By Jenna Everard
The origin and evolution of life as we know it has long been a topic of debate within the scientific community. At the center of that puzzle lies deoxyribonucleic acid, or DNA — the molecule of inheritance that defines life, determining the structures, functions, and capabilities of various organisms.
DNA is composed of four nitrogenous bases, Adenine (A), Thymine (T), Cytosine (C), and Guanine (G), all of which are attached to a molecular backbone of alternating deoxyribose sugars and phosphate groups. In order to form the notorious double helix structure of DNA, a structure that looks like a twisted ladder, hydrogen bonds form between the bases, joining the two backbones together. The rules for these bond formations are relatively strict: C always pairs with G and A always pairs with T. In this manner, the genetic code for life is formed, with different sequences of bases forming different genes that encode different proteins, which determine the various features and functions of living creatures.
As the capabilities of genetic technologies grow, genetic engineering has become a popular approach used for the development of treatments for diseases such as cancer. Traditionally, genetic engineering involves the alteration of genes, such as inserting different ones, removing undesired ones, or changing their expression. While these methods all alter pre-existing DNA, new approaches have begun to explore creating novel genes by adding letters to the DNA alphabet.
In 1962, Alexander Rich first proposed the idea of unnatural base pairs (UBPs), or bases of DNA synthesized in a lab. However, it was not until 2009 that Floyd Romesberg’s lab created the first UBP, labeled X and Y, that could be efficiently amplified and transcribed into proteins. In 2014, Romesberg co-founded Synthorx, a company that strives to use an expanded DNA alphabet made up of six bases rather than the traditional four to develop novel proteins, which they call Synthorins. With their proprietary semi-synthetic bacteria, they are capable of efficiently producing these proteins, and they aim to use them to provide better treatments for cancer and autoimmune disorders.
Synthorx’s first product, THOR-707, has recently been approved for its first in-human clinical trials. It will be both the first Synthorin-based product designed and entered in clinics. THOR-707 is predicted to be an efficient tumor suppressor as it prevents the binding of certain signalling molecules, which increases the activity of cells linked with favorable cancer prognoses while decreasing the activity of cells that suppress immune responses.
Other scientists have followed in Romesberg’s direction of creating UBPs, but not necessarily with the same goals in mind. Just last year, Dr. Steven Benner created an expanded DNA alphabet with 8 letters! In his alphabet, in addition to the normal base pairs, there are 4 UBP’s that form two additional base pairs. His new base pairs fit neatly among normal base pairs and can be easily read by enzymes to make RNA, the molecule that precedes protein formation. In addition to its potential use in diagnosing and treating diseases, Benner’s research to develop his “Hachimoji DNA” begins to hypothesize types of molecules that might sustain extraterrestrial life forms.
Both Romesberg and Benner have achieved remarkable discoveries, expanding on what we have previously considered the fundamental code for life in order to explore possibilities of new lifeforms. Though there is a wide range of useful applications for their respective DNA alphabets, all seem to probe at the basic question: why did life evolve the way that it did? While many have assumed for centuries that a part of the explanation was that the four natural bases of DNA were the only ones that functioned properly in genes, Romesberg and Benner have shown that this is not the case. Their research reveals DNA could have had more bases, but doesn’t, and we are still wondering why.
Demystifying the Origins of Modern Elements: How Astrochemistry Offers Insight About the Nature of Atoms and Molecules
By Victoria Comunale
The massive expanse of space can bring wonder to just about anyone with a simple gaze upward. One might find themselves overwhelmed by the sheer number of stars and planets that are found against the backdrop of the seemingly boundless darkness. But the cosmos offers up so much more than a beautiful scene to look at—it is a mystery, or more appropriately, a puzzle, with clues just waiting to be pieced together. What makes up this enigmatic expanse? What compounds that are incredibly rare on earth might be as abundant as oxygen is to us? The study of such enigmatic molecules and chemical interactions in space, known as astrochemistry, promises to offer insightful clues about the nature of atoms and molecules.
Immediately following the Big Bang, the grand catalyst for the beginning of the universe, activity was rampant. With the collisions of protons and neutrons, traces of hydrogen, helium, and lithium began to form, but all without electrons. Helium was the first to form complete atoms with protons, neutrons, and electrons. Hydrogen and the small amounts of lithium, however, had difficulty acquiring electrons by themselves. So, although helium is a stable noble gas, hydrogen nuclei kept colliding into helium, trying to get a share of its electrons. Through these collisions, the very first molecule of sustained abundance was formed through a chemical bond between helium and hydrogen. This molecule was called helium hydride or helonium (HeH+). This unlikely union of helium and hydrogen was surprising since, as a noble gas, helium has a full valence shell and has no need to share electrons. Yet in the environment of early space, it was the only way hydrogen was able to access electrons.
While HeH+ can be synthesized in laboratory environments, its existence in nature was, until recently, still an important missing piece to the theory. In a recent study, a group of researchers at Max-Planck Institute for Radio Astronomy in Germany confirmed the existence of HeH+ in interstellar space through studying a planetary nebula. Due to advances in spectroscopy, one of the techniques used to determine the existence of HeH+, the search for this molecule that has been eluding scientists has finally concluded in success.
These researchers were prompted to study planetary nebula NGC 7027, which proved to be a model candidate in their search for HeH+. They were specifically interested in focusing on a thin layer in the star where the He+ and H+ layers overlapped. Previous studies of this layer did not prove to be useful because observations with the Infrared Space Obserbatory’s Long Wavelength Spectrometer were inconclusive due to the imprecision of the technology. Yet with the deployment of the new spectrometer called the German Receiver for Astronomy at Terahertz Frequencies (GREAT), the researchers were finally able to prove the existence of HeH+ in nature.
Now HeH+ joins the ranks of the more than 200 molecules that scientists have been able to detect in space. Some of these include water and formaldehyde, chemicals that are ubiquitous here on earth, yet others are more bizarre and only naturally exist outside of earth, such as HeH+.
The corroboration that HeH+ can be formed in space supports and places further credibility on pathways taken for the formation of other molecules in space. For example, the destruction of HeH+ creates a path for the formation of molecular hydrogen. Astrochemistry, although seemingly innocuous, offers us a different avenue with which to explore how atoms interact and how bonding occurs in a strange, new environment. Ultimately, the exploration of this field can help answer questions that have plagued philosophers and scientists for centuries, such as how the Earth and the solar system came to be and how, ultimately, life was able to form.
By Elaine Zhu
With the World Health Organization announcing a global pandemic and schools and large events being canceled across the world, coronavirus, or more formally known as “2019 novel coronavirus” and abbreviated as COVID-19, has been in the global spotlight since the beginning of 2020. COVID-19 is the result of one of a family of viruses called coronaviruses, which are common in various animal species, such as cattle, bats, or camels. Usually, coronaviruses from these species do not infect humans, but in special cases can be spread to humans and lead to a fatal disease. Scientists suspect that COVID-19 originated in a bat and then was transmitted to a pangolin before being spread to a human. This chain of transmission is usually quite rare, as it would need all three hosts to be in the same vicinity. The suspected source of the virus is a wet market in Wuhan, China, where different species of animals are sold for consumption, allowing for the opportunity of transmission to occur. After the initial transmission of COVID-19 to patient zero, the virus has spread to over one million people worldwide and has caused over 53,000 deaths as of April 2020.
An individual usually contracts coronavirus through physical contact with an infected person; respiratory secretions emitting from the coughs or sneezes of an infected person; or coming into contact with the virus on a surface and then touching their eyes, nose, or mouth. After this occurs, the virus can enter the body and begin the process of infection. Generally, a virus is a capsule of genetic material surrounded by a protein shell called the capsid. Spike proteins line the outside of the capsid and then once they come into contact with a cell, bind to human cell receptors, allowing the virus to enter the cell and to hijack it. In COVID-19’s case, the virus binds to the angiotensin-converting enzyme 2 (ACE2) receptor to enter the cell and attacks the lungs, intestines, or spleen in victims. When the virus hijacks the human cell, it uses the cell’s inner mechanisms and the genetic material of the virus to start mass-producing replicas of the virus until it overtakes that cell and destroys it. More virus particles are released in the body and the virus goes on to continue to infect more cells exponentially.
Once the human body detects that a virus has hijacked cells of the body, and triggers an immune response and sends immune cells towards the infection. This immune response triggers the symptoms that are characteristic of COVID-19 infection. Common symptoms include a sore throat, fever, and dry cough. In healthy individuals, the immune system will start to produce specific antibodies, which can identify and neutralize a foreign pathogen. However, COVID-19 cells can infect these immune cells and cause an overdrive in the immune system’s response. In severe cases or in people who are immunocompromised, neutrophils and killer T cells start to destroy both healthy and compromised cells, and soon even healthy tissue starts to get damaged, especially in the lungs. The epithelial cells of the lungs, which comprise its protective lining, can become extremely damaged, leaving the COVID-19 patients more susceptible to outside bacteria that can cause harmful complications or additional infections like pneumonia. With foreign, opportunistic bacteria taking advantage of the weakened and distracted immune system, the body slowly begins to be unable to fight off these bacteria, ultimately leading to organ failure or even death.
To reiterate, the most severe cases of COVID-19 usually occur in the immunocompromised or in the elderly and not in healthy individuals with strong immune systems, though a bulk of the younger population is still at risk. Because a vaccine has yet to be approved for the public’s use, we all must take the appropriate measures to prevent the spread of COVID-19. The Centers for Disease Control and Prevention recommend that we all avoid close contact with people who are sick, stay home as much as possible, and keep a 6-foot distance from others, otherwise known as social distancing. They also recommend that we wash our hands often with soap and water for at least twenty seconds, or use a hand sanitizer that has at least 60% alcohol. In order to contain the spread of COVID-19, we must do all that we can to help the most susceptible members of society and to look out for each other.
By Boyuan Chen
“Try it yourself, just once,” said a voice, low and hoarse.
It was Grandma, smiling.
Grandma, a traditional Chinese countrywoman, always preferred to use the wastewater left from boiling noodles to wash dishes, a practice I have long held doubts about.
As a chemistry enthusiast, I knew by heart that floury water contains mostly starch, a polysaccharide macromolecule that does not qualify as a surfactant, the class of chemicals that common dish soap contains. Generally, dish soap works by the amphiphilicity of the surfactant molecules; this chemical property—having a head attracted to water and a tail attracted to oil—allows these molecules to bind residual oil to running water. As a result, a stable mixture of water and oil, or an emulsion, is formed, further enabling water to wash away the residual oil. How on earth, then, can floury water serve as the role of dish soap?
Figure 1. The molecular structure of a common molecular surfactant, sodium laurylsulfonate (A), and its arrangement around oil droplets in water (B). (C) is what a starch molecule is made of.
Grandma beamed at me understandingly, anticipating my qualms. "It's ancient wisdom,” she chuckled. “It works."
This was Grandma’s habitual answer to my scruples, but sincere as it was, my doubts remained So I started washing. Dipping dishes into the floury water, I wanted to prove my knowledge of chemistry with my own hands. Yet, I was astonished—the thick oil miraculously vanished, leaving the porcelain clean as new. I was as ashamed as I was shocked. Later, I also learned that some families also use the wastewater left from rinsing rice to wash dishes, so starch surely works! But the question remains: how?
After some research, I found out that in addition to molecular surfactants, there exists yet another type of material that may bind water and oil together: Pickering emulsifiers. In these cases, particles with sizes ranging from hundreds of nanometers to a few micrometers function as stabilizers in the water-oil mixture. These particles, which also exhibit both water and oil affinity, may spontaneously attach to the water-oil interface due to surface energy (the same reason that water striders can walk on the surface of water). Thus, a barrier around each oil droplet is formed, allowing them to mix with water as shown in Figure 2.
Figure 2. The diagram of Pickering emulsion.
Natural starch happens to be composed of such particles. Starch is naturally produced and stored in plant cells as small granules ranging from 1 to 100 micrometers in diameter. This fact precisely explains why rice-rinsing water works as a cleaning agent. Rice starch granules have a volume moment mean diameter (the technical term for diameter in fluid mechanics and colloidal science) of 4.61μm, which would easily fall into the size range of Pickering emulsifiers. Therefore, native rice starch can serve as a very efficient emulsifier.
Things only get more interesting when it comes to noodle-cooking water, the one Grandma uses. Wheat starch granules have a volume moment mean diameter of 22.88μm, which would be way too large to qualify as a Pickering emulsifier. Upon heating, however, wheat starch granules start to swell and become sticky. In the floury water, the swollen wheat starch granules acquire a larger surface area, which increases the interfacial force on each granule and decreases density, lessening the destabilizing effect of gravity. The combined result of both factors is a stable emulsion.
Figure 3. Emulsions stabilized by rice starch and wheat starch.
This seemingly magical practice not only challenges our preexisting notions in science, but also holds significant implications for an eco-friendly alternative to traditional surfactants. Rice-rinsing water and floury noodle water are readily available in kitchens and in factories yet are usually disposed of carelessly by those unaware of its potential. They are completely sustainable and biodegradable, which means that starch-based detergents would not only be cheaper but also greener than the non-biodegradable detergents based on molecular surfactants, the production of which also relies on the petrol industry. Beyond cleaning dishes, they may also replace traditional surfactants in personal care products like body wash, shampoo, and certain emulsion-based cosmetics. Grandma’s cleaning formula works, after all.
By Alice Sardarian
In 1999, James Harrison was awarded the Medal of the Order of Australia for saving millions of children’s lives through his blood plasma donations. Harrison, also known as the “man with the golden arm,” has donated plasma almost every week for the past 60 years, spanning the entire range of donor ages permitted by the Australian Red Cross Blood Service. Plasma is a component of blood that contains nutrients, ions, proteins, and more, not including platelets, leukocytes, and erythrocytes. Plasma donation involves continuously withdrawing blood, separating the red blood cells from the plasma, and then returning the red blood cells back to the donor. According to the Red Cross, plasma may be donated much more frequently than whole blood: donors must wait only 7 days for plasma as opposed to between 8 and 16 weeks for whole blood.
Harrison is amongst a rare group of individuals who have Rho(D) immune globulin present in high concentrations within their plasma. Rho(D), also known as anti-D, is an antibody that results from Rh factor incompatibility. Rh factors are proteins found on blood cell surfaces that correlate to the positive and negative qualities assigned to ABO blood types. When blood cells with Rh factor (+) come into contact with blood cells without it (-), Rh incompatibility occurs and leads to hemolysis, the destruction of Rh factor positive red blood cells. Rh incompatibility, or Rhesus disease, occurs in mothers who are Rh-negative and are pregnant, usually for the second time, with Rh-positive babies. As a result of contact with fetal blood in her first pregnancy, the mother develops antibodies to the Rh factor, such that pregnancy with another Rh-positive baby could lead to the destruction of fetal blood cells as a result of the mother’s immune response. Rhesus disease occurs in approximately 276 of 100,000 births globally, with over 50% of cases remaining untreated and leading to newborn brain damage and more frequently, death.
Rho(D) and other antibodies are a component of the immune system and serve to alert the body of foreign entities in order to prevent harm and mount an attack against the “invader.” In instances when maternal blood comes into contact with fetal blood (fetomaternal hemorrhage)—such as during delivery, obstetric procedures like amniocentesis, and after abdominal trauma—the maternal red blood cells detect fetal red blood cells with Rh factors as foreign, and the maternal immune system consequently proceeds to produce antibodies, causing hemolytic anemia in the fetus or newborn, depending on the time of blood exchange. Anemia occurs as a result of red blood cell destruction and an inability to replace them at an effective rate. As a result, the babies are left with insufficient oxygen-carrying capacity and, in severe cases, fatal oxygen deprivation.
This trauma and suffering can be averted by a vaccine developed in part by the contributions of James Harrison and other similarly generous donors. Rho(D) immune globulin was first developed at Columbia University Irving Medical Center, with the first successful treatment occurring in 1968. A product derived from human plasma, the immune globulin contains antibodies to the D antigen in Rh positive individuals. Functionally, administration of the medicine in a vaccine form suppresses the maternal immune response to Rh positive blood, and is consequently protective when given to a mother prior to (if possible) and after fetomaternal hemorrhage, both prenatally and postnatally. A side effect to the baby may include an allergic reaction; however, the benefits of the drug are overwhelmingly positive, halting fetal blood cell destruction and reducing the levels of bilirubin, a byproduct of this process which can put a newborn at risk of brain damage.
Australia was the first nation to establish a donor program within its borders for the anti-D blood type. It is unclear how certain individuals, like Harrison, have this naturally-occurring blood type. Scientists believe it may be due to an Rh positive blood transfusion they may have received as children, which potentially triggered sensitization, prompting the body to begin producing Rho(D). Harrison received transfusions during an extensive surgery, after which he pledged to donate blood in order to give back to those that saved his life with their donations. Since donors are hard to come by, Rh negative men have actually volunteered to receive Rh positive blood transfusions, in order to produce the rare and healing Rho(D) antibody.
While donors like Harrison have saved many lives and contributed to a major milestone in maternal healthcare, as celebrated at Columbia University Irving School of Medicine’s 50th anniversary of the vaccine’s approval by the FDA, this vaccine is not widely accessible to those in less developed countries. Even while the vaccine is on the World Health Organization’s 21st List of Essential Medicines, rhesus disease still impacts over 150,000 children, primarily in sub-Saharan Africa and South Asia. Greater efforts must be made to ensure global prophylaxis and prevention. Several scientists, including pathologist Dr. Steven Spitalnik of the Columbia Department of Pathology and Cell Biology, recently published a call-to-action in which they highlighted the importance of drug affordability as well as Rh and ABO blood typing during pregnancy, which is rarely completed in those nations suffering the highest mortality rates. Early detection of Rh incompatibility and immediate treatment with Anti-D can prevent alloimmunization in 90% of all cases. Alloimmunization refers to the immune response stimulated by detection of foreign antigens, such as the fetal Rh factor. The publication also notes that the vaccine is not available in China due to governmental drug importation regulations.
Within the United States, there are no established means of ensuring compliance and evaluating the effectiveness of Rho(D) immune globulin administration. A study conducted amongst practicing Obstetrics and Gynecology physicians found that most were well-informed of the treatment practices regarding prophylactic measures, but did not know how to calculate the appropriate dosages when potential cases of fetomaternal hemorrhage arise. Better education and emphasis would certainly improve this knowledge gap, though in the last few months, online calculators have been developed to reduce error rates and improve precision in transfusion medicine; amongst the calculators used by millions worldwide, one was curated specifically for Rho (D) immune globulin dosages.
Remarkably, Rho(D) immune globulin may also be used to treat immune thrombocytopenia, an autoimmune blood disorder, frequently developed after viral infections that range from the flu to HIV. Without treatment, individuals suffer from extensive bleeding as a result of low-platelet count and diminished clotting ability. It is evident that Rho(D) is versatile and effective, providing life-saving measures. With improved access, proper education, and routine blood typing across the globe, rhesus disease morbidity rates will continue to decline, and the full potential of the discovery that resulted in part from James Harrison’s lifetime of donations, will be realized. Mothers and their children will be allowed to live happy and healthy lives, free from the burdens of a completely preventable disease.
By Elifsu Gencer
The joy I feel when I spot a perfect little snowflake on my coat sleeve is truly unmatched. Having been taught that every snowflake is unique, I marvel at the level of detail I can see with my bare eyes on something so small in size. I can’t help but think, though, that it does kind of look like every other snowflake that I’ve examined. How do we know that each snowflake is actually unique? And what does “unique” really mean?
The notion that no two snowflakes are alike was introduced by Wilson Bentley in his paper A Study of Snow Crystals, published in 1898. Instead of “snowflakes,” Bentley used the term “snow crystals” to clarify his take on the difference between the two. While a snow crystal is strictly a single crystal of ice, snowflakes may represent a single snow crystal or a “cluster” of snow crystals. Bentley’s fascination with nature, especially the structure of snowflakes, started during his childhood while he lived on his family farm in Vermont, where annual snowfall reached 120 inches. After being gifted a microscope for his fifteenth birthday, Bentley attempted to capture the structure of snowflakes by inspecting them at the microscopic level. Noting the difficulty in studying the structures given that they “ speedily disappeared,” he turned his attention to successfully developing a method in photographing snowflakes.
Bentley cleverly attached a camera to his microscope, and after collecting snowflakes on black velvet, he photographed the snowflakes on pre-chilled glass plates outdoors to prolong the integrity of the snowflakes. After many failed attempts, he successfully photographed his first snowflake in January 1885 at just 20 years old. Bentley eventually accumulated an archive of over 5,000 photographs over the course of his life. His research garnered nationwide interest and slides of his snowflake photographs were sold across the United States. Additionally, jewelers began to copy the snowflake designs in their works. The stunning geometric patterns of snowflakes were also incorporated in the design of wallpapers, textiles, and stained glass windows.
It is important to note that snowflakes are specifically unique at the molecular level based on their general shape and structure. The current widely accepted classification model includes 35 categories, composed of typical shapes, such as stellar dendrites, as well as unexpected shapes, including 12-sided snowflakes composed of two six-branched crystals with one rotated 30 degrees relative to the other.
Snowflakes are formed when water vapor condenses into water droplets on dust particles in the air—aggregates of these suspended water droplets form what we see as clouds. When the clouds begin to cool, the water vapor starts freezing around the dust particles. These heavier droplets fall toward Earth, still growing in size as more water vapor continues to condense and freeze. Ultimately, snowflake formation depends on the temperature and humidity of the air. While the exact reasons for why these conditions result in different shapes is not fully understood, according to Dr. Kenneth G. Libbrecht, a physicist at California Institute of Technology, more intricate snowflake patterns are formed when in humid conditions, while simpler shapes are formed in drier conditions. He also found that snowflakes formed in temperatures below -22 ℃ consisted of simple crystal plates and columns, while those formed in warmer temperatures contained complex branching patterns. Given the impactful influences of factors such as temperature, there are scientists working on developing equations predicting how a snow crystal will grow in certain environmental conditions.
Though many did not see the benefits of Bentley’s work at the time, the study of snowflakes can have many applications. For example, Dr. Libbrecht notes that the study of snowflakes can lead to a better understanding of self-assembly, a process in which disarranged molecules form well-defined structures. Self-assembly is especially important in biological systems, such as in the assembly of proteins to form quaternary structures or in the assembly of capsids containing viral DNA.
Despite their small size, snowflakes had a profound effect on Bentley and he paved the way to a greater understanding of atmospheric science. We honor him today with Jacqueline Briggs Martin’s Snowflake Bentley, a children’s picture book detailing his life story. Although Bentley tragically died of pneumonia at the age of 66 after walking six miles in a blizzard, his photographs remain a spectacle that we enjoy today.