Elsa Vaughn

Biology 1610 -  Blog Assignment

Professor Dr. Michaela Gazdik

December 12, 2016

SCIENTIFIC AMERICAN –naturenews

Topic 1

Biochemists’ Discovery Could Lead to Vaccine Against ‘Flesh-Eating’ Bacteria.-

Biochemists at the University of California San Diego have uncovered patterns in the outer protein coat of group A Streptococcus that could finally lead to a vaccine against these highly infectious bacteria.

The term flesh-eating bacteria refer to a necrotizing fasciitis.  It starts in the tissues just below the skin and spreads along the flat layers of tissue (fascia) that separate different layers of soft tissue, such as muscle and fat, which produce a necrotizing infection that could result in the loss of the affected part.

Flesh-eating disease, caused by the bacterium known as Streptococcus pyogenic, Streptococcus pyogenic,   produces toxins that destroy tissues such as muscles, skin, and fat, and are commonly responsible for mild sore throat (pharyngitis) and skin infections. Rarely, this form of strep bacterium causes severe illnesses such as toxic shock syndrome and necrotizing fasciitis.

“When we become infected with a particular strain of group A Strep, we generally mount an immune response against the particular M protein displayed by that strain,” explains Ghosh. “But this immunity works only against the infecting strain. We remain vulnerable to infection by other group A Strep strains that display other types of M proteins on their surfaces.

Biochemists detailed four crystal structures of four different M protein types, each bound to human C4BP, with common pattern sequences hidden within the differences that linked all these proteins together. The idea is to have antibodies do the same thing as C4BP—that is to recognize many different M protein types. Ghosh says: “That way, the antibody response will not be limited to one M protein and one stain of group A strep. With that purpose chemists are now working on developing a vaccine that will be protective against all strains of group A strep.

Comment 1.- General Comment. -Because our immune system must recognize the different proteins before launching an immune response with antibodies, our immunity system works only against the infected strain. The researchers want to combat C4BP binding a broad variety of M protein types.

Comment 2.- Question.- If M proteins of different types appear to be unrelated in sequence to one another, and the  antibody response is specific and  limited to a single M protein type,  how do they are going to get the effective vaccine?

Comment 3.-Answer. - By blocking the complex interaction between M proteins and C4BP. Two graduate students Sophia Hirakis and Rommie Amaro are studying protein structures by computer. It allowed the researchers to understand that there are common sequence pattern. This sequence pattern is used to recruit C4BP to the surface of group A strep by the different M protein types. 

I found this article very interesting because this job is going to help, individuals who are infected with “flesh-eating bacteria”

Topic 2

Accelerating Tomato Engineering

Source: Cornell University. 

Tomatoes are already an ideal model species for plant research. Scientists at the Boyce Thompson Institute (BTI) just made them even more useful by cutting the time required to modify their genes by six weeks, it means procedure from 17 weeks to just 11. They developed a better method for "transforming" a tomato--a process that involves inserting DNA into the tomato genome and growing a new plant. By adding the plant hormone auxin to the medium that supports growth of tomato cells, they can speed up the plant's growth.

Typically, transformation works by using a soil bacterium called Agrobacterium tumefactions to insert a new segment of DNA into the cells of tomato seedling tissues. The transformed cells are transplanted onto plant regeneration medium, which contains nutrients and hormones that cause the tissue to grow into a tiny new plant.

Researchers in the Van Eck lab perform tomato transformations routinely, as a research method to understand how individual genes affect tomato growth and development “We’re looking at the genes and gene networks involved in stem cell proliferation, meristem development and flowering and branching,” says Van Eck, “with the end goal being that maybe genes that we identify in tomato, which is strictly being used as a model, might help us understand what can be done to increase yield in other crops.”

Comment 1.- General Comment. -While looking for ways to make tomatoes more productive, the researcher’s goal is to use the tomato as a model, to increase yield in other crops.

Comment 2.- Question. -How individual DNA affect tomato grow and development; and, how do the researchers work to insert DNA into the cells of tomato and how do they grow them``    .?

Comment 3.- Answer. - Cuts the time from 17 to11 weeks, and saves money.    They use a soil bacterium called Agrobacterium tumefactions to insert a new segment of DNA into the cells of tomato seedling tissues. The transformed cells are transplanted onto plant generations medium, which contains nutrients and hormones that cause the tissue to grow into a tiny new plants. These plantlets are then transferred to root induction medium where they grow roots, before being planted in soil and hardened in the greenhouse.

I found this article very interesting, because it causes me curiosity to know how do they work; and because in Biology class we were talking about DNA.

“Carbs During Workouts May Fend Off Colds”

By GRETCHEN REYNOLDS DEC. 7, 2016

BIOL 1610 1PM

http://www.biologynews.net/newsfeed/International_Herald_Tribune/2016/12/07/Phys_Ed__Carbs_During_Workouts_May_Fend_Off_Colds

            Here is an interesting article for the cold/flu season we are currently experiencing. This article explains how eating carbohydrates during a workout can help fend off the common cold. I chose this article to potentially inspire exercise in myself and others during these cold winter months. This article also shows how intelligent our bodies are in protecting themselves against sickness.

There is an accepted belief that after exercise the body has a immunodepression. This means that the immune system is compromised during recovery.  In the Journal I chose to use, the article references stated, “Exercise increases circulating neutrophil and monocyte counts.”  In other words: During exercise, white blood cells are circulated throughout the body helping immune defense. Neutrophil and monocytes are white bloods cells in the body that are responsible for protecting the body from infectious diseases and foreign invaders.

                A distinction should be made however. This article is focusing more on vigorous or intense workouts lasting about 90 minutes or more. It is during that time when the body is being stressed that an increased carbohydrate intake is beneficial. It is estimated that about 30-60 grams of carbohydrates should do the trick by helping the body maintain blood sugar levels and reducing the stress response associated with high intensity exercise.

                As a society struggling with obesity, new diseases, and miss information, I believe this article can be used as a motivator for many individuals who struggle with the threat of diabetes or heart disease due to not getting off their couches to properly take exercise their bodies. If that is not motivation enough then perhaps simply avoiding the common cold can lace those shoes for them. I know personally that if I can help control or eliminate the yearly cold I get, I would be exercising daily. I can only assume this may inspire others to get up and hit the gym as well.

Three Parent Child- M. Aldridge

Mitochondrial diseases are deadly and kills many children a year. Many mitochondria diseases like Huntington's disease don't present until adulthood and the carrier has no way of preventing the transmission of this disease to her children. However, during mitosis one of the X chromosomes winds up and becomes dormant in the cell. If these are the chromosomes containing the genes for these mitochondrial diseases, they can still be passed on to their children while never affecting them. By using this new technique, a child will receive DNA from the mother and father, with some from the donor, with no risk of inheriting a mitochondrial DNA. 

Mitochondrial DNA is stored in the protein within the mother’s cells. By using a donor cell that does not contain mitochondrial disease, we can replace the nucleus of the donor cell with the DNA from the mother. Once the and DNA is successively transfer the new egg cell contains DNA from the mother and mitochondrial DNA from the donor that is clear of diseases. This new healthy egg is then fertilized by the father’s sperm and DNA. This fetus is now guaranteed to not develop a mitochondrial disease greatly improving the child’s life.

Once enough children are created through this process, the population could theoretically eradicate the presence of mitochondrial disease in a population, not including the chance of mutation within the mitochondrial DNA. 

This article was very informative and changed the way I look at disease. Instead of simply looking at treatments, we are now able to prevent them on a genetic basis. Once this can be perfected we can look at preventing other genetic disease like Sickle-cell anemia and many other. 

“Five Cutting-Edge Cancer Treatments”

In an article from Scientific American titled “Five Cutting-Edge Cancer Treatments”, the author illustrates five advances in medicine that are changing the way cancer is treated today. The reason why I chose this topic is due to my interest in cancer biology. In the past, I had an aunt who was diagnosed with colon cancer. We were devastated and frankly had no idea what it would take for her to be healed. This has fueled my interest in this subject and although the name of cancer is well-known among society, I think it is simultaneously one of the least understood. A common theme across the board for families who have been affected by cancer is fear of not knowing what will happen to your family member and not fully understanding what cancer is. One day I would like to contribute to this field of research and help further the progression of medicine in this aspect.

The article first introduced one of these treatments titled “precision medicine”. This is a type of treatment that is currently being tested and developed. The article states that in January of this year, there was a precision medicine initiative announced by President Barack Obama. The initiative announced was an emphasis on researching and developing treatment through this method. The benefits of this type of treatment are endless, however, the article focuses on how it applies to the treatment of cancer. Precision medicine is personalized care that treats each individual specifically. This is done directly through a person’s genetics and health history. In the past, precision medicine has given options to patients to have therapy that targets the specific gene mutations that cause a tumor or cancer. Through precision medicine, doctors and physicians will be able to identify mutations in the patient's DNA early on which could lead to prevention of the spread of cancer in the body.

Another method of treatment that has been essential in the fight against cancer is using the patient's own immune system to attack the cancer cells. This is a breakthrough idea because the usual treatment for most types of cancer is chemotherapy and radiation which destroys the cancer cells but also destroys many other types of cells causing extreme sickness and pain in the patient. Using the patient’s immune system is a safer and more effective way to eliminate the cancer. The drugs that have been designed for immunotherapy has been created to boost the immune system to fight off the cancer cells in the body. The article mentions two drugs called nivolumab and ipilimumab that boost the T cells in the immune system which fight off cancer.

The third treatment that the article mentions is: “cell-based therapy”. Cell-based therapy is a form of treatment that manipulates the T cells to attack the cancer cells more readily. Using the T cells that are already present in the patient’s body to fight off the cancer cells is a way that could fight off the cancer cells in the patient’s body.

Another treatment that has been extensively researched in the past several years in “epigenetic therapy”. This uses a method that is quite opposite of chemotherapy and radiation. Rather than poisoning the cells or trying to cut them out, scientists have come up with a treatment that simply turns “off” the cancer cells leaving the rest of the good cells unharmed. A drug called AG 221 has been tested in recent years and according to the article has had a 38% percent positive response rate from the 159 patients who were tested. Scientists hope to make improvements and continue to increase the positive response rate in future patients.

The fifth treatment in the article is research on metastasis. Metastasis is the process whereby cancer is spread from one portion of the body to another by breaking off from the tumor origin and growing in a new part of the body. The states that, “Metastasis causes nine out of ten deaths from cancer, and survival rates haven’t improved much since the 1960s.” It is because of statistics like these that scientists are tirelessly researching the process and how to prevent this from occurring. Groundbreaking discoveries by scientists in 2014 have “open[ed] up a promising new avenue for treatment.” These discoveries include the idea that tumor cells have “remarkable tendency to cling to blood vessels”. Scientists believe that this might explain how cancer cells could “hide out and remain undetected”.

The article concludes with a quote from Joan Massague, PhD that I believe summarizes the conclusions from this article. It states, “Mankind is turning cancer from what we’ve known it to be - the way we’ve related to it in the 20th century as an impossible disease - into a ‘normalized’ disease, Our relationship with it will be much more like the one we have with infectious diseases, for which we have antibiotics and other treatments.” Science is on a road to having reliable treatments for cancers of all types.

--AS

https://www.scientificamerican.com/page/sponsored/memorial-sloan-kettering-cancer-center/five-cutting-edge-cancer-treatments/?wt.ac=SA_Native_MSK_CancerOptimism_BCAD#

Biology News Net, "How ionizing radiation damages DNA and causes cancer."

Biology News Net, "How ionizing radiation damages DNA and causes cancer."

In this article DR Peter Campbell, who lead the study, was trying to find how and if radiation could cause cancer. Him and the others at Wellcome Trust Sanger Institute found two "Fingerprints" of how the ionizing radiation damages the DNA. Firstly, and in my opinion the most frightening, is whats called a balanced inversion. this is where two points in the DNA are cut and then, as if on a pivot, it rotates 180 degrees and reattaches. The second is deletion, where a small number of DNA bases are cut out entirely.

The balanced inversion changes the order of what's read as the RNA transcribes the DNA. with this change it can change what the protein turns out to be, or even terminate it prematurely. A deletion of one of those nitrogenous bases would change the reading frame of the RNA, essentially doing the same thing; changing the outcome of the proteins and/or terminating it before it reaches what it was supposed to be.

I found this article quite interesting because this knowledge will change how some cancers are treated in the future. I have an aunt who passed away this year after a 7 year battle against cancer. she was originally given a year to live, and she fought it for 7 before it finally took her. I would hope that this new advancement in the field of cancer research, and many more as they continue to study, will eventually lead to a cure, and better ways to help treat the cancers without inadvertently causing more damage.

D. Austin Kropushek

Radiation Damages DNA and Causes Cancer

The article is explaining how researchers at the Wellcome Trust Sanger Institute discovered a pattern in human cancers that help doctors better identify if tumors have come about because of radiation. More specifically, they are looking at the DNA damage and mutation signatures and how they can tell the story of whether these cancers came about by radiation or not. They also are looking at if these cancerous tumors from radiation should be treated differently.

In this article I learned that DNA damage can leave what is called a mutational signature. Dr. Peter Campbell from the Wellcome Trust Sanger Institute led a study where the researchers looked for mutational signatures in 12 people with secondary radiation-associated tumors. They compared these with 319 that had not been exposed to the radiation. It was said that from this study they concluded that these mutational signatures can be compared with other DNA sequences of various cancers and will be diagnosis’ tools for the future in learning how radiation causes cancer.

I also learned about balanced inversions and how they do not occur naturally in our bodies. If these inversions were found in a human with cancer, then the researchers concluded that they were caused by high-energy radiation that can cause enough DNA breaks at the same time. One reason the radiation does so much damage to the DNA is because the DNA repair system cannot keep up with the amount of damage that is happening simultaneously.

I thought the article was interesting because I wanted to see what the connection was between DNA and cancer. Also, I’m very interested and hopeful that one day we can cure cancer. Any potential break-through in technology or information about cancer is interesting to learn more about it. If we can figure out the cure for cancer, then not only our society, but the entire world will be changed for the better.