A molecular genetic investigation of the population structure of Atlantic menhaden (Brevoortia tyrannus)

Atlantic menhaden (Brevoortia tyrannus), through landings, support one of the largest commercial fisheries in the United States. Recent consolidation of the once coast-wide reduction fishery to waters within and around Chesapeake Bay has raised concerns over the possibility of the loss of unique genetic variation resulting from concentrated fishing pressure. To address this question, we surveyed variation at the mitochondrial cytochrome c oxidase subunit I (COI) gene region and seven nuclear microsatellite loci to evaluate stock structure of Atlantic menhaden. Samples were collected from up to three cohorts of Atlantic menhaden at four geographic locations along the U.S. Atlantic coast in 2006 and 2007, and from the closely related Gulf menhaden (B. patronus) in the Gulf of Mexico. Genetic divergence between Atlantic menhaden and Gulf menhaden, based on the COI gene region sequences and microsatellite loci, was more characteristic of conspecific populations than separate species. Hierarchical analyses of molecular variance indicated a homogeneous distribution of genetic variation within Atlantic menhaden. No significant variation was found between young-of-the-year menhaden (YOY) collected early and late in the season within Chesapeake Bay, between young-of-the-year and yearling menhaden collected in the Chesapeake Bay during the same year, between YOY and yearling menhaden taken in Chesapeake Bay in successive years, or among combined YOY and yearling Atlantic menhaden collected in both years from the four geographic locations. The genetic connectivity between the regional collections indicates that the concentration of fishing pressure in and around Chesapeake Bay will not result in a significant loss of unique genetic variation.

Use of genetic data to assess the uncertainty in stock assessments due to the assumed stock structure: the case of albacore (Thunnus alalunga) from the Atlantic Ocean

Stock assessments can be problematic because of uncertainties associated with the data or because of simplified assumptions made when modeling biological processes (Rosenberg and Restrepo, 1995). For example, the common assumption in stock assessments that stocks are homogeneous and discrete (i.e., there is no migration between the stocks) is not necessarily true (Kell et al., 2004a, 2004b).

New Nuclear SNP Markers Unravel the Genetic Structure and Effective Population Size of Albacore Tuna (Thunnus alalunga)

In the present study we have investigated the population genetic structure of albacore (Thunnus alalunga, Bonnaterre 1788) and assessed the loss of genetic diversity, likely due to overfishing, of albacore population in the North Atlantic Ocean. For this purpose, 1,331 individuals from 26 worldwide locations were analyzed by genotyping 75 novel nuclear SNPs. Our results indicated the existence of four genetically homogeneous populations delimited within the Mediterranean Sea, the Atlantic Ocean, the Indian Ocean and the Pacific Ocean. Current definition of stocks allows the sustainable management of albacore since no stock includes more than one genetic entity. In addition, short-and long-term effective population sizes were estimated for the North Atlantic Ocean albacore population, and results showed no historical decline for this population. Therefore, the genetic diversity and, consequently, the adaptive potential of this population have not been significantly affected by overfishing.

The relation between translation speed and protein secondary structure

Based on the statistical analysis of 119 human and 92 E. coli proteins it was found that for both human and E. coli, the mRNA sequences consisting of tri-codon and tetra-codon with high translation speed preferably code for alpha helices more than for coils. For beta strand, the preference/ avoidance oscillates with the translation speed. Moreover, the non-homogeneous usages of tri-codon and tetra-codon with different translation speeds in a given secondary structure have also been found. These results cannot be simply explained by the effect of stochastic fluctuation.

Geometry and interaction of structures in homogeneous isotropic turbulence

A strategy to extract turbulence structures from direct numerical simulation (DNS) data is described along with a systematic analysis of geometry and spatial distribution of the educed structures. A DNS dataset of decaying homogeneous isotropic turbulence at Reynolds number Reλ = 141 is considered. A bandpass filtering procedure is shown to be effective in extracting enstrophy and dissipation structures with their smallest scales matching the filter width, L. The geometry of these educed structures is characterized and classified through the use of two non-dimensional quantities, planarity' and filamentarity', obtained using the Minkowski functionals. The planarity increases gradually by a small amount as L is decreased, and its narrow variation suggests a nearly circular cross-section for the educed structures. The filamentarity increases significantly as L decreases demonstrating that the educed structures become progressively more tubular. An analysis of the preferential alignment between the filtered strain and vorticity fields reveals that vortical structures of a given scale L are most likely to align with the largest extensional strain at a scale 3-5 times larger than L. This is consistent with the classical energy cascade picture, in which vortices of a given scale are stretched by and absorb energy from structures of a somewhat larger scale. The spatial distribution of the educed structures shows that the enstrophy structures at the 5η scale (where η is the Kolmogorov scale) are more concentrated near the ones that are 3-5 times larger, which gives further support to the classical picture. Finally, it is shown by analysing the volume fraction of the educed enstrophy structures that there is a tendency for them to cluster around a larger structure or clusters of larger structures. Copyright © 2012 Cambridge University Press.

Electronic structure and optical gain saturation of InAs1-xNx/GaAs quantum dots

The electronic band structures and optical gains of InAs1-xNx/GaAs pyramid quantum dots (QDs) are calculated using the ten-band k . p model and the valence force field method. The optical gains are calculated using the zero-dimensional optical gain formula with taking into consideration of both homogeneous and inhomogeneous broadenings due to the size fluctuation of quantum dots which follows a normal distribution. With the variation of QD sizes and nitrogen composition, it can be shown that the nitrogen composition and the strains can significantly affect the energy levels especially the conduction band which has repulsion interaction with nitrogen resonant state due to the band anticrossing interaction. It facilitates to achieve emission of longer wavelength (1.33 or 1.55 mu m) lasers for optical fiber communication system. For QD with higher nitrogen composition, it has longer emission wavelength and less detrimental effect of higher excited state transition, but nitrogen composition can affect the maximum gain depending on the factors of transition matrix element and the Fermi-Dirac distributions for electrons in the conduction bands and holes in the valence bands respectively. For larger QD, its maximum optical gain is greater at lower carrier density, but it is slowly surpassed by smaller QD as carrier concentration increases. Larger QD can reach its saturation gain faster, but this saturation gain is smaller than that of smaller QD. So the trade-off between longer wavelength, maximum optical, saturation gain, and differential gain must be considered to select the appropriate QD size according to the specific application requirement. (C) 2009 American Institute of Physics. [DOI 10.1063/1.3143025]

Effects of magnetic field on the electronic structure of wurtzite quantum dots: Calculations using effective-mass envelope function theory

The Hamiltonian of the wurtzite quantum dots in the presence of an external homogeneous magnetic field is given. The electronic structure and optical properties are studied in the framework of effective-mass envelope function theory. The energy levels have new characteristics, such as parabolic property, antisymmtric splitting, and so on, different from the Zeeman splitting. With the crystal field splitting energy Delta(c)=25 meV, the dark excitons appear when the radius is smaller than 25.85 A in the absence of external magnetic field. This result is more consistent with the experimental results reported by Efros [Phys. Rev. B 54, 4843 (1996)]. It is found that dark excitons become bright under appropriate magnetic field depending on the radius of dots. The circular polarization factors of the optical transitions of randomly oriented dots are zero in the absence of external magnetic field and increase with the increase of magnetic field, in agreement with the experimental results. The circular polarization factors of single dots change from nearly 0 to about 1 as the orientation of the magnetic field changes from the x axis of the crystal structure to the z axis, which can be used to determine the orientation of the z axis of the crystal structure of individual dots. The antisymmetric Hamiltonian is very important to the effects of magnetic field on the circular polarization of the optical transition of quantum dots.

Investigation of Ge-Si atomic interdiffusion in Ge nano-dots multilayer structure by double crystal X-ray diffraction

The fluctuations of the strained layer in a superlattice or quantum well can broaden the width of satellite peaks in double crystal X-ray diffraction (DCXRD) pattern. It is found that the width of the 0(th) peak is directly proportional to the fluctuation of the strained layer if the other related facts are ignored. By this method, the Ge-Si atomic interdiffusion in Ge nano-dots and wetting layers has been investigated by DCXRD. It is found that thermal annealing can activate Ge-Si atomic interdiffusion and the interdiffusion in the nano-dots area is much stronger than that in the wetting layer area. Therefore the fluctuation of the Ge layer decreases and the distribution of Ge atoms becomes homogeneous in the horizontal Ge (GeSi actually) layer, which make the width of the 0(th) peak narrow after annealing.

Electronic structure and g factors of narrow-gap zinc-blende nanowires and nanorods

The Hamiltonian in the framework of eight-band effective-mass approximation of the zinc-blende nanowires and nanorods in the presence of external homogeneous magnetic field is given in the cylindrical coordinate. The electronic structure, optical properties, magnetic energy levels, and g factors of the nanowires and nanorods are calculated. It is found that the electron states consist of many hole-state components, due to the coupling of the conduction band and valence band. For the normal bands which are monotone functions of |k(z)|, long nanorods can be modeled by the nanowires, the energy levels of the nanorods approximately equal the values of the energy band E(k(z)) of the nanowires with the same radius at a special k(z), where k(z) is the wave vector in the wire direction. Due to the coupling of the states, some of the hole energy bands of the nanowires have their highest points at k(z)=0. Especially, the highest hole state of the InSb nanowires is not at the k(z)=0 point. It is an indirect band gap. For these abnormal bands, nanorods can not be modeled by the nanowires. The energy levels of the nanorods show an interesting plait-like pattern. The linear polarization factor is zero, when the aspect ratio L/2R is smaller than 1, and increases as the length increases. The g(z) and g(x) factors as functions of the k(z), radius R and length L are calculated for the wires and rods, respectively. For the wires, the g(z) of the electron ground state increases, and the g(z) of the hole ground state decreases first, then increases with the k(z) increasing. For the rods, the g(z) and g(x) of the electron ground state decrease as the R or the L increases. The g(x) of the hole ground state decreases, the g(z) of the hole ground state increases with the L increasing. The variation of the g(z) of the wires with the k(z) is in agreement with the variation of the g(z) of the rods with the L.

Electronic structure and optical gain saturation of InAs1-xNx/GaAs quantum dots

The electronic band structures and optical gains of InAs1-xNx/GaAs pyramid quantum dots (QDs) are calculated using the ten-band k . p model and the valence force field method. The optical gains are calculated using the zero-dimensional optical gain formula with taking into consideration of both homogeneous and inhomogeneous broadenings due to the size fluctuation of quantum dots which follows a normal distribution. With the variation of QD sizes and nitrogen composition, it can be shown that the nitrogen composition and the strains can significantly affect the energy levels especially the conduction band which has repulsion interaction with nitrogen resonant state due to the band anticrossing interaction. It facilitates to achieve emission of longer wavelength (1.33 or 1.55 mu m) lasers for optical fiber communication system. For QD with higher nitrogen composition, it has longer emission wavelength and less detrimental effect of higher excited state transition, but nitrogen composition can affect the maximum gain depending on the factors of transition matrix element and the Fermi-Dirac distributions for electrons in the conduction bands and holes in the valence bands respectively. For larger QD, its maximum optical gain is greater at lower carrier density, but it is slowly surpassed by smaller QD as carrier concentration increases. Larger QD can reach its saturation gain faster, but this saturation gain is smaller than that of smaller QD. So the trade-off between longer wavelength, maximum optical, saturation gain, and differential gain must be considered to select the appropriate QD size according to the specific application requirement. (C) 2009 American Institute of Physics. [DOI: 10.1063/1.3143025]

Homogeneous Epitaxial Growth of N,N '-di(n-butyl)quinacridone Thin Films on Ag(110)

The structural evolution of the ordered N-N' dibutyl-substituted quinacridone (QA4C) multilayers (3 MLs) has been monitored in situ and in real time at various substrate temperatures using low energy electron diffraction (LEED) during organic molecular beam epitaxy (MBE). Experimental results of LEED patterns clearly reveal that the structure of the multilayer strongly depends on the substrate temperature. Multilayer growth can be achieved at the substrate temperatures below 300 K, while at the higher temperatures we can only get one ordered monolayer of QA4C. Two kinds of structures, the commensurate and incommensurate one, often coexist in the QA4C multilayer. With a method of the two-step substrate temperatures, the incommensurate one can be suppressed, and the commensurate, on the other hand, more similar to the (001) plane of the QA4C bulk crystal, prevails with the layer of QA4C increasing to 3 MLs. The two structures in the multilayers are compressed slightly in comparison to the original ones in the first monolayer.

Upconversion luminescence of Y2O3 : Er3+, Yb3+ nanoparticles prepared by a homogeneous precipitation method

Y2O3: Er3+, Yb3+ nanoparticles were synthesized by a homogeneous precipitation method without and with different concentrations of EDTA 2Na. Upconversion luminescence spectra of the samples were studied under 980 nm laser excitation. The results of XRD showed that the obtained Y2O3:Er3+,Yb3+ nanoparticles were of a cubic structure. The average crystallite sizes calculated were in the range of 28-40 nm. Green and red upconversion emission were observed, and attributed to H-2(11/2), S-4(3/2) -> I-4(15/2) and F-4(9/2) -> I-4(15/2) transitions of the Er3+ ion, respectively.

Structure and properties of the ordered double perovskites Sr2MWO6 (M = Co, Ni) by sol-gel route

The single-phase double perovskites Sr2MWO6 (M=Co, Ni) were prepared by sol-gel method. Crystal Structure, magnetic properties and the morphology of Sr2CoWO6 and Sr2NiWO6 were investigated. X-ray powder diffraction (XRD) analysis shows single phase structure for Sr2MWO6 (M=Co, Ni) without any traces of impurities and the crystal structure of all the samples belongs to the tetragonal I4/m space group. SEM image for Sr2MWO6 (M=Co, Ni) indicate that the grains are homogeneous and connect each other very well. The Neel temperature for Sr2CoWO6 and Sr2NiWO6 are 23 K and 59 K, respectively. Magnetic measurements showed that the magnetic moment in these double perovskites originates mainly from the interactions between Ni ions and Co ions.

Monte Carlo simulation of miscibility of polymer blends with repulsive interactions: effect of chain structure

The effects of the chain structure and the intramolecular interaction energy of an A/B copolymer on the miscibility of the binary blends of the copolymer and homopolymer C have been studied by means of a Monte Carlo simulation. In the system, the interactions between segments A, B and C are more repulsive than those between themselves. In order to study the effect of the chain structure of the A/B copolymer on the miscibility, the alternating, random and block copolymers were introduced in the simulations, respectively. The simulation results show that the miscibility of the binary blends strongly depends on the intramolecular interaction energy ((ε) over bar (AB)) between segments A and B within the A/B copolymers. The higher the repulsive interaction energy, the more miscible the A/B copolymer and homopolymer C are. For the diblock copolymer/homopolymer blends, they tend to form micro phase domains. However, the phase domains become so small that the blend can be considered as a homogeneous phase for the alternating copolymer/ homopolymer blends. Furthermore, the investigation of the average end-to-end distance ((h) over bar) in different systems indicates that the copolymer chains tend to coil with the decrease Of (ε) over bar (AB) whereas the (h) over bar of the homopolymer chains depends on the chain structure of the copolymers.

Species diversity structure analysis at two sites in the tropical rain forest of Sumatra

Data from a hilly forest study site at Batang Ule, Sumatra, are organized into 30 100-m × 10-m subplots lying perpendicular to the line of maximal topographic gradient, from the valley to the plateau/ridge. The following methodological question is addressed: what species diversity measures are best used in order to reveal the ecologically distinct regions in the site. The main tool used to answer this question is the α-diversity curve (Hα). Graphical examination of tree and species densities, and α-diversity curves identifies an anomalous species diversity behaviour of the ‘ridge above the slope’ subplots which may have implications on land-facet class definitions. Factor analysis of the α-diversity curves indicates that the diversity space is two-dimensional: i.e. two diversity measures are sufficient to characterize the site; the species density (H0), and the Berger-Parker index (H[infty infinity]). In the two-dimensional diversity-space three distinct species diversity groups are found which relate to the topographic gradient at the Batang Ule site. The results are compared with those for a flat homogeneous site at Pasirmayang, Sumatra. The implications of the results on land-classifications in species-diversity mapping and conservation strategy are discussed.