Lifetime visualization of femtosecond laser-induced plasma on GaP crystal.

Gallium phosphide (GaP) is a widely used and promising semiconductor material for photonics devices and we suppose the ultrafast laser can be a competitive tool for GaP processing. We used an 800 nm centered femtosecond (fs) laser with a pulse duration of 50 fs to irradiate the GaP crystal. The ablation threshold was first determined, and then the ultrafast dynamics including plasma expansion, shockwave formation and propagation, and spectral evolution were acquired and analyzed. The evolution of ejected plasma in the initial stage changed from cylindrical to planar propagation with the augment of laser fluence. The study on the propagation properties of shockwaves showed that the energy of propelling shockwaves accounted for 12% to 18% of the laser pulse energy at all fluences above the ablation threshold. A prominent plasma splitting was observed at a fluence slightly higher than the threshold, and a phenomenon that the plasma protruded out of the shockwaves was also found. Finally, the transient temperature and density of electron at different fluences were calculated. The temperature difference between the plasma and the shockwave proved the heating effect of the plasma during ablation.

Supramolecular Design Strategy of a Water-Soluble Diphenylguanidine-Cyclodextrin Polymer Inclusion Complex.

Diphenylguanidine (DPG) is a widely used secondary accelerator for the vulcanization of natural rubber (NR) latex. However, its low water solubility and high toxicity limit its use in high-end NR products. In this study, a water-soluble inclusion complex of DPG and a ß-cyclodextrin polymer (ß-CDP), termed DPG-ß-CDP, was prepared through supramolecular interactions and characterized using Fourier-transform infrared spectroscopy, 1H NMR, scanning electron microscopy, and UV-vis spectroscopy techniques. In comparison with that of DPG, the water solubility of DPG-ß-CDP was greatly enhanced because of the water-soluble host molecule. The molar ratio of DPG to the CD unit in ß-CDP was determined to be 1:1. At 25 °C, the binding constant of DPG-ß-CDP was found to be 9.2 × 105 L/mol by UV-vis spectroscopy. The proposed method for forming inclusion complexes with high potential for use as water-soluble vulcanization accelerators is promising.

Design Strategy for Vulcanization Accelerator of Diphenylguanidine/Cyclodextrin Inclusion Complex for Natural Rubber Latex Foam with Enhancing Performance.

Vulcanization is an essential process to obtain high-performance rubber products. Diphenylguanidine (DPG) is often used as the secondary accelerator in the vulcanization process of natural rubber (NR) latex. However, DPG would make NR latex emulsion exhibit gelation, resulting in the negative vulcanization efficiency. In addition, exposure to DPG might lead to some physiological diseases during the production process of DPG doped NR latex. Hydroxypropyl-ß-cyclodextrin (HP-ß-CD) with the hydrophobic interior and hydrophilic exterior has the advantages of good water solubility, high bioavailability, reliable stability, and low toxicity. In this study, the inclusion complex of diphenylguanidine-hydroxypropyl-ß-cyclodextrin (DPG-HP-ß-CD) is prepared by ball milling with a host-guest molar ratio of 1 : 1, which has also been applied to the foaming process of NR latex. The mechanical properties of DPG-HP-ß-CD inclusion complex/natural rubber latex foam (DPG-HP-ß-CD/NRLF) have been significantly improved, including the tensile strength, elongation at break, hardness, compression set, resilience, and antiaging performance. Further, the usage of DPG has been reduced, leading to the reduction of toxicity and environmental hazards.

Carbon Nanofibers Based on Potassium Citrate/Polyacrylonitrile for Supercapacitors.

Wearable supercapacitors based on carbon materials have been emerging as an advanced technology for next-generation portable electronic devices with high performance. However, the application of these devices cannot be realized unless suitable flexible power sources are developed. Here, an effective electrospinning method was used to prepare the one-dimensional (1D) and nano-scale carbon fiber membrane based on potassium citrate/polyacrylonitrile (PAN), which exhibited potential applications in supercapacitors. The chemical and physical properties of carbon nanofibers were characterized by X-ray diffraction analysis, scanning electron microscopy, transmission electron microscopy, Raman spectroscopy, X-ray photoelectron spectroscopy, and the Brunnauer-Emmett-Teller method. The fabricated carbon nanofiber membrane illustrates a high specific capacitance of 404 F/g at a current density of 1 A/g. The good electrochemical properties could be attributed to the small diameter and large specific surface area, which promoted a high capacity.

High-Sensitivity and Environmentally Friendly Humidity Sensors Deposited with Recyclable Green Microspheres for Wireless Monitoring.

The reliable, high-sensitive, wireless, and affordable requirements for humidity sensors are needed in high-precision measurement fields. Quartz crystal microbalance (QCM) based on the piezoelectric effect can accurately detect the mass changes at the nanogram level. However, water-capture materials deposited on the surface of QCM generally show disadvantages in either cost, sensitivity, or recyclability. Herein, novel QCM-based humidity sensors (NQHSs) are developed by uniformly depositing green microspheres (GMs) of natural polymers prepared by the chemical synthesis of the emulsification/inner gel method on QCM as humidity-sensitive materials. The NQHSs demonstrate high accuracy and sensitivity (27.1 Hz/% RH) owing to the various hydrophilic groups and porous nano-3D deposition structure. Compared with the devices deposited with a smooth film, the frequency of the NQHSs shows almost no changes during the cyclic test and exhibits long-term stability. The NQHSs have been successfully applied to non-contact sensing human activities and remote real-time humidity monitoring via Bluetooth transmission. In addition, the deposited humidity-sensitive GMs and QCM substrate are fully recycled and reused (72% of the original value). This work has provided an innovative idea to construct environmental-friendly, high-sensitivity, and wireless humidity sensors.

Overexpression of VqWRKY31 enhances powdery mildew resistance in grapevine by promoting salicylic acid signaling and specific metabolite synthesis.

Powdery mildew (PM), caused by the fungal pathogen Erysiphe necator, is one of the most destructive diseases of grapevine (Vitis vinifera and other Vitis spp). Resistance to PM is an important goal for cultivar improvement, and understanding the underlying molecular mechanisms conditioning resistance is critical. Here, we report that transgenic expression of the WRKY transcription factor gene VqWRKY31 from the PM-resistant species Vitis quinquangularis conferred resistance to powdery mildew in V. vinifera through promoting salicylic acid signaling and specific metabolite synthesis. VqWRKY31 belongs to the WRKY IIb subfamily, and expression of the VqWRKY31 gene was induced in response to E. necator inoculation. Transgenic V. vinifera plants expressing VqWRKY31 were substantially less susceptible to E. necator infection, and this was associated with increased levels of salicylic acid and reactive oxygen species. Correlation analysis of transcriptomic and metabolomic data revealed that VqWRKY31 promoted expression of genes in metabolic pathways and the accumulation of many disease resistance-related metabolites, including stilbenes, flavonoids, and proanthocyanidins. In addition, results indicated that VqWRKY31 can directly bind to the promoters of two structural genes in stilbene synthesis, STS9 and STS48, and activate their expression. Based on our results, we propose a model where VqWRKY31 enhances grapevine PM resistance through activation of salicylic acid defense signaling and promotion of specific disease resistance-related metabolite synthesis. These findings can be directly exploited for molecular breeding strategies to produce PM-resistant grapevine germplasm.

A Bias Drift Suppression Method Based on ICELMD and ARMA-KF for MEMS Gyros.

The applications of Micro-Electro-Mechanical-System (MEMS) gyros in inertial navigation system is gradually increasing. However, the random drift of gyro deteriorates the system performance which restricting the applications of high precision. We propose a bias drift compensation model based on two-fold Interpolated Complementary Ensemble Local Mean Decomposition (ICELMD) and autoregressive moving average-Kalman filtering (ARMA-KF). We modify CELMD into ICELMD, which is less complicated and overcomes the endpoint effect. Further, the ICELMD is combined with ARMA-KF to separate and simplify the preprocessed signal, resulting improved denoising performance. In the model, the abnormal noise is removed in preprocess by 2σ criterion with ICELMD. Then, continuous mean square error (CMSE) and Permutation Entropy (PE) are both applied to categorize the preprocessed signal into noise, mixed and useful components. After abandon the noise components and denoise the mixed components by ARMA-KF, we rebuild the noise suppression signal of MEMS gyro. Experiments are carried out to validate the proposed algorithm. The angle random walk of gyro decreases from 2.4156∘/h to 0.0487∘/h, the zero bias instability lowered from 0.3753∘/h to 0.0509∘/h. Further, the standard deviation and the variance are greatly reduced, indicating that the proposed method has better suppression effect, stability and adaptability.

Temporal expression study of miRNAs in the crown tissues of winter wheat grown under natural growth conditions.

BACKGROUND: Winter wheat requires prolonged exposure to low temperature to initiate flowering (vernalization). Shoot apical meristem of the crown is the site of cold perception, which produces leaf primordia during vegetative growth before developing into floral primordia at the initiation of the reproductive phase. Although many essential genes for winter wheat cold acclimation and floral initiation have been revealed, the importance of microRNA (miRNA) meditated post-transcriptional regulation in crowns is not well understood. To understand the potential roles of miRNAs in crown tissues, we performed a temporal expression study of miRNAs in crown tissues at the three-leaf stage, winter dormancy stage, spring green-up stage, and jointing stage of winter wheat grown under natural growth conditions. RESULTS: In total, 348 miRNAs belonging to 298 miRNA families, were identified in wheat crown tissues. Among them, 92 differentially expressed miRNAs (DEMs) were found to be significantly regulated from the three-leaf stage to the jointing stage. Most of these DEMs were highly expressed at the three-leaf stage and winter dormancy stage, and then declined in later stages. Six DEMs, including miR156a-5p were markedly induced during the winter dormancy stage. Eleven DEMs, including miR159a.1, miR390a-5p, miR393-5p, miR160a-5p, and miR1436, were highly expressed at the green-up stage. Twelve DEMs, such as miR172a-5p, miR394a, miR319b-3p, and miR9676-5p were highly induced at the jointing stage. Moreover, 14 novel target genes of nine wheat or Pooideae-specific miRNAs were verified using RLM-5' RACE assay. Notably, six mTERFs and two Rf1 genes, which are associated with mitochondrial gene expression, were confirmed as targets of three wheat-specific miRNAs. CONCLUSIONS: The present study not only confirmed the known miRNAs associated with phase transition and floral development, but also identified a number of wheat or Pooideae-specific miRNAs critical for winter wheat cold acclimation and floral development. Most importantly, this study provided experimental evidence that miRNA could regulate mitochondrial gene expression by targeting mTERF and Rf1 genes. Our study provides valuable information for further exploration of the mechanism of miRNA mediated post-transcriptional regulation during winter wheat vernalization and inflorescent initiation.

Transcriptional dynamics of transposable elements when converting fibroblast cells of Macaca mulatta to neuroepithelial stem cells.

BACKGROUND: Transposable elements (TE) account for more than 50% of human genome. It has been reported that some types of TEs are dynamically regulated in the reprogramming of human cell lines. However, it is largely unknown whether some TEs in Macaca mulatta are also regulated during the reprogramming of cell lines of monkey. RESULTS: Here, we systematically examined the transcriptional activities of TEs during the conversion of Macaca mulatta fibroblast cells to neuroepithelial stem cells (NESCs). Hundreds of TEs were dynamically regulated during the reprogramming of Macaca mulatta fibroblast cells. Furthermore, 48 Long Terminal Repeats (LTRs), as well as some integrase elements, of Macaca endogenous retrovirus 3 (MacERV3) were transiently activated during the early stages of the conversion process, some of which were further confirmed with PCR experiments. These LTRs were potentially bound by critical transcription factors for reprogramming, such as KLF4 and ETV5. CONCLUSION: These results suggest that the transcription of TEs are delicately regulated during the reprogramming of Macaca mulatta fibroblast cells. Although the family of ERVs activated during the reprogramming of fibroblast cells in Macaca mulatta is different from those in the reprogramming of human fibroblast cells, our results suggest that the activation of some ERVs is a conserved mechanism in primates for converting fibroblast cells to stem cells.

Sensitive Formaldehyde Detection with QCM Sensor Based on PAAm/MWCNTs and PVAm/MWCNTs.

Two formaldehyde detection methods are proposed by applying composite film quartz crystal microbalance (QCM) sensors. QCM sensor coated with PAAm/MWCNTs and PVAm/MWCNTs shows excellent characteristics of lower limit and high sensitivity. The lower limit of PVAm/MWCNTs is 0.5 ppm, and its detection sensitivity is 0.74 ppm/Hz. Upon working at different concentrations of formaldehyde and fabricating in different proportions, the reuse performance, gas selectivity, and response at room temperature show contrasting results. The main advantages of the two sensors presented are fast reaction, low cost, and easy manufacture. Compared to other formaldehyde sensors based on QCM, the PAAm/MWCNT- and PVAm/MWCNT-coated QCM sensors are able to concurrently show excellent selectivity, reuse performance, and high sensitivity, which is of great significance to detect the environmental quality.

A developmental landscape of 3D-cultured human pre-gastrulation embryos.

Our understanding of how human embryos develop before gastrulation, including spatial self-organization and cell type ontogeny, remains limited by available two-dimensional technological platforms1,2 that do not recapitulate the in vivo conditions3-5. Here we report a three-dimensional (3D) blastocyst-culture system that enables human blastocyst development up to the primitive streak anlage stage. These 3D embryos mimic developmental landmarks and 3D architectures in vivo, including the embryonic disc, amnion, basement membrane, primary and primate unique secondary yolk sac, formation of anterior-posterior polarity and primitive streak anlage. Using single-cell transcriptome profiling, we delineate ontology and regulatory networks that underlie the segregation of epiblast, primitive endoderm and trophoblast. Compared with epiblasts, the amniotic epithelium shows unique and characteristic phenotypes. After implantation, specific pathways and transcription factors trigger the differentiation of cytotrophoblasts, extravillous cytotrophoblasts and syncytiotrophoblasts. Epiblasts undergo a transition to pluripotency upon implantation, and the transcriptome of these cells is maintained until the generation of the primitive streak anlage. These developmental processes are driven by different pluripotency factors. Together, findings from our 3D-culture approach help to determine the molecular and morphogenetic developmental landscape that occurs during human embryogenesis.

PHD2 acts as an oncogene through activation of Ras/Raf/MEK/ERK and JAK1/STAT3 pathways in human hepatocellular carcinoma cells.

Background: Prolyl hydroxylase domain proteins (PHD2) is an oxygen sensor that is able to induce hypoxia-inducible factor-α (HIF-α) degradation under normoxic condition. The present paper designed to reveal the function of PHD2 in hepatocellular carcinoma (HCC) cells proliferation, migration and invasion.Methods: qRT-PCR and Western blot were carried out to see the expression of PHD2 in HCC tissues and cell lines. PHD2 expression in Huh7 and HepG3B cells was overexpressed or suppressed by transfection and then the changes of cell proliferation, migration and invasion were detected by CCK-8 assay, transwell assay and Western blot.Results: PHD2 was highly expressed in HCC tissues and cell lines (Huh7, Hep3B, SK-HEP-1, HCCLM3 and MHCC97) as relative to para-cancerous non-tumour tissues and a normal hepatocyte line MIHA. PHD2 overexpression promoted Huh7 and Hep3B cells viability, migration and invasion. Meanwhile, CyclinD1, c-Myc, MMP-2, MMP-9 and Vimentin were up-regulated, while p53 was down-regulated by PHD2 overexpression. PHD2 silence led to a contrary impact. Further, PHD2 overexpression up-regulated Ras and Raf expression and induced phosphorylation of MEK, ERK, JAK1 and STAT3.Conclusion: PHD2 exhibited pro-tumour functions in HCC cells. PHD2 promoted HCC possibly through Ras/Raf/MEK/ERK and JAK1/STAT3 pathways.HighlightsPHD2 is highly expressed in HCC tissue and cell lines;PHD2 promotes the proliferation of Huh7 and HepG3B cells;PHD2 enhances Huh7 and HepG3B cells migration and invasion;PHD2 activates Ras/Raf/MEK/ERK and JAK1/STAT3 signalling.

An improved method of constructing degradome library suitable for sequencing using Illumina platform.

BACKGROUND: Post-transcriptional gene regulation is one of the critical layers of overall gene expression programs and microRNAs (miRNAs) play an indispensable role in this process by guiding cleavage on the messenger RNA targets. The transcriptome-wide cleavages on the target transcripts can be identified by analyzing the degradome or PARE or GMUCT libraries. However, high-throughput sequencing of PARE or degradome libraries using Illumina platform, a widely used platform, is not so straightforward. Moreover, the currently used degradome or PARE methods utilize MmeI restriction site in the 5' RNA adapter and the resulting fragments are only 20-nt long, which often poses difficulty in distinguishing between the members of the same target gene family or distinguishing miRNA biogenesis intermediates from the primary miRNA transcripts belonging to the same miRNA family. Consequently, developing a method which can generate longer fragments from the PARE or degradome libraries which can also be sequenced easily using Illumina platform is ideal. RESULTS: In this protocol, 3' end of the 5'RNA adaptor of TruSeq small RNA library is modified by introducing EcoP15I recognition site. Correspondingly, the double-strand DNA (dsDNA) adaptor sequence is also modified to suit with the ends generated by the restriction enzyme EcoP15I. These modifications allow amplification of the degradome library by primer pairs used for small RNA library preparation, thus amenable for sequencing using Illumina platform, like small RNA library. CONCLUSIONS: Degradome library generated using this improved protocol can be sequenced easily using Illumina platform, and the resulting tag length is ~ 27-nt, which is longer than the MmeI generated fragment (20-nt) that can facilitate better accuracy in validating target transcripts belonging to the same gene family or distinguishing miRNA biogenesis intermediates of the same miRNA family. Furthermore, this improved method allows pooling and sequencing degradome libraries and small RNA libraries simultaneously using Illumina platform.

Protective Effect of Resveratrol Improves Systemic Inflammation Responses in LPS-Injected Lambs.

Highly intensive livestock production often causes immune stress to animals, which makes them more susceptible to infections. The aim of this study was to examine whether resveratrol (Res) alleviates inflammation in lambs. In Experiment 1, 16 male lambs were injected with lipopolysaccharides (LPS) at an initial dose of 0.25, 1.25, and 2.5 µg/kg body weight (BW) for 9 days. Average daily gain and blood parameters were measured and clinical symptoms were recorded. In Experiment 2, 20 male lambs were injected intravenously with LPS (0 mg/kg) + Res (0 mg), LPS (2.5 µg /kg) + Res (0 mg, 82.5 mg, 165 mg, 330 mg), 4 h after LPS injection. Jugular blood was collected from each lamb to determine white blood cell (WBC) counts and the expression of inflammatory genes. In Experiment 1, all LPS-treated lambs showed clinical signs of sickness including rhinorrhea, lethargy, and shivering, and systemic inflammatory responses of increased inflammatory genes levels and cortisol concentration. The lambs had increased respiratory and heart rates and rectal temperature and decreased average daily gain and feed intake. In Experiment 2, resveratrol significantly reduced WBCs and the expression levels of several genes associated with inflammation response (TLR4, NF-κB, c-jun) and inhibited the signaling cascades of NF-κB and MAPKs by down-regulating the expression levels of inflammatory cytokines (IL-1ß, IL-4, IL-6, TNF-α, IFN-γ) induced by LPS. Resveratrol attenuated the LPS-evoked inflammatory responses in lambs by suppressing expression levels of inflammatory cytokines, and blocking NF-κB and MAPK signaling pathways.

Identification and Temporal Expression Analysis of Conserved and Novel MicroRNAs in the Leaves of Winter Wheat Grown in the Field.

Cold acclimation and vegetative/reproductive transition are two important evolutionary adaptive mechanisms for winter wheat surviving the freezing temperature in winter and successful seeds setting in the next year. MicroRNA (miRNA) is a class of regulatory small RNAs (sRNAs), which plays critical roles in the growth and development of plants. However, the regulation mechanism of miRNAs during cold acclimation and vegetative/reproductive transition of winter wheat is not much understood. In this study, four sRNA libraries from leaves of winter wheat grown in the field at the three-leaf stage, winter dormancy stage, spring green-up stage, and jointing stage were analyzed to identify known and novel miRNAs and to understand their potential roles in the growth and development of winter wheat. We examined miRNA expression using a high-throughput sequencing technique. A total of 373 known, 55 novel, and 27 putative novel miRNAs were identified. Ninety-one miRNAs were found to be differentially expressed at the four stages. Among them, the expression of six known and eight novel miRNAs was significantly suppressed at the winter dormancy stage, whereas the expression levels of seven known and eight novel miRNAs were induced at this stage; three known miRNAs and three novel miRNAs were significantly induced at the spring green-up stage; six known miRNAs were induced at the spring green-up stage and reached the highest expression level at the jointing stage; and 20 known miRNAs and 10 novel miRNAs were significantly induced at the jointing stage. Expression of a number of representative differentially expressed miRNAs was verified using quantitative real-time polymerase chain reaction (qRT-PCR). Potential target genes for known and novel miRNAs were predicted. Moreover, six novel target genes for four Pooideae species-specific miRNAs and two novel miRNAs were verified using the RNA ligase-mediated 5'-rapid amplification of cDNA ends (RLM-5'RACE) technique. These results indicate that miRNAs are key non-coding regulatory factors modulating the growth and development of wheat. Our study provides valuable information for in-depth understanding of the regulatory mechanism of miRNAs in cold acclimation and vegetative/reproductive transition of winter wheat grown in the field.

Identifying microRNAs and Their Editing Sites in Macaca mulatta.

MicroRNAs (miRNAs) are small non-coding RNAs that are critical in post-transcriptional regulation. Macaca mulatta is an important nonhuman primate that is often used in basic and translational researches. However, the annotation of miRNAs in Macaca mulatta is far from complete, and there are no reports of miRNA editing events in Macaca mulatta, although editing may affect the biogenesis or functions of the miRNAs. To improve miRNA annotation and to reveal editing events of miRNAs in Macaca mulatta, we generated 12 small RNA profiles from eight tissues and performed comprehensive analysis of these profiles. We identified 479 conserved pre-miRNAs that have not been reported in Macaca mulatta and 17 species specific miRNAs. Furthermore, we identified 3386 editing sites with significant editing levels from 471 pre-miRNAs after analyzing the 12 self-generated and 58 additional published sRNA-seq profiles from 17 different types of organs or tissues. In addition to 16 conserved A-to-I editing sites, we identified five conserved C-to-U editing sites in miRNAs of Macaca mulatta and Homo sapiens. We also identified 11 SNPs in the miRNAs of Macaca mulatta. The analysis of the potential targets of 69 miRNAs with editing or mutation events in their seed regions suggest that these editing or mutation events severely changed their targets and their potential functions. These results significantly increase our understanding of miRNAs and their mutation/editing events in Macaca mulatta.

Analysis of microRNAs, phased small interfering RNAs and their potential targets in Rosarugosa Thunb.

BACKGROUND: MicroRNAs (miRNAs) are small non-coding RNAs that play important roles by regulating other genes. Rosa rugosa Thunb. is an important ornamental and edible plant, yet there are only a few studies on the miRNAs and their functions in R. rugosa. RESULTS: We sequenced 10 samll RNA profiles from the roots, petals, pollens, stamens, and leaves and 4 RNA-seq profiles in leaves and petals to analysis miRNA, phasiRNAs and mRNAs in R. rugosa. In addition, we acquired a degradome sequencing profile from leaf of R. rugosa to identify miRNA and phasiRNA targets using the SeqTar algorithm. We have identified 321 conserved miRNA homologs including primary transcripts for 25 conserved miRNAs, and 22 novel miRNAs. We identified 592 putative targets of the conserved miRNAs or tasiRNAs that showed significant accumulations of degradome reads. We found differential expression patterns of conserved miRNAs in five different tissues of R. rugosa. We identified three hundred and thirty nine 21 nucleotide (nt) PHAS loci, and forty nine 24 nt PHAS loci, respectively. Our results suggest that miR482 triggers generations of phasiRNAs by targeting nucleotide-binding, leucine-rich repeat (NB-LRR) disease resistance genes in R. rugosa. Our results also suggest that the deregulated genes in leaves and petals are significantly enriched in GO terms and KEGG pathways related to metabolic processes and photosynthesis. CONCLUSIONS: These results significantly enhanced our knowledge of the miRNAs and phasiRNAs, as well as their potential functions, in R. rugosa.

A Comprehensive Map of Intron Branchpoints and Lariat RNAs in Plants.

Lariats are formed by excised introns, when the 5' splice site joins with the branchpoint (BP) during splicing. Although lariat RNAs are usually degraded by RNA debranching enzyme 1, recent findings in animals detected many lariat RNAs under physiological conditions. By contrast, the features of BPs and to what extent lariat RNAs accumulate naturally are largely unexplored in plants. Here, we analyzed 948 RNA sequencing data sets to document plant BPs and lariat RNAs on a genome-wide scale. In total, we identified 13,872, 5199, 29,582, and 13,478 BPs in Arabidopsis (Arabidopsis thaliana), tomato (Solanum lycopersicum), rice (Oryza sativa), and maize (Zea mays), respectively. Features of plant BPs are highly similar to those in yeast and human, in that BPs are adenine-preferred and flanked by uracil-enriched sequences. Intriguingly, ∼20% of introns harbor multiple BPs, and BP usage is tissue-specific. Furthermore, 10,580 lariat RNAs accumulate in wild-type Arabidopsis plants, and most of these lariat RNAs originate from longer or retroelement-depleted introns. Moreover, the expression of these lariat RNAs is accompanied by the incidence of back-splicing of parent exons. Collectively, our results provide a comprehensive map of intron BPs and lariat RNAs in four plant species and uncover a link between lariat turnover and splicing.

Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon.

BACKGROUND: MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stress responses. Watermelon (Citrullus lanatus L.) is one of the important agricultural crops worldwide. However, the watermelon miRNAs and phasiRNAs and their functions are not well explored. RESULTS: Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in watermelon by analyzing 14 small RNA profiles from roots, leaves, androecium, petals, and fruits, and one published small RNA profile of mixed tissues. To identify the targets of miRNAs and phasiRNAs, we generated a degradome profile for watermelon leaf which is analyzed using the SeqTar algorithm. We identified 97 conserved pre-miRNAs, of which 58 have not been reported previously and 348 conserved mature miRNAs without precursors. We also found 9 novel pre-miRNAs encoding 18 mature miRNAs. One hundred and one 21 nucleotide (nt) PHAS loci, and two hundred and forty one 24 nt PHAS loci were also identified. We identified 127 conserved targets of the conserved miRNAs and TAS3-derived tasiRNAs by analyzing a degradome profile of watermelon leaf. CONCLUSIONS: The presented results provide a comprehensive view of small regulatory RNAs and their targets in watermelon.

Phased secondary small interfering RNAs in Panaxnotoginseng.

BACKGROUND: Recent results demonstrated that either non-coding or coding genes generate phased secondary small interfering RNAs (phasiRNAs) guided by specific miRNAs. Till now, there is no studies for phasiRNAs in Panax notoginseng (Burk.) F.H. Chen (P. notoginseng), an important traditional Chinese herbal medicinal plant species. METHODS: Here we performed a genome-wide discovery of phasiRNAs and its host PHAS loci in P. notoginseng by analyzing small RNA sequencing profiles. Degradome sequencing profile was used to identify the trigger miRNAs of these phasiRNAs and potential targets of phasiRNAs. We also used RLM 5'-RACE to validate some of the identified phasiRNA targets. RESULTS: After analyzing 24 small RNA sequencing profiles of P. notoginseng, 204 and 90 PHAS loci that encoded 21 and 24 nucleotide (nt) phasiRNAs, respectively, were identified. Furthermore, we found that phasiRNAs produced from some pentatricopeptide repeat-contain (PPR) genes target another layer of PPR genes as validated by both the degradome sequencing profile and RLM 5'-RACE analysis. We also found that miR171 with 21 nt triggers the generations of 21 nt phasiRNAs from its conserved targets. CONCLUSIONS: We validated that some phasiRNAs generated from PPRs and TASL genes are functional by targeting other PPRs in trans. These results provide the first set of PHAS loci and phasiRNAs in P. notoginseng, and enhance our understanding of PHAS in plants.