Spatially Responsive Multicolor Lanthanide-MOF Heterostructures for Covert Photonic Barcodes.

Micro/nanoscale photonic barcodes based on multicolor luminescent segmented heterojunctions hold potential for applications in information security. However, such multicolor heterojunctions reported thus far are exclusively based on static luminescent signals, thus restricting their application in advanced confidential information protection. Reported here is a strategy to design responsive photonic barcodes with heterobimetallic (Tb3+ /Eu3+ ) metal-organic framework multicolor heterostructures. The spatial colors could be precisely controlled by thermally manipulating the energy-transfer process between the two lanthanides, thus achieving responsive covert photonic barcodes. Also demonstrated is that spatially resolved responsive barcodes with multi-responsive features could be created in a single heterostructure. These findings offer unique opportunities to purposely design highly integrated responsive microstructures and smart devices toward advanced anti-counterfeiting applications.

Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response.

BACKGROUND: Several studies have mined short-read RNA sequencing datasets to identify long non-coding RNAs (lncRNAs), and others have focused on the function of individual lncRNAs in abiotic stress response. However, our understanding of the complement, function and origin of lncRNAs - and especially transposon derived lncRNAs (TE-lncRNAs) - in response to abiotic stress is still in its infancy. RESULTS: We utilized a dataset of 127 RNA sequencing samples that included total RNA datasets and PacBio fl-cDNA data to discover lncRNAs in maize. Overall, we identified 23,309 candidate lncRNAs from polyA+ and total RNA samples, with a strong discovery bias within total RNA. The majority (65%) of the 23,309 lncRNAs had sequence similarity to transposable elements (TEs). Most had similarity to long-terminal-repeat retrotransposons from the Copia and Gypsy superfamilies, reflecting a high proportion of these elements in the genome. However, DNA transposons were enriched for lncRNAs relative to their genomic representation by ~ 2-fold. By assessing the fraction of lncRNAs that respond to abiotic stresses like heat, cold, salt and drought, we identified 1077 differentially expressed lncRNA transcripts, including 509 TE-lncRNAs. In general, the expression of these lncRNAs was significantly correlated with their nearest gene. By inferring co-expression networks across our large dataset, we found that 39 lncRNAs are as major hubs in co-expression networks that respond to abiotic stress, and 18 appear to be derived from TEs. CONCLUSIONS: Our results show that lncRNAs are enriched in total RNA samples, that most (65%) are derived from TEs, that at least 1077 are differentially expressed during abiotic stress, and that 39 are hubs in co-expression networks, including a small number that are evolutionary conserved. These results suggest that lncRNAs, including TE-lncRNAs, may play key regulatory roles in moderating abiotic responses.

Heteroepitaxial Growth of Multiblock Ln-MOF Microrods for Photonic Barcodes.

Micro/nanoscale multicolor barcodes with unique identifiability and a small footprint play significant roles in applications such as multiplexed labeling and tracking systems. Now, a strategy is reported to design multicolor photonic barcodes based on 1D Ln-MOF multiblock heterostructures, where the domain-controlled emissive colors and different block lengths constitute the fingerprint of a corresponding heterostructure. The excellent heteroepitaxial growth characteristics of MOFs enable the effective modulation of the coding structures, thereby remarkably increasing the encoding capacity. The as-prepared multicolor barcodes enable an efficient authentication and exhibit great potential in fulfilling the functions of anti-counterfeiting, information security, and so on. The results will pave an avenue to novel hybrid MOFs for optical data recording and security labels.

Drought-induced changes in root biomass largely result from altered root morphological traits: Evidence from a synthesis of global field trials.

Extreme drought is likely to become more frequent and intense as a result of global climate change, which may significantly impact plant root traits and responses (i.e., morphology, production, turnover, and biomass). However, a comprehensive understanding of how drought affects root traits and responses remains elusive. Here, we synthesized data from 128 published studies under field conditions to examine the responses of 17 variables associated with root traits to drought. Our results showed that drought significantly decreased root length and root length density by 38.29% and 11.12%, respectively, but increased root diameter by 3.49%. However, drought significantly increased root:shoot mass ratio and root cortical aerenchyma by 13.54% and 90.7%, respectively. Our results suggest that drought significantly modified root morphological traits and increased root mortality, and the drought-induced decrease in root biomass was less than shoot biomass, causing higher root:shoot mass ratio. The cascading effects of drought on root traits and responses may need to be incorporated into terrestrial biosphere models to improve prediction of the climate-biosphere feedback.

Organic Microcrystal Vibronic Lasers with Full-Spectrum Tunable Output beyond the Franck-Condon Principle.

The very broad emission bands of organic semiconductor materials are, in theory, suitable for achieving versatile solid-state lasers; however, most of organic materials only lase at short wavelength corresponding to the 0-1 transition governed by the Franck-Condon (FC) principle. A strategy is developed to overcome the limit of FC principle for tailoring the output of microlasers over a wide range based on the controlled vibronic emission of organic materials at microcrystal state. For the first time, the output wavelength of organic lasers is tailored across all vibronic (0-1, 0-2, 0-3, and even 0-4) bands spanning the entire emission spectrum.

Magnetic barcode imaging for contrast agents.

PURPOSE: To demonstrate a new MR imaging approach that unambiguously identifies and quantitates contrast agents based on intrinsic agent properties such as r1 , r2 , r2*, and magnetic susceptibility. The approach is referred to as magnetic barcode imaging (MBI). METHODS: Targeted and bioresponsive contrast agents were imaged in agarose phantoms to generate T1 , T2 , T2*, and quantitative susceptibility maps. The parameter maps were processed by a machine learning algorithm that is trained to recognize the contrast agents based on these parameters. The output is a quantitative map of contrast agent concentration, identity, and functional state. RESULTS: MBI allowed the quantitative interpretation of intensities, removed confounding backgrounds, enabled contrast agent multiplexing, and unambiguously detected the activation and binding states of bioresponsive and targeted contrast agents. CONCLUSION: MBI has the potential to overcome significant limitations in the interpretation, quantitation, and multiplexing of contrast enhancement by MR imaging probes. Magn Reson Med 77:970-978, 2017. © 2016 International Society for Magnetic Resonance in Medicine.

Contrasts between whole-plant and local nutrient levels determine root growth and death in Ailanthus altissima (Simaroubaceae).

UNLABELLED: • PREMISE OF THE STUDY: There is an ongoing debate about the importance of whole-plant control vs. local modular mechanisms for root growth. We conducted a split-root experiment with different patch/background levels of nitrogen to examine whether local root growth and death are controlled by local resource levels or at the whole-plant level.• METHODS: Three microrhizotrons with 0, 10, and 100 µg N/g growth medium levels (74 g growth medium each) were attached to pots of high or low soil N in which one Ailanthus altissima individual was growing. One fine root was guided into each of the microrhizotrons and photographed every 4 d. Plants were harvested after 28 d; root growth and mortality in the microrhizotrons were recorded. Changes in root length, number of laterals, and interlateral length were determined from the photos and analyzed.• KEY RESULTS: While overall plant growth was influenced by background N level, both patch and background N levels influenced root growth and mortality in patches. Local roots proliferated most when the patch N level was high and background level low, and they proliferated least and showed highest mortality when patch N was low and the background level high.• CONCLUSIONS: The fate of roots growing in a patch is influenced by the resource environment of the plant's other roots as well as the resource levels in the patch itself. Thus, the growth and death of roots in patches is determined by both modular and whole-plant mechanisms.

Two-Dimensional Lanthanide Metal-Organic Framework Heterostructures for Noninvasively Photoresponsive High-Security Photonic Barcodes.

Stimuli-responsive micro/nanoscale photonic barcodes show great capacity for encryption and anticounterfeiting technologies due to multiple authentications, yet their application is commonly restricted by invasive stimuli. Herein, we report noninvasive light-stimulated high-security photonic barcodes based on spatially assembled photoresponsive two-dimensional (2D) 1,3,5-benzenetribenzoate (BTB)@Ln-MOF host-guest heterostructures. The photoluminescence (PL) spectra information on BTB@Ln-MOF heterostructures could be precisely controlled by the different wavelengths of ultraviolet (UV) light trigger. By using the PL properties and 2D heterostructures as cryptographic primitives, spatially resolved smart photonic barcodes based on both spectral and graphical coding are realized in BTB@Ln-MOF host-guest materials. These results will pave an avenue for the development of smart stimuli-responsive photonic barcodes for anticounterfeiting applications.

Transcriptome Profiling of Transposon-Derived Long Non-coding RNAs Response to Hormone in Strawberry Fruit Development.

Strawberry is an economically grown horticulture crop required for fruit consumption. The ripening of its fruit is a complex biological process regulated by various hormones. Abscisic acid (ABA) is a critical phytohormone involved in fruit ripening. However, little is known about the long non-coding RNAs (LncRNAs), especially transposon-derived LncRNA (TE-lncRNA), response to hormones during fruit ripening in octoploid strawberry. In the study, the transcriptome data of developing strawberry fruits treated with ABA and its inhibitor Nordihydroguaiaretic acid (NGDA) were analyzed to identify responsive LncRNAs and coding genes. A total of 14,552 LncRNAs were identified, including 8,617 transposon-derived LncRNAs (TE-LncRNAs), 412 LncRNAs (282 TE-LncRNAs), and 382 ABA-sensitive LncRNAs (231 TE-LncRNAs). Additionally, a weighted co-expression network analysis constructed 27 modules containing coding RNAs and LncRNAs. Seven modules, including "MEdarkorange" and "MElightyellow" were significantly correlated with ABA/NDGA treatments, resulting in 247 hub genes, including 21 transcription factors and 22 LncRNAs (15 TE-LncRNAs). Gene ontology enrichment analysis further revealed that ABA/NDGA-responsive modules, including LncRNAs, were associated with various metabolic pathways involved in strawberry fruit development and ripening, including lipid metabolism, organic acid metabolism, and phenylpropanoid metabolism. The current study identifies many high-confidence LncRNAs in strawberry, with a percentage of them being ABA pathway-specific and 22 hub-responsive LncRNAs, providing new insight into strawberry or other Rosaceae crop fruit ripening.

Comprehensive Transcriptome Analysis of GS3 Near-Isogenic Lines During Panicle Development in Rice (Oryza sativa L.).

Panicle architecture is an important agronomic trait in rice that affects rice yields and quality. The GRAIN SIZE 3 (GS3) locus has been identified as a major quantitative trait locus (QTL) affecting grain length and weight. The current understanding of the function of the GS3 gene, especially concerning the regulatory mechanism of panicle development, is still in its infancy. In this study, we generated GS3 near-isogenic lines (NILs) by successive crossing and backcrossing of TD70 (large grain) with Kasalath (small grain), using Kasalath as the recurrent parent. To identify potential transcription dynamic changes in rice panicle formation and grain shape, we deeply analyzed transcriptional profiles for the NILs (NIL-GS3 and NIL-gs3) at three different panicle developmental stages (S, M, and L). A total of 887, 1,768, and 1,478 differentially expressed genes (DEGs) were identified at stages S, M, and L, respectively. We also found 542 differential expressed long non-coding RNAs (lncRNAs). Co-expression analysis further revealed significant clusters associated with different development periods in NIL-gs3 lines. Gene Ontology and KEGG enrichment analysis revealed G-protein signaling and hormones pathway were successively activated at the M and L stages of NIL-gs3, which indicated activation of the G-protein signaling pathway might trigger the down-streaming hormone signaling transduction. we found that other hormones such ABA, Auxin, CK were significantly enriched in the L stage in the NIL-gs3. We highlighted the synergistic interplay of G-protein and multiple hormones signaling pathways and their essential roles in regulating rice panicle formation and the grain shape. Our study provides an invaluable resource for further molecular mechanistic studies that affect rice grain size and provide new insight for directed selection by marker-assisted backcross breeding.

Widely targeted metabolomics analysis reveals the mechanism of quality improvement of flue-cured tobacco.

Flue-curing of top leaves with stems is a widely applied curing technology. Owing to the presence of stems, the quality of flue-cured leaves was significantly improved. However, the contribution of stems to flue-cured leaves is still unknown. In this study, the differences in physicochemical properties and metabolomics data between separated leaves (stem(-)) and leaves with stems (stem(+)) were investigated. The metabolic profiling of stem(+) was significantly different from that of stem(-), with phytohormone indole-3-acetic acid (IAA) being one of the most differential metabolites. The presence of stems reduced the rate of water loss in leaves, which led to less ROS accumulation, higher antioxidant enzyme activities and a lower level of membrane lipid peroxidation in stem(+) than in stem(-). The presence of stems also helped maintain the cellular membrane integrity of leaf cells by preventing the accumulation of IAA in leaf cells. Better cellular membrane integrity during flue-curing means a lower risk of leaf browning. In addition, stem(+) had a lower starch content than stem(-) because of a higher level of amylase activity. In summary, these results indicated that the presence of stems caused metabolism changes in leaves, prevented flue-cured leaves from browning and enhanced starch degradation in leaves during flue-curing.

High-density genetic mapping identified QTLs for anaerobic germination tolerance in rice.

The tolerance of rice anaerobic germination (AG) is the main limiting factor for direct seeding application, yet the genetics mechanism is still in its infancy. In the study, recombinant inbred lines population of TD70 Japonica cultivar and Kasalath Indica cultivar, was employed to construct a high-density genetic map by whole genome re-sequencing. As a result, a genetic map containing 12,328 bin-markers was constructed and a total of 50 QTLs were then detected for CL(coleoptile length), CD (coleoptile diameter), CSA (coleoptile surface area) and CV (coleoptile volume) related traits in the two stages of anaerobic treatment using complete interval mapping method (inclusive composite interval mapping, ICIM). Among the four traits associated with coleoptile, coleoptile volume had the largest number of QTLs (17), followed by coleoptile diameter (16), and coleoptile length had 5 QTLs. These QTLs could explain phenotypic contribution rates ranging from 0.34% to 11.17% and LOD values ranging from 2.52 to 11.57. Combined with transcriptome analysis, 31 candidate genes were identified. Furthermore, 12 stable QTLs were used to detect the aggregation effect analysis. Besides, It was found that individuals with more aggregation synergistic alleles had higher phenotypic values in different environments. Totally, high-density genetic map, QTL mapping and aggregation effect analysis of different loci related to the anaerobic germination of rice seeds were conducted to lay a foundation for the fine mapping of related genes in subsequent assisted breeding.

Comprehensive Transcriptome Analysis Uncovers Hub Long Non-coding RNAs Regulating Potassium Use Efficiency in Nicotiana tabacum.

Potassium (K) is the essential element for plant growth. It is one of the critical factors that determine crop yield, quality, and especially leaf development in tobacco. However, the molecular mechanism of potassium use efficiency (KUE), especially non-coding RNA, is still unknown. In this study, tobacco seedlings were employed, and their hydro-cultivation with K treatments of low and sufficient concentrations was engaged. Physiological analysis showed that low potassium treatment could promote malondialdehyde (MDA) accumulation and antioxidant enzyme activities such as peroxidase (POD), ascorbate-peroxidase (APX). After transcriptomic analysis, a total of 10,585 LncRNA transcripts were identified, and 242 of them were significantly differently expressed under potassium starvation. Furthermore, co-expression networks were constructed and generated 78 potential regulation modules in which coding gene and LncRNAs are involved and functional jointly. By further module-trait analysis and module membership (MM) ranking, nine modules, including 616 coding RNAs and 146 LncRNAs, showed a high correlation with K treatments, and 20 hub K-responsive LncRNAs were finally predicted. Following gene ontology (GO) analysis, the results showed potassium starvation inducing the pathway of antioxidative stress which is consistent with the physiology result mentioned above. Simultaneously, a part of detected LncRNAs, such as MSTRG.6626.1, MSTRG.11330.1, and MSTRG.16041.1, were co-relating with a bench of MYB, C3H, and NFYC transcript factors in response to the stress. Overall, this research provided a set of LncRNAs that respond to K concentration from starvation and sufficient supply. Simultaneously, the regulation network and potential co-functioning genes were listed as well. This massive dataset would serve as an outstanding clue for further study in tobacco and other plant species for nutrient physiology and molecular regulation mechanism.

Single-Crystalline Perovskite p-n Junction Nanowire Arrays for Ultrasensitive Photodetection.

Highly sensitive photodetectors play significant roles in modern optoelectronic integrated circuits. Constructing p-n junctions has been proven to be a particularly powerful approach to realizing sensitive photodetection due to their efficient carrier separation. Recently, p-n-junction photodetectors based on organic-inorganic hybrid perovskites, which combine favorable optoelectronic performance with facile processability, hold great potential in practical applications. So far, these devices have generally been made of polycrystalline films, which exhibit poor carrier-transport efficiency, impeding the further improvement of their photoresponsivities. Here, a type of ultrasensitive photodetector based on single-crystalline perovskite p-n-junction nanowire arrays is demonstrated. The single-crystalline perovskite p-n-junction nanowire arrays not only possess high crystallinity that enables efficient carrier transport but also form a built-in electric field facilitating effective carrier separation. As a result, the devices show excellent photosensitivity over a wide spectral range from 405 to 635 nm with an outstanding responsivity of 2.65 × 102  A W-1 at 532 nm. These results will provide new insights into the design and construction of high-performance photodetectors for practical optoelectronic applications.

Defect engineering in two-dimensional perovskite nanowire arrays by europium(III) doping towards high-performance photodetection.

We demonstrate high-performance photodetectors based on Eu-doped 2D perovskite nanowire arrays. The pure crystallographic orientation enables efficient carrier transport and the doped Eu ions effectively suppress the trap density in the nanowire arrays. As a result, the optimized Eu-doped photodetectors show an excellent responsivity of 6.24 A W-1, an outstanding specific detectivity of 5.83 × 1013 Jones and stable photo-switching behavior with a current on/off ratio of 103.

Transcriptome dynamics uncovers long non-coding RNAs response to salinity stress in Chenopodium quinoa.

Chenopodium quinoa is a crop with outstanding tolerance to saline soil, but long non-coding RNAs (LncRNAs) expression profile driven by salt stress in quinoa has rarely been observed yet. Based on the high-quality quinoa reference genome and high-throughput RNA sequencing (RNA-seq), genome-wide identification of LncRNAs was performed, and their dynamic response under salt stress was then investigated. In total, 153,751 high-confidence LncRNAs were discovered and dispersed intensively in chromosomes. Expression profile analysis demonstrated significant differences between LncRNAs and coding RNAs. Under salt stress conditions, 4,460 differentially expressed LncRNAs were discovered, of which only 54 were differentially expressed at all the stress time points. Besides, strongly significantly correlation was observed between salt-responsive LncRNAs and their closest neighboring genes (r = 0.346, p-value < 2.2e-16). Furthermore, a weighted co-expression network was then constructed to infer the potential biological functions of LncRNAs. Seven modules were significantly correlated with salt treatments, resulting in 210 hub genes, including 22 transcription factors and 70 LncRNAs. These results indicated that LncRNAs might interact with transcription factors to respond to salinity stress. Gene ontology enrichment of the coding genes of these modules showed that they were highly related to regulating metabolic processes, biological regulation and response to stress. This study is the genome-wide analysis of the LncRNAs responding to salt stress in quinoa. The findings will provide a solid framework for further functional research of salt responsive LncRNAs, contributing to quinoa genetic improvement.

Seed priming with selenium: Effects on germination, seedling growth, biochemical attributes, and grain yield in rice growing under flooding conditions.

Prevalent irregular rainfall, flooding for weed control, and unleveled fields in the middle and lower reaches of the Yangtze River all contribute to flooding stress on germination and growth of direct-seeded rice (Oryza sativa L.). Herein, some experiments were conducted so as to assess the effects of seed priming with selenium (Se) on the germination and growth of rice under hypoxia. The experiment was arranged in a completely randomized factorial design with two factors and five replicates. Factors included Se concentration (0, 30, and 60 µmol/L) and duration of flooding stress (0, 2, 4, and 8 days). The experimental results showed that Se accelerated seed germination and increased emergence index and final emergence percentage. Additionally, Se increased shoot and root lengths and dry weights, but high Se concentration (60 µmol/L) reduced 18-day-old seedling dry weight under long-term flooding (8 days). Furthermore, Se reduced malondialdehyde content and increased starch hydrolysis efficiency in seeds, superoxide dismutase, peroxidase, catalase, and glutathione peroxidase activities and seedling soluble protein and total chlorophyll contents. Se improved seedling total Se and organic Se contents while increasing total dry weight and yield. Notably, the highest yield was obtained after a 4-day flooding period. Although Se priming favored rice seedling emergence and growth under flooding conditions, Se concentrations equal or above 60 µmol/L increased the risk of seedling death during long-term flooding (≥8 days).

Facile synthesis of ultrasmall PEGylated iron oxide nanoparticles for dual-contrast T1- and T2-weighted magnetic resonance imaging.

The development of new types of high-performance nanoparticulate MR contrast agents with either positive (T(1)) or dual-contrast (both positive and negative, T(1) + T(2)) ability is of great importance. Here we report a facile synthesis of ultrasmall PEGylated iron oxide nanoparticles for dual-contrast T(1)- and T(2)-weighted MRI. The produced superparamagnetic iron oxide nanoparticles (SPIONs) are of high crystallinity and size uniformity with an average diameter of 5.4 nm, and can be individually dispersed in the physiological buffer with high stability. The SPIONs reveal an impressive saturation magnetization of 94 emu g(-1) Fe(3)O(4), the highest r(1) of 19.7 mM(-1) s(-1) and the lowest r(2)/r(1) ratio of 2.0 at 1.5 T reported so far for PEGylated iron oxide nanoparticles. T(1)- and T(2)-weighted MR images showed that the SPIONs could not only improve surrounding water proton signals in the T(1)-weighted image, but induce significant signal reduction in the T(2)-weighted image. The good contrast effect of the SPIONs as T(1) + T(2) dual-contrast agents might be due to its high magnetization, optimal nanoparticle size for T(1) + T(2) dual-contrast agents, high size monodispersity and excellent colloidal stability. In vitro cell experiments showed that the SPIONs have little effect on HeLa cell viability.

Smart Protein-Based Biolasers: An Alternative Way to Protein Conformation Detection.

Detecting conformational changes in protein is imperative due to its major role in neurodegenerative disorders. Here, we propose an alternative strategy for monitoring the structural change of proteins based on biological microlasers. Smart responsive protein-based microscale biolasers were constructed by incorporating organic gain medium into the microspheres of silk fibroin via emulsion-solvent evaporation. The lasing characteristic of the biolasers exhibited a sensitive response to the structural transformation of the silk fibroin. With narrowed linewidth, the as-prepared biolasers as sensing signals enable highly sensitive protein conformation detection. These results offer an effective approach to monitoring the protein conformational changes and provide valuable guidance for a better understanding of the relationship between bio-microstructures and their photonic properties.

The Landscape of Alternative Splicing Regulating Potassium Use Efficiency in Nicotiana tabacum.

Alternative splicing (AS) occurs extensively in eukaryotes as an essential mechanism for regulating transcriptome complexity and diversity, but the AS landscape regulating potassium (K) use efficiency in plants is unclear. In this study, we performed high-throughput transcriptome sequencing of roots and shoots from allopolyploid Nicotiana tabacum under K+ deficiency. Preliminary physiological analysis showed that root system architecture was dramatically changed due to potassium deficiency and that IAA content was significantly reduced in root and shoot. AS analysis showed that a total of 28,179 genes exhibited 54,457 AS events, and 1,510 and 1,732 differentially alternatively spliced (DAS) events were identified in shoots and roots under low K+ stress. Nevertheless, only 120 DAS events occurred in both shoots and roots, implying that most DAS events were tissue-specific. Both in shoot and the root, the proportion of DAS genes in differentially expressed (DE) genes equaled that in non-DE genes, which indicated that AS might play a unique regulatory role in response to low potassium. Gene ontology analysis further indicated that transcription regulation and AS modulation worked independently in response to low K+ stress in tobacco, as their target biological processes were different. Totally 45 DAS transcription factors (TFs) were found, which were involved in 18 TF families. Five Auxin response factor (ARF) TFs were significantly DAS in root, suggesting that response to auxin was probably subject to AS regulation in the tobacco root. Our study shows that AS variation occurs extensively and has a particular regulatory mechanism under K+ deficiency in tobacco. The study also links changes in root system architecture with the changes in AS of ARF TFs, which implied the functional significance of these AS events for root growth and architecture.