Joel P Joseph Biological Sciences, News

Scientists discover that structures inside mitochondria reshape continuously in living cells

Scientists from Heinrich Heine University Düsseldorf and University of California Los Angeles recently discovered that cristae – structures formed by the inner covering of mitochondria – keep remodelling continuously. The team led by Prof. Andreas S. Reichert made this discovery by seeing live cells using a high-end technique in microscopy. This technique, called stimulated emission depletion (STED) super-resolution nanoscopy, enables one to see details of an organelle in the cell – of the size of 50 nm (about 1000 times smaller than a speck of dust). The study was published in the journal EMBO Reports.     

CJ dyna,ics

STED nanoscopy images showing cristae remodelling 

Mitochondria are organelles in the cell popularly known as the powerhouse of the cell. They form a dynamic network, change their shape, fuse or split. As for their structure, mitochondria have two membranes covering them – the outer membrane and the inner membrane. The inner membrane folds inward to form structures called cristae (sing. crista), on which many important proteins reside. These proteins include ATP synthase – the machine that makes ATP, the energy currency of the cell. Curved, circular or pore-like structures called crista junctions separate the cristae and the rest of the inner membrane.

Other scientists have shown that abnormal or altered cristae in diseases like cancer, diabetes and neurodegeneration. In normal conditions, however, cristae are thought to be static. Scientists from Heinrich Heine University Düsseldorf and University of California Los Angeles led by Prof. Reichert have now found that the cristae membrane and crista junctions reshape continuously. They also found that a protein complex called the mitochondrial contact site and cristae organizing system (MICOS) orchestrate these remodelling events.

 “Prof. Reichert’s lab has been working on the mechanisms of cristae remodelling. We were working on the function of MICOS complex located at the crista junctions,” Dr Arun Kumar Kondadi, one of the first authors of the paper, said. But one could never investigate if the cristae were dynamic or not as there was no technique that enabled researchers to see the details inside an organelle. “For more than half a century, it was rather assumed that cristae are static,” Dr Kondadi said. “Super-resolution microscopy techniques paved us the way to discover something really fascinating.”

In this study, using STED super-resolution nanoscopy, researchers have shown that adjacent crista junctions come together and separate from each other reversibly in human cells. For this, the researchers stained cristae membranes using dyes (or marked proteins present on the inner membrane of mitochondria) and observed how the cristae remodel using STED super-resolution nanoscopy. These experiments showed that cristae undergo membrane remodelling continuously.

According to Prof. Reichert, as quoted in the Press Release from Heinrich Heine University, the observations of this study lead us to a new model – Cristae Fission–Fusion (CriFF) model – that cristae can stay as isolated vesicles within mitochondria and then re-fuse with the inner membrane after fission. The study shows that this fusion is carried out by the MICOS complex. MIC60 – one of the proteins of the complex – initiates the process and marks the crista junction. It then recruits other proteins of the MICOS complex (MIC10, MIC13, MIC19, MIC25, MIC26 and MIC27) and completes the assembly. These crista junctions now become the sites from where cristae form. These junctions keep merging and splitting. The cristae could, therefore, pinch off from these junctions and come back to the same junction or another.

This study has opened a new field in research where one could investigate how a mitochondrion ensures quality control within itself. For all we know now, remodelling and reshaping of mitochondria in a cell can control the fate of the cell. This study has gone one step ahead to show how structures within the mitochondrial remodel continuously. How these events inside mitochondria can affect the mitochondria, and how this impact on mitochondria can influence the cell will be interesting to study.

Read the full paper here

Image Courtesy & Article Source: EMBO Reports

Joel P Joseph Women in Science

Why I do Science: Responses from Women in Science

February 11, 2020: On the occasion of International Day of Women and Girls in Science, I asked a few women in Science one question: “Why do you do Science?” Here are some interesting responses.

Women in Science

I do Science because every day is an adventure as a scientist.

– Dr Vaishnavi Ananthanarayanan (Assistant Professor, IISc)

Everything that happens around is Science. Technology is applied science. I do Science to be a part of everything I do every day.

– Sara Ashok Varghese (Junior Research Fellow, IBAB)

The curiosity to understand the nature around us and my love for solving puzzles were my prime motivation to enter science. Now that I am at ACTREC, I come across cancer patients every day at the hospital associated with the institute. Seeing these patients has added a sense of duty and responsibility towards society as well to my love for science.

– Dr Shilpee Dutt (Principal Investigator, ACTREC)

I do Science because I find the process of discovery exhilarating and humbling at the same time.

– Leeba Ann Chacko (Junior Research Fellow, IISc)

To contribute to the growth of Science, even if it is in a small way, is truly important. For me, research is like cooking. You try different ingredients and recipes to prepare the best dish. Similarly, I try to find different ways to fine-tune a technique or experiment. That’s why I love doing science.

– Dr Devi Arikketh (Associate Professor, SRMIST)

It makes me happy to try something new every single day. That’s why I do Science.

– Sneha Paturi (Research scholar, CCMB)

Biology has been the most fascinating subject for me since school. I always asked questions and decided to become a scientist to answer them. At some point later it changed, I discovered that there are other ways to inquire. Now I use visuals to provoke ideas and discussions around science, definitions, and processes.

– Dr Ipsa Jain (Science Illustrator, Ipsawonders)

I do Science because I love challenges. The harder the path, the stronger I get.

– Gautami Amarnath (PhD student, Ulm University)

I do Science because I enjoy it. My motivation to pursue Science came from my eighth-grade biology classes on the types of animal and plant tissues, which had thrilled me to no end – here was an entire world I did not know of earlier, and it was what constituted life itself! 

– Mitali Shah (PhD student, IISc)

Science is fascinating. And life science, for that matter, is the study of the process of life itself. Many processes of life remain a mystery. Learning about it every day and trying to understand even a little bit of it is greatly satisfying and fun for me.

– Mariam Susan Joseph (Project Fellow, SBRL)

I do Science because I enjoy solving problems and finding the unknown. It adds quality to life.

– Research Scholar, MAHE

I do Science because it thrills me to tap into nature’s unsolved mysteries and build solutions that help people. Also, the small milestones in the journey give me immense joy and satisfaction that no other profession can give.

– Dhanya R. (Research Scholar, IIT-M)

 

PS: These responses are almost entirely from biologists and bioengineers. I’ll try to be more inclusive in covering such occasions in the future.

 

 

 

 

Joel P Joseph Biological Sciences, Interviews, Women in Science

Musings of a woman bioscientist: Interview with Dr Shilpee Dutt

Dr Shilpee Dutt, winner of this year’s Janaki Ammal – National Woman Bioscientist Award for the young category, is a Principal Investigator at Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Mumbai. In this interview, she briefly discusses the research by Shilpee Lab and her journey so far. 

The National Women Bioscientist Award is conferred by the Department of Biotechnology, Government of India, in recognition of the contribution of women scientists in the country who are working in biology and biotechnology. The young category award is given to women scientists below 45 years of age who have contributed significantly towards unravelling challenges in various areas of biosciences and biotechnology.

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Dr Shilpee Dutt and her lab at ACTREC, Mumbai

1. How do you feel winning the Janaki Ammal – National Woman Bioscientist award?

I feel really happy that our research at ACTREC, Navi Mumbai, has been recognized at a national level. It is a teamwork and I am privileged to have students who have made this work possible. This achievement gives a lot of confidence and boost to strive for better.

2. Could you please explain your research?

Resistance to therapy is a longstanding problem in cancer therapeutics and is the major cause of cancer-related deaths. In our lab, we are trying to understand the molecular basis of therapy resistance in cancer with a focus on Glioblastoma (Brain tumours) and Leukemia (Blood cancer). Over the last 8 years, using genetic, molecular biology, biochemical approaches and mouse-xenograft models combined with studies in human patient samples, we have identified that tumour cells are very heterogeneous. We have shown that more than 95% of tumour cells die upon radiation and chemotherapy, but a small set of cells that we call ‘residual resistant’ cells survive and give rise to relapse tumour. We have also identified certain molecules that are responsible for the survival of residual cells thus providing critical information necessary for therapeutic interventions in Glioblastoma and Leukemia.

3. When was the first time you got interested in science?

Although I was always interested in science, it was my research experience at Dr Subrata Sinha’s lab (AIIMS, Delhi) for my M.Sc dissertation that I first realized research was so interesting and something I would want to pursue for the rest of my life.

4. What were the challenges you faced growing up as a girl interested in pursuing science?

There were no challenges growing up as a girl interested in pursuing science. My parents always encouraged me to do what I wanted to do. In fact, I was given a lot of freedom to think on my own and make my own decisions. The way I was brought up has moulded my personality into how it is today.

5. What was the happiest moment in your career so far?

I think the happiest moment was when I started my own lab at ACTREC. This provided me with the opportunity to ask and answer the scientific questions that I was interested in. Setting up your own lab has a lot of challenges and is quite an experience, but I must say I enjoyed every bit of it. I think there cannot be anything better than having your own lab.

6. What was the toughest or saddest moment in your career?

As a researcher, there are always moments when one feels disappointed with the experiments not working, but these are short-lived and they actually provide you with a challenge to start over again, learn from the mistakes and do better.

7. What were the struggles you faced as a woman in science?

Fortunately, I have not faced any gender bias in my scientific career. However, I know everyone is not as privileged. We know that there are fewer women in leadership positions in science as compared to men. It is important that female scientists are promoted to leadership positions. That would provide role models for young researchers and inspire them to take the same path. Providing support systems like campus child-care facilities would help women scientists to balance work and family.

8. Did you find yourself at an advantage anytime being a woman in science?

Not really

9. What is your favourite thing to do when not in the lab?

Reading (fiction), listening to music and watching movies

10. Any advice for those aspiring to pursue a career in scientific research?

Having a research experience like summer training/internship before you apply for a PhD program would help you realize how much you love doing research. Research could be slow and demanding at times, so unless you are passionate about your science you can easily give up. I would suggest pursuing scientific research only if you enjoy both the ups and downs of it.

 

Joel P Joseph Biological Sciences, Interviews, Women in Science

Musings of a woman bioscientist: Interview with Dr Kavita Babu

Dr Kavita Babu, winner of this year’s Janaki Ammal – National Woman Bioscientist Award for the young category, is an Associate Professor at Centre for Neuroscience, Indian Institute of Science (IISc), Bengaluru. Before joining IISc, she worked at the Indian Institute of Science Education and Research (IISER), Mohali. In this interview, she briefly discusses the research by Babu Lab, her journey so far and the principles that drive her. 

The National Women Bioscientist Award is conferred by the Department of Biotechnology, Government of India, in recognition of the contribution of women scientists in the country who are working in biology and biotechnology. The young category award is given to women scientists below 45 years of age who have contributed significantly towards unravelling challenges in various areas of biosciences and biotechnology.

                  Kavita Babu     Babu lab IISER

                                    Dr Kavita Babu and her lab at IISER Mohali

1. How do you feel winning the Janaki Ammal  National Woman Bioscientist award?

It feels good to get an appreciation for our science. The Janaki Ammal – National Woman Bioscientist award was possible because of the work performed by our lab members: postdoctoral fellows, graduate students and undergraduates at IISER Mohali where I set up my lab and spent more than seven and a half years. I have now started setting up my lab at the Centre for Neuroscience, IISc where I have spent the last six months and am currently on lien from IISER Mohali.

2. Could you please explain the research that led you to win this award?

Normal movement occurs when neurons from our brain can “talk” to muscles in our body. The interaction between neurons and muscles occurs at sites called neuromuscular junctions. These regions are sites where the neuron sends a chemical (neurotransmitter) that binds to a class of proteins present on the muscle (called receptors). The activation of these receptors by the neurotransmitters causes contraction or relaxation of muscles and hence movement. We study how surface proteins at the neuromuscular junction affect their functioning. Our work uses a simple non-hazardous worm (C. elegans) to study these proteins. Although we study a small worm, the proteins in these animals are similar to those found in you or me.

Research in our lab has identified proteins that are required for normal neurotransmitter release as well as receptor maintenance. These proteins although found in worms, have counterparts in humans that may be functioning in a similar manner.

3. When did you first decide to become a scientist?

I think I had decided during my undergraduate years that I would become a scientist. During my undergraduate education, I did summer internships at laboratories in TIFR, Bombay and IISc, Bangalore. Those summers convinced me that working in a lab was something I wanted to pursue.

4. What was the best moment of your career so far?

Being able to grow worms for multiple weeks and starting to perform experiments with them was a great moment. It had taken a long time for me to set up a worm lab and it was a great feeling to know that we would soon be able to start performing our experiments in full swing. I am also hoping that this moment will happen fairly soon here at the centre for Neuroscience, IISc where I am currently setting up my lab.

5. What was the greatest struggle in your career so far?

I think struggles and good moments are part of everyday life for many careers. I try to avoid dwelling into past struggles as there are so many present ones that need my attention.

6. What were the struggles you faced as a woman in science?

I think many of the struggles one faces initially while setting up a lab are the same whether you are a man or a woman in science. I try and deal with them by being very organized and fairly prompt with getting things done and avoiding worrying too much about what I can’t change. Although I realise that there are inequalities between how men and women scientists may be treated, I feel that if there is nothing I can do about it, I should just get my work done and carry on instead of worrying too much about these inequalities. Having said that it is clear that there are very few women in professorial positions in most STEM subjects and one hopes that this will change soon. The way forward would be to advocate for more women scientists as this is something that may be more difficult for some women scientists to do for themselves. All things considered, I feel that I have been fortunate in my circumstances and education to be in my current position.

7. Was there any time you were in a privileged position as a woman in science?

I don’t think so.

8. What is your favourite thing to do when not in the lab?

Watching crime and food shows, reading and walking.

9. Any advice for those who wish to pursue a career in science?

Believe in yourself. Do a lot of research on whatever career you want to pursue, there are lots of small things that you won’t know unless you talk to people. Talk to lots and lots of people pursuing careers that you are interested in. However, in the end, make your own decisions on what to pursue based on your strengths, interests and understanding of what the career you want to pursue entails. It helps to go with something that you are passionate about, but there are pros and cons to most decisions, and it helps to think through those carefully while making your final decision. But again, I know a lot of people who have made decisions in an instant and are very happy with the outcome.

Joel P Joseph Biological Sciences, Medicine, News

Scientists identify a compound that protects neurons from degeneration

460711949-56a793d25f9b58b7d0ebda5c     neuron

Scientists from the Bengaluru-based institution Jawaharlal Nehru Center for Advanced Scientific Research (JNCASR), with the help of National Institute of Mental Health and Allied Sciences (NIMHANS) and Center for Cellular and Molecular Platforms (C-CAMP), have identified a molecule that could clear toxic aggregates in the brain and reduce the loss of neurons (neurodegeneration). The study was led by Dr Ravi Manjithaya, Associate Professor, Autophagy laboratory, Molecular Biology and Genetics Unit, and Associate Faculty of Neuroscience, JNCASR. The findings were recently published by the Lancet journal EBioMedicine.

Parkinson’s disease is a neurodegenerative disease that affects 10 million people worldwide. In Parkinson’s disease, misfolded proteins form clumps in a set of neurons in the brain – the neurons that release dopamine (dopaminergic neurons). These aggregates, known as Lewy bodies, majorly constitute a misfolded protein called α-synuclein and result in the loss of dopaminergic neurons. Loss of dopaminergic neurons affects the movement and cognition of a person. The person is unable to walk properly, has shaky hands and legs, and becomes forgetful, drastically affecting his/her quality of life.

Several scientists across the globe have tried to develop drugs that reverse this situation but have failed. In this study, the team of researchers identified a chemical compound that blocks a protein (c-abl kinase), thereby clearing the toxic aggregates formed. The team had to screen numerous small molecules before pinning down on the small molecule, PD180970.

The team overexpressed (forced synthesis beyond natural limit in the cell) α-synuclein in yeast cells, making it toxic for the cells and killing them. This model could mimic how α-synuclein aggregates kill neurons and the researchers tested the small molecules on this. “We screened a small molecule library and identified those that rescued growth of yeast cells expressing the Parkinson’s disease-associated protein, α-synuclein,” Dr Manjithaya said. “Later we narrowed down to molecules that were rescuing the growth defect in an autophagy-dependent manner.”

The team found that PD180970 could inhibit c-abl kinase and induce autophagy to reduce the toxicity in neurons caused by the aggregates. This was evidenced by their studies on neuronal cell lines and in mouse midbrain. In addition to clearing aggregates, preventing the inflammation of neurons is important to stop neurodegeneration. “A small molecule that induces autophagy to clear the aggregates and also has anti-inflammatory property would be more potent in curbing neurodegeneration,” Dr Manjithaya said. “This is how we think PD180970 works,” he added.

The collaborations with Dr Phalguni Alladi, Senior Scientific Officer, NIMHANS, Dr James Clement Chelliah, Neuroscience Unit, JNCASR, and Dr Taslimarif Saiyed, CEO and Director, C-CAMP, were vital in this aspect. “While my lab focuses on the autophagy aspects, my collaborator Phalguni Alladi at NIMHANS mentioned about the impact of neuroinflammation. To this end, we collaborated with Taslim’s lab at C-CAMP to test if any of our molecules had anti-inflammatory properties.” Dr Manjithaya said. “PD180970 was the most effective among the ones they tested.” PD180970 prevented neuroinflammation by inhibiting cytokines like IL-6 (interleukin-6) and MCP-1 (monocyte chemoattractant protein-1), which facilitate inflammation.

Dr Manjithaya is highly appreciative of collaborations in science. “As a young researcher, having collaborations is looked down upon in our country although it is the norm and is encouraged in the western world,” he said. “Good collaborations bring in various aspects that make a study complete. Apart from their unique expertise and direction, there is further confirmation of the work, and more importantly different – sometimes contrasting – views. That makes you think more critically about your data and gives a fresh perspective. This study is a culmination of efforts from four labs across three institutions.”

In mice where the dopaminergic neurons were degenerated by injecting a chemical called MPTP. Treatment with PD180970 along with MPTP injection improved the condition. This was supported by evidence from the changes at a molecular level in the brain and the behavioural changes that occurred in the mice.

That’s not all. The lab is working with Vipragen Bioscience to patent the molecule and take it forward to the next stage in drug development.

Read the full paper here

Pictures from verywellmind.com andeinstein.yu.edu

Joel P Joseph News, Science Outreach

A group of 20-somethings are changing the way biology is taught at school

IMG-20191005-WA0021   IMG_1061

Chennai: Cambrionics Life Science – a community of biologists based in Chennai – is changing the way biology is taught in schools. The enterprise founded by five 20-somethings has reached over 3500 students in Tamil Nadu with their flagship program, Teaching Alternate Biological Science (T.A.B.S). T.A.B.S is a 12-week experimental learning program in Life sciences for school kids in grades 6 to 9.

The program is built on a research-based learning framework, where students spend four weeks experimenting with each model organism. The course includes model systems like Zebrafish or Drosophila, Microbes, and Plants. Through these experiments, students are exposed to various themes in biology including neurobiology, genetics, forensic biology, microbiology, developmental biology, cell biology, toxicology, astrobiology, hydroponics, aquaponics and farming.

The program is designed at three levels – beginner, intermediate and advanced, each level providing varying degrees of exposure to biology. While the beginner level is designed to inspire students and ignite a passion for biology, the intermediate level is aimed to develop critical thinking and the advanced level exposes them to various career opportunities in biology and encourages them to develop scientific solutions to a given problem.

The upcoming T.A.B.S program starts on Saturday, November 30, 2019. The 12-week program is conducted every Saturday from 4:00 PM – 6:00 PM at KK Nagar, Chennai.

To register for this module of T.A.B.S, contact the team at +91-7845133745 or register here. You could also contribute to the cause here.

Joel P Joseph Biological Sciences, Interviews, Medicine

A viral conversation: Interview with Dr G Arun Kumar

Dr G. Arun Kumar, currently heading Manipal Institute of Virology (MIV) under Manipal Academy of Higher Education (MAHE), is a renowned Indian microbiologist and virologist. He also heads the Regional Reference Laboratory for Influenza viruses established by Ministry of Health and Family Welfare, Government of India at Manipal and the ICMR Virology Network Laboratory (Grade-1) at Manipal. He is the pioneering scientist, who established the virology facility in Manipal with the support of the University and the Government. His research interests include viral diseases, epidemiology and diagnostic virology and public health response during infectious disease outbreaks. He led the team that was instrumental in containing the first Nipah Virus outbreak in South India. He is an expert member of several national and international committees pertinent to public health. 

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Dr G. Arun Kumar at Manipal Institute of Virology

How did you come to join Manipal Academy of Higher Education and how was the virology facility set up there?

I came to Manipal in 1994 to pursue MSc in Medical Microbiology after my BSc in Medical Laboratory Technology from Trivandrum Medical College. It was within a year since Manipal had become a deemed university. As soon as I finished MSc, I received the CSIR-JRF fellowship and went to the All India Institute of Medical Sciences (AIIMS), Delhi, to pursue my PhD in Virology.

About six months into AIIMS, as I was preparing to register for PhD there, my Professor from Manipal, Dr P G Shivananda MD, PhD., wrote to me asking me to join them. It was a difficult decision to take as Manipal did not have a virology lab at that time. The risk-benefit analysis showed that it was risky to move to Manipal. But my professor was insistent and promised me to provide a small facility for virology. I also discussed these things with my guide Dr Pradeep Seth, MD at AIIMS, New Delhi, and he also suggested taking up Manipal’s offer. I then thought that moving to Manipal was a challenge I had to take up – to initiate something that would have a lasting impact not only on me but also on the institution.

So, I joined Manipal as a lecturer in Nov 1997. I wrote a proposal to Prof. M. S. Valliathan, the then Vice-Chancellor of MAHE, through my professor, Dr P G Shivananda, to establish a virology laboratory. After a year, INR 500,000 was granted to set up a virology facility. That is how the virology lab was set up in Manipal and I came to be associated with it.

How did this facility grow to be an internationally renowned institute?

In May 1999, we set up a small lab with viral serology, tissue culture and virus isolation facility and started working on some clinically relevant viruses. We started the work with Respiratory Syncytial Virus (RSV) as I had worked on it in AIIMS and was familiar with it. I also started my PhD on RSV and completed it in 2002. By then we were actively working on 4 to 5 viruses and were providing diagnostics for it. This was also the time when we started attending conferences and people started noticing our work.

In 2003, there was a huge outbreak of SARS in Hong Kong. Government of India started looking at developing the capacity to detect and fight this virus. A review committee emphasized the requirement for more virology labs in India. The government also wanted to prepare the country for Avian Influenza (bird flu) Virus. Fortunately for us, without our knowledge, our facility was identified as a potential lab to be supported to work on these programs.

In 2007, we got a letter from the Indian Council of Medical Research (ICMR) asking if we were willing to develop the lab to a state-level virus diagnostic and research laboratory (VRDL). Following an expert site visit and a detailed project proposal review in 2010, they sanctioned a grant of INR 5 crore for a period of five years.  Meanwhile National Centre for Diseases Control (NCDC), Delhi had included our lab under the network of regional influenza laboratories.  This enabled our facility to be notified as a reference laboratory for influenza A H1N1 when the pandemic influenza arrived in India in 2009. The ICMR- VRDL facility was established in March 2010. Subsequently, realizing the potential of the lab, MAHE elevated it as a University department – Manipal Centre for Viral Research (MCVR). Now I had to report directly to the Pro-Vice-Chancellor of the university. This removed many hurdles and facilitated a faster decision-making process. We also moved into a new building with the support of the university. In this way, we grew in close association with the State and Central Health Services in India in the area of disease surveillance

In 2013, we had another quantum leap when we received a foreign grant from the Centre for Disease Control (CDC), USA as part of the global health security agenda (GHSA). We were awarded a sum of USD 250,000 to study emerging pathogens in the human-animal interface. We started the study in Shimoga, Karnataka. It progressed well and we received an upgrade of the award in 2015 to carry out the study in ten states in India. With that our funding had increased and our capacity grew tremendously. This enabled us to become a centre for excellence in disease surveillance and outbreak investigations.

In this way, we grew with the support of the university and the Government of India. We received several grants from the government and the university provided us with the infrastructural support. Manipal provided enormous support, space and freedom to grow and implement some of the dreams I had. The support has continued and now we have been elevated as independent institute – Manipal Institute of Virology (MIV) – under the university with higher containment labs and facilities.

MCVR (now MIV) did an excellent job in checking the Nipah virus outbreak. How did you go about detecting this rare virus?

Since 2009, we have been working very closely with Kerala on the detection of Pandemic Influenza. Besides the Influenza virus, we would also run diagnostic tests for other viruses in many cases. Gradually, many doctors of Kerala gained confidence in our viral detection tests and we developed a close relationship with the doctors. Baby Memorial Hospital at Calicut was one of the hospitals we had been closely working with.

In May 2018, a patient with symptoms of Encephalitis came to Dr Anoop Kumar at Baby Memorial Hospital. His brother had died with a similar illness 12 days earlier and two others in his family were also sick. This cluster of brain fever in a family raised an alarm. There were two possibilities viz., (i) Serial Poisoning (ii) An infection. When Dr Anoop called me around lunchtime on May 17, 2018, and explained the case, I sensed that it was a serious case. I directed him to collect multiple clinical samples and asked him to send it across quickly by hand. In a usual case, the samples are collected through a nodal officer at the district and are sent as a batch by train either daily or on alternate days.

In our primary investigation of this sample, in addition to the test for common Encephalitis agents like Herpes Simplex Virus and Japanese Encephalitis Virus, we tested for Nipah Virus as well. In the usual case of Encephalitis from Kerala of Karnataka, we would never consider testing for Nipah in the first set. But we considered it because of our understanding of Nipah epidemiology and knew that Nipah presents as a family cluster of encephalitis. Nipah virus testing was not new for us. In our fever study program in Assam and Tripura, we had tested samples for Nipah in the border areas close to Bangladesh (Bangladesh has been reporting Nipah cases every year since 2001) but didn’t detect any. That is why we considered it in our primary investigation and it turned out that the patient was positive for Nipah. But since this was from a different region, we were sceptical. We wanted to be sure. So we tested for about 30 other agents and by evening we were sure that it was Nipah only.

How did you tackle the situation when you realized that you were dealing with this deadly virus? What were the measures you took to rise to this public health challenge?

By the evening of May 17, 2018, we knew that we were dealing with Nipah. But you cannot announce it right away as it would have implications on national and international mobility. We also had to be absolutely sure of the agent. But the information had to be conveyed quickly to contain the virus and avoid transmission.

So immediately we sent the samples to National Institute of Virology (NIV), Pune, for a reconfirmation. In the meantime, we alerted the central and the state government authorities about the virus without naming it and urged the hospitals to isolate people who had come in contact with the patient.

Kerala responded to this situation in a very positive way. The health department instructed the hospitals about isolation procedures and patient care. The healthcare workers were pro-active, and the public also responded well.

The Hon. Health Minister of Kerala Smt. KK Shailaja teacher asked me to join them on the field as very little was known about this outbreak and had to be investigated. When we got there, we realized that there were several undiagnosed deaths in the medical college that week. Fortunately, the samples were preserved for few cases at least and they turned out to be positive for Nipah.

But these cases had no obvious connection to the first patient or the family. This was frightening. By this time the public and the government were growing restless and wanted to know what was happening. If these cases were not linked to the first cluster, we would have to consider the case of a biothreat. But Nipah is a difficult agent and is usually not used as a bioweapon. We launched a thorough epidemiological and virological investigation and traced those who had come in contact with the initial patients, isolated them and put them under surveillance. The health department of Kerala had already started isolation procedures on the night on May 18.

We then went into a detailed investigation of the first case, twelve days before the reported death. The patient was hospitalized in the Taluk hospital for one day and in the Medical College Hospital for another day. The Taluk hospital had already been evacuated, but the staff recreated the scene of the original patient in the ward. He had cough, vomiting, and irritability. His father and brother had attended to him and there were some deaths from the same ward because of human to human transmission. Nine cases were thus linked to this hospital.

When we tried to trace the other cases, we found an intriguing association with the radiology corridor of the Calicut medical college. Investigations revealed that the index case when admitted to Calicut medical college was subjected to a CT scanning on 5 May and most of the cases had exposure to index case that day. The index case was moved around the CT scan room and in the corridor for about four hours since it was difficult to get his scan due to his altered sensorium and irritability. CCTV footages helped trace this exposure.  Once this link was established, we were relieved. Health department identified all contacts of these people and isolated all symptomatic cases and the situation came under control.

After this, the health department called for a meeting with News Editors and discussed the situation. We made them aware that Nipah is transmitted by droplets, where the person had to be within one-meter vicinity of the patient for it to be transmitted and not by aerosol (Airborne). At the start of the meeting, about 60% were wearing masks and at the end of it, no one was wearing a mask as the mask was required only for persons in close contact with the patient. This communication helped a lot to clear the public fear.

In retrospect, how do you view this achievement of Nipah intervention and what do you think about it?

Looking back, I think there were some critical junctures where important decisions had to be taken. The district administration was very supportive and was with the health team all the time. There was very good participation and intervention by the state and central health services. Hon. Health minister of Kerala Smt. KK Shailaja Teacher, The Additional Chief Secretary of Health department Sri. Rajeev Sadanandan and the Director of Health Services Dr RL Sarita has provided exceptional leadership. The Nipah emergency operation room at Calicut worked flawlessly in coordinating the response. It was a very good model and I am afraid if it can be replicated in other places.

Recently, Manipal Institute of Virology was added as a centre of Excellence within Global Virus Network (GVN). Could you please tell me a little bit about GVN and how you view this addition?

Global Virus Network (GVN) was founded by Robert Gallo, who won the second Lasker Award for the discovery of HIV, in conjunction with William Hall of University College London and Reinhard Kurth of the Robert Koch Institute. It is a Non-Government network that brings virologists and institutes together in a collaborative effort to fight viral infections.

The idea of the network is to develop expertise through centres for excellence and to exchange it among them to act quickly during an outbreak. The aims of the network include collaboration among virus scholars, expansion of virologist training programs, and evidence-based policy advocacy. The network also collaborates with WHO and gives expert opinion helping in framing evidence-driven policies.

I think our addition to the GVN will help us in building our capacity, be instrumental in framing evidence-based policies and to work on one health – a concept that tells that the health of people is connected to the health of animals and the environment, which is nascent in India. This collaboration is going to help us in the study of these aspects.

What is your vision for MIV for the next 10 years?

As we are transitioning from a centre to an Institute we are redefining our vision and goals. In the next ten years, we envisage transforming MIV to the most preferred place for infectious diseases researchers especially in the area of emerging and re-emerging diseases.  We will enable and nurture basic, translational and public health virology research which is designed to contribute to achieving the sustainable developmental goals.

As a person who has been instrumental in building a centre of excellence in research, what is your advice for other academicians treading the path?

Three things are important to build a department or institution: (i) Your team: You need people who stay with you and understand your vision and philosophy (ii) An enabling leadership and environment (iii) Liaison with government systems and stakeholders.

It is also important that you grow in a niche area. For example, we specialized in disease surveillance, outbreak detection and pathogen detection, which requires quick mobilisation the team in the field.

However, it is important to periodically identify the strengths, weaknesses, opportunities and threats and strategize to reinvigorate the growth rate.

Joel P Joseph Biological Sciences, Medicine, Motivational

The Nobel winners, 2019: Physician-scientists who discovered how cells adapt to changing oxygen levels

The Nobel Prize in Physiology or Medicine, 2019 was awarded to Gregg L. Semenza, William G. Kaelin Jr. and Peter J. Ratcliffe and for their work on how cells sense and adapt to oxygen availability. Their research elucidated the genetic mechanisms through which cells respond to changes in oxygen levels. The findings have implications in treating many diseases, including cancer, anaemia, heart attacks and strokes. These scientists had also shared the Albert Lasker Basic Medical Research Award in 2016. 

Nobel 2019

Left to Right: William G. Kaelin Jr., Sir Peter J. Ratcliffe, Gregg L. Semenza

If Semenza, Kaelin and Ratcliffe had one thing in common, besides their area of research, it is that they chose to publish houses of brick rather than mansions of straw. It sure took a while for the world to notice them, but it did.

About the papers that earned him the Lasker, Kaelin wrote, “Most would be considered quaint, preliminary and barely publishable today.” These papers would get him the Nobel Prize three years later.

Semenza and Kaelin woke up to the call from the Nobel media that day. While Semenza’s first reaction was to hug his wife, Kaelin told Adam Smith – the Chief Scientific Officer of Nobel media – how he missed his late wife on that occasion. Ratcliffe, on the other hand, was working on a grant when Smith called him. “I was writing and will continue to write an EU Synergy grant for collaborative work with friends and colleagues in Finland, and also my good friend and colleague Christopher Schofield, so of course the EU’s on our minds at the moment, and we’re writing a Synergy grant. And despite this good news, I guess I’ll continue doing that and meet the deadline,” Ratcliffe said.

What made these scientists embark on their journey in research is worth knowing. In an interview with The Journal of Clinical Investigation (JCI) in 2016, Semenza said that it was his high school biology teacher, Rose Nelson, who inspired him to pursue biology. “I had her as a freshman for biology and then as a senior for AP biology when it was genetics within biology that I got really excited about. With her help, I was able to enrol in an NSF-sponsored summer program at the Boyce Thompson Institute for plant research. It was really my first exposure to research and experiments,” he said. His interest in genetics and his meeting with a family friend’s child, who had Down syndrome, motivated him to pursue MD-PhD to study genetics and to care for those with genetic disorders.

It wasn’t easy for him at this stage either. Being the first graduate student of the lab with a very ambitious project in hand, he had reached the stage where he felt it wasn’t working out. He then switched to another lab at Children’s Hospital of Philadelphia in the second year, where he studied β-thalassemia.

“I was tasked with studying an unusual family, where one of the alleles was a silent carrier,” Semenza told JCI. “Normally, you can tell from looking at the blood cells whether someone is a carrier. In this case, it was the father who was an obligate carrier, as he had two affected children, but you couldn’t tell he was a carrier. It was suggested that the mutation was in some way different; this was going to be my project. The idea was that you take the blood, isolate the DNA, make a library, pull out the β-globin gene, and sequence it. I did all that and at the end of one year, I got the sequence, and the mutation was the exact same mutation as the previous study, which meant that somehow the clone had become contaminated, and the whole thing had been for nothing. So now I was going to have to start over the third time. I went back, started over again; things went smoothly because technically I’d already done it, and we went through the project and got an answer.”

He then moved to Johns Hopkins for his post-doctoral education, where he worked with Haig Kazazian and Stylianos Antonarakis – leaders in finding the molecular basis of β-thalassemia. He started working on this gene called Erythropoietin (EPO), which Chuck Shoemaker from Genetics Institute in Cambridge had asked Kazazian and Antonarakis to consider. Semenza tried to identify the DNA sequences in the gene responsible for its expression in different tissues. They put different fragments of human DNA spanning the EPO gene into mice and checked if and where the gene was expressed.

This was the turning point for Semenza. He figured that the gene was regulated by oxygen. Now, he had to understand where these DNA sequences regulated by oxygen were located. On investigating further, he realized that this sequence was in the DNA sequence that came after the gene (3’ flanking sequence). This was unusual as such regulating regions usually lie before the gene (5’ flanking sequence). But the data said that it was the 3’ flanking sequence. So, they took this sequence and put them in a plasmid which had a reporter. They then put this plasmid inside human cells grown in the dish and deprived them of oxygen. At low oxygen levels, the EPO gene would be expressed because of the sequence present in the plasmid. They then made smaller fragments of that sequence and repeated the process until they got down to 33 base pairs. On mutating individual nucleotides in this region, they found that the EPO gene expression was stopped.

“We suspected that there was a very important factor, which was binding to that sequence and was responsible for turning on the gene. And so, we tried to find the protein that was the key factor for turning on the EPO gene,” Semenza told JCI.

At this point, he was a young faculty with a post-doctoral fellow, Guang Wang. Semenza and Wang started looking for a protein that would bind to this DNA sequence (Hypoxia Responsive Element). The challenge was to figure out the conditions that allowed binding. They were also hoping to find something that would be present in the nucleus of cells with low oxygen (hypoxic) but absent in those with normal oxygen levels (normoxic). “Guang would do several of these experiments a day and had this stack of blots with negative results on his desk. I was thumbing through them one day, and I came across this one gel where there seemed to be a faint band in the hypoxic lane. I got all excited and said, ‘Did you see this? Did you see this?’ After optimizing the assay in a very short period of time, he generated really strong definitive results of a binding activity that we called hypoxia-inducible factor 1,” Semenza said.

For Ratcliffe, the start was serendipitous. In his Lasker acceptance speech, Ratcliffe reflects on an incident from his days at the Lancaster Royal Grammar School for the boys. “I was a terrible schoolboy chemist and following the career of some distant relative, I was keen to study industrial chemistry. One day the ethereal but formidable headmaster appeared in the chemistry laboratory, summoned me to one side, and said, ‘Ratcliffe, I think you should study medicine.’ I said ‘Yes, Sir’ decisively. Without further thought, the university application papers were changed accordingly,” he said. “To this day, I don’t really know whether he felt I would be a good doctor or a bad chemist. But the moment sticks with me as a reminder of the importance of serendipity in a scientific career, at least in mine,” he added.

He trained in Medicine as a Kidney specialist and started his research career fascinated by the extraordinary sensitivity with which the kidneys regulate the hormone Erythropoietin (EPO) to regulate red blood cell production. “I felt that the problem was interesting, conceivably attractable and there was a new opportunity for study with the cloning of the erythropoietin gene. But some people felt, with the emerging success of recombinant Erythropoietin, that understanding how the hormone was regulated was a niche area unlikely to be of very general importance. They advised me accordingly to study something else,” he said.

In the telephone interview with Nobel Media, Kaelin shared what drew him to science. “You know, I’m a big believer of curiosity-driven, hypothesis-driven research,” he said. “I know that’s complementary to other ways of generating knowledge but I think in the end what drew me to science and what draws a lot of scientists to science is that we like interesting puzzles, like clinical features of patients who had mutations in the VHL gene, were a curious constellation of findings but one way to unify them was there was some abnormality in the way the tumours they were developing were sensing and responding to oxygen, and we thought if we could understand that we could understand more globally how cells and tissues sense and respond to changes in oxygen.”

Little did these physician-scientists know while addressing their research problems, that they were reaching for the Nobel with their findings. But that’s the beauty of Science. Think about these Nobel laureates. As someone who made a serendipitous entry into medicine later pursuing an area of research, which many thought had no scope beyond the niche area of kidney research, Ratcliffe won the Nobel Prize for the findings that have immense physiological importance. Sharing the award with him are Semenza, who struggled in the early days of PhD and found his way through, and Kaelin, whose pre-medical school mentor remarked on his college transcript, “Mr. Kaelin appears to be a bright young man, whose future lies outside of the laboratory.” Their life and work are a testament to the fact that houses of brick stand the test of time.

Sources:

Kaelin Jr., William G. (2017). Publish houses of brick, not mansions of straw. Nature. Retrieved from https://www.nature.com/news/publish-houses-of-brick-not-mansions-of-straw-1.22029

Neill, Ushma S. (2016). A conversation with Gregg Semenza. The Journal of Clinical Investigation.  Retrieved from https://www.jci.org/articles/view/90960

Albert and Mary Lasker Foundation. Peter Ratcliffe, Acceptance Speech, 2016 Lasker Awards. Retrieved from https://www.youtube.com/watch?v=wB5gzwZMvTM

Albert and Mary Lasker Foundation. William Kaelin Jr, Acceptance Speech, 2016 Lasker Awards. Retrieved from https://www.youtube.com/watch?v=K2Ds_S48IWg&t=54s.

Sir Peter J. Ratcliffe Interview. Retrieved from https://www.nobelprize.org/prizes/medicine/2019/ratcliffe/interview/

William G. Kaelin Jr. Interview. Retrieved from https://www.nobelprize.org/prizes/medicine/2019/kaelin/interview/

Gregg L. Semenza Interview. Retrieved from https://www.nobelprize.org/prizes/medicine/2019/semenza/interview/

 

Joel P Joseph Biological Sciences, News, Science & Technology

NOW YOU SEE ME: First Cryo-EM image of New World Hantaviruses

Scientists from the USA recently published the first Cryo-EM image of New World Hantaviruses. The team, led by Colleen B. Jonsson, obtained the Cryo-EM images of three New World Hantaviruses – Andes Virus (ANDV), Sin Nombre Virus (SNV), and Black Creek Canal Virus (BCCV). The study was published in the journal Viruses.     

  SNV      Capture

Left: Cryo-EM image of Sin Nombre Virus (SNV). Right: Members of the research team. L to R: Mariah Taylor, Amar Parvate, Colleen B. Jonsson

The team of seven researchers employed cryo-electron microscopy (cryo-EM) to understand the structural features a group of viruses called Hantaviruses. The technique helped them unravel the features of two types of Hantaviruses – Old World Hantavirus and New World Hantaviruses. While the former is prevalent in Eurasia, the latter is found in the Americas. Old World Hantaviruses include the viruses that cause haemorrhagic fever with renal syndrome (HFRS), whereas New World hantaviruses include those viruses that cause hantavirus pulmonary syndrome (HPS).

“I had not intended to work on these structures from the onset,” Amar Parvate, the first author of the paper says. “The idea was to investigate the spread of hantaviruses through cells using Transmission Electron Microscopy (TEM). But I realized that these viruses were not safe. We had to work on them in a highly contained environment (BSL3). There was no way to safely load them on a cryo-EM.” The team then worked on a method to inactive these viruses, without compromising their quality, and load them safely to see how they look through the cryo-EM. It took Amar and his collaborators three years to optimize the method on a prototype virus. They then applied it to several BSL3 hantaviruses the results of which are published in the paper.

The cryo-EM images of Andes Virus (ANDV), Sin Nombre Virus (SNV), and Black Creek Canal Virus (BCCV) published by this team are the first cryo-EM images of New World Hantaviruses. These images have revealed diverse features and sizes of New World viruses. They are round, tubular or irregular. While BCCV were mostly tubular, SNV were mostly irregular.

“Most of the Hantavirus community was looking at Old World Hantavirus morphology and assuming that the virions are all round. One reason was that they could not put these viruses on a cryo-EM was the containment restriction I mentioned earlier. Even after I had the initial results, other researchers were sceptical if the viruses were inactivated or whether the method itself distorted the morphology. My images proved that there are more diverse features to these viruses rather than just being round” Amar explained. “The most striking finding was the long tube-like morphology of one of the New World Hantaviruses.”

Amar’s method is now available to other researchers working on these kinds of viruses and paves the way to further discoveries in viral studies. “I am hoping other groups use my method to finally tease out structural details of other dangerous (BSL3/4) viruses that had been recalcitrant cryo-EM and structural studies,” Amar said.

Of course, the team had to do some things very differently to achieve this. Electron microscopists have traditionally fixed their room temperature biological samples on the grids using glutaraldehyde. To get an image of higher resolution using cryo-EM, they fixed the samples with a very mild fixation technique using glutaraldehyde. Amar and colleagues combined the two techniques into one. This was the thought that brought the breakthrough.

Amar is excited about the possibilities that his work has opened to researchers studying viruses. “Currently, there are very few cryo-EM facilities in the world that can handle BSL3 samples. Although there are advances being made in this direction, most highly contained (BSL3) labs do not have access to cryo-EM. My method proposes a way to use cryo-EM outside the containment for any BSL3 viruses” Amar said. “Once the virus is inactivated, it can be safely taken out and even shipped to a completely different institute for cryo-EM analysis. This type of extension of my method may eventually help us analyse morphologies of multiple viruses for which the most we have now are one or two TEM images collected in the 1980s.”

The implications of this research, however, do not end there. All these findings will ultimately lead to the greater goal of developing drugs and vaccines to fight these viruses. But those will come only later – when we have a better understanding of the structural features of the viruses. For all we know now, the images published by the group and the method that they have put has given the scientific community a great stride in studying dangerous viruses.

Joel P Joseph Biological Sciences, News

Scientists discover a new gene essential for hearing

Scientists have associated a new gene – Clrn2 – with hearing in mammals. Led by Amraoui and Bowl, the study was a collaborative effort of 32 researchers from institutes in the UK, France, and the USA. The findings were recently published in the journal EMBO Molecular Medicine.

clrn2

Cilia bundle in the inner ear. Picture adopted from EMBO Molecular Medicine

The sense of hearing results from a combination of events of physical and biological sciences. Mechanical energy from sound waves falling on the inner ear must be converted to neuronal signals for a person to hear. The process is taken care of by the specialized hair cells in the inner ear. On the tip of each hair cell is a bundle of cilia, some tall and some short, arranged in a specific manner and tethered to a complex. The movement of the inner ear fluid, caused by sound, deflects these hair cell bundles towards the tallest cilia. The tension created in the tip open the channels in the complex attached to it. The complex releases neuronal signals, completing the conversion of mechanical energy to neuronal signals.

Hearing loss can be caused by environmental factors, genetic factors or a combination of both. Although scientists have managed to understand early-onset hearing loss and hereditary hearing loss to an extent, very little is known about the genetics behind age-related hearing loss. The research conducted by this team has implicated the involvement of Clrn2 in age-related or progressive hearing loss.

The team mutated the Clrn2 gene in mouse and investigated its effect only to discover a progressive hearing loss. To check if the finding applied to humans as well, the group analysed the CLRN2 gene sequences of 5 lakh people from the UK biobank participants data. Data was segregated as hearing loss cases (163, 333) and controls with normal hearing ability (102,832). The cases and controls selected were above 50 years of age. The classification was made based on the participants’ response two questions recorded in the published paper – (i) Do you have any difficulty with your hearing? (ii) Do you find it difficult to follow a conversation if there is background noise (such as TV, radio, children playing)?  Those who answered ‘No’ to both were controls and other were cases. On analysing their CLRN2 gene sequence, the group found that those who had difficulty in hearing harboured mutations in their CLRN2 genes.

With further experiments on mice, the team discovered that while Clrn2 was necessary for the maintenance of the bundle of cilia in the hair cells of the inner ear after they had been formed. Mutations in this gene would, therefore, lead to poor maintenance of the bundle leading to progressive hearing loss.

From this study, scientists and clinicians now have a reference point to test for hearing loss because of ageing. We may be looking at days when the auditory tests, which are subjective, are replaced by the objective genetic tests for deafness.