Haplotype Distribution and Evolutionary Pattern of miR-17 and miR-124 Families Based on Population Analysis

Background: MicroRNAs (miRNAs) are small, endogenously expressed non-coding RNAs that regulate mRNAs posttranscriptionally. Previous studies have explored miRNA evolutionary trend, but evolutionary history and pattern in the miRNA world are still not fully clear. In the paper, we intended to analyze miRNA haplotype distribution and evolutionary network by analyzing miRNA sequences of miR-17 and miR-124 families across animal species as special populations. Principal Findings: 31 haplotypes were detected in miR-17 family while only 9 haplotypes were defined in miR-124 family. The complex miR-17 family was mainly distributed in vertebrates, but miR-124 was shared by more animal species from Caenorhabditis to Homo and had a wide distribution spectrum. Some haplotypes of the two miRNA families appeared discontinuous distributions across animals. Compared with a simple phylogenetic network in miR-124 family, miR-17 family indicated a complex network with some median vectors that might be lost ancestral or potential miRNA haplotypes. By analyzing different miRNAs across 12 animal species, we found these small RNAs showed different haplotype diversities, haplotype distributions and phylogenetic networks. Conclusions: Different miRNAs had quite different haplotype distributions and evolutionary patterns. Discontinuous distributions of miRNAs and median vectors in phylogenetic networks implied more members in the miRNA world. miRN

Pair-barcode high-throughput sequencing for large-scale multiplexed sample analysis

<p>Abstract</p> <p>Background</p> <p>The multiplexing becomes the major limitation of the next-generation sequencing (NGS) in application to low complexity samples. Physical space segregation allows limited multiplexing, while the existing barcode approach only permits simultaneously analysis of up to several dozen samples.</p> <p>Results</p> <p>Here we introduce pair-barcode sequencing (PBS), an economic and flexible barcoding technique that permits parallel analysis of large-scale multiplexed samples. In two pilot runs using SOLiD sequencer (Applied Biosystems Inc.), 32 independent pair-barcoded miRNA libraries were simultaneously discovered by the combination of 4 unique forward barcodes and 8 unique reverse barcodes. Over 174,000,000 reads were generated and about 64% of them are assigned to both of the barcodes. After mapping all reads to pre-miRNAs in miRBase, different miRNA expression patterns are captured from the two clinical groups. The strong correlation using different barcode pairs and the high consistency of miRNA expression in two independent runs demonstrates that PBS approach is valid.</p> <p>Conclusions</p> <p>By employing PBS approach in NGS, large-scale multiplexed pooled samples could be practically analyzed in parallel so that high-throughput sequencing economically meets the requirements of samples which are low sequencing throughput demand.</p

Properties of a Small-scale Short-duration Solar Eruption with a Driven Shock

Large-scale solar eruptions have been extensively explored over many years. However, the properties of small-scale events with associated shocks have been rarely investigated. We present the analyses of a small-scale short-duration event originating from a small region. The impulsive phase of the M1.9-class flare lasted only for four minutes. The kinematic evolution of the CME hot channel reveals some exceptional characteristics including a very short duration of the main acceleration phase ($<$ 2 minutes), a rather high maximal acceleration rate ($\sim$50 km s$^{-2}$) and peak velocity ($\sim$1800 km s$^{-1}$). The fast and impulsive kinematics subsequently results in a piston-driven shock related to a metric type II radio burst with a high starting frequency of $\sim$320 MHz of the fundamental band. The type II source is formed at a low height of below $1.1~\mathrm{R_{\odot}}$ less than $\sim2$ minutes after the onset of the main acceleration phase. Through the band split of the type II burst, the shock compression ratio decreases from 2.2 to 1.3, and the magnetic field strength of the shock upstream region decreases from 13 to 0.5 Gauss at heights of 1.1 to 2.3 $~\mathrm{R_{\odot}}$. We find that the CME ($\sim4\times10^{30}\,\mathrm{erg}$) and flare ($\sim1.6\times10^{30}\,\mathrm{erg}$) consume similar amount of magnetic energy. The same conclusion for large-scale eruptions implies that small- and large-scale events possibly share the similar relationship between CMEs and flares. The kinematic particularities of this event are possibly related to the small footpoint-separation distance of the associated magnetic flux rope, as predicted by the Erupting Flux Rope model.Comment: 20 pages, 16 figure

Mutation analysis of the WNT4 gene in Han Chinese women with premature ovarian failure

BACKGROUND: The WNT4 gene plays an important role in female sex determination and differentiation. It also contributes to maintaining of the ovaries and the survival of follicles. METHODS: We sequenced the coding region and splice sites of WNT4 in 145 Han Chinese women with premature ovarian failure (POF) and 200 healthy controls. RESULTS: Only one novel variation, in Exon 2 (195C > T), was detected among the women with POF. However, this synonymous variation did not result in a change in amino acid sequence (65 Asp > Asp). No further variants were found in any of the samples. CONCLUSION: Although we cannot provide any evidence that it is a possible disease-causing gene, this study is the first attempt to investigate the possible role of WNT4 in Han Chinese women with POF

Observational Signatures of Tearing Instability in the Current Sheet of a Solar Flare

Magnetic reconnection is a fundamental physical process converting magnetic energy into not only plasma energy but also particle energy in various astrophysical phenomena. In this Letter, we show a unique data set of a solar flare where various plasmoids were formed by a continually stretched current sheet. Extreme ultraviolet images captured reconnection inflows, outflows, and particularly the recurring plasma blobs (plasmoids). X-ray images reveal nonthermal emission sources at the lower end of the current sheet, presumably as large plasmoids with a sufficiently amount of energetic electrons trapped in them. In the radio domain, an upward, slowly drifting pulsation structure, followed by a rare pair of oppositely drifting structures, was observed. These structures are supposed to map the evolution of the primary and the secondary plasmoids formed in the current sheet. Our results on plasmoids at different locations and scales shed important light on the dynamics, plasma heating, particle acceleration, and transport processes in the turbulent current sheet and provide observational evidence for the cascading magnetic reconnection process

First determination of 2D speed distribution within the bodies of coronal mass ejections with cross-correlation analysis

Funding: this research has received funding from the the European Union Horizon 2020 research and innovation programme (grant agreement No. 647214).The determination of the speed of coronal mass ejections (CMEs) is usually done by tracking brighter features (such as the CME front and core) in visible light (VL) coronagraphic images and by deriving unidimensional profiles of the CME speed as a function of altitude or time. Nevertheless, CMEs are usually characterized by the presence of significant density inhomogeneities propagating outward with different radial and latitudinal projected speeds, resulting in a complex evolution eventually forming the interplanetary CME. In this work, we demonstrate for the first time how coronagraphic image sequences can be analyzed with the cross-correlation technique to derive two-dimensional (2D) maps of the almost instantaneous plasma speed distribution within the body of CMEs. The technique is first tested with the analysis of synthetic data and then applied to real observations. Results from this work allow us to characterize the distribution and time evolution of kinetic energy inside CMEs, as well as the mechanical energy (combined with the kinetic and potential energy) partition between the core and front of the CME. In the future, CMEs will be observed by two channels (VL and UV Lyα) coronagraphs, such as Metis on board ESA Solar Orbiter mission as well as the Lyα Solar Telescope on board the Chinese Advanced Space-based Solar Observatory mission. Our results will help in the analysis of these future observations, helping in particular to take into account the 2D distribution of Lyα Doppler dimming effect.PostprintPeer reviewe

Three-Dimensional Reconstructions of Coronal Wave Surfaces Using a New Mask-Fitting Method

Coronal waves are large-scale disturbances often driven by coronal mass ejections (CMEs). We investigate a spectacular wave event on 7 March 2012, which is associated with an X5.4 flare (SOL2012-03-07). By using a running center-median (RCM) filtering method for the detection of temporal variations in extreme ultraviolet (EUV) images, we enhance the EUV disturbance observed by the Atmospheric Imaging Assembly (AIA) onboard the Solar Dynamics Observatory (SDO) and the Sun Watcher using Active Pixel System detector and Image Processing (SWAP) onboard the PRoject for Onboard Autonomy 2 (PROBA2). In coronagraph images, a halo front is observed to be the upper counterpart of the EUV disturbance. Based on the EUV and coronagraph images observed from three different perspectives, we have made three-dimensional (3D) reconstructions of the wave surfaces using a new mask-fitting method. The reconstructions are compared with those obtained from forward-fitting methods. We show that the mask fitting method can reflect the inhomogeneous coronal medium by capturing the concave shape of the shock wave front. Subsequently, we trace the developing concave structure and derive the deprojected wave kinematics. The speed of the 3D-wave nose increases from a low value below a few hundred $\mathrm{km\,s^{-1}}$ to a maximum value of about 3800 $\mathrm{km\,s^{-1}}$, and then slowly decreases afterwards. The concave structure starts to decelerate earlier and has significantly lower speeds than those of the wave nose. We also find that the 3D-wave in the extended corona has a much higher speed than the speed of EUV disturbances across the solar disk.Comment: Solar Physics: Topical Collection "Ten Years of Solar Observations with PROBA2", accepte