KERNEL Issue 2, 2021 WHEN BACTERIA BAND - IISc
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Research Newsletter of
the Indian Institute of Science Issue 2, 2021
KERNEL
Editorial
WHEN BACTERIA BAND
TOGETHER
Like humans, bacteria too
can form close-knit groups,
a behaviour usually seen
when they are under duress.
In this issue of Kernel,
read more about sociality
in bacteria: the different
kinds of aggregations,
how they are formed, and
why scientists are keen on
studying them.
Swarming patterns in Pseudomonas aeruginosa bacteria in different concentrations of media (Photo courtesy: Varsha Singh lab)
Also featured in this issue To humans, bacteria appear to lead some from IISc. Their research has led
is an electrical engineering mundane lives. These single-celled to exciting discoveries about how and
prokaryotes – so called because their why bacteria form different types of
lab developing tools and cells lack a distinct nucleus and other collectives.
technologies related to structures – absorb nutrients from their
human speech, besides environment, grow, and multiply on Social bacteria
their own. But how do such relatively The study of social behaviour in
stories on a software rudimentary organisms perform complex bacteria began in 1683, when Dutch
platform for smart video tasks like turn milk into yoghurt or cause scientist Antonie van Leeuwenhoek, the
tracking and a device for diseases? The answer, at least in part, world’s first microscopist, discovered
lies in the ability of several bacteria to a bacterial commune by studying
measuring evaporation. form tightly-knit social groups in certain plaque scraped off his own teeth. But
situations, a behaviour that has attracted it wasn’t until the 1970s that research
the attention of many biologists, including on bacterial sociality gained traction
Continued on page 2
GFP positive Salmonella Typhimurium in strings (Image courtesy: Alan Varghese, Dipankar Nandi lab)
Continued from page 1
when Danish researcher Niels Høiby showed Cell Biology at IISc. For his postdoctoral Talking bacteria
that individuals of a bacterial species research at the Institute of Integrative Before bacteria transform themselves
called Pseudomonas aeruginosa tend to Biology, ETH Zurich, in Switzerland, from their solitary forms to their social
aggregate in the lungs of patients with he investigated social interactions in avatars, they need to communicate with
chronic cystic fibrosis infections. Since then, Myxococcus xanthus, a predatory soil each other about whether and when to
such aggregations, referred to as biofilms, bacterium. When starved, these bacteria make this coordinated switch. Biologists
have been shown to be involved in several aggregate into mounds, become spores have discovered that in order to achieve
bacterial infections in humans, and have also and form a multicellular fruiting body. this lifestyle change, bacteria talk to each
been documented in many other habitats. Upon encountering nutrients again, they other in a chemical language. And the most
germinate and start their lives afresh. popular form of chemical communication
A biofilm is formed when members of a is called quorum sensing, which is seen in
species, or sometimes multiple species, In a recent study published in Current several bacteria, including in P. aeruginosa.
join forces and become embedded in a Biology, Pande and his colleagues have
slimy matrix. Bacteria produce biofilms demonstrated that spores of this bacterium “They use a molecular signal or quorum
often in response to stressful environmental secrete a diffusible “public good” molecule signal to count one another. When the
conditions like a lack of moisture or required for germination. The study also signal reaches a certain threshold, bacteria
nutrients, or the presence of toxins like captures the flipside of sociality: conflict. as a population switch their behaviour,”
antibiotics or disinfectants, according to In a mixed-strain fruiting body, spores explains Singh. She reveals that quorum
Dipankar Nandi, Professor in the Department belonging to a particular strain do not sensing in swarming P. aeruginosa is
of Biochemistry at IISc. Biofilm bacteria work produce and contribute to the common achieved with the help of a chemical called
together to secrete the components of the pool of another important molecule needed C4-homoserine lactone (C4-HSL), which
slime, which protects them from unfriendly for germination. This, according to the can easily diffuse across the population.
environmental conditions. They also authors, constitutes cheating because the “When C4-HSL levels reach a threshold, the
cooperate with each other to share nutrients benefits of being in a collective accrued by population can make a surfactant which is
and remove metabolic waste. these freeloaders come at a cost to other necessary for swarming,” she adds.
group members.
Nandi’s lab also recently discovered a Apart from offering valuable insights into
new mode of cooperation in bacteria. Alan Varsha Singh, Associate Professor in the group behaviour, studying social bacteria
Varghese, a former undergraduate researcher Department of Molecular Reproduction, is helping researchers explore how to make
in his lab, was studying how Salmonella Development and Genetics, studies another human-friendly bacteria more effective,
Typhimurium – which causes gastroenteritis intriguing cooperative behaviour in and hostile bacteria less harmful. For
in humans – responds when it is deprived bacteria called swarming. With the help of instance, Samriddhi Thakur, another former
of iron. During the course of his research, appendages called flagella, groups of some undergraduate student in Nandi’s lab, has
he stumbled upon “string-like structures” species move in unison in a moist medium shown that biofilm formation in Salmonella
formed by these bacteria, which turned out when the situation demands. “For instance, could be inhibited by coumarin, a chemical
to be a novel collective. According to Nandi, we know that P. aeruginosa engages in that plants make to defend themselves
since this kind of multicellular aggregation is swarming when a specific nutrient is against herbivores.
new to science, it was important for his team limiting, such as iron or phosphate,” says
to characterise its structure in detail, and Singh, who wrote a review article on the Understanding bacterial interactions in
also demonstrate how they are different from phenomenon in the Journal of the Indian cooperatives could also address larger
classical biofilms (this bacterium also forms Institute of Science in 2020 along with evolutionary questions, such as how
biofilms but under different conditions). Rahul Jose, an undergraduate student in multicellularity itself may have originated,
Their discovery has just been reported in the her lab. Another paper co-authored by a prospect that many biologists like Pande
journal Frontiers in Microbiology. Singh, also published last year in Physical find exciting. “We can test social evolution
Review E, has shown that these bacteria hypotheses more cleanly and precisely in
A former Junior Research Fellow in Nandi’s can also swarm away from a patch of microbial systems,” he says.
lab, Samay Pande is now Assistant Professor antibiotic.
in the Department of Microbiology and - Karthik Ramaswamy
KERNEL | ISSUE 2, 2021 | Pg 2
Image: Yogesh Simmhan
A SOFTWARE PLATFORM FOR
“SMART” VIDEO TRACKING
Researchers at IISc have developed a Anveshak. It can not only run these dropping the video quality to save on
novel software platform from which apps tracking models efficiently, but also plug bandwidth, while continuing to track the
and algorithms can intelligently track and in advanced computer vision tools and object.
analyse video feeds from cameras spread intelligently adjust different parameters
across cities. Such analysis is not only useful – such as a camera network’s search In 2019, as part of a winning entry for
for tracking missing persons or objects, radius – in real time. the IEEE TCSC SCALE Challenge award,
but also for “smart city” initiatives like Simmhan’s lab showed how Anveshak
automated traffic control. In a recently published paper, his team could potentially be used to control
shows how Anveshak can be used traffic signals and automatically open up
Thousands of video cameras have been to track an object (like a stolen car) “green routes” for ambulances to move
set up across cities worldwide. Machine across a 1,000-camera network. A key faster. The platform used a machine
learning models can scour through the feature of the platform is that it allows learning model to track an ambulance
feeds from these cameras for a specific a tracking model or algorithm to focus on a simulated Bengaluru road network
purpose – tracking a stolen car, for example. only on feeds from certain cameras with about 4,000 cameras. It also
These models cannot work by themselves; along an expected route, and tune out employed a “spotlight tracking algorithm”
they have to run on a software platform other feeds. It can also automatically to automatically restrict which feeds
or “environment” (somewhat similar to a increase or decrease the search radius needed to be analysed based on where the
computer’s operating system). But existing or “spotlight” based on the object’s last ambulance was expected to go.
platforms are usually set in stone, and don’t known position.
offer much flexibility to modify the model as Simmhan’s lab is also working on
the situation changes, or test new models The platform also enables the tracking incorporating privacy restrictions within
over the same camera network. to continue uninterrupted even if the the platform. “We can decide what are the
resources – the type and number of kinds of analyses that we are comfortable
“There has been a lot of research on computers that analyse the feeds – are running. We could say, for example,
increasing the accuracy of these models, limited. “In the field, the amount of that we would allow analytics that track
but sufficient attention hasn’t been paid to computing power you have is not really vehicles, but not analytics that track
how you make [the model] work as part of negotiable on the fly. The devices are people, or analytics that track adults
a larger operation,” says Yogesh Simmhan, static. You have to do the best you but not children,” he says. They are also
Associate Professor at the Department of can with what is available,” explains working on ways to use Anveshak to track
Computational and Data Sciences. Simmhan. For example, if the search multiple objects at the same time.
radius needs to be increased and the
To address this gap, Simmhan’s lab has computer becomes overwhelmed, - Ranjini Raghunath
developed a software platform called the platform will automatically start
KERNEL | ISSUE 2, 2021 | Pg 3
Evaporimeter tested in the lab (Photo courtesy: Navneet Kumar)
AN EFFICIENT WAY TO
MEASURE EVAPORATION
An IISc team has developed a new device change in water level over a day gives the For example, if this device is kept near
that could measure the rate of evaporation evaporation rate from that area for that day. a paddy plant, we could get a better
of a local area within a couple of minutes. measure of the evaporation rate that
The device is a more efficient and “The disadvantages [of existing methods] a particular leaf of that plant might be
inexpensive way to measure evaporation are that the evaporation rates are for one experiencing,” explains Arakeri.
when compared with existing methods. whole day, and over a large area (1 square
“Our method allows you to get a much metre). And one needs an open ground The device would be useful to scientists
more realistic measure of transpiration to place the device. But we have a simple studying the physiological process of
from plants and evaporation from soils,” method of directly measuring evaporation transpiration in plants because of its
says Jaywant H Arakeri, Professor in the from a small surface – at the order of a ability to measure the evaporation rate
Department of Mechanical Engineering, couple of centimetres, and over a short over small areas and over short periods
and senior author of the study published period of time,” Arakeri explains. of time. Stomatal responses can also
in the Journal of Hydrology. now be addressed, in a better and more
The proposed device consists of a filter controlled way, using this device. The
Evaporation is the process by which water paper connected to a capillary tube that authors also suggest that it could be used
turns from liquid to a gaseous state. takes water from a reservoir to the filter in oceans to study changing evaporation
Apart from being an integral process paper, thereby wetting it and thus mimicking patterns in the open sea and in weather
in the water cycle, evaporation also an evaporating water surface. By measuring stations to estimate evaporation rates in
plays a major role in regulating water the distance travelled by the lower meniscus the atmosphere, an important parameter
loss in plants through a process called in the capillary tube over a couple of that is currently not measured.
transpiration. Measuring the evaporation minutes, the evaporation rate is estimated.
rate is useful for farmers to gauge water The innovation lies in being able to measure The next step is to make the device
requirements for their fields and in the very small amount (about 1 microlitre) commercially available. “We are looking
weather stations to characterise the local of water that is lost in evaporation from the for interested companies to take it up to
atmospheric condition. It is also widely surface in a minute. make it into a product. Meanwhile, we
used by botanists to study the dynamics have been doing some experiments in the
underlying transpiration by plants. Since the evaporation rate is affected by polyhouse [a kind of greenhouse used to
a number of factors such as temperature, grow crops in a controlled environment],
Currently, pan evaporimeters are the wind velocity, and humidity, this device and we also want to try it out in the
most commonly used devices to measure could show the evaporation rate within a field,” says Arakeri.
evaporation rates. They resemble large niche environment. “It gives you an idea
pans that are filled with water. The of evaporation rate even from a small leaf. - Rohini Murugan
KERNEL | ISSUE 2, 2021 | Pg 4
Photo: Swapnil Pawar
AGGRESSION BETWEEN LIZARD SPECIES
CAN SHAPE COMMUNICATION
Males of two fan-throated lizard species – between mates of their own and other Thaker’s lab in the Centre for Ecological
Sitana laticeps and Sarada darwini – court species. This apparent confusion triggers Sciences.
females and behave aggressively in front aggression between these species that
of rival males by rapidly flagging their can escalate to chasing and even physical In areas where the two species co-exist,
dewlaps, fan-shaped appendages below combat, which is particularly dangerous Sitana laticeps males have smaller
their throats. for the smaller Sitana laticeps. dewlaps and show reduced courtship
and aggression. These shifts make them
In a small grassland patch in Maharashtra, To avoid aggression, males of the Sitana look a little more like females, reducing
these species overlap with each other. laticeps species have modified their unwanted attention from the aggressive
Males of both species look different but sexual signals and learnt to distinguish males of the other species.
females look almost identical. Males, between rivals of their own and other
therefore, find it difficult to distinguish species, finds a new study from Maria - Maria Thaker and Amod Zambre
Image: N Devabharathi
PRINTED GAS SENSOR TO DETECT TOXIC
NITROGEN DIOXIDE
A fully inkjet-printed gas sensor to detect size. They used an inkjet printer to print 20 parts per billion. It also provided
very low levels of nitrogen dioxide, a toxic this ink onto a substrate, and allowed it stronger response than most currently
gas, has been developed by researchers in to self-assemble into layers of crystalline available gas sensors in the market or
the Department of Materials Engineering tin oxide with well-connected pores 15-20 the ones that the researchers developed
and Materials Research Centre led by nm in size. The printed sensor has a large at the lab scale.
Subho Dasgupta. The sensor is based on surface area to efficiently adsorb and
thin films of mesoporous tin oxide. desorb nitrogen dioxide. It also allows The use of an inkjet printing technique
fast movement of electrons within its also makes it easier to scale up the
To create the “ink” for printing, they crystalline tin oxide ligaments, resulting process to produce inexpensive gas
combined a tin oxide precursor (metal in enhanced sensing. sensors for a wide range of applications.
halide) with a tri-block copolymer and
an additional organic compound called The sensor was able to detect even trace - Ranjini Raghunath
xylene that helps in increasing the pore amounts of nitrogen dioxide – as low as
KERNEL | ISSUE 2, 2021 | Pg 5
Image: Yazhini Arangasamy
COMPARISON OF AFROTHERIAN PROTEINS:
STRENGTH IN NUMBERS
A new study by N Srinivasan’s lab in the sense of smell respectively – were hallmarks elephants have an unusually high
Molecular Biophysics Unit has probed the of Afrotherian proteomes. number of sperm-protecting proteins.
proteomes – the entire set of functional This may be because for animals like
proteins – of a group of mammals The authors also report that although the elephant with low reproductive
collectively referred to as Afrotheria. Afrotherian proteomes are almost 99% rates and fewer offspring, it is critical
Afrotheria includes animals currently similar, comparisons on a finer scale to produce high quality eggs and sperm.
living in or originally from Africa, ranging reveal that elephants have branched The presence of more copies of these
from small insectivorous shrews and out extensively from their Afrotherian proteins may boost sperm protection and
golden moles to elephants. The authors relatives. The number of copies of individual the success rate of reproduction.
found that a large number of ribosomal proteins and their combinations may have
proteins and olfactory receptors – linked contributed to differences between them. - Yazhini Arangasamy
to stress regulation and a heightened In addition, their study highlights that
Image courtesy: P AjitKumar
AN ARMOUR PROTECTS AND PRIMES
TB BACTERIA AGAINST AN ANTIBIOTIC
The bacterium that causes tuberculosis build-up of lethal levels within the cells. mutations in the bacterial DNA. In the
(TB) is notorious for gaining resistance This strategy ensures the survival of these subsequent generations, those bacterial
to antibiotics, which makes treatment cells despite the continued presence of cells that have gained rifampicin-resistant
of the disease difficult. A new study by lethal levels of the drug outside. mutations escape antibiotic-mediated
P AjitKumar and colleagues from the death. These mutant bacteria grow and
Department of Microbiology and Cell The team also discovered that this divide to generate new populations of cells
Biology shows that when TB bacteria capsule consists of certain types of that are entirely rifampicin-resistant and
encounter the common anti-TB drug carbohydrate molecules that make it therefore survive in the presence of lethal
rifampicin, a small proportion of the difficult for rifampicin to enter the cells. doses of the drug.
bacterial cells develop a thick, armour- The small amount of rifampicin that
like capsule. This armour reduces the manages to enter the cells triggers a - Sunreeta Bhattacharya (with inputs from
entry of the drug, thereby preventing the stress reaction, which in turn causes authors)
KERNEL | ISSUE 2, 2021 | Pg 6
Photo courtesy: SPIRE lab
SPEAK, AND YE SHALL BE
HEARD!
PRASANTA KUMAR GHOSH AND HIS TEAM DECODE THE INTRICACIES OF HUMAN SPEECH
Gone are the days when electrical English sentence will sound different. “This they have recently launched an app called
engineering just meant long trails of wires is because of the influence of the accent of “Neurocompanion”, which enables the
and beeping machines. In the age of Siri their mother tongues, and you can tell that I telemonitoring of patients using their
and Alexa, the field has grown to encompass am a Bengali the same way,” he says. Since voice recordings. This research is being
diverse domains. One such area of research English is a must for most jobs, ideally the conducted in collaboration with the
is the study of human speech. Researchers speaker should have a neutral accent so National Institute of Mental Health and
working in this area collect, process and that customers can understand what they Neurosciences (NIMHANS), funded by the
interpret not just sound, but also other are saying. Often, some training is needed Department of Science and Technology,
cues from a speaker. This has been the to reduce the influence of native language Government of India.
focus of the SPIRE lab at the Department of accents, he adds. “English Gyani”, a
Electrical Engineering (EE). software tool being developed in the SPIRE The SPIRE lab also collaborates with the
lab, aims to do just that. Using automated All India Institute of Speech and Hearing
Headed by Prasanta Kumar Ghosh, Associate speech recognition algorithms, it acts as a (AIISH) at Mysore, in developing tools for
Professor, the lab is keenly interested personalised tutor that provides interactive several types of voice therapies. One goal
in the orchestra of organs that generate feedback to the user, based on their voice is to quantify the extent of damage to the
the majority of sounds in our body – the recordings. voice box, using data from high-speed
respiratory and the vocal systems. These videos of the vocal fold vibrations while
organs not only enable us to speak, but the Another major research focus is tracking a person speaks. Another is to develop a
sounds and cues from them also contain the movements of body parts involved tool to help people with severely damaged
tremendous information about their health. in articulating speech – the jaws, lips, or absent voice boxes, by converting their
Combine these vocal signals with facial teeth and tongue. For this, the researchers whisper-like speech into normal-sounding
expressions and body movements when we use a specialised device called the speech.
talk, and the result is a rich set of data that Electromagnetic Articulograph. Special
allows scientists to ask and answer some sensors placed on these body parts Prasanta’s interest in pursuing a career
challenging research questions. record where and how they move during in this area was seeded when he was a
speech. This data can assist doctors to Master’s student at IISc. “Here, I got a
One of the challenges in speech research detect, diagnose and monitor several flavour for doing research for the first
is evaluating one’s English pronunciation, neurodegenerative disorders including time. And the teachers were really great,
particularly when the speaker is from India, Amyotrophic Lateral Sclerosis (ALS) in terms of not just teaching, but helping
a country with a diversity of languages. and Parkinson’s Disease (PD), in which us to see beyond what was taught in
For example, as Prasanta points out, a struggling to speak is a typical sign of class,” he says. In particular, TV Sreenivas
Gujarati and Kannadiga speaking the same disease progression. Towards this goal, from the Department of Electrical
KERNEL | ISSUE 2, 2021 | Pg 7
Speech waveforms and spectrograms linked to each person uttering the syllable ‘pa’ in succession: an ALS patient, a PD patient and a healthy person (Image courtesy: SPIRE lab)
Communication Engineering and YV department at the University of Southern different problems, the depth helps him or
Venkatesh from EE at IISc inspired him California (USC) where he did his PhD, and her to dig deeper into their own research,”
greatly, he adds. the Professor Priti Shankar Teaching Award he says. For that purpose, he ensures
from IISc in 2017. He believes that the goal that each student is involved part-time
After IISc, brief stints as a researcher at of teaching should be to train students to in other projects as well. This also helps
Microsoft and IBM helped him choose develop the ability to weave new ideas out build a social network within the lab; if a
academia over industry. “Everything else of the concepts that they are taught. His student is stuck on a particular topic, they
was great [in the industry], but what teaching strategies are strongly influenced are in touch with their colleagues through
was lacking was the freedom to define by those of Bart Kosko, who taught him at meetings for various other projects that
my own research path. In a company, USC. He also encourages his students to they are involved in, and don’t feel isolated
I can’t really create my own tree of give talks at other institutions, or intern at or depressed, Prasanta explains.
research, with all of the branches that companies to get a feel for the work culture
I’m interested in. I wanted to create a there. “Pre-pandemic, we went on a lot of lab
research environment where I can solve outings – had lunch outside and did other
problems that are impactful for society,” Prasanta strongly believes that to mature activities together. That connects all of us
he says. as a researcher, students should be as a family, and helps us to grow socially
involved in pursuing a variety of questions. as well,” he says. “Otherwise, we will all
Prasanta has also received recognition “The depth and breadth of research ... become like robots.”
as a teacher, including the Centre for that’s important. While the breadth helps a
Excellence in Teaching award from the EE student to gain and share knowledge across - Samira Agnihotri
An electromagnetic articulograph used to collect data from various body parts for speech research (Photo courtesy: SPIRE lab)
Office of Communications (OoC) EDITORIAL TEAM DESIGN
Indian Institute of Science (IISc) Deepika S TheFool.in
Karthik Ramaswamy
Bengaluru - 560012
Ranjini Raghunath (Coordinator)
kernel.ooc@iisc.ac.in | office.ooc@iisc.ac.in Samira Agnihotri
Vaishalli Chandra
KERNEL | ISSUE 2, 2021 | Pg 8
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