Identification and Expression Profiling of MicroRNAs in the Brain, Liver and Gonads of Marine Medaka (Oryzias melastigma) and in Response to Hypoxia

The marine medaka (Oryzias melastigma) has been increasingly used as a fish model for detecting environmental stresses and chemical contaminants in the marine environment. Recent mammalian studies have shown that environmental stresses can alter the expression profiles of microRNAs (miRNAs), leading to transgenerational effects. Here, we use high-throughput Illumina RNA sequencing (RNA-Seq) for miRNA transcriptome analysis of brain, liver, and gonads from sexually mature male and female marine medaka. A total of 128,883,806 filtered sequence reads were generated from six small RNA libraries, identifying a total of 2,125,663 non-redundant sequences. These sequences were aligned and annotated to known animal miRNAs (miRBase) using the BLAST method. A total of 223 distinct miRNA types were identified, with the greatest number expressed in brain tissue. Our data suggested that 55 miRNA types from 34 families are common to all tested tissues, while some of the miRNAs are tissue-enriched or sex-enriched. Quantitative real-time PCR analysis further demonstrated that let-7a, miR-122, and miR-9-3p were downregulated in hypoxic female medaka, while miR-2184 was specifically upregulated in the testis of hypoxic male fish. This is the first study to identify miRNAs in O. melastigma using small RNA deep sequencing technology. Because miRNA expression is highly conserved between marine medaka and other vertebrates, marine medaka may serve as a good model for studies on the functional roles of miRNAs in hypoxia stress response and signaling in marine fish.published_or_final_versio

Taming Charge Transport in Semiconducting Polymers with Branched Alkyl Side Chains

The solid-state packing and polymer orientation relative to the substrate are key properties to control in order to achieve high charge carrier mobilities in organic field effect transistors (OFET). Intuitively, shorter side chains are expected to yield higher charge carrier mobilities because of a denser solid state packing motif and a higher ratio of charge transport moieties. However our findings suggest that the polymer chain orientation plays a crucial role in high-performing diketopyrrolopyrrole-based polymers. By synthesizing a series of DPP-based polymers with different branched alkyl side chain lengths, it is shown that the polymer orientation depends on the branched alkyl chain lengths and that the highest carrier mobilities are obtained only if the polymer adopts a mixed face-on/edge-on orientation, which allows the formation of 3D carrier channels in an otherwise edge-on-oriented polymer chain network. Time-of-flight measurements performed on the various polymer films support this hypothesis by showing higher out-of-plane carrier mobilities for the partially face-on-oriented polymers. Additionally, a favorable morphology is mimicked by blending a face-on polymer into an exclusively edge-on oriented polymer, resulting in higher charge carrier mobilities and opening up a new avenue for the fabrication of high performing OFET devices

Narrowband Biphotons: Generation, Manipulation, and Applications

In this chapter, we review recent advances in generating narrowband biphotons with long coherence time using spontaneous parametric interaction in monolithic cavity with cluster effect as well as in cold atoms with electromagnetically induced transparency. Engineering and manipulating the temporal waveforms of these long biphotons provide efficient means for controlling light-matter quantum interaction at the single-photon level. We also review recent experiments using temporally long biphotons and single photons.Comment: to appear as a book chapter in a compilation "Engineering the Atom-Photon Interaction" published by Springer in 2015, edited by A. Predojevic and M. W. Mitchel

Chinese journals: a guide for epidemiologists.

Chinese journals in epidemiology, preventive medicine and public health contain much that is of potential international interest. However, few non-Chinese speakers are acquainted with this literature. This article therefore provides an overview of the contemporary scene in Chinese biomedical journal publication, Chinese bibliographic databases and Chinese journals in epidemiology, preventive medicine and public health. The challenge of switching to English as the medium of publication, the development of publishing bibliometric data from Chinese databases, the prospect of an Open Access publication model in China, the issue of language bias in literature reviews and the quality of Chinese journals are discussed. Epidemiologists are encouraged to search the Chinese bibliographic databases for Chinese journal articles.Published versio

Tools to Support Policy Decisions Related to Treatment Strategies and Surveillance of Schistosomiasis Japonica towards Elimination

Immunodiagnostic assays are widely applied in the field to control schistosomiasis in P.R. China as the prevalence and infection intensity of schistosome infections decrease. Field evaluations are urgently needed before they can be adopted to support policy decisions of the national programme for the control and elimination of schistosomiasis in P.R. China. We carried out a large scale cross-sectional survey in field settings with different transmission situations to validate immunodiagnostic tools that can be used to formulate new schistosomiasis elimination strategy in P.R. China. Regarding stool examination as gold reference, the validity and screening efficacy of each immunodiagnostic kit were calculated and compared with each other. The association of the prevalence of schistosomiasis and antibody positive rates determined by immunoassays were analyzed using Pearson's correlation coefficient values. The study indicates that which test to use with the elimination strategy is dependent on the purpose of testing, the endemic status of community and the resources available. And more sensitive methods need to be explored and used to target infected individuals for treatment or to eliminate schistosomiasis

Phonon-assisted carrier transport through a lattice-mismatched interface

We showed the distinctive unconventional junction effect of MoS2 junctions: a lattice mismatched MoS2. It is unique to observe the difference originated from the atomic interrelation at the interface. The results revealed the dominant scattering source at the conventional naturally stepwise junction, while the misorientationally stacked layer exhibited effectively decoupled behavior and a significantly smaller junction resistance via phonon assist carrier. Therefore, our finding in this paper clearly shows the different mechanisms in carrier transport at both junction interface of MoS2

Network Analysis of Oyster Transcriptome Revealed a Cascade of Cellular Responses during Recovery after Heat Shock

Oysters, as a major group of marine bivalves, can tolerate a wide range of natural and anthropogenic stressors including heat stress. Recent studies have shown that oysters pretreated with heat shock can result in induced heat tolerance. A systematic study of cellular recovery from heat shock may provide insights into the mechanism of acquired thermal tolerance. In this study, we performed the first network analysis of oyster transcriptome by reanalyzing microarray data from a previous study. Network analysis revealed a cascade of cellular responses during oyster recovery after heat shock and identified responsive gene modules and key genes. Our study demonstrates the power of network analysis in a non-model organism with poor gene annotations, which can lead to new discoveries that go beyond the focus on individual genes

The Role of Histone H4 Biotinylation in the Structure of Nucleosomes

Background: Post-translational modifications of histones play important roles in regulating nucleosome structure and gene transcription. It has been shown that biotinylation of histone H4 at lysine-12 in histone H4 (K12Bio-H4) is associated with repression of a number of genes. We hypothesized that biotinylation modifies the physical structure of nucleosomes, and that biotin-induced conformational changes contribute to gene silencing associated with histone biotinylation. Methodology/Principal Findings: To test this hypothesis we used atomic force microscopy to directly analyze structures of nucleosomes formed with biotin-modified and non-modified H4. The analysis of the AFM images revealed a 13% increase in the length of DNA wrapped around the histone core in nucleosomes with biotinylated H4. This statistically significant (p,0.001) difference between native and biotinylated nucleosomes corresponds to adding approximately 20 bp to the classical 147 bp length of nucleosomal DNA. Conclusions/Significance: The increase in nucleosomal DNA length is predicted to stabilize the association of DNA with histones and therefore to prevent nucleosomes from unwrapping. This provides a mechanistic explanation for the gene silencing associated with K12Bio-H4. The proposed single-molecule AFM approach will be instrumental for studying the effects of various epigenetic modifications of nucleosomes, in addition to biotinylation

Use of Ionic Liquid in Fabrication, Characterization, and Processing of Anodic Porous Alumina

Two different ionic liquids have been tested in the electrochemical fabrication of anodic porous alumina in an aqueous solution of oxalic acid. It was found that during galvanostatic anodization of the aluminum at a current density of 200 mA/cm2, addition of 0.5% relative volume concentration of 1-butyl-3-methylimidazolium tetrafluoborate resulted in a three-fold increase of the growth rate, as compared to the bare acidic solution with the same acid concentration. This ionic liquid was also used successfully for an assessment of the wettability of the outer surface of the alumina, by means of liquid contact angle measurements. The results have been discussed and interpreted with the aid of atomic force microscopy. The observed wetting property allowed to use the ionic liquid for protection of the pores during a test removal of the oxide barrier layer