Genome Evolution: Flies and Humans

The abstract explains how new research has begun on on the factors that influence the population and evolutionary dynamics of transposable elements (TEs) and TE life cycles. What exactly are transposable elements? To answer that question (that most peeps should know the answer to) they are segments of DNA that can move from one site to another. TEs have sometimes been referred to as "jumping genes" because they are inherently mobile. Genomes have several different qualities when it comes to transposable elements, such as the number of TE copies, the level of TE activity, the diversity of TE families and types, and the proportion of old and young TEs.

The abstract focuses on two well-studied genomes with strikingly different architectures, (humans and Drosophila) which represent two extremes in terms of TE diversity and population dynamics. According to the abstract, researchers argue that there are two possibilities for the answers: (1) the larger population size and consequently more effective selection against new TE insertions due to ectopic recombination in flies compared to humans; and (2) in the faster rate of DNA loss in flies compared to humans leading to much faster removal of fixed TE copies from the fly genome.

Article:

Evolution of genome content: population dynamics of transposable elements in flies and humans.

Mighty-Macho Plants! ...and their Genomes

Yup, you read the title right...props for you haha! Anyways, Researchers at the RIKEN Plant Science Center (PSC) have clarified a key epigenetic mechanism by which an enzyme in the model plant Arabidopsis protects cells from harmful DNA elements. Living cells greatly depend on the proper function of their DNA in order to survive. However, certain DNA elements such as transposons (fragments of DNA that replicate within an organism's genome) disrupt this functioning and disable genes.

Ooh question! How are cells able to defend themselves between such harmful elements? Lets contemplate this question for a few seconds.... Eukaryotic cells have both active and inactive DNA; their inactive DNA become tightly-packed, this is called heterochromatin, and these dense structure serves to repress the expression of nearby gene sequences and protect the genome.

According to earlier research, "heterochromatin silencing" in Arabidopsis involves a key enzyme called HDA6. To further their research, scientists investigated the involvement of HDA6 through two processes: DNA methylation and the modification of histone.

How were researchers able to show whether plants with repressed HDA6 function can silence harmful DNA elements? They found their results through a genome-wide comparison, and discovered that these plants with repressed HDA6 function are not able to silence harmful DNA elements. This is because HDA6 binds directly to transposons and silences their activity through specific histone modifications. Therefore, researchers suggest that this enzyme plays an important role in gene silencing for plants.

(The image above shows Arabidopsis thaliana, a small flowering plant that is widely used as a model organism in plant biology and is also discussed in this article.)

Article:

Discovery of DNA Silencing Mechanism Reveals How Plants Protect Their Genome

Chapter 21: Useful Materials

What exactly is this video about? Well it explains the Human Genome Project (HGP), a research effort to identify and map all human genes. The video takes you inside for a close up look at the complexity of the cell. The HGP officially began on October 1, 1990 and was a 13-year project coordinated by the U.S. Department of Energy and the National Institutes of Health.

There were several goals that the HGP had:

1. To identify all human genes
2. To obtain the DNA sequence of the entire human genome
3. To develop technology for the generation and management of human genome information
4. To analyze the genomes of model organisms
5. To develop programs focused on understanding and addressing the ethical, legal, and social implications of results obtained from the HGP

Overall, I think this video was quite interesting in learning more about the Human Genome Project and scientists' thoughts behind this experiment. Watch it!

I LOVE Gene Cloning!

To be honest, when I first read this article it was a bunch of mumbo jumbo in my mind. I was thinking: what the poop is it talking about??? I also doubt the title is relevant to the article but who cares. But, after reading it a few more time, it made more sense...light bulb moment!

Anyways, the abstract talks about how scientists were using the gene encoding endoxylanase (xynA) from Thermoanaerobacterium saccharolyticum B6A-RI. They cloned and expressed this gene in E. coli. Then xynA encoded a hypothetical 33-amino-acid signal peptide, which corresponded to the N-terminal amino acids. From doing this, there were findings of an open reading frame of 3,471 bp, which corresponds to 1,157 amino acid residues. These results gave xynA gene product a molecular mass of 130 kDa (Dalton).

According to the study, xynA from T. saccharolyticum B6A-RI had strong similarity to genes from family F beta-glycanases. The activity of the cloned endoxylanase had a temperature of 70 degrees C and a pH optimum of 5.5. The cloned endoxylanase A was stable at 75 degrees C for 60 min and displayed a specific activity of 227.4 U/mg of protein on oat spelt xylan (a substrate for the specific assay of endo-1,4-ß-D-xylanase). Therefore, scientists concluded that the cloned xylanase was an endo-acting enzyme, meaning that it contained functions within the cell in which it was produced...ain't that spiffy?

Article:

Gene cloning, sequencing, and biochemical characterization of endoxylanase from Thermoanaerobacterium saccharolyticum B6A-RI.

Humans vs. Sheep....which is easier to clone?

So who wins the fight? Well it has to be none other than....humans! Whoot, whoot! Why? Well because humans are just the best, duh. However, in scientific terms this is because humans and primates, in general, have two active copies of a gene called insulin-like growth factor II receptor (IGF2R). This gene prevents fetal overgrowth, which is a problem that has often hindered efforts to clone animals. This problem is due to the fact that nonprimates have only one functional copy of this gene. Thus resulting in genomic imprinting, which effectively silences the other copy and makes these animals have higher risk of exposure to cancer and cloning-related complications.

Scientists at Duke University used single nucleotide polymorphisms (SNPs), which are distinctive genetic markers, to test for imprinted IGF2R in humans and to "reconstruct the evolutionary history of the imprinted gene." The results showed that there was none found in humans; therefore, indicating that primates lost the imprinted gene around 70 million years ago (geez that is a long time). This study basically showed how humans may have a far less complex cloning process compared to sheep.

While, these researchers are positive about this study, other researchers think that the study is flawed because there might be other genes that contribute to the cloning problems in sheep. According to Ian Wilmut (professor at Roslin Institute who created the cloned sheep named Dolly), "it seems that a little knowledge is a dangerous thing, and the authors have allowed themselves to over-interpret their interesting results." Through the years, their has been countless disputes over gene cloning and stem cell research within the general public, the political spectrum, and the scientific and religious communities. What's your opinion on the cloning controversy? Jk I don't really care...or do I? Share your thoughts anyways. :{)

Article:

Genetic Difference May Make Humans Easier to Clone Than Sheep

Chapter 20: Useful Materials

I thought this video showed a cute way in describing the process of gene cloning, which refers to procedures that lead to the formation of many copies of a particular gene. The video goes through gene cloning step by step.

• Step 1: Obtain a plasmid vector and a DNA fragment: these are your starting materials.
• Step 2: Both the vector and DNA are treated with restriction enzymes that cleave double-stranded DNA molecules produced in over-hanging single-stranded nucleotide tails.
• Step 3: The chromosomal and vector DNA are cut into pieces and linked together; the linkage is catalyzed by DNA ligase.
• Step 4: In order to make multiple copies of this molecule the ligation mix is introduced to E. coli cells during the process of transformation
• Step 5: According to the video, the mixture should be placed on ice and then be exposed to 42 degrees celsius to cause a change in temperature.
• Step 6: The cells are then placed on a plate with growth medium. Only the cells that have required the plasmid resistance for the antibiotic can grow in this type of medium.
• Step 7: The plate should be incubated overnight at 37 degrees celsius.

After all these steps, the results should be that each transformed cell produces a colony of cells. Yay we have now gone through the key steps for molecular cloning!

P.S. Didn't you love the guys accent? ...I sure did. :{)

This video explains how scientists obtain a genetic fingerprint at Guy's Hospital in London, England. It shows how a researcher is using an automatic DNA extractor to produce a high purity DNA fragment from a blood sample. Basically, the rest of the video explains how these researchers use gel electrophoresis to produce the needed genetic fingerprint. Why might this be important, you may ask? To answer that question, DNA fingerprinting has gained acceptance as a precise method of identification. Also it is commonly used in forensics by helping provide evidence in a criminal case. Therefore, DNA fingerprinting can be very helpful during these times of identity theft, terrorism, and the TV criminology craze.

Sperm Impaired by HIV-infection... *tear, tear*

The abstract of this article explains how researchers conducted a perspective study on HIV-infected patients. The reason for this experiment was because couples who were serodiscordant (couples with on partner HIV positive and the other HIV negative), had a human immunodeficiency virus type 1 (HIV-1)-infected man, who was most likely on highly active antiretroviral therapy (HAART). The semen alterations are caused by the HIV-1 infection and the antiretroviral drugs. These couples wanted to achieve safe conception by requesting assisted reproductive technology (ART). Therefore, the goal of this study is to investigate the semen parameters in HIV-1-infected patients with and without HAART and to compare their sperm characteristics with those of healthy men.

The experiment:

• The study consisted of 226 men, who attended the university fertility center of Mannheim between May 1996 and July 2003.
• The patients were divided into three groups:
• HIV-infected men taking antiretroviral therapy.
• HIV-infected patients who did not take antiretroviral therapy until now.
• Control group with 93 men consulting our fertility center together with their wives because of tubal sterility.
• Semen samples were examined with regard to ejaculate volume, sperm concentration, motility, and morphology.

The results of this conducted research was that it showed major differences between the ejaculate of HIV-infected and non-infected men. The HIV-infected men as a whole had a lower ejaculate volume compared to the control group. The group with HIV-infection with HAART also had a less slow progressive and more abnormally shaped spermatozoa (motile sperm cell) compared with the control group. Overall, the differences between the groups with and without HAART were not that significant. The spermiogram, which is a microscopic examination of a sample of sperm, was negatively altered in HIV-infected men, especially in men with HARRT, when compared to the control group. This means that the ejaculate volume significantly changed through the course of they study.

I just realized I didn't add any quirky remarks in this post, well until now...oops!

Article:

HIV-infection and modern antiretroviral therapy impair sperm quality.