Genetic structure and systematic relationships within the Ophrys fuciflora aggregate (Orchidaceae: Orchidinae): high diversity in Kent and a wind-induced discontinuity bisecting the Adriatic

A recent phylogenetic study based on multiple datasets is used as the framework for a more detailed examination of one of the ten molecularly circumscribed groups identified, the Ophrys fuciflora aggregate. The group is highly morphologically variable, prone to phenotypic convergence, shows low levels of sequence divergence and contains an unusually large proportion of threatened taxa, including the rarest Ophrys species in the UK. The aims of this study were to (a) circumscribe minimum resolvable genetically distinct entities within the O. fuciflora aggregate, and (b) assess the likelihood of gene flow between genetically and geographically distinct entities at the species and population levels. Fifty-five accessions sampled in Europe and Asia Minor from the O. fuciflora aggregate were studied using the AFLP genetic fingerprinting technique to evaluate levels of infraspecific and interspecific genetic variation and to assess genetic relationships between UK populations of O. fuciflora s.s. in Kent and in their continental European and Mediterranean counterparts. The two genetically and geographically distinct groups recovered, one located in England and central Europe and one in south-eastern Europe, are incongruent with current species delimitation within the aggregate as a whole and also within O. fuciflora s.s. Genetic diversity is higher in Kent than in the rest of western and central Europe. Gene flow is more likely to occur between populations in closer geographical proximity than those that are morphologically more similar. Little if any gene flow occurs between populations located in the south-eastern Mediterranean and those dispersed throughout the remainder of the distribution, revealing a genetic discontinuity that runs north-south through the Adriatic. This discontinuity is also evident in other clades of Ophrys and is tentatively attributed to the long-term influence of prevailing winds on the long-distance distribution of pollinia and especially seeds. A cline of gene flow connects populations from Kent and central and southern Europe; these individuals should therefore be considered part of an extensive meta-population. Gene flow is also evident among populations from Kent, which appear to constitute a single metapopulation. They show some evidence of hybridization, and possibly also introgression, with O. apifera.

SAXS study of crotapotin at low pH

The structure of crotapotin, a protein extracted from the venom of the Crotalus durissus terrificus, in solution at pH = 1.5, was studied by SAXS. The experimental results yield structural parameter values of the molecular radius of gyration R(g) = 13.6 angstrom, volume v = 16.2 x 10(3) angstrom3 and maximal dimension D(max) = 46 angstrom. The distance distribution function deduced from the scattering measurements is consistent with an overall molecular shape of an oblate ellipsoid of revolution with assymetry parameter nu = 0.45.

Quark-antiquark correlation in the pion

The electromagnetic tensor for inclusive electron scattering off the pion Wμν for momentum transfers such that q+ = 0, (q+ = q0 + q3) is shown to obey a sum-rule for the component W++. From this sum-rule, one can define the quark-antiquark correlation function in the pion, which characterizes the transverse distance distribution between the quark and antiquark in the light-front pion wave-function. Within the realistic models of the relativistic pion wave function (including instanton vacuum inspired wave function) it is shown that the value of the two-quark correlation radius (rqq̄) is near twice the pion electromagnetic radius (rπ), where rπ ≈ 2/3 fm. We also define the correlation length lcorr where the two-particle correlation have an extremum. The estimation of lcorr ≈ 0.3-0,5 fm is very close to estimations from instanton models of QCD vacuum. It is also shown that the above correlation is very sensitive to the pion light-front wave-function models. © 1997 Elsevier Science B.V.

SAXS Studies of the Endoglucanase Cel12A from Gloeophyllum trabeum Show Its Monomeric Structure and Reveal the Influence of Temperature on the Structural Stability of the Enzyme

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The subdomain structure of human serum albumin in solution under different pH conditions studied by small angle X-ray scattering

Small-angle X-ray scattering (SAXS) was used to study structural characteristics of human serum albumin (HSA) in solution under different pH conditions. Guinier analysis of SAXS results yielded values of the molecular radius of gyration ranging from 26.7 Å to 34.5 Å for pH varying from 2.5 to 7.0. This suggests the existence of significant differences in the overall shape of the molecule at different pH. Molecular models based on subdomains with different spatial configurations were proposed. The distance distribution functions associated with these models were calculated and compared with those determined from the experimental SAXS intensity functions. The conclusion of this SAXS study is that the arrangement of molecular subdomains is clearly pH dependent; the molecule adopting more or less compact configuration for different pH conditions. The conclusions of this systematic study on the modification in molecular shape of HSA as a response to pH changes is consistent with those of previous investigations performed for particular pH conditions.

Polyelectrolytes and their counterions studied by EPR spectroscopy

In this thesis methods of EPR spectroscopy were used to investigate polyion-counterion interactions in polyelectrolyte solutions. The fact that EPR techniques are local methods is exploited and by employing spin-carrying (i.e., EPR-active) probe ions it is possible to examine polyelectrolytes from the counterions’ point of view. It was possible to gain insight into i) the dynamics and local geometry of counterion attachment, ii) conformations and dynamics of local segments of the polyion in an indirect manner, and iii) the spatial distribution of spin probe ions that surround polyions in solution. Analysis of CW EPR spectra of dianion nitroxide spin probe Fremy’s salt (FS, potassium nitrosodisulfonate) in solutions of cationic PDADMAC polyelectrolyte revealed that FS ions and PDADMAC form transient ion pairs with a lifetime of less than 1 ns. This effect was termed as dynamic electrostatic attachment (DEA). By spectral simulation taking into account the rotational dynamics as a uniaxial Brownian reorientation, also the geometry of the attached state could be characterized. By variation of solvent, the effect of solvent viscosity and permittivity were investigated and indirect information of the polyelectrolyte chain motion was obtained. Furthermore, analysis of CW EPR data also indicates that in mixtures of organic solvent/water PDADMAC chains are preferentially solvated by the organic solvent molecules, while in purely aqueous mixtures the PDADMAC chain segments were found in different conformations depending on the concentration ratio R of FS counterions to PDADMAC repeat units.Broadenings in CW EPR spectra of FS ions were assigned to spin-exchange interaction and hence contain information on the local concentrations and distributions of the counterions. From analysis of these broadenings in terms of a modified cylindrical cell approach of polyelectrolyte theory, radial distribution functions for the FS ions in the different solvents were obtained. This approach breaks down in water above a threshold value of R, which again indicates that PDADMAC chain conformations are altered as a function of R. Double electron-electron resonance (DEER) measurements of FS ions were carried out to probe the distribution of attached counterions along polyelectrolyte chains. For a significant fraction of FS spin probes in solution with a rigid-rod model polyelectrolyte containing charged Ru2+-centers, a bimodal distance distribution was found that nicely reproduced the spacings of direct and next-neighbor Ru2+-centers along the polyelectrolyte: 2.35 and 4.7 nm. For the system of FS/PDADMAC, DEER data could be simulated by assuming a two-state distribution of spin probes, one state corresponding to a homogeneous (3-dimensional) distribution of spin probes in the polyelectrolyte bulk and the other to a linear (1-dimensional) distribution of spin probes that are electrostatically condensed along locally extended PDADMAC chain segments. From this analysis it is suggested that the PDADMAC chains form locally elongated structures of a size of at least ~5 nm.

The PLATO 2.0 mission

PLATO 2.0 has recently been selected for ESA’s M3 launch opportunity (2022/24). Providing accurate key planet parameters (radius, mass, density and age) in statistical numbers, it addresses fundamental questions such as: How do planetary systems form and evolve? Are there other systems with planets like ours, including potentially habitable planets? The PLATO 2.0 instrument consists of 34 small aperture telescopes (32 with 25 s readout cadence and 2 with 2.5 s candence) providing a wide field-of-view (2232 deg 2) and a large photometric magnitude range (4–16 mag). It focusses on bright (4–11 mag) stars in wide fields to detect and characterize planets down to Earth-size by photometric transits, whose masses can then be determined by ground-based radial-velocity follow-up measurements. Asteroseismology will be performed for these bright stars to obtain highly accurate stellar parameters, including masses and ages. The combination of bright targets and asteroseismology results in high accuracy for the bulk planet parameters: 2 %, 4–10 % and 10 % for planet radii, masses and ages, respectively. The planned baseline observing strategy includes two long pointings (2–3 years) to detect and bulk characterize planets reaching into the habitable zone (HZ) of solar-like stars and an additional step-and-stare phase to cover in total about 50 % of the sky. PLATO 2.0 will observe up to 1,000,000 stars and detect and characterize hundreds of small planets, and thousands of planets in the Neptune to gas giant regime out to the HZ. It will therefore provide the first large-scale catalogue of bulk characterized planets with accurate radii, masses, mean densities and ages. This catalogue will include terrestrial planets at intermediate orbital distances, where surface temperatures are moderate. Coverage of this parameter range with statistical numbers of bulk characterized planets is unique to PLATO 2.0. The PLATO 2.0 catalogue allows us to e.g.: - complete our knowledge of planet diversity for low-mass objects, - correlate the planet mean density-orbital distance distribution with predictions from planet formation theories,- constrain the influence of planet migration and scattering on the architecture of multiple systems, and - specify how planet and system parameters change with host star characteristics, such as type, metallicity and age. The catalogue will allow us to study planets and planetary systems at different evolutionary phases. It will further provide a census for small, low-mass planets. This will serve to identify objects which retained their primordial hydrogen atmosphere and in general the typical characteristics of planets in such low-mass, low-density range. Planets detected by PLATO 2.0 will orbit bright stars and many of them will be targets for future atmosphere spectroscopy exploring their atmosphere. Furthermore, the mission has the potential to detect exomoons, planetary rings, binary and Trojan planets. The planetary science possible with PLATO 2.0 is complemented by its impact on stellar and galactic science via asteroseismology as well as light curves of all kinds of variable stars, together with observations of stellar clusters of different ages. This will allow us to improve stellar models and study stellar activity. A large number of well-known ages from red giant stars will probe the structure and evolution of our Galaxy. Asteroseismic ages of bright stars for different phases of stellar evolution allow calibrating stellar age-rotation relationships. Together with the results of ESA’s Gaia mission, the results of PLATO 2.0 will provide a huge legacy to planetary, stellar and galactic science.

New Upper Bounds for Some Spherical Codes

The maximal cardinality of a code W on the unit sphere in n dimensions with (x, y) ≤ s whenever x, y ∈ W, x 6= y, is denoted by A(n, s). We use two methods for obtaining new upper bounds on A(n, s) for some values of n and s. We find new linear programming bounds by suitable polynomials of degrees which are higher than the degrees of the previously known good polynomials due to Levenshtein [11, 12]. Also we investigate the possibilities for attaining the Levenshtein bounds [11, 12]. In such cases we find the distance distributions of the corresponding feasible maximal spherical codes. Usually this leads to a contradiction showing that such codes do not exist.

The global distribution of Banana bunchy top virus reveals little evidence for frequent recent, human-mediated long distance dispersal events

Banana bunchy top virus (BBTV; family Nanoviridae, genus Babuvirus) is a multi-component single-stranded DNA virus, which infects banana plants in many regions of the world, often resulting in large-scale crop losses. Weanalyzed 171 banana leaf samples from fourteen countries and recovered, cloned, and sequenced 855 complete BBTV components including ninety-four full genomes. Importantly, full genomes were determined from eight countries, where previously no full genomes were available (Samoa, Burundi, Republic of Congo, Democratic Republic of Congo, Egypt, Indonesia, the Philippines, and the USA [HI]). Accounting for recombination and genome component reassortment, we examined the geographic structuring of global BBTV populations to reveal that BBTV likely originated in Southeast Asia, that the current global hotspots of BBTV diversity are Southeast Asia/Far East and India, and that BBTV populations circulating elsewhere in the world have all potentially originated from infrequent introductions. Most importantly, we find that rather than the current global BBTV distribution being due to increases in human-mediated movements of bananas over the past few decades, it is more consistent with a pattern of infrequent introductions of the virus to different parts of the world over the past 1,000 years.

Extending Distance-based Ranking Models In Estimation of Distribution Algorithms

Recently, probability models on rankings have been proposed in the field of estimation of distribution algorithms in order to solve permutation-based combinatorial optimisation problems. Particularly, distance-based ranking models, such as Mallows and Generalized Mallows under the Kendall’s-t distance, have demonstrated their validity when solving this type of problems. Nevertheless, there are still many trends that deserve further study. In this paper, we extend the use of distance-based ranking models in the framework of EDAs by introducing new distance metrics such as Cayley and Ulam. In order to analyse the performance of the Mallows and Generalized Mallows EDAs under the Kendall, Cayley and Ulam distances, we run them on a benchmark of 120 instances from four well known permutation problems. The conducted experiments showed that there is not just one metric that performs the best in all the problems. However, the statistical test pointed out that Mallows-Ulam EDA is the most stable algorithm among the studied proposals.

An algorithm of analysis tools on points distribution in high dimension space: The distance of a point and an infinite sub-space

This paper discusses the algorithm on the distance from a point and an infinite sub-space in high dimensional space With the development of Information Geometry([1]), the analysis tools of points distribution in high dimension space, as a measure of calculability, draw more attention of experts of pattern recognition. By the assistance of these tools, Geometrical properties of sets of samples in high-dimensional structures are studied, under guidance of the established properties and theorems in high-dimensional geometry.

Calculation of the average travel distance in a low-level picker-to-part system considering any distribution function within the aisles

The estimation of the average travel distance in a low-level picker-to-part order picking system can be done by analytical methods in most cases. Often a uniform distribution of the access frequency over all bin locations is assumed in the storage system. This only applies if the bin location assignment is done randomly. If the access frequency of the articles is considered in the bin location assignment to reduce the average total travel distance of the picker, the access frequency over the bin locations of one aisle can be approximated by an exponential density function or any similar density function. All known calculation methods assume that the average number of orderlines per order is greater than the number of aisles of the storage system. In case of small orders this assumption is often invalid. This paper shows a new approach for calculating the average total travel distance taking into account that the average number of orderlines per order is lower than the total number of aisles in the storage system and the access frequency over the bin locations of an aisle can be approximated by any density function.