less synaptic pruning than normal mice, so the researchers surmised that the C4 protein was involved in the brain’s neural clipping. Their conclusion: C4 is associated with increased synaptic pruning, which suggests that pruning is an underlying mechanism

brevia.hcura.org

of schizophrenia. The research fits with many previous findings that have suggested a connection between pruning and schizophrenia. Schizophrenia patients have thinner cortices6 (the outer layer of the brain involved in conscious thought) and fewer synapses7 than healthy adults, potentially due to pruning. The adolescent onset of schizophrenia happens at the same time as synaptic pruning.4 And the targets of pruning, scattered around the cerebral cortex, are often the brain regions most impaired in schizophrenia. The study is one of the first to establish a clear biological mechanism by which schizophrenia might arise, and it suggests an entirely new set of drug targets. In contrast to current antipsychotic medications, these drugs could target the fundamental origins of the disease, not just the symptoms.8 Future research is needed, but we may be one step closer to understanding the origins of psychotic disorders--and to finding a cure. Image by MethoxyRoxy via Wikipedia. Creative Commons Attribution. Modified by Erica Newman-Corre.

BREVIA Fall 2016

11


COVERS

The Diagnosis of Difference Comparing the Origins of Autism Spectrum Disorder and Specific Language Impairment By Jennifer Kizza

12

BREVIA Fall 2016

Autism spectrum disorder can sometimes strike very early. This disorder (known as ASD) is associated with impairments in the development and growth of the brain, and some infants exhibit symptoms when they are just 12 months old.1 Such symptoms include repetitive behaviors and difficulties in social communication, especially atypical language development.2 Recent data indicates that 1 in 45 American children have ASD, making the disorder one of the most common diseases affecting brain development.3 Early diagnosis of the disease is crucial for successful treatment: many studies have demonstrated that educational and behavioral therapy for infants who are at high risk for ASD, before the emergence of all ASD symptoms, can improve their language development.4 But for a variety of reasons, ASD can be difficult to diagnose early on. This is especially true because the problems in communication often present in ASD overlap with the symptoms of another disorder called specific language impairment (SLI). SLI is a condition in which a child displays deficiencies in speech acquisition but exhibits no impairments in other cognitive and behavioral functions.5 SLI can be present simultaneously with or exist independently of ASD. Because ASD and SLI symptoms overlap so much and because early identification of ASD is

brevia.hcura.org


COVERS crucial for effective interventions, the goal of our project was to investigate the differences between infants at risk for ASD and those at risk for SLI with respect to language development. These differences can then be used to develop more precise methods for infants at risk for ASD early in their lives. Previous studies have ignored the potential overlap in the developmental trajectories of ASD, SLI, or any other language impairment disorder. As a result, the brain and behavioral development for infants at high risk of ASD and SLI has not been clearly described. Our study sought to distinguish between atypical language development in SLI and atypical language development in ASD. To do this, we followed the development of 274 infants from the age of 12 months, when language first develops, through 36 months, when an ASD or SLI diagnosis is commonly made.6, 7 Because having a sibling with autism or SLI is a major risk factor for both diseases, we categorized the infants into three groups based on whether their siblings had the disease: those at high risk for autism, those at high risk for SLI, and a low-risk control group composed of those who had little familial risk for either disorder.5, 8 We then used a Verbal Intelligence Quotient test to quantify the infants’ language skills.9 We also assessed brain activity in regions connected with language using electroencephalography, a process that measures electrical activity in the brain.10, 11 Lastly, we tested the infants for ASD and SLI when they were 18, 24, and 36 months old in order to determine which infants actually developed a disorder. Overall, our findings support the conclusion that both infants at high risk for autism and those at high

brevia.hcura.org

risk for SLI are delayed in language development when compared to control infants. In particular, from 12 through 18 months of age, infants at high risk for autism or SLI had significantly poorer language skills compared to the controls. However, by 36 months, only those infants at high risk for autism — and especially those who went on to develop autism — had significantly lower language scores than the control group. Differences in brain activity also emerged between groups. Infants at high risk for autism or SLI displayed atypical brain activity from 1218 months when compared to infants in the control group. But by the time the infants were three years old, those at high risk for SLI showed similar electroencephalography results and Verbal Intelligence Quotient scores to those of control infants. Infants at high risk for ASD, however, still differed in these metrics from the control infants when they were three years old. These findings suggest that there are differences in the trajectory of early language development between infants at risk for ASD and infants at risk for SLI. Further studies should explore why infants at risk for ASD differ in their language skills from those at risk for SLI over time. In this way, our research may play a role in helping clinicians distinguish autism from other disorders when children are very young. This work brings us one step closer to a full understanding of ASD. Image by RobertG NL via Flickr. Creative Commons Attribution. Modified by Jeongmin Lee Using https://snorpey.github.io/jpg-glitch/

BREVIA Fall 2016

13


FEATURES Space-time can be bent by any object with mass, creating the attractive force commonly known as gravity.3 How would the bending of space-time result in an attractive force? Physicists allow us to visualize this phenomenon by comparing the 4-dimensional space-time realm to a 2-dimensional fabric. Any object that has mass in the space-time realm is like a Gravitational Waves Explained bowling ball placed on the fabric. Just as a marble By Reece Akana placed near the bowling ball will follow the contours in the fabric created by the ball and move towards it, so objects such as the Earth create bends in the fabric On September 14, 2015, four mirrors moved of space-time that pull other objects towards them. The concept of space-time as a fabric is importhe distance of about 4/1000ths the diameter of a tant for understanding gravitational waves because proton, and this phenomenon made scientific headlines.1 Two Laser Interferometer Gravitational-Wave these waves are “ripples” in the fabric of space4 Observatories (LIGO’s) located in Hanford, Was- time caused by violent cosmic processes. Imagine hington and Livingston, Louisiana reported the that the aforementioned bowling ball is jostled first known direct detection of gravitational waves back and forth so that it creates ripples in the fain a paper published on February 11, 2016. Physi- bric. Einstein predicted that accelerating objects can cists across the globe celebrated this detection be- similarly create fluctuations in the fabric of space4 cause it verified one of Albert Einstein’s last pre- time. These fluctuations are called gravitational dictions before his death.2 For most, though, the waves, but since Einstein first predicted them in 4 news raised the the question: what exactly are 1916, they had not ever been physically detected. In September 2015, physicists at the two LIGO gravitational waves, and why are they important?  In order to answer this question, we should dis- locations were able to gather the first direct, empicuss some basic principles of physics. These prin- rical evidence of gravitational waves. They did so ciples dictate that, to describe the location of an by using giant but precisely calibrated apparatuses. object in a three-dimensional space, we need three Each LIGO observatory consists of two 4-km percoordinates--think of a point whose location can pendicular arms with mirrors at their ends. The lenbe described by its coordinates on the x, y, and z gths of these arms are measured precisely with la5 axes of a graph. But Einstein’s theories suggested sers. When gravitational waves hit both LIGO’s in that a fourth coordinate was needed: time. This re- 2015, the lengths of the arms changed in a specific sults in the concept of a 4-dimensional realm called fashion due to the “ripples,” or the stretching and space-time, which exists everywhere in the universe. compressing, of space-time. It turned out that two

Gazing at Gravity

14

BREVIA Fall 2016

brevia.hcura.org


FEATURES

black holes rapidly orbiting each other approximately 1.3 billion light years away were able to produce such large gravitational waves that the mirrors moved. Their movement was extremely small, but nevertheless detectable by the LIGOs. This detection at last demonstrated the existence of gravitational waves. The fact that gravitational waves exist, in turn, provides direct empirical evidence for the existence of black holes. Black holes are enormously dense objects in space that are so massive that even light cannot escape their gravitational pull.6  Previously, scientists had only inferred their existence by observing the behavior of other celestial objects near locations where black holes might be.6 But after observing the gravitational waves, physicists used Einstein’s equations to deduce that only the motions of two black holes could produce the specific ripples detected at both LIGOs. At the same time, then, the motions of LIGO’s mir-

brevia.hcura.org

rors provided physical confirmation of two important phenomena: gravitational waves and black holes. Einstein’s vision, brilliant as it was, was also incomplete. The theory he developed to explain astronomical phenomena like black holes and gravitational waves--known as the theory of general relativity — conflicts with other theories describing the tiniest phenomena, namely quantum mechanics.7 Through the detection of gravitational waves, we can understand and test Einstein’s theories more rigorously. This enhanced understanding may ultimately help us to unify quantum mechanics and general relativity, providing a single, elegant mathematical description of the universe. Image by Dana Berry via nasa.gov. Creative Commons Attribution.

BREVIA Fall 2016

15


FEATURES

Images of India A Photo Story

By Rubini Naidu Going to Tamil Nadu, India for a documentary photography project was a way for me to deepen my connection to the area native to my family. Though I had been to this area many times before, it was a new experience to walk through the streets with a camera in hand, ready to share the richness of the region with others. I strove to approach locals with humility, respect, and curiosity. I was moved when they reciprocated my interest through participating in interviews that would often bloom into hour-long conversations and sometimes even involve a freshly cooked meal from their farms. Each of these photographs serves as a portal into an aspect of Tamil Nadu’s culture that I have come to cherish and celebrate. One of the main media through which I have compiled this work has been through a handmade fine-art book that includes 30 such photographs, and their respective narratives. I hope that the included sample of images prompts you to reflect on the stories of Tamil Nadu, India that remain behind what meets the eye.

16

BREVIA Fall 2016

brevia.hcura.org


brevia.hcura.org

BREVIA Fall 2016

17


FEATURES Previous Page: This farmer's market is a daily event in which local vendors and customers gather at dawn and remain until the sun is at its highest peak. Each segment of the image could almost be its own photograph — filled with activity, but containing tantalisingly little information about these individuals' stories and identities.

In a narrow street of the Siruvani villages in the western part of Tamil Nadu, a young girl enacts using an empty mortar and pestle to enact grinding food. No one had explicitly taught her this action, but she observed it from the women of the villages.

18

BREVIA Fall 2016

The boys are keeping busy during their lunch break. Their school was less than a block away, and both their teacher and their families were aware of the boys’ mischief. While the teacher was frustrated that her students were not returning to class, the parents were undisturbed: they were satisfied that their children were attending school at all.

brevia.hcura.org


FEATURES

This man is a potter; pottery has been his family’s contribution to society for generations. As he uses his hands to mould the pots out of clay, his wife sits on the floor in front of him, using her hands to spin the wheel on which the clay sits. When his 8-year-old granddaughter was asked what she wanted to do when she grew up, she said she wanted to be a school teacher and a potter.

brevia.hcura.org

BREVIA Fall 2016

19


FEATURES

RACING EVOLUTION

A New Strategy for Antibiotic Synthesis By Alan Yang

When it comes to antibiotics, the pace of our discoveries often lags far behind the rate of bacterial evolution. Recent detections of superbugs resistant to even our last lines of antibiotic defense suggest that antibiotics are changing from miraculous inventions to useless relics.1 The implications are terrifying. Without new antibiotics, banished pestilences can rear their ugly heads again, and even mundane infections can become life-threatening.

20

BREVIA Fall 2016

brevia.hcura.org


FEATURES We need new antibiotics, but it’s not easy to make them. Many current antibiotics were made by harvesting natural products with antimicrobial properties from fungi or bacteria and then modifying them to make drugs that can be used in humans. To make these modifications, scientists typically employ an approach known as semi-synthesis: they attach different chemical groups at specific sites on the natural product to change its pharmacological properties. This approach, however, is laborious and limited in scope because natural products are complex molecules that often cannot be easily modified with high specificity. For instance, the macrolide class of antibiotic — used to treat diseases ranging from STIs to skin infections — are all derived from the natural product erythromycin, which was first harvested from soil samples in 1949. But there are only so many ways one can efficiently modify erythromycin. This means that it is difficult to develop new macrolide antibiotics to overcome antibiotic resistance. However, Professor Andrew G. Myers’s lab at Harvard University has figured out a way to get around both the tediousness and the limitations of semi-synthesis. In a recent paper in Nature, they reported a synthetic strategy based on eight modifiable “chemical building blocks” that can be combined to make an exponential variety of macrolide antibiotics in high quantities.2 These chemical building blocks are small molecular fragments that, when combined in a particular series of steps, react with each other to form a larger macrolide molecule. Unlike semi-synthetic strategies, therefore, Myers’s approach allows

brevia.hcura.org

for the practical and complete synthesis of a diverse range of macrolides without having to start from erythromycin. Because it eliminates the need to work with a natural product, Myers’s strategy drastically reduces the difficulty of producing new drugs. Semi-synthesis relies on making highly specific chemical modifications to erythromycin, a task that requires many arduous synthetic maneuvers. Myers’s “building block” strategy, however, contains fewer than a dozen steps. It is also highly robust: it works well even when the initial building blocks contain modifications, as long as the overall structures of the building blocks are preserved. This versatility means that Myers’s procedure can be used to generate new macrolides with a wide range of chemical flavors. Using their published strategy, Myers’s lab has already synthesized over 300 macrolides, many of which inhibit growth in bacteria that are resistant to erythromycin and other macrolides already on the market. Myers’s strategy therefore demonstrates a practical, simple, and highly versatile method of synthesizing macrolides. Strategies like these might make antibiotic development more attractive to pharmaceutical companies, which have been increasingly reluctant to invest in antibiotic development.3 More importantly, this strategy might help us catch up with bacterial evolution and overcome resistance as it arises in the future. Image via Wikimedia Commons. Creative Commons Attribution.

BREVIA Fall 2016

21


PRIMARY RESEARCH

CLARIFYING CRISPR:

The Bacterial Immune System That Could Change the World By Erin Hollander In the spring of 2015, a group of scientists in China shocked the world with a groundbreaking discovery: certain bacteria have an immune system whose mechanisms can be harnessed to edit the human genome. This system, known as the CRISPR-Cas system, entered into public awareness because some feared it could be used to create “designer babies,” while others hoped it would help to treat devastating illnesses such as sickle cell anemia and beta thalassemia (both disorders of the blood with strong genetic components).1 Despite the controversy surrounding the CRISPR-Cas system and its usage, the mechanisms underlying the system are not well understood. Although the CRISPR-Cas system is often described in terms which make it seem like one unified system, there are actually fourteen different varieties of CRISPR-Cas systems, each designated with a Roman numeral and a letter. Each system has different Cas proteins which may function in different ways during the immune response.2 My research investigated the roles of specific Cas proteins in the CRISPR-Cas system known as Type II-A. Type II-A is found in Strepto-

22

BREVIA BREVIA Fall Fall 2015 2016

coccus thermophilus, a key bacterium in the dairy industry. Because it has only four Cas proteins (Cas1, Cas2, Csn2, and Cas9), the Type II-A system of S. thermophilus is easier to study and manipulate than other, more complex CRISPR-Cas systems. Type IIA’s relative simplicity will allow us to better understand the fundamental attributes of the CRISPR-Cas system and explore its broad range of applications, from novel gene therapy techniques to new methods for combating antibiotic-resistant bacteria.3 My project investigated the role of each Cas protein in the Type II-A system during the three stages of the bacteria’s CRISPR-Cas immune response. The stages are: (1) spacer acquisition, (2) expression, and (3) defense. First, during spacer acquisition, the CRISPR-Cas system of the bacteria incorporates a segment of an invading virus’s genetic material into a part of its own genome called the CRISPR array. Next, the DNA of the CRISPR array, including the foreign genetic material, is transcribed (copied as RNA) and cleaved at specific intervals to create small CRISPR RNAs, or crRNAs. Lastly, during defense, crRNAs attach to specific Cas proteins. The

brevia.hcura.org


PRIMARY RESEARCH crRNA allows the Cas-crRNA complex to recognize an invading virus, as the crRNA contains genetic material that matches the invader’s genome. The Cas protein is then able to cleave the hostile virus’s genome. Once this genome is destroyed, the virus can no longer function and the microorganism has successfully survived the invasion.4 We tested the three stages sequentially to determine whether deleting one of the four Cas proteins resulted in a loss of functionality of the CRISPR-Cas system. We first created four mutant strains of S. thermophilus by deleting one of the four Cas proteins in each strain. To test the spacer acquisition stage of the system, cultures of these mutant S. thermophilus strains were infected with a virus to generate Bacteriophage Insensitive Mutants (BIMs). These BIMs are colonies of S. thermophilus which are able to survive the infection induced by the virus, either through the CRISPR-Cas system or another defense mechanism. We analyzed the genomes of these survivor colonies to find if “spacers” from the virus had been incorporated into the CRISPR array. The analysis demonstrated that in each of the mutant strains, the loss of the Cas protein prevented spacer acquisition. After determining the function of the Cas proteins in spacer acquisition, we tested the last two phases of the CRISPR-Cas mechanism together: expression

brevia.hcura.org

and defense. We inserted circular molecules of DNA called plasmids into the S. thermophilus cells. These plasmids encoded an antibiotic resistance gene as well as a DNA sequence which matched an existing spacer in the CRISPR array of the S. thermophilus. If expression and defense systems are functioning in a mutant strain, then the crRNA and Cas proteins will successfully recognize and cut the plasmids. Because this cutting would also destroy the antibiotic resistance gene in the plasmids, bacterial cells whose CRISPR-Cas systems operated effectively would not be able to survive on plates treated with antibiotics. Using this method, we determined that deletion of Cas9 resulted in loss of defense or expression function, while deletion of Cas1, Cas2, and Csn2 allowed the bacteria to retain expression and defense function. These results indicate that all four Cas proteins are involved in spacer acquisition, whereas only Cas9 is necessary for expression and defense. This research represents a crucial step forward in the quest to understand the CRISPR-Cas system. This quest will not only reveal a new aspect of bacterial biology, but may also revolutionize genetic therapies for human beings. Image by SliderBase via YouTube. Creative Commons Attribution. Modified by Cathy Wang.

BREVIA BREVIA Fall Fall 2015 2016

23


PRIMARY RESEARCH

The Harmonies of Nature and Knowledge Antonio Nardi’s Selva By Teddy Chappell What separates law-bound nature from untamed wilderness? Although we hold the universe to be governed by immutable laws, the impression of the natural world’s chaos is inescapable. We find a surprising take on this problem in the work of Antonio Nardi, a seventeenth century Tuscan mathematician with whom Galileo and his disciples corresponded and worked. A modest body of Italian scholarship on Nardi exists, but beyond a few references to him in works on Galileo, there has been no English scholarship on this important Renaissance figure.1 My work at the University of Minnesota under the supervision of J.B. Shank seeks to remedy this. I suggest that Nardi’s writings portray a complex relationship between nature’s unity and its disharmony: a diverse, varied natural world can still constitute a harmonious whole. Nardi marvels at the overwhelming diversity of nature and the impossibility of comprehending its variety for all except its creator, God. At the same time, however, he continually emphasizes that this seeming chaos produces an ineffable sense of harmony: “the silent parts of the earth (which seem ordered by chance) nevertheless make a secretly

24

BREVIA Fall 2016

manifest harmony” (415). Initially this harmony seems to be present despite nature’s chaos, but Nardi’s continual juxtaposition of the two suggests that their relationship is not entirely antithetical. Nardi was by no means alone: early modern texts abound with the discordia concors trope — Latin for “discord agrees” — which also plays on the concordance or harmony of different musical notes or cordae. Nardi’s ideas are also likely inspired by Johannes Kepler’s 1619 Harmonices Mundi in which he argues for the existence of different kinds of harmony in music, nature, and even society beyond the ancient ones calculated by Pythagoras. All of this points toward a more flexible notion of harmony or perhaps even one that can encompass disharmony. We find even more resonances of this creative tension between order and chaos within Nardi’s Scene (Italian for “Scenes”), a 1,394-page manuscript in Tuscan dialect found today in Galilean collection in Florence.2 Just as Nardi’s vision of nature involved a wide array of different elements, so his written work exhibits a dizzying variety of material ranging from geometry to philology and appears to lack any kind

brevia.hcura.org


PRIMARY RESEARCH of discernible order or organization. A table of contents tucked away around the text’s midpoint, however, indicates that the Scene is not a casually disordered rough draft. Nardi in fact draws four “chords” from what he playfully calls the “chaos” of the Scene, thus “harmonizing” the text’s disorganization (740-1). Indeed, Nardi entitled the earlier versions of his work selva (silva in Latin, meaning wood or forest), which is a reference to the classical genre of ostensibly impromptu or unfinished poems revived during the Renaissance. Like Nardi’s work, however, the seeming jumble of poems in these silvae was actually carefully arranged with a specific purpose in mind.3 Nardi’s composition of the Scene, then, echoes his vision of nature: careful readers will look past the confusing disarray of the selva and be able to perceive its “secretly manifest harmony.” This artistic arrangement also reflects back upon its creator or “author,” an identity which in the early modern period carried more authority than simply being a “writer.” Nardi concludes his essay on nature’s harmony by noting, “It is certain that the highest and sovereign Maker [Artefice] is not only a geometer but also a musician” (419). It is not surprising that God would have multiple capacities as creator, but Nardi praises many other auctores for their multifaceted talents—sometimes in surprising ways. He asserts that Odysseus is as much a sage as an adventurer and that Homer is both poet and philosopher (769). He likewise draws attention to Archimedes’s status as both mathematician and rhetorician, arguing that the ancient geometer uses Euclidian notation despite its complexity because

brevia.hcura.org

“delight and marvel increase with the difficulty of the means” (676). Perhaps most tellingly, he lauds the Roman poet Horace for his ability to effortlessly imitate any kind of individual, whether a Stoic or Epicurean philosopher, or even a libertine courtier (1236). In Nardi’s eyes, then, auctoritas of an early modern auctor comes not from mastery of one field but rather from expertise in many and the ability to move smoothly between them. It is doubtful that Nardi wanted to be known solely as a mathematician, or even as a tripartite mathematician-humanist-philosopher. Indeed, his aim for this virtuosic display in the Scene likely lay outside the world of learning, or at least the narrow sense in which we conceive it today: the apparently off-the-cuff organization of the Scene and its effortless traversal of disciplines points to the intellectual habits of a dilettante-like courtier much more than to those of an academic philosopher.4 Scholars have usually focused on the mathematical and scientific aspects of the Scene, but such an approach not only neglects the rest of the work’s contents but also misses its point altogether.5 Scholars have illustrated how figures of the Scientific Revolution like Galileo were involved in many activities outside of our modern conception of science, ranging from art criticism to court politics.6 Nardi’s work shows us these seemingly disparate personae in dynamic interaction and the urge of a Renaissance author-creator to harmonize them. Image by Steve Slater via Flickr. Creative Commons Attribution. Modified by Erica Newman-Corre. BREVIA Fall 2016

25


PRIMARY RESEARCH

Of Copies and Cures

Type 1 diabetes, previously called juvenile diabetes, is a chronic condition which features irregular blood glucose levels and resulting symptoms including increased thirst and hunger, fatigue and unexplained weight loss.1 Its mechanism involves the destruction of beta cells by the body’s own immune system. Beta cells are found in the pancreas and are responsible for the production of insulin. Insulin is the hormone that signals for absorption of glucose from the blood by muscle and fat cells, and suppression of glucose production by the liver after eating. Once the beta cells that produce insulin are destroyed by the immune system, diabetics lose the ability to regulate their blood glucose levels. Treatment can stabilize these fluctuating blood glucose levels, but for type 1 diabetes, treatment involves lifelong monitoring of blood sugar and daily injections of insulin. Therefore, a curative treatment rather than a daily therapy is highly desirable for the 1.25 million children and adults who suffer from the disease.2 The creation of such a treatment is the goal of Doug Melton’s laboratory. Part of the Harvard Stem Cell In-

By Lizzy Thomas

26

BREVIA Fall 2016

brevia.hcura.org


PRIMARY RESEARCH

stitute, the lab has recently made advances through stem cell work. Specifically, in the fall of 2014, the lab published an article in the journal Cell describing a protocol that can lead human embryonic stem cells through a differentiation pathway from stem cells to beta cells.3 The creation of functional beta cells — cells able to secrete appropriate levels of insulin in response to glucose — from stem cells has never before been done, and was lauded as a significant step toward creating a cure for the disease. Although the stem cell-derived beta cell approach towards diabetes treatment has received much attention, the Melton lab is also investigating other strategies to combat diabetes. One such strategy is boosting beta cell replication, where the goal is ultimately to coax a diabetic individual’s own beta cells to make more of themselves at a higher rate than they normally would. Since I’ve joined the Melton lab, I have assisted in searching for proteins and small molecules that can cause beta cells to increase their replication rate. We assess certain compounds’ ability to increase beta cell replication rate by first “creating” (or, differentiating) beta cells from stem cells according to the new protocol generated by the Melton lab. We then treat these new beta cells with a set of compounds to see if the cells’ replication rates increase when exposed to those compounds. As a control, we compare the rate of replication in cells that have been exposed to various compounds and the replication rate of cells that are untreated. We perform measurement of the replication rates of these cells — also called a repli-

brevia.hcura.org

cation assay — using the fact that dividing cells must replicate their DNA. We expose all the conditions of cells, treated with the different compounds, to a compound called BrdU, an analog to the DNA building block thymidine. We are able to detect BrdU by binding fluorescent antibodies to it. These antibodies can be detected under a fluorescent microscope.4 Since dividing cells incorporate BrdU the newly replicated DNA, this procedure allows us to see which cells are proliferating. Therefore, we can calculate the different levels of replication in different groups of cells. But how does beta cell replication fit into the search for a Type 1 diabetes cure? There is a so-called “honeymoon period” during the progression of the disease, when, after diagnosis and the start of insulin supplementation, a sufficient beta cell mass remains to regulate glucose.5 If a way to silence the destructive immune responses that steadily destroy the beta cells is discovered, a patient’s beta cells could be repopulated by any treatment found to boost their replication. What’s more, there is some evidence that some Type 1 diabetics may retain a miniscule number of beta cells even after most of these cells have been destroyed by the body’s immune system, over long periods of time.6 There is potential, then, that effective beta cell replication boosting therapies could hold promise as a cure for Type 1 diabetes. Images via Asymmetrex and Bella Diva Lifestyle. Creative Commons Attribution. Modified by Cathy Wang.

BREVIA Fall 2016

27


PRIMARY RESEARCH

THE DRUG WAR:

A New Weapon in the Fight Against Antibiotic Resistance By Alan Yang

Antibiotic resistance represents a serious medical crisis that will only worsen with time. Antibiotic resistant bacteria are those that have acquired genetic mutations that allow them to survive even in the presence of antibiotic drugs, which would otherwise kill the bacteria. The CDC currently estimates that two million Americans fall ill to antibiotic-resistant infections yearly, with at least 23,000 dying as a result.1 The numbers are much worse in developing nations.2 Indeed, there are 480,000 cases of multi-drug resistant TB each year around the world--and that’s just one disease.7 Perhaps most alarming are the yearly discoveries of new “superbugs” that have acquired resistance to even our “last resort” antibiotics, transforming from previously treatable pathogens into untreatable ones.3 Antibiotics work by inhibiting the function of essential proteins in bacteria. Despite the problem of antibiotic resistance, in the past 28 years, no new class of antibiotic drugs has been developed.6 One family of proteins present in all bacteria that are currently not targeted by any antibiotic on the market

28

BREVIA Fall 2015 2016

are called the peptidoglycan glycosyltransferases, or PGTs. PGTs join sugar molecules together into long chains, which are then used to build the bacterial cell wall. Inhibiting the activity of PGTs kills bacteria very effectively. We know this through studies on a natural carbohydrate product called moenomycin that kills bacteria by inhibiting PGTs but is unfortunately a poor pharmaceutical candidate because it is poorly absorbed in humans.5 The ultimate goal of this project is to identify molecules that can bind to a particular PGT called penicillin-binding protein 2 (PBP2) from a species of bacteria called Staphylococcus aureus. Ideally, in binding to PBP2, the molecules would block PBP2 from binding to the sugars and building the cell wall. Such molecules, if obtained, would represent the starting point for the development of the first new class of antibiotics in 28 years. This project is still in

brevia.hcura.org


PRIMARY RESEARCH ongoing, but significant strides have been made. One of the best ways to prove that a molecule binds to a protein is to visualize the binding. This atomic-level visualization can be achieved through X-ray protein crystallography, which allows scientists to determine the 3D structure of a protein at the resolution of individual atoms by analyzing the patterns in which a crystallized sample of the protein reflects and bends incoming X-rays. In a protein crystallography experiment, large amounts of the protein in question must be obtained and purified without causing the protein to denature, or unravel into an inactive conformation. The purified protein is then concentrated and placed in a chemical solution that encourages the protein to leave the solution and pack together as solid crystals. Finding the precise recipe for the solution that encourages crystallization largely relies on patient trial and error. Once crystals are obtained, they are exposed to an X-ray beam, which will be diffracted by the crystal. During diffraction, the crystals will bend the X-rays, which will then interfere with each other. By performing complicated calculations on this interference pattern, the atomic-level structure of the protein and any bound molecules can be deduced. After a few months of work, I have developed a protocol that can reliably produce high-quality crystals of PBP2-the S. aureus protein that, when inhibited by the proper molecule, will cause the bacteria to die. I worked off a pro-

brevia.hcura.org

tocol developed by Lovering et al., who were the first to obtain a crystal structure of PBP2.4 My protocol is slightly different than Lovering et al.’s, and these differences allow larger and more viable crystals to form. At this point, I have only produced crystal structures for PBP2 alone, without any molecules bound to it. But the reliability of my protocol is important because it may soon allow me to create co-crystal structures of PBP2 bound to inhibitor molecules. Such co-crystal structures are very useful in drug development because they show scientists exactly how an inhibitor molecule is oriented inside the protein binding pocket and what kinds of bonds it makes with the protein. This information can help scientists design other drugs that can bind similarly to the protein. These co-crystal structures may allow for the development of a new class of drugs, combating the urgent threat of antibiotic resistance. Images via Wallpapers Home and HowStuffWorks. Creative Commons Attribution. Modified by Cathy Wang. BREVIA Fall 2015 2016

29


REFERENCES

Theme: Origins 08 Endless Forms

1. Lenski, R.E. et al. (2015). Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli. Proc. R. Soc. B., 282, 1-9. 2. Scharping, N. (2015). Could Evolution Ever Yield a “Perfect” Organism? Discover. Retrieved from http:// blogs.discovermagazine.com/d-brief/2015/12/16/the-search-for-theperfect-organism/#.V2mrMJMrIdU. 3. Todar, K. (2012). Todar’s Online Textbook of Bacteriology. Retrieved from http://textbookofbacteriology. net/growth_3.html.

10 When the Trimmers Go Wild

1. Mark 5:1-20 2. Tamminga, C. A. and H. H. Holcomb. “Phenotype of schizophrenia: a review and formulation.” Molecular Psychiatry 10 (2005): 27-39. Web. 4 Mar. 2016. 3. Sekar, Aswin et. al. “Schizophrenia risk from complex variation of complement complement 4.” Nature 530 (2016): 177-183. Web. 4 Mar. 2016. 4. Santos, Edalmarys and Chad A. Noggle. “Synaptic Pruning.” Encyclopedia of Child Behavior and Development. Ed. Sam Goldstein and Jack A. Naglieri. 1st ed. New York: Springer US, 2011. Web. 4 Mar. 2016. 5. Riccomagno, Martin M. and Alex L. Kolodkin. “Sculpting Neural Circuits by Axon and Dendrite Pruning. Annual Review of Cell and Developmental Biology 31 (2015): 779-805. Web. 4 Mar. 2016. 6. Cannon, T. D. et. al. “Progressive reduction in cortical thickness as psychosis develops: a multisite longitudinal neuroimaging study of youth at elevated clinical risk.” Biological Psychiatry 77.2 (2015): 147-157. Web. 4 Mar. 2016. 7. Glaussier, J. R. and D. A. Lewis. “Dendritic spine pathology in schizophrenia.” Neuroscience 251 (2013): 90-107. Web. 4 Mar. 2016. 8. Miyamoto, S., Duncan G. E., Marx C. E., & Lieberman J. A. (2004). Treatments for Schizophrenia: a critical review of pharmacology and mechanisms of action of antipsychotic drugs. Molecular Psychiatry, 10: 79-104.

12 The Diagnosis of Difference

1. Jones, E.J., Gliga T, & Bedford, R. (2014). Developmental pathways to autism: A review of prospective studies of infants at risk. Neurosci Biobehav Rev; 39:1-33. Retrieved from http://www.sciencedirect.com/ science/article/pii/S0149763413002984. 2. American Psychiatric Association. (2013). Diagnostic and statistical manual of mental disorders (5th ed.). Arlington, VA: American Psychiatric Publishing. 3. Zablotsky, B., Black, L., Maenner, M., Schieve, L., & Blumberg, S. (2015). Estimated prevalence of autism and other developmental disabilities following

30

BREVIA Fall 2016

questionnaire changes in the 2014 national health interview survey. National Health Statistics Report. Surveillance summaries. Centers for Disease Control, Washington, DC, 2015. 4. Green, J., Charman, T., Pickles, A., Wan, M.W., Elsabbagh, M., Slonims, V., Taylor, C., McNall, J., Booth, R., Gliga, T., Jones, E.J.H., Harrop, C., Bedford, R., Johnson, M.H., & the BASIS Team. (2015). Parent-mediated intervention versus no intervention for infants at high risk of autism: a parallel, single-blind, randomised trial. Lancet, eScholarID:253226. Retrieved from doi.org/10.1016/ S2215-0366(14)00091-1. 5. Bishop, D. (2006). What causes specific language impairment in children? Current Direct Psychological Science, 15(5): 217-221. Retrieved from http://www.ncbi.nlm.nih.gov/pmc/articles/ PMC2582396/. 6. Center for Disease Control (CDC). (2014). 10 things to know about new autism data. National Center on Birth Defects and Developmental Disabilities, 2014. Centers for Disease Control, Washington, DC, 2014. 7. National Institute of Health. (2014). Speech and language developmental milestones. Retrieved from http://www.nidcd.nih.gov/ health/voice/pages/speechandlanguage.aspx. 8. Chaste, P., & Leboyer, M. (2012). Autism risk factors: Genes, environment, and gene- environment interactions. Dialogues Clinical Neuroscience, 14(3): 281-292. Retrieved from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3513682/. 9. Mullen, E. M. (1995). Mullen scales of early learning (AGS ed.). Circle Pines, MN: American Guidance Service Inc. 10. Tierny, A., Gabard-Durnam, L., Vogel-Farley, V., Tager-Flusburg, H., & Nelson, C. (2012). Developmental trajectories of resting EEG power: An endophenotype of autism spectrum disorder. PLoS ONE, 7(6), 1-10. Retrieved from http:// journals.plos.org/plosone/article?id=10.1371/journal.pone.0039127 11. Benasich, A., Guo, Z., Choudhury, N., & Harris, K. (2008). Early cognitive and language skills are linked to resting frontal gamma power across the first three years. Behav Brain Res. 195(2): 215–222. doi:10.1016/j. bbr.2008.08.049.

Features 14 Gazing at Gravity

1. Overbye, Dennis. “Gravitational Waves Detected, Confirming Einstein’s Theory.” The New York Times. The New York Times, 11 Feb. 2016. Web. 03 June 2016. 2. Abbott, B. P., et al. “Observation of gravitational waves from a binary black hole merger.” Physical Review Letters 116.6 (2016): 061102. 3. “Einstein’s Theory of General Relativity.” Space. com. Purch, 11 Feb. 2016. Web. 22 May 2016. 4. “What Are Gravitational Waves?” LIGO Lab. Caltech. Web. 22 May 2016. 5. Cho, Adrian. “Gravitational Waves, Einstein’s Ripples in Spacetime, Spotted for First Time.” Gravitational Waves, Einstein’s Ripples in Spacetime, Spotted for First Time. Science, 11 Feb. 2016. Web. 25 Feb. 2016. 6. Dunbar, Brian. “What

brevia.hcura.org


REFERENCES Is a Black Hole?” NASA. NASA, 30 Sept. 2008. Web. 13 June 2016. 7. Powell, Corey S. “Relativity v Quantum Mechanics – the Battle for the Universe.” The Guardian. Guardian News and Media, 04 Nov. 2015. Web. 25 May 2016.

20 Racing Evolution

1. A. Sun, L.H., Dennis, B. (2016, May 27). The Superbug that doctors have been dreading just reached the U.S. The Washington Post, Retrieved from https://www.washingtonpost.com/. 2. Seiple, I. B. et al. (2016). Fighting evolution with chemical synthesis. Nature, 533, 338–345. 3. Yan, M., Baran, P.S. (2016). Fighting evolution with chemical synthesis. Nature, 533, 326-327.

Primary Research 22 Clarifying CRISPR

1. Wade, N. (2015). Scientists Seek Moratorium on Edits to Human Genome That Could Be Inherited. Retrieved May 05, 2016, from http://www.nytimes.com/2015/12/04/science/crispr-cas9-human-genome-editing-moratorium.html?_r=0 2. Rath, D., Amlinger, L., Rath, A., & Lundgren, M. (2015). The CRISPR-Cas immune system: Biology, mechanisms and applications. Biochimie, 117119-128. doi:10.1016/j. biochi.2015.03.02 3. Bhaya D, Davison M, Barrangou R. CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu. Rev. Genet. 2011;45:273-297. 4. Terns, R. M., & Terns, M. P. (2014). CRISPR-based technologies: prokaryotic defense weapons repurposed. Trends In Genetics,30(3), 111-118. doi:10.1016/j. tig.2014.01.003

24 The Harmonies of Nature and Knowledge

1. Capone-Braga, G. “Un Filosofo dell’estremo Rinascimento.” Atti e Memorie dell’Accademia Petrarca di Scienze, Lettere ed Arti 5-7 (192528): 36-135. Milighetti, Maria Chiara. “Sophia e mathesis negli Scritti di Antonio Nardi.” Bollettino di Storia delle Scienze Matematiche (La Nouva Italia) 26, no. 1 (2006): 9-31. 2. Nardi, Antonio. Scene. Bound manuscript. Gal. Mss. 130. Biblioteca Nazionale Centrale di Firenze. Translations are my own. 3. Van Dam, H. “Wandering Woods Again: From Poliziano to Grotius” in The Poetry of Statius ed. Smolenaars, J., Van Dam, H., and Nauta, R. (Leiden, 2008): 45-64. 4. Biagioli, Mario. Galileo, Courtier: The Practice of Science in the Culture of Absolutism. Science and Its Con-

brevia.hcura.org

ceptual Foundations. Chicago: University of Chicago Press, 1993. Shapin, Stephen. “‘A Scholar and a Gentleman’: The Problematic Identity of the Scientific Practitioner in Early Modern England.” History of Science 29, no. 3 (1991): 279-327. 5. Devoti, Stefania. “Aspetti Scientifico-Matematici del Pensiero di Antonio Nardi.” Per una Storia Critica della Scienza 26 (1995): 207-224. 6. Panofsky, Erwin. “Galileo as a Critic of the Arts: Aesthetic Attitude and Scientific Thought.” Isis 47, no. 1 (1956): 3-15. Peterson, Mark A. Galileo’s Muse: Renaissance Mathematics and the Arts. Cambridge, Mass.: Harvard University Press, 2011. Shank, J.B. “What Exactly Was Torricelli’s ‘Barometer?’” In Science in the Age of Baroque. Edited by Chen-Morris and Offer Gal. Archives Internationales D’histoire Des Idées ; v. 208. Dordrecht; New York: Springer, 2013: 161-195. Wilding, Nick. Galileo’s Idol: Gianfrancesco Sagredo and the Politics of Knowledge. University of Chicago Press, 2014.

26 Of Copies and Cures

1. “Diabetes Symptoms.” American Diabetes Association. N.p., n.d. Web. 30 Aug. 2016. 2. “Type 1 Diabetes.” American Diabetes Association. N.p., n.d. Web. 30 Aug. 2016. 3. Pagliuca F.W. et al. “Generation of Functional Human Pancreatic Beta Cells In Vitro.” Cell 159.2 (2014): 428-439. 4. “BrdU Labeling and Detection Protocol.” Thermo Fisher Scientific. N.p., n.d. Web. 30 Aug. 2016. 5. “Honeymoon Phase.” Honeymoon Period Causes and Duration. N.p., n.d. Web. 30 Aug. 2016. 6. Wang, L., N. F. Lovejoy, and D. L. Faustman. “Persistence of Prolonged C-peptide Production in Type 1 Diabetes as Measured With an Ultrasensitive C-peptide Assay.” Diabetes Care 35.3 (2012): 465-70.

28 The Drug War

1. “Antibiotic Resistance Threats in the United States.” Rep. Atlanta: US CDC, 2013. Print. 2. “Antimicrobial Resistance.” Antimicrobial Resistance. World Health Organization, Apr. 2014. Web. 30 Oct. 2014 3. The Pandemic. (2016). Retrieved from http://www.tballiance.org/why-new-tbdrugs/global-pandemic. 4. Feltman, R. (2015). A ‘superbug’ emerges in China to remind us that antibiotics won’t last forever. The Washington Post Retrieved from https://www.washingtonpost.com/news/speaking-of-science/wp/2015/11/19/a-superbug-emerges-in-china-to-remind-us-that-antibiotics-wont-last-forever/. 5. Roberts, Alice. “Drop the Antibiotics, We Need a New Battle Plan against Bacteria.” The Guardian. Guardian News and Media Limited, 19 Jan. 2013. Web. 13 Feb. 2015. 6. Ostash, B., Walker, S. (2010). Moenomycin family antibiotics: chemical synthesis, biosynthesis, biological activity. Nat Prod Rep, 27(11), 15941617. 7. Lovering, A.L., De Castro, L., Lim, D., Strynadka, N.C.J. (2007). Structural Insight into the Transglycosylation Step of Bacterial Cell-Wall Biosynthesis. Science, 315, 1402.

BREVIA Fall 2016

31


BREVIA is a forum for science, culture and other big ideas. We are committed to bringing all disciplines of research out of the ivory tower and into the discourse of the interested public. Through our features and primary research articles, we explore the myriad connections in the world of intellectual endeavor. Our stories are brief because we want to make knowledge accessible and interesting, providing a palette of perspectives on the world around us.

Brevia Fall 2016: Origins  
Read more
Read more
Similar to
Popular now
Just for you