A recent study by scientists from the International Centre for Genetic Engineering and Biotechnology (ICGEB) published in the journal Nature Scientific Reports sheds light on the mechanisms employed by a family of proteins, called FET proteins, to recognise and bind to RNA.

FET proteins have amino acid sequences that are preserved across species. These proteins, which play an important role in the normal housekeeping of the cell, are implicated in various oncogenic diseases. Mutations in some members of this family—FUS (Fused in sarcoma) or TAF15 (Human TATA binding protein associated factor 2N)—are also known to be involved in neurodegenerative disorders like amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia. FET protein functions range from transcribing DNA to processing RNA sequences with roles such as translation, splicing, transport, stability and localisation. Little was known, at a molecular level, about how these proteins recognise their RNA targets and bind to them.

In macromolecular interactions, like protein-protein or protein-RNA complexes, the interactive forces could be weak, like Van der Waals, electrostatic, hydrophobic or ionic. Strong bonds arise from covalent interactions, such as disulphide bonds. Most RNA binding proteins have multiple binding sites, called domains. To aid binding, the RNA binding domains (RBDs) carry protruding amino acid residues which facilitate weak or strong interactive forces. For most of the RBDs, these interactions are known to be RNA sequence specific.

Researchers in this study used a suite of tools—solution-state NMR spectroscopy, calorimetry, docking and molecular dynamics simulation—to delineate specificities of RBD-RNA interactions in the FET protein TAF15. What they found was that in a manner unique to TAF15, the predominant RBD in this protein, known as RRM (RNA recognition motif), forms hydrogen bond (H-bond) pairs with RNA. The RNA part in this interaction are stem loops—hairpin-shaped intramolecular base pairing patterns—known as the SON (stem in natural left-right configuration of RNA). The bindings were based on RNA’s secondary structural configuration and independent of protein backbone. When further analysed using different RNA sequences, the interactions were found to be independent of the length of the RNA sequence as well. This mechanism of RNA binding is distinctive—other RNA binding proteins are known to rely on non covalent interactions called pi-pi stacking. Since the RRM domains are highly similar in TAF15 and FUS, the authors believe the mechanisms of protein-RNA binding in FUS to be similar as well.

Senior author and Staff Research Scientist, Neel Sarovar Bhavesh described this mechanism of binding with an insightful analogy: “It would be like holding a cricket ball in a glove. TAF15 binds tightly or clamps to the stem loop of RNA, stabilises it and regulates protein production. This interaction is facilitated by the concave face, or the glove, of the protein. The mode of interaction is thus a form of ‘concave-convex’ lock and key model.”

How does this increase our understanding of the neurodegenerative disorders associated with this family of proteins? Bhavesh explains, “Point mutations in RRM surface are known to be implicated in ALS. It is possible that with these mutations, the concave surface of the RRM domain in TAF15/FUS doesn’t form stable interactions with RNA and other protein complexes. These destabilising binding interactions could possibly lead to aggregation of RNA/protein complexes that are a hallmark of ALS.”

While the study did a full structural analysis of TAF15 and eliminated roles of other domains in RNA recognition and binding, the group hopes to work out the full mechanistic details of FET proteins at the cellular level as well. Using different RNA sequences and point mutations, details on what stages of the interaction regulation starts, or at what stages the protein aggregation might occur, would help in understanding of progression of associated neurodegenerative diseases.

This article was originally published in TIFR Science News.

In a recent breakthrough to combat malaria, a collaboration of Indian and American scientists have identified a malarial parasite protein that can be used to develop antibodies when displayed on novel nanoparticles. This approach has the potential to prevent the parasite from multiplying in the human host and also inhibits transmission through mosquitoes. The finding points towards developing a powerful malaria vaccine in the hope of eradicating this debilitating and often fatal disease.

Malaria takes a heavy toll on human lives. About half a million people die every year and several hundred million suffer from this disease across the globe. To add to the disease burden, the malaria parasite is increasingly becoming resistant to commonly used anti-malarial drugs. Development of an anti-malarial vaccine is an integral part of an effort to counter the socio-economic burden of malaria.

Researchers in the malaria labs at Tata Institute of Fundamental Research (TIFR), Mumbai, India, have now identified a five amino acid segment of a Plasmodium parasite protein that is normally involved in producing energy from glucose. Work from Gotam Jarori’s lab has earlier shown that this protein, enolase, is a protective antigen and has several other functions that are essential for parasite growth and multiplication.

Taking this a step further, in a recently published paper in the Malaria Journal, they have shown that a small part of this protein, that is unique to parasite enolase and is absent in human enolases, has protective antigenic properties. “As enolase was implicated in invasion of red blood cells of the host as well as the midgut of mosquitoes, antibodies against this small fragment can potentially have a dual benefit by blocking the multiplication cycle of the parasite in humans, as well as inhibiting transmission through mosquitoes”, says Jarori.

The work was carried out in collaboration with Shiladitya DasSarma’s laboratory at the University of Maryland School of Medicine, Baltimore, USA, who have developed Archaeal gas vesicle nanoparticles (GVNPs). The small unique segment of enolase was genetically fused to a nanoparticle protein and this conjugated system was used to vaccinate mice. Interestingly, a subsequent challenge with a lethal strain of mouse malaria parasite in these vaccinated animals showed considerable protection against malaria. Says DasSarma, “GVNPs offer a designer platform for vaccines and this work is a significant step forward towards a new malaria vaccine.”

This study is a significant advance in the field, since most other vaccine candidate molecules tested so far confer protection against only a single species of parasite, due to the species and strain specific nature of these molecules. “The small segment of five amino acids that forms a protective epitope is present in all human malaria causing species of Plasmodium and hence, antibodies directed against it are likely to protect against all species of the parasite”, says Sneha Dutta, a graduate student at TIFR who conducted these experiments. Efforts are now focused at developing this into an effective vaccine against malaria.

We will never have a universal “cure for cancer,” in part because there is no single type of cancer to cure. Cancer can result from many different kinds of breakdown in the body's regulatory mechanisms, and in most cases we cannot pinpoint the cause closely enough to attack the problem at its root. However, research continues to improve our toolbox of cancer-specific therapies. Recent work by an Indo-US collaboration, involving researchers at the Indian Institute of Technology (IIT), Kanpur and the University of Michigan (UM) at Ann Arbor, has identified potential underlying cellular mechanisms for a sub-type of colorectal cancer, which may in turn give us new therapeutic routes to target the disease.

Colorectal cancer is one of the most common types of cancer diagnosed worldwide, and also one of the leading causes of cancer-related death. We already have targeted therapies approved for colorectal cancer patients, but these show poor response in over 40% of cases, correlating with two genetic mutations in KRAS and BRAF genes, frequently found in colorectal cancer. In their search for alternative therapies for these sub-types, the researchers at IIT Kanpur and UM Ann Arbor focused on one particular abnormality found in an overlapping subset of colorectal cancer cases. Many cases of colorectal (as well as pancreatic, lung, breast and prostate) cancer show over-expression of SPINK1, a gene that encodes a protein whose multiple functions include averting apoptosis, or cell death.

Correlation of SPINK1 over-expression with cancer is far easier to prove than causation, however, and when searching for treatments it is primarily causation that matters. Thus the researchers embarked on the arduous process of trying to find out how exactly SPINK1 might be linked with the underlying mechanisms of colorectal cancer. Searching for the gene's functional effects within colorectal cancer cultures that showed SPINK1 over-expression, they found that blocking the gene's expression reduced cancer proliferation while enhancing its expression had the opposite effect. They discovered, furthermore, that SPINK1 might act by suppressing the expression of Metallothioneins. These are proteins involved in balancing cellular zinc nutrition—or homeostasis—essential for normal function and can increase the responsiveness of cancerous cells to chemotherapy. Targeting the SPINK1 gene therefore has the dual effect of reducing SPINK1 protein levels while increasing the expression of Metallothioneins, making the cells far more sensitive to drug therapies.

Much still remains a mystery, however, says Bushra Ateeq, senior author on the study and Assistant Professor and Intermediate Fellow of the Wellcome Trust/ DBT India Alliance at IIT Kanpur. How precisely does SPINK1 over-expression exacerbate cancerous growth? And how do Metallothioneins have an ameliorative effect? Although we know their effects, the full story of these proteins and their interactions is not yet available to us. “The mechanism behind this phenomenon is poorly understood and demands further attention,” says Ateeq.

This article was originally published in the Journal of Cell Biology: Caitlin Sedwick, 2015, Journal of Cell Biology, Vol. 211, No. 4, 2015

Molecules from outside the cell, or those produced inside the cell, can be packed into membrane-bound vesicles to facilitate their transport to different cellular compartments. This is a highly regulated process that remains poorly understood, even at the most basic level; it is still unclear, for instance, how vesicles form and bud off from their parent membrane.

Having become interested in membrane biology during his graduate work on receptor biology, Thomas Pucadyil first cut his teeth on the problem of membrane fission as a postdoc, where he studied the function and regulation of dynamin, a GTPase essential for vesicle fission from the plasma membrane. Pucadyil says that to comprehend vesicular trafficking, it will be necessary to isolate and study the inherent capabilities of proteins that drive membrane fission. We called him at his laboratory at the Indian Institute of Science Education and Research (IISER) in Pune to hear about the strategies he’s pursuing for this work.

Environmental Influence

Did anyone influence your decision to pursue a career in research?

I would attribute my leanings toward science largely to the environment I grew up in. My father, who’s now retired, was a plasma physicist, so I was exposed to science at a very early age.

What did he do to foster your interests?

My parents never explicitly stated a desire for me to go into science, but I remember that his colleagues would often visit and invariably we’d end up having dinner and discussing their work, or more generally talking about where the world was headed, Indian science policy, and things like that. I think this underlying current made it easier for me to go down this path. My dad is also an avid reader and made sure that there was plenty to read at home. I was exposed to a lot of science fiction novels early on.Other than that, I think the most enjoyable parts of my childhood were spent with my older brother. We were both—and honestly, still are—tremendously interested in LEGO®. My son Nikhil has serious competition from his dad when it comes to LEGO®. [Laughs]

I also liked gardening a lot—probably because of my mom, who was and continues to be very fond of gardening. She passed the gene down to me. Right now I’m cultivating some of the exotic plants collected by my IISER colleagues in my back yard.

Do you still enjoy science fiction?

My favorite author is Arthur C. Clarke. It’s remarkable how Clarke proposed so many things in his writing that eventually ended up coming true. My favorite novel is Clarke’s Childhood’s End, which I think is really pertinent these days. It’s about civilization on Earth coming of age, leaving aside petty squabbles in the face of a monumental challenge.

The future with reach

What led you into a research career in biology?

My bachelor’s and master’s degrees were in biochemistry. I had some exposure to bench work during my master’s dissertation project, and I think that’s when I learned that the ground beneath you is always shaky when it comes to research; I made that transition from taking everything that the textbooks said for granted to actually going out there and testing those ideas.

I did a summer rotation in Amitabha Chattopadhyay’s laboratory at the Centre for Cellular and Molecular Biology in Hyderabad. I would eventually end up doing my PhD there, as well. That summer, I tagged along with a postdoc in Amit’s laboratory named Kaleeckal Harikumar, who was very patient and just a fantastic mentor at the bench. We worked on understanding how a G protein–coupled receptor would respond to covalent modification. These proteins are extremely difficult to express and handle in a laboratory setting, so we would start with a tissue where the protein was expressed, then work our way down through a fairly elaborate biochemical isolation technique to get a more enriched preparation. It was a fairly short project, but it resulted in my first publication.

That was an eye-opener for me. All of a sudden I realized science was actually within reach. Students are raised by reading textbooks, research articles, and reviews, and for some reason, this can all seem very distant. I recall reading articles and looking at the affiliations of the authors in places I’d only heard of. There was no real connection. It seemed so far away. But it was a remarkable experience to see my name with my institution in print. My PhD thesis evolved from that work, studying how membrane lipids influence receptor function.

So you were interested in membrane physiology even before your postdoc?

Amit was really instrumental in getting me excited about membranes, and during my PhD I was already working with membrane preparations isolated from the hippocampus. These were rather complex membranes, and I guess at some point I realized that I needed to strip down that complexity if I wanted to clearly understand what was going on. I needed to be able to reconstitute membranes so that I could know, for example, precisely which kind of lipids or proteins were present. So, toward the end of my PhD, I started working on model membrane systems: liposomes and supported lipid bilayers. I had already decided by then that for my postdoc and later career I wanted to move away from receptor biology and into an area where I could make more original contributions. That’s when I got excited about vesicular transport, and decided to join Sandra Schmid’s laboratory at Scripps.

Building better models

In Schmid’s lab you pioneered a new technology to study membrane fission…

I was determined to come up with an assay to study dynamin-catalyzed membrane vesiculation. But I had been working on supported bilayers for a fairly long time in Sandy’s laboratory—maybe two years—and wasn’t making headway until a paper came out from Jennifer Hovis’ group that just put everything in order. Conventional supported lipid bilayers are formed from lipid vesicles that fuse to cover the surface of a silica bead. They’re fairly taut membranes with little reservoir to bud vesicles from. But her group showed that if you had negatively charged lipids and played around with salt concentrations, you could generate bud-like features or membrane tubes emanating from the beads’ surfaces. The biochemist in me took over and I started testing these conditions until I managed to pack much more membrane onto a bead than is required to cover its surface. This additional membrane reservoir was very useful for studying proteins that deform membranes.

Then I teamed up with another postdoc in Sandy’s laboratory, Rajesh Ramachandran. He worked on a lot of the molecular details about how dynamin binds membranes and how its GTP hydrolysis cycle affects its assembled state, while I perfected assays to allow us to observe regulated vesiculation reactions. We identified some of the key residues important for dynamin’s enzymatic attributes and membrane fission activity, and this gave us some ideas about how the protein might manage membrane fission.

Then you returned to India to start your own lab…

I always knew I wanted to come back to India, and at that time there was a lot of buzz about a new set of institutes being set up by the Indian government as part of the Indian Institute of Science Education and Research Initiative.

My laboratory is a little different from a typical laboratory in the States, perhaps, because most laboratories in India are graduate student–heavy. It’s a lot of fun and a lot of effort working with students! They also seem to have a lot going on in life outside of work. They keep me up to date on movies and music. [Laughs] I spend a lot of time with my group members outside the laboratory.

Do the approaches you used in Schmid’s laboratory still figure in your work today?

Oh, absolutely. Our emphasis is largely on trying to understand vesicular transport, starting with a reconstitution approach. One of our aims is to uncover the intrinsic capabilities of molecules involved in vesicular transport reactions. If we take out the layers of regulation that are built around these processes, can we understand how they are achieved?

We’ve been working quite a bit on clathrin polymerization on membranes, and how this molecule promotes vesicle budding. We’ve set up assays to observe the polymerization reaction taking place in real time under a microscope, that also allow us to interrogate the functions of different clathrin adaptor proteins. There’s a huge variety of clathrin adaptors and they’re not functionally interchangeable, so we’ve begun looking at how different adaptors affect clathrin membrane recruitment.

In addition to that, we’re working on assay systems to study membrane fission. We had a paper come out recently in Nature Cell Biology describing a new generation of model membrane system that we call supported membrane tubes, or SMrT. This technique is fairly straightforward to use and allows us to approach membrane fission from a variety of angles.

Dynamin gets a lot of attention but it’s restricted to the plasma membrane. Surprisingly, Pietro De Camilli’s laboratory published that cells lacking all three dynamin isoforms are viable in culture for a few weeks. That means there must be other molecules that catalyze membrane fission, both at the plasma membrane and elsewhere in the cell. We’re taking a candidate-based approach, revisiting other molecules that have been suggested to function in membrane fission.

When it is time for the female sand fly to hatch her eggs, a nutrient-rich blood meal is an immediate necessity. That means a bite into the nearest mammal or rodent. A sand fly infected with parasitic Leishmania can, during the bite, infect its host, causing the onset of Leishmaniasis. According to the 2014 WHO fact sheet, the disease occurs mainly in 3 forms: Cutaneous, Mucocutaneous and Visceral Leishmaniasis (VL). VL also known as kala-azar (black fever) is the severest of these. Accompanied by fever and ulcers, VL can damage the vital organs (liver, spleen) over time and potentially result in death if left untreated.

A recent article in Parasitology International from Kumarasamy Thangaraj’s lab at Center of Cell and Molecular Biology (CCMB) Hyderabad examines the connection between VL caused by the parasitic protozoa Leishmania donovani and the serum protein Mannose Binding Lectin (MBL). MBL is a blood protein that upon encountering foreign bodies (bacteria, protozoa, fungi or virus), binds to them and activates the ‘complement lectin cascade’—the body’s first mechanism of elimination of infectious gatecrashers. MBL is known to affect Brazilian VL caused by L chagassi. In order to examine the effects of MBL on Indian VL caused by L donovani, Thangaraj’s team conducted a case-controlled study in Bihar, which is an established hotspot for VL. Based on medical records issued by Government Hospitals, 443 subjects were recruited (218 VL patients and 225 healthy controls). Genomic DNA extracted from blood samples were PCR-amplified and sequenced to identify the variants in MBL2 gene and quantify MBL protein levels.

The MBL serum levels in VL patients were significantly higher compared to those in healthy cases. This is in sync with previous studies that indicate higher MBL levels during intracellular infections. Genetic analysis by the researchers has demonstrated that the promoter region of MBL2 gene (78th position) is an important genetic factor for VL occurrence—the presence of a specific variant decreased the susceptibility to the disease. Further higher degree genetic analysis clarified that some genetic segments occur more frequently in healthy subjects, suggesting a correlation with a reduced risk of VL. Interestingly, MBL2 variants have shown different effects in the context of other intracellular infections in other regions of the world. For instance, MBL2*LUPA haplotype is identified as an important risk factor in Brazilian patients with leprosy. Thus it is possible that the role of MBL2 variants differ with different­ geographical settings.

VL is a global health burden with 4,00,000 new cases and 40,000 deaths reported worldwide. A whopping 67% of this global disease burden is shared by India, where VL is a major endemic disease especially in the states of Bihar, West-Bengal and Eastern UP—they account for 90% of Indian VL. VL is treatable, and minimizing exposure to sandflies through covered clothing and careful use of insect-repellants is the best precaution. The lead author Anshuman Mishra, a postdoc at CCMB, who was involved with the yearlong effort of identifying patients in Bihar, notes that lack of hygiene is an important contributor to the continuous presence of VL. However, on a preventive note, there are no vaccines available for human use up to date and this underlines the importance of ongoing research in this area. The findings from this study indicate that the severity of VL in infected patients might differ depending on the genetic variations in MBL2, thus adding a new dimension to the current scientific understanding of Kala-azar.

The auditorium of Alliance française de Bangalore was abuzz with chatter as people filed in. The crowd, which was largely made up of scientists—students and professors alike—and a handful of engineers, doctors and teachers, had gathered together for an evening of science and fun. Six young researchers were nervously preparing to take the stage and share their work with all assembled. Everyone had to understand their research and be entertained by their presentation. The one who managed it best would be the 2015 EURAXESS Science Slam India winner.

Ainhitze Bizkarralegorra Bravo, Country Representative, EURAXESS Links India opened the event with an introduction to EURAXESS - Researchers in Motion. She walked the audience through the format of the event—the contestants would present, following which the audience would be divided in groups that each selected one winner after some discussion and deliberation. The ultimate winner was the one who got the most votes from the groups. In case of a tie, the review panel, which had previously helped to select the 6 finalists, would help resolve it and pick a winner. “The Science Slam provides an opportunity for young researchers to tell people about their research, but with the freedom to decide how to express themselves. It also gives them an opportunity to explore their own talents in ways that they would not have otherwise,” said Karthik Ramaswamy, Visiting Scientist at IISc and one of the members of the review panel.

Arnab Bhattacharya from the Tata Institute for Fundamental Research (TIFR), Mumbai, a member of the review panel took the stage for a demo Slam. He said that the Science Slam was a “wonderful celebration of science that brings people together.” He went on to add that events like this bring scientists out of their lab to share their work, adding, “Most scientists in India work with public money and the public have a right to know what we do.”

The final presentations followed, and covered a whole spectrum of disciplines in quick succession—astrophysics, cognition, disease risk, gravitational waves, animal cloning and animal behavior. Props, music, songs, zany software, demos—some live and others videotaped and even a dance were used to tell the stories of their science. Bollywood made its ever-popular presence felt in the references that peppered the talks. One talk, for instance, adopted the script of a popular movie (DDLJ) while examining whether ones DNA poses a risk of disease. There was time for questions after every “talk”. Technical questions were discouraged—the idea was to keep things light. The audience and the panel worked hard to come up with witty questions. “The level of informality that was stressed upon and executed during presentations was very new to me. I always enjoy any chance of learning something new, and all the presentations had much to offer. Each one of them introduced me to a new topic in varying degrees of rigour. That was very stimulating,” said Rajashree Nori, an aspiring science writer. She went on to add that all the presenters had managed to get people talking about their work—a good sign of public engagement.

The EURAXESS Science Slam India 2015 has been organized by EURAXESS Links India in partnership with the Indian Institute of Science and IndiaBioscience, and the support of Finnair, Philips Innovation Campus and Alliance française de Bangalore.

The Centre for Cellular and Molecular Platforms (C-CAMP) and the California Institute for Quantitative Biosciences (QB3) will collaborate to create an Indo-US life science innovation hub. The two organisations signed a Letter of Intent (LoI) during the Prime Minister Narendra Modi’s recent visit to California.

C-CAMP, a part of the Bangalore BioCluster, which includes NCBS and inStem, is an enabler of life science research and entrepreneurship that has worked with about 50 bioscience startups across India. Based in the Bay Area, QB3 is a research and technology commercialization institute jointly set up by, and across, three University of California (UC) campuses—UC Berkeley, UC San Fransisco and UC Santa Cruz. It promotes innovative research in the “quantitative biosciences” and assists life science entrepreneurs. “The idea is to connect two ecosystems, which are promoting life science innovation in their own cultures, and by doing so, to connect their startups and bring them a global perspective,” said Taslimarif Saiyed, Director and COO, C-CAMP.

At the ground level, the innovation hub will act as a gateway to help startups from India understand the US scenario—the emerging healthcare and life science trends, IP transfer procedures, regulatory hurdles and joint venture possibilities—and vice versa. This kind of knowledge is not documented anywhere in the literature and is largely dissemintated through these kinds of hubs. C-CAMP and QB3 plan to co-invest in startups, co-incubate, facilitate exchanges between scientists and entrepreneurs at both ends, and also offer immersion programs. These programs will allow startups from the US to come to India (and vice versa), and spend a few weeks understanding the needs and nature of the local market. They will also gain insight into whether their technology has potential and whether they can find partners, and how they can get investment. While investors are largely present in the US, there are social impact investors in India who will be willing to invest in US startups addressing Indian needs in the field.

A lot of Indian startups focus on affordability of the technologies they develop. Saiyed feels that an equal focus on quality could help them reach and compete in markets beyond India. “One of the reasons to tie up was to bring that global perspective to our ventures and ask where we stand,” he said.

Across the world, regions at high elevations have been warming at an accelerated pace—with average temperatures in the Himalayas having risen more than twice the global average of 0.7^oC in the last century. What does this mean for the future of Himalayan forests, grasslands and glaciers? A recent collaboration between researchers at the University of Kashmir, Srinagar and the Indian Institute of Science (IISc), Bangalore, published in Climatic Change, projects that under business-as-usual emissions scenarios the face of the Himalayas will dramatically change within the next hundred years. By the year 2085, we might have shrublands, savanna, and evergreen forests in areas now covered with tundra and ice.

Himalayan plant species are already migrating up the mountains as temperatures rise. In order to see how that change might progress, the researchers modelled shifts in vegetation from the present to the end of the 21^st century in the Kashmir Himalayas under three different climate change scenarios called A1B, RCP 4.5 and RCP 8.5. Under each such scenario—standardized by the IPCC (Intergovernmental Panel on Climate Change) to enable easy comparison of results between research groups—greenhouse gas accumulation follows a trajectory determined by underlying socio-economic factors. The A1B scenario belongs to an earlier class of climate change models from 2000, each of which bases itself on a particular storyline of human development. Here, the economy grows rapidly, and so do novel efficient technologies – with a balance between the use of fossil fuel and non-fossil fuel energy. RCP stands for “Representative Concentration Pathways,” a class of models published in 2013. These start with a particular emissions trajectory from now until the end of the century (again, depending on human action), and predict the consequent level of radiation that will be trapped by the earth's atmosphere in 2100.

From emissions, the researchers extrapolated climate—and from climate data, combined with soil type and topography in the Kashmir Himalayas, the researchers modelled possible vegetation changes in the coming decades. At each of these three levels there is uncertainty, however—and any errors will multiply with each subsequent level. Consequently, the researchers fed the averaged output from five different climate models arising from the above scenarios into their vegetation model. They also projected the vegetation model not just into the future but onto the present, to see how well it accorded with observed vegetation data. Model and observation matched by 87.15%, although the authors give the caveat that present vegetation data in Kashmir from satellite maps could not always be confirmed through ground observations.

The results across climate change scenarios showed substantial changes in the vegetation of the Kashmir Himalayas by the end of 21^st century. By 2035, in each case, much of the area presently under polar conditions could be replaced by boreal evergreen forests, with grasslands vanishing. Temperate evergreen broadleaf forests may proliferate at lower altitudes, where there is now open shrubland. By 2085, boreal evergreen forests start to be usurped in turn by shrubland and savanna—most notably in the RCP 8.5 scenario, where the levels of the sun's radiation trapped by Earth's atmosphere continue to rise by the end of this century.

Irfan Rashid, author on the study and Assistant Professor at the University of Kashmir, stresses the effect on water security if the snow and ice-covered regions in the Himalayas were to disappear. “This definitely would have serious implications for streamflows, hydropower generation, tourism, agriculture and drinking water,” he says. He also warns of the loss of livelihoods for forest-dependent communities, and the potential extinction of wildlife as their habitats shift upwards and shrink. Rajiv Chaturvedi, another author on the study and National Environmental Sciences Fellow at IISc, suggests that we need to maintain corridors for flora and fauna to aid their migration in the face of climate change. “The benefit of wildlife and the benefit of trees are not separate,” Chaturvedi says.

The next step is to expand the study to an all-India level, with a 25x25 km² resolution rather than the 50x50 km² resolution used in this study. “This will be the first attempt to project vegetation using observed climatology at India level at a high resolution,” says Rashid.

A sophisticated sound mixer, a projector and a slew of laptops occupied the stage at the Dasheri auditorium in the National Centre for Biological Sciences (NCBS), Bangalore. The stage was set for the last performance of the Sky Island Beatbox Project, an unconventional undertaking that seeks to raise awareness about the distinctive and fragile “sky islands” of the Western Ghats—home to many endemic, and endangered, songbirds.

As the audience trickled in, beatboxer Ben Mirin drew giggles with his vocal acrobatics as he performed a sound check. His fellow performers joined him on stage—bird ecologist VV Robin, Research Fellow at NCBS, and ecologist-turned-photographer Prasenjeet Yadav. What followed was an audio-visual treat, with some serious science thrown into the mix. Mirin matched notes with the birdsongs recorded in his mixer. The catchy tunes had the audience tapping their feet and clapping in time. Yadav’s images of the songbirds filled the projector in the background as the trio shared stories and science about these birds and their shrinking ecosystem. After the presentation, the audience indulged in their share of beatboxing, and even composed a tune or two.

Beatboxers use their voices to imitate drumbeats and other percussion sounds. It turns out that beatboxing is a surprisingly fitting tool to tell the story of the sky islands. For one, it simply makes the science very accessible and enjoyable. The other, deeper connection is that the real scientific way beatboxing works is very similar to the way birdsong works. Beatboxers mimics thing, are constantly engaged with what is around and picking up new things. “This is exactly how birdsong works. Birds in this part of the world are open-ended learners; they learn song almost all through their lives. And are constantly incorporating new things into their repertoire. Songbirds also have regional dialects, just like beatboxers,” said Robin.

The response to the project has been enthusiastic—their performances in Ooty, Kodaikanal, Kochi and Trivandrum saw large turnouts and extensive media coverage. “People from the audience in Kodaikanal showed me photos of some of these birds on their phones,” said Robin. “They said: these are birds we see in our backyards but we didn’t know they were special. Now we know that these are threatened endemic birds. It was very satisfying to see that we made some impact,” he added. Also satisfying to the trio were the insightful questions from the audience about the research and questions from students about their careers—they wanted to know how they could become scientists or photographers or beatboxers too.

“We had a sense that this could work, but we certainly didn’t expect that it would work with everybody,” said Yadav. Their show in Trivandrum was a case in point, where officials from the Forest Department were in attendance. They liked the idea so much that they have expressed interest in having an anthem composed for them based on this music, opening the doors to a unique collaboration between scientists and park rangers.

This blitzkrieg of events was planned in less than two months. An avid birder himself, Mirin had made a music video on birds in New York. Robin, who was introduced to his work through an article in the Guardian, reached out to him. They connected and clicked. What cemented the chemistry was the focus on a common goal—creating awareness about the sky island birds, and the dangers posed to their habitats by human action. “These are birds that offer songs that are really anthems of their natural heritage. By making music from their songs, we wanted to make the people who live in and around the Western Ghats connect with these special birds they find in their backyards,” summed up Mirin.

Imagine yourself at a crowded dinner party, with multiple conversations flying at cross-purposes to each other—greetings between friends, flirtation, heated debate. How do we pick out individual voices across the room, let alone carry the thread of our own conversation?

The “cocktail party problem” described above is faced by many species—including humans—but can have additional challenging layers for some. Animals must communicate and locate potential mates while evading predators and filtering out other noisy species. A new study by researchers at Hyderabad Central University and the Indian Institute of Science, Bangalore has found a species of bushcricket with an unusual solution to this quandary. In response to the male call, females of Onomarchus uninotatus—hidden by jackfruit leaves—stay silent, and may not actively seek the male. Instead, the females send covert vibrations through the tree, guiding the male while leaving eavesdropping predators unaware.

Bushcrickets, or katydids, use camouflage that is difficult to spot, but their evening chorus is unmistakable across the globe. In most species of bushcricket, the female locates the calling male and travels towards him. But that road is perilous: even if the travelling female avoids predators, the male might not. “For many species of cricket and bushcricket, broadcasting an acoustic call comes with disadvantages. Both predators and parasites can eavesdrop on these calls,” says Kaveri Rajaraman, faculty at Hyderabad Central University and co-author of the study.

These predators include bats, well adapted to pick up on the high-frequency courtship calls of their insect prey. But earlier work by Rajaraman and colleagues found that O. uninotatus has evolved an unusually low frequency call, potentially reducing male predation pressure. Theoretically, the balance of predation pressure between sexes should influence who can afford risky mate-seeking behaviour during courtship. Thus a shift in pressure, away from males, could allow a species to evolve novel communication strategies.

Indeed, the researchers found that wild-caught O. uninotatus females did not always search for the source of male song—an often fatal part of the process, as evidenced by the ease with which echo-locating bats catch flying females. A third of the females did not seek out the source of male song, and only about half successfully found the playback speaker.

What females universally did, however, was vibrate in place on their jackfruit tree branch, out of phase with the male chirps. Male bushcrickets in turn were consistently able to follow female vibrations to their source. Curiously, however, males only started searching for the female if they detected both the female's vibration and a male courtship call—either their own or that of another caller. The authors suggest that this may indicate a “satellite strategy” on the part of the males, piggybacking on the communications efforts of others in order to disperse predatory risk.

Vibratory communication combined with sound is unusual in insects. It can be likened, in the noisy party described above, to a woman responding to a man's advances by tapping in Morse code—a strategy that will keep her message discreet, but comes with its own limitations. Vibrations require that bushcrickets be near one another, and are more energy-intensive than acoustic calls.

Tulsi or Ocimum tenuiflorum is mentioned in the ancient Hindu scriptures of the Vedas and Puranas and has long been used by practitioners of Ayurveda, a traditional Indian alternative medicine, to treat a variety of conditions. The plant produces a wide variety of bioactive compounds, which have been found to have anti-cancer, antioxidant, antifungal and anti-inflammatory properties among others. They are believed to be part of the plant’s self-defence mechanism, but a lack of genomic data on their origin means they are poorly understood.

Now, researchers led by Sowdhamini Ramanathan from the National Centre for Biological Sciences (NCBS) in Bangalore have used DNA sequencing technology to create a draft genome of the Krishna subtype of O. tenuiflorum. Despite only assembling 61 per cent of the estimated genome size, the team was able to use the genetic map to identify several major genes responsible for the production of the herb’s medicinal compounds, known as 'metabolites' due to the fact they are a by-product of the plant's metabolism.

Nearly 30 such metabolites with medicinal properties have been reported in the genus Ocimum, of which 14 have complete metabolic pathways, so the team searched for genes from these pathways in the newly produced genome. A total of 458 genes were identified, which were either homologous (have a common ancestor) or directly code for enzymes involved in the synthesis of metabolites. Expression of these genes was confirmed using RNA sequencing and reverse transcription polymerase chain reactions (q-RT-PCR) in both the Krishna and Rama sub-types of O. tenuiflorum, as well as other Tulsi species O. gratissimum, O. saccharinum and O. kilmund.

The team, which included researchers from the Institute for Stem Cell Biology and Regenerative Medicine (inStem) and the Centre for Cellular and Molecular Platforms (C-CAMP), also decided to investigate an important metabolic pathway that involves the production of ursolic acid—a compound with anti-inflammatory, anti-microbial and anti-tumour properties—using q-RT-PCR as well as mass spectrometry to detect the presence of metabolites in the various parts of the plant. They discovered that the metabolites or their precursors appear to be synthesised in the young leaves of the Tulsi plant, but then remain in the mature leaves often in high abundance where they retain their medicinal properties. “The sequence reveals the interesting pathways used by Tulsi to make ursolic acid, a medically important compound. If one could now use modern synthetic biology techniques to synthesise ursolic acid—a compound with multiple chiral centers—it would be of great benefit,” said S. Ramaswamy, from inStem.

The researchers also found high expression levels of a gene that produces the pigment anthocyanin in Krishna Tulsi, which they believe helps explain the purple colouration of the sub-type’s leaves.

A novel wastewater filtration technique developed by a team from the Indian Institute of Science (IISc), Bangalore recently won first place at the Google Pitch Fest in Switzerland. The technology is particularly designed to benefit people in remote and disaster-hit areas that have sources of water, but none that are fit for drinking. No water is wasted in the process, and no membranes or chemicals are used.

“My background is in device physics and circuits. I haven’t really worked in the water technology area before this,” said Sanjiv Sambandan, Assistant Professor at the Department of Instrumentation and Applied Physics, “but when I started my lab, one of the ideas that we discussed was to use electric fields to purify sewage water.” The proposal got a small amount of funding from IISc. The idea uses the understanding of how particles behave in electric fields. If one disperses particles in any fluid—and if there is a permittivity or conductivity difference between the particles and the fluid, the particles will polarize in an electric field. The polarized particles have an attractive force, which will cluster these tiny particles into larger clumps. Using this along with other phenomena that aid clustering, these larger clumps can be removed with a very low-cost sieve, without the need for a very fine membrane.

The system was initially built on a small printed circuit board as a proof of concept. At that time the throughput was one microliter a minute, which is essentially a tiny droplet. The big challenge was in scaling up and building a technology that could purify a few hundred litres of water within an hour. “The engineering behind increasing the throughput while maintaining a low energy currency has been, in some sense, the most important stride in our work,” said Sambandan. What this took was more a psychological change than any adoption of new techniques.

There exist technologies that can achieve a high level of purification of water. However, these technologies are expensive and don’t lend themselves well to very remote settings or disaster-hit areas, which suffer from limited accessibility and little or no electricity. The question the team asked was: “can these people themselves build a water filter from locally available materials that achieve this goal?” They worked backwards keeping in mind the limited resources that may be available in these settings. Sambandan acknowledged that, much to their surprise, the throughput improvement came about when they peeled off unnecessarily fine precision requirements and started working with a crude set-up. “That, in some sense, led to a nice optimization of the engineering problem,” he said.

While the technique is not as good as the reverse osmosis technology, it meets potable water standards—it can remove sub-micron particles, metal oxides, hardness, all coliform bacteria, and also corrects for pH to some extent. The system also desalinates the water to a small extent. A 1-litre water bottle can be purified in just 5 minutes, powered by batteries, a hand crank or a small solar cell.

Diabetes, a disease involving impaired glucose metabolism, has assumed epidemic proportions due to its high prevalence worldwide. India is estimated to have more than sixty-two million diabetic patients, making it one of the epicentres of the global epidemic. The numbers are predicted to increase exponentially in the coming decades. Worryingly, the age of onset of diabetes in Indians is decreasing, indicating that in the coming years, a substantial section of India’s youth will be suffering from the disease. However, research on diabetes in India has been insufficient, making it difficult to formulate an adequate national response.

Scientific efforts worldwide have focussed on finding biomarkers that can aid screening and early detection of diabetes. Indians comprise the ‘Asian Indian Phenotype’, which refers to a gamut of biochemical and clinical peculiarities in the South Asian population that predisposes it to the disease. This makes direct extrapolation of data obtained from western populations to Indians difficult. This motivated a research group from Madras Diabetes Research Foundation (MDRF) to conduct a recent study focussed on finding a biomarker for diabetes specifically tailored for the Indian population.

“The most promising biomarkers should be robust and clinically translatable”, explained Muthuswamy Balasubramanyam, a senior scientist at the foundation and one of the principal investigators of the study. Circulatory microRNAs, small pieces of non-coding RNAs floating in the bloodstream, satisfy both these conditions—they are remarkably stable and require only a blood sample for testing—thus being ideal for large-scale clinical use. MicroRNAs are also known to be master regulators of gene function, affecting a variety of physiological processes. Research has shown that the level of circulating microRNAs changes consistently in various pathophysiologies like cancer and cardiovascular diseases, but little is known about its role in diabetes, especially in the Indian context.

Aiming to identify circulating microRNAs that could serve as biomarkers for diabetes, the investigators recruited three groups of subjects for the study: diagnosed Type 2 Diabetes Mellitus (T2DM) patients, subjects with normal glucose metabolism (NGT: Normal Glucose Tolerance) and those with pre-diabetic state of Impaired Glucose Tolerance (IGT). Blood glucose level was measured in all the participants to confirm the grouping. Candidate microRNAs were searched after characterizing the microRNA profile for each participant. “We found that four microRNAs had different serum levels in IGT and T2DM patients compared to control NGT subjects”, said Balasubramanyam. Levels of two of these microRNAs were also similarly altered in diet-induced diabetic mice, providing further support towards their potential usability as a diabetes biomarker.

“Interestingly, among the altered microRNAs , miR-128 has never been described in previous diabetes studies and appears to be specific for the Indian population”, said Balasubramanyam. Considering that miR-128 has been earlier reported as a biomarker of cognitive impairment and that there exists a neurological component in the etiology of type 2 diabetes, Balasubramanyam speculated that miR-128 could be the connecting link for the cognitive dysfunction and/or depression associated with metabolic diseases like diabetes. miR-128 was further positively correlated with cholesterol both in prediabetic subjects and in diet-induced diabetic mice, suggesting that its increased level might be associated with the development of altered lipid level associated with T2DM.

The results, though preliminary, are exciting because miRNAs are considered to have tremendous potential as non-invasive biomarkers for the screening, monitoring and diagnosis of a disease. The group plans to conduct long-term studies to elucidate the connection of these microRNAs with diabetes to facilitate their use as biomarkers in future. The day might come when a simple blood test would reveal the microRNA profile, facilitating pre-emptive screening of at-risk people. Effective prevention and management can then start right away, before the onset of the disease, which in turn, would lead to a reduction of the burden diabetes imposes on the in Indian nation and society at large.

Delivery of cargo to the correct address requires accurate directions and a dependable machinery for delivery. Any defects in them affect timely delivery or cause the cargo to be misdelivered. This chain of events is not very different at a cellular level. Our cells also have their own transport pathways responsible for the cargo delivery at the right destination at the right time. Any variations to that system shows up as symptoms to fatal diseases. A team of researchers from the Indian Institute of Science (IISc), Bangalore unravels the nitty gritties of one such transport pathway in specialized animal cells where failure to deliver the cargo— melanin synthesizing enzymes in this case—could result in disorders like albinism.

Melanin pigments are responsible for the colour of our skin and also play an important role in protection against radiations and any other damage from light. They are produced by a series of organic chemical reactions that occur in cellular organelles called melanosomes. These cell compartments need melanin synthesizing enzymes transported from other organelles to non-pigmented premature melanosomes where pigment production is initiated. The cargo transport pathways are facilitated with the help of four multi subunit cytosolic protein complexes, BLOC-1, -2, -3 and adaptor protein (AP)-3 complex.

BLOC-1 consists of 8 subunits, functioning in the initial step of transport pathway, while BLOC-2, a 3-subunit protein complex, functions towards the end of the pathway. The team of researchers led by Subba Rao Gangi Setty from the Department of Microbiology and Cell Biology in IISc recently elucidated the role of BLOC-2 in directing the cargo containing vesicles towards maturing melanosomes for subsequent reactions. It does so by the specific method of “tethering” or by stabilizing the two different membranes between which the cargo is transferred through fusion and subsequent cargo delivery.

They went on to show that mutations in any protien subunit of BLOC-2 result in inefficient delivery of melanin synthesizing proteins to maturing melanosomes and thus failure in production of the melanin pigment. This malfunction manifests in the form of albinism of skin and eye, also referred to as occulocutaneous albinism. This is one of the primary clinical symptoms in Hermansky-Pudlak Syndrome (HPS). The other symptoms are lung fibrosis and bleeding. Out of the 16 possible genetic mutations that can result in HPS, only 9 are known in humans so far. Three out of those nine subtypes are a result of mutations in the BLOC-2 protein complex.

Even though it is now established that BLOC-1 and-2 play key respective roles in the overall cargo delivery, how they achieve this is not yet clear. In addition to these key proteins, other cellular machineries are also known to be responsible for membrane fusion and cargo delivery. These proteins are called Soluble NSF (N-ethylmaleimide-sensitive factor)Attachment Protein REceptor (SNARE). SNARE proteins, a family of about 38 proteins has been known for their role in membrane fusion during the delivery of cargo. For the first time, the researchers have identified two members from the SNARE family that are involved in the protein transport pathways to melanosomes. Loss in expression of these proteins mistarget and degarde the enzymes, subsequently affecting melanosome maturation. The team demonstrated that higher expression of a mutant form of SNARE increased cell pigmentation. Furthermore, their study has also shown how these molecules recycle and regulate each other for efficient cargo delivery and melanosome formation.

To most eyes, NIPER Mohali may just seem like a lovely green campus. But the abundance of medicinal plants nurtured at this pharmaceutical institute gave a research idea to Jayeeta Bhaumik, a synthetic organic chemist. Due to their antioxidant properties—the same ones that make plants healthy for humans—some medicinal plants can be used to synthesize and coat nanoparticles.Medicinal plants had the added benefit for Bhaumik of being a local, inexpensive resource—and suitable for biomedical applications, because they pose none of the potential health hazards of more conventional chemical methods of nanoparticle synthesis. Concerns about health have led many other groups to turn to “green” methods of synthesizing nanoparticles in recent years. After initial success using extracts from the jamun fruit to create silver nanoparticles, Bhaumik and her colleagues have now published research that used extracts from green tea leaves and vajradanti roots to produce silver and gold nanoparticles. They attached compounds with diagnostic and therapeutic functions to these nanoparticles, creating basic biomedical delivery vehicles that could one day be refined for cancer treatment.

Nanoparticles range from 1–100 nanometres, larger than a single atom but still small enough to slip inside a cell. Viruses, enzymes and proteins lie within this range. The attraction of nanomaterials for biomedical research lies partly in the simple fact of scale, but also in the changed physical properties at such small sizes. Quantum mechanical effects are still prominent at nanoscales, leading to unusual optical and physical properties that made nanomaterials favourites of ancient artists. Nanotechnology has progressed rapidly in modern times, particularly in the past twenty years—with potential applications in fields as varied as robotics, water purification, energy storage and clothes manufacture.

Bhaumik and colleagues are most interested in nanoparticles as agents that can travel through the body to help us both pinpoint and treat sites of disease. Gold and silver are favoured candidates as nanoparticles in medicine, partly because they have potential therapeutic effects of their own. The natural antibacterial and anticancer properties of gold and silver are believed to become more pronounced at small sizess, as their surface area-to-volume ratio increases. These small sizes are achieved through a simple process of reduction, accomplished here by treating gold and silver salts with antioxidant phytochemicals such as flavonoids and polyphenols present in medicinal plant extracts. Antioxidants reduce positively charged metal ions to a neutral state, by donating negatively charged electrons. The reduced metals naturally aggregate into particles, whose size is capped by a coating of the same phytochemicals, effectively blocking further aggregation. This phytochemical coating is abundant with electron-generous hydroxyl groups, which can bond with complementary compounds of choice.

Bhaumik and co-workers attached two compounds to the surface of their nanoparticles: rhodamine B, a fluorescent molecule that can visually tag the particles wherever they collect, and rose bengal, a photosensitiser that releases reactive oxygen on application of light. Reactive oxygen, in turn, destroys local tissue. Together, these two properties allow for light-directed selective destruction of diseased tissue in the body—so long as nanoparticles can be engineered to collect where the disease is located. In the case of tumour cells, nanoparticles and other macromolecules accumulate automatically, possibly due to a combination of leaky blood vessels and poor drainage of cancerous tissues.

The caveat with all such research is that a long, difficult road tends to lie between promising theory and therapy that can be used on humans. One challenge now facing Bhaumik's group is to reinforce the natural coating of the nanoparticles so that they won't degrade once exposed to blood. Another necessary future step is to road test their engineered particles on live tissues. “We definitely want to shift to in vitro studies,” says Bhaumik. “Long term goals would of course be in vivo animal models.” And after animal models such as mice, and clinical trials on humans—funding permitting—perhaps one day extracts from jamun fruit and green tea leaves will be key components of nanoagents that fight cancer.