Silencing Genes to Prevent Infection

Electron Micrograph of Ebola Virus Particles

Ebola is a virus that causes a deadly hemorrhagic fever and is spread through contact with blood and contaminated needles. About 85 percent of the reported human cases of Ebola have resulted in death. The use of vaccines has protected monkeys, but are only effective when given prior to exposure to the virus. A team of scientists, including Thomas Gesibert, was initially attempting to boost host immunity for people exposed to the virus, but later turned to muting the virus's genes. This would at least buy time for other treatments, including the vaccine, to start working.


Gene silencing, or RNA interference (RNAi) occurs naturally. Some portions of DNA are transcribed into RNA, which are then translated into proteins that keep our cells functioning. However, there are other stretches of DNA that are transcribed into siRNA, or small interfering RNA, that is not translated into proteins. Instead of being translated into protein, these RNA strands are bound to portions of other RNA strands that have complementary sequences. This prevents the RNA from being translated into proteins and offers greater control over gene expression. Geisbert and his team attempted to artificially replicate this process to work on Ebola by creating siRNA that would bind to polymerase L, a gene that is vital for replication to occur.


The researchers were able to silence the gene and prevent replication effectively in cell culture studies, but encountered a new problem when testing the approach on animals infected with Ebola. "Naked" siRNA in blood and body tissues is broken done by enzymes. When the synthetic siRNA was injected into the test animals, the researchers needed to develop a "vehicle" that the infected cells would take up so that the siRNA contained within it would not be broken down by enzymes. The initial packaging system was ineffective, but Geiser then packaged the siRNA into SNALPs, or stable nucleic acid lipid particles. Cells like dendritic cells and macrophages are targeted by Ebola and were capable of taking up the SNALPs, resulting in a successful test with siRNA-containing SNALPs when used on guinea pigs.


When testing the approach on monkeys infected with Ebola, Geiser also included siRNAs to target viral genes that are thought to inhibit the immune system. They injected the SNALPs containing the siRNAs into the monkeys 30 minutes after injecting Ebola and injected the SNALPs every day for a week as well. After seven days, all of the monkeys were virus-free. Gesier hopes to push his approach to work on people infected by Ebola up to 24 hours after infection.


To access the article that I got my information from, click here.

Useful Materials for Chapter 11

The video above reviews the process of how DNA is packaged, how it replicates, and the various proteins and enzymes involved in the process. I found this to be really interesting because it looked less cartoon-ish than biology videos tend to be. It also goes more into topics that we had not focused on in this chapter, such as DNA transcription into RNA. If you are looking for a more detailed version of what we have learned in class, I suggest looking at the lecture I have posted below. I recommend this video particularly for people who have not grasped the basics that are necessary for truly understanding DNA replication. These basics include the structure of the nucleotides in DNA and how this relates to the process of replication. It also goes into more detail about the roles of the various enzymes involved in DNA replication.

There are several parts to this lecture that can all be found on youtube.

Telomerase Structure, Function, and Biogenesis

Telomerase is an enzyme, more specifically a reverse transcriptase, that adds telomeres to the ends of DNA. Telomeres is the end of a eukaryotic chromosome, consisting of a short nucleotide segment that repeats from a few dozen times to several hundred times. They basically make up for the inability of DNA polymerase to fully replicate the 3' linear chromosome ends. Telomerase consists of two parts, TERT (catalytic telomerase reverse transcriptase) and TR (telomerase RNA), and functions as a ribonucleoprotein. There have also been several accessory proteins that have been identified that function in the regulation, biogenesis, and localization of the enzyme. Understanding telomerase's molecular mechanisms is essential to developing therapies for disorders and cancers that are related to telomerase.


Idiopathic pulmonary fibrosis, or IPF, is the most common type of telomere-related disease. Mutations in hTERT and hTR genes are the cause of the defect. These mutations can lead to extra-pulmonary complications that result from telomere shortening. These complications include bone marrow failure. There is also evidence that points towards IPF being a manifestation of telomere syndromes that were autosomal dominant. With each generation, it evolved from pulmonary fibrosis to disorder that is predominantly related to bone-marrow failure. The article goes on to explain the the significance in defects of telomere for understanding the disease patterns, pathophysiology, and genetics of idiopathic pulmonary fibrosis. 


To see the articles that I got my information from click here and here.

The Value of "Junk" DNA

The genetic blueprint of human beings consists of 23 linear chromosomes that contain 3.42 billion nucleotides. The genetic blueprints of most mammals consist of similarly significant amounts of nucleotides. Some extremes in nucleotide numbers do occur in mammals, such as the red vischaca rat (8.21 billion nucleotides) and the bent-winged bat (1.69 billion nucleotides). Regardless of what kind of animal, there is a large excess of DNA that does not code for proteins. Approximately 2% of DNA codes for proteins in humans. For several decades, scientists were confounded by the purpose of such "junk" DNA, which often consisted of repeating segments that are dispersed throughout the genome.


These repeating segments come about when sections of DNA move within the genome to different positions. This process is called transposition. Biologists now believe that these transposable segments are not useless, but instead provide greater ability for the organism to evolve. They serve as areas for genetic recombination and provide new signals for genetic expression. Genomes are dynamic, with certain elements becoming extinct as new elements appear. Functional DNA can therefore be created from "junk" DNA. The term "exaptation" is used when describing how genetic entities can change their role, despite their original role if they had one at all. For example, biologist Gill Bejarano discovered a DNA fragment that was exapted as an enhancer, increasing gene transcription, when it had originally inserted itself anywhere into the genome.


DNA sequences that are nonfunctional in certain organisms could be functional in others, becoming an exon that is transcribed to messenger RNA. While non-functional DNA can be seen as "junk" DNA they actually do actually have a role in the genome. These segments are important to evolution. To access the article that I retrieved my information from, click here.

Useful Materials for Chapter 9

Click here to see a useful animation on signal amplification. It explains how signal transduction pathways, while they may seem unnecessarily complex, amplify a cell's response to a single signal molecule. If each signal only caused a reaction in one particular protein, for example, this would not be a very effective response. This animation uses the hormone epinephrine as an example. Although it only activates a single molecule of adenylyl cyclase, the cellular response is amplified through the pathway. I suggest keeping an eye on amplification count on the right of the screen while moving through the animation.

This video walks you through the fight-or-flight response of the body. I found it useful for making a real-life connection involving the three-stage process of the cells' response to signal molecules. It also included some extra information on the role of nerve signals in the process. I enjoyed the graphics in this video, as they zoomed in and out of the cells and display exactly how the response takes place.

Also, if you are looking for an online flashcard site, I suggest studyblue.com. It's really simple to use and I may share some flashcards that I create on there in the future.

Cancer-Causing Bacteria Induces Apoptosis

Barry Marshall discovered that stomach ulcers are caused by bacteria after he drank a petri-dish containing Helicobacter pylori, a bacteria. He subsequently developed gastritis as a result, then cleared this through the use of antibiotics. The discovery that stomach ulcers could be treated with antibiotics was significant for the medical community as they could lead to stomach cancer and duodenal ulcers.

Helicobacter pylori Micrograph

Researchers have recently identified a bacterial toxin, called vacuolating cytotoxin A or VacA, that plays a role in apoptosis. Apoptosis is a process of programmed cell death. VacA had previously been shown to cause cell death, which is important to the development of gastric cancers. Instead of attacking the cells lining the stomach, Helicobacter pylori causes the cells to undergo apoptosis. Too little or too much apoptosis can lead to several conditions, such as neurodegenerative diseases, cancers, and autoimmune disorders. Apoptosis can occur naturally for several reasons such as well cell population needs to be regulated or as a defense mechanism. Cell death can also be induced due to damage in the cell caused by disease or noxious substances.


VacA is a product of Helicobacter pylori. In order apoptosis to occur, the mitochondria are targeted by VacA, since these parts of the cell are responsible for energy production. VacA makes the outer membrane of the mitochondria permeable,disrupting its electron gradient. This electron gradient is needed for oxidative phosphorylation during cellular respiration. Thus, the mitochondria is unable to produce adequate amounts of usable energy for the cell. In addition, VacA disrupts the structure of mitochondria by preventing them from forming a network and effectively isolating them. Since having functioning mitochondria is essential to cell life, the VacA results in the cell killing itself through apoptosis. Through these mechanisms, Helicobacter pylori causes cell death of stomach cells in small areas, which can then results in gastric cancer and, in less severe cases, peptic ulcers.


Click here to access the article on the cancer-causing bacteria and here to access the article that I got my general information on apoptosis from.

Drug Discovery Opportunities through Allosteric Modulators of G Protein-Coupled Receptors

This article is about the new opportunities for drugs to be discovered through the identification of allosteric ligands. These have generally not been the main focus of GPCR, or G-Protein Couple Receptors. GPCR are located in cell membrane surfaces and respond to a variety of extracellular signaling. They have been investigated for the discovery of several drugs that moderate specific GPCRs. When GPCRs are stimulated by the proper ligand, intracellular signal transduction is initiated. Activation of  β-arrestin pathways and activation of G-proteins are the two mechanisms of signal transduction. The binding of the lingand stabilizes the receptor, allowing it's C-terminal domain to interact with protein complex and its Gα portion to hydrolyse GTP and interact with adenylate cyclase and/or phospholipase C. The receptor is phosphorylated when it reacts with G-protein-coupled receptor kinases and is able to bind β-arrestins. This prevents more G-protein signaling from occurring and also begins a series of intracellular events that are independent from G-proteins.

GPCRs have been pharmacological targets. However, only certain classes of GPCRs are able to be targeted with drugs. The article is proposing that idenitfying allosteric ligands that bind to different sites other than the orthosteric site will provide new opportunities for drugs to be produced. Allosteric modulators allow for enhanced saturability as well as selectivity. Because they cause conformational changes in their receptors, allosteric modulators can alter affinity and capability. Therfore, allosteric modulators can impact how receptors relate and respond to their binding partners, producing selective responses. The article then describes different techniques that can be used to identify allosteric modulators.

For more information, click here to access the article that I got my information from.