Distinct Evolutionary Patterns Between Two Duplicated Color Vision Genes Within Cyprinid Fishes

We investigated the molecular evolution of duplicated color vision genes (LWS-1 and SWS2) within cyprinid fish, focusing on the most cavefish-rich genus-Sinocyclocheilus. Maximum likelihood-based codon substitution approaches were used to analyze the evolution of vision genes. We found that the duplicated color vision genes had unequal evolutionary rates, which may lead to a related function divergence. Divergence of LWS-1 was strongly influenced by positive selection causing an accelerated rate of substitution in the proportion of pocket-forming residues. The SWS2 pigment experienced divergent selection between lineages, and no positively selected site was found. A duplicate copy of LWS-1 of some cyprinine species had become a pseudogene, but all SWS2 sequences remained intact in the regions examined in the cyprinid fishes examined in this study. The pseudogenization events did not occur randomly in the two copies of LWS-1 within Sinocyclocheilus species. Some cave species of Sinocyclocheilus with numerous morphological specializations that seem to be highly adapted for caves, retain both intact copies of color vision genes in their genome. We found some novel amino acid substitutions at key sites, which might represent interesting target sites for future mutagenesis experiments. Our data add to the increasing evidence that duplicate genes experience lower selective constraints and in some cases positive selection following gene duplication. Some of these observations are unexpected and may provide insights into the effect of caves on the evolution of color vision genes in fishes.

Plasmonic graded-index planar lens based on subwavelength features in the effective index regime

We experimentally demonstrate the planar focusing of Surface Plasmon Polaritons using space variant PMMA subwavelength features on top of a metallic film. Focusing is obtained by creating an effective graded refractive index profile. © 2012 OSA.

Plasmonic graded-index planar lens based on subwavelength features in the effective index regime

We experimentally demonstrate the planar focusing of Surface Plasmon Polaritons using space variant PMMA subwavelength features on top of a metallic film. Focusing is obtained by creating an effective graded refractive index profile. © OSA 2012.

Annual variations of biotic integrity in the upper Yangtze River using an adapted index of biotic integrity (IBI)

Adaptive modification and use of Karr's index of biotic integrity (IBI) for the upper Yangtze River, including 12 metrics in five categories, have typically occurred in line with the data collected by 6-year commercial fisheries investigation. These investigations were undertaken annually in four sections of the Upper Yangtze main channel between 1997 and 2002. These four monitoring sections (Yibin - YB, Hejiang - HJ, Mudong - MD, and Yichang - YC) were selected because they represent the part of the river that will be covering a 1000 kin stretch that includes the future Three Gorges Reservoir (TGR), upstream of the Three Gorges Dam (TGD), an area influenced by the construction of TGD. in addition, historical data were used to show changes in the watershed by comparison with field investigations recently. The biotic integrity of the four sections were calculated and classified into different levels annually for recognizing its spatial and temporal variations. It was observed that IBI scores were becoming lower diminishingly since 1997 in all the four sections. Because all the data were collected before the impoundment of the Three Gorges Reservoir, it is obvious that human activities, especially over-fishing, must be crucial factor instead of damming in the upper Yangtze River in that period. (C) 2008 Published by Elsevier Ltd.

Calibration of alkenone unsaturation index with growth temperature for a lacustrine species, Chrysotila lamellosa (Haptophyceae)

Although long chain alkenones (LCKs) occur widely in lacustrine sediments, their origin is not clear. Here, we report a lacustrine source, the non-calcifying species Chrysotila lamellosa Anand (Haptophyceae), collected and isolated from an inland saline water body, Lake Xiarinur (Inner Mongolia, China). Its alketione pattern is similar to those of coastal marine strains of C lamellosa,but the relationship between U-37(K') index and culture temperature for the lacustrine species is quite different from that of the coastal species. A significant feature of the alkenones in this strain of C lamellosa is a lack of C-38 methyl alkenones, which might be used to distinguish the species from the marine haptophyte species Emiliania huxleyi and Gephyrocapsa oceanica. The higher C-38 tetraunsaturated compound abundance might be another important feature for distinguishing the C lamellosa alkenone producer from the coastal species Isochrysis galbana. This alkenone distribution pattern has been detected in many lakes, which suggests that C lamellosa or a closely related species might be a very common alkenone precursor in lacustrine systems. We examined U-37(K') and U-37(K) values for C lamellosa as a function of culture temperature in a batch culture experiment. The calibration for U-37(K') vs. culture temperature (T) was U-37(K') = 0.0011 x T-2 - 0.0157 x T + 0.1057(n = 14, r(2) = 0.99) from 10 degrees C to 22 degrees C or U-37(K') = 0.0257 x T - 0.2608(n = 9, r(2) = 0.97) from 14 degrees C to 22 degrees C. U-37(K) vs. culture temperature was U-37(K) = 0 0377 x T - 0.5992(n = 14, r(2) = 0.98) from 10 degrees C to 22 degrees C. Our experiments show that the alkenone unsaturation index (U-37(K')) is strongly controlled by culture temperature and can be used for palaeoclimate reconstruction. (C) 2007 Elsevier Ltd. All rights reserved.

Novel passive launch scheme for ultimate bandwidth improvement of graded-index multimode fibers

We propose a new practical multimode fiber optical launch scheme, providing near single mode group excitation for >5 times transmission bandwidth improvement. Equalization-free transmission of a 10-Gb/s signal over 220-m fiber is achieved in experimental demonstrations. © 2010 Optical Society of America.

Use of the aquatic protozoa to formulate a community biotic index for an urban water system

Protozoan were collected from 16 stations in water system of Changde City (China) using the PFU method. Sampling programs were conduced on a yearly basis, with seasonal frequency at diverse sites in the water system and 488 species of protozoa was identified. At the same time, Water sampling from these stations was conducted and various water chemical parameters, including DO, COD, BOD5, NH3, TP, and Volatile Phenol, were analyzed. The aim of the research was, on one hand, using chemical method to take an investigation to the water pollution status of Changde City; on the other hand, using protozoan to make an evaluation to the water quality. With the chemical water parameters and protozoa data, a biotic index was derived for the investigated region. The species pollution value (SPV) of 469 protozoa species was established, and the community pollution value (CPV) calculated from SPV was used to evaluate water quality. The method of the biotic index was tested and the result showed that CPV calculated from SPV had a close correlation with the degree of water pollution (p < 0.00001). This indicated that the method of the biotic index is reliable. The water quality degrees divided by CPV were suggested. (c) 2004 Elsevier B.V. All rights reserved.

Identification of a novel C1q family member in color crucian carp (Carassius auratus) ovary

Potential roles of Clq/tumor necrosis factor (TNF) superfamily proteins have been observed in vertebrate oogenesis and oocyte maturation, but no ovary-specific member has been identified so far. In this study, we have cloned and identified a novel member of Clq family with a Clq domain in the C-terminal from fully grown oocyte cDNA library of color crucian carp and demonstrated that the gene might be specifically expressed in ovary and therefore designated as Carassius auratus ovary-specific Clq-like factor, CaOClq-like factor. It encodes a 213 amino acid protein with a 17 amino acid signal peptide. There is only one protein band of about 24.5 kDa in the extracts from phase I to phase IV oocytes, but two positive protein bands are detected in the extracts of mature eggs and fertilized eggs. Furthermore, the mobility shift of the smaller target protein band cannot be eliminated by phosphatase treatment, but the larger protein band increases its mobility on the gel after phosphatase treatment, suggesting that the larger protein might be a phosphorylated form. Immunofluorescence localization indicates that the CaOClq-like proteins localize in cytoplasm, cytoplasm membrane and egg envelope of the oocytes at cortical granule stage and vitellogenesis stage, whereas they were compressed to cytoplasm margin in ovulated mature eggs and discharged into perivitelline space between cytoplasm membrane and egg envelope after egg fertilization. Further studies on distribution and translocation mechanism of the CaOClq-like factor will be benefit to elucidate the unique function in oogenesis, oocyte maturation and egg fertilization. (C) 2004 Elsevier Inc. All rights reserved.

Development of a biotic index using the correlation of protozoan communities with chemical water quality

A method of comparing data on protozoan communities with chemical parameters is presented. Using data from an extensive survey of the River Hanjiang in China, each species of protozoa has been given a species pollution value (SPV) related to its occurrence in waters with different degrees of pollution. A comprehensive chemical index is calculated for each site based on water quality standards for eight chemical parameters. The index is calculated from the relationship between the observed levels of each chemical at a site, compared with the limits of the drinking water quality standards of the People's Republic of China. From the distribution of each species at sites with differing chemical index values, a SPV is calculated. The SPV for each species is obtained by summing the logarithmic value of 10 times the chemical pollution divided by the number of chemical parameters, then divided by the stations where the species occurs. The community pollution value (CPV), which is the average SPVs of all protozoa at a site, is used to evaluate water quality. The CPV has been shown to have a close correlation with the degree of water pollution. It is not necessary for all the protozoa in a sample to have SPVs listed in this paper, provided at least 56% of the protozoa in a sample have an SPV value, the CPV will be applicable.

Application and validation of a new biotic index using data from several water systems

Protozoans of Lake Donghu were collected from five stations using the PFU method. The sampling was conducted for one year and two times a month. The aim of this research was to test the applicability of a new protozoa biotic index, species pollution value (SPV) and community pollution value (CPV), established by the authors using data from the River Hanjiang. Each station's CPV was calculated from the SPV and the correlation analysis between the CPV and the comprehensive chemical index of stations I, II, III showed a significant correlation between them. The pollution status of the five stations was correctly evaluated by the CPV. These results suggested that the biotic index could be applied in water systems other than the River Hanjiang. The SPV of some protozoa species in Lake Donghu, not observed in the River Hanjiang were established. In order to further test the applicability of the biotic index, protozoan and chemistry data from the Rivers Torrente Stirone and Parma of Italy were used. The results showed that the CPV for the two rivers had a close relationship with the chemical water quality, which indicated that the biotic index could be applied in other parts of the world for the monitoring and estimating of water quality. Since the results of testing and verifying the biotic index in some other water systems in China were also satisfactory, this indicated that the biotic index has an extensive suitability for freshwater ecosystems. As long as more than 50% of the species in a sample have a SPV, the CPV calculated from the SPV is reliable for monitoring and evaluating water quality.

Cyclin A2 is differentially expressed during oocyte maturation between gynogenetic silver crucian carp and gonochoristic color crucian carp

Silver crucian carp (Carassius auratus gibelio) is a unique gynogenetic fish. Because of its specific genetic background and reproduction mode, it is an intriguing model system for understanding regulatory mechanism of oocyte maturation division. It keeps its chromosomal integrity by inhibiting the first meiotic division (no extrusion of the first pole body). The spindle behavior during oocyte maturation is significantly different from that in gonochoristic fish. The chromosomes are first arranged in a tripolar spindle, and then they turn around and are reunited mutually to form a normal bipolar spindle. A new member of the fish A-type cyclin gene, cyclin A2, has been isolated by suppression of subtractive hybridization on the basis of its differential transcription in fully-grown oocytes between the gynogenetic silver crucian carp and gonochoristic color crucian carp. There are 18 differing amino acids in the total 428 residues of cyclin A2 between the two forms of crucian carps. In addition, cDNAs of cyclin A1 and cyclin B have also been cloned from them. Thus two members of A-type cyclins, cyclin A1 and cyclin A2, are demonstrated to exist in fish, just as in frog, humans, and mouse. Northern blotting reveals that cyclin A2 mRNA is more than 20-fold and cyclin A1 mRNA is about 2-fold in fully grown oocytes of gynogenetic silver crucian carp compared to gonochoristic color crucian carp. However, cyclin B does not show such a difference between them. Western blot analysis also shows that the cyclin A2 protein stockpiled in fully grown oocytes of gynogenetic crucian carp is much more abundant than in gonochoristic crucian carp. Moreover, two different cyclin A2 expression patterns during oocyte maturation have been revealed in the two closely related crucian carps. For color crucian carp, cyclin A2 protein is translated only after hormone stimulation. For silver crucian carp, cyclin A2 protein can be detected throughout the process of maturation division. The different expression of cyclin A2 may be a clue to understanding the special maturation division of gynogenetic silver crucian carp.

Voltage tunable two-color InAs/GaAs quantum dot infrared photodetector

We report a bias voltage tunable two-color InAs/GaAs quantum dot infrared photodetector working under the normal incidence infared irradiation. The two-color detection of our device is realized by combining a photovoltaic and a photoconductive response by bias voltage tuning. The photovoltaic response is attributed to the transition of electron from the ground state to a high continuum state. The photoconductive response arises from the transition of electron from the ground state to the wetting layer state through the barrier via Fowler-Nordheim tunneling evidenced by a broad feature of the photocurrent peak on the high energy side. (C) 2008 American Institute of Physics.

Direct observation of coherent spin transfer processes in an InGaAs/GaAs quantum well via two-color time-resolved Kerr rotation measurements

A two-color time-resolved Kerr rotation spectroscopy system was built, with a femtosecond Ti:sapphire laser and a photonic crystal fiber, to study coherent spin transfer processes in an InGaAs/GaAs quantum well sample. The femtosecond Ti:sapphire laser plays two roles: besides providing a pump beam with a tunable wavelength, it also excites the photonic crystal fiber to generate supercontinuum light ranging from 500 nm to 1600 nm, from which a probe beam with a desirable wavelength is selected with a suitable interference filter. With such a system, we studied spin transfer processes between two semiconductors of different gaps in an InGaAs/GaAs quantum well sample. We found that electron spins generated in the GaAs barrier were transferred coherently into the InGaAs quantum well. A model based on rate equations and Bloch-Torrey equations is used to describe the coherent spin transfer processes quantitatively. With this model, we obtain an effective electron spin accumulation time of 21 ps in the InGaAs quantum well.

Design and optimization of photonic crystal coupling layer for bi-color quantum well infrared photodetectors

Finite difference time domain (FDTD) method is used for the simulation and analysis of electromagnetic field in the top coupling layer of GaAs/AlGaAs quantum well infrared photodetector (QWIP). Simulation results demonstrated the coupling efficiencies and distributions of electromagnetic (EM) field in a variety of 2D photonic crystal coupling layer structures. A photonic crystal structure for bi-color-QWIP is demonstrated with high coupling efficiency for two wavelengths.

Polarization dependence of absorption in strongly vertically coupled InAs/GaAs quantum dots for two-color far-infrared photodetector

Strongly vertically coupled InAs/GaAs quantum dots (QDs) with modulation doping are investigated, and polarization dependence of two-color absorptions was observed. Analysis of photoluminescence (PL) and absorption spectra shows that s-polarized absorptions at. 10.0 and 13.4 mu m, stem from the first excited state E-1 and the second excited state E-2 in the QDs to the bound state E-InGaAs in the InGaAs spacer, respectively, whereas p-polarized absorptions at 10.0 and 8.2 mu m stem from the first excited state E-1 and the ground E-g in the QDs to the bound state E-InGaAs in the InGaAs spacer, respectively. These measurements illustrate that transitions from excited states are more sensitive to normal incidence, which are very important in designing QD infrared detector. (C) 2007 Elsevier B.V. All rights reserved.