Small RNA profiles in soybean primary root tips under water deficit

Background: Soybean (Glycine max) production is significantly hampered by frequent droughts in many regions of the world including the United States. Identifying microRNA (miRNA)-controlled posttranscriptional gene regulation under drought will enhance our understanding of molecular basis of drought tolerance in this important cash crop. Indeed, miRNA profiles in soybean exposed to drought were studied but not from the primary root tips, which is not only a main zone of water uptake but also critical for water stress sensing and signaling.Methods: Here we report miRNA profiles specifically from well-watered and water-stressed primary root tips (0 to 8 mm from the root apex) of soybean. Small RNA sequencing confirmed the expression of vastly diverse miRNA (303 individual miRNAs) population, and, importantly several conserved miRNAs were abundantly expressed in primary root tips.Results: Notably, 12 highly conserved miRNA families were differentially regulated in response to water-deficit; six were upregulated while six others were downregulated at least by one fold (log2) change. Differentially regulated soybean miRNAs are targeting genes include auxin response factors, Cu/Zn Superoxide dismutases, laccases and plantacyanin and several others.Conclusions: These results highlighted the importance of miRNAs in primary root tips both under control and water-deficit conditions; under control conditions, miRNAs could be important for cell division, cell elongation and maintenance of the root apical meristem activity including quiescent centre whereas under water stress differentially regulated miRNAs could decrease auxin signaling and oxidative stress as well as other metabolic processes that save energy and water.Peer reviewedBiochemistry and Molecular Biolog

Energy absorption mechanisms of modified double-aluminum layers under low-velocity impact

Laminated multiple metal or alloy sheets have been widely used in protective structures. However, energy absorption mechanism remains unclear for those laminates with different interface and surface conditions under low-velocity impact. This study investigates the effect of interface and surface modified double aluminum sheets under drop-weight loading. The experimental results showed that epoxy-bonded double sheets did not dissipate more energy than free-contact sample. The simulation results agree well with the experimental data at low cohesive stress of the epoxy adhesive, and friction plays an important role in absorbing impact energy for free-contact sample. However, at high interface cohesive stress as simulated, epoxy-bonded samples absorb more energy than free-contact ones. Further experiments indicated that sample with grease spread front surface is more sensitive in improving energy absorption than sample with grease applied in between two layers. These results are important reference for designing laminated composites to improve impact resistance

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

Abstract 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

Accurate detection for a wide range of mutation and editing sites of microRNAs from small RNA high-throughput sequencing profiles

© 2016 The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. Various types of mutation and editing (M/E) events in microRNAs (miRNAs) can change the stabilities of pre-miRNAs and/or complementarities between miRNAs and their targets. Small RNA (sRNA) high-throughput sequencing (HTS) profiles can contain many mutated and edited miRNAs. Systematic detection of miRNA mutation and editing sites from the huge volume of sRNA HTS profiles is computationally difficult, as high sensitivity and low false positive rate (FPR) are both required. We propose a novel method (named MiRME) for an accurate and fast detection of miRNA M/E sites using a progressive sequence alignment approach which refines sensitivity and improves FPR step-by-step. From 70 sRNA HTS profiles with over 1.3 billion reads, MiRME has detected thousands of statistically significant M/E sites, including 3′-editing sites, 57 A-to-I editing sites (of which 32 are novel), as well as some putative non-canonical editing sites. We demonstrated that a few non-canonical editing sites were not resulted from mutations in genome by integrating the analysis of genome HTS profiles of two human cell lines, suggesting the existence of new editing types to further diversify the functions of miRNAs. Compared with six existing studies or methods, MiRME has shown much superior performance for the identification and visualization of the M/E sites of miRNAs from the ever-increasing sRNA HTS profiles

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

Interfacial Microstructure and Properties of Carbon Fiber Composites Modified with Graphene Oxide

The performance of carbon fiber-reinforced composites is dependent to a great extent on the properties of fiber–matrix interface. To improve the interfacial properties in carbon fiber/epoxy composites, we directly introduced graphene oxide (GO) sheets dispersed in the fiber sizing onto the surface of individual carbon fibers. The applied graphite oxide, which could be exfoliated to single-layer GO sheets, was verified by atomic force microscope (AFM). The surface topography of modified carbon fibers and the distribution of GO sheets in the interfacial region of carbon fibers were detected by scanning electron microscopy (SEM). The interfacial properties between carbon fiber and matrix were investigated by microbond test and three-point short beam shear test. The tensile properties of unidirectional (UD) composites were investigated in accordance with ASTM standards. The results of the tests reveal an improved interfacial and tensile properties in GO-modified carbon fiber composites. Furthermore, significant enhancement of interfacial shear strength (IFSS), interlaminar shear strength (ILSS), and tensile properties was achieved in the composites when only 5 wt % of GO sheets introduced in the fiber sizing. This means that an alternative method for improving the interfacial and tensile properties of carbon fiber composites by controlling the fiber–matrix interface was developed. Such multiscale reinforced composites show great potential with their improved mechanical performance to be likely applied in the aerospace and automotive industries

Phased secondary small interfering RNAs in Panaxnotoginseng

Abstract 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