Orthogonal Control of Nucleic Acid Function via Chemical Caging-Decaging Strategies.

The ability to precisely control the function of nucleic acids plays an important role in biosensing and biomedicine. In recent years, novel strategies employing biological, physical, and chemical triggers have been developed to modulate the function of nucleic acids spatiotemporally. These approaches commonly involve the incorporation of stimuli-responsive groups onto nucleic acids to block their functions until triggers-induced decaging restore activity. These inventive strategies deepen our comprehension of nucleic acid molecules' dynamic behavior and provide new techniques for precise disease diagnosis and treatment. Focusing on the spatiotemporal regulation of nucleic acid molecules through the chemical caging-decaging strategy, we here present an overview of the innovative triggered control mechanisms and accentuate their implications across the fields of chemical biology, biomedicine, and biosensing.

Lost genome segments associate with trait diversity during rice domestication.

BACKGROUND: DNA mutations of diverse types provide the raw material required for phenotypic variation and evolution. In the case of crop species, previous research aimed to elucidate the changing patterns of repetitive sequences, single-nucleotide polymorphisms (SNPs), and small InDels during domestication to explain morphological evolution and adaptation to different environments. Additionally, structural variations (SVs) encompassing larger stretches of DNA are more likely to alter gene expression levels leading to phenotypic variation affecting plant phenotypes and stress resistance. Previous studies on SVs in rice were hampered by reliance on short-read sequencing limiting the quantity and quality of SV identification, while SV data are currently only available for cultivated rice, with wild rice largely uncharacterized. Here, we generated two genome assemblies for O. rufipogon using long-read sequencing and provide insights on the evolutionary pattern and effect of SVs on morphological traits during rice domestication. RESULTS: In this study, we identified 318,589 SVs in cultivated and wild rice populations through a comprehensive analysis of 13 high-quality rice genomes and found that wild rice genomes contain 49% of unique SVs and an average of 1.76% of genes were lost during rice domestication. These SVs were further genotyped for 649 rice accessions, their evolutionary pattern during rice domestication and potential association with the diversity of important agronomic traits were examined. Genome-wide association studies between these SVs and nine agronomic traits identified 413 candidate causal variants, which together affect 361 genes. An 824-bp deletion in japonica rice, which encodes a serine carboxypeptidase family protein, is shown to be associated with grain length. CONCLUSIONS: We provide relatively accurate and complete SV datasets for cultivated and wild rice accessions, especially in TE-rich regions, by comparing long-read sequencing data for 13 representative varieties. The integrated rice SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in rice.

Time-ordering japonica/geng genomes analysis indicates the importance of large structural variants in rice breeding.

Temperate japonica/geng (GJ) rice yield has significantly improved due to intensive breeding efforts, dramatically enhancing global food security. However, little is known about the underlying genomic structural variations (SVs) responsible for this improvement. We compared 58 long-read assemblies comprising cultivated and wild rice species in the present study, revealing 156 319 SVs. The phylogenomic analysis based on the SV dataset detected the putatively selected region of GJ sub-populations. A significant portion of the detected SVs overlapped with genic regions were found to influence the expression of involved genes inside GJ assemblies. Integrating the SVs and causal genetic variants underlying agronomic traits into the analysis enables the precise identification of breeding signatures resulting from complex breeding histories aimed at stress tolerance, yield potential and quality improvement. Further, the results demonstrated genomic and genetic evidence that the SV in the promoter of LTG1 is accounting for chilling sensitivity, and the increased copy numbers of GNP1 were associated with positive effects on grain number. In summary, the current study provides genomic resources for retracing the properties of SVs-shaped agronomic traits during previous breeding procedures, which will assist future genetic, genomic and breeding research on rice.

Engineering a Reversible Fluorescent Probe for Real-Time Live-Cell Imaging and Quantification of Mitochondrial ATP.

Real-time imaging and quantification of adenosine triphosphate (ATP) fluctuation in cells are significant for understanding the relationship between energy metabolism and cell functions. However, few synthetic fluorescent probes have been reported to tackle this challenge due to lack of accurate fluorescence readout and suitable response concentration. Herein we designed and synthesized a ratiometric fluorescent probe (Rh6G-ACFPN) for quantitatively detecting the fluctuation of mitochondrial ATP in living cells. Rh6G-ACFPN selectively and reversibly responds to ATP with an ideal dissociation constant (Kd) of 4.65 mM (3-10 mM: the range of mitochondrial ATP concentrations). Live-cell imaging allows us to directly monitor the dynamic changes of mitochondrial ATP in high temporal resolution. Moreover, for the first time, mitochondrial ATP in normal and cancer cells lines was successfully quantified and discriminated. These results demonstrate the versatility of Rh6G-ACFPN as a useful imaging tool to elucidate the function of mitochondrial ATP in living cells.

Donor and Ring-Fusing Engineering for Far-Red to Near-Infrared Triphenylpyrylium Fluorophores with Enhanced Fluorescence Performance for Sensing and Imaging.

Fluorescent probes have become an indispensable tool in the detection and imaging of biological and disease-related analytes due to their sensitivity and technical simplicity. In particular, fluorescent probes with far-red to near-infrared (FR-NIR) emissions are very attractive for biomedical applications. However, many available FR-NIR fluorophores suffer from small Stokes shifts and sometimes low quantum yields, resulting in self-quenching and low contrast. In this work, we describe the rational design and engineering of FR-NIR 2,4,6-triphenylpyrylium-based fluorophores (TPP-Fluors) with the help of theoretical calculations. Our strategy is based on the appending of electron-donating substituents and fusing groups onto 2,4,6-triphenylpyrylium. In contrast to the parent TPP with short emission wavelength, weak quantum yields, and low chemical stability, the obtained novel TPP-Fluors display some favorable properties, such as long-wavelength emission, large Stokes shifts, moderate to high quantum yields, and chemical stability. TPP-Fluors demonstrate their biological value as mitochondria-specific labeling reagents due to their inherently positive nature. In addition, TPP-Fluors can also be applied to develop ratiometric fluorescent probes, as the electron-donating ability of the 2,6-phenyl substituents is closely correlated with their emission wavelength. A proof-of-concept ratiometric probe has been developed by derivatizing the amino groups of TPP-Fluor for the detection and imaging of nitroreductase in vitro and in hypoxic cells.

Enhancing the Anti-Solvatochromic Two-Photon Fluorescence for Cirrhosis Imaging by Forming a Hydrogen-Bond Network.

Two-photon imaging is an emerging tool for biomedical research and clinical diagnostics. Electron donor-acceptor (D-A) type molecules are the most widely employed two-photon scaffolds. However, current D-A type fluorophores suffer from solvatochromic quenching in aqueous biological samples. To address this issue, we devised a novel class of D-A type green fluorescent protein (GFP) chromophore analogues that form a hydrogen-bond network in water to improve the two-photon efficiency. Our design results in two-photon chalcone (TPC) dyes with 0.80 quantum yield and large two-photon action cross section (210 GM) in water. This strategy to form hydrogen bonds can be generalized to design two-photon materials with anti-solvatochromic fluorescence. To demonstrate the improved in vivo imaging, we designed a sulfide probe based on TPC dyes and monitored endogenous H2 S generation and scavenging in the cirrhotic rat liver for the first time.

Damage Evolution of Polypropylene-Basalt Hybrid Fiber Ceramsite Concrete under Chloride Erosion and Dry-Wet Cycle.

To investigate the influence of polypropylene-basalt hybrid fibers (PBHFCC) on the durability of ceramsite concrete, this study determined the appearance change, mass loss rate, relative dynamic elastic modulus, compressive strength and splitting tensile strength of ceramsite concrete with four kinds of hybrid fibers volume admixture under chloride erosion and dry-wet cycles. The results reveal that under this effect, the apparent damage of each group of specimens increased with the growth of the erosion time. The quality, compressive strength and splitting tensile strength of the specimens all increased gradually during the erosion age period of the first 72 d and gradually decreased after 72 d. The relative dynamic elastic modulus was similarly mutated in 48 d. When the hybrid fiber content of the specimens is 0.15 vol %, the enhancement effect of ceramsite concrete is better than that of the other three amounts. The relative dynamic elastic modulus value is used as a damage variable to establish the damage equation, and the damage evolution equation of PBHFCC considering the volume of hybrid fiber under chloride erosion and dry-wet cycle is derived. The conclusions can be used as a reference for the durability design and construction of PBHFCC.