Atomic-level characterization of the structural dynamics of proteins

Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic level of detail, but they have been limited to time scales shorter than those of many biologically critical conformational changes. We examined two fundamental processes in protein dynamics--protein folding and conformational change within the folded state--by means of extremely long all-atom MD simulations conducted on a special-purpose machine. Equilibrium simulations of a WW protein domain captured multiple folding and unfolding events that consistently follow a well-defined folding pathway; separate simulations of the protein's constituent substructures shed light on possible determinants of this pathway. A 1-millisecond simulation of the folded protein BPTI reveals a small number of structurally distinct conformational states whose reversible interconversion is slower than local relaxations within those states by a factor of more than 1000.     

A New Approach to Select Doubled Haploid Rice Lines under Salinity Stress Using Indirect Selection Index

This study determined the indirect selection index of doubled haploid(DH) rice using a multivariate analysis approach to select lines adaptive to salinity stress, comprising three experiments. The first experiment involved the selection of good agronomic characters in a field experiment conducted at an experimental station in Bogor, Indonesia. The second experiment involved salinity tolerance screening through hydroponic cultures using 0 and 120 mmol/L NaCl, conducted at a greenhouse in Bogor. The third experiment involved the validation of the indirect adaptability selection index(IASI) through a field experiment in Sukra(saline area). Field experiments followed a randomized complete block design(RCBD), whereas an RCBD nested factorial design was used for the greenhouse experiment. The first and second experiments used 56 DH lines and four check varieties with three replications. In the second experiment, Pokkali and IR29 varieties were also added as tolerant and sensitive checks of salinity, respectively. The third experiment used 28 selected DH lines, Inpari 29 and one sensitive DH line. The good agronomic index(GAI) was 0.465 yield + 0.433 number of productive tillers + 0.31 number of filled grains. This generated 24 DH rice lines with good agronomic traits. The salinity tolerance index(SaTI) was developed through the average of standardized salinity tolerance score and salinity selection index based on discriminant analysis. This generated 34 DH rice lines with good salinity stress tolerance. The IASI(IASI = GAI – Sa TI) selected 28 DH rice lines adaptive to salinity stress and it was considered effective by Sukra validation.     

Zur Mäusenahrung des Fischreihers

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Timber tree regeneration along abandoned logging roads in a tropical Bolivian forest

Sustainable management of selectively logged tropical forests requires that felled trees are replaced through increased recruitment and growth. This study compares road track and roadside regeneration with regeneration in unlogged and selectively logged humid tropical forest in north-eastern Bolivia. Some species benefited from increased light intensities on abandoned logging roads. Others benefited from low densities of competing vegetation on roads with compacted soils. This was the case for the small-seeded species Ficus boliviana C.C. Berg and Terminalia oblonga (Ruiz & Pav.) Steud. Some species, e.g. Hura crepitans L., displayed patchy regeneration coinciding with the presence of adult trees. Our results suggest that current management practices could be improved by intensifying logging in some areas to improve regeneration of light demanding species. Sufficient seed input in logged areas should be ensured by interspersing large patches of unlogged forest with logged areas. This may also assist regeneration of species that perform poorly in disturbed areas.     

Expression of garlic leaf lectin under the control of the phloem-specific promoter Asus1 from Arabidopsis thaliana protects tobacco plants against the tobacco aphid (Myzus nicotianae)

BACKGROUND: To check for correlation between the insecticidal properties and the specificity of lectins, a comparative study was made of the insecticidal activities of two garlic lectins with different biological activities.RESULTS: The insecticidal activity of the garlic (Allium sativum L.) leaf lectin ASAL and bulb lectin ASAII towards the tobacco aphid Myzus nicotianae Blackman was studied using bioassays with transgenic tobacco (Nicotiana tabacum L. cv. Wisconsin 38). Bioassays were started with newborn nymphs of the tobacco aphid. Although during the first 7-8 days when nymphs developed to adults there were no apparent effects, part of the nymphal population was found to develop into winged (alate) forms. Later it became clear that transgenic plants expressing ASAL and ASAII had a significant effect on the reproduction capacity of the resulting adults, with a reduction of up to 40%. Different life table parameters such as prereproductive time, intrinsic rate of natural increase, generation time and doubling time were significantly affected (P < 0.05) in aphids grown on transgenic plant material expressing ASAL and ASAII.CONCLUSION: Bioassays with tobacco plants expressing ASAL and ASAII demonstrated a significant impact on the population growth of M. nicotianae. Therefore, both lectins can be considered as valuable candidate aphid control agents.     

Distribution of Trace Elements in Sediments and Biota of Songkhla Lake, Southern Thailand

The concentrations of Co, Ni, Cu, Zn, Cd, Pb, As, Fe, Mn, and Al were determined in sediments and biota of Songkhla Lake, a shallow coastal lagoon located in southern Thailand. In June 2006, surface sediments were sampled in 44 stations in the three sections of the lake (inner-, middle-, and outer sections). Sediment cores were also sampled in 13 stations in three cross-sections of the lake. In surface sediments, trace and major elements, organic matter, sediment grain size analysis, and sulfides were determined, and in the sediment cores, redox profiles were made. Soil samples were also collected at garbage dumping sites in the vicinity of the lake. In addition, the metal accumulation in two catfish species (Arius maculatus and Osteogeneiosus militaris) and the crustacean (Apseudes sapensis) was also investigated. Trace element concentrations in sediments of Songkhla Lake show that, especially the Outer section of the lake, in particular the sediments at the mouths of the Phawong, U-Taphao, and Samrong Canals are significantly enriched with trace elements due to municipal, agricultural, and industrial discharges entering the lake through the canals. Aluminum-normalized enrichment factors throughout the lake vary from 0.4 to 1.7 for Ni, 0.3 to 3.3 for Cu, 0.2 to 7 for Zn, 0.1 to 14 for As, 1 to 24 for Cd, 0.7 to 6.8 for Pb, and 0.1 to 7.8 for Mn. Correlations between the elements and sediment characteristics show that Cu, Zn, Cd, and Pb are essentially associated with the sulfide fraction; that Ni and Co are predominantly bound to the clay minerals and iron oxy-hydroxides, and that As is principally bound to iron oxy-hydroxides. The accumulation of trace elements between muscle tissue and liver and eggs of A. maculatus and O. militaris is element-specific, but concentrations of trace elements in fish muscle tissue are well within the limits for human consumption.     

Fine‐scale population structure and connectivity of bottlenose dolphins,Tursiops truncatus,in European waters and implications for conservation

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Uptake and residues of aldicarb in sugarbeet leaves

The breakdown of aldicarb and its oxidation products (the sulphoxide and the sulphone, aldoxycarb), under field conditions in 1976, were studied on three different types of soil (a sandy loam, a silt loam and a sandy clay loam that were normally cropped with sugarbeet). Residues were determined in leaves, stems, roots and soil, and related to aphid counts. Higher doses were needed on heavy soils in order to obtain a sufficient concentration in the leaves and thus provide an efficient treatment for aphid control. Weather conditions, especially rainfall, also affected the residue content. At harvest, the sugar beet tops used for fodder can contain residues which vary widely, depending on dosage, soil type and climatic conditions.     

A recent growth increase of European beech (Fagus sylvatica L.) at its Mediterranean distribution limit contradicts drought stress

Future changes in tree growth, associated with a warmer and drier climate, are predicted for many species and locations across the European Mediterranean Basin. However, quantification of the intensity and severity of related consequences for forest ecosystem functioning and productivity remains challenging. Species-specific distribution limits that are particularly sensitive to small changes in the ambient climate may provide an ideal test bed to assess the nature of past growth trends and extremes and their responsible controls. Here, we seek to understand how twentieth century climate change affected the growth of European beech (Fagus sylvatica L.) nearby its south-eastern distribution limit in Albania and Macedonia on the Balkan Peninsula. We sampled 93 living trees from undisturbed mixed forest stands at ~1,450 m a.s.l. and 29 timbers from nearby historical buildings. Application of different tree-ring detrending techniques allowed robust composite chronologies with varying degrees of high- to low-frequency variability to be developed back to 1648 ad. Comparison with local meteorological station measurements and continental grid-box climate indices revealed spatiotemporal instability in growth–climate response patterns. Nevertheless, year-to-year and decadal-long fluctuations in radial beech growth were significantly (P < 0.001) negatively correlated at ?0.61 with June–September temperature over the 1951–1995 period. This (inverse) relationship between increased beech growth and decreased summer temperature is somewhat indicative for the importance of plant-available soil moisture, which likely controls ring width formation near the species-specific south-eastern distribution limit. Significant positive correlations between beech growth and drought (scPDSI; r = 0.57) confirm metabolistic drought constraints. However, an unexpected late twentieth century growth increase not only contradicts the previously observed growth dependency to summer soil moisture, but also denies any putative drought-induced forest ecosystem suppression in this part of the Mediterranean Basin.     

Formation of secondary organic aerosols through photooxidation of isoprene

Detailed organic analysis of natural aerosols from the Amazonian rain forest showed considerable quantities of previously unobserved polar organic compounds, which were identified as a mixture of two diastereoisomeric 2-methyltetrols: 2-methylthreitol and 2-methylerythritol. These polyols, which have the isoprene skeleton, can be explained by OH radical-initiated photooxidation of isoprene. They have low vapor pressure, allowing them to condense onto preexisting particles. It is estimated that photooxidation of isoprene results in an annual global production of about 2 teragrams of the polyols, a substantial fraction of the Intergovernmental Panel on Climate Change estimate of between 8 and 40 teragrams per year of secondary organic aerosol from biogenic sources.