Using 3D photogrammetry from ROV video to quantify cold-water coral reef structural complexity and investigate its influence on biodiversity and community assemblage

Fine-scale structural complexity created by reef-building coral in shallow-water environments is influential on biodiversity, species assemblage and functional trait expression. Cold-water coral reefs are also hotspots of biodiversity, often attributed to the hard surface and structural complexity provided by the coral. However, that complexity has seldom been quantified on a centimetric scale in cold-water coral reefs, unlike their shallow-water counterparts, and has therefore never been linked in a similar way to the reef inhabitant community. Structure from motion techniques which create high-resolution 3D models of habitats from sequences of photographs is being increasingly utilised, in tandem with 3D spatial analysis to create useful 3D metrics, such as rugosity. Here, we demonstrate the use of ROV video transect data for 3D reconstructions of cold-water coral reefs at depths of nearly 1000 m in the Explorer Canyon, a tributary of Whittard Canyon, NE Atlantic. We constructed 40 3D models of approximately 25-m-length video transects using Agisoft Photoscan software, resulting in sub-centimetre resolution reconstructions. Digital elevation models were utilised to derive rugosity metrics, and orthomosaics were used for coral coverage assessment. We found rugosity values comparable to shallow-water tropical coral reef rugosity. Reef and nearby non-reef communities differed in assemblage composition, which was driven by depth and rugosity. Species richness, epifauna abundance and fish abundance increased with structural complexity, being attributed to an increase in niches, food, shelter and alteration of physical water movement. Biodiversity plateaued at higher rugosity, illustrating the establishment of a specific reef community supported by more than 30% coral cover. The proportion of dead coral to live coral had limited influence on the community structure; instead, within-reef patterns were explained by depth and rugosity, though our results were confounded to a certain extent by multi-collinearity. Fine-scale structural complexity appeared to be integral to local-scale ecological patterns in cold-water coral reef communities

Force steps during viral DNA packaging ?

Biophysicists and structural biologists increasingly acknowledge the role played by the mechanical properties of macromolecules as a critical element in many biological processes. This change has been brought about, in part, by the advent of single molecule biophysics techniques that have made it possible to exert piconewton forces on key macromolecules and observe their deformations at nanometer length scales, as well as to observe the mechanical action of macromolecules such as molecular motors. This has opened up immense possibilities for a new generation of mechanical investigations that will respond to such measurements in an attempt to develop a coherent theory for the mechanical behavior of macromolecules under conditions where thermal and chemical effects are on an equal footing with deterministic forces. This paper presents an application of the principles of mechanics to the problem of DNA packaging, one of the key events in the life cycle of bacterial viruses with special reference to the nature of the internal forces that are built up during the DNA packaging process.Comment: 18 pages, 7 figures, To appear in the Journal of Mechanics and Physics of Solid

Is inhaled prophylactic heparin useful for prevention and management of pneumonia in ventilated ICU patients?

Purpose: The purpose was to determine the efficacy of prophylactic inhaled heparin for the prevention and treatment of pneumonia in patients receiving mechanical ventilation (MV)

Quantum Communication

Quantum communication, and indeed quantum information in general, has changed the way we think about quantum physics. In 1984 and 1991, the first protocol for quantum cryptography and the first application of quantum non-locality, respectively, attracted a diverse field of researchers in theoretical and experimental physics, mathematics and computer science. Since then we have seen a fundamental shift in how we understand information when it is encoded in quantum systems. We review the current state of research and future directions in this new field of science with special emphasis on quantum key distribution and quantum networks.Comment: Submitted version, 8 pg (2 cols) 5 fig

Investigation of a Neuronal Nitric Oxide Synthase Gene (NOS1) Polymorphism in a Multiple Sclerosis Population

Multiple Sclerosis (MS) is a chronic neurological disease characterized by demyelination associated with infiltrating white blood cells in the central nervous system (CNS). Nitric oxide synthases (NOS) are a family of enzymes that control the production of nitric oxide. It is possible that neuronal NOS could be involved in MS pathophysiology and hence the nNOS gene is a potential candidate for involvement in disease susceptibility. The aim of this study was to determine whether allelic variation at the nNOS gene locus is associated with MS in an Australian cohort. DNA samples obtained from a Caucasian Australian population affected with MS and an unaffected control population, matched for gender, age and ethnicity, were genotyped for a microsatellite polymorphism in the promoter region of the nNOS gene. Allele frequencies were compared using chi-squared based statistical analyses with significance tested by Monte Carlo simulation. Allelic analysis of MS cases and controls produced a chi-squared value of 5.63 with simulated P=0.96 (OR(max)=1.41, 95% CI: 0.926-2.15). Similarly, a Mann-Whitney U analysis gave a non-significant P-value of 0.377 for allele distribution. No differences in allele frequencies were observed for gender or clinical course subtype (P>0.05). Statistical analysis indicated that there is no association of this nNOS variant and MS and hence the gene does not appear to play a genetically significant role in disease susceptibility

Soil bacterial and fungal communities across a pH gradient in an arable soil

Soils collected across a long-term liming experiment (pH 4.0-8.3), in which variation in factors other than pH have been minimized, were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial taxa, fungi and bacteria. We hypothesized that bacterial communities would be more strongly influenced by pH than fungal communities. To determine the relative abundance of bacteria and fungi, we used quantitative PCR (qPCR), and to analyze the composition and diversity of the bacterial and fungal communities, we used a bar-coded pyrosequencing technique. Both the relative abundance and diversity of bacteria were positively related to pH, the latter nearly doubling between pH 4 and 8. In contrast, the relative abundance of fungi was unaffected by pH and fungal diversity was only weakly related with pH. The composition of the bacterial communities was closely defined by soil pH; there was as much variability in bacterial community composition across the 180-m distance of this liming experiment as across soils collected from a wide range of biomes in North and South America, emphasizing the dominance of pH in structuring bacterial communities. The apparent direct influence of pH on bacterial community composition is probably due to the narrow pH ranges for optimal growth of bacteria. Fungal community composition was less strongly affected by pH, which is consistent with pure culture studies, demonstrating that fungi generally exhibit wider pH ranges for optimal growth. The ISME Journal (2010) 4, 1340-1351; doi: 10.1038/ismej.2010.58; published online 6 May 2010&nbsp

Phylogeography of the iconic Australian pink cockatoo, Lophochroa leadbeateri

The pink cockatoo (Lophochroa leadbeateri; or Major Mitchell’s cockatoo) is one of Australia’s most iconic bird species. Two subspecies based on morphology are separated by a biogeographical divide, the Eyrean Barrier. Testing the genetic basis for this subspecies delineation, clarifying barriers to gene flow and identifying any cryptic genetic diversity will likely have important implications for conservation and management. Here, we used genome-wide single nucleotide polymorphisms (SNPs) and mitochondrial DNA data to conduct the first range-wide genetic assessment of the species. The aims were to investigate the phylogeography of the pink cockatoo, to characterize conservation units and to reassess subspecies boundaries. We found consistent but weak genetic structure between the two subspecies based on nuclear SNPs. However, phylogenetic analysis of nuclear SNPs and mitochondrial DNA sequence data did not recover reciprocally monophyletic groups, indicating incomplete evolutionary separation between the subspecies. Consequently, we have proposed that the two currently recognized subspecies be treated as separate management units rather than evolutionarily significant units. Given that poaching is suspected to be a threat to this species, we assessed the utility of our data for wildlife forensic applications. We demonstrated that a subspecies identification test could be designed using as few as 20 SNPs

DNAJC21 Mutations Link a Cancer-Prone Bone Marrow Failure Syndrome to Corruption in 60S Ribosome Subunit Maturation

This work was funded by The Medical Research Council UK (MR/K000292/1), Children with Cancer UK (2013/144), Barts and The London Charity (845/1796), and Leukaemia Lymphoma Research/Bloodwise (14032)

Observer variability of absolute and relative thrombus density measurements in patients with acute ischemic stroke

Introduction: Thrombus density may be a predictor for acute ischemic stroke treatment success. However, only limited data on observer variability for thrombus density measurements exist. This study assesses the variability and bias of four common thrombus density measurement methods by expert and non-expert observers. Methods: For 132 consecutive patients with acute ischemic stroke, three experts and two trained observers determined thrombus density by placing three standardized regions of interest (ROIs) in the thrombus and corresponding contralateral arterial segment. Subsequently, absolute and relative thrombus densities were determined using either one or three ROIs. Intraclass correlation coefficient (ICC) was determined, and Bland–Altman analysis was performed to evaluate interobserver and intermethod agreement. Accuracy of the trained observer was evaluated with a reference expert observer using the same statistical analysis. Results: The highest interobserver agreement was obtained for absolute thrombus measurements using three ROIs (ICCs ranging from 0.54 to 0.91). In general, interobserver agreement was lower for relative measurements, and for using one instead of three ROIs. Interobserver agreement of trained non-experts and experts was similar. Accuracy of the trained observer measurements was comparable to the expert interobserver agreement and was better for absolute measurements and with three ROIs. The agreement between the one ROI and three ROI methods was good. Conclusion: Absolute thrombus density measurement has superior interobserver agreement compared to relative density measurement. Interobserver variation is smaller when multiple ROIs are used. Trained non-expert observers can accurately and reproducibly assess absolute thrombus densities using three ROIs