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Posted in Literature

Characterizing New Viruses in Rice

Novel mastreviruses identified in Australian wild rice

Simona Kraberger, Andrew D.W. Geering, Matthew Walters, Darren P. Martin, Arvind Varsani

Virus Research, vol 238, pg 193-197, 15 June 2017. Link to article.

The deep sequencing techniques made possible by next-generation sequencing technologies enable research into, among other things, viral diversity. Considering the vast majority of viruses in the world do not affect human existence at all, this might appear to be a rather esoteric pursuit. However, increased understanding of viral populations leads to increased understanding of the characteristics that make certain viruses more or less destructive, or that restrict their targeted host species, or that create vulnerabilities and weaknesses in the virus’s defense.

In this case, the researchers sampled wild rice plants around Australia for viruses, specifically searching for a type of virus called mastrevirus that infects grasses and economically important crops such as chickpeas and maize. Because the genome of this particular type of virus is circular single-stranded DNA. a specific extraction kit could be used that selected for viral DNA to the exclusion of any plant or bacterial contaminant. The resulting DNA was sequenced on an Illumina machine to determine whether any mastrevirus-specific sequence was present, and primers were designed based off of those identified sequence to enable the circular viral genome from each rice sample to be sequenced individually using Sanger sequencing. Based on this, two complete and previously unknown mastrevirus genomes were discovered – the first two mastreviruses shown to infect any variety of rice.

As the authors conclude, the “discovery of novel mastreviruses within both cultivated grasses and their uncultivated relatives [… is] an essential first step in identifying instances where these viruses are in the process of emerging as pathogens of economic significance.”

Posted in Science Stories

Hildegard Lamfrom: building the theory of messenger RNA

Tenacious, skilled, and self-effacing – these are words used to describe Dr. Hildegard Lamfrom by her colleagues and family. Born in 1922 to a Jewish family in Germany, Lamfrom fled with her parents and sisters to Portland, Oregon in 1938, and worked her way through Reed College by working as a welder in wartime shipyards. Twenty years later, with a PhD and years of working on the renin protein system in blood, she began to study protein synthesis as the field of molecular biology was just starting to take off.

Continue reading “Hildegard Lamfrom: building the theory of messenger RNA”

Posted in Biology Basics

RNA: An Introduction

While RNA is built on the same backbone and structural concept as DNA (read this post for a refresher!), its slight biological differences lead to significant functional diversity. We’ll examine the structure of RNA molecules first, then dig more deeply into the myriad of functions performed by these molecules within (and even outside of!) the cell. Continue reading “RNA: An Introduction”

Transposable Element

(also known as a transposon)

A DNA sequence that can move from one section of the genome to another, affecting chromosome shape and structure as well as gene expression.

  1. Cut-and-paste transposons move by excision from their original location and insertion into a new location, catalyzed by a transposase enzyme encoded by the transposon itself.
  2. Replicative transposons are replicated and the copy is inserted at a new location without loss of the transposon at the original location; this is also catalyzed by a transposase enzyme encoded by the transposon.
  3. Retrotransposons move via RNA transcription of the transposon followed by reverse transcription of the RNA molecule and insertion of the newly synthesized DNA.
Posted in Sequencing Technology and Methods

Nucleic Acid Fragmentation: Three Methods

An essential step in preparing total RNA or genomic DNA samples for sequencing is cutting them down into usable fragments. For Illumina instruments, the bridge amplification aspect of the sequencing process works best when these fragments are between 100 and 1000 nucleotides long, and quality is improved by using fragments within a narrow size range (ideally no more than 200bp spread). There are several different techniques for accomplishing this: nebulization, sonication, and enzymatic fragmentation.

Continue reading “Nucleic Acid Fragmentation: Three Methods”