From Pine Cones to Read Clouds: Rescaffolding the Megagenome of Sugar Pine (Pinus lambertiana).

We investigate the utility and scalability of new read cloud technologies to improve the draft genome assemblies of the colossal, and largely repetitive, genomes of conifers. Synthetic long read technologies have existed in various forms as a means of reducing complexity and resolving repeats since the outset of genome assembly. Recently, technologies that combine subhaploid pools of high molecular weight DNA with barcoding on a massive scale have brought new efficiencies to sample preparation and data generation. When combined with inexpensive light shotgun sequencing, the resulting data can be used to scaffold large genomes. The protocol is efficient enough to consider routinely for even the largest genomes. Conifers represent the largest reference genome projects executed to date. The largest of these is that of the conifer Pinus lambertiana (sugar pine), with a genome size of 31 billion bp. In this paper, we report on the molecular and computational protocols for scaffolding the P. lambertiana genome using the library technology from 10× Genomics. At 247,000 bp, the NG50 of the existing reference sequence is the highest scaffold contiguity among the currently published conifer assemblies; this new assembly's NG50 is 1.94 million bp, an eightfold increase

Reply to letter from W.H. Stevens, August 12, 1940.

https://digitalmaine.com/alien_corresp/1022/thumbnail.jp

Structure of cytochrome a3-Cua3 couple in cytochrome c oxidase as revealed by nitric oxide binding studies

The addition of NO to oxidized cytochrome c oxidase (ferrocytochrome c:oxygen oxidoreductase, EC 1.9.3.1) causes the appearance of a high-spin heme electron paramagnetic resonance (EPR) signal due to cytochrome a3. This suggests that NO coordinates to Cu{a3}+2 and breaks the antiferromagnetic couple by forming a cytochrome a3+3-Cu{a3}+2-NO complex. The intensity of the high-spin cytochrome a3 signal depends on the method of preparation of the enzyme and maximally accounts for 58% of one heme. The effect of N3- on the cytochrome a3+3-Cu{a3}+2-NO complex is to reduce cytochrome a3 to the ferrous state, and this is followed by formation of a new complex that exhibits EPR signals characteristic of a triplet species. On the basis of optical and EPR results, a NO bridge between cytochrome a3+2 and Cu{a3}+2 is proposed-i.e., cytochrome a3+2-NO-Cu{a3}+2. The half-field transition observed at g = 4.34 in the EPR spectrum of this triplet species exhibits resolved copper hyperfine splittings with |A{}| = 0.020 cm-1, indicating that the Cu{a3}+2 in the cytochrome a3+2-NO-Cu{a3}+2 complex is similar to a type 2 copper site

Orbital-quenching-induced magnetism in Ba_2NaOsO_6

The double perovskite \bnoo with heptavalent Os ($d^1$) is observed to remain in the ideal cubic structure ({\it i.e.} without orbital ordering) despite single occupation of the $t_{2g}$ orbitals, even in the ferromagnetically ordered phase below 6.8 K. Analysis based on the {\it ab initio} dispersion expressed in terms of an Os $t_{2g}$-based Wannier function picture, spin-orbit coupling, Hund's coupling, and strong Coulomb repulsion shows that the magnetic OsO$_6$ cluster is near a moment-less condition due to spin and orbital compensation. Quenching (hybridization) then drives the emergence of the small moment. This compensation, unprecedented in transition metals, arises in a unified picture that accounts for the observed Mott insulating behavior.Comment: in press at Europhysics Letter

Differences in both prevalence and titre of specific immunoglobulin E among children with asthma in affluent and poor communities within a large town in Ghana.

Background Reports from several African countries have noted an increasing prevalence of asthma in areas of extensive urbanization. Objective To investigate the relevance of allergen-specific sensitization and body mass index (BMI) to asthma/wheezing and exercise-induced bronchospasm (EIB) among children from affluent and poorer communities within a large town in Ghana. Methods Children with physician-diagnosed asthma and/or current wheezing aged 9-16 years (n=99; cases) from three schools with differing socio-economic backgrounds [urban affluent (UA), urban poor (UP) or suburban/rural (SR)] were recruited from a cross-sectional study (n=1848) in Kumasi, Ghana, and matched according to age, sex and area of residence with non-asthmatic/non-wheezy controls. We assayed sera for IgE antibodies to mite, cat, dog, cockroach, Ascaris and galactose-α-1,3-galactose. Results Children from the UA school had the lowest total serum IgE. However, cases from the UA school had a higher prevalence and mean titre of sIgE to mite (71.4%, 21.2IU/mL) when compared with controls (14.3%, 0.8IU/mL) or cases from UP (30%, 0.8IU/mL) and SR community (47.8%, 1.6IU/mL). While similar findings were observed with EIB in the whole population, among cases there was no difference in IgE antibody prevalence or titre between children with or without EIB. BMI was higher among UA children with and without asthma; in UP and SR communities, children with EIB (n=14) had a significantly higher BMI compared with children with asthma/wheezing without EIB (n=38) (18.2 vs. 16.4, respectively, P<0.01). Conclusions and Clinical Relevance In the relatively affluent school, asthma/wheezing and EIB were associated with high titre IgE antibodies to mite, decreased total IgE, and increased BMI. This contrasted with children in the urban poor school and suggests that changes relevant to a Western model of childhood asthma can occur within a short geographical distance within a large city in Africa. © 2011 Blackwell Publishing Ltd

The treatment of zero eigenvalues of the matrix governing the equations of motion in many-body Green's function theory

The spectral theorem of many-body Green's function theory relates thermodynamic correlations to Green's functions. More often than not, the matrix governing the equations of motion has zero eigenvalues. In this case, the standard text-book approach requires both commutator and anti-commutator Green's functions to obtain equations for that part of the correlation which does not lie in the null space of the matrix. In this paper, we show that this procedure fails if the projector onto the null space is dependent on the momentum vector. We propose an alternative formulation of the theory in terms of the non-null space alone and we show that a solution is possible if one can find a momentum-independent projector onto some subspace of the non-null space. To do this, we enlist the aid of the singular value decomposition (SVD) of the equation of motion matrix in order to project out the null space, thus reducing the size of the matrix and eliminating the need for the anti-commutator Green's function. We extend our previous work, dealing with a ferromagnetic Heisenberg monolayer and a momentum-independent projector onto the null space, where both multilayer films and a momentum-dependent projector are considered. We develop the numerical methods capable of handling these cases and offer a computational algorithmus that should be applicable to any similar problem arising in Green's function theory.Comment: 16 pages, 7 figure

The nature of CuA in cytochrome c oxidase

The isolation and purification of yeast cytochrome c oxidase is described. Characterization of the purified protein indicates that it is spectroscopically identical with cytochrome c oxidase isolated from beef heart. Preparations of isotopically substituted yeast cytochrome c oxidase are obtained incorporating [1,3-15N2]histidine or [beta,beta- 2H2]cysteine. Electron paramagnetic resonance and electron nuclear double resonance spectra of the isotopically substituted proteins identify unambiguously at least 1 cysteine and 1 histidine as ligands to CuA and suggest that substantial spin density is delocalized onto a cysteine sulfur in the oxidized protein to render the site Cu(I)-S

Proceedings of the Spacecraft Charging Technology Conference: Executive Summary

Aerospace environments are reviewed in reference to spacecraft charging. Modelling, a theoretical scheme which can be used to describe the structure of the sheath around the spacecraft and to calculate the charging currents within, is discussed. Materials characterization is considered for experimental determination of the behavior of typical spacecraft materials when exposed to simulated geomagnetic substorm conditions. Materials development is also examined for controlling and minimizing spacecraft charging or at least for distributing the charge in an equipotential manner, using electrical conductive surfaces for materials exposed to space environment

Health-related quality of life for pediatric emergency department febrile illnesses: an Evaluation of the Pediatric Quality of Life Inventory™ 4.0 generic core scales

OBJECTIVE: We sought to assess the validity and short-term responsiveness of the Pediatric Quality of Life Inventory™ 4.0 Generic Core Scales (PedsQL™) for febrile illnesses evaluated in the pediatric emergency department (ED). DESIGN: Prospective cohort study of children 2–18 years discharged after ED evaluation for fever (≥ 38°C). Self-administered, parent-report of health-related quality of life (HRQOL) was assessed using the PedsQL™ Acute Version, a validated HRQOL instrument. HRQOL was measured on ED presentation and at 7–10 day follow-up. At follow-up, duration of fever, child functional impairment, missed daycare/school, and disrupted family unit functioning, were assessed. RESULTS: Of 160 subjects enrolled, 97 (61%) completed the study; mean follow-up was 8.7 days. Mean total HRQOL score on ED presentation was 76.4; mean follow-up score was 86.3. Compared to subjects that returned to baseline, statistically significant differences in HRQOL were noted for those with prolonged fever, child functional impairment, and relapse. Significant correlation was observed between HRQOL at follow-up and days of daycare/school missed (r = -0.35, p = .003) and days of family disruption (r = -0.43, p < .001). Mean change in HRQOL within subjects, from ED visit to follow-up, was +9.8 (95% CI: 5.6–14.6). Effect size was 0.53, indicating moderate responsiveness. CONCLUSION: The PedsQL™ appears to be a valid and responsive indicator of HRQOL for short-term febrile illnesses evaluated in the ED

Matter wave pulses characteristics

We study the properties of quantum single-particle wave pulses created by sharp-edged or apodized shutters with single or periodic openings. In particular, we examine the visibility of diffraction fringes depending on evolution time and temperature; the purity of the state depending on the opening-time window; the accuracy of a simplified description which uses ``source'' boundary conditions instead of solving an initial value problem; and the effects of apodization on the energy width.Comment: 11 pages, 11 figure