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Cryogenic Electron Microscopy: A Leap Forward for UC Davis
Photo originally published in Structural Studies of the Giant Mimivirus. PLoS Biol 7(4): e1000092. doi:10.1371/journal.pbio.1000092. License: CC BY 2.5.
By Nathan Levinzon, Neurobiology, Physiology, and Behavior ‘23
Author’s Note: The purpose of this article is to inform the UC Davis community about the arrival and use of a groundbreaking technology to campus. I hope to have provided a comprehensive introduction to Cryo-EM, information on Cryo-EM at UC Davis, and an example of how the technology is already being used to solve problems in biology on campus. I also aim to share my excitement regarding this technology in the hope that I inspire others to pursue this interesting and advancing field of study.
Cryo-electron microscopy, often abbreviated as “Cryo-EM,” is a version of microscopy that uses beams of electrons instead of light to illuminate cryogenically frozen samples. Because the wavelength of an electron is much shorter than the wavelength of light, samples can be imaged at mind-boggling resolutions. After the sample is captured in many orientations, the images are compiled in software to finally resolve a three-dimensional image. “If you want to imagine what it’s like to use this technology,” UC Davis Professor Jawdat Al-Bassam explains in an interview for the College of Biological Sciences, “think about walking into a museum, looking at a statue, taking pictures of it, and figuring out how to put those pictures together to get a three-dimensional picture. In essence, that’s what we do with molecules. They are like small molecular statues, and we take images of them at a variety of angles and orientations. We combine these images to get a design plan for how these molecules are put together ” [1].
As a result of recent advances in technology and software, the progress in the resolution of Cryo-EM seems limitless. New microscopes on the market have brought the lowest resolution down to about two angstroms—twice the diameter of a hydrogen atom—with even higher resolutions yet to come. Before 2010, scientists could achieve maximum resolutions of about four angstroms. This incredible and exciting variant of microscopy stands to shape the future of biological sciences. Dean of Biological Sciences Mark Winey says that “Cryo-EM is certainly part of the portfolio of technology that any campus like UC Davis should have,” and it’s easy to see why [1].
One of the most advanced Cryo-EM microscopes on the market today is the newly released Glacios Cryo-Transmission Electron Microscope (TEM) by Thermo-Fisher. On the surface, the Glacios functions like any other TEM: A cryogenically frozen sample is prepared and shot with electrons that hit a camera in order to resolve a high-resolution, black and white image. What makes this microscope different, however, is its groundbreaking camera. The camera has a pixel size slightly smaller than the area that electrons interact with, which enables a high-speed electron detector to find the center of electron events with sub-pixel precision. The end result is a fourfold increase in resolution from older TEMs while simultaneously reducing aliasing, a sampling error caused by electron interference.
With this microscope, researchers can examine life at the molecular level better than ever before. The closed-system design of the microscope ensures a safe and robust pathway through every step of microscopy, from sample preparation and optimization to image acquisition and data processing of up to twelve samples [2]. Its massive throughput is as impressive as its small footprint, allowing for it to be installed in labs with pre-existing infrastructure. Autonomous sample loading and lense alignment have made Cryo-EM faster and easier for both the budding and seasoned scientist.
UC Davis has recently made a large investment of its own in Cryo-EM. On January 31, 2020, the College of Biological Sciences celebrated the ribbon-cutting for their own ThermoFisher Scientific Glacios Cryo-Transmission Electron Microscope, outfitted with a Gatan K3 direct detector camera. Festivities were short-lived, however, because labs were already in line to use this new machine. Researchers at Professor Al-Bassam’s lab were some of the first to use this microscope while studying kinesin, a motor protein found in eukaryotic cells. By utilizing Cryo-EM to resolve the structure of kinesin, they concluded that kinesin’s tails open a part of the motor that encapsulates ATP, slowing the movement of these motors and allowing kinesin to cluster and work together. With this new microscope in hand, these researchers are now able to unravel the functions of kinesin and how it interacts with other kinesin to move and group. The complete paper discussing the binding between kinesin tail and motor domains and its function in microtubule sliding can be found in the January 2020 edition of eLife [3].
Cryo-EM has never been easier, safer, and more accessible to use UC Davis. With the purchase of the Glacios, UC Davis has made itself ready to introduce a new generation of researchers to the field of modern biology. Resolutions that were thought impossible ten years ago are now a reality, and new advancements continue to push the bounds at which samples can be imaged at. With the quickening pace of advancements in Cryo-EM, there is no telling what mysteries researchers at UC Davis will uncover next.
References
- Slipher, David, et al. “CRYO EM: Unleashing the Future of Biology at UC Davis.” UC Davis College of Biological Sciences, 31 Jan. 2020, biology.ucdavis.edu/cryo-em. Accessed 23 Mar. 2020.
- “Cryo TEM: Cryo-EM.” Thermo Fisher Scientific – US, www.thermofisher.com/us/en/home/electron-microscopy/products/transmission-electron-microscopes/glacios-cryo-tem.html.
- Bodrug, Tatyana, et al. “The Kinesin-5 Tail Domain Directly Modulates the Mechanochemical Cycle of the Motor Domain for Anti-Parallel Microtubule Sliding.” ELife, vol. 9, 2020, doi:10.7554/elife.51131.
Ode to the Eye: Movement of Mitochondria in Retinal Ganglion Cells
By Nicholas Garaffo, Biochemistry and Molecular Biology, 20’
Author Note: I wrote this paper in an attempt to connect my research project to a non-science audience. While this topic is very scientific, I am attempting to translate the molecular biology of the eye to a language any reader could understand. With this paper, I hope more people get interested in basic biology, and have a new appreciation for the eye.
Ode to the Eye
Right now, your irises are contracting, folding, and manipulating to adjust the amount of light allowed in. Photons are reflected from these words, move through your pupil, bypass the aqueous cavity within your eye, and are absorbed by the .2 mm thick retinal cell layer inside your eye (1, 2). These photons are scattered, and absorbed by the photoreceptor cells; these are known as rods and cones. Once absorbed, the cells undergo a rapid change in their membrane potential allowing the signal to transport along its axon. The signal is released from the photoreceptors and received by the bipolar cells which then undergo the same process. Hundreds of photoreceptor cells connect to a single bipolar cell, and hundreds of bipolar cells connect to a single retinal ganglion cell (RGC) (1, 2). RGCs are the bridge between the eye and brain. Without these cells the light ends as a signal, and is never used to create an image. All of this is happening as fast as you can read these words; what a beautiful thing the eye is!
Introduction
The cells within the eye are co-dependent for its overall performance, yet even the smallest alterations can be detrimental. As a fluid filled cavity, the eye expands and contracts in response to external pressures. This is a normal process because every time you blink, rub your eye, or sneeze the pressure within the eye– intraocular pressure (IOP)– spikes. An IOP above 22 mmHg (16-22 mmHg is thought to be physiologically normal) can occur when the muscles, known as the ciliary bodies, responsible for flushing and recycling the internal fluid get clogged (3). Fluid will then begin to increase within the eye, and cause the cavity to expand. While spikes in IOP are rarely damaging, prolonged exposure to high IOP can strain RGCs. Recall, RGCs are the bridge between the eye and the brain. RGCs exit the eye through a pore in the back of the eye, known as the optic nerve head (ONH). To protect and accelerate the signal from the eye to the brain, RGC’s form a tubular structure with other cell types. This structure is called the optic nerve and is composed of RGC’s, blood vasculature, and microglia– a large family of neuronal support cells, but for the focus of this review we will only focus on specifically the astrocytes.
The main area for RGC damage is the ONH, the connecting area of the eye to the optic nerve (2, 3). Like all neuron cells, the axons of RGCs are heavily myelinated– a fatty sheath to increase electrical signaling– however, the RGCs which exit through the eye must remain unmyelinated to maintain the eye’s dynamic motions. These ONH RGCs are most vulnerable to variations in IOP. When the eye’s IOP increases for a prolonged period of time, the ONH and its corresponding cells are pulled. This increase in tension causes cellular strain, and as a consequence, glaucoma– an irreversible blindness commonly attributed to a prolonged increase in IOP (3). Patients first notice blind spots in the periphery, and then the blind spot begins to rainbow across their vision until it elapses the entire eye. Currently, there is no cure, and the main treatments are to decrease IOP, but regulating IOP serves to prolong vision rather than prevent glaucoma.
Interestingly, only 25-50% of all patients with glaucoma have high IOP, and patients with high IOP do not always get glaucoma (2, 3). Increases in IOP may be a correlation with glaucoma rather than a cause of it. Therefore, it is of extreme importance to understand overall RGC health through other methods. Specific research is focused on how debris, including fats, organelles and degraded protein, is moved throughout the optic nerve.
Astrocytes and Retinal Ganglion Cells
Astrocytes are a cell-type within the glial system that interact with neurons to provide metabolic support, signaling and maintain cellular homeostasis. Throughout the entire neuronal network, (brain, spine, optic nerve, etc.) neurons do not exist in isolation. Within the brain, astrocytes are responsible for sending local and wide-ranging signals which actually assist in neuronal communication (4). Within the optic nerve, astrocytes surround every part of RGC that is not covered in myelin to assist similar activities. Astrocytes actually out-number RGCs within the optic nerve.
Recall that neurons function by sending neurotransmitters, most commonly glutamic acid, across synapses to relay information cell to cell. This process is no different for RGCs. Each signal must remain short, and sharp to ensure proper communication. One function that astrocytes play is to uptake lingering glutamic acid when a signal is released thereby preventing misfiring. The sequestered glutamic acid will be converted to glutamine within the astrocyte and sent back to the RGC for future signaling (4). This is only one of the hundreds of functions that astrocytes help RGC’s with.
Transmitophagy and Implications with Glaucoma
Mitochondria, colloquially known as the power-house of the cell, are an indicator of overall cell health because abnormal or reduced amounts of mitochondria are symptomatic of degratory diseases, including parkinson’s disease and glaucoma. Mitochondria normally function to provide the cell with ample ATP through the electron-transport chain which requires a reactive oxygen species (ROS) and electron potential forces (5). As mitochondria age, their ROS begin to interact with their intracellular proteins, including that of the electron transport chain. When the damage accumulates, the mitochondria undergoes fission (i.e. pinching off a piece) to be degraded via the lysosome, or fusion (i.e. fuse to a large, healthy mitochondria) (5). For the context of this article we will only be looking at lysosomal mediated degradation of mitochondria, and mitochondria fragments. This process is known as mitophagy, which is a subset of autophagy. One assumption made with autophagy (or, ‘self-eating’) is that cells will degrade their own organelles. While this may be the case for the majority of degradative processes, there is evidence which supports RGC protrusion of mitochondria to be degraded by neighboring astrocytes, a novel process termed transmitophagy.
In 2014, Chung-Ha et al. provided a new model of mitochondria degradation within ONH RGC’s (6). This study used the Xenopus laevis as their model, and used a series of mitochondria, lysosomal, and astrocytic tags to track mitochondria movement and degradation within the optic nerve. Ultimately, they found fragmented and malformed mitochondria protruding out from the RGC axon, and getting picked up by neighboring astrocytes for degradation (6). Axonal mitochondria are specifically vulnerable to this process because it is an energy costly, and dangerous process to move an ROS-producing mitochondria to the cell soma, where the majority of lysosomes reside.
Conclusion
The eye is a beautiful, yet intricate structure that is dependent on overall cell and organelle health. The mitochondria are perhaps the most important for cellular metabolism and overall health. While it was previously thought that mitochondria are only degraded within the cell, transmitophagy illustrates a potential route that axonal mitochondria can undergo for degradation. However, transmitophagy studies have only been presented in non-disease models. Therefore, future studies must utilize disease models (i.e. induced glaucoma models) to understand how transmitophagy is affected, or affects, eye diseases.
Citations
- Kolb H. Gross Anatomy of the Eye. 2005 May 1. “The Organization of the Retina and Visual System. Salt Lake City (UT): University of Utah Health Sciences Center; 1995.
- Sung, Ching-Hwa, and Jen-Zen Chuang. “The cell biology of vision.” The Journal of cell biology vol. 190,6 (2010): 953-63. doi:10.1083/jcb.201006020
- Weinreb, Robert N et al. “The pathophysiology and treatment of glaucoma: a review.” JAMA vol. 311,18 (2014): 1901-11. doi:10.1001/jama.2014.3192
- Sofroniew, Michael V, and Harry V Vinters. “Astrocytes: biology and pathology.” Acta neuropathologica vol. 119,1 (2010): 7-35. doi:10.1007/s00401-009-0619-8
- Pickrell, Alicia M, and Richard J Youle. “The roles of PINK1, parkin, and mitochondrial fidelity in Parkinson’s disease.” Neuron vol. 85,2 (2015): 257-73. doi:10.1016/j.neuron.2014.12.007
- Davis, Chung-ha O et al. “Transcellular degradation of axonal mitochondria.” Proceedings of the National Academy of Sciences of the United States of America vol. 111,26 (2014): 9633-8. doi:10.1073/pnas.1404651111
The Roots of Chemistry: How the Ancient Tradition of Alchemy Influenced Modern Scientific Thought
By Reshma Kolala, Biochemistry & Molecular Biology 22’
Author’s Note: A scientific education today often omits the origins of modern scientific thought. I was interested in understanding how early philosophers built the foundation of modern scientific disciplines such as chemistry and physics through the ancient tradition of alchemy alongside rational thought and reasoning.
The ancestral equivalents of many modern branches of science have shaped the face of scientific innovation. Alchemy, the predecessor of modern chemistry, has influenced the discovery of several scientific concepts and experimental methodologies that have constructed the foundational basis of empirical science.
Alchemy had roots in philosophy, astronomy, and religion. It spanned beyond empirical science, combining spirituality with experimental observation to decipher the intricacies of nature. Alchemy was infatuated with the creation of new materials, such as transmutation of base metals into precious metals such as gold [1]. Alchemists also strived to uncover or create a universal elixir, “[a] substance that would indefinitely prolong life” [2]. The element of spirituality, specifically the belief in ultimate divine perfection sustained these ideals. Because it was believed that nature always strives to achieve perfection, the transmutation of say, lead, into gold, was considered to simply be a matter of chemical catalyzation. This required an understanding of the composition and complexities of the natural world. In doing so, alchemists contributed to an incredible diversity of what would be later considered as major chemical industries such as metallurgy, the production of paints, inks, and dyes, and cosmetics [3].
Alchemy can be traced back to ancient Egypt, where Jabir Ibn Hayyan, a court alchemist and physician, was the first to introduce experimental methodology into alchemy and is credited with the invention of several chemical processes used in modern chemistry. These include, “crystallization, calcinations, sublimation and evaporation, the synthesis of acids (hydrochloric, nitric citric, acetic and tartaric acids), and distillation. [4]” Hayyan applied this knowledge to improve manufacturing processes that allowed advancements in major industries both then and today, including glass-making, the development of steel, the dyeing of cloth, and the prevention of rust. Hayyan’s contribution to alchemy paralleled the previously developed Aristotelian theory of elements which suggested the existence of four core elements: earth, water, air, and fire. Hayyan suggested the existence of different categories of matter, including spirits (which vaporize upon heating), metals, and stones (which can be converted into powder). Jabir’s work laid the foundation for the structured classification of chemical substances. His practice and encouragement of systematic experimentation began to transform alchemy from a superstitious practice to a proper scientific discipline.
Compared to European alchemy, Chinese alchemy had a more obvious application to medicine and was influenced by Taoism, a philosophical and religious tradition of living in harmony with the natural order of the universe, and traditional Chinese medicine. Acupuncture, Tai Chi, and meditation focus on the purification of the spirit in hopes of achieving immortality, a core value in alchemy [5]. In an attempt to uncover an elixir for eternal life, Chinese alchemists accidentally invented gunpowder, which would go on to have major social and political implications [6].
The Decline of Alchemy and Rise of Modern Chemistry
Alchemy regained popularity in Renaissance Europe and influenced many modern scientists, including Issac Newton and Robert Boyle, both of which were also alchemists. Considered as the father of chemistry, Robert Boyle is most notably known for Boyle’s law, which observed the inverse relationship between the volume of a gas and its pressure. Boyle, however, was far from a scientist in the modern sense and was considered to be a natural philosopher. Boyle was interested in transmutation and constructed the “corpuscularian hypothesis” in which he describes all matter consisting of varied arrangements of identical “corpuscles,” known today as particles [7]. According to his theory, Boyle believed that transmutation was just a matter of rearrangement. Boyle wrote The Sceptical Chymist to assert his hypothesis, officially establishing chemistry as the science of the composition of substances. This marked the official separation of modern chemistry from the mystical qualities of alchemy. Through the span of several millennia, alchemists “were learning fundamental principles of chemistry: breaking down ores, dissolving metals with acids, and precipitating metals out of solution [8].” This laid the foundations of basic scientific experimentation with modern alchemists such as Boyle emphasizing the importance of consistent and accurate results. This pioneered the development of chemical analysis and the scientific method. Boyle also rejected the Aristotelian theory of elements and recognized that certain substances decompose into other substances. This brought forth the first conceptions of a chemical element, a state of matter that cannot be further decomposed [9]. Despite denouncing mysticism, Boyle remained an alchemist and believed, correctly, that one element could be transmuted to another through rearrangement of the basic particles making up the element. This was achieved by Ernest Rutherford in 1919 when he transformed nitrogen into oxygen by aiming alpha particles at nitrogen atoms. This resulted in the formation of hydrogen and oxygen atoms, establishing the first man-made nuclear reaction [10]. Rutherford is considered a father of nuclear physics, illustrating the multidisciplinary influence of alchemy in many modern sciences.
Alchemic practice also had implications in medicine. Philippus Paracelsus, a prominent Swiss physician, applied general alchemic principles to a more realistic model such as the human body. Similar to the idea of transmutation, he believed that organs could be transformed from sick to healthy, implying the use of chemicals to treat illness. Paracelsus pioneered the integration of chemicals and bodily medicine in what would later develop as toxicology [11]. This launched an entirely new branch of science where inorganic materials were used in conjunction with the human body, including the use of mercury to treat syphilis [12]. Paracelsus is also known for his creation of laudanum, otherwise known as opium [13]. The most active substance in opium is morphine, which is a powerful painkiller and is used for anesthetic purposes .
The rise of modern chemistry does not mark the dissolution of alchemy but rather symbolizes a departure from the occultism of the ancient tradition to embrace a more empirical method of scientific discovery. Although alchemy is considered to be an ancient science, it can be regarded as a necessary precursor to the development of modern chemistry and it continues to have implications on scientific discovery today.
References
- King, P. (2007). Routledge encyclopedia of philosophy online: all site license & consortia/ .. Place of publication not identified: Routledge.
- The Editors of Encyclopaedia Britannica. (2007, December 13). Elixir. Retrieved from https://www.britannica.com/topic/elixir-alchemy
- Zimdahl, R. L. (2015). Six Chemicals That Changed Agriculture. Academic Press.
- Amr, S. S., & Tbakhi, A. (2007). Jabir ibn Hayyan. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6077026/
- An Introduction to Taoist Alchemy. (n.d.). Retrieved from https://www.goldenelixir.com/jindan/jindan_intro.html
- Szczepanski, K. (2019, July 3). How China Invented Gunpowder. Retrieved from https://www.thoughtco.com/invention-of-gunpowder-195160
- Corpuscularian hypothesis. (n.d.). Retrieved from https://www.britannica.com/science/corpuscularian-hypothesis
- Principe, L. (2007). Chymists and chymistry: studies in the history of alchemy and early modern chemistry. Sagamore Beach, MA: Science History Publications/USA, a division of Watson Publishing International.
- Home. (n.d.). Retrieved from https://www.famousscientists.org/robert-boyle/
- Rutherford, transmutation and the proton. (2019, June 26). Retrieved from https://cerncourier.com/a/rutherford-transmutation-and-the-proton/
- F., J. (2000, January 1). Paracelsus: Herald of Modern Toxicology. Retrieved from https://academic.oup.com/toxsci/article/53/1/2/1673334
- Stillman, J. M. (1920). Theophrastus Bombastus von Hohenheim called Paracelsus: his personality and influence as physician, chemist and reformer. Chicago: The Open court Publishing Co.
- Sigerist, H. E. (1941). Laudanum in the works of Paracelsus.
Applications of Machine Learning in Precision Medicine
By Aditi Goyal, Statistics, Genetics and Genomics, ‘22
Author’s Note: I wrote about this topic after being introduced to the idea through a speaker series. I think the applications of modern day computer science, genetics and statistics creates a fascinating crossroads between these academic fields, and the applications are simply astounding.
Next Generation Sequencing (NGS) has revolutionized the field of clinical genomics and diagnostic genetic tests. Now that sequencing technologies can be easily accessed and results can be obtained relatively quickly, several scientists and companies are relying on this technology to learn more about genetic variation. There is just one problem: magnitude. NGS and other genome sequencing methods generate data sets in the size of billions. As a result, simple pairwise comparisons of genetic data that have served scientists well in the past, cannot be applied in a meaningful manner to these data sets [1]. Consequently, in efforts to make sense of these data sets, artificial intelligence (AI), also known as deep learning or machine learning, has introduced itself to the biological sciences. Using AI, and its adaptive nature, scientists can design algorithms aimed to identify meaningful patterns within genomes and to highlight key variations. Ideally, with a large enough learning data set, and with a powerful enough computer, AI will be able to pick out significant genetic variations like markers for different types of cancer, multi-gene mutations that contribute to complex diseases like diabetes, and essentially provide geneticists with the information they need to eradicate these diseases, before they manifest in the patient.
The formal definition for AI is simply “the capability of a machine to imitate intelligent human behavior” [2]. But what exactly does that imply? The key feature of AI is simply that it is able to make decisions, much like a human would, based on previous knowledge and the results from past decisions. AI algorithms are designed to take in information, generate patterns from that information, and apply it to new data, about which we know very little about. Using its adaptive strategies, AI is able to “learn as it goes,” by fine-tuning its decision-making process with every new piece of data provided to it, eventually making it the ultimate decision-making tool. While this may sound highly futuristic, AI has been used for several years in applications throughout our daily lives from the self-driving cars being tested in the Silicon Valley, to the voice recognition program available on every smartphone today. Most chess fans will remember the iconic “Deep Blue vs Kasparov” match, where Carnegie Mellon students developed an IBM supercomputer using a basic AI algorithm designed to compete against the reigning chess champion of the world [3]. Back then, in 1997, this algorithm was revolutionary, as it was one of the major signs that AI was on par with human intelligence. [4]. Obviously, there is no question that AI has immense potential to be applied in the field of genomics.
Before we can begin to understand what AI can do, it is important to understand how AI works. Generally speaking, there are two ways AI algorithms are developed: supervised and unsupervised learning. The key difference between the two groups is that in supervised learning, the data sets we provide to AI to “learn” are data sets that we have already analyzed and understand. In other words, we already know what the output will be, before providing it to AI [5]. The goal, therefore, is for the AI algorithm to generate an output as close to our prior knowledge as possible. Eventually, by using larger and more complex data sets, the algorithm will have modified itself enough to the point where it does the job of the data scientist, but is capable of doing so on a much larger scale. Unsupervised learning, on the other hand, does not have a set output predefined. So, in a sense, the user is learning along with the algorithm. This technique is useful when we want to find patterns or define clusters within our data set without predefining what those patterns or clusters will be. For the purposes of genomic studies, scientists use unsupervised learning patterns to analyze their data sets. This is beneficial over supervised learning, since the gigantic data sets produced by omics studies are difficult to fully understand.
Some of the clearest applications of AI in biology are in cancer biology, especially for diagnosing cancer [6]. “AI has outperformed expert pathologists and dermatologists in diagnosing metastatic breast cancer, melanoma, and several eye diseases. AI also contributes to innovations in liquid biopsies and pharmacogenomics, which will revolutionize cancer screening and monitoring, and improve the prediction of adverse events and patient outcomes” [7]. By providing a data set of genomic or transcriptomic information, we can develop an AI program that is designed to identify key variations within the data. The problem lies, primarily, in providing the initial data set.
In the 21st century, an era of data hacks and privacy breaches, the general public is not keen to release their private information, especially when this information contains everything about their medical history. Because of this, “Research has suffered for lack of data scale, scope, and depth, including insufficient ethnic and gender diversity, datasets that lack environment and lifestyle data, and snapshots-in-time versus longitudinal data. Artificial intelligence is starved for data that reflects population diversity and real-world information” [8]. The ultimate goal of using AI is to identify markers and genetic patterns that can be used to treat or diagnose a genetic disease. However, until we have data that accurately represents the patient, this cannot be achieved. A study in 2016 showed that 80% of participants of Genome Wide Association Study (GWAS) were of European descent [9]. At first glance, the impacts of this may not be so clear. But when a disease such as sickle cell anemia is considered, the disparity becomes more relevant. Sickle cell anemia is a condition where red blood cells are not disk-shaped, as they are in most individuals, but rather in the shape of a sickle, which reduces their surface area, which in turn reduces their ability to carry oxygen around the body. This is a condition that disproportionately affects people of African descent, so it is not reasonable to expect to be able to find a genetic marker or cure for this disease when the data set does not accurately reflect this population.
Another key issue is privacy laws. While it is important to note that any genomic data released to a federal agency such as the NIH for research purposes will be de-identified, meaning that the patient will be made anonymous, studies have shown that people can be re-identified using their genomic data, the remaining identifiers still attached to their genome, and the availability of genealogical data and public records [10]. Additionally, once your data is obtained, policies like the Genetic Information Nondiscrimination Act do protect you in some ways, but these pieces of legislation are not all-encompassing, and still leave the window open for some forms of genetic discrimination, such as school admissions. The agencies conducting research have the infrastructure to store and protect patient data, but in the era of data leaks and security breaches, there are some serious concerns that need to be addressed.
Ultimately, AI in genomics could transform the world within a matter of days, allowing Modern biology, defined by the innovation of NGS technologies, has redefined what is possible. Every day, scientists all around the world generate data sets larger than ever before, making a system to understand them all the more necessary. AI could be the solution, but before any scientific revolution happens, it is vital that the legislation protecting citizens and their private medical information be updated to reflect the technology of the times. Our next challenge as a society in the 21st century is not developing the cure for cancer or discovering new secrets about the history of human evolution, but rather it is developing a system that will support and ensure the protection of all people involved in this groundbreaking journey for the decades to come.
References
- https://www.nature.com/articles/s41576-019-0122-6
- https://www.ibm.com/ibm/history/ibm100/us/en/icons/deepblue/
- https://en.chessbase.com/post/kasparov-on-the-future-of-artificial-intelligence
- http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.278.5274&rep=rep1&type=pdf#page=41
- https://www.nature.com/articles/s41746-019-0191-0
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6373233/
- https://www.genengnews.com/insights/looking-ahead-to-2030/
- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5089703/
- https://www.genome.gov/about-genomics/policy-issues/Privacy
Frontiers in Animal Behavior Research: Scientific Application of Krogh’s Principle
By Kaiming Tan, Neurobiology, Physiology, and Behavior, ‘16
Author’s Note: As a student who is engaged in biological sciences research, I often read research publications and perform experiments in laboratory classes and research projects. A common theme across these studies is that different labs use various model organisms. For instance, labs that research infectious human diseases tend to use primates because of their similarity to humans, whereas geneticists tend to use fruit flies because of their clearly defined and inherited traits. I often wondered what drives the selection of specific model organisms and whether there is any scientific justification behind it. This manuscript introduces Krogh’s principle, a principle which is commonly applied in in vivo research studies to aid in determining the appropriate model organism. Additionally, a brief research proposal is presented to demonstrate Krogh’s principle on a practical level.
Key Words
Krogh’s principle, animal behavior, sensory ecology, Leach’s storm-petrel, bladder grasshopper, research proposal
Introduction
Krogh’s principle is the gold standard used to choose experimental models in the fields of animal behavior and sensory ecology. The principle states that for every research question, there is a preferred model organism to study, which allows researchers to produce experimental results that help to answer the research question. These preferred organisms often have one or more specialized traits that are particularly well-suited for a researcher’s objectives [1]. August Krogh developed this principle in the mid 19th century, and ever since, scientists worldwide have adapted this principle when selecting model organisms for their research studies.
Krogh’s Principle in Use
Dr. Robyn Hudson is a world-renowned scientist and a leading expert on the effects of chemical olfactory cues on animal behavior. Dr. Hudson applied Krogh’s principle in her research on olfactory learning and development by choosing the European rabbit as a model for her research. Rabbit pups are born blind, but they have a fully-developed sense of smell, also known as olfaction. Additionally, baby pups are fed in the dark conditions of their underground nests. They are also altricial, meaning they are entirely dependent on their mother’s brief nursing. In Hudson’s experiment, the rabbit pups were only visited by their mother once a day to be nursed for about three to four minutes [2]. Thus, the pups require olfaction to look for their mother’s nipples for milk in order to survive. Given the natural history of this species, scientists can conclude that the baby rabbit’s ability to search for their mother’s nipples is primarily due to olfaction.
Additionally, Krogh’s principle applies to Dr. Hudson’s choice of research subjects because rabbits are easy to rear and observe in a laboratory setting. European rabbit pups have evolved plastic mechanisms calibrated by circumstantial odor experience in preceding and current environments. Olfactory plasticity allows the rabbits to modify their behavior in response to olfactory cues such as different scents. This enables the rabbits to learn behaviors evoked by odors and makes the behavior easy to measure and manipulate by researchers [2,3]. As a result, scientists can measure the rabbits’ behavioral ecology with respect to foraging, which could make the European rabbits a preferred model for olfactory learning. These rabbits are perfectly suited for this type of study because they are born with an innate sense of olfaction, allowing Dr. Hudson and her research team an excellent opportunity for a study aimed at olfactory learning and development.
Another illustrative example of Krogh’s principle in use comes from the work of Dr. Brian Hoover. Dr. Hoover’s research interests included the role of olfaction as it pertained to determining mating preferences in avian species. Dr. Hoover investigated mating patterns in Leach’s storm-petrel (Oceanodroma leucorhoa) to explore the chemical basis of mate choice through avian olfaction. There are several reasons he chose the Leach’s storm-petrel as the model organism for this study. The Leach’s storm-petrel has among the largest olfactory bulbs of any bird, thus they have an excellent sense of smell [4]. Olfaction is critical for the Leach’s storm-petrel to locate prey [5]. In addition, the Leach’s storm-petrels are genetically monogamous and produce only one chick per year. This scenario allows the offspring to have higher genetic quality. An organism’s genotype must be best-fitted for its survival. As the Leach’s storm-petrel only gives one offspring per year, its genetic makeup needs to be suitable to sustain it in its environment so that its survival rate is high. Thus, scientists can collect data about offspring quality and observe the adults’ mating patterns, thereby simplifying the data collection process while maintaining the accuracy of the mating patterns measured.
The population of Leach’s storm-petrel was abundant in the study, which equated to a large and accessible sample size. Sample size is an important consideration for data analysis as it is the determinant of statistical power, the ability to report findings with statistical confidence. There are other species that could have been used in this study, including the mallards (Anas platyrhynchos) due to their large olfactory bulbs. The mallard’s reproductive behavior is also driven by olfactory cues [6]. However, the mallards are not an ideal model organism compared to the Leach’s storm-petrels in this study because the mallards are polygamous. Therefore, the mallards would not show clear mating preferences compared to the monogamous Leach’s storm-petrel [5,7]. Both Dr. Hudson and Dr. Hoover utilized Krogh’s principle when designing their respective research studies. Applying Krogh’s principle allows for the intersection of practical study methodology, high quality data, and conclusions that are generalizable beyond the species studied.
Application of Krogh’s Principle: An Experimental Proposal on the Effect of Noise Pollution on Insect Communication
Now that we have examined historical uses, both recent and distant, of Krogh’s principle, we will now examine an application of Krogh’s principle for future research. In light of how useful Krogh’s principle is, it makes sense to propose an additional study on the auditory interference of grasshoppers. This research proposal will explore whether artificial noise in the environment affects insect hearing or communication. Insect perception of a sound is masked by environmental noise pollution. Based on Krogh’s principle, Bullacris membracioides (the bladder grasshopper) will be the model organism for this study due to their anatomical and behavioral advantages. Male and female bladder grasshoppers (Bullacris membracioides) call each other during mating using the duet behavior. The duet behavior occurs when a male grasshopper produces a song that is then repeated by a receptive female. Therefore, perception of the male call by the female can be measured by the female’s reply [8]. Anatomically, female bladder grasshoppers possess a sensitive auditory system of six pairs of ears (A1-A6). The A1 auditory organ contains 2,000 sensilla, which allows them to hear sounds over great distances of up to two kilometers. This is in contrast to other species of grasshoppers (i.e. Achurum carinatum) where females can only hear male calls only within 1-2 meters [9].
Bladder grasshopper female calls range in frequency from 1.5-3.2 kHz [8]. A common habitat for the bladder grasshopper is on the roadside. Road noises from the motorcycles can be loud (110 dB) and within the frequency range (700 Hz to 1.5 kHz) that could interfere with the auditory system of grasshoppers. Bladder grasshoppers typically mate in daytime, which is the same time as peak traffic noises. As a result, common noise pollution may disrupt perception of grasshopper calls and interfere with mating behavior [10] . In addition, it has been shown that grasshoppers exhibit phonotaxi (an organism’s movement in response to sound) in laboratory conditions [8-11]. To test whether artificial noise can disrupt the duetting behavior of the grasshoppers, a female grasshopper will be placed in a glass aquarium in front of an omnidirectional speaker that plays a recording of a male’s song mounted on a parabolic disk. Testing will be done at distance levels such as 100, 200, 500, 1,000, and 2,000 meters to examine whether distance correlates to the amount of time the female takes to respond. The experiment will be repeated with male calls with traffic noise, traffic noise alone, and no sound at all. Studying the effects of noise pollution on the auditory system using the bladder grasshopper is an example of Krogh’s principle because they are easy to raise and rear in a laboratory setting. Bladder grasshopper’s advantageous hearing made them the model organism of choice in relation to Krogh’s principle, making the hearing behavior more practical to measure and manipulate in response to different noise levels.
Conclusion
Krogh’s principle is an important concept to keep in mind while designing research studies. Many scientists, including Dr. Hudson and Dr. Hoover, around the world have applied this principle in their research to better answer research questions. To further elucidate the utility of Krogh’s principle, an experimental proposal was made concerning the effects of noise pollution on insect communication. The anatomical and behavioral characteristics considered in selecting the bladder grasshopper for this experiment were illustrated. Krogh’s principle provides useful guidance for scientists to select the most representative and practical model organism to study.
Acknowledgments
The author would like to thank Dr. Gabrielle Nevitt (Professor of the Department of Neurobiology, Physiology and Behavior at University of California, Davis) for supporting this research project and providing feedback on early versions of this manuscript.
Editor’s Note: A previous version of this article was published on April 18, 2020. The article was updated on June 19, 2020 to correct citation style.
References
- Lindstedt, S. (2014). Krogh 1929 or ‘the Krogh principle.’ The Journal of Experimental Biology, 217 (Pt 10), 1640-1.
- Kindermann, U., Gervais, R., & Hudson, R. (1991). Rapid odor conditioning in newborn rabbits: Amnesic effect of hypothermia. Physiology & Behavior, 50(2), 457–460.
- Schaal, B., Coureaud, G., Doucet, S., Allam, M. D.-E., Moncomble, A.-S., Montigny, D., et al.(2009). Mammary olfactory signalisation in females and odor processing in neonates: Ways evolved by rabbits and humans. Behavioural Brain Research, 200(2), 346–358.
- Hoover, B., Alcaide, M., Jennings, S., Sin, S., Edwards, S., & Nevitt, G. (2018). Ecology can inform genetics: Disassortative mating contributes to MHC polymorphism in Leach’s storm‐petrels (Oceanodroma leucorhoa). Molecular Ecology, 27(16), 3371-3385.
- Nevitt, G., & Haberman, K. (2003). Behavioral attraction of Leach’s storm-petrels (Oceanodroma leucorhoa) to dimethyl sulfide. The Journal of Experimental Biology, 206 (Pt 9), 1497-501.
- Corfield, J. R., Price, K., Iwaniuk, A. N., Gutierrez-Ibañez, C., Birkhead, T., & Wylie, D. R. (2015). Diversity in olfactory bulb size in birds reflects allometry, ecology, and phylogeny. Frontiers in Neuroanatomy, 9, 102.
- Doherty, P., Nichols, J., Tautin, J., Voelzer, J., Smith, G., Benning, D., et al. (2002). Sources of variation in breeding-ground fidelity of mallards (Anas platyrhynchos). Behavioral Ecology, 13(4), 543-550.
- Hedwig, B. (2014). Insect Hearing and Acoustic Communication.
- Van Staaden, M., & Römer, H. (1997). Sexual signalling in bladder grasshoppers: Tactical design for maximizing calling range. The Journal of Experimental Biology, 200 (Pt 20), 2597-608.
- Chepesiuk R. (2005). Decibel Hell: The Effects of Living in a Noisy World. Environmental Health Perspectives. 113(1): A34-A41.
- Drosopoulos, S., & Claridge, M. (2006). Insect Sounds and Communication: Physiology, Behaviour, Ecology, and Evolution.
Cerebral Palsy: More Than a Neurological Condition
By Anjali Borad, Psychology ‘21
Author’s Note: This paper explores the dynamic relationship between a mother and her son and the complexity of a health condition that the son has. I will look at a specific case of cerebral palsy—my brother—and talk about how his condition came to be and the likely prognosis. I want to delve into the details of how family dynamics play a very important role in the caregiving and caretaking that goes along with having a disabled family member and how that is seen in the relationship between my brother and my mother.
I see two different perspectives of my brother, Sam, and his condition, cerebral palsy: one through his eyes and the other through the eyes of my mother, his caregiver. Observing how my mother has taken care of Sam from the beginning, I began to realize that it takes a lot to be a caregiver and that she plays a significant role in his life. In order to gain more insight into her practices of giving care, I interviewed her. I started off by asking her what it means to be a caregiver and what “care” means to her. She took a deep breath in and expressed her daily routines as a caregiver. “Waking up in the morning, the first thing that you have to do is to attend to him and care for him before yourself,” she said. “You know that from brushing his teeth to giving him a shower and feeding him, we have to do everything from A to Z.”[1] A day in the life of my mother starts and ends with my brother, from getting him out of bed to providing him with basic needs like food and water. She even takes care of specific requests that pertain to his own interests, such as wearing a watch every day and having matching socks and pants.
Cerebral palsy is a neurological disorder. Most cases of cerebral palsy occur under hypoxic conditions during the birthing process. This lack of oxygen to the brain can cause developmental delays and lifelong debilitating conditions [2]. My family and I have experienced the difficulties and limitations that accompany this disease first hand. My brother’s condition of cerebral palsy is in its most extreme form: he has quadriplegia and spasticity. A telltale sign of quadriplegic cerebral palsy is the inability to voluntarily control and use the extremities. Spasticity occurs due to a lesion in the upper motor neuron, located in the brain and spinal cord. It interferes with the signals that your muscles need to move and manifests in the body by increasing muscle tone and making the muscles unusually tight [3]. Dr. Neil Lava, a member of the National Multiple Sclerosis Society and American Academy of Neurology, describes the pathophysiology of a lack of muscular activity. “When your muscles don’t move for a long time, they become weak and stiff,” Lava writes [4]. This physical restraint is evident in my brother’s case because he has been wheelchair-bound since the age of seven.
Upper motor neuron lesions can worsen over time. Major prolonged symptoms include over-responsive reflexes, weakness in the extensor muscles, and slow movement of the body, all of which affect the sensation of balance and coordination. For this kind of condition, occupational and physical therapy can alleviate some of the symptomatic stresses. In the case of therapy, performing the right kind of stretches can help to relax some muscle stiffness. Medication and certain surgical procedures can also treat upper motor neuron symptoms. Some common muscle relaxants prescribed to patients are Zanaflex, Klonopin and Baclofen [5].
At the neurochemical level, “Spasticity results from an inadequate release of gamma-aminobutyric acid (GABA), an inhibitory neurotransmitter in the central nervous system,” according to Mohammed Jan [6]. In a normal neural cell, when GABA interacts with and binds to GABA receptors on the postsynaptic neuron, it decreases the likelihood that the postsynaptic neuron will fire an action potential because of the inhibitory nature of GABA receptors. For a condition like cerebral palsy in which some form of insult or damage has occurred to the brain, especially in the upper motor neurons, the result is hyperactive reflexes (as opposed to the calming sensation). At this point, muscle spasticity begins to become detectable. [6]
Apart from the biological mechanism underlying this condition, particularly significant environmental factors also gravely contributed to Sam’s condition. For eight months, my mother was carrying a normally developing fetus in the womb. However, a few weeks before Sam’s delivery date, my mother could not feel any fetal movement for about three days, so she went to check on it. As she was receiving the examination, Sam unexpectedly made a fluttering movement. If he had not moved, my mother would have had to get a Caesarean section immediately. Since he moved inside, the examiners found nothing to be wrong with the fetus and deemed it safe to send my mother home.
Just a few days later, my mom was rushed to the hospital after her labor pain started. At the time, the primary medical staff mostly consisted of medical interns still honing in on decision-making skills during critical situations. From the time of my mother’s arrival at the hospital, 13 hours passed before a team of doctors and interns determined that she needed a C-section. Once this decision was made, additional time was required by the medical professionals to prepare the room for surgery. All the while, my mom was in labor pain and, unbeknownst to her, the fetus had become separated from the placenta while the umbilical cord suffered damage. By the time the surgery finally ended, Sam had suffered from asphyxiation. According to the Cerebral Palsy Guide, “asphyxiation that occurs during labor or delivery may have been caused by medical malpractice or neglect. Early detachment of the placenta, a ruptured uterus during birth or the umbilical cord getting pinched in a way that restricts blood flow can cause oxygen deprivation.” [7]
The most important aspect of a disease, once established and diagnosed, is treatment and therapy. Asking questions about how to manage pain, how to make daily routines easier to perform, and how to accommodate family members in raising a child with a disability all goes into the planning process of treatment as well. These individuals need more than mere pills in order to get through their daily lives. This is where therapists (i.e. occupational, behavioral, speech, physical, and vocational therapists) and related health advocates, including family members, come into play. While therapists cannot completely remove the condition, they provide a strategy to alleviate psychological symptoms, including feelings of loneliness, fear of who will care for you, or resentment towards oneself. Family psychologists can help children with cerebral palsy by providing an initial assessment in an attempt to gain more insight into the family dynamics. If there seems to be a lack of parental support or lack of child attachment, a family psychologist can address this through therapy sessions with the parents. Therapy sessions allow for parents to individually discuss what they think is working well for the child and other areas that can be improved. The parents are also free to talk about their own personal issues, permitting the psychologist to gain a better understanding of certain triggers for the parents. These triggers can affect caregiving for the child with special needs.
Cerebral palsy is more than just a neurological condition. It is a way of life that, for Sam, is entangled in a web of personal, social, familial, caregiver and medical challenges. One noteworthy concept heavily emphasized in the healthcare field today is the importance of a family-centered management model. The notion of a family-centered approach strives to improve the way of life for individuals with the condition in the family in a mutual way. For a family, it can be quite taxing physically and emotionally to have to take care of someone for the rest of their lives. While it is considerably easier for the receiver to reap the benefits of the caregiver, it is more difficult for the caregiver to constantly provide. The family-centered approach tries to find a middle ground where the caregiver or family and the care-receiver are benefitting from each other as much as possible. In a holistic family-centered model, the needs of each family member are taken into consideration.
A study by Susanne King details the role of pediatric neurologists, therapists, and family members, especially parents, in caring for children with cerebral palsy. This study mainly emphasizes the limiting restraints cerebral palsy places on individuals. For example, families with special needs children often have specific ways of communicating, specialized equipment used at home, and a support system consisting of the family members, therapists, and guidance counselors. The heavy emphasis on familial involvement with medical guidance from professionals is the root of family-centered care. King describes that “these children often have complex long-term needs that are best addressed by a family-centered service delivery model.”[8] Oftentimes, we see that those families who have disabled family members are suffering. Some parents, for example, experience great distress because they do not completely understand what is happening to their child and, thus, fail to acknowledge their limitations at times. Others feel that they are incapable of looking after their child but cannot bear the idea of sending them away to an institution.
King also discusses the lack of investigation of families as a whole practicing care-giving. “Although there is much evidence supporting a family-centered approach in the area of parental outcomes, there has been little work reported on the family unit as a whole,” King writes. “The most common outcome is better psychological well-being for mothers (because they generally were the participants in most of the studies).”[8]
In my family, I can actively see family-centered management of my brother’s condition occurring. I see how both my parents have certain roles in my brother’s life that collectively enable or mobilize him to feel included and respected. I like to call my parents the arms and legs for my brother in a figurative sense, and I like to call myself the eyes for my brother. Working together to the best of our ability, we enable him to see the outside world in a way that’s similar to the way we experience it.
All my life, I have seen my mother perform the role of a caregiver. I have seen so many ups and downs in her situation, and I would always ask myself the following questions. What makes her get up every morning and continue to give the care she does? What makes her not give up? She told me, “I have faith in God, and I know that He creates pathways for me to deal with the physical implications of taking care of a disabled family member and see, I have never had any major problems with your brother. I will continue to give care for as long as my body will allow for me to do so.”[1] Annemarie Mol and John Law of Duke University collaboratively published a research paper detailing how people are more than just the definitions of their disorders or conditions. According to Mol and Law, people actively create and construct their life in a way that either enhances or minimizes the intensity of their conditions. Mol and Law also explain that “there are boundaries around the body we do…so long as it does not disintegrate, the body-we-do hangs together. It is full of tensions, however.”[9] Their conclusion on what makes a person pull through encapsulates the reason my mother still continues to care for my brother.
The definition of cerebral palsy as a condition is very limited. Oftentimes people who have debilitating conditions are missing a network or a support system of people, that once established, can essentially improve that family member’s way of life. With the family-centered approach to managing care, one is essentially enabling the disabled family member by actively being a part of their life, including their day-to-day life activities. For example, through the support system we provide for Sam, he can feel that he is in good hands and that he has established emotional and personal security. Although his condition is permanent, it is comforting to know that our family dynamics allow for an environment in which he can thrive while remaining mentally healthy.
References
- Borad, Geeta. “Practices of Care, Interviews.” 8 Dec. 2018.
- Debello, William, and Lauren Liets. “Motor Systems.” Lecture, NPB 101, Davis, CA, 20 Jan. 2020.
- Emos MC, Rosner J. Neuroanatomy, Upper Motor Nerve Signs. [Updated 9 Apr. 2020]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2020 January. https://www.ncbi.nlm.nih.gov/ books/NBK541082/
- Lava, Neil. “Upper Motor Neuron Lesions: What They Are, Treatment.” WebMD, 11 May 2018, https://www.webmd.com/multiple-sclerosis/upper-motor-neuron-lesions-overview#1.
- Chang, Eric et al. (2013). “A Review of Spasticity Treatments: Pharmacological and Interventional Approaches.” Critical reviews in physical and rehabilitation medicine vol. 25, 1-2: 11-22.
- Jan, Mohammed M S. (2006). “Cerebral palsy: comprehensive review and update.” Annals of Saudi Medicine. vol. 26, 2.
- Cerebral Palsy Guide. “Causes of Cerebral Palsy – What Causes CP.” Cerebral Palsy Guide. 21 Jan. 2017, https://www.cerebralpalsyguide.com/cerebral-palsy/causes/.
- King S, Teplicky R, King G, Rosenbaum P. (2004). “Family-centered service for children with cerebral palsy and the families: a review of the literature.” Semin Pediatr Neurol. Science Direct.
- Mol, A & Law, J. (2004). “Embodied Action, Enacted Bodies: the Example of Hypoglycaemia.” Body & Society, 43–62.
Stem Cells: Miracle Cure or Hoax? A Review of Present Application and Potential Uses of Stem Cells
By Vita Quintanilla, Genetics 23’
Author’s Note: My purpose in writing this piece is to educate the current safe applications of stem cell as misuse and damage due to the same is so prevalent in the US and abroad. While not detracting from the great advances being made in the field currently this piece is to take stock of the reality of this treatment.
Large segments of the American and world population living with medical conditions that cause significant loss of mobility and quality of life are searching for hope in Stem Cell therapy. The unfortunate reality is that many of these “therapies” are not only ineffective but potentially harmful and the clinics that distribute them are not always properly certified. While stem cell therapies are promising, run away hope for a miracle cure coupled with unethical advertising and untested procedures have caused patients in the United States and beyond to be harmed by a potentially life saving tool. Here we will examine the current state of stem cell investigation, treatment, US Regulation, prospects in the future of medicine, and information for consumers to consider in deciding to receive a stem cell treatment.
Stem cells are undifferentiated cells that are at the start of all cell lines. Embryonic stem cells come from the blastocyst, a small clump of cells that forms several days after conception, and are pluripotent, meaning that they can give rise to any cell type (except specific embryonic tissues not present out of utero). [1] While these are the most often referred to type of stem cells there are also multipotent stem cells that can only give rise to a specific kind of tissue and are present into adulthood. Somatic cells, or differentiated cells, can be reverted to a pluripotent state. Induced pluripotent stem cells (IPS) are a growing area of interest in the field as they carry with them the possibility of culturing tissues for transplant using the existing cells of a patient thus eliminating the possibility of rejection.[2]
IPS exemplify an unfortunate reality in the whole of stem cell research, that at present widespread stem cell therapies are not ready for the general public. While these cells have great potential, a major hurdle is the cost in both time and labor required to culture them in a safe and sterile environment. A single vial of research grade cells that will produce fewer than thirty colonies in five days under ideal circumstances can cost over 1,000 dollars. This does not include the cost of facilities, culture equipment, and labor making these therapies cost prohibitive as the resulting therapy can run as far as 10,000 dollars per treatment. [3&4] Furthermore, colonies of cells are far from fully developed tissues that could potentially be implanted. A patient in critical condition in need of a transplant likely cannot wait for the cells to grow into tissue in culture, even if they can afford it.
Difficulties in access however are not the greatest barrier to stem cell therapy, but rather the lack of widespread testing and approval for the treatment of the diverse conditions for which they are sometimes advertised. While these cells are promising for usage in widespread areas of medicine, at present they do not live up to the claims that many unscrupulous clinics make for them. US Stem Cell Clinic, with a sleek website, and moving testimonials, advertises the use of stem cells as a magical cure that make the old feel young again using stem cells to treat a host of orthopedic maladies. These claims are highly suspicious as the FDA website says, as of January 2019, that only stem cell therapies for blood disorders are approved. [5]
These cells have been proclaimed cure-alls and medical miracles by the mass media but the reality is that the research into the application of stem cells for diverse ailments in humans is not conclusive at the present moment. [5] The FDA only approves stem cell treatments for blood disorders using stem cells from umbilical cord blood or bone marrow, but many clinics are offering stem cell treatments for everything from vision problems to COPD. The FDA recently filed two complaints against US Stem Cell Clinic LLC in Florida and California Stem Cell Treatment Inc. for marketing stem cell products that do not have the proper approval and for having unsafe manufacturing conditions that compromised sterility and patient safety. Patients filed lawsuits against California based stem cell supplier Liveyon who sold umbilical cord stem cells contaminated with E. Coli that resulted in sepsis and several patient hospitalizations after the stem cells were used for unapproved treatments. [6] In a recent lawsuit Florida based US Stem Cell was ordered to cease and desist, destroy all stem cells in their possession and pay for twice annual facilities inspections after taking cells from fat and injecting them into the eyes of patients causing five women to be blinded. In a 2018 statement FDA Commissioner Scott Gottlieb, M.D. said “We support sound, scientific research and regulation of cell-based regenerative medicine, and the FDA has advanced a comprehensive policy framework to promote the approval of regenerative medicine products. But at the same time, the FDA will continue to take enforcement actions against clinics that abuse the trust of patients and endanger their health” [7] The FDA, has in the past been accused of slowing down progress with novel treatments, but in the case of stem cells it is apparent that their actions hold patient safety as first priority, protecting the public from doctors and companies that value monetization over public health.
Patients in the United States have been harmed by these clinics including adverse injection site reactions, migration of cells to the improper location, the failure of cells to work in the desired way, and even the growth of tumors. Clinics that operate these studies may even be operating criminally as the FDA has pressed charges against these clinics in the past in the form of permanent injunction, an order to cease and desist permanently. [7]
Patients are often motivated to take these risky treatments because there is no other hope for a cure, however, unapproved treatments can make the condition worse or even lead to death. The dangers of receiving unapproved therapies is illustrated in the case of a 38-year-old man, who developed a spinal tumor after a stem cell treatment in preformed in Portugal where doctors injected cells taken from his nose into his spine. The treatment was attempting to cure paralysis in his legs and arms. It had no effect on his paralysis, but twelve years later the tumor that formed further limited his mobility and quality of life as his bladder control and motor function in arms steadily declined. Complications have been even more dire as a thirteen-year-old male in Israel who was treated at a clinic in Moscow for Ataxia telangiectasia, which affects the nervous system, died of a tumor that arose from donor cells. These are not isolated instances of unsuccessful treatment in patients that were already ill, the stem cells themselves were directly the cause of degeneration in the patients, and more than 19 deaths confirmed by the National Institute of Health as of 2018. [8&9]
Predatory clinics that perform these unapproved procedures can be especially hard to identify. Many have sleek well-designed websites with official looking personnel and lofty claims of unrealistic success rates and propositions for stem cells as cures for many diverse and at times totally unrelated disorders. Many clinics are located in Florida and Southern California however there are hundreds of clinics across the United States. [10]*** Patients should be advised to do some research into these claims and check to see if the clinic in question as well as the treatment has FDA approval. A good strategy for determining the legitimacy of a clinic is to do research on the main doctors performing the procedure. If a clinic is claiming to be able to cure numerous unrelated and debilitating disorders, the doctors performing these procedures should be of high esteem in the community and have visible external measures to the importance of their work or the prestige of their practice. If this is not the case the patient should proceed with great caution.
The issue of deceptive stem cell clinics is not a mere issue of public health but an example of a greater problem, a break between scientific community and the public perpetuated by a few unscrupulous characters for the sake of profit. Stem cells have the potential to be life saving tools and usher in a whole new chapter of regenerative medicine, but if the reputation of this technology continues to be tarnished by clinics that do not abide by the laws and conventions put in place to keep consumers safe, this technology may never get an opportunity to reach its full potential.While stem cells have great potential for diverse treatments at some point in the future, at present their efficacy and safety for regenerative medicine has not been firmly established in the context of current technology. Not all stem cell treatments are to be feared, stem cell treatments for some blood disorders have been shown to be effective and safe. At some point in the future when culture and delivery techniques improve stem cells could revolutionize transplant and regenerative medicine. At present the best course of action for consumers in regard to these therapies is to partake only in treatments or clinical trials operating with the approval of the FDA, and keep up with developments in the field by reading peer reviewed papers published in reputable journals. Exercise great caution but do not lose hope for the future. Stay current with research and, considering the risks and benefits, consumers may choose to enroll in FDA supervised clinical trials that adhere to the three phase clinical trial process, but always be sure to exclusively receive treatment from FDA regulated and approved clinicians.
Sources
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- https://www.atcc.org/search?title=Human%20IPS%20(Pluripotent)#q=%40productline%3DL035&sort=relevancy&f:contentTypeFacetATCC=[Products]
- Office of the Commissioner. “Consumer Updates – FDA Warns About Stem Cell Therapies.” U S Food and DrugAdministration Home Page, Center for Drug Evaluation and Research, 16 Nov. 2016, www.fda.gov/ForConsumers/ConsumerUpdates/ucm286155.htm.
- William Wan, Laurie McGinley. “’Miraculous’ Stem Cell Therapy Has Sickened People in Five States.” The Washington Post, WP Company, 27 Feb. 2019, www.washingtonpost.com/national/health-science/miraculous-stem-cell-therapy-has-sickened-people-in-five-states/2019/02/26/c04b23a4-3539-11e9-854a-7a14d7fec96a_story.html.
- Commissioner, Office of the. “FDA Seeks Permanent Injunctions against Two Stem Cell Clinics.” U.S. Food and Drug Administration, FDA, 9 May 2018, www.fda.gov/news-events/press-announcements/fda-seeks-permanent-injunctions-against-two-stem-cell-clinics.
- Bauer, Gerhard, et al. “Concise Review: A Comprehensive Analysis of Reported Adverse Events in Patients Receiving Unproven Stem Cell-Based Interventions.” Stem Cells Translational Medicine, John Wiley & Sons, Inc., Sept. 2018, www.ncbi.nlm.nih.gov/pmc/articles/PMC6127222/#!po=19.4444.
- Flaherty, Brittany, et al. “Case Highlights the Risks of Experimental Stem Cell Therapy.” STAT, Staten News, 11 July 2019, www.statnews.com/2019/07/11/canada-case-long-term-risks-experimental-stem-cell-therapy/.
- https://usstemcellclinic.com/ [10]
- Commissioner, Office of the. “Step 3: Clinical Research.” U.S. Food and Drug Administration, FDA , 4 Jan. 2018, www.fda.gov/patients/drug-development-process/step-3-clinical-research.
- Hiltznik, Micheal. “Column: Judge Throws the Book at a Clinic Offering Unproven Stem Cell ‘Treatments’.” Los Angeles Times, Los Angeles Times, 26 June 2019, www.latimes.com/business/hiltzik/la-fi-hiltzik-stem-cell-injunction-20190626-story.html.
Gene editing invasive species out of New Zealand
By Jessie Lau, Biochemistry and Molecular Biology ‘20
Authors Note: Since the advent of Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR Associated Protein 9 (CRISPR/Cas9) discovery and biotechnological breakthroughs thereafter, this revolutionary application has been primarily focused on human health, particularly fostering solutions to numerous debilitating ailments. However, the general public has offered little attention towards the use of this engineering feat in a broader ecological system. Upon watching the new Netflix original Unnatural Selection, discussion of considering the use of CRISPR/Cas9 in New Zealand’s effort to completely eradicate invasive species piqued my interest. The following article is an exploration of CRISPR/Cas9 prospect into New Zealand’s bold environmental pursuit and its potential ecological impact.
Abstract
Since it has become feasible to cross oceans to reach unforeseeable land masses, invasive alien species (IAS) are an increasing threat to international biodiversity. Moreover, no other region faces as great of a peril as New Zealand (NZ), which holds the record as the nation with the highest survival rate of threatened avifauna (birds of a particular region) species [5]. In 2012, New Zealand physicist Sir Paul Callaghan introduced a large-scale eradication program to permanently remove eight invasive mammalian predators (rodents: Rattus rattus, Rattus norvegicus, Rattus exulans, Mus musculus; mustelids: Mustela furo, Mustela erminea, Mustela nivalis; and the common brushtail possum: Trichosurus vulpecula) [5]. Four years after this grand proposal, the NZ government committed to a national challenge titled “Predator Free 2050” (PF 2050) to pursue this audacious goal.
Introduction
Approximately 85 million years ago, NZ was one of the first landmasses to split from the supercontinent Gondwana and as it shifted away, it did not carry mammals until bats flew and aquatic species swam to this island. [7]. With the introduction of rodent species initially through Polynesian settlement some 750 years ago and thereafter European seafaring ventures, the endemic species of NZ have been left vulnerable to novel predators. Consequently, at least 51 native bird species that have evolved adaptive skills of remaining close to the ground have been unsuccessful at surviving alongside these rodent predator species [4]. These invasive omnivorous rodents prey on birds, eggs, seeds, snails, lizards, and fruits. As a result, their varied diets prompt competition with the native fauna, further placing pressure on their vulnerable survival [7]. Despite CRISPR/Cas9 modifications offering the greatest potential in gene drive to eliminate these unwanted predators, several techniques implemented to control these invasive populations, such as pesticides, trapping innovations, and biological factors have given favorable results.
Past Successes and Future Endeavors
For decades, the NZ government has pursued eradication initiatives to permanently eliminate foreign invasive species on small local islands. Through concerted efforts, several of these projects have proven successful in the restoration of the natural biodiversity this island nation boasts.
In June of 2009, the NZ Department of Conservation (DOC) undertook a multi-action plan to simultaneously eradicate rodent, rabbit, stout, hedgehog, and cat species in Rangitoto and Motutapu islands. After three years of aerial dispersion of anticoagulant Pestoff 20RTM combined with trapping and indicator dogs, the island witnessed total elimination of the islands’ stoats and four rodent species; declination of rabbit and hedgehog population by 96%; and over 50% reduction in cats [7].
Despite these successful feats, the invasive species fecundity and ability to adapt to these challenges still present an overwhelming challenge to reach the goal of complete eradication. Recently, more direct approaches delving into novel genetic inheritance techniques have been explored to serve as a potential permanent solution. Termed the“Trojan Female Technique” (TFT), the method makes use of the correlation of sperm fitness dependence on the abundance of mitochondrial DNA (mtDNA) [2]. Healthy sperm is dependent on sufficient mitochondrial level for energy production to manage motility and fertilization. For example, experiments conducted on Drosophila melanogaster supports the causation of reduced spermatogenesis and sperm maturation due to induced mutations in cytochrome mitochondrial gene [9]. Contrasting female eggs, the asymmetric greater dependence of sperm on mtDNA for normal functionality results in only male populations to be the sole source of target. Induction of mitochondrial mutations in females to compromise total sperm viability in future male progenies will serve as an effective control to population growth.
Although seemingly promising, TFT is not guaranteed to completely eradicate propagation for several reasons. For starters, males with impaired fertility can still provide sufficient sperm count to fertilize eggs on a population-based scale. Furthermore, in circumstances where females do receive nonviable sperm count, they can still seek adequate functioning sperm through matings with other males. On a larger scale, should the mutation pervade, selection pressures could still inadvertently choose for nuclear modifications to make up for the mitochondrial defects [2]. These flaws raise the need for more pervasive and permanent resolutions.
Daisy Chain CRISPR Gene Drive
The recent biochemical breakthrough underpinning the ability to effectively and precisely modify genes with CRISPR/Cas9 has allowed for potential biotechnology to boom in the realm of ecology. The simple generation of a short RNA sequence into a virus or bacterium to serve as a vector, guides the cutting mechanism of Cas9 to specific regions in the genome to be excised, prompting for these double stranded breaks to be fixed through DNA repair mechanisms. While these fixtures can potentially repair the gene, it can also raise the possibility for the gene to be disabled, introduce a new function, or create an unforeseen mutation. Given the right specific targeting in the germ line, this approach houses the innovation for exterminating entire species through gene drive [6].
The mechanism behind gene drive overthrows the traditional Mendelian sexual reproduction concept of proportional contribution from both the male and female parent. The power comes from the ability of one genetically modified (GM) contributor encoding for the ‘gene drive’ to cut the other set of chromosomes lacking these genes and replace this excision with a self-replicating copy. In effect, this divisive modification would push for an otherwise heterozygous offspring from a wild-type mating with a GM partner to become homozygous for certain genes to be carried on and propagated by future generations. Given that these genetic alterations do not affect the fitness of the organism, dissemination of 1% of the population with CRISPR modified genes can lead to 99% of the local population carrying the genetic indicator in as little as nine generations (The use of gene editing to create gene drives for pest control in New Zealand).
Such a unilateral approach poses political and ethical challenges amongst neighboring nations with diverging ecological approaches to confront pest control. Should this pervasive gene drive program reach beyond its intended border, great difficulty would arise in maintaining this ecological enclosure. For example, possum is on the list of invasive species in NZ while just 2,500 miles west, its neighbor Australia keeps this species of marsupials under protection. As such, scientists have devised a simple model to localize gene alterations, coined The Daisy Chain.
Unlike the original gene drive method in which all components necessary for transformation (CRISPR, edited DNA, and guide RNAs) are provided on the same chromosome, Daisy Chain provides a self-exhaustive means of guaranteeing genetic edits. This tool is designed so that each component required for genetic alteration is dependent on the presence of a different element upstream on the gene found on the same locus to be activated [8]. The most downstream portion of this chain contains the “load” of engineered dominant lethal genes preventing reproduction, which will be promoted to higher frequency in the population within several generations. For instance, should an engineered allele contain three elements A, B, and C, element C would render element B to drive, which will in turn cause element A carrying the final load to drive. The initial element (C in this case) does not actually drive, thus is restricted by the number of altered individuals released into the wild and will be lost via natural selection over time. During initial implementation, the presence of C will increase B in abundance, but B will eventually decline and finally disappear as C is lost in the population. The rapid rise in abundance of B will also cause A to increase in frequency within the local population; however, with the decrease of B, A would not be driven and will ultimately vanish as well [1]. Using MIT Professor Esvelt’s analogy, “… the elements of a daisy drive system are similar to booster stages of a genetic rocket: those at the bottom of the base of the daisy-chain help life the payload until they run out of fuel and are successively lost.”
Challenges with Daisy Chain CRISPR Gene Drive
CRISPR/Cas9 technology’s ability to potentially alter these invasive species’ fecundity provides an avenue of pursuing NZ’s goal of PF 2050. Despite the developed understanding of how to carry out this plan, scientists in NZ are still working to piece together the genomes of stoats and possums in order to understand where to properly facilitate the engineered RNA sequence. Other barriers that must be acknowledged are the unprecedented approach to genetically modify marsupials and the difficulty of implanting hundreds to thousands of oocytes to be dispersed amongst their population.
Beyond these known difficulties, scientists still tread in unknown terrains pertaining to whether these mutations can have pernicious effects in the survival, health, and reproductive success in propagating these mutations within their populations. Further exploration into the development of these modifications, and the potential impacts they can have on these animals, must be investigated on model organisms prior to widespread use.
Of the eight listed mammalian species vied to be permanently eradicated from NZ, Mus musculus holds the most promise, given the extensive knowledge of the Mus musculus genome. With the help of scientists outside of New Zealand, joining in on the efforts to identify which germline gene to focus on, this project has received international attention.
Although the daisy drive provides promising potential, research collaborators at MIT and Harvard have identified a possible risk of, “… DNA encoding a drive component from one element to another, thereby creating a ‘daisy necklace’ capable of a global drive” [1]. Due to this rare recombinatory event arising from the similarity of DNA sequences, these investigators have looked into circumventing the problem by creating numerous alternatives to CRISPR components and selecting the model with the greatest diversity.
Conclusion
From their renowned aviary to reptilian species, New Zealand’s islandic geographical region houses some of the most biodiverse fauna known to man. The arrival of human settlement has introduced predatory species, causing endemic species to experience extinction at concerning rates [4]. With the purpose of preserving their unique remaining diversity, New Zealand has committed to concerted efforts of varying methods to eradicate these invasive vertebrate pests. Investigation into genetic modifications can provide for more expansive and thorough techniques to eliminate these human introduced pests and allow for these endangered species to thrive once again. By further exploring daisy chain CRISPR/Cas9, this effort can be genetically inherited by offspring, allowing for nature to carry out this effort. As opposed to continued efforts of targeting each individual one by one, conservation ecologists can borrow from molecular biologist’s toolkit to revolutionize the means of pursuing pest control and perhaps even pave the road for future endeavors with similar pursuits.
References
- Esvelt, Kevin M. “Daisy Drives.” Sculpting Evolution, www.sculptingevolution.org/daisydrives.
- Gemmell, Neil J., et al. “The Trojan Female Technique: a Novel, Effective and Humane Approach for Pest Population Control.” Proceedings of the Royal Society B: Biological Sciences, vol. 280, no. 1773, 2013, pp. 1–6., doi:10.1098/rspb.2013.2549.
- Griffiths, Richard, et al. “Successful Eradication of Invasive Vertebrates on Rangitoto and Motutapu Islands, New Zealand.” Biological Invasions, vol. 17, no. 5, 2014, pp. 1355–1369., doi:10.1007/s10530-014-0798-7.
- Owens, Brian. “The Big Cull: Can New Zealand Pull off an Audacious Plan to Get Rid of Invasive Predators by 2050?” Nature, vol. 541, 12 Jan. 2017, pp. 148–150.
- Russell, James C., John G. Innes, Philip H. Brown, and Andrea E. Byrom. “Predator-Free New Zealand: Conservation Country.” BioScience 65, no. 5 (October 2015): 520–25. https://doi.org/10.1093/biosci/biv012.
- Saey, Tina Hesman. “Explainer: How CRISPR Works.” Science News for Students, 4 Dec. 2017, www.sciencenewsforstudents.org/article/explainer-how-crispr-works.
- “Why Predator Free 2050?” Department of Conservation. Accessed November 18, 2019. http://www.doc.govt.nz/nature/pests-and-threats/predator-free-2050/why-predator-free-2050/.
- Dearden, Peter K., et al. “The Potential for the Use of Gene Drives for Pest Control in New Zealand: a Perspective.” Journal of the Royal Society of New Zealand, vol. 48, no. 4, 2017, pp. 225–244., doi:10.1080/03036758.2017.1385030.
- Wolff, Jonci N., et al. “Mitonuclear Interactions, MtDNA-Mediated Thermal Plasticity and Implications for the Trojan Female Technique for Pest Control.” Scientific Reports, vol. 6, no. 1, 2016, doi:10.1038/srep30016.
- Min, John, Jason Olejarz, Joanna Buchthal, Alejandro Chavez, Andrea L. Smidler, Erika A. DeBenedictis, George M. Church, Martin A. Nowak, Kevin M. Esvelt, and Charleston Noble. “Daisy-Chain Gene Drives for the Alteration of Local Populations.” PNAS. National Academy of Sciences, April 23, 2019. https://www.pnas.org/content/116/17/8275.
You might have to use more than a microscope, there’s more to genetics than what meets the eye: An interview with Dr. Gerald Quon
By Tannavee Kumar, Genetics & Genomics 20’
Author’s Note: As an undergraduate studying genetics and genomics and computer science, I wanted to interview a former professor to find out the steps he took in order to do computational research in the biological sciences. I was interested in finding out more about the growing field of computational biology and wanted to help shed light on a field to students that may be similarly interested.
Background
You received a Bachelors in Math, then a masters in Biochemistry, then a PhD in Computer Science; did you always know that you wanted to do research in biology? If so, what made you want to start off with a technical education rather than something traditional like biology or chemistry? If not, how did you come to discover applications of computer science in Biology even 15 years ago?
No, I did not start off wanting to do anything related to biology. I started my undergrad thinking I would make computer games. How I kind of got into this was a week before my undergrad, I got an email from my university asking if I wanted to be a part of the first cohort of a bioinformatics program. I initially declined.
As I was looking for my third internship in my co-op program, I had a friend who found a job for a professor in Toronto, and my friend asked if I wanted to work on this cool project about predicting how proteins fold into these 3D structures. I told him I don’t know anything about protein structures, but sure! It was a lot of fun.
Is that what inspired you to pursue Biochemistry for further education?
I think that first internship was very pivotal, because it really nurtured my interest in protein structures. When I finished my undergrad, I was kind of bored of computer science, which is why I thought I would do a PhD studying protein structures.
How do you see life sciences research evolving and progressing in the coming years, given the inclusion of this new field?
In my opinion, we will see more and more blurring of boundaries. In 25 years, there is going to be more undergraduate programs less defined by walls like “life sciences,” “chemistry,” and better recognition that everybody borrows knowledge and skills from many fields. It will be very difficult to do a life sciences degree without learning anything about math or statistics. Similarly, more people in traditional quantitative disciplines will want to take those classes in the life sciences. Essentially there will be fewer walls.
How would undergraduates studying quantitative subjects, like mathematics, statistics, or computer science be made aware of the growing demand for such skills in the Life Sciences?
The classic way to become introduced to such areas would be through coursework, internship with a company, or research with a professor. The last two ways are not very optimal. At the end of the day, in a standard undergraduate program, you have summers, and if you are ambitious you can try to do research during the school year. However, you can only do so many different kinds of internships before you graduate. If you did one every summer of college, and even two before hand, even that would not be sufficient for getting a nice, representative sample for all the things you can work on.
That is where universities need to do a better job of creating opportunities for students to engage with people from industry and research so that they don’t need 4-5 months to figure many essential things out.
Research and Beyond
Can you briefly describe some of the research that your lab does?
We are currently working towards a few different directions. A large project at the moment is studying the genetics of mental disorders and neurodegeneration, for example we look at the genetics of Alzheimer’s disease, schizophrenia, autism, etc. Our main goal is to mechanistically understand how genetic variants associated with these mental conditions modify disease risk. Much of those mechanistic studies currently look at events that happen at the molecular level. This is great and very useful; however, since the majority of the research is geared at the molecular level we don’t have a good understanding of what variants do functionally at the level of the cell. How does it affect the functional properties of the cell, such as neuron electrophysiology? Or, how is the organization of the tissue affected?
Other areas we work on are on building better models to understand how cells are spatially organized in the brain, as well as building models that quantitatively describe cell population behavior. We know that cells behave differently when put into different contexts. It’s of interest to build a model to predict what happens when you put together different kinds of cells in different combinations, orientations, or conditions.
Lastly, a third project being worked on is on the therapeutic end. We are essentially trying to identify the druggable region of the genome. There are a lot of computational problems in trying to determine what is druggable.
How do you think the integration of the computational sciences has shed light on how biological processes are interconnected, and what do they make clear that a molecular approach may not be able to?
In human genetics, computational models play a huge role in hypothesis generation. They do a good job leveraging big data, such as genomics, to prioritize which variants should be tested using molecular approaches, for example, when molecular approaches are costly or too slow to systematically test many variants across a genome. The role of computation is parsing through the many possibilities that you can’t explore molecularly.
For example, a study we worked on four years ago was to try and find a causal variant for obesity. Most human genetic studies only point to a region of the genome where causal variants might hide, but don’t tell you exactly which one is the true causal one. When these regions are big, like hundreds of kilobases long, you need computational tools to identify the precise causal one to test experimentally. In that study, computational tools played the pivotal role of identifying the causal variant that was ultimately tested and shown to drive large changes in obesity risk.
How does computational research like your own lead to the progression of curated care in the health industry?
At a superficial level, in some ways it accelerates some of the biomedical discoveries that are being done today. The obesity study is one example. If you didn’t have the computational resources, you would spend years and years trying to find the right variant. However, we found it relatively quickly with computation.
For healthcare specifically, fields such as machine learning are revolutionizing care today. People from statistics, computer science, and math are working directly with clinicians and hospitals to develop highly accurate ‘digital pathology’ software, they help predict when patients will need to come into the hospital or whether they are high risk for a disease.
Oftentimes, conditions and diseases are misdiagnosed, which leads to inappropriate treatments. How would research in this area begin to remedy this common problem in the healthcare industry?
Most diseases are heterogeneous, which means that a group of people who are diagnosed with the same condition might actually have different underlying conditions, and need different treatments. Many computational approaches based on molecular and clinical data are being developed to identify more homogeneous groups of patients, to help achieve precision medicine. This allows for the most accurate prescription of medication and treatments. This is because these homogenous groups help identify the underlying disease phenotype which means access to better directed medication.
During your time as a PhD student, you also “explored the application of models built from deconvolving gene expression profiles, for personalized medicine.” Can you go more in depth to how these models were built and how it can advance our ability to provide a more accurate prognosis to patients?
During my PhD, we were trying to predict the prognosis of early stage lung cancer patients. If you are diagnosed with early stage lung cancer say stage 1B, clinicians have to make important decisions, such as how much e.g. chemotherapy to give you. If they give you too much, it will get rid of the primary tumor, but you will increase your risk of recurrence. But if you don’t give enough, you don’t get rid of the primary tumor.
Back then, fourteen year ago or so, genome expression profiling was just becoming popular. People were thinking maybe we can predict whether these stage 1B patients were going to be at high risk of recurrence or not. Our motivation for that problem was essentially to build a computational model to predict based on molecular signatures if they should be given extra therapy or not. That in itself is a hard problem. Additionally, before single cell sequencing was available, it was hard to take a sample of a tumor and only sequence the tumor cells. Often times you would have contamination of normal cells that would mess up the signatures you would get. We had to develop a computational method to extract out only the signatures due to tumor cells, and show that once you do that it is much easier to predict prognosis.
Where do you think research will be in the next 10-20 years?
We are going to see a lot more connections across more previously isolated fields. For example, with respect to human psychiatric genetics, a lot of focus right now is at the molecular impact of genetic variants, but in the near future I’d expect there to be much closer integration with clinicians to also study the impact on behavior, and with the experimental biologists to study the impact on brain development and organization.
***Special thanks to Dr. Gerald Quon for this interview
Genetically Engineered Crops: A Food Security Solution?
By Roxanna Pignolet, Biochemistry and Molecular Biology 20’
Author’s Note: Since I started working on plant metabolites as an undergraduate researcher in the Shih Lab, I’ve developed a great appreciation for the power of plant genetic engineering to address a wide variety of problems. A uniquely global and increasingly relevant concern is how to continue to feed the world’s growing population in the face of climate change. I decided to write this paper to provide a snapshot of the current research being done to innovate crop species that will survive in the face of climate change. As part of this review. I also wanted to address ongoing concerns about the safety and impact of GMOs on consumers and the environment, and whether these genetic engineering strategies have the potential to make a positive impact on food security.
Introduction
As the world population continues to rise, climate change is also having an increasingly large impact on agriculture in the form of rising temperatures and intensified weather variations. Population growth is challenging researchers and farmers to find new ways to increase crop yields without access to more land or freshwater. Population is expected to increase from the current 7.7 billion to 9 billion by 2050 (1,2). However, it was found in 2000 that about 70% of the available freshwater was already in use. Meanwhile, climate change is introducing new challenges to crop productivity and stability. By 2050, the global crop demand may increase as much as 110%, which emphasizes the need for new, powerful strategies for crop improvement.
Genetically engineered crops have been used in agriculture since the mid-1990s, and have been instrumental in overcoming serious agricultural challenges such as disease outbreaks and overuse of toxic insecticides (3). In contrast to traditional breeding, genetic engineering allows for a direct transfer of one or more genes of interest from either closely or distantly related organisms. In some cases, a plant is modified solely by turning on or off one of its own genes (4). These methods allow for fast and precise changes that target a specific trait. Since their introduction, numerous studies have measured their potential for health and environmental risks, as well as their benefits. This review will discuss the impacts of genetically engineered crops from an environmental and health perspective. Additionally, I will look at how genetically engineered crops are currently being applied to address food security concerns in the face of climate change.
What is the Impact of Genetically Engineered Crops?
Environment
As genetically engineered crops have now been used in the field for many years, the environmental impacts can be assessed. The most abundant type of genetically engineered crops are insect resistant crops, specifically Bacillus thuringiensis (Bt) resistant corn and cotton. Bt is a soil bacterium which produces proteins that are toxic to certain insects (5). Bt crops have been modified to produce Bt genes as protection against specific pests (3). These crops have been grown commercially since 1996 (2), which has allowed long term environmental studies to be conducted. In a two-year field trial on the impact of transgenic maize on soil fauna, Fan et al. found that there was no impact on biodiversity, abundance or composition of the soil fauna. They compared samples taken in varying conditions from either transgenic maize or non-transgenic maize controls. The researchers found that the insecticide transgene did not affect the soil ecosystem, while factors such as time of year, pH, sampling time, and root-biomass all had significant effects (6). In a 2003 review on Bt crops, Mendelsohn et al. also found that there were no negative impacts observed on species of endangered insects, earthworms, or non-target insects. However, one negative that applies to all insecticides is that pests will eventually gain resistance. Engineering crop varieties to have several different resistance genes has been shown to slow this process (2).
Another class of genetically modified crops that are currently in use are herbicide-tolerant crops. Herbicide-tolerant crops are designed to be tolerant to broad-spectrum herbicides that can be used to control surrounding weeds. Use of herbicide-tolerant corn and soybeans has been shown to decrease the use of highly toxic herbicide sprays in favor of an amino-acid derived, non-toxic alternative (Roundup), and has also encouraged low-till farming practices which have been correlated to significant reductions in greenhouse gasses (2). Weed resistance is a concern with herbicide-resistant crops, especially when a single herbicide gene is overused. In some cases, high selection pressures caused by overuse of a single broad-spectrum herbicide have led to resistant weeds. If unchecked, these resistant weeds can spread across farms and negatively impact crop growth (7). New varieties of crops resistant to multiple types of herbicides should help mitigate this problem by allowing farmers to rotate several types of herbicides. A widespread adaptation of these new varieties and consistent practice of sustainable herbicide application will be important to avoiding negative outcomes of herbicide-tolerant crop use.
Implementing these genetically engineered crops has contributed to overall decreases in the amount of toxic insecticide and herbicide sprayed. Just as with chemical pesticide and herbicide sprays, proper steps must be taken with insect-resistant or herbicide-resistant crops to delay resistance in the affected insect or weed. These steps include rotating planting of herbicide-resistant crops and using weed control tactics with different modes of action to avoid putting high selection pressure on one type of resistance.
Health
The consensus from long term studies carried out to address biosafety concerns of genetically modified crops, is that they are just as safe as their natural counterparts. Genetically engineered crops are subjected to a variety of tests on a case by case basis before they are implemented, and now long term data shows that there have been no side effects from possible unintended chemical compositions of crops, making them just as safe as those derived from traditional breeding. There are, however, concerns about next generation genetic engineering, which targets regulator genes instead of a single functional gene. Targeting regulator genes could allow scientists to target plant stress response pathways, and engineer plants to have multiple desirable traits (8). Additional research must be conducted to assess the plant-wide changes caused by affecting a player in a signaling cascade.
New Approaches to Crop Improvement
While the current genetically engineered crops have been found to have a positive effect on crop yields, the increases are not enough to keep up with projected population growth. Additionally, climate change is predicted to cause stressors to crops such as drought, rising temperatures, and weather variations among other things (2). Therefore, scientists are looking for new and creative genetic engineering techniques to create robust and high-yielding crops for our future.
One of the main targets for genetically engineered crops is adaptions to grow and produce quality yields under higher temperatures. In a study investigating the genes responsible for creating lower quality, chalky rice grains under high temperature conditions, Nakata et al. looked at the role of a starch metabolizing enzyme, known as amylase, in the packing of starch into rice grains. Their team used transgenic rice modified with a reporter gene attached to each isotype of the amylase gene. By comparing the activity of plants overexpressing each variety, they were able to identify specific amylase genes as targets for genetic modification. Rice variants with these modifications would remain higher quality, with tightly packed starch, even if grown under non-optimal higher temperatures (9). Another study tested the responses of a previously created transgenic rice line called HOSUT under high amounts of carbon dioxide (CO2), a heat wave, and nitrogen enriched conditions. They found that the transgenic line, which has enhanced sucrose transport, has a superior yield than the control line (Certo), and that increased CO2 conditions resulted in higher yields in Certo with only minimal increases for HOSUT. They concluded that the minimal response of HOSUT to the increased CO2 was indicative of HOSUT already being saturated due to its optimized transport capabilities. The HOSUT line is already optimized for translocation of carbon, which they were able to show by increases in starch in the grains in HOSUT only. HOSUT also produced more yield in response to increased nitrogen, making it a good option for producing high rice yields under variable climate change conditions (10) The HOSUT line is a great example of how genetic engineering can be used to fortify and optimize crops to both survive under atypical conditions and produce enough yield to keep up with demand.
Another problem that researchers are addressing through genetic engineering, is drought. Selvaraj et al., developed and field tested two drought tolerant rice lines, created by introducing an Arabidopsis stress response gene (galactinol synthase) with a maize promoter. Galactinol synthase produces galactinol, a sugar that functions as an osmoprotectant, keeping water from leaving the cells. These galactinol synthase genes were introduced into two commercially available rice lines and tested in the field under drought and well-watered conditions. Under drought conditions, the collection of galactinol resulted in higher grain yields, while under well-watered conditions no significant yield increase was observed. Galactinol is a sugar that functions as an osmoprotectant, keeping water from leaving the cells. The results of these field trials show that these rice lines are ready to be integrated into ongoing breeding programs (11). Wang et al. also tackled the problem of drought stress caused by global warming on fruit such as apple trees. They transgenically expressed an aquaporin gene found in Fuji apples that has increased expression during fruit growth in tomato. The transgenic plants did have an increased drought tolerance, observed as an increased sensitivity of their stomata to water loss, and a larger fruit size when compared to wild type. This research will be continued in apples next with the goal of producing plants with larger fruits when well-watered, which will also be more tolerant to drought due to increased water transport efficiency (12).
A third target for genetic engineering solutions is circadian rhythms. Understanding and controlling circadian rhythms in crop plants has the potential to adapt plants to radically different environments. One group at the Guru Jambheshwar University of Science and Technology is tackling this challenge in rice. This group expressed an Arabidopsis transcription factor known as Circadian Clock Associated1 (CCA1) under the Timing Of Cab Expression 1 (TOC1) promoter, which are both part of the circadian clock machinery in Arabidopsis. They found that overexpression of the CCA1 in rice had negative results, while repressing it caused positive changes to plant morphology. The researchers used RNAi, which is a biological process where small fragments of RNA are used by the cell to target complementary mRNA for destruction, thus silencing expression of the encoded protein. By comparing RNAi constructs based off of three different parts of the CCA1 gene for silencing the gene expression, they found that the RNAi derived from the 3’-terminal end of the CCA1 gene had the best impact on plant morphology (13). This study is an important first step towards unlocking the power of using circadian clock genes to breed plants better adapted to a changing environment.
One new strategy being considered is a CRISPR/Cas9 genome editing method that could be used to quickly develop improved crop varieties without transgenes. CRISPR/Cas9 can introduce specific changes into a plant genome without being limited by existing variation. Applying this method, scientists will be able to stack multiple edits into a plant within a single generation, resulting in transgene-free progeny. One benefit of this method is that it may allow for more complex changes to polygenetic traits or signaling pathways. For example, this could be helpful for targeting complex plant stress response pathways. This technology is currently limited by the availability of annotated reference genome sequences for plants other than Arabidopsis. Scheben et al. suggest that taking a genomics-based approach would allow for a comparison of species-wide genome diversity, making differences in copy-number visible and thus available for editing. While the authors suggest that this method creates plants that are indistinguishable from those created through natural breeding and random mutations, bans against genetically modified crops may target methodologies rather than the final result (14).
Conclusion
Currently implemented genetically engineered crops, have been shown, through years of testing and trials to be at least as safe, both towards the environment and in terms of human health, as naturally bred varieties. While new transgenic lines must be screened and tested on a case-by-case basis, the overall benefits of this technology make it an important tool that may be necessary to confront upcoming challenges to agriculture. Climate change and population growth are putting steep demands on crops to survive in more hostile environments while also producing higher yields. Current efforts are focusing on vital crops, such as rice, corn, wheat, and fruits, to create drought-tolerant, heat-tolerant, and yield-optimized plants.
References
- “World Population Clock: 7.7 Billion People (2019) – Worldometers.” n.d. Accessed November 18, 2019. https://www.worldometers.info/world-population/.
- Ronald, Pamela. 2011. “Plant Genetics, Sustainable Agriculture and Global Food Security.” Genetics; Bethesda 188 (1): 11–20.
- Mendelsohn, Mike, John Kough, Zigfridais Vaituzis, and Keith Matthews. 2003. “Are Bt Crops Safe?” Nature Biotechnology 21 (9): 1003–9. https://doi.org/10.1038/nbt0903-1003.
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