IISER Pune, IIT-Delhi teams wins Bronze Medal at iGEM 2015 contest in Boston; Congratulations

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IISER Pune iGEM 2015 team-members

A team of undergraduates from IISER Pune has bagged a Bronze Medal at the international Genetically Engineered Machines (iGEM) contest held at Boston, USA from September 24-28, 2015.

iGEM first started in 2003 as an Independent Activity Period (IAP) project of undergraduates at the Massachusetts Institute of Technology (MIT) in Boston. It has since grown and gone international with over 280 teams from all over the world participating in 2015. In this Synthetic Biology contest participants are expected to design molecular “bio-devices” in a manner that combines their understanding of genetically encoded parts with additions from anything ranging from art to nano-fabrication.

This year, a team of ten 2nd year BS-MS students from IISER Pune: Siddhesh Zadey, Prachiti Moghe, Rahul Biradar, Gayatri Mundhe, Prashant Uniyal, Ira Phadke, Snehal Kadam, Harsh Gakhare, Swapnil Bodkhe and Yash Jawale signed up under the guidance of Dr Chaitanya Athale (Assistant Professor, IISER Pune). To help them troubleshoot the experimental and theoretical aspects, two PhD students, from the Athale-Lab, Neha Khetan and Manasi Gangan, volunteered to help out. After a hectic summer and last minute experiments, two novel DNA sequences were submitted to the common repository of iGEM. Finally, six of the members were selected to present their work as a talk and poster to the international audience at the Giant Jamboree in Boston, USA.

The IISER Pune team was amongst a list of Bronze-Medal winners – one of only two from India. Their project “Mycobacterium Revelio” was targeted to develop a cost-effective diagnostic tool for detecting the causative pathogen for tuberculosis (TB). Using ideas from synthetic biology, simulations of genetic networks and combined with basic microbiology, the team designed a genetic device they refer to as “the Terminator”. This sequence in its eventual function aims to cause a cessation of cell division when turned on, to keep the Mycobacterial population at a fixed size. Additional modules, “Detection” for instance aimed to use visible dyes that genetically trigger the appearance of colour in the target organism, M. tuberculosis.

This year the IISER Pune team had also hosted a national meet-up of Indian teams participating in iGEM 2015, with groups from IIT Kharagpur and IIT Delhi visiting the institute. The work was funded by IISER Pune, the Department of Biotechnology and corporate sponsorship from Qiagen, Eppendorf and Merck-Millipore, with additional support from Mathworks and IDT.

We congratulate team Mycobacterium Revelio and wish them success in their future endeavours.

Original news : IISER,Pune News.

All iGEM 2015 Results : Click Here

THE NOBEL PRIZE IN PHYSICS 2015 : Neutrinos, the chameleons of space

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We live in a world of neutrinos. Thousands of billions of neutrinos are flowing through your body every second. You cannot see them and you do not feel them. Neutrinos rush through space almost at the speed of light and hardly ever interact with matter. Where do they come from?

 

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Brain FM tuned by NCBS

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Image : NCBS News

Each of us have our moods when we like to hum an old melody or suddenly feel like tapping our feet to the latest hit. It turns out that cells in our brains can be equally moody, changing the tune of their electrical signals from time to time. In a recent study, scientists Mohini Sengupta and Dr. Vatsala Thirumalai, from the National Centre for Biological Sciences (NCBS), Bangalore, reveal that nerve cells found in the cerebellum (at the base of the brain) send out electrical signals in either a constant hum or in sudden bursts. Which of the two tunes they choose depends on the voltage across their cell membranes and on input from a specific region of the brain.

Our balance, co-ordination and the capacity to learn new skills such as riding a bicycle or playing a piano depends on a small leaf-like structure at the base of our brain called the cerebellum. Within the cerebellum, are nerve cells named ‘Purkinje cells’ that are arranged neatly in a single layer and are vital for carrying out the aforementioned functions. These cells receive signals from many different regions of the brain and send out messages to the deeper layers of the cerebellum.

However, how Purkinje cells communicate with other nerve cells has thus far been a mystery, mainly because it is very difficult to ‘listen’ to these cells in animals that are awake and moving around. Since these nerve cells are very small, scientists employ fine glass capillaries to record their electrical signals using a technique called ‘whole cell patch clamping’. For this technique to work, most experimental animals must be anesthetised, as even small movements can knock the capillaries out of place. Unfortunately, anesthetics themselves alter the electrical signals generated by the brain. This means that previous studies aimed at determining the nature of electrical signals generated by Purkinje cells in awake and moving animals have largely been inconclusive.

The researchers at NCBS overcame these issues by using zebrafish, a fresh water fish found in the Ganga and Brahmaputra, for their experiments. The young zebrafish (called larvae) are transparent and have not yet developed a skull. Furthermore, specific nerve cells in the larvae can be made to glow by injecting DNA into them at the embryonic stage. This made it possible for scientists to insert and precisely place the fine recording equipment onto the Purkinje cells within the fish brains. To prevent the fish from moving, a paralytic agent that does not interfere with electrical signals in the brain was used. This combination of technical advances allowed the team to record electrical signals from Purkinje cells in an intact animal that was not anesthetized.

Results from these experiments showed that Purkinje cells sent out electrical signals in two different modes depending on the voltage at their cell surfaces. The first mode, called the ‘down’ state, occurred when the inside of the cell was more negative compared to the outside. In this state, cells were silent until signals from a different part of the brain arrived, at which time, they sent out a burst of impulses. In the second mode, called the ‘up’ state, the inside of the cell was less negative compared to the outside and the Purkinje cells sent out impulses at a constant rate. In this mode, these cells ignored any impulses coming from other parts of the brain. These states are reminiscent of a person attentively listening to directions and responding accordingly, or simply ‘zoning out’ and going their own way irrespective of instructions.

What does this phenomenon mean for the functioning of the cerebellum? To understand this, the NCBS scientists recorded the instructions of the nervous system to muscles. In normal fish, these instructions would result in swimming. However, since the experimental preparation is paralyzed, no movement is seen, yet the instructions to the muscle continue to be sent. The scientists discovered that such ‘fictive’  motor instructions were always accompanied by bursts of impulses in the Purkinje cells. Mostly, the impulses occurred after the start of these motor instructions and the timing of the bursts varied from cell to cell.

These results demonstrate that Purkinje cells receive a copy of the instructions sent by the nervous system to muscles and that they generate a burst of impulses in response. The researchers propose that the existence of the ‘up’ and ‘down’ states is a possible mechanism by which Purkinje cells choose to listen in on the  instructions sent out to muscles or not. What do these cells do with such instruction copies? Do they alter their signals when the animal is learning a new motor task? The authors are excited to find out answers to these questions in ongoing experiments.

The paper titled “AMPA receptor mediated synaptic excitation drives state-dependent bursting in Purkinje neurons of zebrafish larvae” was published in the journal eLife on 29th September 2015 and can be accessed here.

Original news : NCBS News

 

 

 

 

 

 

Bats and their Pumping-tongue mechanism

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Image: AAAS News

News Update By – Nitali

          Researchers have captured on video what appears to be a new tongue mechanism some bats use to feast on nectar. The research appears in the 25 September issue of the journal Science Advances.

Nectar is a primary food source for many animals but a few, including hummingbirds, honey eaters and sun birds and bats, possess mouthparts specifically designed to slurp up the sweet liquid found in flowers. Specialized nectar-feeding bats typically siphon nectar from flowers using extremely long, protruding tongues sprinkled with hair-like papillae. But some bats sport another type of grooved tongue — one that scientists haven’t studied in depth.

Marco Tschapka at the University of Ulm and colleagues show that grooved-tongued bats in the group of New World leaf-nosed bats known as the Lonchophyllinae display a unique feeding behavior. Using high-speed cameras focused on bats trained to obtain nectar from artificial “test tube” flowers containing honey water in the lab, the researchers’ video captured bats hovering in short flights (rarely lasting a second) over the feeders.

Unlike bats with hairy papillae, which moved their tongues in short lapping movements resembling a cat, the grooved-tongued bats lowered their tongues into the test tubes and did not move them during the entire visit. The bats’ grooved tongues appear to never separate from the liquid nectar, acting a bit like a conveyor belt to transport the food up the tongue and straight into the animals’ mouths.

The researchers aren’t exactly sure how the bats are able to do this, but suspect it occurs by some combination of tongue deformation and the ability of fluids like nectar to flow without external force in certain narrow spaces, a phenomenon known as capillary action.

Both methods for obtaining nectar were effective, but the researchers think that the grooved-tongue bats may have an advantage in acquiring nectar from flowers of certain shapes that hold the sweet liquid differently.

For example, some flowers have diffusely distributed nectar, while others offer one small pool of nectar. Different nectar extraction mechanisms might be useful depending on the flower. The pumping mechanism of Lonchophyllinae bats might work more efficiently in flowers that allow a more complete submersion of the tongue in the nectar pool, the authors suggest.

Another important factor might be nectar viscosity. Nectar from bat-visited flowers is generally dilute, but the sugar concentration in nectar varies between flowers. Nectar with a low sugar concentration that is less viscous and more free-flowing might be more easily harvested by the pumping mechanism compared to nectar of high sugar concentration and viscosity.

Original News : Science Advances