December 2, 2016

As the semester is coming to a close, and this is our final blog, I've decided to end mine with a hopeful literature article on the first steps to neutralizing the Zika virus.

Researchers at Duke-NUS Medical School along with scientists from the University of North Carolina, have discovered the mechanism by which C10, a human antibody previously identified to react with the Dengue virus ( one of the viruses I spoke about in my previous blog), prevents Zika infection at a cellular level. The researchers have determined how C10 is able to prevent infection. To infect a cell, virus particles usually undergo two main steps, docking and fusion. The way Zika works is first by docking, docking then initiates the cell to take the virus to a separate compartment within the cell body. Proteins within the virus coat undergo structural changes to fuse with the membrane of the endosome, which then release the virus genome into the cell, and complete the fusion step of infection. Using cryoelectron microscopy they were able to visualize C10 interacting with Zika at different pHs that they might come across during the infection process. This means that C10 binds to the main protein that makes up the Zika virus coat, regardless of pH, and locks these proteins into place which does NOT allow the changes to be made to the structure that is needed in order for fusion to take place. Without fusion of the virus to the endosome, viral DNA can not enter the cell and the infection will stop. The researchers are hoping that this will open up doors for more research to take place in the development into Zika therapy. They also believe that disrupting fusion with C10 could be more effective in preventing Zika as opposed to working towards disrupting the docking step. Why do they believe that disrupting fusion would be better than disrupting blocking? Because the fusion step is critical for Zika to infect the cell, while the virus can develop other ways to overcome the disruption to the docking step. I sincerely hope that all this research is going to hopefully one day develop a way to eradicate this disease.

Journal Reference:

1. Shuijun Zhang, Victor A. Kostyuchenko, Thiam-Seng Ng, Xin-Ni Lim, Justin S. G. Ooi, Sebastian Lambert, Ter Yong Tan, Douglas G. Widman, Jian Shi, Ralph S. Baric, Shee-Mei Lok. Neutralization mechanism of a highly potent antibody against Zika virus. Nature Communications, 2016; 7: 13679 DOI: 10.1038/NCOMMS13679 

November 18, 2016

I've decided to carry on with my Zika theme from my last blog, but this time looking at it from the mosquitoes point of view and how they are capable of carrying this virus. Researchers Dr. Kevin Myles, Glady "Hazitha" Samuel and Dr. Zach Adelman are Texas A&M AgriLife Research scientists at Texas A&M University, College Station and they have been studying the question of "how the virus gets around the insect's immune response" and the answer they found was that the virus makes a protein that suppresses the immune response. When the mosquitoes are infected with viruses, there's a signal that lets the mosquito's cells know that they are infected, resulting in targeting of the virus by the mosquito's immune response. The team found that the protein that suppresses the immune response is also found in the yellow fever, West Nile, and dengue virus which are all of which can be transmitted by mosquitoes. So basically put, the virus and the mosquitoes immune system are at a constant battle because obviously the mosquitoes don't want the virus but the virus knows that the only way to stay alive is to stay on the mosquito. The researchers called this the "evolutionary arms race". By understanding this, they hope to use gene drive, a method targeting specific genes, to go in and help the mosquito. They could possibly make it to where the virus would actually make the mosquito sick preventing transmission to humans. Researchers are looking to see the protein interferes with the human immune response and if it does interfere with human immune response, it could become a target for vaccine development, not only for Zika virus, but possibly other viruses as well. While they say they are far from reaching this point, they are in the right direction to hopefully understand and preventing this virus.

Journal Reference:

1. Glady Hazitha Samuel, Michael R. Wiley, Atif Badawi, Zach N. Adelman, Kevin M. Myles. Yellow fever virus capsid protein is a potent suppressor of RNA silencing that binds double-stranded RNA. Proceedings of the National Academy of Sciences, 2016; 201600544 DOI: 10.1073/pnas.1600544113

November 11, 2016

So many of us know of the Zika virus and what is causes if you happen to get infected while pregnant; it causes microcephaly along with several other brain disorders. But if you're like myself, you aren't sure how it happens or why, you just know it does. Luckily there is new research that provides clues to how Zika reaches the placental barrier. Zika damages certain cells that affect the formation and function of the placenta. Aside from that, the herpes simplex virus-2 (HSV-2) infection develops placental sensitivity to Zika virus by enhancing the expression of receptors that allow Zika virus to enter cells. Researchers in Brazil suspect that something more than Zika virus is causing the high intensity and severity of cases. Their suggests that the immune response to an early infection, HSV-2, may be the additional factor that increases the risk for severity of Zika virus-induced disease. They are hoping that these findings can explain the mechanism of how Zika reaches the placental barrier to access the fetus.

Journal Reference:

1. Paulomi Aldo, Yuan You, Klara Szigeti, Tamas L Horvath, Brett Lindenbach, Gil Mor. HSV-2 enhances ZIKV infection of the placenta and induces apoptosis in first-trimester trophoblast cells. American Journal of Reproductive Immunology, 2016; DOI: 10.1111/aji.12578

November 4, 2016

Good news, researchers have published a high resolution draft of the barley genome. Why is this important? Because by being able to map out the barley genome it will be possible to see the genes at which point are being switched on and off and the mutations that occur during development, which will result in make better beer! Now, I'm not much of a beer person but I bet beer drinkers are rejoicing about this. Aside from making better beer, this publication is a critical step towards barley varieties being able to cope with the demands of climate change. It is also a helpful way to fight against cereal crop diseases that affect the economy when they destroy millions of pounds each year. Barley is the world's fourth most important cereal crop and is also a major component of the animal feed for meat and dairy industries. Barley straw is a source of nutrition for ruminants and is used for animal bedding and frost protection in the winter.

Why hasn't barely's genome been fully mapped yet you ask? Well that is because it is almost twice the size of humans. Its genome contains a large proportion of closely related sequences that are hard to piece together into a linear order. By developing and applying a series of strategies that allowed them to go around the difficulties, the International Barley Genome Sequencing Consortium (IBSC)has managed to construct a high resolution draft DNA sequence assembly that contains the majority of barley genes in linear order.

Hopefully this leads to better beer soon, oh and the progression and preservation of the worlds fourth most important cereal crop!

Journal Reference:

1. Klaus F. X. Mayer et al. A physical, genetic and functional sequence assembly of the barley genome. Nature, 2012; DOI: 10.1038/nature11543

October 28, 2016

So when you think of onions what do you think of? Bad smell, crying, food (tacos to be specific), or maybe that one line in Shrek that talks about onions having so many layers? Well to add to this list, how about cancer suppressor? Yup, onions are now being researched and have been found to have cancer suppression capabilities.

To be more specific researchers in Japan have isolated a compound that is found in onions, onionin A (ONA) to have several anti-ovarian cancer capabilities. The research that was performed focused on the effects of ONA on a pre-clinical model of epithelial ovarian cancer (EOC) in vivo and in vitro. Since EOC is the most common type of ovarian cancer and it has an 80%  relapse rate, there needed to be a more effective treatment. When the researchers performed the in vitro experiments it showed that EOCs, which usually proliferate in the presence of pro-tumor M2 macrophages, showed inhibited growth after introduction of ONA. This wasn't the only finding in the research, are y'all ready to know what else this wonderful onion can be isolated to do?
- It can inhibit the pro-tumor functions of myeloid derived suppressor cells, which are closely associated with the suppression of the anti-tumor immune response of host lymphocytes
-It can enhance the effects of anti-cancer drugs by strengthening their anti-proliferation capabilities
- When orally administered, ONA  showed that it can give onger lifespans and inhibit the ovarian cancer tumor development

So if that doesn't give you hope that medicine might be getting closer to solving this terrifying disease, I don't know what will. So, three cheers to onion for not only be great on food, but for being great in medicine!

1. Junko Tsuboki, Yukio Fujiwara, Hasita Horlad, Daisuke Shiraishi, Toshihiro Nohara, Shingo Tayama, Takeshi Motohara, Yoichi Saito, Tsuyoshi Ikeda, Kiyomi Takaishi, Hironori Tashiro, Yukihiro Yonemoto, Hidetaka Katabuchi, Motohiro Takeya, Yoshihiro Komohara. Onionin A inhibits ovarian cancer progression by suppressing cancer cell proliferation and the protumour function of macrophages. Scientific Reports, 2016; 6: 29588 DOI: 10.1038/srep29588 

October 21, 2016

Many people view music as therapy, a way to soothe the body, mind, and soul when they are under stress. It has also been known to have positive results when exposed to certain types of music in the womb. It is safe to say that music has it's positive aspects, but have you ever thought of using music to study proteins?

Researchers from Finland, the UK, and the US believe that their musical technique can provide insight into proteins and how they work. They use sonification to identify the different anomalies and holes in proteins. Now, when I hear sonification all I think about is that awful noise that was produced when we used it to break up the cell walls in one of our previous experiments. How can someone stand to hear that noise all day to try and find anomalies? Well they don't, the frequency and noise that is produced is at a different level and by the researchers account, is quite pleasant. With the use of sonification they can turn the data that they obtain about the proteins, and how they work and fold, into different melodies that can hopefully be used as not only to aid further research but also in the  future of teaching about proteins. For now they are sticking to the melodies of proteins to identify irregularities, but they hope to be listening to genomes to further understand the role of junk DNA.

So in the future people can start adding "Protein" and "Genome" to their Spotify playlists.

Journal Reference:

1. Robert P. Bywater, Jonathan N. Middleton. Melody discrimination and protein fold classification. Heliyon, 2016; 2 (10): e00175 DOI: 10.1016/j.heliyon.2016.e00175

October 14, 2016

If you are like myself, and grew up on Disney cartoons from the early 2000s then you know who Rufus is from Kim Possible. Whenever I hear "naked mole rat" I immediately think of Rufus, but naked mole rats have so many awesome aspects to them than just crime-fighting.

Mole rats are said to be the closest thing to having super powers on this earth. This is said because for a small rodent, they are able to live up to 32 years, have cancer-resistant tendencies, and are not phased by certain types of pain. Recent research has found what has made the naked mole rat pain-free by identifying the evolutionary change that causes this to occur. In a nutshell it's basically as if the signal for pain was semi-turned off to allow for the feeling of pain but not completely enough to harm the animal. This happens because the TrkA receptor of the naked mole rat isn't dysfunctional but hypo-functional. The hypo-functionality of this receptor in the mole rats allows them to survuve without neurodegeneration that is found in animals with mutations that have the Nerve Growth Factor shut down. Researchers believe that evolution selected the TrkA receptor that works when they are babies, but goes away when they enter adulthood. Because they live in underground desert regions, evolution has shut down functions, including nerve receptors, to allow them to live in these conditions. Future plans for this research are to inject mice with the TrkA receptor found in naked mole rats and see if the mice will display the features in that of the mole rat.

Journal Reference:

1. Damir Omerbašić, Ewan St. J. Smith, Mirko Moroni, Johanna Homfeld, Ole Eigenbrod, Nigel C. Bennett, Jane Reznick, Chris G. Faulkes, Matthias Selbach, Gary R. Lewin. Hypofunctional TrkA Accounts for the Absence of Pain Sensitization in the African Naked Mole-Rat. Cell Reports, 2016; 17 (3): 748 DOI: 10.1016/j.celrep.2016.09.035 

October 7, 2016

When I came across this article I was so intrigued about it just because it's something I've said several times before. I'm talking about the rule many of us have used, or at least said it at one point or another: 5-second rule.

Donald Schnaffner a Professor at Rutgers University who specializes in food science has decided to put the five second rule to the test. the research tested four differnt surfaces, stainless steel ceramic tile, wood and carpet with four different foods, watermelon, bread, bread and butter, and gummy candy. Four different contact times were 1 second, 5 seconds, 30 seconds, and 300 seconds. The bacteria that was used to inoculate the surfaces was Enterobacter areogenes, a nonpathogenic "cousin" of Salmonella naturally occurring in the human digestive system. The bacteria was inoculated in either tryptic soy broth or peptone buffer. Each of the surfaces was inoculated and allowed to completely dry before the samples were dropped onto them. The results showed that the watermelon had the most contamination and the gummy candy had the least. Simply put the more moisture a food contains the more bacteria the food will contain. This was found because bacteria move with moisture which allows moist food  to have the higher risk of transfer. While it is also true that the longer the exposure on the floor the more risk of bacterial transfer, there were results that showed that transfer happened instantly.


Journal Reference:

Robyn C. Miranda, Donald W. Schaffner. Longer Contact Times Increase Cross-Contamination ofEnterobacter aerogenesfrom Surfaces to Food. Applied and Environmental Microbiology, 2016; AEM.01838-16 DOI: 10.1128/AEM.01838-16

September 29, 2016

For this week's blog, I chose this topic because I've always been fascinated by the beginning. The beginning of time, the beginning of life, the beginning of a species and how it's transformed over time. In a recent study, researchers have discovered proteins in ancient eggshells that has the information to discover DNA almost 50 times older than what they thought had been known. This could in turn provide more facts and insight to how animals and humans interacted in every-day life and why some animals became extinct while others were able to thrive in the conditions they were given and able to evolve over time. The ostrich eggshells come from well-dated sites in Tanzania and South Africa which are known for their extreme heat and harsh conditions. Originally researchers had thought that protein would not survive in the harsh conditions, but upon researching more and more shells, they actually found that it was the exact opposite. The one's in the unstable regions were the ones that survived the best and had the most protein within them. In light of this current finding, this allows them to be much more targeted in their study when looking at fossils and what exactly to look for. I'm excited to see what other information on evolution will come from these findings!


Journal: University of York. "Ancient eggshell protein breaks through DNA time barrier." ScienceDaily. ScienceDaily, 27 September 2016. <www.sciencedaily.com/releases/2016/09/160927082904.htm>.

DOI: 

1. 10.7554/eLife.17092 

September 23, 2016

Recently, a group of researchers at MIT have created tiny freeze dried pellets that upon adding water can translate DNA into proteins. This can be the foundation and pave the way for on-demand production of drugs and vaccines. These pellets are capable of being stored for long periods of time at room temperature and because of their easy storage they can be used in several different aspects: military, hiking, and even be used in everyday first aid kits. Using the growing field of synthetic biology, researchers and scientists can design the cells in the pellets to perform functions that they normally do not have. With the help of synthetic biology, these pellets could be used to form vaccines and produce antibodies. Some of the pellets that they have made are ones that have small proteins that could be used as a diptheria vaccine and antimicrobial peptides that can help fight bacterial infections. They've also made one that can detect the bacterium Clostridium difficile, which is capable of producing severe inflammation of the colon. The researchers on the team have extensive plans to create and mass produce several of these pellets that can be used in every day life. Collins, one of the researchers, wants to purse integrating pellets into "smart bandages" that would detect infection and then produce the microbials needed to treat the infections. I think that these pellets can really change the future of medicine and bio-pharmaceuticals.


Research Article:
DOI: http://dx.doi.org/10.1016/j.cell.2016.09.013

September 16, 2016

In last weeks blog, I wrote about home remedies and how they are being researched with a new approach: systems biology. I figured why not elaborate more on this for my next blog.

Systems biology is a type of research that focuses on the whole instead of the sum of the individual parts. it is a collaborative type of approach the combines the disciplines of several scientific fields such as: biology, computer science, engineering, bioinformatics, and physics to name a few. By using all of these disciplines researchers hope to predict how biological systems change over time depending on the conditions they are faced with. By being able to design multiscale models, scientists are able to discover "new biomarkers for disease, stratify patients based on unique genetic profiles, and target drugs and other treatments". There is a whole institute dedicated to the approach and the research of using systems biology. Institute of Systems Biology, ISB. To learn more about system's biology and how it is being used in several studies you can go to the following website which also includes an informative video describing system's biology.

https://www.systemsbiology.org/about/what-is-systems-biology/

September 9, 2016

For this weeks blog I've decided to touch base on an article I read on ScienceDaily.com, "How Chinese medicine kills cancer cells". I chose this article for one reason, I'm Hispanic, I grew up in Brownsville, which is down by the border, so I have had my fair share of home remedies. Most people I tell about how my grandmother and mother would cure a common cold, or strep throat, takes them by surprise because there isn't much medicine behind it.

I found it rather interesting and satisfying that medical professionals are now starting to investigate and test the effects of home remedies. The China Centre for the Molecular Basis of Traditional Chinese Medicine has begun to run tests and tear apart the components of the medicine at a molecular level to see how these medicines interact. It was stated that individually, they are not very effective, but when combined they are able to interact and that is when they become more useful. They've used what is called a systems biology approach. It's a way of analyzing complex biological systems that attempt to take into account all measurable aspects of the system rather than focusing on a single variable.

To read more about the article go to:
https://www.sciencedaily.com/releases/2016/09/160908084319.htm

Journal Reference:

1. Zhipeng Qu, Jian Cui, Yuka Harata-Lee, Thazin Nwe Aung, Qianjin Feng, Joy M. Raison, Daniel R. Kortschak, David L. Adelson. Identification of candidate anti-cancer molecular mechanisms of compound kushen injection using functional genomics. Oncotarget, 2014; DOI:10.18632/oncotarget.11788