Comparative transcriptome analysis uncovers regulatory roles of long non-coding RNAs involved in resistance to powdery mildew in melon.

BACKGROUND: Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs with more than 200 nucleotides in length, which play vital roles in a wide range of biological processes. Powdery mildew disease (PM) has become a major threat to the production of melon. To investigate the potential roles of lncRNAs in resisting to PM in melon, it is necessary to identify lncRNAs and uncover their molecular functions. In this study, we compared the lncRNAs between a resistant and a susceptible melon in response to PM infection. RESULTS: It is reported that 11,612 lncRNAs were discovered, which were distributed across all 12 melon chromosomes, and > 85% were from intergenic regions. The melon lncRNAs have shorter transcript lengths and fewer exon numbers than protein-coding genes. In addition, a total of 407 and 611 lncRNAs were found to be differentially expressed after PM infection in PM-susceptible and PM-resistant melons, respectively. Furthermore, 1232 putative targets of differently expressed lncRNAs (DELs) were discovered and gene ontology enrichment (GO) analysis showed that these target genes were mainly enriched in stress-related terms. Consequently, co-expression patterns between LNC_018800 and CmWRKY21, LNC_018062 and MELO3C015771 (glutathione reductase coding gene), LNC_014937 and CmMLO5 were confirmed by qRT-PCR. Moreover, we also identified 24 lncRNAs that act as microRNA (miRNA) precursors, 43 lncRNAs as potential targets of 22 miRNA families and 13 lncRNAs as endogenous target mimics (eTMs) for 11 miRNAs. CONCLUSION: This study shows the first characterization of lncRNAs involved in PM resistance in melon and provides a starting point for further investigation into the functions and regulatory mechanisms of lncRNAs in the resistance to PM.

Symplastic phloem loading in poplar.

Sap is driven through phloem sieve tubes by an osmotically generated pressure gradient between source and sink tissues. In many plants, source pressure results from thermodynamically active loading in which energy is used to transfer sucrose (Suc) from mesophyll cells to the phloem of leaf minor veins against a concentration gradient. However, in some species, almost all trees, correlative evidence suggests that sugar migrates passively through plasmodesmata from mesophyll cells into the sieve elements. The possibility of alternate loading mechanisms has important ramifications for the regulation of phloem transport and source-sink interactions. Here, we provide experimental evidence that, in gray poplar (Populus tremula × Populus alba), Suc enters the phloem through plasmodesmata. Transgenic plants were generated with yeast invertase in the cell walls to prevent Suc loading by this route. The constructs were driven either by the constitutive 35S promoter or the minor vein-specific galactinol synthase promoter. Transgenic plants grew at the same rate as the wild type without symptoms of loading inhibition, such as accumulation of carbohydrates or leaf chlorosis. Rates of photosynthesis were normal. In contrast, alfalfa (Medicago sativa) plants, which have limited numbers of plasmodesmata between mesophyll and phloem, displayed typical symptoms of loading inhibition when transformed with the same DNA constructs. The results are consistent with passive loading of Suc through plasmodesmata in poplar. We also noted defense-related symptoms in leaves of transgenic poplar when the plants were abruptly exposed to excessively high temperatures, adding to evidence that hexose is involved in triggering the hypersensitive response.

Total synthesis and determination of the absolute configuration of rakicidin A.

Rakicidin A is a cyclic depsipeptide that has exhibited unique growth inhibitory activity against chronic myelogenous leukemia stem cells. Furthermore, rakicidin A has five chiral centers with unknown stereochemical assignment, and thus, can be represented by one of 32 possible stereoisomers. To predict the most probable stereochemistry of rakicidin A, calculations and structural comparison with natural cyclic depsipeptides were applied. A total synthesis of the proposed structure was subsequently completed and highlighted by the creation of a sterically hindered ester bond (C1-C15) through trans-acylation from an easily established isomer (C1-C13). The analytic data of the synthetic target were consistent with that of natural rakicidin A, and then the absolute configuration of rakicidin A was assigned as 2S, 3S, 14S, 15S, 16R. This work suggests strategies for the determination of unknown chiral centers in other cyclic depsipeptides, such as rakicidin B, C, D, BE-43547, and vinylamycin, and facilitates the investigations of rakicidin A as an anticancer stem cell agent.

Mechanically Durable Superhydrophobic Strain Sensors with High Biocompatibility and Sensing Performance for Underwater Motion Monitoring.

Much progress has been made toward the development of wearable flexible strain sensors with high sensing performance to monitor human motion, but continuous function in harsh aqueous environments remains a significant challenge. A promising strategy has been the design of sensors with highly durable superhydrophobicity and maintenance of unique sensing properties. Herein, an extremely durable superhydrophobic strain sensor with an ultrawide sensing range was simply fabricated by directly brushing conductive carbon black nanoparticles (CBNPs) onto an elastic silicone rubber sheet (SS) with poly(dimethylsiloxane) (PDMS) coatings (i.e., SS/PDMS-CBNPs sensors). First, this method avoided the use of toxic solvents and a conventional prestretching treatment. Second, considering the easily destroyed rough structures and surface chemistry for conventional superhydrophobic sensors during practical applications, the prepared SS/PDMS-CBNP sensors showed excellent mechanical durability of both superhydrophobicity and sensing as examined by harsh abrasion (300 cycles), stretching (up to 200%), and ultrasonication (40 min) treatments. Third, the prepared superhydrophobic strain sensor exhibited high sensitivity (gauge factor of 101.75), high stretchability (0.015-460%), low hysteresis (83 ms), and long-term stability (10000 cycles). Fourth, the high biocompatibility of the SS/PDMS-CBNP sensor was demonstrated by rabbit skin irritation tests. Finally, the remarkable water-repellent and sensing properties of the SS/PDMS-CBNP sensor allowed its application to monitor a swimmer's real-time situation and send distress signals when needed.

Identification and characterization of melon circular RNAs involved in powdery mildew responses through comparative transcriptome analysis.

Circular RNAs (circRNAs) are a class of newly discovered non-coding RNAs that are typically derived from a genome's exonic, intronic, and intergenic regions. Recent studies of circRNAs in animals and plants have shown that circRNAs are vital in response to various abiotic and biotic stresses. Powdery mildew disease (PM) is a serious fungal disease threatening the melon industry. We performed whole transcriptome sequencing using the leaves of a PM-resistant (M1) and a PM-susceptible (B29) melon to identify circRNAs and determine their molecular functions. A total of 303 circRNAs were identified and >50% circRNAs were derived from exonic regions. Expression levels were significantly altered in 17 and 23 circRNAs after PM infections in B29 and M1, respectively. Melon circRNAs may participate in the response to biotic stimuli, oxidation reduction, metabolic processes, and the regulation of gene expression based on the functional annotation of circRNA parental genes. Furthermore, 27 circRNAs were predicted to be potential targets or 'sponges' for 18 microRNAs (miRNAs). Our results are the first to identify and characterize circRNA functions in melon and may contribute to a better understanding of the role and regulatory mechanisms of circRNAs in resisting PM.

Genome-wide characterization, evolutionary analysis of WRKY genes in Cucurbitaceae species and assessment of its roles in resisting to powdery mildew disease.

The WRKY proteins constitute a large family of transcription factors that have been known to play a wide range of regulatory roles in multiple biological processes. Over the past few years, many reports have focused on analysis of evolution and biological function of WRKY genes at the whole genome level in different plant species. However, little information is known about WRKY genes in melon (Cucumis melo L.). In the present study, a total of 56 putative WRKY genes were identified in melon, which were randomly distributed on their respective chromosomes. A multiple sequence alignment and phylogenetic analysis using melon, cucumber and watermelon predicted WRKY domains indicated that melon WRKY proteins could be classified into three main groups (I-III). Our analysis indicated that no recent duplication events of WRKY genes were detected in melon, and strong purifying selection was observed among the 85 orthologous pairs of Cucurbitaceae species. Expression profiles of CmWRKY derived from RNA-seq data and quantitative RT-PCR (qRT-PCR) analyses showed distinct expression patterns in various tissues, and the expression of 16 CmWRKY were altered following powdery mildew infection in melon. Besides, we also found that a total of 24 WRKY genes were co-expressed with 11 VQ family genes in melon. Our comparative genomic analysis provides a foundation for future functional dissection and understanding the evolution of WRKY genes in cucurbitaceae species, and will promote powdery mildew resistance study in melon.

Comparing emissions from a cattle pen as measured by two micrometeorological techniques.

Accurate measurement of ammonia (NH3) emissions from livestock pens is challenging. Two micrometeorological techniques, the integrated horizontal flux (IHF) and the backward Lagrangian stochastic (bLS) dispersion techniques were used to measure NH3 emissions from an isolated cattle pen (20 × 20 m) in Victoria, Australia. The bLS technique is simple and insensitive to the presence of animals, but typically gives discontinuous measurements due to the need for target wind directions and wind conditions above accepted thresholds. In contrast, the IHF technique as implemented here gives near-continuous measurements with no restriction on wind directions. However, IHF needs more complex field measurements, and there are ambiguities when applied to an animal pen due to the presence of animals. Over the 29 days of our experiment, we collected 124 coincidental bLS and IHF emission measurements from the pen (30-min each). We found no statistical difference in the bLS and IHF calculations when the IHF turbulent flux correction factor (TFcor) was set to 15%. Our results confirm that the IHF and bLS techniques, using independent sensors and having very different equipment layouts, gives nearly equivalent results. This suggests the choice of the two methods in future experiments can focus on their different strengths and weaknesses.

Genome-wide analysis of basic/helix-loop-helix gene family in peanut and assessment of its roles in pod development.

The basic/helix-loop-helix (bHLH) proteins constitute a superfamily of transcription factors that are known to play a range of regulatory roles in eukaryotes. Over the past few decades, many bHLH family genes have been well-characterized in model plants, such as Arabidopsis, rice and tomato. However, the bHLH protein family in peanuts has not yet been systematically identified and characterized. Here, 132 and 129 bHLH proteins were identified from two wild ancestral diploid subgenomes of cultivated tetraploid peanuts, Arachis duranensis (AA) and Arachis ipaensis (BB), respectively. Phylogenetic analysis indicated that these bHLHs could be classified into 19 subfamilies. Distribution mapping results showed that peanut bHLH genes were randomly and unevenly distributed within the 10 AA chromosomes and 10 BB chromosomes. In addition, 120 bHLH gene pairs between the AA-subgenome and BB-subgenome were found to be orthologous and 101 of these pairs were highly syntenic in AA and BB chromosomes. Furthermore, we confirmed that 184 bHLH genes expressed in different tissues, 22 of which exhibited tissue-specific expression. Meanwhile, we identified 61 bHLH genes that may be potentially involved in peanut-specific subterranean. Our comprehensive genomic analysis provides a foundation for future functional dissection and understanding of the regulatory mechanisms of bHLH transcription factors in peanuts.

Ammonia deposition in the neighbourhood of an intensive cattle feedlot in Victoria, Australia.

Intensive cattle feedlots are large emission sources of ammonia (NH3), but NH3 deposition to the landscape downwind of feedlots is not well understood. We conducted the first study in Australia to measure NH3 dry deposition within 1 km of a commercial beef cattle feedlot in Victoria. NH3 concentrations and deposition fluxes decreased exponentially with distance away from the feedlot. The mean NH3 concentrations decreased from 419 µg N m(-3) at 50 m to 36 µg N m(-3) at 1 km, while the mean NH3 dry deposition fluxes decreased from 2.38 µg N m(-2) s(-1) at 50 m to 0.20 µg N m(-2) s(-1) at 1 km downwind from the feedlot. These results extrapolate to NH3 deposition of 53.9 tonne N yr(-1) in the area within 1 km from the feedlot, or 67.5 kg N ha(-1) yr(-1) as an area-weighted mean, accounting for 8.1% of the annual NH3-N emissions from the feedlot. Thus NH3 deposition around feedlots is a significant nitrogen input for surrounding ecosystems. Researches need be conducted to evaluate the impacts of NH3 deposition on the surrounding natural or semi-naturals ecosystems and to reduce N fertilizer application rate for the surrounding crops by considering nitrogen input from NH3 deposition.

Effects of lignite application on ammonia and nitrous oxide emissions from cattle pens.

Beef cattle feedlots are a major source of ammonia (NH3) emissions from livestock industries. We investigated the effects of lignite surface applications on NH3 and nitrous oxide (N2O) emissions from beef cattle feedlot pens. Two rates of lignite, 3 and 6kgm(-2), were tested in the treatment pen. No lignite was applied in the control pen. Twenty-four Black Angus steers were fed identical commercial rations in each pen. We measured NH3 and N2O concentrations continuously from 4th Sep to 13th Nov 2014 using Quantum Cascade Laser (QCL) NH3 analysers and a closed-path Fourier Transform Infrared Spectroscopy analyser (CP-FTIR) in conjunction with the integrated horizontal flux method to calculate NH3 and N2O fluxes. During the feeding period, 16 and 26% of the excreted nitrogen (N) (240gNhead(-1)day(-1)) was lost via NH3 volatilization from the control pen, while lignite application decreased NH3 volatilization to 12 and 18% of the excreted N, for Phase 1 and Phase 2, respectively. Compared to the control pen, lignite application decreased NH3 emissions by approximately 30%. Nitrous oxide emissions from the cattle pens were small, 0.10 and 0.14gN2O-Nhead(-1)day(-1) (<0.1% of excreted N) for the control pen, for Phase 1 and Phase 2, respectively. Lignite application increased direct N2O emissions by 40 and 57%, to 0.14 and 0.22gN2O-Nhead(-1)day(-1), for Phase 1 and Phase 2, respectively. The increase in N2O emissions resulting from lignite application was counteracted by the lower indirect N2O emission due to decreased NH3 volatilization. Using 1% as a default emission factor of deposited NH3 for indirect N2O emissions, the application of lignite decreased total N2O emissions.

Structure-Activity Relationship Study of Rakicidins: Overcoming Chronic Myeloid Leukemia Resistance to Imatinib with 4-Methylester-Rakicidin A.

Natural product rakicidin A induces cell death in TKI-resistant chronic myelogenous leukemia (CML) cells. Therefore, 14 rakicidin A analogues were synthesized via a highly efficient combinatorial strategy and were evaluated against CML cell lines. The conjugated diene moiety was found to be crucial for the anti-CML activity of rakicidin A, and the changes in the configuration(s) at C-2, C-3, C-14, C-15, and C-16 resulted in lower levels of anti-CML activity. The most promising compound was 4-methylester rakicidin A (1a). Compared with rakicidin A, 1a exhibited 2.8-fold greater potency against the imatinib-resistant cell line K562/G(+) and approximately 100-fold enhanced potency compared with that of imatinib. Furthermore, compound 1a demonstrated a significantly lower resistance index against Ba/F3 cells expressing BCR-ABL(T315I) than bosutinib, dasatinib, nilotinib, and ponatinib, while 1a exhibited less effect on normal hematopoietic cells. Preliminary results indicated that 1a down-regulated caspase-3 and PARP, which contributes to its K562 cell inhibitory activity.

A new cost-effective method to mitigate ammonia loss from intensive cattle feedlots: application of lignite.

In open beef feedlot systems, more than 50% of dietary nitrogen (N) is lost as ammonia (NH3). Here we report an effective and economically-viable method to mitigate NH3 emissions by the application of lignite. We constructed two cattle pens (20 × 20 m) to determine the effectiveness of lignite in reducing NH3 emissions. Twenty-four steers were fed identical commercial rations in each pen. The treatment pen surface was dressed with 4.5 kg m(-2) lignite dry mass while no lignite was applied in the control pen. We measured volatilised NH3 concentrations using Ecotech EC9842 NH3 analysers in conjunction with a mass balance method to calculate NH3 fluxes. Application of lignite decreased NH3 loss from the pen by approximately 66%. The cumulative NH3 losses were 6.26 and 2.13 kg N head(-1) in the control and lignite treatment, respectively. In addition to the environmental benefits of reduced NH3 losses, the value of retained N nutrient in the lignite treated manure is more than $37 AUD head(-1) yr(-1), based on the current fertiliser cost and estimated cost of lignite application. We show that lignite application is a cost-effective method to reduce NH3 loss from cattle feedlots.

Measurement and mitigation of nitrous oxide emissions from a high nitrogen input vegetable system.

The emission and mitigation of nitrous oxide (N2O) from high nitrogen (N) vegetable systems is not well understood. Nitrification inhibitors are widely used to decrease N2O emissions in many cropping systems. However, most N2O flux measurements and inhibitor impacts have been made with small chambers and have not been investigated at a paddock-scale using micrometeorological techniques. We quantified N2O fluxes over a four ha celery paddock using open-path Fourier Transform Infrared spectroscopy in conjunction with a backward Lagrangian stochastic model, in addition to using a closed chamber technique. The celery crop was grown on a sandy soil in southern Victoria, Australia. The emission of N2O was measured following the application of chicken manure and N fertilizer with and without the application of a nitrification inhibitor 3, 4-dimethyl pyrazole phosphate (DMPP). The two techniques consistently demonstrated that DMPP application reduced N2O emission by 37-44%, even though the N2O fluxes measured by a micrometeorological technique were more than 10 times higher than the small chamber measurements. The results suggest that nitrification inhibitors have the potential to mitigate N2O emission from intensive vegetable production systems, and that the national soil N2O emission inventory assessments and modelling predictions may vary with gas measurement techniques.

The effect of using a geotextile in a monolithic (evapotranspiration) alternative landfill cover on the resulting water balance.

This paper examines the potential effects of a geotextile layer used in a lysimeter pan experiment conducted in a monolithic (evapotranspiration) soil cover trial on its resulting water balance performance. The geotextile was added to the base of the lysimeter to serve as a plant root barrier in order to delineate the root zone depth. Both laboratory data and numerical modelling results indicated that the geotextile creates a capillary barrier under certain conditions and retains more water in the soil above the soil/geotextile interface than occurs without a geotextile. The numerical modelling results also suggested that the water balance of the soil cover could be affected by an increase in plant transpiration taking up this extra water retained above the soil/geotextile interface. This finding has a practical implication on the full-scale monolithic cover design, as the absence of the geotextile in the full-scale cover may affect the associated water balance and hence cover performance. Proper consideration is therefore required to assess the final monolithic cover water balance performance if its design is based on the lysimeter results.