Upinder S. Bhalla, Ph.D.
Professor & Dean, NCBS, Bengaluru, India
Watching the network change during the formation of associative memory
The process of learning is measured through behavioural changes, but it is of enormous interest to understand its cellular and network basis. We used 2-photon imaging of hippocampal CA1 pyramidal neuron activity in mice to monitor such changes during the acquisition of a trace conditioning task. One of the questions in such learning is how the network retains a trace of a brief conditioned stimulus (a sound), until the arrival of a delayed unconditioned stimulus (a puff of air to the eye). During learning, the mice learn to blink when the tone is presented, well before the arrival of the air puff.
The mice learnt this task in 20-50 trials. We observed that in this time-frame the cells in the network changed the time of their peak activity, such that their firing times tiled the interval between sound and air puff. Thus the cells seem to form a relay of activity. We also observed an evolution in functional connectivity in the network, as measured by groupings of correlated cells. These groupings were stable till the learning protocol commenced, and then changed. Thus we have been able to observe two aspects of network learning: changes in activity (relay firing), and changes in connectivity (correlation groups).
S. Ramaswamy, Ph.D.
CEO of c-CAMP, Dean, inStem, NCBS, Bangalore, India
Discovery, engineering and applications of Blue Fish Protein with Red Fluorescence
Swagatha Ghosh, Chi-Li Yu, Daniel Ferraro, Sai Sudha, Wayne Schaefer, David T Gibson and S. Ramaswamy
Fluorescent proteins and their applications have revolutionized our understanding of biology significantly. In spite of several years since the discovery of the classic GFP, proteins of this class are used as the standard flag bearers. We have recently discovered a protein from the fish Sanders vitrius that shows interesting fluorescent properties – including a 280 nm stoke shift and infrared emission. The crystal structure of the wild type protein shows that it is a tetramer. We have engineered mutations to make a monomer with very similar fluorescent properties. We have used this protein for tissue imaging as well as for in cell-fluorescence successfully
Claudia AM Wheeler-Kingshott, Ph.D.
University Reader in Magnetic Resonance Physics, Department of Neuroinflammation, UCL Institute of Neurology, London, UK
Abstract
Detecting neuronal activity in vivo non-invasively is possible with a number of techniques. Amongst these, in 1990 functional magnetic resonance imaging (fMRI) was proposed as a technique that has a great ability to spatially map brain activity by exploiting the blood oxygenation level dependent (BOLD) contrast mechanism [1, 2]. In fact, neuronal activation triggers a demand for oxygen and induces a localised increase in blood flow and blood volume, which actually exceeds the metabolic needs. This in turns causes an increase of oxyhaemoglobin in the venous compartment, which is a transient phenomenon and is accompanied by a transient change (decrease) in the concentration of deoxyhaemoglobin. Due to its paramagnetic properties, the amount of deoxyhaemoglobin present in the venous blood affects the local magnetic field seen by the spins (protons) and determines the local properties of the MR signal. A decrease in deoxyhaemoglobin during neuronal activity, therefore, induces local variations of this magnetic field that increases the average transverse relaxation time of tissue, measured via the T2* parameter [3]. This means that there is an increase of the MR signal (of the order of a few %, typically <5%) linked to metabolic changes happening during brain function. Activation can be inferred at different brain locations by performing tasks while acquiring the MR signal and comparing periods of rest to periods of activity.
The macroscopic changes of the BOLD signal are well characterised, while the reason for the increased blood supply, exceeding demands, needs further thoughts. Here we will discuss two approaches for explaining the BOLD phenomenon, one that links it to adenosine triphosphate production [4] and enzyme saturation, the other that relates it to the very slow diffusion of oxygen through the blood-brain-barrier with a consequent compensatory high demand of oxygen [5]. Some evidence of restricted oxygen diffusion has been shown by means of hypercapnia [6], although it is not excluded that both mechanisms may be present.
Overall, the BOLD signal changes theory and its physiological basis will be presented and discussed.
References
- Ogawa, S., et al., Brain magnetic resonance imaging with contrast dependent on blood oxygenation. Proc Natl Acad Sci U S A, 1990. 87(24): p. 9868-72.
- Kwong, K.K., et al., Dynamic magnetic resonance imaging of human brain activity during primary sensory stimulation. Proc Natl Acad Sci U S A, 1992. 89(12): p. 5675-9.
- Bandettini PA, et al. Spin-echo and gradient-echo EPI of human brain activation using BOLD contrast: a comparative study at 1.5 T. NMR Biomed. 1994 Mar;7(1-2):12-20
- Fox, P.T., et al., Nonoxidative glucose consumption during focal physiologic neural activity. Science, 1988. 241(4864): p. 462-4.
- Gjedde, A., et al. Reduction of functional capillary density in human brain after stroke. J Cereb Blood Flow Metab, 1990. 10(3): p. 317-26.
- Hoge, R.D., et al., Linear coupling between cerebral blood flow and oxygen consumption in activated human cortex. Proc Natl Acad Sci U S A, 1999. 96(16): p. 9403-8.
Nader Pourmand, Ph.D.
Director, UCSC Genome Technology Center,University of California, Santa Cruz
Biosensor and Single Cell Manipulation using Nanopipettes
Approaching sub-cellular biological problems from an engineering perspective begs for the incorporation of electronic readouts. With their high sensitivity and low invasiveness, nanotechnology-based tools hold great promise for biochemical sensing and single-cell manipulation. During my talk I will discuss the incorporation of electrical measurements into nanopipette technology and present results showing the rapid and reversible response of these subcellular sensors to different analytes such as antigens, ions and carbohydrates. In addition, I will present the development of a single-cell manipulation platform that uses a nanopipette in a scanning ion-conductive microscopy technique. We use this newly developed technology to position the nanopipette with nanoscale precision, and to inject and/or aspirate a minute amount of material to and from individual cells or organelle without comprising cell viability. Furthermore, if time permits, I will show our strategy for a new, single-cell DNA/ RNA sequencing technology that will potentially use nanopipette technology to analyze the minute amount of aspirated cellular material.
Kal Ramnarayan, Ph.D.
Co-founder President & Chief Scientific Officer, Sapient Discovery, San Diego, CA, USA
A cost-effective approach to Protein Structure-guided Drug Discovery: Aided by Bioinformatics, Chemoinformatics and computational chemistry
With the mapping of the human genome completed almost a decade ago, efforts are still underway to understand the gene products (i.e., proteins) in the human biological and disease pathways. Deciphering such information is very important for the discovery and development of small molecule drugs as well as protein therapeutics for various human diseases for which no cure exists. As an example, with more than 500 members, the kinase family of protein targets continues to be an important and attractive class for drug discovery. While how many of the members in this family are actually druggable is still to be established, there are several ongoing efforts on this class of proteins across a broad spectrum of disease categories. Even though in general the protein structural topology might looks similar, there are issues with respect selectivity of identified small molecule inhibitors when, the lead molecule discovery is carried out at the ATP binding site. As an added complexity, allosteric modulators are needed for some of the members, but the actual site for such modulation on the protein target can not resolved with uncertainty. In this presentation we will describe a bioinformatics and computational based platform for small molecule discovery for protein targets that are involved in protein-protein interactions as well as targets like kinases and phosphatases. We will describe a computational approach in which we have used an informatics based platform with several hundred kinases to sort through in silico and identify inhibitors that are likely to be highly selective in the lead generation phase. We will discuss the implication of this approach on the drug discovery of the kinase and phosphatase classes in general and independent of the disease category.
Satheesh Babu T. G., Ph.D.
Associate Professor, Department of Sciences, School of Engineering, Amrita University, Coimbatore, India
Nanomaterials for ‘enzyme-free’ biosensing
Enzyme based sensors have many draw backs such as poor storage stability, easily affected by the change in pH and temperature and involves complicated enzyme immobilization procedures. To address this limitation, an alternative approach without the use of enzyme, “non-enzymatic” has been tried recently. Choosing the right catalyst for direct electrochemical oxidation / reduction of a target molecule is the key step in the fabrication of non-enzymatic sensors.
Non-enzymatic sensors for glucose, creatinine, vitamins and cholesterol are fabricated using different nanomaterials, such as nanotubes, nanowires and nanoparticles of copper oxide, titanium dioxide, tantalum oxide, platinum, gold and graphenes. These sensors selectively catalyse the targeted analyte with very high sensitivity. These nanomaterials based sensors combat the drawbacks of enzymatic sensors.
![Delegate Talk: Novel Cell-Based Biosensors for High Throughput Toxin Detection and Drug Screening Applications @ Amriteshwari Hall | Vallikavu | Kerala | India](http://www.amritabioquest.org/conference/2013/wp-content/uploads/sites/2/2015/02/biomed.jpg)
Anupama Natarajan, James Hickman and Peter Molnar
Novel Cell-Based Biosensors for High Throughput Toxin Detection and Drug Screening Applications
Over the last decade there has been focus on the development of cellbased biosensors to detect environmental toxins or to combat the threats of biological warfare. These sensors have been shown to have multiple applications including understanding function and behaviour at the cellular and tissue levels, in cell electrophysiology and as drug screening tools that can eliminate animal testing. These factors make the development of cell-based biosensors into high throughput systems a priority in pharmacological, environmental and defence industries (Pancrazio J J et al. 1999, Kang G et al. 2009, Krinke D et al. 2009). We have developed a high through-put in vitro cell-silicon hybrid platform that could be used to analyze both cell function and response to various toxins and drugs. Our hypothesis was that by utilizing surface modification to provide external guidance cues as well as optimal growth conditions for different cell types (Cardiac and Neuronal), we could enhance the information output and content of such a system. An intrinsic part of this study was to create ordered or patterned functional networks of cells on Micro-electrode arrays (MEA). Such engineered networks had a two-fold purpose in that they not only aided in a more accurate analysis of cell response and cell and tissue behaviour, but also increased the efficiency of the system by increasing the connectivity and placement of the cells over the recording electrodes. Here we show the response of this system to various toxins and drugs and the measurement of several vital cardiac parameters like conduction velocity and refractory period (Natarajan A et al. 2011)
Jeff Perry, Ph.D.
Assistant Professor, University of California, Riverside
Combined Crystallography and SAXS Methods for Studying Macromolecular Complexes
Recent developments in small angle X-ray scattering (SAXS) are rapidly providing new insights into protein interactions, complexes and conformational states in solution, allowing for detailed biophysical quantification of samples of interest1. Initial analyses provide a judgment of sample quality, revealing the potential presence of aggregation, the overall extent of folding or disorder, the radius of gyration, maximum particle dimensions and oligomerization state. Structural characterizations may include ab initio approaches from SAXS data alone, or enhance structural solutions when combined with previously determined crystal/NMR domains. This combination can provide definitions of architectures, spatial organizations of the protein domains within a complex, including those not yet determined by crystallography or NMR, as well as defining key conformational states. Advantageously, SAXS is not generally constrained by macromolecule size, and rapid collection of data in a 96-well plate format provides methods to screen sample conditions. Such screens include co-factors, substrates, differing protein or nucleotide partners or small molecule inhibitors, to more fully characterize the variations within assembly states and key conformational changes. These analyses are also useful for screening constructs and conditions that are most likely to promote crystal growth. Moreover, these high throughput structural determinations can be leveraged to define how polymorphisms affect assembly formations and activities. Also, SAXS-based technologies may be potentially used for novel structure-based screening, for compounds inducing shape changes or associations/diassociations. This is addition to defining architectural characterizations of complexes and interactions for systems biology-based research, and distinctions in assemblies and interactions in comparative genomics. Thus, SAXS combined with crystallography/NMR and computation provides a unique set of tools that should be considered as being part of one’s repertoire of biophysical analyses, when conducting characterizations of protein and other macromolecular interactions.
1 Perry JJ & Tainer JA. Developing advanced X-ray scattering methods combined with crystallography and computation. Methods. 2013 Mar;59(3):363-71.