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Soil salt-alkalization seriously impacts crop growth and productivity worldwide. Breeding and applying tolerant varieties is the most economical and effective way to address soil alkalization. However, genetic resources for breeders to improve alkali tolerance are limited in mung bean. Here, a genome-wide association study (GWAS) was performed to detect alkali-tolerant genetic loci and candidate genes in 277 mung bean accessions during germination. Using the relative values of two germination traits, 19 QTLs containing 32 SNPs significantly associated with alkali tolerance on nine chromosomes were identified, and they explained 3.6 to 14.6% of the phenotypic variance. Moreover, 691 candidate genes were mined within the LD intervals containing significant trait-associated SNPs. Transcriptome sequencing of alkali-tolerant accession 132–346 under alkali and control conditions after 24 h of treatment was conducted, and 2565 DEGs were identified. An integrated analysis of the GWAS and DEGs revealed six hub genes involved in alkali tolerance responses. Moreover, the expression of hub genes was further validated by qRT-PCR. These findings improve our understanding of the molecular mechanism of alkali stress tolerance and provide potential resources (SNPs and genes) for the genetic improvement of alkali tolerance in mung bean.

Salt-alkaline stress generally leads to soil compaction and fertility decline. It also restricts rice growth and nutrient acquisition, so reduces rice yield. However, little is known about the effect of salt-alkaline stress on the carbon and nitrogen metabolism of rice. In this study, two relatively salt-alkaline tolerant (Changbai 9 and Dongdao 12) and sensitive (Jinongda 138 and Tongyu 315) rice cultivars were grown in a field experiment conducted with two soil types including black soil and salt-alkaline soil to evaluate the characteristics of yield, carbon and nitrogen metabolism in rice. Results showed that yield and nitrogen use efficiency (NUE) in rice greatly decreased under salt-alkaline stress. Changbai 9 (CB9) and Dongdao 12 (DD12) showed higher NUE than Jinongda 138 (JND138) and Tongyu 315 (TY315) under the salt-alkaline stress. Additionally, carbon and nitrogen metabolism enzyme activity and compound content were significantly affected by salt-alkali stress; different performances were observed between cultivars under salt-alkaline stress. In conclusion, our results indicate that salt-alkaline tolerant rice cultivars may have more stable carbon and nitrogen metabolism than sensitive genotypes under salt-alkaline conditions.

Tetrastigma hemsleyanum Diels & Gilg ex Diels is a liana plant with promising medicinal and ornamental values. Its calabash-shaped roots (CRs) are served as a traditional Chinese herb. However, it takes a long growth period to form CRs. In this study, three types of architectural roots, including fibrous roots (FRs), bar-shaped roots (BRs) and CRs, were employed as materials, and the characteristics of histo-anatomy and digital RNA-seq transcriptome profiles were analyzed. Among the three types of roots, the vascular bundles in FRs were intact, while some of the vascular bundles degenerated in BRs, and only few traces of vascular bundles existed in CRs. Meanwhile, no obvious cell inclusions were found in the cytoplasm of FRs, while a few inclusions were found in BRs, and abundant inclusions were detected in CRs, which might be the main source of medicinal components in roots. The transcriptome profiles and qRT-PCR validation indicated that seven upregulated genes, encoding xyloglucan glycosyltransferase, ACC oxidase, CYP711A1, SHORT-ROOT transcript factor, galacturonosyltransferas, WAT1 and WRKY, and two downregulated genes, encoding LRR receptor-like serine/threonine-protein kinase and CYP83B1, were probably involved in the formation and development of CRs. In addition, Gene Ontology terms of intrinsic component of membrane, integral component of membrane, cell periphery, membrane part, plasma membrane, membrane, intrinsic component of plasma membrane, cellular chemical homeostasis and plasma membrane part were probably related to the formation of CRs. Kyoto Encyclopedia of Genes and Genomes pathways related to the development of CRs probably included MAPK signaling pathway–plant, plant hormone signal transduction and circadian rhythm–plant. Our finding suggested a probable mode for the formation of CRs.

Motivated by recent experimental studies of fluorescence resonant energy transfer (FRET), we consider the influence of the temperature-dependent microscopic spectral overlap and relative orientation of the transition dipoles of fluorophores on the nanosecond dynamics of photon statistics and energy transfer efficiency in semiconductor nanocrystal–DNA–organic dye conjugates using Monte-Carlo simulations. Our calculated mean energy transfer efficiencies are found to be well consistent with those measured in experiment at low temperatures. For the higher temperatures, our results demonstrate that the use of Forster radius estimated from the isotropic dynamic average value of 2/3 for the orientation parameter term may lead to overestimation of energy transfer efficiency for the cases of the rigid arrangement of fluorophore transition moments, and thereby deteriorate the precision of the analysis of donor–acceptor distances. Our theoretical results here underline the importance of a detailed understanding of the microscopic picture of FRET for exploiting this spectroscopic technique in various nano- and bio-applications.

Motivated by the recent pioneering advances on nanoscale plasmonics and also nanophotonics technology based on the surface plasmons (SPs), in this work, we give a master equation model in the Lindblad form and investigate the quantum optical properties of single quantum dot (QD) emitter coupled to the SPs of a metallic nanowire. Our main results demonstrate the QD luminescence results of photon emission show three distinctive regimes depending on the distance between QD and metallic nanowire, which elucidates a crossover passing from being metallic dissipative for much smaller emitter-nanowire distances to surface plasmon (SP) emission for larger separations at the vicinity of plasmonic metallic nanowire. Besides, our results also indicate that, for both the resonant case and the detuning case, through measuring QD emitter luminescence spectra and second-order correlation functions, the information about the QD emitter coupling to the SPs of the dissipative metallic nanowire can be extracted. This theoretical study will serve as an introduction to understanding the nanoplasmonic imaging spectroscopy and pave a new way to realize the quantum information devices.

Electronic structure and optical properties of deformed single-wall carbon nanotubes (SWNTs) varies widely depending on their chirality and deformation mode. Here we present a theoretical framework to analyze the electronic structures and optical properties of deformed SWNTs by quantifying the dispersion relation and density of states (DOS). Based on the tight-binding model of deformed nanotubes under stretching, compression, torsion, and bending, we describe and unify the energy band and optical spectra studies and predict that the shifting, merging, and splitting of Van Hove singularities in the DOS, and optical absorption properties change with strains. The results can be employed to understand and guide experimental studies of electronic and optoelectronic devices based on the carbon nanotubes.

Here we theoretically investigate a new laser device structure model based on a single semiconductor quantum dot (QD) gain emitter, where the lasing occurs through discrete conduction states. A single QD is selectively placed in a high quality microcavity, called a microdisk, which is resonant with an intersublevel QD transition. The quantitative results of fully quantum-mechanical treatment here show that, when adjusting the QD-cavity coupling parameters to be appropriate values, the microcavity coupling mode would lead to a very high photon intensity of the single QD microcavity laser. The QD-cavity coupling interaction is modeled in the strong-coupling regime, and we conclude that the present QD microcavity system itself can serve as a new novel terahertz laser with low threshold.

Dynamic structural changes of macromolecules undergoing biochemical reactions can be studied using a novel single pair fluorescence resonance energy transfer (sp-FRET) tool which can be used as a nanoscale spectroscopic ruler. Although recent advances in applying such a nanoscale ruler to biological systems have been made, improvements in photon detectors and photophysical properties of the single FRET pair are still being studied. Motivated by the recent progresses in single-atom laser, we have investigated the ability to use the optical microcavity to amplify the sp-FRET signal. When the single FRET pair and the attached macromolecule of interest are placed inside an optical cavity with the emission mode of the acceptor dye in resonance with the cavity mode, quantitative modeling shows that, when adjusting the acceptor-cavity coupling parameters to be appropriate values, the acceptor fluorescence emission signal amplified by the cavity coupling mode would reach a significant value, leading to a much brighter sp-FRET spectroscopic signal. Possible applications to sp-FRET measurement of biological molecules are quantitatively examined.

Single-molecule fluorescence spectroscopy in condensed phases has many important chemical and biological applications. The single-molecule fluorescence measurements contain information about conformational dynamics on a vast range of time scales. Based on the data analysis protocols methodology proposed by X. Sunney Xie, the theoretical study here mainly focuses on the single-molecule studies of single RNA with interconversions among different conformational states, to with a single FRET pair attached. We obtain analytical expressions for fluorescence lifetime correlation functions that relate changes in fluorescence lifetime to the distance-dependent FRET mechanism within the context of the Smoluchowski diffusion model. The present work establishes useful guideline for the single-molecule studies of biomolecules to reveal the complicated folding dynamics of single RNA molecules at nanometer scale.