<?xml version="1.0" encoding="UTF-8"?><feed xmlns="http://www.w3.org/2005/Atom" xml:lang="en"><title>IndiaBioscience - Conversations from 2021</title><link
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    /><id>https://indiabioscience.org/columns/conversations/2021/feed</id><updated>2026-07-13T19:36:52+05:30</updated><entry><title>10 Leaders, 10 Questions: Sanghamitra Bandyopadhyay</title><link
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                <p>Sanghamitra Bandyopadhyay is currently the director of the Indian Statistical Institute (ISI), Kolkata. Among other accolades, she received the Infosys Prize in Engineering and Computer Science in 2017 and was the second woman scientist to receive the Shanti Swarup Bhatnagar Prize in Engineering Sciences (2010). We recently had the opportunity to chat with her regarding her thoughts on leadership.</p>              ]]></summary><id>tag:indiabioscience.org,2021-07-16:/columns/conversations/10-leaders-10-questions-sanghamitra-bandyopadhyay</id><published>2021-07-16T00:00:00+05:30</published><updated>2021-07-16T05:44:19+05:30</updated><author><name>Shreya Ghosh</name><uri>https://indiabioscience.org/authors/ShreyaGhosh</uri></author><content type="html"><![CDATA[
                
<p>Sanghamitra Bandyopadhyay is currently the director of the <a href="https://indiabioscience.org/orgs/isi">Indian Statistical Institute (ISI), Kolkata</a>. She received the Infosys Prize in Engineering and Computer Science in 2017 and was the second woman scientist to receive the Shanti Swarup Bhatnagar Prize in Engineering Sciences (2010). Her other accolades include the Young Scientist Award from the <a href="https://indiabioscience.org/orgs/insa">Indian National Science Academy (INSA)</a> in 2000, the Young Engineer Award from <a href="https://www.inae.in/" target="_blank" rel="noreferrer noopener">Indian National Academy of Engineers (INAE) </a>in 2002, the Swarnajayanti Fellowship from the <a href="https://indiabioscience.org/orgs/dst">Department of Science and Technology</a> in 2006, the JC Bose Fellowship in 2017 and the TWAS Prize in 2018 . We recently had the opportunity to chat with her regarding her thoughts on leadership.</p><figure><a href="https://indiabioscience.org/columns/conversations/10-leaders-10-questions-sanghamitra-bandyopadhyay"><img
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                src="https://cdn.indiabioscience.org/media/articles/10L10Q_Sanghamitra_2.png"></a></figure><p><strong>What role does able leadership play in scientific/academic environments?</strong></p><p>Strong and able leadership naturally plays a very important role in a scientific organisation because science works well when many people work together, collaborate, and have mutual respect for one another. And that comes when the leader also shows respect to all the people working in the institution. In addition to that, if the leader is herself/himself academically very sound, then s/he also attracts a lot of respect and recognition by the virtue of the science that s/he does. When you are running a scientific organisation, you are leading not just the scientists, but also the supporting staff, the students – everyone who works in the organisation. So the leader should be a role model to all of these people and make sure to take them along on her/his journey. </p><blockquote class="pull-quote">The leader has to be above petty allegations and should consciously ensure that the integrity of their actions is not doubted. <br></blockquote><p>For a scientific organisation, the vision – what the scientific organisation wants to be down the line – must be strongly established. And then the scientific work that goes on in the institution has to be nudged to go in that direction. Science cannot be regimented – you cannot say “you have to do this” or “you cannot do that”. You cannot stop scientists from doing what they like to do. At the most, you can say that this is important, this is what the country needs, this is where science is going these days etc., but you cannot do anything beyond that. Instead, it is very important for a leader to be able to create an environment where the research naturally moves in that direction, perhaps with a slight nudge now and then – an environment where there is a healthy competition and whatever comes out of it takes the institution towards the vision which has been established. </p><p><strong>According to you, what are the key qualities of a leader?</strong></p><p>For a scientific organisation, in particular, the leader should be a reputed academician/scientist who is known for the strength of their science. The other quality which is an absolute must is very high level of integrity. The leader has to be above petty allegations and should consciously ensure that the integrity of their actions is not doubted. Of course, there will always be people who are dissatisfied, but one’s own conscience should be absolutely clear that one’s actions have been in the best interest of the institution. The actions taken should be very rational and should be backed up by strong logic. </p><p>The leader also has to be fair, to everybody – friends or foes – and must also be <em>seen</em>
to be fair. It is important to have that transparency, to demonstrate that there’s fairness. A leader should also be willing to listen to others, but make decisions on their own. It is very important to listen to others, because with one brain, one mind, there’s only so much that you can think of. With five people coming together, you are exposed to different opinions and views, and it is important to be flexible enough to accommodate those. <br></p><p>And finally, a leader has to learn to say no. They should always be trying to find a solution, to facilitate things, but at times when saying no is important, the leader should be able to say no. </p><p><strong>When did you first realize that you are on a path towards leadership? </strong></p><p>No, actually I never realized that. I realized only when my selection <em>[as the director of ISI]</em> was announced. I had been nominated for the position, but had not expected my selection. I had very clearly stated that if the institute gives me a responsibility, I will not turn away from that challenge, but I will not go running behind that opportunity. In fact, when my selection as the director was announced in 2015, many people in my own institution did not know who I was. That was the day when I realized that, yes, I'm now on the way to leading this institution. I decided that I have to give it my best shot. So, whatever I did, I did it to the best of my capability.</p><p><strong>What do you consider your biggest successes or failures and what have these taught you?</strong></p><p>There's nothing like a <em>biggest</em> success or a <em>biggest </em>failure. There have been successes, there have been failures, but nothing that I can quantify as such. By nature, I'm never too happy with successes and never too sad with failures. What has always mattered to me is whether I've given it my best shot or not. And once I have done that, I take the results as they come, whether they are successes or failures. But not giving up is something which has been very important to me.</p><blockquote class="pull-quote">Old institutions have very fixed mindsets and changing mindsets is much, much more challenging than building buildings.</blockquote><p>Over the years, there have been a number of successes as well as failures. My institution is very theoretical research-oriented. To me, that is very important, but at the same time, looking outwards is also important. I've been trying to get more industry collaborations and get more of my colleagues interested in industrial applications. I have tried to set up facilities, instruments, cells and departments which can facilitate such interactions. Seeing this interaction with the industrial world grow is something I was quite happy with. And as for failures, there have been many instances I have tried to do something, but because of certain problems, I was not able to achieve it.</p><p>Of course, it's important to me that when I leave my office, I leave the institution in a better position than when I took up this responsibility. I have always tried to do that. Old institutions have very fixed mindsets and changing mindsets is much, much more challenging than building buildings. In that too, there have been successes and failures. Overall, I would say that I have tried my best and I'm not unhappy.</p><p><strong>Is this a skill that you feel scientists should learn, how to take successes and failures in their stride?</strong></p><p>Oh, certainly, I think everybody has to learn that. When you are successful, if you look around, you will find people who have achieved greater things. If you fail and you look around, you will see people who have had greater failures than you. So, you need to remember that your experience is not the end of it. This will give you a proper perspective, which I think not only scientists, but everybody should imbibe. I think this mindset is also important just from a social point of view, as this helps people to not get depressed. It's also important to be able to celebrate successes, which, to some extent, <em>I</em> don't. But then, I've been fortunate because some of my successes, many others have celebrated. It's important to present role models in front of the young, in particular. </p><p><strong>How much value do you give to human relationships?</strong></p><p>Oh, human relationships are extremely important. Human relationships are what an organisation is built on, because an organisation is not the set of buildings that we have, it's the humans that work in them. And especially in research organisation like ours, there are scientists, but there are also non-scientists – the administrative staff, accounts staff, etc. It's very important for them to also realize the role that they're playing – that without them, the science that we are doing would not happen. They are <em>facilitating</em> research, and if they believe that, then they will have more involvement in whatever they are doing. </p><p>In this institution, we have, to a large extent, been able to maintain these human relationships. We have a family-like environment where the interaction between the faculty, the students, and the non-scientific staff is very open and friendships are quite strong. In organisations like ours, the official hierarchies are limited to the administrative staff section. Among the faculty, there is no such strong hierarchy, it's quite flat. So, there, unless the human relationships are very strong and understanding is clear, work quality will suffer. These relationships are very important and have to be nurtured.</p><p><strong>How do you keep your team happy and motivated?</strong></p><p>As a supervisor, when it comes to my research students, we have regular talks and get-togethers. With the pandemic, it’s been a challenge to have the students on the campus. It’s very important that a research group works together, not just in the form of collaborations, but also in the form of just talking to each other and having a good time together. It is also the supervisor’s primary responsibility to see that the research team is happy and that if there are problems that the students are facing, they can share them openly. </p><blockquote class="pull-quote">[An] important part of keeping your team motivated is telling them “I value you”...<br></blockquote><p>But as an institution leader, the team is so big. When you look from the institute's point of view, the team is <em>huge</em>. And not everybody will be with you always. As an institution head, first of all, you need to know all the people – that’s very important. There will also inevitably be times when you have to turn someone down due to certain rules, regulations, bureaucratic hurdles etc. It’s important to be able to explain why you were not able to do something at those times. If you are not able to say yes to something, but if you're able to explain the reason behind this decision, then I think people often agree and are reasonably happy. You can also try to facilitate and find ways to help such people while working within the rules. After all, as the leader of a scientific institution, your main role is to see that science flourishes. So, it is important that the leader creates an environment where the scientists can do their science well. </p><p>Another important part of keeping your team motivated is telling them “I value you” – that you value their contribution, you value what they are doing, you value them for whoever they are, irrespective of successes or failures. </p><p><strong>How do you deal with difficult situations or difficult people?</strong></p><p>I try to explain my reasoning. If someone is unhappy, then they're unhappy for some particular reason. What I have always tried to do is to explain my point of view clearly to that person. Of course, while many people understand after receiving an explanation, there's a small percentage who fail or refuse to understand even if they see your logic. There’s not much you can do in such cases. You view it as living in a family. There are many types of people in a family, and not everyone may be happy with you always. But you don’t exclude anyone for that reason, you move on with everybody and you take care of everyone. I think we have to take everybody along and demonstrate fairness, which I have always tried to do. There have been people who have been publicly unhappy with me, but I apply the same yardstick to them as to everyone else.</p><p><strong>How and where did you pick up the leadership traits/​skills that were necessary to bring you where you are now? </strong></p><p>I learnt them on the job. It was what I call a “baptism by fire” – I was pushed into the water and I learned to swim. I had no particular experience and no particular training before that point. There were certain characteristics, maybe, which helped me adapt to the role. Being a quick learner, being able to take everybody along, even when they are not in agreement with you, knowing how to say a firm no etc. are some such characteristics. And as I said earlier, you learn from your failures as well as from your successes. Now that I’m on my second tenure, I can apply some of the training I received on the job in my first tenure. </p><p><strong>What, according to you, is the most important principle of leadership?</strong></p><p>The single most important principle, if you ask me, is to be fair to everybody. Your own conscience should be clear that any action you have taken, any decision you have made, you have tried to be as fair as possible. It is also important to be extremely logical and rational in decision making. </p>
              ]]></content><category term="advice" label="Advice" /><category term="leadership" label="Leadership" /></entry><entry><title>Science as a community enterprise: In conversation with Mriganka Sur</title><link
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                <p>Mriganka Sur is the Newton Professor of Neuroscience and Director of the Simons Center for the Social Brain at MIT. He has also acted as the jury chair for the Infosys Prize in the field of life sciences for the past several years. IndiaBioscience recently had the opportunity to chat with him about the current status of life science research in India, some of the common challenges, and the road ahead for the community. The interview has been edited for clarity and brevity. </p>              ]]></summary><id>tag:indiabioscience.org,2021-06-21:/columns/conversations/science-as-a-community-enterprise-in-conversation-with-mriganka-sur</id><published>2021-06-21T04:17:00+05:30</published><updated>2021-06-21T04:25:24+05:30</updated><author><name>Shreya Ghosh</name><uri>https://indiabioscience.org/authors/ShreyaGhosh</uri></author><content type="html"><![CDATA[
                
<p>Mriganka Sur is the Newton Professor of Neuroscience and Director of the Simons Center for the Social Brain at MIT. He has also acted as the jury chair for the Infosys Prize in the field of life sciences for the past several years. IndiaBioscience recently had the opportunity to chat with him about the current status of life science research in India, some of the common challenges, and the road ahead for the community. The interview has been edited for clarity and brevity. </p><figure><a href="https://indiabioscience.org/columns/conversations/science-as-a-community-enterprise-in-conversation-with-mriganka-sur"><img
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                src="https://cdn.indiabioscience.org/media/articles/Sur-6.png"></a></figure><p dir="ltr"><strong>In your opinion, what are some of the most significant achievements or contributions of the Indian life science community in the last 20 years or so? </strong></p><p dir="ltr">I think there are lots of achievements and some important milestones. If the COVID-19 vaccine made by Bharat Biotech holds up to peer review, I think that's a major achievement. There has also been work on rotavirus, which affects infants. I must say that what I am mentioning is the tip of the iceberg. Underneath, there are many smaller achievements that may go unnoticed by the media, but nonetheless form the backbone of progress in science. The Indian life science community has built capacity, as well as a knowledge base along with a technical base over the last 20 years. I think it has been very impressive in this regard.</p><p dir="ltr"><strong>Can you tell me some ways in which the Indian scientific ecosystem has grown and changed over the last few decades?</strong></p><p dir="ltr">While my scientific life, for the last 46 or so years, has been in the US, I have tried to stay engaged with India. And so, my view is from that very limited perspective. I do see major changes at many levels. I see changes in the way that Indian science has matured. Indian science needs critical mass in many different areas, but in certain areas like molecular biology, structural biology, virology, infectious diseases research, neurobiology, there has been major progress in the last 20 or 30 years. </p><p dir="ltr">This has happened mainly by bringing in talented researchers and by expanding the base of people who are doing their PhDs and becoming independent researchers in their own right. This has been enabled by a number of institutions dedicated to different components of life sciences research that have come up recently, as well as by entities such as the Infosys Science Foundation and public-private partnerships like DBT/Wellcome Trust India Alliance. </p><p dir="ltr">The results are now emerging in terms of significant growth and progress in the Indian life sciences community as well as in the discoveries and maturation of the field in India. There was a time not too long ago when almost all life sciences research was related to medicine, which is completely understandable for a country like India where the need for medical professionals is so high. At the same time, we need to build a base of fundamental research on which the translation or understanding of medical conditions can be built. And out of that, comes therapeutics that are rational and mechanism based. This fundamental base of knowledge and basic life sciences research has received a major boost in the last 20-30 years. I must say there is still a ways to go and there are areas in India that I think would benefit from more concerted attention or bringing in more people. But that's an issue for almost every country and India is no exception.</p><blockquote dir="ltr" class="pull-quote"><em>Ideas don't necessarily just come from one individual and their brain, but from a community in which there is conversation, there is discussion, there is critical evaluation, and there is sifting of evidence regarding what things are worth studying and what can we solve using our collective knowledge and genius.</em></blockquote><p dir="ltr"><strong>Could you elaborate on the concept of “Critical Mass”?</strong></p><p dir="ltr">Science is, in many ways, an enterprise of a community. An individual working in their garage or in their individual laboratory can perhaps achieve a lot - but increasingly, science requires collaboration. Science requires technologies that are not necessarily available in one laboratory or one institution. And science requires <em>knowledge</em> that often goes much beyond a single person’s expertise. This is demonstrably true for the life sciences, perhaps more than the physical or mathematical sciences. Life itself involves fundamental mechanisms from the level of genes and molecules to the level of organisms. The process of enquiry thus involves not only just knowledge of life sciences, but knowledge of statistics, knowledge of mathematics, and knowledge of physics and chemistry. </p><p dir="ltr">Here, the community plays an important role. It allows the embedding of life sciences research in a larger enterprise that builds on the understanding of life at the deepest level. It also involves the social and intellectual life of scientists, where they can talk to others who are doing similar things, in order to build ideas. </p><p dir="ltr">Where do ideas come from? Ideas don't necessarily just come from one individual and their brain, but from a community in which there is conversation, there is discussion, there is critical evaluation, and there is sifting of evidence regarding what things are worth studying and what can we solve using our collective knowledge and genius. </p><p dir="ltr">So these are all the ways in which the community matters - the number of people who are in a field and around the field matter. And India has been developing that. As I said before, these are issues for every country, for every society. And given how many people India has, the more India can bring young people into the field, the more Indian science will progress.<br></p><p dir="ltr"><strong>To build these communities, we need to recruit talented individuals and get them motivated to stay in science and do good research. Do you have any suggestions for how India can do this? </strong></p><p dir="ltr">I think being able to foster scientific thinking and temper among young people is perhaps the most important thing. Out of that, and out of curiosity about the world or a desire to solve problems, a subset of young people will choose science as a career. But that is the outcome of a whole process by which a society develops scientific knowledge and critical thinking. <br></p><blockquote dir="ltr" class="pull-quote"><em>Even in high school and certainly in undergraduate colleges, students should be exposed to scientific research, even in the humblest way, so that they can get a feel for how discoveries happen.</em></blockquote><p dir="ltr">Scientific knowledge is defined not only by curiosity about the world, but also by being able to understand that science is not something that exists external to us - it is a part of us. We live in a world that is amazing, that is wonderful, that has rules of cause and effect. This is not a world of superstition, where things are mystical. How does knowledge get built? Knowledge gets built on the basis of <em>discovery</em>, which happens through <em>experimentation</em>, which happens through <em>analysis</em>. Scientific knowledge doesn't just drop into textbooks. This is, in my opinion, a very important part of building a scientific environment. </p><p dir="ltr">So even in high school and certainly in undergraduate colleges, students should be exposed to scientific research, even in the humblest way, so that they can get a feel for how discoveries happen. They get a chance to see science is the accumulation, sifting, and appreciation of evidence to build relationships between cause and effect.</p><p dir="ltr">So, this is all part of what I think a society needs to do. And the more our society does it, the better citizens are prepared for science and to be scientists later on. Of course, society should also make this an important value and mission for young people – it should convey that science is something worth doing. There are few nobler things a young person can do than to find out a little bit about the world and make it a better place. And scientists do that with their lives.</p><p dir="ltr"><strong>What do you think are the major challenges that the Indian life science ecosystem is facing right now?</strong></p><p dir="ltr">Like I said earlier, I don't have a day-to-day or a very granular knowledge of the all the problems that are faced. I don't think that the problems are unique to India. For instance, I think that the issues of availability of resources - whether reagents or technologies - are nothing new. Many things have also become better, for instance, the integration of Indian science and scientists with the international stage is infinitely better today than some decades ago. Resources matter; science costs money. In particular, fundamental science is usually funded almost entirely by the government. So stable and sufficient funding is a very big driver of the quality and the quantity of science. And that's certainly the case in India. So, if all of these issues are dealt with, I think Indian science will progress. It <em>has</em> progressed and will continue to progress.<br></p><p dir="ltr"><strong>Where do you see the Indian life science ecosystem in relation to the global ecosystem?</strong></p><p dir="ltr">I think that the Indian life sciences community is definitely a part of the global ecosystem. It is often driven by the individual scientist and her/his individual collaborations, but a lot of Indian scientists, particularly young scientists, have trained abroad, gone back to India, and set up laboratories. That itself sets up a base on which these researchers can then build to advance their scientific linkages across the world. </p><p dir="ltr">I think that this should be promoted, enhanced, and strongly encouraged because science is not the province of one country. Science deals with global problems, even if they have local manifestations. For example, the coronavirus doesn't respect national borders. The solution to the pandemic, therefore, has to be international. And that's just the most recent example. </p><p dir="ltr">So, Indian science, demonstrably, needs to be linked to global science. And that is already happening. More, certainly, can happen - there can be steps taken by institutions, by funding agencies, and even by the global community itself. It's not just a one-way street - Indian scientists looking abroad. Global scientists also need to be aware of the capabilities and the contributions of Indian science.</p><blockquote dir="ltr" class="pull-quote"><em>Society can never progress unless science is available as a vision, as a means of participation for </em><em><strong>all</strong></em> its people.</blockquote><p dir="ltr"><strong>You have been working with the Infosys Science Foundation for several years now. What role do you think organizations like this can play in promoting the culture of doing science in India?</strong></p><p dir="ltr">My major interaction with the Infosys Science Foundation has been through the Infosys Prize. I know that they do many other things, but I'll confine my comments to the Infosys prize. I think that the Infosys Prize is a unique prize in that it is, unequivocally, based on evaluation of merit, and on recognizing scientific contributions based on international criteria. And that is reflected in the award and the awardees. This is important because having a vision that Indian science can be on the world stage and recognizing Indian scientists who are at par with the best of international scientists makes the statement that Indian science is certainly a contributor to international excellence. So that's the first and most important idea. And the second is that Infosys prize awardees act as a role model for young scientists. A unique thing about the Infosys prize is that it's given to mid-career scientists, which means that some of their best work has been done, but there is more to <em>come</em>. And in that way, it recognizes the importance of continual progress of science as an explicit mission. Those are the ways in which I see the Infosys prize, which is an important component of the Infosys Science Foundation, as playing a role. </p><p dir="ltr"><strong>Is there any message that you would like to give someone who's just starting their career in science in India right now? </strong></p><p>I would offer strong encouragement to every young person who wishes to start her/his career in science, and particularly to those from communities that have been underrepresented. The representation of women and other minorities in Indian science, I must say, has been much less than their proportion in the population. And society can never progress unless science is available as a vision, as a means of participation for <em>all</em> its people. And so, I would have a special word of encouragement for women and minority scientists to be involved in science. As I said before, there be few more noble goals in one's life than to find out a little bit more about the world and to make it a better place and demonstrably, a career in science does that<em>.</em></p>
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                <p>With several new COVID variants emerging in recent months, the importance of analysing and drawing insights from vast amounts of viral genome sequencing data cannot be understated. To address this need, A team of researchers at the Advanced Centre for Treatment Research &amp; Education in Cancer (ACTREC), Navi Mumbai, have come up with a computational tool called the Infectious Pathogen Detector (IPD).</p>              ]]></summary><id>tag:indiabioscience.org,2021-03-30:/columns/conversations/a-computational-tool-that-can-rapidly-identify-and-analyse-coronavirus-mutations</id><published>2021-03-30T14:30:00+05:30</published><updated>2021-03-30T22:40:37+05:30</updated><author><name>Susheela</name><uri>https://indiabioscience.org/authors/ANQdMn8qkRK6OE7</uri></author><content type="html"><![CDATA[
                
<p>With several new COVID variants emerging in recent months, the importance of analysing and drawing insights from the vast amounts of viral genome sequencing data we currently have available cannot be understated. A team of researchers at the Advanced Centre for Treatment Research &amp; Education in Cancer (ACTREC), Navi Mumbai, have come up with a computational tool called the Infectious Pathogen Detector (IPD), which can quickly process large amounts of DNA sequencing data to spot pathogens and mutations in their genomes.</p><figure><a href="https://indiabioscience.org/columns/conversations/a-computational-tool-that-can-rapidly-identify-and-analyse-coronavirus-mutations"><img
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                src="https://cdn.indiabioscience.org/media/articles/Featured_Sequencing_COVID3.png"></a></figure><p dir="ltr"><em><a href="https://www.genome.gov/about-genomics/fact-sheets/DNA-Sequencing-Fact-Sheet">Gene sequencing </a>has expanded our understanding of genetic codes and provided valuable insights into genomic mutations. A recent example is the analysis of the emerging dominant strains of the SARS-CoV-2. However, advanced sequencing methods - collectively called the <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3841808/">next-generation sequencing (NGS)</a> platforms - generate diverse sequencing datasets. They pose challenges in scrutinising and comparing a new sample's genetic data with the existing global data. A tool that can integrate such varied data and quickly identify locally circulating dominant mutants can prove indispensable at this juncture. </em></p><p dir="ltr"><em>A team of researchers led by Amit Dutt at the <a href="https://indiabioscience.org/orgs/actrec">Advanced Centre for Treatment Research & Education in Cancer (ACTREC), Navi Mumbai,</a> have developed a computational tool called the <a href="https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbaa437/6105766">Infectious Pathogen Detector (<strong>IPD</strong>)</a>. The tool, enabled with a graphic user interface, can identify 1060 pathogens, including the SARS-CoV-2 virus, from a biological sample's genetic data.</em></p><p dir="ltr"><em>We catch up with Amit Dutt to gain insights into the IPD and its <a href="https://www.biorxiv.org/content/10.1101/2021.01.21.427574v1">SARS-CoV-2 module</a>. </em></p><p dir="ltr"><strong>What is the Infectious Pathogen Detector?</strong></p><p dir="ltr">The Infectious Pathogen Detector (<strong>IPD</strong>) is an open-source computational tool useful for identifying pathogen strains in a given biological sample based on DNA sequencing data. To use the IPD, the user has to upload the genomic sequence (genetic code) of a biological sample. The IPD runs a rapid analysis on the sample from which it can identify the presence of 182 viral strains (including SARS-CoV-2) and 868 bacterial strains as well as their mutations.</p><p dir="ltr">The IPD automatically generates molecular reports such as the abundance of a pathogen or the number of mutations (mutation-rate) present in the sample. Also, the IPD identifies if the sample contains any new mutations. Notably, the tool can recognise <a href="https://pubmed.ncbi.nlm.nih.gov/12888108/">'mutation hotspots'</a> - the regions in the pathogen's genome where mutations are predominantly seen - which is crucial to our understanding of how the pathogen is evolving. After identifying these parameters, the IPD then rapidly compares the observations with a global genomic database and classifies the pathogen as a novel variant or one of the commonly occurring ones. </p><p dir="ltr">We initially designed the IPD to detect cancer-causing pathogens. However, when the pandemic broke out, we included a SARS-CoV-2 module for rapid analysis of the COVID-19 viral genomic <a href="https://www.gisaid.org/">database</a> (<a href="https://www.gisaid.org/">GISAID</a>). </p><p dir="ltr">To use the IPD's SARS-CoV-2 module, a researcher can upload the molecular sequence of a COVID-19 sample to the IPD server hosted at ACTREC. The IPD detects the viral abundance in the sample, then analyses the mutations and classifies them with reference to the original Wuhan viral strain. The classification, called the <a href="https://biologydictionary.net/clade/">phylogenetic clade</a>, shows if the sample is the common prevailing local variant or if a newer one has emerged. The user can then opt to generate detailed reports of the analysis.</p><p dir="ltr"><strong>How does the IPD work and what are its features?</strong></p><p dir="ltr">The IPD comprises data processing elements or computerised algorithms that are linked serially to form a data pipeline. The processing elements work sequentially — they are so connected that one stage's data output becomes the next stage's input data.</p><p dir="ltr">The most important feature of the IPD is its versatility. There are currently several genome sequencing methods that generate heterogeneous genomic data, for example, <a href="https://medlineplus.gov/genetics/understanding/testing/sequencing/#:~:text=Together%2C%20all%20the%20exons%20in,only%20a%20select%20few%20genes">whole exome, whole transcriptome or whole genome</a>. Some of the sequences generated by gene sequencing methods are long-read data that comprise the entire DNA sequence, running into thousands of base pairs. In contrast, others are short-read — of a few hundred base pairs — obtained from a DNA fragment. Analysing such heterogeneous data can be a challenge.</p><p dir="ltr">However, The IPD normalises data from any of these inputs. It employs computational subtraction methodology and statistical analysis to eliminate the sample sequence's non-relevant parts and zeroes in on the pathogen's genetic codes. The sample is then rapidly compared for mutations, running through a comprehensive reference library of genomic databases corresponding to 1060 different pathogens.</p><p dir="ltr"><strong>What are some of your findings so far using IPD's SARS-CoV-2 module?</strong></p><p dir="ltr"><a href="https://www.biorxiv.org/content/10.1101/2021.01.21.427574v1">Our study</a><em>(preprint submitted to BioRxiv)</em> describes a comprehensive dataset of 200865 samples collected from COVID-19 patients across 155 countries from the GISAID database. In all, the IPD detected 2.58 million mutations from these samples.</p><figure style="float: right; width: 812px; max-width: 295px; margin-left: 20px; margin-right: 20px;"><grammarly-extension data-grammarly-shadow-root="true" style="position: absolute; top: 0px; left: 0px; pointer-events: none;" class="cGcvT"></grammarly-extension><img src="https://cdn.indiabioscience.org/media/articles/The-team-of-researchers-at-Dutt-Lab.jpg" data-image="238518" alt="Team of researchers working on this project at Dutt Lab" width="295" height="278"><figcaption spellcheck="false">The team of researchers working on this project at Dutt Lab. Standing (from left to right): Bhasker Dharavath, Asim Joshi and Amit Dutt; Sitting: Aishwarya Rane and Sanket Desai</figcaption></figure><p dir="ltr">Our analysis revealed 13 mutation hotspots in the SARS-CoV-2 genome. These occurred at least in one-fifth of the samples. In 40,000 or more samples, we found that of the 27 proteins encoded by the SARS-CoV-2 genome, more than half of all the nonsilent mutations were found in 5 genes — S, N, M, ORF7a and ORF10. Nonsilent mutations lead to protein changes that are more likely to alter protein function and result in a 'fitter' virus. In that case, those changes may be favoured and naturally chosen for replication in the virus' evolutionary cycle leading to a dominant variant. Also, the ORF-proteins are presently understood to have no known function and are considered as non-essential. However, we found that they exhibited an equal natural selection bias by the virus.</p><p dir="ltr">When we ran an analysis for the recently reported mutants - B1.1.7, B.1.351, and P.1 (commonly known as the UK, South Africa, and Brazil strains, respectively) - none of them were significantly abundant in the samples accessed until 28 December 2020. This could be due to their inadequate representation in the database as they were emerging strains at that time. </p><p dir="ltr"><strong>Can you elaborate on what the above data may imply?</strong></p><p dir="ltr">The SARS-CoV-2 virus has around 29,000 bases in its genome, and each of the bases can mutate, leading to 'point -mutations'. However, point-mutations are finite in number as they are a function of the number of bases. Our study found more than 2 million point-mutations occurring across 21,016 unique bases. In my opinion, a catalogue of all possible such mutations would soon reach its limit. </p><p dir="ltr">However, with continued human-human transmission during the pandemic, combination mutations with higher transmission rates or with the ability to hoodwink the immune system will get selected and enriched in a population. These can emerge as new viral variants which can severely impact the disease outcome. This could also be the reason for the varying fatality or transmission rates observed in different countries. </p><p dir="ltr"><strong>Did you also perform this analysis with Indian samples? What were your observations?</strong></p><p dir="ltr">We analysed 3,361 full-length viral genomes derived from about 6,000 Indian COVID-19 patient samples present in the GISAID database (as available on 28 December 2020). In all, we found that the mutation rate was comparable with the global rate. We noticed 5.17 nonsilent and 4.39 silent mutations per sample, along with 4,422 unique mutations not reported elsewhere. The Indian samples also shared the same hotspots as the global samples. There were no significant occurrences of the UK, Brazil and South Africa variants. However, as the Indian database is very small compared to the global database, we cannot rule out any emerging occurrence of these variants in our population. </p><p dir="ltr"><strong>Why is the Indian dataset small compared to the global dataset?</strong></p><p dir="ltr">Presently in India, the emphasis is more on detecting COVID-19 cases than on sequencing. Most of the public sequencing data we used comprised submissions made by researchers from institutes like the Centre for Cellular & Molecular Biology (CCMB), Hyderabad, CSIR-Institute of Genomics & Integrative Biology (IGIB), New Delhi, ACTREC, National Centre for Biological Sciences (NCBS), Bengaluru, to name a few. Subsequently, the authorities have undertaken an active and concrete step by constituting the <a href="http://dbtindia.gov.in/pressrelease/indian-sars-cov-2-genomic-consortia-insacog-launchedcoordinated-department">Indian SARS-CoV-2 genome consortium (INSACOG</a>), similar to a few prominent consortiums abroad (e.g. COVID-19 genomics UK consortium (<a href="https://www.cogconsortium.uk/">COG-UK</a>) and the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance (<a href="https://www.cdc.gov/coronavirus/2019-ncov/covid-data/spheres.html">SPHERES</a>), USA). With a concerted effort under the ambit of INSACOG, we are hopeful that India will soon be a significant contributor to the GISAID database.</p><p dir="ltr"><strong>How can the IPD analysis reports impact the current situation? </strong></p><p>Different centres employ different sequencing processes or use various reagents; their equipment's sensitivity may also differ. These variations give different data outcomes for which statistical analysis, downstream processing, and data integration are time-consuming and challenging tasks. The IPD is a handy tool in such a situation, specifically in a consortium-based format. The IPD can be helpful to establish uniformity for standardising the reports and comparing the data across centres. With such diverse SARS-CoV-2 genomic information in hand, vaccines can be suitably tweaked. They can be updated to match the predominant variant, providing a quick strategy to combat the disease outbreak effectively.</p>
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                <p>Jaishree Subrahmanium is a botanist who did her PhD in ecological genomics from the French National Institute of Agricultural Research. She has been working with Lotus STEMM, a Canadian NGO working on representing South Asian women in STEM careers, where she established a mental health support community -‘Paksh’. We spoke with Jaishree about her experience with this initiative and lessons from the same.</p>              ]]></summary><id>tag:indiabioscience.org,2021-03-04:/columns/conversations/building-an-international-mental-health-support-group-for-people-in-science</id><published>2021-03-04T14:00:00+05:30</published><updated>2021-07-28T16:32:32+05:30</updated><author><name>Zill-e-Anam</name><uri>https://indiabioscience.org/authors/jaXZ1ydEJaKDwzO</uri></author><content type="html"><![CDATA[
                
<p>Jaishree Subrahmanium is a botanist who did her PhD in ecological genomics from the French National Institute of Agricultural Research. She has recently ventured into science communication, as well as advocacy for equal rights of women and better mental health. She has been working with Lotus STEMM, a Canadian NGO working on representing South Asian women in STEM careers, where she established a mental health support community - ‘Paksh’. We spoke with Jaishree about her experience with this initiative and lessons from the same.</p><figure><a href="https://indiabioscience.org/columns/conversations/building-an-international-mental-health-support-group-for-people-in-science"><img
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                src="https://cdn.indiabioscience.org/media/articles/Paksh_Featured_V2.png"></a></figure><p><strong>What motivated you to establish Paksh?</strong></p><p>As a masters’ student, I harboured a dream of going abroad to study. Apart from experiencing a new culture, I wanted to explore the world. A lot of international students have the same dreams. I ended up moving to a country where I did not speak the language and did not know anybody except for my supervisor whom I had met only once before. The culture shock was huge. I had a very hard time dealing with people and integrating myself into a completely different environment. I was the outcast: the only woman and the only non-French student in the lab. </p><p>Being an international student, I had also put a lot of pressure on myself to perform well since I believed I had been given an incredible chance that many would die for. I wanted to come in early and stay out late in the lab, read as much as I could, and basically lived for my work. Nobody asked me to do these things – I just felt this pressure and I thought I needed to keep going to make myself believe that I was doing a good job. What I didn’t realize was that my mental health was gradually deteriorating as a result. </p><p>I realized towards the end of my PhD that I was not the only one suffering. Being in academia brings some common challenges that people don’t talk about. Along with homesickness and the anxiety of finishing my PhD, I was also facing the problem of having no one to talk to about my problems and challenges. When I talked to people, most were very supportive of talking about their personal journeys but when asked to form a community or be a part of something much bigger than their own career, people would shy away and fear the outcomes. </p><p>While I have finished my PhD and am no longer in that mental state, I know that many PhD students continue to suffer in silos. They think their journeys, problems, thoughts are not valid or worth asking for advice over. I wanted to help these people and didn’t want anybody to ever go through what I went through myself. This led me to establish Paksh. </p><p><strong>How exactly does Paksh work? What are its key activities?</strong></p><p>Paksh was initially created for students who are living abroad. But knowing that there are many students who are living in their home countries who are also going through the same academic challenges, we decided to make this community open to graduate students and postdocs from across the globe. </p><p>The core idea behind Paksh is creating a safe space, a no-judgment community for academics to freely express their thoughts. People from all walks of life share their experiences, thoughts, and opinions. It is a community based on kindness. They help and support each other. I translated everything I learnt during my PhD about altruism - the ability to help one another without thought of personal gain - into Paksh. I learnt that people form bonds with each other; they can empathize with and support one another no matter where they are from. </p><p>Paksh reinforces that every journey, every experience needs to be acknowledged, talked about, and shared. I think stories matter and storytelling can be an incredible way of empowering and encouraging people to stand up to whatever struggles they are facing. </p><p>At Paksh, I see people coming together irrespective of backgrounds. We need to understand that people can form groups, become part of something that is bigger than themselves, and these groups can be kind and cooperative under stressful circumstances. We tend to find ample reasons to divide people and create borders between them. But at the end of the day we are all from the same species and what connects us together is the love for what we do. Nobody should struggle while doing what they love.</p><p><strong>What were the initial challenges you faced while establishing Paksh?</strong></p><p>The initial idea of Paksh came to me when I was writing my PhD thesis, which was a very challenging and exhausting period of my life. When I approached people with the idea, many supported me in private but didn’t come forward in public. I approached heads of labs who felt that this was not a strong enough idea for people to be spending their time and resources on. Other major hindrances were the fear of losing my career path, the fact that mental health was not a common priority, and fear of judgement. Later, unexpectedly, I met Roopali, CEO of Lotus STEMM, and that one conversation changed everything. </p><p><strong>Phase 1 of Paksh has now ended. What are your major learnings and how has your journey been?</strong></p><p>It has been an incredible journey for me. Starting from the very first session, all the participants were discussing their individual journeys and I think they were experiencing what I wanted them to experience. I was never giving them advice - that was not my job. Our idea was to encourage them to learn from one another. I could see that happening and it was so rewarding for me. We were handling six different time zones and no matter where these people were from, they were able to empathize with one another. </p><p>The major learning from Phase I was that if you want to bet on collective human kindness, you can, and I think Paksh is a testament to that. I have also learnt that if humans can come together under the right circumstances, they can become an altruistic community and this is the most stable strategy in the long run. </p><p>I also realized that a support community can only do so much. There are some underlying issues that really need to be addressed that go much beyond what students face. These problems need to be addressed at the institutional level. Organizations like Dragonfly Mental Health are trying to understand systemic problems and make systematic changes by talking to universities and institutions. I would like to see something like that in the Indian context as well. </p><p>Another major issue is the lack of statistics for issues like academic bullying. I think we need to have many more conversations and that’s the only way we can acknowledge problems and potentially try to find solutions. Scientists spend an incredible amount of time becoming who they are and their loss is a loss to science.</p><p><strong>How do you plan to take forward the second phase of Paksh?</strong></p><p>In its second phase, Paksh will be much more than a support community. We are planning to divide members into two groups (1) international community and (2) people who are living in their home countries. Because we will be growing bigger in the second phase, I will also have a co-host or a co-facilitator. I would also like to bring in trained people and specialists to give more concrete advice to solve problems that the members are facing.</p><p><strong>From your experience, is it also necessary to distinguish "Indians living abroad" vs just "people living outside their own country"? Are the principles universal or does being Indian pose any special challenges?</strong></p><p>There is a theory in evolutionary biology called group selection theory. It essentially talks about the survival of not the fittest but the kindest. It is a theory of compassion that says that a group of organisms that are there for each other and support each other, will always be better off in the long run as compared to individuals that follow selfish interests. And the point I’m trying to make here is that every individual is different and has a role to play. Every story, every journey is important and needs to be acknowledged. I feel you don’t have to distinguish between Indians living abroad and people living outside the country because stories vary at the individual level. The individual stories then become the basis of that community through sharing and learning and result in bonding. I don’t think it matters where you’re coming from as long as you are part of a group and you are able to open up to one another, which requires courage and practice.</p><p><strong>Many Indian students dream of going abroad for their doctoral and postdoctoral studies. What kind of mental health challenges are associated with working outside your home country/home state?</strong></p><p>It does not always have to be about leaving your country, it is about leaving your comfort zone and the supportive network of your family and friends. Troubles associated with communicating, not having the people that you are used to around, separation anxiety, and homesickness are some common challenges. Moving to a new place means adjusting to an entirely different environment, culture, and way of doing things. It’s a constant battle between keeping in touch with the ones that you left behind and forming new bonds with people with whom you are now. This really challenges your mental well-being. Having a support system, community and network during this process really helps. That’s the niche I’m trying to fill with Paksh.</p><p><strong>What steps can early career researchers take in order to keep mental health issues associated with being ‘away from home’ at bay? As a young Indian woman in STEM working abroad, what advice do you have for Indians planning to go abroad who want to maintain their mental well-being?</strong></p><p>Early career researchers often put in much more work and experience much more stress than what is required, just to be validated by the scientific community. I think international students take this even more to heart due to the high pressure to perform. They wear sleeplessness or not eating food as badges of honour and I was one of them too. And that’s where I think we are going wrong. While academia is a great place to be in at the service of science, it can be incredibly brutal. Mental health challenges are not seen in the light they are supposed to be seen in and not just students, but institutions also treat mental health topics as taboo. There’s the idea that if you’re talking about your mental health, it means you’re not strong enough or cut out for being a scientist. </p><p>Studying overseas was a dream for me. However, it came with a lot of challenges and there was a very steep learning curve. I think what helped me the most was to keep the connection with the people I left behind. Humans are social beings and we have forgotten how to form connections and once we find a support network, I think that really eases the journey. </p><p>It is also important to make an effort to integrate yourself into the environment and learn how life works in the new place. There are cultural differences that need to be appreciated and learning the language also helps. Another thing that is very crucial is having realistic expectations. Not everybody gets to change the world. I think, as a scientist, each one of us needs to take responsibility for building a healthy academic environment.</p><p>I also think storytelling and sharing real experiences brings people together. The atmosphere of toxicity that we all know exists in academia, partly arises because people don’t talk about their issues. Try to appreciate why you are in science, and make your mental health a priority. Even though we know this, we often don’t take care of ourselves because we don’t think we deserve it. One has to acknowledge that there will always be somebody who will be better than you, no matter where you go, or what you do. At the end of the day, find your identity beyond being just a scientist.</p><p><strong>In your opinion, what makes a supportive and reliable mental health community?</strong></p><p>Shared experiences make a reliable non-judgmental community. I think COVID has taught us that people can be brought together like never before. Researchers need to understand that you can connect to people beyond your scientific collaborations. It’s really hard to admit to your weaknesses, failures, and fears in front of people and to be able to open up like that requires courage. Ultimately, a reliable community will grow organically, one cannot force these things.</p>
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