Estimation of advective methane flux in gas hydrate potential area offshore SW Taiwan and its tectonic implications

With the discoveries of Bottom Simulating Reflectors (BSRs), large and dense chemosynthetic communities and rapid sulfate reductions in pore space sediments, gas hydrates may exist in offshore southwestern Taiwan. Methane concentrations in pore space sediments have been measured to investigate if fluids and gases are derived from dissociation of gas hydrates. Very high methane concentrations and very shallow depths of sulfate methane interface (SMI) imply the high methane flux underneath the seafloor. Linear sulfate gradients, low total organic carbon (TOC) have been combined to describe the process of anaerobic methane oxidation (AMO) and calculate the iffusive methane flux in Chuang et al. (2010). However, the appearance of concave (or non-linear) profiles of sulfate in some cores might indicate advective fluid flows. Hence, the methane flux may be much greater under advective conditions. In this study, numerical transport-reaction models were applied to calculate the methane flux including diffusion and advection of dissolved sulfate and methane and the anaerobic methane oxidation of methane. According to the modeled results of three giant piston cores (MD05-2911, MD05-2912 and MD05-2913) collected during the r/v Marion Dufresne cruise in 2005, gas bubbling or bioirrigation may occur in these site. Values of the methane flux ranging from 1.91 to 5.17 mmol m-2yr-1 and upward fluid flow velocities around 0.05-0.13 cm yr-1 are related to different geologic structures in the active continental margin. Site MD05-2912 is located on the Tainan Ridge where anticlines and blind thrusts are the dominate structures. Site MD052911 is on the Yung-An Ridge characterized by emergent and imbricate thrusts

Determination of Nucleopolyhedrovirus’ Taxonomic Position

To date , over 78 genomes of nucleopolyhedroviruses (NPVs) have been sequenced and deposited in NCBI. How to define a new virus from the infected larvae in the field is usually the first question. Two NPV strains, which were isolated from casuarina moth (L. xylina) and golden birdwing larvae (Troides aeacus), respectively, displayed the same question. Due to the identity of polyhedrin (polh) sequences of these two isolates to that of Lymantria dispar MNPV and Bombyx mori NPV, they are named LdMNPV-like virus and TraeNPV, provisionally. To further clarify the relationships of LdMNPV-like virus and TraeNPV to closely related NPVs, Kimura 2-parameter (K-2-P) analysis was performed. Apparently, the results of K-2-P analysis that showed LdMNPV-like virus is an LdMNPV isolate, while TraeNPV had an ambiguous relationship to BmNPV. Otherwise, MaviNPV, which is a mini-AcMNPV, also exhibited a different story by K-2-P analysis. Since K-2-P analysis could not cover all species determination issues, therefore, TraeNPV needs to be sequenced for defining its taxonomic position. For this purpose, different genomic sequencing technologies and bioinformatic analysis approaches will be discussed. We anticipated that these applications will help to exam nucleotide information of unknown species and give an insight and facilitate to this issue

A Bayesian measurement error model for two-channel cell-based RNAi data with replicates

RNA interference (RNAi) is an endogenous cellular process in which small double-stranded RNAs lead to the destruction of mRNAs with complementary nucleoside sequence. With the production of RNAi libraries, large-scale RNAi screening in human cells can be conducted to identify unknown genes involved in a biological pathway. One challenge researchers face is how to deal with the multiple testing issue and the related false positive rate (FDR) and false negative rate (FNR). This paper proposes a Bayesian hierarchical measurement error model for the analysis of data from a two-channel RNAi high-throughput experiment with replicates, in which both the activity of a particular biological pathway and cell viability are monitored and the goal is to identify short hair-pin RNAs (shRNAs) that affect the pathway activity without affecting cell activity. Simulation studies demonstrate the flexibility and robustness of the Bayesian method and the benefits of having replicates in the experiment. This method is illustrated through analyzing the data from a RNAi high-throughput screening that searches for cellular factors affecting HCV replication without affecting cell viability; comparisons of the results from this HCV study and some of those reported in the literature are included.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS496 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Genomic sequencing and analyses of Lymantria xylina multiple nucleopolyhedrovirus

<p>Abstract</p> <p>Background</p> <p>Outbreaks of the casuarina moth, <it>Lymantria xylina </it>Swinehoe (Lepidoptera: Lymantriidae), which is a very important forest pest in Taiwan, have occurred every five to 10 years. This moth has expanded its range of host plants to include more than 65 species of broadleaf trees. LyxyMNPV (<it>L. xylina </it>multiple nucleopolyhedrovirus) is highly virulent to the casuarina moth and has been investigated as a possible biopesticide for controlling this moth. LdMNPV-like virus has also been isolated from <it>Lymantria xylin</it>a larvae but LyxyMNPV was more virulent than LdMNPV-like virus both in NTU-LY and IPLB-LD-652Y cell lines. To better understand LyxyMNPV, the nucleotide sequence of the LyxyMNPV DNA genome was determined and analysed.</p> <p>Results</p> <p>The genome of LyxyMNPV consists of 156,344 bases, has a G+C content of 53.4% and contains 157 putative open reading frames (ORFs). The gene content and gene order of LyxyMNPV were similar to those of LdMNPV, with 151 ORFs identified as homologous to those reported in the LdMNPV genome. Two genes (Lyxy49 and Lyxy123) were homologous to other baculoviruses, and four unique LyxyMNPV ORFs (Lyxy11, Lyxy19, Lyxy130 and Lyxy131) were identified in the LyxyMNPV genome, including a <it>gag-like </it>gene that was not reported in baculoviruses. LdMNPV contains 23 ORFs that are absent in LyxyMNPV. Readily identifiable homologues of the gene <it>host range factor-1 </it>(<it>hrf-1</it>), which appears to be involved in the susceptibility of <it>L. dispar </it>to NPV infection, were not present in LyxyMNPV. Additionally, two putative <it>odv-e27 </it>homologues were identified in LyxyMNPV. The LyxyMNPV genome encoded 14 <it>bro </it>genes compared with 16 in LdMNPV, which occupied more than 8% of the LyxyMNPV genome. Thirteen homologous regions (<it>hr</it>s) were identified containing 48 repeated sequences composed of 30-bp imperfect palindromes. However, they differed in the relative positions, number of repeats and orientation in the genome compared to LdMNPV.</p> <p>Conclusion</p> <p>The gene parity plot analysis, percent identity of the gene homologues and a phylogenetic analysis suggested that LyxyMNPV is a Group II NPV that is most closely related to LdMNPV but with a highly distinct genomic organisation.</p

A novel randomly textured phosphor structure for highly efficient white light-emitting diodes

We have successfully demonstrated the enhanced luminous flux and lumen efficiency in white light-emitting diodes by the randomly textured phosphor structure. The textured phosphor structure was fabricated by a simple imprinting technique, which does not need an expensive dry-etching machine or a complex patterned definition. The textured phosphor structure increases luminous flux by 5.4% and 2.5% at a driving current of 120 mA, compared with the flat phosphor and half-spherical lens structures, respectively. The increment was due to the scattering of textured surface and also the phosphor particles, leading to the enhancement of utilization efficiency of blue light. Furthermore, the textured phosphor structure has a larger view angle at the full width at half maximum (87°) than the reference LEDs

Preparation and Bioactivity Properties of a Novel Composite Membrane of Fructose Mediated β

A novel composite membrane of β-tricalcium pyrophosphate (β-TCP) and fructose- (F-) mediated chitosan/poly(ethylene glycol) (CS/PEG) was prepared by thermally induced phase separation technique. The prepared composite membranes were characterized using scanning electron microscopy (SEM) and X-ray diffraction (XRD). The mechanical property, swelling, degradation, and cytotoxicity of the composite membranes were evaluated in vitro with respect to its potential for use as biodegradable guided tissue regeneration (GTR) membrane. In vitro degradation tests showed the composite membrane with a controllable degradation rate when changing the β-TCP content. The incorporation of β-TCP granules also caused a significant enhancement of tensile strength. When β-TCP content is controlled to 50 wt%, homogeneous composite membranes with well mechanical property and enzymatic degradation rate can be obtained. Cytotoxicity assay demonstrates that the composite membranes were nontoxic and had very good cell compatibility. Most importantly, the release of calcium ions and glucosamine from the composite membranes was proved to increase the cell proliferation of NIH3T3. The results of this study have indicated that this novel F-β-TCP/CS/PEG composite can be a suitable material for GTR applications

Sialolipoma of the Floor of the Mouth: A Case Report

Intra-oral lipoma is a well-known entity, but lipomatous tumors including salivary gland tissue containing clustered or peripherally located ducts and acinar cells are uncommon. They are a newly recognized entity of salivary gland lipoma, designated sialolipoma. We describe a case of sialolipoma arising in the floor of the mouth presenting with apparently normal salivary gland tissue, as demonstrated by both histologic and immunohistochemical findings, in a 67-year-old female. Complete surgical removal of the tumor with preservation of the sublingual gland was implemented after a careful examination confirming that the lesion did not originate from the sublingual gland