Archive for the “Technology” Category

The term “superbug” is nothing new to the microbiology world but has only been under the spotlight for a few years, which consequently led to an increasing interest in antibiotic resistance by researchers. A superbug refers to a multidrug resistant bacterium which can therefore cause untreatable and fatal infections. This particular aspect has sparked global worry that our known antibiotics will eventually fail us.

With the interest in superbugs at its highest, scientists from Indiana University and Harvard University had their share in the investigation, using multi-colored dyes called fluorescent D-amino acids (FDAAs), aka rainbow dyes, which turned out to be just as cheerful to the researchers as actual rainbows. These dyes enabled them to visualize the detailed process of cell division, particularly the movement of the filaments FtsZ and FtsA (cytoskeletal polymers and prokaryotic homologs of the protein tubulin) that determine the site of cell division by driving peptidoglycan synthesizing enzymes to the correct sites. Cytokinesis starts with the formation of a Z-ring at the site of cell division, and both FtsZ and FtsA are required for this process.

When visualized, the filaments appeared to move in circular concentric rings, in a movement which was described as “treadmilling” in which the FtsZ filament loses a molecule at one end and gains a molecule at the other end, resulting in the circular motion. With the guidance of these rings, peptidoglycan was shown to begin forming a septum dividing the cell.

A more detailed aspect of the FtsZ and FtsA system is the lack of any means to convert chemical energy into mechanical force. However, the rearrangement is primarily dependent on FtsZ polymerization dynamics under the influence of conflicting regulation by FtsA, first, by promoting FtsZ assembly and second, by inhibiting FtsZ network organization. The result of this regulation is the formation of higher ordered structures by FtsZ as tubules, circles and sheets.

These findings might be a magnificent aid in combating superbugs by visualizing so accurately their division and offering a broader comprehension of their mechanisms.

Finally, if you ever find yourself anxious about superbugs, just remember: there always comes a RAINBOW after a rainy day.


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Though risky, transplants are crucial treatment interventions for many patients.They can save lives of cancer patients, others with severely ill organs and recently there are trials to make them a mainstream treatment for autoimmune disease patients ( i’ve just read an article about that topic and i’d really love to write about it soon too).

But the major problem with transplants, other than the agonizing wait for the right donor on endless lists for sometimes many years, is that when things go wrong with transplants, the patient’s life becomes at mortal risk. Almost 40% of transplant patients will show rejection episodes within the first year after the operation. The detection of these immunological reactions are usually so late, and the only solution will be to flush the patient’s system with huge doses of immunosuppressive drugs that are toxic themselves and can have debilitating effects on cancer patients for instance. Also, to be able to detect rejection reactions, the doctors should take biopsies of the new organ, a process that can cause damage to the organ itself, let alone the stress and the already fragile patient condition. Transplant patients have to undergo exploratory biopsies monthly for one year after the operation!!!!!

Will these risky, life-saving procedures be safer in the future?

Early detection of these reactions was an interesting topic and a field of research for the cardiologist Hannah Valantine of Stanford University School of Medicine in Palo Alto, California. In 2009, she devised a new test that detects the immunological changes in a transplant patient in an episode of rejection. The test, called AlloMap, became the first of its kind to be approved by the FDA for use in the detection of heart transplant rejections. Yet, it failed to detect the rejections early in about half the patients.This, of course, didn’t satisfy Valantine.

Along with biophysicist Stephen Quake of Stanford, they came out with a much more sensitive test. The idea was that DNA from the new organ constitutes around 1% of the free DNA in blood of transplant patients. This DNA is foreign from the DNA of the patient and using her test, it can be very sensitively detected, despite the fact that it is circulating in minute amounts. To validate their test, they used it on stored plasma samples from transplant patients that later showed rejection signs. It was found that the amounts of the rejected organ’s DNA in such episodes are elevated soon after the surgery and constitutes around 3% of the free DNA in plasma, and of course, will be much elevated later, in the peak of the episode. They reported the results in The Proceedings of National Academy of Sciences.

The good thing about this test, besides its high sensitivity, is that it is much less invasive than a biopsy, and the biopsy will not be needed except for confirmation, in case the test is positive and the DNA % is higher than normal. Also, early detection will allow doctors to use much smaller doses of immunosuppressives to control the case and therefore, less side effects will be experienced. Valantine is a cardiologist, but believes the test can be used with other types of transplanted organs, other than hearts.

Source: ScienceMag



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Infections in the teeth implants are dreaded, running a high risk of potentially affecting the jaw bones. It is actually not that uncommon. The overall number of performed teeth implantations in the US and Europe has doubled over the last decade, yet studies show that 10 percent of the implants are associated with problems, usually in the first year directly after the operation. To prevent any further deterioration, the implants sometimes have to be removed.

New methods are now being developed by researchers in the University of Zurich to keep inflammation-causing bacteria at bay. In their PLoS ONE article, they present their materials and methods, which have successfully eliminated 99% of the microbes after a 15-minute electrical treatment.

Conventional treatment methods of this sort of inflammation depend on the utilization of topical antibiotics, which is surely a burden for the patient. The aim of the study was to develop a non-invasive approach to efficiently fight off the bacteria, or, as the researchers phrase it in their paper, to develop “an in-situ decontamination of the dental implants”.

The whole idea is based on the process of water treatment, where sterile water is produced through electrolysis. In order to simulate the conditions in the jaw, an Escherichia coli bacterial film was coated onto the titanium implants, which were impregnated in a gelatinous preparation. In the experimental design, one implant functioned as the cathode and the other as the anode. The implants were subjected to a 15-minute-long electrical treatment, of an intensity ranging between 0 and 10 Milliampere. This artificially generated electrical field caused the hydroxyl ions of the water molecules to migrate to the cathode, and thus raising the pH. A color change of the indicators, used in the gelatin, prove that an alkaline environment predominates at the cathode. On the other hand, the pH value drops at the anode, forming an acidic milieu.

The numerous experimental models with various electrical intensities show that in cases, where an acidic ambience was produced around the implants, 99% of the bacteria died off after a 15-minute treatment. Therefore, the patient implants in the future will take up the role of the anode. A clip at the lip will be used as a cathode.

What at first glance might seem as a torture mechanism is in reality completely harmless. The minute amount of Milliampere, which is sufficient to conquer the bacteria, is hardly even perceived by the patient and would tops cause a mild muscle twitching.




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If you have ever been one of the unlucky ones waiting for a cancer diagnosis biopsy, or having a friend or a relative undergoing the process, then you must know how the wait is nerve wrecking. The standard procedure is using a biopsy needle to extract some cells of the tissue suspected for cancer, and then waiting for about a week, until the results come out. To make matters worse, results can sometimes be inconclusive or 100% correct.

Simple smartphone applications might be able to rapidly diagnose cancer in the future

Fortunately, a group of scientists at Massachusetts General Hospital (MGH) in Boston, were able to develop a new technology, that is much more rapid and almost 100% accurate in the diagnosis process. They developed a small NMR device (detects compounds by the mode of oscillation of their nuclei in a magnetic field) the size of about a coffee cup, and they were also able to synthesize magnetic Nanoparticles, which stick to certain tumor specific proteins. So now all I have to do, is head to the clinic, have the needle biopsy performed and the cells taken. Then they are mixed with the magnetic Nanoparticles and the results are taken from the small NMR device and read using a simple smartphone application.

This technique was used in the first trial on 50 patients, taking less than an hour to diagnose each. Also, as the device can detect 9 tumor associated proteins, combining the results for 4 of these gave accurate results in 48 out of the 50 patients. In another trial, the accuracy was 100% in the 20 patients tested. The conventional tests’ average accuracy is 74-84 %.

This new technology will also cut down on the cost of repeat biopsies, which can be very expensive, and scientists hope it will have many other applications as well, like patient cancer follow-up, through quantitative analysis of the tumor associated proteins. Maybe the biopsy will not be needed in the future and a simple blood test will also do….

Source: Science/AAAS

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Man or Machine? Bioinformaticians at McGill university are betting on man. They want to put, what was previously wasted, time on the internet into use. Thus, Phylo was created. That is the name of an online interactive game, aiming to solve the problem of multiple sequence alignments, one that has been agonizing researchers for some time now. The human mind is evolved in a way, that even computers supposedly can’t beat. We are capable of recognizing certain patterns and forming interrelations between them, a skill which numerous lines of codes can not easily accomplish.

So what to do? Once you open the link, go ahead and sign up, although it is possible to play as a guest. But hey, if I am taking time off to contribute to science, I want to be able to brag about it later on. 🙂 The creators of the game have formed a very comprehensive tutorial, explaining how the game works. They use down-to-earth terms and comparisons to simplify matters, so people from all walks of life can jump in as well.

The coloured blocks: Those symbolize the nucleotides. Correspondingly, there are four of them: Orange, Green, Blue, Purple. I wasn’t able to find exactly which colour codes for which nucleotide, something which particularly intrigued me, since purple blocks were scanty in my alignment.

Aim of the game: Our job is to align these blocks, as best as possible, so that the blocks’ colour in the first line are matching those in the second line. Matching blocks gives you a score of 1 point and mismatched ones deduct 1 point. This should be preferably done WITHOUT having to create gaps. They point out that gaps represent the mutations, which the sequences have incurred during evolution. In the easier stages, the sequences are provided on two lines, representing two different species. As it gets more difficult, more lines are provided and related together through a mini-phylogenetic tree, to allow you to pinpoint your priorities. Once you have reached the same score a computer had previously provided “par”, a star will blink to indicate that you are ready to move on, as the alignments are stored in a database for future use.

My experience: I stumbled upon a feature, where you can choose the type of sequences you want to work with. They are arranged according to disease, level ID, or simply random. I chose the blood and immune system disorders and was granted sequences, related to essential thrombocytopenia.

Statistics: At the end, I was provided with the following astonishing numbers. So far, 5344 users have submitted 70196 alignments for 2137 different levels. Personally, I think this number is quite surprising, since that many people are joining in since only November 29th, the date of the official launch.

Interested in more: In the “about” page, the following sentence is provided: “For more information about any one of these topics, click here“.

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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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