Data assimilation: From photon counts to Earth System forecasts

Data assimilation – the set of techniques whereby information from observing systems and models is combined optimally – is rapidly becoming prominent in endeavours to exploit Earth Observation for Earth sciences, including climate prediction. This paper explains the broad principles of data assimilation, outlining different approaches (optimal interpolation, three-dimensional and four-dimensional variational methods, the Kalman Filter), together with the approximations that are often necessary to make them practicable. After pointing out a variety of benefits of data assimilation, the paper then outlines some practical applications of the exploitation of Earth Observation by data assimilation in the areas of operational oceanography, chemical weather forecasting and carbon cycle modelling. Finally, some challenges for the future are noted.

Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold

The nuclear magnetic resonance (NMR) structure of a central segment of the previously annotated severe acute respiratory syndrome (SARS)-unique domain (SUD-M, for "middle of the SARS-unique domain") in SARS coronavirus (SARS-CoV) nonstructural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3 residues 528 to 648, and there is a flexibly extended N-terminal tail with the residues 513 to 527 and a C-terminal flexible tail of residues 649 to 651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527 to 651 [SUD-M(527-651)]. NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly(A) and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In a further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1 ''-phosphatase nsp3b, although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows three-dimensional structure homology with several helicases and nucleoside triphosphate-binding proteins, but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection.

NMR structure shows that the SARS-unique domain contains a macrodomain fold

The NMR structure of a central segment of the previously annotated "SARS-unique domain" (SUD-M; "middle of the SARS-unique domain") in the SARS coronavirus (SARS-CoV) non-structural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3-residues 528-648, and there is a flexibly extended N-terminal tail with the residues 513-527 and a C-terminal flexible tail of residues 649-651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527-651 [SUD-M(527-651)]. NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly-A and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1''-phosphatase nsp3b, although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows 3D structure homology with several helicases and NTP-binding proteins, but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection.

The effect of temperature, photosynthetic photon flux density, and photoperiod on the vegetative growth and flowering of 'Autumn Bliss' raspberry

The effects of temperature, photosynthetic photon flux density (PPFD) and photoperiod on vegetative growth and flowering of the raspberry (Rubus idaeus L.) 'Autumn Bliss' were investigated. Increased temperature resulted in an increased rate of vegetative growth and a greater rate of progress to flowering. Optimum temperatures lay in the low to mid 20degreesC range. Above this the rate of plant development declined. Increased PPFD also advanced flowering. While photoperiod did not significantly affect the rate of vegetative growth, flowering occurred earliest at intermediate photoperiods and was delayed by extreme photoperiods. These responses suggest that there is potential for adjusting cropping times of raspberry grown under protection by manipulating the environment, especially temperature.

A monoaqua zinc complex. Unique acid dissociation behaviour

Using the I : 2 condensate of benzil dihydrazone and 2-acetylpyridine as the ligand L, two complexes of zinc, [ZnL(CH3COO)]PF6 (1) and [ZnL(H2O)CIO4]CIO4 H2O (2), are synthesised from Zn(CH3COO)(2).2H(2)O and Zn(CIO4)(2).6H(2)O, respectively. From X-ray crystallography, both the complexes are found to be single helical with the metal in distorted octahedral N4O2 environment. In 1, the two oxygen atoms come from the bidentate acetate while 2 is a monoaqua complex with a perchlorate anion bound to the metal in monodentate fashion. The perchlorate in 2 is not at all weakly bound [Zn-O(perchlorate) 2.256(4) A]. Still in acetonitrile solution, the coordinated perchlorate ion dissociates upon deprotonation [reaction (i)].

(Ni-2), (Ni-3), and (Ni-2 + Ni-3): A Unique Example of Isolated and Cocrystallized Ni-2 and Ni-3 Complexes

Structural and magnetic characterization of compound {[Ni-2(L)(2)(OAC)(2)][Ni-3(L)(2) (OAc)(4)]) center dot 2CH(3)CN (3) (HL = the tridentate Schiff base ligand, 2-[(3-methylaminb-propylimino)-methyl]-phenol) shows that it is a rare example of a crystal incorporating a dinuclear Ni(II) compound, [Ni-2(L)(2)(OAc)(2)], and a trinuclear one, [Ni-3(L)(2)(OAC)(4)]. Even more unusual is the fact that both Ni (II) complexes, [Ni-2(L)(2)(OAc)(2)] (1) and [Ni-3(L)(2)(OAc)(4)(H2O)(2)] center dot CH2Cl2 center dot 2CH(3)OH (2), have also been isolated and structurally and magnetically characterized. The structural analysis reveals that the dimeric complexes [Ni-2(L)(2)(OAc)(2)] in cocrystal 3 and in compound 1 are almost identical-in both complexes, the Ni(II) ions possess a distorted octahedral geometry formed by the chelating tridentate ligand (L), a chelating acetate ion, and a bridging phenoxo group with very similar bond angles and distances. On the other hand, compound 2 and the trinuclear complex in the cocrystal 3 show a similar linear centrosymmetric structure with the tridentate ligand coordinated to the terminal Ni(II) and linked to the central Ni(II) by phenoxo and carboxylate bridges. The only difference is that a water molecule found in 2 is not present in the trinuclear unit of complex 3; instead, the coordination sphere is completed by an additional bridging oxygen atom from an acetate ligand. Variable-temperature (2-300 K) magnetic susceptibility measurements show that the dinuclear unit is antiferromagnetically coupled in both compounds (2J = -36.18 and -29.5 cm(-1) in 1 and 3, respectively), whereas the trinuclear unit shows a very weak ferromagnetic coupling in compound 3 (2J = 0.23 cm(-1)) and a weak antiferromagnetic coupling in 2 (2J = -8.7(2) cm(-1)) due to the minor changes in the coordination sphere.

Relatives of patients with severe mental disorders: unique traits and experiences of primary, nonprimary, and lone caregivers

The authors examined caregivers' characteristics and experiences. Previously suggested principles for identifying the primary caregiver in 22 multiple-caregiver families were assessed, but none reliably distinguished the primary caregiver. The authors then compared primary (n = 22), nonprimary (n = 22), and lone caregivers' (n = 43) appraisals of caregiving and psychological distress. Lone and primary caregivers' experiences were similar. but nonprimary caregivers' experiences were less adverse. Despite these findings, greater psyhcological distress in primary caregivers indicated greater psychological distress in nonprimary caregivers.

SARS coronavirus unique domain: three-domain molecular architecture in solution and RNA binding

Nonstructural protein 3 of the severe acute respiratory syndrome (SARS) coronavirus includes a "SARS-unique domain" (SUD) consisting of three globular domains separated by short linker peptide segments. This work reports NMR structure determinations of the C-terminal domain (SUD-C) and a two-domain construct (SUD-MC) containing the middle domain (SUD-M) and the C-terminal domain, and NMR data on the conformational states of the N-terminal domain (SUD-N) and the SUD-NM two-domain construct. Both SUD-N and SUD-NM are monomeric and globular in solution; in SUD-NM, there is high mobility in the two-residue interdomain linking sequence, with no preferred relative orientation of the two domains. SUD-C adopts a frataxin like fold and has structural similarity to DNA-binding domains of DNA-modifying enzymes. The structures of both SUD-M (previously determined) and SUD-C (from the present study) are maintained in SUD-MC, where the two domains are flexibly linked. Gel-shift experiments showed that both SUD-C and SUD-MC bind to single-stranded RNA and recognize purine bases more strongly than pyrimidine bases, whereby SUD-MC binds to a more restricted set of purine-containing RNA sequences than SUD-M. NMR chemical shift perturbation experiments with observations of (15)N-labeled proteins further resulted in delineation of RNA binding sites (i.e., in SUD-M, a positively charged surface area with a pronounced cavity, and in SUD-C, several residues of an anti-parallel beta-sheet). Overall, the present data provide evidence for molecular mechanisms involving the concerted actions of SUD-M and SUD-C, which result in specific RNA binding that might be unique to the SUD and, thus, to the SARS coronavirus.

Thiolytic screening method for exploring condensed tannin variation in a unique sainfoin germplasm bank

This EU funded 'HealthyHay'project stablished a sainfoin (Onobrychis vicifolia) germplasm bank at NIAB, Cambridge, with 306 accessions from around the world. A screening method was developed to characterise tannins by thiolytic degradation [1] directly in green plants for the first time. the method was validated by separate analysis of unextractable, extractable and purified tannins using thiolysis, HPLC-GPC and MALDI-TOF MS. Most tannins (58 to 73% of the total) could be recovered after Toyopearl HW50 fractionation with water, aqueous methanol and acetone. the greatest losses during purification occurred amongst larger molecular weight tannins with mean degree of polymerisation (mDP) > 18. The composition of water-,aqueous methanol- and acetone-soluble tannins differed considerably in their mDP and trans/cis ratios, but not in their prodelphinidin/orocyanidin (PD/PC) ratios.

A unique example of structural and magnetic diversity in four interconvertible copper(II)−azide complexes with the same Schiff base ligand: a monomer, a dimer, a chain, and a layer

Four new Cu(II)-azido complexes of formula [CuL(N-3)] (1), [CuL(N-3)](2) (2), [Cu7L2(N-3)(12)](n) (3), and [Cu2L(dmen)-(N-3)(3)](n) (4) (dmen = N,N-dimethylethylenediamine) have been synthesized using the same tridentate Schiff base ligand HL (2-[1-(2-dimethylaminoethylimino)ethyl]phenol, the condensation product of dmen and 2-hydroxyacetophenone). The four compounds have been characterized by X-ray structural analyses and variable-temperature magnetic susceptibility measurements. Complex 1 is mononuclear, whereas 2 is a single mu-1,1 azido-bridged dinuclear compound. The polymeric compound 3 possesses a 2D structure in which the Cu(II) ions are linked by phenoxo oxygen atoms and two different azide bridges (mu-1,1 and mu-1,1,3). The structure of complex 4 is a double helix in which two mu-1,3-azido-bridged alternating one-dimensional helical chains of CuL(N-3) and Cu(dmen)(N-3)(2) are joined together by weak mu-1,1 azido bridges and H-bonds. The complexes interconvert in solution and can be obtained in pure form by carefully controlling the conditions. The magnetic properties of compounds 1 and 2 show the presence of very weak antiferromagnetic exchange interactions mediated by a ligand pi overlap (J = -1.77) and by an asymmetric 1,1-N-3 bridge (J = -1.97 cm(-1)), respectively. Compound 3 presents, from the magnetic point of view, a decorated chain structure with both ferro- and antiferromagnetic interactions. Compound 4 is an alternating helicoidal chain with two weak antiferromagnetic exchange interactions (J -1.35 and -2.64 cm(-1)).