When I read DRACO paper, my adviser ask me the question (on the title).

My primitive idea is the following text. (2011.08)

On the beginning, I also send a letter to Dr. Rider, but I didn’t receive his reply T_T (2011.08.21)

This question can be divided into two parts: one is why viruses produce long dsRNAs, the other is why endogenous dsRNAs are short.

In August,I guess endogenous long dsRNA is unstable in cells.Dicer can cleaves endogenous dsRNAs to produce siRNA. Long endogenous dsRNAs can induce complete Gene silencing in mammalian cells and primary cultures. So endogenous dsRNA are shorter than exogenous dsRNA.

But, there are some questions on my guess.

What RNA belong to dsRNA?

As we know, mircoRNA is not siRNA, though it as little as siRNA. So, what RNA is dsRNA? tRNA and rRNA has some hairpin structure (cloverleaf structure). Does this structure is double strand structure? All RNA viruses must produce at least a transient dsRNA intermediate. In replicating + or - RNA, you have to produce the opposite sense RNA, thus forming a dsRNA molecule. tRNA has only one strand, and the hairpin structure isn’t made of double strands.

I think dsRNA must made of two strands perfectly complementary, the secondary structure isn’t reflect strand type.

On the molecular biology class, I learn mircoRNA is single strand. (2011.10.14)

Why endogenous dsRNAs are short?

In the DRACO paper, it said that uninfected mammalian cells don’t produce long dsRNA. Information generally transfer from DNA to RNA (central dogma). RNA can not replication in human cells.So endogenous dsRNAs are not existence in human cells.

Why viruses produce long dsRNAs but not short ones?

RNA viruses’ genetic information are all in the RNA, so it longer.

However, I think I have misunderstanding the question. (2011.10.09)

Why viruses produce dsRNAs?

Positive-strand RNA, dsRNA, or DNA viruses produce dsRNA.

RNA polymerase synthesizes an RNA strand complementary to the genome. This produces a dsRNA. RNA can not replication in human cells.So endogenous dsRNAs are not existence in human cells.

Negative-strand RNA viruses doesn’t produce dsRNA. (Double-Stranded RNA Is Produced by Positive-Strand RNA Viruses and DNA Viruses but Not in Detectable Amounts by Negative-Strand RNA Viruses)

A big news from MIT: MIT Lincoln Laboratory researchers develop a technique to cure a broad range of viruses

Dr. Todd Rider and his team have developed and demonstrated a novel broad-spectrum antiviral approach, called DRACO (for Double-stranded RNA dsRNA Activated Caspase Oligomerizer). DRACO selectively induces apoptosis, or cell suicide, in cells containing any viral dsRNA, rapidly killing infected cells without harming uninfected cells. As a result, DRACO should be effective against virtually all viruses, rapidly terminating a viral infection while minimizing the impact on the patient.

BUT, Should DRACO be effective against virtually all viruses?

I think there are many problem. First, DRACO can only senses double-stranded RNA, and DRACO just senses long ( >~23nt ) dsRNA, so it just can senses a limit of viruses. Second, DRACO is a chimeric protein, how to delivery it into our body without proteolysis? The delivery mechanism may a big problem. Third, viruses have some tricks use to inhibit apoptosis. So, DRACOs seems not effective against virually all viruses.

BTW: Is Dr. Todd a fan of Harry Potter ? ;)

I haven’t check my code for 7 years ago, thanks to all the visitors who left a comment.

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[How to do with R] is a category about use R to deal with problems. Maybe you can use web search find this, when you have the same problems.

I need to calculate “number of times” same word appear in some text documents. There are many ways to do it. One simple way is using R. To calculate word frequencies have three mainly steps.

• Read the text into R.
• Split sentence into words.
• Calculate word frequencies.

R can read any text file using readLines() or scan().

readLines("Textname.txt",encoding="UTF-8")
scan("Textname.txt","character",sep="\n")

Reference: Reading and writing text files

Use strsplit to split sentence into words.

strsplit(string,"")

Reference: ?strsplit

Use table to calculate word frequencies.

table(sentences)

Reference: ?table

Hear is a Example

Calculate word frequencies in TEXTname.txt

TEXTname.txt: It was the age of wisdom, it was the age of foolishness, it was the epoch of belief, it was the epoch of incredulity, it was the season of Light, it was the season of Darkness, it was the spring of hope, it was the winter of despair, we had everything before us, we had nothing before us.

sentences<-scan("TEXTname.txt","character",sep="\n");
#Replace full stop and comma
sentences<-gsub("\\.","",sentences)
sentences<-gsub("\\,","",sentences)
#Split sentence
words<-strsplit(sentences," ")
#Calculate word frequencies
words.freq<-table(unlist(words));

The source code can be found in github

Result:
cbind(names(words.freq),as.integer(words.freq)) ## You might consider using cbind.data.frame instead of cbind

  [1,] "age" "2"
  [2,] "before" "2"
  [3,] "belief" "1"
  [4,] "Darkness" "1"
  [5,] "despair" "1"
  [6,] "epoch" "2"
  [7,] "everything" "1"
  [8,] "foolishness" "1"
  [9,] "had" "2"
  [10,] "hope" "1"
  [11,] "incredulity" "1"
  [12,] "it" "7"
  [13,] "It" "1"
  [14,] "Light" "1"
  [15,] "nothing" "1"
  [16,] "of" "8"
  [17,] "season" "2"
  [18,] "spring" "1"
  [19,] "the" "8"
  [20,] "us" "2"
  [21,] "was" "8"
  [22,] "we" "2"
  [23,] "winter" "1"
  [24,] "wisdom" "1"

Hello world! This site is my first English blog. You can contact me in this page.