BioQuakes

AP Biology class blog for discussing current research in Biology

Author: edcowinsystem

CRISPR-ing the Code: Deciphering Gene Regulation with Epigenome Editing

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On May 13, 2024

In Student Post

Let’s embark on a journey through the labyrinth of our genetic blueprint, scientists wield a powerful new tool, epigenome editing. Imagine having the ability to fine tune the orchestra of our genes, adjusting the volume of each instrument to compose the perfect symphony of life. In a groundbreaking study recently unveiled in Nature Genetics, researchers from the Hackett Group at EMBL Rome have unveiled a modular epigenome editing platform. This revolutionary system offers a glimpse into the intricate dance between our DNA and the proteins that regulate it, shedding light on how subtle molecular tweaks can orchestrate the grand narrative of biological existence. Join us as we delve into the captivating realm of chromatin modifications, CRISPR technology, and the tantalizing secrets they unveil about gene regulation.

CRISPR CAS9 technology

The researchers used CRISPR technology to precisely program nine important chromatin marks in the genome. The CRISPR technology served as the magic wand in the hands of researchers, enabling them to meticulously sculpt the epigenetic landscape of the genome. With CRISPR’s unparalleled precision and accuracy, scientists from the Hackett Group at EMBL Rome were able to program nine crucial chromatin marks at precise locations within the genome. This level of control allowed them to investigate the cause-and-consequence relationships between these chromatin modifications and gene regulation. CRISPR technology facilitates the development of reporter systems, which enable researchers to measure changes in gene expression at the single-cell level. This high-resolution analysis provides deeper insights into the dynamics of gene regulation and allows for the exploration of how different factors, such as chromatin structure and DNA sequence, interact to modulate gene activity. Additionally, CRISPR facilitated the creation of a ‘reporter system’, empowering researchers to measure changes in gene expression at the single-cell level. This enabled them to investigate the causal relationships between chromatin marks and gene regulation, shedding light on how these marks affect transcription, the process of copying genes into mRNA for protein synthesis. By employing a reporter system, they could measure changes in gene expression at the single-cell level and explore how DNA sequence influences the effects of each chromatin mark.

CRISPR Cas9 technology

Surprisingly, they discovered a new role for a chromatin mark called H3K4me3, which was previously thought to be a consequence of transcription. Their findings suggest a complex regulatory network involving multiple factors such as chromatin structure, DNA sequence, and genomic location.The researchers aim to further explore the implications of their findings by targeting genes across different cell types and at scale. This technology not only provides insights into the role of epigenetic changes in gene activity during development and disease but also offers potential applications in precision health by enabling the programming of desired gene expression levels.

The research conducted at he Hackett Group at EMBL Rome connects to a topic we have done in AP Biology. This is Gene Expression and Regulation. gene expression and regulation are fundamental concepts that delve into how genetic information stored in DNA is utilized by cells to produce proteins and carry out various functions. Here’s how the study conducted by scientists from the Hackett Group at EMBL Rome connects to gene expression and regulation in AP Biology. Chromatin Modifications and Transcription. The study investigates how chromatin modifications, such as histone methylation, influence the process of transcription, where genes are copied into mRNA molecules. This aligns with the AP Biology curriculum’s focus on understanding the role of chromatin structure in regulating access to DNA and controlling gene expression. Another way is Regulatory Mechanisms. The study provides insights into the regulatory mechanisms that govern gene expression by examining the causal relationships between chromatin marks and transcriptional activity. Students can learn about the intricate interplay between transcription factors, chromatin modifications, and regulatory DNA sequences in controlling gene expression levels.

Immune Evasion Unveiled: The Thrilling Genetic Drama of Tumor Suppressors and Their Sneaky Dance with Cancer Cells

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On February 27, 2024

In Student Post

Cancer, an unwelcome antagonist in our lives, often emerges as the thief of precious moments with our loved ones and friends. Ever wondered how it manages to disrupt the narrative of our lives, stealing the scenes we hold dear? Or perhaps, reflecting on those stolen moments, have you found yourself questioning the resilience of the human spirit in the face of such a formidable foe? Cancer perfectly reflects the quote that Alfred from  “The Dark Knight” said to Bruce  ‘Some men just want to watch the world burn”. In this case Cancer just wants to watch the world burn because it gains nothing.

Cancer stem cells text resized it

A study conducted recently at Howard Hughes Medical Institute by Stephen Elledge highlights the strange role played by altered tumor suppressor genes. Compared to the common belief that implies mutations in these genes only encourage unrestricted cell growth. The study revealed that in excess of 100 defective cancer suppressor genes in mice may impair the immune system’s ability to identify and eliminate cancerous cells.  Do you know how the immune system is able to detects and eliminate cancerous cells? If not this is how. The immune system is able to identify and eliminate the cancerous cells by using  T cells. These T cells constantly patrol the body to identify cells that display abnormal or mutated proteins on their surfaces. These proteins, known as antigens, can be indicative of cancerous changes. Dendritic cells then engulf and process abnormal proteins from cancer cells. They then present these antigens on their surfaces. They then present the cancer antigens to T cells.This activates specific T cells (cytotoxic T cells) that are capable of recognizing and targeting cells with the presented antigens. Activated cytotoxic T cells travel to the site of the cancer cells and release substances, such as perforin and granzymes, that induce apoptosis (programmed cell death) in the cancer cells. Successful elimination of cancer cells leads to the development of memory T cells. These memory cells “remember” the cancer antigens, providing a faster and more efficient response if the same cancer cells reappear. This challenges the conventional understanding that mutations in tumor suppressor genes primarily trigger unrestricted cell division. Instead, it suggests that such mutations can also impact the immune system’s ability to identify and eliminate cancerous cells through the T cell-mediated recognition process. This broader perspective underscores the complex interplay between genetic mutations, immune responses, and cancer development.

Tumor Growth

This has several key concepts that we covered in our AP Biology class, particularly related to cell regulation, cancer, and the immune system.

The immune system’s role in identifying and eliminating cancer cells is a significant aspect of the AP Biology curriculum. The discussion of T cells, dendritic cells, and the process of presenting cancer antigens aligns with the immune system’s functions and responses to abnormal cells. This aligns with what we learned in AP Bio regarding the immune system’s crucial role in defending the body against abnormal or potentially harmful cells, including cancerous cells because we got to see how the T Cells, Dendritic Cells, and Memory T Cells really work. We also got to see how the immune system also works directly with blood sugar levels. With various activities in class with the skittles as glucose and how the pancreases would either send a message to produce insulin or  glucagon depending on which the body needed to maintain a balanced blood sugar level.

 

Unmasking Covid: A Rollercoaster of Well Being

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On December 11, 2023

In Student Post

Covid for many of us, is a villain. It tore society away from each other. Making us hide inside and distancing ourselves because we were scared. Covid also had many effects on us because it attacked people with health issues such as diabetes, fatigue, or blood clots.

SARS-COV-2 Impfstoff (50745105642)

A study based on the health records of about 140,000 U.S. veterans. shows the risk people with health issues such as diabetes, fatigue, or blood clots can have even with COVID being around for 2 years.  The study compared veterans who were infected with SARS-CoV-2 early in the pandemic with those who did not test positive. Even two years after their infections, individuals who had COVID-19 were at a higher risk for various health problems, including heart disease and gastrointestinal issues. Hospitalized patients during their initial COVID-19 cases were more likely to experience these issues, but those with milder infections were also at higher risk for certain medical problems. The study highlights the long-term risks and burden of disease associated with COVID-19, even for individuals with mild cases. However, the study has limitations, including its reliance on electronic health records. The use of electronic health records is a limitation in the study because electronic health records or EHRs, contain data that is available within the healthcare system. They may not capture information about symptoms or conditions that patients experience outside of the healthcare setting. EHRs may focus on medical events and diagnoses, potentially missing information about the broader impact of long COVID on patients’ daily lives and well-being. The study’s reliance on EHRs from a veteran population may introduce biases. For example, the data may be skewed towards men, as about 90 percent of the veteran records included in the study were from men. This may not fully represent the experiences of women, who are also affected by long COVID. People with health issues are much more vulnerable because certain health conditions do increase the risk of complications and severe illness if infected with the virus.Diabetes, can weaken the immune system, making it more challenging for the body to mount an effective defense against the virus. Diabetes, especially uncontrolled diabetes, can impair the function of various immune cells, including neutrophils and macrophages. These cells play a crucial role in recognizing and eliminating pathogens, such as bacteria and viruses. Diabetes also affects T cells,  which are a type of white blood cell that plays a central role in the immune response. In diabetes, there may be a reduced activity of T cells, which can compromise the body’s ability to identify and destroy infected cells.

Primary immune response 1

In AP Bio we saw the process in Pathogen Specific Recognition which is a part in the Immune System. First a pathogen would appear and the macrophage would ingest the pathogen, allowing the lysosome to come and kill the pathogen. Then the macrophage would present a antigen fragment with MHC proteins to helper T cells. This then causes the helper T cell to bind with the antigen fragment allowing it to produce interleukin. The interleukin would then either trigger cell-mediated response with T cells or humoral response which include B cells. The difference between the two types of response are with cell-mediated response T-cells make killer T-cells which kill infected or cancerous cells and  humoral response secrete antibodies which bind to and neutralize pathogens. How has the journey with COVID-19 unfolded within your family over the past two years? What challenges have you faced, and what lessons or changes have emerged from this unique experience?

 

A Sustainable Breakthrough To Rescue Drinking Water

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On October 31, 2023

In Student Post

Water is a necessity for all living things. Water is fundamental component of cells and is essential for various biological processes. Water serves as a medium for the transport of nutrients in both plants and animals. In plants, water is crucial for the uptake of minerals from the soil and their movement within the plant. For humans, access to clean and safe drinking water is crucial for survival and good health. Lack of clean water can lead to waterborne diseases and other health issues.

Water drop impact on a water-surface - (2)

According to a study conducted at the University of Bath, Swansea, and Edinburgh students found a breakthrough method to supply drinking water to disaster zones with limited electrical power. Unlike your typical way of  reverse osmosis where a high pressure pump is used to increase the pressure on the salt from the seawater so that the salt can be extracted from the water. The water is then forced to cross semi-permeable RO membrane. The primary purpose of an RO membrane is to selectively allow the passage of water molecules while preventing the passage of contaminants. In the students’ approach they use a small amount of electrical power to draw the ions to go though the membrane which also bring the water molecules with them. This also reduces the risk for membrane clogging but also less electrical power. The Professor Frank Marken also stated that with this breakthrough they could also be able to use it in the medical field by such as applications for dosing systems like insulin. This refers to the adaptability of the technology for medical use. The process, which utilizes a small amount of electrical energy to move ions through a membrane, could be miniaturized and applied to create precise dosing systems. The method allows for precise control over the movement of ions through the membrane. In a medical context, this could translate to a highly controlled and precise dosing mechanism. For medications like insulin, where accuracy is crucial to manage blood sugar levels effectively, such precision is highly desirable

Reverse osmosis

In AP Biology, We tried to use the principles of osmosis to determine different concentrations of various unlabeled solutions. In osmosis, water moves through the membrane to equalize the concentration of solute on both sides. The driving force behind osmosis is the difference in concentration, commonly referred to as the concentration gradient. The side with lower solute concentration is often called hypotonic, while the side with higher solute concentration is hypertonic. There are three main types of solutions based on their osmotic pressure and their effects on cells, isotonic solution, hypertonic solution, and hypotonic solution. The direction of water movement in osmosis is influenced by the relative concentrations of solutes on either side of the membrane. Water moves from areas of lower solute concentration (hypotonic) to areas of higher solute concentration (hypertonic) until equilibrium is reached. With the principles of osmosis we then would calculate each different solution to find the water potential. This scientific breakthrough of being able to make seawater into drinkable water with less electrical power is breathtaking. Not only does this new technique use a small amount of electrical energy. This makes the process more energy-efficient and reduces energy waste. This method could be applied on a smaller scale, making it suitable for areas where there is a need for drinking water but limited infrastructure for example, deserts and other remote areas which can help people who can not obtain fresh drinkable water a bigger chance to obtain water. Can you think of any other places that can benefit from this experiment?

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