AP Biology class blog for discussing current research in Biology

Tag: inflammation

A “Coffee-With-Milk” A Day Keeps The Doctor Away

In a recent study, researchers at the Department of Food Science, in collaboration with researchers from the Department of Veterinary and Animal Sciences, at the University of Copenhagen have discovered evidence that the mixture of coffee and milk has anti-inflammatory effects when consumed.

On January 30th, a study was published in the Journal of Agricultural and Food Chemistry (led by Professor Marianne Nissen Lund) that explains how this common combination of ingredients can limit inflammation.  To test the theory, the study “applied artificial inflammation to immune cells.  Some cells received various doses of polyphenols that had reacted with an amino acid, while others only received the same doses. A control group received nothing” (Science Daily).

The results showed that cells that received a dosage of polyphenols and amino acids were twice as effective as cells that received purely polyphenols.  Now, you may be asking how this relates to coffee and milk?  The answer to this question lies in the definitions of terms used above.  Polyphenols are a “category of plant compounds that offer health benefits” (Healthline).  They are found in coffee beans, and therefore, coffee.  Amino acids are “molecules that combine to form proteins,” and therefore are found in a majority of animal products, including milk (Medline Plus).

It is an established fact in the scientific community that polyphenols and amino acids bond, and therefore, the link between the two substances and anti-inflammatory effects is believable to scientists after the recent study performed by the Department of Food Science.  Furthermore, considering how common both substances are, it is likely that a similar reaction occurs when protein is combined with other fruits and vegetables with high amounts of polyphenol.  According to Marianne Nissen Lund, “I can imagine that something similar happens in, for example, a meat dish with vegetables or a smoothie, if you make sure to add some protein like milk or yogurt”.

The immune system is incredibly important to the function of the human body, as it serves to maintain order and defend against both foreign and local threats. When pathogens are able to infiltrate the body, they trigger innate immunity defenses, which in turn causes inflammation (as histamines which are released dilate local blood vessels and increase capillary permeability and cause the area to swell with fluid, which thus, causes inflammation).

Although immune cells (and in particular, innate immunity) cause inflammation, it is also the job of the immune system to limit inflammation by fighting off any unwanted antigen quickly, as the faster the antigen is killed, the faster inflammation goes away.  Immune cells of all types serve this function, ranging from innate to adaptive.  Thus, a compound that can increase the reaction rate of immune cells is incredibly valuable to animal health, including human health.

The results of the study show that polyphenols that have reacted with amino acids can double the effectiveness of the anti-inflammatory process of immune cells.  So, next time you are ordering a coffee, remember to ask for a splash of milk – you just might thank me later.

Coffee with milk (563800) (cropped)

Why are some people’s sense of smell unable to recover after COVID-19?

A recent finding published on December 21, 2022, in Science Daily, regarding the topic on why COVID-19 affects our ability to smell in the long run, was uncovered by the Duke University Medical Center. The biological mechanisms that are behind the loss of smell many people face who have had COVID-19, may also be the reason for some of the other symptoms of COVID-19 such as fatigue, shortness of breath, and brain fog.

SARS-CoV-2 without background


Although many people recover from the side effects of being infected with SARS-CoV2 within a few weeks, there are many cases where some people’s smell is still altered for several months after. An experiment at Duke University conducted by  Bradley Goldstein, M.D., Ph.D., associate professor in Duke’s Department of Head and Neck Surgery and Communication Sciences and the Department of Neurobiology, collected 24 biopsies and examined the olfactory epithelial in each one. Using a single- cell analysis to examine the biopsies, it was discovered that multiple T-cells were heavily inflamed in the olfactory epithelium and that there was a loss of multiple olfactory sensory neurons. This is why many people have had a loss of smell even in the absence of SARS-CoV-2. 

In biology class when learning about the immune system and can fight and prevent viruses, such as SARS-CoV-2. We also learned about the importance of T-cells, which are a large group of lymphocytes that play an important role in the immune response. We also specifically touch upon the central roles of T- cells and how “helper T- cells” recognize antigens and stimulate humoral and cell mediated immunity by releasing cytokines. We have discussed how vital T- cells are to our bodies while fighting off viruses because they protect us from infection and Without T cells, every exposure of pathogens that we face daily could be life-threatening to us. This relates to why our smell could be altered for so long after being infected with SARS-CoV-2 virus because our T-cells aren’t able to properly function since they are inflamed in the olfactory epithelium.

Healthy Human T Cell
According to Goldstien, other COVID-19 symptoms might be caused by a similar inflammation that affected people’s loss of smell. 


Can Reactive Oxygen Species Maintain Stem Cell Function and Prevent Inflammation?

Have you ever wondered what “gut health” really means? What keeps your gut microbiome functioning properly, maintaining homeostasis, and preventing inflammation? Originating from oxygen, reactive oxygen species (ROS) that are highly reactive function as central indicators of cellular flaws and issues in the body, such as inflammation. Nai-Yun Hsu of Mount Sinai has stated that “Reactive oxygen species released by stem cells are critical in maintaining a heathy gut via maintaining proper balance of intestine barrier cell types.”

File:Inflammatory Bowel Disease MTK.jpg 

A team of researchers from the Ichan School of Medicine at Mount Sinai have gone in depth about the importance of these oxygen species for stem cell function, avoiding inflammation, and repairing wounds in a recent study. Using mice as models, the researchers were also able to conclude that microfold cells, called “m cells” regulate an organism’s gut immune response, and emerged from a loss of ROS in mice and humans. 


The experiment was conducted in vino and in vitro conditions with the mice cells, and ex vivo conditions with human intestinal biopsies post-colonoscopy. Both the human intestinal biopsies and mouse cells were utilized to determine the amount of ROS in the body to support a finding. In addition to determining the amount of the oxygen species, the biopsies and mice were used to analyze the “gene expression profile” of barrier cells in intestines of mice and humans that are diagnosed with a “subtype of IBD known as ulcerative colitis.”  


A decrease in these oxygen species can lead to TNF’s emergence in the body, which is a substance that attempts to maintain homeostasis in the body and avoid inflammatory diseases, like IBD and ulcerative colitis. They have concluded that losing species like NOX1, a protein that creates these species, is directly linked with inflammatory diseases like Inflammatory Bowel Disease (IBD). Judy H. Cho, MD, has stated that the study is a breakthrough “in defining the key role of oxygen species in maintaining a healthy epithelial barrier for IBD.” These reactive oxygen species are relevant to AP Bio considering the information we have learned about general biological systems and cells, which function to maintain homeostasis in the body. The mitochondria, which is an organelle of the cell covered in AP Bio, receives signals from gut bacteria that reveals inflammation. While the mitochondria is typically known as the site of cell respiration and performing reactions, new evidence has shown a relationship between the gut microbiota and mitochondria to trigger immune responses and activate barrier cell function. These processes relate to changes to the mitochondria that occur from gut-related issues in IBD patients, meaning that there is a connection to ROS. 


Gut Microbiota

As a conclusion to proving the direct link between the highly reactive oxygen species and treating inflammation, these researchers encourage and plan to conduct further study on this topic, but for using “oxygen species-stem cell modulation therapy” to potentially treat IBD patients. 



Vitamin D Points to Potential Life-saving Therapeutics for Severe Cases of SARS-CoV-2

A promising new joint study by Purdue University and the National Institutes of Health (NIH) suggests that active metabolites of vitamin D are linked to reducing lung inflammation after SARS-COV2 infection. And no, before you break out your vitamin D pills, the vitamins inside your capsules are quite different from the active metabolites studied. Because of this, these researchers are warning those infected with COVID-19 against taking excessive supplements of vitamin D in hopes of reducing lung inflammation.

The researchers identified an autocrine loop involving vitamin D which allows T-helper (Type 1) cells to activate and respond to the active metabolites of Vitamin D which represses the signaling protein, Interferon Gamma. Distinguishing features of Interferon Gamma is the central role it plays in promoting inflammation

Interferon Gamma

Structure of interferon gamma. The two chains are colored in red (chain A) and green (chain B).

Although interferon gamma sounds wildly unrecognizable at first, we have actually learned about these proteins more broadly in our AP Biology class. Interferon Gamma is actually a type of cytokine! Regarding this cytokine’s structure, the proteins that compose interferon gamma are dimerized (sounds familiar? This is because we have also previously learned about dimerization through the tyrosine kinase receptor pathway in class!). 

Along with the suppression of Interferon Gamma, Interleukin 10, a cytokine with potent anti-inflammatory properties, is amplified. This is significant because this cytokine prevents damage to the host and maintains normal tissue homeostasis by reducing inflammation.

IL10 Crystal Structure.rsh

Structure of interleukin 10 as published in the Protein Data Bank.

In the near future, these pathways could be exploited therapeutically to accelerate the shutdown program of hyper-inflammatory lung cells in patients with severe SARS-CoV-2 infections. But for now, before vitamin D is adopted to treat COVID-19, clinical trials are still needed. However, research findings like these are critical to creating effective treatment not just for those infected with SARS-CoV-2, but also other respiratory diseases as well.

What do you think about this new discovery? Do you think this could lead to scientific progress regarding the treatment of inflammation?

How Dandruff Can Lead to Crohn’s Cures

The Intro

Crohn’s disease is an inflammatory bowel disease (IBD) that causes inflammation of the digestive tract. Symptoms can include abdominal pain, malnutrition, stunted growth, and more on the gross side, diarrhea. There is no known cure for the condition, but a research team under David Underhill, “research chair for inflammatory bowel diseases at Cedars-Sinai Medical Center in Los Angeles,” has made a promising discovery in the gut microbiome. The researchers’ observations involve a microfungus present in and on our bodies, but before we unpack their findings, let’s figure out why the heck there are fungi inside our bodies and how all this relates back to dandruff!

The Mycobiome

There is a vast array of microbes that make their home in and around our person. This collection of organisms is known as the microbiome. While our microbiome consists of thousands of different microbial species, a whopping “99.9% of the total number of microbial cells belong to only a few species.” That other 0.1% of microbes is known as the “rare biosphere,” and within this diverse collection of organisms lies the mycobiome, the assortment of microscopic fungi that inhabit each and every one of us. While the microbiome has received lots of attention, especially in our gut area, research on the mycobiome’s effects on the human body is just beginning. Underhill’s team’s discovery gives us a glimpse into just how impactful these relatively rare organisms can be.

The Dandruff

So, what does dandruff from our scalp have to do with the fungi in our gut, and how does all this involve Crohn’s disease? Underhill and his researchers studied Malassezia, a fungus pretty much omnipresent in and around our bodies. It’s been known that a concentration of Malassezia on our scalps causes irritation that leads to dandruff. However, this fungus also inhabits our digestive tract. The research team found that “people with Crohn’s had high concentrations of Malassezia on their intestine walls, while healthy patients had almost none. The researchers then demonstrated that simply adding this type of fungi to the gut — at least, in mice — was enough to exacerbate the inflammation seen in Crohn’s.” Therefore, the same fungal substance that can cause minor dandruff may also be heavily responsible for a serious IBD that affects about 780,00 Americans. 

The Significance

Even though some patients may achieve permanent remission, as we noted before, there is not yet an established cure for Crohn’s disease. However, Underhill’s team’s study raises some questions that could help shape the future of IBD medical development. Could the current expensive, 60% effective anti-inflammatory medicine be replaced with simple antifungal drugs? If we prove that reducing fungus reduces intestinal inflammation, then antifungal Crohn’s cures could be accessible and affordable for thousands of people! In 5th grade, I was diagnosed with Crohn’s, and while my condition has improved, it’s far from cured. It’s exciting to hear about new discoveries that could lead to advances in treatment to help people like myself. Underhill’s team and another team of researchers in Montreal have already begun clinical trials with antifungal drugs, so depending on their results, we may be one big step closer to curing Crohn’s and other inflammatory bowel diseases alike!

I think these discoveries are important and worth talking about, so if you have anything to add, challenge, or discuss, feel free to comment below! Thanks for reading!


Using CRISPR to Prevent Chronic Pain & Inflammation


Researchers at the University of Utah have recently figured out a way to use CRISPR gene-editing techniques to reduce chronic pain and inflammation.

Normally, inflammation around damaged tissue signals various cells to produce molecules that destroy the damaged tissue. However, this can quickly devolve into chronic pain when the tissue destruction does not stop.

The researchers have found a way to use CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) to relieve and prevent chronic pain. Unlike most popular CRISPR techniques, theirs does not involve altering the gene sequences– it instead relies upon epigenetics, and modifying the expression of the genes in the cytokine receptors in inflammatory areas, to prevent cells from producing the molecules that destroy tissue.

The treatment is delivered through a virus, which is injected into the inflammatory site. It is more potentially therapeutic than current treatments for chronic pain, in that it actually prevents tissue destruction and future pain, rather than just relieving present pain. The method is approximately ten years away from being used to treat human patients.

Dysbiosis: Does Imbalance Help?

The gut microbiome is a very large collection of mutualistic relationships between microorganisms and an animal. In our case, these microorganisms control very much of the digestive tract and have influences throughout the body. Crohn’s disease is something that can happen due to imbalance in this microbiome or “dysbiosis“. Usually marked by inflammation in the digestive tract, this disease is a result of an autoimmune response against possibly microbial antigens. Although there is no cure, scientists have determined the best course of action is to relieve the symptoms. This results in disruptions to the gut microbiome.

Inflammation of the colon due to Crohn’s disease

Scientists studying responses in the gut microbiome have found that treatment for Crohn’s disease have caused various responses in the people in the experiment. Antibiotics have been found to decrease bacterial growth in the tract while allowing fungus to grow more freely. Formula diets relieved inflammation and other symptoms but didn’t repair bacterial balance in the microbiome. Immunosuppressants decreased inflammation and bacterial dysbiosis at the expense of increasing fungal dysbiosis. All these methods don’t seem to work out.

But what if the microbiome does not need to be restored to remain healthy? Formula diets caused more dysbiosis but were able to alleviate symptoms. Suddenly, the microbiome does not seem to be as necessary as previous studies suggest. However, this experiment only measures a few variables. Results beneficial to treatments for Crohn’s disease may cause something bad to happen elsewhere in the microbiome. Replacing the gut microbiome would definitely have massive side effects.

Perhaps one day, we could find some way to substitute parts of our mutualistic relationship with the bacteria inhabiting our gut. However, that day seems far off. For now, we should probably stick with what we have.

Original Article

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