Identification of microRNAs Actively Involved in Fatty Acid Biosynthesis in Developing Brassica napus Seeds Using High-Throughput Sequencing

Seed development has a critical role during the spermatophyte life cycle. In Brassica napus, a major oil crop, fatty acids are synthesized and stored in specific tissues during embryogenesis, and understanding the molecular mechanism underlying fatty acid biosynthesis during seed development is an important research goal. In this study, we constructed three small RNA libraries from early seeds at 14, 21 and 28 days after flowering (DAF) and used high-throughput sequencing to examine microRNA (miRNA) expression. A total of 85 known miRNAs from 30 families and 1,160 novel miRNAs were identified, of which 24, including 5 known and 19 novel miRNAs, were found to be involved in fatty acid biosynthesis. bna-miR156b, bna-miR156c, bna-miR156g, novel_mir_1706, novel_mir_1407, novel_mir_173, and novel_mir_104 were significantly down-regulated at 21 DAF and 28 DAF, whereas bna-miR159, novel_mir_1081, novel_mir_19 and novel_mir_555 were significantly up-regulated. In addition, we found that some miRNAs regulate functional genes that are directly involved in fatty acid biosynthesis and that other miRNAs regulate the process of fatty acid biosynthesis by acting on a large number of transcription factors. The miRNAs and their corresponding predicted targets were partially validated by quantitative RT-PCR. Our data suggest that diverse and complex miRNAs are involved in the seed development process and that miRNAs play important roles in fatty acid biosynthesis during seed development

Discovery of Stable and Selective Antibody Mimetics from Combinatorial Libraries of Polyvalent, Loop-Functionalized Peptoid Nanosheets.

The ability of antibodies to bind a wide variety of analytes with high specificity and high affinity makes them ideal candidates for therapeutic and diagnostic applications. However, the poor stability and high production cost of antibodies have prompted exploration of a variety of synthetic materials capable of specific molecular recognition. Unfortunately, it remains a fundamental challenge to create a chemically diverse population of protein-like, folded synthetic nanostructures with defined molecular conformations in water. Here we report the synthesis and screening of combinatorial libraries of sequence-defined peptoid polymers engineered to fold into ordered, supramolecular nanosheets displaying a high spatial density of diverse, conformationally constrained peptoid loops on their surface. These polyvalent, loop-functionalized nanosheets were screened using a homogeneous Förster resonance energy transfer (FRET) assay for binding to a variety of protein targets. Peptoid sequences were identified that bound to the heptameric protein, anthrax protective antigen, with high avidity and selectivity. These nanosheets were shown to be resistant to proteolytic degradation, and the binding was shown to be dependent on the loop display density. This work demonstrates that key aspects of antibody structure and function-the creation of multivalent, combinatorial chemical diversity within a well-defined folded structure-can be realized with completely synthetic materials. This approach enables the rapid discovery of biomimetic affinity reagents that combine the durability of synthetic materials with the specificity of biomolecular materials

Effects of Different Surface Heat Transfer Coefficients on Predicted Heating and Cooling Loads towards Sustainable Building Design

The transfer of surface heat between a building and the outdoor environment is the energy transfer channel and it is important for the energy efficiency of buildings. Early stage building design is a critical stage and it can directly determine the energy consumption by a building. Therefore, selecting appropriate surface heat transfer coefficients (SHTCs) is a key issue in building energy consumption prediction. In this study, EnergyPlus was employed to investigate the building load in Chinese cities with different SHTCs: (1) constant SHTCs based on national standards; and (2) dynamically changing SHTCs based on the Thermal Analysis Research Program (TARP). Based on investigations of the hourly load, daily cumulative load in a typical day, and annual cumulative load with different SHTCs, corrections for the annual cumulative load were obtained according to the relative deviations between the results produced with the TARP model and traditional SHTCs. The greatest relative deviations were 67.5% and 25.3% for the building shape factor φ = 0.49 and 0.29 in Lhasa. The relative deviations were 13.3% and 12.0% for φ = 0.49 in Xi’an and Beijing, respectively. Corrections were not essential for other conditions because the relative deviations were lower than 5.0%. Considering the current characteristics of engineering calculations and the need to obtain more accurate design results, dynamically changing SHTCs should be applied. These correction factors can obtain more accurate results for the current building energy efficiency system with traditional SHTCs

Effects of Different Surface Heat Transfer Coefficients on Predicted Heating and Cooling Loads towards Sustainable Building Design

The transfer of surface heat between a building and the outdoor environment is the energy transfer channel and it is important for the energy efficiency of buildings. Early stage building design is a critical stage and it can directly determine the energy consumption by a building. Therefore, selecting appropriate surface heat transfer coefficients (SHTCs) is a key issue in building energy consumption prediction. In this study, EnergyPlus was employed to investigate the building load in Chinese cities with different SHTCs: (1) constant SHTCs based on national standards; and (2) dynamically changing SHTCs based on the Thermal Analysis Research Program (TARP). Based on investigations of the hourly load, daily cumulative load in a typical day, and annual cumulative load with different SHTCs, corrections for the annual cumulative load were obtained according to the relative deviations between the results produced with the TARP model and traditional SHTCs. The greatest relative deviations were 67.5% and 25.3% for the building shape factor φ = 0.49 and 0.29 in Lhasa. The relative deviations were 13.3% and 12.0% for φ = 0.49 in Xi’an and Beijing, respectively. Corrections were not essential for other conditions because the relative deviations were lower than 5.0%. Considering the current characteristics of engineering calculations and the need to obtain more accurate design results, dynamically changing SHTCs should be applied. These correction factors can obtain more accurate results for the current building energy efficiency system with traditional SHTCs

Designed Metal-Containing Peptoid Membranes as Enzyme Mimetics for Catalytic Organophosphate Degradation.

The detoxification of lethal organophosphate (OP) residues in the environment is crucial to prevent human exposure and protect modern society. Despite serving as excellent catalysts for OP degradation, natural enzymes require costly preparation and readily deactivate upon exposure to environmental conditions. Herein, we designed and prepared a series of phosphotriesterase mimics based on stable, self-assembled peptoid membranes to overcome these limitations of the enzymes and effectively catalyze the hydrolysis of dimethyl p-nitrophenyl phosphate (DMNP)─a nerve agent simulant. By covalently attaching metal-binding ligands to peptoid N-termini, we attained enzyme mimetics in the form of surface-functionalized crystalline nanomembranes. These nanomembranes display a precisely controlled arrangement of coordinated metal ions, which resemble the active sites found in phosphotriesterases to promote DMNP hydrolysis. Moreover, using these highly programmable peptoid nanomembranes allows for tuning the local chemical environment of the coordinated metal ion to achieve enhanced hydrolysis activity. Among the crystalline membranes that are active for DMNP degradation, those assembled from peptoids containing bis-quinoline ligands with an adjacent phenyl side chain showed the highest hydrolytic activity with a 219-fold rate acceleration over the background, demonstrating the important role of the hydrophobic environment in proximity to the active sites. Furthermore, these membranes exhibited remarkable stability and were able to retain their catalytic activity after heating to 60 °C and after multiple uses. This work provides insights into the principal features to construct a new class of biomimetic materials with high catalytic efficiency, cost-effectiveness, and reusability applied in nerve agent detoxification

Genome-Wide Analysis of the PYL Gene Family and Identification of PYL Genes That Respond to Abiotic Stress in Brassica napus

Abscisic acid (ABA) is an endogenous phytohormone that plays important roles in the regulation of plant growth, development, and stress responses. The pyrabactin resistance 1-like (PYR/PYL) protein is a core regulatory component of ABA signaling networks in plants. However, no details regarding this family in Brassica napus are available. Here, 46 PYLs were identified in the B. napus genome. Based on phylogenetic analysis, BnPYR1 and BnPYL1-3 belong to subfamily I, BnPYL7-10 belong to subfamily II, and BnPYL4-6 and BnPYL11-13 belong to subfamily III. Analysis of BnPYL conserved motifs showed that every subfamily contained four common motifs. By predicting cis-elements in the promoters, we found that all BnPYL members contained hormone- and stress-related elements and that expression levels of most BnPYLs were relatively higher in seeds at the germination stage than those in other organs or at other developmental stages. Gene Ontology (GO) enrichment showed that BnPYL genes mainly participate in responses to stimuli. To identify crucial PYLs mediating the response to abiotic stress in B. napus, expression changes in 14 BnPYL genes were determined by quantitative real-time RT-PCR after drought, heat, and salinity treatments, and identified BnPYR1-3, BnPYL1-2, and BnPYL7-2 in respond to abiotic stresses. The findings of this study lay a foundation for further investigations of PYL genes in B. napus

Underway mapping of coastal seawater pH using an automated shipboard analyzer with spectrophotometric detection

Highlights • High-precision spectrophotometric determination of pH. • Robust automated field-deployable analyzer for mapping pH. • Accurate pH measurement of dynamic estuarine-coastal samples. • A powerful monitoring tool for addressing ocean acidification and facilitating marine carbon dioxide removal. Abstract The development of field-deployable methods and instruments for the measurement of pH and other carbonate parameters is important for the assessment of the marine carbon cycle, ocean acidification and marine carbon dioxide removal techniques. In this study, a high-precision fully automated integrated syringe-pump-based environmental-water analyzer for pH (iSEA-pH) was developed. The pH is determined spectrophotometrically using purified indicator dye with a high precision (better than ±0.001) and high frequency (3.5 min/sample). For the short-term analysis, the measurement frequency was 18 h−1, which revealed pH = 7.8148 ± 0.0005 (n = 104) for aged surface seawater (S = 35) from the western Pacific. For long-term analysis, the measurement frequency was 2 h−1 for 4 days, and the results showed that pH = 7.8148 ± 0.0010 (n = 200). Three commonly used pH indicators (meta-cresol purple, thymol blue and phenol red) were purified with improved flash chromatography procedures. The autonomous iSEA-pH can automatically correct for the influence of temperature, salinity and other factors on pH measurements to achieve rapid and accurate on-site measurements, which meet the “climate” goal of the Global Ocean Acidification Observing Network (uncertainty is ±0.003). Three identical iSEA-pH systems were developed and successfully applied in mesocosm experiments and several coastal and open ocean cruises with excellent in field performance

Genome-Wide Identification of the LAC Gene Family and Its Expression Analysis Under Stress in <i>Brassica napus</i>

Lignin is an important biological polymer in plants that is necessary for plant secondary cell wall ontogenesis. The laccase (LAC) gene family catalyzes lignification and has been suggested to play a vital role in the plant kingdom. In this study, we identified 45 LAC genes from the Brassica napus genome (BnLACs), 25 LAC genes from the Brassica rapa genome (BrLACs) and 8 LAC genes from the Brassica oleracea genome (BoLACs). These LAC genes could be divided into five groups in a cladogram and members in same group had similar structures and conserved motifs. All BnLACs contained hormone- and stress- related elements determined by cis-element analysis. The expression of BnLACs was relatively higher in the root, seed coat and stem than in other tissues. Furthermore, BnLAC4 and its predicted downstream genes showed earlier expression in the silique pericarps of short silique lines than long silique lines. Three miRNAs (miR397a, miR397b and miR6034) target 11 BnLACs were also predicted. The expression changes of BnLACs under series of stresses were further investigated by RNA sequencing (RNA-seq) and quantitative real-time polymerase chain reaction (qRT-PCR). The study will give a deeper understanding of the LAC gene family evolution and functions in B. napus.</i

In Liquid Infrared Scattering Scanning Near-Field Optical Microscopy for Chemical and Biological Nanoimaging

Imaging biological systems with simultaneous intrinsic chemical specificity and nanometer spatial resolution in their typical native liquid environment has remained a long-standing challenge. Here, we demonstrate a general approach of chemical nanoimaging in liquid based on infrared scattering scanning near-field optical microscopy (IR s-SNOM). It is enabled by combining AFM operation in a fluid cell with evanescent IR illumination via total internal reflection, which provides spatially confined excitation for minimized IR water absorption, reduced far-field background, and enhanced directional signal emission and sensitivity. We demonstrate in-liquid IR s-SNOM vibrational nanoimaging and conformational identification of catalase nanocrystals and spatio-spectral analysis of biomimetic peptoid sheets with monolayer sensitivity and chemical specificity at the few zeptomole level. This work establishes the principles of in-liquid and in situ IR s-SNOM spectroscopic chemical nanoimaging and its general applicability to biomolecular, cellular, catalytic, electrochemical, or other interfaces and nanosystems in liquids or solutions