Clinical and molecular study of a new form of hereditary myotonia in Murrah water buffalo

Hereditary myotonia caused by mutations in CLCN1 has been previously described in humans, goats, dogs, mice and horses. The goal of this study was to characterize the clinical, morphological and genetic features of hereditary myotonia in Murrah buffalo. Clinical and laboratory evaluations were performed on affected and normal animals. CLCN1 cDNA and the relevant genomic region from normal and affected animals were sequenced. The affected animals exhibited muscle hypertrophy and stiffness. Myotonic discharges were observed during EMG, and dystrophic changes were not present in skeletal muscle biopsies; the last 43 nucleotides of exon-3 of the CLCN1 mRNA were deleted. Cloning of the genomic fragment revealed that the exclusion of this exonic sequence was caused by aberrant splicing, which was associated with the presence of a synonymous SNP in exon-3 (c.396C>T). The mutant allele triggered the efficient use of an ectopic 5' splice donor site located at nucleotides 90-91 of exon-3. The predicted impact of this aberrant splicing event is the alteration of the CLCN1 translational reading frame, which results in the incorporation of 24 unrelated amino acids followed by a premature stop codon. Copyright © 2012 Elsevier B.V. All rights reserved.

The effects of water molecules on the electronic and structural properties of peptide nanotubes

The self-assembly of short amino acid chains appears to be one of the most promising strategies for the fabrication of nanostructures. Their solubility in water and the possibility of chemical modification by targeting the amino or carboxyl terminus give peptide-based nanostructures several advantages over carbon nanotube nanostructures. However, because these systems are synthesized in aqueous solution, a deeper understanding is needed on the effects of water especially with respect to the electronic, structural and transport properties. In this work, the electronic properties of l-diphenylalanine nanotubes (FF-NTs) have been studied using the Self-Consistent Charge Density-Functional-based Tight-Binding method augmented with dispersion interaction. The presence of water molecules in the central hydrophilic channel and their interaction with the nanostructures are addressed. We demonstrate that the presence of water leads to significant changes in the electronic properties of these systems decreasing the band gap which can lead to an increase in the hopping probability and the conductivity. © the Owner Societies 2013.

Circulation and salt intrusion in the Piaçaguera Channel, Santos (SP)

A análise de dados termohalinos e correntes medidos em uma estação fixa no Canal de Piaçaguera (Estuário de Santos) no inverno foi feita em termos de condições cíclicas da maré (quadratura e sizígia) e quase-estacionária, com o objetivo de caracterizar a estratificação da massa de água estuarina, sua circulação e transporte de sal forçados pela modulação quinzenal da maré. Foram utilizados métodos clássicos de análise de dados observacionais horários e quase sinóticos e de simulações analíticas de perfis estacionários de salinidade e do componente longitudinal da velocidade. Durante o ciclo de maré de quadratura as velocidades de enchente (v<0) e vazante (v>0) variaram de -0.20 m/s a 0.30 m/s, associadas à pequena variação de salinidade entre a superfície e o fundo (26.4 psu a 30.7 psu). No ciclo de sizígia a velocidade aumentou de -0.40 m/s a 0.45 m/s, mas a estratificação de salinidade permaneceu praticamente a mesma. Os perfis estacionários teóricos de salinidade e de velocidade apresentaram boa concordância (Skill próximo a 1,0) quando comparados aos perfis observacionais. Durante a modulação quinzenal da maré não houve alteração na classificação do canal estuarino (tipo 2a-parcialmente misturado e fracamente estratificado), pois a taxa de aumento da energia potencial não foi suficiente para ocasionar a erosão da haloclina. Esses resultados, associados à alta estabilidade vertical (RiL >20) e ao número de Richardson estuarino (1,6), permitem as seguintes conclusões: i) o mecanismo que forçou a circulação e os processos de mistura foi principalmente o balanço da descarga fluvial com a maré, associado ao componente baroclínico da força de gradiente de pressão; ii) não houve variações nas principais características termohalinas e da circulação devido à modulação quinzenal da maré; e iii) os perfis quase estacionários de salinidade e da velocidade foram adequadamente simulados com um modelo analítico clássico.

Photomorphogenic modulation of water stress in tomato (Solanum lycopersicum L.): the role of phytochromes A, B1, and B2

Phytochromes are red/far-red light photoreceptors that mediate a variety of photomorphogenic processes in plants, from germination to flowering. In addition, there is evidence that phytochromes are also part of the stress signalling response, especially in response to water deficit stress, which is the major abiotic factor limiting plant growth and crop productivity worldwide. In this study, we used the phyA (far red-insensitive; fri), phyB1 (temporary red-insensitive; tri) and phyB2 mutants of tomato (Solanum lycopersicum L.) to study the roles of these three phytochromes in drought stress responses. Compared to wild type (WT) plants grown under water-deficit stress conditions, the fri, tri, and phyB2 mutants did not exhibit altered dry weights, leaf areas, stomatal densities, or stomatal opening. The stomatal conductance of all three mutants was severely reduced under both fully-hydrated and water-deficit conditions. Although relative water contents did change after drought stress in each mutant, the most significant reduction in water potential during water stress was observed in the fri mutant. However, this mutant returned its water status to WT levels during rehydration. Although the phyB2 mutant lost more water from detached leaves during abscisic acid (ABA) treatment, phyB2 behaved like WT plants, indicating that this mutant was not insensitive to ABA. Overall, these results indicate that the phytochromes phyA, phyB1, and phyB2 modulate drought stress responses in tomato.

The Oligocene-Neogene deep-sea Columbia Channel system in the South Brazilian Basin: Seismic stratigraphy and environmental changes

The Columbia Channel (CCS) system is a depositional system located in the South Brazilian Basin, south of the Vitoria-Trindade volcanic chain. It lies in a WNW-ESE direction on the continental rise and abyssal plain, at a depth of between 4200 and 5200 m. It is formed by two depocenters elongated respectively south and north of the channel that show different sediment patterns. The area is swept by a deep western boundary current formed by AABW. The system has been previously interpreted has a mixed turbidite-contourite system. More detailed study of seismic data permits a more precise definition of the modern channel morphology, the system stratigraphy as well as the sedimentary processes and control. The modern CCS presents active erosion and/or transport along the channel. The ancient Oligo-Neogene system overlies a ""upper Cretaceous-Paleogene"" sedimentary substratum (Unit U1) bounded at the top by a major erosive ""late Eocene-early Oligocene"" discordance (D2). This ancient system is subdivided into 2 seismic units (U2 and U3). The thick basal U2 unit constitutes the larger part of the system. It consists of three subunits bounded by unconformities: D3 (""Oligocene-Miocene boundary""), D4 (""late Miocene"") and D5 (""late Pliocene""). The subunits have a fairly tabular geometry in the shallow NW depocenter associated with predominant turbidite deposits. They present a mounded shape in the deep NE depocenter, and are interpreted as forming a contourite drift. South of the channel, the deposits are interpreted as a contourite sheet drift. The surficial U3 unit forms a thin carpet of deposits. The beginning of the channel occurs at the end of U1 and during the formation of D2. Its location seems to have been determined by active faults. The channel has been active throughout the late Oligocene and Neogene and its depth increased continuously as a consequence of erosion of the channel floor and deposit aggradation along its margins. Such a mixed turbidite-contourite system (or fan drift) is characterized by frequent, rapid lateral facies variations and by unconformities that cross the whole system and are associated with increased AABW circulation. (C) 2009 Elsevier B.V. All rights reserved.

CIRCULATION AND SALT INTRUSION IN THE PIACAGUERA CHANNEL, SANTOS (SP)

Analysis of thermohaline properties and currents sampled at an anchor station in the Piacaguera Channel (Santos Estuary) in the austral winter was made in terms of tidal (neap and spring tidal cycles) and non-tidal conditions, with the objective to characterize the stratification, circulation and salt transport due to the fortnightly tidal modulation. Classical methods of observational data analysis of hourly and nearly synoptic observations and analytical simulations of nearly steady-state salinity and longitudinal velocity profiles were used. During the neap tidal cycle the flood (v<0) and ebb (v>0) velocities varied in the range of -0.20 m/s to 0.30 m/s associated with a small salinity variation from surface to bottom (26.4 psu to 30.7 psu). In the spring tidal cycle the velocities increased and varied in the range of -0.40 m/s to 0.45 m/s, but the salinity stratification remained almost unaltered. The steady-state salinity and velocity profiles simulated with an analytical model presented good agreement (Skill near 1.0), in comparison with the observational profiles. During the transitional fortnightly tidal modulation period there was no changes in the channel classification (type 2a - partially mixed and weakly stratified), because the potential energy rate was to low to enhance the halocline erosion. These results, associated with the high water column vertical stability (RiL > 20) and the low estuarine Richardson number (RiE = 1.6), lead to the conclusions: i) the driving mechanism for the estuary circulation and mixing was mainly balanced by the fresh water discharge and the tidal forcing associated with the baroclinic component of the gradient pressure force; ii) there was no changes in the thermohaline and circulation characteristics due to the forthnigtly tidal modulation; and iii) the nearly steady-state of the vertical salinity and velocity profiles were well simulated with a theoretical classical analytical model.

Experimental investigation of gravitational gas separation in an inclined annular channel

The oil industry uses gas separators in production wells as the free gas present in the suction of the pump reduces the pumping efficiency and pump lifetime. Therefore, free gas is one of the most important variables in the design of pumping systems. However, in the literature there is little information on these separators. It is the case of the inverted-shroud gravitational gas separator. It has an annular geometry due to the installation of a cylindrical container in between the well casing and pioduction pipe (tubing). The purpose of the present study is to understand the phenomenology and behavior of inverted-shroud separator. Experimental tests were performed in a 10.5-m-length inclinable glass tube with air and water as working fluids. The water flow rate was in the range of 8.265-26.117 l/min and the average inlet air mass flow rate was 1.1041 kg/h, with inclination angles of 15 degrees, 30 degrees, 45 degrees, 60 degrees, 75 degrees, 80 degrees and 85 degrees. One of the findings is that the length between the inner annular level and production pipe inlet is one of the most important design parameters and based on that a new criterion for total gas separation is proposed. We also found that the phenomenology of the studied separator is not directly dependent on the gas flow rate, but on the average velocity of the free surface flow generated inside the separator. Maps of efficiency of gas separation were plotted and showed that liquid flow rate, inclination angle and pressure difference between casing and production pipe outlet are the main variables related to the gas separation phenomenon. The new data can be used for the development of design tools aiming to the optimized project of the pumping system for oil production in directional wells. (C) 2012 Elsevier Inc. All rights reserved.

Circulation and salt intrusion in the Piaçaguera Channel, Santos (SP)

Analysis of thermohaline properties and currents sampled at an anchor station in the Piaçaguera Channel (Santos Estuary) in the austral winter was made in terms of tidal (neap and spring tidal cycles) and non-tidal conditions, with the objective to characterize the stratification, circulation and salt transport due to the fortnightly tidal modulation. Classical methods of observational data analysis of hourly and nearly synoptic observations and analytical simulations of nearly steady-state salinity and longitudinal velocity profiles were used. During the neap tidal cycle the flood (v<0) and ebb (v>0) velocities varied in the range of -0.20 m/s to 0.30 m/s associated with a small salinity variation from surface to bottom (26.4 psu to 30.7 psu). In the spring tidal cycle the velocities increased and varied in the range of -0.40 m/s to 0.45 m/s, but the salinity stratification remained almost unaltered. The steady-state salinity and velocity profiles simulated with an analytical model presented good agreement (Skill near 1.0), in comparison with the observational profiles. During the transitional fortnightly tidal modulation period there was no changes in the channel classification (type 2a - partially mixed and weakly stratified), because the potential energy rate was to low to enhance the halocline erosion. These results, associated with the high water column vertical stability (RiL >20) and the low estuarine Richardson number (RiE=1.6), lead to the conclusions: i) the driving mechanism for the estuary circulation and mixing was mainly balanced by the fresh water discharge and the tidal forcing associated with the baroclinic component of the gradient pressure force; ii) there was no changes in the thermohaline and circulation characteristics due to the forthnigtly tidal modulation; and iii) the nearly steady-state of the vertical salinity and velocity profiles were well simulated with a theoretical classical analytical model.

Movement of NH3 through the human urea transporter B: a new gas channel

Aquaporins and Rh proteins can function as gas (CO2 and NH3) channels. The present study explores the urea, H2O, CO2, and NH3 permeability of the human urea transporter B (UT-B) (SLC14A1), expressed in Xenopus oocytes. We monitored urea uptake using [14C]urea and measured osmotic water permeability (Pf) using video microscopy. To obtain a semiquantitative measure of gas permeability, we used microelectrodes to record the maximum transient change in surface pH (∆pHS) caused by exposing oocytes to 5% CO2/33 mM HCO3- (pHS increase) or 0.5 mM NH3/NH4+ (pHS decrease). UT-B expression increased oocyte permeability to urea by >20-fold, and Pf by 8-fold vs. H2O-injected control oocytes. UT-B expression had no effect on the CO2-induced ∆pHS but doubled the NH3-induced ∆pHS. Phloretin reduced UT-B-dependent urea uptake (Jurea * ) by 45%, Pf * by 50%, and (- ∆pHS * )NH3 by 70%. p-Chloromercuribenzene sulfonate reduced Jurea * by 25%, Pf * by 30%, and (∆pHS * )NH3 by 100%. Molecular dynamics (MD) simulations of membrane-embedded models of UT-B identified the monomeric UT-B pores as the main conduction pathway for both H2O and NH3 and characterized the energetics associated with permeation of these species through the channel. Mutating each of two conserved threonines lining the monomeric urea pores reduced H2O and NH3 permeability. Our data confirm that UT-B has significant H2O permeability and for the first time demonstrate significant NH3 permeability. Thus the UTs become the third family of gas channels. Inhibitor and mutagenesis studies and results of MD simulations suggest that NH3 and H2O pass through the three monomeric urea channels in UT-B.

Hydrologic and Water Quality Assessment of Miller Run: A Study of Bucknell University’s Impact

Human development causes degradation of stream ecosystems due to impacts on channel morphology, hydrology, and water quality. Urbanization, the second leading cause of stream impairment, increases the amount of impervious surface cover, thus reducing infiltration and increasing surface runoff of precipitation, which ultimately affects stream hydrologic process and aquatic biodiversity. The main objective of this study was to assess the overall health of Miller Run, a small tributary of the Bull Run and Susquehanna River watersheds, through an integrative hydrologic and water quality approach in order to determine the degree of Bucknell University’s impact on the stream. Hydrologic conditions, including stage and discharge, and water quality conditions, including total suspended solids, ion, nutrient, and dissolved metal concentrations, specific conductivity, pH, and temperature, were measured and evaluated at two sampling sites (upstream and downstream of Bucknell’s main campus) during various rain events from September 2007 to March 2008. The primary focus of the stream analysis was based on one main rain event on 26 February 2008. The results provided evidence that Miller Run is impacted by Bucknell’s campus. From a hydrologic perspective, the stream’s hydrograph showed the exact opposite pattern of what would be expected from a ‘normal’ stream. Miller run had a flashier downstream hydrograph and a broader upstream hydrograph, which was more than likely due to the increased amount of impervious surface cover throughout the downstream half of the watershed. From a water quality perspective, sediment loads increased at a faster rate and were significantly higher downstream compared to upstream. These elevated sediment concentrations were probably the combined result of sediment runoff from upstream and downstream construction sites that were being developed over the course of the study. Sodium, chloride, and potassium concentrations, in addition to specific conductivity, also significantly increased downstream of Bucknell’s campus due to the runoff of road salts. Calcium and magnesium concentrations did not appear to be impacted by urbanization, although they did demonstrate a significant dilution effect downstream. The downstream site was not directly affected by elevated nitrate concentrations; however, soluble reactive phosphorus concentrations tended to increase downstream and ammonium concentrations significantly peaked partway through the rain event downstream. These patterns suggest that Miller Run may be impacted by nutrient runoff from the golf course, athletic fields, and/or fertilizers applications on the main campus. Dissolved manganese and iron concentrations also appeared to slightly increase downstream, demonstrating the affect of urban runoff from roads and parking lots. pH and temperature both decreased farther downstream, but neither showed a significant impact of urbanization. More studies are necessary to determine how Miller Run responds to changes in season, climate, precipitation intensity, and land-use. This study represents the base-line analysis of Miller Run’s current hydrologic and water quality conditions; based on these initial findings, Bucknell should strongly consider modifications to improve storm water management practices and to reduce the campus’s overall impact on the stream in order to enhance and preserve the integrity of its natural water resources.

Length of the annular regime for condensing flows inside a horizontal channel - the experimental determination of its values and its trends

The experiments observe and measure the length of the annular regime in fully condensing quasi-steady (steady-in-the-mean) flows of pure FC-72 vapor in a horizontal condenser (rectangular cross-section of 2 mm height, 15 mm width, and 1 m length). The sides and top of the duct are made of clear plastic that allows flow visualization. The experimental system in which this condenser is used is able to control and achieve different quasi-steady mass flow rates, inlet pressures, and wall cooling conditions (by adjustment of the temperature and flow rate of the cooling water flowing underneath the condensing-plate). The reported correlations and measurements for the annular length are also vital information for determining the length of the annular regime and proposing extended correlation (covering many vapors and a larger parameter set than the experimentally reported version here) by ongoing independent modeling and computational simulation approach.

Fluidic oscillator design for water removal enhancement in a PEM fuel cell

This research initiative was triggered by the problems of water management of Polymer Electrolyte Membrane Fuel Cell (PEMFC). In low temperature fuel cells such as PEMFC, some of the water produced after the chemical reaction remains in its liquid state. Excess water produced by the fuel cell must be removed from the system to avoid flooding of the gas diffusion layers (GDL). The GDL is responsible for the transport of reactant gas to the active sites and remove the water produced from the sites. If the GDL is flooded, the supply gas will not be able to reach the reactive sites and the fuel cell fails. The choice of water removal method in this research is to exert a variable asymmetrical force on a liquid droplet. As the drop of liquid is subjected to an external vibrational force in the form of periodic wave, it will begin to oscillate. A fluidic oscillator is capable to produce a pulsating flow using simple balance of momentum fluxes between three impinging jets. By connecting the outputs of the oscillator to the gas channels of a fuel cell, a flow pulsation can be imposed on a water droplet formed within the gas channel during fuel cell operation. The lowest frequency produced by this design is approximately 202 Hz when a 20 inches feed-back port length was used and a supply pressure of 5 psig was introduced. This information was found by setting up a fluidic network with appropriate data acquisition. The components include a fluidic amplifier, valves and fittings, flow meters, a pressure gage, NI-DAQ system, Siglab®, Matlab software and four PCB microphones. The operating environment of the water droplet was reviewed, speed of the sound pressure which travels down the square channel was precisely estimated, and measurement devices were carefully selected. Applicable alternative measurement devices and its application to pressure wave measurement was considered. Methods for experimental setup and possible approaches were recommended, with some discussion of potential problems with implementation of this technique. Some computational fluid dynamic was also performed as an approach to oscillator design.

Searching the Rhone delta channel in Lake Geneva since François‐Alphonse Forel

In the late 19th century, F.A. FOREL led investigations of the Rhone River delta area of Lake Geneva that resulted in the dis- covery of a textbook example of a river-fed delta system containing impressive subaquatic channels. Well ahead of the marine counterparts, scientific observations and interpretations of water currents shaping the delta edifice for the first time documented how underflow currents carry cold, suspension-laden waters from the river mouth all the way to the deep basin. These early investigations of the Rhone delta laid the basis for follow-up studies in the 20th and 21th centuries. Sediment coring, water-column measurements, manned submersible diving, seismic reflection profiling and bathymetric sur- veying eventually provided a rich database to unravel the key erosional and depositional processes, further documenting the impact of human-induced changes in the catchment. With the merging of old and new scientific knowledge, today a comprehensive understanding prevails of how a delta changes through time, how its channels are formed, and what potential natural hazards may be related to its evolution. New and efficient bathymetric techniques, paired with novel coring operations, provided a time-series of morphologic evolution showing and quantifying the high dynamics of the delta/channel evolution in an unprecedented temporal and spatial reso- lution. Future investigations will continue to further quantify these dynamic processes and to link the evolution of the subaquatic domain with changes and processes in the catchment and with natural hazards. Its size, easy access, and large variety of states and processes will continue to make the Rhone delta area a perfect ‘laboratory’ in which general processes can be studied that could be upscaled or downscaled to other marine and lacustrine deltas.

Sediment dynamics in the subaquatic channel of the Rhone delta (Lake Geneva, France/Switzerland)

bstract With its smaller size, well-known boundary conditions, and the availability of detailed bathymetric data, Lake Geneva’s subaquatic canyon in the Rhone Delta is an excellent analogue to understand sedimentary pro- cesses in deep-water submarine channels. A multidisciplinary research effort was undertaken to unravel the sediment dynamics in the active canyon. This approach included innovative coring using the Russian MIR sub- mersibles, in situ geotechnical tests, and geophysical, sedimentological, geochemical and radiometric analysis techniques. The canyon floor/levee complex is character- ized by a classic turbiditic system with frequent spillover events. Sedimentary evolution in the active canyon is controlled by a complex interplay between erosion and sedimentation processes. In situ profiling of sediment strength in the upper layer was tested using a dynamic penetrometer and suggests that erosion is the governing mechanism in the proximal canyon floor while sedimen- tation dominates in the levee structure. Sedimentation rates progressively decrease down-channel along the levee structure, with accumulation exceeding 2.6 cm/year in the proximal levee. A decrease in the frequency of turbidites upwards along the canyon wall suggests a progressive confinement of the flow through time. The multi-proxy methodology has also enabled a qualitative slope-stability assessment in the levee structure. The rapid sediment loading, slope undercutting and over-steepening, and increased pore pressure due to high methane concentrations hint at a potential instability of the proximal levees. Fur- thermore, discrete sandy intervals show very high methane concentrations and low shear strength and thus could cor- respond to potentially weak layers prone to scarp failures.

Impact of dams, dam removal and dam-related river engineering structures on sediment connectivity and channel morphology of the Fugnitz and the Kaja Rivers

In terms of changing flow and sediment regimes of rivers, dams are often regarded as the most dominant form of human impact on fluvial systems. Dams can decrease the flux of water and sediments leading to channel changes such as upstream aggradation and downstream degradation. The opposite effects occur when dams are removed. Channel degradation often requires further intervention in terms of river bed and bank protection works. The situation evolves more complex in river systems that are impacted by a series of dams due to feedback processes between the different system compartments. A number of studies have recently investigated geomorphic systems using connectivity approaches to improve the understanding of geomorphic system response to change. This paper presents a case study investigating the impact of dam construction, dam removal and dam-related river bed and bank protection measures on the sediment connectivity and channel morphology of the Fugnitz and the Kaja Rivers using a combination of DEM analyses, field surveys and landscape evolution modelling. For both river systems the results revealed low sediment connectivity accompanied by a fine river bed sediment facies in river sections upstream of active dams and of removed dams with protection measures. Contrarily, high sediment connectivity which was accompanied by a coarse river bed sediment facies was observed in river sections either located downstream of active dams or of removed dams with upstream protection. In terms of channel changes, significant channel degradation was examined at locations downstream of active dams and of removed dams. Channel bed and bank protection measures prevent erosion and channel slope recovery after dam removal. Landscape evolution modeling revealed a complex geomorphic response to dam construction and dam removal as sediment output rates and therefore geomorphic processes have been shown to act in a non-linear manner. These insights are deemed to have major implications for river management and conservation, as quality and state of riverine habitats are determined by channel morphology and river bed sediment composition.