Category: Blog Posts

  • Jacques Dubochet: Putting the Cool in Cryo-EM

    Jacques Dubochet: Putting the Cool in Cryo-EM

    JacquesDubochet
    Dr. Jacques Dubochet, a Nobel Prize Winner of Chemistry (5).

    By Shivani Manikandan

    It might be hard to believe that a dyslexic student who nearly failed high school and was even a college dropout is now a Nobel prize-winner in chemistry, but this is exactly the life story of Dr. Jacques Dubochet (2). 

    Dubochet is a Swiss biophysicist who won the Nobel Prize in Chemistry in 2017. His groundbreaking research in cryogenic-electron microscopy (Cryo-EM) has revolutionized the field of structural biology, allowing scientists to visualize the structures of biological molecules in unprecedented detail (1).

    Despite his many achievements, Dubochet’s academic journey was not always easy. He struggled with dyslexia as a child, which made reading and writing a challenge (2). Throughout his schooling years, Dubochet did not get good grades and nearly failed high school. His academics were so poor that he had to receive special permission to advance through his coursework and not be held back. This continued into his college years, and Dubochet says that at times dyslexia fueled his laziness and allowed him to not put in the effort he should have. Fortunately, he had very supportive parents that pushed him to excel in other areas, and teachers that believed in his abilities despite his poor grades. However, after his second year, Dubochet was dismissed from college for his failing grades, and took on some temporary jobs before returning to college and getting a PhD (1). 

    Dubochet describes his approach to life as follows, “The need for understanding is my way of finding my way in life”, and this was exactly his approach to his career as well (1). His pathway to obtaining a PhD and studying biology was also unconventional. Hoping to fulfill the need to better understand the world around him, Dubochet first earned a diploma in physics. However, he was later influenced by prominent discoveries of the time by researchers like Watson and Crick and wanted to solve biological problems under the framework of physics. In order to do so, he worked to obtain a PhD in Biology and became a biophysicist. 

    This ultimately led to one of his greatest contributions to the field of biology. Dubochet, along with Joachim Frank and Richard Henderson, was awarded the Nobel Prize for Chemistry for their discovery of Cryo-EM. Specifically, Dubochet’s contribution to this finding was centered around a process called vitrification (4). At the time of his discovery, it was difficult to understand the molecular structure of biological compounds. Most studies related to this had to be conducted with the help of X-ray Crystallography, a process that requires the biomolecule to be frozen down to crystals. However, this was problematic as it was not always possible to force biomolecules into a crystalline structure. This is where Dubochet comes in. Vitrification is a process of rapid cooling that allows one to preserve the structure of a biomolecule and allows for observation of the structure in solution, without crystallization (4). This method, in combination with Henderson’s discovery that samples can be understood by their interaction with a beam of electrons and Frank’s analysis of this data, allowed for Cryo-EM. This made a large impact on the scientific community (7). Specifically, it allowed for a broader range of molecules to be visualized and enabled the pharmaceutical industry to customize drugs to be able to bind to the specific shapes of molecules (3). 

    In the real world, it made a large impact on the development of many medications, notably the vaccine for the Zika Virus (3, 6). During a time when there was overwhelming spread of the Zika Virus, the Cryo-EM structure discovery of the virus was crucial in progressing the development of the vaccine, because it helped scientists visualize the changes of virus as it develops over the course of its life cycle, which provided important insight into how to stop the virus life cycle (3, 6). In addition to the Zika Virus, Cryo-EM also helped scientists understand the respiratory syncytial virus, SARS-CoV-2, and other proteins important to the progression of cancer (7). The applications of Cryo-EM are immense, and it’s especially remarkable considering the atypical path that led Dubochet to help make this discovery.

    At the University of Iowa, the departments of Biophysics and Biochemistry are applying Dubochet’s discovery, Cryo-EM, in a variety of ways to help solve problems in biology. Specifically, some experts are studying the role of a specific transcription factor’s structure in binding to different areas of the genome and regulating gene expression. Others are studying the role of specific protein structure in relation to muscular dystrophy and potential ways to combat it (8, 9).

    Cryo-EM Structure of the Zika Virus (3).

    In terms of studying transcription factors, experts hope to better understand what change in the transcription factor, the Glucocorticoid Receptor, causes it to bind to a specific region of the genome over another. Additionally, they hope to better understand the role of glucocorticoid receptors in the treatment of acute lymphoblastic leukemia. They hope to explore these questions by looking at the structures of the molecules involved (8).

    With regards to muscular dystrophy, changes to a specific protein complex called dystrophin-glycoprotein can affect the type of dystrophy a person has. Experts are working to uncover how changes to the structure of this complex can affect the way it interacts with its surroundings and its overall function. This information could provide insight into possible treatment options for this disease. The structural study of such a project relies on methods like Cryo-EM (9).

    Even though Dubochet’s journey to the scientific field was unconventional, he was able to make such a large impact on the way we see the biomolecules within us. Dubochet serves as a reminder that no student should be judged solely by their grades or their ability to conform to conventional standards of intelligence, and that a true scientist is defined not by their career path but by their curiosity, perseverance, and willingness to learn.

    Links to research groups in the University of Iowa:

    1)    Transcription Factors

    2)    Muscular Dystrophy

     

    The information for this article was obtained from the following sources:

    1)    https://www.nobelprize.org/prizes/chemistry/2017/dubochet/biographical/

    2)    https://www.thelocal.ch/20171006/i-was-very-bad-in-school-swiss-nobel-prize-in-chemistry-2017-winner

    3)    https://www.thermofisher.com/blog/atomic-resolution/cryo-em-gives-researchers-a-detailed-view-of-the-zika-virus-structure/

    4)    https://www.chemistryworld.com/features/cryo-em-a-cold-hard-look-at-biology/3008131.article

    5)    https://www.biozentrum.unibas.ch/news/detail/mini-symposium-with-nobel-laureate-jacques-dubochet

    6)    https://www.pnas.org/doi/10.1073/pnas.1609721113

    7)    https://pubs.acs.org/doi/10.1021/acscentsci.0c01048

    8)    https://medicine.uiowa.edu/biochemistry-molecular-biology/profile/miles-pufall

    9)    https://medicine.uiowa.edu/physiology/profile/kevin-campbell

  • The Knight In The Shining Lab Coat and His Journey to the Nobel Prize

    The Knight In The Shining Lab Coat and His Journey to the Nobel Prize

    image of john gurdon
    Sir John Gurdon, a Nobel Prize winner for Medicine (11).

    By Shivani Manikandan

    “I believe he has ideas about becoming a scientist; on his present showing, this is quite ridiculous […] and it would be sheer waste of time, both on his part, and of those who have to teach him. (1)”

    Imagine you are 15 years old, opening your report card with your parents, and your teacher has written that. Imagine being told you are so bad at your science courses that you are no longer allowed to study them, and instead you are to study ancient and modern languages. Unfortunately for Sir John Gurdon, he did not have to imagine these things, because he experienced them firsthand. Fortunately, he went on to have a very successful career in science, one that led him to win the Nobel Prize in medicine and to be knighted by the queen of England (2).

    Growing up, Gurdon was always interested in the development of moths and butterflies and initially wanted to pursue zoology (1). Sadly, because of his academic struggles, he continuously faced obstacles on his career path. For example, because he was forced to study languages prior to applying to college, he was unable to get into the zoology program he wanted to study (2). Without being disheartened, Gurdon took a year to study the course work he missed out on and reapplied and was accepted to the zoology program at Oxford University! However, after his undergraduate years, upon applying to doctoral programs in entomology, he was rejected despite having discovered a new species of flies. Still devoted to science, he decided to pursue developmental biology with Dr. Michael Fischberg (2).

    While his career path was anything but streamlined, science would not be the same today without his contributions to developmental biology. During his time, biologists were unsure if all the cells in the human body have the same genetic composition. Specifically, some researchers of his time found that once cells became a part of a specific organ (through a process called cell differentiation), they no longer contained the genetic material to become any other type of cell (3). However, Robert Briggs and Thomas King challenged this idea by demonstrating that when the nucleus of a cell in an intermediate stage of development is transplanted into a frog egg cell lacking a nucleus, a healthy frog can be grown (6). Curiously, their success rate decreased as the developmental stage of the transplanted nucleus progressed. This ultimately sparked Gurdon’s work, in which he transplanted the nucleus of a well-differentiated intestinal cell into a frog egg cell lacking a nucleus. After numerous failures, he was able to show that a healthy frog can be grown, which helped prove that cells do not lose genetic material as they differentiate and that they all contain the same genetic material. This was his Nobel Prize winning discovery (3).

    Screen Shot 2023-03-09 at 1.12.30 AM
    The above figure outlines the foundational discovery behind Sir John Gurdon’s work. His work showed that when a nucleus from a differentiated cell is transplanted into a frog egg cell without a nucleus, a healthy frog can be produced (2).

    The work of Gurdon and his joint Nobel Prize winner Dr. Shinya Yamanaka has made a dramatic impact on stem cell research. Gurdon’s work laid the foundation for the Yamanka’s discoveries on how pluripotent stem cells can be induced from differentiated cells. Pluripotent cells can differentiate into most of the cells in our body. This discovery has huge implications for stem cell therapies because it allows for a patient’s own cells to be used in their transplants or other treatments, which decreases risk of immune rejection (10). Additionally, induced pluripotent stem cells are used in creating disease models that capture the patient-specific causes of a disease and aid in creating a more realistic model for study (7). The implications of Gurdon’s discovery are still being explored, and he still continues to work in this field today. Now, he hopes to understand the mechanisms involved in inducing pluripotent stem cells (5).

    At the University of Iowa, there are many researchers working on projects that Gurdon’s work laid the foundation for. You can find work that is related to Gurdon’s discoveries in the links below. Specifically, you can find experts studying the development of facial structures and experts that are working on using stem cells to develop gene therapies for cystic fibrosis (8, 9).

    Working off the understanding that all cells have the same genetic material, researchers in the study of facial structure development are attempting to selectively express the necessary gene to regenerate specific tissues from stem cells. These tissues can then be transplanted to patients for various ailments. If the stem cells used in this process are iPSC from the patient, this could help reduce the risks associated with such a procedure (8).

    In terms of the studies related to cystic fibrosis, researchers are working to understand the mechanisms behind the process of stem cells repairing the airway within our lungs. Using this understanding, they hope to use gene therapy to control stem cell proliferation and induce repair in patients with cystic fibrosis (9). 

    Even though Gurdon began studying this question when he was a PhD student, it was not until he was an established scientist, more than 50 years later, that he was recognized for this discovery (4). In his talks, Gurdon emphasizes that he faced challenges that did not have readily available solutions and oftentimes he had to build the equipment he needed. Additionally, he talks about how even when he had the tools, his experiments failed repeatedly in the early stages of the project (1). His story highlights the commonality of failures in science and the importance of perseverance and resilience despite them. If he had not been persistent throughout his scientific career, our understanding of human development would not be the same.

    Links to research groups in the University of Iowa:

    1)    Development of Facial Structures

    2)    Therapies for Cystic Fibrosis

     

    The information for this article was obtained from the following sources:

    1)    https://www.oxfordstudent.com/2019/10/27/prof-sir-john-gurdon-from-failure-to-nobel-prize/

    2)    https://achievement.org/achiever/sir-john-gurdon/

    3)    https://www.youtube.com/watch?v=YNvMg1C1WK4&ab_channel=FacultyofMedicineLundUniversity

    4)    https://www.nobelprize.org/prizes/medicine/2012/gurdon/facts/

    5)    https://www.gurdon.cam.ac.uk/people/john-gurdon/

    6)    https://embryo.asu.edu/pages/transplantation-living-nuclei-blastula-cells-enucleated-frogs-eggs-1952-robert-briggs-and

    7)    https://www.thermofisher.com/blog/behindthebench/disease-modeling-using-induced-pluripotent-stem-cells/#:~:text=iPSCs%20are%20a%20valuable%20tool,modeling%3A%20Parkinson’s%20disease%20and%20cardiomyopathy.

    8)    https://medicine.uiowa.edu/acb/profile/brad-amendt

    9)    https://medicine.uiowa.edu/acb/profile/john-engelhardt

    10) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313779/#:~:text=The%20use%20of%20iPSCs%20may,disease%20modeling%20and%20gene%20therapy.

    11) https://nieuws.kuleuven.be/en/content/2018/nobel-prize-winner-john-gurdon-growing-body-parts-is-not-science-fiction

  • Charles Darwin: His Evolution from Bad Grades to Big Theories

    Charles Darwin: His Evolution from Bad Grades to Big Theories

    image of charles darwin
    72 year old Charles Darwin getting ready to go on a stroll (2).

    By Shivani Manikandan

    “You care for nothing but shooting, dogs, and rat-catching, and you will be a disgrace to yourself and all your family” (2).

    Who do you think this quote is about? You may be surprised to know it is about one of the most well-known scientists of the 19th century. Charles Darwin, often called the father of evolution, is credited with making pivotal discoveries that transformed the field of biology. The quote above is from Darwin’s autobiography, where he describes his own father’s disappointment with his academics. In his own words, “When I left the school I was for my age neither high nor low in it; and I believe that I was considered by all my masters and by my Father as a very ordinary boy, rather below the common standard in intellect” (2).

    In simpler words, Darwin, like many of us, was an average C student in school. His father, a respected physician, was so disappointed with his work that he sent Darwin off to sea aboard the HMS Beagle in 1831 (2). However, to everyone’s surprise, this voyage resulted in the development of one of the most influential theories in biology: natural selection.

    While we often think of scientists as lone thinkers, the greatest discoveries are really the culmination of years of gradual progress by many individuals. Darwin’s discovery of natural selection was no different. During the Beagle voyage, Darwin had time to read the theories of thinkers like Thomas Malthus and Charles Lyell. Malthus drew connections between food resources and populations, suggesting that the environment of a population impacts its growth (1). Additionally, scientists like Lyell discussed the geological evolution of the world over long periods of time. These ideas and more led Darwin to think about how major environmental changes can cause species to change over time (6).

    Aside from proposing transformational theories like natural selection, Darwin also changed how the natural world was studied. Unlike other theorists of his time, he was committed to an evidence-based approach to science. From finches to pigeons and beetles to barnacles, Darwin spent much of his later life collecting evidence to support his theories (1, 4). 

    Like any good theory, natural selection led the scientific community to many more questions. In his book explaining natural selection, The Origin of Species, Darwin admitted to not knowing the mechanism of evolution. What inside an organism causes variations? How are variations passed on (6)? Natural selection was a steppingstone for various fields of science and is a foundational concept in our understanding of the past, present, and future. From the origins of the human species to the inheritance of genetic diseases to the impact of humanity on the ecological future of the planet, our understanding of the natural world stems in part from the work of an average C student (3).

    At the University of Iowa, you can find work that is related to Darwin’s discoveries in the links below. Specifically, you can find experts studying the evolution of sexual reproduction and its importance to biodiversity, the origin of eukaryotes and how they differ from prokaryotes, the stress responses within species that result in adaptation, and more (7, 8, 9).

    labeled image of darwin's finches
    There are 17 finches that are considered Darwin’s finches and above are eight that are endemic to the Galapagos Islands (10).

    In the study of sexual reproduction, one question that UIowa researchers are investigating is the role of sexual reproduction on the composition of genes and their structure in snails. They are also working to understand how rare asexual reproduction is and its relation to the accumulation of harmful mutations (7). These questions will help us understand the value of biodiversity in a world where global warming and other environmental changes pose a threat to it. 

    In relation to the origin of eukaryotes, researchers are working to understand how important processes such as meiosis came to exist, and how different eukaryotes relate to each other (8). These finds can help improve our understanding of how eukaryotes became so diverse and provide insight into the cellular processes in our body. 

    Regarding the evolution of stress responses, researchers believe that a better understanding of how species respond to stress and how this is passed on can shed light on how the microbiota inside humans evolve over time to become pathogenic as their environment changes (9). These are just a few examples of how Darwin’s work continues today, and how far his ideas have come.

    I hope Darwin’s story serves as a reminder that your academic struggles do not define your ability to contribute to science or prevent you from being a revolutionary. In the words of Darwin himself, “One lives only to make blunders” (5). Don’t let your academic blunders hold you back. Darwin serves as an example that the most important characteristic of a scientist is curiosity, so follow your curiosity and learn more with the links below!

    Links to research groups in the University of Iowa:

    1)        The Evolution of Sexual Reproduction

    2)        The Origin of Eukaryotes

    3)        The Evolution of Stress Responses

     

    The information for this article was obtained from the following sources:

    1)        https://evolution.berkeley.edu/the-history-of-evolutionary-thought/1800s/natural-selection-charles-darwin-alfred-russel-wallace/

    2)        http://darwin-online.org.uk/content/frameset?viewtype=text&itemID=F1497&pageseq=28

    3)        https://www.nature.com/scitable/spotlight/charles-darwin-7567158/

    4)        https://education.nationalgeographic.org/resource/hms-beagle-darwins-trip-around-world

    5)        The Correspondence of Charles Darwin, Volume 9: 1861

    6)        https://www.youtube.com/watch?v=dfsUz2O2jww&ab_channel=CrashCourse

    7)        https://biology.uiowa.edu/people/maurine-neiman

    8)        https://biology.uiowa.edu/people/john-logsdon

    9)        https://biology.uiowa.edu/people/bin-z-he

    10)   https://galapagosconservation.org.uk/wildlife/darwins-finches/

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