Thursday, May 28, 2009

Quantum: Ancient immunity

A QUANTUM OF SCIENCE

New findings show adaptive immune system may not be new invention

Recently, scientists at Emory University in Atlanta reported that lampreys - a cartilaginous fish which evolved around 500 million years ago - is the oldest organism yet found to possess an adaptive immune system like that of humans. Previously, the adaptive immune system was believed to have originated in sharks, which evolved around 400 million years ago. This extra 100 million years is a big deal because the lamprey is a much earlier splinter from the vertebrate branch of the tree of life, and could mean that other even more ancient predecessors had already figured out how to "record" microbial invaders and repel them better in future infections.

Another interesting note: the age of cartilaginous fishes was known as the Silurian period, a time culminating in the so-called Law Event in which approximately 60% of aquatic species became extinct through a series of rapid climatic changes. Could the adaptive immune system have helped lampreys and sharks survive?

For more information:
The Scientist: Ancient organism, modern immunity

© A Quantum of Science / Peter Smalley (2009)
Reproduction with attribution is appreciation

Tuesday, May 26, 2009

Curing the Mosquito

A QUANTUM OF SCIENCE

How can bacteria help protect humans from malaria?

Malaria is a deadly but neglected tropical disease that has received more money and attention in the last decade than in perhaps the preceding century. The disease is spread by mosquitoes in whose gut live one or more of five protozoan species of the Plasmodium genus. As a protozoa, it is neither a virus nor a bacteria but more like an amoeba or an algae, and thus it is more difficult to fight because its cells look more like human ones than either viruses or bacteria. Malaria is contracted by 350-500 million people every year, and approximately 1-3 million die of it annually - mostly sub-Saharan children. Now a scientist at the Johns Hopkins University Malaria Research Institute think he might have a unique way to help break the cycle of malarial infection.

The answer? Cure the mosquito.

For a long time it was thought that malaria could be controlled by using insecticides and bed screens to keep the mosquitoes away, but these approaches have both proven only partially effective. Insecticides also have their own toll on both human health and the environment, and rapidly become ineffective. But Dr. George Dimopoulos has found a species of bacteria living in the gut of the mosquito whose presence seems to inhibit the growth of the malaria protozoa. When he treated mosquitoes with an antibiotic, the bacteria died and the protozoa multiplied manyfold, making the mosquito a much deadlier vector for the disease. By helping this specific bacterium to stimulate the mosquito's immune system and cure it of the protozoans it carries, Dr. Dimopoulos believes, the spread of malaria could be controlled more effectively than with insecticides or bed screens alone.

If so, this could be a new and unprecedented breakthrough in fighting malaria, one of the great scourges of Africa.

For more information:
VOA News article

Public Library of Science article by Dr. Dimopoulos

Wikipedia entry on protozoa


© A Quantum of Science / Peter Smalley (2009)

Reproduction with attribution is appreciation

Sunday, May 24, 2009

A Cure for the Common Cancer

A QUANTUM OF SCIENCE

What can the common cold do to help fight cancer?

Behold one of the most successful organisms in the history of the world: the humble adenovirus, better known as the cold. Human have recorded suffering from this virus since at least Hippocritas, and likely much earlier. Every year humans around the world come down with runny noses, coughs and fevers associated with the cold. And then they spread it to others, and recover - until the next round. Adenoviruses are among the handful of true success stories in biology. Now, scientists have found a way to harness the infectivity of the common cold to make it serve a therapeutic function, not an epidemiological one.

Recently, a group of scientists led by Dr. Leonard Seymour of Oxford University reported successfully removing the "disease" genes from a adenovirus and replacing them with genes for cancerous proteins. Why would this help? In the same way that your body's immune system eventually learns to recognize and attack normal adenoviruses that manage to infect you, the modified adenovirus contains cancer-linked genes that provide the immune system with the opportunity to "learn" that these proteins are invaders to be fought, potentially turning the immune system into the most potent and selective anti-cancer fighter possible.

Scientists have managed similar feats before but to do so they have had to weaken the virus, making it less effective at stimulating the immune system and teaching it to recognize cancer proteins as invaders to be fought. With this achievement, Dr. Seymour and his collaborators have taken a large step forward into a burgeoning field of therapeutics drawn from biological strategies older than humanity itself.

For more inforation:
http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1000440

(C) AQOS / Peter Smalley (2009)

Thursday, May 21, 2009

A single amino acid

A QUANTUM OF SCIENCE

Why does the more lethal H5N1 Avian flu not infect humans more readily?

Several references have been made now to the "nightmare scenario" in which genes from the more lethal Avian flu (H5N1) reassort with the less dangerous but more infective Swine flu (H1N1), generating a hybrid that is both lethal and infective. We have yet to talk much about why the H5N1 strain is harder for people to catch – so hard that in some years there are only a single-digit number of cases.

Certainly, the lethality of H5N1 inhibits its spread. In epidemiological terms, the virus kills faster than it spreads, leading to a reproduction number at or below one. In a recent paper, researchers show that a single amino acid change in the sequence of the viral polymerase gene (PB2) results in a dramatic difference in both temperature tolerance and infectivity.

Scientists at University of North Carolina at Chapel Hill found that the H5N1 virus required the higher temperatures found in its bird hosts (around 40 degrees Celsius) in order to be highly infective. At 32 degrees Celsius - the temperature of the cells found in human nasal passages called HAE, or human airway epithelium – the H5N1 virus became sticky and did not effectively infect those cells. The reason for this? A single amino acid at position 627 of the polymerase protein of the H5N1 virus was changed, allowing it to be glycosylated - chemically modified to bear a particular sugar residue. Researchers were able to prove this by genetically altering a human influenza virus (which infected cells optimally at 32 degrees Celsius) at position 627, changing just that one amino acid to one that could be glycosylated. The resulting human virus was not capable of creating an infection in human airway epithelial cells, demonstrating an attenuation of the formerly infective human influenza virus. Further modification of viral coat proteins fully attained an "avian" level of temperature sensitivity.

This research is important because it significantly adds to our understanding of the molecular process by which the influenza virus mounts a successful infection in either of its principal hosts (birds or humans). Scientists who sequence previously unknown strains of influenza isolated from patients can now rapidly assess the polymerase gene (PB2) and determine quickly whether it is an avian strain or one more evolved for humans. Not only the treatments recommended but also the course of a widespread epidemiological event could be affected by this. Further, scientists searching for the molecular keys to understanding the mutations of various influenza strains can now look more effectively for such alterations, granting insight into the process of interspecies spread of the virus.

Perhaps most importantly, these findings help to partially allay fears that H5N1 is likely to reassort with H1N1 – since avian flu infects HAE cells poorly due to their intolerance for colder temperatures, we are less likely to endure that kind of hybrid virus.

For more information:
Avian Influenza Virus Glycoproteins Restrict Virus Replication and Spread through Human Airway Epithelium at Temperatures of the Proximal Airways.

© A Quantum of Science / Peter Smalley (2009)
Reproduction with attribution is appreciation

Wednesday, May 20, 2009

Mapping H1N1

A QUANTUM OF SCIENCE

Where in the world is H1N1?

The spread of H1N1 around the world has significant implications for the etiology and epidemiology of the disease, as well as the global health infrastructure’s response to it. Raw numbers alone do not tell the story as well as this single image, taken from the WHO pandemic alert and response website.

This map is current: as of today there are a global total of 10,243 laboratory-confirmed cases of H1N1 influenza that have been reported to the WHO, including 80 deaths (making the global mortality rate one death out of every 128 cases). While the actual number of total cases is inevitably somewhat higher due to the lagging nature of lab confirmations and reporting, what is more interesting is the distribution of the cases – and deaths – and what this might tell us about the past and future of H1N1.

Originally dubbed as Swine Flu, the official name for this strain of H1N1 is North American influenza, and indeed the overwhelming majority of the cases are in North America (93.8%). What is interesting to note is that 79 of the 80 confirmed deaths are also in North America (98.75%). Digging a little deeper into the distribution of deaths, we find that this is due to the large contribution of deaths from H1N1 in Mexico, where the mortality rate is one death for every 50.6 cases. That is two and a half times the global mortality rate, and eighteen times the mortality rate in the adjacent United States. With the sequencing of the H1N1 genome in Canada that was announced yesterday, no significant differences were found in strains isolated in Mexico versus those in the United States or Canada. While this is somewhat reassuring because it means there is not a more virulent strain on the loose in Mexico, it requires a different explanation. Some authorities have suggested Mexico has deficiencies in its health infrastructure, but others cite a cultural inhibition that may play a more pervasive role in preventing infected persons from seeking help until it is too late. In either case, however, countries with similar health infrastructures and cultures would be expected to have a similar mortality rate, and this has not yet been borne out (as the map’s number for Central and South America show).

Another point of interest brought out by the map of H1N1 cases to date are the non-North American hot spots. Japan is the leader of these, with 210 cases, followed almost evenly by Spain (107) and the United Kingdom (102). What is interesting about this is the far-flung locations of the hotspots outside North America. Nothing like the close distribution of cases in Mexico-US-Canada have been seen in these Asian and European hotspots. This could mean that there is something particular to North America that supports the infectivity of the viral strain; or it could mean that it is simply too soon, and the neighbors of these hotspots will soon show a commensurate rise in cases. It is worth noting that strains of influenza are known to show a strong geographical preference; the deadly Bird flu (H5N1) is almost unknown outside of the Far East, for reasons that scientists are still trying to elucidate. This also brings up the potential for reassortment of viral genes between H1N1 and H5N1, now that the former has entered the latter’s territory. Still, Japan has been aggressive about treating flu cases and currently Roche (the maker of Tamiflu) estimates that 35 million of the 50 million people who have been treated with Tamiflu are in Japan. It can be hoped that this aggressive treatment schedule will be effective in containing the possible hybridization of H1N1 with H5N1.

For more information:
WHO Epidemic and Pandemic Alert and Response

WHO H1N1 map (20-May-2009 version)

Tamiflu (Oseltamivir) information, including use in Japan

© A Quantum of Science / Peter Smalley (2009)
Reproduction with attribution is appreciation

Tuesday, May 19, 2009

Canadian scientists sequence H1N1 genome

A QUANTUM OF SCIENCE

Now we know the complete blueprint for H1N1; now what?

Today it was announced that scientists in Canada have fully sequenced the entire genome of the H1N1 influenza virus. While it's not the first viral genome to be fully sequenced, it is a landmark achievement and all the more so for having been completed in one week of around-the-clock work by scientists at Canada's National Microbiology Laboratory in Winnipeg. This is, as the saying goes, kind of a big deal.

These findings shed some intriguing light on the outbreak of H1N1 but raises even more questions, as most scientific discoveries do. For example, researchers found virtually no difference between the Mexican strains and those occurring in the US or Canada. Why, then, have so many more cases in Mexico proven fatal? The answers may not lie in the genes themselves, but rather in differences of health infrastructure and health policy. Benefits of this breakthrough include faster analysis of future strains, a better understanding of how and why H1N1 mutations or reassortments occur, and a better H1N1 vaccine - with this last being of crucial importance as major pharmaceutical companies begin the laborious process of choosing which sequences to use for their vaccines. With an improved understanding of the variations in the H1N1 genome, conserved sequences can be selected for use vaccines, resulting in a stronger, more robust protection against future infection.

Perhaps it is a little cynical, but one might consider that the timing of this announcement seems a little too convenient considering that today is the second day of the 62nd World Health Assembly, the annual meeting of the World Health Organization whose handling of the H1N1 outbreak has been criticized by many science and health professionals. Then again, maybe it is simply a case of serendipity; regardless, it is good news and that's worth remembering.

Plus, if you want to apply for the position of Viral Genome Curator at a company in Bethesda, MD, you now have one more fully-sequenced genome to add to the list.

For more information:
http://www.canada.com/Health/Canadian+completes+sequencing+virus/1569084/story.html

© A Quantum of Science / Peter Smalley (2009)
Reproduction with attribution is appreciation

Quantum: Influenza tutorial (powerpoint)

A QUANTUM OF SCIENCE

This powerpoint presentation may be a little advanced in places but there is some great information to be extracted even with just a casual viewing, especially among the pictures. The author, Dr. Mustafa Ababneh, is a molecular virologist at the Department of Veterinary Clinical Sciences, Jordan University of Science and Technology.

For more information:
Dr. Ababneh's publication record on PubMed

© A Quantum of Science / Peter Smalley (2009)
Reproduction with attribution is appreciation

Quantum: flu expert fears H5N1 nightmare

A QUANTUM OF SCIENCE

What happens when the lethal but less-infective H5N1 strain of influenza mingles with the relatively benign but more-infective H1N1?

Dr. Yi Guan of Hong Kong Kong University is one of the leading flu experts in the world. His claim to fame was the isolation of the SARS virus in wild civets in 2003; his recommendation to eliminate the population of captive civets may have prevented a re-emergence of SARS since then. Now he has some strong criticisms of the World Health Organization's handling of H1N1, and worries about the potential for a sharing of lethal H5N1 genes with H1N1, which has proven itself far better at spreading itself around than H5N1.

The difference between the two strains' ability to infect may be in the gene encoding hemagglutinin, the protein that helps the virus get into cells and infect them. Recently published data shows that the genetic sequence for the hemagglutinin (HA) gene is only 9.7% similar between H5N1 and H1N1, by far the largest difference between their genetic codes. Because influenza is capable of rapid reassortment - the shuffling of genes like decks of cards - it may only be a matter of time before the HA gene from H1N1 is adopted by H5N1. That could have profoundly dire effects if experts like Dr. Guan are to be believed. So far the only ray of hope that nightmare scenario will not happen is the H1N1 seems restricted to North America, while H5N1 is only found in Asia. Critics of the WHO like Dr. Guan seem to be quite justified in calling for increased attention to transcontinental spread of H1N1 and more aggressive use of TamiFlu and other treatments to curb the spread of H1N1 into Asia.

More information:
http://blogs.sciencemag.org/scienceinsider/2009/05/exclusive-meet.html

© A Quantum of Science / Peter Smalley (2009)
Reproduction with attribution is appreciation

Monday, May 18, 2009

Quantum: Counting H1N1

A QUANTUM OF SCIENCE

First let's tackle the jargon.

Prevalence is the total number of cases of a disease or infection in a given population. The important thing to remember about prevalence is that it is all the cases, not just the new ones, so the longer it takes to recover from a particular infection, the higher the prevalence will be. Most of the H1N1 figures you hear or read about are prevalence numbers, and as such are not as accurate a reflection as they might be.

Incidence is the rate at which new cases occur in a population, and is a better measure of how fast a disease is spreading because it takes out the duration-of-illness factor included in prevalence. Incidence is usually reported per capita ("3 new infections per 1000 people") or even with a time-element ("14 per 1000 persons-years"). The latter is useful because it lets researchers compare the instantaneous rate of a disease’s spread even in disparate time periods (for example, an incidence of 14 per 1000 persons-years could mean 14 cases would be expected for 1000 persons observed for 1 year, or 50 persons observed for 20 years). The only caveat to this use of incidence is the assumption that the rate will always be linear over the period in question, so longer time periods are more susceptible to incidence errors.

Finally there is the reproduction ratio, which is a measure of how many people each infected person will spread the disease to before they recover. In order for a disease to spread at all that ratio has to be greater than 1 (such that each infected person infects at least one more person). Up to now the ratios estimated for H1N1 Swine flu have been between 1.4 and 1.6. Recently, however, researchers at the National Institute of Health and Medical Research in Paris have re-estimated the ratio using some different assumptions and found it to be between 2.2 and 3.1 in Mexico, well within the range of numbers required for a pandemic. With the recent report of 135 new cases of H1N1 in Japan, the World Health Organization still denies an official pandemic is underway but evidence is mounting that H1N1 may have a higher incidence than previously thought.

For more information:
http://blogs.sciencemag.org/scienceinsider/2009/05/swine-flus-rate.html

http://blogs.sciencemag.org/scienceinsider/2009/05/h1n1-rocks-japa.html

http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=19205

© A Quantum of Science / Peter Smalley (2009)
Reproduction with attribution is appreciation

Saturday, May 16, 2009

Smoking AIDS

A QUANTUM OF SCIENCE

Anti-retrovirals are now drugs of abuse in South Africa; will this lead to resistant HIV?

The newest chapter in the AIDS saga in Africa is unfolding in the townships of South Africa, where the demographic of 15-21 year olds are engaging in a new practice: grinding up anti-retroviral drugs designed to suppress HIV and prevent it from becoming AIDS, mixing the powder with tobacco or marijuana, and smoking it to achieve hallucinogenic and anxiolytic effects.

A recent BBC article goes into further detail, but mainly focuses on the social aspect of the new form of drug abuse. Doctors and health care policy activists in South Africa are gravely concerned about not only the interruption of the intended use of the drugs - which has led to shortages and long lines in many areas - but also the possibility that this abuse of the drugs will cause resistant strains of HIV to arise.

This seems unlikely for several reasons. First, smoking a pharmaceutical innately changes the molecular structure of the drug. The heat involved might well be expected to break down the structure into inactive forms, or combine key parts of the molecule with oxygen and likewise eliminate its antiviral activity. Without activity, the drug cannot cause resistance to arise. The second reason this fear is ungrounded is that in order to cause resistance, those abusing this drug must also be HIV-positive. While there is likely to be some overlap in a country whose HIV-positive population is 3.2% among that age/sex demographic [LINK], it is unlikely to be enough to cause undue concern from a health policy standpoint.

Clearly there is a health policy crisis in South Africa regarding the proper administration of anti-retroviral drugs. Concerns about drug abuse aside, the phenomenon is preventing those who really need such drugs from obtaining them, and this alone is sufficient reason to take action. But fears of a super-HIV, resistant to the anti-retroviral cocktails of drugs currently capable of controlling (though not eradicating) HIV, are overblown in this case.

© AQOS / Peter Smalley (2009)
Reproduction with attribution is appreciation

Wednesday, May 13, 2009

Quantum: Tracking H1N1 mutations in real time

A QUANTUM OF SCIENCE

How do scientists around the world collaborate rapidly in real time when a pandemic looms?

Today marks a departure from the established format of longer, more detailed essays with the first "quantum" post designed to provide a short, sweet snapshot of a small corner of Science. The intent of such quantum posts is to give readers tools to make use of on their own to extend their knowledge of the cutting edge of science and technology.

Today's quantum is the Human/Swine A/H1N1 Influenza Origins and Evolution project: a wiki site maintained by Oliver Pybus of Oxford University and Andrew Rambaut of the University of Edinburgh. The purpose of this wiki is to provide a place for scientists around the world to post and discuss the genetic sequences of H1N1 influenza strains they have isolated and characterized. Based on these sequences, scientists can build a more accurate picture of where the flu virus is spreading and - most importantly - how fast it is mutating... in real time. This is key because a mutation that increases virulence could make the difference between a regular annual flu season and a global pandemic.

Of particular note: the phylogeography link has a great discussion of how fast different strains of the virus are spreading, and where. This ties in nicely with the phylogenetic analysis of the virus, a look at the genetic history of H1N1 as it has spread over time.

© AQOS / Peter Smalley (2009)
Reproduction with attribution is appreciation

Tuesday, May 12, 2009

The End of Antibiotics

A QUANTUM OF SCIENCE

As antibiotic after antibiotic becomes useless, where will we turn to fight the advancing tide of bacterial infection?

Most American adults are aware of the problem of antibiotic resistance: the rapid and aggressive evolution of pathogenic bacteria capable of tolerating even the most potent antibiotics that Western medicine has come up with. Less than a century ago penicillin would knock out any bacterial infection known; today we live in the age of MRSA, a strain of Staphylococcus aureus resistant to not just one but multiple antibiotics. Doctors are running out of ways to prevent even mild infections from becoming life-threatening because bacteria develop resistance can share genetic information with one another, spreading the resistance even further. While there are things we can do to slow the advance of antibiotic resistance, the pace of resistance is accelerating far beyond the ability of pharmaceutical companies to develop new drugs. Is there no hope?

One source of hope may be simpler - and far older - than we think. Mammals have a powerful adaptive immune system to protect them, but what about the lower animals, insects, and plants that lack a sophisticated immune system? How do they avoid succumbing to microbial infections? In the last thirty years scientists have begun to discover that living things have long since developed ways to fight bacteria. One of the most ancient and endemic of these are a class of proteins call antimicrobial peptides (AMP).

First a bit of nomenclature. The majority of your body is made of protein: a polymer of up to 21 different amino acids strung together in long chains. A shorter chain of amino acids (less than a hundred) is called a peptide. Both peptides and proteins have their sequence determined by genes: deoxyribonucleic acid (DNA), which is made up for four basic nucleic acids in repeating sequences. Antimicrobial peptides are encoded by special genes that first evolved, scientists estimate, over a hundred million years ago.

Scientists now know of over nine hundred antimicrobial peptides, and the number is growing at an exponential rate. The diversity of these peptides is astounding: even closely related species have a different set of AMP that little resemble those of even their closest evolutionary siblings. And almost every animal or insect examined has not merely one, but a palette of antimicrobial peptides in their genome, expressed as peptides found in epithelial tissues, blood cells, haemolymph and saliva. Not only the sequence of these peptides is diverse. Their structure also spans an amazing range of shapes, sizes and architectures. Some resemble a helix, others form two-dimensional sheets, and still others form complex rings and branches through multiple internal bonds. Further, many of these AMPs are processed by the cell after being translated from genes into peptides: glycosylation, amidation, halogenation and proteolytic cleavage are common modifications. Given the diversity of genes and structures, scientists have spent a long time trying to understand the unique effectiveness of AMP in combating microbial infections.

The first question that arose after the discovery of antimicrobial peptides was why resistant strains of bacteria had not evolved, especially since AMP genes were so evolutionarily ancient. The first key to this is the very diversity that has confounded scientists. Imagine if each species of plant and animal had evolved the genetic ability to produce between five and twenty broad-spectrum antibiotics, all of which were available for use as a kind of antibiotic "cocktail" whenever infection threatened! This diversity makes it very hard for bacteria to evolve resistance – just when it figures out how to evade one AMP, nineteen more are there to make sure it doesn't pass on that knowledge. Further, the target of antimicrobial peptides is almost impossible for bacteria to avoid: the bacterial membrane itself.

Bacterial membranes are made up of a double layer of molecules called phospholipids. Briefly, the "phospho" part of the membrane molecule is hydrophilic and prefers to be in water, thus facing both the inside and the outside of the bacterium. The "lipid" part of the membrane molecule is hydrophobic, preferring not to be exposed to water, and so gets sandwiched in the middle of the membrane. (Touch your four fingertips together in front of you; the fingers are like the lipid part of the membrane, the palms are like the phospho part. To the left of your hands is inside the cell, to the right is outside.) This makes an effective barrier because most molecules are either overall-hydrophilic or overall-hydrophobic; either way, the phospolipid bilayer will prevent both kinds of molecules from crossing into (or out of) the cell.

The exception, of course, are antimicrobial peptides. Regardless of the diverse sequences they possess, all AMP have the characteristic of being "amphipathic" – possessing both hydrophobic and hydrophilic sequences of amino acids in the same peptide. Carefully spaced, these amino acids first carpet the bacterial membrane, merging with the hydrophilic phospho exterior of the membrane and thinning it. The AMP then swing around so that their hydrophobic amino acids can merge with the lipid layer of the membrane. As this happens, pores begin to form in the membrane and more AMP are able to slip inside the bacterium, repeating the process from the inside. Pores expand and soon the membrane collapses, destroying the bacterium and freeing the AMP to find another target.

Because the target of the AMP is the bacterial membrane, this strategy has been effective for a remarkably long time – more than a hundred million years in some cases (Nicolas, 2003). The phospholipid membrane was one of the earliest innovations of the primordial unicellular world, and unlike genes and protein, it is not easily susceptible to evolutionary advance. While bacteria have learned how to add or subtract elements from their membranes – and do, often, to disguise themselves from the immune system – they cannot alter the basic phospholipid building block of their membranes.

There is even more to the story. In higher animals, their repertoire of AMP work in concert with their immune systems, giving T-cells and antibodies greater access to invade bacterial cells and defeat them – and more importantly, to recognize them and store that memory against future invasions. Additionally, commensal bacteria (the "helpful bacteria" that do things like help humans digest their food) seem to be considerably more tolerant of AMP and even play a role in stimulating the body to produce AMPs and keep the defenses active. This is part of why you are more likely to develop an infection after a course of treatment with broad-spectrum antibiotics that kill these commensal bacteria as well as the pathogenic ones.

So if antibiotics are unable to keep up with the rate of resistance and AMP are so much better, why aren’t we already using them? The answer is that pharmaceutical companies are exploring many potential AMP therapies but their nature makes them difficult to use as drugs. AMPs work in a mass-action fashion, mobbing a single bacterium with hundreds of copies and dozens of different specific AMPs; because of this, effective dosages of AMP are quite high and can result in potentially toxic side-effects. Still, topical uses of AMP are the most accessible application and several are in clinical trials or consideration by the FDA. Oral and systemic AMP drugs are still in development as scientists search for molecules with high activity that could be supplied in lower dosages, but the use of AMP in combination with antibiotics has resulted in some exciting drug cocktails of considerable potency.

AMP also have an array of very exciting applications even outside direct use as drugs, however. AMP molecules have been used as imaging probes, allowing doctors to better visualize the spread of a bacterial infection in the body. Biofilms of AMP have been shown to protect surgical instruments against airborne bacteria that could infect patients on the operating table. AMP genes have been introduced into crops such as tobacco and potatoes to noticeable improvement in their disease resistance. AMP constructs have also been shown to aid considerably in combating STDs, as well as the pulmonary infections associated with cystic fibrosis. A novel class of human therapeutics is even being explored that works by stimulating natural AMP production.

Antibiotics are powerful tools, but more and more doctors and researchers are turning to alternatives as resistance to antibiotics renders them ineffective. In the future, expect to see greater emphasis placed on peptide pharmaceuticals as an expanding answer to the threat of pathogenic bacterial infections – an answer that Nature has already tried and found effective for the last hundred million-odd years.

For more inforation:
Molecular strategies in biological evolution of antimicrobial peptides. P Nicolas, D Vanhoye, M Amiche – Peptides, 2003 [Link]

Antimicrobial Sequences Database (Tossi group, University of Trieste)

Antimicrobial peptides of multicellular organisms. Zasloff, Nature, 415 (24) 2002 [Link]

Antimicrobial Activity and Stability to Proteolysis of Small Linear Cationic Peptides with D-Amino Acid Substitutions. Hamamoto et al. Microbiology and Immunology
Vol. 46 (2002) , No. 11 pp.741-749 [Link]


© AQOS / Peter Smalley, 2009
Reproduction with attribution is appreciation

Thursday, May 7, 2009

The Upside of Food Poisoning

A QUANTUM OF SCIENCE

In the future, food poisoning might keep you from developing cancer

Food poisoning occurs when a microbial pathogen enters the food supply and multiplies, leading to a high enough concentration of viable cells to cause an infection when the food is consumed. Most frequently this is a gastrointestinal infection, leading to nausea and diarrhea as the body tries to flush the invader out of its system. In severe cases, especially among the very young and very old, severe cases of dehydration can result in death. This was the case during the recent outbreak of Salmonella in peanut butter, where hundreds were sickened around the US. But is there any upside to food poisoning?

Surprisingly, yes. One particular food-borne pathogen is a common bacterium known as Staphylococcus aureus. Most strains of this microbe are harmless and actually help protect you by competing with the more sinister strains and effectively out-growing them. A few strains are deadly, however, such as the growing frequency of hospital infections of MRSA (multiply-resistant S. aureus, strains that are resistant to all but the newest antibiotics). In between these two extremes are those strains of S. aureus that produce a special protein called staphylococcal enterotoxin. This protein, belonging to a class known as superantigens, is the immune system equivalent of shouting "BOMB!" in an airport. All the body’s defensive systems are activated and a red alert is sounded, sending active T-cells scrambling to produce antibodies and hopefully fight off whatever invader has come calling. But recent research has shown that this is not always a bad thing, at least in small, controlled doses. Enterotoxins have been shown to stimulate the immune system in novel ways, even to generating protective antibodies against unusual targets – targets such as the body’s own cancerous cells.

In their review article "Superantigens: The Good, the Bad, and the Ugly," researchers at Duke and the University of Florida tested the protective effect of superantigens when healthy mice were vaccinated with melanoma cells that had been chemically inactivated – making them unable to grow and become tumors, but allowing the mouse immune system to make antibodies against them. Some of these mice were then given a dose of superantigen (equivalent to a case of food poisoning, roughly speaking) and all the mice were exposed to live, infective melanoma cells. The usual result of this is death after 14 days from massive skin cancer tumors. In this study, however, the results were startling: 100% of the untreated mice in the study expired after 14 days; 100% of vaccinated mice after 17 days; but after 136 days only 40% of the vaccine+superantigen mice had expired, and none of these mice displayed any sign of melanoma tumors. The mice who survived to this stage were given another dose of live melanoma cells and 80% of them survived for another 50 days, showing that the protective antibodies were now a permanent part of their immune repertoire.

Does this mean you should go eat some potato salad that has sat at room temperature on the counter overnight? Well, no. First of all, only the T-cells that are actively making antibodies are stimulated by the superantigen; all others are switched off, the better to concentrate the body’s resources on making protective antibodies. This means that unless you are currently being exposed to an invader and making antibodies against it, receiving a dose of superantigenic staphylococcal enterotoxin isn’t going to do you any good (and while food poisoning won't kill you, the symptoms are far from pleasant). On the other hand, superantigen therapy has the potential to help the human body fight off infections that even modern antibiotics are helpless against. Imagine a patient infected with MRSA – now, his own immune system could be revved up by administration of superantigen and potentially mount a much stronger offense against the current, active infection. The irony here is that MRSA is also a member of the S. aureus species from which the superantigenic enterotoxin is derived, meaning that the invader itself has helped teach us how to fight off its more virulent sibling.

The potential for superantigenic anti-cancer vaccine therapies in humans is still a ways off, but not so far that it cannot be seen. Many researchers are looking for the most effective way to balance the protection gained from superantigenic treatment against the potential harms – which include a range of autoimmune diseases (such as multiple sclerosis and other degenerative disorders). Clearly the potential exists to improve human health and longevity against one of the most prevalent causes of mortality; and with a healthy dollop of caution, the downside of superantigens can be avoided.

Pass the potato salad.



Want to know more? Full text of the cited article can be found here:

http://www.ebmonline.org/cgi/reprint/226/3/164


© A Quantum of Science / Peter Smalley, 2009
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Wednesday, May 6, 2009

Down With the Sickness

A QUANTUM OF SCIENCE

Down With the Sickness,
or why you should be glad to have the flu now (as opposed to later)


Being sick is no fun. Congestion, fever, coughing – there’s nothing good about it. Or is there? For a single human being the answer may be "no" but for large groups of humans the grim reality of a multi-stage pandemic makes beating the rush a smart strategy.

First let’s talk about the adaptive immune system. Every time your body encounters a foreign protein such as a virus, your immune system kicks in and starts the process of identifying the invader, teaching other cells how to recognize it, and systematically degrading the virus wherever it is found in the body. There are many different cells involved in this process but the big players are the special white blood cells known as T-cells, B-cells, and macrophages. Just a few words about each will be sufficient for our later discussion.

T-cells mature in the thymus (hence "T") and are responsible for several important immune activities: secretion of cytokines (small chemical triggers that turn on various parts of the immune system), destruction of infected cells, and eventual suppression of immune response (if your immune system doesn't know when to turn off it eventually attacks itself). B-cells are maintained in the bone marrow (hence "B") and work by engulfing an invader, chewing it up and displaying bits and pieces of it on the cell surface. T-cells that are already on alert for the same invader bind to the B-cell and secrete cytokines telling the B-cell to multiply and mature, after which it churns out antibodies that bind to the invader and signal its destruction. B-cells that survive this process through multiple rounds are called memory B-cells and are the repository of much of humans’ adaptive immune repertoire. Finally, macrophages ("big eaters") literally swallow viral particles and even whole bacteria, digesting them and displaying bits and pieces of them in much the same way that B-cells do, eventually recruiting T-cells to flag the invader and make it easier to find and consume. A single macrophage can consume a hundred bacteria before its own digestive enzymes break it down from the inside.

Now that we now a bit more about the major players of the immune system, let’s talk about one particular invader: the influenza virus. A virus is a small bundle of proteins that can be thought of as a kind of microscopic mosquito, with long "legs" that latch onto a target cell and a dense "body" containing its own genes for making more copies of itself. 

The influenza virus is a rough sphere or filament coated with proteins that bind to human cells using a protein called hemagglutinin (abbreviated HA) that works by binding to a particular sugar modification called sialic acid. Once bound, the cell "ingests" the virus in a special bubble called an endosome, the purpose of which is to isolate the virus and fuse the endosome with an acidic lysozome in order to degrade the virus down to harmless nuts and bolts. HA is specifically adapted to this use strategy against the cell, however; the acidic environment causes it to alter its shape and helps the virus escape the lysozome, where its RNA genes can be released directly into the cell and the copying process can begin. Once this happens, the cell cannot tell which RNA is viral and which is its own, so its cellular machinery begins turning viral RNA into protein – new copies of the virus – and the battle is effectively over for that cell.

The other major player for the influenza virus is called neuraminidase (NA), an enzyme that is critical for release of the many-times-copied virus out of the cell. The HA part of these copied viruses would like nothing better than to bind to the sialic acid in the cell wall once again, just as it did when entering the cell; in order to prevent that, NA cleaves the sialic acid off of sugar molecules in the cell membrane and helps the viral copies escape the cell and spread out to look for new cells to infect. Some of the most potent anti-influenza drugs currently available, including TamiFlu, specifically inhibit viral neuraminidase, a perfect target because humans do not possess that enzyme.

Because these two enzymes (hemagglutinin and neuraminidase) are so critical for the activity and pathogenicity of the influenza virus, virologists classify strains of influenza based on which versions of those two enzymes characterize that strain. There are 16 types of HA and 9 types of NA, meaning that there is a range of 144 individual influenza strains in this group. Strains of related pairings of these two enzymes compose the major classifications of the flu virus, such as the avian flu that was the specter of the 1990’s (H5N1) as well as the current strain of interest: H1N1 swine flu. 

H1N1 is a subtype of the Influenza A class, and is composed of eight single-stranded RNA molecules that code for eight individual proteins. Unlike many viruses, however, these eight genes are not all part of a single long string of nucleic acid; and because they are physically separate, they lend themselves well to a process called reassortment in which a cell infected by different strains of the influenza virus will package genes from different viruses together into a new, hybrid virus. By analogy, imagine the cell as a car manufacturing plant: viral proteins are assembled into cars (viruses), all of which look pretty similar. The owner’s manual (RNA genes) that goes into each car, however, might be made up of pages taken from two different models (viral strains), so when a particular car (virus) later infects a new cell, the hybrid owner's manual it comes with gives rise to an entirely new model of car (virus). Reassortment is what allows influenza viruses from different species to commingle and generate new, more pathogenic hybrid strains of the virus, as well as helping them continue to elude the best efforts of the immune system to recognize and eradicate the virus. It also makes it difficult for scientists to predict which strain of influenza should be included in this year's flu shot. The current H1N1 model is what is known as a triple reassortment - a virus carrying genes from avian, swine and human influenza strains.

So what about the H1N1 model? Scientists are concerned about the current outbreak of H1N1 that began in Mexico in March 2009 because this model is also responsible for one of the worst pandemics in human history, the 1918 "Spanish Flu" epidemic. In just two years, between 70 and 100 million humans died due to this strain of flu, largely due to a specific pathogenicity that turned the human immune system into its own worst enemy. Remember the T-cells, the immune system player that secretes cytokines and stimulates the overall immune response? The 1918 strain of H1N1 was incredibly good at causing T-cells to secrete cytokines, to such an extent that the victims were overcome by what is now termed a "cytokine storm" in which a positive feedback loop was created between cytokines and immune cells. This is why the majority of victims of the 1918 epidemic were not the very young and very old, but rather healthy adults – their immune systems were the strongest, and thus most easily turned against them.

So far the North American H1N1 shows no signs of being capable of creating a cytokine storm effect in its victims. So we’re home free, right? As it turns out, it’s not that simple. Researchers who have charted the progression of the 1918 epidemic show a peculiar three-stage pattern in which the H1N1 strain killed 5 people per thousand in July of 1918, then 25 per thousand in November of that year, and finally 12 per thousand in March 1919. The current scientific explanation of this pattern, based on viral RNA extracted from well-preserved victims who died at different stages of the epidemic, is that there was a critical mutation of the strain in just four brief months between the first and second emergence of the H1N1 virus. Normally when a virus gains in strength its victims are more likely to stay home and not spread it, but in late 1918 World War I was still raging, and it is theorized that the concentration of military personnel around the world fostered the spread of the more pathogenic mutant. Because the mutant was so lethal, it actually inhibited its own reproduction and thus the third emergence showed another new mutant, this one less pathogenic. By that time the war was over and sociological pressures that favored the spread of the virus were far reduced; there was no fourth emergence.



So what does this teach us regarding the current H1N1 outbreak? Quite a bit, actually. Our world today is much different than the world of 1918. Air travel can now spread a virus around the world literally overnight, exposing vast numbers of people in a far shorter span than was ever true in the crowded field hospitals and trenches of World War I. The speed at which a pandemic could take hold in many major cities around the world means the window for an effective response time is also much shorter. On the other hand, we now know about cytokine storms and how to prevent them using a variety of drugs like corticosteroids, free radical scavengers and TNF-alpha inhibitors. Further, powerful drugs like TamiFlu provide an effective answer to pandemics, especially among healthcare professionals who are on the front lines in any major public health threat. And most reassuringly of all, epidemiologists are well aware of the possibility of pandemic and are, if anything, overeager in their efforts to spread the word about that possibility. This may create some annoying overdramatization in the media, but considering that electronic media now encircle the globe far faster even than air travel, any increase in public awareness remains the first, best line of defense against a pandemic outbreak. 

And one more thing about the 1918 H1N1 pandemic: those who caught the earliest, least pathogenic strain of the virus were largely immune to later mutants. So if you’re a parent thinking about keeping your child out of school, or if the guy next to you at work keeps coughing in your direction, just remember that if things go bad, you’re probably better off catching that flu now when it’s in the mildest form – just in case.


For more information:

http://www.newscientist.com/article/dn17072-first-genetic-analysis-of-swine-flu-reveals-potency.html

http://www.newscientist.com/article/dn17077-flu-outbreak-the-pig-connection.html

http://www.cnn.com/video/?/video/health/2009/04/28/am.gupta.swine.flu.model.cnn


© AQOS, Peter Smalley (2009)
Distribution with attribution is appreciation