A transcriptome analysis of mitten crab testes (Eriocheir sinensis)

The identification of expressed genes involved in sexual precocity of the mitten crab (Eriocheir sinensis) is critical for a better understanding of its reproductive development. To this end, we constructed a cDNA library from the rapid developmental stage of testis of E. sinensis and sequenced 3,388 randomly picked clones. After processing, 2,990 high-quality expressed sequence tags (ESTs) were clustered into 2,415 unigenes including 307 contigs and 2,108 singlets, which were then compared to the NCBI non-redundant (nr) protein and nucleotide (nt) database for annotation with Blastx and Blastn, respectively. After further analysis, 922 unigenes were obtained with concrete annotations and 30 unigenes were found to have functions possibly related to the process of reproduction in male crabs – six transcripts relevant to spermatogenesis (especially Cyclin K and RecA homolog DMC1), two transcripts involved in nuclear protein transformation, two heat-shock protein genes, eleven transcription factor genes (a series of zinc-finger proteins), and nine cytoskeleton protein-related genes. Our results, besides providing valuable information related to crustacean reproduction, can also serve as a base for future studies of reproductive and developmental biology

A Novel OxyR Sensor and Regulator of Hydrogen Peroxide Stress with One Cysteine Residue in Deinococcus radiodurans

In bacteria, OxyR is a peroxide sensor and transcription regulator, which can sense the presence of reactive oxygen species and induce antioxidant system. When the cells are exposed to H2O2, OxyR protein is activated via the formation of a disulfide bond between the two conserved cysteine residues (C199 and C208). In Deinococcus radiodurans, a previously unreported special characteristic of DrOxyR (DR0615) is found with only one conserved cysteine. dr0615 gene mutant is hypersensitive to H2O2, but only a little to ionizing radiation. Site-directed mutagenesis and subsequent in vivo functional analyses revealed that the conserved cysteine (C210) is necessary for sensing H2O2, but its mutation did not alter the binding characteristics of OxyR on DNA. Under oxidant stress, DrOxyR is oxidized to sulfenic acid form, which can be reduced by reducing reagents. In addition, quantitative real-time PCR and global transcription profile results showed that OxyR is not only a transcriptional activator (e.g., katE, drb0125), but also a transcriptional repressor (e.g., dps, mntH). Because OxyR regulates Mn and Fe ion transporter genes, Mn/Fe ion ratio is changed in dr0615 mutant, suggesting that the genes involved in Mn/Fe ion homeostasis, and the genes involved in antioxidant mechanism are highly cooperative under extremely oxidant stress. In conclusion, these findings expand the OxyR family, which could be divided into two classes: typical 2-Cys OxyR and 1-Cys OxyR

Bioinformatics in China: A Personal Perspective

Biochemical Research MethodsMathematical & Computational BiologySCI(E)PubMed3EDITORIAL MATERIAL4e1000020

Mode-dependent characterization of photonic lanterns

We propose and experimentally demonstrate a simple method for characterizing the power transfer matrix of photonic lanterns (PLs) used for mode division multiplexing (MDM) transmission. Due to the optical reflection arising at output facet of the few-mode fiber (FMF), we are able to detect the power at the individual single-mode fiber (SMF) input port and exploit a series of equations based on the theory of energy conservation to obtain mode-dependent characteristics of the PL, including the property of mode selectivity, insertion loss (IL), and channel-dependent loss (CDL). The proposed method is experimentally verified for both the mode selective and the nonmode selective photonic lanterns

Characterization of Rayleigh backscattering arising in various two-mode fibers

\u3cp\u3eWe experimentally characterize the mode dependent characteristics of Rayleigh backscattering (RB) arising in various two-mode fibers (TMFs). With the help of an all-fiber photonic lantern, we are able to measure the RB power at individual modes. Consequently, mode dependent power distribution of RB light caused by arbitrary forward propagation mode superposition can be obtained. The total RB power of the TMFs under test is higher than that of single mode fiber by at least 2 dB over the C band. Meanwhile, the RB light occurs among all guided modes in the TMFs with specific power ratios. The experimental characterization agrees well with the theoretical calculations.\u3c/p\u3

Light-controllable fiber interferometer utilizing photoexcitation dynamics in colloidal quantum dot

The development of highly efficient light-controlled functional fiber elements has become indispensable to optical fiber communication systems. Traditional nonlinearity-based optical fiber devices suffer from the demerits of complex/expensive components, high peak power requirements, and poor efficiency. In this study, we utilize colloidal quantum dots (CQDs) to develop a light-controlled optical fiber interferometer (FI) for the all-optical control of the transmission spectrum. A specially designed exposed-core microstructure fiber (ECMF) is utilized to form the functional structure. Two types of PbS CQDs with absorption wavelengths around 1180 nm and 1580 nm, respectively, are deposited on the ECMF to enable the functional FI. The wavelength and power of control light are key factors for tailoring the FI transmission spectrum. A satisfactory recovery property and linear relationship between the spectrum shift and the power of control light at certain wavelength are achieved. The highest wavelength shift sensitivity of our light-controlled FI is 4.6 pm/mW, corresponding to an effective refractive index (RI) change of 5 × 10-6 /mW. We established a theoretical model to reveal that the RI of the CQD layer is governed by photoexcitation dynamics in CQD with the light absorption at certain wavelength. The concentration of charge carriers in the CQD layer can be relatively high under light illumination owing to their small size-related quantum confinement, which implies that low light power (mW-level in this work) can change the refractive index of the CQDs. Meanwhile, the absorption wavelength of quantum dots can be easily tuned via CQD size control to match specific operating wavelength windows. We further apply the CQD-based FI as a light-controllable fiber filter (LCFF) in a 50-km standard single-mode fiber-based communication system with 12.5-Gbps on-off keying direct modulation. Chirp management and dispersion compensation are successfully achieved by using the developed LCFF to obtain error-free transmission. CQDs possess excellent solution processability, and they can be deposited uniformly and conformally on various substrates such as fibers, silicon chips, and other complex structure surfaces, offering a powerful new degree of freedom to develop light control devices for optical communication.Feng Gao, Yang Wang, Liang Xu, Zhenhua Feng, Qiong Wu, Baohui Zhang, Jingyao Liu, Jiang Tang, Ming Tang, Huan Liu, Songnian Fu, Yinlan Ruan, Heike Ebendorff-Heidepriem and Deming Li