Drafts

Structural inequalities are found in societies not only create environments were disease can thrive within those of lower position but also increase the stress of those same people's life which increases their stress even more.  One of the most impactful stories from these week's reading that resonated with these issues was the increased change of pre-term births as well as infant mortality.  This pattern was found across education levels of African Americans (an atypical birthing pattern) in the United States which indicated not just a case of structural violence but as well as cultural violence.  Cultural violence is key in normalizing all the structural violence which is why it took so long for these patterns to be recognized and accepted by science.  Structural violence is often hidden within society.  Those who created the system of violence and power are often those who benefit from the structure and do not want to accept its flaws to the minority for the sake of it turning on them.  Another key theory in violence theory is the fear of the unknown (additional stress).  When in a medical system with no understanding of what is going on around them and in their body brings this fear to the forefront of worry.  As a result, violence entails either in aggression to the medical system or it riddles the human body.

Today is Halloween, which means dining halls at the University of Massachusetts - Amherst will be preparing for their annual fresh lobster special. Fresh lobsters must be prepared in a particular way. Seafood should always be prepared with extra care because shellfish is a common allergen to the public. One topic that is talked about around lobsters is their innate ability to be immortal. Biological immortality in lobsters is expressed through the telomerase gene. When DNA is replicated, we lose DNA at the ends of our chromosomes (telomeres). Studies have linked the shortage of telomeres with aging. Telomerase is an enzyme that reduces the loss of telomeres. 

 Aquaculture is a growing industry but has yet to take hold in most of the countries across the world. Seaweed aquaculture is primarily used for food, medicine, and cosmetics. Increasing seaweed production for food markets appears to be the best course in order to increase seaweed cultivation and subsequently it’s beneficial carbon-sequestering effects. Seaweed aquaculture is not an end-all solution to climate change and carbon buildup. There would need to be significant increases in aquaculture alongside reductions and reforms of the biggest CO2 production industries and locations for seaweed aquaculture to have a significant benefit. Currently, this method of carbon sequestering has gone relatively undeveloped and should be implemented world-wide where growth conditions are right as an ecologically- beneficial method of reducing carbon and CO2 buildup in the environment.  

I think that one of the most interesting things that I've encountered while working in a lab is how a large number of samples affect how the scientists behave around the samples. I have been in labs where the main experiment was to do PCR, and I've worked in labs where PCR is just a chore that no one else really wants to do. I think one of the biggest differences between the people who are still learning and the people who do this for a career is that people who do it as a career really does not care about the things that are not the most important things. for example, when teaching in the lab, one of the ways that the students do it is to make each master mix for a specific gene and then add to the DNA and everything is carefully calculated. This is different if a person does this for a living. They are much less likely to be careful and count the concentration of the cells. they are far more likely to just add enough that will give them the results that are needed to do the experiment that can actually be published because of this, when I worked in labs, I was told that I should have some idea of how much 1ul looks like in the pipette and be able to add that much instead of going back and forth between the DNA and the PCR tubes.  Being careful isn't as important as getting things done at work especially if there are a lot of resources and there is high pressure to get results like at a company.  Being careful is very good when starting out, but it quickly becomes a burden when there are over 100 PCR to do and that isn't even the main focus of the experiment. I have also taught people in trypsonizing the cell cultures that the amount that is added is whatever that will trypsinize the cells without killing the cells. I will usually just pour the reagent instead of taking careful measurements of it. this was a big change from how I did it at the beginning where I spent most of the time splitting cells and each time there was a new experience. now because the focus isn't n splitting the cells, I just do whatever is the fastest and still get the result that I want. I think that something like this is not really something that can be really be taught at a class but can only be learned through working in a lab. although, the idea of having a class where the main objective is to find better ways to do simple and common lab technique is interesting. 

one of the techniques that I use in the lab the most often in culturing cells. this is also the technique that I encountered most often when analyzing studying biochemistry. it is also one of the hardest one to talk about because there are so many different variations on it. One of the biggest differences between different cell lines is the media used. Depending on the different cell lines used, there are different media used and different things that are added to cells. While immortalized cells need very few things, only FBS that provides nutrients and antibiotics to prevent contamination, primary normal cell lines can be incredibly fussy, with things like growth hormones and other things that are needed to keep them alive. Making the media itself can be a bit of a challenge because there is a need for many different things at specific concentrations. to cultivate a cell there is a need for a flask or a plate. while some cells are able to grow in a suspension, others must be grown in a container with a surface that the cells can adhere to. the cells are then left in the incubating, which is typically at 37 degrees to grow, however, if the cells are allowed to grow for too long, they will become too confluent, and as a result, the properties of the cell will change. This may or may not be desirable depending on the experiment that the cells are needed for. If the cells cannot be confluent, the cells would need to be split. to do this, the media is removed and the cell surface is washed with PBS and trypsinized so that the cells can detach (if the cell is an adherent cell). Then trypsin is neutralized using media and put into the centrifuge tube to be spun. after it is spun, the media is removed, and new media is added. then the cells are resuspended in the tube and a portion of it is put into a new flask to allow for growth along with the new media that is added. 

Many students, including myself drink alcohol, ignoring the possible effects it can cause on our brain. We all know that while under the influence, it has an immediate effect on our brain, but I am curious about the long term effects. It wasn't until I did some research about it where I found out it was harmful to our brain and its' developement. While under the influence of alcohol, there will be a difficulty walking, blurred vision, surred speech, slower reaction times and an impaired memory. These by itself are very harmful to the brain. Of course, if someone drinks alcohol once, that does not mean they will forever be impaired, but it is drinking over and over again that can harm the individual. Alcohol can produce detectable impairments in memory after only a few drinks and, as the amount of alcohol increases, so does the degree of impairment. Large quantities of alcohol, especially when consumed quickly and on an empty stomach, can produce a blackout, or an interval of time for which the intoxicated person cannot recall key details of events, or even entire events. Additionally, you do not retain information because we do not go through "REM" sleep when intoxicated. People who have been drinking large amounts of alcohol for long periods of time run the risk of developing serious and persistent changes in the brain. Damage may be a result of the direct effects of alcohol on the brain or may result indirectly, from a poor general health status or from severe liver disease.

Many students, including myself drink alcohol, ignoring the possible effects it can cause on our brain. It wasn't until I did some research about it where I found out it was harmful to our brain and its' developement. While under the influence of alcohol, there will be a difficulty walking, blurred vision, surred speech, slower reaction times and an impaired memory. These by itself are very harmful to the brain. Of course, if someone drinks alcohol once, that does not mean they will forever be impaired, but it is drinking over and over again that can harm the individual. Alcohol can produce detectable impairments in memory after only a few drinks and, as the amount of alcohol increases, so does the degree of impairment. Large quantities of alcohol, especially when consumed quickly and on an empty stomach, can produce a blackout, or an interval of time for which the intoxicated person cannot recall key details of events, or even entire events. People who have been drinking large amounts of alcohol for long periods of time run the risk of developing serious and persistent changes in the brain. Damage may be a result of the direct effects of alcohol on the brain or may result indirectly, from a poor general health status or from severe liver disease.

I realized while working on a project on CMT 1a, specifically a project where I have to describe the lives of those who are affected by CMT1A, that the clinical descriptions and the stories that the patients tell each other and others do not quite line up. While the descriptions given by doctors are cold and clinical, as they should be there is so much more than the description of the disease in patients who were affected by this disorder. For example, some of the classic symptoms are muscle loss feet and extremities deformities and loss of sensation. While this is interesting from a clinical point of view, this is made even more interesting hearing the patient's personal account of how this affects them personally and how the severity of different symptoms causes trouble or at times odd moments of hilarity in their daily lives. according to the patients because there are feet deformities, if they walk very long, they are liable to have their feet bleed. While this sounds horrifying to the people who do not have the disease to those who do, it is their daily lives, and since the disease also leads to a loss of sensation, this means that they cannot feel it. Symptoms can provide moments of levity as well. few people have told stories of friends or family trying to shock people using a shocking pen, and it not affect the person who was affected at all. Another thing that surprised me is how much the patients were knowledgeable about the drugs that were in a trial in order to treat this disease and their willingness to go any length to get better. In treating CMT, there is a drug combination treatment that is called PTX3003, which consists of three drugs, and laxative, an anti-addiction medication, and antiseizure medication. through the use of these three drugs, studies have proven that it can alleviate the symptoms of CMT 1A. The medicine is currently in phase 3 trials. However, since there are improvements in phase 2 trials, there are patients who have got their doctors to prescribe the three medication that makes up PXT3003 and take them with some visible improvement.  I think that as I learn more about medicine and how it works as well as the process in which science is created, I realize more and more that it is incredibly human and relies on so many soft skills to get anything done. this is endlessly frustrating for someone like me tho is not sociable, but it is also a reminder that scientists may have the image of logic, they are human and will have flaws stemming from that. 

Genomic analysis is the identification, comparison of genetic features and their expression through the use of techniques such as DNA sequencing and bioinformatics. Genomic analysis is generally considered to be divided into two categories; structural genomics which identifies certain genomic structures in the genome and functional genomic analysis which analyses the expression of genes and their interactions often also called transcriptomes. Genomic analysis was made available through the prevalence and availability of gene sequencing. While human genome project sequenced the entire human genome most of the genomic analysis would not be possible would not be possible without the further accessibility of sequencing to the point where currently it is extremely affordable to have a genome sequenced, and other techniques such as next-gen sequencing and whole-genome sequencing that does not depend on the isolation of cells in order to sequence the genes. Because these data that are generated from sequencing are generally put online in databases, these data are both available and able used to be used for purposes that are not intended by the researchers who have originally made the sequence. The data set is so large that a single sequencing can be the basis of several papers. Because of this, there is a data analysis bottleneck where there is so much data that needs to be analyzed but there is not enough time or computing power to analyze the entire genome for all the information that it can yield. Because there are so many different venues that use bioinformatics, there is a major need for people who are able to analyze the data that is available and easily accessible.  Degrees in Bioinformatics is quickly becoming one of the highest-paid and available jobs on the market.

Hox genes are a superfamily of genes that specify an organism’s body plans. Within the protein made by the HOX genes, there is a homeobox domain is a domain that controls anatomical development in eukaryotes. In animals, there are 16 major classes of homeodomains. HOX genes were originally discovered in 1994 in fruit flies. The HOX gene is especially important in the regulation of development. A mutation in the HOX gene can have a crippling effect on the development, often resulting in physical disorganizes or termination of pregnancy. Because HOX genes are most vital to the development of the fetus, the HOX gene is mostly conserved across species. A mutation in HOX gene that gets fixed in a population can result in a completely new plan such as those that are present in snakes. In snakes, they specifically have a mutation in the HOX6 gene which causes the snake to lose the forelimb. Because of this, snakes have a widely different body plan compared to those of its close relatives who have forelimbs. In labs, hox gene regulation and expression can be manipulated to make certain body parts grow where there normally isn’t a certain body part. The most famous example of this is in fruit flies where researchers caused legs to grow where the eyes should be by manipulating a hox gene called antp. Experiments show the importance of HOX gene in maintaining the general structure of the body plan.