BioQuakes

AP Biology class blog for discussing current research in Biology

Author: cytokinesav

Instead of Bringing Back Dinosaurs, These Scientists are Bringing Back the Extinct Christmas Island Rat

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On March 20, 2022

In Student Post

Majestic dinosaurs and mammoths on our planet both underwent extinction millions and millions of years ago. The Christmas Island rat? In 1908. De-extinction techniques, also known as resurrection biology, garnered popularity within the science world in the 1990s. The Encyclopedia Britannica defines it as, “the process of resurrecting species that have died out or gone extinct.” Here is how these scientists are attempting to bring back a rat species that you have probably never heard of, and what that can mean for the future.

De-extinction using CRISPR gene-editing

 

File:MaclearsRat-PLoSOne.png - Wikimedia Commons

path of extinction of the Christmas Island rat

The process of de-extinction with the Christmas Island rat is driven by the method of CRISPR gene-editing, which allows for the genome of organisms to be modified, or edited, meaning that an organism’s DNA can be changed by us humans. This allows for genetic material to be added, removed, or modified at specific locations said genome. The idea behind the de-extinction of an animal through CRISPR gene-editing is to take surviving DNA of an extinct species and compare it to the genome of a closely-related modern species, then use CRISPR to edit the modern species’ genome in the places where it differs from the extinct one. The edited cells can then be used to create an embryo implanted in a surrogate host.

CRISPR thought to be “genetic scissors”

Thomas Gilbert, one of the scientists on the team of this project, says old DNA is like a “book that has gone through a shredder”, while the genome of a modern species is like an intact “reference book” that can be used to piece together the fragments of its degraded counterpart.

What is the difference between a genome and a gene?

File:Human genome to genes.png

Gene depicted within genome

Genes, a word you are most likely familiar with, carry the information which determines our traits, or features/characteristics that are passed on to us from our parents. Like chromosomes, genes come in pairs. Each of your parents has two alleles of each of their genes, and each parent passes along just one to make up the genes you have. Genes that are passed on to you determine many of your traits, such as your hair color and skin color. Known dominant traits are dark hair and brown eyes, while known recessive traits are blonde hair and blue or green eyes. If the two alleles that you receive from your parents are the same, you are homozygous for that gene. If the alleles are different, you are heterozygous, but you only express the dominant gene.

Each cell in the human body contains about 25,000 to 35,000 genes, and genes exist in animals and plants as well. Each gene is a small section of DNA within our genomes. That is the link between them, and they are not the same.

Is this possible? Can we really bring back the dead?

Reconstructed image of the extinct woolly mammoth

See, CRISPR gene-editing itself is of great interest for having shown promising results in terms of human disease prevention and treatment for diseases and single-gene disorders such as cystic fibrosis, hemophilia, and sickle cell disease, and shows promise for more complicated illnesses such as cancer, HIV infection, and mental illness–not so much with de-extinction. Here’s a simple diagram displaying the process.

File:Crispr.png

In this scenario, it is not looking very likely that these rats can come back. Gilbert and his team of 11 other scientists, through extensive processes and attention to small-detail, have in total reconstructed 95% of the Christmas Island rat genome. While 95% may be an A on a test, in regards to genomes, that 5% is crucial. In this case, the missing 5% is linked to the control of smell and immunity, meaning that if we were to bring this animal back, it would lose key functionality. Gilbert says 100% accuracy in genome reconstructing of this species is “never” going to happen.

The success of de-extinction is quite controversial in itself. Restoring extinct species can mean an increase in biodiversity and helping out our ecosystems which are suffering greatly from climate change.  However, research also suggests it can result in biodiversity loss through possibly creating invasive species (yes, I wrote this) or for other reasons.

While the science is interesting, the reality of the unlikeliness of de-extinction becoming a normal and official process is kind of dream-crushing. Who knows, maybe as technology advances, hopefully, we can make all of this happen without harmful side effects, aid our ailing ecosystems, and visit some mammoths on a safari vacation!

Super-Spreader Plants: The #2 Cause of Biodiversity Loss Worldwide

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On February 14, 2022

In Student Post

According to the results of a global research project, conducted by the University of Konstanz and posted in December 2021, “super-invader” plants are a huge problem and greatly reduce biodiversity.

What even is biodiversity? What do the results mean? How does this even happen? Here’s what you need to know about these invasive plants that spread like wildfire.
Large-leaved Lupine (Lupinus polyphyllus). Invasive | Free Photo - rawpixelLarge-leaved Lupine (Lupinus polyphyllus). Invasive species in the wild of Ukraine.

What exactly are ‘invasive’ plants?

Coming from all around the world, invasive plant species cause harm to the environment, the economy, and/or to human health through rapid overpopulation. Most invasive plants come from other continents and countries, but few are native to other regions of the United States.

The extremely harmful side effects of invasive plants

  • a reduction in native biodiversity which adds to climate change, pollution, and more (I encourage you to self-educate on the importance of biodiversity here)
  • alteration of disturbance regimes
  • habitat degradation and loss (the loss of native fish, wildlife and tree species)
  • loss of habitat for dependent and native species (including wildlife)
  • changes in biogeochemical cycling
  • the loss of recreational opportunities and income
  • crop damage and diseases in humans and livestock
Free photo Asian Berry Red Honeysuckle Bush Invasive Plants - Max PixelJapanese honeysuckle

What makes these plants invasive?

Here are some characteristics of invasive plants, through both their properties and how they are distributed over large distances.

  • Can produce large quantities of seed
    • For example, each garlic mustard plant produces hundreds of thousands of seeds–which is a great abundance
  • Seeds are often distributed by birds, wind, or humans which allows them to travel significant distances
  • Many produce chemicals that make it difficult for other plants to grow nearby (ex: garlic mustard plant)
  • Some plants arrive accidentally in air or water cargo
  • Tourism: travelers from one country to another actually commonly spreads things such as insect pests or weed seeds across
  • Produce seeds and leaves that germinate and ‘leaf out’ way early in the spring. As an example, the Norway maple‘s seeds can be 6 inches tall before the plant sprouts, and buckthorns keep their leaves into November, long after native plants have lost theirs.
    • This results in the plant’s leaves being kept late into fall, allowing them to photosynthesize earlier and later than native plants

Looking deeper into this on a molecular level…

File:Photosynthesis.gifphotosynthesis drawing

Looking at the basic science of plants is helpful to understand why this earlier photosynthesis is so important. Plants use sunlight, water, and carbon dioxide to create sugars and oxygen in energy form in the process called photosynthesis. Plants contain chloroplasts that perform this process, which is comprised of light-dependent reactions and the Calvin Cycle (light-independent reactions).

The goal of the light-dependent reactions of photosynthesis is to collect energy from the sun and break down water molecules to produce energy-storing molecules ATP and NADPH. These are then used in the Calvin Cycle to turn carbon dioxide from the air into sugar, providing food for plants.

File:Simple photosynthesis overview.svg - Wikimedia Commons simple photosynthesis diagram

Plants with high photosynthetic rates will grow and reproduce earlier than their native counterparts, often out-competing them and leaving little space for them to thrive. They then can spread really fast due to their other properties listed above.

Why should we care?

Following habitat destruction, invasive species are the second leading cause of biodiversity loss around the world, contributing to climate change and pollution. Forty-two percent of threatened and endangered plants and animals in the United States are directly harmed by the presence of invasive organisms. That’s basically half! Governments around the globe spend billions of dollars each year to control the harm caused by these plants. Yikes.

What can we do?

Here’s what you can do to prevent the super-spread of invasive plants:

  • Learn how to identify these plants and educate your friends about them.
  • Don’t pick, gather, or bring home wildflowers that you can’t identify.
  • Check for weeds and seeds from shoes and clothing after a hike. Also, check your pet’s fur for them! Remove anything that you find before arriving home.
  • Try to keep your car off of weed-infested roads and trails.
  • Be on the lookout for seeds while camping and coming back from vacation!
  • Try to join a plant-removal project! Shown below is the happy result of an invasive species removal project completed by The Southeastern States District Office.

Dr. Mark van Kleunen, Professor of Ecology in the Department of Biology at the University of Konstanz and senior author of the research project’s publication, brings up the most important point: “Unless more effective protective measures are taken to counter the ongoing spread and naturalization of alien plants in the future, they will continue to destroy the uniqueness of our ecosystems — making the world a less diverse place.”

Cocaine’s Abuse on the Body: How Far Does it Go?

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On December 17, 2021

In Student Post

Cocaine powder on black table | 🇩🇪Professional Photographe… | FlickrCocaine pictured above

When it comes to cocaine, there is a long list of the drastic. negative effects it has on the human body–not only physically, but mentally as well. When we see major celebrities such as Mac Miller, Don Rogers, and Whitney Houston pass from a cocaine overdose, what do you think plays a part in it?

What is cocaine?

Cocaine is a powerful and highly addictive stimulant drug, which first arose in the US in the late 1800s. It can be snorted, injected, rubbed in one’s mouth, and smoked. It is made from the coca plant of South America. It raises our dopamine levels which cause us to feel joy and relief, however, it damages the natural communication cycle in our brain, leading people to take highter and more frequent doses in an attempt to achieve the same high as when they first began using.

Effect of cocaine on our bodies

Short-term health effects of cocaine include, but are not limited to:

  • extreme happiness and energy
  • mental alertness
  • hypersensitivity to sight, sound, and touch irritability
  • paranoia—extreme and unreasonable distrust of others

Some long-term effects of cocaine abuse include, but are not limited to:

  • headaches
  • extreme weight loss
  • cardiac complications such as irregular heartbeat, cardiomyopathy, and acute myocardial infarction (heart attack)
  • loss of smell/olfactory function
  • mood swings
  • movement disorders, including Parkinson’s disease
  • paranoia
  • auditory hallucinations
  • irregular heartbeat
  • death by overdose
On a cellular level…

Once in our system, cocaine rapidly crosses the blood-brain barrier and binds to various plasma membrane transporters on neurons. Neurons are the main focus here, as our brains are comprised of 3 to 6 layers. What are they? They are “the fundamental units of the brain and nervous system, the cells responsible for receiving sensory input from the external world, for sending motor commands to our muscles, and for transforming and relaying the electrical signals at every step in-between” (Queensland Brain Institute). Neurons contain cytoplasm, mitochondria and other organelles. Neurons carry out basic cellular processes such as protein synthesis and energy production. Regarding basic cell types and structure, neurons have a cell body comprised of a nucleus and cytoplasm, and also have a mitochondria. The nucleus produces ribosomes which are involved in protein production. The cytoplasm acts as a suspension medium for organelles, and the mitochondria is involved in complex processes of neurotransmission. Overall, this cell body is essential to the neuron’s function as it carries genetic information, maintains the neuron’s structure, and provides energy to drive important cellular activities.

File:Blausen 0657 MultipolarNeuron.png - Wikimedia CommonsNeuron structure pictured

Or, to put it very simply, cocaine alters our brains and DNA in a complex manner, relating to several neurotransmitter systems, leading to seizures and neurological disorders such as Parkinson’s disease, as well as the more mild symptoms listed above.

Crack and cocaine users: are they bad?

Yes, crack and cocaine use is objectively terrible. They can alter our behavior, emotions, physical abilities, and our future children in drastic ways. However, it is important not to villainize those suffering from substance abuse. Rather, we should focus on what causes these people to turn to drugs. Systemic racism plays a large role in who uses and is distributed crack/cocaine. Lack of access to mental healthcare is yet another factor. As a society, we need to do better and be aware of all these things. If you or someone you know may be susceptible or vulnerable to drug abuse, please contact the Substance Abuse National Helpline at 1-800-662-4357.

 

 

 

How does the Omicron variant of COVID-19 compare to the deadly Delta variant?

By

On December 6, 2021

In Student Post

With news of the new variant of the COVID-19 virus reaching 16 states here in the US, many are asking: What is this Omicron variant?

The Omicron variant of COVID-19 was first reported to the World Health Organization by the Head of South African Medical Association, Dr. Angelique Coetzee. As of December 6, 2021, there are about 59,000 Americans hospitalized due to said variant.  The Delta variant, more than twice as contagious than previous variants according to the CDC, still continues to be the leading cause of COVID-related hospitalization and deaths today in the US and many other countries. However, medical experts are saying that Omicron has a few different key mutations that make it very likely to outperform Delta. How does this Omicron variant compare to the deadly Delta variant which we’ve been battling this year? Here are the main things you need to know.

Symptoms of the Omicron variant:

  • Fever or chills
  • Cough
  • Shortness of breath or difficulty breathing
  • Fatigue
  • Muscle or body aches
  • Headache
  • New loss of taste or smell
  • Sore throat
  • Congestion or runny nose
  • Nausea or vomiting
  • Diarrhea

Infection and Spread:

So far, people who have been diagnosed with the Omicron variant of SARS-Cov-2 in the US have or had mild symptoms, yet it is said to be much more contagious. Why? The difference in the structure of the spike protein. Variants of COVID-19 have mutations present in the spike protein due to copying errors in our DNA.

File:Omicron.jpg - Wikimedia Commons

Omicron Structure pictured

The Delta variant has 18 mutations in its spike proteins…Omicron has a whopping 43! That is many, many more than Delta. Jeremy Kamil, associate professor of microbiology and immunology at Louisiana State University Health Shreveport, said, “The number of changes blew people’s minds…It’s an exaggeration to say we’re back at square one, but this is not a good development.”

Around 30 countries have detected said variant so far; 19 states in the US have. The high number of mutations it contains does not necessarily mean it’s more dangerous. As previously stated, Omicron patients have thus far exhibited milder symptoms. Dr. Coatzee said that she first discovered Omicron’s appearance as her patients exhibited “unusual symptoms” in comparison to the Delta variant. However, don’t be too scared; experts say our immune systems have grown more equipped to fight the COVID-19 virus.

We still have yet to learn more about Omicron and its nature, infection, etc., as it is very new.

Free COVID-19 Illustrations - Innovative Genomics Institute (IGI)The original COVID-19 virus’s structure is pictured above

With Omicron having more than double the mutations as Delta, the likeliness of transmission/level of contagiousness is quite high–also meaning that the efficacy of our vaccine could be compromised. The Omicron spike protein has similar components that of the Delta, beta, and gamma variants, meaning that the rate of transmissibility is similar. With Omicron having the largest number of mutations, however, transmissibility can be increased more than 2x!

What should you do?

Well, continue to follow the standard COVID-19 measures. Wear a mask, social distance, wash your hands, travel less, and just be careful. These methods have proven time and time again to help. Travel restrictions on the rise can be tough with the holidays coming, but remember that they are only in place for the sake of our safety. It is important to follow these rules as the pandemic is not over.

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