Effects of agricultural cropping systems on micronutrients transformation

Summary The effect of cropping systems of wheat-maize (WM), wheat-rice (WR), wheat-groundnut (WG), gram-bajra (GrB), potato-guara (PGu), and raya-mash (RaMa) in combination with treatments of dummy (uncultivated area) and applied Zn 0.0 (Zn₀), 2.8 (Zn₁), 5.6 (Zn₂) 11.2 (Zn₃) kg/ha was studied on the transformation of labile Zn fractions: exchangeable (Exch.), adsorbed (TAd) [weakly (WAd), moderately (MAd), strongly (SAd)], and organic matter (OM) in different layers of sandy loam soil. The added Zn stayed largely in the 0–30 cm layer and was associated with the WAd- and OM-Zn fractions. About 70% of the total labile Zn (PAv) remained in the WAd- and OM-Zn, that is, 33 and 39% in 0–15 cm layer, and 33–39% and 31–36% in 16–150 cm layer. All the Zn fractions in 0–15 cm layer, and only of WAd in 16–30 cm layer, significantly increased with rates of Zn addition. These were also significantly higher in Zn_1–3 than Zn₀ and dummy treatments because of the residual Zn. Diverse effects of cropping systems on soil properties, residual Zn, and labile Zn fractions were found. The influence was strong in 0–15 cm layer decreasing gradually with soil depth due largely to differences in Zn requirement, crop intake of various Zn fractions and the cultural practices of the systems. All the crops and rotations appreciabilly responded to Zn application. Uptake of Zn by crops markedly and successively increased with increasing rates of Zn application. The WR caused a significant increase in soil organic matter whereas WR and WM in CaCO₃. The WR, WM and GrB resulted in a decrease in pH while WG and GrB in CaCO₃. The RaMa and PGu maintained much higher residual Zn than other systems. The systems which caused the maximum decrease in Zn fractions were: cereal-cereal (WM) in Exch. legume-millet (GrB) in all the adsorbed, PAv and the Zn associated with CaCO₃, vegetable-legume (PGu) also in MAd and SAd; and cereal-legume (WG) in OM and PAv. Hence GrB, WG and WM in that order will cause the deficiency of Zn much earlier than the other systems due to greater use and or transformation of WAd- andOM-Zn. Such effects were least under RaMa because it increased the WAd-, MAd- and OM-Zn.     

Palladium in plant ash

Summary Palladium is taken up by vegetation, generally with a ratio ash/soil>1. A high concentration in leaves ofJuglans hindsii in early spring is followed by a large drop during initial growth. The concentration increases toward the end of the season and is resorbed before abscission.     

Considerations for measuring genetic variation and population structure with multilocus fingerprinting

Multilocus DNA fingerprinting provides a cost-effective means to rapidly assay genetic variation at many loci. While this makes the technique particularly attractive for studies of evolution and conservation biology, fingerprint data can be difficult to interpret. Measurement errors inherent with the technique force investigators to group similar-sized alleles (bands) into discrete bins before estimating genetic parameters. If too little error is accounted for in this process homologous alleles will not be grouped in a common bin, whereas overestimated error can produce bins with homoplasic alleles. We used simulations and empirical data for two frog species ( Rana luteiventris and Hyla regilla ) to demonstrate that mean band-sharing ( S¯_xy ) and heterozygosity ( H ¯_E) are a function of both bin width and band profile complexity (i.e. number and distribution of bands). These estimators are also sensitive to the number of lanes included in the analysis when bin width is wide and a floating bin algorithm is employed. Multilocus estimates of H ¯_E were highly correlated with S¯_xy and thus provide no additional information about genetic variation. Estimates of population subdivision ( F ^ and Φ^_ST) appeared robust to changes in bin size. We also examined the issue of statistical independence for band-sharing data when comparisons are made among all samples. This analysis indicated that the covariance between band-sharing statistics was very small and not statistically different from zero. We recommend that sensitivity analyses for bin size be used to improve confidence in the biological interpretation of multilocus fingerprints, and that the covariance structure for band-sharing statistics be examined.     

Inverted patterns of genetic diversity in continental and island populations of the heather Erica scoparia s.l.

Aim Using the heather Erica scoparia s.l. as a model, this paper aims to test theoretical predictions that island populations are genetically less diverse than continental ones and to determine the extent to which island and continental populations are connected by pollen‐ and seed‐mediated gene flow. Location Macaronesia, Mediterranean, Atlantic fringe of Europe. Methods Patterns of genetic diversity are described based on variation at two chloroplast DNA (cpDNA) loci and one nuclear DNA (nDNA) locus for 109 accessions across the entire distribution range of the species. Global patterns of genetic differentiation were investigated using principal coordinates analysis. Genetic differentiation between island and continental areas, estimations of pollen‐ and seed‐mediated gene flow, and the presence of phylogeographical signal were assessed by means of F_st /N_ST (continental scale) and F_ij/N_ij (local scale). Extant and past distribution ranges of the species were inferred from niche modelling using layers describing present and Last Glacial Maximum (LGM) macroclimatic conditions. Results The Azores exhibited a significantly higher genetic diversity than the continent. The lowest levels of genetic differentiation were observed between the Azores and the western Mediterranean, and the diversity observed in the Azores resulted from at least two colonization waves. Within the Azores, kinship coefficients showed a significant and much steeper decrease with geographical distance in the cpDNA than in the nDNA. The distribution predicted by LGM models was markedly different from the current potential distribution, particularly in western Europe, where no suitable areas were predicted by LGM models, and along the Atlantic coast of the African continent, where LGM models predicted highly suitable climatic conditions. Main conclusions The higher diversity observed in Azorean than in continental populations is inconsistent with MacArthur and Wilson’s equilibrium model and derived theoretical population genetic expectations. This inverted pattern may be the result of extinction on the continent coupled with multiple island colonization events and subsequent allopatric diversification and lineage hybridization in the Azores. The results highlight the role of allopatric diversification in explaining diversification on islands and suggest that this process has played a much more significant role in shaping Azorean biodiversity than previously thought.     

De novo inference of protein function from coarse‐grained dynamics

Inference of molecular function of proteins is the fundamental task in the quest for understanding cellular processes. The task is getting increasingly difficult with thousands of new proteins discovered each day. The difficulty arises primarily due to lack of high‐throughput experimental technique for assessing protein molecular function, a lacunae that computational approaches are trying hard to fill. The latter too faces a major bottleneck in absence of clear evidence based on evolutionary information. Here we propose a de novo approach to annotate protein molecular function through structural dynamics match for a pair of segments from two dissimilar proteins, which may share even <10% sequence identity. To screen these matches, corresponding 1 µs coarse‐grained (CG) molecular dynamics trajectories were used to compute normalized root‐mean‐square‐fluctuation graphs and select mobile segments, which were, thereafter, matched for all pairs using unweighted three‐dimensional autocorrelation vectors. Our in‐house custom‐built forcefield (FF), extensively validated against dynamics information obtained from experimental nuclear magnetic resonance data, was specifically used to generate the CG dynamics trajectories. The test for correspondence of dynamics‐signature of protein segments and function revealed 87% true positive rate and 93.5% true negative rate, on a dataset of 60 experimentally validated proteins, including moonlighting proteins and those with novel functional motifs. A random test against 315 unique fold/function proteins for a negative test gave >99% true recall. A blind prediction on a novel protein appears consistent with additional evidences retrieved therein. This is the first proof‐of‐principle of generalized use of structural dynamics for inferring protein molecular function leveraging our custom‐made CG FF, useful to all. Proteins 2014; 82:2443–2454. © 2014 Wiley Periodicals, Inc.