Deep sequencing reveals important roles of microRNAs in response to drought and salinity stress in cotton

Drought and salinity are two major environmental factors adversely affecting plant growth and productivity. However, the regulatory mechanism is unknown. In this study, the potential roles of small regulatory microRNAs (miRNAs) in cotton response to those stresses were investigated. Using next-generation deep sequencing, a total of 337 miRNAs with precursors were identified, comprising 289 known miRNAs and 48 novel miRNAs. Of these miRNAs, 155 miRNAs were expressed differentially. Target prediction, Gene Ontology (GO)-based functional classification, and Kyoto Encyclopedia of Genes and Genomes (KEGG)-based functional enrichment show that these miRNAs might play roles in response to salinity and drought stresses through targeting a series of stress-related genes. Degradome sequencing analysis showed that at least 55 predicted target genes were further validated to be regulated by 60 miRNAs. CitationRank-based literature mining was employed to determinhe the importance of genes related to drought and salinity stress. The NAC, MYB, and MAPK families were ranked top under the context of drought and salinity, indicating their important roles for the plant to combat drought and salinity stress. According to target prediction, a series of cotton miRNAs are associated with these top-ranked genes, including miR164, miR172, miR396, miR1520, miR6158, ghr-n24, ghr-n56, and ghr-n59. Interestingly, 163 cotton miRNAs were also identified to target 210 genes that are important in fibre development. These results will contribute to cotton stress-resistant breeding as well as understanding fibre development

Formation of Highly Oxidized Radicals and Multifunctional Products from the Atmospheric Oxidation of Alkylbenzenes

Aromatic hydrocarbons contribute significantly to tropospheric ozone and secondary organic aerosols (SOA). Despite large efforts in elucidating the formation mechanism of aromatic-derived SOA, current models still substantially underestimate the SOA yields when comparing to field measurements. Here we present a new, up to now undiscovered pathway for the formation of highly oxidized products from the OH-initiated oxidation of alkyl benzenes based on theoretical and experimental investigations. We propose that unimolecular H-migration followed by O-2-addition, a so-called autoxidation step, can take place in bicyclic peroxy radicals (BPRs), which are important intermediates of the OH -initiated oxidation of aromatic compounds. These autoxidation steps lead to the formation of highly oxidized multifunctional compounds (HOMs), which are able to form SOA. Our theoretical calculations suggest that the intramolecular H-migration in BPRs of substituted benzenes could be fast enough to compete with bimolecular reactions with HO2 radicals or NO under atmospheric conditions. The theoretical findings are experimentally supported by flow tube studies using chemical ionization mass spectrometry to detect the highly oxidized peroxy radical intermediates and closed-shell products. This new unimolecular BPR route to form HOMs in the gas phase enhances our understanding of the aromatic oxidation mechanism, and contributes significantly to a better understanding of aromatic-derived SOA in urban areas.Peer reviewe

Single-Locus and Multi-Locus Genome-Wide Association Studies in the Genetic Dissection of Fiber Quality Traits in Upland Cotton (Gossypium hirsutum L.)

A major breeding target in Upland cotton (Gossypium hirsutum L.) is to improve the fiber quality. To address this issue, 169 diverse accessions, genotyped by 53,848 high-quality single-nucleotide polymorphisms (SNPs) and phenotyped in four environments, were used to conduct genome-wide association studies (GWASs) for fiber quality traits using three single-locus and three multi-locus models. As a result, 342 quantitative trait nucleotides (QTNs) controlling fiber quality traits were detected. Of the 342 QTNs, 84 were simultaneously detected in at least two environments or by at least two models, which include 29 for fiber length, 22 for fiber strength, 11 for fiber micronaire, 12 for fiber uniformity, and 10 for fiber elongation. Meanwhile, nine QTNs with 10% greater sizes (R2) were simultaneously detected in at least two environments and between single- and multi-locus models, which include TM80185 (D13) for fiber length, TM1386 (A1) and TM14462 (A6) for fiber strength, TM18616 (A7), TM54735 (D3), and TM79518 (D12) for fiber micronaire, TM77489 (D12) and TM81448 (D13) for fiber uniformity, and TM47772 (D1) for fiber elongation. This indicates the possibility of marker-assisted selection in future breeding programs. Among 455 genes within the linkage disequilibrium regions of the nine QTNs, 113 are potential candidate genes and four are promising candidate genes. These findings reveal the genetic control underlying fiber quality traits and provide insights into possible genetic improvements in Upland cotton fiber quality

Fluorescent Nanodiamonds for Tracking Single Polymer Particles in Cells and Tissues

Polymer nanoparticles are widely used in drug delivery and are also a potential concern due to the increased burden of nano- or microplastics in the environment. In order to use polymer nanoparticles safely and understand their mechanism of action, it is useful to know where within cells and tissues they end up. To this end, we labeled polymer nanoparticles with nanodiamond particles. More specifically, we have embedded nanodiamond particles in the polymer particles and characterized the composites. Compared to conventional fluorescent dyes, these labels have the advantage that nanodiamonds do not bleach or blink, thus allowing long-term imaging and tracking of polymer particles. We have demonstrated this principle both in cells and entire liver tissues.</p

A Chinese SCA36 pedigree analysis of NOP56 expansion region based on long-read sequencing

Introduction: Spinocerebellar ataxias 36 (SCA36) is the neurodegenerative disease caused by the GGCCTG Hexanucleotide repeat expansions in NOP56, which is too long to sequence using short-read sequencing. Single molecule real time (SMRT) sequencing can sequence across disease-causing repeat expansion. We report the first long-read sequencing data across the expansion region in SCA36.Methods: We collected and described the clinical manifestations and imaging features of Han Chinese pedigree with three generations of SCA36. Also, we focused on structural variation analysis for intron 1 of the NOP56 gene by SMRT sequencing in the assembled genome.Results: The main clinical features of this pedigree are late-onset ataxia symptoms, with a presymptomatic presence of affective and sleep disorders. In addition, the results of SMRT sequencing showed the specific repeat expansion region and demonstrated that the region was not composed of single GGCCTG hexanucleotides and there were random interruptions.Discussion: We extended the phenotypic spectrum of SCA36. We applied SMRT sequencing to reveal the correlation between genotype and phenotype of SCA36. Our findings indicated that long-read sequencing is well suited to characterize known repeat expansion

Experiments and CFD-DEM simulations of cohesive particles sedimentation in stilled fluid

Particle agglomeration is observed in slurry loop reactors due to the presence of cohesive force between the swollen polyethylene (PE) particles, which has direct impact on the hydrodynamics predictions. However, a qualitative study of the cohesive forces in the suspensions of swollen PE particle at the microscopic level is still lacking. In this study, a simulation contrast experiment method for quantification of cohesive force is proposed. The simulation method is based on a coupled computational fluid dynamics and discrete element method (CFD-DEM) approach, which have been used to study and explain the effects of cohesion on fluidization of particles. The DEM allows the dynamic simulation of the solid phase motion by tracking individual particles, whereas a CFD algorithm is commonly used to simulate the flow field of the continuous fluid phase. The swollen PE particles, initially arranged within a cylinder region in a quiescent hot dodecane, are made to fall, and their sedimentation induces the liquid flow around them. The interactions between the particle motion and the liquid flow are favorably compared with the experimental data, demonstrating the value of the cohesive energy density for the swollen PE particles is between 4000 J/m(3) and 5000 J/m(3). (C) 2019 Published by Elsevier B.V

New Mechanism for the Atmospheric Oxidation of Dimethyl Sulfide. The Importance of Intramolecular Hydrogen Shift in a CH₃SCH₂OO Radical

Theoretical study has been carried out on the fate of methylthiomethylperoxy radical (CH₃SCH₂OO, <b>MSP</b>) in the atmosphere. The intramolecular H-shift followed by recombination with O₂, <b>MSP</b> → CH₂SCH₂OOH → OOCH₂SCH₂OOH (<b>MSPO</b>_<b>2</b>), is found to be fast enough, that is, 2.1 s^–1 at 293 K, to compete with and even surpass the possible bimolecular reactions of <b>MSP</b> with NO_<i>x</i>, HO₂, and RO₂ in the remote marine atmosphere. <b>MSPO</b>_<b>2</b> would also undergo another intramolecular H-shift and decompose to the most important intermediate HOOCH₂SCHO instead of the CH₃SCH₂O radical. HOOCH₂SCHO would be further oxidized via the route as HOOCH₂SCO (by OH radical) → HOOCH₂S (by decomposition) → HOOCH₂SO (by O₃ or NO₂) → HOOCH₂SO₂ (by O₃ and NO₂) → OH + CH₂O + SO₂ (by decomposition). Our calculations suggest a drastically different oxidation mechanism for dimethyl sulfide (CH₃SCH₃, DMS) in the remote marine atmosphere

Atmospheric Oxidation Mechanism of Benzene. Fates of Alkoxy Radical Intermediates and Revised Mechanism

The fate of alkoxy radicals formed in the atmospheric oxidation of benzene initiated by OH radical is investigated by using quantum chemistry and kinetics calculations. The two alkoxy radicals (R2 and R3), formed from the commonly accepted bicyclic radical intermediates, are found to undergo ring-closure preferentially, in addition to the ring-breakage, as suggested in previous studies. The ratio between the ring-closure and ring-breakage is ∼2:1. The ring-closure route will lead to equal amounts of glyoxal and 2,3-epoxybutandial, while the ring-breakage route leads to glyoxal and butenedial. Overall, the new mechanism suggests the yield of glyoxal to be three times that of butenedial, consistent with the previous experimental measurements. The new mechanism calls for the search of the newly proposed product 2,3-epoxybutandial

MicroRNA expression profiles during cotton (Gossypium hirsutum L) fiber early development

The role of microRNAs (miRNAs) during cotton fiber development remains unclear. Here, a total of54 miRNAs belonging to 39 families were selected to characterize miRNA regulatory mechanism in eight different fiber development stages in upland cotton cv BM-1. Among 54 miRNAs, 18 miRNAs were involved in cotton fiber initiation and eight miRNAs were related to fiber elongation and secondary wall biosynthesis. Additionally, 3,576 protein-coding genes were candidate target genesof these miRNAs, which are potentially involved in cotton fiber development. We also investigatedthe regulatory network of miRNAs and corresponding targets in fiber initiation and elongation, and secondary wall formation. Our Gene Ontology-based term classification and KEGG-based pathway enrichment analyses showed that the miRNA targets covered 220 biological processes, 67 molecular functions, 45 cellular components, and 10 KEGG pathways. Three of ten KEGG pathways were involved in lignan synthesis, cell elongation, and fatty acid biosynthesis, all of which have important roles in fiber development. Overall, our study shows the potential regulatory roles of miRNAs in cotton fiber development and the importance of miRNAs in regulating different cell types. This is helpful to design miRNA-based biotechnology for improving fiber quality and yield