In the first section of this page, you will write a daily summary of that day's class.  For example in  your chapter 2 blog, your first entry should be titled 9/3/10.  You should then write a one or two paragraph summary of that day's lecture, outlining the major points.  In the second section, you are required to add two items (link to a website, video, animation, student-created slide show, student-created PowerPoint presentation) and one journal article pertaining to a topic in this chapter.  A one-paragraph summary must accompany each item describing the main idea and how it applies to the lecture topic.  Please see the PBWorks help guide for assistance embedding video and other items directly in the page.  I will also produce a how-to video on using tables to wrap text around items and other useful tips.  Please see the syllabus for organization and grading details.

A.  Daily Blog

This chapter is all about the genetics of viruses and bacteria.

Viruses are small infectious particles that consist of nucleic acid enclosed in a protein coat. There are over 4,000 different types of viruses. They vary greatly in their host range, structure, and genome composition. The host range is the number of species and cell types a virus can infect. The structure of a virus can be helical, polyhedral, or complex. The helical structure is a helical capsid surrounding the nucleic acid. The polyhedral structure is like a regular polygon, with protein fibers on the capsid. There may also be a viral envelope. The complex structure has a head with the nucleic acid, the shaft, and a base plate, and almost looks like a robot. The viral envelope, as mentioned before, is an additional layer made up of phospholipids and protein that is non-selective and aids in recognition. This envelope is acquired when exiting the host cell.

The viral reproductive cycle contains several steps. The first is the attachment and entry of the viral nucleic acid into the host cell. Once inside, the nucleic acid will be integrated into the host DNA, either as DNA directly, or being reverse-transcribed from RNA into DNA, and then into the host DNA. The viral DNA is then expressed, and the viral components are synthesized. Then the virus is assembled, and is released. The virus may run a lysogenic cycle where the viral DNA is reproduced passively, or may run a lytic cycle, lysing the host cell when reproduced.

The genetics of bacteria is the next part. Bacteria have circular DNA, unlike eukaryotic linear DNA. They lack a nucleus, but have their DNA in a nucleoid region. Another aspect of bacterial DNA are plasmids. These are small, circular pieces of DNA independent of the bacterial chromosome. They have their own origin of replication. They are usually not essential for survival, but aid in the life of the bacteria. Some plasmids can integrate into the bacterial chromosome, and they are called episomes. There can also be multiple copies of plasmids to increase the amount of expression. Plasmids can be Resistance plasmids, Degradative plasmids (which enable the bacterium to digest and utilize an unusual substance), Col-plasmids (which produce a protein to kill other bacteria), Virulence plasmids (which turn the bacterium into a pathogenic strain) or Fertility plasmids (which allow bacteria to mate). The reproduction of bacteria is near constant. They reproduce quickly, even exponentially. They also die exponentially. Bacteria divide through binary fission, where identical copies are produced. Plasmids in a bacteria may replicate independent of the bacterial chromosome.

The last part of the chapter is the genetic diversity of bacteria. There are two causes: mutations, or gene transfer. Gene transfer can occur in three ways. Conjugation is when a bacterium with an Fertility plasmid that directly transfers genetic material from the donor to the recipient. Transformation is a process in which the DNA from a dead bacterium is taken up by another bacterium. Only cells with competency factors can do this. The last process is transduction, in which a virus transfers genetic information from one bacterium to another. This usually occurs through an error in the bacteriophage lytic cycle, where newly assembled phages incorporate host DNA instead of their own.

B.  Useful Materials

This is a video that illustrates the process of conjugation.... In a very interesting way....

In this video, the HIV virus reproductive cycle is explained. We can see that HIV is a retrovirus, as its nucleic acid is normally RNA, and is turned into DNA by reverse transcriptase.

A lentiviral vector pseudotype suitable for vaccine development

This experiment was designed to develop vaccines. I found it cool to see an application of the science outside of class, something that always makes me think about what I've learned, and how it is actually practical. Nonetheless, the experiment was made to find the best viral envelope to use for the lentiviral vaccine. The researchers selected the Ross River Virus envelope so that they could test in a clinical setting. From their tests, they found that this envelope was a good candidate for the vaccine. The ultimate goal of this research is mass-produce vaccines.