BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: light

Why are Blueberries Blue?

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On March 8, 2024

In Student Post

Have you ever wondered how certain fruits are such vibrant colors? Scientists globally have also pondered such characteristics. Some people think that objects obtain their colors by simply having the pigment inside. However, how our eyes perceive color is much more complicated than simply seeing the pigmentation.

Recently, research has been conducted on the color of blueberries. Blueberries are considered to be a “bloom” fruit, in that it has an epicuticular wax layer and dark pigmentation. This color does not come from smushing the fruit and watching the juice emerge, which led researchers to wonder where exactly it does come from. Researchers have discovered that blueberries are covered by a thin, waxy coating that is two microns thick. The researchers discovered this by removing the waxy layer and recrystallizing it to view the particles within the layer itself.

Within this layer, there are scattered particles in a random crystalline structure that reflect blue and UV light. Photons of light have certain pigments, and only a few of which are visible to humans. The photo below depicts which light is visible to humans. It is also notable that the pigment in blueberries reflects UV light, which is visible to birds.

FIO117: Figure 8.1

This directly relates to our AP Bio Photosynthesis Unit. In this unit we learned the reason why leaves are green. This is because leaves contain certain pigments (one being chlorophyll a) that absorb all wavelengths of light except for green, which is reflected.

Additionally, we learned in AP Bio that leaves are surrounded by a non-polar, waxy substance. This is the same on blueberries. It is interesting that learn that water will not easily penetrate through the skin of leaves as well as certain fruits due to the repulsion of non-polar and polar substances.

Do you know of any other epicuticular fruits? Can we investigate their pigmentation as well?

The Fluorescent Frontier: Glow in the Dark Proteins in Disease Research

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On April 23, 2023

In Student Post

We all know that although science is improving rapidly on a global scale, diagnostic tests for diseases remain sensitive and require complicated techniques. One evident example is the tests for COVID-19. This complexity can range from their preparation to an interpretation of their results. However, recent research from the American Chemical Society has developed a method that is able to analyze viral or infected nucleic acids in less than 30 minutes and in just one step. This is all due to “glow in the dark” proteins.

Bioluminescence is a scientific phenomenon that powers many animals: a firefly’s flash, an anglerfish’s glowing head, and even phytoplankton’s blue color.  Here a chemical reaction occurs, involving the luciferase protein. This protein essentially causes the “glow in the dark” effect. The protein is incorporated into sensors which emit a light when a target is located. Although the simplicity of these sensors is idyllic for clinical diagnostic testing, they still lack the sensitivity

One solution to this problem is presented by a particular gene editing technique: CRISPR. The Broad Institute defines CRISPR as; Clustered Regularly Interspaced Short Palindromic Repeats. It is essentially an efficient and customizable alternative to other existing genome editing tools. With this new technique, Maarten Merkx and his coworkers wished to use CRISPR-connected proteins while combining them with a bioluminescence form whose glow could be seen by humans, through a digital camera for example.

CRISPR CAS9 technology

To ensure that there was an ample amount of DNA or RNA to analyze, they used a technique known as Recombinase Polymerase Amplification, or RPA. This is a simple method which works continuously at a temperature of 100 F. With this  two CRISPR proteins specific for different parts of a viral genome each have a different fragment of luciferase attached. In other words, the new treatment known as LUNAS (Luminescent Nucleic Acid Sensor), takes two CRISPR proteins for different parts of a viral genome and has a distinct fragment of luciferase added to each.

Moreover, if one specific viral genome that the researchers were testing was present, the two CRISPR proteins would bind to the targeted nucleic acid sequence. This would allow them to come together and promote the full luciferase protein to form and glow. Additionally, to account for the luciferase being depleted, the researchers used a control reaction which turned green. In the event of a positive viral detection the color would change from green to blue. To prove the validity of this method, the researchers tested LUNAS on clinical samples of nasal swabs testing COVID-19. The method successfully detected the virus in less than 20 minutes, even at low concentrations. With this, the LUNAS method holds great potential in detecting other viruses in a concise and efficient manner.

Zika-chain-colored

To connect to our AP Bio class, we learned about how specific proteins code for specific actions or results in our bodies. At their tertiary and quaternary structures, proteins have a myriad of functions ranging from acting as a receptor to interacting with an enzyme. This parallels with the luciferase’s specific function of creating a glow affect. Additionally we learned about cell communication and how interaction with a receptor would result, or cause a specific occurrence. This connects to luciferase’s binding to its sensor, causing the glow affect. This cell communication also connects to the two CRISPR proteins attaching to a specific nucleid acid sequence. If the nucleid acid holds the viral genome and the luciferase, it would connect and form a glow response – a direct example of intercellular communication. Continually, we learned about DNA manipulation and alteration and how segments can be added in, substituted, or even removed. This occurs in CRISPR gene editing’s nature as a genome editing tool. It exemplifies all these manipulations to both DNA and RNA. We also learned about ideal protein function at a variety of temperatures, pHs, and environmental settings. This idyllic setting in seen in RPA’s function at a continuous 100 F.

To close, I feel that the use of luciferase, or “glow in the dark” proteins fronts an entirely new way of combating diseases and supporting disease identification. It would provide a new way for doctors and scientists to diagnose patients in a time efficient manner. And frankly, the idea of being diagnosed by something “glow in the dark” is entirely lightening and provides some relief to the gravity of the situation. I invite any and all comments regarding this specific method of disease identification or any other relevant discussion points.

Leading Science with Light

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On March 8, 2021

In Student Post

Emmett Chappelle

Emmett Chappelle: The father of Bioluminescence

Emmett Chappelle was a African American Scientist and one who contributed greatly to Medicine, Philanthropy, and Astrochemistry. Chapelle was born on October 24, 1925 in Phoenix, Arizona where he grew up to attend Phoenix College. During his time at Phoenix college, he received an Associate’s Degree in electrical engineering and then a Bachelor’s of Science in biology at the University of California. Following, Emmett Chappelle taught biochemistry at Meharry Medical College. He received many offers for his graduate studies which he completed for his Master’s Degree at the University of Washington. Continuing his studies, Chappelle earned a Ph.D at Stanford University for 4 years before leaving for a research position at the Research Institute for Advanced Studies in Maryland. After years of hard work, he moved on to work at NASA before moving on to work at the Goddard Space Flight.

While at NASA, where Chappelle worked as a Exobiologist and Astrochemist, he made several discoveries. Perhaps the most important aspect of his work in the field of biology was his exploration of how light is given off by different organisms. Chappelle learned that certain chemicals give off light when mixed with living cells as long as adenosine triphosphate is present, and use this finding to detect bacteria in various samples, including bodily fluids, water, and other foods. Chappelle used this knowledge to develop a means to determine the health of plants. By measuring the amount of fluorescents emitted by plants in a forest, he was able to determine the amount of photosynthesis occurring within that forest. Chappelle’s study of the enzymes luciferin and luciferase, used by fireflies, to make their cells glow paved the path for many current scientists who still use these chemicals as florescent tags to see cancer cells.

firefly 8823 | common eastern (USA) firefly - photinus pyral… | Flickr

The glow created by Luciferin and Luciferase

Chappelle was inducted into the National Inventors Hall of Fame for his discoveries related to bioluminescence and the important roles they have played in many fields of science. Aside from his recognition for his scientific discoveries that earned him 14 US patents, Chappelle was also respected for his service in the United States Army and for the time he spent mentoring minority high school and college students. Although he passed away in October of 2019, Chappelle will long be remembered for his many contributions to science.

 

 

 

 

“What Does Light Taste Like?” I Don’t Know, Ask A Nematode.

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On November 28, 2016

In Student Post

csiro_scienceimage_2818_group_of_nematodes

by Entomology on scienceimage.csiro.au

The vision of light is a beautiful blessing brought to us by our sight receptor cells. Since the sight of light is so great, the taste of it must be even better. Though we don’t know the taste of light, there may be a very tiny someone who does, the nematode. In the article Tasting Light: New type of photoreceptor is 50 times more efficient than the human eye, published on sciencedaily.com, it states that, at the University of Michigan, researchers have discovered a new photoreceptor amidst a bunch of taste receptor cells in nematodes and other invertebrates. This new receptor is called, LITE-1. Because of the receptor’s unusual location, it is believed that these animals have an ability to taste light. New studies have also shown that LITE-1 is no average photoreceptor.

LITR-1 was discovered in nematodes, which are eyeless roundworms only measuring about a millimeter in length. You might be thinking, “Nematodes don’t have eyes. So why would they need photoreceptors?” Shawn Xu, a senior study author who has a lab at University of Michigan Life Sciences Institute, where he is also a faculty member, demonstrated in his lab that even though nematodes are  eyeless, they still move away from flashes of light. The purpose of photoreceptors is to transform light into a signal that is usable for the body. This fact leads scientists to believe that it’s possible for that the roundworm uses this photoreceptor, located among its taste receptors, so that it can convert light into something that the worm can taste in order to perceive it. Xu also says that “LITE-1 actually comes from a family of taste receptor proteins first discovered in insects.”

Though these nematodes are extremely tiny, their peculiar LITE-1 photoreceptors are nothing to be looked over. Something that makes LITE-1 strange is that it has the astounding ability to absorb UVA and UVB light. Another unusual trait of LITE-1 is that it is unlike other photoreceptor proteins. Photoreceptors consist of two parts: a base protein and a chromophore. Breaking these two sections apart does not destroy all of their ability to function. However, LITE-1, when broken apart loses its ability to absorb light entirely.

LITE-1 also has a range possible future uses, such as being applied as a sunscreen that can absorb harmful rays or being used to promote the development light sensitivity in new types of cells. The future of LITE-1 shows great promise  and could open doors for the potential of other animals, besides invertebrates, to have a new and possibly delicious way of sensing light.

 

http://www.cell.com/cell/abstract/S0092-8674(16)31518-5

http://www.natureworldnews.com/articles/32317/20161119/animals-taste-light-new-type-photoreceptor-found-invertebrates.htm

 

 

Sensing neuronal activity with light

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On September 24, 2014

In Student Post

neurons

Researches have recently developed a tool that may help in mapping the neural networks of living organisms using light. Observing these electrical signals of neurons can lead to numerous advancements in our understanding of neural circuitry.

In a collaborative study between Viviana Gradinaru, Frances Arnold and Barbara Dickinson, they developed a method to sense neuronal activity with light. These researchers used a protein named Archaerhodopsin (Arch) and exploited its light responsive qualities. They were able to optimize Arch through a process known as directed evolution. Using this method they created a variant of the Arch protein, called archer1 that acted as a voltage sensor under a red light and an inhibitor under a green light, while generating a light intensive enough to detect. When this protein acts as a voltage sensor it can show which neurons are active and synaptically connected and which aren’t under certain stimuli.

These researchers were able to test Archer1 in the worm C. elegans, which was chosen for its near transparent tissue that made it ideal for observing the luminescent protein. This was the first place they were able to observe the circuits of the neurons light up if they were expressed and dim down if they were repressed. For future studies they hope to make Archer1 bright enough to be detected through opaque tissue and accurate enough to detect voltage changed in more complex, behaving mammals. This study can prove to help us in our understanding of neural networks.

Original papers:

http://www.pnas.org/content/111/36/13034

http://www.nature.com/ncomms/2014/140915/ncomms5894/full/ncomms5894.html  (You can only read abstracts; you have to pay to read the full text)

Dr. Light

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On November 18, 2013

In Student Post

Cardiac arrhythmia is a problem with the rate of heart beat that currently affects 4 million Americans. During arrhythmia, the heart may beat too fast, too slow, or have an obvious irregular rhythm. In some cases, this heart condition may be life-threatening with the ability to damage the brain, heart, and other organs due to the lack of blood flow.

Oscar Abilez, a cardiovascular physician at Stanford University has developed the solution to this condition: light. With his team, he is working to create a new biological pacemaker that is able to control the heart with light. The first phase of his research involves optogenetics. This uses techniques from both optics and genetics to control the activity of individual neurons in living tissue. In 2002, German scientists were able to isolate the genes for the proteins called opsins. Before this discovery, algae and few other organisms were the only know carriers of light sensitive cells. These opsins, however, are responsible for cells’ light sensitivity in humans and modify the genetic code of other cells so that they, too, would produce these opsins. 

The next phase of his research involves stem cells. Oscar Abilez hopes to convert the stem cells light-sensitive cardiomyocytes from a person who is suffering from this condition.  These cells that make up the muscle tissue in the heart  would be able to be “grafted” onto a person’s heart. This would then ideally carry out Abilez’s vision, which he hopes will be achieved in the next decade or so, allowing physicians to control the whole heart’s rhythm using light.VPC_1

Jet Lag Prevention

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On January 7, 2013

In Student Post

Jet lag can be a difficult issue to deal with when traveling across time zones and no one wants to be drowsy while on their vacation. Jet Lag is caused when your circadian rhythm  is out of sync with the environment you are in. Circadian rhythm is the internal, biological clock that drive changes within most organisms. Normally, your circadian rhythm is controlled by several factors such as exercise and melatonin levels but the most prevalent factor is light exposure. Light exposure can cause phase shifts which are changes in your circadian rhythm. With this information, scientist have shown in a recent study that you can follow four simple steps to minimize jet lag:

1. Estimate when your body temperature reaches a minimum. If sleeping 7 or fewer hours per night, assume this is 2 hours before your usual wake time. If sleeping more, assume this is 3 hours before your usual wake time.

2. Determine whether you need to advance or delay your circadian rhythms. If you are flying east (to a later time zone), such as from Los Angeles to New York, you will need to phase advance. Otherwise, if you are flying west, you will need to phase delay.

3. If you need to phase advance, avoid light for 4 hours before your body temperature minimum, and seek light for 4 hours after it. Otherwise, do the opposite.

4. Shift your estimated body temperature minimum by one hour earlier per day if phase advancing, or one and a half hours later per day if phase delaying.

Photo taken by Mary Lane

 

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