The human biological clock is composed of several molecular mechanisms which are synchronous with the day-night cycle or circadian rhythm. Disruption in the cycle can lead to chronic metabolic disorders.

Among other things, the circadian rhythm keeps a check on the proliferation of cells in the body. However, when cells become cancerous, they break away from the circadian rhythm and escape from the circadian control system to undergo uncontrolled proliferation.

The processes that promote cancerous growth can hijack the metabolic balance to fuel the rapidly proliferating cancer cells. The dysregulated metabolic balance in cancer cells results in the increased generation of a substance called lactate.  Further, cancer cells produce large quantities of a protein called IL-1β that promotes the growth of tumors. Till now, it was not clear how cancer cells sustain the high rate of production of lactate and IL-1β in conjunction with the cellular circadian rhythm.

The researchers at NBRC have now unraveled the mystery. They have found that cancer cells modify the molecular components of cellular circadian rhythm to create a new regulatory network that produces more lactate and IL-1β. The network has been named as Lactate-Inflammation-Clock (LIC).

In their first set of experiments, the research team used chemicals to activate/inhibit lactate and IL-1β in glioma cells, a type of tumor that occurs in the brain and spinal cord.

They found that, when activated, lactate and IL-1β induce the expression of important circadian proteins called Clock and Bmal1. Further molecular experiments revealed that Clock/Bmal1 transcriptionally activates the expression of LDH-A (Lactate producing enzyme) and IL-1β thus confirming the existence of the LIC regulatory network.

The team found that LIC controls the key pathways of glioma progression such as cell cycle, DNA damage and repair of cytoskeletal architecture and modification of chromatin,which is a complex of DNA and proteins that forms chromosomes within the nucleus of cells.

In further studies, the researchers found that similar LIC regulatory networks were present in stomach and cervical cancer cells as well and that disruption of these networks can interfere with their tumor-promoting signals too.

Speaking to India Science Wire, leader of the team, Ellora Sen, said, “We noted significant correlation of LIC circuit with patient survival and anti-cancer drug sensitivity. Patients with stomach, cervical or brain cancers survived longer when they had lower levels of Clock, Bmal1, LDHA and IL1-β protein. We found that clinically approved EGFR inhibitors such as gefitinib and erlotinib can be utilized for disrupting the LIC regulatory loop in cancer cells”.

She and her team are now working in collaboration with IIT-Mumbai to develop the mathematical model for the LIC regulatory circuit. “The model, when fitted to the patient molecular profile of LIC components, could serve as a framework for a new approach to cancer treatment based on the body clock. It may be called cancer chronotherapy”.

The study team included Pruthvi Gowda, KirtiLathoria, Shalini Sharma, Shruti Patrick and Sonia B. Umdor. The study has been accepted for publication in American Society for Microbiology journal `Molecular and Cellular Biology’.

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keywords: National Brain Research Centre, NBRC, molecular mechanism, cancer, circadian rhythm, metabolic, proliferation, protein, tumour, glioma, brain, spinal cord, DNA, chromosomes, cervical, mathematical model

TB has been associated with mankind since the beginning of human civilization. It is caused by a bacterium called Mycobacterium tuberculosis (M.tb). It travels through the air from one human to another human till it finds its happy home in the lungs. Tuberculosis is a curable disease if treated properly and timely. There is a need for a fast and advanced detection system for the diagnosis of tuberculosis disease, like a smoke detector, that could detect fire and blare alarm before the fire could go out of hand. Identification of important virulent proteinsof M.tb is important for TB care and management program. The arsenal of M.tb is equipped with several such proteins which help the bacterium to avoid and weakenthe host immune-responses. A protein called PPE2 is one such.

Earlier studies by the group of researchers had shown that PPE2 protein works by blocking the production of compounds called reactive nitrogen species (RNS) and reactive oxygen species (ROS) which are some of the key elements of the human immune system.

The new study has taken the work forward by getting new insights that suggest that PPE2 could also be playing an important role in regulating the synthesis of Vitamin B₁₂ in the bacterium. Vitamin B₁₂ plays a fundamental role in bacterial metabolism and gene regulation.The human body cannot synthesize Vitamin B₁₂ and depends upon gut microbiota or external food supplements to meet the daily requirement of Vitamin B₁₂. M.tb, on the other hand, has genes for Vitamin B₁₂ synthesis. The true nature of the Vitamin B₁₂ pathway in the bacterium, however, is still a mystery. The new study gives some insight into this.

A striking feature in M.tb physiology is the presence of a regulatory RNA element or riboswitch in a cluster of genes known as an operonin a functioning unit of its DNA. The cluster has three genes – ppe2, cobq, and cobu. While cobq and cobu genes are already known to be part of the Vitamin B₁₂ biosynthesis process, not much is known about PPE2’s role.

The new study has helped unravel the mystery to some extent. In this study, it has been observed that PPE2 could bind to DNA located beforeoperon ppe2–cobq–cobu suggesting thatPPE2 protein might be playing a role in the regulation of the ppe2-cobq1-cobucluster.

Speaking to India Science Wire, the leader of the team, Dr. Sangita Mukhopadhyay stressed that it was only a first step and more research is needed in the form of a detailed understanding of the underlying mechanism. “Vitamin B₁₂ has a fundamental role in bacterial metabolism and gene regulation and if carefully investigated, ppe2-cobq1-cobu cluster and riboswitch together, may present opportunities to translate the basic knowledge of microbial metabolism into effective therapeutic methods”, she added.

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Keywords: Hyderabad, Centre for DNA Fingerprinting and Diagnostics, CDFD, molecular mechanism, bacterium, immune system, Mycobacterium tuberculosis,M.tb, lung, diagnosis, protein, Vitamin B_12, gut, microbiota,RNA, DNA, genes

Cryo-EM has revolutionized structural investigations of macromolecules in recent times. It is a testimonial for a revolutionary technology for structural biologists, chemical biologists, and ligand discovery, which has gained a clear edge over contemporary x-ray crystallography. In light of these advancements, cryo-electron microscopy technique was recognized with the Nobel Prize for the high-resolution structure determination of biomolecules in solution (2017). The revolution in resolution resulted in atomic-level understanding of the Zika virus surface proteins, thus aiding structure-based drug discovery, deciphering of structure of hard-to-crystallize membrane proteins and other macromolecular complexes.

The National Facilities supported by the Science & Engineering Research Board (SERB), an institution under the Department of Science & Technology (DST), would help explore Macromolecular Structures and Complexes” and create research knowledge base and skills for cryo-EM research in India to establish leadership in structural biology, enzymology, ligand/drug discovery.

The establishment of these facilities in all directions of the country–Indian Institute of Technology, Chennai; Indian Institute of Technology, Bombay; Indian Institute of Technology, Kanpur; and Bose Institute, Kolkata would help in scaling up cryo-EM based structural biology research in different corners across the country. These centers are designated as SERB National Facility for Cryo-Electron Microscopy and will work on the identified thrust areas. They will be accessible to all researchers.

Housed with 200kV machines have added advantages like lesser maintenance and can help generate human resources through training, which can also help sustain the facility for longer duration. Each Cryo-EM facility costs about Rs. 28.5 crore for a period of five years and an amount of Rs. 114 crores for research in the critically important research areas.

While IIT Chennai will focus on nano-biointerfaces (e.g. materials–microbes, materials–human tissue), IIT Bombay will execute research on ribosome translation and its implication in disease and antibiotic resistance, neurodegenerative disorders and tackle problems to address solutions to cancer, membrane structure, composition, dynamics & transport. IIT Kanpur will conduct research focused on macromolecular structures and drug discovery with a specific focus on membrane proteins, and Bose Institute, Kolkata will focus on transforming the structure-guided drug discovery and therapeutics research for communicable and non-communicable diseases, allosteric drugs, transcription, and epigenetics.

The first national cryo-EM facility was established at National Centre for Biological Sciences (NCBS) in 2017 and then subsequently in IISc, Bangaluru, and RCB Faridabad. However, it was felt that the existing cryo-EM research facilities in the country are not adequate to leave a mark at the global stage. Historically, Indian scientists have contributed significantly in the area of Prof. GN Ramachandran and Dr. G. Kartha made a remarkable contribution to structural biology, biological, chemical, physical, computational, and theoretical crystallography and materials crystallography. Given significant advances in cryo-EM of large structures, SERB has taken the responsibility that concerted funding should be provided to establish leadership in this area to enable and empower Indian researchers to lead from the front.

DNA conformation, in particular, its supercoiling, plays an important structural and functional role in gene accessibility as well as in DNA condensation.Alteration in DNA affects their expression and functions. DNA controls cell survival through the genetic code as well as via modifications to its structure. The scientific community was looking for a technique with very high resolution to measure such modifications of DNA structures and observe and understand the molecular mechanisms associated with it to track rare diseases.

The novel nanopore-based platform developed by the scientists can directly measure such modifications or branched DNA properties with the single-molecule resolution even with extremely low amounts of sample.The platform and associated analysis techniques developed by the team can quantitatively assess the distribution of supercoiled branches on DNA plasmids (DNA molecule outside the chromosome).

“Further optimization of the technique can help in the development of portable nano-bio sensors for detection and quantification of protein aggregates and cell-free DNA or nucleosomes. This may help in the early diagnosis of many diseases like Cancer, Alzheimer’s, and Parkinson’s diseases” said Prof Gautam Vivek Soni, the lead researcher. Currently, researchers at RRI are also exploring applications of this method for virus detection.

The measurement principle of the novel platform is analogous to the Archimedes principle. Individual analyte molecules are driven through a nanopore under an applied voltage, which, during translocation, results in a tiny electrical blip. Charges excluded by the analyte(supercoiled DNA) in the  nanopore are directly proportional to the volume of the particle and are directly measured as the current change. This method utilizes extremely low amounts of sample and can measure DNA structural changes ranging to a few nanometers resolution in the axis perpendicular to the translocation and few tens of nanometers along the translocation axis.

The research team comprises Dr Sumanth Kumar Maheshwaram, Dr Koushik Sreenivasaa and Prof Gautam Vivek Soni. The research findings have been recently published in the journal ‘Nanoscale’. (India Science Wire)

Keywords: DNA Modification, nanopore, new technique, RRI

‘DBT-ILS has excelled in application of science and technology for improving livelihoods of the tribal population’, said Dr Harsh Vardhan. He also praised the scientific achievements of the institute during COVID-19 pandemic, in his online address. “The institute has sequenced around 500 viral genomes and established 17 virus cultures that will enable furthering the research and development efforts of COVID-19 in the coming days. DBT-ILS has excelled in application of science and technology for improving livelihoods of the tribal population,” said Dr. Harsh Vardhan.  He also appreciated DBT-ILS for testing over 1,50,000 samples from across Odisha.

Dr Harsh Vardhanalso laid the foundation stone for the “Animal Challenge Study platform” at DBT-ILS and inaugurated Biorepository for COVID-19 clinical samples at ILS. The Minister dedicated ILS-IBSD partnership centre to the scientific community of the north east and also launchesdthe Himalayan Bioresources Mission, on this occasion.

Animal Challenge Study platform at DBT-ILS will undertake evaluation studies of potential drug and vaccine candidates. Biorepository for the COVID-19 clinical samples at ILS now holds more than 1000 samples of nasopharyngeal swabs, blood, urine and saliva etc from 202 COVID patients. The ILS-IBSD partnership centre aims at skill and capacity development of scientific communities of North East region, especially in the area of advanced biotechnology. The Himalayan Bioresources Mission will carry out advanced research focusing on agriculture, horticulture, medicinal and aromatic plants, livestock and microbial resources, while taking up translational research for societal development. Speaking on the occasion, Shri Dharmendra Pradhan, Minister for Petroleum and Natural Gases, said that DBT-ILS is one of the premier institutions in Odisha and Eastern India and expressed satisfaction that ILS is working to create a visible impact on lives and livelihoods of the people of Odisha.  The Minister further said that Odisha’s coastline has been in focus for Prime Minister Shri Narendra Modi’s vision of a blue economy. He requested Dr Harsh Vardhan that a Centre of Excellence on Marine Biotechnology at ILS be set up which will help unlock the true potential of a marine-led sustainable economic growth in Odisha.

Dr. RenuSwarup, Secretary, Department of Biotechnology, mentioned about the impressive progress made by DBT-ILS particularly in the area of tribal health and nutrition using multi-omics approach which will have far reaching implications. Dr. Ajay Parida, Director, DBT-ILS gave a detailed presentation on the work carried out in the area of research and development, COVID management, societal work as well as entrepreneurship development. (India Science Wire)

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Keywords: DBT-ILS, Bio repository, COVID-19, Animal Challenge Study platform, Himalayan Bio resources Mission, Biotechnology