Description: Background: Degradation is essential for RNA maturation, turnover, and quality control. RNA degradome sequencing that integrates a modified 5[prime]-rapid amplification of cDNA ends protocol with next-generation sequencing technologies is a high-throughput approach for profiling the 5[prime]-end of uncapped RNA fragments on a genome-wide scale. The primary application of degradome sequencing has been to identify the truncated transcripts that result from endonucleolytic cleavage guided by microRNAs or small interfering RNAs. As many pathways are involved in RNA degradation, degradome data should contain other RNA species besides the cleavage remnants of small RNA targets. Nevertheless, no systematic approaches have been established to explore the hidden complexity of plant degradome. Results: Through analyzing Arabidopsis and rice RNA degradome data, we recovered 11 short motifs adjacent to predominant and abundant uncapped 5[prime]-ends. Uncapped ends associated with several of these short motifs were more prevalent than those targeted by most miRNA families especially in the 3[prime] untranslated region of transcripts. Through genome-wide analysis, five motifs showed preferential accumulation of uncapped 5[prime]-ends at the same position in Arabidopsis and rice. Moreover, the association of uncapped 5[prime]-ends with a CA-repeat motif and a motif recognized by Pumilio/Fem-3 mRNA binding factor (PUF) proteins was also found in non-plant species, suggesting that common mechanisms are present across species. Based on these motifs, potential sources of RNA ends that constitute degradome data were proposed and further examined. The 5[prime]-end of small nucleolar RNAs could be precisely captured by degradome sequencing. Position-specific enrichment of uncapped 5[prime]-ends was seen upstream of motifs recognized by several RNA binding proteins especially for the binding site of PUF proteins. False uncapped 5[prime]-ends produced from capped transcripts through non-specific PCR amplification were common artifacts among degradome datasets. Conclusions: The complexity of plant RNA degradome data revealed in this study may contribute to the alternative applications of degradome in RNA research.

Description: Chinese tradition and culture developed from Taoism, Confucianism, and Buddhism and have influenced ethnic Chinese for thousands of years, particularly thoughts on death. Many ethnic Chinese, particularly olde...

Description: Background: Diabetes mellitus (DM) has been associated with the cancer risk. This study investigated relationship between DM and esophageal cancer using Taiwan's insurance data. Methods: We identified 549 patients with esophageal cancer newly diagnosed in 2000-2009 and randomly selected 2196 controls without any cancer, frequency matched by sex, age and diagnosis year of cases. Logistic regression model estimated odds ratios (ORs) and 95% confidence intervals (CI) of esophageal cancer associated with DM, sex, age. co-morbidities and medications. Results: Cases were more prevalent than controls for alcoholism and esophageal disorders and using nonsteroidal anti-inflammatory drugs (NSAIDs) and cyclooxygenase-2 inhibitors but not DM. Esophageal cancer had no association with DM (OR 0.99, 95% CI 0.71-1.37), but significantly associated with alcoholism (OR 14.1, 95% CI 7.87-25.4), esophageal ulcer (OR 10.1, 95% CI 5.70-17.9), esophageal reflux (OR 3.47, 95% CI 2.14-5.26) and uses of NSAIDs (OR 2.73, 95% CI 1.80-4.13). An elevated risk of esophageal cancer appeared in DM patients taking insulin (OR 2.57, 95% CI 1.08-6.15) or sulfonyurea (OR 3.80, 95% CI 1.16-12.5). Conclusions: Patients with DM are not at higher risk for esophagus cancer. However, esophageal disorders and anti-diabetic drugs are associated with the risk of the disease.

Description: Background: The aims of this study were to evaluate the antioxidant activity and to identify the antioxidant components of a traditional Chinese medicine formula consisting of a combination of Shanzha (the fruit of Crataegus pinnatifida Bge. var. major N.E.Br., SZ) and Danshen (the root of Salvia miltiorrhiza Bge., DS). This medicine is extensively used to treat cardiovascular disease. Methods: Twelve samples extracted and fractionated from SZ, DS and the formula (SZ+DS) were analyzed. The concentrations of eight phenolic compounds were determined by high performance liquid chromatography. Oxygen radical absorbance capacity (ORAC) assay and 1,1-diphenyl-2-picrylhydrazyl assay were conducted to explore the antioxidant activities of the samples and of the 15 phenolic compounds detected. Correlation analysis of the antioxidant activity of herb samples and their phenolic components was performed. Results: The main phenolic component in all SZ+DS samples was salvianolic acid B, which exhibited strong antioxidant activity (ORAC value: 16.73 +/- 2.53, IC50 value: 8.80 +/- 0.06 muM) compared with the other phenolic compounds. For all samples, there was a positive relationship between their total phenolic components and their antioxidant activities. Conclusions: Phenolic compounds were the bioactive components of the herb samples, and salvianolic acid B was identified as the main bioactive compound in the SZ+DS formula.

Description: Although topological defects, such as domain walls (DWs) or vortices, are naturally protected by topological invariance, yet, we discover an exception that the six-state topology of the vortex with Z2 × Z3 symmetry is broken by a partial edge dislocation (PED) in hexagonal Y 0.67 Lu 0.33 MnO 3 , where the topologies of the four-state vortex or closed DWs emerges. Using aberration-corrected scanning transmission electron microscopy, we found that the PED plays an important role in changing the phase of translation domain. The PED at the vortex core leads to the formation of the four-state vortex, while the ones at closed DWs connect different types of DWs, both corresponding to continuous phase changes. These results indicate that PEDs can change the topology of translation-related domain vortices and more vortices with even domains can be expected.

Description: Silver nanorod (Ag NR) arrays with average diameter about 18 nm and period about 50 nm were electrodeposited in anodic aluminum oxide (AAO) templates. The filling factor of Ag NRs in the AAO nanopores could be adjusted by the deposition temperature. The filling factor increased to ∼98% when the deposition temperature decreased to 1 °C. As the filling factor increased, the plasmon absorption intensity of Ag NR arrays was greatly enhanced, and the longitudinal surface plasmon resonance increased faster. Meanwhile, the AgNR:AAO exhibit strong photoluminescence at ∼570 nm, obviously different with that of the bare AAO at ∼495 nm. Our observation revealed the strong near-field plasmon coupling among the Ag NR arrays.

Description: The cellular signal transduction is commonly believed to rely on the direct “contact” or “binding” of the participating molecule reaction that depends positively on the corresponding molecule concentrations. In living systems, however, it is somewhat difficult to precisely match the corresponding rapid “binding,” depending on the probability of molecular collision, existing in the cellular receptor-ligand interactions. Thus, a question arises that if there is another mechanism (i.e., bindingless ) that could promote this signal communication. According to this hypothesis, we report a cellular model based on the examination of intracellular calcium concentration to explore whether the unidentified signal delivery in cells exists, via a microfluidic device. This device was designed to isolate the cells from directly contacting with the corresponding ligands/molecules by the particular polydimethylsiloxane (PDMS) membranes with different thicknesses. Results show a significant increment of calcium mobilization in human prostate cancer PC-3 cells by the stimulation of endothelin-1, even up to a separated distance of 95  μ m. In addition, these stimulated signals exhibited a bump-shaped characteristics depending on the membrane thickness. When the PDMS membrane is capped by SiO 2 , a particular trait that resembles the ballistic signal conduction was observed. A theoretical model was developed to describe the signal transport process across the PDMS membrane. Taken together, these results indicate that the unidentified signal (ligand structural information) delivery could occur in cells and be examined by the proposed approach, exhibiting a bindingless communication manner. Moreover, this approach and our finding may offer new opportunities to establish a robust and cost-effective platform for the study of cellular biology and new drug development.

Description: Background: Chronic kidney disease (CKD) is more prevalent in Taiwan than in most countries. This population-based cohort study evaluated the dementia risk associated with CKD. Methods: Using claims data of 1,000,000 insured residents covered in the universal health insurance of Taiwan, we selected 37049 adults with CKD newly diagnosed from 2000--2006 as the CKD cohort. We also randomly selected 74098 persons free from CKD and other kidney diseases, frequency matched with age, sex and the date of CKD diagnosed. Incidence and hazard ratios (HRs) of dementia were evaluated by the end of 2009. Results: Subjects in the CKD cohort were more prevalent with comorbidities than those in the non-CKD cohort (p

Description: Background: Phosphatase of regenerating liver (PRL) family is classified as class IVa of protein tyrosine phosphatase (PTP4A) that removes phosphate groups from phosphorylated tyrosine residues on proteins. PRL phosphatases have been implicated in a number of tumorigenesis and metastasis processes and are highly conserved. However, the understanding of PRL expression profiles during embryonic development is very limited. Results: In this study, we demonstrated and characterized the comprehensive expression pattern of Drosophila PRL, amphioxus PRL, and zebrafish PRLs during embryonic development by either whole mount immunostaining or in situ hybridization. Our results indicate that Drosophila PRL is mainly enriched in developing mid-guts and central nervous system (CNS) in embryogenesis. In amphioxus, initially PRL gene is expressed ubiquitously during early embryogenesis, but its expression become restricted to the anterior neural tube in the cerebral vesicle. In zebrafish, PRL-1 and PRL-2 share similar expression patterns, most of which are neuronal lineages. In contrast, the expression of zebrafish PRL-3 is more specific and preferential in muscle. Conclusions: This study, for the first time, elucidated the embryonic expression pattern of Drosophila, amphioxus, and zebrafish PRL genes. The shared PRL expression pattern in the developing CNS among diverse animals suggests that PRL may play conserved roles in these animals for CNS development.