Archive for the “Virology” Category

A 70-year-old man can enjoy the blessing of fatherhood to perfectly healthy children. That is practically a miracle quality-wise because the male gametes are being produced in huge amounts, 1000 per second to be exact. That amounts to about 30 billion a year. Each and every one of those sperms could potentially contribute by half to the formation of a human being. So how could this rapid production preserve and maintain the critical quality required? How could errors during the sperm production be avoided? Researchers have recently gained an insight into the molecular mechanism as released in the “Proceedings of the National Academy of Sciences”.

During the sperm production, there is an automatic quality control process. This control mechanism is strengthened by a specific genetic addition, present in both humans and great apes. The triggering factor is comprised of parts of an endogenous retrovirus, incorporated in our genome. 15 million years ago, this viral DNA was presumably incorporated in the genetic makeup of one of our ancestors. A lucky coincidence? Perhaps, but the researchers claim it catched on during the process of evolution. The site of insertion of this viral DNA is close to a gene, responsible for the production of a crucial control factor.
The control factor, termed p63, drives faulty cells straight to their apoptosis. It imposes a strict quality control of the genome because even in cases of a slight damage to the DNA, the cells ultimately die. As a result, the passing on of a flawed genome to the next generation is prevented. Some cells definitely fall as victims in the process. In addition, this mechanism could protect against certain types of cancer as testicular carcinoma. They refer that, p63 represents a barrier to the formation of tumors in normal healthy tissues. In cases of testicular cancer, the administration of drugs, that restore the function of p63, could prove potentially useful in the near future.

Source: Pharmazeutische Zeitung and original PNAS paper (thanks to Mariam and Steve Moss for sharing)

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Viruses are defined as “ small highly specialized infectious agent”. This definition has been common for the last decades or century to define nature’s microorganisms, which tend to infect most living organisms from humans down to bacteria. Now, it seems that the definition would be widened to include even these little malicious computer codes –that they used to call worms– but now the word virus would seem more appropriate.

In July 2010, a malicious code was discovered and assigned the name “Stuxnet” the powerful virus, and –unlike the previous ones– this one simulates the biological virus in the way it acts. Speaking biologically, a common flu virus would enter the human body through the respiratory tract, bind to special receptors and infect the entire respiratory tract causing the common flu symptoms, this could have been applied to older computer viruses. The new Stuxnet virus, however, would resemble a more specialized biological viruses as hepatitis viruses or HIV; the Stuxnet virus gains entrance to the computer via “Universal Serial Bus“ –commonly known as “USB port”– and then spreads like wild fire in the entire network its device is connected to.

Up to this part, Stuxnet would be a common garden-variety computer virus, but this is not enough for Stuxnet. Just like HIV searches for CD4 cells and hepatitis virus searches for hepatic cells, the malicious code Stuxnet searchs the infected computer for its target, which is a special control program called “Supervisory Control and Data Acquisition (SCADA) developed by Siemens Co. for operation of industrial systems, and used to control manufacturing processes from centralized locations, for example it can be used to alter the motor work rate of a machine on a factory floor, or the pressure in a pipeline, so typical environments could be oil pipelines and power plants.

This highly specialized virus is also unique in its mode of action; the sophisticated virus uses a four “zero-day” vulnerabilities –zero-day vulnerability or zero-day attack is a security hole or breach in a program which the developer is unaware of. Using four of these zero-day vulnerabilities is quite weird because these zero-days are of great value ( for hacker and malware makers )and using 4 of them in a single code is quite odd. Again the code still surprises us with its resemblance to biological viruses, for examples, like flu virus that has the ability to mutate and change forms via multiple ways, and like any bacterium that acquires resistance through plasmids or other pathways, Stuxnet can upgrade itself via peer-to-peer architecture (p2p, a distributed application architecture that partitions tasks or workloads between peers) allowing it to be updated after the initial command and control server (the initial computer) is disabled.

Symantec Corp., one of the world computer security leaders, estimates that 45.000 computers have been infected, and like biological threats and biological warfare viruses, Symantec also estimates nearly 30.000 of these infected computers in Iran only, and earlier today (27 September 2010) undisclosed Iranian sources said the nuclear plant have indeed been hit by Stuxnet with no damage to the plant.

I guess Arnold Schwarzenegger (The terminator) wasn’t lying after all when he said “I’ll be back!! “



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When you have to make a tough decision, a difficult choice, one that will affect your life and the lives of those around you, you always have to involve them in the process, and you will find that the wisest thing to do is to unite and make the decision collectively…

Starting from us, humans, and reaching bacteria, collective decision making can be a matter of life and death, yet many factors can influence the way we think and switch our behavior from one way to another. In quorum sensing, bacteria behave in a completely different way upon reaching a certain population density, from the way each one would behave individually.

This is all obvious, but I was lately wondering, do viruses exhibit any form of such “attitude”?? What is the equivalent to quorum sensing in the world of viruses?

The work in this field was all focused on bacterial viruses or bacteriophages, and especially on the temperate lambda virus (a phage that infects E. coli).Temperate means that upon infecting a bacterial cell, the virus will be allowed to choose between two scenarios:

Either: the lytic pathway, in which the virus will use the bacterial resources to replicate itself several times, then bursting out of the cell, killing it and releasing the viral progeny.

Or: the latency or lysogenic pathway, in which the virus integrates its genetic material into that of the host, undergoing minimal transcription and translation, and just replicating and vertically transferring it as the cell divides.

So what really helps or even forces the virus into a certain direction? For a long time, it was thought that the choice is completely random, and greatly affected by environmental conditions. But Joshua Weitz (assistant professor in the school of biology, Georgia Tech) and his team were not satisfied by this answer. They wanted to justify the experimental observation that when one virus infects the cell, the result would be lysis and cell death, whereas if two or more co-infect the host, the result would be latency.

Their mathematical model, based on the gene regulatory dynamics of the λ phage, shows us that the true answer lies in the levels of “gene expression”. Apparently, the process turned out to be controlled by three key genes: cro, cI, and cII. These genes are bound together by a decision loop (a feedback system) that is nonlinear and thus is tremendously affected by minimal changes in the levels of their expression into proteins, which depends on the total number of viral genomes in the host.

The negative feedback system was linked to the “cro” gene, and was triggered by the overall lower rate of mRNA transcription present at this stage, and thus its protein products inhibited the genes responsible for the production of the lysogenic proteins, and so lysis takes place.

In case of co-infection by two or more viruses, as the overall level of viral mRNA transcription is higher (although the increase could be so small!)& the products activate the “c I” gene transcription, translated into lysogenic proteins that activate & accelerate the positive feedback system, leading to even higher levels of production of the lysogenic proteins, and the cell is kept alive and kicking for a certain time period.

The “c II” gene represents a “gate” to the activation of the lysogenic cascade, activated prior to the c I gene. This is a figure I designed to simplify the idea.

Although it is far from settled, but proposing the ability of viruses to make collective decisions based on the number of viral genomes in the surrounding environment can be a very important “life” history trait. Having this trait may be critical to the evolution and survival of certain types of viruses and can explain a lot about that. But what I thought to be most interesting is this: knowing about these mechanisms can allow us to manipulate them in the future! We might be able to slow down the aggressiveness of some viral infections by driving them to latency. Even if is not a radical cure, it can greatly improve the life quality of lots of patients. Maybe in the future we would be able to find other viral functions that are driven by the same mechanisms like host resource usage or cellular penetration, and so defeating viruses in some new unconventional ways… let us hope and work!


Original paper: collective decision making in bacterial viruses

Biophysical journal 15 Sept 2008 (available online)

References (Citation by ResearchBlogging)
WEITZ, J., MILEYKO, Y., JOH, R., & VOIT, E. (2008). Collective Decision Making in Bacterial Viruses☆ Biophysical Journal, 95 (6), 2673-2680 DOI: 10.1529/biophysj.108.133694

Edited on Sep 24, 2010 (07:21 CLT)

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A team of Harvard scientists has taken the first step to solve mystery about why HIV patients are more susceptible to TB infection.

According to USAID, 42 million people are HIV infected & almost one third of them are also TB infected. It is believed that HIV interferes with the cellular and molecular mechanisms used by the lungs to fight TB infection. The HIV replication cycle

This mystery has been solved when scientists extracted immune cells called “alveolar macrophages” from the lungs of asymptomatic HIV +ve patients as well as healthy patients ” HIV –ve.” They observed a decrease in response towards TB bacterium in HIV +ve patients when compared to HIV –ve patients.

A further examination of lung specimens showed an increased level of a molecule called IL-10, which elevates the amount of a protein called “BCL-3” in alveolar macrophages and this reduces their ability to ward off TB infection.

It seems that HIV increases severity of TB infection, where both represent two of the most significant health challenges in human history.

Source: Science Daily.

Image credits: The HIV replication cycle.

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Researchers at Massachusetts General Hospital (MGH) are investigating a new way to block replication of hepatitis C virus “HCV” by targeting not the virus itself, but the genes that the virus exploits during its life cycle.

HCV has a high rate of replication that it can replicate a trillion particles per day. Also, due to its high rate of mutation, it can escape our immune system.

HCV replicates mainly within hepatocytes in liver by binding to receptors on the surface of the liver “CD81″ and human scavenger receptor class B1 “SR-BI”. Then it utilizes the intracellular machinery necessary for its replication. Upper right, virus particle enters cell followed by uncoating and release of positive-stranded HCV RNA genome. Viral genome is translated at the endoplasmic reticulum into the viral polypeptide (upper left). Viral replication complexes (red) are then assembled onto host-derived small membranous vesicles (yellow ovoids).

Transmission occurs by blood to blood contact, where it causes chronic liver infection in about 70-80% of patients & long term infections can cause liver failure or liver cancer.

HCV infection is usually treated with a six to eleven month regimen combining peginterferon and the antiviral drug ribavirin, but unfortunately, treatment is not successful in many patients and has serious side effects that some cannot tolerate.

Many drugs target viral enzymes, but due to the great ability of HCV to mutate, such approach lead to the emergence of resistant strains.

Recently, a new strategy has developed, which is to block human genes, which act as a cofactors for HCV infection. Using small interfering RNAs (siRNAs), researchers examined blocking of approximately 21,000 predicted messenger RNA transcripts in the human genome.

The siRNA scan found 96 genes that appear to have a role in viral replication, one gene codes for an enzyme called PI4KA, which is believed to be involved in the formation of membrane structures within the cell. Another group of genes contribute to formation of the coat.

So, by blocking these genes, HCV replication is stopped. At this time, these tested agents might not be suitable for therapeutic use.

Source & Image credits : Harvard Science.


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South Djoum ChimpIf you try to search in the library or over the internet for AIDS, you will find a huge amount of information available. You will also figure out that all scientists reach a dead end at the step of treating or vaccinating against AIDS. Their stop makes you never stop thinking: why can’t they continue? Why is there no cure for such a disease? Or at least why can’t they stop the progress of this illness by simply making a vaccine? It is like reading the same book millions of times without understanding its end, then you re-read the last chapters but still “YOU CAN’T”!!

I think that we need to restart reading the book from its beginning. We need to re-read about the origin of AIDS infections, to know more about HIV genome, and how its genes function; then we may know how to slow down or terminate progression of the virus inside the human body or at least to stop its passage from an individual to another. Hence, we may be able to read the book again and this time we can understand its end.

AIDS was initially reported on June 5th, 1981. But, it is more precise to mention the first documented AIDS case, which was in 1959. At that time, no one was able to define such an illness; however, scientists did a favor for the humankind by preserving the infected tissues till someone would be able to define HIV, i.e. after 1981. I may ask why not before 1959? But who can answer a question like this?

The origin of AIDS has so many controversial theories, including conspiracy theories. One of these is that HIV arose as a result of leakage in the US governmental or military labs during the development of a biological weapon. You may ask Dr. Leonard G. Horowitz (the author of Emerging Viruses: AIDS & Ebola. Nature, Accident or Intentional? And Death in the Air: Globalism, Terrorism and Toxic Warfare) for evidence to prove such an idea. As wikipedia page of ” AIDS origins opposed to scientific consensus” mentions his theory which claims that AIDS virus was engineered by such U.S. Government defense contractors as Litton industries for the purposes of bio-warfare and “population control”.

Dr. Alan Cantwell (the author of AIDS and the Doctors of Death) supported this theory, by naming one scientist that led the US military research on homosexual and bisexual men between 1979 and 1981; he attributed these research activities to Dr. Wolf Szmuness. And, when Dr. Alan was asked about the cases that were reported before 1979, his answer was that the American media masked the truth at that time! This has been also mentioned on “AIDS origins opposed to scientific consensus” Wikipedia webpage.

Another unreliable hypothesis had been advanced by Edward Hooper, as he accused Hilary Koprowski, the polish virologist and immunologist who was preparing polio vaccine using tissue cultures from non-human primates during 1950s, that he might have transferred AIDS from monkeys to human. This idea couldn’t be evidenced when one of these vaccine vials had been checked in 2000 to show negative HIV or SIV (Simian immune-deficiency virus that infects chimpanzees). Also, by checking the protocols of that old research, it is clear they were working on monkeys’ kidney cells that cannot transmit AIDS. But can one negative vial become a prove for the whole negativity?!

The most accepted and recent theory assumes that HIV is an evolution from SIV. This Cameroon Chimpanzees theory was suggested in 2006 after a study on genetic samples from more than 1300 chimpanzees within 7 years by Dr. Beatrice Hahn. It seems that one person had been bitten by one of these apes or got cut while he or she was trying to slaughter one of these animals, maybe for eating purposes!!

If this Chimpanzee in the picture is the main suspect now for HIV triggering on earth, the question now is: Do we have current reports for the same transmission from apes to human? If yes or no, I think we need to re-study and search that SIV which might tell us something about its “daughter” HIV (as accepted by most of the scientists). It is like reading the book from its beginning not the last chapters, sure it will tell us new things.. Like what? I really dont know, it may be like the first idea that led to inventing the nuclear bomb, would you believe me if I told you more than 60 years ago that there is an idea to bombard the nucleus to make a huge bomb? It was just an idea, but the know how was not known. I think it is the same for the AIDS book: we need to re-read but we still don’t know what is going to happen after that reading. All I know that we need to re-read with a new vision, not the same ordinary way of reading.

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Nothing is impossible..

Things, you think are absolutely harmful, may be highly beneficial if we use them in a new way.

Viruses can be used in the treatment of cancer, a field known as oncolytic virotherapy.

But can you imagine that they are safer & highly specific than other traditional chemotherapy???

You will get the key when you know that they destroy cancer cells with a high accuracy that scientists called them “magic bullet”.

Simply, the mechanism of most viruses is to infect our cells, then to use them as a factory to produce more & more viruses.

Viruses are highly specific, they replicate in cells having receptors for them. So, we need to change viruses to selectively bind to tumors.

In fact, a virus consists of a coat & genome.

So, we got two methods to generate tumor selectivity.

First: By making modification on viral coat in order to increase adhesion between coat & cancer cells “Transductional Targeting”.

Second: By altering viral genome, so it can only replicate in cancer cells “Non-Transductional targeting”.

However, many primary cancers were resistant to conventional virotherapy.

Researchers at McGill University and the affiliated Lady Davis Research Institute of the Jewish General Hospital, along with colleagues at the University of Ottawa and the Ottawa Health Research Institute (OHRI) have discovered that a family of compounds called histone deacetylase inhibitors “HDI” which convert oncolytic viruses into more potent weapon.

So, HDI can augment the ability of the virus to target & kill the cancer cells.Vesicular stomatitis virus

Many viruses can be used especially those with dsDNA
genomes “as
adenovirus and herpes simplex virus
where they have a higher stability & less susceptible for mutations.

Researchers utilize Vesicular Stomatitis Virus “VSV” as it is not a human pathogen. So, most individuals don’t have antibodies against it & can be treated before they gain immunity.

Human trials have been already approved & the results of these experiments will determine if this viral bullet is really a “magic bullet”.

Source: ScienceDaily

Image credits: Vesicular Stomatitis Virus

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Did you ever think about only one disease that causes the death of 50 million people? and around a year!!!!

Unfortunately, it already happened between 1918-1919 and is known as Spanish flu.

Flu (influenza) is a highly contagious respiratory infection caused by influenza viruses, which are divided into three types A, B and C.

Type A influenza is the most frightening and epidemic.

Type B influenza  causes milder symptoms than type A.

Type C influenza tends to be mild and does not spark epidemics.

Type A flu virus is subdivided into subtypes based on two surface proteins, hemagglutinin (HA) and  neuraminidase (NA).

Now, Scientists know 16 HA subtypes and 9 NA subtypes of the flu virus.

A (H1N1) and A (H3N2) are the  subtypes of influenza A viruses found in people, and there are no subtypes of influenza B virus.


The influenza viruses contain eight segments of single-strand RNA ,  continually change over time through “antigenic drift” or “antigenic shift”.

So, there is new flu vaccine every year and from time to time we face a new flu outbreaks.

Now, there is real fear between scientists and people of transmission of influenza viruses from animals to people.

There is a promising trial of new flu vaccine , targeting the internal proteins of the virus, this vaccine may be used in vaccination of many viruses like flu in mechanism of infection. (you can see BBC report Here).

References :


What Is Flu?

Types of flu

Influenza virus

History of Flu Epidemics

The Influenza (Flu) Viruses

Types of Influenza Viruses

Flu Virus Can Change: “Drift” and “Shift”

For Further reading

Seasonal Flu

Flu Channel

Cold Channel

Bacterial Pneumonia and 1918 flu

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Image Source: College of Agriculture & Natural resourcesIn an on-going study at the University of Rochester Medical Center, scientists have come across a new form of inheritance which would probably astonish Mendel himself. Research has shown that parents pass on the human herpes virus 6 “HHV-6” to their offspring because the virus has integrated itself into the infected parent’s chromosomes. And it is actually not as odd as it sounds. One in every 116 newborns is affected by this unique congential infection. The virus appears to integrate itself into a position in the chromosome concerned with the maintenance of the body’s normal immune function.

Typically, HHV-6 causes roseola which is characterized by high fever, rash, and mild gastrointestinal symptoms. However, the number of viruses found in children, who carry the virus within their genes, is much higher than those who were infected merely through the placenta. 86% of the children included in the study had the virus integrated within their chromosomes. The HHV-6 DNA itself was found in a hair sample provided by one of the parents. Only six of the congenitally infected babies were infected by the mother through the placenta.

The odd part about this does not lay in the fact that the virus has integrated itself within the chromosomes, but that it was actually passed on. So far, the long-term consequences on the children’s immune system is unknown but to have a virus lying around like that in their DNA…simply frightening, yet fascinating.

Source: Biology News Net

Press release: URMC website

Original research paper: Chromosomal integration of human herpesvirus 6 is the major mode of congenital human herpesvirus 6 infection. Pediatrics. 2008 Sep;122(3):513-20. PMID: 18762520. (Vote for the abstract on Biowizard)

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“It’s an honor to announce that we’ve successfully discovered, cloned & characterized the densonucleosis virus (DNV) Antigen, which will be able to infect Anopheles gambiae. That will hinder its ability to transmit Malaria parasite, Plasmodium or, at least, reduce its lifespan. I’ve to tell you this: This will be the latest in Malaria control.” Well.. those are my words but, of course, it is not my discovery. It’s the team of researchers from Johns Hopkins who discovered it. To realize how big it’s; we first need to know the previous approaches & trials in Malaria control.

To think, just think, about control/ prevention of any of those vector-borne parasites; automatically researchers think about these:
1- Prevent infection – disease – transmission.
2- By looking at: the parasite’s life cycle – the mosquito – the human immune system.
3- So, it’ll look like that: get humans vaccinated – develop genetically modified mosquitoes incapable of transmitting the parasite or simply “I was so naive to think that it’s simple” kill them with insecticides (anti-vector measures) – target the parasite at any stage of its life cycle.

For decades, DDT (dichloro-diphenyl-trichloroethane) & Chloroquine were successfully used in eradication of Anopheles & Plasmodium respectively, “I do like this word, makes me sound like a pro”. Chloroquine was used in treatment as well as prevention, till the emergence of chloroquine-resistant Plasmodium parasites and DDT-resistant Anopheles mosquitoes. Yes, they overcame the humans’ arsenal. So, preventing spread of resistant parasites is the #1 priority.

We can’t talk about all control strategies today, so we’ll talk about anti-vector measures. What do they use in control programs as anti-vector measures?
1- Insecticide-treated bednets (ITNs) & long-lasting ITNs (LLINs) it helped kids to survive. The only allowed insecticides to be used in ITNs are pyrethroid insecticides, so when the pyrethroid resistance emerged, as usual, it was really bad.
2- Indoor residual spraying (IRS) using DDT
One word about the mechanism of action of DDT & pyrethroids, both target voltage-gated Na-channels. So, when a set of mutations change the protein structure; Congratulations! It’s resistance to both DDT & pyrethroids.
3- New approach: Molecular talk; Know more about “blood meal” host selection. Yes, Anopheles smells the host, so researchers want to identify that pathway.
4- Another new approach: They are investigating genes which encode proteins that may interrupt the development of the parasite in the Anopheles.

The latest as an anti-vector measure is using Paratransgenesis or “the genetic manipulation of insect symbiotic (mutualistic, commensal or parasitic) microorganisms”, I can’t get the term or the definition. I’ll say it like that: “Any other m.o. has a relationship with the vector”. The steps are:
1- Know the Ag (Pick the gift)
2- Get the gene(s) engineered to be successfully expressed (Wrap the gift)
3- Delivery to Anopheles (Deliver the gift)
So the gift will be the non-enveloped ssDNA virus called (DNV). Its genome is very small, when they say for a viral genome that it’s small, so it has to be small (4–6 kb). The entire genome can be placed in a plasmid.

Back to the story of the discovery, they were doing a totally unrelated experiment when they found that strange band/ zone. They isolated it from the gel, cloned, sequenced, ran through BLAST which showed that it looks like DNV of Aedes aegypti (AeDNV) but not the man himself. They did multiple tests to identify the Ag, e.g. Immunofluorescence assay. There was a trial to infect Anopheles gambiae with DNV of Aedes aegypti which wasn’t successful in infecting adults from Anopheles gambiae. But the novel “AgDNV is highly infectious to An. gambiae larvae, disseminates to adult tissues, and is passed on to subsequent generations.”

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