Unveiling the underestimated direct emissions of nitrous acid (HONO).

Gaseous nitrous acid (HONO) is a critical source of hydroxyl radicals (OH) in the troposphere. While both direct and secondary sources contribute to atmospheric HONO, direct emissions have traditionally been considered minor contributors. In this study, we developed δ15N and δ18O isotopic fingerprints to identify six direct HONO emission sources and conducted a 1-y case study on the isotopic composition of atmospheric HONO at rural and urban sites. Interestingly, we identified that livestock farming is a previously overlooked direct source of HONO and determined its HONO to ammonia (NH3) emission ratio. Additionally, our results revealed that spatial and temporal variations in atmospheric HONO isotopic composition can be partially attributed to direct emissions. Through a detailed HONO budget analysis incorporating agricultural sources, we found that direct HONO emissions accounted for 39~45% of HONO production in rural areas across different seasons. The findings were further confirmed by chemistry transport model simulations, highlighting the significance of direct HONO emissions and their impact on air quality in the North China Plain. These findings provide compelling evidence that direct HONO emissions play a more substantial role in contributing to atmospheric HONO than previously believed. Moreover, the δ15N and δ18O isotopic fingerprints developed in this study may serve as a valuable tool for further research on the atmospheric chemistry of reactive nitrogen gases.

DNA-Programmed Four-Bit Quaternary Fluorescence Encoding (FLUCO) Enables 51-Colored Bioimaging Analysis.

Color encoding plays a crucial role in painting, digital photography, and spectral analysis. Achieving accurate, target-responsive color encoding at the molecular level has the potential to revolutionize scientific research and technological innovation, but significant challenges persist. Here, we propose a multibit DNA self-assembly system based on computer-aided design (CAD) technology, enabling accurate, target-responsive, amplified color encoding at the molecular level, termed fluorescence encoding (FLUCO). As a model, we establish a quaternary FLUCO system using four-bit DNA self-assembly, which can accurately encode 51 colors, presenting immense potential in applications such as spatial proteomic imaging and multitarget analysis. Notably, FLUCO enables the simultaneous imaging of multiple targets exceeding the limitations of channels using conventional imaging equipment, and marks the integration of computer science for molecular encoding and decoding. Overall, our work paves the way for target-responsive, controllable molecular encoding, facilitating spatial omics analysis, exfoliated cell analysis, and high-throughput liquid biopsy.

Enzyme Reaction-Assisted Programmable Transcriptional Switches for Bioactive Molecule Detection.

Bioactive molecules are highly worthwhile to recognize and explore the latent pathogenic mechanism. Conventional methods for bioactive molecule detection, including mass spectrometry and fluorescent probe imaging, are limited due to the complex processing and signal interference. Here, we designed enzyme-reaction-assisted programmable transcriptional switches for the detection of bioactive molecules. The approach is based on the use of programmable enzyme site-specific cleavage-assisted DNA triplex-based conformational switches that, upon responding to bioactive molecules, can trigger the transcription of fluorescent light-up aptamers. Thanks to the programmable nature of the sensing platform, the method can be adapted to different bioactive molecules, and we demonstrated the enzyme-small molecule catalytic reaction combination of myeloperoxidase (MPO)-hydrogen peroxide (H2O2) as a model that transcriptional switches was capable of detecting H2O2 and possessed the specificity and anti-interference ability in vitro. Furthermore, we successfully applied the switches into cells to observe the detection feasibility in vivo, and dynamically monitored changes of H2O2 in cellular oxidative stress levels. Therefore, we attempt to amalgamate the advantages of enzyme reaction with the pluripotency of programmable transcriptional switches, which can take both fields a step further, which may promote the research of biostimuli and the construction of DNA molecular devices.

Dissecting Drivers of Ozone Pollution during the 2022 Multicity Lockdowns in China Sheds Light on Future Control Direction.

In 2022, many Chinese cities experienced lockdowns and heatwaves. We analyzed ground and satellite data using machine learning to elucidate chemical and meteorological drivers of changes in O3 pollution in 27 major Chinese cities during lockdowns. We found that there was an increase in O3 concentrations in 23 out of 27 cities compared with the corresponding period in 2021. Random forest modeling indicates that emission reductions in transportation and other sectors, as well as the changes in meteorology, increased the level of O3 in most cities. In cities with over 80% transportation reductions and temperature fluctuations within -2 to 2 °C, the increases in O3 concentrations were mainly attributable to reductions in nitrogen oxide (NOx) emissions. In cities that experienced heatwaves and droughts, increases in the O3 concentrations were primarily driven by increases in temperature and volatile organic compound (VOC) emissions, and reductions in NOx concentrations from ground transport were offset by increases in emissions from coal-fired power generation. Despite 3-99% reduction in passenger volume, most cities remained VOC-limited during lockdowns. These findings demonstrate that to alleviate urban O3 pollution, it will be necessary to further reduce industrial emissions along with transportation sources and to take into account the climate penalty and the impact of heatwaves on O3 pollution.

Proximity-Enhanced Functional Imaging Analysis of Engineered Tumors.

Functional imaging (FI) techniques have revolutionized tumor imaging by providing information on specific tumor functions, such as glycometabolism. However, tumor cells lack unique molecular characteristics at the molecular level and metabolic pathways, resulting in limited metabolic differences compared to normal cells and increased background signals from FI. To address this limitation, we developed a novel imaging technique termed proximity-enhanced functional imaging (PEFI) for accurate visualization of tumors. By using "two adjacent chemically labeled glycoproteins" as output signals, we significantly enhance the metabolic differences between tumor and normal cells by PEFI, thereby reducing the background signals for analysis and improving the accuracy of tumor functional imaging. Our results demonstrate that PEFI can accurately identify tumors at the cellular, tissue, and animal level, and has potential value in clinical identification and analysis of tumor cells and tissues, as well as in the guidance of clinical tumor resection surgery.

Computer-Aided Design of DNA Self-Limited Assembly for Relative Quantification of Membrane Proteins.

Immunofluorescence imaging of cells plays a vital role in biomedical research and clinical diagnosis. However, when it is applied to relative quantification of proteins, it suffers from insufficient fluorescence intensity or partial overexposure, resulting in inaccurate relative quantification. Herein, we report a computer-aided design of DNA self-limited assembly (CAD-SLA) technology and apply it for relative quantification of membrane proteins, a concept proposed for the first time. CAD-SLA can achieve exponential cascade signal amplification in one pot and terminate at any desired level. By conjugating CAD-SLA with immunofluorescence, in situ imaging of cell membrane proteins is achieved with a controllable amplification level. Besides, comprehensive fluorescence intensity information from fluorescent images can be obtained, accurately showing relative quantitative information. Slight protein expression differences previously indistinguishable by immunofluorescence or Western blotting can now be discriminated, making fluorescence imaging-based relative quantification a promising tool for membrane protein analysis. From the perspectives of both DNA self-assembly technology and immunofluorescence technology, this work has solved difficult problems and provided important reference for future development.

Types and Applications of Nicking Enzyme-Combined Isothermal Amplification.

Due to the sudden outbreak of COVID-19 at the end of 2019, rapid detection has become an urgent need for community clinics and hospitals. The rapid development of isothermal amplification detection technology for nucleic acids in the field of molecular diagnostic point-of-care testing (POCT) has gained a great deal of attention in recent years. Thanks to intensive research on nicking enzymes, nicking enzyme-combined isothermal amplification has become a promising platform for rapid detection. This is a novel technique that uses nicking enzymes to improve ordinary isothermal amplification. It has garnered significant interest as it overcomes the complexity of traditional molecular diagnostics and is not subject to temperature limitations, relying on cleavage enzymes to efficiently amplify targets in a very short time to provide a high level of amplification efficiency. In recent years, several types of nicking enzyme-combined isothermal amplification have been developed and they have shown great potential in molecular diagnosis, immunodiagnosis, biochemical identification, and other fields. However, this kind of amplification has some disadvantages. In this review, the principles, advantages and disadvantages, and applications of several nicking enzyme-combined isothermal amplification techniques are reviewed and the prospects for the development of these techniques are also considered.

Worsening ozone air pollution with reduced NOx and VOCs in the Pearl River Delta region in autumn 2019: Implications for national control policy in China.

Ozone (O3) pollution has emerged as a major air quality issue in China. Here we emphasize the great challenges in controlling O3 pollution by analyzing the recent experience of the Pearl River Delta (PRD) in southern China in reducing the autumn O3 peaks. Despite significant reductions in the concentration of O3 precursors, i.e., nitrogen oxides (NOx) and volatile organic compounds (VOCs), regional O3 pollution in the PRD was largely worse in autumn 2019 than in autumn 2018. We found that the supra-regional and regional background concentrations of O3 increased significantly in the PRD in autumn 2019 due to increased concentrations of O3 in the vast surrounding areas. We also observed slight increases in the concentrations of PRD-regionally and Guangzhou-locally produced O3. A chemical box-model analysis confirmed a slight increase in the in-situ production of O3 and revealed that increased biogenic VOCs (BVOCs) and decreased NOx levels negated the effect of significant decrease in the anthropogenic VOCs. Taken together, these aspects exacerbated O3 pollution in the PRD region in autumn 2019 relative to autumn 2018. The findings from this study highlight the strong interactions of O3 pollution over multiple regions and the need for collaborative inter-regional efforts to control O3 pollution. The experience of PRD also underlines the key role of BVOCs and the importance of science-based strategies to decrease VOCs and NOx.

mRNA Delivery by a pH-Responsive DNA Nano-Hydrogel.

The delivery of mRNA to manipulate protein expression has attracted widespread attention, since that mRNA overcomes the problem of infection and mutation risks in transgenes and can work as drugs for the treatment of diseases. Although there are currently some vehicles that deliver mRNA into cells, they have not yet reached a good balance in terms of expression efficiency and biocompatibility. Here, a DNA nano-hydrogel system for mRNA delivery is developed. The nano-hydrogel is all composed of DNA except the target mRNA, so it has superior biocompatibility compared with those chemical vehicles. In parallel, the nano-hydrogel can be compacted into a nanosphere under the crosslinking by well-designed "X"-shaped DNA scaffolds and DNA linkers, facilitating the delivery into cells through endocytosis. In addition, smart intracellular release of the mRNA is achieved by incorporating a pH-responsive i-motif structure into the nano-hydrogel. Thus, taking the efficient delivery and release together, mRNA can be translated into the corresponding protein with a high efficiency, which is comparable to that of the commercial liposome but with a much better biocompatibility. Due to the excellent biocompatibility and efficiency, this nano-hydrogel system is expected to become a competitive alternative for delivering functional mRNA in vivo.

Measurements of Volatile Organic Compounds During the COVID-19 Lockdown in Changzhou, China.

The COVID-19 outbreak in 2020 prompted strict lockdowns, reduced human activity, and reduced emissions of air pollutants. We measured volatile organic compounds (VOCs) using a proton-transfer-reaction mass spectrometry instrument in Changzhou, China from 8 January through 27 March, including periods of pre-lockdown, strict measures (level 1), and more relaxed measures (level 2). We analyze the data using positive matrix factorization and resolve four factors: textile industrial emissions (62 ± 10% average reduction during level 1 relative to pre-lockdown), pharmaceutical industrial emissions (40 ± 20%), traffic emissions (71 ± 10%), and secondary chemistry (20 ± 20%). The two industrial sources showed different responses to the lockdown, so emissions from the industrial sector should not be scaled uniformly. The quantified changes in VOCs due to the lockdowns constrain emission inventories and inform chemistry-transport models, particularly for sectors where activity data are sparse, as the effects of lockdowns on air quality are explored.

Multiple N-glycans cooperate in balancing misfolded BRI1 secretion and ER retention.

KEY MESSAGE: N-glycans play a protective or monitoring role according to the folding state of associated protein or the distance from structural defects. Asparagine-linked (Asn/N-) glycosylation is one of the most prevalent and complex protein modifications and the associated N-glycans play crucial roles on protein folding and secretion. The studies have shown that many glycoproteins hold multiple N-glycans, yet little is known about the redundancy of N-glycans on a protein. In this study, we used BRI1 to decipher the roles of N-glycans on protein secretion and function. We found that all 14 potential N-glycosylation sites on BRI1 were occupied with oligosaccharides. The elimination of single N-glycan had no obvious effect on BRI1 secretion or function except N154-glycan, which resulted in the retention of BRI1 in the endoplasmic reticulum (ER), similar to the loss of multiple highly conserved N-glycans. To misfolded bri1, the absence of N-glycans next to local structural defects enhanced the ER retention and the artificial addition of N-glycan could help the misfolded bri1-GFPs exiting from the ER, indicating that the N-glycans might serve as steric hindrance to protect the structure defects from ER recognition. We also found that the retention of misfolded bri1-9 by lectins and chaperones in the ER relied on the presence of multiple N-glycans distal to the local defects. Our findings revealed that the N-glycans might play a protective or monitoring role according to the folding state of associated protein or the distance from structural defects.

N-glycosylation is involved in stomatal development by modulating the release of active abscisic acid and auxin in Arabidopsis.

Asparagine-linked glycosylation (N-glycosylation) is one of the most important protein modifications in eukaryotes, affecting the folding, transport, and function of a wide range of proteins. However, little is known about the roles of N-glycosylation in the development of stomata in plants. In the present study, we provide evidence that the Arabidopsis stt3a-2 mutant, defective in oligosaccharyltransferase catalytic subunit STT3, has a greater transpirational water loss and weaker drought avoidance, accompanied by aberrant stomatal distribution. Through physiological, biochemical, and genetic analyses, we found that the abnormal stomatal density of stt3a-2 was partially attributed to low endogenous abscisic acid (ABA) and auxin (IAA) content. Exogenous application of ABA or IAA could partially rescue the mutant's salt-sensitive and abnormal stomatal phenotype. Further analyses revealed that the decrease of IAA or ABA in stt3a-2 seedlings was associated with the underglycosylation of ß-glucosidase (AtBG1), catalysing the conversion of conjugated ABA/IAA to active hormone. Our results provide strong evidence that N-glycosylation is involved in stomatal development and participates in abiotic stress tolerance by modulating the release of active plant hormones.

Application of DNA nanodevices for biosensing.

Deoxyribonucleic acid (DNA), the carrier of genetic information in living life, is an essential biomacromolecule in almost all living systems. DNA has advantages including, programmability, predictability, high rigidity, and stability. Through self-assembly or combination with other nanomaterials (such as gold nanoparticles, graphene oxides, quantum dots, and polymers), DNA can be applied to construct specific, stable, biocompatible, and functional nanodevices. DNA nanodevices have made greater contributions in a plethora of fields. In this review, we discuss the recent progress of DNA nanodevices in molecular detection and analysis. Meanwhile, we prospect the development of various DNA devices in biological analysis, clinical diagnosis and biomedical research.

Rhodopsin-Like Ionic Gate Fabricated with Graphene Oxide and Isomeric DNA Switch for Efficient Photocontrol of Ion Transport.

Rhodopsin, composed of opsin and isomeric retinal, acts as the primary photoreceptor by converting light into electric signals. Inspired by rhodopsin, we have fabricated a light-regulated ionic gate on the basis of the design of a graphene oxide (GO)-biomimetic DNA-nanochannel architecture. In this design, photoswitchable azobenzene (Azo)-DNA is introduced to the surface of porous anodic alumina (PAA) membrane. With modulation of the interaction between the GO blocker and Azo-DNA via flexibly regulating trans and cis states of Azo under the irradiation of visible and ultraviolet light, alternatively, the ionic gate is switched between ON and OFF states. This newly constructed ionic gate can possess high efficiency for the control of ion transport because of the high blocking property of GO and the rather tiny path within the barrier layer which are both first employed to fabricate ionic gate. We anticipate that this rhodopsin-like ionic gate may provide a new model and method for the investigation of ion channel, ion function, and ion quantity. In addition, because of the advantages of simple fabrication, good biocompatibility, and universality, this bioinspired system may have potential applications as optical sensors, in photoelectric transformation, and in controllable drug delivery.

DNA-Oriented Shaping of Cell Features for the Detection of Rare Disseminated Tumor Cells.

Metastasis of tumors is the major cause of death in cancer patients. The efficient detection of disseminated tumor cells (DTCs) is found to be critical for the early warning of tumor metastasis. However, it is technically difficult to identify DTC among circulation tumor cells (CTCs). In this work, we have proposed a DNA-oriented shaping strategy to convert the metastasis-associated feature of CTC into a dominant signature, making DTCs discernible. In detail, by performing the in situ DNA rolling circle amplification, invasive biomarkers at cell surface are specifically labeled with large amount of biotin-incorporated DNA strands. Therefore, isolation and detection processes of DTCs are significantly simplified. On a streptavidin immobilized ITO electrode, we demonstrated that these biotin-featured DTCs are efficiently captured, and as few as two cells can be electrochemically detected, with a linear detection range from 5 to 320 cells/cm2. Therefore, on the basis of the DNA-oriented shaping of cell, detection of DTCs becomes simple and sensitive, which may facilitate the process of rare DTC analysis. Besides, it is also promising to distinguish other cell types with this method in fields such as cell-based clinical diagnosis, systematic cell census, and tissue engineering.

pH-Based immunoassay: explosive generation of hydrogen ions through an immuno-triggered nucleic acid exponential amplification reaction.

In this work, we propose a novel concept and a proof-of-concept strategy for the fabrication of a pH-based immunoassay platform with a certain degree of universality and scalability to make it adaptable for different application scenarios. The immunoreactions for the target detection are converted to pH changes through an engineered and optimized isothermal nucleic acid amplification, named exponential amplification reaction (EXPAR). Thus, a variety of well-developed methods for pH analysis, e.g. pH indicators, pH-strips and pH meters, can be applied for immunoassay directly. Here, we show that this proof-of-concept strategy is applicable for both macromolecular and micromolecular antigens by adopting human platelet-derived growth factor-BB (PDGF-BB) and chloramphenicol (CAP) as the model targets, respectively. The detection can be achieved using a colorimetric pH indicator after a 15 min reaction of the immuno-triggered isothermal nucleic acid amplification. In addition, compared with the traditional enzyme-linked immunosorbent assay (ELISA), the performance of our strategy, especially the detection limits, is improved to varying degrees for different targets, making the strategy a promising alternative for diverse application scenarios of immunoassay.

New method for detection of T4 polynucleotide kinase phosphatase activity through isothermal EXPonential amplification reaction.

As a bifunctional enzyme, T4 polynucleotide kinase phosphatase (T4 PNKP) catalyzes the phosphorylation of 5'-hydroxyl, and also removes the terminal 3'-phosphate group. This is closely related to the restructuring, replication, and damage repair of nucleic acid. In this paper, we describe a new method for the sensitive detection of T4 PNKP activity based on the isothermal EXPonential amplification reaction (EXPAR). T4 PNKP can be linearly assayed in the range from 0.001 to 0.01 U mL-1 with a detection limit of 7.9 × 10-4 U mL-1. Moreover, the method exhibits high specificity and sensitivity and can be applied in the enzyme analysis of complex serum samples. In view of its simplicity and moderate experimental conditions, the method may suitable for use in a commercial kit for the analysis of T4 PNKP activity.

A Dual-Enzyme-Assisted Three-Dimensional DNA Walking Machine Using T4 Polynucleotide Kinase as Activators and Application in Polynucleotide Kinase Assays.

T4 polynucleotide kinase (T4 PNK), an intracellular kinase, catalyzes the phosphorylation of 5'-hydroxyl termini in nucleic acids and plays a crucial role in DNA-related physiological activities. Malfunctioning of PNK is associated with the deregulation of many cellular activities and eventually induces a variety of human diseases. Herein, we report a smart three-dimensional (3D) DNA walking machine using PNK as an effective activator when coupled with the duplex DNA nuclease-assisted cleavage reaction. The 3D DNA tracks benefit from high DNA loading capacity of gold nanoparticles, and the high efficiency of duplex nuclease-mediated cyclic cleavage facilitates the movement of the DNA machine in response to T4 PNK. The DNA machine is also applied for the PNK assay based on the signal amplification from point to area during the DNA walking process. The method achieves an excellent detection limit of 0.0067 U/mL with a linear range from 0.01 to 0.3 U/mL and a favorable specificity even in complex serum samples. Therefore, the 3D DNA machine shows great potential in biochemical and molecular biology studies, drug discovery, and clinic diagnostics.

DNA Nanotechnology for Cancer Diagnosis and Therapy.

Cancer is one of the leading causes of mortality worldwide, because of the lack of accurate diagnostic tools for the early stages of cancer. Thus, early diagnosis, which provides important information for a timely therapy of cancer, is of great significance for controlling the development of the disease and the proliferation of cancer cells and for improving the survival rates of patients. To achieve the goals of early diagnosis and timely therapy of cancer, DNA nanotechnology may be effective, since it has emerged as a valid technique for the fabrication of various nanoscale structures and devices. The resultant DNA-based nanoscale structures and devices show extraordinary performance in cancer diagnosis, owing to their predictable secondary structures, small sizes, and high biocompatibility and programmability. In particular, the rapid development of DNA nanotechnologies, such as molecular assembly technologies, endows DNA-based nanomaterials with more functionalization and intellectualization. Here, we summarize recent progress made in the development of DNA nanotechnology for the fabrication of functional and intelligent nanomaterials and highlight the prospects of this technology in cancer diagnosis and therapy.

Understanding unusually high levels of peroxyacetyl nitrate (PAN) in winter in Urban Jinan, China.

Peroxyacetyl nitrate (PAN), as a major secondary pollutant, has gained increasing worldwide attentions, but relevant studies in China are still quite limited. During winter of 2015 to summer of 2016, the ambient levels of PAN were measured continuously by an automatic gas chromatograph equipped with an electron capture detector (GC-ECD) analyzer at an urban site in Jinan (China), with related parameters including concentrations of O3, NO, NO2, PM2.5, HONO, the photolysis rate constant of NO2 and meteorological factors observed concurrently. The mean and maximum values of PAN concentration were (1.89 ±â€¯1.42) and 9.61 ppbv respectively in winter, and (2.54 ±â€¯1.44) and 13.47 ppbv respectively in summer. Unusually high levels of PAN were observed during severe haze episodes in winter, and the formation mechanisms of them were emphatically discussed. Study showed that high levels of PAN in winter were mainly caused by local accumulation and strong photochemical reactions during haze episodes, while mass transport played only a minor role. Accelerated photochemical reactions (compared to winter days without haze) during haze episodes were deduced by the higher concentrations but shorter lifetimes of PAN, which was further supported by the sufficient solar radiation in the photolysis band along with the high concentrations of precursors (NO2, VOCs) and HONO during haze episodes. In addition, significant PAN accumulation during calm weather of haze episodes was verified by meteorological data.