Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions

Single-stranded DNA (ssDNA) plays a major role in several biological processes. It is therefore of fundamental interest to understand how the elastic response and the formation of secondary structures are modulated by the interplay between base pairing and electrostatic interactions. Here we measure force-extension curves (FECs) of ssDNA molecules in optical tweezers set up over two orders of magnitude of monovalent and divalent salt conditions, and obtain its elastic parameters by fitting the FECs to semiflexible models of polymers. For both monovalent and divalent salts, we find that the electrostatic contribution to the persistence length is proportional to the Debye screening length, varying as the inverse of the square root of cation concentration. The intrinsic persistence length is equal to 0.7 nm for both types of salts, and the effectivity of divalent cations in screening electrostatic interactions appears to be 100-fold as compared with monovalent salt, in line with what has been recently reported for single-stranded RNA. Finally, we propose an analysis of the FECs using a model that accounts for the effective thickness of the filament at low salt condition and a simple phenomenological description that quantifies the formation of non-specific secondary structure at low forces.

Assessment of rubber tree panels under crowns resistant to South American leaf blight

The objective of this work was to assess the performance of panel clones under crowns resistant to South American leaf blight (Microcyclus ulei). The experiment was carried out with 18 panel clones crown-budded with Hevea pauciflora x H. guianensis, in a Xanthic Ferralsol (Oxisol) in Manaus, AM, Brazil. The following parameters were evaluated: dry rubber yield, plant nutritional status, and anatomical and physiological characteristics of the latex vessels. In the first three years of evaluation, the panel clones IAN 2878, IAN 2903, CNS AM 7905, CNS AM 7905 P1, and PB 28/59 showed the highest dry rubber yield potential, while the clones IAN 6158, IAN 6590, and IAN 6515 should not be recommended for crown budding. Higher potassium and copper foliar content in panel clones were associated to an increase in dry rubber yield. The simultaneous evaluation of anatomical and physiological characteristics of latex is fundamental for the selection of panel clones in the Amazon region. Crown budding is an efficient technology for South American leaf blight management in endemic regions.

Temporal trends in chemical parameters of upland forest soils in southern Finland

Abstract

Correlation of Locally-Based Performance of Asphalts with Their Physicochemical Parameters, Progress Report 2, HR-298, 1989

This project was undertaken to study the relationships between the performance of locally available asphalts and their physicochemical properties under Iowa conditions with the ultimate objective of development of a locally and performance-based asphalt specification for durable pavements. Physical and physicochemical tests were performed on three sets of asphalt samples including: (a) twelve samples from local asphalt suppliers and their TFOT residues, (b) six core samples of known service records, and (c) a total of 79 asphalts from 10 pavement projects including original, lab aged and recovered asphalts from field mixes, as well as from lab aged mixes. Tests included standard rheological tests, HP-GPC and TMA. Some specific viscoelastic tests (at 5 deg C) were run on b samples and on some a samples. DSC and X-ray diffraction studies were performed on a and b samples. Furthermore, NMR techniques were applied to some a, b and c samples. Efforts were made to identify physicochemical properties which are correlated to physical properties known to affect field performance. The significant physicochemical parameters were used as a basis for an improved performance-based trial specification for Iowa to ensure more durable pavements.

Estimating parameters for generalized mass action models using constraint propagation.

As modern molecular biology moves towards the analysis of biological systems as opposed to their individual components, the need for appropriate mathematical and computational techniques for understanding the dynamics and structure of such systems is becoming more pressing. For example, the modeling of biochemical systems using ordinary differential equations (ODEs) based on high-throughput, time-dense profiles is becoming more common-place, which is necessitating the development of improved techniques to estimate model parameters from such data. Due to the high dimensionality of this estimation problem, straight-forward optimization strategies rarely produce correct parameter values, and hence current methods tend to utilize genetic/evolutionary algorithms to perform non-linear parameter fitting. Here, we describe a completely deterministic approach, which is based on interval analysis. This allows us to examine entire sets of parameters, and thus to exhaust the global search within a finite number of steps. In particular, we show how our method may be applied to a generic class of ODEs used for modeling biochemical systems called Generalized Mass Action Models (GMAs). In addition, we show that for GMAs our method is amenable to the technique in interval arithmetic called constraint propagation, which allows great improvement of its efficiency. To illustrate the applicability of our method we apply it to some networks of biochemical reactions appearing in the literature, showing in particular that, in addition to estimating system parameters in the absence of noise, our method may also be used to recover the topology of these networks.

The kinetic parameters and energy cost of the Hsp70 chaperone as a polypeptide unfoldase.

Hsp70-Hsp40-NEF and possibly Hsp100 are the only known molecular chaperones that can use the energy of ATP to convert stably pre-aggregated polypeptides into natively refolded proteins. However, the kinetic parameters and ATP costs have remained elusive because refolding reactions have only been successful with a molar excess of chaperones over their polypeptide substrates. Here we describe a stable, misfolded luciferase species that can be efficiently renatured by substoichiometric amounts of bacterial Hsp70-Hsp40-NEF. The reactivation rates increased with substrate concentration and followed saturation kinetics, thus allowing the determination of apparent V(max)' and K(m)' values for a chaperone-mediated renaturation reaction for the first time. Under the in vitro conditions used, one Hsp70 molecule consumed five ATPs to effectively unfold a single misfolded protein into an intermediate that, upon chaperone dissociation, spontaneously refolded to the native state, a process with an ATP cost a thousand times lower than expected for protein degradation and resynthesis.

Construction mechanisms and thermal evolution of upper crustal intrusions : the Saint-Jean-du-Doigt bimodal intrusion (Brittany, France)

Understanding the emplacement and growth of intrusive bodies in terms of mechanism, duration, ther¬mal evolution and rates are fundamental aspects of crustal evolution. Recent studies show that many plutons grow in several Ma by in situ accretion of discrete magma pulses, which constitute small-scale magmatic reservoirs. The residence time of magmas, and hence their capacities to interact and differentiate, are con¬trolled by the local thermal environment. The latter is highly dependant on 1) the emplacement depth, 2) the magmas and country rock composition, 3) the country rock thermal conductivity, 4) the rate of magma injection and 5) the geometry of the intrusion. In shallow level plutons, where magmas solidify quickly, evi¬dence for magma mixing and/or differentiation processes is considered by many authors to be inherited from deeper levels. This work shows however that in-situ differentiation and magma interactions occurred within basaltic and felsic sills at shallow depth (0.3 GPa) in the St-Jean-du-Doigt (SJDD) bimodal intrusion, France. This intrusion emplaced ca. 347 Ma ago (IDTIMS U/Pb on zircon) in the Precambrian crust of the Armori- can massif and preserves remarkable sill-like emplacement processes of bimodal mafic-felsic magmas. Field evidence coupled to high precision zircon U-Pb dating document progressive thermal maturation within the incrementally built ioppolith. Early m-thick mafic sills (eastern part) form the roof of the intrusion and are homogeneous and fine-grained with planar contacts with neighboring felsic sills; within a minimal 0.8 Ma time span, the system gets warmer (western part). Sills are emplaced by under-accretion under the old east¬ern part, interact and mingle. A striking feature of this younger, warmer part is in-situ differentiation of the mafic sills in the top 40 cm of the layer, which suggests liquids survival in the shallow crust. Rheological and thermal models were performed in order to determine the parameters required to allow this observed in- situ differentiation-accumulation processes. Strong constraints such as total emplacement durations (ca. 0.8 Ma, TIMS date) and pluton thickness (1.5 Km, gravity model) allow a quantitative estimation of the various parameters required (injection rates, incubation time,...). The results show that in-situ differentiation may be achieved in less than 10 years at such shallow depth, provided that: (1) The differentiating sills are injected beneath consolidated, yet still warm basalt sills, which act as low conductive insulating screens (eastern part formation in the SJDD intrusion). The latter are emplaced in a very short time (800 years) at high injection rate (0.5 m/y) in order to create a "hot zone" in the shallow crust (incubation time). This implies that nearly 1/3 of the pluton (400m) is emplaced by a subsequent and sustained magmatic activity occurring on a short time scale at the very beginning of the system. (2) Once incubation time is achieved, the calculations show that a small hot zone is created at the base of the sill pile, where new injections stay above their solidus T°C and may interact and differentiate. Extraction of differentiated residual liquids might eventually take place and mix with newly injected magma as documented in active syn-emplacement shear-zones within the "warm" part of the pluton. (3) Finally, the model show that in order to maintain a permanent hot zone at shallow level, injection rate must be of 0.03 m/y with injection of 5m thick basaltic sills eveiy 130yr, imply¬ing formation of a 15 km thick pluton. As this thickness is in contradiction with the one calculated for SJDD (1.5 Km) and exceed much the average thickness observed for many shallow level plutons, I infer that there is no permanent hot zone (or magma chambers) at such shallow level. I rather propose formation of small, ephemeral (10-15yr) reservoirs, which represent only small portions of the final size of the pluton. Thermal calculations show that, in the case of SJDD, 5m thick basaltic sills emplaced every 1500 y, allow formation of such ephemeral reservoirs. The latter are formed by several sills, which are in a mushy state and may interact and differentiate during a short time.The mineralogical, chemical and isotopic data presented in this study suggest a signature intermediate be¬tween E-MORB- and arc-like for the SJDD mafic sills and feeder dykes. The mantle source involved produced hydrated magmas and may be astenosphere modified by "arc-type" components, probably related to a sub¬ducting slab. Combined fluid mobile/immobile trace elements and Sr-Nd isotopes suggest that such subduc¬tion components are mainly fluids derived from altered oceanic crust with minor effect from the subducted sediments. Close match between the SJDD compositions and BABB may point to a continental back-arc setting with little crustal contamination. If so, the SjDD intrusion is a major witness of an extensional tectonic regime during the Early-Carboniferous, linked to the subduction of the Rheno-Hercynian Ocean beneath the Variscan terranes. Also of interest is the unusual association of cogenetic (same isotopic compositions) K-feldspar A- type granite and albite-granite. A-type granites may form by magma mixing between the mafic magma and crustal melts. Alternatively, they might derive from the melting of a biotite-bearing quartz-feldspathic crustal protolith triggered by early mafic injections at low crustal levels. Albite-granite may form by plagioclase cu¬mulate remelting issued from A-type magma differentiation.

Genetic parameters and estimated genetic gains in young rubber tree progenies

The objective of this work was to assess the genetic parameters and to estimate genetic gains in young rubber tree progenies. The experiments were carried out during three years, in a randomized block design, with six replicates and ten plants per plot, in three representative Hevea crop regions of the state of São Paulo, Brazil. Twenty-two progenies were evaluated, from three to five years old, for rubber yield and annual girth growth. Genetic gain was estimated with the multi-effect index (MEI). Selection by progenies means provided greater estimated genetic gain than selection based on individuals, since heritability values of progeny means were greater than the ones of individual heritability, for both evaluated variables, in all the assessment years. The selection of the three best progenies for rubber yield provided a selection gain of 1.28 g per plant. The genetic gains estimated with MEI using data from early assessments (from 3 to 5-year-old) were generally high for annual girth growth and rubber yield. The high genetic gains for annual girth growth in the first year of assessment indicate that progenies can be selected at the beginning of the breeding program. Population effective size was consistent with the three progenies selected, showing that they were not related and that the population genetic variability is ensured. Early selection with the genetic gains estimated by MEI can be made on rubber tree progenies.

Mating system parameters in a high density population of andirobas in the Amazon forest

The objective of this work was to estimate the mating system parameters of a andiroba (Carapa guianensis) population using microsatellite markers and the mixed and correlated mating models. Twelve open‑pollinated progeny arrays of 15 individuals were sampled in an area with C. guianensis estimated density of 25.7 trees per hectare. Overall, the species has a mixed reproductive system, with a predominance of outcrossing. The multilocus outcrossing rate (t m = 0.862) was significantly lower than the unity, indicating that self‑pollination occurred. The rate of biparental inbreeding was substantial (t m ‑ t s = 0.134) and significantly different from zero. The correlation of selfing within progenies was high (r s = 0.635), indicating variation in the individual outcrossing rate. Consistent with this result, the estimate of the individual outcrossing rate ranged from 0.598 to 0.978. The multilocus correlation of paternity was low (r p(m) = 0.081), but significantly different from zero, suggesting that the progenies contain full‑sibs. The coancestry within progenies (Θ = 0.185) was higher and the variance effective size (Ne(v) = 2.7) was lower than expected for true half‑sib progenies (Θ = 0.125; Ne(v) = 4). These results suggest that, in order to maintain a minimum effective size of 150 individuals for breeding, genetic conservation, and environmental reforestation programs, seeds from at least 56 trees must be collected.

Repeatability of adaptability and stability parameters of common bean in unpredictable environments

The objective of this work was to estimate the repeatability of adaptability and stability parameters of common bean between years, within each biennium from 2003 to 2012, in Minas Gerais state, Brazil. Grain yield data from trials of value for cultivation and use common bean were analyzed. Grain yield, ecovalence, regression coefficient, and coefficient of determination were estimated considering location and sowing season per year, within each biennium. Subsequently, a analysis of variance these estimates was carried out, and repeatability was estimated in the biennia. Repeatability estimate for grain yield in most of the biennia was relatively high, but for ecovalence and regression coefficient it was null or of small magnitude, which indicates that confidence on identification of common bean lines for recommendation is greater when using means of yield, instead of stability parameters.

Use of individual race results in the estimation of genetic parameters of trotting performance for Finnhorse and Standardbred trotters

Selostus: Ravikilpailumenestysmittojen periytymisasteet ja toistumiskertoimet kilpailukohtaisten tulosten perusteella

Genetic parameters and simultaneous selection for root yield, adaptability and stability of cassava genotypes

The objective of this work was to estimate genetic parameters and to evaluate simultaneous selection for root yield and for adaptability and stability of cassava genotypes. The effects of genotypes were assumed as fixed and random, and the mixed model methodology (REML/Blup) was used to estimate genetic parameters and the harmonic mean of the relative performance of genotypic values (HMRPGV), for simultaneous selection purposes. Ten genotypes were analyzed in a complete randomized block design, with four replicates. The experiment was carried out in the municipalities of Altamira, Santarém, and Santa Luzia do Pará in the state of Pará, Brazil, in the growing seasons of 2009/2010, 2010/2011, and 2011/2012. Roots were harvested 12 months after planting, in all tested locations. Root yield had low coefficients of genotypic variation (4.25%) and broad-sense heritability of individual plots (0.0424), which resulted in low genetic gain. Due to the low genotypic correlation (0.15), genotype classification as to root yield varied according to the environment. Genotypes CPATU 060, CPATU 229, and CPATU 404 stood out as to their yield, adaptability, and stability.

Quantum transport phenomena and shallow impurity states in CdSb

This work is dedicated to investigation of the energy spectrum of one of the most anisotropic narrow-gap semiconductors, CdSb. At the beginning of the present studies even the model of its energy band structure was not clear. Measurements of galvanomagnetic effects in wide temperature range (1.6 - 300 K) and in magnetic fields up to 30 T were chosen for clarifying of the energy spectrum in the intentionally undoped CdSb single crystals and doped with shallow impurities (In, Ag). Detection of the Shubnikov - de Haas oscillations allowed estimating the fundamental energy spectrum parameters. The shapes of the Fermi surfaces of electrons (sphere) and holes (ellipsoid), the number of the equivalent extremums for valence band (2) and their positions in the Brillouin zone were determined for the first time in this work. Also anisotropy coefficients, components of the tensor of effective masses of carriers, effective masses of density of states, nonparabolicity of the conduction and valence bands, g-factor and its anisotropy for n- and p-CdSb were estimated for the first time during these studies. All the results obtained are compared with the cyclotron resonance data and the corresponding theoretical calculations for p-CdSb. This is basic information for the analyses of the complex transport properties of CdSb and for working out the energy spectrum model of the shallow energy levels of defects and impurities in this semiconductor. It was found out existence of different mechanisms of hopping conductivity in the presence of metal - insulator transition induced by magnetic field in n- and p-CdSb. Quite unusual feature opened in CdSb is that different types of hopping conductivity may take place in the same crystal depending on temperature, magnetic field or even orientation of crystal in magnetic field. Transport properties of undoped p-CdSb samples show that the anisotropy of the resistivity in weak and strong magnetic fields is determined completely by the anisotropy of the effective mass of the holes. Temperature and magnetic field dependence of the Hall coefficient and magnetoresistance is attributed to presence of two groups of holes with different concentrations and mobilities. The analysis demonstrates that below Tcr ~ 20 K and down to ~ 6 - 7 K the low-mobile carriers are itinerant holes with energy E2 ≈ 6 meV. The high-mobile carriers, at all temperatures T < Tcr, are holes activated thermally from a deeper acceptor band to itinerant states of a shallower acceptor band with energy E1 ≈ 3 meV. Analysis of temperature dependences of mobilities confirms the existence of the heavy-hole band or a non-equivalent maximum and two equivalent maxima of the light-hole valence band. Galvanomagnetic effects in n-CdSb reveal the existence of two groups of carriers. These are the electrons of a single minimum in isotropic conduction band and the itinerant electrons of the narrow impurity band, having at low temperatures the energies above the bottom of the conduction band. It is found that above this impurity band exists second impurity band of only localized states and the energy of both impurity bands depend on temperature so that they sink into the band gap when temperature is increased. The bands are splitted by the spin, and in strong magnetic fields the energy difference between them decreases and redistribution of the electrons between the two impurity bands takes place. Mobility of the conduction band carriers demonstrates that scattering in n-CdSb at low temperatures is strongly anisotropic. This is because of domination from scattering on the neutral impurity centers and increasing of the contribution to mobility from scattering by acoustic phonons when temperature increases. Metallic conductivity in zero or weak magnetic field is changed to activated conductivity with increasing of magnetic field. This exhibits a metal-insulator transition (MIT) induced by the magnetic field due to shift of the Fermi level from the interval of extended states to that of the localized states of the electron spectrum near the edge of the conduction band. The Mott variablerange hopping conductivity is observed in the low- and high-field intervals on the insulating side of the MIT. The results yield information about the density of states, the localization radius of the resonant impurity band with completely localized states and about the donor band. In high magnetic fields this band is separated from the conduction band and lies below the resonant impurity bands.

Random regression models to estimate genetic parameters for milk production of Guzerat cows using orthogonal Legendre polynomials

The objective of this work was to compare random regression models for the estimation of genetic parameters for Guzerat milk production, using orthogonal Legendre polynomials. Records (20,524) of test-day milk yield (TDMY) from 2,816 first-lactation Guzerat cows were used. TDMY grouped into 10-monthly classes were analyzed for additive genetic effect and for environmental and residual permanent effects (random effects), whereas the contemporary group, calving age (linear and quadratic effects) and mean lactation curve were analized as fixed effects. Trajectories for the additive genetic and permanent environmental effects were modeled by means of a covariance function employing orthogonal Legendre polynomials ranging from the second to the fifth order. Residual variances were considered in one, four, six, or ten variance classes. The best model had six residual variance classes. The heritability estimates for the TDMY records varied from 0.19 to 0.32. The random regression model that used a second-order Legendre polynomial for the additive genetic effect, and a fifth-order polynomial for the permanent environmental effect is adequate for comparison by the main employed criteria. The model with a second-order Legendre polynomial for the additive genetic effect, and that with a fourth-order for the permanent environmental effect could also be employed in these analyses.

Seed biometric parameters in oil palm accessions from a Brazilian germplasm bank

The objective of this work was to evaluate the morphological diversity of oil palm seeds and to cluster the accessions according to their morphological characteristics. Forty-one accessions from the oil palm germplasm bank of Embrapa Amazônia Ocidental were evaluated - 18 of Elaeis oleifera and 23 of E. guineensis. The groups were formed based on morphological characteristics, by principal component analysis. In E. oleifera, four groups were formed, tied to their region of origin, but with significant morphological differences between accessions from the same population. For tenera-type E. guineensis seeds, three widely divergent groups were formed, especially as to external parameters, which differentiated them from the other ones. The parameter endocarp thickness stood out in intra- and inter-population differentiation. For dura-type E. guineensis, three groups were formed, with larger seeds and thicker endocarps, which differed from all the other ones. The variability observed for seed characteristics in the analyzed accessions allows the establishment of different groups, to define strategies for genetic improvement.