marcochondria – BioQuakes

Author: marcochondria

Cas9/10

On March 24, 2022

Gene editing sounds to most like an intriguing opportunity at the very least, if not a groundbreaking advancement in human development, however it does not come without any flaw. We are not living in “Gattaca”quite yet to say the least. One of the most common gene editing processes, CRISPR, is equipped with a relatively predictable flaw in particular; an error taking place at the molecular level that results in the wrong genome being altered than what had been intended, therefore leading to potentially dangerous or life altering mutations in said gene. A team of specialized professionals at the University of Texas at Austin decided to revamp a significant component used for the CRISPR gene editing process. Their new version of Cas9 reduces the chances of the wrong genome being manipulated by thousands. This is a figurative unicorn of scientific discovery, it is groundbreaking on top of groundbreaking, it is cloth cut from the fabric of similar discoveries that have changed the course of human history and still – it is only the beginning.

When there is an error in the way the genomes are adjusted, it is a rather simple explanation as to how, and even simpler when describing how the new version of Cas9 can fix it. When the letters making up the DNA’s structure are incorrectly assembled or mismatched, causing a lack of stability in the structure of the DNA itself. Due to this, Cas9 is not capable of making the necessary adjustments to the DNA in order to properly execute the procedure. The new version of Cas9 is far more capable and strong, meaning that it can in fact execute the procedure.

Although this new Cas9 is an answer to a previously inherent setback to gene editing, it doesn’t come without its own respective setbacks. A primary caveat to the increased accuracy of this Cas9 is that it works at a much slower pace than Cas9 that is naturally occurring.

There is a self awareness that seeps through this accomplishment to the people that set it in motion. Kenneth Johnson, a professor at the University of Texas at Austin and co-author of the study even says that this newfound tool “could really be a game changer” when it comes to further use of gene editing among the public. It is truly a tremendous feat conquered by this group of experts in the field of genetic engineering.

Ultimately, further advancements in genetic editing could very well change the human race and the world as we know it so long as quality time and effort is put into it, as seen with this study. With the incentive of the potential advancement of human kind as a whole, its anyone’s guess as to what could one day be possible.

iDNA

By marcochondria

On March 20, 2022

In Student Post

DNA is often referred to as “storing genetic code” or “data”. Information of sorts. While this is true, it is a bit different from data when referring to it in layman’s terms; data is often associated with the internet and computers. However, the line creating this barrier of difference is becoming very blurred. A study at the Beckman Institute of Science and Technology claims that DNA and its double helical structure can be used to store anything; including virtual media.

Though DNA is microscopic in size, its ability to store information is colossal. According to Kasra Tabatabaei, a researcher who helped conduct the study, “Only one gram of DNA would be sufficient” to store the several petabytes of data that are created from the internet each day. To say that this is staggering would be terribly understated. Furthermore, DNA is quite durable. It has a longevity to it that is rivaled by few other mechanisms on the planet. The material can last for thousands of years without severe damage to its ability to store information as it’s supposed to. There is also little competition with DNA when it comes to abundance. Due to the fact that there is DNA present within each living thing, there is quite a lot, to say the least. This makes it a very sustainable source of storage, as the odds that there will be a shortage is extremely unlikely.

Of course DNA has a large capacity but it seems almost necessary to expand upon it in order for the material to truly be able to slay the informational beast that is the internet. DNA already has 4 naturally occurring chemicals; Adenine,Guanine, cytosine and Thymine, that allow for it to have such capacity. To allow for its capabilities to transcend adequacy, the researchers added seven artificial nucleases. To find which would work, they experimented with “77 different combinations of the 11 nucleotides”. This change expands DNA’s capabilities tremendously, as it opens doors for a much larger range of data that can be stored.

The internet is boundless. Where technology takes the human race next is still largely unknown. However, none of it can be done without data, and the future of data storage may be exactly where it started.

How We Can Potentially Manage The Overwhelming Amount of Carbon Dioxide Emissions That Destroy The Planet

By marcochondria

On February 25, 2022

In Student Post

Due to the annual trend of an increase in global carbon dioxide emissions, it has now manifested itself as something that exists in abundance. While it is of course a knee jerk reaction to look at the negative effects of this, whether it be in the long term or in the short term, potential benefits should not be completely discounted. Perhaps “benefits” is not the right word but more so… ability to capitalize on it. After all, just like any material on earth, carbon dioxide can quickly be seen as a resource rather than a waste product if applied to the proper endeavor. For example, Researchers at Lund University in Sweden found in a study that there is potential way to use solar power in order to convert carbon dioxide into fuel.

It is explained in simplest terms as a two step process. Initially, solar power is absorbed by panels, and using “ultra fast laser spectroscopy“, the researches are able to understand how to use said absorbed sun rays in order to convert carbon dioxide into fuel. Through this process, they learned that by adding a material that they had studied – covalent organic framework – the mechanism they created will be able to take in sunlight at a much more efficient rate than without it. In order to ensure that there would be no extra energy used, a catalytic complex was added to the covalent organic framework. The result of this strenuous, though short, process is the conversion of carbon dioxide to carbon monoxide.

There were other components that contributed to the result of this study as well. As explained by Kaibo Zheng, one of the researchers at Lund University who specializes in chemistry, “The conversion to carbon monoxide requires two electrons”. Due to this, it drove the researchers to see how they could access electrons with exceptional longevity and energy levels. Thus, further measures were taken, and it was found that photons with blue light were best at producing electrons with these preferred characteristics. Once these electrons were accessed, the covalent organic framework could then be charged with them so that they can properly execute their intended task.

While this study was performed on a small scale, the results of it allows for it to be done on a much larger, and potentially global stage. More often than not when it comes to innovation, the most significant obstacle is if the task can be done. With these results, we now know that it is, and that’s half the battle.

Pesticide Homicide

By marcochondria

On January 17, 2022

In Student Post

Typically what comes to mind as staples of a healthy diet for most people is an abundant amount of fruits and vegetables and while I agree with this and there seems to be nothing wrong with them on the surface…there kind of is. In fact the issue is precisely what’s on the surface. Some research done at the University of Queensland in Australia points to pesticide as a lurking contributor to one’s risk of developing chronic kidney disease (referred to in the article as “CKD”).

CKD essentially prevents the kidney’s ability to filter waste and it’s a gradual process. As it gets worse and the person suffering from CKD experiences renal failure, waste builds up to an amount that can simply not be handled by the body, and one can experience a laundry list of complications due to the illness including but not limited to irreversible damage to the kidneys, excessive fluid retention, and damage to the central nervous system.

The study was observed among over 41,000 participants (41,847 to be perfectly accurate) and utilized data from the USA National Health and and Nutrition Examination Survey. The results were alarming to say the least. According to the data collected, those exposed to higher amounts of the insecticide Malathion “had 25 percent higher risk of kidney dysfunction”. Dr. Richard Osbourne, an Associate Professor at the School of Public health claims that “Nearly one in 10 people in high income countries show signs of CKD”. As one can imagine, that fraction of the population adds up rather quickly, resulting in millions of people at risk of or suffering from CKD. It seems very plausible that Malathion is the culprit, especially considering that it is quite literally designed to kill other organisms.

Dr. Osbourne also points to “environmental contamination, pesticide residues, and herbal medicines potentially containing heavy metals” as other possible contributors to this correlation between the consumption of Malathion and CKD. It seems as though ultimately the main issue is foreign particles being in our food.

Washing produce has always been important and should be an absolute must if one is to expect to get the best that they possibly can out of their food. If not, they just may have a consequence for an unwanted accessory to their vegetables. Not the most desired dressing, I’d imagine.

Something’s In the Water

By marcochondria

On January 17, 2022

In Student Post

Global temperatures have been on the rise for generations now and this is no different for the UK and there are some quite interesting effects from it. The hotter temperatures may be bringing more people to the beaches despite the northern country not being known for sunny coasts however there is something else in the water that researchers from the University of Exeter couldn’t help but notice in their study.

What they found is not as cinematic as say a killer shark but they did find an organism, or rather organisms that are not typically found in their waters; two Vibrio bacteria. Vibrio rotiferianus and Vibrio jasicida have both “never been recorded in UK waters before”, and in a perfect world it would have stayed that way. Not only can the bacteria be harmful to other sea life but it can be harmful to humans as well. As written in the study. “Vibrio bacteria can cause gastroenteritis when eaten in raw or undercooked shellfish” and can even cause “skin infections”. Due to rising global temperatures, there has been a great increase in Vibrio infections in both humans and sea life.

Most simply put, as sea levels rise and the waters are warm enough for Vibrio bacteria to prosper, the bacteria will only grow. With this growth comes mutation and the emergence of new breeds from the same species of bacteria. This increases their genetic diversity and ultimately allows them to become a stronger species.

Not only can the bacteria be injected through seafood but also through sea water. If contaminated seawater were to enter one’s body through an open cavity, such as the mouth or an open wound, one runs the risk of being infected by the Vibrio bacteria.

While for now there is not an alarming amount of casualties due to the bacteria’s flourishing in the U.K, measures should be taken in order to make sure that never happens.

Catch Some Z’s

By marcochondria

On January 17, 2022

In Student Post

A study published by the University of Zurich displayed findings that are relatively unsurprising yet are still worth noting, these findings being that while students last year were largely learning at home, they were sleeping for a more adequate amount of time. Of course, while this is considered to be a positive result of less than desirable circumstances, it would be most ideal to attain these same benefits while avoiding the negatives.

There was a tremendous amount of baggage that came with this up-tick in sleep per night on average. The pandemic surging through Switzerland (where the study was done) and the rest of the world has been documented thoroughly, but on top of that due to the social isolation that came with the many lockdowns in order to combat the spread of the virus, many people including the teens saw a dramatic lack of satisfaction with their lives paired with a rise in anxiety and depression.

Although these findings were not made during the best circumstances for the greater whole of society, there was definitely something positive to take away from it, and not just COVID tests. According to the researchers in Zurich, students experienced an increase of up to “75 minutes more sleep per day” during lockdown while school was virtual. This could perhaps be due to the absence of a morning commute time and leaving certain household obligations that are typically done in the morning for later in the day, due to their consistent proximity to said obligations. Furthermore, the researchers noticed an increase in the student’s quality of life health-wise as well in certain areas. For example, due to a lack of vigor now that their academics are virtual and social gatherings became obsolete in the time of lockdown, caffeine and alcohol consumption rates dropped quite significantly. While this secondary positive effect is also great, it was not the focal point of the study and is currently not the focal point of this post. The amount of sleep students were getting as opposed to their previous amounts is the most

important result of the study.

Photoshop by Bryce Martin from google images.

The study, conducted online and focusing on “high school students in the Canton of Zurich” surveyed 3,664 students and questioned them on their daily sleeping patterns and was taken over the course of 3 months. The results were then compared with data from a similar study conducted in 2017 among 5,308 participants. The results were borderline staggering. The students slept an average of 90 minutes later than they normally would pre-virtual school despite only going to sleep an average of 15 minutes later.

It’s no secret that being well-rested improves overall health and well being, especially in the long term. “Chronic lack of sleep” is mentioned in the study as being an all-too-typical problem for most teens and not only contributes to poor overall health but also poor daily functioning as fatigue, lack of focus, and a general indifference to tasks are described as effects of this. Overall, one of the few joys that these students were able to experience during this unprecedented time of human existence was also one of the most needed and most simple; a good night’s sleep.

You Are What You Eat – And You May Prevent COVID-19 Depending What You Eat!

By marcochondria

On December 20, 2021

In Student Post

It’s no secret that a clean diet containing nutrient dense foods is optimal for one’s health and the body’s overall ability to function. Due to the mass spread of COVID-19, health and wellness has become more relevant to daily life and more present in the mouths of the general public than ever. A study done by a team of researches at Massachusetts General Hospital provides information that supports the idea that not only can individuals lower their risk of contracting COVID-19 by following a healthy (and primarily plant-based diet), but they can also significantly lower their risk of having severe COVID-19 or further complications from the illness if contracted.

While the researchers still consider cooperation amongst the public in regards to getting vaccinated and wearing masks when in public spaces, they can’t help but notice a significant link between the dietary status of the people partaking in their nearly year long study and their susceptibility to COVID-19. To be precise, those that were considered to be eating healthiest had a 9% lower risk of contracting the virus, and a 41% lower risk of the virus and its complications becoming severe.

Though the primary intention of running this study was to address the global public health issue that is the COVID-19 pandemic, the acknowledgement of diet being an important factor in the defense against COVID-19 brought attention to an important social issue as well: food insecurity and a lack of access to healthy foods for many people. There was a direct correlation found in the study between the participants with the least healthy diets and “socioeconomic deprivation”. It’s absolutely necessary to consider that in order for people to eat healthy, they need access to healthy foods. Due to the rampant income inequality worldwide and lack of social safety nets in the United States in particular, it is very difficult for many, many people to get foods that allow them to achieve optimal levels of nutrition.

More often than not, even if certain unhealthy foods do have adequate macronutrients (most commonly they are high in fat and carbohydrates), they severely lack in micronutrients, thus causing them to earn their “unhealthy” status.

Nevertheless, this link between diet and COVID-19 acts as further proof that maintaining a healthy lifestyle (so long as one is financially capable of doing so), in the midst of a pandemic or not, is absolutely necessary for the body to effectively function whether it be for defense or performance.

Fungi’s Pacifist Defense Strategy

By marcochondria

On November 3, 2021

In Student Post

Recently, it’s been discovered by a group of student researchers at the University of Göttingen, Germany that the cells found in fungi that are typically responsible for the reproductive structures of the organism during overwintering periods also play a large role in the production of chemicals that protect the fungi from potential predators.

Due to the fact that fungi cannot move on its own in order to evade predators, they use chemicals to defend themselves by producing secondary metabolites. Secondary metabolites are not essential to the life of organisms, however they absolutely aid the fungi in their pursuit of avoiding predators and are beneficial for the organism’s survival. Some fungal secondary metabolites can even be fatal when eaten by humans, however most only consist of unappealing odor, color, and other physical attributes. Though not classified as plants, fungi and plants share many qualities and their production of secondary metabolites happens to be one of them and they produce them for the exact same reason too (their cells also both have a cell wall; that’s not really relevant but I wanted to include that because I find it interesting).

The proteins that are largely responsible for the production of most of these secondary metabolites are located in the Hülle cells of the fungus. Hülle cells play a vital role of the development and structure of fungi’s reproductive mechanisms. In order for the production of these secondary metabolites to be limited to that of an appropriate quantity, the “velvet complex” acts as a regulator for the pathways needed for production itself. A nearly perfect system. A flaw though, is if this process is interrupted for some reason, the organisms system of protection and its reproductive structures will both be impacted severely. Due to the fact that the protective chemicals use the reproductive structures as its main hub of production and storage, an interruption of the process would lead to a lack of development in both. This would be devastating to the organism not only because it is now vulnerable to predators but this lack of development of reproductive structures also inhibits the organism’s ability to reproduce.

In the study, researchers observed woodlice and other arthropods that are predators of the fungi (they used A. nidulans for this study, a self fertilizing fungus (pictured above)) and how they respond to these secondary metabolites. It’s important to note that in this case the chemicals were not toxic to the arthropods, they simply made the parts of the fungus containing secondary metabolites undesirable for consumption (I include that not only to provide ethical clarity regarding the study for any readers that are curious but also to provide more information about the study as a whole). What the researchers found was that the predators only consumed parts of the organism that did not possess any secondary metabolites and they left areas that had many, such as its reproductive structures, completely alone. While I, like presumably many, don’t find this particularly surprising on the one hand; on the other it confirms that there is some sort of significance to the chemicals being produced and stored primarily in this region of the organism. Previous to this study, the importance of Hülle cells regarding the protection of fungi was completely unknown. In science, no matter what the field, discovery of any kind is a step in the right direction.

This study has shown that despite fungi’s immobility and lack of obvious protection, it has evolved in such a way that its system of shielding itself from potential threat is sophisticated, effective, and deceiving.

BioQuakes

AP Biology class blog for discussing current research in Biology

Author: marcochondria

Cas9/10

iDNA

How We Can Potentially Manage The Overwhelming Amount of Carbon Dioxide Emissions That Destroy The Planet

Pesticide Homicide

Something’s In the Water

Catch Some Z’s

You Are What You Eat – And You May Prevent COVID-19 Depending What You Eat!

Fungi’s Pacifist Defense Strategy

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