A novel ultrasensitive RNase H assay based on phosphorothioated-terminal hairpin formation and self-priming extension reaction.

We herein present a novel ultrasensitive RNase H assay based on phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP) reaction. The detection probe employed as a key component in this technique serves as a substrate for RNase H and triggers the PS-THSP reaction upon the RNase H-mediated degradation of the probe. As a consequence, a large number of long concatemeric amplification products could be produced and used to identify the RNase H activity through the fluorescence signals produced by the nucleic acid-specific fluorescent dye, SYTO 9. Importantly, the use of the gp32 protein allowed the PS-THSP reaction to be performed at 37 °C, ultimately enabling an isothermal one-step RNase H assay. Based on this sophisticated design principle, the RNase H activity was very sensitively detected, down to 0.000237 U mL-1 with high specificity. We further verified its practical applicability through its successful application to the screening of RNase H inhibitors. With its operational convenience and excellent analytical performance, this technique could serve as a new platform for RNase H assay in a wide range of biological applications.

Multifunctional self-priming hairpin probe-based isothermal nucleic acid amplification and its applications for COVID-19 diagnosis.

We herein present a multifunctional self-priming hairpin probe-based isothermal amplification, termed MSH, enabling one-pot detection of target nucleic acids. The sophisticatedly designed multifunctional self-priming hairpin (MSH) probe recognizes the target and rearranges to prime itself, triggering the amplification reaction powered by the continuously repeated extension, nicking, and target recycling. As a consequence, a large number of double-stranded DNA (dsDNA) amplicons are produced that could be monitored in real-time using a dsDNA-intercalating dye. Based on this unique design approach, the nucleocapsid (N) and the open reading frame 1 ab (ORF1ab) genes of SARS-CoV-2 were successfully detected down to 1.664 fM and 0.770 fM, respectively. The practical applicability of our method was validated by accurately diagnosing 60 clinical samples with 93.33% sensitivity and 96.67% specificity. This isothermal one-pot MSH technique holds great promise as a point-of-care testing protocol for the reliable detection of a wide spectrum of pathogens, particularly in resource-limited settings.

A novel electrochemical strategy to detect hydrogen peroxide by utilizing peroxidase-mimicking activity of cerium oxide/graphene oxide nanocomposites.

We herein describe a novel electrochemical strategy to detect hydrogen peroxide (H2O2) by utilizing the peroxidase-mimicking activity of cerium oxide nanoparticles (CeO2 NP) and reduced graphene oxide (rGO). Particularly, CeO2 NP/rGO nanocomposites were deposited on the commercial electrode by a very convenient and direct electrochemical reduction of graphene oxide. Due to the peroxidase-mimicking activity of CeO2 NP and the outstanding electrochemical properties of reduced graphene oxide, the reduction current of H2O2 was greatly enhanced. Based on this strategy, we reliably determined H2O2 down to 1.67 µM with excellent specificity and further validated its practical capabilities by robustly detecting H2O2 present in heterogeneous human serum samples. We believe that this work could serve as a new facile platform for H2O2 detection.

A CRISPR/Cas12 trans-cleavage reporter enabling label-free colorimetric detection of SARS-CoV-2 and its variants.

We present a label-free colorimetric CRISPR/Cas-based method enabling affordable molecular diagnostics for SARS-CoV-2. This technique utilizes 3,3'-diethylthiadicarbocyanine iodide (DISC2(5)) which exhibits a distinct color transition from purple to blue when it forms dimers by inserting into the duplex of the thymidine adenine (TA) repeat sequence. Loop-mediated isothermal amplification (LAMP) or recombinase polymerase amplification (RPA) was used to amplify target samples, which were subsequently subjected to the CRISPR/Cas12a system. The target amplicons would activate Cas12a to degrade nearby TA repeat sequences, preserving DISC2(5) in its free form to display purple as opposed to blue in the absence of the target. Based on this design approach, SARS-CoV-2 RNA was colorimetrically detected very sensitively down to 2 copies/µL, and delta and omicron variants of SARS-CoV-2 were also successfully identified. The practical diagnostic utility of this method was further validated by reliably identifying 179 clinical samples including 20 variant samples with 100% clinical sensitivity and specificity. This technique has the potential to become a promising CRISPR-based colorimetric platform for molecular diagnostics of a wide range of target pathogens.

A label-free and washing-free method to detect biological thiols on a personal glucose meter utilizing glucose oxidase-mimicking activity of gold nanoparticles.

We herein developed a label-free and washing-free method to detect biological thiols (biothiols) on a personal glucose meter (PGM) utilizing the intrinsic glucose oxidase (GOx)-mimicking activity of gold nanoparticles (AuNPs). By focusing on the fact that this activity could be diminished by target biothiols through their binding onto the AuNP surface, we correlated the concentration of biothiols with that of glucose readily measurable on a PGM and successfully determined cysteine (Cys), homocysteine (Hcy), and glutathione (GSH) down to 0.116, 0.059, and 0.133 µM, respectively, with high specificity against non-target biomolecules. We further demonstrated its practical applicability by reliably detecting target biothiol in heterogeneous human serum. Due to the meritorious features of PGM such as simplicity, portability, and cost-effectiveness, we believe that this work could serve as a powerful platform for biothiol detection in point-of-care settings.

Assessment of sources variability of riverine particulate organic matter with land use and rainfall changes using a three-indicator (δ13C, δ15N, and C/N) Bayesian mixing model.

In intensive agricultural watersheds, riverine particulate organic matter (POM) may be transported from many sources such as rice paddies, crop uplands, forests, and livestock farming areas during rainy seasons. However, the impacts of land-use and rainfall changes on the POM sources are not well understood. In this study, changes in the sources of riverine POM were investigated in an agricultural area of Korea between 2014 and 2020/21. During this period, land-use and rainfall patterns changed dramatically. The δ13C, δ15N, and C/N of the POM sources as well as those of riverine POM were analyzed, and a stable isotope analysis in R (SIAR) model was utilized for source apportionment. There were differences in δ13C, δ15N, and C/N among the sources. For example, manure had higher δ13C (-22.6 ± 3.3‰) and δ15N (+10.6 ± 5.9‰) than soils (from -28.0 ± 0.8‰ to -25.1 ± 1.2‰ for δ13C and +3.6 ± 1.7‰ to +9.8 ± 1.4‰ for δ15N). For soils, the δ13C and δ15N were higher for upland soils, while C/N was greater for forest soils than for others. For riverine POM, the δ15N marginally changed; however, the δ13C and C/N increased from -26.1 ± 0.9‰ to -20.8 ± 5.3‰ and from +7.7 ± 1.7 to +18.8 ± 8.3 between 2014 and 2020/21, respectively. The SIAR model showed that the contributions of paddy (from 41.0% to 14.9%) and upland fields (from 48.1% to 23.7%) to riverine POM decreased between the periods due to decreased paddy area and the implementation of best management practice on upland fields, respectively. However, the contribution of forests (from 3.5% to 28.0%) and manure (from 7.4% to 33.5%) increased probably due to improper management of forest clear-cutting sites and livestock manure storage sites. The contributions of agricultural soils to riverine POM decreased in drier years. Our study suggests that land management rather than land-use area is critical in riverine POM management, particularly in wetter years.

Colorimetric detection of individual biothiols by tailor made reactions with silver nanoprisms.

We herein described a rapid, sensitive, and selective colorimetric sensing platform for biothiols in human serum, which relies on the dual functions of biothiols as anti-etching and aggregating agent for silver nanoprisms (AgNPRs). In principle, the target biothiols that bind to the surface of AgNPRs through Ag-S covalent interactions protect the AgNPRs from being etched by chloride ion (Cl-) in human serum, thus exhibiting the blue/purple color that is indicative of AgNPRs. On the other hand, the color of AgNPRs turned to yellow in the absence of biothiols or the presence of non-sulfur-containing amino acids, indicating the formation of small silver nanoparticles (AgNPs). Importantly, we found that individual biothiols (Hcy, Cys, and GSH) exert not only the anti-etching effect, but also the aggregating effect on AgNPRs, which can be modulated by simply tuning the pH conditions, and this consequently allows for the discriminative detection of each biothiol. Based on this simple and cost-effective strategy, we successfully determined the Hcy, Cys, and GSH in human serum with high sensitivity and selectivity within 10 min, demonstrating the diagnostic capability and potential in practical applications.

Rice straw cover decreases soil erosion and sediment-bound C, N, and P losses but increases dissolved organic C export from upland maize fields as evidenced by δ13C.

Soil surface with crop residue is effective in reducing soil erosion and carbon (C), nitrogen (N), and phosphorus (P) losses from sloping fields. However, there is a high possibility that surface cover increases export of dissolved organic C (DOC) though relevant field studies under natural rainfall are lacking. In this study, the effects of surface cover with rice (Oryza sativa L.) straw on soil and CNP losses in both dissolved and sediment-bound forms from maize (Zea mays L.) fields were investigated under two fertilization levels (standard and double) × two types of runoff experiments (natural rainfall and artificial irrigation). Changes in soil properties including moisture, temperature, nutrients, and C concentration as well as maize yield were also examined. Surface cover decreased soil and total CNP losses by up to 82% across the experimental plots with some exceptions. However, surface cover increased DOC export in both natural (by 68-82% in total across all events) and artificial (by 3-4 fold) runoff, suggesting that crop residue cover may act as a DOC pollution source of water bodies. The contribution of rice straw to DOC, which was calculated using the δ13C of DOC from covered plots (-24.1 to -28.0‰) and control plots (-19.6 to -25.1‰), was 52.5-95.8%. The concentrations of K2SO4-extractable and microbial biomass C of the soils did not differ between covered and control plots, suggesting that DOC produced from rice straw was not incorporated into the soils, but rather, was washed out with surface runoff in this study. Surface cover increased maize growth and yield, particularly in double fertilization plots, through improved soil moisture, temperature, and nutrient conditions. To take full advantage of surface cover with crop residue, a further study on reducing DOC loss from crop residue needs to be conducted.