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Culturing and Enumerating Bacteria from Soil Samples

JoVE 10099

Source: Laboratories of Dr. Ian Pepper and Dr. Charles Gerba - Arizona University
Demonstrating Authors: Bradley Schmitz and Luisa Ikner


Surface soils are a heterogeneous mixture of inorganic and organic particles that combine together to form secondary aggregates. Within and between the aggregates are voids or pores that visually…

 Environmental Microbiology

Gram Staining of Bacteria from Environmental Sources

JoVE 10092

Source: Laboratories of Dr. Ian Pepper and Dr. Charles Gerba - Arizona University
Demonstrating Author: Luisa Ikner


The spectrum of research in environmental microbiology is broad in scope and application potential. Whether the work is bench-scale with known bacterial isolates, or in the field collecting soil or water samples…

 Environmental Microbiology

Restriction Enzyme Digests

JoVE 5070

Restriction enzymes or endonucleases recognize and cut DNA at a specific sequence. These enzymes occur naturally in bacteria as a defense against bacteriophages - viruses that infect bacteria. Bacterial restriction enzymes cut the invading bacteriophage DNA while leaving the bacterial genomic DNA unharmed due to addition of methyl groups.


This video explains the basic principles …

 Basic Methods in Cellular and Molecular Biology

Bioremediation

JoVE 10937

Bioremediation is the use of prokaryotes, fungi, or plants to remove pollutants from the environment. This process has been used to remove harmful toxins in groundwater as a byproduct of agricultural run-off and also to clean up oil spills.

Bioremediation is a useful process in which microbes and bacteria are used to remove toxins and pollutants from the environment. In agricultural practices, the use of fertilizers and pesticides can result in leaching of chemicals into the groundwater, streams and lakes. For example, atrazine—an environmental toxin found in many fertilizers—can be broken down and removed from soils using two common environmental bacterial species, Rhizobium and Tricoderma sp. Oil spills often contribute to the loss of marine biodiversity. However, nutrient addition to aquatic areas affected by an oil spill promote the growth of hydrocarbon-degrading bacteria that will break down petroleum. For example, in one study, scientists tested the ability of a naturally occurring consortium of bacterial symbionts of the coral Mussismilia hartii, to break down oil. Not only can they degrade petroleum hydrocarbons minimizing effects of oil on the health of the coral species, but they can dually promote photosynthetic efficiency of the coral.

 Core: Biology

Mismatch Repair

JoVE 10791

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.

The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic information needs to be replicated. Despite the proofreading ability of the DNA polymerase, a copying error occurs approximately every 1 million base pairs. One type of error is the mismatch of nucleotides, for example, the pairing of A with G or T with C. Such mismatches are detected and repaired by the Mutator protein family. These proteins were first described in the bacteria Escherichia coli (E. coli), but homologs appear throughout prokaryotes and eukaryotes. Mutator S (MutS) initiates the mismatch repair (MMR) by identifying and binding to the mismatch. Subsequently, MutL identifies which strand is the new copy. Only the new strand requires fixing while the template strand needs to remain intact. How can the molecular machinery identify the newly synthesized strand of DNA? In many organisms, cytosine and adenine bases of the new strand receive a methyl group some time after replication. Therefore,

 Core: Biology
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