AP Biology class blog for discussing current research in Biology

Author: walkabuffalo

Are Fish Mind Readers?

Several inherited behavioral mechanisms in humans and animals are deeply rooted in prehistoric animals. Some of these mechanisms, for example, fear, as well as the ability to fall in or out of love, humans have possessed for thousands of years and are found in our ancient genetic pathways. Although scientists are hesitant to attribute human-like feelings to animals, it has been proven that many animals, including fish, have moods. A recent study published in the journal; Science, demonstrated that fish can identify fear in other fish. This ability is regulated by the hormone oxytocin. This is the same “brain chemical” that controls the feeling of empathy in humans. The researchers discovered that fish could detect fear in other fish by deleting genes linked to producing and absorbing oxytocin. These fish became fearful as well.


Deleting genes involves various techniques, which is specific to the organism and the purpose for the deletion. Generally, there are two main approaches for deleting genes: Targeted Deletion and Random Deletion. In Targeted Deletion, very specific regions of the DNA sequence are removed or replaced to eliminate the gene of interest. Random Deletion occurs when large sections of the DNA sequence are randomly deleted in the hope of removing the gene of interest. The research focused on zebrafish brains; a small tropical fish often used for such research. The fish used in this experiment became practically antisocial and failed to change their behavior and could no longer detect when other fish were anxious. Scientists then injected oxytocin into some of the altered fish, and the fish’s ability to sense and react to the feelings of other fish was re-established. Fish behave just like humans in that they respond to other individuals being frightened. During this experiment, fish were seen paying considerably more attention to previously stressed or frightened fish.

Oxytocin is a hormone that plays a key role in social bonding and emotional communication in mammals, including humans. It is produced in the hypothalamus and released into the bloodstream by the pituitary gland. One of the primary functions of oxytocin is to produce social bonding between individuals. It has been shown to increase trust and cooperation between people, and it is often referred to as the love hormone because of its role in promoting feelings of love and intimacy.

Oxytocin with labels

Hans Hofmann, an evolutionary neuroscientist at the University of Texas at Austin, said that it’s less of a “love hormone” and more of a “scale” that helps fish recognize the most noticeable social situation. This recognition activates neural circuits that may make one run from danger or engage in behavior that results in mating. This ability is essential to certain species of fish survival.

CRISPR-Cas9 – The Human Editor

What is CRISPR-Cas9? CRISPR-Cas9 (Clustered, Regularly Interspaced Short Palindromic Repeats) is a powerful technology that allows geneticists to modify or “edit” parts of the target genome by adding or removing whole sections of the DNA sequence. Currently, CRISPR is the most versatile and accurate DNA modification tool globally. This tool allows scientists to fix flaws in most organisms’ DNA and has minimal risk of off-target damage.

Cas9 cleavage position

CRISPR-Cas9 has two main molecules that carry out the change in DNA, an enzyme called Cas9, and a piece of RNA called guide RNA (gRNA). The Cas9 enzyme locates the target area and can cut the DNA in a specific location in the genome so that small pieces of DNA can either be added or removed. The gRNA is made of a small piece of a lab-designed RNA sequence, roughly 20 bases long, located within the RNA scaffold. To ensure that the Cas9 enzyme cuts at the right point in the genome, the scaffold binds to the DNA, and the lab-designed sequence pilots the Cas9 enzyme to the correct location. The gRNA has RNA bases that match those of the target DNA sequence in the genome. The Cas9 enzyme follows the gRNA to the specific area and makes a precise cut across both strands of the DNA. During this stage, the cell recognizes that the DNA has been damaged and will try to repair itself. Scientists use this DNA repair system to add or remove changes in one or multiple genes. This technology is consistent with our most recent AP Biology Unit, DNA Replication, and Gene Expression/Replication.

In my opinion, CRISPR-Cas9 is an incredible technology as it has so many practical applications. The future of this technology has potential in many diverse fields such as genetic engineering, bioengineering, and molecular biology, among other areas of study.

The technology has been tested on dogs with Duchenne Muscular Dystrophy, a gene mutation adversely affecting muscle proteins. In this case, a CRISPR gene-editing treatment demonstrated promising signs of permanently fixing the genetic mutation responsible for this disease, which in humans, affects approximately 1 in 3,500 male births worldwide. The mutation prevents an organism from producing an appropriate level of functioning dystrophin which causes muscles to be weak and not respond efficiently. Researchers at the University of Texas Southwestern found that gene editing restored the functioning dystrophin levels in the dog’s muscles and heart tissue. The increase in the dystrophin levels would need to be more significant for it to work in humans, but researchers have been making substantial progress in advancing this developing CRISPR-Cas9 technology.

New Generation of Coral!

As global warming continues to increase the temperature of the atmosphere and water column across our planet, the coral populations in our oceans are decreasing. Normally, to survive, coral hosts microscopic algae in its structure, which provides the coral with the energy it needs to grow. The algae produce glucose through photosynthesis, which the corals use to survive and to build their skeletons. This coral then releases oxygen that the algae takes back in. The stability of this symbiotic relationship is critical to corals’ survival. When a coral loses these symbiotic algae due to increases in water temperature, it causes the coral to turn white, as the coral struggles to meet its energy needs, which can often prove fatal. This phenomenon is called “bleaching.”

Bleached Staghorn Coral
Scientists studying coral bleaching have found evidence that some species of coral appear to be adapting to climate change and increasing their tolerance to warming ocean waters by changing the symbiotic algae communities they host. This allows the photosynthetic process to continue and provides them with the energy they need to live. This more resilient species of coral have been found in eastern tropical Pacific places such as Costa Rica, Mexico, and Colombia. These locations are projected to have higher coral cover through 2060. Pocillopora is one such species of coral and is an important genus found within the shallow coral reefs in the eastern tropical Pacific Ocean and the Indian Ocean.
I selected this article for my blog as it embodies several key biological concepts that we have studied and discussed in detail in class this year. These include the photosynthetic process and its important energy-producing biochemical reactions, the various types of successful symbiotic relationships between different organisms, and the role that DNA and genetics play in the evolutionary process of advancing successful biological adaptation.

Consistent with Darwin’s theory of evolution, it appears that Mother Nature, once again, may have found a way to overcome climate change, at least in this specific instance, and we may be witnessing it firsthand!

A View into Life Millions of Years Ago

In an obscure geological valley at the very northern tip of Greenland’s large ice sheet, investigators have uncovered scientifically derived evidence of the existence of a lush, ancient ecosystem that was functioning over 2 million years ago. The clues to this ecosystem come from the oldest DNA ever recovered, bits and pieces of genetic material, carefully and tediously extracted from buried sediments representing more than 100 kinds of animals and plants. The investigators painstakingly extracted and “sequenced” the DNA strands and compared them to libraries of existing DNA “reads” from living species today.

DNA double helix horizontal
This is an incredibly impressive example of the power of environmental DNA (eDNA), as it is genetic material collected from the ambient environment and not individual organisms. The investigative team aimed to collect hundreds of samples from different locations within the ancient valley and reconstruct what this ecosystem looked like before the ice age. They found many different types of conifers, including poplars, thujas, and species like black geese and horseshoe crabs, that are now common further south of Greenland, but most of which are no longer found in the Arctic at all.
There are many reasons that I believe this discovery is important, not the least of which is that it may give scientists clues as to how some species were able to adapt to climate change in the past and give us some insight into climate change and evolution as we advance. It may also turn the time-honored discipline of paleontology on its head by driving it from its almost all fieldwork mode into the molecular biology laboratory.

The DNA/RNA biochemical process plays a very important role within the nucleus of each cell which defines the existence and evolutionary success of living plants and animals on the planet. The article which I selected from “Nature” discussed above, really emphasizes importance of these chemical structures regardless of whether we are investigating the past, looking into possible future biological scenarios, or looking to “improve”, correct or modify existing biological systems. Understanding both the future and historic past of the biology of the planet is no longer simply relegated to the desktop microscope, but more appropriately is a function of understanding the complex biochemical reactions at the molecular level, not just the cellular level. The extraction of biological (environmental DNA) material from historic sediments thousands of years old underscores the important changes taking place in this exciting new field and emphasized to me that the study of DNA/RNA biochemistry is very relevant to understanding all living systems, past, present and likely into the future.


Fears of a Winter COVID-19 Surge

         In March 2020, our planet was invaded, as we were threatened by the very initial strain of the SARS-CoV-2 virus. This event was commonly referred to as the Coronavirus pandemic. Little did we know then that there would also be several increasingly virulent variants facing us in the immediate future. This highly infectious and adaptive virus forced virtually everyone on Earth to quarantine and patiently wait for a worldwide team of multi-disciplined scientists and medical practitioners to develop an approvable and effective vaccine. For at least a year, we sat before our TV sets and awaited the daily numbers of the newly infected, hospitalized, and deaths. Populations throughout the world were being sent to hospitals in an effort to survive this dangerous virus. The hospitals and healthcare workers across the globe were stretched way beyond capacity, and the untold emotional effects on care providers, in itself, reached epidemic proportions.

SARS-CoV-2 without background
The SARS-CoV-2 virus enters and attacks our lungs through our normal respiratory process. The virus causes our lungs to become inflamed, making it challenging for us to breathe. This can lead to pneumonia, an infection of the tiny air sacs inside your lungs where your blood exchanges oxygen and carbon dioxide. These viral effects made it difficult for middle-aged and older adults to cope and often left them vulnerable to the disease. Once the vaccines were advancing to a stage of government approval and being administered to the general population, we began to see statistically significant improvements in the overall ability of our immune systems to “take on” the virus and win the battle. As people were receiving the vaccine, most people were choosing the mRNA vaccines. These vaccines teach your cells to produce a harmless piece of the coronavirus spike protein that triggers an immune response to build antibodies. A spike protein is a specialized combination of amino acids designed to help the immune system know how to respond to the spike protein. In this way, one begins to build immunity to COVID-19, which results in mitigating the adverse effects of the virus or, in some cases, not succumbing to the effects of the virus. Once it does its job, the mRNA quickly breaks down, and the body clears it away in a few days.
All vaccines leave the body with a supply of T-lymphocytes and B-lymphocytes that will remember how to fight that virus in the future. Since COVID-19 is highly adaptive, as evidenced by the emergence of its numerous variants, biomedical researchers have to quickly produce a new vaccine to prevent a new SARS-CoV-2 virus variant from spreading.

Janssen COVID-19 vaccine (2021) F (cropped) 2
New concerns are now arising in the medical community with the threat of yet another new variant strand of SARS-CoV-2 emerging onto the scene as winter approaches. According to the Centers for Disease Control and Prevention, we could be looking at two new omicron subvariants becoming increasingly more dominant in the United States, raising fears that they could start another surge of COVID-19 infections. The new subvariants known as BQ.1 and BQ.1.1 are raising concerns because it appears to be proficient at evading the defenses of currently available vaccination formulations. According to the CDC, in recent weeks, BQ.1 and BQ.1.1 has quickly risen to 44% of all new infections nationwide and is approaching nearly 60% in some parts of the country, such as New York and New Jersey. Additionally, this viral landscape takes on even greater significance as we seem to be in a “viral trifecta” with the more common Influenza (flu) Virus and the Respiratory Syncytial Virus (RSV) taking the stage front and center this Fall and Winter season. Perhaps the best advice is to see your health care practitioner and see if a vaccination or booster shot is right for you!

HABs – The Tiny Killers

Harmful Algal Blooms (HABs) occur when algae, which can range from microscopic, single-celled organisms to large seaweed, produce harmful toxins that grow in extremely high numbers and are in dense concentrations at the surface of lakes and in marine environments. These HABs are killing fish, mammals, and birds and may cause human illness or even death in extreme cases. In some instances, the algae blooms can be nontoxic but, in any event, consume all the oxygen in the water as they die off and decay, which can clog the gills of fish and invertebrates or smother corals. They are becoming a growing concern because they affect the health of humans, freshwater, and marine ecosystems. One research study indicates that the economic loss resulting from algal blooms, including regular phytoplankton algal blooms and what is now referred to as “harmful algal blooms or “HABs” formed by cyanobacteria, is on the order of approximately $4 billion annually.

River algae SichuanIn October 2019, a research article was published in the prestigious scientific journal; Nature, which documented a significant increase in phytoplankton (algal) blooms worldwide since the 1980s. This was reported by a detailed study of worldwide LANDSAT satellite photography utilizing three decades of satellite imagery. Using these satellites, 71 large lakes throughout the world were studied.

These phytoplankton populations form the basis of the food chain and contribute or are engaged in numerous biological, chemical, and biochemical processes that are important to everyday life on our planet. Many of these blooms can be caused by cyanobacteria which are prokaryotic cells that still can generate oxygen via photosynthesis, much like the eukaryotic microscopic plant cells, better known as phytoplankton. Some cyanobacteria can “fix” atmospheric nitrogen as well. Several cyanobacteria species also produce toxins as a bi-product of their metabolism that can adversely affect the liver, kidney, and nervous systems in humans and animals.

NOAA is at the forefront of HAB research to better understand how and why these blooms form and to improve the detection and forecasting of these seasonal events. The causes of this significant increase in algal blooms are somewhat unclear; however, it seems to be linked to precipitation, trends in fertilizer use, changing weather patterns, nitrogen concentrations, phosphorus concentrations, and perhaps climate change; as increases in temperature worldwide are occurring, but this data is inconclusive. Humans may also impact how frequently they occur and their intensity. Increased pollution, food web alterations, introduced species, water flow modifications, and climate change are all human activities that may play a role in creating these blooms.

These blooms concern me because, for the first time in many years, I have observed several algal blooms where I spend my summers on Upper Saranac lake, a freshwater lake in the Adirondack Park. While these are not HABs (harmful algal blooms) produced by cyanobacteria, they indicate changes in the lake’s biochemical, chemical, and perhaps physical parameters. The lake is monitored 24/7 via a telemetric sampling station that runs typical water quality parameters, which are being studied as we speak by local researchers. I feel we must continue to research the causes and effects of this situation to better manage algal blooms in the future. Can you think of any methods to reduce the likelihood of these Harmful Algal Blooms from forming?

Harmful Algal Bloom in Western Lake Erie, July 9, 2018

Powered by WordPress & Theme by Anders Norén

Skip to toolbar