04.09.2015
Instead of creating BioBricks, as is the IGEM project norm, we focussed on creating novel ways for existing BioBricks to be used by ordinary citizen scientists to investigate their neighborhoods.
We also borrowed some techniques of grassroot cartographers to build our own maps of the soil samples and map GEL bands on to them. We collected various soil samples from which we extracted DNA and ran it through a PCR machine (using standard Biobrick primers) followed by gel electrophoresis to characterize the combined flora and fauna of a site visually; the ecology’s fingerprint, if you will. 3.After the protein is removed the DNA can be precipitated using cold ethanol or isopropanol (propan-2-ol). 6.Presence of DNA can be confirmed by electrophoresing on an agarose gel containing ethidium bromide, or another fluorescent dye that reacts with the DNA, and checking under UV light.
1.For dissolving the DNA present in the soil, mix the soil sample (5 g) in Tris Buffer (5 mL of 25 mM buffer) and mix thoroughly. 2.Then in order to separate the cells out of the solution, filter using 5?m cellulose nitrate filter.
4.The pellet, containing the concentrated DNA (after centrifugation) is separated from the supernatant, and dissolved in 100?L autoclaved milliQ water.
1.For dissolving the DNA present in the soil, mix the soil sample in Tris Buffer (2 gm soil sample in 2 mL 25mM Tris Buffer) and mix thoroughly. 2.Freeze the eppendorf tubes containing the above mixture in liquid nitrogen, and then boil (at 100°C for 20 mins). 5.Presence of DNA can be confirmed by electrophoresing on an agarose gel containing ethidium bromide, or another fluorescent dye that reacts with the DNA, and checking under UV light.
1.Add the tris buffer to the agarose powder, heat at 50 degrees centigrade till you obtain a clear solution and add Ethidium bromide.
2.Pour into the Gel box, add the comb to form wells, get rid of any air bubbles and let it settle for 30 minutes. Sickle Cell Anemia is a common genetic disease that causes long rods in red blood cells, giving them a “sickled“ appearance. Gel Electrophoresis gel electrophoresis – moving DNA through a gel medium using an electric current Why can we move DNA with electricity? Trends in the Occurrence of Extreme Events: An Example From the North Sea Manfred Mudelsee Department of Earth Sciences Boston University, USA. Two Types of Gels 1)Agarose gels Medium to Large DNA fragments or RNA Made from polysaccharides found in various marine species of red algae (Agar)— Some found right here in California! History of Restriction Enzymes Restriction enzymes are called restriction endonucleases- cut DNA strand at certain nucleotide sequences usually 4-6 base pairs long Occur naturally in some species of bacteria where their role is “defense” These enzymes “restrict” foreign (e.g.
Different gel [] The concentration of the gel (matrix density) is critical The more agarose = the more compact and tighter the matrix = harder for charged particles to move through the gel Most agarose gels are made between 0.6% and 3%.


Different gel [] –A 2%-3% gel will show good resolution for small DNA fragments (200-1,000 bp) Lower percentage gels (0.6%) are very weak and may break when you try to lift them.
Brighter bands= high concentration of DNA Lighter bands = low concentration of DNA **Each band that you see is a collection of millions of DNA molecules, all of the same length!! Visualizing DNA Ethidium Bromide is a mutagen So we will use trace amounts of EtBr in our gels to minimize student exposure to the compound Listen to instructions when pouring your gels or analyzing your gels! Troubleshooting Guide DNA Science: A First Course in Recombinant DNA Technology, by David A.
Features First-of-its-kind blue LED light box that allows you to visualize and cut out the DNA bands without a protective mask, shield or filter obstructing your access to the gel. If you are cutting bands with a UV transilluminator, you are probably trying to limit the exposure of your sample to the damaging effects of UV as much as you can. UV-transilluminators are used in molecular biology labs to view DNA (or RNA) that has been separated by electrophoresis through an agarose gel. For the UV transilluminator enclosure and lid, download the design file attached below (svg or PDF file). Take one of the 1" long 10-32 machine screws and thread it through one of the rubber feet and the corner holes on the bottom enclosure part.
The top part of the transilluminator includes the transilluminator glass covered with the solacryl UV-transmissive protective cover. Once you have your gel prepared, place it onto the transilluminator above the viewing window, put the hinged safety lid down and switch on the transilluminator. These cells get stuck in small capillaries of the blood stream leading to oxygen deprivation that causes pain and organ damage. Thakral Group from Singapore Orion Former state owned Hungarian company Orion Electronics Ltd Budapest, Hungary Manufacturing. MIGAO CORPORATION PRESENTATION 2 Forward looking statement The contents of this presentation contain statements that. Swyx Technology Conference 2011 Smart Call Routing with Persistent Variables Tom Wellige, Swyx Solutions AG. Electro- = flow of electricity -phoresis = to carry across A gel is a suspension of tiny particles in a medium, occurring in a solid form (like gelatin) Gel electrophoresis = a process that uses electricity to separate charged molecules- DNA, RNA, and proteins, on a gel slab.
Agar is composed of both agarose and agaropectin molecules and provides support to the cell walls within the marine algae.
When DNA is cut by restriction enzymes*, the result is a mixture of DNA segments of varying lengths It is useful to be able to separate the pieces (for forensic work or for DNA sequencing) *Reminder: …. When the power supply is turned on, an electric current runs into the gel box, and an electric field is established between the positive and negative electrodes.


DNA fragments migrate toward the positive electrode at a rate that depends on their size and the size of the pores in the gel.
The PrepOne Image Catcher includes a 12.0 megapixel or higher digital camera* that allows you to send your picture directly to your email or computer via WiFi. Its oblique illumination design features a light source that enters the gel from the side, hence exciting the fluorescent dye enough so you can see the bands with the naked eye without over-saturating the background of the gel. With the PrepOne, you can take your time to cut out the optimal band with minimum attached agarose to get the most efficient recovery rate. We know your computer is not always right next to your illuminator so rather than walking back and forth, press send! During or immediately after electrophoresis, the agarose gel is stained with a fluorescent dye which binds to nucleic acid.
The photographs from these were sown together to produce a comprehensive map of the immediate surroundings.
We did this by vortexing using phenol-chloroform, and further the addition of SDS (a detergent) to remove the membranes of lipids. Sickle Cell Anemia is caused by a single point mutation in the hemoglobin gene that results in a faulty protein.
It DOES NOT tell us the sequence of those fragments –DNA sequencing is the next step to determining the actual nucleotide sequence of the DNA fragment(s). Simply connect to your WiFi network with the intuitive instructions on the camera, select your picture and press send or backup! If you do not have access to a laser cutter, you can send the files to any laser cutting service such as Pololu. In this experiment, your students will investigate the restriction enzyme that discriminates between HbA (normal) and HbS (disease) genes and perform a simulated test on a patient. This technique is used wherever the researcher needs to be able to view their sample, for example sizing a PCR product, purifying DNA segment after a restriction enzyme digest, quantifying DNA or verifying RNA integrity after extraction. Materials for laser cutting can be found at any supplier of acrylic materials (McMaster-Carr, US Plastics etc) except for the solacryl (UV-transmissive) which can be bought from Loop Acrylics.
Other users are strongly recommended to use SYBR-Safe instead, which can be handled and disposed of more safely.
However, when the lid is not in place, safety glasses must be worn when operating the UVB bulb.



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