Reported: The First Known Case of a Child Being Cured of HIV

HIV might have finally met its match. We report the first documented case of a child being cured of HIV after antiretroviral therapy. Dr. Deborah Persaud of John Hopkins University presented this remarkable case yesterday at the 2013 Conference on Retroviruses and Opportunistic Infections, Atlanta, Georgia. The breakthrough was confirmed by various ultra-sensitive test on the child, all coming out negative for the presence of the HIV viral load.

Scanning Electron Micrograph of an HIV attacking a live cell.

The child was born HIV positive, since the mother was also HIV positive. At the age of 2 years, the child in Mississippi was diagnosed with the deadly virus and immediately put on antiretrovirals. This therapy continued for 18 months. After five more months, during which the child was off treatment, the child was tested and the absence of HIV was confirmed via highly sensitive tests. Dr. Persaud said that it was beyond any doubt that the child showed no signs of being HIV positive.

The treatment for HIV depends crucially on the patient’s immune system makeup. Also, an infant’s immune system differs from that of an adult. Scientists want to study the individual’s immune system, especially since the treatment of the patient happened via only very cheap antiretroviral therapy, rather than expensive treatment. No one is really sure how this cure happened.

This is only the second documented case of an HIV cure, the first one being the famous ‘Berlin Patient’, Timothy Ray Brown. He has founded his own AIDS Foundation, the Timothy Ray Brown Foundation, dedicated exclusively to finding a cure for the deadly disease.

However, the Ray Brown case is quite different from this. Even though, the Ray Brown involved a longish course of antiretrovirals, there was a diagnosis of myeloid leukemia in case of Ray Brown. His heamatologist, Dr. Gero Hutter, make a stem-cell bone-marrow transplant from a doner who had a very rare HIV immunity called the CCR5 mutation. A few months later, there was no active HIV viral load in his body.

Nothing nearly as drastic as a stem-cell bone-marrow implant was done in this present case. And that makes this case all the more special.

More info here:

Google Celebrates Pioneer Copernicus’ Birthday With Cool Doodle

He pioneered a revolution so strong that it lasts to this day. While Galileo is considered to be the first real scientist, Nicolaus Copernicus, yes, the one of the heliocentric model of the universe, was the one who started it all off!

Copernicus was the first great proponent of the theory that the Earth goes round the Sun and the Sun is the center of the Universe. This hypothesis served to explain why we see retrograde motion of the planets (meaning, sometimes, the planets like Venus seemed to go back and then again start moving forward; today this is known as epicyclic motion). His hypothesis contained little mathematical formalism and mostly comprised logical deductions from a set of seven assumptions about the ‘firmament’, Earth and Sun.

The Copernican Google Doodle

Google celebrates the 540th birthday of the pioneer with a brilliant doodle. The doodle sketches the Copernican universe having 5 bodies and the Earth revolving around a central Sun on circular paths. The moon for the Earth has also been indicated. I hope the speeds are in proper ratio but I haven’t checked that. As is usual, clicking the doodle leads you to search results for Copernicus.

Ideas and acceptance

One might have expected a wildfire-like spread of Copernicus’ idea, since it was almost universally accepted, and also severe backlash from the Church, as the basic tenet of the theory violates the geocentric view of the religious majority. None of the two happened. The idea was slow to catch on and the fact that Copernicus was a Catholic cleric – and that too an active one – helped with the latter part of the above. Copernicus himself suspected a backlash, and thus delayed publishing his ideas in a book.

It strikes me as odd how these ideas, about a quarter of a century before Galileo was accepted largely because it hailed from a Catholic cleric, while Galileo, with no direct links to the gentry, was ostracized and threatened with torture.

Science has since made giant strides. Happy Birthday Nicolaus.

New Mechanism of Regulating Gene Expression Discovered

A few months ago, much ado was made about results from the ENCODE project on the human genome, publicized as having made the discovery that 80% of the human genome has a biochemical function. While this is true (with ‘biochemical function’ being defined loosely and broadly), we don’t yet know how or why most of the long stretch of DNA in our cells is important. ‘Genes’ as we know them make up less than 2% of the total DNA. What purpose does the rest of it serve?

What Purpose does “Junk DNA” Serve?

The ENCODE project suggested that the rest of the genome had a strong regulatory potential. How do our cells control when to turn on certain genes, when to ramp up production of one protein and when to slow down? A lot of these regulatory mechanisms remain unknown. A team of researchers at Wistar Institute have now discovered one additional mechanism of regulation.

Before we move on, let’s briefly review how genes function. ‘Genes’ are essentially regions of the genome which are processed into intermediate molecules called ‘RNA’, also linear strings. These RNA strings are further processed to yield the protein that performs the gene’s function. Think of the gene as a ‘recipe’ for a protein, with the RNA molecule being the unfinished product halfway along the recipe. There are, however, some regions of the genome which are processed to form RNAs, but do not form proteins. They often have regulatory functions.

ncRNA-a (the region of the genome on upper segment of the loop) helps the mediator protein complex to gain a foothold on the right region, so that the gene (shown by ‘mRNA’ on the lower segment of the loop) can be transcribed. [Image Credit: Nature Publishing Group]

Long Non-Coding RNAs Regulate Gene Expression

Moving back to the research team, they had previously discovered that a class of these ‘non-coding RNAs’, which they have termed ‘ncRNA-a’, serve to activate processing of their neighbouring genes. But how do they do this? There are certain proteins called mediators which facilitate the processing of genes to RNA. They have now discovered that ncRNA-a helps these mediator proteins bind to these genes at the right place. To determine this, the team removed proteins known to be involved in gene processing (called transcription) one by one, and looked for changes in ncRNA-a mediated activation. And voilà, components of the mediator complex came up immediately. They also found that the chromosome forms a loop between the ncRNA-a locus and the gene locus, for the mediator complex to be able to gain a stronghold at the gene locus using the ncRNA-a as a base.

Why is this result important? It gives us a better idea of the factors controlling gene expression. And as importantly, it helps us understand our DNA just a little better. You can read about this research here.

Poachers 11100: Conservation 0

Shocking figures on elephant conservation have just been released by the Wildlife Conservation Society (WCS). The Minkebe National Park in Gabon has lost as many as 11,100 elephants to the ivory trade in the last 9 years.

Rampant Elephant Poaching in Gabon

Gabon is home to more than half of Africa’s elephants, and elephant poaching in this region was believed to be less than in other regions of Africa, where 31000 elephants are estimated to have been lost due to poaching. However, there has been increased human activity seen in this National Park, with there being around 5000 miners, poachers and arms and drugs dealers on its premises. Authorities believe that 50-100 elephants could be killed everyday.

Image Source: Wikimedia commons
Gabon’s elephant population is estimated to be 40,000. This number may not be safe. [Image Source: Wikimedia commons]

Increasing Demand for Ivory

According to a previous report by the CNN, there is an increased demand for ivory which can be attributed to economic growth in Asia, where ivory is valued for ceremonial and cultural purposes. The price of ivory has reached $1000 per pound. The statistics released highlight the extent of the threat these pose to conservation.

Authorities Respond

These statistics are dramatic enough to have evoked reactions from the Gabonese government. The president has vowed to introduce further legislation to dissuade poachers, including longer prison terms. He also called for an integrated effort to meet this problem. He was echoed by the president and CEO of WCS. “This sad news from Gabon confirms that without a global commitment, great elephant populations will soon become a thing of the past,” said WCS President and CEO Cristián Samper. “We believe that elephants can still be saved – but only if nations greatly increase their efforts to stop poaching while eliminating the illegal ivory trade through better enforcement and reduced demand.”

The surveys were conducted by WCS, WWF and Gabon’s National Parks Agency. This report was sourced from a press release by WCF, which you can read here.

How Does Our Brain Create Fear?

Why do we feel fear? For years, a part of the brain called the amygdala has been implicated in this emotional response. This region links memories with emotional responses, one of which might be fear. A patient (known as S.M.) with dysfunctional amygdalae on both sides of her brain has been known to show no fear in response to various fear-inducing stimuli, including life-threatening traumatic events.

Everyday Gas Induces Fear in the Brain

Another stimulus that is known to evoke fear is carbon dioxide. Inhaling this gas turns on a protein which in turn plays a role in fear and anxiety (how this protein works in inducing fear remains unknown). How would patients with damaged amygdalae react to this stimulus? A team of researchers at the University of Iowa tried to find out.

fear center in the brain
The first image is a scan from a normal patient and the next three are from patients with damaged amgydalae. The area marked in red shows the lesions present in their brains. [Image Source: Iowa Neurological Patient Registry at the University of Iowa]

‘Fearless’ Patients Show Fear

To their surprise, they found that the 3 people with lesion in their amygdalae (let’s call them patients) showed a greater degree of panic than a group of patients with normal amygdalae. The patients described having experienced emotions they had never felt before, with their descriptions residing well under the category of ‘fear’. Clearly, these results show that the amygdala is not an absolute necessity for fear. However, anticipatory responses to the inhalation, such as an increased heart rate before inhalation, were shown to be significantly increased in controls when compared to patients.

These results led the authors to believe that the carbon dioxide activated a previously unused pathway in patients with damaged amygdalae. One possibility is that most stimuli that normally induce fear are external—perceived visually or auditorily—, whereas inhalation of carbon dioxide represents a physiological, internal, change that does not need processing by the amygdala to generate fear. Another conclusion that the authors came to was that the amygdala might, to some degree, inhibit fear, since the degree of panic attacks was milder in the control group.

Fear is an important survival mechanism, and this experiment gives important clues to its origin. You can read about this research here.

Novel Method To Invade Cells

One of the current paradigms of molecular biology research is to study cells by manipulating them. Insert a piece of DNA and see what changes. Add a protein and see if the cell can now become cancerous. Inactivate a protein and see if a diseased cell becomes normal.

One of the trickiest steps in such processes is often getting the foreign substance inside a cell. Living cells have membranes designed to keep out foreign substances and to absorb just what the cell wants. How do we let particularly large molecules in?

Infiltrating the Cell’s Walls

Pieces of DNA are usually inserted into a longer fragment of DNA called a vector (to keep the DNA stable). The cell is then shocked to jolt the proteins in its membrane and make it temporarily porous. This method can work for small molecules, and another method is the chemical disruption of the membrane temporarily. The problem with these methods is that they change some properties of the cell, and the goal of such experiments is to observe changes in the cell that is ONLY because of the inserted molecule, and not due to other factors (such that the result of a shock might lead to). Another method is to deliver the molecule inside nanoparticles which can then enter the cell, but the nanoparticle is often captured by an organelle of the cell, and the molecule is then not released. The cell’s membrane also allows certain protein to pass through it—think of it like a gatekeeper, letting proteins of certain charges and small enough sizes go through while keeping out the others.

This image gives the workflow of the microfluidics device. Figure A shows cells flowing through a tube with a constriction. After being squeezed, these cells are now have the delivery material inside them. [Image Credit: Sharei et al; PNAS]

Squeezing Cells to Make Them Yield

A general method of insertion would thus be a useful tool in research. Researchers at MIT have come up with the solution mothers use when their children don’t eat food—they press in the child’s cheeks till their mouths open. This team has developed a microfluidics device that does something similar. Cells (and the delivery material) flow through a tubes under external pressure and are forced to pass through a tiny constriction in the tube (see figure). During this phase, the cells are compressed to such tiny sizes that their membranes ‘split’ temporarily, leaving gaps for molecules to enter.

The team used this method to generate stem cells (by inserting the necessary factors into cells) and found that this method had an efficiency 10 to 100 times greater than other existing methods. Their next step is to use this for therapeutic purposes, wherein a patient’s cells could be taken out of his body, injected with the necessary DNA/protein, and re-injected into his/her body.

You can read about this research here.

Deadly Ebola Strain Could Infect Asian Bats

Ebola is a viral disease that has been a threat for more than a decade. Detected in Africa, this virus causes a serious haemorrhagic fever and has high fatality rates. There have been indications that it is from bats that these viruses infect humans, and a new study in Bangladesh lends this further credence.

Source of the Disease

Diseases like Ebola emerge periodically in human populations, and just as suddenly, disappear following an outbreak. This patterns owes itself to the virus being ‘zoonotic’—a virus that infects humans via another organism. Zoonotic diseases are hard to eradicate because we can’t immunize animals in the wild. This is why we have effective vaccines for Measles (not zoonotic), but Ebola or the flu is always on the radar for health officials. Thus, a crucial step in studying zoonotic diseases is determining their primary hosts. One criterion for primary hosts is that the virus shouldn’t be too harmful to them. If it were, it would kill the host organism and would not be able to circulate for long periods of time, as it does. Humans are definitely not its primary hosts—each outbreak subsides soon after its origin because it is so lethal.

This innocuous virion is the cause of a deadly disease. [Image Source: wikipedia]

Ebola Virus in Bats

The organism which is the original reservoir of Ebola virus has not been known for certain, though previous studies have found a few species of bats infected with Ebola. Now, researchers have studied 276 bats in three regions of Bangladesh and identified antibodies against the Ebola virus in 4% of these, meaning that the bats have, at some point, been exposed to the Ebola virus. However, they haven’t found live virus in bats, which is the piece of evidence necessary to confirm that bats are a reservoir, i.e. a permanent ‘store’ of the virus.

What Does this Study Tell Us?

Bats harbouring antibodies for Ebola has already been found—what new information does this study yield? This study tested bats for 2 strains of the virus: the Reston strain which has been seen in animals across the world (and has not caused human disease), and the more deadly Zaire strain, which has a whopping mortality rate of around 80% and was previously seen only in Africa. Antibodies for both these strains were found by this study, which means that a Zaire Ebola infectious outbreak in Asia remains a distinct possibility. How possible? We don’t know, until we have more evidence on prevalence of the virus in its primary hosts.

This research was conducted by the EcoHealth Alliance. You can read about this study here.

Ancient Link Between India and Australia

The study of the human genome continues to yield new insights about our history. A new study on the variation seen across human populations has revealed an ancient migration from India to Australia 141 generations ago, one that hadn’t been on record.

It is accepted that human populations migrated out of Africa and subsequently colonized the world. Some previous studies have shown that a wave of migration (called the ‘southern route’ of migration) to the Australian landmass occurred around 45000 years ago, following which this population remained isolated until colonization by Europeans in the 18th Century. This study upends this conclusion.

How Does Such Genetic Analysis Work?

Before the era of airplanes and global migration, populations across the world were relatively isolated, mainly because of geographical barriers, and often because of cultural and social barriers. Thus, members of each population would only breed with other members of the same population. Over time, this lack of interbreeding, or genetic mixing between different populations, led to distinct patterns that could be seen in each population. It is by looking at similarities and differences in these that we can compare genetic data.

A Study of Global Populations

The distribution of samples used in the study. [Image Source: PNAS: doi: 10.1073/pnas.1211927110]

Researchers at the Max Planck Institute for Evolutionary Anthropology collected ‘genotype data’—genetic data only at commonly varying locations in the genome—from different populations across the world (see figure above), and looked for patterns of similarities across these populations in terms of their genetic data. Using this genetic data and known rates of genetic change, they found a genetic link between populations from Australia, New Guinea and Mamanwa (an ancient group from the Philippines). This is consistent with the ‘southern route’ theory. What was novel was a significant similarity between Indian populations and Australian populations. This indicates a pattern of gene flow from India to Australia approximately 4230 years ago, a period called the Holocene.

Genetic Link Matches Archaeological Record—Coincidence?

This is fascinating because of an archaeological factoid of this period. This represents the period when changes in tool technology, food processing and a dog native to Australia called the dingo emerged on the Australian subcontinent. Could this emergence be related to the migration occurring in the same period?

It is plausible that this wave of migration was not direct, i.e., it could have been through the region of S.E. Asia, which shares long cultural links with Australia. However, the patterns of similarity seen between the Indian and Australian populations are not seen in the South-East Asian populations which were also included in this study. This means that there was a direct migration between India and Australia.

The study of our past is a fascinating one. Genetic data is an invaluable tool in this pursuit, and provides a tangible way for mankind to trace its evolutionary past.

You can read about this research here.

Achieved: Negative Temperature For A Quantum Gas!

There exists nothing as negative temperature (in Kelvin scale), at least not in ‘normal’ systems; this is something we learn in physics. This is a scale devised by Lord Kelvin (and hence the name of the unit) and according to this scale, there can be no negative value of temperature. Temperature was thought to be the measure of the energy of the particles in a system. While this isn’t untrue, the modern definition of temperature is broader.

For a system with energy levels, temperature is a measure of the probability of the occupation of an energy level with respect to energy. As we access more and more energetic states, the probability of occupation generally decreases and this leads to a positive temperature state. Now, imagine a system having the reverse configuration, like the higher energy states being more populated than the lower energy states. This kind of system will then have a negative temperature.

Try and note that negative temperature states are extremely rare and do not occur in our day-to-day lives. Particles will always like to occupy the lower energy states first and then go for the higher energy ones. In a room of air, you’ll always find more molecules with very low energies than molecules with very high energies. This is because the energy has a lower limit, viz E=0. The lowest energy possible is if the molecule were completely static. However, there is no upper limit.

Interesting systems

But if you did have an upper limit, things would be interesting! Say there is an upper limit of the energy spectrum, meaning that no particle can have any energy beyond this limit (just like no particle could go below the lower limit). Now, under certain conditions, the system would occupy the upper energy levels more than the lower ones! This causes an inversion of the sign of temperature, according to the modern definition. Thus, we have negative temperature!

The temperature on the right half is negative. We do not live in that half, but some systems do! (taken from the Nature paper – link given below)

So what’s the big deal, you ask? Negative temperatures have been known for magnetic systems (which have an upper and a lower limit), but we haven’t known of any system with motional degrees of freedom (like an atom free to move in 3 dimensions) to have such an energy spectrum.

The Experiment

Ulrich Schneider, a physicist at the Ludwig Maximilian University in Munich, Germany and his team created an ultra-cold quantum gas made up of potassium atoms and they confined these atoms to a lattice (i.e. a crystal like arrangement). At positive temperatures, the atoms repelled each other, but the team was able to flip the magnetic field fast enough for the atoms to start attracting each other. This also flips the sign of the temperature. Explains Prof. Schneider:

This suddenly shifts the atoms from their most stable, lowest-energy state to the highest possible energy state, before they can react. It’s like walking through a valley, then instantly finding yourself on the mountain peak.

The temperature measured was a billionths of a degree below absolute zero! Wolfgang Ketterle, Nobel Laureate, called this an ‘experimental Tour de Force’. It truly is!

Link to paper in Naturedoi:10.1038/nature.2013.12146

Quadrantids Meteor Shower Kicks off the New Year; Moon Plays Spoilsport

Another meteor shower is upon us. The Quadrantids are all set to blaze across the night sky. The only problem? The bright Moon!

The elusive Quadrantids

The full moon day happened only a few days back on the 28th of December and the moon is in its gibbous phase. They start off this year’s journey for meteor hunters and are known for intense and numerous. The maximum is a short intense one which lasts for something like an hour or so. After that you’ll find practically zero meteors. After the incredible Geminids a few days back, you might have trouble believing that meteor shower maxima can be so very short!

The location of the Quadrantids

The Quadrantids are named after the constellation Quadrans Muralis, which is now an obsolete constellation. So, in terms of the modern constellations, it’s near the head of Draco, the snake or the arm of the Big Dipper, if you prefer

The meteor shower will peak late tonight and continue on till the morning of 3rd January. But being the intense peak, if you’re late – or looking the other way – you’ll miss it.

The chances of missing it are really high, unfortunately. The moon will be bright and it being winter in the northern latitudes, the fog is expected to play major spoilsport. And since, the peak is late at night, when the fog formation is the strongest, you’ll definitely need to be insanely lucky.

In North America, the peak is expected to be at about 2-3 AM at about 30 degrees from the horizon on the east. As you go to the east, the morning comes earlier and the sky grows brighter when the peak actually arrives, making it hard to see the meteors.

No wonder Quadrantids are not as popular as the Geminids or the Perseids.

Best of luck.