• Skip to main content
  • Skip to primary sidebar
virology blog

virology blog

About viruses and viral disease

nucleic acid

TWiV 162: Transcription

18 December 2011 by Vincent Racaniello

transcriptionHosts: Vincent Racaniello, Rich Condit, and Alan Dove

Vincent, Rich, and Alan continue Virology 101 with a discussion of transcription, the process of making mRNA from a DNA template.

Please help us by taking our listener survey.

[powerpress url=”http://traffic.libsyn.com/twiv/TWiV162.mp3″]

Click the arrow above to play, or right-click to download TWiV 162 (56 MB .mp3, 93 minutes).

Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, by email, or listen on your mobile device with the Microbeworld app.

Links for this episode:

  • Slides for this episode (pdf)
  • Propose an ASM General Meeting session
  • TWiV on Facebook
  • Letters read on TWiV 162
  • Video of this episode – different file types available.
    Right-click and save as:
    Large version for your computer (482 MB | .mov)
    iPad/Apple TV (333 MB | .mp4)
    iPhone (130 MB | .mp4)
    iPod (154 MB | .mp4)
    for PCs (517 MB | .wmv)
    or just view it below

Weekly Science Picks

Rich – 3D vaccinia virion
Alan – Happy Holidays from NOAA (YouTube)
Vincent – 17 year old wins $100,000 science prize

Listener Pick of the Week

Sarah – Critical Thinking (pdf),  diagnosing respiratory infections by gene signature (Cell Host Micro), and One Health Initiative (CDC page)

Send your virology questions and comments (email or mp3 file) to twiv@microbe.tv, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twiv.

Filed Under: This Week in Virology Tagged With: cap, dna dependent rna synthesis, nucleic acid, pol I, pol II, pol III, polyA, polymerase, rna splicing, transcription, viral, virology, virus

Har Gobind Khorana, master decoder

11 November 2011 by Vincent Racaniello

genetic codeMost students of elementary biology will have seen the table at left that depicts the genetic code. HG Khorana was one of several scientists who determined, in the 1960s, the amino acids specified by each three-letter combination of bases. As long as I have been at Columbia University I have had a copy of this table on my office wall.

Khorana reminisces how the finding that genes are nucleic acids set the stage for his work on decoding:

While it is always difficult, perhaps impossible, to determine or clearly define the starting point in any area of science, the idea that genes make proteins was an important step and this concept was brought into sharp focus by the specific one gene-one enzyme hypothesis of Beadle and Tatum. The field of biochemical genetics was thus born. The next step was taken when it was established that genes are nucleic acids. The transformation experiments of Avery and coworkers followed by the bacteriophage experiments of Hershey and Chase established this for DNA and the work with TMV-RNA a few years later established the same for RNA. By the early 1950’s it was, therefore, clear that genes are nucleic acids and that nucleic acids direct protein synthesis, the direct involvement of RNA in this process being suggested by the early work of Caspersson and of Brachet.

The first triplet to be decoded was UUU, which specifies the amino acid phenylalanine. This work was done by Nirenberg who found that an RNA consisting of repeating U residues could be translated into a protein containing only phenylalanine. Codons for lysine (AAA) and proline (CCC) were similarly discovered using RNAs containing only A or C. Khorana used both enzymatic and chemical synthesis of oligonucleotides to decipher much of the remaining code. A good account of his work can be found in his Nobel lecture (pdf).

Khorana, together with Robert Holley (structure of tRNA) and Marshall Nirenberg, received the Nobel Prize in Physiology or Medicine in 1968 for their work on deciphering the genetic code.

Filed Under: Events, Information Tagged With: amino acid, DNA, genetic code, har gobind khorana, nucleic acid, RNA, virus

Viral bioinformatics: Introduction to multiple sequence alignment

15 October 2010 by Vincent Racaniello

This week’s addition to the virology toolbox was written by Chris Upton

Generating multiple sequence alignments (MSA) is one of the most commonly used bioinformatics techniques. The “sequences” to be compared can be DNA (promoters, genes, genomes) or proteins. Note that the length and number of sequences to be aligned has an impact on the methods (algorithms) that can be used; what is suitable for aligning 20 proteins probably won’t work for alignment of 5 poxvirus genomes (200 kb each).

Some useful links:

  • Wikipedia: multiple sequence alignment
  • Wikipedia: sequence alignment
  • Wikipedia: list of sequence alignment software
  • Protein Multiple Sequence Alignment: Book chapter by Chuong B. Do and Kazutaka Katoh
  • Sequence alignment: Lecture notes by Per Kraulis
  • Another list of tools

So you see, there lots of options (did you say: “too many!”?). Further confusion may arise because 1) the same algorithm may be used in many different software programs, and 2) referencing a software package may give no clue to the algorithm used. For many molecular biologists, Clustal is synonymous with sequence alignment. However, newer algorithms such as T-Coffee and MUSCLE are often offered in current software packages, and may be faster and more accurate.

Specialized alignment tools are almost always needed for long, genome sized DNA sequences.

In this set of posts, I’ll provide some information on favorite general MSA tools (that are free) that should be useful to the average molecular virologist. The lists noted above provide a multitude of tools, but many are for specific analyses.

Filed Under: Toolbox Tagged With: bioinformatics, clustal, multiple sequence alignment, muscle, nucleic acid, protein, t-coffee, Toolbox, viral, virology, virus

Virology lecture #6: RNA-directed RNA synthesis

9 February 2010 by Vincent Racaniello


Download: .wmv (324 MB) | .mp4 (76 MB)

Visit the virology W3310 home page for a complete list of course resources.

Filed Under: Basic virology, Information Tagged With: alphavirus, course w3310, DNA, influenza, lecture, nucleic acid, poliovirus, polymerase, reovirus, replication, RNA, viral, virology, virus, vsv

Virology lecture #3: Genomes and genetics

29 January 2010 by Vincent Racaniello


Download: .wmv (333 MB) | .mp4 (75 MB)

Visit the virology W3310 home page for a complete list of course resources.

Filed Under: Basic virology Tagged With: columbia university, DNA, genetics, genomes, nucleic acid, RNA, viral, virology, virology course, virus, w3310

TWiV 60: Making viral RNA

29 November 2009 by Vincent Racaniello

TWiV_AA_200Hosts: Vincent Racaniello and Dickson Despommier

Vincent and Dick continue Virology 101 with a discussion of how RNA viruses produce mRNA and replicate their genomes.

[powerpress url=”http://traffic.libsyn.com/twiv/TWiV060.mp3″]

Click the arrow above to play, or right-click to download TWiV #60 (51 MB .mp3, 71 minutes)

Subscribe to TWiV in iTunes, by the RSS feed, or by email

Links for this episode:

  • Diagrams of viral RNA synthesis
  • Animations of influenza virus and HIV-1 replication
  • Video for this episode – see below

Weekly Science Picks
Dick The Double Helix by James D. Watson
Vincent
Worms and Germs Blog

Send your virology questions and comments (email or mp3 file) to twiv@microbe.tv or leave voicemail at Skype: twivpodcast. You can also send articles that you would like us to discuss to delicious and tag them with to:twivpodcast.

Below is a video of TWiV 60, which highlights the diagrams I referred to during the podcast.

Get the Flash Player to see this video.

Download TWiV 60 video. These videos are slightly larger (800 x 512) than the flash version shown above

186 MB .mov video file

584 MB .wmv video file

Filed Under: This Week in Virology Tagged With: genome, genome replication, influenza, mRNA, nucleic acid, poliovirus, polymerase, rabies, replication, RNA polymerase, rna synthesis, rotavirus, viral, virology, virus

  • Go to page 1
  • Go to page 2
  • Go to Next Page »

Primary Sidebar

by Vincent Racaniello

Earth’s virology Professor
Questions? virology@virology.ws

With David Tuller and
Gertrud U. Rey

Follow

Facebook, Twitter, YouTube, Instagram
Get updates by RSS or Email

Contents

Table of Contents
ME/CFS
Inside a BSL-4
The Wall of Polio
Microbe Art
Interviews With Virologists

Earth’s Virology Course

Virology Live
Columbia U
Virologia en Español
Virology 101
Influenza 101

Podcasts

This Week in Virology
This Week in Microbiology
This Week in Parasitism
This Week in Evolution
Immune
This Week in Neuroscience
All at MicrobeTV

Useful Resources

Lecturio Online Courses
HealthMap
Polio eradication
Promed-Mail
Small Things Considered
ViralZone
Virus Particle Explorer
The Living River
Parasites Without Borders

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.