“Minimal cell raises stakes in race to harness synthetic life”. Really??

29 March, 2016

Genomics entrepreneur Craig Venter has created a synthetic cell that contains the smallest genome of any known, independent organism. Functioning with 473 genes, the cell is a milestone in his team’s 20-year quest to reduce life to its bare essentials and, by extension, to design life from scratch.

Venter, who has co-founded a company that seeks to harness synthetic cells for making industrial products, says that the feat heralds the creation of customized cells to make drugs, fuels and other products. But an explosion in powerful ‘gene-editing’ techniques, which enable relatively easy and selective tinkering with genomes, raises a niggling question: why go to the trouble of making new life when you can simply tweak what already exists?

Thomas Deerinck and Mark Ellisman/NCMIR/UCSD
Each cell of JCVI-syn3.0 contains just 473 genes, fewer than any other independent organism.
Unlike the first synthetic cells made in 20101, in which Venter’s team at the J. Craig Venter Institute in La Jolla, California, copied an existing bacterial genome and transplanted it into another cell, the genome of the minimal cells is like nothing in nature. Venter says that the cell, which is described in a paper released on 24 March in Science2, constitutes a brand new, artificial species.

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

So: JC Venter and team have stripped down a pre-existing organism to what appears to be the essential set of genes, added “watermarks” and inspirational quotes – and this is part of a race to harness synthetic life?  If so, they’re pretty much racing themselves, because precious few others are trying to do the same things.
And if you DID want to, why make a completely artificial cell genome?  Why not use tailored viruses?  It’s a great development, don’t get me wrong, but it is very much part of the “because we can” school of biology, rather than anything directed towards something as coherent as a race to harness synlife*.
* = I should TM that…B-)

See on Scoop.itVirology News

Thabo Mbeki rides again. Let’s knock him off his horse, then!

7 March, 2016

Sixteen years ago, two colleagues and I wrote a letter to Nature expressing our concern about our then-President Thabo Mbeki’s denialist views on HIV and AIDS – views he then tried to push into national policy, and which almost certainly were highly influential in delaying the rollout of ARVs in South Africa.  I was also active for several years in the media and in public lectures in trying to negate some of the damage he was causing – and I was very relieved when he took a back seat eventually, and then effectively vanished from the public stage.

However, in an unwelcome development as of this week, it appears that Mr Mbeki has finally, in his ongoing quest to rewrite history, addressed the elephant in the room: his views on HIV/AIDS.

To say this “letter” is self-serving would be to pay it a compliment.  Indeed, he himself has this to say concerning the awful “Castro Hlongwane, Cats, Geese, Caravans, Foot and Mouth and Statistics…” that he almost certainly was the main author of, back there in 2002:

“Thirteen (13) years later today I would stand by everything said in this excerpt and still ask that the questions posed should be answered by those who have the scientific capacity to do so!”

So in other words, he still holds with much of the rubbish he wrote then.  Right – well, so will I revisit something I helped write, back in 2000, after reading that Mbeki had written to Bill Clinton to dispute conventional ideas on HIV/AIDS.

Nature 405: 273, 2000

AIDS dissidents aren’t victims – but the people their ideas kill will be

Sir – As South African scientists working in the field of HIV/AIDS vaccine research, we are extremely concerned about the letter president Thabo Mbeki recently sent other heads of state (Nature 404, 911; 2000). As an individual Mr Mbeki is entitled to his point of view, but as our head of state we feel he risks binding our country to an untenable position.

We would like Mr Mbeki and others to consider how the mass of South Africans would react if he were to give a sympathetic ear to unrepentant proponents of apartheid. His willingness to be influenced by people with no credibility causes as much anguish to those of us working to combat HIV/AIDS.

The simple facts, as shown by a huge volume of scientific and medical research, are that HIV causes AIDS; that in Africa (as in other developing regions) the disease is mainly spread heterosexually; and that AIDS kills poor people in disproportionate numbers. We most emphatically do not need to revisit the debate on the causation of AIDS. What we do urgently need is to educate, train and medicate, to save lives.”

This is germane, because Mbeki has the gall to go back to his Castro Hlongwane crap at the end of his latest letter, and say:

“Beneath the heartening facts about decreased mortality and increasing life expectancy, and many other undoubted health advances, lie unacceptable disparities in wealth. The gaps between rich and poor, between one population group and another, between ages and between sexes, are widening. For most people in the world today every step of life, from infancy to old age, is taken under the twin shadows of poverty and inequity, and under the double burden of suffering and disease.”

“Castro Hlongwane…” says: “Given that our minds on this matter (of HIV and AIDS) have become thoroughly clogged by the information communicated by the omnipotent apparatus, a miracle will have to be achieved to get all our people to use their brains, rather than perish on emotional responses based on greatly heightened levels of fear.”

Really, Thabo??  You’re going to harp on about poverty, again?  Oh, and the “omnipotent apparatus” that is Western Pharma, and of course US capitalism?

Please do us a favour, Comrade: go back to your pipe, and your old friends Johnny and Jack, and stop trying to justify the indefensible.  And I will close with something I wrote for the Mail & Guardian on March 1st back in 2002:

“It does not seem to matter what happens in our country; it does not matter how many people try to engage the slippery python that is the president’s policy and thinking on HIV/Aids; it does not seem to matter how many people die of Aids, and how many babies are needlessly born with HIV – there remains the stubbornness and wilful failure to comprehend that is leading us into disaster. Mr Mbeki, you make an idiot of yourself, and fools of us all for putting up with your views. Leave health policy alone, or resign. Please.

Ed Rybicki, Pinelands”

I see no reason to change my views either, Comrade.

Was I wrong on HIV/AIDS: Thabo Mbeki. Answer: yes. Yes, you were.

7 March, 2016

In 2002 a few of us here in South Africa wrote a booklet entitled “Castro Hlongwane…”‚ and sub-titled it “HIV/AIDS and the Struggle for the Humanisation of the African”.


Here is an excerpt from that booklet, which speaks for itself: “The first report on the incidence of HIV in South and Southern Africa was published in the “New England Journal of Medicine” and the “South African Medical Journal”, both in 1985. Two of the most important findings in this report were that in our country and region: 

HIV infection was confined to male homosexuals; and,

HIV was not endemic in this region of the world.

To quote this report, it said: “The only positive subjects were in the group compromising male homosexuals. The majority of these positive subjects had either recently been to the United States or had had sexual contact with other homosexuals who had visited the United States…

Sourced through Scoop.it from: www.timeslive.co.za

Yes, Cde Mbeki, yes: you were wrong on HIV/AIDS, and you continue to be wrong.  And if you are going to revisit your nonsense, then I am going to revisit mine – just to show what some people thought of you.
Because you wrote that “booklet”, Cde Mbeki. There are those of us who know how to see who authored something, and the copy I had of that scurrilous piece of rubbish said it came from your laptop. It was rubbish then, and can be seen to be even more rubbish now.
And if you are still a denialist, then I sincerely hope that there is a tribunal in your future.

See on Scoop.itVirology News

How Mbeki’s character and his AIDS denialism are intimately linked

3 March, 2016

Critics say that Thabo Mbeki’s character matters less than his AIDS denialism. But these things are actually intimately linked.

Sourced through Scoop.it from: theconversation.com

So Thabo Mbeki is attempting to rewrite history, or at least his place in it, and he may or may not get to writing about his beliefs on HIV/AIDS.
As someone who was actively involved in telling him how wrong he was, I cannot say I am looking forward to seeing him attempt to explain himself.
Because he was wrong in so many ways: wrong in his disbelief; wrong in his actively courting the loony dissidents; wrong in buying into the “ARVs are just poisons” belief; wrong in buying into the conspiracy theories around Big Pharma.
And wrong not to believe scientists in his own country, who did their very best to convince him, using the best evidence on hand, that HIV causes AIDS, and ARVs mitigate the effects.

I think he should appear before a tribunal of some kind, one day, to explain himself – and be prepared to take the withering criticism of those like me who believe he was partially culpable in the deaths of several hundreds of thousands of people in South Africa who could otherwise have been saved by ARVs.
Manto Tshabala-Msimang should be alongside him, of course – but she has taken herself and her several livers off to the grave, and he would stand alone.

See on Scoop.itVirology News

‘Alien DNA’ raining down on Earth could mix with Zika and form super disease – NOT!

2 March, 2016

“Scientists have warned that  panspermia – the theory of genetic material raining down from space – could make Zika stronger and more deadly”

Genetic material falling on Earth from outer space could create a supercharged version of the Zika virus, scientists have warned.

Experts claim that the virus, which is spreading across the globe, will become more prevalent and deadly in the future.

Changes in Zika have already been noted, as it’s changed to be passable through sexual contact.

The disease, first discovered in monkeys in 1947, had previously only been transferable by mosquito bite.

But now, scientists are warning that it could mutate, growing stronger and spreading more easily – with its victims suffering more serious consequences.

They have warned that future strains could become worse thanks to panspermia – the theory of genetic material constantly raining down on Earth from outer space.

Sourced through Scoop.it from: www.mirror.co.uk

The bullshirt is strong with this one…I have to include some conspiracy nonsense from time to time, just to show what’s out there!
And what’s out there for Zika is Fred Hoyle’s old mate, Chandra Wickramasinghe, who really should stick to astronomy or astrophysics – because he’s just making an idiot of himself.
Consider these statements:
“Genetic material falling on Earth from outer space could create a supercharged version of the Zika virus, scientists have warned.”
“Changes in Zika have already been noted, as it’s changed to be passable through sexual contact.”
“Professor Chandra Wickramasinghe, of the University of Buckingham, has long held panspermia as a common route of viral and bacterial mutation….
Worryingly, he said, is the apparent ability of the Zika virus to pick up foreign DNA and adapt quickly to become more virulent.”
OK: just how, exactly, is Zika supposed to be able to interact with the genetic material falling from space? And how in heaven’s name can anyone tie sexual transmission of Zika – which has only not been documented before, NOT shown not to happen – with picking up genetic material? Which, if Professor W is to be believed, is DNA – and Zika is a (+)sense RNA virus, which are not much given to picking up DNA fragments?
As I said, bullshirt: Zika is quite capable of mutating all by itself, without extraplanetary influences.

See on Scoop.itVirology News

Structural and molecular basis for Ebola virus neutralization by protective human antibodies

27 February, 2016

Ebola virus causes hemorrhagic fever with a high mortality rate and for which there is no approved therapy. Two human monoclonal antibodies, mAb100 and mAb114, in combination, protect nonhuman primates against all signs of Ebola virus disease, including viremia. Here, we demonstrate that mAb100 recognizes the base of the Ebola virus glycoprotein (GP) trimer, occludes access to the cathepsin-cleavage loop, and prevents the proteolytic cleavage of GP that is required for virus entry. We show that mAb114 interacts with the glycan cap and inner chalice of GP, remains associated following proteolytic removal of the glycan cap, and inhibits binding of cleaved GP to its receptor. These results define the basis of neutralization for two protective antibodies and may facilitate development of therapies and vaccines.

Sourced through Scoop.it from: science.sciencemag.org

Why is it that structural / molecular immunologic studies always "may facilitate development of therapies and vaccines"?  Really??  How about looking at what the actual vaccines did in terms of eliciting sterilising immunity, or controlling viral load?

So nice work, but it characterises the mode of action of just two monoclonal antibodies from the spectrum of many thousand that would be involved in reaction to infection, and of the hundreds that are involved in vaccine responses, and the many in any single individual that would be involved in actual neutralisation of infectivity / ADCC / infected cell killing, etc.

What I’m getting at is that whole protein responses, in the context of live vaccine vector inoculations, are almost certainly more complex than anything that involves just these two antibodies, and elegant immunological / structural studies are a minor part of understanding the whole problem.

See on Scoop.itVirology News

GM viruses could help prevent animal diseases jumping to humans

23 February, 2016

Vaccinating wildlife with genetically-modified viruses could one day help stop diseases like Ebola and MERS jumping from animals to humans, researchers say.

Sourced through Scoop.it from: www.abc.net.au

In principle, a great idea – BUT, as was pointed out, using live viruses in an effectively uncontrolled manner COULD result in all sort of unforeseen outcomes.

Like making a killer virus that drastically reduces numbers of a given species, like myxomatosis and RHDV did to rabbits [OK, they were supposed to].

Like making a virus that spreads to NON-target animals, and does…what?  Start a zombie plague?  Mutate to virulence, and cause havoc?

The point is, WE DON’T KNOW what may happen – and in circumstances like that, it may be safer to leave well alone!

See on Scoop.itVirology News

+strand RNA viruses stimulate host phosphatidylcholine synthesis at viral replication sites

22 February, 2016

Positive-strand RNA viruses [(+)RNA viruses] include many important human, animal, and plant pathogens. A highly conserved and indispensable feature of (+)RNA virus infection is that these viruses proliferate and reorganize host membranes to assemble viral replication complexes (VRCs). We show that brome mosaic virus (BMV) stimulates phosphatidylcholine (PC) synthesis at the viral replication sites. BMV recruits a host enzyme involved in PC synthesis to support proper VRC formation and genomic replication. We further show that hepatitis C virus and poliovirus also promote accumulation of PC at the viral replication sites, revealing a feature common to a group of (+)RNA viruses. This virus-specific step can be targeted to develop a broad-spectrum antiviral strategy with the least side effects on host growth.


Sourced through Scoop.it from: www.pnas.org

This is a big deal: it demonstrates a common requirement among very different (+)strand RNA viruses – picornaviruses, flaviviruses and bromoviruses – for the same lipid – phosphatidylcholine (PC) – and makes the point that inhibiting PC synthesis significantly inhibits viral replication.  That means the same therapy could be used for viruses that are otherwise so different as to have no obvious similarity at all, other than genome polarity.  Great stuff!

See on Scoop.itVirology News

World hunger: what the Ebola virus can teach us about saving crops

19 February, 2016

Rapid genetic disease screening will be the key to saving East Africa’s crops – just as it was during West Africa’s ebola crisis.

When the deadly Ebola virus struck West Africa last year, one thing that became clear was that the region lacked access to quick diagnostic toolsthat could help identify those infected and help contain the virus’s spread.

As the world swung into action to combat the emergency, one crucial factor that helped to curb the epidemic was the arrival of backpacks containing portable genetic sequencing computers – a technology not readily available in the affected countries.

What has that story got to do with world hunger, beyond the fact that both hunger and disease are featured in the United Nations’ Sustainable Development Goals?

If we can bring the same technologies to bear against crop diseases as well as human ones, we can help eradicate hunger – a less newsworthy and more slow-burning problem than Ebola, but far more deadly in terms of the human toll.

Sourced through Scoop.it from: theconversation.com

Interesting insight – because in 2007, some of the same folk who wrote this were involved in two workshops that I attended, in Bellagio and in Zanzibar, on setting up a plant disease diagnostic network for Africa.  We had folk from the Rockefeller Foundation there, Gates Foundation too, and we did a lot of good work – to no end, because the proposal did not fly.

Their points are highly valid: I have pointed out elsewhere, and others too, that plant diseases can kill people just as human diseases can.  Indirectly, maybe, and due to lack of food caused by plant pathogens, but taking a deadly toll nonetheless (see here: https://rybicki.files.wordpress.com/2012/01/plvidis-final-11-6-99.pdf).

The sad fact is that there is next to nothing in place in most of Africa for the kinds of molecular diagnostics that folk working with human diseases take for granted.  Oh, there are a few centres in the more sophisticated African countries where ELISA kits can be used, and places like Uganda, Kenya and even Malawi have labs and dedicated people – but these are the exceptions, and the overall picture is dismal.

What we need are comprehensive surveys of crops across Africa, in all of the breadbasket countries that supply most of the maize, cassava, sweet potatoes and the like, and of vegetable-growing areas in all countries, to see what is there.

Once that is known, then surveillance programmes could be set up, to monitor outbreaks of dangerous diseases, insect vector populations and their role in spreading plant disease – and provide information to assess real and potential crop losses.

All it would take is money – and some of the kit that came to Africa for the Ebola outbreak in West Africa recently.  We even have a plan that could be dusted off – and a good Africa-wide network to help make it happen.

Oh, and some political will, and some planning.  That’s the difficult bit….

See on Scoop.itVirology News

The scientific journey of AIDS from despair to cautious hope

18 February, 2016

Despite the breakthroughs in HIV and AIDS research, without an effective vaccine, the world will not get to zero new infections and deaths.

Sourced through Scoop.it from: theconversation.com

Nice series of articles – I covered the first one earlier.

HIV/AIDS for many of has been a long and sustained learning experience that has paralleled the pandemic: it has provided numerous invaluable insights into the workings of the human immune system, into how retroviruses work, how they evolve – and how to treat the diseases HIV infection leads to, as well as how to develop therapies for those infected.

I hope we are past the midpoint of the pandemic curve now: as a young academic, I remember the first reports of AIDS the syndrome, the discovery of the viruses involved.

As an old academic who has been involved in research on candidate vaccines against it, I am still hoping that we will conquer the virus in my lifetime.

See on Scoop.itVirology News


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