Through seed : Seed can be infected with virus either due to external contamination of the seed with virus particles, or due to infection of the living tissues of the embryo. Transmission by this route leads to early outbreaks of disease in new crops which are usually initially focal in distribution, but may subsequently be transmitted to the remainder of the crop by other mechanisms.

Vegetative propagation/grafting: These techniques are cheap and easy methods to allow more growth but provide the ideal opportunity for viruses to spread to new plants.

Vectors: Many different groups of living organisms can act as vectors and spread viruses from one plant to another: i.e. are inscects like beetle,grasshopper. When this inscects sucks or bite the plant tissues, viruses is transmitted. In some cases, the virus may also infect and multiply in the tissues of the insect, and so these inscects not only serves as a vectors but also of amplifying the infection.

Mechanical: Plant viruses rely on a mechanical breach of the integrity of a cell wall to directly introduce a virus particle into a cell. Thus, when an inscect bite or sucks it makes the plant vulnerable for infectious. Sometimes, virus from the soil or the air can infect the plant.

Spraying of pesticide or insecticide will damage the plant cell wall thus it make plants vulnerable to infectious. Most of the time this form of action will cause the whole crop population to be infected. Farmers will be the only suffering the lose of crops but it can cause food shortage in this century of times as many farmers are using pesticide or insecticide and with the climate changing virus can spread rapidly from one crops to the next killing them. Crops are important to human for food so thus plants in the wild, they also give off oxygen which is the breath of every living creature on this earth. If we would to eat this virus infected plants this virus may start mutating to start infecting humans too. Everything that seems impossible will be possible with nature so we should not only should learn our nature but should start repairing this very damage earth if not we will become extinct.

Done by me, Jiani

In this post, in studying the molecular virology,
I would be talking about the

Analysis of viral genome

the analysis of viral genome,
• Agarose gels
• Restriction analysis
• Sequencing
• Southern blot
• Northern blog
• PCR/ RT- RCP

is used. one by one, I will explain to you how do they work.


There are many different ways of extracting DNA bands using agarose gels. And using different methods, different yield or purity of the DNA is produced after extraction. In extraction of the DNA, many different enzymes are being used and hence, there may be various impurities which may inhibit downstream reactions if not efficiently removed from the DNA. After the DNA is exctracted, agarose gels could also be used to purify it.

Below are Videos, explaining how the extraction is made and


More detailed videos on how procedures involved in the production of an agarose gel and on running an Agarose Gel






From the extracting DNA bands using agarose gels, protein sequencing could be used to predict the amino acid sequence of a protein, indirectly from the mRNA of the organism. From there, the restriction enzymes are used to cut the DNA sequence into smaller pieces for an easier deduction of the amino acids sequence. It is done by isolating the mRNA coding for the protein and replicate a certain yield of the DNA, using PCR(polymerase chain reaction).

Next, is the Southern blot. It is a method used to check for the presence of a DNA sequence in a DNA sample combining agarose gel electrophoresis for size separation of DNA and transferring the separated DNA to a filter membrane for probe hybridization. (Where fragment of either DNA or RNA of certain length is used to detect the presence of nucleotide sequences in the sample that are complementary to the sequence in the probe.)

The method for the northern blot is similar to the Southern blot but RNA rather than DNA is analyzed in the northern blot.

Below are 2 videos on southern and northern blot.


Southern blot


Northern blot


Then is the polymerase chain reaction (PCR). It is steps repeated 20 to 30 times to clone copies of DNA. For more information on the procedure, please view the videos below.



Lastly is the reverse transcriptase PCR (RT-PCR) is a method used to convert the RNA back to DNA called cDNA(complementary DNA) As RNA is single stranded, it is fragile and unstable. Therefore, by using the enzymes reverse transcriptase, the double strand form of the cDNA is produced. Then, it goes on to the normal PCR cycle to replicate more of the DNA.

For more information, do go to this website to know more about RT-PCR




And, for a bit for humor, let’s watch this!
The PCR song.




Thanks! signing off, Yanling

Continued from Manhua's Methods of study of Viruses i am going to talk about the physical methods used to view virus.


They are mainly:

• X-ray crystallography
• Electron microscopy - Transmission Electron microscopy, Scanning Electron microscopy and the STEM (Scanning Transmission Electron Microscope)
• Ultracentrifugation where purification is used.


Basically, they are used to study the virus and the virus genome.
X-ray crystallography is a method used to determine atoms in the crystals with an illustration of the picture is on the right. The rays are being scattered on to the crystal, forming a lot of rays which gives an density make up of the virus.


The Electron microscopy is a microscope used to enlarge objects up to 2 million times, using electrons to give an idea of the object. As compared to a light microscope which can only magnify up to 2000 times, the electron microscope have a higher resolution due to the wavelength of the electron. With a electrostatic and electromagnetic lenses, the image is then formed by controlling the electron beam to focus on the object to form the magnified image.

The difference between the 3 Electron microscope is that the Transmission Electron microscope uses a high voltage electron beam to create an image.

While the
Scanning Electron microscope,( picture of it is at the right) produces the image with a electron beam that is focus and scan over the specimen.
Unlike the Transmission Electron microscope, it does not carry a complete image of the specimen.

Lastly, the Scanning Transmission Electron Microscope
STEM use beam like
use of SEM’s beam which transmits and simplifies dark-field images. Thus, the specimen is taken in serial but not in parallel fashion.



Then, is the Ultracentrifugation where purification is used. In ultracentrifugation, either sucrose gradients or organelles. gradients of caesium salts are used to study the virus.
Using the sucrose gradient, the cellular organelles are being separated followed by the gradient of caesium salts are used to separate the nucleic acids. Then, the sample are being spun at high speed for sufficient time to produce the separation for the gradient to be isolated and then separated.

Breaking news!! Viruses infect plants. Yes, the very plants that we use to beautify our landscapes, purify our air and also consume.