Visualisation of a 2′-5′ parallel stranded double helix at atomic resolution: crystal structure of cytidylyl-2′,5′-adenosine

X-ray crystallographlc studies on 3′–5′ ollgomers have provided a great deal of information on the stereochemistry and conformational flexibility of nucleic acids and polynucleotides. In contrast, there is very little Information available on 2′–5′ polynucleotides. We have now obtained the crystal structure of Cytidylyl-2′,5′-Adenoslne (C2′p5′A) at atomic resolution to establish the conformational differences between these two classes of polymers. The dlnucleoside phosphate crystallises in the monocllnlc space group C2, with a = 33.912(4)Å, b =16.824(4)Å, c = 12.898(2)Å and 0 = 112.35(1) with two molecules in the asymmetric unit. Spectacularly, the two independent C2′p5′A molecules in the asymmetric unit form right handed miniature parallel stranded double helices with their respective crystallographic two fold (b axis) symmetry mates. Remarkably, the two mini duplexes are almost indistinguishable. The cytosines and adenines form self-pairs with three and two hydrogen bonds respectively. The conformation of the C and A residues about the glycosyl bond is anti same as in the 3′–5′ analog but contrasts the anti and syn geometry of C and A residues in A2′p5′C. The furanose ring conformation is C3′endo, C2′endo mixed puckering as in the C3′p5′A-proflavine complex. A comparison of the backbone torsion angles with other 2′–5′ dinucleoside structures reveals that the major deviations occur in the torsion angles about the C3′–C2′ and C4′-C3′ bonds. A right-handed 2′–5′ parallel stranded double helix having eight base pairs per turn and 45° turn angle between them has been constructed using this dinucleoside phosphate as repeat unit. A discussion on 2′–5′ parallel stranded double helix and its relevance to biological systems is presented.

Field-dependent changeover from current-to voltage-limiting characteristics by non-linear n-type BaTiO3 ceramics

Non-linear resistors having current-limiting capabilities at lower field strengths, and voltage-limiting characteristics (varistors) at higher field strengths, were prepared from sintered polycrystalline ceramics of (Ba0.6Sr0.4)(Ti0.97Zr0.03)O3+0.3 at % La, and reannealed after painting with low-melting mixtures of Bi2O3 + PbO +B2O3. These types of non-linear characteristics were found to depend upon the non-uniform diffusion of lead and the consequent distribution of Curie points (T c) in these perovskites, resulting in diffuse phase transitions. Tunnelling of electrons across the asymmetric barrier at tetragonak-cubic interfaces changes to tunnelling across the symmetric barrier as the cubic phase is fully stabilized through Joule heating at high field strengths. Therefore the current-limiting characteristics switch over to voltage-limiting behaviour because tunnelling to acceptor-type mid-bandgap states gives way to band-to-band tunnelling.

The Madras Triple Helix:Origins and Current Status

Madras triple helix’ was the name assigned by the scientific community in the West, to the molecular model proposed for the fibrous protein collagen, by G N Ramachandran’s group at the University of Madras. As mentioned jocularly in a recent retrospective of this work by Sasisekharan and Yathindra [1], the term was possibly coined due to the difficulty of Western scientists in pronouncing the Indian names of Ramachandran and his associates. The unravelling of the precise nature of collagen structure indeed makes for a fascinating story and as succinctly put by Dickerson [2]: “... to trace the evolution of the structure of collagen is to trace the evolution of fibrous protein crystallography in miniature”. This article is a brief review highlighting the pioneering contributions made by G N Ramachandran in elucidating the correct structure of this important molecule and is a sincere tribute by the author to her mentor, doctoral thesis supervisor and major source of inspiration for embarking on a career in biophysics

Stereochemistry of 2'-5' linked nucleic acids: crystal and molecular structure of ammonium adenylyl-2',5'-adenosine tetrahydrate: a core fragment of 2'-5' oligo A's produced by interferon induced adenylate synthetase

The preponderance of 3'-5' phosphodiester links in nucleic acids is well known. Albeit less prevalent, the 2'-5' links are specifically utilised in the formation of 'lariat' in group II introns and in the msDNA-RNA junction in myxobacterium. As a sequel to our earlier study on cytidylyl-2',5'-adenosine we have now obtained the crystal structure of adenylyl-2',5'-adenosine (A2'p5'A) at atomic resolution. This dinucleoside monophosphate crystallizes in the orthorhombic space group P2(1)2(1)2(1) with a = 7.956(3) A, b = 12.212(3) A and c = 36.654(3) A. CuK alpha intensity data were collected on a diffractometer. The structure was sloved by direct methods and refined by full matrix least squares methods to R = 10.8%. The 2' terminal adenine is in the commonly observed anti (chi 2 = 161 degrees) conformation and the 5' terminal base has a syn (chi 1 = 55 degrees) conformation more often seen in purine nucleotides. A noteworthy feature of A2'p5'A is the intranucleotide hydrogen bond between N3 and O5' atoms of the 5' adenine base. The two furanose rings in A2'p5'A show different conformations - C2' endo, C3' endo puckering for the 5' and 2' ends respectively. In this structure too there is a stacking of the purine base on the ribose O4' just as in other 2'-5' dinucleoside structures, a feature characteristically seen in the left handed Z DNA. In having syn, anti conformation about the glycosyl bonds, C2' endo, C3' endo mixed sugar puckering and N3-O5' intramolecular hydrogen bond A2'p5'A resembles its 3'-5' analogue and several other 2'-5' dinucleoside monophosphate structures solved so far. Striking similarities between the 2'-5' dinucleoside monophosphate structures suggest that the conformation of the 5'-end nucleoside dictates the conformation of the 2' end nucleoside. Also, the 2'-5' dimers do not favour formation of miniature classical double helical structures like the 3'-5' dimers. It is conceivable, 2-5(A) could be using the stereochemical features of A2'p5'A which accounts for its higher activity.

Ring Resonators and Micro Fluidics: Novel Design for Drug/Disease Detection

MEMS systems are technologically developed from integrated circuit industry to create miniature sensors and actuators. Originally these semiconductor processes and materials were used to build electrical and mechanical systems, but expanded to include biological, optical fluidic magnetic and other systems 12]. Here a novel approach is suggested where in two different fields are integrated via moems, micro fluidics and ring resonators. It is well known at any preliminary stage of disease onset, many physiological changes occur in the body fluids like saliva, blood, urine etc. The drawback till now was that current calibrations are not sensitive enough to detect the minor physiological changes. This is overcome using optical detector techniques 1]. The basic concepts of ring resonators, with slight variations can be used for optical detection of these minute disease markers. A well known fact of ring resonators is that a change in refractive index will trigger a shift in the resonant wavelength 5]. The trigger for the wavelength shift in the case discussed will be the presence of disease agents. To trap the disease agents specific antibody has to be used (e. g. BSA).

Matching sender and receiver: poikilothermy and frequency tuning in a tree cricket

Animals communicate in non-ideal and noisy conditions. The primary method they use to improve communication efficiency is sender-receiver matching: the receiver's sensory mechanism filters the impinging signal based on the expected signal. In the context of acoustic communication in crickets, such a match is made in the frequency domain. The males broadcast a mate attraction signal, the calling song, in a narrow frequency band centred on the carrier frequency (CF), and the females are most sensitive to sound close to this frequency. In tree crickets, however, the CF changes with temperature. The mechanisms used by female tree crickets to accommodate this change in CF were investigated at the behavioural and biomechanical level. At the behavioural level, female tree crickets were broadly tuned and responded equally to CFs produced within the naturally occurring range of temperatures (18 to 27 degrees C). To allow such a broad response, however, the transduction mechanisms that convert sound into mechanical and then neural signals must also have a broad response. The tympana of the female tree crickets exhibited a frequency response that was even broader than suggested by the behaviour. Their tympana vibrate with equal amplitude to frequencies spanning nearly an order of magnitude. Such a flat frequency response is unusual in biological systems and cannot be modelled as a simple mechanical system. This feature of the tree cricket auditory system not only has interesting implications for mate choice and species isolation but may also prove exciting for bio-mimetic applications such as the design of miniature low frequency microphones.

Ethnobotany of the Monpa ethnic group at Arunachal Pradesh, India

Background: The present paper documents the uses of plants in traditional herbal medicine for human and veterinary ailments, and those used for dietary supplements, religious purpose, local beverage, and plants used to poison fish and wild animals. Traditional botanical medicine is the primary mode of healthcare for most of the rural population in Arunachal Pradesh. Materials and methods: Field research was conducted between April 2006 and March 2009 with randomly selected 124 key informants using semi-structured questionnaire. The data obtained was analyzed through informant consensus factor (F(IC)) to determine the homogeneity of informant's knowledge on medicinal plants. Results: We documented 50 plants species belonging to 29 families used for treating 22 human and 4 veterinary ailments. Of the medicinal plants reported, the most common growth form was herbs (40%) followed by shrubs, trees, and climbers. Leaves were most frequently used plant parts. The consensus analysis revealed that the dermatological ailments have the highest F(IC) (0.56) and the gastro-intestinal diseases have F(IC) (0.43). F(IC) values indicated that there was high agreement in the use of plants in dermatological and gastro-intestinal ailments category among the users. Gymnocladus assamicus is a critically rare and endangered species used as disinfectant for cleaning wounds and parasites like leeches and lice on livestocks. Two plant species (Illicium griffithii and Rubia cordifolia) are commonly used for traditional dyeing of clothes and food items. Some of the edible plants recorded in this study were known for their treatment against high blood pressure (Clerodendron colebrookianum), diabetes mellitus (Momordica charantia), and intestinal parasitic worms like round and tape worms (Lindera neesiana, Solanum etiopicum, and Solanum indicum). The Monpas of Arunachal Pradesh have traditionally been using Daphne papyracea for preparing hand-made paper for painting and writing religious scripts in Buddhist monasteries. Three plant species (Derris scandens, Aesculus assamica, and Polygonum hydropiper) were frequently used to poison fish during the month of June-July every year and the underground tuber of Aconitum ferrox is widely used in arrow poisoning to kill ferocious animals like bear, wild pigs, gaur and deer. The most frequently cited plant species; Buddleja asiatica and Hedyotis scandens were used as common growth supplements during the preparation of fermentation starter cultures. Conclusion: The traditional pharmacopoeia of the Monpa ethnic group incorporates a myriad of diverse botanical flora. Traditional knowledge of the remedies is passed down through oral traditions without any written document. This traditional knowledge is however, currently threatened mainly due to acculturation and deforestation due to continuing traditional shifting cultivation. This study reveals that the rural populations in Arunachal Pradesh have a rich knowledge of forest-based natural resources and consumption of wild edible plants is still an integral part of their socio-cultural life. Findings of this documentation study can be used as an ethnopharmacological basis for selecting plants for future phytochemical and pharmaceutical studies.

Air Pollution Control

The air we breathe is being polluted by activities such as vehicles; burning coal, oil, and other fossil fuels; and manufacturing chemicals. Air pollution can even come from smaller, everyday activities such as cooking, space heating, and degreasing and painting operations. These activities add gases and particles to the air we breathe. When these gases and particles accumulate in the air in high enough concentrations, they can harm us and our environment. The module on Air Pollution deals with the various sources of air pollution and the associated environmental and health impacts. It also discusses the appropriate measures to control/prevent the same.

Changing resonator geometry to boost sound power decouples size and song frequency in a small insect

Despite their small size, some insects, such as crickets, can produce high amplitude mating songs by rubbing their wings together. By exploiting structural resonance for sound radiation, crickets broadcast species-specific songs at a sharply tuned frequency. Such songs enhance the range of signal transmission, contain information about the signaler's quality, and allow mate choice. The production of pure tones requires elaborate structural mechanisms that control and sustain resonance at the species-specific frequency. Tree crickets differ sharply from this scheme. Although they use a resonant system to produce sound, tree crickets can produce high amplitude songs at different frequencies, varying by as much as an octave. Based on an investigation of the driving mechanism and the resonant system, using laser Doppler vibrometry and finite element modeling, we show that it is the distinctive geometry of the crickets' forewings (the resonant system) that is responsible for their capacity to vary frequency. The long, enlarged wings enable the production of high amplitude songs; however, as a mechanical consequence of the high aspect ratio, the resonant structures have multiple resonant modes that are similar in frequency. The drive produced by the singing apparatus cannot, therefore, be locked to a single frequency, and different resonant modes can easily be engaged, allowing individual males to vary the carrier frequency of their songs. Such flexibility in sound production, decoupling body size and song frequency, has important implications for conventional views of mate choice, and offers inspiration for the design of miniature, multifrequency, resonant acoustic radiators.

Evaluation of mechanical losses in a linear motor pressure wave generator

A moving magnet linear motor compressor or pressure wave generator (PWG) of 2 cc swept volume with dual opposed piston configuration has been developed to operate miniature pulse tube coolers. Prelimnary experiments yielded only a no-load cold end temperature of 180 K. Auxiliary tests and the interpretation of detailed modeling of a PWG suggest that much of the PV power has been lost in the form of blow-by at piston seals due to large and non-optimum clearance seal gap between piston and cylinder. The results of experimental parameters simulated using Sage provide the optimum seal gap value for maximizing the delivered PV power.

Manually operated piston-driven shock tube

A simple hand-operated shock tube capable of producing Mach 2 shock waves is described. Performance of this miniature shock tube using compressed high pressure air created by a manually operated piston in the driver section of the shock tube as driver gas with air at 1 atm pressure as the test gas in the driven tube is presented. The performance of the shock tube is found to match well with the theoretically estimated values using normal shock relations. Applications of this shock tube named Reddy tube, include study of blast-induced traumatic brain injuries and high temperature chemical kinetics.

Simulations and experiments in punching spring-steel devices with sub-millimeter features

This work demonstrates the feasibility of mesoscale (100 μm to mm) punching of multiple holes of intricate shapes in metals. Analytical modeling, finite element (FE)simulation, and experimentations are used in this work. Two dimensional FE simulations in ABAQUS were done with an assumed material modeling and plane-strain condition. A known analytical model was used and compared with the ABAQUS simulation results to understand the effects of clearance between the punch and the die. FE simulation in ABAQUS was done for different clearances and corner radii at punch, die, and holder. A set of punches and dies were used to punch out a miniature spring-steel gripper. Comparison of compliant grippers manufactured by wire-cut electro discharge machining(EDM) and punching shows that realizing sharp interior and re-entrant corners by punching is not easy to achieve. Punching of circular holes with 5 mm and 2.5 mm diameter is achieved. The possibility of realizing meso-scale parts with complicated shapes through punching is demonstrated in this work; and some strategies are suggested for improvement.

Corticosterone targets distinct steps of synaptic transmission via concentration specific activation of mineralocorticoid and glucocorticoid receptors

Hippocampal neurons are affected by chronic stress and have a high density of cytoplasmic mineralocorticoid and glucocorticoid receptors (MR and GR). Detailed studies on the genomic effects of the stress hormone corticosterone at physiologically relevant concentrations on different steps in synaptic transmission are limited. In this study, we tried to delineate how activation of MR and GR by different concentrations of corticosterone affects synaptic transmission at various levels. The effect of 3-h corticosterone (25, 50, and 100nM) treatment on depolarization-mediated calcium influx, vesicular release and properties of miniature excitatory post-synaptic currents (mEPSCs) were studied in cultured hippocampal neurons. Activation of MR with 25nM corticosterone treatment resulted in enhanced depolarization-mediated calcium influx via a transcription-dependent process and increased frequency of mEPSCs with larger amplitude. On the other hand, activation of GR upon 100nM corticosterone treatment resulted in increase in the rate of vesicular release via the genomic actions of GR. Furthermore, GR activation led to significant increase in the frequency of mEPSCs with larger amplitude and faster decay. Our studies indicate that differential activation of the dual receptor system of MR and GR by corticosterone targets the steps in synaptic transmission differently.

Time-Optimal Convergence to a Rectilinear Path in the Presence of Wind

This paper considers the problem of determining the time-optimal path of a fixed-wing Miniature Air Vehicle (MAV), in the presence of wind. The MAV, which is subject to a bounded turn rate, is required to eventually converge to a straight line starting from a known initial position and orientation. Earlier work in the literature uses Pontryagin's Minimum Principle (PMP) to solve this problem only for the no-wind case. In contrast, the present work uses a geometric approach to solve the problem completely in the presence of wind. In addition, it also shows how PMP can be used to partially solve the problem. Using a 6-DOF model of a MAV the generated optimal path is tracked by an autopilot consisting of proportional-integral-derivative (PID) controllers. The simulation results show the path generation and tracking for cases with steady and time-varying wind. Some issues on real-time path planning are also addressed.

Optimal Trajectory Generation for Convergence to a Rectilinear Path

This paper presents a strategy to determine the shortest path of a fixed-wing Miniature Air Vehicle (MAV), constrained by a bounded turning rate, to eventually fly along a given straight line, starting from an arbitrary but known initial position and orientation. Unlike the work available in the literature that solves the problem using the Pontryagin's Minimum Principle (PMP) the trajectory generation algorithm presented here considers a geometrical approach which is intuitive and easy to understand. This also computes the explicit solution for the length of the optimal path as a function of the initial configuration. Further, using a 6-DOF model of a MAV the generated optimal path is tracked by an autopilot consisting of proportional-integral-derivative (PID) controllers. The simulation results show the path generation and tracking for different cases.