Heat shock protein 40 of Streptococcus pneumoniae induces immune response of human dendritic cells via TLR4-dependent p38 MAPK and JNK signaling pathways.

INTRODUCTION: Heat shock protein 40 (HSP40) is a vaccine adjuvant candidate for Streptococcus pneumoniae. The mechanism by which HSP40 activates the human dendritic cells (DCs) is unclear. METHODS: DCs were isolated from human peripheral blood and their markers (HLA-DR, CD86, CD83, and CD80) were detected by flow cytometry. The messenger RNA (mRNA) and secretion levels of inflammary cytokines were measured after DCs were stimulated with recombinant HSP40 (rHSP40). Short hairpin RNAs were used to knock down toll-like receptor 2 (TLR2) and TLR4. The TLR2- or TLR4-deficient DCs were treated with lipopolysaccharides, rHSP40, or peptidoglycan, and then the secretion levels of tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) were measured. Moreover, the secretion levels of TNF-α and IL-6 were measured after DCs were treated with mitogen-activated protein kinase (MAPK) inhibitors including SB203580, SP600125, and U0126. In addition, the phosphorylation levels of p38 MAPK and Jun N-terminal kinase (JNK) in DC cells were determined using western blot analysis after treatment with rHSP40 for different times. RESULTS: DCs were successfully isolated and cultured. rHSP40 treatment significantly increased cytokine levels in a concentration-dependent manner. TLR4 deficiency, but not TLR2 deficiency, significantly suppressed the rHSP40-induced secretion of tumor necrosis factor-α  (TNF-α) and interleukin-6 (IL-6). SB203580 and SP600125 significantly inhibited the rHSP40-induced secretion of TNF-α and IL-6. rHSP40 significantly enhanced the phosphorylation of p38 MAPK and JNK. CONCLUSION: HPS40 stimulates the immune response of DCs via the p38 MAPK and JNK signaling pathways, which depend on TLR4.

Impact of LncRNA GAS5 Genetic Variants and the Epidermal Growth Factor Receptor Phenotypes on the Clinicopathological Characteristics of Lung Adenocarcinoma Patients.

The aim of the current study was to evaluate the combined effect of the single nucleotide polymorphism (SNP) in long non-coding RNA growth arrest-specific 5 (GAS5) and the phenotypes of epidermal growth factor receptor (EGFR) on the clinicopathological characteristics of lung adenocarcinoma. The present study examined the relationship between the GAS5 single-nucleotide polymorphisms (SNPs; rs145204276 Ins/Del, rs55829688 T/C) and the clinicopathological factors in 539 lung adenocarcinoma patients with or without EGFR mutations. We found that the genotype distributions of the two GAS5 SNPs between different EGFR genotypes were similar after adjusting for age, gender and smoking history. The GAS5 SNP rs145204276 Ins/Del + Del/Del illustrated a higher distribution with an advanced tumor stage (p = 0.030), larger tumor T status (p = 0.019), positive lymph node status (p = 0.014) and distal metastases (p = 0.011) in the EGFR wild type group. In the subgroup analysis of the EGFR wild type population, the presence of GAS5 SNP rs145204276 Ins/Del + Del/Del was correlated to an advanced tumor stage (p = 0.014) and distal metastases (p = 0.020) in non-smokers. In conclusion, these data indicate that the GAS5 SNP rs145204276 variant may help predict tumor stage, lymph node metastasis and distal metastases in patients with EGFR wild type lung adenocarcinoma.

Impact of carbonic anhydrase 9 gene polymorphism on the progression of colorectal cancer.

Colorectal cancer (CRC) is a commonly occurring tumor type worldwide, and its development is governed by a connection between genetic variations and acquired factors. Carbonic anhydrase 9 (CA9) is a cell-surface pH modulator that has been demonstrated to contribute to key steps of cancer progression. Here, we attempted to interrogate the effect of CA9 gene polymorphisms on the development of CRC in 470 cases and 470 gender- and age-matched non-cancer controls. We found that none of three CA9 single-nucleotide polymorphisms (SNPs) tested, including rs2071676, rs3829078, and rs1048638, was significantly associated with the occurrence of CRC. Yet, while evaluating the clinicopathological variables, cases carrying at least one reference allele (G allele) of rs2071676 tended to develop poorly differentiated tumors less frequently than those who are homozygous for the alternative allele (A allele) of rs2071676 (GA+GG vs AA; OR, 0.483; 95% CI, 0.242-0.963; p=0.036). Further stratification revealed that as compared to homozygous carriers of the alternative allele (AA), cases of colon cancer bearing at least one reference allele of rs2071676 (GA+GG) less frequently developed poorly differentiated tumors (OR, 0.449; 95% CI, 0.221-0.911; p=0.024) and lymphovascular invasion (OR, 0.570; 95% CI, 0.361-0.900; p=0.015). Such genetic effect was exclusively observed in colon cancer but not in rectal cancer. Our results indicate an anatomical site-specific impact of CA9 gene polymorphisms on modulating the progression of colorectal malignancies.

Gender differences in femoral trochlea morphology.

PURPOSE: This study aimed to analyze the morphology of the anterior femoral condyle using a quantitative three-dimensional reconstruction method. The morphological data were compared between genders. METHODS: Computed tomography scans of femurs were taken from 90 healthy subjects and then reconstructed in 3D modeling software. Coaxial cutting planes were created at 10° increments to measure the lateral and medial anterior condylar heights (LACH and MACH, respectively), lateral and medial trochlear groove widths (LTW and MTW, respectively), and for trochlear groove tracking. The absolute values and normalized data were compared between male and female subjects. The sulcus angle and deepest point of the trochlear groove at each cross-section were also analyzed to determine the differences in the depth of the trochlear groove. RESULTS: The absolute dimensions of LACH, MACH, LTW, and MTW were significantly smaller in the female subjects, by 10.5%, 36.9%, 10.3%, and 11.0%, respectively, than in the males (p < 0.05). After normalization, no significant difference was found in the condylar height between the genders. However, the female subjects had a significantly larger value of approximately 7.9% for the normalized trochlear width. CONCLUSION: Male subjects had greater condylar heights and widths than the female subjects. Although the trajectory of the trochlear groove varied greatly among the subjects, the trochlear groove appeared to be wider and shallower in the female subjects than in the male subjects. These results provide important information for the design of femoral trochlea to fit Asian female patients. LEVEL OF EVIDENCE: III.

Impact of Matrix Metalloproteinase-11 Gene Polymorphisms on Biochemical Recurrence and Clinicopathological Characteristics of Prostate Cancer.

Prostate cancer is among the most common malignant tumors worldwide. Matrix metalloproteinase (MMP)-11 is involved in extracellular matrix degradation and remodeling and plays an essential role in cancer development and metastasis. This study investigated the association of MMP-11 polymorphisms with the clinicopathological characteristics and biochemical recurrence of prostate cancer. Five single-nucleotide polymorphisms (SNPs) of the MMP-11 were analyzed in 578 patients with prostate cancer through real-time polymerase chain reaction analysis. A prostate-specific antigen level of >10 ng/mL, Gleason grade groups 4 + 5, advanced tumor stage, lymph node metastasis, invasion, and high-risk D'Amico classification were significantly associated with biochemical recurrence in the patients (p < 0.001). MMP-11 rs131451 "TC + CC" polymorphic variants were associated with advanced clinical stage (T stage; p = 0.007) and high-risk D'Amico classification (p = 0.015) in patients with biochemical recurrence. These findings demonstrate that MMP-11 polymorphisms were not associated with prostate cancer susceptibility; however, the rs131451 polymorphic variant was associated with late-stage tumors and high-risk D'Amico classification in prostate cancer patients with biochemical recurrence. Thus, the MMP-11 SNP rs131451 may contribute to the tumor development in prostate cancer patients with biochemical recurrence.

Study of GaN-Based Thermal Decomposition in Hydrogen Atmospheres for Substrate-Reclamation Processing.

This study investigates the thermal decomposition behavior of GaN-based epilayers on patterned sapphire substrates (GaN-epi/PSSs) in a quartz furnace tube under a hydrogen atmosphere. The GaN-epi/PSS was decomposed under different hydrogen flow rates at 1200 °C, confirming that the hydrogen flow rate influences the decomposition reaction of the GaN-based epilayer. The GaN was completely removed and the thermal decomposition process yielded gallium oxyhydroxide (GaO2H) nanostructures. When observed by transmission electron microscopy (TEM), the GaO2H nanostructures appeared as aggregates of many nanograins sized 2⁻5 nm. The orientation relationship, microstructure, and formation mechanism of the GaO2H nanostructures were also investigated.

Photovoltaic Performance Characterization of Textured Silicon Solar Cells Using Luminescent Down-Shifting Eu-Doped Phosphor Particles of Various Dimensions.

This paper reports on efforts to enhance the photovoltaic performance of textured silicon solar cells through the application of a layer of Eu-doped silicate phosphor with particles of various dimensions using the spin-on film technique. We examined the surface profile and dimensions of the Eu-doped phosphors in the silicate layer using optical microscopy with J-image software. Optical reflectance, photoluminescence, and external quantum efficiency were used to characterize the luminescent downshifting (LDS) and light scattering of the Eu-doped silicate phosphor layer. Current density-voltage curves under AM 1.5G simulation were used to confirm the contribution of LDS and light scattering produced by phosphor particles of various dimensions. Experiment results reveal that smaller phosphor particles have a more pronounced effect on LDS and a slight shading of incident light. The application of small Eu-doped phosphor particles increased the conversion efficiency by 9.2% (from 12.56% to 13.86%), far exceeding the 5.6% improvement (from 12.54% to 13.32%) achieved by applying a 250 nm layer of SiO2 and the 4.5% improvement (from 12.37% to 12.98%) observed in cells with large Eu-doped phosphor particles.

Electrical and Optical Characterization of Sputtered Silicon Dioxide, Indium Tin Oxide, and Silicon Dioxide/Indium Tin Oxide Antireflection Coating on Single-Junction GaAs Solar Cells.

This study characterized the electrical and optical properties of single-junction GaAs solar cells coated with antireflective layers of silicon dioxide (SiO2), indium tin oxide (ITO), and a hybrid layer of SiO2/ITO applied using Radio frequency (RF) sputtering. The conductivity and transparency of the ITO film were characterized prior to application on GaAs cells. Reverse saturation-current and ideality factor were used to evaluate the passivation performance of the various coatings on GaAs solar cells. Optical reflectance and external quantum efficiency response were used to evaluate the antireflective performance of the coatings. Photovoltaic current-voltage measurements were used to confirm the efficiency enhancement obtained by the presence of the anti-reflective coatings. The conversion efficiency of the GaAs cells with an ITO antireflective coating (23.52%) exceeded that of cells with a SiO2 antireflective coating (21.92%). Due to lower series resistance and higher short-circuit current-density, the carrier collection of the GaAs cell with ITO coating exceeded that of the cell with a SiO2/ITO coating.

Plasmonic Light Scattering in Textured Silicon Solar Cells with Indium Nanoparticles from Normal to Non-Normal Light Incidence.

In this study, we sought to improve the light trapping of textured silicon solar cells using the plasmonic light scattering of indium nanoparticles (In NPs) of various dimensions. The light trapping modes of textured-silicon surfaces with and without In NPs were investigated at an angle of incidence (AOI) ranging from 0° to 75°. The optical reflectance, external quantum efficiency (EQE), and photovoltaic performance were first characterized under an AOI of 0°. We then compared the EQE and photovoltaic current density-voltage (J-V) as a function of AOI in textured silicon solar cells with and without In NPs. We observed a reduction in optical reflectance and an increase in EQE when the cells textured with pyramidal structures were coated with In NPs. We also observed an impressive increase in the average weighted external quantum efficiency (∆EQEw) and short-circuit current-density (∆Jsc) in cells with In NPs when illuminated under a higher AOI. The ∆EQEw values of cells with In NPs were 0.37% higher than those without In NPs under an AOI of 0°, and 3.48% higher under an AOI of 75°. The ∆Jsc values of cells with In NPs were 0.50% higher than those without In NPs under an AOI of 0°, and 4.57% higher under an AOI of 75°. The application of In NPs clearly improved the light trapping effects. This can be attributed to the effects of plasmonic light-scattering over the entire wavelength range as well as an expanded angle of incident light.

R3D-BLAST2: an improved search tool for similar RNA 3D substructures.

BACKGROUND: RNA molecules have been known to play a variety of significant roles in cells. In principle, the functions of RNAs are largely determined by their three-dimensional (3D) structures. As more and more RNA 3D structures are available in the Protein Data Bank (PDB), a bioinformatics tool, which is able to rapidly and accurately search the PDB database for similar RNA 3D structures or substructures, is helpful to understand the structural and functional relationships of RNAs. RESULTS: Since its first release in 2011, R3D-BLAST has become a useful tool for searching the PDB database for similar RNA 3D structures and substructures. It was implemented by a structural-alphabet (SA)-based method, which utilizes an SA with 23 structural letters to encode RNA 3D structures into one-dimensional (1D) structural sequences and applies BLAST to the resulting structural sequences for searching similar substructures of RNAs. In this study, we have upgraded R3D-BLAST to develop a new web server named R3D-BLAST2 based on a higher quality SA newly constructed from a representative and sufficiently non-redundant list of RNA 3D structures. In addition, we have modified the kernel program in R3D-BLAST2 so that it can accept an RNA structure in the mmCIF format as an input. The results of our experiments on a benchmark dataset have demonstrated that R3D-BLAST2 indeed performs very well in comparison to its earlier version R3D-BLAST and other similar tools RNA FRABASE, FASTR3D and RAG-3D by searching a larger number of RNA 3D substructures resembling those of the input RNA. CONCLUSIONS: R3D-BLAST2 is a valuable BLAST-like search tool that can more accurately scan the PDB database for similar RNA 3D substructures. It is publicly available at http://genome.cs.nthu.edu.tw/R3D-BLAST2/ .

iPARTS2: an improved tool for pairwise alignment of RNA tertiary structures, version 2.

Since its first release in 2010, iPARTS has become a valuable tool for globally or locally aligning two RNA 3D structures. It was implemented by a structural alphabet (SA)-based approach, which uses an SA of 23 letters to reduce RNA 3D structures into 1D sequences of SA letters and applies traditional sequence alignment to these SA-encoded sequences for determining their global or local similarity. In this version, we have re-implemented iPARTS into a new web server iPARTS2 by constructing a totally new SA, which consists of 92 elements with each carrying both information of base and backbone geometry for a representative nucleotide. This SA is significantly different from the one used in iPARTS, because the latter consists of only 23 elements with each carrying only the backbone geometry information of a representative nucleotide. Our experimental results have shown that iPARTS2 outperforms its previous version iPARTS and also achieves better accuracy than other popular tools, such as SARA, SETTER and RASS, in RNA alignment quality and function prediction. iPARTS2 takes as input two RNA 3D structures in the PDB format and outputs their global or local alignments with graphical display. iPARTS2 is now available online at http://genome.cs.nthu.edu.tw/iPARTS2/.

Optical and Electrical Performance of MOS-Structure Silicon Solar Cells with Antireflective Transparent ITO and Plasmonic Indium Nanoparticles under Applied Bias Voltage.

This paper reports impressive improvements in the optical and electrical performance of metal-oxide-semiconductor (MOS)-structure silicon solar cells through the incorporation of plasmonic indium nanoparticles (In-NPs) and an indium-tin-oxide (ITO) electrode with periodic holes (perforations) under applied bias voltage. Samples were prepared using a plain ITO electrode or perforated ITO electrode with and without In-NPs. The samples were characterized according to optical reflectance, dark current voltage, induced capacitance voltage, external quantum efficiency, and photovoltaic current voltage. Our results indicate that induced capacitance voltage and photovoltaic current voltage both depend on bias voltage, regardless of the type of ITO electrode. Under a bias voltage of 4.0 V, MOS cells with perforated ITO and plain ITO, respectively, presented conversion efficiencies of 17.53% and 15.80%. Under a bias voltage of 4.0 V, the inclusion of In-NPs increased the efficiency of cells with perforated ITO and plain ITO to 17.80% and 16.87%, respectively.

Inactivation kinetics of beta-N-acetyl-D-glucosaminidase from green crab (Scylla serrata) in dioxane solution.

Beta-N-acetyl-D-glucosaminidase (NAGase, EC.3.2.1.52), which catalyzes the cleavage of N-acetylglucosamine polymers, is a composition of chitinase and cooperates with endo-chitinase and exo-chitinase to disintegrate chitin into N-acetylglucosamine (NAG). In this investigation, A NAGase from green crab (Scylla serrata) was purified and the effects of dioxane on the enzyme activity for the hydrolysis of p-Nitrophenyl-N-acetyl-beta-D-glucosaminide (pNP-NAG) were studied. The results show that appropriate concentrations of dioxane can lead to reversible inactivation of the enzyme and the inactivation is classified as mixed type. The value of IC50, the dioxane (inactivator) concentration leading to 50% activity lost, is estimated to be 0.68%. The kinetics of inactivation of NAGase in the appropriate concentrations of dioxane solution has been studied using the kinetic method of the substrate reaction. The rate constants of inactivation have been determined. The results showed that k+0 is much larger than k'+0, indicating the free enzyme molecule is more fragile than the enzyme-substrate complex in the dioxane solution. It is suggested that the presence of the substrate offers marked protection of this enzyme against inactivation by dioxane.

Rule extraction for glaucoma detection with summary data from StratusOCT.

PURPOSE: To extract and induce rules of association for differentiating between normal and glaucomatous eyes based on the quantitative assessment of summary data reports from the StratusOCT (optical coherence tomography; Carl Zeiss Meditec, Inc., Dublin, CA) in a Taiwan Chinese population. METHODS: One randomly selected eye of each of the 64 patients with glaucoma and each of the 71 normal subjects was included in the study. Measurements of glaucoma variables (retinal nerve fiber layer thickness and optic nerve head analysis results) were obtained with the StratusOCT. A self-organizing map and decision tree were applied to extract features and determine rules of association for glaucoma detection. RESULTS: The average visual field mean deviation was -0.55 +/- 0.57 dB in the normal group and -4.30 +/- 3.32 dB in the glaucoma group. Vertical cup-to-disc (C/D) ratio and inferior quadrant thickness were extracted from the decision tree, and three association rules were determined for glaucoma detection. CONCLUSIONS: The precise rules of association induced by a novel application of the decision tree may enhance glaucoma detection.

Effects of mercuric ion on the conformation and activity of Penaeus Vannamei beta-N-acetyl-d-glucosaminidase.

beta-N-acetyl-d-glucosaminidase (NAGase, EC.3.2.1.52), a composition of the chitinases, catalyzes the cleavage of N-acetylglucosamine polymers into N-acetylglucosamine. In this paper, the effects of mercuric ion on the activity of NAGase from Penaeus vannamei for the hydrolysis of pNP-NAG have been studied. The results show that HgCl2 can lead to irreversible inactivation to this enzyme. The inactivation process follows a first-order reaction and the inactivation rate constants have been determined. The relationship between the inactivation rate constants and HgCl2 concentration has been studied and the result shows that only one molecule of HgCl2 binds to the enzyme molecule to lead the enzyme lose its activity. Moreover, the conformational changes of the enzyme inactivated by HgCl2 were studied by following changes in the intrinsic fluorescence emission and ultraviolet absorption spectra.

The chemical modification of the essential groups of beta-N-acetyl-D-glucosaminidase from Turbo cornutus Solander.

The chemical modification of beta-N-acetyl-D-glucosaminidase (EC3.2.1.30) from Turbo cornutus Solander has been first studied. The results demonstrate that the sulfhydryl group of cysteine residues and the hydroxyl group of serine residues are not essential to the enzyme's function. The modification of indole group of tryptophan of the enzyme by N-bromosuccinimide (NBS) can lead to the complete inactivation, accompanying the absorption decreasing at 278 nm and the fluorescence intensity quenching at 335 nm, indicating that tryptophan is essential residue to the enzyme. The modification of amino group of lysine residue by formaldehyde and trinitrobenzenesulfonic acid also inactivates the enzyme completely. The results show that lysine and tryptophan are probably situated in the active site of the enzyme. The modification of the imidazole residue and carboxyl group leads to inactivate incompletely, indicating they are not the composing groups of the enzyme active center, and they are essential for maintaining the enzyme's conformation which is necessary for the catalytic activity of the enzyme.

Putative hAPN receptor binding sites in SARS_CoV spike protein.

AIM: To obtain the information of ligand-receptor binding between the S protein of SARS-CoV and CD13, identify the possible interacting domains or motifs related to binding sites, and provide clues for studying the functions of SARS proteins and designing anti-SARS drugs and vaccines. METHODS: On the basis of comparative genomics, the homology search, phylogenetic analyses, and multi-sequence alignment were used to predict CD13 related interacting domains and binding sites in the S protein of SARS-CoV. Molecular modeling and docking simulation methods were employed to address the interaction feature between CD13 and S protein of SARS-CoV in validating the bioinformatics predictions. RESULTS: Possible binding sites in the SARS-CoV S protein to CD13 have been mapped out by using bioinformatics analysis tools. The binding for one protein-protein interaction pair (D757-R761 motif of the SARS-CoV S protein to P585-A653 domain of CD13) has been simulated by molecular modeling and docking simulation methods. CONCLUSION: CD13 may be a possible receptor of the SARS-CoV S protein, which may be associated with the SARS infection. This study also provides a possible strategy for mapping the possible binding receptors of the proteins in a genome.

Prediction of prokaryotic promoters based on prediction of transcriptional units.

Identification of promoters is very important in understanding gene regulating relationships in an organism, and computational identification of promoters has been a long standing problem in computational biology. A new method was presented to predict promoter regions in prokaryotic organism. The method predicted transcription unit (TU) first and the TU was divided into singlet that contains only one single gene in a TU, and operon that contains more than one gene. Based on these predicted TUs, promoter was predicted for each TU using hidden Markov model including explicit state duration density. Both predicted TUs and promoters were satisfying.