deepBase: a database for deeply annotating and mining deep sequencing data

Advances in high-throughput next-generation sequencing technology have reshaped the transcriptomic research landscape. However, exploration of these massive data remains a daunting challenge. In this study, we describe a novel database, deepBase, which we have developed to facilitate the comprehensive annotation and discovery of small RNAs from transcriptomic data. The current release of deepBase contains deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana. By analyzing ∼14.6 million unique reads that perfectly mapped to more than 284 million genomic loci, we annotated and identified ∼380 000 unique ncRNA-associated small RNAs (nasRNAs), ∼1.5 million unique promoter-associated small RNAs (pasRNAs), ∼4.0 million unique exon-associated small RNAs (easRNAs) and ∼6 million unique repeat-associated small RNAs (rasRNAs). Furthermore, 2038 miRNA and 1889 snoRNA candidates were predicted by miRDeep and snoSeeker. All of the mapped reads can be grouped into about 1.2 million RNA clusters. For the purpose of comparative analysis, deepBase provides an integrative, interactive and versatile display. A convenient search option, related publications and other useful information are also provided for further investigation. deepBase is available at: http://deepbase.sysu.edu.cn/

Functional analysis of distraction arthroplasty in the treatment of ankle osteoarthritis

BACKGROUND: Ankle joint distraction arthroplasty (AJDA) is an alternative surgical procedure for the management of moderate to severe ankle osteoarthritis. However, the benefit of this procedure and failure relative factors are still in debate. The purpose of the current study was to evaluate the functional outcomes of AJDA in treatment of moderate to severe ankle OA and to evaluate the relative factors correlated with treatment failure. METHODS: Forty-six van Dijk stages II and III ankle osteoarthritis patients were included. Fifteen males and 31 females with a mean age of 54.8 (range, 42–71) years were followed with a mean of 42.8 (range, 24–68) months. The Ankle Osteoarthritis Scale (AOS) and American Orthopaedic Foot and Ankle Society (AOFAS) ankle-hindfoot score were used for functional outcome evaluation. The talar tilt (TT) angle and ankle joint space distance (AJSD) were evaluated. The risk ratio (RR) was calculated for each potential failure relative factor. RESULTS: The AOS and AOFAS scores were significantly improved at the last follow-up time (P < 0.01). The AJSD was improved in 61% of patients and with a significant improvement compared with the preoperative conditions (P < 0.01). The TT angle and range of motion reached no significant difference. The failure rate was 21.7%. Patients with large TT (≥5°) angle (RR = 3.81, 95% CI 1.28–11.33, P = 0.02) and obesity (RR = 3.58, 95% CI 1.30–9.89, P = 0.01) were found to have positive correlation with failure. No correlation was found between failure and gender, or overweight, or side, or age, or type and stage of OA, or pin infection. CONCLUSIONS: The current study confirmed the early functional outcomes of ankle distraction arthroplasty. However, this procedure still has a relatively high failure rate, especially for those obese patients and patients with large TT angles. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13018-017-0519-x) contains supplementary material, which is available to authorized users

Two-dimensional Transport Induced Linear Magneto-Resistance in Topological Insulator Bi2_2Se3_3 Nanoribbons

We report the study of a novel linear magneto-resistance (MR) under perpendicular magnetic fields in Bi2Se3 nanoribbons. Through angular dependence magneto-transport experiments, we show that this linear MR is purely due to two-dimensional (2D) transport, in agreement with the recently discovered linear MR from 2D topological surface state in bulk Bi2Te3, and the linear MR of other gapless semiconductors and graphene. We further show that the linear MR of Bi2Se3 nanoribbons persists to room temperature, underscoring the potential of exploiting topological insulator nanomaterials for room temperature magneto-electronic applications.Comment: ACS Nano, in pres

Diversification of importin-α isoforms in cellular trafficking and disease states.

The human genome encodes seven isoforms of importin α which are grouped into three subfamilies known as α1, α2 and α3. All isoforms share a fundamentally conserved architecture that consists of an N-terminal, autoinhibitory, importin-β-binding (IBB) domain and a C-terminal Arm (Armadillo)-core that associates with nuclear localization signal (NLS) cargoes. Despite striking similarity in amino acid sequence and 3D structure, importin-α isoforms display remarkable substrate specificity in vivo. In the present review, we look at key differences among importin-α isoforms and provide a comprehensive inventory of known viral and cellular cargoes that have been shown to associate preferentially with specific isoforms. We illustrate how the diversification of the adaptor importin α into seven isoforms expands the dynamic range and regulatory control of nucleocytoplasmic transport, offering unexpected opportunities for pharmacological intervention. The emerging view of importin α is that of a key signalling molecule, with isoforms that confer preferential nuclear entry and spatiotemporal specificity on viral and cellular cargoes directly linked to human diseases

Molecular identification of endophytic fungi from Aquilaria sinensis and artificial agarwood induced by pinholes-infusion technique

Agarwood, the resinous portions of Aquilaria plants, have been used as medicines and incenses. Aquilaria sinensis is the major producer of agarwood in China. Agarwood are generally viewed as pathological products formed as defense symptom against fungal infection. In this study, microbial communities inhabiting the leaves of non-resinous and agarwood-producing wounded A. sinensis tree were investigated by cultivation-independent approaches, such as PCR, restriction fragment length polymorphism (RFLP) analysis and sequencing of rDNA internal transcribed spacer (ITS) library. Molecular phylogenetic analysis demonstrated that Botryosphaeria, Colletotrichum gloeosporioides, Phomopsis and Cylindrocladium species are members of the agarwood-producing wounded tree, while Phoma, Mycosphaerella, Sagenomella, Alternaria and Ramichloridium species is able to colonize the non-resinous tree internally. C. gloeosporioides was the only fungus shared by the two rDNA ITS libraries. C. gloeosporoides, Botryosphaeria, and Cylindrocladium were considered to be related to agarwood formation. A pinholes-infusion method to induce the generation of agarwood by chemically stimulated and/or inoculate combined method was established. One to two years after the artificial inoculation, resinous wood were collected and the inoculating effects were detected by ethanol extraction content, thin layer chromatography (TLC) and gas chromatography-mass spectrometry (GCMS) techniques. The results reveal that chemically stimulated with formic acid and infected by Botryosphaeria dothidea produced high yield and high quality artificial agarwood in a relatively short time.Keywords: Agarwood, endophytic fungi, Aquilaria sinensis, molecular identification, artificial induce of agarwoodAfrican Journal of Biotechnology Vol. 12(21), pp. 3115-313