Identification of RNA editing in the human exome and development of DARNED DatabaseSF

RNA editing is a biological phenomena that alters nascent RNA transcripts by insertion, deletion and/or substitution of one or a few nucleotides. It is ubiquitous in all kingdoms of life and in viruses. The predominant editing event in organisms with a developed central nervous system is Adenosine to Inosine deamination. Inosine is recognized as Guanosine by the translational machinery and reverse-transcriptase. In primates, RNA editing occurs frequently in transcripts from repetitive regions of the genome. In humans, more than 500,000 editing instances have been identified, by applying computational pipelines on available ESTs and high-throughput sequencing data, and by using chemical methods. However, the functions of only a small number of cases have been studied thoroughly. RNA editing instances have been found to have roles in peptide variants synthesis by non-synonymous codon substitutions, transcript variants by alterations in splicing sites and gene silencing by miRNAs sequence modifications. We established the Database of RNA EDiting (DARNED) to accommo-date the reference genomic coordinates of substitution editing in human, mouse and fly transcripts from published literatures, with additional information on edited genomic coordinates collected from various databases e.g. UCSC, NCBI. DARNED contains mostly Adenosine to Inosine editing and allows searches based on genomic region, gene ID, and user provided sequence. The Database is accessible at http://darned.ucc.ie RNA editing instances in coding region are likely to result in recoding in protein synthesis. This encouraged me to focus my research on the occurrences of RNA editing specific CDS and non-Alu exonic regions. By applying various filters on discrepancies between available ESTs and their corresponding reference genomic sequences, putative RNA editing candidates were identified. High-throughput sequencing was used to validate these candidates. All predicted coordinates appeared to be either SNPs or unedited.

Effect of particle concentration on erosion rate of mild steel bends in a pneumatic conveyor

Particle concentration is known as a main factor that affects erosion rate of pipe bends in pneumatic conveyors. With consideration of different bend radii, the effect of particle concentration on weight loss of mild steel bends has been investigated in an industrial scale test rig. Experimental results show that there was a significant reduction of the specific erosion rate for high particle concentrations. This reduction was considered to be as a result of the shielding effect during the particle impacts. An empirical model is given. Also a theoretical study of scaling on the shielding effect, and comparisons with some existing models, are presented. It is found that the reduction in specific erosion rate (relative to particle concentration) has a stronger relationship in conveying pipelines than has been found in the erosion tester.

Comparisons between “sand blast” and “centripetal effect accelerator” type erosion testers

There are two major types of erosion testing devices that are used throughout the world for quantifying particle impact erosion against a solid surface. The first of these uses pressurised air to accelerate abrasive particles through a nozzle so that they impinge upon a target specimen. The second adopts a rotating disc to accelerate abrasive particles using the centripetal effect so that they impinge upon a series of targets arranged around the periphery of the disc. This paper reports the findings of a collaborative project that was designed to compare the performance and results obtained from a rig of each of the two types mentioned above. The sand blast type rig was provided by The Department of Powder Science Technology (POSTEC) at The Telemark Technological Research and Development Centre (TEL-TEK), Porsgrunn, Norway while the centripetal effect accelerator was provided by The Wolfson Centre for Bulk Solids Handling Technology, University of Greenwich, London, UK. The test programme included tests against a wide range of materials that are commonly used in pneumatic handling facilities. (Pneumatic handling is a means of conveying and transporting powders and granular solid materials in bulk in industrial process plant, through pipelines using a gas as the carrier medium.) Olivine sand was used as the abrasive and it was projected against the test specimens at velocities and concentrations commensurate with those seen in pneumatic conveyors. In all instances the materials used in the test programme were taken from the same batch so that scatter of experimental results due to specimen variation was minimised. The paper contains a series of recommendations for erosion testing equipment. A discussion based on the results and their applicability to the prediction of wear in pneumatic conveyors concludes the paper.

A Marine Environmental Recorder

An inexpensive Marine Environmental Recorder is described. The instrument system is small, lightweight and of low-power consumption. It is flexible, simple to operate and economical. It can be used remotely in a moored, buoyed or towed instrument system, recording measurements continuously for up to 24 h, or intermittently for 1 min every hour, for a period of up to 60 d. It has been used extensively in the Continuous Plankton Recorder and the Undulating Oceanographic Recorder to measure temperature, depth and occasionally chlorophyll and radiant energy; as a temperature recorder, it has a resolution of 0.1 Co, an uncertainty of measurement of ±0.1 Co and a stability of calibration within ±0.1 Co over a period of several months. With optional additional sensors for pitch, roll, vibration, acceleration and water-flow, the instrument system has been used to measure the performance of underwater towed vehicles and plankton samplers. The Marine Environmental Recorder is being incorporated into an instrument system in a data buoy, for automatically monitoring the marine environment in estuaries around the British Isles.

Growth and production of Pacific ocean perch (Sebastes alutus) in nursery habitats of the Gulf of Alaska

Nursery areas for juvenile fishes are often important for determining recruitment in marine populations by providing habitats that can maximize growth and thereby minimize mortality. Pacific ocean perch (POP, Sebastes alutus) have an extended juvenile period where they inhabit rocky nursery habitats. We examined POP nursery areas to link growth potential to recruitment. Juvenile POP were captured from nursery areas in 2004 and 2008, and estimated growth rates ranged from −0.19 to 0.60 g day−1 based on differences in size between June and August. Predicted growth rates from a bioenergetics model ranged from 0.05 to 0.49 g day−1 and were not significantly different than observed. Substrate preferences and the distribution of their preferred habitats were utilized to predict the extent of juvenile POP nursery habitat in the Gulf of Alaska. Based on densities of fish observed on underwater video transects and the spatial extent of nursery areas, we predicted 278 and 290 million juvenile POP were produced in 2004 and 2008. Growth potential for juvenile POP was reconstructed using the bioenergetics model, spring zooplankton bloom timing and duration and bottom water temperature for 1982–2008. When a single outlying recruitment year in 1986 was removed, growth potential experienced by juvenile POP in nursery areas was significantly correlated to the recruitment time-series from the stock assessment, explaining ∼30% of the variability. This research highlights the potential to predict recruitment using habitat-based methods and provides a potential mechanism for explaining some of the POP recruitment variability observed for this population.

Investigating the inter-relationships between water attenuated irradiance, primary production and DMS(P)

Both solar irradiance and primary production have been proposed as independent controls on seawater dimethyl sulphide (DMS) and dimethylsulphoniopropionate (DMSP) concentrations. However, irradiance also drives photosynthesis, and thus influences a complex set of inter-related processes that modulate marine DMS. We investigate the potential inter-relationships between the rate of primary production (carbon assimilation), water-attenuated irradiance and DMS/DMSP dynamics by applying correlation analysis to a high resolution, concurrently sampled in situ data set from a range of latitudes covering multiple biogeochemical provinces from 3 of the 4 Longhurst biogeochemical domains. The combination of primary production (PP) and underwater irradiance (Iz) within a multivariate regression model is able to explain 55% of the variance in DMS concentrations from all depths within the euphotic zone and 66% of the variance in surface DMS concentrations. Contrary to some previous studies we find a variable representing biological processes is necessary to better account for the variance in DMS. We find that the inclusion of Iz accounts for variance in DMS that is independent from the variance explained by PP. This suggests an important role for solar irradiance (beyond the influence of irradiance upon primary production) in mediating the relationship between the productivity of the ecosystem, DMS/DMSP production and ambient seawater DMS concentrations.

Estimating Oceanic Primary Production Using Vertical Irradiance and Chlorophyll Profiles from Ocean Gliders in the North Atlantic

An autonomous underwater vehicle (Seaglider) has been used to estimate marine primary production (PP) using a combination of irradiance and fluorescence vertical profiles. This method provides estimates for depth-resolved and temporally evolving PP on fine spatial scales in the absence of ship-based calibrations. We describe techniques to correct for known issues associated with long autonomous deployments such as sensor calibration drift and fluorescence quenching. Comparisons were made between the Seaglider, stable isotope (13C), and satellite estimates of PP. The Seaglider-based PP estimates were comparable to both satellite estimates and stable isotope measurements.

Paisajes para el Medioambiente. Estudio de caso.

Una de las cuencas hidrográficas más importante de la Península es la del río Tajo, por su extensión y por su caudal. Se trata de una fosa tectónica calificable de modélica. Dos moles montañosas, el Sistema central y los Montes de Toledo en sentido amplio, la flanquean al Norte y al Sur. La dovela hundida, formada por idénticos materiales que las Sierras, granitos y gneis, alcanza una gran profundidad. Al Este el Sistema Ibérico castellano, principalmente calizo y mesozoico, cierra Castilla y la cuenca, viniendo a dar vida con el agua de sus nieves a un Tajo niño’. El inicio de su Historia Geológica podemos situarlo en el Paleozoico, tiempo geológico durante el cual los territorios donde hoy se sitúa la Meseta estaban formando grandes cordilleras producto de la Orogenia Herciniana. La última etapa de la formación de los relieves actuales de la cuenca la encontramos en la reactivación de los antiguos macizos arrasados. Se inicia con los materiales de la raña y sus equivalentes en el centro de la Cuenca o Fosa del Tajo, y se caracteriza por una progresiva individualización de los procesos, pasándose de las grandes superficies generalizadas en macizos y cuencas, Sierras y Fosa del Tajo, a las pequeñas llanuras en franja u orla, que quedan localizadas en cada cuenca fluvial a medida que éstas se van consolidando por jerarquización, y partir de un río generatriz o emisario principal, el Tajo. La tectónica, procesos posteriores de captura, reajustes climáticos..., no permiten aún determinar cuál fue el orden de jerarquía en los ríos que hoy conocemos; no obstante, puede aventurarse que Jarama-Henares, Perales-Alberche y Guadarrama serían los primeros y Manzanares, Guadalix, Tajuña, los siguientes, y así sucesivamente. La síntesis de la realidad geológica, litológica y climática va a coadyuvar, frenando o favoreciendo, el desarrollo y la diferenciación entre los paisajes vegetales de las zonas montañosas y los de las depresiones terciarias y penillanuras paleozoicas, en un territorio marcado por el predominio del clima mediterráneo continentalizado, con matices de montaña y áreas de influencia atlántica.

Seasonal and diurnal variations in ultraviolet-B and ultraviolet-A irradiances at and below the sea surface at Helgoland (North Sea) over a 6-year period

Ultraviolet(UV) radiation at four wavelengths (305, 320, 340 and 380 nm) and photosynthetically active radiation (PAR) were measured from May 1994 to October 1999 using Biospherical UV radiometers. A surface reference sensor located on the roof of the Marine Station at Helgoland recorded values every 5 min, and an equivalent profiling underwater sensor was used for measurements in the sea at approximately monthly intervals. The ratio of 305-nm radiation to PAR varied seasonally, with a 14-fold increase from winter to summer. A much weaker seasonal trend (ca. 1.5-fold) was apparent in the ratio of 320-nm radiation to PAR, but there was no seasonal trend in the ratios of 340- or 380-nm radiation to PAR. The year-to-year variations in 305-nm radiation were also much greater relative to PAR than for the other UV wavelengths, but there was no evidence of a change in the 305 nm:PAR ratio over the study period. The ratios of both 305- and 320-nm radiation to PAR increased from dawn to midday, but those of 340- and 380-nm radiation were almost constant through the day, except shortly before sunrise and after sunset when the proportions of 340- and 380-nm radiation increased. Underwater measurements of PAR and UV suggest that the 1% depth for 305-nm radiation was little more than 1 m, but this estimate is valid only for summer and autumn because, in other seasons, few reliable readings for 305-nm radiation could be obtained underwater, and no attenuation coefficient could be calculated. The 1% depths recorded for the other UV wavelengths in the middle 6 months of the year were 2.0 m for 320 nm, 2.6 m for 340 nm and 4.6 m for 380 nm, compared with 12 m for PAR, but the attenuation of all wavebands increased sharply in October and remained higher until March. An analysis of the influence of sun angle, total column ozone concentration, the proportion of skylight, and cloud cover on the ratio of UV wavelengths to PAR in surface irradiance demonstrated that solar angle has a greater influence than ozone concentration on the irradiance at 305 nm, and that the typical occurrence of ozone

Kinetics of the oxidation of methyl tert-butyl ether (MTBE) by potassium permanganate

The occurrence of the fuel oxygenate methyl tert-butyl ether (MTBE) in the environment has received considerable scientific attention. The pollutant is frequently found in the groundwater due to leaking of underground storage tanks or pipelines. Concentrations of more than several mg/L MTBE were detected in groundwater at several places in the US and Germany in the last few years. In situ chemical oxidation is a promising treatment method for MTBE-contaminated plumes. This research investigated the reaction kinetics for the oxidation of MTBE by permanganate. Batch tests demonstrated that the oxidation of MTBE by permanganate is second order overall and first order individually with respect to permanganate and MTBE. The second-order rate constant was 1.426 x 10(-6) L/mg/h. The influence of pH on the reaction rate was demonstrated to have no significant effect. However, the rate of MTBE oxidation by potassium permanganate is 2-3 orders of magnitude lower than of other advanced oxidation processes. The slower rates of MTBE oxidation by permanganate limit the applicability of this process for rapid MTBE cleanup strategies. However, permanganate oxidation of MTBE has potential for passive oxidation risk management strategies. (C) 2002 Elsevier Science Ltd. All rights reserved.

Under-water scene investigation using ground penetrating radar (GPR) in the search for a sunken jet ski, Northern Ireland

A search for a submerged jet ski and the lost limb of its driver involved in a collision with a speedboat was made in a shallow lake in Northern Ireland. The location of both was crucial to establishing events at the time of the accident. Local intelligence suggested both objects were likely to be partially-buried by lacustrine silt. To avoid sediment churning, this required non-invasive, completely non-destructive assessment and mapping of the scene. A MALA RAMAC ground-penetrating radar system (GPR) mounted on floats for surveying from walkways and jetties or placed in a small rubber dinghy for offshore profiling was used. A grid was established and each line surveyed with 100, 200 and 400MHz antennae. In waters over 6m deep GPR data showed the form of the lake floor but excessive ringing occurred in the data. In waters less than 6m deep ringing diminished on both 100 and 200MHz data, the latter displaying the best trade-off between depth penetration and horizontal object resolution. 400MHz data failed to be of use in waters over 2m deep and at these depths showed only limited improvement of image quality compared to 200MHz data. Surface objects such as a wooden walkway caused interference on 200 and 400MHz data when antennae were oriented both normal and parallel to survey direction; this may be a function of the low attenuation of radar waves in freshwater, allowing excellent lateral and vertical radar wave penetration. On 200MHz data the damaged jet-ski was clearly imaged in a location that contradicted the speedboat driver's account of the accident.