Preferential attachment in the protein network evolution

The Saccharomyces cerevisiae protein-protein interaction map, as well as many natural and man-made networks, shares the scale-free topology. The preferential attachment model was suggested as a generic network evolution model that yields this universal topology. However, it is not clear that the model assumptions hold for the protein interaction network. Using a cross genome comparison we show that (a) the older a protein, the better connected it is, and (b) The number of interactions a protein gains during its evolution is proportional to its connectivity. Therefore, preferential attachment governs the protein network evolution. The evolutionary mechanism leading to such preference and some implications are discussed.Comment: Minor changes per referees requests; to appear in PR

Photon echo quantum memories in inhomogeneously broadened two level atoms

Here we propose a solid-state quantum memory that does not require spectral holeburning, instead using strong rephasing pulses like traditional photon echo techniques. The memory uses external broadening fields to reduce the optical depth and so switch off the collective atom-light interaction when desired. The proposed memory should allow operation with reasonable efficiency in a much broader range of material systems, for instance Er3+ doped crystals which have a transition at 1.5 um. We present analytic theory supported by numerical calculations and initial experiments.Comment: 7 pages, 8 figure

Lignin biomarkers as tracers of mercury sources in lakes water column

This study presents the role of specific terrigenous organic compounds as important vectors of mercury (Hg) transported from watersheds to lakes of the Canadian boreal forest. In order to differentiate the autochthonous from the allochthonous organic matter (OM), lignin derived biomarker signatures [Lambda, S/V, C/V, P/(V ? S), 3,5-Bd/V and (Ad/Al)v] were used. Since lignin is exclusively produced by terrigenous plants, this approach can give a non equivocal picture of the watershed inputs to the lakes. Moreover, it allows a characterization of the source of OM and its state of degradation. The water column of six lakes from the Canadian Shield was sampled monthly between June and September 2005. Lake total dissolved Hg concentrations and Lambda were positively correlated, meaning that Hg and ligneous inputs are linked (dissolved OM r2 = 0.62, p\0.0001; particulate OM r2 = 0.76, p\0.0001). Ratios of P/(V ? S) and 3,5-Bd/V from both dissolved OM and particulate OM of the water column suggest an inverse relationship between the progressive state of pedogenesis and maturation of the OM in soil before entering the lake, and the Hg concentrations in the water column. No relation was found between Hg levels in the lakes and the watershed flora composition—angiosperm versus gymnosperm or woody versus non-woody compounds. This study has significant implications for watershed management of ecosystems since limiting fresh terrestrial OM inputs should reduce Hg inputs to the aquatic systems. This is particularly the case for largescale land-use impacts, such as deforestation, agriculture and urbanization, associated to large quantities of soil OM being transferred to aquatic systems

Global priorities for conservation across multiple dimensions of mammalian diversity

Conservation priorities that are based on species distribution, endemism, and vulnerability may underrepresent biologically unique species as well as their functional roles and evolutionary histories. To ensure that priorities are biologically comprehensive, multiple dimensions of diversity must be considered. Further, understanding how the different dimensions relate to one another spatially is important for conservation prioritization, but the relationship remains poorly understood. Here, we use spatial conservation planning to (i) identify and compare priority regions for global mammal conservation across three key dimensions of biodiversity-taxonomic, phylogenetic, and traits-and (ii) determine the overlap of these regions with the locations of threatened species and existing protected areas. We show that priority areas for mammal conservation exhibit low overlap across the three dimensions, highlighting the need for an integrative approach for biodiversity conservation. Additionally, currently protected areas poorly represent the three dimensions of mammalian biodiversity. We identify areas of high conservation priority among and across the dimensions that should receive special attention for expanding the global protected area network. These high-priority areas, combined with areas of high priority for other taxonomic groups and with social, economic, and political considerations, provide a biological foundation for future conservation planning efforts

Hybrid Soybean Seed Production: Comparison of Three Methods

Improved methods to produce hybrid soybean [Glycine max (L.) Merr.] seed could augment several types of research. Two previously described methods, the traditional method and the dilution method, require insect-facilitated cross-pollination of ms ms nuclear male-sterile plants. The traditional method requires a substantial time investment during flowering to remove fertile siblings, and the dilution method requires a substantial amount of land and pollen-parent seed. Because time, land, and seed are limited, a more efficient method would be valuable. The cosegregation method was developed, utilizing close genetic linkage between the W1 locus and the Ms6 locus. The W1 ___, seedling has a purple hypocotyl; the w1 w1 seedling has a green hypocotyl. The ms6 ms6 plant is male sterile and female fertile. Approximately 97% of the purple-hypocotyl seedlings, W1 ___, in a line segregating for the w1 and ms6 alleles in coupling phase will he fertile, Ms6 ___, and can be removed as a pollen source at the first-trifoliolate stage. Our objective was to evaluate and compare the three methods of hybrid soybean seed production for seed yield, efficiency, and hybrid seed purity and quality. We used a randomized complete-block design (three replications per location, three locations, two years). The cosegregation method gave higher seed yield, better efficiency, and equal or better seed quality (percentage germination, 100-seed weight) than the other methods. Male-sterile plants yielded an average of 28.6 seeds plant−1 with the cosegregation method, 18.2 seeds plant−1 with the traditional method, and 9.5 seeds plant−1 with the dilution method. The cosegregation method will be useful in several research areas, including genetic control of complex traits, prediction of parental value, recurrent selection, and commercialization of hybrid soybean

The limits of social class in explaining ethnic gaps in educational attainment

This paper reports an analysis of the educational attainment and progress between age 11 and age 14 of over 14,500 students from the nationally representative Longitudinal Study of Young People in England (LSYPE). The mean attainment gap in national tests at age 14 between White British and several ethnic minority groups were large, more than three times the size of the gender gap, but at the same time only about one-third of the size of the social class gap. Socio-economic variables could account for the attainment gaps for Black African, Pakistani and Bangladeshi students, but not for Black Caribbean students. Further controls for parental and student attitudes, expectations and behaviours indicated minority ethnic groups were on average more advantaged on these measures than White British students, but this was not reflected proportionately in their levels of attainment. Black Caribbean students were distinctive as the only group making less progress than White British students between age 11 and 14 and this could not be accounted for by any of the measured contextual variables. Possible explanations for the White British-Black Caribbean gap are considered

Consistent alleviation of abiotic stress with silicon addition: a meta-analysis

1. Hundreds of single species studies have demonstrated the facility of silicon (Si) to alleviate diverse abiotic stresses in plants. Understanding of the mechanisms of Si-mediated stress alleviation is progressing, and several reviews have brought information together. A quantitative assessment of the alleviative capacity of Si, however, which could elucidate plant Si function more broadly, was lacking. 2. We combined the results of 145 experiments, predominantly on agricultural species, in a meta-analysis to statistically assess the responses of stressed plants to Si supply across multiple plant families and abiotic stresses. We interrogated our database to determine whether stressed plants increased in dry mass and net assimilation rate, oxidative stress markers were reduced, antioxidant responses were increased and whether element uptake showed consistent changes when supplied with Si. 3. We demonstrated that across plant families and stress types, Si increases dry weight, assimilation rate and chlorophyll biosynthesis and alleviates oxidative damage in stressed plants. In general, results indicated that plant family (as a proxy for accumulator type) and stress type had significant explanatory power for variation in responses. The consistent reduction in oxidative damage was not mirrored by consistent increases in antioxidant production, indicative of the several different stress alleviation mechanisms in which Si is involved. Silicon addition increased K in shoots, decreased As and Cd in roots and Na and Cd in shoots. Silicon addition did not affect Al, Ca or Mn concentration in shoots and roots of stressed plants. Plants had significantly lower concentrations of Si accumulated in shoots but not in roots when stressed. 4. Meta-analyses showed consistent alleviation by Si of oxidative damage caused by a range of abiotic stresses across diverse species. Our findings indicate that Si is likely to be a useful fertilizer for many crops facing a spectrum of abiotic stresses. Similarities in responses across families provide strong support for a role of Si in the alleviation of abiotic stress in natural systems, where it has barely been explored. We suggest this role may become more important under a changing climate and more experiments using non-agricultural species are now needed

Inclusion of additional studies yields different conclusions: Comment on Sedikides, Gaertner, & Vevea (2005), Journal of Personality and Social Psychology

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75100/1/j.1467-839X.2007.00211.x.pd