MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences

<p>Abstract</p> <p>Background</p> <p>MicroRNAs are a family of ~22 nt small RNAs that can regulate gene expression at the post-transcriptional level. Identification of these molecules and their targets can aid understanding of regulatory processes. Recently, HTS has become a common identification method but there are two major limitations associated with the technique. Firstly, the method has low efficiency, with typically less than 1 in 10,000 sequences representing miRNA reads and secondly the method preferentially targets highly expressed miRNAs. If sequences are available, computational methods can provide a screening step to investigate the value of an HTS study and aid interpretation of results. However, current methods can only predict miRNAs for short fragments and have usually been trained against small datasets which don't always reflect the diversity of these molecules.</p> <p>Results</p> <p>We have developed a software tool, miRPara, that predicts most probable mature miRNA coding regions from genome scale sequences in a species specific manner. We classified sequences from miRBase into animal, plant and overall categories and used a support vector machine to train three models based on an initial set of 77 parameters related to the physical properties of the pre-miRNA and its miRNAs. By applying parameter filtering we found a subset of ~25 parameters produced higher prediction ability compared to the full set. Our software achieves an accuracy of up to 80% against experimentally verified mature miRNAs, making it one of the most accurate methods available.</p> <p>Conclusions</p> <p>miRPara is an effective tool for locating miRNAs coding regions in genome sequences and can be used as a screening step prior to HTS experiments. It is available at <url>http://www.whiov.ac.cn/bioinformatics/mirpara</url></p

Sequential Reassortments Underlie Diverse Influenza H7N9 Genotypes in China

Initial genetic characterizations have suggested that the influenza A (H7N9) viruses responsible for the current outbreak in China are novel reassortants. However, little is known about the pathways of their evolution and, in particular, the generation of diverse viral genotypes. Here we report an in-depth evolutionary analysis of whole-genome sequence data of 45 H7N9 and 42 H9N2 viruses isolated from humans, poultry, and wild birds during recent influenza surveillance efforts in China. Our analysis shows that the H7N9 viruses were generated by at least two steps of sequential reassortments involving distinct H9N2 donor viruses in different hosts. The first reassortment likely occurred in wild birds and the second in domestic birds in east China in early 2012. Our study identifies the pathways for the generation of diverse H7N9 genotypes in China and highlights the importance of monitoring multiple sources for effective surveillance of potential influenza outbreaks.National Natural Science Foundation (China) (31125016)National Natural Science Foundation (China) (31371338)National Center for Biotechnology Information (U.S.) (Major National Earmark Project for Infectious Diseases, 2013ZX10004611-002)National Basic Research Program of China (973 Program)National Basic Research Program of China (973 Program, grant, 2009CB918503)National Science and Technology Major Projects (2012ZX10004214001002)Jiangsu Sheng (China) (Priority Academic Program Development of Jiangsu Higher Education Institutions)National Natural Science Foundation (China) (31100950)MIT International Science and Technology Initiative

The Survey of H5N1 Flu Virus in Wild Birds in 14 Provinces of China from 2004 to 2007

The highly pathogenic H5N1 avian influenza emerged in the year 1996 in Asia, and has spread to Europe and Africa recently. At present, effective monitoring and data analysis of H5N1 are not sufficient in Chinese mainland.)) were obviously higher than those in other 13 provinces. The results of sequence analysis indicated that the 17 strains isolated from wild birds were distributed in five clades (2.3.1, 2.2, 2.5, 6, and 7), which suggested that genetic diversity existed among H5N1 viruses isolated from wild birds. The five isolates from Qinghai came from one clade (2.2) and had a short evolutionary distance with the isolates obtained from Qinghai in the year 2005.We have measured the prevalence of H5N1 virus in 56 species of wild birds in 14 provinces of China. Continuous monitoring in the field should be carried out to know whether H5N1 virus can be maintained by wild birds

Wild Bird Migration across the Qinghai-Tibetan Plateau: A Transmission Route for Highly Pathogenic H5N1

BACKGROUND: Qinghai Lake in central China has been at the center of debate on whether wild birds play a role in circulation of highly pathogenic avian influenza virus H5N1. In 2005, an unprecedented epizootic at Qinghai Lake killed more than 6000 migratory birds including over 3000 bar-headed geese (Anser indicus). H5N1 subsequently spread to Europe and Africa, and in following years has re-emerged in wild birds along the Central Asia flyway several times. METHODOLOGY/PRINCIPAL FINDINGS: To better understand the potential involvement of wild birds in the spread of H5N1, we studied the movements of bar-headed geese marked with GPS satellite transmitters at Qinghai Lake in relation to virus outbreaks and disease risk factors. We discovered a previously undocumented migratory pathway between Qinghai Lake and the Lhasa Valley of Tibet where 93% of the 29 marked geese overwintered. From 2003-2009, sixteen outbreaks in poultry or wild birds were confirmed on the Qinghai-Tibet Plateau, and the majority were located within the migratory pathway of the geese. Spatial and temporal concordance between goose movements and three potential H5N1 virus sources (poultry farms, a captive bar-headed goose facility, and H5N1 outbreak locations) indicated ample opportunities existed for virus spillover and infection of migratory geese on the wintering grounds. Their potential as a vector of H5N1 was supported by rapid migration movements of some geese and genetic relatedness of H5N1 virus isolated from geese in Tibet and Qinghai Lake. CONCLUSIONS/SIGNIFICANCE: This is the first study to compare phylogenetics of the virus with spatial ecology of its host, and the combined results suggest that wild birds play a role in the spread of H5N1 in this region. However, the strength of the evidence would be improved with additional sequences from both poultry and wild birds on the Qinghai-Tibet Plateau where H5N1 has a clear stronghold

Bird migration and risk for H5N1 transmission into Qinghai Lake, China

The highly pathogenic avian influenza H5N1 virus still cause devastating effects to humans, agricultural poultry flocks, and wild birds. Wild birds are also detected to carry H5N1 over long distances and are able to introduce it into new areas during migration. In this article, our objective is to provide lists of bird species potentially involved in the introduction of highly pathogenic avian influenza H5N1 in Qinghai Lake, which is an important breeding and stopover site for aquatic birds along the Central Asian Flyway. Bird species were classified according to the following behavioral and ecological factors: migratory status, abundance, degree of mixing species and gregariousness, and the prevalence rate of H5N1 virus. Most of the high-risk species were from the family Anatidae, order Anseriformes (9/14 in spring, 11/15 in fall). We also estimated the relative risk of bird species involved by using a semi-quantitative method; species from family Anatidae accounted for over 39% and over 91% of the total risk at spring and fall migration periods, respectively. Results also show the relative risk for each bird aggregating site in helping to identify high-risk areas. This work may also be instructive and meaningful to the avian influenza surveillance in the breeding, stopover, and wintering sites besides Qinghai Lake along the Central Asian Flyway

A Filmy Black-Phosphorus Polyimide Saturable Absorber for Q-Switched Operation in an Erbium-Doped Fiber Laser

We demonstrate an erbium-doped fiber laser passively Q-switched by a black-phosphorus polyimide film. The multi-layer black-phosphorus (BP) nanosheets were prepared via a liquid exfoliation approach exploiting N-methylpyrrolidone as the dispersion liquid. By mixing the BP nanosheets with polyimide (PI), a piece of BP–PI film was obtained after evaporating the mixture in a petri dish. The BP–PI saturable absorber had a modulation depth of 0.47% and was inserted into an erbium-doped fiber laser to realize passive Q-switched operations. The repetition rate of the Q-switched laser increased from 5.73 kHz to 31.07 kHz when the laser pump was enhanced from 31.78 mW to 231.46 mW. Our results show that PI is an excellent host material to protect BP from oxidation, and the BP–PI film can act as a promising nonlinear optical device for laser applications

Broad-spectrum mildew resistance in Arabidopsis thaliana mediated by RPW8

Plant disease resistance (R) genes control the recognition of specific pathogens and activate subsequent defense responses. We show that the Arabidopsis thaliana locus RESISTANCE TO POWDERY MILDEW8 (RPW8) contains two naturally polymorphic, dominant R genes, RPW8.1and RPW8.2, which individually control resistance to a broad range of powdery mildew pathogens. Although the predicted RPW8.1 and RPW8.2 proteins are different from the previously characterized R proteins, they induce localized, salicylic acid–dependent defenses similar to those induced by R genes that control specific resistance. Apparently, broad-spectrum resistance mediated by RPW8 uses the same mechanisms as specific resistance