Classification of Nonenzymatic Homologues of Protein Kinases

Protein Kinase-Like Non-kinases (PKLNKs), which are closely related to protein kinases, lack the crucial catalytic aspartate in the catalytic loop, and hence cannot function as protein kinase, have been analysed. Using various sensitive sequence analysis methods, we have recognized 82 PKLNKs from four higher eukaryotic organisms, namely, Homo sapiens, Mus musculus, Rattus norvegicus, and Drosophila melanogaster. On the basis of their domain combination and function, PKLNKs have been classified mainly into four categories: (1) Ligand binding PKLNKs, (2) PKLNKs with extracellular protein-protein interaction domain, (3) PKLNKs involved in dimerization, and (4) PKLNKs with cytoplasmic protein-protein interaction module. While members of the first two classes of PKLNKs have transmembrane domain tethered to the PKLNK domain, members of the other two classes of PKLNKs are cytoplasmic in nature. The current classification scheme hopes to provide a convenient framework to classify the PKLNKs from other eukaryotes which would be helpful in deciphering their roles in cellular processes.

Vertical distribution of aerosols over the east coast of India inferred from airborne LIDAR measurements

The information on altitude distribution of aerosols in the atmosphere is essential in assessing the impact of aerosol warming on thermal structure and stability of the atmosphere.In addition, aerosol altitude distribution is needed to address complex problems such as the radiative interaction of aerosols in the presence of clouds. With this objective,an extensive, multi-institutional and multi-platform field experiment (ICARB-Integrated Campaign for Aerosols, gases and Radiation Budget) was carried out under the Geosphere Biosphere Programme of the Indian Space Research Organization (ISRO-GBP) over continental India and adjoining oceans during March to May 2006. Here, we present airborne LIDAR measurements carried out over the east Coast of the India during the ICARB field campaign. An increase in aerosol extinction (scattering + absorption) was observed from the surface upwards with a maximum around 2 to 4 km. Aerosol extinction at higher atmospheric layers (>2 km) was two to three times larger compared to that of the surface. A large fraction (75-85%) of aerosol column optical depth was contributed by aerosols located above 1 km. The aerosol layer heights (defined in this paper as the height at which the gradient in extinction coefficient changes sign) showed a gradual decrease with an increase in the offshore distance. A large fraction (60-75%) of aerosol was found located above clouds indicating enhanced aerosol absorption above clouds. Our study implies that a detailed statistical evaluation of the temporal frequency and spatial extent of elevated aerosol layers is necessary to assess their significance to the climate. This is feasible using data from space-borne lidars such as CALIPSO,which fly in formation with other satellites like MODIS AQUA and MISR, as part of the A-Train constellation.

Effect of pulse profile variations on measurement of eccentricity in orbits of Cen X-3 and SMC X-1

It has long been argued that better timing precision allowed by satellites like Rossi X-ray Timing Explorer (RXTE) will allow us to measure the orbital eccentricity and the angle of periastron of some of the bright persistent high-mass X-ray binaries (HMXBs) and hence a possible measurement of apsidal motion in these system. Measuring the rate of apsidal motion allows one to estimate the apsidal motion constant of the mass losing companion star and hence allows for the direct testing of the stellar structure models for these giant stars present in the HMXBs. In the present paper, we use the archival RXTE data of two bright persistent sources, namely Cen X-3 and SMC X-1, to measure the very small orbital eccentricity and the angle of periastron. We find that the small variations in the pulse profiles of these sources, rather than the intrinsic time resolution provided by RXTE, limit the accuracy with which we can measure arrival time of the pulses from these sources. This influences the accuracy with which one can measure the orbital parameters, especially the very small eccentricity and the angle of periastron in these sources. The observations of SMC X-1 in the year 2000 were taken during the high-flux state of the source and we could determine the orbital eccentricity and omega using this data set.

Real-time kinematic positioning over long baselines using triple-frequency BeiDou signals

The BeiDou system is the first global navigation satellite system in which all satellites transmit triple-frequency signals that can provide the positioning, navigation, and timing independently. A benefit of triple-frequency signals is that more useful combinations can be formed, including some extrawide-lane combinations whose ambiguities can generally be instantaneously fixed without distance restriction, although the narrow-lane ambiguity resolution (NL AR) still depends on the interreceiver distance or requires a long time to achieve. In this paper, we synthetically study decimeter and centimeter kinematic positioning using BeiDou triple-frequency signals. It starts with AR of two extrawide-lane signals based on the ionosphere-free or ionosphere-reduced geometry-free model. For decimeter positioning, one can immediately use two ambiguity-fixed extrawide-lane observations without pursuing NL AR. To achieve higher accuracy, NL AR is the necessary next step. Despite the fact that long-baseline NL AR is still challenging, some NL ambiguities can indeed be fixed with high reliability. Partial AR for NL signals is acceptable, because as long as some ambiguities for NL signals are fixed, positioning accuracy will be certainly improved.With accumulation of observations, more and more NL ambiguities are fixed and the positioning accuracy continues to improve. An efficient Kalman-filtering system is established to implement the whole process. The formulated system is flexible, since the additional constraints can be easily applied to enhance the model's strength. Numerical results from a set of real triple-frequency BeiDou data on a 50 km baseline show that decimeter positioning is achievable instantaneously.With only five data epochs, 84% of NL ambiguities can be fixed so that the real-time kinematic accuracies are 4.5, 2.5, and 16 cm for north, east, and height components (respectively), while with 10 data epochs more than 90% of NL ambiguities are fixed, and the rea- -time kinematic solutions are improved to centimeter level for all three coordinate components.

Multi-GNSS precise point positioning with raw single-frequency and dual-frequency measurement models

The emergence of multiple satellite navigation systems, including BDS, Galileo, modernized GPS, and GLONASS, brings great opportunities and challenges for precise point positioning (PPP). We study the contributions of various GNSS combinations to PPP performance based on undifferenced or raw observations, in which the signal delays and ionospheric delays must be considered. A priori ionospheric knowledge, such as regional or global corrections, strengthens the estimation of ionospheric delay parameters. The undifferenced models are generally more suitable for single-, dual-, or multi-frequency data processing for single or combined GNSS constellations. Another advantage over ionospheric-free PPP models is that undifferenced models avoid noise amplification by linear combinations. Extensive performance evaluations are conducted with multi-GNSS data sets collected from 105 MGEX stations in July 2014. Dual-frequency PPP results from each single constellation show that the convergence time of undifferenced PPP solution is usually shorter than that of ionospheric-free PPP solutions, while the positioning accuracy of undifferenced PPP shows more improvement for the GLONASS system. In addition, the GLONASS undifferenced PPP results demonstrate performance advantages in high latitude areas, while this impact is less obvious in the GPS/GLONASS combined configuration. The results have also indicated that the BDS GEO satellites have negative impacts on the undifferenced PPP performance given the current “poor” orbit and clock knowledge of GEO satellites. More generally, the multi-GNSS undifferenced PPP results have shown improvements in the convergence time by more than 60 % in both the single- and dual-frequency PPP results, while the positioning accuracy after convergence indicates no significant improvements for the dual-frequency PPP solutions, but an improvement of about 25 % on average for the single-frequency PPP solutions.

Assessment of code bias variations of BDS triple-frequency signals and their impacts on ambiguity resolution for long baselines

Carrier phase ambiguity resolution over long baselines is challenging in BDS data processing. This is partially due to the variations of the hardware biases in BDS code signals and its dependence on elevation angles. We present an assessment of satellite-induced code bias variations in BDS triple-frequency signals and the ambiguity resolutions procedures involving both geometry-free and geometry-based models. First, since the elevation of a GEO satellite remains unchanged, we propose to model the single-differenced fractional cycle bias with widespread ground stations. Second, the effects of code bias variations induced by GEO, IGSO and MEO satellites on ambiguity resolution of extra-wide-lane, wide-lane and narrow-lane combinations are analyzed. Third, together with the IGSO and MEO code bias variations models, the effects of code bias variations on ambiguity resolution are examined using 30-day data collected over the baselines ranging from 500 to 2600 km in 2014. The results suggest that although the effect of code bias variations on the extra-wide-lane integer solution is almost ignorable due to its long wavelength, the wide-lane integer solutions are rather sensitive to the code bias variations. Wide-lane ambiguity resolution success rates are evidently improved when code bias variations are corrected. However, the improvement of narrow-lane ambiguity resolution is not obvious since it is based on geometry-based model and there is only an indirect impact on the narrow-lane ambiguity solutions.

Wide area kinematic positioning with BeiDou triple frequency signals

A key challenge of wide area kinematic positioning is to overcome the effects of the varying hardware biases in code signals of the BeiDou system. Based on three geometryfree/ionosphere-free combinations, the elevation-dependent code biases are modelled for all BeiDou satellites. Results from the data sets of 30-day for 5 baselines of 533 to 2545 km demonstrate that the wide-lane (WL) integer-fixing success rates of 98% to 100% can be achieved within 25 min. Under the condition of HDOP of less than 2, the overall RMS statistics show that ionospheric-free WL single-epoch solutions achieve 24 to 50 cm in the horizontal direction. Smoothing processing over the moving window of 20 min reduces the RMS values by a factor of about 2. Considering distance-independent nature, the above results show the potential that reliable and high precision positioning services could be provided in a wide area based on a sparsely distributed ground network.

Evolution of domain combinations in protein kinases and its implications for functional diversity

Protein kinases phosphorylating Ser/Thr/Tyr residues in several cellular proteins exert tight control over their biological functions. They constitute the largest protein family in most eukaryotic species. Protein kinases classified based on sequence similarity in their catalytic domains, cluster into subfamilies, which share gross functional properties. Many protein kinases are associated or tethered covalently to domains that serve as adapter or regulatory modules,naiding substrate recruitment, specificity, and also serve as scaffolds. Hence the modular organisation of the protein kinases serves as guidelines to their functional and molecular properties. Analysis of genomic repertoires of protein kinases in eukaryotes have revealed wide spectrum of domain organisation across various subfamilies of kinases. Occurrence of organism-specific novel domain combinations suggests functional diversity achieved by protein kinases in order to regulate variety of biological processes. In addition, domain architecture of protein kinases revealed existence of hybrid protein kinase subfamilies and their emerging roles in the signaling of eukaryotic organisms. In this review we discuss the repertoire of non-kinase domains tethered to multi-domain kinases in the metazoans. Similarities and differences in the domain architectures of protein kinases in these organisms indicate conserved and unique features that are critical to functional specialization. (C) 2009 Elsevier Ltd. All rights reserved.

Role of Magmas in protein transport and human mitochondria biogenesis

Magmas, a conserved mammalian protein essential for eukaryotic development, is overexpressed in prostate carcinomas and cells exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF). Reduced Magmas expression resulted in decreased proliferative rates in cultured cells. However, the cellular function of Magmas is still elusive. In this report, we have showed that human Magmas is an ortholog of Saccharomyces cerevisiae Pam16 having similar functions and is critical for protein translocation across mitochondrial inner membrane. Human Magmas shows a complete growth complementation of delta pam16 yeast cells at all temperatures. On the basis of our analysis, we report that Magmas localizes into mitochondria and is peripherally associated with inner mitochondrial membrane in yeast and humans. Magmas forms a stable subcomplex with J-protein Pam18 or DnaJC19 through its C-terminal region and is tethered to TIM23 complex of yeast and humans. Importantly, amino acid alterations in Magmas leads to reduced stability of the subcomplex with Pam18 that results in temperature sensitivity and in vivo protein translocation defects in yeast cells. These observations highlight the central role of Magmas in protein import and mitochondria biogenesis. In humans, absence of a functional DnaJC19 leads to dilated cardiac myophathic syndrome (DCM), a genetic disorder with characteristic features of cardiac myophathy and neurodegeneration. We propose that the mutations resulting in decreased stability of functional Magmas:DnaJC19 subcomplex at human TIM23 channel leads to impaired protein import and cellular respiration in DCM patients. Together, we propose a model showing how Magmas:DnaJC19 subcomplex is associated with TIM23 complex and thus regulates mitochondrial import process.

Characterization of non-imaging semiconductor X-ray solar monitors

The first observations of solar X-rays date back to late 1940 s. In order to observe solar X-rays the instruments have to be lifted above the Earth s atmosphere, since all high energy radiation from the space is almost totally attenuated by it. This is a good thing for all living creatures, but bad for X-ray astronomers. Detectors observing X-ray emission from space must be placed on-board satellites, which makes this particular discipline of astronomy technologically and operationally demanding, as well as very expensive. In this thesis, I have focused on detectors dedicated to observing solar X-rays in the energy range 1-20 keV. The purpose of these detectors was to measure solar X-rays simultaneously with another X-ray spectrometer measuring fluorescence X-ray emission from the Moon surface. The X-ray fluorescence emission is induced by the primary solar X-rays. If the elemental abundances on the Moon were to be determined with fluorescence analysis methods, the shape and intensity of the simultaneous solar X-ray spectrum must be known. The aim of this thesis is to describe the characterization and operation of our X-ray instruments on-board two Moon missions, SMART-1 and Chandrayaan-1. Also the independent solar science performance of these two almost similar X-ray spectrometers is described. These detectors have the following two features in common. Firstly, the primary detection element is made of a single crystal silicon diode. Secondly, the field of view is circular and very large. The data obtained from these detectors are spectra with a 16 second time resolution. Before launching an instrument into space, its performance must be characterized by ground calibrations. The basic operation of these detectors and their ground calibrations are described in detail. Two C-flares are analyzed as examples for introducing the spectral fitting process. The first flare analysis shows the fit of a single spectrum of the C1-flare obtained during the peak phase. The other analysis example shows how to derive the time evolution of fluxes, emission measures (EM) and temperatures through the whole single C4 flare with the time resolution of 16 s. The preparatory data analysis procedures are also introduced in detail. These are required in spectral fittings of the data. A new solar monitor design equipped with a concentrator optics and a moderate size of field of view is also introduced.

Hybrid Modelling of Titan's Interaction with the Magnetosphere of Saturn

In this dissertation we study the interaction between Saturn's moon Titan and the magnetospheric plasma and magnetic field. The method of research is a three-dimensional computer simulation model, that is used to simulate this interaction. The simulation model used is a hybrid model. Hybrid models enable individual tracking or tracing of ions and also take into account the particle motion in the propagation of the electromagnetic fields. The hybrid model has been developed at the Finnish Meteorological Institute. This thesis gives a general description of the effects that the solar wind has on Earth and other planets of our solar system. Planetary satellites can also have similar interactions with the solar wind but also with the plasma flows of planetary magnetospheres. Titan is clearly the largest among the satellites of Saturn and also the only known satellite with a dense atmosphere. It is the atmosphere that makes Titan's plasma interaction with the magnetosphere of Saturn so unique. Nevertheless, comparisons with the plasma interactions of other solar system bodies are valuable. Detecting charged plasma particles requires in situ measurements obtainable through scientific spacecraft. The Cassini mission has been one of the most remarkable international efforts in space science. Since 2004 the measurements and images obtained from instruments onboard the Cassini spacecraft have increased the scientific knowledge of Saturn as well as its satellites and magnetosphere in a way no one was probably able to predict. The current level of science on Titan is practically unthinkable without the Cassini mission. Many of the observations by Cassini instrument teams have influenced this research both the direct measurements of Titan as well as observations of its plasma environment. The theoretical principles of the hybrid modelling approach are presented in connection to the broader context of plasma simulations. The developed hybrid model is described in detail: e.g. the way the equations of the hybrid model are solved is shown explicitly. Several simulation techniques, such as the grid structure and various boundary conditions, are discussed in detail as well. The testing and monitoring of simulation runs is presented as an essential routine when running sophisticated and complex models. Several significant improvements of the model, that are in preparation, are also discussed. A main part of this dissertation are four scientific articles based on the results of the Titan model. The Titan model developed during the course of the Ph.D. research has been shown to be an important tool to understand Titan's plasma interaction. One reason for this is that the structures of the magnetic field around Titan are very much three-dimensional. The simulation results give a general picture of the magnetic fields in the vicinity of Titan. The magnetic fine structure of Titan's wake as seen in the simulations seems connected to Alfvén waves an important wave mode in space plasmas. The particle escape from Titan is also a major part of these studies. Our simulations show a bending or turning of Titan's ionotail that we have shown to be a direct result of the basic principles in plasma physics. Furthermore, the ion flux from the magnetosphere of Saturn into Titan's upper atmosphere has been studied. The modelled ion flux has asymmetries that would likely have a large impact in the heating in different parts of Titan's upper atmosphere.

Hall thruster sequencer using Intel-8051 microcontroller for ion thrust measurement

Hall thrusters, such as Stationary Plasma Thruster (SPT), have been widely used on board modern satellites placed in geo-synchronows orbits for reasons such as orbit maintenance, repositioning and attitude control. In order to study the performance of the stationary plasma thruster, the thrust produced by it has been measured, using a thrust balance with strain gauge sensors under vacuum conditions, by activating the thruster. This activation of thruster has been carried out by switching ON and switching OFF of the necessary power supplies and control of other feed system such as the propellant flow in a particular sequence. Hitherto, these operations were done manually in the required sequence. This paper reports the attempt made to automate the sequential operation of the power supplies and the necessary control valves of the feed system using Intel 8051 microcontroller. This automation has made thrust measurements easier and more sophisticated.

Variations in the satellited chromosomes ofCicer arietinum Linn.

The diversity in the morphology of the SAT-chromosomes of C. arietinum in different roots are analysed in the context of similar variations observed in the different cells of one of the roots. Intergrades between the two pairs of chromosomes with normal satellites and those with tandem ones were observed in anaphases. The differences in the number as well as the size of the SAT-grains of replicated chromosomes indicate that non-reciprocal translocations between sister chromosomes may be of parts of SAT-grains and not of entire ones.

A new ELISA plate based microtiter well assay for mycobacterial topoisomerase I for the direct screening of enzyme inhibitory monoclonal antibody supernatants

Antigen specific monoclonal antibodies present in crude hybridoma supernatants are normally screened by ELISA on plates coated with the relevant antigen. Screening for inhibitory monoclonals to enzymes would require the evaluation of purified antibodies or antibody containing supernatants for their inhibition of enzyme activity in a separate assay. However, screening for inhibitory antibodies against DNA transacting enzymes such as topoisomerase I (topo I) cannot be done using hybridoma supernatants due to the presence of nucleases in tissue culture media containing foetal calf serum which degrade the DNA substrates upon addition. We have developed a simple and rapid screening procedure for the identification of clones that secrete inhibitory antibodies against mycobacterial topo I using 96 well ELISA microtiter plates. The principle of the method is the selective capture of monoclonal antibodies from crude hybridoma supernatants by topo I that is tethered to the plate through the use of plate-bound polyclonal anti-topo I antibodies. This step allows the nucleases present in the medium to be washed off leaving the inhibitor bound to the tethered enzyme. The inhibitory activity of the captured antibody is assessed by performing an in situ DNA relaxation assay by the addition of supercoiled DNA substrate directly to the microtiter well followed by the analysis of the reaction products by agarose gel electrophoresis. The validity of this method was confirmed by purification of the identified inhibitory antibody and its evaluation in a DNA relaxation assay. Elimination of all enzyme-inhibitory constituents of the culture medium from the well in which the inhibitory antibody is bound to the tethered enzyme may make this method broadly applicable to enzymes such as DNA gyrases, restriction enzymes and other DNA transaction enzymes. Further, the method is simple and avoids the need of prior antibody purification for testing its inhibitory activity. (C) 2010 Elsevier B.V. All rights reserved.