Evolution of a stream ecosystem in recently deglaciated terrain

Climate change and associated glacial recession create new stream habitat that leads to the assembly of new riverine communities through primary succession. However, there are still very few studies of the patterns and processes of community assembly during primary succession for stream ecosystems. We illustrate the rapidity with which biotic communities can colonize and establish in recently formed streams by examining Stonefly Creek in Glacier Bay, Alaska (USA), which began to emerge from a remnant glacial ice mass between 1976 and 1979. By 2002, 57 macroinvertebrate and 27 microcrustacea species had become established. Within 10 years of the stream's formation, pink salmon and Dolly Varden charr colonized, followed by other fish species, including juvenile red and silver salmon, Coast Range sculpin, and sticklebacks. Stable-isotope analyses indicate that marine-derived nitrogen from the decay of salmon carcasses was substantially assimilated within the aquatic food web by 2004. The findings from Stonefly Creek are compared with those from a long-term study of a similarly formed but older stream (12 km to the northeast) to examine possible similarities in macroinvertebrate community and biological trait composition between streams at similar stages of development. Macroinvertebrate community assembly appears to have been initially strongly deterministic owing to low water temperature associated with remnant ice masses. In contrast, microcrustacean community assembly appears to have been more stochastic. However, as stream age and water temperature increased, macroinvertebrate colonization was also more stochastic, and taxonomic similarity between Stonefly Creek and a stream at the same stage of development was,<50%. However the most abundant taxa were similar, and functional diversity of the two communities was almost identical. Tolerance is suggested as the major mechanism of community assembly. The rapidity with which salmonids and invertebrate communities have become established across an entire watershed has implications for the conservation of biodiversity in freshwater habitats

Beyond Outerplanarity

We study straight-line drawings of graphs where the vertices are placed in convex position in the plane, i.e., convex drawings. We consider two families of graph classes with nice convex drawings: outer $k$-planar graphs, where each edge is crossed by at most $k$ other edges; and, outer $k$-quasi-planar graphs where no $k$ edges can mutually cross. We show that the outer $k$-planar graphs are $(\lfloor\sqrt{4k+1}\rfloor+1)$-degenerate, and consequently that every outer $k$-planar graph can be $(\lfloor\sqrt{4k+1}\rfloor+2)$-colored, and this bound is tight. We further show that every outer $k$-planar graph has a balanced separator of size $O(k)$. This implies that every outer $k$-planar graph has treewidth $O(k)$. For fixed $k$, these small balanced separators allow us to obtain a simple quasi-polynomial time algorithm to test whether a given graph is outer $k$-planar, i.e., none of these recognition problems are NP-complete unless ETH fails. For the outer $k$-quasi-planar graphs we prove that, unlike other beyond-planar graph classes, every edge-maximal $n$-vertex outer $k$-quasi planar graph has the same number of edges, namely $2(k-1)n - \binom{2k-1}{2}$. We also construct planar 3-trees that are not outer $3$-quasi-planar. Finally, we restrict outer $k$-planar and outer $k$-quasi-planar drawings to \emph{closed} drawings, where the vertex sequence on the boundary is a cycle in the graph. For each $k$, we express closed outer $k$-planarity and \emph{closed outer $k$-quasi-planarity} in extended monadic second-order logic. Thus, closed outer $k$-planarity is linear-time testable by Courcelle's Theorem.Comment: Appears in the Proceedings of the 25th International Symposium on Graph Drawing and Network Visualization (GD 2017

Clinical biological and genetic heterogeneity of the inborn errors of pulmonary surfactant metabolism

Pulmonary surfactant is a multimolecular complex located at the air-water interface within the alveolus to which a range of physical (surface-active properties) and immune functions has been assigned. This complex consists of a surface-active lipid layer (consisting mainly of phospholipids), and of an aqueous subphase. From discrete surfactant sub-fractions one can isolate strongly hydrophobic surf acta nt proteins B (SP-B) and C (SP-C) as well as collectins SP-A and SP-D, which were shown to have specific structural, metabolic, or immune properties. Inborn or acquired abnormalities of the surfactant, qualitative or quantitative in nature, account for a number of human diseases. Beside hyaline membrane disease of the preterm neonate, a cluster of hereditary or acquired lung diseases has been characterized by periodic acid-Schiff-positive material filling the alveoli. From this heterogeneous nosologic group, at least two discrete entities presently emerge. The first is the SP-B deficiency, in which an essentially proteinaceous material is stored within the alveoli, and which represents an autosomal recessive Mendelian entity linked to the SFTPB gene (MIM 1786640). The disease usually generally entails neonatal respiratory distress with rapid fatal outcome, although partial or transient deficiencies have also been observed. The second is alveolar proteinosis, characterized by the storage of a mixed protein and lipid material, which constitutes a relatively heterogeneous clinical and biological syndrome, especially with regard to age at onset (from the neonate through to adulthood) as well as the severity of associated signs. Murine models, with a targeted mutation of the gene encoding granulocyte macrophage colony-stimulating factor (GM-CSF) (Csfgm) or the beta subunit of its receptor (II3rb1) support the hypothesis of an abnormality of surfactant turnover in which the alveolar macrophage is a key player. Apart from SP-B deficiency, in which a near-consensus diagnostic chart can be designed, the ascertainment of other abnormalities of surfactant metabolism is not straightforward. The disentanglement of this disease cluster is however essential to propose specific therapeutic procedures: repeated broncho-alveolar ravages, GM-CSF replacement, bone marrow grafting or lung transplantation

Performance of Small Cluster Surveys and the Clustered LQAS Design to estimate Local-level Vaccination Coverage in Mali

<p>Abstract</p> <p>Background</p> <p>Estimation of vaccination coverage at the local level is essential to identify communities that may require additional support. Cluster surveys can be used in resource-poor settings, when population figures are inaccurate. To be feasible, cluster samples need to be small, without losing robustness of results. The clustered LQAS (CLQAS) approach has been proposed as an alternative, as smaller sample sizes are required.</p> <p>Methods</p> <p>We explored (i) the efficiency of cluster surveys of decreasing sample size through bootstrapping analysis and (ii) the performance of CLQAS under three alternative sampling plans to classify local VC, using data from a survey carried out in Mali after mass vaccination against meningococcal meningitis group A.</p> <p>Results</p> <p>VC estimates provided by a 10 × 15 cluster survey design were reasonably robust. We used them to classify health areas in three categories and guide mop-up activities: i) health areas not requiring supplemental activities; ii) health areas requiring additional vaccination; iii) health areas requiring further evaluation. As sample size decreased (from 10 × 15 to 10 × 3), standard error of VC and ICC estimates were increasingly unstable. Results of CLQAS simulations were not accurate for most health areas, with an overall risk of misclassification greater than 0.25 in one health area out of three. It was greater than 0.50 in one health area out of two under two of the three sampling plans.</p> <p>Conclusions</p> <p>Small sample cluster surveys (10 × 15) are acceptably robust for classification of VC at local level. We do not recommend the CLQAS method as currently formulated for evaluating vaccination programmes.</p

The ‘algebra of evolution’: the Robertson–Price identity and viability selection for body mass in a wild bird population

By the Robertson–Price identity, the change in a quantitative trait owing to selection, is equal to the trait’s covariance with relative fitness. In this study, we applied the identity to long-term data on superb fairy-wrens Malurus cyaneus, to estimate phenotypic and genetic change owing to juvenile viability selection. Mortality in the four-week period between fledging and independence was 40%, and heavier nestlings were more likely to survive, but why? There was additive genetic variance for both nestling mass and survival, and a positive phenotypic covariance between the traits, but no evidence of additive genetic covariance. Comparing standardized gradients, the phenotypic selection gradient was positive, βP = 0.108 (0.036, 0.187 95% CI), whereas the genetic gradient was not different from zero, βA = −0.025 (−0.19, 0.107 95% CI). This suggests that factors other than nestling mass were the cause of variation in survival. In particular, there were temporal correlations between mass and survival both within and between years. We suggest that use of the Price equation to describe cross-generational change in the wild may be challenging, but a more modest aim of estimating its first term, the Robertson–Price identity, to assess within-generation change can provide valuable insights into the processes shaping phenotypic diversity in natural populations. This article is part of the theme issue ‘Fifty years of the Price equation’G.K.H. was supported by the U.K. Natural Environment Research Council (grant no. NE/L002558/1) through the University of Edinburgh’s E3 Doctoral Training Partnership, and L.E.B.K. was funded by an ARC Future Fellowship FT110100453. The long-term superb fairy-wren study research has been facilitated by a series of Discovery Project grants from the Australian Research Council to A.C. and L.E.B.K., most recently DP150100298

Benchmarking the power of amateur observatories for TTV exoplanets detection

This document is the Accepted Manuscript version of the following article: Roman v. Baluev, et al, ‘Benchmarking the power of amateur observatories for TTV exoplanets detection’, Monthly Notices of the Royal Astronomical Society, Vol. 450(3): 3101-3113, first published online 9 May 2015. The version of record is available at doi: https://doi.org/10.1093/mnras/stv788 © 2015 The Authors. Published by Oxford University Press on behalf of the Royal Astronomical Society.We perform an analysis of ~80000 photometric measurements for the following 10 stars hosting transiting planets: WASP-2, -4, -5, -52, Kelt-1, CoRoT-2, XO-2, TrES-1, HD 189733, GJ 436. Our analysis includes mainly transit lightcurves from the Exoplanet Transit Database, public photometry from the literature, and some proprietary photometry privately supplied by other authors. Half of these lightcurves were obtained by amateurs. From this photometry we derive 306 transit timing measurements, as well as improved planetary transit parameters. Additionally, for 6 of these 10 stars we present a set of radial velocity measurements obtained from the spectra stored in the HARPS, HARPS-N, and SOPHIE archives using the HARPS-TERRA pipeline. Our analysis of these TTV and RV data did not reveal significant hints of additional orbiting bodies in almost all of the cases. In the WASP-4 case, we found hints of marginally significant TTV signals having amplitude 10-20 sec, although their parameters are model-dependent and uncertain, while radial velocities did not reveal statistically significant Doppler signals.Peer reviewe

Minimum-Uncertainty Angular Wave Packets and Quantized Mean Values

Uncertainty relations between a bounded coordinate operator and a conjugate momentum operator frequently appear in quantum mechanics. We prove that physically reasonable minimum-uncertainty solutions to such relations have quantized expectation values of the conjugate momentum. This implies, for example, that the mean angular momentum is quantized for any minimum-uncertainty state obtained from any uncertainty relation involving the angular-momentum operator and a conjugate coordinate. Experiments specifically seeking to create minimum-uncertainty states localized in angular coordinates therefore must produce packets with integer angular momentum.Comment: accepted for publication in Physical Review

Asymptotic normalization coefficients (nuclear vertex constants) for p+7Be→8Bp+^7Be\to ^8B and the direct 7Be(p,γ)8B^7Be(p,\gamma)^8B astrophysical S-factors at solar energies

A new analysis of the precise experimental astrophysical S-factors for the direct capture $^7Be(p,\gamma)$ $^8B$ reaction [A.J.Junghans et al.Phys.Rev. C 68 (2003) 065803 and L.T. Baby et al. Phys.Rev. C 67 (2003) 065805] is carried out based on the modified two - body potential approach in which the direct astrophysical S-factor, ${\rm S_{17}(E)}$, is expressed in terms of the asymptotic normalization constants for $p+^7Be\to ^8B$ and two additional conditions are involved to verify the peripheral character of the reaction under consideration. The Woods-Saxon potential form is used for the bound ($p+^7Be$)- state wave function and for the $p^7Be$- scattering wave function. New estimates are obtained for the ^{\glqq}indirectly measured\grqq values of the asymptotic normalization constants (the nuclear vertex constants) for the $p+^7Be\to ^8B$ and $S_{17}(E)$ at E$\le$ 115 keV, including $E$=0. These values of $S_{17}(E)$ and asymptotic normalization constants have been used for getting information about the ^{\glqq}indirectly measured\grqq values of the $s$ wave average scattering length and the $p$ wave effective range parameters for $p^7Be$- scattering.Comment: 27 pages, 6 figure

RNA polymerase II stalling promotes nucleosome occlusion and pTEFb recruitment to drive immortalization by Epstein-Barr virus

Epstein-Barr virus (EBV) immortalizes resting B-cells and is a key etiologic agent in the development of numerous cancers. The essential EBV-encoded protein EBNA 2 activates the viral C promoter (Cp) producing a message of ~120 kb that is differentially spliced to encode all EBNAs required for immortalization. We have previously shown that EBNA 2-activated transcription is dependent on the activity of the RNA polymerase II (pol II) C-terminal domain (CTD) kinase pTEFb (CDK9/cyclin T1). We now demonstrate that Cp, in contrast to two shorter EBNA 2-activated viral genes (LMP 1 and 2A), displays high levels of promoter-proximally stalled pol II despite being constitutively active. Consistent with pol II stalling, we detect considerable pausing complex (NELF/DSIF) association with Cp. Significantly, we observe substantial Cp-specific pTEFb recruitment that stimulates high-level pol II CTD serine 2 phosphorylation at distal regions (up to +75 kb), promoting elongation. We reveal that Cp-specific pol II accumulation is directed by DNA sequences unfavourable for nucleosome assembly that increase TBP access and pol II recruitment. Stalled pol II then maintains Cp nucleosome depletion. Our data indicate that pTEFb is recruited to Cp by the bromodomain protein Brd4, with polymerase stalling facilitating stable association of pTEFb. The Brd4 inhibitor JQ1 and the pTEFb inhibitors DRB and Flavopiridol significantly reduce Cp, but not LMP1 transcript production indicating that Brd4 and pTEFb are required for Cp transcription. Taken together our data indicate that pol II stalling at Cp promotes transcription of essential immortalizing genes during EBV infection by (i) preventing promoter-proximal nucleosome assembly and ii) necessitating the recruitment of pTEFb thereby maintaining serine 2 CTD phosphorylation at distal regions

The Ctf18 RFC-like complex positions yeast telomeres but does not specify their replication time

Peer reviewedPreprin