Controling HIV-like virus in monkeys by early intervention

HIV photo-Optimized

The paper was published in Nature on March 13.

In an interesting study, the immune system of monkeys was found capable of controlling HIV-like virus (simian-human immunodeficiency virus (SHIV)) when treatment with a combination of two broadly neutralising antibodies was started three days after infection. The immune system of the animals was found to control the virus even after the anti-HIV antibodies were no longer present in the monkeys.

In a paper published on March 13 in the journal Nature, researchers from the National Institutes of Health and other institutes infected 13 macaque monkeys with SHIV virus. Unlike earlier studies where intervention began late, the researchers started treating the monkeys with two broadly neutralizing HIV antibodies from the third day of infection. The monkeys were infused with the two drugs three times over a two-week period.

Compared with controls, six monkeys were able to suppress the virus for 56 days to as long as six months; in one monkey the virus was below detectable level for 150 days. Once the antibodies level dropped to a very low in the animals, the virus resurfaced. The time taken to rebound was directly related to the concentration of the neutralising antibodies in the plasma.

Quite unexpectedly, five to 22 months after the virus resurfaced, the immune system of the six monkeys spontaneously regained control of the virus and brought it down to undetectable levels for another five to 13 months. Four other monkeys could never fully regain complete control of the virus but the viral load was “very low level” for more than two years. Of the 13 monkeys studied, 10 were able to benefit from two neutralising antibodies administered.

A particular kind of immune cells called CD8+ T cells were found to be higher in all the animals that were infected with SHIV virus. To ascertain if CD8+ T cells were responsible for mediating sustained suppression of virus replication, the researchers purposely depleted the CD8+ T cells in the six monkeys. What followed was a sharp increase in the viral load in all the animals. This helped the researchers conclude that the CD8+ T cells controlled the virus multiplication following the administration of the neutralising antibodies.

The study shows that a combination therapy of two neutralising antibodies given early after infection can control SHIV viral load for nearly six months and facilitate the emergence of potent CD8+ T cells that “durably suppress virus replication”.

Though SHIV infection in macaque monkeys differs from HIV-1 infection in humans in many ways, based on the study, the researchers suggest that immunotherapy should be explored to control the spread of virus, contain the damage to CD8+ T cells, mobilise a robust immune response and control HIV infection in humans.

Published in The Hindu on March 14, 2017

Indian researcher uses light to speed up electronics by one million times


Manish Garg used high intensity laser to generate very high frequency electric current.

A researcher from India has taken the first definitive step to produce high-speed electronic devices that can operate one million times faster than modern electronics. At Max Planck Institute of Quantum Optics in Garching, Germany, Manish Garg and other researchers used laser light to generate very high frequency electric current inside a solid material. The electrons were found to be moving at a speed close to 1015 (one million billion) hertz; the best achievable speed in modern transistors is only 109 (one billion) hertz. The results were published in Nature.

Conventionally, the motion of electrons (conductivity) is achieved by applying voltage. But Dr. Garg and others controlled the motion of electrons inside the solid material by using laser pulses. “Light waves are electromagnetic in nature and have very high oscillation frequency of electric and magnetic fields. This ultrahigh frequency of light waves can be used to drive and control electron motion in semiconductors. Electronics when driven by such light waves will be inherently faster than current state of electronics,” says Dr. Garg, who is the first author of the paper.

The conductivity increases by more than 19 orders of magnitude in presence of the laser pulse.“When we shine high intensity laser on silicon dioxide nanofilm charge carriers (electrons) are generated. When the electrons move in the presence of electric field of the laser it generates current,” he says. “Initially, the nanofilm behaves like an insulator but when we shine high intensity laser it behaves like a conductor. The conductivity increases by more than 19 orders of magnitude in presence of the laser pulse.”

The performance of high-speed circuits rely on how quickly electric current can be turned on and off inside a material. “We showed that we could turn the conductivity of silicon dioxide nanofilm from zero to very high values in a time interval of 30 attoseconds (an attosecond is 1×10-18 of a second), which is one million times faster than modern electronics,” he says.

The high speed of electrons was achieved only in the presence of the laser pulse. Once the pulse (flash) is gone, the nanofilm is restored to its original configuration (insulating). “The whole idea of doing light-wave-electronics is based solely on this fact. So in terms of binary logic, the nanofilm will be in a ‘zero’ state (insulating) when there is no laser and when it interacts with laser it would become conducting ‘one state’” he says.

The very short time interval needed to turn silicon dioxide from an insulator to a conductor was possible as the team used high intensity and extremely short laser pulses and silicon dioxide was in the form of a nanofilm. In the bulk form, silicon dioxide tends to get damaged by high intensity laser as the material tends to accumulate heat produced by the laser pulse. But as a nanofilm, silicon dioxide becomes nearly transparent to laser and absorbs less heat and therefore gets less damaged.

“In our earlier work, which was also published in Nature, we obtained signatures of very high frequency current, but we were not able to measure it. But now we are able to measure current in real time by measuring the time-structure of emitted extreme ultraviolet radiation using an attosecond streak camera,” he says. Current produced in the nanofilm manifests as extreme UV radiation.

The coupling of dipole moment of electrons inside the nanofilm with the electric field of the laser pulse gets the electrons to make a transition from the valence band to the conduction band whereas the motion of electrons inside the conduction band gives rise to an electric current.

“We envision in future we will be able to use transistors driven by laser pulses instead of electronic transistors in electronic devices. The technical challenges is to make use of high frequency currents to perform logic operations similar to the ones performed inside an electronic transistor and also make it feasible on integrated chips,” Dr. Garg says.

Scientists have long debated whether transition of electrons from the valence to the conduction band or the motion of electrons inside the conduction band gives rise to extreme to extreme ultraviolet radiation. “Our study has resolved this by showing that the motion of electrons in the conduction band is the real mechanism for extreme UV radiation,” he says. “When we resolved this we found the motion of electrons in the conduction band is the same as the motion of electrons in modern electronics.”

Published in The Hindu on January 31, 2017

A novel compound prevents, cures malaria


The novel compound acts on all three life stages of the malaria parasite -Photo: James Gathany/CDC

In a pathbreaking discovery, scientists from New Delhi’s International Centre for Genetic Engineering and Biotechnology (ICGEB), Broad Institute of MIT and Harvard and other institutions have isolated a compound that is able to completely clear malaria parasites with just a single, low-dose treatment.

The compound acts on all three life stages of the malaria parasite, has prophylactic property and prevents disease transmission in mice. The prophylactic effect lasted for as long as 30 days. The compound had activity against a number of malaria-causing Plasmodium strains with a variety of resistant mechanisms.

The researchers found a series of novel compounds (bicyclic azetidine series) that shows great promise in the battle against malaria. Four candidate agents were characterised and one compound was tested in mice.

The results of the study were published on September 7 in the journal Nature.

“A single, low-dose is able to target the parasite so very effectively due to the high potency of the compound and by targeting an essential cellular function in the malaria parasite,” Dr. Amit Sharma, one of the authors of the paper from ICGEB, said in an email to me. The compound has low metabolism, long half-life and good oral bioavailability.

Since the target is so essential for the parasite’s functioning, it is quite unlikely that it would undergo mutations.

One of the issues with malaria is the reappearance of the Plasmodium parasite (recrudescence). The parasite can persist for a few months in blood without causing apparent symptoms. “It was for this reason that we carried out 30-day studies with both P. berghei (a mouse strain) and P. falciparum (the parasite responsible for most malaria deaths worldwide). A dose of 25 mg/kg showed no recrudescence for 30 days that we monitored,” Dr. Nobutaka Kato, the first author of the paper from the Broad Institute of MIT and Harvard, said in an email. “No recrudescence for 30 days means we killed all the parasites.”

Effective at every stage

The compound was able to achieve extraordinary results in mice as it targets the parasite’s protein translation machinery (phenylalanine tRNA synthetase), which is the very core of the parasite’s housekeeping function of synthesising about 5,000 proteins. Protein translation is vital at every stage of the Plasmodium life cycle.


Broad Institute – Photo: Len Rubenstein

Since the target is so essential for the parasite’s functioning, it is quite unlikely that it would undergo mutations. So, there are less chances of the parasite developing resistance against the compound. “In a standard tool for measuring for generation of resistance, we found a low propensity for resistance,” Dr. Marshall L. Morningstar, a co-author of the paper from Broad Institute of MIT and Harvard said in an email.

Addition of a highly potent drug component to the already very successful artemisinin combination therapy will go a long way in stemming malaria infections, and may present therapeutic options when artemisinin drug-resistance becomes a problem.

“A lot of studies will be needed to ensure that the findings in mice get translated into humans. Fortunately, we have a great group of researchers spanning the globe to help us complete the necessary studies,” Dr. Morningstar says. The team says that it would take 5-7 years before a potent drug becomes available for commercial use. “What is important is that there are now new molecules in the development pipeline and therefore we can expect more therapeutic arsenals against the parasite in the coming years,” Dr. Sharma says.

DOS library

The Diversity Oriented Synthesis (DOS) library, from where the compounds were selected, is a unique collection of 100,000 chemical compounds that are not traditionally represented in pharmaceutical libraries and were designed to emulate small molecules found in nature. “By employing build/couple/pair strategy, the library was built utilising a variety of chemistry routes,” Dr. Kato says.

From this library, 478 compounds that had potent activity against chloroquine-resistant Plasmodium strain were identified. Compounds that targeted two common mechanisms of action in malaria were removed and those that showed in vitro inhibitory activity in gametocyte and liver stage assays were prioritised. “The bicyclic azetidine series was the lead series from this cascade effort,” Dr. Morningstar says.

“We have made all structures and screening data available online at a new Malaria Therapeutics Response Portal and invite the scientific community to use this database as a jumping-off point for other anti-malarial development efforts,” Dr. Kato says.


UPDATE (September 13, 9.30 am)

The Director-General of the Indian Council of Medical Research (ICMR) Dr. Soumya Swaminathan has shown interest in the study and tweeted saying: “ICMR will be happy to partner in further drug development and human trials.” Now that’s what is called a lightning response to a promising study.

Published in The Hindu on September 13, 2016

A novel, powerful antibiotic found inside human nose

MRSA - Photo National Institute of Allergy and Infectious Diseases (NIAID)

The novel antibiotic ludunin, found inside human nose, has antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA). – Photo: NIAD

A novel antibiotic — lugdunin — produced by a bacterium found inside the human nose has been found to kill the bacterium Staphylococcus aureus, including drug-resistant forms such as the methicillin-resistant S. aureus (MRSA). The study found S. aureus does not develop resistance against the novel antibiotic. The findings could aid the development of new therapies for hard-to-treat bacterial infections. The results were published today (July 28, 2016) in the journal Nature.

The human body is home to an immense variety of microorganisms known collectively as the microbiota. Several bacteria species including Staphylococcus are found inside the human nose and these bacterial species are fewer in number when the pathogenic S. aureus bacterium is present. However, in about 70 per cent of human population, colonisation by S. aureus inside human nose is absent. The reasons for this were not clear.

On screening a collection of nasal Staphylococcus species for antimicrobial activity against S. aureus, a team of scientists led by Andreas Peschel from the University of Tubingen, Germany, found that Staphylococcus lugdunensis bacterial strain had a particularly strong capacity to prevent the growth of S. aureus.

On screening S. lugdunensis mutants, Dr. Peschel and colleagues identified the compound that resisted the growth of S. aureus and called it lugdunin. Lugdunin causes the breakdown of S. aureus.

Peptide antibiotic

The novel compound represents the first known example of a new class of peptide antibiotics.


The bacteria producing the novel antibiotic reduced the S. aureus colonisation by six times. – Photo: R. Prasad

The lugdunin’s role in inhibiting S. aureus growth was first proved in the lab. To test the efficacy in animals, the researchers infected mice skin with S. aureus and then treated it with the novel antibiotic 24, 30 and 42 hours after infection had set in. Lugdunin was found to completely clear all viable S. aureus from the surface and in the deeper layers of the skin.

Next, lugdunin’s ability to inhibit S. aureus’ growth in the nose was tested using cotton rats. When both S. aureus and S. lugdunensis bacteria were introduced into the cotton rat nose, relatively fewer S. aureus cells were retrieved proving that lugdunin production effectively prevented S. aureus colonisation inside the nose.

The nasal swabs of 187 hospitalised patients were tested for the presence of S. aureus, S. lugdunensis or both. When both the bacterial species were found in a patient’s nose, S. aureus colonisation was nearly six times lower than in those people who had only S. aureus.

The researchers found lugdunin had bacterial activity against many major pathogens, and S. aureus isolates had “pronounced susceptibility” to lugdunin in all nasal and clinical samples. So it may be quite difficult for S. aureus to develop resistance against lugdunin, they say.

Published in The Hindu on July 28, 2016

First CRISPR trial on humans set to begin

HIV - Researchers   successfully modified the T cells of 12 HIV patients to resist infection. - Photo Penn Medicine

Researchers from the Perelman School of Medicine successfully used a genome-editing technology to modify the T cells of 12 HIV patients to resist infection. – Photo: Penn Medicine

On June 21, the National Institutes of Health gave permission for starting the first ever clinical trial using CRISPR genome-editing technology, Nature news notes. The trial, which  will begin before the end of the year, will be carried out on 18 cancer patients to “help augment cancer therapies that rely on enlisting a patient’s T cells, a type of immune cell”.

The goal of the trial is not to cure cancer but to test the safety of CRISPR-Cas9 technology. According to Nature, the T cells from the patients suffering from melanoma, sarcoma or myeloma will be removed and three edits will be performed using CRISPR.

The first one will be to insert a gene for a protein engineered to detect cancer cells and instruct the T cells to target them, the second edit will be clean up the T cells so they don’t interfere with the process and finally the third edit will be to “remove the gene for a protein that identifies the T cells as immune cells and prevent the cancer cells from disabling them”. The cells will be returned to the patients once all the three edits are completed.

CRISPR is not the only genome-editing technology around.  However, CRISPR is far better than other technologies as editing is far easier and more efficient. But it does have some inherent problems.  According to the journal, CRISPR has a propensity for going in off-target edits. “These are instances in which the system cuts or mutates unintended parts of the genome. And despite precautions, the immune system could still attack the edited cells,” it says.

Though this is the first time that permission has been granted for a human clinical trial involving CRISPR, another genome-editing technology was used in the past.  The enzymes called zinc-finger nucleases (ZFNs) were used to genetically engineer the immune cells of 12 people with HIV, to resist infection, and decrease the viral load of some patients taken off antiretroviral therapy. The results published in The New England Journal of Medicine on March 5, 2014 was the first time gene editing approach was used in a trial on humans.

After four weeks of infusing the edited immune cells back into the patients, six subjects were taken off HIV medications for 12 weeks. While two were put back on treatment, the viral load decreased on average by 10 fold at the end of the 12-weeks treatment interruption.

Also, one week after the initial infusion, the decrease in the modified T cells was significantly less than the unmodified T cells during the period of treatment interruption. “The modified cells were also observed in the gut-associated lymphoid tissue, which is a major reservoir of immune cells and a critical reservoir of HIV infection, suggesting that the modified cells are functioning and trafficking normally in the body,” a release notes.

“This study shows that we can safely and effectively engineer an HIV patient’s own T cells to mimic a naturally occurring resistance to the virus, infuse those engineered cells, have them persist in the body, and potentially keep viral loads at bay without the use of drugs,” corresponding author Carl H. June from Perelman School of Medicine, University of Pennsylvania said in the release.

Potential drug target identified for Zika virus

img_0317At a time when no vaccines or therapeutic drugs are available against Zika and other diseases caused by flaviviruses, researchers have successfully found that disabling or silencing one single gene can effectively leave the flaviviruses unable to leave the cell that has been infected, thereby preventing the spread of infection.

Unlike bacteria, viruses must necessarily infect cells to multiply. If, however, the cells lack a gene that the virus requires for infection, the virus cannot get into the cell or infect it.

The results were published on June 17, in the journal Nature.

The researchers performed a genome-wide CRISPR/Cas9-based screen to identify host genes that reduced flavivirus infection when edited. Of the 19,000-odd genes of West Nile virus studied, only nine genes were required for flavivirus infectivity. All of them are associated with an important part of the cell that processes viral particles, which is essential to spreading the infection.

Editing of the nine genes using CRISPR resulted in reduction in West Nile virus antigen expression following infection. The same result was seen in other four diseases caused by flavivirus – Zika, Japanese encephalitis, yellow fever and dengue serotype 2.

As insects transmit pathogenic flaviviruses, scientists studied the orthologues (sequences that have common ancestor and have split due to speciation event) of these genes in insect cells. In fruit fly, silencing the genes reduced the infection of West Nile virus and dengue serotype-2. However, the viability of the cells was not affected.

Of the nine genes studied, Rong Zhang, the first author from the Washington University School of Medicine, Saint Louis, U.S., found that one single gene – SPCS1 – particularly affected flavivirus infection. “Loss of SPCS1 expression resulted in markedly reduced yield” of all five flaviviruses (Zika, West Nile, dengue and yellow fever and Japanese encephalitis) studied.

Despite the huge effect that the SPCS1 gene had on flavivirus protein processing, the expression of host proteins was only “modestly affected” by the absence of the gene, the researchers found.

“Flaviviruses appear to be uniquely dependent on this particular gene to release the viral particle,” senior author Michael S. Diamond from Washington University School of Medicine said no in a release. “In these viruses, this gene sets off a domino effect that is required to assemble and release the viral particle. Without it, the chain reaction doesn’t happen and the virus can’t spread. So we are interested in this gene as a potential drug target because it disrupts the virus and does not disrupt the host infectivity.”

Landmark experiment improves coral calcification by 7% in Great Barrier Reef

Aerial photograph of One Tree Reef. — Photo  One Tree Island Research Station at the University of Sydney-Optimized

Aerial photograph of One Tree Reef. – Photo: One Tree Island Research Station at the University of Sydney

A first-of-its kind, field-controlled experiment carried out for 22 days between September 16, 2014 and October 10, 2014 in a natural coral-reef community in the Great Barrier Reef has allowed scientists to unequivocally show the detrimental effects of ocean acidification on coral reefs across the world. According to the study published on February 25 in the journal Nature, the net coral-reef growth would have been seven per cent more in the absence of ocean acidification.

The unique design of the study allowed the researchers to pinpoint the role of ocean acidification in diminishing the coral-reef growth even without altering or removing other compounding factors such as elevated sea surface temperature due to global warming, land-based pollution and overfishing. Coral reefs, which provide marine ecosystems comparable to tropical rain forests, are most vulnerable to ocean acidification.

Ocean acidification arises when nearly 25 per cent of carbon dioxide released into the atmosphere and absorbed by the oceans reacts with water to form carbonic acid.  The carbonic acid thus produced leads to ocean acidification by decreasing the pH of the ocean, reducing the concentration of carbonate ion (which is essential for organisms such as corals and clams to build their shells and skeletons) and a decreased aragonite mineral saturation state (“a measure of the availability of dissolved carbonate and calcium ions”).

According to Nature, today’s oceans are already 30 per cent more acidic than they were before the Industrial Revolution.

Increasing the pH of the ocean to make it more alkaline than acidic will provide an ideal condition for coral reefs to grow.  While it is nearly impossible to do so on a large scale and study its impact on coral growth, the unique conditions seen in the One Tree Reef that encloses three lagoons in the southern Great Barrier Reef provided an ideal location to test this.

All the three lagoons in the One Tree Reef get cut off from the ocean during low tide, and water tends to flow from the first lagoon to the third lagoon as a result of elevation difference of 30 cm. A reef made of live corals separates the two lagoons and water flows over the reef in one direction for one full hour a day during peak low tide.

Experimental seawater flowing over the reef flat study site. A pink dye tracer was used to track the movement of seawater. — Photo Rebecca Albright-Optimized

Experimental seawater flowing over the reef flat study site.  A pink dye tracer was used to track the movement of water. – Photo: Rebecca Albright

The team artificially increased the alkalinity of the water flowing from one lagoon to another over the reef flat by introducing sodium hydroxide solution once a day for 15 days.  An active tracer in the form non-reactive dye solution was introduced into the reef flat during the entire duration of the study — 22 days. The first seven days when no sodium hydroxide was added along with the tracer served as control.

“By measuring the concentrations of dye and sodium hydroxide the scientists were able to calculate the overall increase in calcification across the reef when the seawater chemistry was altered,” notes Nature.  What they found was truly dramatic — net coral-community increased by 7 per cent. In addition, they found that around 17 per cent of the added sodium hydroxide was taken up by the reef community and the increase in alkalinity led to 0.6 per cent increase in aragonite saturation state.

The experiment helped prove that restoring the ocean chemistry to pre-industrialisation conditions led to an increase in coral growth.  “We provide evidence that net community calcification is depressed compared with values expected for preindustrial conditions, indicating that ocean acidification may already be impairing coral reef growth”, writes Rebecca Albright, the first author of the paper from the Carnegie Institution for Science, Stanford, California. The reduction in calcification as a result of acidification is “projected to shift coral reefs from a state of net accretion to one of net dissolution this century”.

Global warming has not only increased the acidity of the oceans but has also elevated the sea surface temperature. While a warming ocean would have initially favoured coral reefs and led to more growth, the continued increase has proved harmful. Hence, coral reefs suffer from the combined onslaught of both acidification and elevated sea surface temperature. Future studies need to look at the combined effect on coral reefs.

While the researchers have been able to temporarily reverse the ocean chemistry at a very local scale, the only way to achieve this globally is by reducing the amount of carbon dioxide emitted. Even the Paris climate agreement has able to reach a consensus to keep the global temperature “well below the 2 degree C above the pre-industrial levels would mean little for the health of coral reefs; they run the highest risk of acidification and ocean warming.

“Caldeira’s team is planning a second experiment — scheduled for September — that will help them to take a peek at possible future ocean conditions. Rather than adding an antacid to seawater, the researchers will add carbon dioxide to boost acidity to levels that would be expected in 2100 if emissions continue to rise,” notes Nature.

Published in The Hindu on February 28, 2016