Molecular mechanism of salinity and waterlogging tolerance in mangrove Kandelia obovata.

Mangrove forests are colloquially referred to as "Earth's kidneys" and serve many important ecological and commercial functions. Salinity and waterlogging stress are the most important abiotic stressors restricting the growth and development of mangroves. Kandelia obovata (K. obovata) is the greatest latitudinally-distributed salt mangrove species in China.Here, morphology and transcriptomics were used to study the response of K. obovata to salt and waterlogging stress. In addition, weighted gene co-expression network analysis of the combined gene expression and phenotypic datasets was used to identify core salinity- and waterlogging-responsive modules. In this study, we observed that both high salinity and waterlogging significantly inhibited growth and development in K. obovata. Notably, growth was negatively correlated with salt concentration and positively correlated with waterlogging duration, and high salinity was significantly more inhibitive than waterlogging. A total of 7, 591 salt-responsive and 228 waterlogging-responsive differentially expressed genes were identified by RNA sequencing. Long-term salt stress was highly correlated with the measured physiological parameters while long-term waterlogging was poorly correlated with these traits. At the same time, 45 salinity-responsive and 16 waterlogging-responsive core genes were identified. All 61 core genes were mainly involved in metabolic and biosynthesis of secondary metabolites pathways. This study provides valuable insight into the molecular mechanisms of salinity and waterlogging tolerance in K. obovata, as well as a useful genetic resource for the improvement of mangrove stress tolerance using molecular breeding techniques.

Physiological and transcriptomic analysis of the mangrove species Kandelia obovata in response to flooding stress.

Flooding stress on mangroves is growing continually with rising sea level. In this study, the physiology and transcriptome of the mangrove species Kandelia obovata under flooding stress were analyzed. With increasing inundation time, malondialdehyde (MDA), superoxide dismutase (SOD), glutathione (GSH), soluble sugar (SS), soluble protein (SP), and proline (Pro) content declined, while peroxidase (POD) and ascorbate peroxidase (APX) activity rose significantly. According to the KEGG pathway enrichment analysis, upregulated differentially expressed genes (DEGs) were enriched in the plant hormone signaling pathway. Furthermore, MYB44 and MYB108 genes from the MYB transcription factor family and RAP2.12, DREB2B, and ERF4 genes from the AP2/ERF family were up-regulated under flooding conditions. A strong correlation was established between the expression levels of 12 DEGs under flooding stress and RNA sequencing data and was verified by qRT-PCR. These results provide new insights into the molecular mechanism of K. obovata in response to flooding stress.

Ion recognition properties of 2,2'-bibenzimidazole regulated by ammonium-modified pillar[5]arenes.

With the increasing issues of environmental degradation and health problem, the selective detection of toxic ions has attracted considerable attention from researchers. Chemical fluorescent sensors with the advantages of facile operation, high sensitivity, rapid response, and easy visualization are emerging as powerful detection tools towards ions. However, the selective recognition of ions is always hindered by the presence of other interfering substances. Herein, we show that supramolecular host-guest interaction based on a pillar[5]arene provides a new opportunity to regulate the ionic recognition properties of guest molecules. A pillar[5]arene-based host-guest complex HG was constructed through the host-guest interaction between ammonium functionalized pillar[5]arene (HAP5) and 2,2'-bibenzimidazole (G). The host-gust complex HG can realize the successive, highly selective, and sensitive detection of specific ions. It was found that only in the presence of HAP5, the sensitivity towards cations was evidently enhanced, and selective successive recognition for I- and HSO4- was achieved. Those results indicate that the introduction of HAP5 can effectively improve the ion recognition performance of 2,2'-bibenzimidazole, so it is a feasible strategy using supramolecular host-guest interaction to regulate the ionic recognition properties of guest molecules.

Learning to Extract Building Footprints From Off-Nadir Aerial Images.

Extracting building footprints from aerial images is essential for precise urban mapping with photogrammetric computer vision technologies. Existing approaches mainly assume that the roof and footprint of a building are well overlapped, which may not hold in off-nadir aerial images as there is often a big offset between them. In this paper, we propose an offset vector learning scheme, which turns the building footprint extraction problem in off-nadir images into an instance-level joint prediction problem of the building roof and its corresponding "roof to footprint" offset vector. Thus the footprint can be estimated by translating the predicted roof mask according to the predicted offset vector. We further propose a simple but effective feature-level offset augmentation module, which can significantly refine the offset vector prediction by introducing little extra cost. Moreover, a new dataset, Buildings in Off-Nadir Aerial Images (BONAI), is created and released in this paper. It contains 268,958 building instances across 3,300 aerial images with fully annotated instance-level roof, footprint, and corresponding offset vector for each building. Experiments on the BONAI dataset demonstrate that our method achieves the state-of-the-art, outperforming other competitors by 3.37 to 7.39 points in F1-score. The codes, datasets, and trained models are available at https://github.com/jwwangchn/BONAI.git.

Role of exogenous abscisic acid in freezing tolerance of mangrove Kandelia obovata under natural frost condition at near 32°N.

BACKGROUND: Mangroves possess substantial ecological, social, and economic functions in tropical and subtropical coastal wetlands. Kandelia obovata is the most cold-resistance species among mangrove plants, with a widespread distribution in China that ranges from Sanya (18° 12' N) to Wenzhou (28° 20' N). Here, we explored the temporal variations in physiological status and transcriptome profiling of K. obovata under natural frost conditions at ~ 32oN, as well as the positive role of exogenous abscisic acid (ABA) in cold resistance. RESULTS: The soluble sugar (SS) and proline (Pro) functioned under freezing stress, of which SS was more important for K. obovata. Consistently, up-regulated DEGs responding to low temperature were significantly annotated to glycometabolism, such as starch and sucrose metabolism and amino sugar and nucleotide sugar metabolism. Notably, the top 2 pathways of KEGG enrichment were phenylpropanoid biosynthesis and flavonoid biosynthesis. For the antioxidant system, POD in conjunction with CAT removed hydrogen peroxide, and CAT appeared to be more important. The up-regulated DEGs responding to low temperature and ABA were also found to be enriched in arginine and proline metabolism, starch and sucrose metabolism, and peroxisome. Moreover, ABA triggered the expression of P5CS and P5CR, but inhibited the ProDH expression, which might contribute to Pro accumulation. Interestingly, there was no significant change in malondialdehyde (MDA) content during the cold event (P > 0.05), suggesting foliar application of ABA effectively alleviated the adverse effects of freezing stress on K. obovata by activating the antioxidant enzyme activity and increasing osmolytes accumulation, such as Pro, and the outcome was proportional to ABA concentration. CONCLUSIONS: This study deepened our understanding of the physiological characters and molecular mechanisms underlying the response of K. obovata to natural frost conditions and exogenous ABA at the field level, which could provide a sound theoretical foundation for expanding mangroves plantations in higher latitudes, as well as the development coastal landscape.

IsoSeq and RNA-Seq analyses uncover the molecular response of Dalbergia odorifera T. Chen to low temperature.

In previous studies, we found young plants propagated from acclimated D. odorifera T. Chen trees displayed increased cold tolerance. To understand the molecular and physiological mechanisms underlying this phenomenon, we prepared acclimated and non-acclimated young D. odorifera T. Chen trees for physiological, RNA-Seq, and IsoSeq analyses. First, both the acclimated and non-acclimated young trees were grown in 10 ℃ condition, then treated at -3 ℃ for one day, and finally recovered at 10 ℃. The measurement of physiological parameters, including superoxide dismutase, peroxidase, malondialdehyde, thiobarbituric acid, and soluble sugar, showed that the physiological change of acclimated plants is smoother than non-acclimated plants. The RNA-Seq analyses pointed out that cold acclimation already fixed the different gene expression patterns of D. odorifera T. Chen trees. The hormone-related, secondary metabolic, and signal transduction related biological genes tend to show different expressions between the acclimated and non-acclimated D. odorifera T. Chen trees. Moreover, the change of gene expression for some biological processes, such as alpha-Linolenic acid metabolism and its response to hydrogen peroxide, seems to occur earlier in non-acclimated than acclimated plants. The ISOSeq analyses pointed out that alternative splicing (AS) of some genes was also found, and these AS events were predicted to play important roles in regulating different expression patterns between non-acclimated and acclimated plants. Therefore, according to the performance of this study, we are able to provide some novel understanding of cold tolerance enhanced by cold acclimation in perennial trees.

Integrative Analyses of Transcriptomics and Metabolomics in Sex Differentiation of Mulberry Flowers.

Sex determination and sex differentiation of plants are important physiological processes of plant development. Mulberry (Morus indica L.) is an important economic tree being cultivated in sericulture countries, and mulberry leaf is commonly used for sericulture. The transcriptomic and metabolomic differences between the staminate flowers (SFs) and pistillate flowers (PFs) of mulberry were investigated by RNA sequencing and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Overall, we uncovered 4,230 genes and 209 metabolites are significantly differentially expressed between the SFs and PFs of mulberry. The combined transcriptomic and metabolomic analysis revealed these differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) are involved in flavonoid biosynthesis, galactose metabolism, plant-pathogen interaction, and starch and sucrose metabolism, and these detected DEGs and DEMs may be associated with sex differentiation of mulberry through the regulation of the enrichment pathways, such as the MAPK pathway, flavonoid biosynthesis, galactose metabolism, plant-pathogen interaction, and starch and sucrose metabolism. This study will provide a rich source for the analysis of the molecular mechanism of mulberry sex differentiation processes.

RNA-seq and phytohormone analysis reveals the culm color variation of Bambusa oldhamii Munro.

BACKGROUND: The clumping bamboo Bambusa oldhamii Munro, known as "green bamboo", is famous for its edible bamboo shoots and fast-growing timber. The green and yellow striped-culm B. oldhamii variety, named B. oldhamii f. revoluta W.T. Lin & J. Y. Lin, is an attractive system for researching the culm color variation of B. oldhamii. METHODS: Millions of clean reads were generated and assembled into 604,900 transcripts, and 383,278 unigenes were acquired with RNA-seq technology. The quantification of ABA, IAA, JA, GA1, GA3, GA4, and GA7 was performed using HPLC-MS/MS platforms. RESULTS: Differential expression analysis showed that 449 unigenes were differentially expressed genes (DEGs), among which 190 DEGs were downregulated and 259 DEGs were upregulated in B. oldhamii f. revoluta. Phytohormone contents, especially GA1 and GA7, were higher in B. oldhamii. Approximately 21 transcription factors (TFs) were differentially expressed between the two groups: the bZIP, MYB, and NF-YA transcription factor families had the most DEGs, indicating that those TFs play important roles in B. oldhamii culm color variation. RNA-seq data were confirmed by quantitative RT-PCR analysis of the selected genes; moreover, phytohormone contents, especially those of ABA, GA1 and GA7, were differentially accumulated between the groups. Our study provides a basal gene expression and phytohormone analysis of B. oldhamii culm color variation, which could provide a solid fundamental theory for investigating bamboo culm color variation.

The rhizosphere effect of native legume Albizzia julibrissin on coastal saline soil nutrient availability, microbial modulation, and aggregate formation.

In the coastal zones, numerous ecological shelterbelt projects were conducted to protect against natural hazards. However, it is still not fully understood whether phytoremediation with native legume Albizzia julibrissin plantation can improve saline soil structural development or microbial community structure. In this study, a field experiment was conducted to investigate the responses of rhizosphere soil salinity, nutrients, bacterial community, and aggregate structure to A. julibrissin plantation in a recently reclaimed area along Zhejiang coast, China. After ~3-year plantation, rhizosphere soil pH and EC reduced to 8.25 and 0.14 dS·m-1, respectively, belonging to non-saline soil. Meanwhile, total organic carbon (TOC), permanganate-oxidizable carbon (POXC), total nitrogen (TN), alkali-hydrolyzable nitrogen (AN), and ammonium nitrogen (NH4+-N) were significantly increased in rhizosphere soil compared with bare land (P < 0.05). Consequently, rhizosphere soil had favorable habitat condition for copiotrophic bacterial taxa (e.g., Chloroflexi, Acidobacteria, and Bacteroidates), as well as high diversity, complex co-occurrence network, and catabolism related with nutrient cycling. The soil particle size of bare land was < 0.053 mm, while microaggregate (0.053-0.25 mm) and macroaggregate (0.25-2 mm) were formed in the rhizosphere and coupled with C accumulation and Fe removal. Soil aggregates were of great importance to soil fertility with more efficient bacterial network and biogeochemical cycles of nutrients. N-fixing Rhizobiales preferred to inhabit large soil particle and might primarily contribute to N accumulation. Generally, A. julibrissin was a suitable pioneer tree for mudflat reclamation projects, which effectively improved saline soil rhizosphere environment by reducing salinity, accumulating C and N, and promoting microbial community succession, as well as aggregate structure formation.

The complete chloroplast genome sequence of Bambusa stenoaurita (Bambusoideae).

Bambusa stenoaurita is an excellent sympodial bamboo species, which is cultivated for its shoots in some parts of China. Here, we sequenced and reported the complete chloroplast genome of B. stenoaurita for the first time. The complete chloroplast genome sequence of B. stenoaurita was generated by de novo assembly using whole-genome next-generation sequencing. The genome was 139,451 bp in total length, including a large single-copy region of 82,958 bp, a small single-copy region of 12,897 bp, a pair of invert repeats regions of 21,798 bp. The plastid genome contained 134 genes including 87 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 23 chloroplast genomes demonstrates that B. stenoaurita is closely related to B. emeiensis in Bambusoideae.

Nutrient uptake and assimilation in fragrant rosewood (Dalbergia odorifera T.C. Chen) seedlings in growing media with un-composted spent mushroom residue.

The purpose of this study was to detect nutrient uptake and assimilation in woody plants subjected to growing media with some peat replaced by spent mushroom residue (SMR). Fragrant rosewood (Dalbergia odorifera T.C. Chen) seedlings were cultured in five types of growing media with SMR and peat in volumetric proportions of 0% (control), 25%, 50%, 75%, and 100%. With the increase of SMR proportion, ammonium- and nitrate-nitrogen (N) concentrations declined but available phosphorus (P) concentration and electrical conductance both increased. Seedlings in the full SMR substrates showed obvious mortality. Seedlings in substrates with SMR in proportions higher than 25% showed symptoms of excessive N and P toxicities. The utilization efficiency for P was highest in the 25% SMR growing-media. Mineral N in substrates had a positive relationship with growth and biomass but not with glutamine synthetase activity. Available P was negatively related with acid phosphatase activity in both leaves and roots. Un-composted SMR can replace 25% of peat in growing media for fragrant rosewood seedlings, benefitting P uptake and assimilation.

Development of an Autonomous Unmanned Aerial Manipulator Based on a Real-Time Oriented-Object Detection Method.

Autonomous Unmanned Aerial Manipulators (UAMs) have shown promising potential in mobile 3-dimensional grasping applications, but they still suffer from some difficulties impeding their board applications, such as target detection and indoor positioning. For the autonomous grasping mission, the UAMs need ability to recognize the objects and grasp them. Considering the efficiency and precision, we present a novel oriented-object detection method called Rotation-SqueezeDet. This method can run on embedded-platforms in near real-time. Besides, this method can give the oriented bounding box of an object in images to enable a rotation-aware grasping. Based on this method, a UAM platform was designed and built. We have given the formulation, positioning, control, and planning of the whole UAM system. All the mechanical designs are fully provided as open-source hardware for reuse by the community. Finally, the effectiveness of the proposed scheme was validated in multiple experimental trials, highlighting its applicability of autonomous aerial rotational grasping in Global Positioning System (GPS) denied environments. We believe this system can be deployed to many potential workplaces which need UAM to accomplish difficult manipulation tasks.

Nab-paclitaxel plus S-1 as first-line followed by S-1 maintenance for advanced pancreatic adenocarcinoma: a single-arm phase II trial.

PURPOSE: We conducted a single-arm prospective phase II study to determine the efficacy and safety of the first-line treatment of advanced pancreatic cancer with nab-paclitaxel and S-1 followed by S-1 maintenance therapy. METHODS: Nab-paclitaxel was administered intravenously on days 1 and 8 at 120 mg/m2. S-1 at 120 mg/day (for surface area ≥ 1.5 m2), 100 mg/day (for surface area between 1.25-1.5 m2), and 80 mg/day (for surface area < 1.25 m2) were given two times daily on days 1-14 every 3 weeks. Patients who achieved response and stable disease after 6 cycles were given S-1 maintenance treatment in the same schedule until disease progression or unacceptable toxicity developed. The primary endpoint was objective response rate (ORR), and the secondary endpoints were disease control rate (DCR), progression-free survival (PFS), overall survival (OS) and safety. Between 01/2015 and 07/2017, 32 patients were enrolled. RESULTS: The ORR in the intention-to-treat (ITT) population (N = 32) was 53.1%, and the DCR was 87.5%. In the 30 evaluable patients, the ORR and DCR were 56.7 and 93.3%, respectively. The median follow-up time was 18 (range 12-36) months, the median PFS was 6.2 (range 4.4-8) months, and the median OS was 13.6 (range 8.7-18.5) months. The incidence of grade 3/4 neutropenia was 27.6%. Other grade 3 adverse events included 1 (3.1%) hand-foot syndrome, 1 (3.1%) rash and 2 (6.3%) diarrheas. CONCLUSIONS: Nab-paclitaxel and S-1 regimen has presented encouraging ORR, OS, and manageable toxicities as first-line therapy for advanced pancreatic cancer.

Response of submerged plant (Vallisneria spinulosa) clones to lead stress in the heterogenous soil.

In order to evaluate risk spreading among clones and antioxidant defence response of clonal ramets, turions of Vallisneria spinulosa, the dominant clonal plant of the submerged plant community in most of the lakes in Middle and Lower Reaches of Yangtze Rive, China, were planted in the heterogeneous soils contaminated with 40 and 160 microg g(-1) Pb (dry weight) in a greenhouse. After 100 d, the ranking order of tissue Pb concentrations in organs of the ortets (parental plants) was root>turion>rhizome>leaf, but that of tissue Pb quantities was leaf>turion>rhizome>root, due to their different biomass. Some of Pb was transferred from the ortets exposed in the Pb-supplied soil to leaves of the offspring growing in the favorable patch through rhizome (connective organ). A high foliar Pb concentration induced a significant decrease in superoxide dismutases, peroxidase and catalase activities. Catalase was more sensitive to Pb than the other two antioxidant enzymes. However, a low foliar Pb concentration, in the ortets exposed to 40 microg g(-1) Pb and in all of the offspring, slightly increased the activities of superoxide dismutases and peroxidase. The biomass accumulation per ortet and the biomasses percentages allocation to the roots and the leaves in Pb treatments decreased markedly. Nevertheless, there was no significant difference in biomass accumulation of the offspring between the low Pb level treatment and the control. The biomass percentage allocated to the root of the offspring was found to be larger than that of the ortets.