After returning from a relaxing winter break, the AP Bio Team has jumped right back into the swing of things. We started a new unit, continuing our studies on gene regulation and focusing on DNA tools and biotechnology. Last week we completed multiple virtual labs and online explorations covering topics such as stem cells, cancer genetics and bacterial identification. It was really interesting to learn about the different types of stem cells and how they can lead to potential treatments to cure diseases like leukemia. At the same time, we uncovered many ethical questions regarding stem cell research. Many people do not feel comfortable with destroying a human embryo, and scientists have struggled with questions such as "When does a human life truly begin?" or "Can the destruction of one human embryo be justified if it saves a countless number of other patients?". It will be interesting to see where stem cell research goes in the future.
The main purpose of the bacterial identification lab was to familiarize us with the science and techniques used to identify different types of bacteria using their DNA sequence. The four basic steps involved in this process are:
1. Prepare a sample from a patient and isolate whole bacterial DNA
2. Make many copies of the desired piece of DNA
3. Sequence the DNA
4. Analyze the sequence and identify the bacteria
The lab showed us how the PCR (polymerase chain reaction) machines allow many copies of DNA to be made, and how gel electrophoresis is a method used to separate molecules based on difference of size or charge. We were able to identify the bacteria by determining whether the sequence we found had a significant degree of similarity to another known sequence on the BLAST database.
Later in the week we conducted our own mini-lab using gel electrophoresis to identify whether or not each patient was normal, had sickle cell disease or was a carrier of sickle cell disease. The first sample was of normal hemoglobin, the second sample was sickled hemoglobin and the third sample was a carrier of sickle cell. Those three samples represented the control of the experiment. The fourth and fifth samples were patients with unknown hemoglobin. The wells are placed on the negative end of the gel electrophoresis box. Because the sickle cell hemoglobin is slightly more positive compared to normal hemoglobin, the sickle cell hemoglobin will travel slower across the gel. The carrier hemoglobin shows two bands instead of one. After the gel ran, the results showed that patient 1 was normal and patient 2 was a carrier.
In another mini lab, we conducted a microarray analysis to a newly diagnosed breast cancer patient to determine her gene expression profile. We then proceeded to decide on her course of treatment. In order to perform the microarray analysis we had to collect healthy and cancerous tissue samples from the patient. That way we were able to look at what genes are turned on and off in the healthy cells compared to the cancerous cells. Based on the results we were able to match the patient with the cancer treatment that would be most effective.
Next, we learned about epigenetics, the study of heritable traits that are not caused by changes in the DNA sequence. We watched the documentary "Ghost in Your Genes", which discussed how different experiences could affect gene expression. Scientists following the mapping of the human genome scientists discovered chemical markers on DNA that effectively turn genes on or off, dramatically influencing growth and development. The markers vary widely from person to person and are influenced not just by the environment but by experiences. Most remarkably the markers can be inherited generation after generation. A study was done on identical twins where researchers collected cells from twins ages 3 to 74. It revealed epigenetic tags that showed younger twins having extremely similar epigenomes, but the older twins had very different epigenomes. This supports the idea that experiences are linked to one's epigenome. A different study was done with rats, specifically looking at the behavior of the mothers. The research showed that the care the rats receive as babies can affect long term health conditions. A chemical mark somehow captures the memory of a nurturing mother. Stress levels of the neglected rats soared. This shows how personality traits could potentially be linked to one's epigenome. In the last study conducted in the documentary, information was gathered from a Swedish village that showed how a famine might affect people a century later, even if they haven't personally experienced it. According to the research, if the grandfather had experienced a surplus of food in early childhood, the chances of his grandson having diabetes would be four times greater. This study focused on the environment molding one's epigenome. These discoveries have changed the face of inheritance it can lead us to believe that the decisions we make today can have a big impact on the lives of our children and grandchildren.
Continuing to study gene expression, the AP Bio Team acted out the functions of the lac operon!
The last major activity of these past 2 weeks was a really cool lab where we were able to make bacteria glow! The process of introducing foreign DNA into a host is called transformation. Biofluorescence is the ability of an organism to produce proteins that make the organism glow. The gene that codes for this Green Fluorescent Protein (GFP), known as the gfp gene, can be isolated from a source (an organism such as a jellyfish) and used to transform another organism. The bacterium E. coli is ideal for transformation because this bacterial cell is small and reproduces quickly. Arabinose is a sugar that bacteria break down for nutrients. The arabinose operon contains a promoter and three genes that code for three enzymes that digest arabinose. In the modified operon, these genes have been replaced by the gfp gene, so that when arabinose is present, the pathway to produce GFP will be triggered and the transformed bacteria will fluoresce.
Thanks so much for reading! It has been a crazy 2 weeks packed full of information. I can't wait to see what comes next!
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