Rhodovarius crocodyli sp. nov., isolated from a crocodile pond

Bacterial strain CCP-6^T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain CCP-6^T is affiliated with species in the genus Rhodovarius. Strain CCP-6^T was most closely related to Rhodovarius lipocyclicus CCUG 44693^T with a 98.9% 16S rRNA gene sequence similarity. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and formed light pink-coloured colonies. Optimal growth occurred at 30 °C, pH 6 and in the absence of NaCl. The major fatty acids of strain CCP-6^T were C_{18 : 1} ω7c, C_{16 : 0} and C_{19 : 0} cyclo ω8c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, phosphatidylmethylethanolamine, diphosphatidylglycerol, three unidentified aminophospholipids and an unidentified phospholipid. The predominant polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content of the genomic DNA was 69.3 mol%. Strain CCP-6^T showed 85.8% average nucleotide identity and 14.5% digital DNA-DNA hybridization identity with Rhodovarius lipocyclicus CCUG 44693^T. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain CCP-6^T represents a novel species in the genus Rhodovarius, for which the name Rhodovarius crocodyli sp. nov. is proposed. The type strain is CCP-6^T (=BCRC 81095^T=LMG 30310^T=KCTC 62188^T).

Sphingomonas lacunae sp. nov., isolated from a freshwater pond

A novel bacterial strain, designated CSW-10^T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and formed yellow-coloured colonies. Optimal growth occurred at 30 °C, pH 7, and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain CSW-10^T formed a phylogenetic lineage in the genus Sphingomonas. The 16S rRNA gene sequence similarity indicated that strain CSW-10^T was most closely related to Sphingomonas fonticola TNR-2^T (97.6%). Strain CSW-10^T showed 69.8-70.7% average nucleotide identity and 19.0-23.0% digital DNA-DNA hybridization identity with the strains of other related Sphingomonas species. The major fatty acids of strain CSW-10^T were summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c) and C_17:1 ω6c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylcholine, one uncharacterized sphingoglycolipid, five uncharacterized aminophospholipids, one uncharacterized phospholipid and one uncharacterized lipid. The predominant polyamines were homospermidine and spermidine. The major isoprenoid quinone was Q-10. Genomic DNA G+C content of strain CSW-10^T was 62.0 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain CSW-10^T should represent a novel species of the genus Sphingomonas, for which the name Sphingomonas lacunae sp. nov. is proposed. The type strain is CSW-10^T (=BCRC 81190^T =LMG 31340^T).

Novosphingobium ovatum sp. nov., isolated from a freshwater mesocosm

A bacterial strain, designated FSY-8^T, was isolated from a freshwater mesocosm in Taiwan and characterized using the polyphasic taxonomy approach. Cells of strain FSY-8^T were aerobic, Gram-stain-negative, rod-shaped, non-motile and formed yellow coloured colonies on Reasoner's 2A agar. Growth occurred at 20-40 °C (optimum, 30-37 °C) and pH 5-7 (optimum, pH 6) and in the presence of 0-0.5 % NaCl (optimum, 0 %, w/v). The major fatty acids (>10 %) of strain FSY-8^T were summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c) and summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c). The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, diphosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized glycolipid and an uncharacterized lipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 64.8 mol %. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain FSY-8^T formed a phylogenetic lineage in the genus Novosphingobium. Strain FSY-8^T showed 71.6-77.2 % average nucleotide identity and 19.9-22.8 % digital DNA-DNA hybridization identity with the strains of other Novosphingobium species. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain FSY-8^T should be classified in a novel species of the genus Novosphingobium, for which the name Novosphingobium ovatum sp. nov. is proposed. The type strain is FSY-8^T (=BCRC 81051^T=LMG 30053^T=KCTC 52812^T).

Ideonella livida sp. nov., isolated from a freshwater lake

A novel bacterial strain, designated TBM-1^T, isolated from a freshwater lake in Taiwan, was characterized using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain TBM-1^T formed a phylogenetic lineage in the genus Ideonella. Analysis of 16S rRNA gene sequences showed that strain TBM-1^T was most closely related to Ideonella dechloratans CCUG 30898^T with 98.4 % sequence similarity. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain TBM-1^T and closely related strains of the genus Ideonella were 74.4-77.5 %, 69.7-75.4 % and 19.8-21.8 %, respectively, supporting that strain TBM-1^T represents a novel species of the genus Ideonella. Cells were Gram-stain-negative, motile by means of a single polar flagellum, rod-shaped and formed blue colonies. Optimal growth occurred at 30 °C, pH 6 and 0 % NaCl. The predominant fatty acids of strain TBM-1^T were summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c), C_18 : 1  ω7c and C_16 : 0. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two uncharacterized aminophospholipids and two uncharacterized phospholipids. The main polyamine was putrescine. The major isoprenoid quinone was Q-8. The estimated genome size was 5.26 Mb, with an average G+C content of 70.0 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain TBM-1^T should be classified in a novel species of the genus Ideonella, for which the name Ideonella livida sp. nov. is proposed. The type strain is TBM-1^T (=BCRC 81199^T =LMG 31339^T).

Identification and expression analysis of 19 CC chemokine genes in orange-spotted grouper (Epinephelus coioides)

In this study, we describe 19 different CC chemokine genes from the orange-spotted grouper, Epinephelus coioides, identified by the analysis of the spleen transcriptome. Multiple sequence alignment of the 19 CC chemokines showed that although two genes, EcSCYA115 and EcSCYA117, shared 80% amino acid similarity (72% identity), the majority exhibited low similarity to each other. Phylogenetic analysis divided the 19 CC chemokines into six major groups. Tissue distribution analysis by RT-PCR showed that most of these chemokines were ubiquitously expressed in the 9 examined tissues, whereas some exhibited tissue-preferential expression patterns. For example, EcSCYA103 was preferentially expressed in fin and gill; EcSCYA109 in head kidney and spleen; EcSCYA114 in fin, gill, and liver; and EcSCYA119 in fin and stomach. Quantitative RT-PCR showed that after challenge with grouper iridovirus (GIV), four of the 19 CC chemokine genes, EcSYCA102, EcSYCA103, EcSYCA116, and EcSYCA118, were highly induced in the spleen. The expression of these four genes could also be upregulated by LPS and poly (I:C) challenges, suggesting that these four genes might be involved in immune response against invading pathogens.

Determining the cleavage site for the mature antimicrobial peptide of Nile tilapia β-defensin using 2D electrophoresis, western blot, and mass spectrometry analysis

Several proteomic techniques were used to determine the cleavage site of the mature antimicrobial peptide of Nile tilapia β-defensin. The computer-predicted Nile tilapia β-defensin (²⁵ASFPWSCLSLSGVCRKVCLPTELFFGPLGCGKGSLCCVSHFL⁶⁶) composed of 42 amino acids was chemically synthesized and prepared to produce an antibody for Western blotting. Total proteins from the skin of the Nile tilapia were separated on two-dimensional electrophoresis, and the spot of Nile tilapia β-defensin was recognized using Western blot analysis. It was then excised and extracted from the gel. The precise molecular mass of this spot was determined by LC-MS/MS spectrometry. Four major peptides were discovered, with molecular weights of 4293.2 Da, 4306.5 Da, 4678.9 Da, and 4715.0 Da. The calculated mass of the 40-amino-acid sequence (²⁷FPWSCLSLSGVCRKVCLPTELFFGPLGCGKGSLCCVSHFL⁶⁶) of Nile tilapia β-defensin starting from Phe27 and ending with Leu66 was 4293.18 Da, which completely matched the 4293.2 Da peptide that was obtained from the mass spectrometry analysis. This result confirmed that the cleavage site for the mature C-terminal Nile tilapia β-defensin is at residue Ser26-Phe27, not at Ala24-25 as predicted by computer analysis. This study provides a simple but reliable model to determine the cleavage site for a mature antimicrobial peptide.

Comparative proteomic analysis of Litopenaeus vannamei gills after vaccination with two WSSV structural proteins

White spot syndrome virus (WSSV) is one of the most devastating viral pathogens of cultured shrimp worldwide. Recently published papers show the ability of WSSV structural protein VP28 to vaccinate shrimp and raise protection against the virus. This study attempted to identify the joining proteins of the aforementioned shrimp quasi-immune response by proteomic analysis. The other envelope protein, VP36B, was used as the non-protective subunit vaccine control. Shrimp were intramuscularly injected with rVPs or PBS on day 1 and day 4 and then on day 7 their gill tissues were sampled. The two-dimensional electrophoresis (2-DE) patterns of gill proteins between vaccinated and PBS groups were compared and 20 differentially expressed proteins identified by mass spectrometry, some of which were validated in gill and hemocyte tissues using real-time quantitative RT-PCR. Many of identified proteins and their expression levels also linked with the shrimp response during WSSV infection. The list of up-regulated protein spots found exclusively in rVP28-vaccinated shrimp include calreticulin and heat shock protein 70 with chaperone properties, ubiquitin, and others. The two serine proteases, chymotrypsin and trypsin, were significantly increased in shrimp of both vaccinated groups compared to PBS controls. The information presented here should be useful for gaining insight into invertebrate immunity.

Transformation optofluidics for large-angle light bending and tuning

Transformation optics is a new art of light bending by designing materials with spatially variable parameters for developing wave-manipulation devices. Here, we introduce a transformation optofluidic Y-branch splitter with large-angle bending and tuning based on the design of a spatially variable index. Differing from traditional splitters, the optofluidic splitter is achieved in an inhomogeneous medium by coordinate transformation. The designed bidirectional gradient index (GRIN) distribution can be achieved practically by the convection-diffusion process of liquid flowing streams. The transformation optofluidic splitter can achieve a much larger split angle with little bend loss than the traditional ones. In the experiments, a large tunable split angle up to 30° is achieved by tuning the flow rates, allowing optical signals to be freely transferred to different channels. Besides the symmetrical branch splitting, asymmetrical Y-branch splitting with approximately equal power splitting is also demonstrated by changing the composition of the liquids. The optofluidic splitter has high potential applications in biological, chemical and biomedical solution measurement and detection.

Force-induced optical nonlinearity and Kerr-like coefficient in opto-mechanical ring resonators

This paper demonstrates the optical nonlinearity in opto-mechanical ring resonators that consist of a bus waveguide and two ring resonators, which is induced by the optical gradient force and characterized by the Kerr-like coefficient. Each ring resonator has a free-hanging arc that is perpendicularly deformable by an optical gradient force and subsequently this deformation changes the effective refractive index (ERI) of the ring resonator. The change of the ERI induces optical nonlinearity into the system, which is described by an equivalent Kerr coefficient (Kerr-like coefficient). Based on the experimental results, the Kerr-like coefficient of the ring resonator system falls in the range from 7.64 × 10(-12) to 2.01 × 10(-10) m(2)W(-1), which is at least 6-order higher than the silicon's Kerr coefficient. The dramatically improved optical nonlinearity in the opto-mechanical ring resonators promises potential applications in low power optical signal processing, modulation and bio-sensing.

A nano-opto-mechanical pressure sensor via ring resonator

This paper reports a nano-opto-mechanical pressure sensor based on nano-scaled ring resonator. The pressure is measured through the output spectrum shift which is induced via mechanical deformation of the ring resonator. The sensitivity as high as 1.47 pm/kPa has been experimentally achieved which agrees with numerical prediction. Due to the strong variation of sensitivity with different ring radius and thickness of the diaphragm, the pressure sensor can be used to form an array structure to detect the pressure distribution in highly accurate measurement with low-cost advantages. The nano-opto-mechanical pressure sensor has potential applications such as shear stress displacement detection, pressure wave detector and pressure mapping etc.

Identification of the nucleocapsid, tegument, and envelope proteins of the shrimp white spot syndrome virus virion

The protein components of the white spot syndrome virus (WSSV) virion have been well established by proteomic methods, and at least 39 structural proteins are currently known. However, several details of the virus structure and assembly remain controversial, including the role of one of the major structural proteins, VP26. In this study, Triton X-100 was used in combination with various concentrations of NaCl to separate intact WSSV virions into distinct fractions such that each fraction contained envelope and tegument proteins, tegument and nucleocapsid proteins, or nucleocapsid proteins only. From the protein profiles and Western blotting results, VP26, VP36A, VP39A, and VP95 were all identified as tegument proteins distinct from the envelope proteins (VP19, VP28, VP31, VP36B, VP38A, VP51B, VP53A) and nucleocapsid proteins (VP664, VP51C, VP60B, VP15). We also found that VP15 dissociated from the nucleocapsid at high salt concentrations, even though DNA was still present. These results were confirmed by CsCl isopycnic centrifugation followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and liquid chromatography-nanoelectrospray ionization-tandem mass spectrometry, by a trypsin sensitivity assay, and by an immunogold assay. Finally, we propose an assembly process for the WSSV virion.

The unique stacked rings in the nucleocapsid of the white spot syndrome virus virion are formed by the major structural protein VP664, the largest viral structural protein ever found

One unique feature of the shrimp white spot syndrome virus (WSSV) genome is the presence of a giant open reading frame (ORF) of 18,234 nucleotides that encodes a long polypeptide of 6,077 amino acids with a hitherto unknown function. In the present study, by applying proteomic methodology to analyze the sodium dodecyl sulfate-polyacrylamide gel electrophoresis profile of purified WSSV virions by liquid chromatography-mass spectrometry (LC-MS/MS), we found that this giant polypeptide, designated VP664, is one of the viral structural proteins. The existence of the corresponding 18-kb transcript was confirmed by sequencing analysis of reverse transcription-PCR products, which also showed that vp664 was intron-less. A time course analysis showed that this transcript was actively transcribed at the late stage, suggesting that this gene product should contribute primarily to the assembly and morphogenesis of the virion. Several polyclonal antisera against this giant protein were prepared, and one of them was successfully used for immunoelectron microscopy analysis to localize the protein in the virion. Immunoelectron microscopy with a gold-labeled secondary antibody showed that the gold particles were regularly distributed around the periphery of the nucleocapsid with a periodicity that matched the characteristic stacked ring subunits that appear as striations. From this and other evidence, we argue that this giant ORF in fact encodes the major WSSV nucleocapsid protein.

Genomic and proteomic analysis of thirty-nine structural proteins of shrimp white spot syndrome virus

White spot syndrome virus (WSSV) virions were purified from the hemolymph of experimentally infected crayfish Procambarus clarkii, and their proteins were separated by 8 to 18% gradient sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to give a protein profile. The visible bands were then excised from the gel, and following trypsin digestion of the reduced and alkylated WSSV proteins in the bands, the peptide sequence of each fragment was determined by liquid chromatography-nano-electrospray ionization tandem mass spectrometry (LC-nanoESI-MS/MS) using a quadrupole/time-of-flight mass spectrometer. Comparison of the resulting peptide sequence data against the nonredundant database at the National Center for Biotechnology Information identified 33 WSSV structural genes, 20 of which are reported here for the first time. Since there were six other known WSSV structural proteins that could not be identified from the SDS-PAGE bands, there must therefore be a total of at least 39 (33 + 6) WSSV structural protein genes. Only 61.5% of the WSSV structural genes have a polyadenylation signal, and preliminary analysis by 3' rapid amplification of cDNA ends suggested that some structural protein genes produced mRNA without a poly(A) tail. Microarray analysis showed that gene expression started at 2, 6, 8, 12, 18, 24, and 36 hpi for 7, 1, 4, 12, 9, 5, and 1 of the genes, respectively. Based on similarities in their time course expression patterns, a clustering algorithm was used to group the WSSV structural genes into four clusters. Genes that putatively had common or similar roles in the viral infection cycle tended to appear in the same cluster.

Simultaneous detection of white spot syndrome virus (WSSV) and Taura syndrome virus (TSV) by multiplex reverse transcription-polymerase chain reaction (RT-PCR) in pacific white shrimp Penaeus vannamei

An assay using a single-tube, 1-step multiplex reverse transcription-polymerase chain reaction (RT-PCR) was established for the simultaneous detection of white spot syndrome virus (WSSV) and Taura syndrome virus (TSV). Three primer sets, 9195 F/9992 R, 94 F2/R2, and ITS F/28S R, were mixed at a ratio of 3:1:1 to amplify specific fragments of the TSV, WSSV, and Penaeus vannamei genome, respectively, in the RT-PCR reaction. Shrimp samples were experimentally infected with WSSV and TSV. PCR-amplified products detected in the nucleic acid extraction of shrimp pleopods produced 4 kinds of results. With no virus infection, 1 fragment of 892 base pairs (bp) was amplified from a ribosomal RNA gene by primer set ITS F/28S R as an internal control. In samples only infected by WSSV or TSV, 2 fragments could be seen: either from WSSV (530 bp) plus the internal control or TSV (231 bp) plus the internal control, respectively. In cases of co-infection with both viruses, all 3 amplified products were detected simultaneously. This study is the first report of Penaeus vannamei specimens co-infected with WSSV and TSV being detected using a PCR method via experimental infection.

Depletion of glutathione by buthionine sulfoxine is cytotoxic for human neuroblastoma cell lines via apoptosis

Buthionine sulfoximine (BSO) selectively inhibits glutathione (GSH) synthesis and has been used to sensitize tumor cells to alkylating agents, but has minimal single-agent cytotoxicity for most cell types. We determined the cytotoxicity of BSO for 18 (12 MYCN amplified; 6 MYCN nonamplified) human neuroblastoma cell lines using DIMSCAN, a digital image microscopy cytotoxicity assay. D-L(R:S) BSO was highly cytotoxic (>3 logs of cell kill) for most neuroblastoma cell lines, with 17/18 cell lines having IC90 values (range 2. 1->1000 microM) below equivalent steady state plasma levels of L(R:S) BSO reported in adult human trials. Cell lines with genomic amplification of MYCN were more sensitive to BSO than MYCN nonamplified cell lines (P = 0.04). D-L(R:S) BSO (500 microM for 72 h) induced apoptosis as detected by DNA laddering, nuclear morphology, and TUNEL staining of DNA fragments using flow cytometry. Maximal cell killing occurred within 48 h and was antagonized byic value in neuroblastoma.

Inhibition of platelet-derived growth factor and epidermal growth factor receptor signaling events after treatment of cells with specific synthetic inhibitors of tyrosine kinase phosphorylation

The receptor kinase activity associated with the epidermal growth factor (EGF) receptor and platelet-derived growth factor (PDGF) receptor plays an important role in ligand-induced signaling events. The effect of specific, synthetic chemical inhibitors of PDGF- and EGF-mediated receptor tyrosine autophosphorylation on receptor signaling were examined in NIH 3T3 cells overexpressing PDGF or EGF receptors. Specific inhibition of ligand-dependent receptor autophosphorylation, PI3K activation, mitogen-activated protein kinase (MAPK) activation, cyclin E-associated kinase activity and cell proliferation was measured after treatment of cells with these inhibitors. A synthetic PDGF receptor kinase inhibitor exhibited specific inhibitory properties when tested for PDGF-induced receptor autophosphorylation, MAPK activity, PI3K activation, entry into S phase and cyclin E-associated kinase activity. A synthetic EGF receptor kinase inhibitor showed selective inhibitor properties when tested for EGF-induced receptor autophosphorylation, MAPK activation, PI3K activation, entry into S phase and cyclin E-associated kinase activity. In both cases, these compounds were found to be effective as inducers of growth arrest and accumulation of cells in the G1 phase of the cell cycle after ligand treatment. However, at high concentrations, the EGF receptor kinase inhibitor was observed to exhibit some nonspecific effects as demonstrated by attenuation of PDGF-induced receptor autophosphorylation and cell cycle progression. This demonstrates that it is critical to use the lowest concentration of such an inhibitor that will alter the response under investigation, to have confidence that the conclusions derived from the use of such inhibitor are valid. We conclude that these experimental parameters signify useful end points to measure the relative selectivity of tyrosine kinase inhibitors that affect receptor-mediated signal transduction.