Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes

CpG islands (CGIs) are often considered as gene markers, but the number of CGIs varies among mammalian genomes that have similar numbers of genes. In this study, we investigated the distribution of CGIs in the promoter regions of 3,197 human-mouse ortholo

Stepwise loss of motilin and its specific receptor genes in rodents

Specific interactions among biomolecules drive virtually all cellular functions and underlie phenotypic complexity and diversity. Biomolecules are not isolated particles, but are elements of integrated interaction networks, and play their roles through specific interactions. Simultaneous emergence or loss of multiple interacting partners is unlikely. If one of the interacting partners is lost, then what are the evolutionary consequences for the retained partner? Taking advantages of the availability of the large number of mammalian genome sequences and knowledge of phylogenetic relationships of the species, we examined the evolutionary fate of the motilin (MLN) hormone gene, after the pseudogenization of its specific receptor, MLN receptor (MLNR), on the rodent lineage. We speculate that the MLNR gene became a pseudogene before the divergence of the squirrel and other rodents about 75 mya. The evolutionary consequences for the MLN gene were diverse. While an intact open reading frame for the MLN gene, which appears functional, was preserved in the kangaroo rat, the MLN gene became inactivated independently on the lineages leading to the guinea pig and the common ancestor of the mouse and rat. Gain and loss of specific interactions among biomolecules through the birth and death of genes for biomolecules point to a general evolutionary dynamic: gene birth and death are widespread phenomena in genome evolution, at the genetic level; thus, once mutations arise, a stepwise process of elaboration and optimization ensues, which gradually integrates and orders mutations into a coherent pattern.

The hearing gene Prestin unites echolocating bats and whales

This work was supported by a grant from Key Disciplines of Zoology in Sowthwest Forestry University (XKX200903).

A reappraisal of complete mtDNA variation in East Asian families with hearing impairment

In a number of recent studies, we summarized the obvious errors and shortcomings that can be spotted in many (if not most) mitochondrial DNA (mtDNA) data sets published in medical genetics. We have reanalyzed here the complete mtDNA genome data published

Depletion of Vipp1 in Synechocystis sp PCC 6803 affects photosynthetic activity before the loss of thylakoid membranes

A vipp1 mutant of Synechocystis sp. PCC 6803 could not be completely segregated under either mixotrophic or heterotrophic conditions. A vipp1 gene with a copper-regulated promoter (P-petE-vipp1) was integrated into a neutral platform in the genome of the merodiploid mutant. The copper-induced expression of P-petE-vipp1 allowed a complete segregation of the vipp1 mutant and observation of the phenotype of Synechocystis 6803 with different levels of vesicle-inducing protein in plastids 1 (Vipp1). When P-petE-vipp1 was turned off by copper deprivation, Synechocystis lost Vipp1 and photosynthetic activity almost simultaneously, and at a later stage, thylakoid membranes and cell viability. The photosystem II (PSII)-mediated electron transfer was much more rapidly reduced than the PSI-mediated electron transfer. By testing a series of concentrations, we found that P-petE-vipp1 cells grown in medium with 0.025 mu M Cu2+ showed no reduction of thylakoid membranes, but greatly reduced photosynthetic activity and viability. These results suggested that in contrast to a previous report, the loss of photosynthetic activity may not have been due to the loss of thylakoid membranes, but may have been caused more directly by the loss of Vipp1 in Synechocystis 6803.

Identification of one intron loss and phylogenetic evolution of Dfak gene in the Drosophila melanogaster species group

Intron loss and its evolutionary significance have been noted in Drosophila. The current study provides another example of intron loss within a single-copy Dfak gene in Drosophila. By using polymerase chain reaction (PCR), we amplified about 1.3 kb fragment spanning intron 5-10, located in the position of Tyr kinase (TyK) domain of Dfak gene from Drosophila melanogaster species group, and observed size difference among the amplified DNA fragments from different species. Further sequencing analysis revealed that D. melanogaster and D. simulans deleted an about 60 bp of DNA fragment relative to other 7 Drosophila species, such as D. elegans, D. ficusphila, D. biarmipes, D. takahashii, D. jambulina, D. prostipennis and D. pseudoobscura, and the deleted fragment located precisely in the position of one intron. The data suggested that intron loss might have occurred in the Dfak gene evolutionary process of D. melanogaster and D. simulans of Drosophila melanogaster species group. In addition, the constructed phylogenetic tree based on the Dfak TyK domains clearly revealed the evolutionary relationships between subgroups of Drosophila melanogaster species group, and the intron loss identified from D. melanogaster and D. simulans provides a unique diagnostic tool for taxonomic classification of the melanogaster subgroup from other group of genus Drosophila.

Effect of wind speed on loss of water from Nostoc flagelliforme colonies

The effects of wind speed on loss of water from N. flagelliforme colonies were investigated indoors in an attempt to assess its ecological significance in field. Wind enhanced the process of waterless; the half-time of desiccation at wind speeds of 2.0 and 3.4 m s(-1) was, respectively, shortened to one-third and one-fifth at 20 degrees C and, to one-sixth and one-eighth at 27 degrees C that of still air. Photosynthetic efficiency was not affected before the wet alga lost about 50% water.

Fabrication of a Low-Loss SSC Using High-Dose Electron Beam Lithography Exposure With Negative PMMA Resist

A silicon-on-insulator optical fiber-to-waveguide spot-size converter (SSC) using Poly-MethylMethAcrylate (PMMA) is presented for integrated optical circuits. Unlike the conventional use of PMMA as a positive resist, it has been successfully used as a negative resist with high-dose electron exposure for the fabrication of ultrafine silicon wire waveguides. Additionally, this process is able to reduce the side-wall roughness, and substantially depresses the unwanted propagation loss. Exploiting this technology, the authors demonstrated that the SSC can improve coupling efficiency by as much as over 2.5 dB per coupling facet, compared with that of SSC fabricated with PMMA as a positive resist with the same dimension.

Investigation of mode radiation loss for microdisk resonators with pedestals by FDTD technique

Mode radiation loss for microdisk resonators with pedestals is investigated by three-dimensional (3D) finite-difference time-domain (FDTD) technique. For the microdisk with a radius of 1 mu m, a thickness of 0.2 mu m, and a refractive index of 3.4, on a pedestal with a refractive index of 3.17, the mode quality (Q) factor of the whispering-gallery mode (WGM) quasi-TE7,1 first increases with the increase of the radius of the pedestal, and then quickly decreases as the radius is larger than 0.75 mu m. The mode radiation loss is mainly the vertical radiation loss induced by the mode coupling between the WGM and vertical radiation mode in the pedestal, instead of the scattering loss around the perimeter of the round pedestal. The WG M can keep the high Q factor when the mode coupling is forbidden.

Mode Analysis and Design of a Low-Loss Photonic Crystal 60 degrees Waveguide Bend

The guided modes of a two-dimensional photonic crystal straight waveguide and a waveguide bend are studied in order to find the high transmission mechanism for the waveguide bend. We find that high transmission occurs when the mode patterns and wave numbers match, while the single-mode condition in the waveguide bend is not necessarily required. According to the mechanism, a simply modified bend structure with broad high transmission band is proposed. The bandwidth is significantly increased from 19 to 116 nm with transmission above 90%, and covers the entire C band of optical communication.

Coherence loss and recovery of an electron spin coupled inhomogeneously to a one-dimensional interacting spin bath: An adaptive time-dependent density-matrix renormalization group study

Coherence evolution and echo effect of an electron spin, which is coupled inhomogeneously to an interacting one-dimensional finite spin bath via hyperfine-type interaction, are studied using the adaptive time-dependent density-matrix renormalization group method. It is found that the interplay of the coupling inhomogeneity and the transverse intrabath interactions results in two qualitatively different coherence evolutions, namely, a coherence-preserving evolution characterized by periodic oscillation and a complete decoherence evolution. Correspondingly, the echo effects induced by an electron-spin flip at time tau exhibit stable recoherence pulse sequence for the periodic evolution and a single peak at root 2 tau for the decoherence evolution, respectively. With the diagonal intrabath interaction included, the specific feature of the periodic regime is kept, while the root 2 tau-type echo effect in the decoherence regime is significantly affected. To render the experimental verifications possible, the Hahn echo envelope as a function of tau is calculated, which eliminates the inhomogeneous broadening effect and serves for the identification of the different status of the dynamic coherence evolution, periodic versus decoherence.

Mode coupling and vertical radiation loss for whispering-gallery modes in 3-D microcavities

The characteristics of whispering-gallery modes (WGMs) in 3-D cylindrical, square, and triangular microcavities with vertical optical confinement of semiconductors are numerically investigated by the finite-difference time-domain (FDTD) technique. For a microcylinder with a vertical refractive index 3.17/3.4/3.17 and a center layer thickness 0.2 mu m, Q-factors of transverse electric (TE) WGMs around wavelength 1550 nm are smaller than 10(3), as the radius R < 4 mu m and reach the orders of 10(4) and 10(6) as R = 5 and 6 mu m, respectively. However, the Q-factor of transverse magnetic (TM) WGMs at wavelength 1.659 mu m reaches 7.5 x 10(5) as R = 1 mu m. The mode coupling between the WGMs and vertical radiation modes in the cladding layer results in vertical radiation loss for the WGMs. In the microcylinder, the mode wavelength of TM WGM is larger than the cutoff wavelength of the vertical radiation mode with the same mode numbers, so TM WGMs cannot couple with the vertical radiation mode and have high Q-factor. In contrast, TE WGMs can couple with the corresponding vertical radiation mode in the 3-D microcylinder as R < 5 mu m. However, the mode wavelength of the TE WGM approaches (is larger than) the cutoff wavelength of the corresponding radiation modes at R = 5 mu m (6 mu m), so TE WGMs have high Q-factors in such microcylinders too. The results show that a critical lateral size is required for obtaining high, Q-factor TE WGMs in the 3-D microcylinder. For 3-D square and triangular microcavities, we also find that the Q-factor of TM WGM is larger than that of TE WGM.

Confinement factor and absorption loss of AlInGaN based laser diodes emitting from ultraviolet to green

Confinement factor and absorption loss of AlInGaN based multiquantum well laser diodes (LDs) were investigated by numerical simulation based on a two-dimensional waveguide model. The simulation results indicate that an increased ridge height of the waveguide structure can enhance the lateral optical confinement and reduce the threshold current. For 405 nm violet LDs, the effects of p-AlGaN cladding layer composition and thickness on confinement factor and absorption loss were analyzed. The experimental results are in good agreement with the simulation analysis. Compared to violet LD, the confinement factors of 450 nm blue LD and 530 nm green LD were much lower. Using InGaN as waveguide layers that has higher refractive index than GaN will effectively enhance the optical confinement for blue and green LDs. The LDs based on nonpolar substrate allow for thick well layers and will increase the confinement factor several times. Furthermore, the confinement factor is less sensitive to alloys composition of waveguide and cladding layers, being an advantage especially important for ultraviolet and green LDs.

Optical waveguide propagation loss measurement using multiple reflections method

Optical waveguide propagation loss measurement method based on optical multiple reflections detection is presented in this paper. By using a precision reflectometer, uncertain influence on waveguide propagation loss measurement caused by fiber-waveguide coupling can be eliminated effectively and the waveguide net propagation loss can be measured accurately. To demonstrate this, the propagation loss of a Silicon-on-Insulator (SOI) rib waveguide fabricated by RIE is measured with the obtained value being 4.3 dB/cm. This method provides a non-destructive means for evaluating waveguide propagation loss. (c) 2005 Elsevier B.V. All rights reserved.

Rearrangeable nonblocking SOI waveguide thermooptic 4x4 switch matrix with low insertion loss and fast response

A rearrangeable nonblocking 4 x 4 thermooptic silicon-on-insulator waveguide switch matrix at 1.55-mu m integrated spot size converters is designed and fabricated for the first time. The insertion losses and polarization-dependent losses of the four channels are less than 10 and 0.8 dB, respectively. The extinction ratios are larger than 20 dB. The response times are 4.6 mu s for rising edge and 1.9 mu s for failing edge.