Investigations into the molecular effects of single nucleotide polymorphism

Objectives: DNA sequences are very rich in short repeats and their pattern can be altered by point mutations. We wanted to investigate the effect of single nucleotide polymorphism (SNP) on the pattern of short DNA repeats and its biological consequences. Methods: Analysis of the pattern of short DNA repeats of the Thy-1 sequence with and without SNP. Searching for DNA-binding factors in any region of significance. Results: Comparing the pattern of short repeats in the Thy-1 gene sequences of Turkish patients with ataxia telangiectasia (AT) with the `wild type' sequence from the DNA database, we identified a missing 8-bp repeat element due to an SNP in position 1271 (intron II) in AT-DNA sequences. Only the mutated sequence had the potential for the formation of a stem loop in DNA or pre-mRNA. In super-shift experiments we found that DNA oligomers covering the area of this SNP formed a complex with proteins amongst which we identified the proliferating cell nuclear antigen (PCNA) protein. Conclusion: SNPs have the potential to alter DNA or pre-mRNA conformation. Although no SNP-depeding formation of the DNA-protein complex was evident, future investigations could reveal differential molecular mechanisms of cellular regulation. Copyright (C) 2001 S. Karger AG, Basel

Forward Skirt Structural Testing on the Space Launch System (SLS) Program

Structural testing was performed to evaluate heritage forward skirts from the Space Shuttle program for use on the Space Launch System (SLS) program. One forward skirt is located in each solid rocket booster. Heritage forward skirts are aluminum 2219 welded structures. Loads are applied at the forward skirt thrust post and ball assembly. Testing was needed because SLS ascent loads are roughly 40% higher than Space Shuttle loads. Testing objectives were to determine margins of safety, demonstrate reliability, and validate analytical models. Two forward skirts were structurally tested using the test configuration. The test stand applied loads to the thrust post. Four hydraulic actuators were used to apply axial load and two hydraulic actuators were used to apply radial and tangential loads. The first test was referred to as FSTA-1 (Forward Skirt Structural Test Article) and was performed in April/May 2014. The purpose of FSTA-1 was to verify the ultimate capability of the forward skirt subjected to ascent ultimate loads. Testing consisted of two liftoff load cases taken to 100% limit load followed by an ascent load case taken to 110% limit load. The forward skirt was unloaded to no load after each test case. Lastly, the forward skirt was tested to 140% limit and then to failure using the ascent loads. The second test was referred to as FSTA-2 and performed in July/August of 2014. The purpose of FSTA-2 was to verify the ultimate capability of the forward skirt subjected to liftoff ultimate loads. Testing consisted of six liftoff load cases taken to 100% limit load followed by the six liftoff cases taken to 140% limit load. Two ascent load cases were then tested to 100% limit load. The forward skirt was unloaded to no load after each test case. Lastly, the forward skirt was tested to 140% limit and then to failure using the ascent loads. The forward skirts on FSTA-1 and FSTA-2 successfully carried all applied liftoff and ascent load cases. Both FSTA-1 and FSTA-2 were tested to failure by increasing the ascent loads. Failure occurred in the forward skirt thrust post radius. The forward skirts on FSTA-1 and FSTA-2 had nearly identical failure modes. FSTA-1 failed at 1.72 times limit load and FSTA-2 failed at 1.62 times limit load. This difference is primarily attributed to variation in material properties in the thrust post region. Test data were obtained from strain gages, deflection gages, ARAMIS digital strain measurement, acoustic emissions, and high-speed video. Strain gage data and ARAMIS strain were compared to finite element (FE) analysis predictions. Both the forward skirt and tooling were modeled. This allows the analysis to simulate the loading as close as possible to actual test configuration. FSTA-1 and FSTA-2 were instrumented with over 200 strain gages to ensure all possible failure modes could be captured. However, it turned out that three gages provided critical strain data. One was located in the post bore and two on the post radius. More gages were not specified due to space limitations and the desire to not interfere with the use of the ARAMIS system on the post radius. Measured strains were compared to analysis results for the load cycle to failure. Note that FSTA-1 gages were lost before failure was reached. FSTA-2 gages made it to the failure load but one of the radius gages was lost before testing began. This gage was not replaced because of the time and cost associated with disassembly of the test structure. Correlation to analysis was excellent for FSTA-1. FSTA-2 was not quite as good because there was more residual strain from previous load cycles. FSTA-2 was loaded and unloaded with 12 liftoff cases and two ascent cases before taking the skirt to failure. FSTA-1 only had two liftoff cases and one ascent case before taking the skirt to failure. The ARAMIS system was used to determine strain at the post radius by processing digital images of a speckled paint pattern. Digital cameras recorded images of the speckled paint pattern. ARAMIS strain results for FSTA-2 just prior to failure. Note a high strain location develops near the left side. This high strain compares well to analysis prediction for both FSTA-1 and FSTA-2. The strain at this location was also plotted versus limit load. Both FSTA-1 and FSTA-2 had excellent correlation between ARAMIS and analysis strains. Acoustic emission (AE) sensors were used to monitor for damage formation that may occur during testing (e.g., crack formation and growth or propagation). AE was very important because after disassembly of FSTA-1, a crack was observed in the ball fitting radius. The ball fitting did not crack on FSTA-2. AE data was used to reconstruct when the crack occurred. The AE energy versus time plot for FSTA. The energy increased considerably at 850 seconds (152% limit load), indicating a crack could have formed at this point. The only visual evidence found that could have corresponded to this was the crack that initiated in the ball fitting. The cracks in the forward skirt aluminum structures would likely have been lower energy due to a lower modulus and all that were found after failure correlated to occurring after the initial crack in the post radius. This was verified by high-speed cameras used to record the failure

Forward Skirt Structural Testing on the Space Launch System (SLS) Program

Introduction: (a) Structural testing was performed to evaluate Space Shuttle heritage forward skirts for use on the Space Launch System (SLS) program, (b) Testing was required because SLS loads are approximately 35% greater than shuttle loads; and (c) Two forwards skirts were tested to failure

Forward Skirt Structural Testing on the Space Launch System (SLS) Program

Structural testing was performed to evaluate heritage forward skirts from the Space Shuttle program for use on the NASA Space Launch System (SLS) program. Testing was needed because SLS ascent loads are 35% higher than Space Shuttle loads. Objectives of testing were to determine margins of safety, demonstrate reliability, and validate analytical models. Testing combined with analysis was able to show heritage forward skirts were acceptable to use on the SLS program

Benthic Structure and Pelagic Food Sources Determine Post-settlement Snapper (Chrysophrys auratus) Abundance

Nursery habitats provide increased survival and growth and are a crucial early life-stage component for many fish and invertebrate populations. The biogenic structures that provide this nursery function, however, are increasingly degraded. Therefore, any effort to conserve, restore or replace habitat with artificial structure should be guided by an understanding of the value provided by that nursery habitat. Here, we experimentally manipulated structure across a number of sites by inserting pinnind bivalve mimics into the seabed and deploying video cameras to observe the response of post-settlement stage snapper, Chrysophrys auratus (Forster in Bloch and Schneider 1801). We also collected a range of environmental variables across these sites to determine the relative importance to snapper of benthic vs. pelagic productivity. While the abundance of snapper was low, our results demonstrated a strong association to structure relative to control plots. The environmental variable with the highest correlation to snapper abundance was the abundance of zooplankton eaten by snapper. This result was well supported by the dominance of zooplankton over small benthic invertebrates in snapper gut contents, and the weak influence of benthic infauna in our regression models. These regressions also demonstrated that when combined with zooplankton abundance, turbidity had a negative relationship to snapper abundance. This highlights the importance of relatively clear water in estuaries, which allows post-settlement snapper to more efficiently consume the zooplankton that are present in the water column. The third component that post-settlement snapper require is of course the presence of benthic structure. While benthic habitat structure was the strongest factor affecting juvenile snapper abundance, we did not find any correlations to suggest that this importance was related to energetic sheltering and access to locations with high food flux

An atlas of seabed biodiversity for Aotearoa New Zealand

\ua9 2023 Copernicus GmbH. All rights reserved. The waters of Aotearoa New Zealand span over 4.2ĝ€\uafmillionĝ€\uafkm2 of the South Pacific Ocean and harbour a rich diversity of seafloor-Associated taxa. Due to the immensity and remoteness of the area, there are significant gaps in the availability of data that can be used to quantify and map the distribution of seafloor and demersal biodiversity, limiting effective management. In this study, we describe the development and accessibility of an online atlas of seabed biodiversity that aims to fill these gaps. Species distribution models were developed for 579 taxa across four taxonomic groups: demersal fish, reef fish, subtidal invertebrates and macroalgae. Spatial layers for taxa distribution based on habitat suitability were statistically validated and then, as a further check, evaluated by taxonomic experts to provide measures of confidence to guide the future use of these layers. Spatially explicit uncertainty (SD) layers were also developed for each taxon distribution. We generated layer-specific metadata, including statistical and expert evaluation scores, which were uploaded alongside the accompanying spatial layers to the open access database Zenodo. This database provides the most comprehensive source of information on the distribution of seafloor taxa for Aotearoa New Zealand and is thus a valuable resource for managers, researchers and the public that will guide the management and conservation of seafloor communities. The atlas of seabed biodiversity for Aotearoa New Zealand is freely accessible via the open-Access database Zenodo under 10.5281/zenodo.7083642 (Stephenson et al., 2022)

Population-Level Metrics of Trophic Structure Based on Stable Isotopes and Their Application to Invasion Ecology

Biological invasions are a significant driver of human-induced global change and many ecosystems sustain sympatric invaders. Interactions occurring among these invaders have important implications for ecosystem structure and functioning, yet they are poorly understood. Here we apply newly developed metrics derived from stable isotope data to provide quantitative measures of trophic diversity within populations or species. We then use these to test the hypothesis that sympatric invaders belonging to the same functional feeding group occupy a smaller isotopic niche than their allopatric counterparts. Two introduced, globally important, benthic omnivores, Louisiana swamp crayfish (Procambarus clarkii) and carp (Cyprinus carpio), are sympatric in Lake Naivasha, Kenya. We applied our metrics to an 8-year data set encompassing the establishment of carp in the lake. We found a strong asymmetric interaction between the two invasive populations, as indicated by inverse correlations between carp abundance and measures of crayfish trophic diversity. Lack of isotopic niche overlap between carp and crayfish in the majority of years indicated a predominantly indirect interaction. We suggest that carp-induced habitat alteration reduced the diversity of crayfish prey, resulting in a reduction in the dietary niche of crayfish. Stable isotopes provide an integrated signal of diet over space and time, offering an appropriate scale for the study of population niches, but few isotope studies have retained the often insightful information revealed by variability among individuals in isotope values. Our population metrics incorporate such variation, are robust to the vagaries of sample size and are a useful additional tool to reveal subtle dietary interactions among species. Although we have demonstrated their applicability specifically using a detailed temporal dataset of species invasion in a lake, they have a wide array of potential ecological applications

An atlas of seabed biodiversity for Aotearoa New Zealand

The waters of Aotearoa New Zealand span over 4.2 million km2 of the South Pacific Ocean and harbour a rich diversity of seafloor-associated taxa. Due to the immensity and remoteness of the area, there are significant gaps in the availability of data that can be used to quantify and map the distribution of seafloor and demersal biodiversity, limiting effective management. In this study, we describe the development and accessibility of an online atlas of seabed biodiversity that aims to fill these gaps. Species distribution models were developed for 579 taxa across four taxonomic groups: demersal fish, reef fish, subtidal invertebrates and macroalgae. Spatial layers for taxa distribution based on habitat suitability were statistically validated and then, as a further check, evaluated by taxonomic experts to provide measures of confidence to guide the future use of these layers. Spatially explicit uncertainty (SD) layers were also developed for each taxon distribution. We generated layer-specific metadata, including statistical and expert evaluation scores, which were uploaded alongside the accompanying spatial layers to the open access database Zenodo. This database provides the most comprehensive source of information on the distribution of seafloor taxa for Aotearoa New Zealand and is thus a valuable resource for managers, researchers and the public that will guide the management and conservation of seafloor communities. The atlas of seabed biodiversity for Aotearoa New Zealand is freely accessible via the open-access database Zenodo under https://doi.org/10.5281/zenodo.7083642 (Stephenson et al., 2022).</p

Comparing the Invasibility of Experimental “Reefs” with Field Observations of Natural Reefs and Artificial Structures

Natural systems are increasingly being modified by the addition of artificial habitats which may facilitate invasion. Where invaders are able to disperse from artificial habitats, their impact may spread to surrounding natural communities and therefore it is important to investigate potential factors that reduce or enhance invasibility. We surveyed the distribution of non-indigenous and native invertebrates and algae between artificial habitats and natural reefs in a marine subtidal system. We also deployed sandstone plates as experimental ‘reefs’ and manipulated the orientation, starting assemblage and degree of shading. Invertebrates (non-indigenous and native) appeared to be responding to similar environmental factors (e.g. orientation) and occupied most space on artificial structures and to a lesser extent reef walls. Non-indigenous invertebrates are less successful than native invertebrates on horizontal reefs despite functional similarities. Manipulative experiments revealed that even when non-indigenous invertebrates invade vertical “reefs”, they are unlikely to gain a foothold and never exceed covers of native invertebrates (regardless of space availability). Community ecology suggests that invertebrates will dominate reef walls and algae horizontal reefs due to functional differences, however our surveys revealed that native algae dominate both vertical and horizontal reefs in shallow estuarine systems. Few non-indigenous algae were sampled in the study, however where invasive algal species are present in a system, they may present a threat to reef communities. Our findings suggest that non-indigenous species are less successful at occupying space on reef compared to artificial structures, and manipulations of biotic and abiotic conditions (primarily orientation and to a lesser extent biotic resistance) on experimental “reefs” explained a large portion of this variation, however they could not fully explain the magnitude of differences