Next Generation Sequencing Meets Traditional medicine

June 4th, 2015

Traditional knowledge in combination with modern scientific techniques could help unravel deep hidden mysteries. Scientists from NCBS, Bangalore, have revisited the age old knowledge of “Tulsi and its medicinal effects” in their labs, only to be overwhelmed by their scientific findings. Ocimum tenuiflorum or commonly known as Tulsi has been mentioned in ancient Indian scriptures and has found wide usage in the Indian traditional system of medicine, Ayurveda. Known for producing many aromatic compounds, Tulsi gained an informal name as the “Queen of Herbs”. It is considered sacred in Hindu households and mostly used for spiritual and religious purposes in India.

Tulsi grows extensively in tropical climate, hence found in most parts of Asia, Africa, Central and South America. It consists of a wide range of bioactive compounds which are known for their anti-bacterial, anti-fungal, anti-pyretic and anti-cancer properties. These compounds or plant metabolites are very poorly understood because of absolute lack of genomic information. Prof. Ramanathan Sowdhamini and team have produced the first draft genome of O. tenuiflorum Krishna subtype which is a huge leap in understanding and identifying the genes responsible for production of metabolites with medicinal properties. Focussing on the important metabolite genes, the team used five different types of Tulsi, (Ocimum tenuflorium subtype Rama, O. tenuflorium subtype Krishna, O. gratissimum, O. saccharicum and O. kilmund) to collect the genomic data and compare it with the nearest genetically related species. “The genome sequencing projects involved generation of huge quantity of data. The genes were identified from this enormous amount of data using complex prediction models and then they were numbered for easy identification. This assembled genome and the set of genes served as a start point for all downstream analysis”, said Adwait Joshi, one of the team members.

Like every other plant, Tulsi also produces specialized metabolites as a part of its defence mechanism. Linalool, Linalyl, Geraniol, Camphor, Thymol, Safrol, Apigenin, Citral, Eugenol, Taxol and Urosolic acid are few examples among the important secondary metabolites of Ocimum species. “Apigenin, Taxol and Urosolic acid are implicated in anti-cancer properties of the plant, Citral for its anti-septic nature and Eugenol for its anti-infective properties and so on”, says Prof. Sowdhamini. Few metabolites have been used in the perfume and cosmetic industries. While others have been exploited in curing human ailments like malaria, bronchitis, diarrhea and dysentery, etc. The metabolic pathway concerning the synthesis of Ursolic acid was investigated as a case study. Studying mature roots, leaves, flowers, seeds and other parts of the plant, the team found that the precursors of these metabolites are synthesized in young tissues and retain their specific medicinal properties in their mature counterparts.

Owing to the 3000 years of cultivation of Krishna Tulsi and extensive descriptions in the Vedas and Puranas, it is assumed to be of Indian origin. The findings of the experiments at CCAMP, NCBS, reinstate the household knowledge passed on by grandma, even when prodded by the modern scientific techniques. Prof. Sowdhamini said, “This is the first report of draft genome sequencing of a plant species from NCBS and we hope to do more”. Convinced of the huge array of genes and their respective downstream compounds yet to be unraveled in further research, the team looks forward to working in collaboration with an independent parallel initiative by CAMP, Lucknow, to provide the next version of the draft of Tulsi genome.

Conference report

INTERNATIONAL CONFERENCE ON BRAIN DISORDERS  & TREATMENTS

16-18 November 2015

Faculty Hall, Indian Institute of Science Bangalore

What is dementia and how is it caused?

The underlying genetic bases of Alzheimer’s disease

Can we prevent the onset of dementia in Alzheimer’s disease?

These are some of the key areas that will come under the lens at the international conference: “Neurodegenerative Diseases: Pathogenesis to Therapy” conference, which will be held between 16-18 November 2015 at the Faculty Hall, Indian Institute of Science, Bangalore. The conference is being organised by the Centre for Brain Research, an autonomous centre at the IISc. Scientists from various national and international research institutes and Universities will present their studies and findings during these three days and explore novel therapies. The main focus will be on neurological disorders related to age: their causes, mitigation and possible treatments.

Dementia refers to a range of symptoms that includes the loss of memory and decline in mental abilities like thinking, problem solving and language, caused due to brain degeneration. It is a common symptom of Alzheimer’s disease (AD) and has been noted in people in their mid-60s. Research suggests the onset of dementia could be delayed, and that there are treatments for the symptoms of the disease which can slow down the progression of dementia.

The degeneration of the brain as we age is primarily a medical problem. But, with the increasing ageing population across the world, it has now become an economic issue also. “Age related neurological  disorders have been a cause for public health concern in developed countries. In the near future, India and China will see the largest increase in new cases of dementia. So, there is growing global concern about ageing disorders, in general and dementia, in particular”, said Professor Vijayalakshmi Ravindranath, chairman, Centre for Neuroscience, IISc, Bangalore.

The first day of the conference will focus on Alzheimer disease- its causes, symptoms and possible therapy of its primary symptom – dementia. The day’s talks include

• John C. Morris, a lifetime achievement award winner from the Alzheimer’s Association for his contributions to this field, currently at the Washington University School of Medicine will speak about delaying the onset of dementia in AD and the ongoing trials.
• Yves Joanette, University of Montreal, Canada, will talk about the challenge that dementia poses and the collaborative efforts at a global level to understand the origins of the diseases causing dementia.
• Arthur Toga, founder of the Laboratory of NeuroImaging, University of California, Los Angeles, describing his work on making data from various laboratories accessible, and using a wide range of instruments and different protocols, to discover meaningful patterns.
• Sudha Seshadri from Boston University School of Medicine, will present the genetic aspect of Alzheimer disease research.
• The possible links between Dementia and type 2 diabetes will be discussed by Prof. Velandai Srikanth, a geriatrician at the Monash medical centre, Monash University, Melbourne.
• Suvarna Alladi, Nizam Institute of medical Sciences, Hyderabad, will address the possible role of multilingualism in the delay of onset of dementia.
• Mary Ganguli, University of Pittsburgh will speak about the relationship of brain’s function and dysfunction to the overall population as opposed to an individual.
• Murali Krishna will present his research from populations of Mysore and how nutrition and growth in early life and socio-economic adversities affect cognition in individuals.

The second day will be a range of topics on factors and mitigation of neurodegeneration due to age, how lifestyle factors and other diseases can influence brain damage owing to AD, Parkinson, Lafora disease or Amylotrophic Lateral Sclerosis. Dr. Ana Ines Ansaldo from University of Montreal, Canada, will talk about mitigation of neurodegenerative symptoms. Dr. Rosalyn Moran from Virginia Tech Carilion Research Institute, will present a mathematical predictive model to examine the impact of life experiences in aging neurobiology. Dr. Stanley Fahn, Columbia University Medical centre, followed by Dr. Uday Muthane’s, (Parkinson aging and research foundation, Bangalore) talk on Parkinson’s disease and mitigation probabilities.

 

The last day will be a presentation by Dr. Sangram Sisodia from University of Chicago, on genetic mutations causing Alzheimer followed by Dr. M. M. Panicker’s (NCBS, Bangalore) research on stem cell modelling on late onset of the disease. Prof. Colin Masters, University of Melbourne, will speak on possible gene therapy in Alzheimers before the concluding session of the conference – a panel discussion on dementia.

 

 

Day 1

16-18 November 2015

Faculty Hall, Indian Institute of Science Bangalore

“By 2050, more than 50% of the ageing population will be in South East Asia”, said Prof Yves Joanette, during the first session of the International Conference ‘Neurodegenerative Diseases: Pathogenesis to Therapy’ at the IISc today. “Globally, about 30% of the population would be 60+ very soon”, she added.

This immediately implies an increase in incidence of dementia. With an increasing aged population, dementia is becoming more of an economic problem, rather than a medical problem.

“India will contribute to dementia research both within the country and globally”, said Joanette, pointing out to the Rs 225 crore grant provided by Kris Gopalakrishnan to IISc. During his speech at the inauguration, Gopalakrishnan said “Understanding the human brain would help us improve the condition of people whose lives are affected by these diseases. There is a huge avenue for computational research, where India can really provide inputs”.

Dementia refers to a range of symptoms that includes the loss of memory and decline in mental abilities like thinking, problem solving and language, caused due to brain degeneration. It is a common symptom of Alzheimer’s disease (AD) and has been noted in people in their mid-60s. Dementia is also caused by other factors, said Joanette. “We need to examine the cascade of events that end up in dementia”, she said.

“We also need to find ways to deal with dementia-affected population – their quality of life and strengthening services for caregivers and families”, she added.

AD, first diagnosed in 1906, is a disease where neurons in the brain die and the brain wastes away as a result. Dr John Morris from the Washington University in St Louis called it a ‘global epidemic’. “The first stage of the disease is generally silent, and cannot be detected by current diagnosis methods”, he said. “The second phase is characterised by dementia and cognitive impairment. We currently have no therapy for the underlying cause of AD – the neuronal degeneration”, he added.

“We need population level studies to complement clinical ones”, said Dr Mary Ganguli from the University of Pittsburgh. Human beings are hetergenous subjects, not uniform like lab rats, she said. “It is crucial to examine the external factors from the population around a patient. Such data is lacking from countries like India”.

Ganguli has developed an India-specific questionnaire which can be used for population level dementia surveys. Neuro-physiological tests, the usual norm for diagnosis, were not feasible with illiterate people. She found an incidence of 1.17% in a population in Haryana, as opposed to 8% at a locality in the US. “The study needs to be expanded to other socio-economic classes, and across the country”, she said.

Dr Sudha Seshadri, an alumnus of CMC Vellore who is now at Boston University, has been “looking at new genes or new targets for understanding the biology of AD, which would help discover new drugs and therapeutic approaches”. She suggested genome-wide surveys to look at possible targets for gene therapy.

Murali Krishna, an Early Career Wellcome Trust-DBT fellow from Mysore, examined the hypothesis that a smaller birth weight, because of a smaller head, increases chances of dementia when the person ages. Examining more than 1000 people born in a particular hospital in Mysore, he was able to establish that low birth weight, combined with low socio-economic status, increased the prevalence of dementia and cardiometabolic disorders.

Suvarna Alladi of Nizam’s Institute of Medical Sciences, Hyderabad, said that India was ideal to test the hypothesis of whether speaking more than one language maintains cognitive functions better. “Switching between languages maintains higher cognitive functioning”, she said. “Irrespective of literacy, being multi-lingual helps to delay dementia. Illiterate but skilled workers like artisans, potters and weavers had heightened cognitive abilities and hence late onset of dementia”, she added.

 

http://cbr.iisc.ernet.in/conference.php

Prof. John C. Morris http://neuro.wustl.edu/aboutus/facultybiographies/morris

Mary Ganguli http://www.wpic.pitt.edu/research/dementia_epidemiology/

Murali Krishna http://wellcomedbt.org/fellowsprofile/dr-murali-krishna-125

 

 

Day 2

17 November 2015

Faculty Hall, Indian Institute of Science Bangalore

“Sitting is the new smoking. Eight hours of sitting does similar damage to what smoking does to you”, said Manjari Tripathi, a Professor of Neurology at the All India Institute of Medical Sciences, New Delhi. Life expectancy in India has shot up in the last 50 years, thanks to better medical facilities.

“Soon, India will have the third largest ageing population following the US and China”, she said. “One in six women beyond 55 are likely to develop dementia. However, the factors leading to dementia are still an enigma”. Tripathi has initiated a study that will monitor the health of a rural and an urban group, over the next couple of decades.

Dementia refers to a range of symptoms that includes the loss of memory and decline in mental abilities like thinking, problem solving and language, caused due to brain degeneration. It is a common symptom of Alzheimer’s disease (AD) and has been noted in people in their mid-60s.

Can we remodel the brain after it has aged? At a very interesting talk during the second day of the International Conference ‘Neurodegenerative Diseases: Pathogenesis to Therapy’ at the IISc today, Ana Ines Ansaldo from the University of Montreal discussed brain remodelling as a therapy for Alzheimer’s Disease.

The brain is capable of some degree of plasticity, or remodelling. With age, this ability typically decreases. Ansaldo has found that engaging the brain in novel, complex tasks provides it with an ‘enriched environment’ that delays onset of brain degeneration. Therapy induced plasticity can potentially prove beneficial for Alzheimer’s patients, her research has shown.

Stanley Fahn from Columbia University spoke on the symptoms and pathogenesis of Parkinson’s Disease. The disease is caused due to degeneration of neurons, and it progresses slowly in most people; the person’s brain slowly stops producing dopamine, a neurotransmitter – a chemical used to communicate between neurons. Hirsch Etienne from the Brain and spine institute, Paris, spoke on the unmet therapeutic needs in Parkinson’s disease. K P Mohan Kumar spoke on the specific protein Prohibitin and its relation with Parkinson’s.

Jean-Pierre Julien from Laval university, Canada, spoke on possible therapies for the disease Amylotrophic Lateral Sclerosis (ALS). The disease affects motor neurons, the brain and spinal cord, causing muscle weakness and paralysis.

Rosalyn Moran from Virginia Tech spoke about her research on the mathematical modelling of the brain, which can help predict long term ageing patterns and propensity for disease.

LINKS

http://cbr.iisc.ernet.in/conference.php

Ana Ines Ansaldo: http://www.laboansaldo.com/ana_ines_e.html

Manjari Tripathi: http://www.aiims.edu/aiims/departments/spcenter/nsc/neurology/manjari-t.htm

K P Mohan Kumar: http://iicb.res.in/divisionwiselistofscientists/cbp/kpmohankumar.html

 

 

Day 3

18 November 2015

Faculty Hall, Indian Institute of Science Bangalore

The last day of the International Conference ‘Neurodegenerative Diseases: Pathogenesis to Therapy’ was packed with discussions regarding the latest research about Alzheimer’s and dementia, especially detection and therapy.

A panel discussion in the afternoon discussed the Dementia Network – designed to improve the system of care for individuals with Alzheimer’s Disease and dementia. Stanley Fahn from Columbia University stressed the need for collaboration among institutes, and among different streams – doctors, nurses, academicians, caregivers and families of affected people. Such a network can be used to establish common protocols and assessments for diagnosis, treatment and data collection.

Sangram Sisodia from the University of Chicago stressed the need for scientists to network together and use technology to the best possible extent. Yves Joanette from the University of Montreal stressed on the need for Big Data; and the need for large international collaborations to generate Big Data. Narahari from IISc stressed further on the need for complex algorithms that can handle the kind of data needed to understand neurological diseases. He spoke of the need to complement crowdsourced data with expert data, to get a good picture.

Upinder Bhalla from the National Centre for Biological Sciences said that the Centre for Brain Research established at IISc was an excellent starting point to setup the Dementia Network in India. Mathew Varghese from NIMHANS also stressed the same – when setting up the network was discussed 6 years ago, he said “research into Alzheimer’s Disease was in its infancy”.

In other talks, Sisodia from the University of Chicago has been working on the function of presenilin, a protein that is involved in the generation of beta-amyloid, which accumulates to form the ‘amyloid plaques’ typical of Alzheimer’s Disease. Deepak Nair from the Centre for Neurosciences, IISc has been studying the Amyloid Precursor Protein, which generates the beta-amyloid that leads to plaques. Vijayalakshmi Ravindranath studies how the plaques accumulate.

Balaji Jayaprakash from the Centre for Neurosciences, IISc has been studying mice affected by Alzheimer’s Disease to test memory and how it disappears with time.

Using laboratory strains of patient cells, Mitradas Panicker from the National Centre for Biological Sciences has developed a ‘gene map’ of the neural cells, which can help in earmarking the genes responsible for Alzheimer’s Disease.

Interviews

Prof. John Morris is the Harvey A. and Dorismae Hacker Friedman Distinguished Professor of Neurology, Professor of Pathology and Immunology, Professor of Physical Therapy, and Professor of Occupational Therapy at Washington University. He also is the Director and Principal Investigator of the Charles F. and Joanne Knight Alzheimer’s Disease Research Center. He studies various aspects of Alzheimer disease.

Based on your experience in dementia research in the western world, what would be you suggestions to Indian researchers or researchers focussing on dementia in India?

In the US, the only area where we have done really well in approaching the issue of dementing illness is a combination of clinical research in following patients and healthy control people to see how the disease progresses in them in conjunction with basic science. So the two work together and not separately. In IISc, there is tremendous basic research but no or very little clinical research. In the US, we have exclusive Alzheimer’s research centres that are funded by national institute of health which started in 1984 and since then they have brought clinical and basic science people together. It’s not a tradition in India but I would say that is the only way to advance research in dementia here.

Do you think that lifestyle changes in Indians could help curb the rising number of dementia affected people here?

No one knows the answer yet but it might be possible. That makes India a wonderful place for this kind of research because of the diverse populations, cultures and lifestyles – diet, aging, obesity etc. factors can be checked for their links to dementia. India makes for a perfect laboratory to check for these questions and examine them in clinical cohorts. There will be a lot of challenges to that. Also the population above 65 is much lower in India as opposed to the US or Japan but the existing number is huge and it is only going to get bigger. Hence there is an imperative to do this research.

Available drugs have failed to stop or delay dementia. The ongoing genetic research in that direction is also in its nascent stages. Is there any other alternative that can help deal with dementia in the present situation?

Two paths that we haven’t tried –

1. Administering past failed drugs during the earlier course of the disease, right when the symptoms show up. The research has just begun in that aspect.
2. Using combination of drugs- each drug attacking a different mechanism leading to dementia. This is yet to start.

 

 

Perfectionism on part of proteins in cargo delivery could save lives

August 2015

A minor fault in any member of the team of proteins carrying structural elements for melanin pigment maturation could deprive us of not just our colour, but could be fatal when combined with few other factors.

Trucks and lorries rule the world of cargo delivery. Any malfunction in them affects the timely delivery of the cargo at the destination and where and how they are used in the further processes. This chain of events is not very different at a cellular level. Our cells also have their own transport pathways responsible for the cargo delivery at the right destination at the right time. Any variations to that system shows up as symptoms to fatal diseases. Dr. Subba Rao and team from the Indian Institute of Science, Bangalore, unravel the nitty gritties of one such transport pathway in animal cells where failure to deliver the cargo, in this case melanin synthesizing enzymes, could result in fatalities.

Melanin pigments are responsible for the colour of our skin and also play an important role in protection against radiations and any other damage from light. Melanin pigment is produced in cellular organelles called melanosomes which need melanin synthesizing enzymes transported from other organelles. The enzymes transported into premature melanosomes facilitate the maturation into fully pigmented melanosomes. The transport pathway is completed with the help of four multi subunit protein complexes, BLOC 1, 2, 3 and Adaptor protein 3 complex.

BLOC 1 consists of 8 subunits, functioning in the upstream of the pathway while BLOC 2, a 3-subunit protein complex, functions towards the end of the pathway in directing the transfer of molecules towards maturing melanosomes for subsequent reactions. It does so by the specific method of “tethering” or by stabilizing the intermediate molecules that need to be transported.

Mutations in BLOC 1 or BLOC 2 proteins result in inefficient delivery of melanin synthesizing proteins to melanosomes and thus failure in full expression of the melanin pigment. This malfunction manifests in the form of albinism of skin, ear and eye, also referred to as oculocutaneous albinism. This is one of the primary symptoms in Hermansky-Pudlak Syndrome (HPS). The other symptoms are lung infections, which are mistaken as Tuberculosis in most cases in India. Both the lung pathology and albinism put together result in HPS but the confirmatory diagnosis is genetic sequencing of the patient and the parents. HPS generally shows up in children within the age group of 4-6. Out of the 16 possible genetic mutations that can result in HPS, only 9 are known so far. Three out of those nine subtypes are a result of mutations to the BLOC 2 protein.

Even though BLOC 1 and 2 play their respective roles in the overall transport pathway, their molecular functions are not yet clear. There are additional proteins that are responsible for membrane trafficking throughout the cell in most transport pathways. These proteins are called Soluble NSF (N-ethylmaleimide sensitive fusion proteins) Attachment Protein REceptor (SNARE). SNARE proteins, a family of about 60 proteins has been known for their role in membrane fusion during transfer of information. For the first time, the team from IISc has identified two members from the SNARE family that are involved in the transport pathway to melanosome. Immortal melanocyte cell lines from mice, both wild type and mutated, were used for the experiments. The expression of these cell lines were estimated by their absorbance at certain wavelengths and compared with levels of protein expressions found in healthy cells. The team concluded that not only do SNAREs play a vital role in the endosome and melanosome membrane trafficking but are also responsible for maintaining the melanosomal proteins in their stable states until delivered to the maturing melanosomes. Very strong interactions between the SNARE proteins and BLOC 1 has been reported in the initial steps of the transport pathway.

Dr. Subba Rao and team intends to further work on uncovering the details of the interactions between the SNAREs and BLOC 1 and 2 complexes. It is important to understand the specific roles that BLOC 2 plays in the cell and would help in filling the gaps in the transport pathway. How and what delivers the cargo at the destination is yet to be understood. Whether the membranes actually fuse for the transport of the proteins or only the proximity of molecules with the opposite membrane to the surface completes the transport? What are the guiding proteins? If the SNAREs go back to their respective states after the transfer is completed? These are few questions the team is looking forward to resolve in their future research.

 

A biosensor to peer into the insides of a HIV infected cell

December 8, 2014

One of the unique features of the AIDS virus, HIV-1, is that it can exist inside human cells for years without causing any harm. It then reactivates to cause infection when conditions are suitable. Researchers from IISc, Bangalore, the International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi and Jamia Millia Islamia, New Delhi have exploited a non-invasive biosensor that can measure what is going on within HIV-1 infected cells in real-time.

This technology can offer insights which can help in controlling the AIDS infection and also provide insight on the interactions between HIV-1 and the tuberculosis causing bacteria, Mycobacterium tuberculosis (Mtb),within the cells.

Acquired Immune Deficiency Syndrome or AIDS is a devastating disease, which is unfortunately quite common. Since its discovery, AIDS has caused an estimated 36 million deaths worldwide (as of 2012). Its causative agent, the Human Immunodeficiency Virus (HIV), has thus been a hot topic of research.

Our body produces oxygen free radicals called Reactive Oxygen Species or ROS, during routine cellular metabolism. When not regulated properly, accumulation of these ROS can lead to oxidative stress. Heightened oxidative stress is one of the primary causes of reactivation of HIV-1 in infected cells.

Oxidative stress also decreases proliferation of disease fighting immune cells; besides, it causes loss of memory in immune cells. These factors reduce the efficiency of the immune response toward the HIV. A major cellular antioxidant called glutathione (GSH) functions as a protective shield against the oxidative stress. GSH levels in infected cells and tissues are indicators of the level of infection.

The team has devised a non-invasive biosensor methodology for precise measurements of GSH levels within HIV-1 infected cells. Earlier methods use whole cell or tissue extracts, which destroy detailed information related to the GSH levels in different areas within an infected cell. Study discovered that a modest increase in oxidative stress is sufficient to reactivate virus from latency. This may allow researchers to adopt a “shock-and-kill” strategy in which virus could be reactivated by oxidative stress inducing compounds and subsequently killed/flushed by current anti-HIV drugs. The fluctuation of GSH levels detected by the biosensor also helps understand the expression of antioxidant genes and related pathways during latent and active stages of infection.

The sensitivity and specificity of this biosensor could be further used in understanding the physiological changes in HIV-1 infected cells and the mechanism of drug action.

“Importantly, we also discovered that Mycobacterium tuberculosis, another major human pathogen, specifically disturbs glutathione balance to increase the replication of HIV. Since TB is the major cause of HIV related deaths, our findings have major mechanistic and therapeutic potential for both TB and AIDS (among the main causes of human death)”, said Dr. Singh.

The paper appeared in The Journal of Bilogical Chemistry on 18th November. DOI: 10.1074/jbc.M114.588913

Taking help from ageing cells to suppress tumours

December 8, 2014

As cells grow older, their DNA gets damaged. Depending on the extent of damage, the cell can repair the DNA and continue its life, or self destruct and die. A molecule called ATM kinase is involved in this decision making process.

Deepak Saini’s lab at IISc has delineated the role of ATM kinase in this important process. The extent of DNA damage either triggers activation of cancer causing genes, or deactivation of tumour suppressor genes. Both these processes can initiate uncontrollable multiplication of cells, leading to cancer. The other possible outcome of DNA damage, especially if very severe, is cell death. The decision of the cell’s fate lies in the hands of the genetic errors accumulated. If the errors cannot be repaired, or can be detrimental if left unrepaired, the cells enter cellular senescence, which is basically ageing. Cell function deteriorates and ageing of the organism is the inevitable result.

The senescent condition of the cells depend on their respective abilities to maintain a persistent DNA damage state without inducing death or repair. There are a number of molecules like ATM kinase and ROS (reactive oxygen species) that play a critical role in regulating cell fate after the genomic damage.

Cellular senescence can be divided into two distinct phases – initiation or early senescence and the maintenance of senescence. The present research delineates the roles of ATM kinase in the initiation of senescence and importance of ROS in maintaining senescence. ATM kinase is one of the key proteins which decides the fate of a cell; it also acts as a quantitative sensor for DNA damage. When DNA damage is not so severe, the cell repairs its DNA and continues growth; in severe damaged states, the cell dies.

In the intermediate stages of damage, the cell enters the senescent stage activated by ATM kinase. “Our studies show that senescence or aging is one of the cell fates in response to DNA damage and the decision is dependent on the dose of damage and ATM kinase protein. Aged cells generate free radicals which is critical in maintaining their status quo”, said Dr. Saini.

Since the other two alternatives after DNA damage – death and cancer – are obviously harmful, a possible way to push a cell toward senescence instead of the other options can have possible therapeutic value. Cell senescence can be induced in tumour and cancer cells by using a sub-lethal dose of stress, by agents like gamma rays, hydrogen peroxide etc. which triggers the DNA damage response leading to senescence. Further research on this could help us devise a very simple yet attractive tumour suppressing mechanism.

The paper will be published in the Journal of Cell Science and appeared online on 21^st November. http://jcs.biologists.org/content/early/2014/11/20/jcs.159517.abstract

– See more at: http://iisc.researchmedia.center/article/taking-help-ageing-cells-suppress-tumours#sthash.Ui6FYTu7.dpuf

A potential therapeutic for septic shock

January 5, 2015

We sometimes hear of post-surgery infections, which can even result in untimely death. The life-saving surgery at times leads to a life threatening recovery. In the intensive care units of hospitals, microbial contamination induces massive inflammation leading to sepsis or septic shock. This has been a rising cause of mortality worldwide in the hospital intensive care unit admissions.

As the famous saying goes “the more the merrier” does not necessarily hold true with new drugs because “less is always more”. All we need is a single efficient drug to combat the sudden and rapid spread of sepsis in the intensive care units of hospitals.

Sepsis is caused by the uncontrolled expression of several inflammatory genes in the host, leading to irreparable damages. The sudden onset and excessive expression of these genes leads to accumulation of harmful metabolic end products, resulting in multiple organ failure. During such cellular stress, some proteins are activated. Development of inhibitors to these stress activated proteins can help devise treatment of such disorders.

The stress activated proteins are comprised of two main subsets- c-Jun N-terminal Kinase (JNK) and p38 Mitogen Activated Protein Kinase (MAPK). It is interesting to note that this work stems out of an extensive collaborative work by three groups from IISc, K. Durga Prasad and T. N. Guru Row from SSCU, J. Trinath and K. N. Balaji from MCBL and Anshuman Biswas and K. Sekar from Bioinformatics. Carefully planned chemical modifications on the commercially available and expensive JNK inhibitor SP600125 improve its ability to bind and inhibit JNK at very low concentrations. The inhibitor also reduces the expression of the inflammatory genes, which in turn cascade into septic shock.“Our study is among the first reports of the description and meticulous biochemical characterisation of selective JNK inhibitors” says Professor Balaji K. N.

This selective and more efficient inhibition activity of JNK inhibitors could facilitate the generation of novel therapeutics to treat sepsis and other inflammatory disorders. It can also pave the way to understand the essential biological function of signalling pathways related to JNK.

The paper appeared in the journal Scientific Reports in end November 2015. http://www.nature.com/srep/2014/141127/srep07214/full/srep07214.html

– See more at: http://iisc.researchmedia.center/article/potential-therapeutic-septic-shock#sthash.Tq5AOAub.dpuf

How your brain helps you see

February 2, 2015

You may worry that intelligent robots will replace humans any day, but that isn’t happening anytime soon. For now, the best computer algorithms cannot do even simple visual tasks like recognizing distorted letters. This is exploited each time we are asked to recognize distorted letters on website. These tests – called CAPTCHAS (for Completely Automated Public Turing test to tell Computers and Humans Apart) – are ubiquitous on the internet because they can prevent access to malicious computer programs. So what makes our brain so good at vision?

Through decades of research, neuroscientists have now found that there’s much more to vision than meets the eye. The eye works much like a camera. Light enters through the pupil and the lens focuses light onto a screen called the “retina”, which is akin to a camera film. Neurons leaving the retina carry information about the image to the visual areas in the brain, which occupy as much as 40% of the total real estate in the brain. This disproportionate area occupied by vision in the brain shows that vision is not easy for the brain either.

Dr SP Arun and his team have been studying biological vision at the Centre for Neuroscience, Indian Institute of Science, Bangalore. In a recent study, Arun and PhD student Ratan Murty have shed light on how the brain interprets the 2-dimensional image falling on the retina. “The image on the retina contains relevant as well as irrelevant information,” Arun says, “The same object can produce different images because of changes in lighting, size, position and three dimensional rotations. These irrelevant variations have to be factored out by the brain for it to understand that all these images belong to the same object. This computation is performed by neurons in the visual cortex.”

Ratan and Arun have performed recordings from the inferior temporal cortex of the monkey brain — an area that is known to be crucial for visual object recognition. They have found that flashing an image results in neural activity that builds up and drops over a period of time. During the build-up of the response, neurons are sensitive to irrelevant variations such as changes in the view point of an object. But in the later portion of the response, neurons respond to the same object ignoring irrelevant stimuli. “This transition from view dependence to view invariance has never been shown before, and it shows that neurons in this area perform this important computation dynamically over time”, said Ratan.

Ratan and Arun are performing a number of other experiments to understand how the brain processes three dimensional information. “Precisely how the brain ignores all the irrelevant variations is a fundamental problem in vision,” Ratan adds, “My experiments will help us understand at least the problem of viewpoint invariance better.” The researchers believe it is something that the brain has learned to solve over the course of evolution. Robots may beat us at algorithmic games like chess but they are nowhere near human competence in real-world tasks like vision.

The paper appeared online in the Journal of Neurophysiology during early 2015. http://jn.physiology.org/content/early/2015/01/16/jn.00810.2014

See more at: http://iisc.researchmedia.center/article/how-your-brain-helps-you-see#sthash.CNa4F6MR.dpuf

Decoding transmembrane communication in living cells

April 24th, 2015

Living cells aren’t self-sufficient; they need to interact with their environment in order to survive. But these interactions are extensively controlled by the barrier called the cell membrane, a dynamic entity made up of lipids and proteins. Molecules are constantly passing in and out of the cell through the semi-permeable cell membrane, their movement often orchestrated by different forces and membrane components. This was the level of understanding of this barrier’s structure and function, posited by the ‘fluid mosaic’ model developed by Singer and Nicholson in 1972. Little was known then about minute details of the driving forces at the nano scale.

Until now, the nitty-gritty of how information traverses the membrane had been left to cell biologists’ countless hypotheses. Fast-forward to the 21^st century, some of those assumptions have been put to rest by a recent study at NCBS. An interdisciplinary team has used living cells, synthetic lipid analogs and molecular dynamic simulations to understand transbilayer communication between molecules on either side of the bilayered cell membrane. The team consists of cell biologist Satyajit Mayor along with soft matter physicist Madan Rao and their teams at the National Centre for Biological Sciences, Bangalore, and synthetic chemists Ram Viswakarma (IIIM, Jammu) and Zhongwu Guo (Wayne State University, USA).

The team’s studies at the nanoscale have revealed that Phosphatidylserine (PS) is a key component that mediates the communication between the lipids on the inner leaflet, and actin and lipid-anchored proteins on the outer leaflet. PS gets the message across because of the presence of long chain-containing lipids such as those found in ‘solid fats’. That’s how the components on inner and outer leaflets communicate.  These studies show how integral PS is to signalling pathways of the cell, and therefore when absent results in irreparable damage.

“The uniqueness of the study lies in discovering a specific role for PS in nanocluster formation, a building block of ‘lipid rafts’ and how the chemistry of both the outer and inner leaflet facilitate this process. For this we have adopted an array of methods which combines biology, genetics, chemistry and physics to provide an explanation for the formation of nanoclusters” says Anupama Ambika Anilkumar, one of the first authors of the paper published online on 23 April, 2015, in the journal Cell.

Lipid rafts are microenvironments in the membrane made up of clusters of lipids and protein receptors, and are involved in molecule trafficking and assembly. Refuting early theories on the random combination of lipids to construct these lipid rafts, this study shows that the formation of these “nanoclusters” of lipids is an active process templated by the actin cytoskeleton on the inner leaflet. This understanding also points to further clues about the role of these clusters. They have been hypothesized to function as a ‘sorting station’ for components to be recruited for signalling events on the cell surface.

The discovery of PS as a vital component in the transmembrane communication would advance our understanding of the cell membrane’s microenvironment. It would also help scientists understand how these nanoclusters function and what proteins are involved in their assembly. Additional experiments in Mayor’s lab are underway to draw the complete picture of the cell’s communications and the anchors of the PS species. These entities also play an important role in various other cell functions and are hence important problems to pursue.

“There is no earlier evidence of how these clusters are formed by lipidic interactions. My colleague and co-first author, Riya Raghupathy established methods to assay the role of long-acyl chain lipid species, and along with Parvinder Pal Singh, developed the synthetic analogues used in this study. Anirban Polley, working with Madan, conducted molecular dynamic simulations; both of these are an integral part of this study and I am grateful for having such terrific collaborators,” said Anupama Anilkumar.

Decrypting this communication could help explain how signals are both read and interpreted by the cell, with implications for a number of diseases caused by alteration in lipid balance or composition. Understanding how these lipids, the “gatekeepers” of the cell, function might also help deter the progression of viral diseases, by potentially disrupting the interaction of membrane components with the viruses.

The paper can be accessed at:
http://dx.doi.org/10.1016/j.cell.2015.03.048

Replacement with a single atom alters thyroid biochemical cascade in the body

June 8, 2015

More than 200 million people worldwide suffer from thyroid related disorders like hyperthyroidism, hypothyroidism, goitre, Hashimoto’s thyroiditis, thyroid cancer etc. Hyperthyroidism is also associated with various diseases like Grave’s disease, thyroid storm and toxic thyroid nodule. Most of these are treated with synthetic form of T4 for hypothyrodism and thiouracil-based drugs for hyperthyroidism. However, small variations in the drug concentration can lead to adverse effects.

Thyroxine or T4, having four iodine atoms is the thyroid pro-hormone, while the biologically more active metabolite tri-iodothyronine (T3) regulates body temperature, growth and heart rate. Thyroxine is produced by the thyroid gland and its metabolism is tightly regulated in human body. The activation or inactivation of thyroid hormones are mediated by enzymes in various cells/tissues. The activation occurs when T4 is converted to T3, but an inactivation occurs when T4 is converted to reverse T3 (rT3).

Earlier studies showed that simple chemical compounds containing sulfur or selenium atoms can remove iodine atoms selectively from T4 to produce rT3, thereby, mimicking the enzymes that mediate the inactivation pathway. For the first time, K Raja and Prof. G Mugesh from the department of Inorganic and Physical Chemistry, IISc, Bangalore, show that the replacement of sulfur or selenium by tellurium atoms dramatically alters the rate of the reaction. The compounds that mediated the conversion of T4 to rT3 can also mediate the conversion of T4 to T3 upon introduction of a tellurium atom. This study shows how a single atom change in a chemical compound can alter a very important biochemical reaction.

The team of scientists have developed a novel set of compounds that can mimic the function of the enzymes to activate or inactivate thyroxine (i.e. remove iodine atoms from T4 under physiologically relevant conditions). Prof. Mugesh said, “While the primary aim of this study is to understand the various mechanisms proposed for the model reactions as well as those catalysed by the natural deiodinases, the compounds developed are considered as potential candidates for the development of drugs for thyroid related disorders such as hyperthyroidism.”

The team aims to develop compounds that can control the thyroxine metabolism in the body rather than inhibiting the thyroxine biosynthesis or supplementing with thyroxine. Depending upon the nature of disease, a suitable enzyme mimic can be administered. The advantage of the current set of compounds is that they are highly reactive and the deiodination reactions can be performed in water at physiological conditions. The previous studies used organic solvents for the chemical transformations, and such conditions are not suitable for drug development. Though the current studies indicate that the compounds have potential applications in the treatment of hyperthyroidism, they need to be tested in human cell lines and animal models to understand the efficacy and toxicity.

The article appeared in the “Early View” section of Angewandte Chemie on 12th May 2015. http://onlinelibrary.wiley.com/doi/10.1002/anie.201502762/abstract

– See more at: http://iisc.researchmedia.center/article/replacement-single-atom-alters-thyroid-biochemical-cascade-body#sthash.SOcHTTQI.dpuf