Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing

Background In plants, microRNAs (miRNAs) are endogenous ~22 nt RNAs that play important regulatory roles in many aspects of plant biology, including metabolism, hormone response, epigenetic control of transposable elements, and stress response. Extensive studies of miRNAs have been performed in model plants such as rice and Arabidopsis thaliana. In maize, most miRNAs and their target genes were analyzed and identified by clearly different treatments, such as response to low nitrate, salt and drought stress. However, little is known about miRNAs involved in maize ear development. The objective of this study is to identify conserved and novel miRNAs and their target genes by combined small RNA and degradome sequencing at four inflorescence developmental stages. Results We used deep-sequencing, miRNA microarray assays and computational methods to identify, profile, and describe conserved and non-conserved miRNAs at four ear developmental stages, which resulted in identification of 22 conserved and 21-maize-specific miRNA families together with their corresponding miRNA*. Comparison of miRNA expression in these developmental stages revealed 18 differentially expressed miRNA families. Finally, a total of 141 genes (251 transcripts) targeted by 102 small RNAs including 98 miRNAs and 4 ta-siRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs. Moreover, the differentially expressed miRNAs-mediated pathways that regulate the development of ears were discussed. Conclusions This study confirmed 22 conserved miRNA families and discovered 26 novel miRNAs in maize. Moreover, we identified 141 target genes of known and new miRNAs and ta-siRNAs. Of these, 72 genes (117 transcripts) targeted by 62 differentially expressed miRNAs may attribute to the development of maize ears. Identification and characterization of these important classes of regulatory genes in maize may improve our understanding of molecular mechanisms controlling ear development

A Genome-Wide SNP Scan Reveals Novel Loci for Egg Production and Quality Traits in White Leghorn and Brown-Egg Dwarf Layers

Availability of the complete genome sequence as well as high-density SNP genotyping platforms allows genome-wide association studies (GWAS) in chickens. A high-density SNP array containing 57,636 markers was employed herein to identify associated variants underlying egg production and quality traits within two lines of chickens, i.e., White Leghorn and brown-egg dwarf layers. For each individual, age at first egg (AFE), first egg weight (FEW), and number of eggs (EN) from 21 to 56 weeks of age were recorded, and egg quality traits including egg weight (EW), eggshell weight (ESW), yolk weight (YW), eggshell thickness (EST), eggshell strength (ESS), albumen height(AH) and Haugh unit(HU) were measured at 40 and 60 weeks of age. A total of 385 White Leghorn females and 361 brown-egg dwarf dams were selected to be genotyped. The genome-wide scan revealed 8 SNPs showing genome-wise significant (P<1.51E-06, Bonferroni correction) association with egg production and quality traits under the Fisher's combined probability method. Some significant SNPs are located in known genes including GRB14 and GALNT1 that can impact development and function of ovary, but more are located in genes with unclear functions in layers, and need to be studied further. Many chromosome-wise significant SNPs were also detected in this study and some of them are located in previously reported QTL regions. Most of loci detected in this study are novel and the follow-up replication studies may be needed to further confirm the functional significance for these newly identified SNPs

Different acid pretreatments at room temperature boost selective saccharification of lignocellulose via fast pyrolysis

Fermentable sugars are a group of pivotal intermediates and platform compounds achieved by the conversion of lignocellulose. Fast pyrolysis, as a little-explored way to liberate levoglucosan from biomass, may have a potential capability to overcome the technical barriers and fundamental limitations for efficient saccharification. Pretreatment prior to fast pyrolysis is essential to improve levoglucosan yield from lignocellulose. Contrary to typical high-temperature acid pretreatments, a pretreatment under mild conditions was evaluated and optimized, where different acid (formic acid, acetic acid, oxalic acid, nitric acid, phosphoric acid, sulphuric acid and hydrochloric acid) were employed at room temperature prior to fast pyrolysis of lignocellulose. Due to the alteration of chemical compositions and physical structures of biomass, especially the elimination of alkali and alkaline earth metals, the levoglucosan yield of dilute acid pretreated biomass was improved remarkably as compared with that of raw material, meanwhile claimed that acid pretreatments at room temperature had an enough capability in efficient utilization of biomass. In sum, this study offered a novel and economical strategy for selective saccharification of lignocellulose for industrialized bio-refinery

Extended Model on Structural Stability and Robustness to Bounded Rationality

In this article, we focus on an extended model M¯ of bounded rationality. Based on a rationality function with lower semicontinuity, we analyze the relationship between structural stability and robustness of Ω¯. To further demonstrate the applicability of our theory, we introduce a model Ω¯0 containing an abstract rationality function and generalize abstract fuzzy economies. We demonstrate the structural stability of the extended model Ω¯0 at ξ¯,ɛ. That is to say, Ω¯0 is robust to the ξ¯,ɛ-equilibria

Catalytic co-pyrolysis of cellulose and waste polyoxymethylene to improve producing pyridines compounds over commercial HZSM-5 zeolites under ammonia atmosphere

Polyoxymethylene resin, one of the five major engineering materials with excellent comprehensive performance, was widely used in the industry. Pyridines, a kind of important heterocyclic compounds, were widely used as substrates for synthesis pharmaceutical, agro-chemical and dye industries. In this study, N-containing chemicals could be produced from waste polyoxymethylene (POM) plastic and cellulose via catalytic pyrolysis over commercial zeolite under ammonia atmosphere. Zeolite acidity and pyrolysis temperature affected product distribution significantly. Suitable catalyst for pyridines production was HZSM-5 (Si/Al = 83.3), and lower temperature (500 degrees C) prefer to form pyridines, nitriles and pyrroles and higher temperature could increase pyridines selectivity while decreased its yield. In addition, significant synergetic effects have been observed when cellulose was added, which improved pyridines yield by 40.64 % to 11.32 C% at the mixing weight ratio of cellulose to POM of 5:1. The synergistic effect between cellulose and POM for enhancing pyridines production were that POM pyrolytic intermediate (HCHO) can be used not only as substrate to form pyridines but also as an alkylation reagent to produce alkylation substituted pyridines. Catalytic pyrolysis with ammonia process has been proved to be a promising method for producing N-containing chemicals from biomass and wasted oxygencontaining plastics