Analysis of mRNA transcripts improves the success rate of molecular genetic testing in OTC deficiency

BACKGROUND: Ornithine transcarbamylase (OTC) deficiency is the most common inborn error of urea metabolism that can lead to hyperammonemic crises and orotic aciduria. To date, a total of 341 causative mutations within the OTC gene have been described. However, in about 20% of the patients with enzymatically confirmed OTC deficiency no mutation can be detected when sequencing of genomic DNA analyzing exons and adjacent intronic segments of the OTC gene is performed. METHODS: Standard genomic DNA analysis of the OTC gene in five consecutive patients from five families revealed no mutation. Hence, liver tissue was obtained by needle sampling or open biopsy and RNA extracted from liver was analyzed. RESULTS: Complex rearrangements of the OTC transcript (three insertions and two deletions) were found in all five patients. CONCLUSION: In patients with a strong suspicion of OTC deficiency despite normal results of sequencing exonic regions of the OTC gene, characterization of liver OTC mRNA is highly effective in resolving the genotype. Liver tissue sampling by needle aspiration allows for both enzymatic analysis and RNA based diagnostics of OTC deficiency.

Anelastic strain recovery and elastic properties of ODP Leg 123 oceanic basalt samples

A knowledge of rock stress is fundamental for improving our understanding of oceanic crustal mechanisms and lithospheric dynamic processes. However, direct measurements of stress in the deep oceans, and in particular stress magnitudes, have proved to be technically difficult. Anelastic strain recovery measurements were conducted on 15 basalt core samples from Sites 765 and 766 during Leg 123. Three sets of experiments were performed: anelastic strain recovery monitoring, dynamic elastic property measurements, and thermal azimuthal anisotropy observations. In addition, a range of other tests and observations were recorded to characterize each of the samples. One common feature of the experimental results and observations is that apparently no consistent orientation trend exists, either between the different measurements on each core sample or between the same sets of measurements on the various core samples. However, some evidence of correspondence between velocity anisotropy and anelastic strain recovery exists, but this is not consistent for all the core samples investigated. Thermal azimuthal anisotropy observations, although showing no conclusive correlations with the other results, were of significant interest in that they clearly exhibited anisotropic behavior. The apparent reproducibility of this behavior may point toward the possibility of rocks that retain a "memory" of their stress history, which could be exploited to derive stress orientations from archived core. Anelastic strain recovery is a relatively new technique. Because use of the method has extended to a wider range of rock types, the literature has begun to include examples of rocks that contracted with time. Strong circumstantial evidence exists to suggest that core-sample contractions result from the slow diffusion of pore fluids from a preexisting microcrack structure that permits the rock to deflate at a greater rate than the expansion caused by anelastic strain recovery. Both expansions and contractions of the Leg 123 cores were observed. The basalt cores have clearly been intersected by an abundance of preexisting fractures, some of which pass right through the samples, but many are intercepted or terminate within the rock matrix. Thus, the behavior of the core samples will be influenced not only by the properties of the rock matrix between the fractures, but also by how these macro- and micro-scale fractures mutually interact. The strain-recovery curves recorded during Leg 123 for each of the 15 basalt core samples may reflect the result of two competing time dependent processes: anelastic strain recovery and pore pressure recovery. Were these the only two processes to influence the gauge responses, then one might expect that given the additional information required, established theoretical models might be used to determine consistent stress orientations and reliable stress magnitudes. However, superimposed upon these competing processes is their respective interaction with the preexisting fractures that intersect each core. Evidence from our experiments and observations suggests that these fractures have a dominating influence on the characteristics of the recovery curves and that their effects are complex.

Seawater carbonate chemistry, growth rate and light sensitivity of marine diatom Chaetoceros muelleri (strain CSIRO CS-176) during experiments, 2011

This study investigated the impact of photon flux and elevated CO2 concentrations on growth and photosynthetic electron transport on the marine diatom Chaetoceros muelleri and looked for evidence for the presence of a CO2-concentrating mechanism (CCM). pH drift experiments clearly showed that C. muelleri has the capacity to use bicarbonate to acquire inorganic carbon through one or multiple CCMs. The final pH achieved in unbuffered cultures was not changed by light intensity, even under very low photon flux, implying a low energy demand of bicarbonate use via a CCM. In short-term pH drift experiments, only treatment with the carbonic anhydrase inhibitor ethoxyzolamide (EZ) slowed down the rise in pH considerably. EZ was also the only inhibitor that altered the final pH attained, although marginally. In growth experiments, CO2 availability was manipulated by changing the pH in closed flasks at a fixed dissolved inorganic carbon (DIC) concentration. Low-light-treated samples showed lower growth rates in elevated CO2conditions. No CO2 effect was recorded under high light exposure. The maximal photosynthetic capacity, however, increased with CO2 concentration in saturating, but not in subsaturating, light intensities. Growth and photosynthetic capacity therefore responded in opposite ways to increasing CO2 availability. The capacity to photoacclimate to high and low photon flux appeared not to be affected by CO2treatments. However, photoacclimation was restricted to growth photon fluxes between 30 and 300 µmol photons m-2 s-1. The light saturation points for photosynthetic electron transport and for growth coincided at 100 µmol photons m-2 s-1. Below 100 µmol photons m-2 s-1 the light saturation point for photosynthesis was higher than the growth photon flux (i.e. photosynthesis was not light saturated under growth conditions), whereas at higher growth photon flux, photosynthesis was saturated below growth light levels.

Packaging and testing of fiber Bragg gratings for use as strain sensor for rock specimens

This paper reports a packaging and calibration procedure for surface mounting of fiber Bragg grating (FBG) sensors to measure strain in rocks. The packaging of FBG sensors is performed with glass fiber and polyester resin, and then subjected to tensile loads in order to obtain strength and deformability parameters, necessaries to assess the mechanical performance of the sensor packaging. For a specific package, an optimal curing condition has been found, showing good repeatability and adaptability for non-planar surfaces, such as occurs in rock engineering. The successfully packaged sensors and electrical strain gages were attached to standard rock specimens of gabbro. Longitudinal and transversal strains under compression loads were measured with both techniques, showing that response of FBG sensors is linear and reliable. An analytical model is used to characterize the influences of rock substrate and FBG packaging in strain transmission. As a result, we obtained a sensor packaging for non-planar and complex natural material under acceptable sensitivity suitable for very small strains as occurs in hard rocks.

Development and Testing of a Fiber Bragg Grating Strain Sensor for Uniaxial Compression of Rock Specimens

Los sensores de fibra óptica son una tecnología que ha madurado en los últimos años, sin embargo, se requiere un mayor desarrollo de aplicaciones para materiales naturales como las rocas, que por ser agregados complejos pueden contener partículas minerales y fracturas de tamaño mucho mayor que las galgas eléctricas usadas tradicionalmente para medir deformaciones en las pruebas de laboratorio, ocasionando que los resultados obtenidos puedan ser no representativos. En este trabajo fueron diseñados, fabricados y probados sensores de deformación de gran área y forma curvada, usando redes de Bragg en fibra óptica (FBG) con el objetivo de obtener registros representativos en rocas que contienen minerales y estructuras de diversas composiciones, tamaños y direcciones. Se presenta el proceso de elaboración del transductor, su caracterización mecánica, su calibración y su evaluación en pruebas de compresión uniaxial en muestras de roca. Para verificar la eficiencia en la transmisión de la deformación de la roca al sensor una vez pegado, también fue realizado el análisis de la transferencia incluyendo los efectos del adhesivo, de la muestra y del transductor. Los resultados experimentales indican que el sensor desarrollado permite registro y transferencia de la deformación fiables, avance necesario para uso en rocas y otros materiales heterogénos, señalando una interesante perspectiva para aplicaciones sobre superficies irregulares, pues permite aumentar a voluntad el tamaño y forma del área de registro, posibilita también obtener mayor fiabilidad de resultados en muestras de pequeño tamaño y sugiere su conveniencia en obras, en las cuales los sistemas eléctricos tradicionales tienen limitaciones. ABSTRACT Optical fiber sensors are a technology that has matured in recent years, however, further development for rock applications is needed. Rocks contain mineral particles and features larger than electrical strain gauges traditionally used in laboratory tests, causing the results to be unrepresentative. In this work were designed, manufactured, and tested large area and curved shape strain gages, using fiber Bragg gratings in optical fiber (FBG) in order to obtain representative measurement on surface rocks samples containing minerals and structures of different compositions, sizes and directions. This reports presents the processes of manufacturing, mechanical characterization, calibration and evaluation under uniaxial compression tests on rock samples. To verify the efficiency of rock deformation transmitted to attached sensor, it was also performed the analysis of the strain transfer including the effects of the bonding, the sample and the transducer. The experimental results indicate that the developed sensor enables reliable measurements of the strain and its transmission from rock to sensor, appropriate for use in heterogeneous materials, pointing an interesting perspective for applications on irregular surfaces, allowing increasing at will the size and shape of the measurement area. This research suggests suitability of the optical strain gauge for real scale, where traditional electrical systems have demonstrated some limitations.

(Table 2) Rate of reduction in cell size (apical length) and growth rate for seven Fragilariopsis kerguelensis strains sampled during POLARSTERN cruise ANT-XXI/3

The planktonic diatom Fragilariopsis kerguelensis plays an important role in the biogeochemical cycles of the Southern Ocean, where remains of its frustules form the largest deposit of biogenic silica anywhere in the world. We assessed the genetic identity of 26 strains, from cells collected at various sites in the Southern Ocean, using three molecular markers, LSU and ITS rDNA and rbcL. The LSU sequences were identical among the tested strains, ITS sequences were highly similar, and only one base pair difference was detected among the rbcL sequences. These results, together with a large number of successful mating experiments demonstrated that the strains belong to a single biological species. We investigated the mating system and life cycle traits of F. kerguelensis. Cell size diminished gradually in clonal strains. Gamete formation only occurred when strains of opposite mating type - within a cell size range of 7-36 µm - were mixed together. Two binucleate gametes were formed in each gametangium and gamete conjugation produced a zygote that had four nuclei and was surrounded by thin siliceous scales. Two out of the four nuclei subsequently degenerated and the zygote expanded to form an auxospore surrounded by a transverse and a longitudinal perizonium. Staining with the fluorochrome PDMPO provided for the first time a clear demonstration that the longitudinal perizonium is formed after auxospore expansion is complete. Initial cells produced within the mature auxospores were 78-101 µm in length. Various authors have shown that the average valve size of F. kerguelensis varies in sediment samples collected in regions and seasons with different primary production regimes and this parameter has thus been proposed as a biological proxy for palaeo-productivity. A better understanding of the life cycle of F. kerguelensis should help the design of future investigations aimed at testing the link between cell size distribution in the natural environment and the role that environmental factors might have in the regulation of population cell size.

Long-term effects of land application of domestic wastewater : Roswell, New Mexico, slow rate irrigation site /

Mode of access: Internet.

Long-term effects of land application of domestic wastewater : Dickinson, North Dakota, slow rate irrigation site /

Mode of access: Internet.

Heat stress, heat strain, and productivity in Washington State tree fruit harvesters

Thesis (Master's)--University of Washington, 2016-06

Seawater carbonate chemistry, nutrients, and Calcidiscus leptoporus (strain RCC1135) growth rate and calcification rate during experiments, 2012

The coccolithophore Calcidiscus leptoporus was grown in batch culture under nitrogen (N) as well as phosphorus (P) limitation. Growth rate, particulate inorganic carbon (PIC), particulate organic carbon (POC), particulate organic nitrogen (PON), and particulate organic phosphorus (POP) production were determined and coccolith morphology was analysed. While PON production decreased by 70% under N-limitation and POP production decreased by 65% under P-limitation, growth rate decreased by 33% under N- as well as P-limitation. POC as well as PIC production (calcification rate) increased by 27% relative to the control under P-limitation, and did not change under N-limitation. Coccolith morphology did not change in response to either P or N limitation. While these findings, supported by a literature survey, suggest that coccolith morphogenesis is not hampered by either P or N limitation, calcification rate might be. The latter conclusion is in apparent contradiction to our data. We discuss the reasons for this inference.

Seawater carbonate chemistry, growth rate and Emiliania huxleyi (strain AC481) biological processes during experiments, 2010

The impact of ocean acidification and increased water temperature on marine ecosystems, in particular those involving calcifying organisms, has been gradually recognised. We examined the individual and combined effects of increased pCO2 (180 ppmV CO2, 380 ppmV CO2 and 750 ppmV CO2 corresponding to past, present and future CO2 conditions, respectively) and temperature (13 °C and 18 °C) during the exponential growth phase of the coccolithophore E. huxleyi using batch culture experiments. We showed that cellular production rate of Particulate Organic Carbon (POC) increased from the present to the future CO2 treatments at 13 °C. A significant effect of pCO2 and of temperature on calcification was found, manifesting itself in a lower cellular production rate of Particulate Inorganic Carbon (PIC) as well as a lower PIC:POC ratio at future CO2 levels and at 18 °C. Coccosphere-sized particles showed a size reduction with both increasing temperature and CO2concentration. The influence of the different treatments on coccolith morphology was studied by categorizing SEM coccolith micrographs. The number of well-formed coccoliths decreased with increasing pCO2 while temperature did not have a significant impact on coccolith morphology. No interacting effects of pCO2 and temperature were observed on calcite production, coccolith morphology or on coccosphere size. Finally, our results suggest that ocean acidification might have a larger adverse impact on coccolithophorid calcification than surface water warming.

Neuromuscular adaptations in football athletes with prior history of hamstring strain injury

Background: Hamstring strain injuries (HSI) are one of the most common injuries in a wide variety of running-sports, resulting in a considerable loss of competition and training time. One of the most problematic consequences regarding HSI is the recurrence rate and its non-decrease over the past decades, despite increasing evidence. Recent studies also found several maladaptations post-HSI probably due to neuromuscular inhibition and it has been proposed that these adaptations post-injury may contribute as risk factors for the injury-reinjury cycle and high recurrence rates. Furthermore it has been recently proposed not to disregard the inter-relationship between these adaptations and risk-factors post-injury in order to better understand the mechanisms of this complex injury. Objective: To determine, analyze and correlate neuromuscular adaptations in amateur football players with prior history of HSI per comparison to uninjured athletes in similar conditions. Methodology: Every participant was subjected to isokinetic concentric (60 and 240deg.sec) and eccentric (30 and 120deg.sec¯¹) testing, and peak torque, angle of peak torque and hamstrings to quadriceps (H:Q) conventional ratios were measured, myoelectrical activity of Bicep Femoris (BF) and Medial Hamstrings (MH) were also measured during isokinetic eccentric testing at both velocities and muscle activation percentages were calculated at 30, 50 and 100ms after onset of contraction. Furthermore active and passive knee extension, knee joint position sense (JPS) test, triple-hop distance (THD) test and core stability (flexors and extensors endurance, right and left side bridge test) were used and correlated. Results: Seventeen players have participated in this study: 10 athletes with prior history of HSI, composing the Hamstring injury group (HG) and 7 athletes without prior severe injuries as control group (CG). We found statistical significant differences between HG injured and uninjured sides in the BF myoelectrical activity at almost all times in both velocities and between HG injured and CG non-dominant sides at 100ms in eccentric 120deg.sec¯¹ velocity (p<.05). We found no differences in MH activity. Regarding proprioception we found differences between the HG injured and uninjured sides (p=.027). We found no differences in the rest of used tests. However, significant correlation between myoelectrical activation at 100ms in 120deg.sec¯¹ testing and JPS with initial position at 90º (r-.372; p=0.031) was found, as well as between isokinetic H:Q ratio at 240deg.sec and THD score (r=-.345; p=.045). Conclusion: We found significant differences that support previous research regarding neuromuscular adaptations and BF inhibition post-HSI. Moreover, to our knowledge, this was the first study that found correlation between these adaptations, and may open a door to new perspectives and future studies.

Small strain elastic behaviour of unsaturated soil investigated by bender/extender element testing

The aim of this project was to investigate very small strain elastic behaviour of soils under unsaturated conditions, using bender/extender element (BEE) testing. The behaviour of soils at very small strains has been widely studied under saturated conditions, whereas much less work has been performed on very small strain behaviour under unsaturated conditions. A suction-controlled double wall triaxial apparatus for unsaturated soil testing was modified to incorporate three pairs of BEEs transmitting both shear and compression waves with vertical and horizontal directions of wave transmission and wave polarisation. Various different techniques for measuring wave travel time were investigated in both the time domain and the frequency domain and it was concluded that, at least for the current experimental testing programme, peak-to-first-peak in the time domain was the most reliable technique for determining wave travel time. An experimental test programme was performed on samples of compacted speswhite kaolin clay. Two different forms of compaction were employed (i.e. isotropic and anisotropic). Compacted kaolin soil samples were subjected to constant suction loading and unloading stages at three different values of suction, covering both unsaturated conditions (s= 50kPa and s= 300kPa) and saturated conditions (s=0). Loading and unloading stages were performed at three different values of stress ratio (η=0, η=1 and η=-1 ). In some tests a wetting-drying cycle was performed before or within the loading stage, with the wetting-drying cycles including both wetting-induced swelling and wetting-induced collapse compression. BEE tests were performed at regular intervals throughout all test stages, to measure shear wave velocity Vs and compression wave velocity Vp and hence to determine values of shear modulus G and constrained modulus M. The experimental test programme was designed to investigate how very small strain shear modulus G and constrained modulus M varied with unsaturated state variables, including how anisotropy of these parameters developed either with stress state (stress-induced anisotropy) or with previous straining (strain-induced anisotropy). A new expression has been proposed for the very small strain shear modulus G of an isotropic soil under saturated and unsaturated conditions. This expression relates the variation of G to only mean Bishop’s stress p* and specific volume v, and it converges to a well-established expression for saturated soils as degree of saturation approaches 1. The proposed expression for G is able to predict the variation of G under saturated and unsaturated conditions at least as well as existing expressions from the literature and it is considerably simpler (employing fewer state variables and fewer soil constants). In addition, unlike existing expressions from the literature, the values of soil constants in the proposed new expression can be determined from a saturated test. It appeared that, in the current project at least, any strain-induced anisotropy of very small strain elastic behaviour was relatively modest, with the possible exception of loading in triaxial extension. It was therefore difficult to draw any firm conclusion about evolution of strain-induced anisotropy and whether it depended upon the same aspects of soil fabric as evolution of anisotropy of large strain plastic behaviour. Stress-induced anisotropy of very small strain elastic behaviour was apparent in the experimental test programme. An attempt was made to extend the proposed expression for G to include the effect of stress-induced anisotropy. Interpretation of the experimental results indicated that the value of shear modulus was affected by the values of all three principal Bishop’s stresses (in the direction of wave transmission, the direction of wave polarisation and the third mutually perpendicular direction). However, prediction of stress-induced anisotropy was only partially successful, and it was concluded that the effect of Lode angle was also significant.