The effects of explicit versus parameterized convection on the MJO in a large-domain high-resolution tropical case study. Part I: Characterization of large-scale organization and propagation

High-resolution simulations over a large tropical domain (∼20◦S–20◦N and 42◦E–180◦E) using both explicit and parameterized convection are analyzed and compared to observations during a 10-day case study of an active Madden-Julian Oscillation (MJO) event. The parameterized convection model simulations at both 40 km and 12 km grid spacing have a very weak MJO signal and little eastward propagation. A 4 km explicit convection simulation using Smagorinsky subgrid mixing in the vertical and horizontal dimensions exhibits the best MJO strength and propagation speed. 12 km explicit convection simulations also perform much better than the 12 km parameterized convection run, suggesting that the convection scheme, rather than horizontal resolution, is key for these MJO simulations. Interestingly, a 4 km explicit convection simulation using the conventional boundary layer scheme for vertical subgrid mixing (but still using Smagorinsky horizontal mixing) completely loses the large-scale MJO organization, showing that relatively high resolution with explicit convection does not guarantee a good MJO simulation. Models with a good MJO representation have a more realistic relationship between lower-free-tropospheric moisture and precipitation, supporting the idea that moisture-convection feedback is a key process for MJO propagation. There is also increased generation of available potential energy and conversion of that energy into kinetic energy in models with a more realistic MJO, which is related to larger zonal variance in convective heating and vertical velocity, larger zonal temperature variance around 200 hPa, and larger correlations between temperature and ascent (and between temperature and diabatic heating) between 500–400 hPa.

Structure and magnetic properties of a tetranuclear Cu(II) complex containing the 2-(pyridine-2-yliminomethyl)-phenol ligand

A tetranuclear Cu(II) complex [Cu4L4(H2O)4](ClO4)4 has been synthesized using the terdentate Schiff base 2-(pyridine-2-yliminomethyl)-phenol (HL) (the condensation product of salicylaldehyde and 2-aminopyridine) and copper perchlorate. Chemical characterizations such as IR and UV/Vis of the complex have been carried out. A single-crystal diffraction study shows that the complex contains a nearly planar tetranuclear core containing four copper atoms, which occupy four equivalent five-coordinate sites with a square pyramidal environment. Magnetic measurements have been carried out over the temperature range 2–300K and with 100Oe field strengths. Analysis of magnetic susceptibility data indicates a strong antiferromagnetic (J1=−638cm−1) exchange interaction between diphenoxo-bridged Cu(II) centers and a moderate antiferromagnetic (J2=−34cm−1) interaction between N–C–N bridged Cu(II) centers. Magnetic exchange interactions (J’s) are also discussed on the basis of a computational study using DFT methodology. The spin density distribution (singlet ground state) is calculated to visualize the effect of delocalization of spin density through bridging groups.

Electrochemical reductive deprotonation of an imidazole ligand in a bipyridine tricarbonyl rhenium(I) complex

The reduction path of the complex fac-[ReΙ(imH)(CO)3(bpy)]+ was studied in situ by UV-Vis-NIR-IR spectroelectrochemistry within an OTTLE cell. The complex undergoes 1e‒ reduction of the 2,2'-bipyridine (bpy) ligand and intramolecular electron transfer resulting in the conversion of the axial imidazole (imH) ligand to 3-imidazolate (3-im–). This step is followed by two bpy-based 1e– reductions producing ultimately the five-coordinate complex [Re(CO)3(bpy)]‒ and free 3-im‒. The identity of the reduction product fac-[Re(3-im–)(CO)3(bpy)] has been proven by partial chemical deprotonation of the parent complex followed by IR spectroelectrochemistry. This is the first time when an electrochemical conversion of metal-coordinated imidazole to terminal 3-imidazolate has been observed.

The R1441C mutation alters the folding properties of the ROC domain of LRRK2

LRRK2 is a 250 kDa multidomain protein, mutations in which cause familial Parkinson's disease. Previously, we have demonstrated that the R1441C mutation in the ROC domain decreases GTPase activity. Here we show that the R1441C alters the folding properties of the ROC domain, lowering its thermodynamic stability. Similar to small GTPases, binding of different guanosine nucleotides alters the stability of the ROC domain, suggesting that there is an alteration in conformation dependent on GDP or GTP occupying the active site. GTP/GDP bound state also alters the self-interaction of the ROC domain, accentuating the impact of the R1441C mutation on this property. These data suggest a mechanism whereby the R1441C mutation can reduce the GTPase activity of LRRK2, and highlights the possibility of targeting the stability of the ROC domain as a therapeutic avenue in LRRK2 disease.

Effect of an ancillary ligand on single helix-double helix interconversion in copper complexes. Copper(I)-water bond

Reaction of Cu(ClO(4))(2)center dot 6H(2)O with the 1:2 condensate of benzildihydrazone and 2-acetylpyridine, in methanol in equimolar ratio yields a green compound which upon recrystallisation from 1:1 CH(2)Cl(2)-C(6)H(6) mixture affords [CuL(H(2)O)](ClO(4))(2)center dot 1/2C(6)H(6). The complex crystallises in the space group P-1 with a = 8.028(11) angstrom, b = 12.316(17) angstrom, c = 18.14(3) angstrom, alpha = 97.191(10)degrees, beta = 94.657(10)degrees and gamma = 108.039(10)degrees. It is single helical with the metal having a distorted trigonal bipyramidal N(4)O coordination sphere. The acid dissociation constant of the Cu(I) complex in CH(3)CN is 3.34 +/- 0.19. The X band EPR spectrum of the compound is rhombic with g(1) = 2.43, g(2) = 2.10 g(3) = 2.02 and A(1) = 79.3 x 10(-4) cm(-1). The Cu(II/I) potential of the complex in CH(2)Cl(2) at a glassy carbon electrode is 0.43 V vs SCE. It is argued that the copper-water bond persists in the corresponding copper(I) species. Its implications on the single helix-double helix interconversion in copper helicates are discussed. DFT calculations at the B3LYP/6-311G** level shows that the binding energy of water in the single helicol live-coordinate copper(I) species [CuL(H(2)O)](+) is similar to 40 kJ mol(-1).

Structural and magnetic studies of Schiff base complexes of nickel(ii) nitrite: change in crystalline state, ligand rearrangement and a very rare μ-nitrito-1κO:2κN:3κO′ bridging mode

Four new nickel(II) complexes, [Ni2L2(NO2)2]·CH2Cl2·C2H5OH, 2H2O (1), [Ni2L2(DMF)2(m-NO2)]ClO4·DMF (2a), [Ni2L2(DMF)2(m-NO2)]ClO4 (2b) and [Ni3L¢2(m3-NO2)2(CH2Cl2)]n·1.5H2O (3) where HL = 2-[(3-amino-propylimino)-methyl]-phenol, H2L¢ = 2-({3-[(2-hydroxy-benzylidene)-amino]-propylimino}-methyl)-phenol and DMF = N,N-dimethylformamide, have been synthesized starting with the precursor complex [NiL2]·2H2O, nickel(II) perchlorate and sodium nitrite and characterized structurally and magnetically. The structural analyses reveal that in all the complexes, NiII ions possess a distorted octahedral geometry. Complex 1 is a dinuclear di-m2-phenoxo bridged species in which nitrite ion acts as chelating co-ligand. Complexes 2a and 2b also consist of dinuclear entities, but in these two compounds a cis-(m-nitrito-1kO:2kN) bridge is present in addition to the di-m2-phenoxo bridge. The molecular structures of 2a and 2b are equivalent; they differ only in that 2a contains an additional solvated DMF molecule. Complex 3 is formed by ligand rearrangement and is a one-dimensional polymer in which double phenoxo as well as m-nitrito-1kO:2kN bridged trinuclear units are linked through a very rare m3-nitrito-1kO:2kN:3kO¢ bridge. Analysis of variable-temperature magnetic susceptibility data indicates that there is a global weak antiferromagnetic interaction between the nickel(II) ions in four complexes, with exchange parameters J of -5.26, -11.45, -10.66 and -5.99 cm-1 for 1, 2a, 2b and 3, respectively

Genome dynamics explain the evolution of flowering time CCT domain gene families in the Poaceae

Numerous CCT domain genes are known to control flowering in plants. They belong to the CONSTANS-like (COL) and PREUDORESPONSE REGULATOR (PRR) gene families, which in addition to a CCT domain possess B-box or response-regulator domains, respectively. Ghd7 is the most recently identified COL gene to have a proven role in the control of flowering time in the Poaceae. However, as it lacks B-box domains, its inclusion within the COL gene family, technically, is incorrect. Here, we show Ghd7 belongs to a larger family of previously uncharacterized Poaceae genes which possess just a single CCT domain, termed here CCT MOTIF FAMILY (CMF) genes. We molecularly describe the CMF (and related COL and PRR) gene families in four sequenced Poaceae species, as well as in the draft genome assembly of barley (Hordeum vulgare). Genetic mapping of the ten barley CMF genes identified, as well as twelve previously unmapped HvCOL and HvPRR genes, finds the majority map to colinear positions relative to their Poaceae orthologues. Combined inter-/intra-species comparative and phylogenetic analysis of CMF, COL and PRR gene families indicates they evolved prior to the monocot/dicot divergence ~200 mya, with Poaceae CMF evolution described as the interplay between whole genome duplication in the ancestral cereal, and subsequent clade-specific mutation, deletion and duplication events. Given the proven role of CMF genes in the modulation of cereals flowering, the molecular, phylogenetic and comparative analysis of the Poaceae CMF, COL and PRR gene families presented here provides the foundation from which functional investigation can be undertaken.

Delivery of AAV2/9-microdystrophin genes incorporating helix 1 of the coiled-coil motif in the C-terminal domain of dystrophin improves muscle pathology and restores the level of α1-syntrophin and α-dystrobrevin in skeletal muscles of mdx mice. Level of α1-Syntrophin and α-Dystrobrevin in Skeletal Muscles of mdx Mice

Duchenne muscular dystrophy is a severe X-linked inherited muscle wasting disorder caused by mutations in the dystrophin gene. Adeno-associated virus (AAV) vectors have been extensively used to deliver genes efficiently for dystrophin expression in skeletal muscles. To overcome limited packaging capacity of AAV vectors (<5 kb), truncated recombinant microdystrophin genes with deletions of most of rod and carboxyl-terminal (CT) domains of dystrophin have been developed. We have previously shown the efficiency of mRNA sequence–optimized microdystrophin (ΔR4-23/ΔCT, called MD1) with deletion of spectrin-like repeat domain 4 to 23 and CT domain in ameliorating the pathology of dystrophic mdx mice. However, the CT domain of dystrophin is thought to recruit part of the dystrophin-associated protein complex, which acts as a mediator of signalling between extracellular matrix and cytoskeleton in muscle fibers. In this study, we extended the ΔR4-23/ΔCT microdystrophin by incorporating helix 1 of the coiled-coil motif in the CT domain of dystrophin (MD2), which contains the α1-syntrophin and α-dystrobrevin binding sites. Intramuscular injection of AAV2/9 expressing CT domain–extended microdystrophin showed efficient dystrophin expression in tibialis anterior muscles of mdx mice. The presence of the CT domain of dystrophin in MD2 increased the recruitment of α1-syntrophin and α-dystrobrevin at the sarcolemma and significantly improved the muscle resistance to lengthening contraction–induced muscle damage in the mdx mice compared with MD1. These results suggest that the incorporation of helix 1 of the coiled-coil motif in the CT domain of dystrophin to the microdystrophins will substantially improve their efficiency in restoring muscle function in patients with Duchenne muscular dystrophy.

The domain derivative in rough-surface scattering and rigorous estimates for first-order perturbation theory

We investigate Fréchet differentiability of the scattered field with respect to variation in the boundary in the case of time–harmonic acoustic scattering by an unbounded, sound–soft, one–dimensional rough surface. We rigorously prove the differentiability of the scattered field and derive a characterization of the Fréchet derivative as the solution to a Dirichlet boundary value problem. As an application of these results we give rigorous error estimates for first–order perturbation theory, justifying small perturbation methods that have a long history in the engineering literature. As an application of our rigorous estimates we show that a plane acoustic wave incident on a sound–soft rough surface can produce an unbounded scattered field.

Evaluation of a boundary integral representation for the conformal mapping of the unit disk onto a simply-connected domain

A representation of the conformal mapping g of the interior or exterior of the unit circle onto a simply-connected domain Ω as a boundary integral in terms ofƒ|∂Ω is obtained, whereƒ :=g -l. A product integration scheme for the approximation of the boundary integral is described and analysed. An ill-conditioning problem related to the domain geometry is discussed. Numerical examples confirm the conclusions of this discussion and support the analysis of the quadrature scheme.

The FunFOLD2 server for the prediction of protein-ligand interactions

The FunFOLD2 server is a new independent server that integrates our novel protein–ligand binding site and quality assessment protocols for the prediction of protein function (FN) from sequence via structure. Our guiding principles were, first, to provide a simple unified resource to make our function prediction software easily accessible to all via a simple web interface and, second, to produce integrated output for predictions that can be easily interpreted. The server provides a clean web interface so that results can be viewed on a single page and interpreted by non-experts at a glance. The output for the prediction is an image of the top predicted tertiary structure annotated to indicate putative ligand-binding site residues. The results page also includes a list of the most likely binding site residues and the types of predicted ligands and their frequencies in similar structures. The protein–ligand interactions can also be interactively visualized in 3D using the Jmol plug-in. The raw machine readable data are provided for developers, which comply with the Critical Assessment of Techniques for Protein Structure Prediction data standards for FN predictions. The FunFOLD2 webserver is freely available to all at the following web site: http://www.reading.ac.uk/bioinf/FunFOLD/FunFOLD_form_2_0.html.

The contributions of domain-general and numerical factors to third-grade arithmetic skills and mathematical learning disability

Explanations of the marked individual differences in elementary school mathematical achievement and mathematical learning disability (MLD or dyscalculia) have involved domain-general factors (working memory, reasoning, processing speed and oral language) and numerical factors that include single-digit processing efficiency and multi-digit skills such as number system knowledge and estimation. This study of third graders (N = 258) finds both domain-general and numerical factors contribute independently to explaining variation in three significant arithmetic skills: basic calculation fluency, written multi-digit computation, and arithmetic word problems. Estimation accuracy and number system knowledge show the strongest associations with every skill and their contributions are both independent of each other and other factors. Different domain-general factors independently account for variation in each skill. Numeral comparison, a single digit processing skill, uniquely accounts for variation in basic calculation. Subsamples of children with MLD (at or below 10th percentile, n = 29) are compared with low achievement (LA, 11th to 25th percentiles, n = 42) and typical achievement (above 25th percentile, n = 187). Examination of these and subsets with persistent difficulties supports a multiple deficits view of number difficulties: most children with number difficulties exhibit deficits in both domain-general and numerical factors. The only factor deficit common to all persistent MLD children is in multi-digit skills. These findings indicate that many factors matter but multi-digit skills matter most in third grade mathematical achievement.

Analytical solutions of a minimal model of species migration in a bounded domain

A minimal model of species migration is presented which takes the form of a parabolic equation with boundary conditions and initial data. Solutions to the differential problem are obtained that can be used to describe the small- and large-time evolution of a species distribution within a bounded domain. These expressions are compared with the results of numerical simulations and are found to be satisfactory within appropriate temporal regimes. The solutions presented can be used to describe existing observations of nematode distributions, can be used as the basis for further work on nematode migration, and may also be interpreted more generally.

RuII(α-diimine) or RuIII(α-diimine·–)? Structural, spectroscopic, and theoretical evidence for the stabilization of a prominent metal-to-Ligand charge- transfer excited-state configuration in the ground state

The new compounds [Ru(R-DAB)(acac)2] (R-DAB = 1,4-diorganyl- 1,4-diazabuta-1,3-diene; R = tert-butyl, 4-methoxyphenyl, 2,6-dimethylphenyl; acac– = 2,4-pentanedionate) exhibit intrachelate ring bond lengths 1.297ligand to produce UV/Vis/NIR and electron paramagnetic resonance (EPR) spectroelectrochemically detectable RuIII species, whereas the reduction proceeds less reversibly and yields predominantly (R-DAB)-ligand-based spin for the 4-methoxyphenyl derivative, measured at low temperature. The results are discussed with respect to metal-to-ligand chargetransfer (MLCT) excited states of conventional (α-diimine)- ruthenium(II) complexes and in view of other (α-diimine)- metal complexes with ambiguous oxidation-state assignments.

A MATLAB GUI for learning controller design in the frequency domain

A MATLAB GUI is presented which is used to help students learn to design controllers in the frequency domain. It complements the author’s two previous GUIs for plotting and identification of systems in the frequency domain. It also incorporates the concept used in the “electronic calculator that makes students think” to assist learning. Positive student feedback affirms that the GUI has helped their understanding.