Global analysis of mRNA half-lives and de novo transcription in a dinoflagellate, Karenia brevis

Dinoflagellates possess many physiological processes that appear to be under post-transcriptional control. However, the extent to which their genes are regulated post-transcriptionally remains unresolved. To gain insight into the roles of differential mRNA stability and de novo transcription in dinoflagellates, we biosynthetically labeled RNA with 4-thiouracil to isolate newly transcribed and pre-existing RNA pools in Karenia brevis. These isolated fractions were then used for analysis of global mRNA stability and de novo transcription by hybridization to a K. brevis microarray. Global K. brevis mRNA half-lives were calculated from the ratio of newly transcribed to pre-existing RNA for 7086 array features using the online software HALO (Half-life Organizer). Overall, mRNA half-lives were substantially longer than reported in other organisms studied at the global level, ranging from 42 minutes to greater than 144 h, with a median of 33 hours. Consistent with well-documented trends observed in other organisms, housekeeping processes, including energy metabolism and transport, were significantly enriched in the most highly stable messages. Shorter-lived transcripts included a higher proportion of transcriptional regulation, stress response, and other response/regulatory processes. One such family of proteins involved in post-transcriptional regulation in chloroplasts and mitochondria, the pentatricopeptide repeat (PPR) proteins, had dramatically shorter half-lives when compared to the arrayed transcriptome. As transcript abundances for PPR proteins were previously observed to rapidly increase in response to nutrient addition, we queried the newly synthesized RNA pools at 1 and 4 h following nitrate addition to N-depleted cultures. Transcriptome-wide there was little evidence of increases in the rate of de novo transcription during the first 4 h, relative to that in N-depleted cells, and no evidence for increased PPR protein transcription. These results lend support to the growing consensus of post-transcriptional control of gene expression in dinoflagellates.

Changes in the hydrometeorological regime in the Pacific Southwest [abstract]

EXTRACT (SEE PDF FOR FULL ABSTRACT): Selected hydrometeorological (HM) data for the Pacific Northwest and atmospheric and North Pacific sea-surface temperature (SST) data are examined for three successive periods that are subsets of the historical record to estimate if their characteristics have changed.

Effects of turbulent reynolds number on the displacement speed statistics in the thin reaction zones regime of turbulent premixed combustion

The effects of turbulent Reynolds number on the statistical behaviour of the displacement speed have been studied using three-dimensional Direct Numerical Simulation of statistically planar turbulent premixed flames. The probability of finding negative values of the displacement speed is found to increase with increasing turbulent Reynolds number when the Damkhler number is held constant. It has been shown that the statistical behaviour of the Surface Density Function, and its strain rate and curvature dependence, plays a key role in determining the response of the different components of displacement speed. Increasing the turbulent Reynolds number is shown to reduce the strength of the correlations between tangential strain rate and dilatation rate with curvature, although the qualitative nature of the correlations remains unaffected. The dependence of displacement speed on strain rate and curvature is found to weaken with increasing turbulent Reynolds number when either Damkhler or Karlovitz number is held constant, but the qualitative nature of the correlation remains unaltered. The implications of turbulent Reynolds number effects in the context of Flame Surface Density (FSD) modelling have also been addressed, with emphasis on the influence of displacement speed on the curvature and propagation terms in the FSD balance equation. © 2011 Nilanjan Chakraborty et al.

Tracing sediment transport and bed regime in Nha Trang Bay

Three spatial structure groups of radionuclides in U and Th series, 210Pb-excess and 137Cs, and 40K were found based on analyzing temporal and spatial datum of their content by factor analysis with oblique rotation in Nhatrang bay. U and Th spatial structure with their contours decreased toward the offshore, ran longshore and divided seawater of bay into two parts with strong gradient on both sides. Inside part located from center of Nhatrang bay toward the seashore with three main deposit centers of their contents higher than 23 Bq/kg.dry for 238U and 40 Bq/kg.dry for 232Th, indicated unstability of shoreline. Almost sediments coming from river extended toward the offshore, were stopped and transported toward southeastern. The outside part was less than above mentioned content. The boundary line between two parts superposed with the constantly limit line of turbid plume in the rainy season. Direct influence of the continental runoff was limited by the 9 Bq/kg.dry contour of 238U, 19 Bq/kg.dry contour of 232Th. Longshore current was a predominant process whereas lateral transport as sifting and winnowing process of finer grains in sediments of Nhatrang bay. Areas that had very low content of 137Cs and 210 Pb-excess adjoining shoreline showed areas being eroded. Accumulation of 137Cs and 210 Pbexcess nearby river mouth characterized for fine compositions of sediments controlled by seasonal plumes and sites further toward the south indicated finer materials transported from river and accumulated in lack of hydrodynamic process. Near shore accumulation of 40K revealed the sediments there originated from bed erosion.

Photosynthetic bacteria in the marine environment at Porto-Novo

Sediment and water samples were collected from mangrove and estuarine biotopes at fortnightly intervals. The physico-chemical characters of the overlying water were studied. In the mangrove biotope maximum temperature (31.5°C) and in the estuarine biotope maximum salinity (35.6‰) were recorded during the summer season, whereas in post-monsoon period the sulphate content was increased to 516 p.p.m. and the pH was reduced to 7.4. Invariably both in the enriched sediment and water samples four major peaks (at wavelengths 460, 705, 772 and 850 nm) and two minor peaks (at wavelengths 580 and 663 nm) of absorption spectra were noticed. A pure culture of Chromatium sp., isolated from mangroves sediment, showed three peaks of absorption spectra at wavelengths, 500, 580 and 850 nm. The effect of sodium chloride on the growth of Chromatium sp., was also studied and it was observed that maximum growth occurred in the range 1-3% sodium chloride concentration. This isolate was also capable of utilizing various sulphur and carbon compounds. Glycerol and glucose did not show any specific effect whereas pyruvate, malate and acetate increased the growth.

De novo origination of a new protein-coding gene in Saccharomyces cerevisiae

Origination of new genes is an important mechanism generating genetic novelties during the evolution of an organism. Processes of creating new genes using preexisting genes as the raw materials are well characterized, such as exon shuffling, gene duplicat

A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand

Recent transcription profiling studies have revealed an unexpectedly large proportion of antisense transcripts in eukaryotic genomes. These antisense genes seem to regulate gene expression by interacting with sense genes. Previous studies have focused on the non-coding antisense genes, but the possible regulatory role of the antisense protein is poorly understood. In this study, we found that a protein encoded by the antisense gene ADF1 acts as a transcription suppressor, regulating the expression of sense gene MDF1 in Saccharomyces cerevisiae. Based on the evolutionary, genetic, cytological and biochemical evidence, we show that the protein-coding sense gene MDF1 most likely originated de novo from a previously non-coding sequence and can significantly suppress the mating efficiency of baker's yeast in rich medium by binding MAT alpha 2 and thus promote vegetative growth. These results shed new light on several important issues, including a new sense-antisense interaction mechanism, the de novo origination of a functional gene, and the regulation of yeast mating pathway.