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To meet the growing demand of the soybean consumer market, cultivars increasingly early, productive and resistant to biotic and abiotic stress are sought. Several populations are obtained in soybean breeding programmes, but progeny are selected without being weighted for their respective population effect. As a consequence, progeny originating from high‐merit populations may be discarded too early. Given this scenario, this study proposes to employ the selection index with progeny and population effect via best linear unbiased prediction (SIPP‐BLUP) for the genetic selection of early and productive soybean progeny. A total of 180 progeny derived from three populations were evaluated for yield‐related traits. Genetic gains from selection, Spearman correlation and coincidence index were used to check the efficiency of the models with and without the population effect. The SIPP‐BLUP index achieved greater selection accuracy and was efficient in the identification and future selection of early soybean progeny. Therefore, this study demonstrates that soybean breeding programmes should consider the population effect via SIPP‐BLUP in progeny selection to obtain future lines that really contribute to genetic gain.

This paper introduces InSAR (Interferometric Synthetic Aperture Radar) as an advanced tool for measuring and monitoring surface ground movements over time, with interest in all phases of a tunnel project, both in urban and non-urban areas. Following a preliminary overview of the technology used to compile radar images of the earth's surface, the multi-image techniques (Persistent Scatterers Interferometry, PSI) and the InSAR algorithm (SqueeSAR) are briefly outlined. Two examples of InSAR data applied to tunnelling projects are presented. In the first case, the integration of InSAR surface measurements into monitoring by conventional methods is discussed as a tool for providing useful information to study the relationship between tunnelling and surface settlements. In the second case, the temporal evolution of ground displacements provided by SqueeSAR is applied in order to understand the link between tunnel excavation and surface movements, along a slope under passed by two large tunnels. (A)

This article reports a stratigraphic and structural analysis of the Neogene-Quaternary Valdelsa Basin (Central Italy), filled with up to 1000 m of uppermost Miocene to lower Pleistocene strata. The succession is subdivided into seven unconformity-bounded stratigraphic units (synthems, or large-scale depositional sequences) that include fluvio-deltaic and shallow-marine deposits. Structures related to basin shoulders and internal boundaries controlled the Neogene location and geometry of different depocentres. During the Tortonian-Messinian, a buried NE-trending high related to regional, basin-transverse lineaments separated two adjacent sub-basins. During the lower Pliocene, compressional displacement along NW-trending, thrust-related highs controlled the distribution of depocentres and dispersal of sediment. Extensional tectonics, although previously considered the dominant deformation style affecting the rear of the Northern Apennines since the late Miocene, is no longer considered a dominant control on tectono-sedimentary development of the Valdelsa basin. Instead,the Valdelsa Basin shares features with continental hinterland basins of orogenic belts where compression, extension, and transcurrent stress fields determine a complex spatial and temporal record of accommodation and sediment supply. In the Valdelsa Basin tectonics and eustatic sea-level fluctuations were dominant in forcing the deposition of sedimentary cycles at several scales. Zanclean and Gelasian large-scale depositional sequences were mainly controlled by crustal shortening, whereas a eustatic signal was preferentially recorded during the Piacenzian. Smaller scale depositional sequences, common to most synthems, were controlled by orbitally forced glacio-eustatic cycles.

Often, deregulation of protein activity and turnover by tyrosine nitration drives cells toward pathogenesis. Hence, understanding how the nitration of a protein affects both its function and stability is of outstanding interest. Nowadays, most of the in vitro analyses of nitrated proteins rely on chemical treatment of native proteins with an excess of a chemical reagent. One such reagent, peroxynitrite, stands out for its biological relevance. However, given the excess of the nitrating reagent, the resulting in vitro modification could differ from the physiological nitration. Here, we determine unequivocally the configuration of distinct nitrated-tyrosine rings in single-tyrosine mutants of cytochrome c. We aimed to confirm the nitration position by a non-destructive method. Thus, we have resorted to 1H- 15N heteronuclear single quantum coherence(HSQC) spectra to identify the 3J(N-H) correlation between a 15N-tagged nitro group and the adjacent aromatic proton. Once the chemical shift of this proton was determined, we compared the 1H- 13C HSQC spectra of untreated and nitrated samples. All tyrosines were nitrated at ε positions, in agreement to previous analysis by indirect techniques. Notably, the various nitrotyrosine residues show a different dynamic behaviour that is consistent with molecular dynamics computations. Nitrotyrosines in a protein context: Unveiling of the configuration and dynamics of nitrotyrosines in proteins, such as cytochrome c, requires the development of a non-damaging method based on recording 1H- 15N heteronuclear single quantum coherence (HSQC) NMR spectra optimized for the detection of 3J(N-H) couplings between a 15N-tagged nitro group and the adjacent aromatic proton (see figure). Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Methionine sulfoxide reductases are antioxidant enzymes that repair oxidatively damaged methionine residues in proteins. Mammals have three members of the methionine-R-sulfoxide reductase family, including cytosolic MsrB1, mitochondrial MsrB2 and endoplasmic reticulum MsrB3. Here, we report the solution structure of reduced Mus musculus MsrB2 using high resolution NMR spectroscopy. MsrB2 is a β-strand rich globular protein consisting of eight all anti-parallel β-strands and three N-terminal α-helical segments. The latter secondary structure elements represent the main structural difference between mammalian MsrB2 and MsrB1. Structural comparison of mammalian and bacterial MsrB structures indicates that the general topology of this MsrB family is maintained and that MsrB2 more resembles bacterial MsrBs than MsrB1. Structural and biochemical analysis supports the catalytic mechanism of MsrB2 that, in contrast to MsrB1, does not involve a resolving cysteine (Cys). pH dependence of catalytically relevant residues in MsrB2 was accessed by NMR spectroscopy and the pKa of the catalytic Cys162 was determined to be 8.3. In addition, the pH-dependence of MsrB2 activity showed a maximum at pH 9.0, suggesting that deprotonation of the catalytic Cys is a critical step for the reaction. Further mobility analysis showed a well-structured N-terminal region, which contrasted with the high flexibility of this region in MsrB1. Our study highlights important structural and functional aspects of mammalian MsrB2 and provides a unifying picture for structure-function relationships within the MsrB protein family.

S100B contributes to cell proliferation by binding the C terminus of p53 and inhibiting its tumor suppressor function. The use of multiple computational approaches to screen fragment libraries targeting the human S100B-p53 interaction site is reported. This in silico screening led to the identification of 280 novel prospective ligands. NMR spectroscopic experiments revealed specific binding at the p53 interaction site for a set of these compounds and confirmed their potential for further rational optimization. The X-ray crystal structure determined for one of the binders revealed key intermolecular interactions, thus paving the way for structure-based ligand optimization.

The solution structure of homodimeric Cu2Zn2 superoxide dismutase (SOD) of 306 aminoacids was determined on a 13C, 15N and 70% 2H labeled sample. Two-thousand eight-hundred and five meaningful NOEs were used, of which 96 intersubunit, and 115 dihedral angles provided a family of 30 conformers with an rmsd from the average of 0.78 +/- 0.11 and 1.15 +/- 0.09 A for the backbone and heavy atoms, respectively. When the rmsd is calculated for each subunit, the values drop to 0.65 +/- 0.09 and 1.08 +/- 0.11 A for the backbone and heavy atoms, respectively. The two subunits are identical on the NMR time scale, at variance with the X-ray structures that show structural differences between the two subunits as well as between different molecules in the unit cell. The elements of secondary structure, i.e. eight beta sheets, are the same as in the X-ray structures and are well defined. The odd loops (I, III and V) are well resolved as well as loop II located at the subunit interface. On the contrary, loops IV and VI show some disorder. The residues of the active cavity are well defined whereas within the various subunits of the X-ray structure some are disordered or display different orientation in different X-ray structure determinations. The copper(I) ion and its ligands are well defined. This structure thus represents a well defined model in solution relevant for structure-function analysis of the protein. The comparison between the solution structure of monomeric mutants and the present structure shows that the subunit-subunit interactions increase the order in loop II. This has the consequences of inducing the structural and dynamic properties that are optimal for the enzymatic function of the wild-type enzyme. The regions 37-43 and 89-95, constituting loops III and V and the initial part of the beta barrel and showing several mutations in familial amyotrophis lateral sclerosis (FALS)-related proteins have a quite extensive network of H-bonds that may account for their low mobility. Finally, the conformation of the key Arg143 residue is compared to that in the other dimeric and monomeric structures as well as in the recently reported structure of the CCS-superoxide dismutase (SOD) complex.

Mutation of arginine (Arg) 143 with Ile in the monomeric mutant (Phe50Glu, Gly51Glu, Vall48Lys, Ile151Lys) of copper-zinc superoxide dismutase (R143I M4SOD, where M4SOD is the above mutant) leads to a protein with low copper content. Cobalt(II) binds the demetalized protein with a low and comparable affinity for the two metal sites, whereas it binds first and stochiometrically at the zinc site in the M4SOD protein and in the dimeric wild type SOD. However, a CuCo SOD derivative can be obtained whose NMR spectra indicate the structural changes induced by monomerization plus those induced by the Arg ---> Ile mutation. The electronic, circular dichroism, and EPR spectra provide structural information on the copper site. The low activity of the enzyme is accounted for on the basis of the structural properties of the active cavity.

An extensive series of three-dimensional, triple resonance experiments were performed on a fully labeled 13C, 15N monomeric form of human copper/zinc superoxide dismutase which contains 153 amino acids. The present system, in addition to the mutations at the subunit–subunit interface (Phe50Glu, Gly51Glu) which lead to the monomeric form, carries the mutation of the Glu133 to Gln, a residue at the active channel entrance. Firm assignment was found for 97% of the protons, 99% of the 13Cα, 91% of the 15N, 98% of 13C(O) and 90% of the 13Cβ backbone resonances. Analysis of the chemical shift values of 13Cα, Hα, 13Cβ and 13CO, of 3JHNHα coupling constants, of NOEs between backbone protons and of the H–D exchange behavior of amide protons permits the unequivocal detection of elements of secondary structure. The secondary structure of the present monomeric form is very similar to that of the WT enzyme, although the enzymatic activity is 20% of that of the WT protein. © 1997 John Wiley & Sons, Ltd.