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