A search for the 55 MHz OH line

The OH molecule, found abundantly in the Milky Way, has four transitions at the ground state rotational level(J = 3/2) at cm wavelengths. These are E1 transitions between the F+ and F- hyperfine levels of the Lambda doublet of the J=3/2 state. There are also forbidden M1 transitions between the hyperfine levels within each of the doublet states occuring at frequencies 53.171 MHz and 55.128 MHz. These are extremely weak and hence difficult to detect. However there is a possibility that the level populations giving rise to these lines are inverted under special conditions, in which case it may be possible to detect them through their maser emission. We describe the observational diagnostics for determining when the hyperfine levels are inverted, and identify a region near W44 where these conditions are satisfied. A high-velocity-resolution search for these hyperfine OH lines using the low frequency feeds on four antennas of the GMRT and the new GMRT Software Backend(GSB) was performed on this target near W44. We place a 3-sigma upper limit of ~17.3 Jy (at 1 km/s velocity resolution) for the 55 MHz line from this region. This corresponds to an upper limit of 3 X 10^8 for the amplification of the Galactic synchrotron emission providing the background.Comment: 5 pages, 4 figures, accepted for publication in MNRAS. The definitive version is available at www.blackwell-synergy.co

Inquiries into Wheat Streak Mosaic Virus and Other WSM Associated Viruses

Wheat Streak Mosaic WSM) is a complex disease found to cause severe impact on wheat yield. Wheat streak mosaic virus (WSMV Triticum Mosaic Virus (TMV) and Wheat Mosaic Virus (WMOV) are all transmitted by Aceria tosichella, the wheat cun mite, and have been reported as the viruses associated with WSM. There is a research project on the genetic composition of the associated viruses as well as determining any novel viruses that may be involved in the disease. The process has begun with the virus assessment of neid samples by RT-PCR and sanger Sequencing in a different study, the potential of a common Insect in wheat fields. Rhopalosiphum padi, the Bird cherry oat aphid, to be a vector for WSMV was Investigated. R. Daar was found to be not a vector of WSMV through RT-PCR. The other proiect screened some wid-relative wheat plants for WSMV resistance Various lines of Aeglos tauschii, a landrace wheat, were tested for viral resistance by assessing the viral copy number by RT-PCR. The Initial result has demonstrated that one of the four selected lines may have promising tolerance The preliminary tests performed for each Inquiry provides Insight to Improving the respective experiment design for further understanding of how concerned parties such as farmers may better combat the disease

Multiplex Chromosomal Exome Sequencing Accelerates Identification of ENU-Induced Mutations in the Mouse

Forward genetic screens in Mus musculus have proved powerfully informative by revealing unsuspected mechanisms governing basic biological processes. This approach uses potent chemical mutagens, such as N-ethyl-N-nitrosourea (ENU), to randomly induce mutations in mice, which are then bred and phenotypically screened to identify lines that disrupt a specific biological process of interest. Although identifying a mutation using the rich resources of mouse genetics is straightforward, it is unfortunately neither fast nor cheap. Here we show that detecting newly induced causal variants in a forward genetic screen can be accelerated dramatically using a methodology that combines multiplex chromosome-specific exome capture, next-generation sequencing, rapid mapping, sequence annotation, and variation filtering. The key innovation of our method is multiplex capture and sequence that allows the simultaneous survey of both mutant, parental, and background strains in a single experiment. By comparing variants identified in mutant offspring with those found in dbSNP, the unmutagenized background strains, and parental lines, induced causative mutations can be distinguished immediately from preexisting variation or experimental artifact. Here we demonstrate this approach to find the causative mutations induced in four novel ENU lines identified from a recent ENU screen. In all four cases, after applying our method, we found six or fewer putative mutations (and sometimes only a single one). Determining the causative variant was then easily achieved through standard segregation approaches. We have developed this process into a community resource that will speed up individual labs’ ability to identify the genetic lesion in mutant mouse lines; all of our reagents and software tools are open source and available to the broader scientific community

Silencing of the XAF1 gene by promoter hypermethylation in cancer cells and reactivation to TRAIL-sensitization by IFN-β

BACKGROUND: XIAP-associated factor 1 (XAF1) is a putative tumor suppressor that exerts its proapoptotic effects through both caspase-dependent and – independent means. Loss of XAF1 expression through promoter methylation has been implicated in the process of tumorigenesis in a variety of cancers. In this report, we investigated the role of basal xaf1 promoter methylation in xaf1 expression and assessed the responsiveness of cancer cell lines to XAF1 induction by IFN-β. METHODS: We used the conventional bisulfite DNA modification and sequencing method to determine the methylation status in the CpG sites of xaf1 promoter in glioblastoma (SF539, SF295), neuroblastoma (SK-N-AS) and cervical carcinoma (HeLa) cells. We analysed the status and incidence of basal xaf1 promoter methylation in xaf1 expression in non-treated cells as well as under a short or long exposure to IFN-β. Stable XAF1 glioblastoma knock-down cell lines were established to characterize the direct implication of XAF1 in IFN-β-mediated sensitization to TRAIL-induced cell death. RESULTS: We found a strong variability in xaf1 promoter methylation profile and responsiveness to IFN-β across the four cancer cell lines studied. At the basal level, aberrant promoter methylation was linked to xaf1 gene silencing. After a short exposure, the IFN-β-mediated reactivation of xaf1 gene expression was related to the degree of basal promoter methylation. However, in spite of continued promoter hypermethylation, we find that IFN-β induced a transient xaf1 expression, that in turn, was followed by promoter demethylation upon a prolonged exposure. Importantly, we demonstrated for the first time that IFN-β-mediated reactivation of endogenous XAF1 plays a critical role in TRAIL-induced cell death since XAF1 knock-down cell lines completely lost their IFN-β-mediated TRAIL sensitivity. CONCLUSION: Together, these results suggest that promoter demethylation is not the sole factor determining xaf1 gene induction under IFN-β treatment. Furthermore, our study provides evidence that XAF1 is a crucial interferon-stimulated gene (ISG) mediator of IFN-induced sensitization to TRAIL in cancer

Determinants of barley grain yield in drought-prone Mediterranean environments

The determinants of barley grain yield in drought-prone Mediterranean environments have been studied in the Nure x Tremois (NT) population. A large set of yield and other morpho-physiological data were recorded in 118 doubled haploid (DH) lines of the population, in multi-environment field trials (18 site-year combination). Agrometeorological variables have been recorded and calculated at each site too. Four main periods of barley development were considered, vegetative, reproductive early and late grain filling phases, to dissect the effect on yield traits of the growth phases. Relationships between agrometeorological variables, grain yield (GY) and its main components (GN and GW) were also investigated by correlation. Results firstly gave a clear indication of the involvement of water consumption in determining GY and GW (r2=0.616, P=0.007 and r2=0.703, P=0.005, respectively) calculated from sowing to the early grain filling period, while GN showed its highest correlation with the total photothermal quotient (PQ) calculated for the same period (r2=0.646, P=0.013). With the only exception of total PQ calculated during the vegetative period, all significant correlations with GY were associated to water-dependent agrometeorological parameters. As a second result, the NT segregating population allowed us to weight the amount of interaction due to genotypes over environments or to environments in relation to genotypes by a GGE analysis; 47.67% of G+GE sum of squares was explained by the first two principal components. Then, the introduction of genomic information at major barley genes regulating the length of growth cycle allowed us to explain patterns of adaptation of different groups of NT lines according to the variants (alleles) harbored at venalization (Vrn-H1) in combination with earliness (Eam6) genes. The superiority of the lines carrying the Nure allele at Eam6 was confirmed by factorial ANOVA testing the four possible haplotypes obtained combining alternative alleles at Eam6 and Vrn-H1. Maximum yield potential and differentials among the NT genotypes was finally explored through Finlay-Wilkinson model to interpret grain yield of NT genotypes together with yield adaptability (Ya), as the regression coefficient bi; Ya ranged from 0.71 for NT77 to 1.20 for NT19. Lines simply harboring the Nure variants at the two genes behaved as highest yielding (3.04 t ha-1), and showed the highest yield adaptability (bi=1.05). The present study constitutes a starting point towards the introduction of genomic variables in agronomic models for barley grain yield in Mediterranean environments

Determinants of barley grain yield in drought-prone Mediterranean environments

The determinants of barley grain yield in drought-prone Mediterranean environments have been studied in the Nure x Tremois (NT) population. A large set of yield and other morpho-physiological data were recorded in 118 doubled haploid (DH) lines of the population, in multi-environment field trials (18 site-year combination). Agrometeorological variables have been recorded and calculated at each site too. Four main periods of barley development were considered, vegetative, reproductive early and late grain filling phases, to dissect the effect on yield traits of the growth phases. Relationships between agrometeorological variables, grain yield (GY) and its main components (GN and GW) were also investigated by correlation. Results firstly gave a clear indication of the involvement of water consumption in determining GY and GW (r2=0.616, P=0.007 and r2=0.703, P=0.005, respectively) calculated from sowing to the early grain filling period, while GN showed its highest correlation with the total photothermal quotient (PQ) calculated for the same period (r2=0.646, P=0.013). With the only exception of total PQ calculated during the vegetative period, all significant correlations with GY were associated to water-dependent agrometeorological parameters. As a second result, the NT segregating population allowed us to weight the amount of interaction due to genotypes over environments or to environments in relation to genotypes by a GGE analysis; 47.67% of G+GE sum of squares was explained by the first two principal components. Then, the introduction of genomic information at major barley genes regulating the length of growth cycle allowed us to explain patterns of adaptation of different groups of NT lines according to the variants (alleles) harbored at venalization (Vrn-H1) in combination with earliness (Eam6) genes. The superiority of the lines carrying the Nure allele at Eam6 was confirmed by factorial ANOVA testing the four possible haplotypes obtained combining alternative alleles at Eam6 and Vrn-H1. Maximum yield potential and differentials among the NT genotypes was finally explored through Finlay-Wilkinson model to interpret grain yield of NT genotypes together with yield adaptability (Ya), as the regression coefficient bi; Ya ranged from 0.71 for NT77 to 1.20 for NT19. Lines simply harboring the Nure variants at the two genes behaved as highest yielding (3.04 t ha\u20131), and showed the highest yield adaptability (bi=1.05). The present study constitutes a starting point towards the introduction of genomic variables in agronomic models for barley grain yield in Mediterranean environments

A search for soft X-ray emission associated with prominent high-velocity-cloud complexes

We correlate the ROSAT 1/4 keV all-sky survey with the Leiden/Dwingeloo HI survey, looking for soft X-ray signatures of prominent high-velocity-cloud (HVC) complexes. We study the transfer of 1/4 keV photons through the interstellar medium in order to distinguish variations in the soft X-ray background (SXRB) intensity caused by photoelectric absorption effects from those due to excess X-ray emission. The X-ray data are modelled as a combination of emission from the Local Hot Bubble (LHB) and emission from a distant plasma in the galactic halo and extragalactic sources. The X-ray radiation intensity of the galactic halo and extragalactic X-ray background is modulated by the photoelectric absorption of the intervening galactic interstellar matter. We show that large- and small-scale intensity variations of the 1/4 keV SXRB are caused by photoelectric absorption which is predominantly traced by the total N(HI) distribution. The extensive coverage of the two surveys supports evidence for a hot, X-ray emitting corona. We show that this leads to a good representation of the SXRB observations. For four large areas on the sky, we search for regions where the modelled and observed X-ray emission differ. We find that there is excess X-ray emission towards regions near HVC complexes C, D, and GCN. We suggest that the excess X-ray emission is positionally correlated with the high-velocity clouds. Some lines of sight towards HVCs also pass through significant amounts of intermediate-velocity gas, so we cannot constrain the possible role played by IVC gas in these directions of HVC and IVC overlap, in determining the X-ray excesses.Comment: 16 pages, 8 figures, accepted for publication in Astronomy & Astrophysics main journa

Wavelength Accuracy of the Keck HIRES Spectrograph and Measuring Changes in the Fine Structure Constant

We report on an attempt to accurately wavelength calibrate four nights of data taken with the Keck HIRES spectrograph on QSO PHL957, for the purpose of determining whether the fine structure constant was different in the past. Using new software and techniques, we measured the redshifts of various Ni II, Fe II, Si II, etc. lines in a damped Ly-alpha system at z=2.309. Roughly half the data was taken through the Keck iodine cell which contains thousands of well calibrated iodine lines. Using these iodine exposures to calibrate the normal Th-Ar Keck data pipeline output we found absolute wavelength offsets of 500 m/s to 1000 m/s with drifts of more than 500 m/s over a single night, and drifts of nearly 2000 m/s over several nights. These offsets correspond to an absolute redshift of uncertainty of about Delta z=10^{-5} (Delta lambda= 0.02 Ang), with daily drifts of around Delta z=5x10^{-6} (Delta lambda =0.01 Ang), and multiday drifts of nearly Delta z=2x10^{-5} (0.04 Ang). The causes of the wavelength offsets are not known, but since claimed shifts in the fine structure constant would result in velocity shifts of less than 100 m/s, this level of systematic uncertainty makes may make it difficult to use Keck HIRES data to constrain the change in the fine structure constant. Using our calibrated data, we applied both our own fitting software and standard fitting software to measure (Delta alpha)/alpha, but discovered that we could obtain results ranging from significant detection of either sign, to strong null limits, depending upon which sets of lines and which fitting method was used. We thus speculate that the discrepant results on (Delta alpha)/alpha reported in the literature may be due to random fluctuations coming from under-estimated systematic errors in wavelength calibration and fitting procedure.Comment: 19 pages, 10 figures, to appear in ApJ, Dec 2009 Many corrections and changes made, some new figure