Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication

Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication(1,2). To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data(3). Furthermore, we find a surprising correspondence between genetic and phenotypic/functional breed groupings but there are exceptions that suggest phenotypic diversification depended in part on the repeated crossing of individuals with novel phenotypes. Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages. More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity.

Genome-wide computational identification of microRNAs and their targets in the deep-branching eukaryote Giardia lamblia

Using a combined computational program. we identified 50 potential microRNAs (miRNAs) in Giardia lamblia. one of the most primitive unicellular eukaryotes. These miRNAs are unique to G. lamblia and no homologues have been found in other organisms; miRNAs.

Genome-wide identification and characterization of cytochrome P450 monooxygenase genes in the ciliate Tetrahymena thermophila

Background: Cytochrome P450 monooxygenases play key roles in the metabolism of a wide variety of substrates and they are closely associated with endocellular physiological processes or detoxification metabolism under environmental exposure. To date, however, none has been systematically characterized in the phylum Ciliophora. T. thermophila possess many advantages as a eukaryotic model organism and it exhibits rapid and sensitive responses to xenobiotics, making it an ideal model system to study the evolutionary and functional diversity of the P450 monooxygenase gene family. Results: A total of 44 putative functional cytochrome P450 genes were identified and could be classified into 13 families and 21 sub-families according to standard nomenclature. The characteristics of both the conserved intron-exon organization and scaffold localization of tandem repeats within each P450 family clade suggested that the enlargement of T. thermophila P450 families probably resulted from recent separate small duplication events. Gene expression patterns of all T. thermophila P450s during three important cell physiological stages (vegetative growth, starvation and conjugation) were analyzed based on EST and microarray data, and three main categories of expression patterns were postulated. Evolutionary analysis including codon usage preference, sit-especific selection and gene-expression evolution patterns were investigated and the results indicated remarkable divergences among the T. thermophila P450 genes. Conclusion: The characterization, expression and evolutionary analysis of T. thermophila P450 monooxygenase genes in the current study provides useful information for understanding the characteristics and diversities of the P450 genes in the Ciliophora, and provides the baseline for functional analyses of individual P450 isoforms in this model ciliate species.

Range-wide Yangtze freshwater dolphin expedition: The last chance to see Baiji?

Background, Aim and Scope. There are two species of fresh water cetaceans surviving in the Yangtze River system in China: Baiji (Lipotes vexillifer) and Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis). As a result of the expansion of human activities on the river, their distribution ranges appear to be decreasing and in the case of the Baiji, are even being restricted to several sections. The Baiji is the world's most critically endangered cetacean species with a population estimated at only a few tens of individuals. The Yangtze finless porpoise is the world's only freshwater-adapted population of the species, and it has been estimated that only around 1,000 individuals remain in the river system. In order to prevent the extinction of Baiji and a sharp decline in the abundance of the porpoise, in situ conservation (i.e. in the river) and two ex situ conservation (i.e. in semi-natural reserves and in captivity) strategies were proposed and have been implemented since the early 1990s. In view of both the severely endangered status of the animals and the severely degraded conditions of their habitats, the feasibility and actual status of these two strategies are raised for discussion. Main Features. The threats faced by the cetaceans are mainly from the unfettered exploitation of the river's resources. In the past 20 years, five nature reserves have been established along the river. Imposing maximum prohibition of harmful and illegal fishing methods in the reserves might prolong the process of extinction of these cetaceans in the wild, but so far, the administrative measures taken in the reserves have not yet kept the abundance from sharply declining. As human use of the river and its resources is expected to intensify for many decades into the future, the ability of the river to continue to support these species is certainly undecided. Therefore, rescuing animals from the river and establishing viable breeding populations in semi-natural reserves, in which the environment is similar to the main stream of the river, and in captivity, has to be considered urgently as the short-term goal of ex situ strategies. Since the abundance of porpoises is higher than that of the Baiji, we have first established breeding populations of them in the semi-natural reserves and in captivity. But, considering the extremely low density of Baiji in the river, an immediate range-wide Yangtze Baiji survey is an urgent need for locating and capturing sufficient Baiji for successfully establishing a breeding population of them in semi-natural reserves. Results. Two semi-natural reserves (in Shishou, Hubei Province, and Tongling, Anhui Province) have been set up along the river in order to establish breeding populations of the Baiji and the porpoises. So far, several small groups of porpoises that were caught in the main stream of the river have successively been introduced into the semi-natural reserves. Under careful management, these animals in both of the semi-natural reserves not only survive, but can also reproduce naturally and successfully. At least one or three calves were born in each reserve each year. Additionally, a breeding group of porpoises is being established at the Baiji Dolphinarium at the Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan. There are presently four adults and one calf living in the Dolphinarium. The calf, born in July, 2005, is the first captive bred Yangtze Finless Porpoise in the world. In preparation for the range-wide Yangtze cetacean survey, a 9-day pilot expedition on the river near Wuhan was conducted in March, 2006, in order to develop methods for locating the Baiji. No Baiji were expected to be seen in such a short period but about 40 porpoise sightings were observed. Results of the pilot survey indicated that traditional visual and acoustical survey methods for cetaceans should be adapted to find the elusive Baiji in the river. Currently, the range-wide Yangtze cetacean survey is in preparation. The survey will cover over 1,700 km of the Yangtze River from Yichang to Shanghai, and is expected to provide detailed information on Baiji and porpoise numbers and distribution patterns in the river. Discussion. Although the short-term goal of ex situ conservation is to rescue cetaceans from the river and to establish viable breeding populations in semi-natural reserves and in captivity, the long-term goal of releasing the animals back into the river when the threats have decreased and the natural environment has been improved, should not be neglected. Moreover, the in situ conservation efforts in the natural reserves, and even in the entire Yangtze River system, including the lakes, should not be ignored or abandoned at any time. The activities contributing to the conservation of the Baiji and the porpoise in the wild have the incidental effect of benefiting the entire Yangtze ecosystem and other rare threatened species. The dynamics of the groups of porpoises in semi-natural reserves should be monitored continually, in order to guide the establishment of breeding groups of Baiji in these semi-natural reserves in the near future. Conclusions. Under the existing severely degraded conditions of the Yangtze system, the sharply fall populations of Baiji and porpoises will not be suspended in the foreseeable future. Therefore, ex situ conservation should be emphasized, and the severely threatened Baiji in the river should be removed and translocated to semi-natural reserves for establishing viable breeding populations. The successful program of capturing, translocating and maintaining finless porpoises in the Shishou semi-natural reserve has demonstrated its adequacy as an ex situ environment for cetaceans. Following the successful pilot survey in the river, the immediate range-wide Yangtze cetacean survey is proposed and is in preparation. The range-wide survey is expected to ensure that any remaining Baiji can be found reliably and captured successfully after the survey. Recommendations and Perspectives. During the range-wide survey, not only the Baiji but also the porpoise as well as their habitats should be investigated based on visual and acoustical methods that adapted to the river and the animals. Meanwhile, the current risk levels to the Baiji and porpoises should be evaluated at each area where Baiji or porpoises can be reliably sighted. Any capture efforts should be targeted on the most threatened areas, or where there is maximum risk of injury or death. The immediate track of the Baiji should be carried out once a Baiji is sighted during the range-wide survey in order to obtain the movement route of the animals, which is crucial information for the successful capture operation. Additionally, the need to establish new semi-natural reserves for the porpoises should be placed on the agenda of local and central governments in the near future.

Sonar gain control in echolocating finless porpoises (Neophocaena phocaenoides) in an open water (L)

Source levels of echolocating free-ranging Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis) were calculated using a range estimated by measuring the time delays of the signals via the surface and bottom reflection paths to the hydrophone, relative to the direct signal. Peak-to-peak source levels for finless porpoise were from 163.7 to 185.6 dB re:1 mu Pa. The source levels are highly range dependent and varied approximately as a function of the one-way transmission loss for signals traveling from the animals to the hydrophone. (c) 2006 Acoustical Society of America.

Theoretical gain of strained GeSn0.02/Ge1-x-y ' SixSny ' quantum well laser

Using effective-mass Hamiltonian model of semiconductors quantum well structures, we investigate the electronic structures of the Gamma-conduction and L-conduction subbands of GeSn/GeSiSn strained quantum well structure with an arbitrary composition. Our theoretical model suggests that the band structure could be widely modified to be type I, negative-gap or indirect-gap type II quantum well by changing the mole fraction of alpha-Sn and Si in the well and barrier layers, respectively. The optical gain spectrum in the type I quantum well system is calculated, taking into account the electrons leakage from the Gamma-valley to L-valley of the conduction band. We found that by increasing the mole fraction of alpha-Sn in the barrier layer and not in the well layer, an increase in the tensile strain effect can significantly enhance the transition probability, and a decrease in Si composition in the barrier layer, which lowers the band edge of Gamma-conduction subbands, also comes to a larger optical gain.

High efficiency and broad bandwidth grating coupler between nanophotonic waveguide and fibre

A high efficiency and broad bandwidth grating coupler between a silicon-on-insulator (SOI) nanophotonic waveguide and fibre is designed and fabricated. Coupling efficiencies of 46% and 25% at a wavelength of 1.55 mu m are achieved by simulation and experiment, respectively. An optical 3 dB bandwidth of 45 nm from 1530 nm to 1575 nm is also obtained in experiment. Numerical calculation shows that a tolerance to fabrication error of 10 nm in etch depth is achievable. The measurement results indicate that the alignment error of +/-2 mu m results in less than 1 dB additional coupling loss.

Investigation of gain recovery for InAs/GaAs quantum dot semiconductor optical amplifiers by rate equation simulation

The gain recoveries in quantum dot semiconductor optical amplifiers (QD SOAs) are numerically studied by rate equation simulation. Similar to the optical pump-probe experiment, the injection of double 150 fs optical pulses is used to simulate the gain recovery of a weak continuous signal under different injection levels, inhomogeneous broadenings, detuning wavelengths, and pulse signal energies for the QD SOAs. The obtained gain recoveries are then fitted by a response function with multiple exponential terms to determine the response times. The gain recovery can be described by three exponential terms with the time constants, which can be explained as carrier relaxation from the excited state to the ground state, carrier captured by the excited state from the wetting layer, and the supply of the wetting layer carriers. The fitted lifetimes decrease with the increase of the injection currents under gain unsaturation, slightly decrease with the decrease of inhomogeneous broadening of QDs, and increase with the increase of detuning wavelength between continuous signal and pulse signal and the increase of the pulse energy.

NUMERICAL ANALYSIS OF A NOVEL 980nm MICROCAVITY SEMICONDUCTOR OPTICAL AMPLIFIER WITH HIGH GAIN AND LOW NOISE

A novel microcavity semiconductor optical amplifier ( MCSOA) was proposed by incorporating top and bottom distributed Bragg reflectors ( DBRs) into the waveguide structure of conventional traveling-wave semiconductor optical amplifiers(TW-SOAs). The incoming( outgoing) light beam incidented onto (escaped from) the waveguide structure at a oblique angle through two optical windows, where the top DBR was etched away, and anti-reflection coating was deposited. The light beams inside the optical cavity were reflected repeatedly between two DBRs and propagated along waveguide in a zigzag optical path. The performance of the MCSOA was systematically investigated by extensive numerical simulation based on a traveling-wave model by taking into account the comprehensive effects of DBRs on both the amplification of signals and the filtering of spontaneous emission( SE). Our results show that the MCSOA is capable of achieving a fiber-to-fiber gain as high as 40dB and a low noise figure is less than 3.5dB.

Numerical analysis of gain saturation, noise figure, and carrier distribution for quantum-dot semiconductor-optical amplifiers

The gain saturation behaviors and noise figure are numerically analyzed for quantum-dot semiconductor optical amplifiers (QD-SOAs). The carrier and photon distributions in the longitudinal direction as well as the photon energy dependent facet reflectivity are accounted in the rate equations, which are solved with output amplified spontaneous emission spectrum as iterative variables. The longitudinal distributions of the occupation probabilities and spectral-hole burning are presented for electrons in the excited and ground states of quantum dots. The saturation output power 19.7 dBm and device gain 20.6 dB are obtained for a QD-SOA with the cavity length of 6 rum at the bias current of 500 mA. The influences of them electron intradot relaxation time and the QD capture time on the gain spectrum are simulated with the relaxation time of 1, 30, and 60 ps and capture time of 1, 5, and 10 ps. The noise figure as low as 3.5 dB is expected due to the strong polarization sensitive spontaneous emission. The characteristics of gain saturation and noise figure versus input signal power for QD-SOAs are similar to that of semiconductor. linear optical amplifiers with gain clamping by vertical laser fields.

Enhanced modulation bandwidth of a Fabry-Perot semiconductor laser subject to light injection from another Fabry-Perot laser

Variations in optical spectrum and modulation band-width of a modulated Fabry-Perot (FP) semiconductor laser subject to the external light injection from another FP Laser is investigated in this paper. Optimal wavelength matching conditions for two FP lasers are discussed. A series of experiments show that two FP lasers should have a central wavelength overlapping and a mode spacing difference of several gigahertz. Under these conditions both the magnitude and phase frequency responses can be improved significantly.

Electronic structure and optical gain of wurtzite ZnO nanowires

The electronic structure and optical gain of wurtzite ZnO nanowires are investigated in the framework of effective-mass envelope-function theory. We found that as the elliptical aspect ratio e increases to be larger than a critical value, the hole ground states may change from optically dark to optically bright. The optical gain of ZnO nanowires increases as the hole density increases. For elliptical wire with large e, the y-polarized mode gain can be several thousand cm(-1), while the x-poiarized mode gain may be 26 times smaller than the former, so they can be used as ultraviolet linearly polarized lasers. (C) 2008 American Institute of Physics.

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

The shape of truncated square-based pyramid quantum dots (QDs) is similar to that of real QDs in experiments. The electronic band structures and optical gain of InAs1-xNx/GaAs QDs are calculated by using the 10-band k.p model, and the strain is calculated by the valence force field (VFF) method. When the top part of the QD is truncated, greater truncation corresponds to a flatter shape of the QD. The truncation changes the strain distribution and the confinement in the z direction. A flatter QD has a greater C1-HH1 transition energy, greater transition matrix element, less detrimental effect of higher excited transition, and higher saturation gain and differential gain. The trade-off between these properties must be considered. From our results, a truncated QD with half of its top part removed has better overall performance. This can provide guidance to growing QDs in experiments in which the proper growing conditions can be controlled to achieve required properties. (C) 2009 Elsevier Ltd. All rights reserved.

Optical bistability in InP/GaInAsP equilateral-triangle-resonator microlasers

Optical bistability is reported in InP/GaInAsP equilateral-triangle-resonator (ETR) microlasers, which are fabricated by planar technology. For a 30 mu m side ETR microlaser with a 2-mu m-wide output waveguide connected to one of the vertices of the ETR, hysteresis loops are observed for the output power versus the injection current from 215 to 235 K. The laser output spectra are measured in the upper and lower states of the hysteresis loop, which show strong mode competition among transverse modes. The hysteresis loops are demonstrated by two-mode rate equations with asymmetric cross gain saturation and different output efficiencies. (C) 2009 Optical Society of America

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]