Transcriptomics profiling of Indian mustard (Brassica juncea) under arsenate stress identifies key candidate genes and regulatory pathways

© 2015 Srivastava, Srivastava, Sablok, Deshpande and Suprasanna. Arsenic (As) is a non-essential element, a groundwater pollutant, whose uptake by plants produces toxic effects. The use of As-contaminated groundwater for irrigation can affect the crop productivity. Realizing the importance of the Brassica juncea as a crop plant in terms of oil-yield, there is a need to unravel mechanistic details of response to As stress and identify key functional genes and pathways. In this research, we studied time-dependent (4–96 h) transcriptome changes in roots and shoots of B. juncea under arsenate [As(V)] stress using Agilent platform. Among the whole transcriptome profiled genes, a total of 1,285 genes showed significant change in expression pattern upon As(V) exposure. The differentially expressed genes were categorized to various signaling pathways including hormones (jasmonate, abscisic acid, auxin, and ethylene) and kinases. Significant effects were also noticed on genes related to sulfur, nitrogen, CHO, and lipid metabolisms along with photosynthesis. Biochemical assays were conducted using specific inhibitors of glutathione and jasmonate biosynthesis, and kinases. The inhibitor studies revealed interconnection among sulfur metabolism, jasmonate, and kinase signaling pathways. In addition, various transposons also constituted a part of the altered transcriptome. Lastly, we profiled a set of key functional up- and down-regulated genes using real-time RT-PCR, which could act as an early indicators of the As stress

On the variability and increasing trends of heat waves over India

Over India, heat waves occur during the summer months of April to June. A gridded daily temperature data set for the period, 1961–2013 has been analyzed to examine the variability and trends in heat waves over India. For identifying heat waves, the Excess Heat Factor (EHF) and 90th percentile of maximum temperatures were used. Over central and northwestern parts of the country, frequency, total duration and maximum duration of heat waves are increasing. Anomalous persistent high with anti-cyclonic flow, supplemented with clear skies and depleted soil moisture are primarily responsible for the occurrence of heat waves over India. Variability of heat waves over India is influenced by both the tropical Indian Ocean and central Pacific SST anomalies. The warming of the tropical Indian Ocean and more frequent El Nino events in future may further lead to more frequent and longer lasting heat waves over India

Development of a high resolution daily gridded temperature data set (1969-2005) for the Indian region

A high resolution daily gridded temperature data set for the Indian region was developed using temperature data of 395 quality controlled stations for the period 1969–2005. A modified version of the Shepard's angular distance weighting algorithm was used for interpolating the station temperature data into 1° latitude × 1° longitude grids. Using the cross validation, errors were estimated and found less than 0.5 °C. The data set was also compared with another high resolution data set and found comparable. Mean frequency of cold and heat waves, temperature anomalies associated with the monsoon breaks have been presented

Biomarkers and Surrogate Endpoints in Uveitis: The Impact of Quantitative Imaging

PURPOSE: Uveitis is a major cause of sight loss across the world. The reliable assessment of intraocular inflammation in uveitis (‘disease activity') is essential in order to score disease severity and response to treatment. In this review, we describe how ‘quantitative imaging', the approach of using automated analysis and measurement algorithms across both standard and emerging imaging modalities, can develop objective instrument-based measures of disease activity. METHODS: This is a narrative review based on searches of the current world literature using terms related to quantitative imaging techniques in uveitis, supplemented by clinical trial registry data, and expert knowledge of surrogate endpoints and outcome measures in ophthalmology. RESULTS: Current measures of disease activity are largely based on subjective clinical estimation, and are relatively insensitive, with poor discrimination and reliability. The development of quantitative imaging in uveitis is most established in the use of optical coherence tomographic (OCT) measurement of central macular thickness (CMT) to measure severity of macular edema (ME). The transformative effect of CMT in clinical assessment of patients with ME provides a paradigm for the development and impact of other forms of quantitative imaging. Quantitative imaging approaches are now being developed and validated for other key inflammatory parameters such as anterior chamber cells, vitreous haze, retinovascular leakage, and chorioretinal infiltrates. CONCLUSIONS: As new forms of quantitative imaging in uveitis are proposed, the uveitis community will need to evaluate these tools against the current subjective clinical estimates and reach a new consensus for how disease activity in uveitis should be measured. The development, validation, and adoption of sensitive and discriminatory measures of disease activity is an unmet need that has the potential to transform both drug development and routine clinical care for the patient with uveitis

Characterisation of atmospheric aerosol by SEM-EDX and Ion-chromatography techniques for eastern Indo-Gangetic plain location, Varanasi, India

Atmospheric aerosol consists of both natural and anthropogenic origin. Studies have shown that continuous exposure to these particles is associated with a high percentage of death from respiratory and cardiovascular disease. In the present study, we have first time used both SEM-EDX analysis as well as chemical analysis to understand the differences in morphology and elemental composition of aerosols sample from a suburban clean and green area of Banaras Hindu University campus and some much polluted urban areas of the Varanasi city situated in the eastern Indo-Gangetic plain. The analysis was done by using scanning electron microscope (SEM) coupled with energy dispersive X-ray microanalyzer (EDX) and ionchromatography (IC). Analyses show that C, Ca, Na, S, Si, Al have dominated the sample

Evaluation of Patient Radiation Doses in Skull Radiography

Purpose: Exposures to medical ionizing radiations elevate the risk of stochastic effects such as cancer in exposed individuals. It is of utmost importance to monitor the radiation doses delivered to patients and their optimization to reduce the associated radiation risks without limiting the diagnostic information. Methods: Entrance surface air kerma (ESAK) in a total of 64 adult patients in diagnostic digital Xray examinations were calculated and effective doses were estimated as per International Atomic Energy Agency (IAEA). Results: Median ESAK (mGy) and associated effective doses obtained were skull PA (0.45mGy, 0.005mSv) and skull Lat (0.25mGy, 0.003mSv). Results were compared with UK diagnostic reference levels and studies in India.Conclusion: The comparison revealed that the calculated ESAK and effective dose values wereless than the published literature. ESAK values reported in this study could further contribute toestablishing LDRLs

Ab-initio study of structure and dynamics properties of crystalline ice

We investigated the structural and dynamical properties of a tetrahedrally coordinated crystalline ice from first principles based on density functional theory within the generalized gradient approximation with the projected augmented wave method. First, we report the structural behaviour of ice at finite temperatures based on the analysis of radial distribution functions obtained by molecular dynamics simulations. The results show how the ordering of the hydrogen bonding breaks down in the tetrahedral network of ice with entropy increase in agreement with the neutron diffraction data. We also calculated the phonon spectra of ice in a 3x1x1 supercell by using the direct method. So far, due to the direct method used in this calculation, the phonon spectra is obtained without taking into account the effect of polarization arising from dipole-dipole interactions of water molecules which is expected to yield the splitting of longitudinal and transverse optic modes at the Gamma-point. The calculated longitudinal acoustic velocities from the initial slopes of the acoustic mode is in a reasonable agreement with the neutron scatering data. The analysis of the vibrational density of states shows the existence of a boson peak at low energy of translational region a characteristic common to amorphous systems.Comment: International symposium on structure and dynamics of heterogeneous system SDHS'0

Inferring aerosol types over the Indo-Gangetic Basin from ground based sunphotometer measurements

A discrimination of aerosol types over the Indo-Gangetic Basin (IGB) region during pre-monsoon period was made using multi-year ground based sun/sky radiometer measured aerosol products associated with the size of aerosols and radiation absorptivity. High dust enriched aerosols (i.e. polluted dust, PD) were found to contribute more over the central IGB station at Kanpur (KNP, 62) as compared to the eastern IGB station at Gandhi College (GC, 31) whereas vice-versa was observed for polluted continental (PC) aerosols, which contain high anthropogenic and less dust aerosols. Contributions of carbonaceous particles having high absorbing (mostly black carbon, MBC) and low absorbing (mostly organic carbon, MOC) aerosols were found to be 11 and 10, respectively at GC, which was ~. 46 and 62 higher than the observed contributions at KNP; however, very less contribution of non-absorbing (NA) aerosols was observed only at GC (2). Variability in aerosol types together with single scattering albedo (SSA) at both the stations were also studied during the forenoon (FN) and afternoon (AN) hour, which suggests their strong association with emission sources. Results were well substantiated with the air mass back-trajectories and the fire products. Spectral information of SSA for each aerosol type discriminates the dominance of natural dust (SSA increases with increasing wavelength) with anthropogenic aerosols (SSA decreases with increasing wavelength) at both the locations. The estimated absorption à ngström exponent (AAE) values suggest relative dominance of absorbing type aerosols over the central part of IGB (due to dominant dust absorption) as compared to the eastern part during pre-monsoon period

Aerosol optical depth, ozone and water vapor measurements over Gadanki, a tropical station in peninsular India

This paper reports the results of a study related to the optical and physical characteristics of columnar aerosols and variation in total column ozone (TCO) and precipitable water content (PWC) over Gadanki (13.45°N, 79.18°E), a tropical station in peninsular India, for the first time, using MICROTOPS-II (Microprocessor-based Total Ozone Portable Spectrometer), comprising of both sun photometer and ozonometer. Results show wavelength dependence of AOD, having mean value of �0.4 (± 0.09) at 500 nm optical channel. Daily mean aerosol size spectra shows, most of the time, power-law distribution. However, its diurnal variations show significant changes in aerosol size spectra modulated by a combination of both power-law and bi-modal distributions. To characterize AOD, the Angstrom parameters (i.e., a and β) were used. The day-to-day variations in TCO were found to be in fair agreement with that derived from TOMS satellite data for all the experimental days, having mean observed value of ~253 (± 8) DU over the station. Interestingly, an inverse relationship between TCO and AOD or PWC was observed over the station, on some times of the day, which could be attributed to the mixing of significant fraction of ozone with aerosol and water vapor-rich air mass. However, a significant positive correlation was observed between AOD and PWC

Phylogenetic diversity analysis of Trichoderma species based on internal transcribed spacer (ITS) marker

The phylogeny of Trichoderma and the phylogenetic relationships of its species was investigated by maximum parsimony analysis and distance analysis of DNA sequences from multiple genetic loci 18S rDNA sequence analysis suggests that the genus Trichoderma evolved at the same time as Hypomyces and Fusarium and thus about 110 Myr ago 28S rDNA sequence analysis shows that the genus Trichoderma is part of a monophyletic branch within the Hypocreaceae. Most isolates of the genus Trichoderma were found to act as mycoparasites of many economically important aerial and soil-borne plant pathogens. Trichoderma has attained importance as a substitute for chemical pesticides and hence an attempt was intended to corroborate the positive relatedness of molecular and morphological characters. Two fungal strains, Trichoderma koningii Tk-5201/CSAU and Trichoderma virens Tvi-4177/CSAU were isolated from a soil sample collected from CSA Farm, Kanpur district of Uttar Pradesh, India. The universal primers (internal transcribed spacer, ITS) were used for the amplification of 18S rRNA gene fragment and strains were thus characterized with the help of ITS marker. It is proposed that the identified strains T. koningii Tk-5201/CSAU and T. virens Tvi-4177/CSAU be assigned as the type strains of a species of genus Trichoderma based on phylogenetic tree analysis together with the 18S rRNA gene sequence search in Ribosomal Database Project, small subunit rRNA and large subunit rRNA databases. The sequence was deposited in GenBank with the accession numbers KC800923 and KC800924, respectively. Thus an integrated approach of morphological and molecular markers can be employed to identify a superior strain of Trichoderma for its commercial exploitation.Keywords: 18S ribosomal RNA gene, Trichoderma, phylogenetic analysis, internal transcribed spacer (ITS), DNA sequencing, GenBankAfrican Journal of Biotechnology, Vol. 13(3), pp. 449-455, 15 January, 201