IISc’s potent molecules show promise for TB therapy

SEM photo of Mycobacterium tuberculosis bacteria. - Photo NIAD-Optimized

The two molecules were able to prevent biofilm formation and even disrupt biofilms that had formed.

Scientists at the Indian Institute of Science (IISc) Bengaluru have developed two new, potent molecules that can severely impact the survival of mycobacteria, including Mycobacterium tuberculosis that causes TB. The results were published in the journal Antimicrobial Agents and Chemotherapy.

Unlike most antibiotics that target the bacterial metabolism by aiming at the cellular components, the novel molecules inhibit the stress response pathway of mycobacteria. The stress response pathway is crucial for bacteria to survive during hostile conditions such as lack of nutrients and the presence of antibiotics, to name a few. So any inhibition of this pathway will lead to its death.

The master regulator of stress pathway in the case of mycobacteria is (p)ppGpp (Guanosine pentaphospahte or Guanosine tetraphosphate). Though a molecule that inhibits the (p)ppGpp formation has already been synthesised, the efficacy is not much. “Very high concentration of Relacin molecule is needed to inhibit the pathway and, therefore, the efficacy is low. So we synthesised two new molecules — acetylated compound (AC compound) and acetylated benzoylated compound (AB compound) — by bringing about a modification in the base of the Relacin molecule,” says Prof. Dipankar Chatterji from the Division of Biological Sciences at IISc and the corresponding author of the paper.

“We found both the molecules to be very good inhibitors of stress response. The two compounds affected the rate of synthesis of (p)ppGpp and also reduced the cell survival,” he says. Laboratory studies showed that the two molecules were not toxic to human cells and were able to penetrate the human lung epithelial cells.

IMG_0508

Inhibiting (p)ppGpp synthesis would target the survival of the bacteria, says Dr. Kirtimaan Syal.

“We found our compounds were targeting the Rel gene. The Rel gene makes Rel protein, which in turn synthesises (p)ppGpp. When the Rel gene is knocked out, the long-term survival of Mycobacterium smegmatis decreases,” says Prof. Chatterji.

“The Alarmone molecule “(p)ppgpp”, a modified nucleotide, is ubiquitous in bacteria and absent in humans. Inhibiting (p)ppgpp synthesis would specifically target the survival of bacteria without having any effects on humans,” says Dr. Kirtimaan Syal from the Division of Biological Sciences, IISc and the first author of the paper.

Earlier studies have shown that when the rel gene is deleted, the long-term survival ability under stress was lost; the M. tuberculosis bacteria was unable to persist in mice and unable to form tubercle lesions in guinea pigs.

“The major reason for prolonged treatment of TB is the bacterium’s ability to persist in dormant form, which is tolerant to most antibiotics used in the treatment regimen. So inhibition of (p)ppGpp-mediated persistence could help in shortening the treatment regime, dealing with the emergence of multiple drug resistance and treatment of chronic infections, Dr. Syal says.

Inhibiting biofilm

Under hostile conditions, bacteria tend to form biofilms, which protect the bacteria from stress and induce tolerance to antibiotics. Recent studies have shown that tuberculosis bacteria that cannot form a biofilm cannot survive inside the host. Evidences have shown that at the time of infection, the M. tuberculosis display a biofilm-like phenotype and this helps the bacteria to survive inside the host.

Studies carried out by the researchers showed that both the molecules were able to inhibit biofilm formation by M. tuberculosis and M. smegmatis and also disrupt the already formed biofilm. “The biofilm formed by TB bacteria is very dangerous. The ability of the molecules to destroy the biofilm and even prevent its formation is a very important achievement,” says Prof. Chatterji.

Since there are very few antibiotics that target the stress response pathway of the bacteria, the two molecules offer great promise. “The next step is to test the molecules on animals. We have not thought about it. It will also be interesting to see if the bacteria develop resistance against these molecules,” Prof. Chatterji says.

Published in The Hindu on April 15, 2017

IISc designs a novel graphene electrical conductor

Ghosh-Optimized-1

(From left) T. Phanindra Sai, Amogh Kinikar, Arindam Ghosh have produce single- to few-layers thick graphene that conducts current along one particular edge.

Researchers from the Indian Institute of Science (IISc), Benagluru have been able to experimentally produce a new type of electrical conductor that was theoretically predicted nearly 20 years ago.

A team led by Prof. Arindam Ghosh from the Department of Physics, IISc successful produced graphene that is single or a few layers thick to conduct current along one particular edge — the zigzag edge. The zigzag edge of graphene layer has a unique property — it allows flow of charge without any resistance at room temperature and above.

“This is the first we found the perfect edge structure (zigzag structure of the carbon atoms) in graphene and demonstrated electrical conductance along the edge,” says Prof. Ghosh. The results of the study were published in the journal Nature Nanotechnology.

A few-layers thick graphene that conducts current along one edge does not experience any resistance and so can lead to realising power-efficient electronics, to quantum information transfer, even at room temperature.

Many groups over the world have been trying to access these edges since the emergence of graphene in 2004, but have been largely unsuccessful because when current flows through graphene, it flows through both the edge as well as the bulk. “We succeeded in this endeavour by creating the bulk part of graphene extremely narrow (less than 10 nanometre thick), and hence highly resistive, thus forcing the current to flow through the edge alone,” he says.

The edges conduct current without any resistance as long as the edges don’t come in contact with any chemicals.“While the bulk is totally insulating, the edge alone has the ability to conduct because of the unique quantum mechanics of the edge. Because of the zigzag orientation of carbon atoms [resulting from the hexagonal lattice], the electron wave on each carbon atom overlaps and forms a continuous train of wave along the edge. This makes the edge conducting,” explains Prof. Ghosh. The edge will remain conductive even if it is very long but has to be chemically and structurally pristine.

In the past, others researchers had tried making narrow graphene through chemical methods. But the use of chemicals destroys the edges. So the IISc team resorted to mechanical exfoliation to make graphene that are single- and few-layers thick. They used a small metal robot to peel the graphene from pyrolytic graphite. “If you take a metal tip and crash it on graphite and take it back, a part of the graphite will stick to the tip. The peeling was done slowly and gradually (in steps of 0.1 Å),” says Amogh Kinikar from the Department of Physics at IISc and the first author of the paper.

The exfoliation was carried out at room temperature but under vacuum and the electrical conductance was measured at the time of exfoliation before the pristine nature of the edge was affected. The unsatisfied bonds of the carbon atoms make them highly reactive and they tend to react with hydrogen present in the air. “The edges conduct without any resistance as long as the edges don’t come in contact with any chemicals,” says Prof. Ghosh. “It is very easy to passivate [make the surface unreactive by coating the surface with a thin inert layer] the edges to prevent contamination [when narrow graphene is used for commercial purposes].”

As the carbon atoms have a hexagonal structure, exfoliation is by default at 30 degree angle and one of the edges has a zigzag property. “The steplike changes observed for small values of conductance when other variables were changed were surprising. Through theoretical work we were able to link this to edge modes in graphene,” says Prof. H.R.Krishnamurthy from the Department of Physics, IISc and one of the authors of the paper.

There are currently several chemical methods to produce very narrow graphene nanoribbons. If the chemicals are non-destructive to the edges then it is possible to have a perfect quantum circuit at room temperature. “So the challenge is to produce graphene nanoribbons using chemicals that do not destroy the edges,” Prof. Ghosh says. “We believe that this successful demonstration of the dissipation-less edge conduction will act as great incentive to develop new chemical methods to make high-quality graphene nano-ribbons or nano-strips with clean edges.”

Published in The Hindu on April 8, 2017

IISc researchers’ novel, eco-friendly way of recycling e-waste

e-waste-Optimized

Prof. Mahapatra (left) and Prof. Chattopadhyay took advantage of cryo-mill’s ability to crush e-waste into individual components — polymer, oxides and metals.

Indian Institute of Science (IISc) researchers have found a novel way of recycling the mounting pile of electronic waste more efficiently and in an environmentally friendly manner. According to the United National Environmental Programme, about 50 million tonnes of e-waste is generated annually across the world.

The new approach is based on the idea of crushing e-waste into nanosize particles using a ball mill at very low temperature ranging from -50 to -150 degree C.

When crushed to nanosize particles for about 30 minutes, different classes of materials — metals, oxides and polymer — that go into making of electronic items get physically reduced into their constituent phases, which can then be separated without using any chemicals. The use of low-temperature grinding eliminates noxious emission. The results of the study were published in the journal Materials Today.

“The behaviour of individual materials is different when they are pulverised at room temperature. While metal and oxides get mixed, the local temperature of polymer increases during grinding and so the polymer melts instead of breaking,” says Dr. Chandra Sekhar Tiwary from the Materials Engineering Department at IISc and the first author of the paper. “The polymer starts reacting with the rest of the components and forms a chunk. So we can’t separate the individual components.”

“The deformation behaviour at low temperature is very different from room temperature. There are two processes that happen when milling. The polymer material breaks but metals get welded, some sort of solid-state welding resulting in mixing; the welded metals again get broken during milling. At low temperature mixing does not happen,” says Prof. K. Chattopadhyay from the Materials Engineering Department at IISc and the corresponding author of the paper.

Tiwary 2

Dr. Tiwary designed the cryo-mill.

There is also a lower limit to which materials can be broken into when e-waste is milled at room temperature. The maximum size reduction that can be achieved is about of 200 nanometre. But in the case of low temperature ball milling the size can be reduced to 20-150 nanometres.

The low-temperature ball mill was designed by Dr. Tiwary. The cryo-mill grinding chamber is cooled using liquid nitrogen and a small hardened steel ball is used for grinding the material in a controlled inert atmosphere using argon gas. “The interface remains clean when broken in an inert atmosphere,” says Prof. Chattopadhyay.

“One of the main purposes of ball milling [at room temperature] is to mix materials. But in the case of ball milling at low temperature we did not observe any mixing; the individual components separate out really well. We wanted to use this property more constructively. So we took two printed circuit boards from optical mouse and milled them for 30 minutes,” recalls Dr. Tiwary, who is currently at Rice University, Houston, Texas.

The polymer becomes brittle when cooled to -120 degree C and ball milling easily breaks it into a fine power. Metals and oxides too get broken but are a bit bigger in size.

Separation of individual components

The milled e-waste powder was then mixed with water to separate the components into the individual classes of materials using gravity. The powder separated into two layers — the polymer floats at the top due to lower density, while metals and oxides of similar size and different density settle at the bottom. The bottom layer when diluted further separated into oxides at the top and metals at the bottom. The oxides and metals were present as individual elements.

“Our low-temperature milling separates the components into single phase components without using any chemicals, which is not possible using other techniques,” says Prof. Chattopadhyay. “Our process is scalable and is environment friendly though it uses higher energy.”

The technology has been patented and transferred to a Bengaluru-based company.

Published in The Hindu on April 2, 2017

Bengaluru researchers mimic nature to produce richer colours

sood-optimized

(From left) Prof. Rajesh Ganapathy, Chandan Mishra and Prof. Ajay Sood have taken the first step to make crystalline materials that produce structural colours by scattering light

In a novel approach that mimics nature, Bengaluru-based researchers have designed crystalline materials that selectively scatter specific colours of light. Dyes and pigments produce colour predominantly through selective absorption of light. But scattering of light by particles which are arranged in an ordered, periodic pattern produces structural colour, which gives butterfly wings their colour and sheen.

The backlit colour display of a mobile or laptop monitor becomes difficult to read under intense light. But if the front panel were to be made of structural colour then the ambient light would become a source of colour. By producing crystals that scatter wavelengths corresponding to  red, green and blue light, structural colours can be used in place of the conventional LED and LCD monitors, too.

In nature, nanosized particles and colloids are responsible for producing structural colours. Compared with atoms, colloidal particles are 10,000 times bigger, and, so, conventional lab techniques to move the particles over long distances to form an ordered, periodic pattern have been riddled with problems.

The novel approach adopted by researchers at the Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) and Indian Institute of Science (IISc) has overcome the challenge of transporting the particles to target sites; the size and symmetry of the growing crystallites are also controlled. The results were published in the journal Proceedings of the National Academy of Sciences.

structural colours can be used in place of the conventional LED and LCD monitors.“We need some mechanism which will drive the particle in a given direction to a long distance. We solved this by creating an energy gradient on the surface of a Moiré pattern. The energy gradient dictates where the colloidal particle should go and nucleate and grow in an ordered fashion,” says Chandan K. Mishra from the Chemistry and Physics of Materials Unit, JNCASR, and the first author of the paper.

To produce the Moiré pattern the researchers first imprinted an optical grating (which has linear trenches drilled on a glass surface) on a soft polymer. Rotating the optical grating at a small angle and repeating the imprinting on the soft polymer led to the creation of a geometrical pattern. The Moiré pattern with channels of non-uniform depth was the template on which the colloidal particles get deposited at specific sites in an orderly pattern.

“There is an energy gradient within the geometric pattern which drives the particles to the desired locations,” says Prof. Ajay Sood of the Department of Physics, IISc and a coauthor of the paper. The energy gradient comes from the variation in the depth of the channels and the presence of small particles driving the colloidal particles to the specific sites in the pattern.

In the presence of smaller particles (which are added along with the colloidal particles), the colloidal particles are attracted towards the channel wall. “Since the channel has a gradient in depth, the smaller particles drive the colloidal particles to the deeper portions of the channel where the particle is surrounded by tall ridges on either side.  This is the final resting place of the colloidal particle. If all the particles come to this point they form a crystal,” says Prof. Rajesh Ganapathy from JNCASR and one of the corresponding authors of the paper.

The nucleation initially begins at the sites where the ridges have maximum height and then progressively spreads to sites where the channel height is less. The distance between two nucleation sites is predetermined to scatter a particular colour, for instance, red.

The process is repeated with colloidal particles of a different size which will grow into crystals with a different separation distance between them (periodicity). Due to a different separation distance the crystals will then scatter light of a different wavelength. “Our eventual goal is to make these patterns and drop particles of three different sizes at the same time and the Moiré pattern will decide where each particle size should go and form crystals that scatter red, green and blue wavelength,” says Prof. Ganapathy. “What we have done is the first step — controlling the colloidal self-assembly using the Moiré pattern.”

Published in The Hindu on December 18, 2016

IISc produces a novel salt to better combat bacterial infections

img_0386

The salt developed by Dr. Shanmukha Prasad Gopi (left) and Prof. Gautam Desiraju (right) of IISc is highly efficacious than a physical mixture of the two drugs.

Using crystal engineering, a team of researchers from the Indian Institute of Science (IISc) Bangalore has successfully produced a highly efficacious binary salt of two commonly used drugs — norfloxacin (antibacterial) and sulfathiazole (antimicrobial). The salt is more effective than a physical mixture of the two drugs. The results were published in the journal Molecular Pharmaceutics.

Better solubility

The two drugs were ground for nearly 30 minutes and made into a solution from which the salt was produced. It has enhanced pharmaceutical effects compared to the physical mixture of the two drugs.

The underlying reason for the salt’s improved efficacy is the better solubility and diffusion of the drugs, particularly norfloxacin and, therefore, enhanced bioavailability and pharmaceutical activity.

“Norfloxacin in a pure form or in a physical mixture has low solubility and permeability, so the amount of the drug that goes through the membrane and gets into tissues is less. To compensate for this, higher dosages of norfloxacin drug are generally used,” says Prof. Gautam R. Desiraju from the Solid State and Structural Chemistry Unit at IISc and the corresponding author of the paper.

The salt has properties that are more than the aggregate of the individual drug properties.But in the case of the binary salt, a “large enhancement in overall solubility” was seen at pH 7.4, which is generally seen in the small intestine where most of the absorption takes place. Most importantly, both the drugs showed comparable solubility when present in the salt form.

Similarly, in the case of permeability, the amount of binary salt diffusing through the membrane was much higher in the first hour. In contrast, the parent drugs show much lower diffusion. When the drugs are present together in a physical mixture, each one has a different rate of diffusion across the membrane. “But in the case of the binary salt both diffuse together. It is like sulfathiazole pulls norfloxacin across the membrane so both the drugs are available at the same time at the site of action to combat the microbes together,” he says.

“We are trying to study the mechanism behind the increased diffusion so that we have molecular level understanding of what precisely is happening,” Prof. Desiraju says.

“Generally the salt form increases solubility and because of high solubility or concentration gradient diffusion gets enhanced,” says Dr. Shanmukha Prasad Gopi from IISc and the first author of the paper.

Potency tested

The potency of the salt and the physical mixture of the drugs was tested on E. coli, Staphylococcus aureus and fungi. Studies showed that the salt was able to achieve the same result of inhibiting bacterial and fungal growth at about half the concentration of the physical mixture.

For the same dosage, the salt had nearly five times greater area that was clear of microbes than the physical mixture of the two drugs. The greater inhibition of microbes around the salt might be due to greater solubility and faster release of norfloxacin from the salt compared with the pure form and the simultaneous presence of both the drugs at the site of action when present as a salt. “The salt has properties that are more than the aggregate of the individual properties,” Prof. Desiraju says.

Due to enhanced solubility, the amount of norfloxacin required will be less and, therefore, lesser chances of developing resistance against the drug. The team has patented the salt. A Mumbai-based pharmaceutical company has already shown interest in the salt.

Published in The Hindu on November 3, 2016

IISc’s self-powered UV photodetector can power electronic devices

buddha

The UV light that gets into the pores of the nanoflakes undergoes multiple reflections and finally gets absorbed, says Buddha Deka Boruah.

In a novel approach, researchers from the Indian Institute of Science (IISc), Bangalore, have developed a cost-effective, high-performance, self-powered UV photodetector that can use the harvested optical energy for direct self-charging of energy storage devices such as supercapacitor. It can also be used for operating electronic devices in the absence of external power source.

The researchers developed the photodetector by integrating semiconducting vanadium doped zinc oxide (VZnO) nanoflakes with a conducting polymer. The photodetector has superior performance in terms of faster detection of photo signals in the order of milliseconds even when UV light intensity is low.

The Vanadium Zinc Oxide material has 98 per cent light harvesting efficiency.The results were published in the journal ACS Applied Materials & Interfaces.

Zinc oxide (ZnO), the base material for UV detection, can be doped with vanadium to produce photodetectors that are self-powered. When doped with vanadium, the microstructure of ZnO changes from nanorods to closely-packed nanoflakes, causing an increase in the surface area to volume ratio of the material.

Doping ZnO with vanadium also creates surface defects within the band gap (between the conduction and valence bands) of ZnO, which helps in trapping the UV radiation that falls on the nanoflakes.

“The nanoflakes are 80 per cent more porous than nanorods.  The nanorods are one-dimensional and so the possibility of light reflection from the top surface is more. But nanoflakes are two-dimensional and the light penetration is more,” says Buddha Deka Boruah from the Department of Instrumentation and Applied Physics at IISc and the lead author of the paper. The UV light that gets into the pores undergoes multiple reflections and finally gets absorbed.

detector-optimized

Once hydrogenated, the  nanoflakes’ photocurrent generation capacity increased to 1,000 nA.

“The vanadium-doped zinc oxide nanoflake material has 98 per cent light-harvesting efficiency, which is much higher than the 84 per cent seen in zinc oxide nanorods,” says Prof. Abha Misra from the department who is the corresponding author of the paper.

The VZnO nanoflakes were annealed (heated and allowed to cool slowly) in the presence of hydrogen gas at 350 degree C (hydrogenated) to increase the conductivity and reduce the recombination of photo-generated charge carriers.

More photocurrent

Compared with ZnO, which generates only 40 nA photocurrent, the VZnO nanoflakes produced five times more photocurrent. Once the nanoflakes were hydrogenated, the current generation capacity further increased to 1,000 nA, says Boruah.

If the increased optically active surface area of the nanoflakes enhanced the generation of electron-hole pairs (photo response), resulting in increased current generation, hydrogenation brought about a further enhancement in the electron-hole pair generation as well as increased free electron density, leading to more current generation.

When exposed to UV light, the device, after hydrogenation, was able to detect photo signal within milliseconds, which is nearly 100 times faster than conventional UV photodetectors, says Prof. Misra.

Published in The Hindu on October 15, 2016

Voila! IISc’s catalyst uses sunlight to make water E. coli-free

giridhar

The catalyst developed by Eswar (left) and Dr. Giridhar Madras can reduce the E. coli load from 10 million to zero in an hour.

Drinking water can now be made completely free of E. coli in about 30 minutes by exposing it to sunlight thanks to a catalyst developed by researchers at the Indian Institute of Science (IISc), Bangalore. The E. coli bacteria is responsible for most of the water-borne bacterial infections. The results were published on September 2, 2016 in the journal RSC Advances.

Conventional methods that rely on UV light to kill pathogenic bacteria are often expensive and need relatively more sophisticated process. Now, IISc researchers have made it possible to easily rid the water of E. coli bacteria by synthesising a zinc oxide photocatalyst that absorbs both UV and visible light to kill the bacteria. “We studied E. coli but the photocatalyst can potentially kill all harmful bacteria,” says Prof. Giridhar Madras from the Department of Chemical Engineering at IISc and the corresponding author of the paper.

“Our catalyst is unique as we have doped it with a metal and a non-metal (copper and nitrogen) so that it absorbs both visible and UV light,” says Prof. Madras. “Our catalyst is far efficient than conventional catalysts as it absorbs both wavelengths.”

The visible light comprises more than 40 per cent of the electromagnetic spectrum and UV light 4 per cent. The catalyst absorbs both spectrums and generates free radicals that kill the bacteria. Such is the efficiency of the catalyst in the presence of sunlight that it is able to reduce the E. coli load in water from 10 million to zero in an hour. “The rate of killing the bacteria increases with an increase in the intensity of sunlight.  We did out experiments between 11 am and 3 pm,” Prof. Madras says.

gupta

The zinc oxide catalyst was doped with copper and nitrogen, says Rimzhim Gupta, the first author of the paper.

But to be effective, the catalyst (in powder form) must be kept in suspension so there is a greater chance of the catalyst interacting with the bacteria and killing them. “We kept stirring the water to keep the catalyst in suspension, else it will settle at the bottom and its efficacy in killing the bacteria will be reduced. We are now trying to coat the catalyst on a glass plate and suspend the glass plate in water to kill the bacteria,” says Prof. Madras.

How it works

“Conventional catalysts like TiO2 are active only in the UV region as it has a wide band gap. In the case of ZnO we have reduced the band gap by by co-doping it with copper and nitrogen,” says Rimzhim Gupta from IISc and the first author of the paper. “The co-doped ZnO catalyst will be able to absorb even the longer wavelength of 400-700 nm which is the visible range of the spectrum.”

The band gap of a semiconductor determines the wavelength of light required to activate a photocatalyst and kill the bacteria by producing free radicals. In this case, copper and nitrogen have their unique roles in reducing the band gap. While nitrogen shifts the valence band, copper shifts the conduction band.

“When you shine light of appropriate wavelength on a photocatalyst the electrons and holes get separated. The electrons and holes can themselves produce free radicals that kill the bacteria. And free radicals like superoxide radicals and hydroxyl radicals too can kill E. coli. Superoxide radicals can be generated when electrons from the conduction band react with dissolved oxygen and holes in the valence band react with hydroxyl (OH) group and produce hydroxyl radicals,” says Neerugatti KrishnaRao Eswar from IISc and a coauthor of the paper. “We found superoxide and hydroxyl radicals were more effective in rupturing the cell wall of the bacteria and killing them.”

Published in The Hindu on October 2, 2016