Factors regulating the transcription of eukaryotic protein coding genes and their mechanism of action- a review

Protein factors play a crucial role in establishing gene-specific and cell-specific regulation of the process of transcription. These include general transcription factors which recognize TATA and CCAAT boxes and which form components of the RNA polymerase II system. Specific transcription factors interact with characteristic promoter elements of individual genes. Some of the examples are SP1, glucocorticoid receptor, GCN4, GAL4 and many others. Transcription factors have a DNA binding domain demarcated from the transcription activation domain. Some factors may have an additional ligand (small molecule) binding domain. Typical structural features such as helix-turn-helix motif, zinc finger and leucine zipper have been recognized in the DNA binding domain of the transcription factors. The acidic domain of the protein factors is involved in the transcription activation process. It appears that activation is the result of the combined action of several regulatory proteins binding at different regions of the promoter. Interaction between proteins bound to DNA but seperated by long stretches of nucleotides is facilitated by DNA bending. Functional specificity as well as diversity are feasible with a limited number of transcription factors through alterations in the architecture of interaction between a group of proteins bound to promoter elements

Genetic analysis of foot-and-mouth disease virus serotype A of Indian origin and detection of positive selection and recombination in leader protease- and capsid-coding regions

The leader protease (Lpro) and capsid-coding sequences (P1) constitute approximately 3 kb of the foot-and-mouth disease virus (FMDV). We studied the phylogenetic relationship of 46 FMDV serotype A isolates of Indian origin collected during the period 1968-2005 and also eight vaccine strains using the neighbour-joining tree and Bayesian tree methods. The viruses were categorized under three major groups-Asian, Euro-South American and European. The Indian isolates formed a distinct genetic group among the Asian isolates. The Indian isolates were further classified into different genetic subgroups ( < 5% divergence). Post-1995 isolates were divided into two subgroups while a few isolates which originated in the year 2005 from Andhra Pradesh formed a separate group. These isolates were closely related to the isolates of the 1970s. The FMDV isolates seem to undergo reverse mutation or convergent evolution wherein sequences identical to the ancestors are present in the isolates in circulation. The eight vaccine strains included in the study were not related to each other and belonged to different genetic groups. Recombination was detected in the Lpro region in one isolate (A IND 20/82) and in the VP1 coding 1D region in another isolate (A RAJ 21/96). Positive selection was identified at aa positions 23 in the Lpro (P < 0.05; 0.046∗) and at aa 171 in the capsid protein VP1 (P < 0.01; 0.003∗∗)

Stripped Spiral Galaxies as Promising Targets for the Determination of the Cepheid distance to the Virgo Cluster

The measurement of precise galaxy distances by Cepheid observations out to the distance of the Virgo cluster is important for the determination of the Hubble constant ($H_0$). The Virgo cluster is thereby often used as an important stepping stone. The first HST measurement of the distance of a Virgo galaxy (M100) using Cepheid variables provided a value for $H_0=80(\pm 17)$ km/s/Mpc (Freedman et al. 1994). This measurement was preceeded by a ground based study of the Virgo spiral NGC4571 (Pierce et al. 1994) formally providing $H_0= 87\pm7$ km/s/Mpc. These determinations rely on the accuracy with which the position of this observed spiral galaxy can be located with respect to the Virgo cluster center. This uncertainty introduces a major error in the determination of $H_0$, together with the uncertainty in the adopted Virgo infall velocity of the Local Group. Here we propose the use of spiral galaxies which show clear signs of being stripped off their interstellar medium by the intracluster gas of the Virgo cluster as targets for the Cepheid distance measurements. We show that the stripping process and the knowledge of the intracluster gas distribution from ROSAT X-ray observations allow us to locate these galaxies with an at least three times higher precision with respect to M87 than in the case of other spirals like M100. The X-ray observations further imply that M87 is well centered within the intracluster gas halo of the Virgo cluster and that M86 is associated with a group of galaxies and a larger dark matter halo. The combination of these informations could enable us to locate the two stripped spiral galaxies quite precisely within the Virgo cluster and could greatly improve the determination of the Virgo cluster distance.Comment: 21 pages, Latex(aaspp.sty), including 6 figures, accepted for publication in ApJL (shortened abstract:

Chandra Observations of Gas Stripping in the Elliptical Galaxy NGC 4552 in the Virgo Cluster

We use a 54.4 ks Chandra observation to study ram-pressure stripping in NGC4552 (M89), an elliptical galaxy in the Virgo Cluster. Chandra images in the 0.5-2 keV band show a sharp leading edge in the surface brightness 3.1 kpc north of the galaxy center, a cool (kT =0.51^{+0.09}_{-0.06} keV) tail with mean density n_e ~5.4 +/- 1.7 x 10^{-3} cm^{-3} extending ~10 kpc to the south of the galaxy, and two 3-4 kpc horns of emission extending southward away from the leading edge. These are all features characteristic of supersonic ram-pressure stripping of galaxy gas, due to NGC4552's motion through the surrounding Virgo ICM. Fitting the surface brightness profile and spectra across the leading edge, we find the galaxy gas inside the edge is cooler (kT = 0.43^{+0.03}_{-0.02} keV) and denser (n_e ~ 0.010 cm^{-3}) than the surrounding Virgo ICM (kT = 2.2^{+0.7}_{-0.4} keV and n_e = 3.0 +/- 0.3 x 10^{-4} cm^{-3}). The resulting pressure ratio between the free-streaming ICM and cluster gas at the stagnation point is ~7.6^{+3.4}_{-2.0} for galaxy gas metallicities of 0.5^{+0.5}_{-0.3} Zsolar, which suggests that NGC4552 is moving supersonically through the cluster with a velocity v ~ 1680^{+390}_{-220} km/s (Mach 2.2^{+0.5}_{-0.3}) at an angle xi ~ 35 +/- 7 degrees towards us with respect to the plane of the sky.Comment: 31 pages, 12 figures, ApJ, in press; paper split into 2 parts, Paper I(sec 1-3) here, added figs and discussion to conform to published version; Paper II (sec. 4) in astro-ph/060440

Metal-coated magnetic nanoparticles for surface enhanced Raman scattering studies

We report the optimization and usage of surfactantless, water dispersible Ag and Au-coated γ–Fe2O3 nanoparticles for applications in Surface-enhanced Raman Scattering (SERS). These nanoparticles, with plasmonic as well as super paramagnetic properties exhibit Raman enhancement factors of the order of 106 (105) for Ag (Au) coating, which are on par with the conventional Ag and Au nanoparticles. Raman markers like 2-naphthalenethiol, rhodamine-B and rhodamine-6G have been adsorbed to these nanoparticles and tested for nonresonant SERS at low concentrations. Further, to confirm the robustness of Ag-coated nanoparticles, we have performed temperature-dependent SERS in the temperature range of 77–473 K. The adsorbed molecules exhibit stable SERS spectra except at temperatures >323 K, where the thermal desorption of test molecule (naphthalenethiol) were evident. The magnetic properties of these nanoparticles combined with SERS provide a wide range of applications

Evolution of Multiphase Hot Interstellar Medium in Elliptical Galaxies

We present the results of a variety of simulations concerning the evolution of multiphase (inhomogeneous) hot interstellar medium (ISM) in elliptical galaxies. We assume the gases ejected from stars do not mix globally with the circumferential gas. The ejected gas components evolve separately according to their birth time, position, and origin. We consider cases where supernova remnants (SNRs) mix with local ISM. The components with high metal abundance and/or high density cool and drop out of the hot ISM gas faster than the other components because of their high metal abundance and/or density. This makes the average metal abundance of the hot ISM low. Furthermore, since the metal abundance of mass-loss gas decreases with radius, gas inflow from outer region makes the average metal abundance of the hot ISM smaller than that of mass-loss gas in the inner region. As gas ejection rate of stellar system decreases, mass fraction of mass-loss gas ejected at outer region increases in a galaxy. If the mixing of SNRs is ineffective, our model predicts that observed [Si/Fe] and [Mg/Fe] should decrease towards the galactic center because of strong iron emission by SNRs. In the outer region, where the cooling of time of the ISM is long, the selective cooling is ineffective and most of gas components remain hot. Thus, the metal abundance of the ISM in this region directly reflects that of the gas ejected from stars. Our model shows that supernovae are not effective heating sources in the inner region of elliptical galaxies, because most of the energy released by them radiates. Therefore, cooling flow is established even if the supernova rate is high. Mixing of SNRs with ambient ISM makes the energy transfer between supernova explosion and ambient ISM more effective.Comment: 21 pages (AASTeX), 14 figures, accepted for publication in The Astrophysical Journa

Fused Deposition of Ceramics: Progress Towards a Robust and Controlled Process for Commercialization

The feasibility of using the Fused Deposition ofCeramics (FDC) process to rapidly fabricate functional quality advanced ceramic components has been demonstratedl - 5 . This direct manufacturing technique, by eliminating the need for costly tooling, dramatically reduces functional prototype development time. This makes it suitable for small quantity production runs and complex parts. The move from 'feasibility" to a robust, reliable commercial fabrication tool requires that every aspect ofthe manufacturing be understood and brought under control. An overview ofthe five basic process steps in FDC: batch compounding, filament fabrication, fused deposition, binder burnout and sintering will be presented in light ofthis drive toward a robust process. Tools such as Statistical Process Control and Experimental Design techniques are being used to monitor, improve, and stabilize each step and sub-process. Hardware and software modifications have been made to the FD machine to effect the required changes. This paper will identify the remaining technical barriers to commercialization and our progress in addressing these issues.Mechanical Engineerin

Dust Streamers in the Virgo Galaxy M86 from Ram Pressure Stripping of its Companion VCC 882

The giant elliptical galaxy M86 in Virgo has a ~28 kpc long dust trail inside its optical halo that points toward the nucleated dwarf elliptical galaxy, VCC 882. The trail seems to be stripped material from the dwarf. Extinction measurements suggest that the ratio of the total gas mass in the trail to the blue luminosity of the dwarf is about unity, which is comparable to such ratios in dwarf irregular galaxies. The ram pressure experienced by the dwarf galaxy in the hot gaseous halo of M86 was comparable to the internal gravitational binding energy density of the presumed former gas disk in VCC 882. Published numerical models of this case are consistent with the overall trail-like morphology observed here. Three concentrations in the trail may be evidence for the predicted periodicity of the mass loss. The evaporation time of the trail is comparable to the trail age obtained from the relative speed of the galaxies and the trail length. Thus the trail could be continuously formed from stripped replenished gas if the VCC 882 orbit is bound. However, the high gas mass and the low expected replenishment rate suggest that this is only the first stripping event. Implications for the origin of nucleated dwarf ellipticals are briefly discussed.Comment: 22 pages, 7 figures, Astronomical Journal, August 2000, in pres

ROSAT Evidence for Intrinsic Oxygen Absorption in Cooling Flow Galaxies and Groups

Using spatially resolved, deprojected ROSAT PSPC spectra of 10 of the brightest cooling flow galaxies and groups with low Galactic column densities we have detected intrinsic absorption over energies ~0.4-0.8 keV in half of the sample. Since no intrinsic absorption is indicated for energies below ~0.4 keV, the most reasonable model for the absorber is collisionally ionized gas at temperatures T=10^{5-6} K with most of the absorption arising from ionized states of oxygen but with a significant contribution from carbon and nitrogen. The soft X-ray emission of this warm gas can explain the sub-Galactic column densities of cold gas inferred within the central regions of most of the systems. Attributing the absorption to ionized gas reconciles the large columns of cold H and He inferred from EINSTEIN and ASCA with the lack of such columns inferred from ROSAT. Within the central ~10-20 kpc, where the constraints are most secure, the estimated mass of the ionized absorber is consistent with most (perhaps all) of the matter deposited by a cooling flow over the lifetime of the flow. Since the warm absorber produces no significant H or He absorption the large absorber masses are consistent with the negligible atomic and molecular H inferred from HI and CO observations of cooling flows. It is also found that if T > ~2x10^5 K then the optical and UV emission implied by the warm gas does not violate published constraints. Finally, we discuss how the prediction of warm ionized gas as the product of mass drop-out in these and other cooling flows can be verified with new CHANDRA and XMM observations. (Abridged)Comment: 17 pages (5 figures), Accepted for publication in ApJ, expanded discussion of multiphase spectral models, theoretical implications of warm gas in cooling flows, and the statistical significance of the oxygen absorptio

Working Group Report: Neutrino and Astroparticle Physics

This is the report of neutrino and astroparticle physics working group at WHEPP-8. We present the discussions carried out during the workshop on selected topics in the above fields and also indicate progress made subsequently. The neutrino physics subgroup studied the possibilites of constraining neutrino masses, mixing and CPT violation in lepton sector from future experiments. Neutrino mass models in the context of abelian horizontal symmetries, warped extra dimensions and in presence of triplet Higgs were studied. Effect of threshold corrections on radiative magnification of mixing angles was investigated. The astroparticle physics subgroup focused on how various particle physics inputs affect the CMBR fluctuation spectrum, and on brane cosmology. This report also contains an introduction on how to use the publicly available code CMBFAST to calculate the CMBR fluctuations.Comment: Prepared for the 8th Workshop on High-Energy Physics Phenomenology (WHEPP-8), IIT Mumbai, India, 5-16 Jan 200