Gene Therapy - The Walton

Here is a copy of the article I did for the Spring Edition of The Walton. You can read more here.

Over the past year in Ireland, there has been much excitement with regards to gene therapy, with a couple of potentially ground-breaking developments occurring. So let’s pause and look at what gene therapy is, how it is currently being used and perhaps look towards the future.

Gene Therapy is an umbrella term for many types of treatments. Ultimately it involves changing, fixing or replacing genes that are defective or mutated in someone’s cell such that the cells can function again. Remember that genes represent the code by which just about everything that happens in the body follows; an instruction manual for all the processes of the body. So if some of that code is missing, or incorrect, the body functions won’t work properly. Examples of such diseases would be cystic fibrosis, Huntington’s disease, Sickle-cell anaemia and a huge range of immunity disorders. Even cancer is caused by genetic mutations. So if there was a way to fix the code, repair it in some way, this would have huge benefits to thousands of people.

One way to fix a broken code involves using viruses. This may sound alarming, but it is actually quite effectively used. The basic principal revolves around using a harmless virus i.e. one that will only infect certain cells and won’t replicate, to carry the corrected gene code to cells. Viruses do this anyway – when they infect a person, they are often actually infecting the cells, their own gene codes being incorporated into the host cell. Usually this is extremely detrimental, and cell death ensues, but by controlling what gene sequences are included in the virus, you can potentially tailor what happens when a virus infects a cell.

The diagram shown here shows a virus (called a vector because it is basically a transport vehicle) attaching to a cell. It is an adenovirus vector. Adenovirus is associated with respiratory, intestinal, and eye infections in humans (especially the common cold). As shown in the diagram, the virus is taken into the cell and then travels to the nucleus (the pink thing). It attaches to the surface of the nucleus and injects the DNA into to core of the nucleus. Remember that the nucleus of the cell is where we hold all our own genetic material.

The DNA type molecule in this case isn’t a double-stranded molecule, but instead is a single strand, and can thus be read by the cells replication molecules. These molecules are called messenger RNA, and they are part of the process by which new proteins are formed. Thus, if the correct DNA is present, the correct proteins will be made, and so any dysfunction that occurred before may be rectified.

There are two methods to introduce the genetic material into the patient. Ex vivo gene therapy involves removing cells from an individual’s body, modifying them to include the correct genetic material using a vector, and then transferring these cells back into the patient’s body. In Vivo gene therapy involves injecting the viral vector directly into the patient, in the hopes that the virus with infect and ‘fix’ the damaged cells. Both methods have seen varying levels of success.

Cystic fibrosis is a genetic disease which is particularly common in Ireland and results in a build-up of mucous in the lungs of affected individuals. Vital research in University College Cork is currently underway to cure cystic fibrosis. The central tenet to this research involves creating breaks in both strands of the DNA at targeted sites. This process is enabled by the use of Zinc-finger nucleases which are specially designed DNA-binding proteins, with high specificity.

By intentionally creating a break in the DNA strands, you can induce homologous recombination (a time of genetic repair) between the broken strands. This can allow you to include the correct sequence in the genome at that point. More in-depth analysis of the current status of research, both here and in the UK will be presented in next issue of Walton Magazine.

Similarly, a novel treatment for bacterial infection of Pseudomonas aeruginosa in cystic fibrosis patients is also seeing some success, also using gene therapy. The research was carried out the Alimentary Pharmabiotic Centre [APC], a Science Foundation Ireland funded research centre based in UCC, Teagasc Moorepark Research Centre and CIT.

The researchers, led by Professor Colin Hill in UCC and Professor Paul Ross in Teagasc, took advantage of a method called phage therapy. This involves identifying and characterising bacterial viruses which can attack and kill Pseudomonas aeruginosa within minutes of initial contact. One of the advantages of phage therapy is that any viruses which ‘find’ a target multiply at the target site, generating more viruses and amplifying the therapeutic effect. This research is paving the way for the development of new treatments for Pseudomonas infections in cystic fibrosis patients.

So with two keen and different ways of tackling the disease, either by treating the infections that occur or by curing the disease itself, it goes without saying that there is bound to be some new revelation this year. We have barely scratched the iceberg in this article with all research for other diseases that could be treated, so maybe that’s for the next time!

New Blog

Here is another blog I write: cleverbugblog.wordpress.com

Pigs, Ferrets and Flu

And so the panic may begin again. 

A new flu virus found in pigs in Korea may have the potential to infect humans. We aren’t that similar to pigs in our genes, but we are pretty close to ferrets… and they are getting sick too. And the virus grew in human tissue in the lap.

It is interesting to note, and I did not know this, is that ferrets are the favoured proxy for humans in flu research.

 “That makes it a bit scary,” says Robert Webster, a virologist at St. Jude Children’s Research Hospital in Memphis, who co-wrote the research paper. So far, the virus has not been found in people, but “if it is in the pig, beware,” he says.

All that has to happen is a bit of genetic mixing or reassortment in the virus for it to start infecting us. Unfortunately, pigs are known to be perfect mixing vessels for the virus, so this is a major cause for concern. H1N1 (back in 2009 – remember?!) made ferrets sick.

Many different mutations could occur, from changing the proteins on the virus’s outer surface (which affects adhesion to our respiratory cells) to changing other proteins which are involved in making them more infectious.

But don’t panic, just because our weasely friends get sick, doesn’t mean we will. Yet. *insert dramatic music here*

Article Source: www.sciencenews.org

So What is Software Licensing, Anyway?

So I started a new job working in software licensing - I had no idea what I was getting myself into. Little did I know, that this is something we are all involved in, and it pays to know a little more about what it's all about. Sure, it's not quite science, but unless you are careful you can end up getting into trouble. So here it is - what software licensing is all about!

People often seem to think that software is a commodity – something you buy from a retailer which you then own and use. But in actual fact, with software, you license, not purchase it. Why? Well, when you license the software, the primary value comes not from an object (such as the disk it is stored on) but instead from the knowledge of the people who wrote the software – the ‘cleverness’, if you like. You can’t own that knowledge, you merely acquire a limited right to use it. Put simply, software is intellectual property.

It’s tricky to define or identify the value of intellectual property and thus, such things are copyrighted (copyrights, trademarks, and patents). This allows whoever owns the material, in this case, software to define who can access and use their property, protecting it from unauthorized use. This is in an attempt to define the value of the software.

In this line, a software license provides the legal right to install, use, access, display, run, or otherwise interact with a software program. This doesn’t always include right to media, manuals, or support. Remember checking the ‘I agree’ box whenever you install something? That is you agreeing to the terms of use of the software.

If you breech these terms and conditions, you are in violation of the law and can run into trouble.

So yea, it's important. I may start blogging about more technologically oriented things from now on... maybe!

Licensing Software

It has been far too long, and I promise to find some newsy item to write on, but for now, check out this new blog that I am managing... http://wp.me/p11yyP-4W (its all about what software licencing, which is actually really important (it's news to me!)

enjoy

Cloudy Computing?

Being asked to define or explain cloud computing is like being asked to pet Schrodinger’s cat: you just can’t. Not easily anyway. The name suggests as much, but is it really that vague? A buzzword made so popular recently with the likes of iCloud, Dropbox and Microsoft Sharepoint, is it just that, a buzzword? Or is there something more? With headlines littering the news daily, and with every company beginning to carry the tagline ‘We use cloud’, some myths need to be dispelled and facts shared.

Technically speaking, cloud computing is the practice of using a network of remote servers or computers hosted on the internet to store, manage and process data. This is usually managed by a third party company, (a vendor) who is responsible for everything; management, administration and trouble shooting. Often, these servers (or hosting devices) are located in various locations. 

Often, companies offer either a dedicated or shared server agreement. If dedicated, only your information is stored on a server, which is more expensive. Shared is the converse of this. Clearly, if you are in a shared environment you run the risk that others might have access to your data or bring down the server completely. Also, location wise, it is rare that you know exactly where the data you are storing is. This has become an all-to-apparent problem with shutting down of MegaUpload.



Traditionally, these activities would be done using a local server or personal computer. So any data you are saving or accessing is stored locally, on your premises. In large businesses, this would typically involve a large room filled with servers in the basement of the building, to which each staff computer has access. For personal users, it just entails using hard disks or simply storing data on your PC or laptop. So, most websites and server-based applications ran on particular computers and servers. What is different with the cloud is that the cloud utilizes the resources from the computers as a collective virtual computer. Applications can run independently from particular computer or server configurations. With broadband internet, the need to have the software run on your computer or on a company’s site is becoming less and less essential. 


A lot of the software that people use nowadays are completely web-based. The cloud takes advantage of that to bring it to the next level. Thus, the hardware is less important.

A summary of what is being offered by vendors is as follows. The most basic is called Infrastructure-as-a-Service (IaaS), which is just servers ‘in the cloud’. This is mostly for tech companies who just want access to computing power but don’t want to be responsible for installing or maintaining it.


The next tier is Platform-as-a-Service (Paas) which is a cloud-based platform that companies can use to develop their custom applications or write software that integrates with existing applications. These environments are often equipped with software technologies like Jave, Python and Ruby on Rails (coding languages) to allow customers to start writing code quickly. The vendor then hosts the code and makes it widely available. This is often used by companies looking to outsource a piece of their infrastructure.


Lastly is Software-as-a-Service (SaaS), which is the largest and most mature part of the cloud. It is an application or suite of applications that sits in the cloud instead of on the user’s hard drive or in a data centre. One of the earliest SaaS successes was Salesforce.com’s customer relationship management software. It was an ideal alternative to on-premise CRM systems when it was launched in 2000. Further developments now include productivity and collaboration software such as Google Apps, Microsoft Office 365 among other things.

Have you noticed how much more dynamic webpages are? This is somewhat due to the development of Html5, which allows everything you are browsing to be cached (temporarily stored) to the cloud (e.g. Google server) which means you have less caching on your computer, taking up less space, and thus, ultimately less processing power. This means instant loading web pages, which are more dynamic. It also allows companies to give their users/customers more scope in business world online; just another aspect of internet progression.

Other less technical benefits of the cloud include a significant reduction in cost. In fact, previously, companies had to fork out excessive budgets to manage servers and server management teams, whereas now, it can all be done by a third party, who often offer ‘pay as you use’ contracts, marking the end of user organization demand. Companies no longer have to manage the servers (they break down often), they don’t have to have an IT staff, and basically, the old headache has been alleviated’. Somewhat. Maybe.


It also offers a collaborative atmosphere – take Microsoft Sharepoint, for example, which allows transfer and access of documents between groups. And it is being given out like candy to companies at the moment. Also, some smaller companies can use cloud analytic services, as they have access to big data that has been generated by other companies, and thus, can analyze their customers, or employees, or anything they want to. Another attraction is that access is given to cutting edge technology, with no need for the risk of ownership.

The problems that are starting to come out of the woodwork are things like data ownership, security and contract obligations. Data ownership is an interesting one. You, the client, have asked a third party to look after your files and information. They have it stored on their servers, which is accessed using their applications and portals.

Megaupload.com was a file hosting service, run by a Hong Kong-based company. The site was shut down by the U.S. Justice Department on January 19^th following the indictment and arrests of the owners in New Zealand, who are charged with copyright infringement. They argue that they just offer a service, and that it is not their responsibility that the users upload content (onto the cloud) that is illegal.

So who takes the fall? The users cannot be easily tracked, and the owners now face the charges. This is an important thing to consider about the cloud. That said, it is only if the content being stored is illegal in the country it is being stored in, that problems will occur. Who polices this, and how does a vendor or client know what the law is of the country that the servers are based in? In effect, the cloud is breaking the usual boundaries, making it exceedingly difficult for law-makers to predict.

Other minor issues include integrating new technologies with existing legacy systems in established companies, and thus issues with compatibility can arise. But usually, whole aspects of a process is outsourced to the cloud, so this may not actually be a particular problem. One way of looking at cloud computing, is as the industrialization of enterprise technology. This suggests a decrease in jobs, especially in areas that manage data centers.

So it seems that the cloud is not quite as ‘wafty’ as it would at first appear.  Also, considering that this technology, although newly revolutionized and popularized, is not actually new, it is most likely here to stay.

Marijuana and Memory

This time of year, memory is on everybody’s minds. With late night cramming and early morning panicking – ‘tis the season of exams. So with all this stress you may want dabble with various calming chemicals – rescue remedy, copious amounts of tea and cigarettes, perhaps all with dash of alcohol, and maybe a shneaky shmoke, but is that actually a good idea?

Mary-jane, gunja, weed, pot, whatever you call it, research shows that marjiuana significantly impairs working memory – the memory that you would need to use to cram in those last minute facts about Chaucer or Freud or Boyle. But until recently, it was not clear exactly what the source of the memory lapses were.

The major psuchoactive ingredient (THC) impairs memory independently of its direct effects on neurons. The side effects stem instead from the drug's action on astroglia, which are passive support cells to neurons in the brain supporting, protecting and feeding neurons. Support cells typically help the propagation of electrical signals along neural cells.

It was actually thought that that was all that the astroglial cells do – support. But now evidence has accumulated that suggests these cells play a more active role in forging connections between one neuron and another.

The researchers didn't set out to discover how marijuana causes its cognitive side effects. Rather, they wanted to understand the receptors found on the cells. Mice lacking these receptors on the astroglial cells are protected from impairments to spatial working memory that would usually follow a dose of THC. These receptors are found on other neurons as well, yet if the receptors are lacking in only in neurons, then the mice still suffer the memory problems.

"The study shows that one of the most common effects of cannabinoid intoxication is due to activation of astroglial receptors," the researchers wrote.

Given that different cell types express different variants of that receptor, there might be a way to therapeutically activate the receptors on neurons while leaving the astroglial cells out. Thus, these findings offer important new insight into the brain and raise the possibility that marijuana's benefits for the treatment of pain, seizures and other ailments might someday be attained without hurting memory, the researchers say.

The findings further suggest that astrocytes might be playing unexpected roles in other forms of memory in addition to spatial working memory, Zhang said. The researchers hope to explore the activities natural endocannabinoids (things that are like cannabis), which naturally trigger the receptors, on astroglial and other cells. The endocannabinoid system is involved in appetite, pain, mood, memory and many other functions. "Just about any physiological function you can think of in the body, it's likely at some point endocannabinoids are involved," Marsicano said.

And that means an understanding of how those natural signalling molecules act on astroglial and other cells could have a real impact. For instance, Zhang said, "we may find a way to deal with working memory problems in Alzheimer's."

But back to the marijuana effects – it is clear that this drug triggers memory impairment, so perhaps it would be best to stave off the stuff for a while, and give your astroglial cells a rest!

Science Spin- Cloud Computing

Check this out: http://www.sciencespin.com/, especially the February issue, page 22!

Mushrooms Don't Make You Grow...

When Timothy Leary (renowned psychologist) advised his generation to “turn on” by taking psychedelic drugs, he got it all wrong. The truth is, turning off parts of the brain may be the real secret to expanding your mind, a new study of hallucinogenic mushrooms finds.

(A version of this article appeared in Motley, UCC's official magazine in the Feb Issue, 2012)

The study involved 15 people who had previous experiences taking hallucinogens. These ‘lucky’ volunteers were then injected with psilocybin which is the ingredient responsible for mind trips thanks to mushrooms. The effect was immediate, peaking in just minutes and lasting for about an hour.

Some described the experience as ‘dissolving’, while another said they were ‘kneeling at the foot of God’. Their brains were scanned before and after the trips. It was shown that there were decreases in the amount of blood flowing through parts of their brains. The reduction of brain activity was seen in particular in the thalamus.

This reduction in action is not what would be expected. For years, people have thought that hallucinogens ‘turn-on’ brain activity. Even I, with my limited and naive knowledge perused that these kinds of drugs were activating other pathways in the brain. Stimulation, not depression. Stimulation would more likely explain the kaleidoscopic hallucinations often experienced by magic mushroom users.

So what is going on?

It may be suppressing core regions that help to coordinate and control the brain that has deeper, more philosophical consequences. It fits with how Aldous Huxley described the effects of mescaline — a hallucinogen that, in his words, flung wide the “doors of perception.”

So, decreased activity in certain parts of the brain may allow for a more unconstrained conscious experience, in a way lifting the ‘filters that are at play in terms of limiting our perception of reality’ according to Matthew Johnson, an experimental psychologist at Johns Hopkins University in Baltimore.

Scientists believe that the highly interconnected brain that we all have is essential for maintaining a person’s sense of self. So, by turning off some of these networks, it may be possible to treat certain psychological conditions by opening the brain to new ways of thinking, researchers hope.

Several studies have shown that psilocybin can change people’s attitudes for the better and may be useful for treating depression, a condition linked to too much activity in the normal network pathways of the brain.

“Chemically switching off might have very profound beneficial effects,” says Nutt, who suspects that psilocybin could also be useful for treating obsessive-compulsive disorder. “It may help people completely locked into a mindset that drives their lives.”

I have to add though that using psychedelic drugs is dangerous. Many people argue that taking mushrooms is safer than any of the other hallucinogens, and that could be the case, but one has to remember that altering your perception of reality can have lasting effects e.g persisting anxiety, psychological disturbances or even ‘post-traumatic stress disorder’.

It is seriously messing with your mind. So please, don’t use this article as an excuse to experiment. Studies like this are done to try and find ways to cure disorders in a controlled manner. Not to reason that it’s ok for drug misuse.

Dublin - City of Science 2012

 This is all gonna be pretty exciting - stay tuned for more news concerning this...

'Dublin has been chosen to host Europe’s largest science conference, ESOF 2012 (Euroscience Open Forum), from 11-15 July, 2012. To celebrate this prestigious, international event in Dublin, the City of Science 2012, an innovative science themed festival will run throughout the year across the island of Ireland combining the best of Irish culture, arts and science.'

For now, check out: http://www.dublinscience2012.ie/

Its the power of... MUSIC!

I always knew that there was power in music, but this blows my mind!

A new type of miniature medical sensor that is implanted in the body can be powered by a driving bass rhythm. The sensor would be used to measure pressure changes in parts of the body, helping those with aneurisms or incontinence due to paralysis. 


The way that it works is thus: There is a tiny vibrating cantilever at the heart of the sensor. A cantilever is a thin beam attached at one end, kind of like a diving board. Music within a certain range, between 200 and 500 hertz has been found to be able to cause this little lever to vibrate. These vibrations generate electricity which can store a charge in a capacitor.

Babak Ziai (what a name, right?!), a professor of electrical and computer engineering and biomedical engineering said, ‘The music reaches the correct frequency only at certain times, for example, when there is a strong bass component.’

What’s really cool is that the acoustic energy can bass through body tissue. Thus if the sensor is implanted in the body, it can be recharged.

It’s a clever little device such that when the frequency falls outside of the proper range, the cantilever stops vibrating, automatically sending the electrical charge to the sensor, which then takes a pressure reading. This data is then transmitted as radio signals. Because frequencies continually change in songs, the sensor can be switch between storing charge and transmitting data.

"You would only need to do this for a couple of minutes every hour or so to monitor either blood pressure or pressure of urine in the bladder," Ziaie said. "It doesn't take long to do the measurement."

It is possible to play tones within the frequency range instead of music, but that would be boring. The researchers experimented with a few types of music: rap, blues, jazz and rock. Rap turned out to be the best as it contains a lot of bass! 

To reiterate, this sensor can measure pressure in the urinary bladder on in the blood vessel damaged by an aneurysm. When pressure in the bladder rises, the spinal cord can be stimulated to control urine flow. It can also be used as a diagnostic tool instead of a painful catheter. 

These exciting findings will be presented in the upcoming IEEE MEMS conference in a few days in Paris, and the patent is pending.

My computer should yawn too...

Getting too hot? Sitting by the fire for too long? Try yawning... apparently...


According to researchers from Yale University and the University of Maryland, YAWNING may act to cool the brain when it gets too hot. Yawning opes up the sinuses located to the left and right of the nose, so that letting air into these places would reduce brain temperature.

Researchers argue that yawining is a symptom of conditions that cause an increase in the brain or core temperature. It is true that fits of yawning have been noticed to precede epileptic seisures and migraines.

Studies done in mice do demonstrate that the brains of mice increased in temperature just before a yawn and decreased directly after. A potential cause for this is that the mucus in the sinuses may constantly evaporate, and thus cool the surrounding blood vessels and cerebrospinal fluid. Bringing in new air into the sinues would speed up this process, cooling the brain.

Now I am going to refues to stifle that yawn, whether it happens in class, or in a job interview... or when meeting the Queen. I do not want to overheat my brain.

To Sleep or to Not Sleep?!

I dont know why so many of these articles have to do with sleep patterns - I must be lacking in those REM cycles. Its not surprising though, two jobs and a full-time masters would keep anyone running in circles. Ah, but I do love that feeling, just when you are dozing off, when you no longer think...well here is something you can think of when you can't sleep!

Never let the sun go down on your anger! This biblical warning may actually have a scientific founding according to new research. Sleeping apparently seers bad feeling into the brain, while be awake can take the emotional edge off. The study appeared in a report in the Jan 18 Journal of Neuroscience. It was known that sleep locks in memories - studying the second before you go to sleep and when you wake up fortifies long-term memory. But scientists didn't know whether feelings accompanying painful memories are locked in too. This question is of particular importance to people who suffer post-traumatic stress disorder.

“If we really want to know if this is relevant to trauma survivors, then we need to know if sleep not just changes the memory, but if it changes how you feel about it if you experience it again,” says study coauthor Rebecca Spencer of the University of Massachusetts Amherst.

In the study, Spencer and her colleagues showed participants pictures of neutral scenes, such as a street, or negative scenes, such as an upsetting car crash, to 106 young adults. Participants then rated the emotion inspired by the image on a one-to-nine scale ranging from sad to happy. After that, they were either sent to bed for a full night’s sleep or asked to stay awake for 12 hours. The researchers then retested the participants by showing some of the same pictures mixed in with new images. 

The results were as expected. The participant who had slept were better at remembering which images they had seen the day before. But it wasn't only the memory that remained: sleepers held on tighter to their feelings. Sadness scores given by people who stayed awake tended to weaker in the second session.

These results are to preliminary to base any reccomendations about how much or little sleep should be had after experiencing trauma. So more needs to be researched.

It should be noted that sleep deprivation is actually known to increase stress, so while the bad feeling may be seered into the brain, the temporary effects can be detrimental. “In most cases, it’s better to sleep than to not sleep,” Cognitive neuroscientist Jessica Payne of the University of Notre Dame in Indiana states.

But wait! There are conflicting study results: a study published in December that found that a night of sleep takes the emotional edge off unpleasant experiences — what some scientists call overnight therapy. That study, led by Matthew Walker of the University of California, Berkeley, used different methods and measurements, which may be responsible for the seemingly opposite findings, says neuroscientist Penny Lewis of the University of Manchester in England.

Ah this often happens when you did deeper - there are so few facts in Science! You haven't learnt anything new really, except that you musn't take things at their face value, I started this thinking there was a new discovery to be made - but the case is still open. Watch this space. If you are pained by this, the maybe you should stay awake all night so the pain doesn't imprint itself. Or not, cos it might be better if you slept... AHHHHH!

Who knows the nose?

Apparently, according to research done at the Weizmann Institute (in Israel), how we rate a certain smells (i.e. whether they are pleasant or not) has to do with an organizing principle for the way we smell. At a deeper level, certain nerves respond to particular scents and it is this connection that allowed researchers to tell whether their test subject found a smell pleasant or unpleasant.

This kind of organisation is seen in other sensory organs. For example, in the eye, the receptors are arranged to map out visual coordinates. The inner ear, as well, is set up based on tonal scale. But until now, the organizational principle for a sense of smell has remained a mystery. 

                                                                                                   

As scientists began delving into this conundrum, they began noticing that there was a connection between the chemical structure of an odour molecule and its place on the ‘pleasantness scale’. Professor Noam Sobel figured that maybe the smell receptors in the nose were arranged on the nasal membrane according to this scale. Note that this idea goes against what was thought previously, which was that the various receptors were mixed, distributed evenly, but randomly on the membrane.

Using lots of tiny electrodes attached to many (presumably very patient) volunteers’ noses, scientists found that the strength of response from each nerve varied from place to place in reaction to different smells. Further investigation showed that the intensity of any reaction was linked to the odour’s place on the pleasantness scale. Therefore, their hypothesis seems correct.

'We uncovered a clear correlation between the pattern of nerve reaction to various smells and the pleasantness of those smells. As in sight and hearing, the receptors for our sense of smell are spatially organized in a way that reflects the nature of the sensory experience,' says Sobel. This doesn’t mean that individuals may experience smells differently, but instead suggests that cultural context and personal experiences may cause a certain amount of reorganization in smell perception over a person’s lifetime.

I knew that my obsession with coriander leaf had something to do with having Indian neighbours when growing up!

Credits:

Long Nose Fish Fine Art Print - Sara Raber

New Scientist

Science Daily

Double-Bagging?

It's been a while since I posted here. This article interested me and I wanted people to know about the study. I’m from South Africa where just under 20% of the population is living with HIV/Aids. This is all news to me!

Apparently using hormonal contraception (i.e. the pill or Depo injection) are at double the risk of getting infected with HIV. On top of that, HIV-infected women who use hormonal contraception are twice more likely to five their HIV to their uninfected partners.

Acquired immune deficiency syndrome (AIDS) is a disease of the human immune system caused by the human immunodeficiency virus (HIV). So someone can be infected with the virus, (HIV-positive) and then only later develop AIDS.

This study, run by the University of Washington is probably the first study to the risk to male
partners of HIV-infected woman using contraception, according a prof. of global health at the international clinical research centre. It examined almost 3,800 couples in Africa. Each couple had one partner with HIV infection, and the other without. I’m amazed they could find people willing to participate in this sort of study, never to mind couples who knew that their partner was HIV-positive! Ultimately, the statistics showed that using either the pill or the depo injection doubled an uninfected woman’s chances of becoming infected. The same is true for women who are infected – they are twice as likely to transmit their HIV to their partners.

"Women should be counseled about potentially increased risk of HIV acquisition and transmission with hormonal contraception, particularly injectable methods, and about the importance of dual protection with condoms to decrease HIV risk," said Renee Heffron a key author of the study.

The findings of this study were presenting in July in Rom at the meeting of the International AIDS Society. According to UNAIDS estimats, there are 2.2million people living with HIV/AIDS in Europe.

So if you aren’t into abstinence, and if you are sleeping around, double-bagging is the way to go!

Disclaimer: Abstinence is the safest form of contraception.

Secret Life of a Solar Flare

I watched The Knowing last night, and despite negative reviews, I actually quite liked it. *SPOILER ALERT*. It ends with the entire planet Earth being incinerated by a gigantic solar flare. What really interested me was that my weekly NASA Science News email that I got today was about solar flares. So instead of writing a big spiel dissecting the workings of the sun, I thought I would instead include this sweet little video. I would recommend watching just before bed time…

Thanks to NASA Science News

Its definitely a lazy blog entry, but it's back to school time and it's sunny... days like these when little asteroids are being burnt to bits in our outer atmosphere...

Breakfast on Planet Tiffany's?

While travelling recently, I made the mistake of wandering into Tiffany's in the airport. I was quite tempted to have breakfast, but resisted the urge. I have always liked diamonds, but those sparkling, glittering magnificent stones, set so perfectly were something else - I am in love. I just hope my boyfriend doesn't mind. I think I now know their secret...

An international research team with scientists from Australia, Germany, Italy, the UK, and the United States have discovered a pulsar with an interesting neighbour. Pulsars are highly magnetized, rotating neutron starts that emit a pulsing beam of radiation. They are formed when the core of a massive star is compressed during a supernova (a huge explosion), which collapses into a neutron star. Most pulsars have no companions whatsoever, but this one appears to have a very special one.

The orbiting neighbour has a mass close to that of Jupiter and appears to be a remnant of a carbon- and oxygen-rich white dwarf star that measures no more than 55,000 kilometers across. It's make-up and mass mean that it may have a very interesting quality.

''It's highly speculative, but if you shine a light on it, I can't see any reason why it wouldn't sparkle like a diamond," says Travis Metcalfe of the National Center for Atmospheric Research in Boulder, Colorado, talking to New Scientist.

This find is very rare considering the nature of pulsars. Also, a planet that dense is also a rare find.

Some interesting facts...

On Earth, diamonds are formed at pressures of 45-60 kbar.  A kilobar is a metric unit used to measure high pressure. This high pressue corresponds to a depth of 125-200 kilometres below the Earth’s surface where the pressure is around fifty thousand times that of atmospheric pressure at the Earth’s surface.

Some diamonds form at depths of 300-400 kilometres, or even deeper, but these diamonds are particularly rare.

Diamonds are formed at temperatures between 900°C and 1,300°C.

So it makes sense that an old star (very hot) that has collapsed and compressed (very high pressure) that was composed mostly of carbon may indeed ressemble a very, very large diamond.

Guess I know where to have brunch... just hope I don't suffer from space-sickness!

Pass me the Yoghurt, I Feel Sad

In honour of the fact that I am graduating next week, I thought I would scout out some of the new developments that are happening in my college. Seems like I will be eating more yoghurt from now on...


An article publishind in the journal Proceedings of the National Academy of Sciences USA outlined a collaborative project that showed that mice who were fed with a type of bacteria showed less stress, anxiety and depression-related behaviours than those fed with just broth. Importantly, these mice showed lower levels of corticosterone, which is a hormone associated with stress.


What's interesting about this study is that it highlights the important role that probiotic bacteria play in the communication between the gut and the brain. Remember that there are lots of different types of bacteria in the gut, many of which are involved not only in digestion, but also in maintenance of a healthy gut and production of vitamins. According to John F. Cryan, Professor at University College Cork, these findings ''open up the intriguing opportunity of developing unique microbial-based strategies for treatment for stress-related psychiatric disorders such as anxiety and depression.''


Further findings show that feeding mice with this bacteria causes changes in the number of receptors for a neurotransmitter in the brain (called GABA). This is the first time that it has been shown that probiotics can have a direct effect on brain chemistry in normal situations. The communications between the brain and gut is three-way, involving the Vagus nerve as well, and perhaps this axi can be exploited in the future to treat other disorders that involve the brain.


So pass me an Actimel* and perhaps I can fight these 'Back-to-College' blues.

* Just to clarify, Actimel doesn't contain the exact same bacteria that they fed the mice. They used Lactobacillus rhamnosus JB-1, whereas Actimel has some other Lactobacilli.

Sleeping Beauty Had it Wrong...

Apparently that beloved fairytale had it backwards. According to a new study, there is a reason why women wake before men, and tire more easily in the evenings. Here I thought it was just so they could fetch coffee and breakfast in the morning...

A previous article (http://suupedupscience.blogspot.com/2011/07/less-rhythm-less-sleep.html) talked about circadian rhythm (the body clock) and how neural rhythms determine so many body functions. A new study shows that men and women are biologically designed to go to bed at different times. Female circadian rhythm runs faster, and therefore they tire earler and wake up ealier than men. Male rhythm predisposes them to sleep and wake later, and are therefore more likely to be night owls.

The study was led by Jeanne F Duffy, associate professor of medicine at Harvard Medical School, and is the first to find a difference in the body clocks of different sexes. She said 'We found that women are twice as likely to have a circadian rhythm shorter than the normal 24 hrs and mre likely to get sleepy in the evening.'

By contrast, men are more likely to have a rhythm that is longer than 24 hours.

The study involved 200 people and took a month. The subjects were not told the time and were kept in subdued light. The production of melatonin (a hormone that is involved in circadian rhythm) was measured and showed that the average male internal cycle lasts 24 hours and 11 minutes, 6 minutes longer than for woman.

This may not seem like a big difference, but becaus circadian rhythm affects your sensitivity to multiple external factors (like light), it can effectively mean a matter of hours. Duffy explains, 'Morning light exposure aligns us to the 24-hour clock, so if you in on Sunday, it's harder to wake up on Monday.' So if women expose themselves to light in the evenings, they can slow down their cycle, whereas men can do the opposite.

Now I know there is a reason why my mother always insisted on my going to bed at the same time every night. I wonder if there is a reason female cycles are faster. I think back to our hunter-gather days, men would so often be working harder chasing things to kill, so perhaps those who got too tired died out, and so the ones that could stay up later survived, whereas with women, it didn't matter because they were just looking after the cave hearth...

Credits:The Sunday Times 28.08.11,

www.npr.org/2011/05/03/135954176

www.macmillandictionary.com/dictionary/american/circadian

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Gene Therapy 2: Nitty Gritty Cell Stuff

Rise of the Planet of the Apes (or as I like to mockingly call it 'Beginning of the Story of the Rise of the Planet of the Apes') was surprisingly good. No spoilers here, however, in light of the fact that the main storyline involves the use of viral gene therapy to enhance (or heal) ape brains, I figured it would be appropriate to write instalment number two of the gene therapy introduction.

Viruses are used to deliver the correct genetic material to cells in the hopes that this genetic material will be incorporated as part of the cells own genetic code. But how does this actually work?

The above diagram shows a virus (called a vector because it is basically a transport vehicle) attching to a cell. It is an adenovirus vector. Adenovirus is associated with respiratory, intestinal, and eye infections in humans (especially the common cold). As shown in the diagram, the virus is taken into the cell and then travles to the nuclues (the pink thing). It attaches to the surface of the nucleus and injects the DNA into to core of the nucleus. Remember that the nucleus of the cell is where we hold all our own genetic material.

The DNA molecule isn't a double-stranded molecule, but instead is a single strand, and can thus be read by the cells replication molecules. These molecules are called messenger RNA, and they are part of the process by which new proteins are formed. Thus, if the correct DNA is present, the correct proteins will be made, and so any disfunction that occured before may be rectified.

That's the nitty gritty of what is happening in the cells when infected with a virus vector carrying the corret DNA sequence. Next up we'll look at what diseases and disorders have been cured or treated to date, and what side effects have occured.

Will gene therapy one day become the ultimate application of genetic technology? Gene Therapy, the newest booklet in the Special Topics in Biology Series, addresses this question by exploring gene therapy as a complex technology for delivering therapeutic genes as a way to treat and cure human genetic diseases.
Author Mary Colavito provides an overview of the basic science involved in gene therapy methods and chronicles the history of gene therapy by discussing successful and ongoing gene therapy treatments as well as adverse outcomes in some cases of gene therapy. Also discussed are challenges that must be overcome for gene therapy to become a more reliable and readily accessible approach for treating a multitude of genetic diseases that affect humans.