Jumping Genes

I found this video interesting because it talks about the effects of transposons, or jumping genes. They use chromosomes of organisms and "jump" between different parts of the genome.  It has been observed that transpons avoid inserting themselves into active genes, allowing their hosts to continue functioning. According to this video, it seems as though transposons are helpful parasites that attempt to "live" longer by allowing the organism in which they inhabit, or their host, to survive. For example, transposons can cells capable of surviving in stressful conditions, such as in cold and salty environments. 98% of DNA of some plants are derived from transposons, which seem to diversify genetic material.

ENCODE Project

The ENCODE, or Encyclopedia of DNA Elements, Project's objective is to aid the biology and medical community by helping them interpret the human genome. It uses several different types of technology to identify all of the functional elements within the human genome. The main purpose is to make all of this information available to public databases for widespread use. This project was launched by the National Human Genome Research Institute to identify all of the regions within the genome that codes for a defined product or a biochemical signature. These signatures can mark important sequences within the genome, such as those for silencers, enhancers, and promoters. The main focus currently is to annotate genes and their RNA transcripts and also regulatory regions for transcription. Click here to access the article that I got my information from. Overall, this project is an important development within bioinformatics and it will be interesting to see how large the database grows.

Transposons and New Discoveries

Transposons are an important topic within our bioinformatics chapter in which short segments of DNA move from one site within a genome to a different site. This article discusses how scientists have re-created a precursor gene to two current human genes. This gene is called Harbringer3_DR and is a transposon. This research could be enlightening to scientists who are attempting to more precisely control where genes incorporate themselves during gene therapy. This particular transposon, Harbringer3_DR, is unique for its ability to insert itself into a genome in a specific manner by recognizing certain DNA sequences.

Transposons typically code for transposase, an enzyme that facilitates transposition, but this transposon also codes for another molecule that resembles a known protein. For this reason, researchers called this molecule Myb-like. The Harbringer3_DR gene exists in other animals, such as zebra fish. Scientists were able to synthesize Harbringer3_DR  using the gene in zebra fish as a template, then placed their constructed gene within a human cell. They were interested to find that the Myb-like protein allowed the transposon to enter the nucleus and brought it within the transposon's tips vicinity. This sparked further interest in discovering how the Myb-like protein and transposase work together to control where the gene is inserted.

In the future, scientists hope to use transposons as vehicles for therapeutic genes that can deliver these genes to specific locations.While inactivated viruses can also be used for this purpose, they are fairly random in their insertion site. Researchers intend to investigate a method of disabling the ability of a transposon to further jump from one location to another after it has been inserted into the desired spot. If this is discovered, there may be a major breakthrough in gene therapy!

Plasmid Cloning Animation

Click here to go to an animation about plasmid cloning. I liked this video because it walks you through the various stages of DNA cloning alongside animations that really clarify the process. It begins with inserting target DNA into a vector, such as a plasmid. It then moves on to the various sites of vectors and how exogenous DNA can be inserted into the vector. I liked how the example used in the animation is the ampicillin-resistance gene, which we discussed in our bacterial transformation lab. The animation goes on to explain how restriction enzymes are used to cleave the vector at specific cloning sites and sticky ends are produced. A recombinant vector, or hybrid vector, is formed and is put into a host cell so that the genes can be cloned. The recombinant plasmid is amplified to produce many copies of it. The animation ends with the long-term effects of this kind of cloning, as multiple daughter cells are formed that have the same recombinant plasmid.

Bioremediation

One of the topics within genetic technology is bioremediation, in which living organisms are used to detoxify environmental pollutants. Basically, microorganisms or plants are used to reduce pollution. A pollutant's structure can be altered so that it is no longer harmful. Enzymes produced by microorganisms can carry out this alteration.

This article is about a species of bacteria than can detoxify contaminated groundwater by removing any uranium that may be present. This species, Geobacter sulfurreducens , gets energy by reducing metal. If you can recall for chemistry, reducing is when a substance gains electrons. This bacteria adds electrons to metals within its environment, including uranium. When uranium is reduced, it becomes less soluble and does not spread as efficiently as it did before, therefore reducing contamination.

Researchers are attempting to discover how this species is able to remove uranium. They strongly believe that the pilli of these bacteria plays an important role in this process. Without pilli, this species reduces uranium in the environment within its cell envelope, which is fatal to the cell. When pilli are present, the bacteria are able to survive the process since it is occurring farther away from the cell and the pilli also increase the surface area at which electron transfer can take place.

Research into the ability of the pilli to conduct electricity and transfer electrons to power the bacteria may help scientists understand more about bioremediation. There is also a possibility of producing non-living devices that can perform the same type of function as these bacteria if enough research is conducted into how the bacteria function. It is also possible that this species can be manipulated to remove other radioactive isotopes of elements, such as plutonium. Overall, research into bioremediation could be very beneficial to the environment.

Rapid PCR

So...this might be my shortest blog post until now. Well, here goes. Do you recall our GMO experiment in which we had to use polymerase chain reactions, or PCR? And do you remember how the thermal cycling involved meant that we would not be able to retrieve our results the day of, and the lab was split between two weeks? Well, it is possible that PCR can be sped up so that it is completed under three minutes!

To brush up, polymerase chain reactions make many, many copies of a specific DNA sequence (as specified by the primers used in the reaction). This amplification allows scientists (or us) to perform genetic tests on these sequences for various purposes. This article states that PCR amplification can be completed in as little time as two minutes and eighteen seconds. Basically, a rapid thermal cycler was created in which the sample's temperature is altered 45 degrees Celsius every second. 30 cycles of PCR can be completed within this time. DNA amplification enzymes, such as polymerases, that are able to work under these conditions were also discovered.

The ability to almost instantly amplify genes could be extremely beneficial to the medical community specifically in addition to the scientific community as a whole.

HIV Life Cycle Video

This video shows the life cycle of HIV, which we know is a retrovirus. This video displays the entire life cycle, starting from attachment and moving on to entry, integration, synthesis of viral components, viral assembly, and release. I really liked the visuals in this video and felt that they enhanced the understanding of the life cycle of HIV. While the video did not explicitly state where each step started and stopped, I was able to track the various stages. There was also some interesting extra information in the video, such as how the virus uses GP120 surface glycoprotein to attach to a CD4 membrane protein as well as its corecepotor. The video then proceeds to explain how the viral envelope and the cell membrane fuse and allow the capsid to enter the cytosol. Overall, I felt that this video included all the information about the life cycle of a retrovirus that is present in the book and also added on to it by including extra information that is specific to HIV.

Bacterial Conjugation

As we learned in class, gene transfer in bacteria can occur through transformation, transduction, and conjugation. In this post, I will be focusing on conjugation. In conjugation, there is direct contact between the donor cell and the recipient cell through which a strand of DNA is transferred. See the picture below for a visual of how conjugation occurs. It has been found that conjugative plasmids contain genes that are resistant to several types of antibiotics. Therefore, if resistance to a particular antibiotic is selected, resistance to other types of antibiotics will be simultaneously selected. Plasmids involved in gene transfer also code for conjugative pilli that facilitates the transfer of DNA by binding to the recipient cell from the donor cell. At the end of conjugation, both cells have the plasmid that was transferred.



According to my article, this is the main method of the transfer of antibiotic resistance between bacteria. It may be useful to develop a method of preventing conjugation in order to prevent the development of bacteria that are resistant to multiple antibiotics. Several decades ago, it was found that filamentous bacteriophages are capable of preventing conjugation. Further investigation showed that this was accomplished by closing up the conjugation pilus (or sex pilus). This is mainly mediated by g3p, a phage protein within the phage coat that seems to lower conjugation rates. These results indicate that certain proteins from the phage can be used to slow down antibiotic resistance in bacterial cells.

Click here to view the abstract of the article I used and click here to view the full article.

To Share and Share Alike

This chapter in biology has been all about the genetics of viruses and bacteria. One of the topics that we covered in class was horizontal gene transfer, in which genetic information is trasnferred between bacterial cells. This leads to increased genetic variation. I found the picture below to be helpful in understanding the difference between horizontal and vertical gene transfer.

According to my article, it was originally thought that horizontal gene transfer in bacterial cells only occurred in certain situations, such as in the presence of strong antibiotics. In actuality, prokaryotes (which include bacteria and archaea) are able to receive genes rather frequently either through a bridge or a virus. This can even occur when the two prokaryotes transferring genes are from different species. Researchers have found that 88 to 98% percent of new genes in bacteria come from horizontal gene transfer. The genes that are transferred are usually next to genes that are not similar in function. Genes that evolve within a bacteria are often located near genes that serve similar functions. The study shows that the majority of new DNA in bacteria comes from horizontal gene transfer. It has also been observed that newly transferred DNA usually stay longer within the genome and evolve more efficiently. Overall, horizontal gene transfer allows prokaryotes to evolve quickly to fit a new environment. This is also the cause of rapid development of antibiotic resistance in bacteria.

To access the article from which I retrieved my information, click here.