new treatment possibilities for vision loss

The article that I stumbled on this week covers stem cells. Researchers at John Hopkins have developed a method to transform human stem cells into retinal ganglion cells. The researchers define that retinal ganglion cells are types of nerve cells that are located within the retina that transmit visual signals from the eye to the brain. They also state that if someone were to lose the cells, they would suffer a complete or partial loss of vision. The death of the cells could arise from conditions such as glaucoma and multiple sclerosis. The way that the researchers were able to transform the stem cells is by using the tool CRISPR-Cas9. The researchers inserted the fluorescent protein gene into the stem cells' DNA. This fluorescent protein would be fluoresced only if a gene named BRN3B (POU4F2) was expressed. According to the researchers “BRN3B is expressed by mature retinal ganglion cells, so once a cell differentiated into a retinal ganglion cell, it would appear red under a microscope”. This is because the fluorescent protein would fluoresce red. The researchers then sorted the cells via a technique called fluorescence-activated cell sorting. They were then able to study the transformed stem cells to the point where they discovered that they showed similar biological and physical properties seen in retinal ganglion cells that are produced naturally. This research is important because it could lead to other treatment options for patients with glaucoma and MS.

here is the link to the article:

http://www.news-medical.net/news/20151201/Johns-Hopkins-researchers-develop-method-to-turn-stem-cells-into-retinal-ganglion-cells.aspx

Aspirin as a Cancer Prevention

We take aspirin is used to reduce fever and relieve mild to moderate pain from conditions such as muscle aches, toothaches, common cold, and headaches. It may also be used to reduce pain and swelling in conditions such as arthritis. Researchers at Huntsman Cancer Institute in Salt Lake City have found that aspirin could be used as a cancer prevention for colorectal cancer. In the study they found statistically significant changes in a metabolite that has been found to drive cancer development, 2-hydroxyglutarate, which was reduced by 12%. This study is important because it shows that aspirin has some level of cancer prevention for corolectal cancer. The next step in this study is to see if aspirin has any effect of prevention on other cancers. One thing to keep in mind is that Aspirin is acting as a prevention not a cure.

here is the link to the article:

http://www.news-medical.net/news/20151119/Identifying-new-mechanism-for-aspirin-in-cancer-prevention.aspx

Advancements in Cancer detection

Today while I was looking for articles I came across one that I found really interesting. A research team from the School of Engineering & Applied Science at Washington University in St. Louis was able to see early-developing cancer cells deeper in tissue. The way they achieved this was using two embodiments of photoacoustic tomography that they developed themselves. Photoacoustic tomgraphy is an analysis technique busing photoacoustic imaging, which uses ultrasonic emissions to take images of the tissue. This method uses red or near-infrared light, as well as sound to take high resolution images. For this method they used a protein called BphP1. According to this article, this protein has the ability to sense different types of light and shift its absorption properties accordingly. This is why they used red or near-infrared light. they subtracted the image created from the red light scan from the infrared light scan and recovered an image that revealed the cancer cells deep in the tissue. This research is important because it provides a way to better detect cancer as well as detect it early. This article was interesting because this method could potentially save lives. However, this method does no good if people do not go to get checked out.

here is the link to the paper. 

http://www.sciencedaily.com/releases/2015/11/151109134457.htm

The importance of sleep on a cellular level

Sleep is very important. its recommended that a person should get around 8 hrs of sleep. But as a college student getting 8 hours of sleep is rare. A research conducted by team at the University of Tennessee, Knoxville revealed how not getting enough sleep effects us on the cellular level. the researchers state that not getting enough sleep can "short-circuit your system and interfere with a fundamental cellular process that drives physical growth, physiological adaptation and even brain activity". They based this claim off a prior study conducted on protein synthesis in plants. This study showed that "protein synthesis activity changed over the course of the day, but also that it was under the influence of the circadian clock". When we disrupt our circadian clock by studying all night or staying up till 2 or 3 in the morning watching netflix, it affects some of our bodily functions such as muscle contraction, and brain activity. The researchers stated that these functions depend on proteins that are regulated like those that were looked at in the study conducted on plants, therefore they claimed that if the regulation of proteins that deal with these functions are disrupted this could possible lead to side effects on a cellular level. This study has not incorporated any human test subjects. I am interested in how they plan to proceed with this study, and what the results of human studies could mean. 

here is a link to the article
http://www.news-medical.net/news/20151030/Lack-of-adequate-sleep-can-interfere-with-fundamental-cellular-process.aspx

New role of Nuclear Membrane?

The nuclear membrane has been thought to have one sole purpose, to protect the nuclear material and provide channels to allow molecules that are necessary to transport into and out of the nucleus. According to a team of scientists from USC, it plays a part in repairing DNA. In the nucleus there are two forms of DNA that are found. The first is the DNA that we known of that codes for everything, this form is called euchromatin. The second type of DNA that is found in the nucleus is refereed to some as junk DNA, but is actually called heterochromatin. This form is referred to as junk DNA because it has been mostly ignored. A team of scientists has found evidence that this form of DNA is dragged back to the nucleus for repairs. Heterochromatin, as defined by the scientists in the paper, are mostly composed of repeated DNA sequences. A graduate student on the team stated that "repeated sequences tend to recombine with each other during DNA repair, which would lead to chromosome aberrations as frequently observed in cancer cells".  The team of scientists discovered that "breaks in heterochromatin are repaired after damaged sequences move away from the rest of the chromosome to the inner wall of the nuclear membrane". They then stated that this process was done away from other chromosomes in the membrane so that they are not tangled. As organisms age they become prone to developing cancer. This is because over time the nuclear membrane breaks down and and the repair process previously stated ceases. The team intends to study this process more to understand the mechanisms that drive the repair process. This discovery is important so that researchers can relate these findings to human cells to prevent the degradation of the membrane to the point where the process of repair continues to stop cancer from forming as we age. 


here is the link for this article:
http://www.sciencedaily.com/releases/2015/10/151029185601.htm

improving cancer treatments one step at a time

Chemotherapy is a widely used treatment for cancer. One of the side affects that can come from chemotherapy is chemotherapy induced anemia in ovarian and breast cancer patients. My aunt had breast cancer and went through several rounds of chemotherapy, luckily for her she did not have to deal with this side affect. The article i read this week states that several studies have been conducted and have shown that a popular method called Epo-based therapies can shorten survival times in some patients by inadvertently stimulating tumor growth when treating the anemia. The article states that "EphB4 is the cell receptor that is linked to the cancer anemia therapy known as recombinant human erythropoietin (rhEPO)." The article states that EphB4 can "enhance tumor growth via STAT3, a protein or transcription factor vital to gene regulation". The researchers stated that with knowledge of the Epo signaling pathway, the shortening of time of survival can be stopped by adjusting the pathway of the Epo treatment. This break through is important because it produces a path in which researchers can take to further improve the anemia treatment drug. Not everyone chooses chemotherapy, and those that do very little are affected by the chemotherapy induced anemia. However its comforting to know that researchers are constantly improving treatment techniques.

Here is a link to this article:

http://www.news-medical.net/news/20151016/Study-shows-why-cancer-anemia-therapy-stimulates-tumor-growth.aspx

Breakthroughs in sequncing

Today's topic is off subject from DNA barcoding, however, the article i'll be talking about discusses a new device that is efficient for sequencing DNA. We all know by now that "DNA is the blueprint to life" and that RNA interprets it. The authors of this article state that the old sequencing technique wont work on molecules they called  "choose your own adventure genes". these genes are hard to sequence because each copy can be different from the next. Different forms of these genes are called isoforms and when these genes get chopped up the authors state that "it becomes impossible to compare the pieces". a new breakthrough in technology has made this impossible now possible. It is a nano sequencer called a MinION. developed by Oxford Nanopore, this device works by reading the bases 5 at a time, making a possible 1,024 possibilities that produce different electrical signals. The researchers at UConn then sequenced "the most complex choose-your-own-adventure gene, they chose the most complex one known, Down Syndrome cell adhesion molecule 1 (Dscam1)". this gene controls the wiring of fruit fly brains. The researchers took  the brain of a fruit fly, "extracted the RNA, converted it into DNA, isolated the DNA copies of the Dscam1 RNAs, and then ran them through the MinION's nanopores". The results of this experiment showed that "they not only found 7,899 of the 38,016 possible isoforms of Dscam1 were expressed but also that many more can be expressed". This break through is important not only because a complex gene was sequenced but that it showed that the MinION had much more potential. The MinION is brand new and is probably super expensive, but think of the possibilities that this new technique could introduce.

Next Gen Sequencing

The standard protocol for DNA Barcoding is to perform PCR amplifications followed by Sanger sequencing.  Sanger sequencing uses dideoxynucleotides and normal nucleotides from DNA. The writers of the paper I read this week propose a new method claiming that its more effective, faster, and cheaper than the standard methods used today. This "next gen" method is called 454 pyrosequencing. this method uses tags that are attached to the primers. The tags are set of oligonucleotides with a known sequence. To prove their statement they performed  side by side experiments using both the standard method and the "next gen" method to generate barcodes for 190 species of Lepidoptera. The results of this experiment were that the 454 pyrosequencing method outperformed the standard method. the "next gen" method produced 189 complete barcodes after only 1/8 of a complete run compared to the standard Sanger sequencing only producing 127 complete barcodes. The authors I feel have proved their point. This new method is more accurate and produces results at a much faster rate. This method, in my opinion, should be considered to be the new standard, because with the amount of time and resources saved it could save the barcoding community some money. 

Here is the link to the paper:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4276293/

A New Aspect to the Genetic Code

This week I have decided to discuss some news that I found interesting while looking at possible grad schools. I had googled UT Southwestern and a news article regarding a unknown genetic code showed up. In almost all of my biology classes we have discussed cells in some manner. Its no news to anyone that cells are are made up of proteins, and that proteins are made up of amino acids. We also know that there is a genetic code that is used to build the proteins. The genetic code as we know it assigns the 20 different amino acids with 3 codons. Amino acids can have several different codon sequences. But does the speed at which these amino acids are assembled affect the overall function of the protein? Researchers from UT Southwestern claim that it does. They stated in this news article that "the speed with which a protein is assembled from amino acid building blocks can affect protein folding, which is the process that allows a protein to form the right shape to perform a specific function". This means that if the protein folds differently the function of the protein will be different. This discovery also has important implications for identifying mutations that cause diseases. this is because the findings of their research "indicate that a mutation does not have to change amino acid identity to cause a disease". If these findings hold true and a paper from this research is published, could we see a change in the genetic code that we have been taught all  our lives.

Here is the link to the news article.
http://www.news-medical.net/news/20150924/UT-Southwestern-researchers-find-a-previously-unknown-genetic-code.aspx

Putting it in to perspective

As I read more papers covering DNA barcoding I had a few questions of my own. one of these questions was why does every paper focus on the cytochrome c oxidase gene. why is it the special one. the answer was pretty simple. According to ibol.org this gene is used because its short enough to be sequenced quickly and cheaply. My next question was does this gene work well for barcoding other living things such as plants. Plants are barcoded using two genes from the chloroplasts, matK and rbcL. This website also gives an overall descripition of the barcoding process.

Here is the link to the website for more information:

http://www.ibol.org/about-us/background/
http://www.ibol.org/about-us/what-is-dna-barcoding/

Problems with barcoding

Like any identification system there are do’s and don’ts. For DNA barcoding there are seven major don’ts or as the paper calls them “seven deadly sins”. The sins are as follows failure to test clear hypotheses, inadequate a priori identification of specimens, the use of the term ‘species identification, inappropriate use of neighbor-joining trees, inappropriate use of bootstrap resampling, inappropriate use of fixed distance thresholds, and the one that I will be discussing today incorrectly interpreting the barcoding gap. The paper states that incorrectly interpreting the barcoding gap has “two distinct scenarios”, the first being for specimen identification and the second being species discovery.

The first scenario just means that the organism is so close to another organism in its species that t is identified incorrectly as the other organism. The second scenario means that a new species could be incorrectly identified as a pre-existing species. I feel like all the sins listed above could be easily avoided just by being careful when examining the species. But I think instead of having a system that relies on the barcoding “sequence” of one gene, have a system that if questions or errors like this are possible add an extra position that is barcoded on that gene.

Here is the link to the article:

http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12046/full

DNA Barcoding

Today I will be discussing a paper that I found on DNA barcoding. For those that do not know, DNA barcoding is a way to identify a species using a genetic marker in the organisms DNA. The author of this project discusses how this “project was initially was conceived as a standard system for fast and accurate identification of animal species” but now is used to “assign” and “enhance the discovery of new species”(Frézal and Leblois). This paper discusses that it uses a region of “648 base pair (bp) of the cytochrome c oxidase gene”(Frézal and Leblois).  This region is used to identify all eukaryotic species. The author then states that they are also working on a way to use this system for identifying microscopic eukaryotic life. For this they are looking at a 600 bp region of a ribosomal subunit (Frézal and Leblois). This paper did a good job explaining the idea of DNA barcoding for eukaryotes, but can this idea be used to classify prokaryotes (using RNA instead of DNA)?

Here is the link to the paper as well as the citation.

http://www.sciencedirect.com/science/article/pii/S1567134808001238

Frézal, Lise, and Raphael Leblois. “Four Years of DNA Barcoding: Current Advances and Prospects.” Infection, Genetics and Evolution 8.5 (2008): 727–736. ScienceDirect. Web. 11 Sept. 2015.