Development of polymorphic EST markers in Penaeus monodon: applications in penaeid genetics

The objective of this study was to develop type I markers for genome mapping and other genetic studies of Penaeus monodon. Primers were designed based on expressed sequence tags (ESTs) from a P monodon cephalothorax cDNA library to amplify 100-300 bp products. 34 of the primer pairs successfully amplified PCR products from genomic DNA. Single-strand conformation polymorphism analysis showed that similar to 30% of the ESTs tested exhibit polymorphism in a test panel of P monodon individuals. Mendelian inheritance of the EST-derived markers has been established in two international reference mapping families of P monodon, and mapping of these markers is in progress. Some ESTs were successfully amplified from other Penaeus species (P. chinensis, P japonicus and P vannamei), indicating that the markers are applicable in cross-species comparison. Two populations of P. japonicus could be differentiated using one of the ESTS. In conclusion, the polymorphic EST markers developed in this study are applicable in genome mapping and population genetic studies of penaeid shrimp. (C) 2002 Elsevier Science B.V. All rights reserved.

Karyotype evolution in Rhinolophus bats (Rhinolophidae, Chiroptera) illuminated by cross-species chromosome painting and G-banding comparison

Rhinolophus (Rhinolophidae) is the second most speciose genus in Chiroptera and has extensively diversified diploid chromosome numbers (from 2n=28 to 62). In spite of many attempts to explore the karyotypic evolution of this genus, most studies have been

Uncertainties in estimates of cropland area in China: a comparison between an AVHRR-derived dataset and a Landsat TM-derived dataset

The large uncertainties in estimates of cropland area in China may have significant implications for major cross-cutting themes of global environmental change-food production and trade, water resources, and the carbon and nitrogen cycles. Many earlier studies have indicated significant under-reporting of cropland area in China from official agricultural census statistics datasets. Space-borne remote sensing analyses provide an alternative and independent approach for estimating cropland area in China. In this study, we report estimates of cropland area from the National Land Cover Dataset (NLCD-96) at the 1:100,000 scale, which was generated by a multi-year National Land Cover Project in China through visual interpretation and digitization of Landsat TM images acquired mostly in 1995 and 1996. We compared the NLCD-96 dataset to another land cover dataset at I-km spatial resolution (the IGBP DIScover dataset version 2.0), which was generated from monthly Advanced Very High Resolution Radiometer (AVHRR)-derived Normalized Difference Vegetation Index (NDVI) from April, 1992 to March, 1993. The data comparison highlighted the limitation and uncertainty of cropland area estimates from the DIScover dataset. (C) 2003 Elsevier Science B.V. All rights reserved.

Characterization and Comparison of the Tissue-Related Modules in Human and Mouse

Background: Due to the advances of high throughput technology and data-collection approaches, we are now in an unprecedented position to understand the evolution of organisms. Great efforts have characterized many individual genes responsible for the interspecies divergence, yet little is known about the genome-wide divergence at a higher level. Modules, serving as the building blocks and operational units of biological systems, provide more information than individual genes. Hence, the comparative analysis between species at the module level would shed more light on the mechanisms underlying the evolution of organisms than the traditional comparative genomics approaches. Results: We systematically identified the tissue-related modules using the iterative signature algorithm (ISA), and we detected 52 and 65 modules in the human and mouse genomes, respectively. The gene expression patterns indicate that all of these predicted modules have a high possibility of serving as real biological modules. In addition, we defined a novel quantity, "total constraint intensity,'' a proxy of multiple constraints (of co-regulated genes and tissues where the co-regulation occurs) on the evolution of genes in module context. We demonstrate that the evolutionary rate of a gene is negatively correlated with its total constraint intensity. Furthermore, there are modules coding the same essential biological processes, while their gene contents have diverged extensively between human and mouse. Conclusions: Our results suggest that unlike the composition of module, which exhibits a great difference between human and mouse, the functional organization of the corresponding modules may evolve in a more conservative manner. Most importantly, our findings imply that similar biological processes can be carried out by different sets of genes from human and mouse, therefore, the functional data of individual genes from mouse may not apply to human in certain occasions.

A single amino acid defines cross-species reactivity of tree shrew (Tupaia belangeri) CD1d to human invariant natural killer T (iNKT) cells

P>The non-classical major histocompatibility complex (MHC) class I molecule CD1d presents lipid antigens to invariant natural killer T (iNKT) cells, which are an important part of the innate immune system. CD1d/iNKT systems are highly conserved in evoluti

Identification of a novel gene K23 over-expressed in fish cross-subfamily cloned embryos

A novel gene-K23, differentially expressed in cross-subfamily cloned embryos, was isolated by RACE-PCR technique. It had 2580 base pairs (bp) in length, with a 1,425 bp open reading frame (ORF) encoding a putative protein of 474 amino acids (aa). Bioinformatic analysis indicated that K23 had 22 phosphorylation sites, but it had no signal peptides. Developmental expression analysis in zebrafish showed that K23 transcripts were maternally expressed in ovum and the amount of K23 transcripts increased gradually from zygote to pharyngula period. Subcellular localization analysis revealed that K23 protein was homogeneously distributed both in nuclei and cytoplasm. Taken together, our findings indicate that K23 gene is a novel gene differentially expressed in fish cross-subfamily cloned embryos.

Comparison of stationary acoustic monitoring and visual observation of finless porpoises

The detection performance regarding stationary acoustic monitoring of Yangtze finless porpoises Neophocaena phocaenoides asiaeorientalis was compared to visual observations. Three stereo acoustic data loggers (A-tag) were placed at different locations near the confluence of Poyang Lake and the Yangtze River, China. The presence and number of porpoises were determined acoustically and visually during each 1-min time bin. On average, porpoises were acoustically detected 81.7 +/- 9.7% of the entire effective observation time, while the presence of animals was confirmed visually 12.7 +/- 11.0% of the entire time. Acoustic monitoring indicated areas of high and low porpoise densities that were consistent with visual observations. The direction of porpoise movement was monitored using stereo beams, which agreed with visual observations at all monitoring locations. Acoustic and visual methods could determine group sizes up to five and ten individuals, respectively. While the acoustic monitoring method had the advantage of high detection probability, it tended to underestimate group size due to the limited resolution of sound source bearing angles. The stationary acoustic monitoring method proved to be a practical and useful alternative to visual observations, especially in areas of low porpoise density for long-term monitoring.

A comparison of silicon oxide and nitride as host matrices on the photoluminescence from Er3+ ions

This paper compares the properties of silicon oxide and nitride as host matrices for Er ions. Erbium-doped silicon nitride films were deposited by a plasma-enhanced chemical-vapour deposition system. After deposition, the films were implanted with Er3+ at different doses. Er-doped thermal grown silicon oxide films were prepared at the same time as references. Photoluminescence features of Er3+ were inspected systematically. It is found that silicon nitride films are suitable for high concentration doping and the thermal quenching effect is not severe. However, a very high annealing temperature up to 1200 degrees C is needed to optically activate Er3+ which may be the main obstacle to impede the application of Er-doped silicon nitride.

Comparison and combination of several stress relief methods for cubic boron nitride films deposited by ion beam assisted deposition

Cubic boron nitride (c-BN) films were prepared by ion beam assisted deposition (IBAD) technique, and the stresses were primary estimated by measuring the frequency shifts in the infrared-absorption peaks of c-BN samples. To test the possible effects of other factors, dependencies of the c-BN transversal optical mode position on film thickness and c-BN content were investigated. Several methods for reducing the stress of c-BN films including annealing, high temperature deposition, two-stage process, and the addition of a small amount of Si were studied, in which the c-BN films with similar thickness and cubic phase content were used to evaluate the effects of the various stress relief methods. It was shown that all the methods can reduce the stress in c-BN films to various extents. Especially, the incorporation of a small amount of Si (2.3 at.%) can result in a remarkable stress relief from 8.4 to similar to 3.6 GPa whereas the c-BN content is nearly unaffected, although a slight degradation of the c-BN crystallinity is observed. The stress can be further reduced down below I GPa by combination of the addition of Si with the two-stage deposition process. (c) 2008 Elsevier B.V. All rights reserved.

Comparison of short period InAs/GaSb superlattices on GaSb and GaAs substrates

Type II superlattices (SLs) short period InAs(4ML)/GaSb(8ML) were grown by molecular-beam epitaxy on lattice-mismatched GaAs substrates and on GaSb substrates. A smooth GaSb epilayer was formed on GaAs substrates by inserting mulit-buffer layers including an interfacial misfit mode AlSb quantum dot layer and AlSb/GaSb superlattices smooth layer. SLs grown on GaAs substrates (GaAs-based SLs) showed well-resolved satellite peaks in XRD. GaSb-based SLs with better structural quality and smoother surface showed strong photoluminescence at 2.55 mu m with a full width at half maximum (FWHM) of 20 meV, narrower than 31 meV of GaAs-based SLs. Inferior optical absorption of GaAs-based SL was observed in the range of 2-3 mu m. Photoresponse of GaSb-based SLs showed the cut-off wavelength at 2.6 mu m.

Quantum mechanical simulation of nanosized metal-oxide-semiconductor field-effect transistor using empirical pseudopotentials: A comparison for charge density occupation methods

The atomistic pseudopotential quantum mechanical calculations are used to study the transport in million atom nanosized metal-oxide-semiconductor field-effect transistors. In the charge self-consistent calculation, the quantum mechanical eigenstates of closed systems instead of scattering states of open systems are calculated. The question of how to use these eigenstates to simulate a nonequilibrium system, and how to calculate the electric currents, is addressed. Two methods to occupy the electron eigenstates to yield the charge density in a nonequilibrium condition are tested and compared. One is a partition method and another is a quasi-Fermi level method. Two methods are also used to evaluate the current: one uses the ballistic and tunneling current approximation, another uses the drift-diffusion method. (C) 2009 American Institute of Physics. [doi:10.1063/1.3248262]

Single-mode condition for silicon rib waveguides with large cross sections

The single-mode condition for silicon rib waveguides with large cross sections is obtained using a numerical method based on the finite-difference beam propagation method (FD-BPM). An ultrawide computation window is used to contain the wide mode profile near cutoff. Comparison with previous results shows that the formula predicted by the mode-matching technique is in a better agreement with our results. (C) 2004 Society of Photo-Optical Instrumentation Engineers.

Single-mode condition for silicon rib waveguides with trapezoidal cross-section

Single-mode condition for silicon rib waveguides with trapezoidal cross-section was obtained using a numerical method based on imaginary-distance beam propagation method with non-uniform discretization. Both quasi-transverse-electric and quasi-transverse-magnetic modes were investigated. Simulated single-mode condition is given by a modified equation. Comparison with reported results shows that the Marcatili's method is in a better agreement with our results. (C) 2003 Elsevier B.V. All rights reserved.

Wurtzite-to-tetragonal structure phase transformation and size effect in ZnO nanorods

The deformation of [0001]-oriented ZnO nanorods with hexagonal cross sections under uniaxial tensile loading is analyzed through molecular statistical thermodynamics (MST) simulations. The focus is on the size dependence of mechanical behavior in ZnO nanorods with diameters ranging from 1.95 to 17.5 nm. An irreversible phase transformation from the wurtzite (P6(3)mc space group) structure to a tetragonal structure (P4(2)/mnm space group) occurs during the tensile loading process. Young's modulus before the transformation demonstrates a size dependence consistent with what is observed in experiments. A stronger size dependence of response is seen after the transformation and is attributed to the polycrystalline nature of the transformed structure. A comparison of the MST and molecular dynamics (MD) methods shows that MST is 60 times faster than MD and yields results consistent with the results of MD.

Shell effect and capture cross sections in the synthesis of superheavy nuclei

The shell effect is included in the improved isospin dependent quantum molecular dynamics model in which the shell correction energy of the system is calculated by using the deformed two-center shell model. A switch function is introduced to connect the shell correction energy of the projectile and the target with that of the compound nucleus during the dynamical fusion process. It is found that the calculated capture cross sections reproduce the experimental data quantitatively at the energy near the Coulomb barrier. The capture cross sections for reaction (35) (80) Br + (82) (208) Pb -> (117) (288) X are also calculated and discussed.