Direct identification of A-to-I editing sites with nanopore native RNA sequencing.

Inosine is a prevalent RNA modification in animals and is formed when an adenosine is deaminated by the ADAR family of enzymes. Traditionally, inosines are identified indirectly as variants from Illumina RNA-sequencing data because they are interpreted as guanosines by cellular machineries. However, this indirect method performs poorly in protein-coding regions where exons are typically short, in non-model organisms with sparsely annotated single-nucleotide polymorphisms, or in disease contexts where unknown DNA mutations are pervasive. Here, we show that Oxford Nanopore direct RNA sequencing can be used to identify inosine-containing sites in native transcriptomes with high accuracy. We trained convolutional neural network models to distinguish inosine from adenosine and guanosine, and to estimate the modification rate at each editing site. Furthermore, we demonstrated their utility on the transcriptomes of human, mouse and Xenopus. Our approach expands the toolkit for studying adenosine-to-inosine editing and can be further extended to investigate other RNA modifications.

Fractionation of metals in soil for strawberry cultivation: Effect on metal migration in food chain and application in risk assessment.

Although trace metals in strawberry production system have attracted growing attention, little is known about metal fractionation in soil for strawberry cultivation. We hypothesized that the metal fractions in soil influenced by strawberry production had significant effect on food chain transport of metals and their risk in soil. Here, samples of strawberries and soil were gathered in the Yangtze River Delta, China to verify the hypothesis. Results showed that the acid-soluble Cr, Cd, and Ni in soil for strawberry cultivation were 21.5%-88.3% higher than those in open field soil, which enhanced uptake and bioaccessible levels of these metals in strawberries. Overall, the ecological, mobility, and health risks of Pb, Zn, Ni, and Cu in soil were at a low level. However, the ecological risk of bioavailable Cd, mobility risk of Cd, and cancer risk of bioavailable Cr in over 70% of the soil samples were at moderate, high, and acceptable levels, respectively. Since the increased acid-soluble Cr and Ni in soil were related to soil acidification induced by strawberry production, nitrogen fertilizer application should be optimized to prevent soil acidification and reduce transfer of Cr and Ni. Additionally, as Cd and organic matter accumulated in soil, the acid-soluble Cd and the ecological and mobility risks of Cd in soil were enhanced. To decrease transfer and risk of Cd in soil, organic fertilizer application should be optimized to mitigate Cd accumulation, alter organic matter composition, and subsequently promote the transformation of bioavailable Cd into residual Cd in soil.

Swimming ability of Schizothoracinae fishes in Yarlung Zangbo River of China.

The Yarlung Zangbo River is a river with abundant hydropower resources but fragile biodiversity in China. As an important benchmark for both research and ecological management, there is still a lack of knowledge about the swimming ability of fishes in the Yarlung Zangbo River. The induced flow velocity (Uind), critical swimming speed (Ucrit), and burst swimming speed (Uburst) of five Schizothoracinae species were tested in this study. Relative swimming ability related to body length and body shape was calculated. The results indicated that the average absolute swimming speeds (Uind-a, Ucrit-a, and Uburst-a) of all the experimental fish were 10.20 ± 0.01, 57.58 ± 3.28, and 69.54 ± 2.94 cm/s, respectively, and the corresponding relative Uind, Ucrit, and Uburst related to body length (Uind-l, Ucrit-l, Uburst-l) were 1.15 ± 0.07, 5.04 ± 0.26, and 7.23 ± 0.28 BL/s, respectively. Moreover, relative Uind, Ucrit, and Uburst related to body shape (Uind-s, Ucrit-s, and Uburst-s) were 0.80 ± 0.13, 2.49 ± 0.51, and 4.32 ± 0.57 cm-2/s, respectively. No significantly differences in relative swimming speeds existed among five species. Only Oxygymnocypris stewartii was significantly weaker in Uburst-s than Schizothorax o'connori. The body shape showed a stronger relationship with swimming speed than the body length did. Schizothoracinae fish in the Yarlung Zangbo River basin are less sensitive to the water flow and performed weaker Ucrit and Uburst compared to those in the Yangtze River basin, indicating that Schizothoracinae fish in the Yarlung Zangbo River may be more susceptible to threats from environmental changes. The paper enriched the research on the swimming ability of Schizothoracinae fishes and provided efficient data for the fish conservation in the Yarlung Zangbo River.

Estimating the water quality index based on interpretable machine learning models.

The water quality index (WQI) is an important tool for evaluating the water quality status of lakes. In this study, we used the WQI to evaluate the spatial water quality characteristics of Dianchi Lake. However, the WQI calculation is time-consuming, and machine learning models exhibit significant advantages in terms of timeliness and nonlinear data fitting. We used a machine learning model with optimized parameters to predict the WQI, and the light gradient boosting machine achieved good predictive performance. The machine learning model trained based on the entire Dianchi Lake water quality data achieved coefficient of determination (R2), mean square error, and mean absolute error values of 0.989, 0.228, and 0.298, respectively. In addition, we used the Shapley additive explanations (SHAP) method to interpret and analyse the machine learning model and identified the main water quality parameter that affects the WQI of Dianchi Lake as NH4+-N. Within the entire range of Dianchi Lake, the SHAP values of NH4+-N varied from -9 to 3. Thus, in future water environmental governance, it is necessary to focus on NH4+-N changes. These results can provide a reference for the treatment of lake water environments.

Valence Fluctuation of Uranium Ions in Uranium Sesquinitride Revealed by Dynamical Mean-field Theory Merged with Density Functional Theory.

The electronic properties, in particular, the occupation number of 5f electrons and the valence state of U ions in uranium sesquinitride (U2 N3 ) are studied by using density functional theory (DFT) calculations merged with dynamical mean-field theory (DMFT). The results demonstrate that j=5/2 and j=7/2 manifolds are in the weakly correlated metallic and weakly correlated insulating regimes, respectively. The quasi-particle weights indicate that LS coupling scheme is more feasible for 5f electrons, which are not in the orbital-selective localized state. The weighted summation of the occupation probabilities of 5fn (n=0,1,2,3,4) atomic configurations suggests that 5f electrons have the inter-configuration fluctuation, or the mixed-valence state for U ions, together with an average occupation number of 5f electrons n5f ∼2.234, which is in good agreement with the electron localization function (ELF) and occupation analysis based on other DFT-based calculations. The 5fn -mixing-driven inter-configuration fluctuation might originate from the dual nature of 5f electrons, and the flexible electronic configuration of U ions. Finally, the so-called quasiparticle band structure is also discussed.

Restoration of a fish-attracting flow field downstream of a dam based on the swimming ability of endemic fishes: A case study in the upper Yangtze River basin.

The construction of fish passage facilities can mitigate the negative effects of dams and other water engineering construction on river connectivity and have a significant positive effect on the conservation of local fish diversity. To attract target fishes into fish passage facilities effectively, the optimal flow velocity range to attract fish must be determined. Three local endemic species of the Mishi Reservoir were considered as the protection targets. However, their swimming abilities remain unclear. Therefore, the induced swimming speed (Uind), critical swimming speed (Ucrit) and burst swimming speed (Uburst) of three fish species were tested. Based on these results, we identified the optimal flow velocity to attract fish, which falls within the range of 0.15-0.51 m/s. A validated three-dimensional hydrodynamic model was used to simulate different schemes. By comparing the flow field simulation results of different schemes, we obtained the optimal measure to restore the flow field, namely, a multiple engineering measure combining increased the fish attraction flow in the fish collection pond and the construction of a spur dike. This study offers a solution for the specific case and enhances the database of swimming characteristics of endemic fish in the upstream reaches of the Yangtze River. It also provides a valuable reference for designing fish-attracting flows and potential measures for restoring flow fields in similar future projects.

Total dissolved gases induced tolerance and avoidance behaviors in pelagic fish in the Yangtze River, China.

Total dissolved gas (TDG) supersaturation caused by dam operations can cause fish gas bubble disease (GBD) and even fish kill. Few studies have examined the effects on pelagic species. Here, we examined the tolerance and avoidance characteristics of silver carp (Hypophthalmichthys molitrix), a pelagic fish widely distributed in the Yangtze River basin in China, under stress caused by TDG supersaturation. Silver carp had an average mortality rate of 7.5% ±â€¯1.8%, 92.5% ±â€¯1.8%, and 97.5% ±â€¯1.8% under 130%, 140% and 150% TDG supersaturation for 72 h of exposure, respectively. The average median lethal time (LT50) of silver carp was 18.1 h and 8.0 h under 140% and 150% TDG supersaturation, respectively. Bubbles and congestion appeared in the fins, gills and skin of silver carp. Silver carp can detect and avoid high TDG supersaturation. Significant avoidance behaviors were displayed by silver carp and the final avoidance rate was over 80% under 130% or above TDG conditions. The results of this study indicate that 130% TDG supersaturation triggered silver carp avoidance behaviors, and can be considered as the tolerance threshold.

Interleukin-33 Promotes Th2/Th17 Response in Eosinophilic and Non-Eosinophilic Nasal Polyps.

BACKGROUND: Interleukin-33 (IL-33) is reported to be involved in Th2-skewed eosinophilic inflammation. A recent study also found that IL-33 exerted opposite effects on Th17 response in different diseases. However, the role of IL-33 in chronic rhinosinusitis with nasal polyps (NPs) was not explored. OBJECTIVES: The purpose of this study was to investigate the expression and function of IL-33 in chronic rhinosinusitis with NPs. MATERIALS AND METHODS: NP tissues from 60 NP patients and normal tissues of the inferior turbinate from 20 controls were sampled in operation. Immunochemistry was performed to identify eosinophilic or non-eosinophilic NPs. The expressions of IL-33 and Th1/2/17 cytokines were compared between different subtypes of NPs. The effect of IL-33 on Th response was detected in dispersed nasal polyp cells (DNPCs), and the signaling pathways involved in the process were detected using Western blot. RESULTS: The concentration of IL-33 was significantly elevated in both eosinophilic and non-eosinophilic NPs compared with controls. By in vitro study, we found that IL-33 can induce IL-4 and IL-5 production from eosinophilic DNPCs through the PI3K/AKT pathway, whereas IL-33 can induce IL-17 production from non-eosinophilic DNPCs through the ERK1/2 pathway. CONCLUSION: IL-33 is involved in Th2/Th17 response in NPs. Our study suggests that different types of NPs need a different treatment target.

A chemical-inducible CRISPR-Cas9 system for rapid control of genome editing.

CRISPR-Cas9 has emerged as a powerful technology that enables ready modification of the mammalian genome. The ability to modulate Cas9 activity can reduce off-target cleavage and facilitate precise genome engineering. Here we report the development of a Cas9 variant whose activity can be switched on and off in human cells with 4-hydroxytamoxifen (4-HT) by fusing the Cas9 enzyme with the hormone-binding domain of the estrogen receptor (ERT2). The final optimized variant, termed iCas, showed low endonuclease activity without 4-HT but high editing efficiency at multiple loci with the chemical. We also tuned the duration and concentration of 4-HT treatment to reduce off-target genome modification. Additionally, we benchmarked iCas against other chemical-inducible methods and found that it had the fastest on rate and that its activity could be toggled on and off repeatedly. Collectively, these results highlight the utility of iCas for rapid and reversible control of genome-editing function.

Asp141 and the Hydrogen-Bond Chain Asp141-Asn109-Asp33 Are Respectively Essential for GT80 Sialyltransferase Activity and Structural Stability.

Sialyltransferases are key enzymes involved in the biosynthesis of biologically and pathologically important sialic acid-containing molecules in nature. In this study, the activity of a putative sialyltransferase (Pm0160) harboring an inherent mutation D141Y in the conserved DDG motif, which has been identified in GT52 and GT80 families, was restored by reverse mutation. More interestingly, a hydrogen-bond chain was found to form between three conserved residues (Asp141, Asn109, and Asp33) of GT80 sialyltransferases based on recently determined crystal structures. Our mutagenesis experiments demonstrated that the hydrogen-bond chain connecting the general base Asp141 with Nß4, Nß1, and Nα1 plays an essential role in maintaining protein structural stability other than keeping the general base Asp141 in a productive orientation for sialic acid transfer.

Characterization of the zebrafish Ugt repertoire reveals a new class of drug-metabolizing UDP glucuronosyltransferases.

The zebrafish genome contains a gene superfamily of 40 Ugt genes that can be divided into Ugt1, Ugt2, and Ugt5 families. Because the encoded zebrafish UDP glucuronosyltransferase (UGT) proteins do not display orthologous relationships to any of the mammalian and avian UGT enzymes based on molecular phylogeny, it is difficult to predict their substrate specificity. Here, we mapped their tissue-specific expression patterns. We showed that the zebrafish UGT enzymes can be glycosylated. We determined their substrate specificity and catalytic activity toward diverse aglycone substrates. Specifically, we measured mRNA levels of each of the 40 zebrafish Ugt genes in 11 adult tissues and found that they are expressed in a tissue-specific manner. Moreover, functional analyses with the donor of UDP glucuronic acid (UDPGA) for each of the 40 zebrafish UGT proteins revealed their substrate specificity toward 10 important aglycones. In particular, UGT1A1, UGT1A7, and UGT1B1 displayed good glucuronidation activities toward most phenolic aglycones (4-methylumbelliferone, 4-nitrophenol, 1-naphthol, bisphenol A, and mycophenolic acid) and the two carboxylic acids (bilirubin and diclofenac). Importantly, some members of the UGT5, a novel UGT family identified recently, are capable of glucuronidating multiple aglycones with the donor cofactor of UDPGA. In particular, UGT5A5, UGT5B2, and UGT5E1 glucuronidate phenols and steroids with high specificity toward steroid hormones of estradiol and testosterone and estrogenic alkylphenols 4-tert-octylphenol. These results shed new insights into the mechanisms by which fish species defend themselves against vast numbers of xenobiotics via glucuronidation conjugations and may facilitate the establishment of zebrafish as a model vertebrate in toxicological, developmental, and pathologic studies.

A design of a nature-like fishway to solve the fractured river connectivity caused by small hydropower based on hydrodynamics and fish behaviors.

Achieving a harmonious alignment between the biological characteristics of fish and hydrodynamics patterns is crucial for ensuring the efficacy of fish passage facilities. In this study, based on the hydrodynamic characteristics of the river and the biological characteristics of fish, we evaluated the internal flow field in the nature-like fishway of Congen II hydropower station located along the Chabao river and explored methods to improve the operation efficiency. Based on comprehensive considerations of the flow field, turbulent kinetic energy, and the migration pathways of fish, it is found that the implementation of a continuous oblique bottom slope represents a more cost-effective and operationally convenient solution. The influence of different permutation of bulkheads in the nature-like fishway on operational efficiency was further examined. Our investigation revealed that the nature-like fishway with the continuous slope of 2% and the arrangement of three bulkheads in each row (model 3) exhibited a relatively simple velocity distribution and linear flow line, which poses challenges for fish in locating resting areas. In addition, the distribution of low turbulence kinetic energy area in the mainstream made it less favorable for fish to transition from the mainstream to the rest area within the fishway. The nature-like fishway with the continuous slope of 2% and the arrangement of two or three bulkheads in staggered rows (model 4) demonstrated better performance. Several potential fish migration routes for both model 3 and model 4 were proposed based on the numerical simulation results. In model 3, fish exhibited a continuous sprint through the concentrated high-speed area, which was less favorable for fish to rest and forage. In contrast, model 4 exhibited a diversified flow velocity distribution, enabling fish to make timely changes in their direction during migration. This feather proved to be advantageous in enhancing fish migration within the passage. The design of nature-like fishway in this study provides an important reference and technical support for the construction and optimization of the nature-like fishway for low dams, and is of great significance for restoring river connectivity destroyed by small hydropower construction and improving fish migration.

Tolerance threshold of a pelagic species in China to total dissolved gas supersaturation: from the perspective of survival characteristics and swimming ability.

Total dissolved gas (TDG) supersaturation downstream of dams can occur in the Yangtze River basin and is known to cause stress and even death in fish. Consequently, it is important to establish tolerance thresholds of endemic fish to protect local aquatic resources. We conducted experiments to assess survival characteristics and swimming ability of bighead carp, an important commercial fish dwelling in the Yangtze River, to evaluate its tolerance threshold to TDG supersaturation. The typical external symptoms of gas bubble trauma (GBT) were observed and the time when the fish lost equilibrium and died were recorded. The results showed that the mortality occurred when TDG level exceeded 125%, with obvious symptoms such as exophthalmos and bubbles on the head. The interval between loss of equilibrium and mortality decreased with an increase in TDG level. Neither exposure time nor TDG level significantly affected the critical swimming speed (Ucrit) of fish exposed to non-lethal exposure (110%, 120% and 125% TDG) over a 7 day period. Significant reductions in Ucrit were found under 130% and 135% TDG conditions when the exposure lasted 52.0 h and 42.9 h, respectively. The Ucrit also significantly decreased after exposure of 1.6 h under 140% TDG condition. Moreover, after exposure to 140% TDG for 39.2 h, 135% TDG for 56.5 h and 130% TDG for 95.9 h, bighead carp were transferred into air saturated water to recover for 24 h or 48 h; however, swimming performance remained impaired. The results of this study indicate that 125% TDG was the highest TDG level where limited mortality was observed and the swimming ability was not impaired, showing that 125% TDG can be set as the tolerance threshold of this species to guide the operation of dams in the Yangtze River Basin.

A wearable and flexible lactic-acid/O2 biofuel cell with an enhanced air-breathing biocathode.

The performance of biocathode in an enzymatic biofuel cell (EBFC) in the real application is somehow overlooked. Herein, a wearable and flexible lactic-acid/O2 EBFC enhanced with an air-breathing biocathode is designed to solve the limitation of biocathode that arises from the low solubility and slow mass transfer of the dissolved oxygen. To improve the oxygen supply efficiency for the air-breathing biocathode, a superhydrophobic base electrode creating an efficient air-solid-liquid triphase interface is developed. The designed EBFC with an 'island-bridge' configuration is integrated by assembling the current collectors of air-breathing biocathode and bioanode on a commercial laminating film (LF) screen-printed with a noninterfering circuit. It is found that the biocathode/bioanode area ratio should exceed 9:1 so that the designed EBFC (1A//9C) can achieve the optimal performance. This EBFC delivers an open circuit voltage of ca. 0.75 V and outputs a maximum power density of ca. 1.78 mW cm-2. In addition, a scaled-up EBFC (total bioanode area: 1.5 cm2) successfully powers a self-developed low-power device of heartrate in the pulse operation mode when applied on a volunteer's arm.

Conflict between urbanization and water environmental protection: Lessons from the Xiangjiang River Basin in China.

China, the largest developing country, has experienced rapid urbanization since its reform and opening-up. However, the increasing pollution load from urban areas has deteriorated urban river water quality, contradicting the concept of sustainable and green development promoted by the Chinese government. This situation elucidates governmental shortcomings in systematic environmental protection. Our study revealed that the current wastewater treatment plant (WWTP) discharge standards in urban areas are insufficient for attaining the desired urban river water quality and thus intensify the conflict between urbanization and water environmental protection. As urbanization continues, the urban population will grow, further exacerbating pollution and conflict. Our focus was the Xiangjiang River basin in Zunyi, a typical urbanized city in China. Using a validated one-dimensional mathematical model, we compared the water quality in the Xiangjiang River between current and upgraded WWTP discharge standards. The results showed that the water quality in the Xiangjiang River falls short of the standards, with more than 60 % of the river exceeding limits. However, upgrading WWTP discharge standards significantly reduces the proportion of river sections exceeding limits, with only 0.4 % exceeding standards during specific periods. This enhancement greatly improved the Xiangjiang River's water quality, aided in restoring the entire water environment in the basin, and supported water environmental protection goals. Our research findings offer crucial support for local governments in shaping comprehensive water environmental protection policies and insights for addressing similar environmental challenges caused by rapid urbanization in other developing regions.

Determining the position of a fish passage facility entrance based on endemic fish swimming abilities and flow field.

Hydropower development can significantly mitigate climate change and reduce carbon emissions, but it can also have substantial negative impacts on river environments and fish biodiversity. Fish passage facilities are built to ensure sustainable hydropower development and the biodiversity of fish populations. The locations of the entrances to these facilities play a key role in their efficiency. This study presents a reliable approach that combines the swimming ability of fish and a numerical flow field simulation to determine the optimal location for a fish passage facility entrance. In this study, we used the Gujun Reservoir upstream of the Yangtze River as a case study. A field experiment was conducted, and the swimming abilities of eight endemic fish species in the upstream region of the Yangtze River were measured. Among the tested species, the fastest induced swimming speed (0.14 m/s) was achieved by Glyptothorax sinense, while the slowest critical swimming speed (0.30 m/s) was observed for Paracobitis potanini. We propose that the velocity near the fish passage facility entrance should be higher than the maximum induced swimming speed and lower than the minimum critical swimming speed, making the suitable range between 0.14 and 0.30 m/s. On this basis, velocity fields 500 m downstream of the dam of the Gujun Reservoir under 4 operating conditions with discharge flows of 5.7 m3/s, 23.3 m3/s, 32.5 m3/s, and 41.1 m3/s were calculated. The results showed that the flow field variation downstream of the dam was between 0.1 and 0.9 m/s. After comparing the suitable areas for the target species, the left bank at location 2 was recommended as the optimal location for the fish passage facility entrance in the Gujun Reservoir.

Effect of total dissolved gas supersaturation and flow velocity on survival and swimming ability of juvenile Schizothorax prenanti.

Although developing large-scale hydropower cascades in the upper Yangtze River effectively improves the hydropower resource utilization, it produces total dissolved gas (TDG) supersaturation. In the flood season, the high level of TDG supersaturation (TDGS) frequently occurs in the downstream of dams, causing migratory fish to suffer from gas bubble trauma (GBT) and reducing their survival and swimming ability. Currently, there is a deficiency in particular approaches to evaluate the ecological hazard posed by TDGS on migratory fish as they traverse different flow velocities within their migratory routes. This study assessed the vulnerability of juvenile Schizothorax prenanti (S. prenanti) to GBT from the static setting to 9.0 BL/s during exposure to nominal levels of 100%, 110%, 120% and 130% TDG. The mortality occurs when the flow velocity surpasses 6.0 and 7.5 BL/s in 100% and 110% TDG levels, respectively. For fish exposed to 120% and 130% TDG levels, the relationship between survival time and flow velocity is an approximately inverse bell-shaped curve with increasing velocity. The optimal velocity of maximal survival time of juvenile S. prenanti is 3.0 and 4.5 BL/s in 120% and 130% TDG-supersaturated water. Both TDG level and flow velocity significantly affect burst swimming speed (Uburst) and critical swimming speed (Ucrit). The cases involving GBT showed substantial declines in Uburst and Ucrit, exceeding 6.0 BL/s and TDG levels greater than 120%. The results may contribute to formulating a specific management strategy for hydropower operation during the migratory period and conserving vulnerable species in the Yangtze River.

Quantitative assessment methodology framework of the impact of global climate change on the aquatic habitat of warm-water fish species in rivers.

Global climate change (GCC), with global warming as the main characteristic, has become a global issue widely concerned by people. GCC impacts the hydrological regime at the watershed scale and affects the hydrodynamic force and the habitat conditions of freshwater ecosystems at the river scale. The impact of GCC on water resources and the water cycle is a research hotspot. However, there are few studies on water environment ecology related to hydrology and the influence of changes in discharge and water temperature on warm-water fish habitats. This study proposes a quantitative assessment methodology framework for predicting and analyzing the impact of GCC on the warm-water fish habitat. This system integrates GCC, downscaling, hydrological, hydrodynamic, water temperature and habitat models and was applied to the middle and lower reaches of the Hanjiang River (MLHR), where there are four major Chinese carps resource reduction problems. The results showed that the calibration and validation of the statistical downscaling model (SDSM) and the hydrological, hydrodynamic, and water temperature models were carried out using the observed meteorological factors, discharge, water level, flow velocity and water temperature data. The change rule of the simulated value was in good agreement with the observed value, and the models and methods used in the quantitative assessment methodology framework were applicable and accurate. The rise of water temperature caused by GCC will ease the problem of low-temperature water in the MLHR, and the weighted usable area (WUA) for spawning of the four major Chinese carps will appear in advance. Meanwhile, the increase in future annual discharge will play a positive role in WUA. In general, the rise in confluence discharge and water temperature caused by GCC will increase WUA, which is beneficial to the spawning ground of four major Chinese carps.

Protein engineering for electrochemical biosensors.

The development of electrochemical biosensors has gained tremendous attention. Protein engineering has been applied for enhancing properties of native redox enzymes, such as selectivity, sensitivity, and stability required for applicable biosensors. This review highlights recent advances of protein engineering to improve enzymatic catalysis of biosensors, facilitate electron transfer and enzyme immobilization, and construct allosteric protein biosensors. The pros and cons of different protein engineering strategies are briefly discussed, and perspectives are further provided.