Showing papers by "Alok Chakrabarti published in 2013"

Infection with influenza A viruses causes changes in promoter DNA methylation of inflammatory genes.

Abstract: Background Replication of influenza virus in the host cells results in production of immune mediators like cytokines. Excessive secretion of cytokines (hypercytokinemia) has been observed during highly pathogenic avian influenza virus (HPAI-H5N1) infections resulting in high fatality rates. Objective The exact mechanism of hypercytokinemia during influenza virus infection is still not known completely. As promoter DNA methylation changes are linked with expression changes in genes, we intend to identify whether changes in promoter DNA methylation have any role in expression of cytokines during influenza A virus infection. Methods A panel of 24 cytokine genes and genes known to be involved in inflammatory response were analyzed for their promoter DNA methylation changes during influenza A virus infections. Four different strains of influenza A viruses, viz. H5N1, H1N1, pandemic (2009) H1N1, and a vaccine strain of H5N1, were used for the study. Results We found seven of the total 24 inflammatory genes studied, showing significant changes in their promoter methylation levels in response to virus infection. These genes included proinflammatory cytokines CXCL14, CCL25, CXCL6, and interleukines IL13, IL17C, IL4R. The changes in DNA methylation levels varied across different strains of influenza viruses depending upon their virulence. Significant promoter hypomethylation in IL17C and IL13 genes was observed in cells infected with HPAI-H5N1 virus compared with other influenza viruses. This decrease in methylation was found to be positively correlating with the increased expression of these genes. Analysis of IL17C promoter region using bisulfite sequencing resulted in identification of a CpG site within Retinoid X receptor-alpha (RXR-α) transcription factor binding site undergoing demethylation specifically in H5N1-infected cells but not in other influenza-infected cells. Conclusion Thus, the study could demonstrate that changes in promoter methylation in certain specific cytokine genes actually have a possible role in their expression changes during influenza A virus infection.

The ANURIB project at VECC – Plans and preparations

Abstract: VECC is planning to develop a rare ion beam facility called ANURIB 1 (Advanced National facility for Unstable and Rare Isotope Beams) at the upcoming new campus at New Town in Kolkata. ANURIB aims to attract a wide user community in nuclear physics, nuclear-astrophysics, material science and biology and will provide India with world class accelerator facilities. ANURIB will be built around a 50 MeV 100 kW superconducting electron linac (e-Linac) photo-fission driver and is planned to be a combined ISOL and PFS type facility. Construction of the facility will also enable next generation research into production of medical isotopes. In preparation for ANURIB, a low energy ISOL type facility has been built around the existing K130 cyclotron at VECC. Developed for the past decade, this facility was aimed at completing major R&D steps involved in the construction of ANURIB. Presently this facility accelerates beams up to energy of 415 keV/u and recently first radioactive beams have been produced. Development of a 10 MeV Injector Cryo Module for the e-Linac has been started in collaboration with TRIUMF. In this paper the plans for ANURIB project and present status of the R&D activities will be presented.

The role of carbon in ion beam nano-patterning of silicon

Abstract: We report a comparative study of nano-pattern formations on a carbon film and a smooth Si(100) surface following inert and chemically active ion bombardment. For the case of carbon film, patterns could be formed both by inert (Ar+) and self (C+) ion bombardment with the former producing ripples at relatively lower fluence. In contrast, bombardment by inert Ar+ failed to form the nano patterns on Si surface, while bombardment by the same energy C+ generated the ripples. Thus, impurity induced chemical effect seems to be crucial rather than the Bradley-Harper or Carter-Vishnyakov effects for destabilizing the surface for ripple formation.

Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the influenza A virus subtypes responsible for the 20th-century pandemics.

Abstract: Please cite this paper as: Pasricha et al. (2012) Comprehensive global amino acid sequence analysis of PB1F2 protein of influenza A H5N1 viruses and the Influenza A virus subtypes responsible for the 20th-century pandemics. Influenza and Other Respiratory Viruses 7(4), 497–505. Background PB1F2 is the 11th protein of influenza A virus translated from +1 alternate reading frame of PB1 gene. Since the discovery, varying sizes and functions of the PB1F2 protein of influenza A viruses have been reported. Selection of PB1 gene segment in the pandemics, variable size and pleiotropic effect of PB1F2 intrigued us to analyze amino acid sequences of this protein in various influenza A viruses. Methods Amino acid sequences for PB1F2 protein of influenza A H5N1, H1N1, H2N2, and H3N2 subtypes were obtained from Influenza Research Database. Multiple sequence alignments of the PB1F2 protein sequences of the aforementioned subtypes were used to determine the size, variable and conserved domains and to perform mutational analysis. Results Analysis showed that 96·4% of the H5N1 influenza viruses harbored full-length PB1F2 protein. Except for the 2009 pandemic H1N1 virus, all the subtypes of the 20th-century pandemic influenza viruses contained full-length PB1F2 protein. Through the years, PB1F2 protein of the H1N1 and H3N2 viruses has undergone much variation. PB1F2 protein sequences of H5N1 viruses showed both human- and avian host-specific conserved domains. Global database of PB1F2 protein revealed that N66S mutation was present only in 3·8% of the H5N1 strains. We found a novel mutation, N84S in the PB1F2 protein of 9·35% of the highly pathogenic avian influenza H5N1 influenza viruses. Conclusions Varying sizes and mutations of the PB1F2 protein in different influenza A virus subtypes with pandemic potential were obtained. There was genetic divergence of the protein in various hosts which highlighted the host-specific evolution of the virus. However, studies are required to correlate this sequence variability with the virulence and pathogenicity.

Optical switching in a Ξ system: A comparative study on DROP and EIT

Abstract: In this experimental work we address the issue of optical switching through pump induced atomic coherence in pump-probe spectroscopy of Doppler broadened medium of Rubidium atoms. Here a cascade system 5S → 5P → 5D is chosen as the medium for optical switching. The merit of using this level scheme for current study lies in the fact that two photon spectroscopy conducted in the above-mentioned manifold results into a combination of double resonance optical pumping (DROP) and electromagnetically induced transparency (EIT) signals. Within an intensity modulation frequency range of 10 Hz → 10 MHz, DROP and EIT behave differently. This fact may be attributed to the distinctive difference in mechanisms giving rise to DROP and EIT signals. Though both DROP and EIT stem from two photon spectroscopy, unlike DROP, which arises due to population transfer between dipole forbidden 5S → 5D levels, EIT originates from destructive quantum interference mechanism. This subtle difference is well evidenced when optical switching is conducted through the coherently prepared alkali vapour sample. The EIT is found to be more agile towards faster optical switching while DROP acts as an over damped medium for the same. A simple qualitative discussion is included to explain our results on optical switching.

Defects in 6 MeV H+ irradiated hydrothermal ZnO single crystal.

Abstract: The effect of 6 MeV H+ irradiation on hydrothermally grown ZnO single crystal has been investigated using high resolution x-ray diffraction (HRXRD) and optical absorption (ultraviolet–visible) spectroscopy. The increase of the diffuse scattering in the reciprocal space maps measured using HRXRD indicates an increase of the point defect density upon irradiation. Within the penetration depth of x-rays of several micrometres, the defect density increased with increasing distance from the sample surface. On the other hand, the near band gap optical absorption became sharper for the irradiated crystal. This reflects enhanced band to band absorption and reduced sub-band gap absorption due to defects. Temperature dependent photoluminescence spectra of the pristine sample show negative thermal quenching (NTQ) of the luminescence which is due to the presence of two or more donor related defects. Upon irradiation, a single dominant donor bound transition can be found without any temperature induced NTQ. Enhancement of the band edge luminescence and reduction of the defect related luminescence is observed at 10 K. Such changes have been discussed in the light of the hydrogen present in the as-grown state of hydrothermal ZnO.

First online production of radioactive ion beams at VECC

Abstract: Radioactive ion beams (RIB) have been recently accelerated for the first time at the VECC-RIB facility. Beams of 14 O (71 s), 42 K (12.4 h), 43 K (22 h) and 41 Ar (1.8 h) have been produced by bombarding 1 atm nitrogen and argon gas targets with 1 micro-ampere proton and alpha particle beams from the K130 cyclotron. Radioactive atoms were transported 15 m away to the ECR ion-source using a gas-jet transport system. Typical measured intensity of RIB at the separator focal plane is few times 10 3 pps. About 3300 pps of 1.4 MeV 14 O was measured after acceleration through a 3.4 m long RFQ linac. The details of the gas-jet coupled ECR and RIB production experiments are presented.

A gas-jet transport and catcher technique for on-line production of radioactive ion beams using an electron cyclotron resonance ion-source

Abstract: Radioactive ion beams (RIB) have been produced on-line, using a gas-jet recoil transport coupled Electron Cyclotron Resonance (ECR) ion-source at the VECC-RIB facility Radioactive atoms/molecules carried through the gas-jet were stopped in a catcher placed inside the ECR plasma chamber A skimmer has been used to remove bulk of the carrier gas at the ECR entrance The diffusion of atoms/molecules through the catcher has been verified off-line using stable isotopes and on-line through transmission of radioactive reaction products Beams of 14O (71 s), 42K (124 h), 43K (222 h), and 41Ar (18 h) have been produced by bombarding nitrogen and argon gas targets with proton and alpha particle beams from the K130 cyclotron at VECC Typical measured intensity of RIB at the separator focal plane is found to be a few times 103 particles per second (pps) About 32 × 103 pps of 14 MeV 14O RIB has been measured after acceleration through a radiofrequency quadrupole linac The details of the gas-jet coupled ECR ion-source and RIB production experiments are presented along with the plans for the future

Study of the effect of repump laser on atomic line filter

Abstract: The improvement in the performance of an atomic line filter (ALF) under the action of a repump laser is reported in the current experimental work We address the issue of repumping by including an additional laser coupling the 5S1/2(F=1)→5P3/2(F′′=2,1,0) hyperfine levels whereas the optical filter action is exhibited through a pump–probe laser-induced excited state absorption {5S1/2(F=2)→5P3/2(F′=3)→5D3/2(F′′=3)} of the Rb87 atom It is found that the application of the repump mechanism considerably influences the characterizing parameters (ie, transmittance and width) of the ALF To optimize the performance of the ALF, it is required to carefully choose the detuning and intensity of the repump laser for a fixed set of pump–probe combination For this purpose, the effect of systematic change in detuning and intensity of the repump laser on the ALF signal is studied in detail For example, it is experimentally found that ALF considerably benefits (∼30%) in transmittance from selective repumping of atoms It is to be noted that, unlike earlier reports, where the frequency scale of the filter is calibrated with Faby–Perot etalons of comparatively larger free spectral range, the marking is done here with the help of double resonance optical pumping (DROP) signals The DROP signals, which originate from two-photon coupling within the 5S→5P→5D hyperfine domain, also act as an indicator of the existing “Radiation Trapping” process in the cascade medium The current study may help in improving the performance of narrow-bandwidth ALF, which is useful for free space optical communication systems and laser spectroscopy

Impact of Microarray Technology in Influenza Virus Research and Diagnostics

Abstract: Influenza A viruses cause 300,000-500,000 deaths every year across the globe and are continues threat to public health. There have been five influenza pandemics till date. In spite of the recent advances in the field of virus research there is no steady vaccine against influenza A viruses. Flu shots are given every year in many countries but remain effective only for one season. One of the main reasons of vaccine ineffectiveness is the high mutation rate in the influenza A genome caused by a poor error prone replication mechanism and virus recombination in the host cells resulting in variation in antigenic proteins. In order to overcome this problem scientists have enabled different strategies to control virus infectivity. Now in place of viruses, host responses are studied and modified in order to obtain an effective immune response against the viruses. Also, new strategies like rapid large scale virus diagnosis and development of effective vaccines using reverse genetics technique are being used for improvement of antiviral counter measures. Microarray technique, which is a high throughput method for diagnosis as well as assessment of large number of biomolecules in one attempt, has played an important role in understanding the etiology and pathogenesis of influenza A viruses. In this review we have discussed significance of microarray technology in influenza virus research during last one decade and highlighted its application in extensive diagnostics and genome wide transcriptional profiling of host responses to virus infection.

Development of a fast scintillator based beam phase measurement system for compact superconducting cyclotrons.

Abstract: In an isochronous cyclotron, measurements of central phase of the ion beam with respect to rf and the phase width provide a way to tune the cyclotron for maximum energy gain per turn and efficient extraction. We report here the development of a phase measurement system and the measurements carried out at the Variable Energy Cyclotron Centre's (VECC’s) K = 500 superconducting cyclotron. The technique comprises detecting prompt γ-rays resulting from the interaction of cyclotron ion beam with an aluminium target mounted on a radial probe in coincidence with cyclotron rf. An assembly comprising a fast scintillator and a liquid light-guide inserted inside the cyclotron was used to detect the γ-rays and to transfer the light signal outside the cyclotron where a matching photo-multiplier tube was used for light to electrical signal conversion. The typical beam intensity for this measurement was a few times 1011 pps.

Alternate phase focusing in sequence of independent phased resonators as superconducting linac boosters

Abstract: Theoretical study of an alternate phase focusing (APF) structure, realized in a long chain of double gap quarter wave resonators, capable of accelerating heavy ions from 1.3 to 7 MeV/u has been carried out. Mathieu-Hill stability analysis for the focusing periods consisting of independent resonators with phase variation satisfying square-wave law has been used to evaluate parameters such as the electric field and phase for the resonators. Furthermore, a smooth approximation method taking into account the acceleration in the linac has been employed to find out the rf bucket parameters (energy and phase width acceptance) of the focusing periods. Corroborative particle tracking (longitudinal and transverse) has been carried out using simulated 3D fields for double gap quarter wave resonators (QWR). Steering effects in QWRs over the period have also been studied. In one APF period, the individual phase of resonators changes sign resulting in a vertical steering kick in a particular direction, which is less as compared to the case where all the individual resonators operate in the same phase.

Tunable offset locking in a Ξ system: an experimental study on the rubidium atom

Abstract: In this report, we present an experimental investigation on atomic frequency offset locking (AFOL) of a laser under ladder (Ξ) level coupling scheme. The 5S1/2 → 5P3/2 → 5D5/2 two-photon transition manifold of the rubidium (Rb) atom is chosen to demonstrate the performance of stabilization scheme in terms of frequency stability and tunability. The coherent pump–probe spectroscopy performed on the 5S → 5P → 5D levels results in signatures of two-photon absorption (TPA) and electromagnetically induced transparency (EIT). Here the pump laser is locked to the fringe of a scanning Fabry–Perot interferometer with the help of frequency modulation spectroscopy. The probe laser is subsequently stabilized on the resulting EIT (TPA) signals. It is found that the probe laser attains relative frequency stability as a square root of Allan variance calculated from the frequency noise power density under closed-loop condition. Further, the current locking scheme has wide tuning range {Doppler width of transition manifold. This particular tunable AFOL (TAFOL) scheme can provide large tuning range without compromising the frequency stability and such implementation of TAFOL may open new opportunities in research areas like metrology, ultra precision coherent spectroscopy, etc.

Measurement of radial oscillation and phase of accelerating beam in kolkata superconducting cyclotron

Abstract: This paper describes various measurements performed on the beam behaviour with the help of the main probes and the differential probe to have a clear insight of the accelerating beam and the difficulties of beam -extraction process in the K500 superconducting cyclotron at Kolkata. Beam shadow measurements with three probes at three sectors were done to get the information of beamcentering and radial oscillations. The radial oscillation amplitude is estimated from the measurements. A differential probe was used to measure the turn separation and its modulation due to radial oscillation. With the help of magnetic field detuning method, the beam phase history was also measured.