A legume genomics resource: The Chickpea Root Expressed Sequence Tag Database

Chickpea, a lesser-studied grain legume, is being investigated due to its taxonomic proximity with the model legume genome Medicago truncatula and its ability to endure and grow in relatively low soil water contents making it a model legume crop for the study of agronomic response to drought stress. Public databases currently contain very few sequences from chickpea associated with expression in root tissues. However, root traits are likely to be one of the most important components of drought tolerance in chickpea. Thus, we have generated a set of over 2800 chickpea expressed sequence tags (ESTs) from a library constructed after subtractive suppressive hybridization (SSH) of root tissue from two closely related chickpea genotypes possessing different sources of drought avoidance and tolerance (ICC4958 and Annigeri respectively). This database provides researchers in legume genomics with a major new resource for data mining associated with root traits and drought tolerance. This report describes the development and utilization of the database and provides the tools we have developed to facilitate the bioinformatics pipeline used for analysis of the ESTs in this database. We also discuss applications that have already been achieved using this resource

LRRK2 and RIPK2 variants in the NOD 2-mediated signaling pathway are associated with susceptibility to Mycobacterium leprae in Indian populations

In recent years, genome wide association studies have discovered a large number of gene loci that play a functional role in innate and adaptive immune pathways associated with leprosy susceptibility. The immunological control of intracellular bacteria M. leprae is modulated by NOD2-mediated signaling of Th1 responses. In this study, we investigated 211 clinically classified leprosy patients and 230 ethnically matched controls in Indian population by genotyping four variants in NOD2 (rs9302752A/G), LRRK2 (rs1873613A/G), RIPK2 (rs40457A/G and rs42490G/A). The LRRK2 locus is associated with leprosy outcome. The LRRK2 rs1873613A minor allele and respective rs1873613AA genotypes were significantly associated with an increased risk whereas the LRRK2 rs1873613G major allele and rs1873613GG genotypes confer protection in paucibacillary and leprosy patients. The reconstructed GA haplotypes from RIPK2 rs40457A/G and rs42490G/A variants was observed to contribute towards increased risk whereas haplotypes AA was observed to confer protective role. Our results indicate that a possible shared mechanisms underlying the development of these two clinical forms of the disease as hypothesized. Our findings confirm and validates the role of gene variants involved in NOD2-mediated signalling pathways that play a role in immunological control of intracellular bacteria M. leprae

Drained and undrained response of fully saturated specimen in resonant column tests subjected to large number of torsional vibrations

In this paper, the drained and undrained responses of the saturated sand specimens have been investigated when subjected to small strain torsional excitation cycles using the resonant column apparatus. The sand specimens were reconstituted at an identical relative density of 40%. The fully saturated sand samples were then subjected to different effective isotropic consolidation stresses of 65, 100, and 150 kPa. For each test, thousands of vibration cycles were applied to the specimen by keeping the amplitude of cyclic driving torque constant. The response of the specimen was evaluated in both drained and undrained conditions. Beyond threshold strain, the undrained response of the saturated specimen demonstrated a considerable increase in pore water pressure and decrease in shear modulus, whereas axial strain increased substantially in case of vibrations applied to the specimen in drained conditions This type of study would be beneficial to determine deformational characteristics of fully saturated sand stratum beneath various vibratory machines which impart small stain and high-frequency vibrations

Assessing the liquefaction potential of a sand specimen by using resonant column test

The liquefaction potential of soils is usually assessed based on cyclic simple/triaxial/torsional shear tests. These tests are generally associated with low frequency vibrations in a range of 0.5–10 Hz which are often induced by an earthquake. There is, however, hardly any literature to assess the liquefaction potential when subjected to high frequency (20–100 Hz) and low shearing strain amplitude excitation (approximately 0.0001%–0.1%) - often associated with the foundations of different operating vibratory machines. In the present research, it is attempted to determine the liquefaction potential of a cylindrical saturated sand specimen based on resonant column (RC) tests. The effect of effective confining pressure, relative density of sand and the number of excitation cycles on the liquefaction potential has been investigated. Beyond a threshold shearing strain of 0.01%, a continuous rise in the porewater pressure was experienced when subjected to excitations which eventually lead to the liquefaction of saturated sand. The onset of liquefaction was also revealed by the Poisson ratio - which tends to become close to 0.5 as was observed from the bender and extended elements tests. The number of excitation cycles to cause initial liquefaction increases with (i) a decrease in the cyclic stress ratio, and (ii) an increase in the relative density of the sand. The present research clearly reveals that with a provision of continuous excitation in a RC apparatus, it becomes possible to assess the liquefaction potential of a specimen when subjected to high frequency low strain excitation. On account of low shearing strain in RC tests, the numbers of cycles required to cause liquefaction were found to be much greater than that reported in literature on the basis of cyclic shear tests

Interpretation of bender element test results using sliding Fourier transform method

Identification of the arrival point of the shear wave in bender element tests is a task that can have ambiguous results. The contamination of the received shear wave signal with a weak P-wave component, which can emerge either directly from the transmitter or reflect from the side boundary, makes the judgement involved in this task dubious. The different available procedures to mark the arrival times of the shear wave are often prone to errors. A method is proposed to identify the time of the arrival of the shear wave. The predominant frequency of the received signal is first evaluated and then, with the help of the sliding Fourier transform approach, the arrival of the shear wave is identified. The method does not require any manual intervention. The proposed approach is applied to bender element tests performed on dry and saturated sand and glass beads by varying (i) input frequency of the signal, (ii) confining pressure, and (iii) void ratio. Results for different cases, including those obtained by using resonant column tests, are found to be very promising

Calibration exercise of fixed-free resonant column apparatus

In this paper, the conventional calibration exercise for resonant column apparatus has been re-examined and some recommendations were provided to improve the accuracy of the test results. During the testing, specimen is assumed to be fixed at bottom and dynamic torsional vibrations are applied at the top using drive system consisting of four magnets. Due to complicated geometry of the drive system, its mass polar moment of inertia (Jd) is found to be difficult to estimate. So, calibration exercise is performed to determine Jd. In this present study, calibration rods of aluminum of known stiffness were used. The diameter of each aluminum rod was varied from 8 to 15 mm and keeping the constant height of 100 mm. The study revealed that the mass polar moment of inertia of the resonant column system is frequency dependent. Also, the solid cylindrical sand specimens were tested using resonant column tests and bender elements tests with varying confining pressure and relative density

Effect of slenderness ratio of the specimen on resonant column test results

To investigate the effect of the slenderness ratio (L/d) of the specimen, resonant column (RC) tests were conducted on dry sand specimens by using three different values of L/d, namely 2, 3, and 4, keeping the same diameter (d = 50 mm) to measure the shear moduli and material damping associated with the shear strain varying approximately from 0.0004 to 0.03 %. For the sake of the comparison, bender element (BE) tests were also performed on the same specimens to examine the effect of L/d on the shear moduli. Different combinations of relative densities and isotropic confining pressures were employed. The current experimental findings based on the simplified theory, which is widely used for analyzing the RC test results, reveal that the measured shear moduli of the specimens become higher for a slender specimen. On the other hand, the damping values were found to be only marginally affected with the changes in L/d. For greater L/d, generally the damping values were found to be slightly higher, especially with greater relative densities. The BE tests, on the other hand, hardly illustrate any variation in shear moduli with the changes in L/d. The shear wave velocities (Vs) from the BE tests were found to be a little greater as compared with the RC tests, and the difference between two sets of results becomes narrower with an increase in L/d. This study reveals that it will be more appropriate to use a L/d equal to 4 rather than 2, especially when testing at isotropic confining pressure ≥ 500 kPa