The abstract of this article talks about RT-PCR. Well what exactly is RT-PCR? RT-PCR stands for Reverse Transcription-Polymerase Chain Reaction. It is a technique used in genetic studies that allows the detection and quantification of mRNA , particularly in samples with limited quantities of extracted RNA. It is a very sensitive method that shows whether or not a specific gene is being expressed in a given sample. RT-PCR is a very important test in the field of Genetically-Modified Organisms (GMO's) because it gives researchers a mechanism to test whether any specific gene is turned on (active) or turned off (inactive). This allows researchers to identify the benefits of genetically-modified organisms with respect to their "natural" counterparts and search for any significant differences in which genes are expressed in the two types of organisms.
Saturday, December 10, 2011
Has it all been a lie???
According to the latest findings from researchers of the Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch of the Helmholtz Association, Germany, control mainly occurs in the cytoplasm of the cell and not in the 'high-security tract' of the cell nucleus. Their results also highlight where gene expression (the activation of a gene for protein production) can get out of control. This study was researched by a team of scientists led by biologists Björn Schwanhäusser and Matthias Selbach, biomathematician Jana Wolf (all from MDC) and the biotechnologist Wei Chen of the Berlin Institute for Medical Systems Biology (BIMSB) of the MDC.
As described in my previous post, transcription is the process of creating a complementary RNA copy of a sequence of DNA. Translation is the process that converts an mRNA sequence into a string of amino acids that form a protein. Both of these processes work in cohesion with one another to go through the journey from DNA sequence to a functional protein. The researchers questioned which of the two processes (transcription or translation) plays the dominant role in regulating cellular protein levels.
To answer this question the MDC researchers measured the turnover of cellular mRNAs and proteins and mRNA and protein levels as their starting point. They used high-throughput technologies such as quantitative mass spectrometry and the latest sequencing techniques. In total, they evaluated proteins and mRNAs for more than 5,000 genes. The researchers drew conclusions from the collected data about the control of protein levels by using mathematical modeling. They observed that cellular protein levels mainly depend on translation of mRNAs in the protein factories of the cytoplasm.
The researchers found that cells use their resources very efficiently. Most mRNAs and proteins of abundantly expressed housekeeping genes (these genes maintain the normal operations of the body) are very stable. This is good because the cells will save worthy energy for future needs. However, the proteins responsible for rapid signaling processes are usually unstable. Therefore, cells can quickly adapt to changes in their surroundings. This may also explain why the decisive control step takes place in the cytoplasm and not in the nucleus.
According to Matthias Selbach, "so far, this is purely basic research. But we also know that the production of proteins is disturbed in many diseases, for example cancer." There is not much information about where the process gets out of control. Until now, researchers focused mainly on the nucleus to find answers to this question. However, the new findings show that the protein factories in the cytoplasm have great significance.
Chapter 12: Useful Materials
These animations for both transcription (CLICK HERE: TRANSCRIPTION) and translation (CLICK HERE: TRANSLATION) are from the Institute of Agriculture and Natural Resources at the University of Nebraska. I think these animations are interesting because they go into detail about the process of transcription and translation.
Now I shall somewhat explain both these processes...yay!
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. During transcription, a DNA sequence is read by RNA polymerase, which produces a complementary, antiparallel RNA strand. Transcription is initiated when the RNA polymerase complex assembles at the promoter. RNA polymerase catalyzes the elongation of the RNA while the DNA template is unwound and rewound.
Translation is the process that converts an mRNA sequence into a string of amino acids that form a protein. This fundamental process is responsible for creating the proteins that make up most cells. It also marks the final step in the journey from DNA sequence to a functional protein; the last piece of the central dogma to molecular biology.
Sunday, November 27, 2011
DNA Polymerase and its Conformational Transitions
The abstract of this article explains the conformation transitions in DNA polymerase. DNA polymerase is an enzyme that catalyzes the polymerization of deoxyribonucleotides into a DNA strand. DNA polymerases are best-known for their role in DNA replication, in which the polymerase "reads" an intact DNA strand as a template and uses it to synthesize the new strand. DNA polymerases depend on a series of early steps in the reaction pathway. This allows the selection of the correct nucleotide substrate before the enzyme carries out the chemical step of nucleotide incorporation. The conformational transitions that are involved in these early steps are easily detectable with a variety of fluorescence analysis, which include the fingers-closing transition that has been characterized in structural studies. Scientists have developed a FRET-based assay for the fingers-closing conformational transition that occurs when a binary complex of DNA polymerase I (Klenow fragment) with a primer-template binds a complementary dNTP; they have used this and other fluorescence assays to place the fingers-closing step within the reaction pathway.
Breakdown of DNA in Cancer Cells
This article talks about researchers at the Hebrew University of Jerusalem and how they discovered why cells suffer from insufficient building blocks to support normal DNA replication, during the early stages of cancer development. DNA replication is the process of making an identical copy of a section of duplex (double-stranded) DNA, using existing DNA as a template for the synthesis of new DNA strands.
There is a possibility that cancer development can be ceased by externally supplying the building blocks of DNA. Thus, resulting in reduced DNA damage and significant lower potential of the cells to develop cancerous features. Researchers at the Hebrew University of Jerusalem demonstrated that insufficient levels of the DNA building blocks (nucleotides) required to support normal DNA replication is caused by abnormal activation of cellular generation, which drives many different cancer types. By using laboratory cultures in which cancerous cells were introduced, the researchers were able to show that it is possible to reactivate normal DNA synthesis through external supply of those DNA building block. Thus, opposing the damage caused by the cancerous cells and the cancerous potential it may of caused.
Chapter 11: Useful Materials
This video describes the structure of DNA and everything involved with it. Nucleotides are the building blocks of DNA (and RNA). Each nucleotide consists of a 5-carbon sugar (deoxyribose), a nitrogen containing base attached to the sugar, and a phosphate group. There are four different types of nucleotides found in DNA, differing only in the nitrogenous base; adenine, guanine, thymine, and cytosine. Adenine and guanine are purines, which are the larger of the two types of bases found in DNA. Cytosine and thymine are pyrimidines; like purines, all pyrimidine ring atoms lie in the same plane. This is just an overview on the structure of DNA. But I thought this video was helpful in knowing the basic components of DNA.
This website (CLICK HERE) provides an animation about DNA replication. I thought this website was quite interesting because it breaks down DNA replication into eight sections to better help you learn. You can also pause, rewind, and fast forward the animation. There are also review questions after each section to check if you retained the knowledge that you just learned. I advise you check out this website!
Monday, November 14, 2011
Cell Adhesion
Cellular adhesion is the binding of a cell to a surface, extracellular matrix or another cell using cell adhesion molecules such as integrins, cadherins, and selectins. Cell adhesion is critical for the genesis and maintenance of both three-dimensional structure and normal function in tissues. Cell adhesion receptors are typically transmembrane glycoproteins that mediate binding to extracellular matrix molecules (ECM) or to counter-receptors on other cells; these molecules determine the specificity of cell-to-cell or cell-to-ECM interaction.
The integrins are cell-surface glycoproteins that act as receptors for ECM proteins, or for membrane-bound counter-receptors on other cells. They also play a role in cell signaling and therefore regulate cellular shape, motility, and the cell cycle. Each integrin is a heterodimer that contains an α and a β subunit with each subunit having a large extracellular domain, a single membrane-spanning region, and in most cases, a short cytoplasmic domain.
The cadherins are a class of type-1, transmembrane proteins. They share an extracellular domain consisting of multiple repeats of a cadherin-specific motif. They play important roles in cell adhesion, ensuring that cells within tissues are bound together. Their name is derived from the fact that they are dependent on calcium (Ca2+) ions to function. This subfamily includes the N-, P-, R-, B-, and E-cadherins, also including 10 other members. These molecules localize in specialized sites of cell-to-cell adhesion that are termed adherence junctions; at these sites cadherins can establish linkages with the actin-containing cytoskeleton.
The selectins are lectin-like adhesion receptors composed of three members, L-, E-, and P-selectin. P-selectin is present in latent form in endothelial cells and platelets; it is rapidly translocated from secretory granules to the cell surface upon cell activation by thrombin or other agonists. E-selectin is synthesized and expressed on endothelial cells in response to inflammatory cytokines such as tumor necrosis factor (TNF) or IL-1. L-selectin is expressed constitutively on leukocytes, but its presentation at the cell surface may be regulated. All selectins are single-chain transmembrane glycoproteins that share similar properties to C-type lectins due to a related amino terminus and calcium-dependent binding.
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