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News Article | July 30, 2015
Site: www.zdnet.com

CVS Health and IBM said they are partnering to use the Watson cognitive computing system to better manage chronic disease treatment. The companies on Thursday outlined a partnership where CVS Health will use Watson to allow practitioners to tap health information, medical records, pharmacy, claims and other data from fitness devices to track progress and goals. CVS is best known for its drug stores and pharmacies, but also has health clinics and the Caremark pharmacy benefit management unit. According to IBM, CVS and Big Blue will collaborate on a joint Watson Health system that's optimized to treat hypertension, heart disease, diabetes and obesity. The Watson system will focus on predicting people at risk for declining health, encourage healthy behavior and suggesting cost-effective treatment. On the back-end, CVS will use IBM's Watson Health Cloud and analytics systems and merge it with its own data from its pharmacy and medication data. IBM has aimed Watson at the healthcare industry and has recently acquired Phytel, Explorys, and Curam to build out its patient treatment capabilities.


Kalaimathy S.,NCBS | Sowdhamini R.,National Center for Biological science | Kanagarajadurai K.,NCBS
Briefings in Bioinformatics | Year: 2011

Accurate sequence alignments are crucial for modelling and to provide an evolutionary picture of related proteins. It is well-known that alignments are hard to obtain during distant relationships. Three thousand and fifty-two alignments of 218 pairs of protein domain structural entries, with <40% sequence identity, belonging to different structural classes, of diverse domain sizes and length-rigid/variable domains were performed using 12 programs. Structural parameters such as root mean square deviation, secondary-structural content and equivalences were considered for critical assessment. Methods that compare fragments and permit twists and translations align well during distant relationships and length variations. © The Author 2011. Published by Oxford University Press. Source


News Article
Site: http://phys.org/biology-news/

Three channel time lapse of myosin-induced actin contraction into polar asters. (Scale bar: 10 µm). Credit: Image credits: Through WikiCommons, William CrochotGIF copyright 2016 Köster et al., PNAS Like the phenomena of flocking birds and shoaling fish, the dance of molecules across a cell's surface has long fascinated theorists, physicists and biologists alike. Unlike bird and fish behaviour, however, cell surface dynamics cannot be observed and studied easily. However, it is important to understand these processes as they are crucial for cells to gain information about their environment and respond. So how does one understand the rules that govern movement of molecules across this arena? By reconstructing the cell surface from scratch, perhaps? Now, scientists from the National Centre for Biological Sciences (NCBS) in Bangalore have managed to do exactly that - construct a simplified cell surface from its constituent parts, namely, a mixture of fats and proteins. This reconstruction creates a crucial new tool that researchers can use to test theories on cell surface dynamics. Molecular movements on the cell surface are known to be non-random, incredibly complex, and do not seem to follow simple thermodynamic rules. Until recently, there were few experimental tools available to study such phenomena to really understand how the cell surface functioned. This has changed with the new experimental system that has been developed by a close collaboration between experimental biologists from Prof. Satyajit Mayor's group at NCBS, scientists from the University of California San Francisco (UCSF) and theoretical physicists from Prof. Madan Rao's group at NCBS and RRI (Raman Research Institute). The experimental system is a minimal model of the cell surface constructed from its basic components - purified fats and proteins known to be part of the cell surface. This tool could be the key to understanding how the surface of a living cell works. "This is just a beginning but an important one," says Prof Satyajit Mayor. "Important because it allows one to test ideas that have come from theory built around providing an explanation for active organization at the surface of a living cell. It's an exciting beginning since the feasibility of this simple minimal system opens up huge possibilities to explore the world of a living cell in a test tube system where every element is under our control. This work is inspired by the adage 'what we understand we should be able to build' and this is in trying to understand the principles behind how a living material, the cell surface, works," he adds. The 'active composite model' of the cell surface is one of the latest theories that attempts to explain the behaviour of cell surface molecules. This model visualises the cell surface as not just the cell membrane, but as an amalgamation of two elements - the cell membrane, made of fats and an interwoven mesh of the protein 'actin' that forms a thin layer just below the cell membrane. Another protein, 'myosin' that interacts with actin, behaves like a molecular motor and creates movement in the actin meshwork when supplied with energy. Many of the cell surface proteins whose movements have baffled scientists are often linked to the dynamic actin meshwork that lies just below the cell membrane. As proposed by the active composite model, the researchers decided to recreate a cell surface as an assembly of a fat-based membrane and an actin meshwork. This artificial cell surface was therefore constructed using a fat bilayer, actin and a fluorescent protein specially designed to be embedded in the membrane while also being linked to actin. Using various microscopic techniques, the group was able to study the behaviour of the construct via the patterns formed by the fluorescent proteins. As predicted by the 'active composite model', the dynamics of actin-bound fluorescent proteins were found to be dependent on the dynamics of the actin meshwork. When the molecular motor, myosin, was added and chemical energy provided, the forces generated by actin-myosin interactions drove the movements of these proteins. When the chemical energy was exhausted, the actin-bound proteins aggregated to form distinct bundle or aster-like structures based on the organisation of the actin meshwork. "The importance of active or energy consuming processes in understanding biological phenomena is becoming more and more evident. This is an emerging field in biology called 'active mechanics'. Often, the emerging organisation of biological molecules are not clear, and theoretical explanations for such observations are also far from complete. This makes it important to have proper experimental tools that go hand in hand with theory to test and improve our understanding of such systems. Our current study describes the creation of an experimental system that will serve us in this," says Darius Köster, the lead author of the study that was published in the leading journal PNAS (Proceedings of the Natural Academy of Sciences of the United States of America). "The motivation behind this work is to analyse mechanisms influencing the dynamics and organisation of molecules on the cell surface," says Kabir Husain, another author in this study. Processes like cell growth, division, immune recognition and many others are dependent on the organisation of protein receptors and other associated molecules on the cell surface. This implies that the ability of the cell to reliably control the organisation of its surface molecules is crucial to its survival and function. With the recreation of the cell surface in a testube, scientists have gained a solid experimental footing in the race to comprehend the mechanics of cell surface organisation. Explore further: Mitosis mystery solved as role of key protein is confirmed More information: Darius Vasco Köster et al. Actomyosin dynamics drive local membrane component organization in an in vitro active composite layer, Proceedings of the National Academy of Sciences (2016). DOI: 10.1073/pnas.1514030113


News Article
Site: http://phys.org/biology-news/

"A bend and a twist, then stretch and turn, now relax". What sounds like a series of exercise instructions, are also words that describe the various shapes a piece of DNA can assume. The classic double helix structure that one associates with DNA is but an extremely limited view of its physical 'shape'. The molecule that holds the codes of life is capable of further winding itself into myriad complex shapes called 'supercoils' that are capable of affecting gene expression patterns. Now, researchers from the National Centre for Biological Sciences (NCBS), Bangalore, and the National Institutes of Health (NIH), USA, have elucidated this pattern of supercoiling across the genome of the much studied bacterium E. coli. DNA molecules are wound and rewound into complex structures that condense their immense lengths to a fraction of their actual size in order to fit their long strings of information into microscopic cells. But this 'packed' DNA that fits neatly into a cell also needs to be 'unpacked' periodically for gene expression and replication. When a gene is expressed, it is 'read' by protein machineries to create a messenger transcript that codes for more proteins. This requires DNA to be unwound from its double helix - a process that causes further twisting and coiling or 'overwinding' in regions of DNA elsewhere on the genome. Similarly, unwinding and overwinding also occurs when the genome replicates during reproduction. Therefore, at any given time, a cell's genetic material is in a constant state of structural flux - coils, supercoils, bends, twists and turns are formed, lost and reformed depending on the cell's state of activity. A bacterial cell can be exposed to various environmental changes which include periods of starvation, lack of oxygen and unfavourable temperatures. Surviving these situations would require the bacterium to change its protein repertoire by altering the corresponding genetic expression profiles. Scientists have long thought that these changes could be effected through variations in the supercoiled structure of DNA. For example, the genomes of actively dividing cells under rich-nutrient conditions are known to be more underwound than the genomes of cells from the stationary phase when nutrients are scarce. In other words, supercoiling is likely to be sensitive to changes in the environment. Although recent advancements in methodology have allowed researchers to study DNA supercoiling in human and yeast cells at local scales, this methodology has never been applied to bacterial genomes. Researchers from Aswin S. N. Seshasayee's group at NCBS and Prof. Sankar Adhya's team at NIH have currently applied these methods to study DNA supercoiling in bacteria at a fine-scale level. Using the chemical trimethylpsoralen, exposure to UV light and microarray technology, the research team have gained information on section-specific variations in genomic supercoiling within bacteria exposed to different external conditions. "We have measured DNA supercoiling at a fine-scale resolution in bacteria for the first time. This study provides proof-of-concept that the supercoiling of a genome is not uniform and that it varies locally across genes. It also provides evidence to support the hypothesis that bacterial cells could be regulating gene expression and their own physiologies by altering the structure of their genomes," says Avantika Lal, the first author of the publication in the journal Nature Communications that details these findings. In order to study the effect of environmental stimuli on the supercoiling status of the bacterial genome, two populations of E. coli were used to simulate two different external conditions. One simulated a nutrient-rich situation where actively dividing cells represented a growing population; whereas the other represented a condition where a population had exhausted its nutrients and was in a 'stationary' phase. Since the binding of trimethylpsoralen to DNA is proportional to the amount of supercoiling in the DNA, one could study genome-wide patterns of winding under these two settings. The results have shown that E. coli cells in the 'stationary' phase display a gradient of supercoiling across their circular genomes. In actively dividing cells, however, this gradient was missing though the entire genome was more supercoiled than the genomes of cells from the 'stationary' phase. "It is very early days yet, but this work paves the way to understanding which genes' expression are affected by the environment," says Avantika. "This work can potentially teach us how we could control cell physiology by altering genetic expression via changes to DNA supercoiling by altering external conditions," she adds. More information: Avantika Lal et al. Genome scale patterns of supercoiling in a bacterial chromosome, Nature Communications (2016). DOI: 10.1038/ncomms11055


News Article
Site: http://phys.org/biology-news/

Ordinarily, of course a fly does not shimmer green. Here, researchers - with the help of genetic tricks -  succeeded in making a muscle protein glow, which they can then locate under a fluorescence microscope. Credit: MPI for Biochemistry The human genome codes for more than 20,000 different proteins, however the molecular role for many of these proteins is not known. As most proteins are conserved from fly to humans, understanding the molecular role of a protein in flies can be the first step towards a therapy against a variety of human diseases that are often caused by aberrantly behaving proteins. A consortium of scientists from the Max Planck Institutes of Biochemistry in Martinsried and Molecular Cell Biology and Genetics in Dresden, and the National Centre for Biological Sciences (NCBS) in Bangalore have now reached a milestone towards understanding the function of these proteins by using the fruit fly. The human body is built by many hundreds of different cell types; each one has a very particular function in the body. Red blood cells transport oxygen, nerve cells exchange signals and muscle cells generate mechanical forces. The majority of cellular functions is produced by the action of 20,000-25,000 proteins coded in the human genome. Although sequencing and annotation of human genome were completed in 2004, to date the function of many thousands of these proteins is still mysterious. It is often unknown, which cell types produce which proteins, and particularly where these proteins are located within the cells. Are they in the nucleus or within membranous vesicles, are they within neuronal dendrites or synapses, or are they within the contractile machinery of muscles? Protein localisation is an important piece of information, as it is the first step towards identifying a molecular function for a protein. Unravelling the function of a protein is often started in simpler model organisms such as worms or flies. Like humans, fruit flies have muscles, neurons, oocytes, sperm and many other essential cells types. The fly genome contains about 13,000 protein coding genes, which are responsible for building and maintaining all fly organs. Importantly, many of these proteins are very similar to the human proteins, thus studying a protein in flies will teach us about its role in the human body. To boost these protein studies onto a systematic level, groups headed by Frank Schnorrer at the Max-Planck Institute in Martinsried, Pavel Tomancak and Mihail Sarov at the Max-Planck Institute in Dresden and K VijayRaghavan at the NCBS in Bangalore have generated a large resource for visualizing proteins in Drosophila melanogaster. By using modern molecular biology tricks, the scientists have attached a green fluorescent protein (GFP) tag to 10,000 of these protein coding genes in the test tube. Each tagged gene can then be re-introduced into the fly genome as a 'transgene', creating the fly 'TransgeneOme'. "Together, we thus far generated 880 different fly strains, each of which expresses a different fluorescently tagged protein", explains Frank Schnorrer, "these proteins can then be observed by fluorescent video microscopy in various cell types of the developing fruit fly". For more than 200 proteins, the scientists documented where they are located during fly development, starting with an oocyte that develops into an embryo and finally into the mature fly. The Tomancak group used the so-called light sheet microscopy to film how proteins emerge in cells of the embryo during the first day of its development. The Schnorrer group used this resource to study the localisation of proteins in muscles. As in human skeletal muscles, fly muscles contain complex mini-machines called sarcomeres that produce the mechanical forces enabling animal movements. "We have looked so far at only 200 of these transgenic lines. The future challenge lies in systematically imaging the localization of these proteins in many fly tissues and this is best achieved by involving the powerful Drosophila research community" predicts Pavel Tomancak. The resource will have enormous impact on the understanding of not only fly biology but also on the understanding of protein function in the different human cell types." More information: Mihail Sarov et al. A genome-wide resource for the analysis of protein localisation in , eLife (2016). DOI: 10.7554/eLife.12068

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