Obtaining two distinct contigs from a sequencing reaction suggests that either this virus has two separate chromosomes, or that there is some type of error in the sequencing reaction. 

The most direct way to test this would be to run a Northern blot analysis with probes against the two potential chromosomes. If they are unique chromosomes, we would expect to see a band that matches the length of the sequenced product on the gel per chromosome. If it is an error, both probes should yield a band of the same size, suggesting that there is only one chromosome.

A Southern blot tests for the presence of DNA; therefore, that would not be useful. A protein gel would also not be useful in this case since we are trying to determine the presence of RNA. A PCR will also not be fruitful since it cannot be conducted on RNA.

Note that a reverse-transcription PCR could potentially be useful because it would convert the RNA into DNA; in that case, you can design mulitple combinations of primers if you think it is a single chromosome.

These are all important steps to create a usable DNA extraction. First, the tissues are homogenized, generally chemically or mechanically. The proteins are then removed from the sample by denaturation. Any contaminants can be removed by multiple methods with organic solvents. Depending on the situation, some other steps are involved, such as removal of RNA from the extract. Lastly, the DNA is precipitated via an alcohol into a pure DNA extract.

The correct answer is SDS. SDS disrupts non-covalent bonds in proteins ultimately denaturing these proteins. Both ammonium persulfate and TEMED are reagents used to polymerize (or solidify) SDS-page gels for western blot applications. EDTA chelates cations in solution preventing the activity of proteases that may degrade the primary amino acid structure. Acrylamide is the substance that is polymerized in the SDS-gel, giving the viscous physical characteristics to the gel. 

Flow cytometry utilizes antibodies specific to a protein expressed by a single cell type. Antibodies can be coated onto magnetic beads, and those antibodies will bind only cells with the proper proteins, thus becoming "stuck" to the beads which can be separated out from the sample. Centrifugation will not be able to detect such small differences, and is only useful if the density is different. Co-IP is more appropriate when looking for proteins that interact or colocalize. Southern blotting is for DNA detection, and X-ray crystallography is for understanding protein structure. 

One function of DNA footprinting involves looking for binding sites by using nucleases to cleave DNA. Wherever the transcription factor is bound should be blocked and protected from cleavage. A sample of DNA can be run in a gel without transcription factors bound and compared to a gel run with DNA that has been exposed to the transcription factor. The difference in DNA sequence can be analyzed based on cleavage differences to identify the transcription factor binding region.

Northern blotting helps identify gene expression by looking at RNA. Western blotting helps identify specific proteins in a sample. PCR helps amplify a sample of DNA.

The secondary antibody is designed to interact specifically with the primary antibody. This is a crucial step because the secondary antibody will contain a detectable marker (usually a fluorescent marker).

The primary antibody interacts with the protein of interest. The membrane is blocked with milk or some other substance prior to addition of the antibodies to prevent nonspecific binding. Ponceau S dye is used to quickly and reversibly detect quantities of proteins on nitrocellulose membranes.

The correct answer is the student performed a gram stain and the bacteria is virulent. A gram stain specifically stains peptidoglycan, which is in the outer membrane layer of some bacteria, purple. The presence of peptidoglycan marks a bacteria as gram-positive. If peptidoglycan is not present, the bacteria will not stain purple, and the bacteria is said to be gram-negative. Gram-negative bacteria contain an outer layer of lipopolysaccharides that confer antibiotic resistance and virulence. Since we know that the bacteria in question doe not have an outer peptidoglycan layer, we know that it is virulent.

Northern blots are used to study RNA. When run on the gel used in a Northern, you can observe the length of the RNA (by how far it moves on the gel), the number of transcripts (the number of dark bands), and the expression level (how dark the bands are). Southern blots are used to study DNA, and Western blots are used to study proteins.

The correct answer is to determine which plasmids promote proliferative bacteria growth. In this experiment, the researcher wants to identify enzymes that, when over expressed in bacteria, allow the bacteria to grow in unfavorable (minimal) conditions. Since this researcher grows all 3000 transformed bacteria, each expressing a different enzyme, in one minimal media culture, he needs to be able to identify which enzymes promote growth. A barcode is an engineered unique DNA sequence that can be inserted on the plasmid expressing the enzyme. The researcher barcodes each unique plasmid. If a certain enzyme promotes bacteria growth, there will be bacterial replication and replication of the plasmid. Sequencing of the entire bacterial culture will determine which barcodes are overrepresented. Each barcode is then associated with the unique enzymes that allow for proliferative growth in minimal media. 

The correct answer is co-immunoprecipitation. During this experiment, protein-protein complexes are cross linked then pulled down by an antibody specific to one of the proteins of interest. Then, these protein elutes are run on a western blot and probed for with a second antibody specific for the other protein believed to be in complex. An electrophoretic mobility shift assay measures the DNA-binding ability of a protein. A TUNEL assay is a measure for apoptosis by quantifying fragmented DNA. Protein binding microarrays determine the preferred DNA binding sequences for a given protein. ChIA-PET measures distal chromatin interactions within the genome.