VenChar

Quorum sensing

Interesting Sciam article on bacterial communication. Yes, that's right. It turns out that if enough of them are around, they can communicate and coordinate their activities towards some shared goal.

As its moniker suggests, quorum sensing describes the ways in which bacteria determine how many of them there are in the vicinity. If enough are present (a quorum), they can get down to business or up to mischief. For instance, millions of bioluminescent bacteria might decide to emit light simultaneously so that their host, a squid, can glow--perhaps to distract predators and escape. Or salmonella bacteria might wait until their hordes have amassed before releasing a toxin to sicken their host; if the bacteria had acted as independent assassins rather than as an army, the immune system most likely would have wiped them out.

The ability to communicate and coordinate allows the bacteria to be more effective. It also suggests a medical strategy in dealing with infectious bacteria: interfere with the communication channel and you reduce the effectiveness of the bacteria.

It turns out that the bacteria release chemicals that allow neighbors to infer their presence. Now, interestingly, there seems to be a general chemical (Al-2, used across species, to identify other bacteria generally) as well as a species-specific chemical. So bacteria have the ability to distinguish "one of us" from "other". This means they can actually communicate across species!

In addition, the article suggests the intriguing implications of this finding in thinking about the evolution of multicellular organisms - such primitive communication and coordination might have been the precursor of larger scale organization.

Link via the always interesting Language Log.

Using viruses to cure cancer

Researchers at the NYU School of Medicine (link via ScienceDaily) have identified a virus carried by mosquitoes that targets tumorous cells and kills them, thereby causing the cancer to go into remission. Early testing of this virus (named Sindbis) on mice has yielded positive results.

According to the study, published in the January 2004 issue of the journal Nature Biotechnology, the Sindbis virus is effective at killing tumors in mice at every location tested--whether the growths occur under the skin, in the pancreas, in the main body cavity, or in the lungs. The amount of time and the number of injections needed to cause tumor remission varied, depending on the type of cancer, but in general mice were given injections of the virus daily. Within a month to two months later, many tumors disappeared completely.

Viruses aren't usually thought of as beneficial, but in recent years scientists have started to take advantage of the ability of viruses to infiltrate human cells, enlisting these infectious agents to treat disease. Most of these viruses have been genetically engineered so that they will not cause disease, but will infect rapidly dividing cancer cells. At least 10 different oncolytic, or cancer-killing, viruses are in early clinical trials.

Sindbis is different from these other cancer-killing viruses in that most of the others have to undergo some kind of genetic manipulation to target cancer cells, and they also have to be injected directly into tumors. The NYU School of Medicine team found that Sindbis requires no such manipulation to be effective, and it can apparently be injected anywhere into mice but still find its way through the bloodstream unscathed to the target area.

It is not known exactly why the virus prefers to bind to tumor cells. But Sindbis enters cells through a receptor for laminin, a substance that helps to glue cells together to form tissues, and tumor cells tend to over-express this receptor. Dr. Meruelo theorizes that since tumor cells are far more likely than healthy cells to have free laminin receptors on their surfaces, they are more likely to take up the virus.

Similarities between biological and computer viruses

Slashdot linked to this CNet article on the similarities between computer viruses and their biological brethren. Drawing on a botanical analaogy, the article makes the argument that the existence of "digital monocultures" increases the risk of emergence and proliferation of malware:

Computer security experts see similarities between the way a disease can devastate agricultural crops and the way a virus can attack Internet infrastructure. The reliance on one type of technology, software or protocol has created digital "monocultures," a phrase borrowed from botany that refers to ecosystems vulnerable to disastrous harm from a single disease... Just as biologists advise farmers to diversify their plantings, computer researchers believe that developers should be given tools to vary characteristics of the same program so that not all would be hobbled by a virus written for a specific version... "You only get epidemics when your target populations are alike enough that they can all get the same disease," said Dan Geer, chief scientist at information security firm Verdasys

Obvious examples of digital monocultures: predominance of Windows at the OS level, of Outlook at the application level, of SNMP at the protocol level, etc.

Also interesting is this letter Contagion on the Internet to a journal titled 'Emerging Infectious Diseases' that draws parallels between biological and computer viruses in terms of their emergence, mutation, propagation and mode of action. It also suggests ways in which computer security can learn virus control strategies from the immune system and from immunology. Here are some of the lessons:
* Good hygiene helps: periodically back up data, avoid installing suspicious software, etc.
* Avoid monocultures if at all possible: use a Mac rather than a PC, for instance. Somewhat infeasible as a strategy.
* "Pathogens do not reinvent the wheel. Virulence genes are constantly “stolen” and reused." Self-evident - as soon as a vulnerability is discovered, it should be plugged, regardless of the contagiousness or deadliness of the worm/virus that exploits it.
* R&D ideas: adaptive immunity software that learns from exposure, "“virtual vaccines” that are beneficial to the computers carrying them (e.g., by blocking preferred sites of entrance for viruses or repairing viral damage automatically) and let these “good” microbes circulate on the Internet just as malignant viruses do."

Lethal, non-contagious, vaccine-resistant viruses

More on viruses, this time the biological kind. The New Scientist reports on research into deadly variants on viruses created through genetic engineering. Basically, the virus is enhanced through the addition of a gene (the IL-4 gene) that is responsible for the production of an immuno-suppressant protein. This modification renders the virus immune to traditional vaccines and gives it a lethality rate of 100%. Also, interestingly (and mysteriously), the virus is rendered non-contagious - this means that only directly-infected individuals will succumb: so it would be possible to infect a population and reliably kill all members of the infected population without running the risk of having the disease spread outside this population. All in all, this sounds like a deadly bioterror tool in the making.

Merck alliance with Alnylam

Merck and Alnylam (a biotech startup funded by Polaris, Atlas Ventures and others) recently announced an alliance aimed at developing and bringing to market drugs using RNAi technology.

RNAi (or RNA interference) is a powerful new technique that can be used to "silence" or block the expression of specific genes in a very targeted way by introducing a species of RNA into the cell. The technique can therefore be used either as a way of discovering the function of specific genes or as a means of disabling the production of a disease-causing protein. The latter enables the creation of RNA-based drugs that can target gene-based diseases including viral diseases (related to entry of foriegn genetic material into the cell), cancers (related to gene mutations) and inflammations (related to overexpression of specific genes).

(click below to continue reading)

RNAi is a form of post-transcriptional regulation - acting after a gene has been transcribed from DNA into RNA but before the RNA has been translated into protein. During transcription, the genetic code is transferred from DNA into mRNA (messenger RNA) segments that travel out of the nucleus. The RNAi technique involves the introduction of siRNA (small interfering RNA - short pieces of double-stranded RNA whose code matches that of the corresponding mRNA) segments that can be targeted to destroy a specific mRNA corresponding to a particular gene, thereby controlling the expression of that gene.