BioQuakes

AP Biology class blog for discussing current research in Biology

Author: papanagopoulos

Crispr Gene Editing Aids in Sustainable Bioenergy Production

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On April 23, 2023

In Student Post

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CRISPR/Cas-9 is the most precise gene editing tool. It is a specific, efficient and versatile gene-editing technology used to modify, delete or correct precise regions in our DNA.

Miscanthus sinensis ja01

New research shows that for the first time, researchers have successfully demonstrated precision gene editing in miscanthus. Miscanthus is a promising crop for sustainable bioenergy production due to its high yield and superior environmental adaptability.

A study was done by the Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), a Bioenergy Research Center (BRC) funded by the U. S. Department of Energy. In this study they edited the genomes of three miscanthus species using CRISPR/Cas9.

In this study researchers demonstrated gene-editing in three species of miscanthus: Miscanthus x giganteus, M. sacchariflorus, and M. sinensis. These plants are paleo-polyploids which refer to ancient genome duplications which occurred at least several million years ago. Since these plants are paleo-polyploids the design of the RNAs that locate genetic material for editing needed to target all copies of a gene.

The researchers used the information from what they know about miscanthus and identified RNAs that could target homoeologs, or duplicated gene copies, of the phenotypes in miscanthus plant tissue. To identify miscanthus lines that transformed well, the researchers screened germplasm from commercial vendors and others that help research the study.

Prior to this study, the bioengineering work was limited to sorghum and cane because the methods for precise engineering in miscanthus had not been developed.

This relates to AP biology because CRISPR/Cas 9 technology allows scientists to edit genes and manipulate gene expression with a level of ease that was no possible using other methods. In AP biology we learned how gene expression works and what happens when the encoded gene is changed. Gene expression is accomplished in two main steps: transcription and translation. In transcription an RNA transcript is created from one strand of template DNA. In this stage RNA polymerase binds to prometer, DNA unwinds, polymerase initiates RNA synthesis. The polymerase then moves downstream, unwinding DNA and adding RNA nucleotides. The RNA transcript is then released and RNA polymerase detaches. After transcription translation occurs where cells make proteins using the genetic information carried by the mRNA. This is different in the use of CRISPR/Cas 9 as, unlike coding DNA which gets transcribed and eventually translated into proteins, these regions gets transcribed but never translated.

Can Concussions Lead to Higher Risks of Dementia?

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On March 5, 2023

In Student Post

According to new research, repeated concussions are linked to worsen brain function in later life, including higher risks of Alzheimers and Parkinson’s disease.

Concussion Anatomy

A concussion is a type of traumatic brain injury caused by a bump, blow, or jolt to the head or by a hit to the body that causes the head and brain to move rapidly back and forth. This sudden movement can cause the brain to bounce around or twist in the skull, creating chemical changes in the brain and sometimes stretching and damaging brain cells.

A study led by the University of Oxford and the University of Exeter, published in the Journal of Neurotrauma, included data from over 15,000 participants found that people who reported three or more concussions had significantly worse cognitive function, which got worse with each concussion after that.

The researchers found that reporting even one moderate-to-severe concussion was associated with worsened attention, completion of complex tasks and processing speed capacity. Participants who reported 3 concussions, even mild concussions, throughout their lives had significantly worse attention and ability to complete complex tasks. Those who reported 4 or more mild concussions showed worsened processing speed and working memory. Each additional reported concussion was linked to progressively worse cognitive function.

According to Dr. Vanessa Raymont, senior author of the study from the University of Oxford, head injuries are a major risk factor for dementia and “this large-scale study gives the greatest detail to date on a stark finding — the more times you injure your brain in life, the worse your brain function could be as you age.”

The research indicates that people who have experienced three or more even mild episodes of concussion should be counselled on whether to continue high-risk activities.

This article relates to AP biology because when a concussion occurs this affects the body’s ability to send signal to the brain (cell signaling). Cell signaling occurs when a cell detects a signaling molecule from the outside of the cell. A signal is detected when the chemical signal (also known as a ligand) binds to a receptor protein on the surface of the cell or inside the cell. When the signaling molecule binds the receptor it changes the receptor protein in some way. This change initiates the process of transduction. Signal transduction is usually a pathway of several steps. Each relay molecule in the signal transduction pathway changes the next molecule in the pathway. Finally, the signal triggers a specific cellular response. In cell signaling the axon sends electrical impulses from the neuron travel away to be received by other neurons. After a concussion, damage to axons is much more common than damage to other parts of the cell. The axon in the brain is a long extension of the cell which transmits impulses. The axon carries electrical impulses that help communicate within the brain and between the brain. When the axon is damaged neurons cannot properly communicate, a damaged axon has more trouble sending its signals, interfering with the brain’s ability to do its job. A concussion also makes it difficult for the cells to distribute chemicals and materials to all areas of the cell, this occurs in the synapse where impulses are transmitted from one neuron to another.

Gardening May Help Reduce Cancer Risk and Boost Mental Health

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On January 16, 2023

In Student Post

“Get more exercise. Eat right. Make new friends.”

SF Japanese Garden

A new study reveals that community gardening helps lower stress and anxiety, and reduces cancer risks. Researchers have found that those who gardened had elevated fiber intake and increased physical activity.

A study conducted by Jill Litt, a professor in the Department of Environmental Studies at CU Boulder, funded by the American Cancer Society, was the first-ever, controlled trial of community gardening found that those who started gardening ate more fiber and got more physical activity — two known ways to reduce risk of cancer and chronic diseases. They also saw their levels of stress and anxiety significantly decrease.

During this study, in the spring, Litt recruited 291 non-gardening adults and assigned half of them to the community gardening group and the other half to a control group. The adults in the control group were asked to wait one year to start gardening.

By fall, the adults in the gardening group were eating on average 1.4 grams more fiber per day than the control group. The gardening group’s fiber intake increased around 7%.

Fiber exerts a profound effect on inflammatory and immune responses, influencing everything from how we metabolize food to how healthy our gut microbiome is to how susceptible we are to diabetes and certain cancers. It also helps regulate the body’s use of sugars, helping to keep hunger and blood sugar in check.

The gardening group also increased their physical activity levels by about 42 minutes per week. The CDC recommends at least 150 minutes of physical activity per week. Only a quarter of the U.S. population meet the exercise guidelines. With just two to three visits to the community garden weekly, participants met 28% of that requirement.

The participants in this study also saw that their stress and anxiety levels decrease. Those who came into the study most stressed and anxious saw the greatest reduction in mental health issues.

This article relates to AP biology because as we learned in the blood glucose regulation simulation, exercise and eating well helps regulate blood glucose levels. Fiber also plays an important role in regulating blood glucose levels. It is important to keep your blood sugar levels in range to help prevent or delay long-term health problems. Staying in your target range can also help improve your energy and mood. This is also an example of a negative feedback loop.

 

 

Can Keeping Indoor Humidity at a “Sweet Spot” Reduce the Spread of COVID-19?

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On December 6, 2022

In Student Post

Sars cov2The COVID-19 pandemic has taught us that indoor air quality matters. It has also taught us that indoor spaces need clean air in order to protect the health and well-being of the people inside. According to a study done by MIT, researchers found that indoor relative humidity may also influence the transmission of the virus. 

In a recent study appearing in the Journal of the Royal Society Interface, the MIT team reports that maintaining an indoor relative humidity between 40 and 60 percent is associated with relatively lower rates of COVID-19 infections and deaths, while indoor conditions outside this range are associated with worse COVID-19 outcomes. To put this into perspective most people are comfortable between 30 and 50 percent relative humidity, and an airplane cabin is 20 percent relative humidity. 

To conduct this research, the MIT team focused on the early period of the pandemic when vaccines were not yet available. This is important because with vaccinated populations it would be unclear the influence of any other factor, such as humidity. 

In order for the MIT team to find this “sweet spot” between 40 and 60 percent relative humidity, the researchers found that whenever a region experienced a rise in COVID-19 cases and deaths, the estimated indoor relative humidity was below 40 percent or above 60 percent. 

According to co-author Lydia Bourouiba, director of the MIT Fluid Dynamics of Disease Transmission Laboratory, “indoor ventilation is still critical.” However, “maintaining an indoor relative humidity in that sweet spot — of 40 to 60 percent — is associated with reduced Covid-19 cases and deaths.”

This study relates to AP Biology as COVID-19 affects the immune system. When the virus first enters the body, the body’s response starts by engaging two kinds of immune cells: B cells, which produce antibodies that fight off the virus, and T cells, which destroy infected cells. After this initial response, levels of antibodies in the bloodstream begin to fall. The humidity in the air also relates to biology because in low humidity environments below 40 percent our mucous membranes dry and this “mucociliary clearance” process is impaired. This leaves us more susceptible to airborne infections, like the flu or common cold. When the relative humidity is above 60 percent, as in the case of humid weather, the sweat your body produces cannot evaporate, leaving our bodies feeling hot and sticky. To cool off, our bodies must work even harder. This results in excessive sweating, increased rate and depth of blood circulation and increased respiration. This generates a negative feedback loop to help our body return to a normal state (homeostasis).

105 Negative Feedback Loops

Can Mouthwashes Suppress SARS-CoV-2?

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On October 24, 2022

In Student Post

Various Listerine Products

SARS-CoV-2, the COVID causing virus, could spread from the oral and nasal cavities (mouth and nose). Along with infecting the cells of the respiratory tract, the virus also also infects the cells of the lining of the mouth and salivary glands.

A recent study led by Professor Kyoko Hida at Hokkaido University suggests that a component found in mouthwashes could have an antiviral affect on SARS-CoV-2. Low concentrations of the chemical cetylpyridinium chloride, a component of some mouthwashes, has an antiviral affect on SARS-CoV-2.

Mouthwashes contain antibiotic and antiviral ingredients that fight oral bacteria. It has been demonstrated that cetylpyridinium chloride (CPC) reduces the viral load of SARS-CoV-2 by disturbing the lipid membrane surrounding the virus. While there are other chemicals with similar effects, CPC has the benefit of being tasteless and odorless.

In this study, researchers were interested in studying the effects of CPC in Japanese mouthwashes. Japanese mouthwashes typically contain a fraction of the CPC compared to previously tested mouthwashes. Researchers tested the effects of CPC on cell cultures that express trans-membrane protease serine 2 (TMPRSS2), which is required for SARS-CoV-2 entry into the cell.

During this study researchers found that within 10 minutes of treatment CPC decreased SARS-capacity CoV-2’s for cell entrance and infectivity. They also discovered that mouthwashes that contain CPC perform better than CPC alone.

This study relates to AP biology because the chemical found in mouthwash helps breakdown the lipid membrane surrounding the virus just like the cells on your tongue produce lipase which helps break triglycerides down.

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