SEanalysis 2.0: a comprehensive super-enhancer regulatory network analysis tool for human and mouse.

Super-enhancers (SEs) play an essential regulatory role in various biological processes and diseases through their specific interaction with transcription factors (TFs). Here, we present the release of SEanalysis 2.0 (http://licpathway.net/SEanalysis), an updated version of the SEanalysis web server for the comprehensive analyses of transcriptional regulatory networks formed by SEs, pathways, TFs, and genes. The current version added mouse SEs and further expanded the scale of human SEs, documenting 1 167 518 human SEs from 1739 samples and 550 226 mouse SEs from 931 samples. The SE-related samples in SEanalysis 2.0 were more than five times that in version 1.0, which significantly improved the ability of original SE-related network analyses ('pathway downstream analysis', 'upstream regulatory analysis' and 'genomic region annotation') for understanding context-specific gene regulation. Furthermore, we designed two novel analysis models, 'TF regulatory analysis' and 'Sample comparative analysis' for supporting more comprehensive analyses of SE regulatory networks driven by TFs. Further, the risk SNPs were annotated to the SE regions to provide potential SE-related disease/trait information. Hence, we believe that SEanalysis 2.0 has significantly expanded the data and analytical capabilities of SEs, which helps researchers in an in-depth understanding of the regulatory mechanisms of SEs.

VARAdb: a comprehensive variation annotation database for human.

With the study of human diseases and biological processes increasing, a large number of non-coding variants have been identified and facilitated. The rapid accumulation of genetic and epigenomic information has resulted in an urgent need to collect and process data to explore the regulation of non-coding variants. Here, we developed a comprehensive variation annotation database for human (VARAdb, http://www.licpathway.net/VARAdb/), which specifically considers non-coding variants. VARAdb provides annotation information for 577,283,813 variations and novel variants, prioritizes variations based on scores using nine annotation categories, and supports pathway downstream analysis. Importantly, VARAdb integrates a large amount of genetic and epigenomic data into five annotation sections, which include 'Variation information', 'Regulatory information', 'Related genes', 'Chromatin accessibility' and 'Chromatin interaction'. The detailed annotation information consists of motif changes, risk SNPs, LD SNPs, eQTLs, clinical variant-drug-gene pairs, sequence conservation, somatic mutations, enhancers, super enhancers, promoters, transcription factors, chromatin states, histone modifications, chromatin accessibility regions and chromatin interactions. This database is a user-friendly interface to query, browse and visualize variations and related annotation information. VARAdb is a useful resource for selecting potential functional variations and interpreting their effects on human diseases and biological processes.

High repetition rate 102 W middle infrared ZnGeP2 master oscillator power amplifier system with thermal lens compensation.

We demonstrate a 102 W middle infrared ZnGeP2 (ZGP) optical parametric amplifier (OPA) pumped by a 2097-nm Q-switched Ho:YAG laser at a pulse repetition frequency of 10 kHz. The seed middle infrared laser was produced by a ZGP optical parametric oscillator. Its average power was 28.4 W pumped by a 50 W 2097-nm laser. By thermal lens compensation, the beam factor M2 reduced from 3.1 to 2.1. When the incident Ho pump power was 120 W, the middle infrared ZGP OPA yielded the maximum average output power of 102 W and slope efficiency of 61.7%. The overall optical conversion efficiency of 60% from Ho to middle infrared was obtained for the whole middle infrared laser system. In addition, at the maximum average output power, the beam quality factors of the middle infrared ZGP OPA were measured to be about 2.7 and 2.8 for horizontal and vertical directions, respectively.

A 41-W ZnGeP2 optical parametric oscillator pumped by a Q-switched Ho:YAG laser.

We reported a high-power ZnGeP2 (ZGP) optical parametric oscillator (OPO) pumped by a Q-switched Ho:YAG laser. The maximum output power of the ZGP OPO was 41.2 W at 107.0 W incident Ho pump power, corresponding to a slope efficiency of 44.6%. The ZGP OPO produced 16-ns mid-IR pulse laser in the 3.74-3.98 µm and 4.38-4.76 µm spectral regions simultaneously. The beam quality was measured to be M²<4.37. The continuous wave maximum average output power of the Ho:YAG laser was 128 W, corresponding to a slope efficiency of 65.8%.

103 W in-band dual-end-pumped Ho:YAG laser.

An efficient 2 µm in-band pumped Ho:YAG laser was demonstrated. The resonator involves two Ho:YAG crystals, each of which was dual-end-pumped by two orthogonally polarized diode-pumped Tm:YLF lasers. The maximum continuous wave output power of 103 W was achieved, corresponding to a slope efficiency of 67.8% with respect to the incident pump power and an optical-to-optical conversion efficiency of 63.5%. Under Q-switched mode, we obtained 101 W laser output at 30 kHz, corresponding to a slope efficiency of 66.2%. The beam quality or M2 factor was found to be less than 2.

Resonantly pumped high efficiency Ho:YAG laser.

High-efficient CW and Q-switched Ho:YAG lasers resonantly dual-end-pumped by two diode-pumped Tm:YLF lasers at 1908 nm were investigated. A maximum slope efficiency of 74.8% in CW operation as well as a maximum output power of 58.7 W at 83.2 W incident pump power was achieved, which corresponded to an optical-to-optical conversion efficiency of 70.6%. The maximum pulse energy of 2.94 mJ was achieved, with a 31 ns FWHM pulse width and a peak power of approximately 94.7 kW.

High-efficiency resonantly pumped room temperature Ho:YVO4 laser.

An efficient 2 µm room temperature Ho:YVO(4) laser resonantly pumped by a 1.94 µm Tm:YAP laser is demonstrated, for the first time to our knowledge, in this Letter. Up to 8.58 W of laser output at 2053 nm is obtained with the optical-to-optical conversion efficiency as much as 41.2%. The output beam had quality of M2 factor with Mx(2) of 3.58 and My(2) of 1.76 at 8 W output level. In addition, we also obtained 4.18 W laser output at 2066 nm and 7.04 W at 2040 nm from the Ho:YVO(4) laser with conversion efficiency of 27.8% and 33.8%, respectively.

Room temperature efficient actively Q-switched Ho:YAP laser.

We report on efficient actively Q-switched Ho:YAP laser double-pass pumped by a 1.91-microm laser. At room temperature, when the incident pump power was 20.9 W, a maximum average output power of 10.9 W at 2118 nm was obtained at the repetition rate of 10 kHz, and this corresponds to a conversion efficiency of 52.2% and a slope efficiency of 63.5%. Moreover, a maximum pulse energy of approximately 1.1 mJ and a minimum pulse width of 31 ns were achieved, with the peak power of 35.5 kW.

Continuous-wave laser action around 2-microm in Ho3+:Lu2SiO5.

Continuous-wave (cw) laser action around 2 microm in Ho(3+)-doped Lu(2)SiO(5) (LSO) was demonstrated in this paper. Cryogenically cooled by liquid nitrogen, a 10-mm long Tm-sensitized (6% at.) Ho(0.4% at.):LSO produced a maximum output power of 3 W at 2.07 microm for incident diode power of 11 W at 786 nm, and a slope efficiency of 35% with respect to incident pump power. To achieve room-temperature operation of Tm, Ho:LSO laser, a 1-mm long microchip crystal was pumped by a high brightness diode, generating an output power of greater than 80 mW and a slope efficiency of 26% at 2.08 microm. Using a 1.91 microm Tm:YLF laser as an in-band pump source, room-temperature cw operation of singly-doped Ho: Lu(2)SiO(5) laser at 2106 nm was attained with a maximum output power of 2.8 W and a slope efficiency of 35% corresponding to absorbed pump power.

Diode-pumped continuous wave and Q-switched operation of a c-cut Tm,Ho:YAlO(3) laser.

We report on a diode-pumped, cryogenic and room temperature operation of a Tm,Ho:YAlO3 (c-cut) laser. In a temperature of 77 K, an optical-optical conversion efficiency of 27% and a slope efficiency of 29% were achieved with the maximum continuous-wave (CW) output power of 5.0 W at 2.13 microm. Acousto-optic switched operation was performed at pulse repetition frequency (PRF) from 1 kHz to 10 kHz, the highest pulse energy of 3.3 mJ in a pulse duration of 40 ns was obtained. In room temperature (RT), the maximum CW power of Tm,Ho:YAlO3 laser was 160 mW with a slope efficiency of 11% corresponding to the absorbed pump power.

Continuous-wave and Q-switched operation of a resonantly pumped Ho:YAlO3 laser.

We demonstrated continuous-wave (CW) and Q-switched operation of a room-temperature Ho:YAlO(3) laser that is resonantly end-pumped by a diode-pumped Tm:YLF laser at 1.91 microm. The CW Ho:YAlO(3) laser generated 5.5 W of linearly polarized (EII c ) output at 2118 nm with beam quality factor of M(2) approximately 1.1 for an incident pump power of 13.8 W, corresponding to optical-to-optical conversion efficiency of 40%. Up to 1- mJ energy per pulse at pulse repetition frequency (PRF) of 5 kHz, and the maximum average power of 5.3-W with FWHM pulse duration of 30.5 ns at 20 kHz were achieved in Q-switched mode.

Diode-pumped efficient Tm,Ho:GdVO(4) laser with near-diffraction limited beam quality.

A diode-pumped efficient 2.05-mum Tm,Ho:GdVO(4) laser with high beam quality is reported. The cavity configuration was optimized for weakening influence of thermal effect to resonator stability and mode-coupling. A conversion efficiency of 46% and a slope efficiency of 50% were obtained with continuous-wave (CW) output power of 10.5 W at 77 K. A repetitively Q-switched laser also achieved 10.1 W of output power at 10 kHz. A beam quality factor of M(2) < 1.1 was measured by the traveling knife-edge method. In addition, the energy per pulse of 1.9 mJ was obtained at 5 kHz, corresponding to the peak power of 0.14 MW.

Gain-switched Tm3+-doped double-clad silica fiber laser.

A gain-switched Tm-doped double-clad silica fiber laser operating at a wavelength of approximately 2microm with moderate output energy of 14.7mJ per pulse and a slope efficiency of 39.5% (with respect to launched pump energy) is realized pumped at 1.064microm from a Nd:YAG laser. The gain-switched fiber laser pulses are built up by a series of relaxation spikes, and every spike pulse duration is nearly 1micros. The output wavelength becomes longer, and the slope efficiency increases with the increase in fiber length.

Performance of AO Q-switched Tm,Ho:GdVO4laser pumped by a 794nm laser diode.

Acousto-optically Q-switched operation of Tm (5 at. %), Ho(0.5 at. %):GdVO4 laser was reported in this paper. The Tm,Ho:GdVO4 crystal was cooled by liquid nitrogen and end-pumped by a 13.6 W fiber-coupled laser diode at 794 nm. Average power of 3.9W was obtained at pulse repetition frequency (PRF) from 10 to 50 kHz, with corresponding to optical-to-optical conversion efficiency of 29 %, and slope efficiency of 35%. The highest energy per pulse of 1.1 mJ in 23 ns was achieved at 3 kHz with peak power of 46 kW.

Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites.

Of the two cultivated species of allopolyploid cotton, Gossypium barbadense produces extra-long fibers for the production of superior textiles. We sequenced its genome (AD)2 and performed a comparative analysis. We identified three bursts of retrotransposons from 20 million years ago (Mya) and a genome-wide uneven pseudogenization peak at 11-20 Mya, which likely contributed to genomic divergences. Among the 2,483 genes preferentially expressed in fiber, a cell elongation regulator, PRE1, is strikingly At biased and fiber specific, echoing the A-genome origin of spinnable fiber. The expansion of the PRE members implies a genetic factor that underlies fiber elongation. Mature cotton fiber consists of nearly pure cellulose. G. barbadense and G. hirsutum contain 29 and 30 cellulose synthase (CesA) genes, respectively; whereas most of these genes (>25) are expressed in fiber, genes for secondary cell wall biosynthesis exhibited a delayed and higher degree of up-regulation in G. barbadense compared with G. hirsutum, conferring an extended elongation stage and highly active secondary wall deposition during extra-long fiber development. The rapid diversification of sesquiterpene synthase genes in the gossypol pathway exemplifies the chemical diversity of lineage-specific secondary metabolites. The G. barbadense genome advances our understanding of allopolyploidy, which will help improve cotton fiber quality.

Metabolic profiles of prokaryotic and eukaryotic communities in deep-sea sponge Neamphius huxleyi [corrected]. indicated by metagenomics.

The whole metabolism of a sponge holobiont and the respective contributions of prokaryotic and eukaryotic symbionts and their associations with the sponge host remain largely unclear. Meanwhile, compared with shallow water sponges, deep-sea sponges are rarely understood. Here we report the metagenomic exploration of deep-sea sponge Neamphius huxleyi [corrected] . at the whole community level. Metagenomic data showed phylogenetically diverse prokaryotes and eukaryotes in Neamphius huxleyi [corrected]. MEGAN and gene enrichment analyses indicated different metabolic potentials of prokaryotic symbionts from eukaryotic symbionts, especially in nitrogen and carbon metabolisms, and their molecular interactions with the sponge host. These results supported the hypothesis that prokaryotic and eukaryotic symbionts have different ecological roles and relationships with sponge host. Moreover, vigorous denitrification, and CO2 fixation by chemoautotrophic prokaryotes were suggested for this deep-sea sponge. The study provided novel insights into the respective potentials of prokaryotic and eukaryotic symbionts and their associations with deep-sea sponge Neamphius huxleyi [corrected].

The first complete genome sequence of the class Fimbriimonadia in the phylum Armatimonadetes.

In this study, we present the complete genome of Fimbriimonas ginsengisoli Gsoil 348T belonging to the class Fimbriimonadia of the phylum Armatimonadetes, formerly called as candidate phylum OP10. The complete genome contains a single circular chromosome of 5.23 Mb including a 45.5 kb prophage. Of the 4820 open reading frames (ORFs), 3,000 (62.2%) genes could be classified into Clusters of Orthologous Groups (COG) families. With the split of rRNA genes, strain Gsoil 348T had no typical 16S-23S-5S ribosomal RNA operon. In this genome, the GC skew inversion which was usually observed in archaea was found. The predicted gene functions suggest that the organism lacks the ability to synthesize histidine, and the TCA cycle is incomplete. Phylogenetic analyses based on ribosomal proteins indicated that strain Gsoil 348T represents a deeply branching lineage of sufficient divergence with other phyla, but also strongly involved in superphylum Terrabacteria.

The Composition of Microbiome in Larynx and the Throat Biodiversity between Laryngeal Squamous Cell Carcinoma Patients and Control Population.

The throat is an ecological assemblage involved human cells and microbiota, and the colonizing bacteria are important factors in balancing this environment. However, this bacterial community profile has thus been poorly investigated. The purpose of this study was to investigate the microbial biology of the larynx and to analyze the throat biodiversity in laryngeal carcinoma patients compared to a control population in a case-control study. Barcoded pyrosequencing analysis of the 16S rRNA gene was used. We collected tissue samples from 29 patients with laryngeal carcinoma and 31 control patients with vocal cord polyps. The findings of high-quality sequence datasets revealed 218 genera from 13 phyla in the laryngeal mucosa. The predominant communities of phyla in the larynx were Firmicutes (54%), Fusobacteria (17%), Bacteroidetes (15%), Proteobacteria (11%), and Actinobacteria (3%). The leading genera were Streptococcus (36%), Fusobacterium (15%), Prevotella (12%), Neisseria (6%), and Gemella (4%). The throat bacterial compositions were highly different between laryngeal carcinoma subjects and control population (p = 0.006). The abundance of the 26 genera was significantly different between the laryngeal cancer and control groups by metastats analysis (p<0.05). Fifteen genera may be associated with laryngeal carcinoma by partial least squares discriminant analysis (p<0.001). In summary, this study revealed the microbiota profiles in laryngeal mucosa from tissue specimens. The compositions of bacteria community in throat were different between laryngeal cancer patients and controls, and probably were related with this carcinoma. The disruption of this bio-ecological niche might be a risk factor for laryngeal carcinoma.

[Effects of Schistosoma japonicum heat-shock protein 40 on macrophage activation].

OBJECTIVE: To clone and express heat-shock protein 40 gene of Schistosoma japonicum (SjHSP40) and analyze its effect on macrophage activation. METHODS: The fragment of gene encoding SjHSP40 was amplified by PCR. The gene was sub-cloned into the prokaryotic expression vector pGEX-6P-1. The recombinant plasmid pGEX-6P-1-SjHSP40 was transformed into E. coli BL21 (DE3) and induced with IPTG. The recombinant protein was purified with Glutathione-Sepharose 4B resin and analyzed by SDS-PAGE and Western-blot. The fusion protein of GST-SjHSP40 was loaded to the macrophage cell-line RAW264.7 for 48 h. Following that, the surface molecules of the macrophages were analyzed by flow cytometry. RESULTS: DNA sequencing showed that the recombinant plasmid, pGEX-6P-1-SjHSP40, was successfully constructed. The fusion protein of GST-SjHSP40 was induced, purified and specifically recognized by anti-GST antibody. Compared to GST and medium control groups, this fusion protein significantly induced the expression of co-stimulatory molecules (CD40, CD80, and CD86) and MHC-II on the surface of the macrophages. CONCLUSIONS: SjHSP40 significantly up-regulates the expression of co-stimulatory molecules and MHC-II on the surface of the macrophages. These data indicate that SjHSP40 may initiate macrophage activation.