AP Biology class blog for discussing current research in Biology

Author: charlottersmosis

Genetically Engineering the Food We Eat to Increase Consumer Desire

Solanaceae is an order of classification for a group of plants known as nightshades. The Solanaceae are a family of plants that ranges from annual and perennial herbs to vines, shrubs, and trees. Included in this family of variety are also a number of agricultural crops like tomatoes, medicinal plants like jimson weed, spices, weeds, and ornamentals. This group of plants are given the term “nightshade” because some of these plants prefer to grow in shady areas, and some flowers at night.Solanum americanum, fruits

The Solanaceae is one of humankind’s most utilized and important families. It contains some of the world’s most important vegetables as well as some of the most deadly toxic plants. Foods like potato, tomato, peppers, ground cherries, and eggplant all hail from this incredible plant. With the benefits of this plant family also comes the dangerous variety of plants. The belladonna, mandrake, Jimson weed, and tobacco also come from this family. Solanum trilobatum flowersNot only does this family of plants produce important vegetables and deadly plants, various chemicals and drugs can be harvested. Some of these include nicotine, solanine, capsaicin, atropine, scopolamine, and hyoscyamine.

CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. It is a gene editing tool that can be used to edit DNA in cells. It used a specific enzyme called Cas9, which stands for CRISPR associated nuclease 9, and a specific RNA guide to either disrupt host genes or insert sequences of interest. CRISPR was initially used in bacteria as an adaptive immunity response but is now being used as an alternative in genome engineering.CRISPR illustration gif animation 1

In the agricultural world, plant breeding has always been the way to improve the traits wanted in a plant. With technological improvements, increased production has been vastly upgraded. Recent advances in gene editing have revolutionized the field of plant breeding. The process of genetic engineering has allowed people to target specific genes to improve rather than continuous breeding to produce the desired trait. 

Consumers choose the type of foods they want to eat by the traits of the fruit/vegetable, and in response, it leads the path to ensure that plant breeding will produce that trait again. In the horticulture industry, fruits are an important food that many people buy. Fruits are known to have a crucial source of energy, vitamins, fibers, and mineral components. The larger the fruit, the less sour and more nutrients it tends to store, influencing consumers to buy fruits that are bigger in size and shape. As a plant family with various crops, Solanaceae crops have a variety of fruit sizes and shape features. With advancing gene editing technology, Solanaceae fruit crops have been on the receiving end of being genetically modified to increase desirable traits of fruit size, fruit weight, fruit quality, and plant architecture.Maduración del tomate (Solanum lycopersicum)

Many of the vegetables and fruits we eat today are slowly being improved with CRISPR. For instance, in tomatoes, the ARGONAUTE7 (SlAGO7) gene function in leaf shape development was one of the first edits done with CRISPR Cas9. Tomatoes have been at the forefront of CRISPR Cas9 gene editing on plants because it is a model crop that is able to grow variability. Many more plants of the Solanaceae family, like the goji berry and groundcherry, have been engineered to produce the best product and CRISPR gene editing will continue to enhance the fruit and plant.

This CRISPR gene editing research on the order of Solanaceae plants is relevant to AP Biology because of gene editing. In the first year of biology, we learned about the taxonomy of species and the order of specificity. The order of Solanaceae plants indicates that it isn’t a particular family of plants that includes the different genus and species. Instead, it is a broader classification. We didn’t specifically learn about CRISPR gene editing in class this year, but we learned about DNA and RNA and their replication process. In a way, we learned about CRISPR because it relies on a strand of RNA with the preferred traits that is then transcribed into DNA.

Chimeric Antigen Receptor T-Cell Therapy: Successful Research to Improve Cancer Treatments

Cancer is when abnormal cells divide without control and spread to other parts of the body through the bloodstream and lymph systems to cause illnesses. Immunotherapy is a type of treatment that utilizes a person’s immune system to battle diseases like cancer. Under the branch of immunotherapy, there is a specific therapy that has been recently improved upon.

Chimeric antigen receptor (CAR) T-cell therapy is a treatment that stimulates T-cells to fight cancer by editing them in the lab so they can be released into the body to find and destroy cancer cells. This treatment has been successful in treating certain types of hematologic malignancies but unsuccessful on solid tumors. Hematologic malignancies are cancers that begin in blood-forming tissues such as the bone marrow and in the immune system. Examples of cancers that can be treated with the CAR T-cell therapy include leukemia, lymphoma, and multiple myeloma.CAR T-Cell Therapy 

CAR stimulates macrophage phagocytosis function against tumor cells and its immunomodulation capacity. Scientists have already achieved success with this therapy in B cell leukemia/lymphoma but are still caught up on complications with solid tumors. The main challenge about solid tumors arise from its immunosuppressive tumor microenvironment. There is also a limited effect on infiltration into the dense extracellular matrix of the solid tumors.

In this type of therapy, the macrophages are the most important aspect of the success in treatment. Macrophages play a central role in the crosstalk between the adaptive and innate immune system. The immune system defends the body and marks pathogens and cancer cells for macrophages to fight and engulf. The researchers at Zhejiang University partnered with a researcher at the Fujian Medical University and The First Affiliated Hospital and Center for Stem Cell and Regenerative Medicine to study macrophage specific CARs and the development of EGFRvIII (epidermal growth factor receptor variant III) Targeting CAR-iMACs. The chimeric antigen receptors were further genetically engineered into induced pluripotent stem cell (iPSC) derived macrophages (iMACs) so that the CAR treatment was more effective toward solid tumors. The firefly luciferase gene (Ffluc) was discovered to promote the research through the bioluminescence signal response from tumor cells.

Macrophages were equipped with receptors called pattern recognition receptors (PRRs) through the discovery of the importance of bioluminescence cell signaling. The chimeric antigen receptor was then reprogrammed to contain Toll/IL-1R (TIR), a domain containing adapter inducing interferon β. The TIR-containing CAR is a novel engineered PRR that recognizes antigen associated molecular patterns and enables macrophages with antigen dependent polarization to be more pro-inflammatory to aid immune cell therapies in cancer.

Connection to AP Biology:

The chimeric antigen receptor T cell therapy has a great deal of connections to our AP Biology class.


CAR treats certain types of cancers, usually those in the blood-forming tissues. As we learned in AP Bio, cancers form when a cell does not properly divide and bypasses the checkpoints in the mitosis cycle. These abnormal cells don’t always become cancerous but they no longer follow the signals to stop dividing, causing masses that could one day become cancerous. 

Macrophages & Phagocytosis:

Macrophages and phagocytosis was something that we learned about in the first semester. Macrophages are specialized cells that are involved in pathogen detection so that phagocytosis can occur and destroy bacteria and other harmful substances.

Phagocytosis occurs when a cell engulfs solid things into the cell. We learned about phagocytosis along with pinocytosis and receptor-mediated endocytosis. In CAR therapy, phagocytosis occurs to engulf pathogens and cancer cells.

Bioluminescence:PanellusStipticusAug12 2009

In AP Bio, we did not directly learn about bioluminescence but we learned about cell communication and cell signaling. In bacteria, there is quorum sensing and it allows bacteria to share information about cell density and adjust gene expression. In bioluminescence bacteria, the power to produce light is controlled by quorum sensing. One bioluminescent bacteria cannot light up on its own, but when multiple bioluminescent bacteria gather together, quorum sensing signals for the “light” to shine once it senses enough of the bacteria together.


Can HCQ(Hydroxychloroquine) Prevent COVID-19 Infection and Help Recovery? The Research Says “No”

Have you ever wondered what chemicals and such are being used to treat and illness you have? HydroxychloroquineWell, for treatment of the COVID-19 vaccine, one of the chemicals used is hydroxychloroquine (HCQ), also known as Plaquenil. HCQ is a immunosuppressive drug and anti-parasite that can treat and prevent malaria, lupus, and arthritis.

HCQ was used as pre-exposure prophylaxis against COVID-19 infection in healthcare workers as a study. There were 1294 participants from ages 24-38 with 61% being women. 273 (21.1%) of the participants were healthcare workers but still 83 (6.4%) of them tested positive after duty. This showed that the use of HCQ had no effect on the prevention of the COVID-19 virus.

What made hydroxychloroquine an option used in preventing COVID-19 in the first place? Symptoms of coronavirus disease 2019 2.0There are typically four phases of a more severe version of COVID-19. The first phase would be the incubation period that has a median of 5.1 days. After that is the second phase which lasts around 5-10 days where flu-like symptoms arise. These include, fever, cough, muscle pain/soreness, fatigue, nausea, and diarrhea. Up until the second phase, the severity of the illness can be considered normal. After the second phase, there is normally a progression to a hyperinflammatory acute respiratory distress syndrome (ARDS). ARDS is a life-threatening lung injury that makes breathing difficult. As the second phase progresses onto the third phase, ARDS causes dyspnea, tachypnea, and sometimes hypoxemia making a person extremely out of breath and in need for hospital care. During this third phase, a person affected severely of COVID-19 will normally have high fevers with elevated inflammatory markers and progressive formation of organ failure. For some of these severe cases of COVID-19, effective treatments were desperately needed.

From data of previous epidemics, HCQ have been widely used around the world for Ebola, H7N9 influenza, and SARS virus infection. HCQ has been used to treat a number of auto-immune diseases by raising intracellular pH and affect endosomal activity. However, in the case of COVID-19, HCQ has no positive effect in preventing the coronavirus and may even cause more harm to our bodies.


As an immunosuppressive drug, it made sense to give HCQ to patients with early onset of COVID-19 and as a pre-exposure prophylaxis. HCQ impacts cytokine production and suppresses antigen presentation. The medication was used in various ways: as an oral medication by itself to take before contracting COVID-19, taking it after contracting COVID-19, and combined therapy with azithromycin. None of these ways had a surprising result in preventing COVID-19 or with helping a person recover. It was then believed that the impact of cytokine production and suppression of antigen presentation may cause immunologic consequences resulting in the hampering of the innate and adaptive antiviral immune response, possible making it more dangerous with patients with COVID-19. It has been determined that HCQ is not suitable for the treatment of COVID-19.

The process of proving HCQ effectiveness in fighting COVID-19 can be related to AP Biology because of the way the medication works with the immune system. Hydroxychloroquine is a medication that can raise intracellular pH and affect endosomal activity. Acidity of cell pH and endosomes are topics that we learned first quarter. In relation to the second quarter, HCQ is a immunosuppressive drug known to impact cytokine production and antigen presentation. Cytokines and antigens are part of the innate and adaptive immune system that we learned about recently.

Regeneration of Lost Limbs in Axolotls

Many salamanders have the special ability to regenerate a lost limb, but adult mammals cannot. The axolotl is a Mexican salamander that is an endangered species in the wild. However, it is unlike most salamanders.

Metamorphosis frog Meyers

Normally, amphibians, like salamanders and frogs, go through the process of metamorphosis which begins with an egg that hatches into a larvae with gills to live underwater. As they gradually reach the adult stage, salamanders and frogs begin to lose and gain certain traits that allow them to adapt from an aquatic environment to a terrestrial habitat.


Axolotls are adorable creatures that are a special species of salamanders. Instead of going to the process of metamorphosis, they go through the process of paedomorphosis in which they retain their aquatic juvenile state for the rest of their life cycle.

Most salamanders have regenerative abilities but none to the extent of the axolotl. Axolotls can regenerate almost any body part, including the brain, heart, lungs, spinal cord, skin, tail and more. This possibly has to do with their juvenile state. Mammalian embryos and juveniles have the ability to regenerate to some extent, such as the heart tissue and fingertips. However, once mammals reach the adult stage, regeneration just simply isn’t the solution anymore. Mammals being to form a scar at the location of injury.

A team of scientists led by James Godwin, Ph.D., of the Mount Desert Island Biological Laboratory in Bar Harbor, Maine, approached the mystery of molecular regeneration by studying the axolotl, a highly regenerative salamander, versus an adult mouse, a mammal that has limited regenerative ability. In this research, Godwin compared immune cells called macrophages in the axolotl to the macrophages in the mouse to identify the factor that contributed to regeneration. It turns out that the macrophages are crucial to the process of regeneration. When the macrophages were depleted in the axolotl, it formed a scar like mammals do instead of regenerating. Macrophage signalling was similar in both axolotls and mammals when exposed to pathogens such as bacteria, funguses, and viruses. However, when the axolotl was exposed to these pathogens, the signalling promoted new tissue growth while in the mouse, it promoted scarring. Continual research of macrophage signalling in axolotls might one day be able to pull us closer to human regeneration.

In the future, when we need to surgically remove parts of our organs, axolotl regeneration might come in quite handy to regrow our important organs!

This research article relates back to AP Biology because macrophages work together with the its lysosomes to break down foreign pathogens. These macrophages will engulf these invading pathogens into intracellular membrane vesicles through the process of phagocytosis. Once entrapped in the vesicles, the pathogens will be killed with acid.

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