Archive for the ‘phages’ Category

The Internet Journal of Comprehensive Virology

15 July, 2016

 

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Testing out a textbook on Virology

5 December, 2015

Like my recent books on History of Viruses and Influenza, I’m constructing an ebook Introduction to Virology textbook – and I’d like people’s opinions.

It’s going to look something like this:

Virus_Picture_Book_copy_2_iba

 

It will be based on my web pages that were so cruelly destroyed, but will be PROFUSELY illustrated, using all of the bells and whistles built into the iBooks Author app, with liberal use of Russell Kightley’s very excellent virus picture library.

And I will sell it for US$20 or less.

Tell me what you think of the taster – and there will be more.

So that’s what you lot like, is it?

21 October, 2015

My_Stats_—_WordPress_com

The tree of life should be a garden. With bushes.

21 September, 2015

Biologists like to talk of and depict, “the” tree of life. This is shown here as in most places, with a bacterial and an archaeal bifurcation coming off a LUCA base, and then another bifurcation of archaea into modern archaea and eukaryotes.

Of course, there are also the anastomoses: an early intracellular colonisation of a eukaryote ancestor by a bacterium, which gave rise to mitochondria, and then another later event, where a cyanobacterium became chloroplasts in the ancestor of green plants and algae.

What is not generally appreciated is that the latter occurred more than once – with different photosynthetic bacteria providing distinctly different types of chloroplasts in the various lineages of algae, The situation then becomes more complicated, with minor and more complex anastomoses among eukarya, with unicellular eukaryotic algae becoming intracellular symbionts and then complex organelles – with evidence in some cases that this happened more than once, as evidenced by multiple layers of membranes surrounding chloroplasts in photosynthetic organisms whose closest relatives are non-photosynthetic.

Thus,”the” Tree of Life already has some internal interconnections that make parts of it more a reticulated network than a bifurcating tree – but this complication pales into insignificance when one takes into account the fact that “the” Tree does not take into account the wildly bushy garden of shrubs that would be viruses.

Seriously: despite repeated urging by folk like me, the multitude of Tree designers have consistently ignored the majority of organisms on this planet. Indeed, in a comment in a recent Twitter exchange on a new Tree, answering my comment that it took no notice of viruses, @phylogenomics: wrote “it does say tree of “Life” not tree of weird parasites of still unknown origin ….”

So I just HAD to reply ” …that happen to be life forms in good standing. In everyone B-) And [which] outnumber everything else.”

A good-natured exchange followed, which prompted the writing of this post – because, really, the Tree of Life SHOULD be a Garden of Life, with one tree and a collection of distinct bushes, some pretty big, representing different virus lineages. The biggest bushes would probably be the so-called megaviruses, and collections of viruses dignified by being grouped into taxonomic Orders, such as the tailed phages in the order Caudovirales and the ssRNA(-) viruses grouped as Mononegavirales.

And of course, some components of those bushes meet up with some of the roots of the tree – in the form of specific genes like DNA polymerases, which may well have a common origin with cellular genes.

Some of those bushes also inerconnect underground, like some of the reverse transcriptase-dependent viruses which have nothing else in common; the RNA viruses which share RNA-dependent RNA pol enzymes, but with other components from different origins – the okapi-like viruses, as they were termed by Rob Goldbach.

Some bushes in fact parasitise the tree, just like parasitic plants grow on other plants: the polydnaviruses of wasps, for example, are effectively genome components, and are used by their hosts to aid in parasitising their target hosts.

So, a garden – and one that it would be challenging to portray.

Which I would like to leave up to someone with far more artistic ability than me B-)

New header graphic: something old, something new; something borrowed – and something blue

8 September, 2015

That’s right: a new header graphic after lo, these many years.

Something old: Maize streak virus, in all its geminate glory, on the left. Picture taken by RG (Bob) Milne in Cape Town, 1978.

Something new: unidentified phycodnaviruses, middle right. Picture by Hendrik Els, 2015.

Something borrowed: T4-like phage particles, right. Picture by Mohammed Jaffer, 2005.

Something blue: Bluetongue orbivirus particles, centre left. Picture by Ayesha Mohamed, 2015.

Virology Africa 2015: Update and Registration

19 August, 2015

REGISTRATION IS NOW OPEN – VIROLOGY AFRICA 2015

On behalf of the Institute of Infectious Disease and Molecular Medicine of the University of Cape Town and the Poliomyelitis Research Foundation, we are pleased to invite you to Virology Africa 2015 at the Cape Town Waterfront.

VENUE AND DATES:

The conference will run from Tuesday 1st – Thursday 3rd December 2015. The conference venue is the Radisson Blu Hotel with a magnificent view of the ocean. The hotel school next door will host the cocktail party on the Monday night 30th November and in keeping with Virology Africa tradition, the dinner venue is the Two Oceans Aquarium.

IMPORTANT DATES

Early Bird Registration closes – 30 September 2015
Abstract Submissions deadline – 30 September 2015

The ACADEMIC PROGRAMME will include plenary-type presentations from internationally recognised speakers. We wish to emphasise that this is intended as a general virology conference – which means we will welcome plant, human, animal and bacterial virology contributions. The venue will allow for parallel workshops of oral presentations. There will also be poster sessions. Senior students will be encouraged to present their research. We have sponsorship for students to attend the meeting and details will be announced later in the year.

A program outline has been added to the website

WORKSHOPS

Our preliminary programme includes two workshops.

There is a hands-on workshop on “Plant cell packs for transient expression: Innovating the field of molecular biopharming”, with the contact person being Dr Inga Hitzeroth – Inga.Hitzeroth@uct.ac.za. This workshop will run at UCT one day before the conference, 30th November, and a second day, 4th December, after the conference.

The second workshop is on “”Viromics for virus discovery and viral community analysis”. The workshop at UCT will be on 4 and 5 December with the contact person being Dr Tracy Meiring – tracy.meiring@uct.ac.za.

Some of the workshop presenters will be integrated into the conference programme but the practical components will be run at University of Cape Town. Separate applications are necessary for each workshop.

If you are prepared to fund an internationally recognised scientist to speak at the conference or if you wish to organise a specialist workshop as part of the conference, please contact
Anna-Lise Williamson or Ed Rybicki.

For any enquiries please contact
Miss Bridget Petersen/ Email: conference1@onscreenav.co.za or phone: +27 21 486 9111
Ms Deborah McTeer/Email: conference@onscreenav.co.za or +27 83 457 1975

How should we preserve old viruses?

12 August, 2015

I was reminded via Twitter by Vincent Racaniello, he of “virology blog” fame, of the problem of preserving stocks of old viruses.

Particularly, in his case, of stocks of a virus that may be eradicated in the wild in a few years, and then – according to him – will need to be destroyed.

Surely we need to at least preserve sequence information of these pathogens before we let them go into oblivion, the way variola and rinderpest viruses have already gone?

So I wrote this to him:

“Great that you have preserved these samples – but a longer-term strategy needs to be adopted, before completely irreplaceable specimens are lost forever, to you and to science in general.

tmv sedimI have the same problem: a colleagues’ samples of plant viruses; beautifully preserved in heat-sealed glass vials, dried over silica gel, dating back in some cases to the early 1960s. For that matter, I have about a thousand glass bottles of liquid plant virus samples at 4degC, dating back in some cases over 40 years – and still viable.

Surely there is a case to be made for preserving some of these viruses? Mining them for sequence in this metagenomic age is not that difficult; preserving their infectivity, however – another matter. Some of my plant viruses are probably bomb-proof; your poliovirus samples, on the other hand – probably slowly deteriorating as we watch.

A wider conversation is needed: I know of other archives, of old poxvirus collections for example, that will be lost forever in a few years. Should we not get an international effort going to log them, sequence them, preserve them?

I think so.

Want to join in?

Yours,

Ed”

If any of you out there have a similar problem, let’s hear from you – and maybe we can do something to at least preserve the genetic information in unique collections.

Anyone interested? A candidate virology textbook…

28 July, 2015

I would like to test the response to a Introduction to Virology ebook that I want to develop from my extant Web-based material, given that this is likely to disappear soon with our Web renewal project here at UCT.

Virus_Picture_Book_copy_iba

Download the Virus Picture Book excerpt here. And then please tell me what you think / whether you would buy one (projected price US$15 – 20)?  Ta!

Superbug threat prompts West to revisit Soviet-era virus therapy

4 July, 2015

Alarmed by rising resistance to antibiotics scientists and governments are taking a fresh look at bacteria-chomping viruses first isolated a century ago from the stools of patients recovering from

Sourced through Scoop.it from: www.reuters.com

So nearly 100 years after Felix d’Herelle started championing phage therapy, the West is finally taking notice?  I’t actually way past time that they were taken seriously: the Eliava Institute in Georgia has nearly that long a history (d’Herelle influenced the founder to start their enormous collection of phages) of successful treatment of bacterial infections, but westerners have stayed wedded to increasingly ineffective antibiotics for the last 70-something years.

I know what I might work on in my old age….

See on Scoop.itVirology News

A Short History of the Discovery of Viruses

6 March, 2015

Now much updated, streamlined, added to and otherwise tarted up!  This is the Web version of an eBook, which you can now get here:

A Short History of the Discovery of Viruses – Edward Rybicki

Slide1

See also here for a “pocket reference version” of the discovery of viruses

Part 1: Filters and Discovery

Part 2: The Ultracentrifuge, Eggs and Flu

Part 3: Phages, Cell Culture and Polio

Part 4: RNA Genomes and Modern Virology

Sidebar 1: The Discovery of Filoviruses

Sidebar 2: Papillomaviruses and Human Cancer

Sidebar 3: Epstein-Barr Virus and Hepatitis B Virus

Sidebar 4: Human Retroviruses and Cancer

Sidebar 5: Maize Streak Virus: The Early History

Sidebar 6: Rinderpest and Its Eradication

Sidebar 7: Viruses and human cancer: the molecular age

Copyright Edward P Rybicki and Russell Kightley, February and March 2015, except where otherwise noted.