Le Bioinformatics

This website is all about bioinformatics.
It talks about how the major advances and excess amounts of information needed to be organized and stored in a database, thus resulting in bioinformatics. It explains why bioinformatics is important and necessary. It provides scientists with a more global perspective in experimental design and is able to fund on the surfacing technology of database-mining (process in which testable hypotheses are generated by the function or structure of a gene or protein of interest by finding smaller sequences in better characterized organisms).
It also talks about biological databases, evolutionary biology, protein modeling, genome mapping, and tools used in bioinformatics. For example, "Map Viewer" is used to visualize whole genomes or single chromosomes.
Go check it out!

Bioinformatics: Challenge Accepted.

This article talks about some bioinformatics challenges for genome-wide association studies.
In chapter 21, we learned that bioinformatics is a field of study that uses computers, mathematical tools, and statistical techniques to record, store, and analyze biological information. to study biological information. This fast advancing branch of biology is very interdisciplinary and incorporates principles from mathematics, statistics, information science, chemistry, and physics.
We need bioinformatics because it helps us analyze an enormous amount of data in a reasonable amount of time. By sequencing the human genome, we have been able to identify over one million single nucleotide polymorphisms (SNPs) that can all be used to carry out genome-wide association studies (GWASs). New biostatistical methods have been needed for quality control, imputation, and analysis issues with multiple testing; this is because of the large amounts of GWAS data that has accumulated.
The work has had success and allowed for the discovery of new associations that have been copied in many studies. Most of the SNPs discovered through GWAS have little effects on disease susceptibility and are therefore deemed unsuitable for improving health care through genetic testing. An explanation for the mixed results of GWAS is that the biostatistical analysis example is by design agnostic or unbiased because it does not take into account the previous information on disease pathobiology. The linear modeling framework that is employed in GWAS usually only takes one SNP into account at any given time. This ignores the genomic and environmental context.
Now there is a shift away from the biostatistical approach and more towards a holistic approach. This recognizes the complication of the genotype-phenotype relationship that is set apart by significant heterogeneity along with gene-gene and gene-environment interaction.
The article goes on to assert that bioinformatics plays an important role in addressing the complexity of the
fundamental genetic basis of common human disease. The article identifies and goes into detail about the GWAS challenges that will necessitate computational methods.

Flowchart for bioinformatics analyses of GWAS data. The use of filter and wrapper algorithms along with computational modeling approaches is recommended in addition to parametric statistical methods. Biological knowledge in public databases has a very important role to play at all levels of the analysis and interpretation.

Jumping Genes in Flies

This article talks about transposable elements (TEs) that may be beneficial to fruit flies. In chapter 21, we learned that transposable elements are segments of DNA that can move from one location to another. They are inherently mobile. The ends of TEs have inverted repeats which are short DNA sequences that are present in many copies throughout the genome. All organisms contain pieces of DNA that aren't necessarily theirs, aka TEs. The finer points about factors that govern the spread of transposable elements within a population are still very unclear. The University of Veterinary Medicine, Vienna  has work that may help us increase our information about the intracellular battle that is constantly being played out between the host and invading DNA.
With new sequencing technologies, Robert Kofler and Andrea Betancourt in Schlotterer's group at the Vetmeduni Vienna's Institute of Population Genetics, were able to examine the difference in TEs in a small population of fruit flies. All the TEs in that population were catalogued. The researchers found how often TEs occur at certain sites of insertion as well.

This picture shows the function of a transposable element. It basically carries the genes and gets inserted into the bacterial chromosome.

The flies contain TEs at many sites throughout the genome despite there being many insertion sites that are actually only affected in few individuals. Researchers say that these sites were sites of recent insertion and soon we will be able to find out whether the elements are maintained there. The majority of TEs are somehow purged before they become established. Schlotterer summarized the results: "the genome is like a record of past wars between hosts and the parasitic DNA. There have been waves of attacks and the majority of them have been repelled, with only few transposable elements managing to survive and spread throughout the population."
Many sites of insertion that were more recurrent in the population than would have been expected for their age, were also found . This means that there is positive selection for TEs at these sites. This suggests that insertion has a beneficial effect on the host. 
We can conclude that TEs aren't like parasites at all, but actually very helpful. They provide organisms with an opportunity to increase their genetic collection. This is important and can be very advantageous in helping them overcome future challenges.

Plasmids

This video describes the function of plasmids. It uses diagrams and pictures to explain what plasmids do in a cell. It talks about how bacteria provide genetic engineers with restriction enzymes and plasmids. Then it talks about plasmids and restriction enzymes in further detail. Plasmids are tiny rings of DNA. Plasmids are independent and self-replicating. They allow for DNA recombination. This video is very informative regarding plasmids and bacteria. I would suggest you watch this video if you are having trouble grasping this concept.

Genetically Modified Bacteria

This article talks about how we can filter out pesticides using genetically modified bacteria.
In this chapter we learned that researchers can introduce cloned genes into oocytes, fertilized eggs, and embryonic cells to produce animals that carry the cloned genes. An organism that carries genes that were introduced using molecular techniques, like gene cloning, are called transgenic. Another name for them is genetically modified organism.
E. coli is often used in research for many beneficial experiments. Researchers have found that a genetically modified bacteria can be used in a biofilter to help remove pesticides, parathion, and methyl parathion from the air.

Biofilters use living material to capture and biologically degrade process pollutants.

A group of researchers in Beijing used a biofilter with an engineered E. coli BL21 and found the removal efficiencies of 95.2% for parathion and 98.6% for methyl parathion. Optimizing the system may allow for 100% removal. The team explained why their biofilter is better than the average, conventional biofilter. Their system was more effective, especially in the initial stages of filtering. They also explained how their biofilters work. The pesticides are broken down to p-nitrophenol as well as nitrate and sulfate byproducts. The byproducts are mineralized by other naturally occurring microbes present in the biofilter.
These two pesticides that these researchers have been focusing on are highly effective pesticides and contribute to more than a third of agricultural crop protection throughout the world. However, if they accumulate in the environment, they can seriously harm human health. This is why we are currently developing bioremediation of water and soil using bacteria that can break down these harmful compounds. These Beijing researchers focused on one aspect, air purification, using biofilters.

Baby Got BAC

^I just died for like 10 minutes. ohmygod. Why am I so funny?

This article talks about the development of a bacterial artificial chromosome recombineering procedure using galK-untranslated region for the mutation of diploid genes.
A common aim of researching genomics is to clone and analyze the entire genome of a species. For large eukaryotic genomes, it is easier when cloning vectors can accept larger chromosomal DNA inserts. Most plasmid and viral vectors can accommodate inserts that are a few thousands to tens of thousands of nucleotides in length. If a plasmid or viral vector has a DNA insert that is too large, it will have difficulty with DNA replication and is likely to suffer deletions in the insert. On the other hand, there is another type of cloning vector known as bacterial artificial chromosome (BAC). It can contain much larger inserted DNA fragments. BACs are derived from F factors, large plasmids. BACs are used in genomic research with the same use that other vectors are used for.

BAC doin' work.

BAC recombineering using galK lets cloned DNA from E. coli to be modified without letting unwanted selectable markers (gene whose presence can allow organisms to grow under a certain set of conditions) in at the modification site. Certain genomes contain pairs of inverted repeat sequences that make it difficult to bring in mutations into duplicate genes using galKs selection method. A galK-UTR BAC recombineering procedure was created to mutate duplicate genes. This procedure blocks one copy of the target duplicate gene and allows the simple mutation of the other copy. Blocked copies are now able to be replaced with a UTR-specific primer pair.
In this experiment, mutant IR2 promoters that contained three Sp-1-binding motifs and a consensus TATA box were used in place of the two IR2 promotors in EHV-1 BAC. The results from this showed that there was a 4-fold increase of the expression level of the IR2 protein. This means that the galK-UTR method will prove as a useful tool in studies of herpesviruses.

Viruses and the Lytic Cycle

This is a helpful video in which Professor George Wolfe talks about viruses, their structure, their function and their parts. The video also uses diagrams to help explain. Viruses are acellular, they have no metabolic processes, and they are parasitic. They have a capsid which is the outside layer made out of protein. The inside contains the nucleic acid. Some viruses "steal" things from their host cells. He explains that viruses are lytic or lysogenic. He walks through they lytic cycle. He explains whether or not viruses are living or non-living and goes into detail to explain why. Overall, I found this video to be very useful in explaining the function of viruses.

Prions= The Biggest of Bods :)

I'm sure you've all heard of mad cow disease? Well, mad cow disease was actually sparked by a protein called a prion. This led to fatal brain problems in the cattle. This was dangerous because it could affect any humans that ate contaminated meat. As we learned in this chapter prions are infectious proteins that cause diseases by inducing the abnormal folding of other protein molecules. So, more recently, a "mad deer" disease has come about. It targets deer, moose, and elk in the U.S. Fortunately, there are naturally occurring disinfectants found in lichen that may stop the dangerous prions in the wild.

Le Lichen (aka biggerbods than the prions)

This article talks about how lichens are natural born prion killers and how they can help us solve this dangerous disease.
These types of diseases are scary because they are produced by prions and we all know prions are super bigbods. They're super indestructible. You could be all like "aww yeahh I'm gonna boil all the bacteria outta you" and they're just like, "no". Dry heat, ionizing radiation, you name it... nothing will faze them. After all, one of the main reasons mad cow spread so fast is due to prions resistance to inactivation.
These wild animals spread the disease through their urine, feces, and saliva.
Christopher Johnson of the U.S. Geological Survey of the National Wildlife Health Center in Madison, Wisconsin, and his team found that three species of lichen have an enzyme that can break down the infamous prion!!!! Scientists concluded that when prions come into contact with lichens or soil near them, they inactivate. aka... prions are'nt so big anymore :)

Plasmids Will be the Death of Meee!!!

In this article researchers discovered that plasmids were the main reason that antibiotic resistance was spreading through bacteria. This is an important study because  more and more bacteria are resisting our antibiotics. UH OHHH! The problem is called multi-resistance. This is when an organism is able to survive even when exposed to multiple antibiotics. The antibiotic resistance can be transferred to the bacteria, even non-related bacteria, and can lead to human diseases. So how can this resistance be transferred to other bacteria, thus creating the bigger problem? Through conjugative plasmids, of course!
Conjugative plasmids help transfer genetic material between bacteria. A plasmid is a small DNA molecule that can separate from, and replicate independently of, the chromosomal DNA. These are those tiny circular things that we learned about in class.

This is picture shows the two different types of plasmid integrations into their host bacteria. The top shows non-integrating plasmids and the bottom shows episomes, where the plasmids integrate into the chromosome.

This research team studied IncP-1 plasmids. They mapped the origin of different IncP-1 plasmids and their ability to move and transfer informatoin between different species of bacteria. Peter Norberg, a researcher at IBUG stated, "Our results show that plasmids from the IncP-1 group have existed in, and adapted to, widely differing bacteria. They have also recombined, which means that a single plasmid can be regarded as a composite jigsaw puzzle of genes, each of which has adapted to different bacterial species" So the results showed that the plasmids can easily adapt. This tells us that despite the specie of 

the bacteria, these plasmids can move between and survive quickly in the different environments.

These plasmids are probably the #1 source in transferring the resistance genes between different bacteria. This is why this antibiotic resistance is becoming so widespread so fast.

In conclusion, this study showed that plasmids are the key source in spreading antibiotic resistance. It proved that IncP-1 plasmids move between different species of bacteria and interact directly with each other; thus, increasing the potential for the gene to be spread.