Vibration-tolerant narrow-linewidth semiconductor disk laser using novel frequency-stabilisation schemes

This paper will present developments in narrow-linewidth semiconductor-disk-laser systems using novel frequency-stabilisation schemes for reduced sensitivity to mechanical vibrations, a critical requirement for mobile applications. Narrow-linewidth single-frequency lasers are required for a range of applications including metrology and high-resolution spectroscopy. Stabilisation of the laser was achieved using a monolithic fibre-optic ring resonator with free spectral range of 181 MHz and finesse of 52 to act as passive reference cavity for the laser. Such a cavity can operate over a broad wavelength range and is immune to a wide band of vibrational frequency noise due to its monolithic implementation. The frequency noise of the locked system has been measured and compared to typical Fabry-Perot-locked lasers using vibration equipment to simulate harsh environments, and analysed here. Locked linewidths of < 40 kHz have been achieved. These developments offer a portable, narrow-linewidth laser system for harsh environments that can be flexibly designed for a range of applications

Results of the 2016 Indianapolis Biodiversity Survey, Marion County, Indiana

Surprising biodiversity can be found in cities, but urban habitats are understudied. We report on a bioblitz conducted primarily within a 24-hr period on September 16 and 17, 2016 in Indianapolis, Indiana, USA. The event focused on stretches of three waterways and their associated riparian habitat: Fall Creek (20.6 ha; 51 acres), Pleasant Run (23.5 ha; 58 acres), and Pogue’s Run (27.1 ha; 67 acres). Over 75 scientists, naturalists, students, and citizen volunteers comprised 14 different taxonomic teams. Five hundred ninety taxa were documented despite the rainy conditions. A brief summary of the methods and findings are presented here. Detailed maps of survey locations and inventory results are available on the Indiana Academy of Science website (https://www.indianaacademyofscience.org/)

Field-Grown Transgenic Switchgrass (Panicum virgatum L.) with Altered Lignin Does Not Affect Soil Chemistry, Microbiology, and Carbon Storage Potential

Cell wall recalcitrance poses a major challenge on cellulosic biofuel production from feedstocks such as switchgrass (Panicum virgatum L.). As lignin is a known contributor of recalcitrance, transgenic switchgrass plants with altered lignin have been produced by downregulation of caffeic acid O-methyltransferase (COMT). Field trials of COMT-downregulated plants previously demonstrated improved ethanol conversion with no adverse agronomic effects. However, the rhizosphere impacts of altering lignin in plants are unknown. We hypothesized that changing plant lignin composition may affect residue degradation in soils, ultimately altering soil processes. The objective of this study was to evaluate effects of two independent lines of COMT-downregulated switchgrass plants on soils in terms of chemistry, microbiology, and carbon cycling when grown in the field. Over the first two years of establishment, we observed no significant differences between transgenic and control plants in terms of soil pH or the total concentrations of 19 elements. An analysis of soil bacterial communities via high-throughput 16S rRNA gene amplicon sequencing revealed no effects of transgenic plants on bacterial diversity, richness, or community composition. We also did not observe a change in the capacity for soil carbon storage: There was no significant effect on soil respiration or soil organic matter. After five years of establishment, δ13C of plant roots, leaves, and soils was measured and an isotopic mixing model used to estimate that 11.2 to 14.5% of soil carbon originated from switchgrass. Switchgrass-contributed carbon was not significantly different between transgenic and control plants. Overall, our results indicate that over the short term (two and five years), lignin modification in switchgrass through manipulation of COMT expression does not have an adverse effect on soils in terms of total elemental composition, bacterial community structure and diversity, and capacity for carbon storage

A study of the impacts of variable factors on built environment graduates’ prospects

This paper investigates the impacts of variable factors, such as practical experience and factors related to study style, on employment outcomes and patterns of built environment graduates in Australia. This paper also compares the employment prospects of different built environment sub-disciplines, including Architecture, Construction, Real Estate and Urban Planning and Regional Studies. Practical experience and the possibility of work with final year employers after graduation were found to have a statistically significant impact on the employment outcomes for graduates of built environment and all of its sub-disciplines. However, degree level and type of university attended were not found to have a statistically significant impact. Attendance type and employment mode in the final year of study had a statistically significant impact on the employment patterns for graduates of built environment and all of its sub-disciplines. The graduates who studied part-time and worked full-time in their final year of study were more likely to secure full-time jobs after graduation. The findings of this paper can be used by built environment graduates to identify the variable factors which they can change in order to enhance their employment prospects

Connectivity: insights from the U.S. Long Term Ecological Research Network

Ecosystems across the United States are changing in complex and surprising ways. Ongoing demand for critical ecosystem services requires an understanding of the populations and communities in these ecosystems in the future. This paper represents a synthesis effort of the U.S. National Science Foundation-funded Long-Term Ecological Research (LTER) network addressing the core research area of “populations and communities.” The objective of this effort was to show the importance of long-term data collection and experiments for addressing the hardest questions in scientific ecology that have significant implications for environmental policy and management. Each LTER site developed at least one compelling case study about what their site could look like in 50–100 yr as human and environmental drivers influencing specific ecosystems change. As the case studies were prepared, five themes emerged, and the studies were grouped into papers in this LTER Futures Special Feature addressing state change, connectivity, resilience, time lags, and cascading effects. This paper addresses the “connectivity” theme and has examples from the Phoenix (urban), Niwot Ridge (alpine tundra), McMurdo Dry Valleys (polar desert), Plum Island (coastal), Santa Barbara Coastal (coastal), and Jornada (arid grassland and shrubland) sites. Connectivity has multiple dimensions, ranging from multi-scalar interactions in space to complex interactions over time that govern the transport of materials and the distribution and movement of organisms. The case studies presented here range widely, showing how land-use legacies interact with climate to alter the structure and function of arid ecosystems and flows of resources and organisms in Antarctic polar desert, alpine, urban, and coastal marine ecosystems. Long-term ecological research demonstrates that connectivity can, in some circumstances, sustain valuable ecosystem functions, such as the persistence of foundation species and their associated biodiversity or, it can be an agent of state change, as when it increases wind and water erosion. Increased connectivity due to warming can also lead to species range expansions or contractions and the introduction of undesirable species. Continued long-term studies are essential for addressing the complexities of connectivity. The diversity of ecosystems within the LTER network is a strong platform for these studies

Hundreds of variants clustered in genomic loci and biological pathways affect human height

Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P < 0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.

Adaptor protein-2 sigma subunit mutations causing familial hypocalciuric hypercalcaemia type 3 (FHH3) demonstrate genotype-phenotype correlations, codon bias and dominant-negative effects

The adaptor protein-2 sigma subunit (AP2σ2) is pivotal for clathrin-mediated endocytosis of plasma membrane constituents such as the calcium-sensing receptor (CaSR). Mutations of the AP2σ2 Arg15 residue result in familial hypocalciuric hypercalcaemia type 3 (FHH3), a disorder of extracellular calcium (Ca(2+) o) homeostasis. To elucidate the role of AP2σ2 in Ca(2+) o regulation, we investigated 65 FHH probands, without other FHH-associated mutations, for AP2σ2 mutations, characterized their functional consequences and investigated the genetic mechanisms leading to FHH3. AP2σ2 mutations were identified in 17 probands, comprising 5 Arg15Cys, 4 Arg15His and 8 Arg15Leu mutations. A genotype-phenotype correlation was observed with the Arg15Leu mutation leading to marked hypercalcaemia. FHH3 probands harboured additional phenotypes such as cognitive dysfunction. All three FHH3-causing AP2σ2 mutations impaired CaSR signal transduction in a dominant-negative manner. Mutational bias was observed at the AP2σ2 Arg15 residue as other predicted missense substitutions (Arg15Gly, Arg15Pro and Arg15Ser), which also caused CaSR loss-of-function, were not detected in FHH probands, and these mutations were found to reduce the numbers of CaSR-expressing cells. FHH3 probands had significantly greater serum calcium (sCa) and magnesium (sMg) concentrations with reduced urinary calcium to creatinine clearance ratios (CCCR) in comparison with FHH1 probands with CaSR mutations, and a calculated index of sCa × sMg/100 × CCCR, which was ≥ 5.0, had a diagnostic sensitivity and specificity of 83 and 86%, respectively, for FHH3. Thus, our studies demonstrate AP2σ2 mutations to result in a more severe FHH phenotype with genotype-phenotype correlations, and a dominant-negative mechanism of action with mutational bias at the Arg15 residue

A genome-wide association study of early menopause and the combined impact of identified variants

Early menopause (EM) affects up to 10% of the female population, reducing reproductive lifespan considerably. Currently, it constitutes the leading cause of infertility in the western world, affecting mainly those women who postpone their first pregnancy beyond the age of 30 years. The genetic aetiology of EM is largely unknown in the majority of cases. We have undertaken a meta-analysis of genome-wide association studies (GWASs) in 3493 EM cases and 13 598 controls from 10 independent studies. No novel genetic variants were discovered, but the 17 variants previously associated with normal age at natural menopause as a quantitative trait (QT) were also associated with EM and primary ovarian insufficiency (POI). Thus, EM has a genetic aetiology which overlaps variation in normal age at menopause and is at least partly explained by the additive effects of the same polygenic variants. The combined effect of the common variants captured by the single nucleotide polymorphism arrays was estimated to account for ∼30% of the variance in EM. The association between the combined 17 variants and the risk of EM was greater than the best validated non-genetic risk factor, smokin