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43 results on '"Rajamani Vignesh"'

1. Generation of single stranded DNA with selective affinity to bovine spermatozoa

Author

Sivadasan Pathiyil Vinod, Rajamani Vignesh, Mani Priyanka, Krishnaswamy Gopalan Tirumurugaan, Salem Nagalingam Sivaselvam, and Gopal Dhinakar Raj

Subjects
aptamers, binding, selective enrichment, surface characteristics, Zoology, QL1-991
Abstract

Objective This study was conducted to generate single stranded DNA oligonucleotides with selective affinity to bovine spermatozoa, assess its binding potential and explore its potential utility in trapping spermatozoa from suspensions. Methods A combinatorial library of 94 mer long oligonucleotide was used for systematic evolution of ligands by exponential enrichment (SELEX) with bovine spermatozoa. The amplicons from sixth and seventh rounds of SELEX were sequenced, and the reads were clustered employing cluster database at high identity with tolerance (CD-HIT) and FASTAptamer. The enriched nucleotides were predicted for secondary structures by Mfold, motifs by Multiple Em for Motif Elicitation and 5′ labelled with biotin/6-FAM to determine the binding potential and binding pattern. Results We generated 14.1 and 17.7 million reads from sixth and seventh rounds of SELEX respectively to bovine spermatozoa. The CD-HIT clustered 78,098 and 21,196 reads in the top ten clusters and FASTAptamer identified 2,195 and 4,405 unique sequences in the top three clusters from the sixth and seventh rounds, respectively. The identified oligonucleotides formed secondary structures with delta G values between −1.17 to −26.18 kcal/mol indicating varied stability. Confocal imaging with the oligonucleotides from the seventh round revealed different patterns of binding to bovine spermatozoa (fluorescence of the whole head, spot of fluorescence in head and mid- piece and tail). Use of a 5′-biotin tagged oligonucleotide from the sixth round at 100 pmol with 4×106 spermatozoa could trap almost 80% from the suspension. Conclusion The binding patterns and ability of the identified oligonucleotides confirms successful optimization of the SELEX process and generation of aptamers to bovine spermatozoa. These oligonucleotides provide a quick approach for selective capture of spermatozoa from complex samples. Future SELEX rounds with X- or Y- enriched sperm suspension will be used to generate oligonucleotides that bind to spermatozoa of a specific sex type.

Published
2021
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3. Generation of single stranded DNA with selective affinity to bovine spermatozoa

Author

Sivadasan Pathiyil Vinod, Mani Priyanka, K.G. Tirumurugaan, Gopal Dhinakar Raj, Rajamani Vignesh, and Salem Nagalingam Sivaselvam

Subjects
chemistry.chemical_classification, General Veterinary, Physiology, Oligonucleotide, Chemistry, Surface Characteristics, Aptamer, Amplicon, Binding, Animal Breeding and Genetics, Aptamers, Article, Selective Enrichment, chemistry.chemical_compound, QL1-991, Biochemistry, Biotin, Multiple EM for Motif Elicitation, Genetics, Animal Science and Zoology, Nucleotide, Zoology, Systematic evolution of ligands by exponential enrichment, DNA, Food Science
Abstract

Objective: This study was conducted to generate single stranded DNA oligonucleotides with selective affinity to bovine spermatozoa, assess its binding potential and explore its potential utility in trapping spermatozoa from suspensions.Methods: A combinatorial library of 94 mer long oligonucleotide was used for systematic evolution of ligands by exponential enrichment (SELEX) with bovine spermatozoa. The amplicons from sixth and seventh rounds of SELEX were sequenced, and the reads were clustered employing cluster database at high identity with tolerance (CD-HIT) and FASTAptamer. The enriched nucleotides were predicted for secondary structures by Mfold, motifs by Multiple Em for Motif Elicitation and 5’ labelled with biotin/6-FAM to determine the binding potential and binding pattern.Results: We generated 14.1 and 17.7 million reads from sixth and seventh rounds of SELEX respectively to bovine spermatozoa. The CD-HIT clustered 78,098 and 21,196 reads in the top ten clusters and FASTAptamer identified 2,195 and 4,405 unique sequences in the top three clusters from the sixth and seventh rounds, respectively. The identified oligonucleotides formed secondary structures with delta G values between –1.17 to –26.18 kcal/mol indicating varied stability. Confocal imaging with the oligonucleotides from the seventh round revealed different patterns of binding to bovine spermatozoa (fluorescence of the whole head, spot of fluorescence in head and mid- piece and tail). Use of a 5’-biotin tagged oligonucleotide from the sixth round at 100 pmol with 4×106 spermatozoa could trap almost 80% from the suspension.Conclusion: The binding patterns and ability of the identified oligonucleotides confirms successful optimization of the SELEX process and generation of aptamers to bovine spermatozoa. These oligonucleotides provide a quick approach for selective capture of spermatozoa from complex samples. Future SELEX rounds with X- or Y- enriched sperm suspension will be used to generate oligonucleotides that bind to spermatozoa of a specific sex type.

Published
2020

6. Validation of Modal/MoM in shielding effectiveness studies of rectangular enclosures with apertures

Author

Rajamani, Vignesh, Bunting, Charles F., Deshpande, Manohar D., and Khan, Zulfiqar A.

Subjects
Finite element method -- Usage, Electromagnetic fields -- Research, Magnetic shielding -- Research, Business, Computers, Electronics, Electronics and electrical industries
Abstract

This paper discusses the validation of Modal/method of MoMents (MoM) including cases when the apertures are made as big as the wall of the enclosure (equivalent to having one side of the cavity open). The validation is done using field computations involving bodies of arbitrary shape (FEKO), a commercially available code. The results show that Modal/MoM predicts the results close to the analytical results of Robinson et al. Electron. Lett., 32 (17), 1996; Robinson et al., IEEE Trans. Electromagn. Compat., 40 (3), 240-247, 1998 for single-aperture cases and for most double-aperture cases. Also, for the cases of considering oblique incident plane waves, through validation, it has been found that Modal/MoM can predict the shielding effectiveness close to measured results for smaller angles and not for larger angles of incidence due to the edge effects. In this work, the shielding effectiveness is calculated at only one point, the center of the cavity assuming it to be the worst case. This work discovers the limitation of Modal/MoM for certain applications. Index Terms--FEKO, MoM, shielding effectiveness, validation.

Published
2006

39. Accurate and Efficient Numerical Simulation of the Random Environment Within an Ideal Reverberation Chamber.

Author

West, James C., Bunting, Charles F., and Rajamani, Vignesh

Subjects
COMPUTER simulation, ELECTROMAGNETISM, MOMENTS method (Statistics), SURFACE waves (Fluids), ENGINEERING design, GAUSSIAN distribution, GREEN'S functions, MONTE Carlo method
Abstract

An electromagnetic susceptibility test within an ideal reverberation chamber is numerically simulated using the moment method (MM). The random field environment within the chamber is synthesized using a superposition of plane waves that are propagating in fixed directions determined rigorously from spectral sampling theory. Randomness is introduced in the complex field amplitudes associated with each plane wave. This approach yields field statistics within a designated test region that approach ideal. Moreover, the fixed propagation directions allow very efficient calculation of the currents induced at specific test points on an equipment-under-test due to the random field realizations. MM calculations show that the proposed sampling method yields a better prediction of the statistics of the induced current while requiring far less computation time than the currently used technique of superimposing randomly propagating plane waves to yield field realizations. [ABSTRACT FROM AUTHOR]

Published
2012
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42. HEAT TRANSFER IN CONTINUUM AND NON-CONTINUUM PLASMA FLOWS IN MATERIALS PROCESSING APPLICATIONS

Author

RAJAMANI, VIGNESH

Subjects
Plasma, Knudsen, Temperature Jump, Kinetic theory, Continuum, Non-Continuum
Abstract

Computational analysis of heat transfer in continuum and non-continuum plasma flow is presented in this thesis. First a continuum, laminar, mid-temperature range (1200K-1600K) plasma flow over a cylinder has been considered. The steady form of continuity and momentum conservation equations are solved in the plasma by a finite volume method. The conjugated transient heat transfer in the cylinder and in the plasma is obtained by simultaneous solution of the transient energy conservation equations. The ion and electron fluxes at the solid surface and the self-consistent electric field are evaluated. An inverse heat transfer problem is considered by using available experimental measurements of temperature rise in the cylinder to characterize the degree of ionization in the plasma flow. Comparing computational predictions of heat transfer in plasma flow with those for air flow, it is shown that the heat transfer to the cylinder is higher from plasma flow than that in flow of unionized air under identical flow and temperature conditions. The enhancement of heat transfer in plasma is due to the energy deposited at the solid surface by charged species during recombination reaction at the solid surface. An important finding is that even a small degree of ionization (< 1%) provides significant enhancement in heat transfer. This enhancement in heat transfer can lead to productivity increase in materials processing applications using mid-temperature convective plasma devices. When small particles are introduced in plasma flow, the ratio of mean free path to particle radius, which is known as the Knudsen number (Kn), may not be very small. As such a continuum treatment is not valid under such conditions. In the second part of this thesis, heat transfer to a spherical solid particle from a non-continuum stagnant plasma is considered. A kinetic theory formulation is developed by considering two-sided velocity and temperature distributions for neutral molecules. Governing equations obtained by taking moments of the Boltzmann equation are solved by a Newton-Raphson method along with a shooting technique and a fourth-order Runge-Kutta method. The temperature distribution in the plasma and heat transfer to the particle is obtained at different Knudsen numbers. Results show that the model accurately captures both continuum (Kn 0) and free-molecular regimes (Kn) and the agreement with available experimental data for heat transfer in the entire range of Knudsen number is excellent. The heat transfer to the particle decreases with increase in Knudsen number. The model is used to ascertain validity of the commonly used temperature jump approximation in non-continuum flows. It is shown that the temperature jump approach can be used under near-continuum conditions (Kn < 0.1) and the predictions of heat transfer by this approximation deviate significantly from the developed model. The model developed here can predict the heat transfer in the entire range of Knudsen number and can be applied to accurately evaluate plasma heat transfer in plasma-aided manufacturing applications involving small length scales.

Published
2005

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