Moving Towards Zero Hunger, One Genome at a Time

Farmer and a pile of cassava bulbs.

Have you ever thought about plant viruses? Unless you’re a farmer or avid gardener, probably not. And yet, for many people the battle against agricultural viruses never ends. Plant viruses cause billions of dollars in damage every year and leave millions of people food insecure (1–2), making viruses a major barrier to meeting the United Nations’ global sustainable development goal of Zero Hunger by 2030.

At the University of Western Australia, Senior Research Fellow Dr. Laura Boykin is using genomics and supercomputing to tackle the problem of viral plant diseases. In a recent study, Dr. Boykin and her colleagues used genome sequencing to inform disease management in cassava crops. For this work, they used the MinION, a miniature, portable sequencer made by Oxford Nanopore Technologies, to fully sequence the genomes of viruses infecting cassava plants.

Cassava (Manihot esculenta) is one of the 5 most important calorie sources worldwide (3). Over 800 million people rely on cassava for food and/or income (4). Cassava is susceptible to a group of viruses called begomoviruses, which are transmitted by whiteflies. Resistant cassava varieties are available. However, these resistant plants are usually only protected against a small number of begomoviruses, so proper deployment of these plants means farmers must know both whether their plants are infected and, if so, the strain of virus that’s causing the infection. Continue reading

Will Warmer Weather Wake the Sleeping Giant (Viruses)?

Artist's conception of Mimivirus structure, the first of the giant viruses identified.

Artist’s conception of Mimivirus structure, the first of the giant viruses identified.

Following the discovery of Mimivirus (1) the first virus with a particles large enough to be visible under the light microscope, two additional “giant” viruses infecting Acanthamoeba have been discovered Pandoravirus (2) and Pithovirus sibericum (3), the latter from a 30,000 year old Siberian permafrost. A fourth type was recently isolated from the same sample of permafrost by Legendre et al, and named Mollivirus sibericum (4).

Mollivirus sibericum has an approximately spherical virion (0.6 µm diameter) with a 651kb GC-rich genome that encodes 523 proteins. To further characterize the virus the researchers performed transcromic- and proteomic-based time course experiments.

For the particle proteome and infectious cycle analysis, proteins were extracted and then run a 4–12% polyacrylamide gel, and trypsin digests were performed in-gel before nano LC-MS/MS analysis of the resulting peptides. Proteomic studies of the particle showed that it lacked an embarked transcription apparatus, but revealed an unusual presence of many ribosomal and ribosome-related proteins.

When the researchers explored the proteome during the course of an entire infectious cycle, the relative proportions of Mollivirus-, mitochondrion-, and Acanthamoeba encoded proteins were found to vary consistently with an infectious pattern that preserved the cellular host integrity as long as possible and with the release of newly formed virus particles through exocytosis.

In an interesting footnote, the authors of this study point out the fact that two different viruses retain their infectivity in prehistorical permafrost layers should be a concern in the context of global warming and the potential to expose humans to primeval viruses.

References

1. La Scola, B. et al.   (2003) A giant virus in amoebae. Science  299, 2033.
2. Philippe, N. et al. (2013) Pandoraviruses. Amoeba virus with genomes up to 2.5Mb reaching that of parasitic eukaryotes. Science 341,281–6.
3. Legendre, M. et al. (2014) Thirty thousand year old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. Proc.Natl. Acad. Sci. 111, 4274–9.
4. Legendre, M. et al. (2015)  In depth study of Mollivirus sibercum, a new 30,000 year old giant virus infecting Acanthamoeba.  Proc. Natl. Acad. Sci. 112, E5327–35 (online).

Move Over Genome, Here’s the Virome

Papilloma virusThe availability of next-generation sequencing, and the accompanying capability to process and analyze large amounts of data, has made many previously unthinkable projects possible. Examples include the sequencing of entire microbial genomes to track the spread of antibiotic-resistant infections in a hospital setting, sequencing all the contents of a particular foodstuff to identify meat sources and contaminants, and the microbiome project—a multi-national research effort to characterize the microrganisms colonizing the human body to look for associations with health and disease.

The ability to both get and process data on this large a scale has led to numerous advances in our understanding of the complex relationships between ourselves and our microbial colonizers. Over the last couple of years the microbiome project has generated data suggesting previously unimagined connections between bacteria colonizing our bodies and obesity, cardiac disease, and even personal identification.

As if the complex inter-relationship between bacterial and human cells isn’t enough to grapple with, there is also the virome to consider. Continue reading

Virophages: The Enemy of My Enemy is My Friend

Algae and, quite possibly, some virophages

Algae and, quite possibly, some virophages


Viruses are small DNA- or RNA-based infectious agents that can replicate only inside living cells of a host organism. Most people know what a virus is, and many of us harbor at least one or two of them at some point during the cold and flu season. However, I would guess that many of us do not know what a virophage is, even though they seem to be more common than previously thought.

Virophages were first discovered and characterized by LaScola et al. in 2008 (1) during studies with Acanthamoeba polyphaga mimivirus (APMV), the largest known virus—so large that it is visible by optical microscopy. Continue reading

I Can Haz Meme-Gene Parallelz?

It’s a darn good time to be a meme these days, especially on the Internet. The lightning fast transmission of links and videos and funny pictures between millions of people on any number of social media outlets or email means the viral spread and replication of the latest “you’ve got to see this” thing may sometimes occur even more quickly than with, well, actual viruses or gene replication. I know a tiny bit about genes and viruses and maybe a tiny bit more about memes, but had never realized there were such parallels between the biological and the sociobiological. I also never knew that there was any amount of intention behind that commonality, but apparently, that was no accident. Continue reading