DNA topology regulates PAM-Cas9 interaction and DNA unwinding to enable near-PAMless cleavage by thermophilic Cas9.

CRISPR-Cas9-mediated genome editing depends on PAM recognition to initiate DNA unwinding. PAM mutations can abolish Cas9 binding and prohibit editing. Here, we identified a Cas9 from the thermophile Alicyclobacillus tengchongensis for which the PAM interaction can be robustly regulated by DNA topology. AtCas9 has a relaxed PAM of N4CNNN and N4RNNA (R = A/G) and is able to bind but not cleave targets with mutated PAMs. When PAM-mutated DNA was in underwound topology, AtCas9 exhibited enhanced binding affinity and high cleavage activity. Mechanistically, AtCas9 has a unique loop motif, which docked into the DNA major groove, and this interaction can be regulated by DNA topology. More importantly, AtCas9 showed near-PAMless editing of supercoiled plasmid in E. coli. In mammalian cells, AtCas9 exhibited broad PAM preference to edit plasmid with up to 72% efficiency and effective base editing at four endogenous loci, representing a potentially powerful tool for near-PAMless editing.

N-Heterocyclic Carbene-Derived 1,3,5-Trimethylenebenzene: On-Surface Synthesis and Electronic Structure.

1,3,5-Trimethylenebenzene (1,3,5-TMB), a 3-fold-symmetric triradical with a high-spin ground state, is an attractive platform for investigating the unique spin properties of π-conjugated triangular triradicals. Here, we report the on-surface synthesis of N-heterocyclic carbene (NHC)-derived 1,3,5-TMB (N-TMB) via surface-assisted C-C and C-N coupling reactions on Au(111). The chemical and electronic structures of N-TMB on the Au(111) surface are revealed with atomic precision using scanning tunneling microscopy and noncontact atomic force microscopy, combined with density functional theory (DFT) calculations. It is demonstrated that there is substantial charge transfer between N-TMB and the substrate, resulting in a positively charged N-TMB on Au(111). DFT calculations at the UB3LYP/def2-TZVP level of theory and multireference method, e.g., CASSCF/NEVPT2, indicate that N-TMB possesses a doublet ground state with reduced Cs symmetry in the gas phase, contrasting the quartet ground state of 1,3,5-TMB with D3h symmetry, and exhibits a doublet-quartet energy gap of -0.80 eV. The incorporation of NHC structures and the extended π-conjugation promote the spin-orbital overlaps in N-TMB, leading to Jahn-Teller distortion and the formation of a robust doublet state. Our results not only demonstrate the fabrication of polyradicals based on NHC but also shed light on the effect of NHC and π-conjugation on the electronic structure and spin coupling, which opens up new possibilities for precisely regulating the spin-spin exchange coupling of organic polyradicals.

Silver Surface-Assisted Dehydrobrominative Cross-Coupling between Identical Aryl Bromides.

Cross-coupling reactions represent an indispensable tool in chemical synthesis. An intriguing challenge in this field is to achieve selective cross-coupling between two precursors with similar reactivity or, to the limit, the identical molecules. Here we report an unexpected dehydrobrominative cross-coupling between 1,3,5-tris(2-bromophenyl)benzene molecules on silver surfaces. Using scanning tunneling microscopy, we examine the reaction process at the single-molecular level, quantify the selectivity of the dehydrobrominative cross-coupling, and reveal the modulation of selectivity by substrate lattice-related catalytic activity or molecular assembly effect. Theoretical calculations indicate that the dehydrobrominative cross-coupling proceeds via regioselective C-H bond activation of debrominated TBPB and subsequent highly selective C-C coupling of the radical-based intermediates. The reaction kinetics plays an important role in the selectivity for the cross-coupling. This work not only expands the toolbox for chemical synthesis but also provides important mechanistic insights into the selectivity of coupling reactions on the surface.

Plasma neuron specific enolase (NSE), tumour necrosis factor-alpha (TNF-α) and soluble IL-2 receptor alpha (sIL-2Rα) levels in children with developmental delay (DD): Use of combined ROC curves to increase their diagnostic value.

BACKGROUND: Developmental delay (DD) occurs when children fail to reach developmental milestones in comparison to peers of the same age range. However, there are no valuable biomarkers for the early diagnosis of DD. Since there is no specific marker for screening the disease, we evaluated plasma NSE, TNF-α and sIL2-Rα as potential markers for this purpose. METHODS: In this cross-sectional randomized case-control study, a total of 174 DD patients and 49 matched elderly controls aged between 2 months and 60 months were recruited. A sensitive enzyme-linked immunosorbent assay and an immunoradiometric assay were used to evaluate the levels of plasma IL-1, IL-6, IL-8, IL-10, sIL2-Rα, TNF-α, and NSE. Statistical analyses using t test, χ2, ANOVA, ROC curves and binary logistic regression models were performed. RESULTS: In comparison to the control group, the DD group had greater levels of NSE, TNF-α, and sIL2-Rα(p < 0.05). In the binary logistic regression analysis of DD, NSE had an odds ratio (OR) of 1.783 (95 % CI 1.297 to 2.451, p = 0.000), indicating that NSE was an independent risk factor for DD. The plasma TNF-α level was positively correlated with plasma NSE and sIL2-Rα levels in the DD group (r = 0.366 and 0.433, respectively), and the DQ score and plasma sIL2-Rα level in the DD group were positively correlated. The ROC curve revealed that the respective areas under the NSE, TNF-α, and sIL2-Rα ROC curves were 0.9797, 0.9365, and 0.8533, respectively. Moreover, a significant increase in AUC was observed using combined ROC curve analysis. CONCLUSIONS: Children with DD have significantly altered plasma concentrations of sIL2-Rα, NSE, and TNF-α. NSE, TNF-α and sIL2-Rα can be used as DD blood biomarkers. This information may be helpful in early diagnosis and intervention.

Incidence of noninvasive ventilation failure and mortality in patients with acute respiratory distress syndrome: a systematic review and proportion meta-analysis.

BACKGROUND: Noninvasive ventilation (NIV) is commonly used in patients with acute respiratory distress syndrome (ARDS). However, the incidence and distribution of treatment failure are unclear. METHODS: A comprehensive online search was conducted to select potentially eligible studies with reports of the rate of NIV failure in patients with ARDS. A manual search was also performed to identify additional studies. Data were extracted to calculate the pooled incidences of NIV failure and mortality. Based on oxygenation, the severity of the disease was classified as mild, moderate, or severe ARDS. Based on etiologies, ARDS was defined as being of pulmonary origin or extrapulmonary origin. RESULTS: We enrolled 90 studies in this meta-analysis, involving 98 study arms. The pooled incidence of NIV failure was 48% (n = 5847, 95% confidence interval [CI]: 43-52%). The pooled incidence of ICU mortality was 29% (n = 2363, 95%CI: 22-36%), and that of hospital mortality was 33% (n = 2927, 95%CI: 27-40%). In patients with mild, moderate, and severe ARDS, the pooled incidence of NIV failure was 30% (n = 819, 95%CI: 21-39%), 51% (n = 1332, 95%CI: 43-60%), and 71% (n = 525, 95%CI: 62-79%), respectively. In patients with pulmonary ARDS, it was 45% (n = 2687, 95%CI: 39-51%). However, it was 30% (n = 802, 95%CI: 21-38%) in those with extrapulmonary ARDS. In patients with immunosuppression, the incidence of NIV failure was 62% (n = 806, 95%CI: 50-74%). However, it was 46% (n = 5041, 95%CI: 41-50%) in those without immunosuppression. CONCLUSIONS: Nearly half of patients with ARDS experience NIV failure. The incidence of NIV failure increases with increasing ARDS severity. Pulmonary ARDS seems to have a higher rate of NIV failure than extrapulmonary ARDS. ARDS patients with immunosuppression have the highest rate of NIV failure.

PaCO2 is nonlinearly associated with NIV failure in patients with hypoxemic respiratory failure.

OBJECTIVE: To explore the association between PaCO2 and noninvasive ventilation (NIV) failure in patients with hypoxemic respiratory failure. METHODS: A retrospective study was performed in a respiratory ICU of a teaching hospital. Patients admitted to ICU between 2011 and 2019 were screened. We enrolled the patients with hypoxemic respiratory failure. However, patients who used NIV due to acute-on-chronic respiratory failure or heart failure were excluded. Data before the use of NIV were collected. Requirement of intubation was defined as NIV failure. RESULTS: A total of 1029 patients were enrolled in final analysis. The rate of NIV failure was 45% (461/1029). A nonlinear relationship between PaCO2 and NIV failure was found by restricted cubic splines (p = 0.03). The inflection point was 32 mmHg. The rate of NIV failure was 42% (224/535) in patients with PaCO2 >32 mmHg. However, it increased to 48% (237/494) in those with PaCO2 ≤ 32 mmHg. The crude and adjusted hazard ratio (HR) for NIV failure was 1.36 (95%CI:1.13-1.64) and 1.23(1.01-1.49), respectively, if the patients with PaCO2 >32 mmHg were set as reference. In patients with PaCO2 ≤ 32 mmHg, one unit increment of PaCO2 was associated with 5% reduction of NIV failure. However, it did not associate with NIV failure in patients with PaCO2 >32 mmHg. CONCLUSIONS: PaCO2 and NIV failure was nonlinear relationship. The inflection point was 32 mmHg. Below the inflection point, lower PaCO2 was associated with higher NIV failure. However, it did not associate with NIV failure above this point.

Genome-wide identification of Aux/IAA and ARF gene families reveal their potential roles in flower opening of Dendrobium officinale.

BACKGROUND: The auxin indole-3-acetic acid (IAA) is a vital phytohormone that influences plant growth and development. Our previous work showed that IAA content decreased during flower development in the medicinally important orchid Dendrobium officinale, while Aux/IAA genes were downregulated. However, little information about auxin-responsive genes and their roles in D. officinale flower development exists. RESULTS: This study validated 14 DoIAA and 26 DoARF early auxin-responsive genes in the D. officinale genome. A phylogenetic analysis classified the DoIAA genes into two subgroups. An analysis of cis-regulatory elements indicated that they were related by phytohormones and abiotic stresses. Gene expression profiles were tissue-specific. Most DoIAA genes (except for DoIAA7) were sensitive to IAA (10 µmol/L) and were downregulated during flower development. Four DoIAA proteins (DoIAA1, DoIAA6, DoIAA10 and DoIAA13) were mainly localized in the nucleus. A yeast two-hybrid assay showed that these four DoIAA proteins interacted with three DoARF proteins (DoARF2, DoARF17, DoARF23). CONCLUSIONS: The structure and molecular functions of early auxin-responsive genes in D. officinale were investigated. The DoIAA-DoARF interaction may play an important role in flower development via the auxin signaling pathway.

Identification of the CONSTANS-like family in Cymbidium sinense, and their functional characterization.

BACKGROUND: Cymbidium sinense is an orchid that is typically used as a potted plant, given its high-grade ornamental characteristics, and is most frequently distributed in China and SE Asia. The inability to strictly regulate flowering in this economically important potted and cut-flower orchid is a bottleneck that limits its industrial development. Studies on C. sinense flowering time genes would help to elucidate the mechanism regulating flowering. There are very few studies on the genetic regulation of flowering pathways in C. sinense. Photoperiod significantly affects the flowering of C. sinense, but it was unknown how the CONSTANS gene family is involved in regulating flowering. RESULTS: In this study, eight CONSTANS-like genes were identified and cloned. They were divided into three groups based on a phylogenetic analysis. Five representative CsCOL genes (CsCOL3/4/6/8/9) were selected from the three groups to perform expression characterization and functional study. CsCOL3/4/6/8/9 are nucleus-localized proteins, and all five CsCOL genes were expressed in all organs, mainly in leaves followed by sepals. The expression levels of CsCOL3/4 (group I) were higher in all organs than other CsCOL genes. Developmental stage specific expression revealed that the expression of CsCOL3/4/9 peaked at the initial flowering stage. In contrast, the transcript level of CsCOL6/8 was highest at the pedicel development stage. Photoperiodic experiments demonstrated that the transcripts of the five CsCOL genes exhibited distinct diurnal rhythms. Under LD conditions, the overexpression of CsCOL3/4 promoted early flowering, and CsCOL6 had little effect on flowering time, whereas CsCOL8 delayed flowering of Arabidopsis thaliana. However, under SD conditions, overexpression of CsCOL4/6/8 promoted early flowering and the rosette leaves growth, and CsCOL3 induced flower bud formation in transgenic Arabidopsis. CONCLUSION: The phylogenetic analysis, temporal and spatial expression patterns, photoperiodic rhythms and functional study indicate that CsCOL family members in C. sinense were involved in growth, development and flowering regulation through different photoperiodic pathway. The results will be useful for future research on mechanisms pertaining to photoperiod-dependent flowering, and will also facilitate genetic engineering-based research that uses Cymbidium flowering time genes.

High-performance anti-reflection micro-forests on aluminium alloy fabricated by laser induced competitive vapor deposition.

Surfaces with strong anti-reflection properties have attracted the wide attention of scientists and engineers due to their great application potential in many fields. Traditional laser blackening techniques are limited by the material and surface profile, which are not able to be applied to film and large-scale surfaces. Inspired by the rainforest, a new design for anti-reflection surface structures was proposed by constructing micro-forests. To evaluate this design, we fabricated micro-forests on an Al alloy slab by laser induced competitive vapor deposition. By controlling the deposition of the laser energy, the surface can be fully covered by forest-like micro-nano structures. The porous and hierarchical micro-forests performed a minimum and average reflectance of 1.47% and 2.41%, respectively, in the range of 400-1200 nm. Different from the traditional laser blackening technique, the micro-scaled structures were formed due to the aggregation of the deposited nanoparticles instead of the laser ablation groove. Therefore, this method would lead to little surface damage and can also be applied to the aluminum film with a thickness of 50 µm. The black aluminum film can be used to produce the large-scale anti-reflection shell. Predictably, this design and the LICVD method are simple and efficient, which can broaden the application of the anti-reflection surface in many fields such as visible-light stealth, precision optical sensors, optoelectronic devices, and aerospace radiation heat transfer device.

Large scanning field laser concurrent drilling system with a five-axis independent control for special-shaped holes.

Five-axis laser scanning technology is an effective drilling method for special-shaped holes. Due to a gap in laser angle-of-incidence (AOI) control within a large scanning field, current technologies are challenging for fabricating large-size holes or special-shaped hole arrays. In this paper, a large scanning field five-axis laser concurrent drilling system was proposed. The laser AOI was independently controlled using two pairs of synchronous deflection mirrors. The laser control deviations under a large scanning field were investigated systematically by simulation and experiment. By establishing a complete correction method, the laser AOI control within a scanning field diameter of up to 35 mm was achieved. A series of special-shaped holes were fabricated concurrently on a 3.6 mm thick glass fiber reinforced plastic (GFRP), verifying that the AOI can be controlled by the five-axis laser scanning system. Our work provides a novel method to increase the scanning field of the five-axis laser scanning technology, expanding the application scope of the five-axis laser processing.

Tunable metasurface for independent controlling radar stealth properties via geometric and propagation phase modulation.

Metasurfaces have been verified as an ideal way to control electromagnetic waves within an optically thin interface. In this paper, a design method of a tunable metasurface integrated with vanadium dioxide (VO2) is proposed to realize independent control of geometric and propagation phase modulation. The reversible conversion of VO2 between insulator phase and metal phase can be realized by controlling the ambient temperature, which enables the metasurface to be switched quickly between split-ring and double-ring structures. The phase characteristics of 2-bit coding units and the electromagnetic scattering characteristics of arrays composed of different arrangements are analyzed in detail, which confirms the independence of geometric and propagation phase modulation in the tunable metasurface. The experimental results demonstrate that the fabricated regular array and random array samples have different broadband low reflection frequency bands before and after the phase transition of VO2, and the 10 dB reflectivity reduction bands can be switched quickly between C/X and Ku bands, which are in good agreement with the numerical simulation. This method realizes the switching function of metasurface modulation mode by controlling the ambient temperature, which provides a flexible and feasible idea for the design and fabrication of stealth metasurfaces.

Single-pass cutting of frosted glass via change of laser incident medium.

We report a water medium-assisted composite laser cutting (WMACLC) technology for what is believed to be the first time to achieve single-pass separation of frosted glass (FG). The water medium was used to flatten the surface of FG to reduce the diffuse reflection and random refraction of the incident laser. The simulation results of picosecond pulsed laser Bessel beam (PPLBB) intensity distribution in FG showed that the peak intensity in the presence of water can reach about 24 times and 2.3 times that in the absence of water when the PPLBB is 0.08 mm and 0.3 mm below the upper surface of FG, respectively. A PPLBB with higher intensity can be formed along the thickness direction to realize the material modification. A coaxial CW laser provides the thermal tensile stress required for separation. Finally, high-quality separation of FG was achieved using the WMACLC technology with a speed of 50 mm/s. No deviation in the separation track and no edge collapse occurred. The roughness Sa of the separated sidewall is less than 0.3 µm.

Extending the 3D scanning range of reflective dynamic focusing device-based laser scanners.

Reflective dynamic focusing devices (RDFDs) have shown their potential in laser scanning as high-performance laser Z-direction focusing devices. However, the scanning range of RDFD-based scanners is limited by aberrations during dynamic focusing. An aspheric symmetry correction (ASC) method was proposed to extend the effective scanning range. An aspheric lens was introduced to correct the optical path difference (OPD) and optimize aberrations. As a result, the scanning range in the three-dimensional (3D) space increased by 15.2%. The ASC method has been proven to extend the 3D scanning range of RDFD-based scanners and may have broad application prospects.

A GH42 ß-galactosidase from Bifidobacterium thermophilum: Biochemical characterization and synthesis of galactosyl glycerol by reverse hydrolysis.

In this study, a ß-galactosidase gene (btgal42) was first cloned from Bifidobacterium thermophilum and successfully expressed in Escherichia coli. The molecular weight of the purified BtGal42 was estimated to be 78 kDa by the sodium dodecyl sulfate-polyacrylamide gel electrophoresis and 225 kDa by the size-exclusion chromatography, indicating that the native BtGal42 was a homotrimer. BtGal42 belonged to the glycosidase hydrolase family 42, exhibiting the maximum activity at pH of 7 and at temperature of 50°C. The enzyme displayed a strictly specific activity toward substrates with ß-galactosyl linkages at the nonreducing ends, of which the activity on 4-nitrophenyl-ß-d-galactopyranoside was the highest, followed by 2-nitrophenyl-ß-d-galactopyranoside and lactose. Among the tested metals and reagents, BtGal42 showed tolerance in the presence of various organic solvents. Importantly, BtGal42 exhibited a high reverse hydrolysis activity when using galactose as the donor and the di-alcohol ethylene glycol and the trialcohol glycerol as the acceptors. Under unoptimized reaction conditions, the galactosyl glycerol yield reached 62.2 g/L (galactose conversion rate, 41.2%). This study might provide a feasible method for the biosynthesis of galactosyl glycerol from low-cost glycerol and galactose, which was associated with high conversion efficiency and few byproducts.

Shengjie Tongyu Decoction Regulates Cardiomyocyte Autophagy Through Modulating ROS-PI3K/Akt/mTOR Axis by LncRNA H19 in Diabetic Cardiomyopathy.

Context: Diabetic cardiomyopathy (DCM) is particularly dangerous in diabetes mellitus (DM). The Shengjie Tongyu decoction (SJTYD) is a well-known, traditional Chinese medicinal formulation that practitioners use to treat myocardial diseases in China; however, its role in DCM remain unclear. Objective: The study intended to investigate: (1) SJTYD's role in the treatment of DCM and its underlying mechanisms, (2) the association of autophagy with DCM, and (3) the involvement of mammalian target of rapamycin (mTOR) signaling in the regulation of DCM. Design: The research team performed an animal study. Setting: The study took place in the Department of Endocrinology in the No. 2 ward-Traditional and Complementary Medicine(TCM) of the China-Japan Friendship Hospital in Beijing, China. Animals: The animals were 60 C57/BL6 mice weighing 200-250 g. Intervention: To determine the role of SJTYD in treating DCM, the research team established a mouse model of DM using streptozotocin (STZ). The team randomly divided the mice into three groups with 20 mice each: (1) a negative control group, which didn't receive injections of STZ or treatment with SJTYD; (2) a model group, the Model group, which received injections of STZ but didn't receive treatment with SJTYD; and (3) an SJTYD group, which received injections of STZ and treatment with SJTYD. Outcome Measures: The research team: (1) conducted a differential analysis to identify the differentially expressed genes; (2) performed deep sequencing of the long noncoding RNAs (lncRNAs) expressed in cardiomyocytes from the control, Model, and SJTYD groups ; (3) performed a bioinformatics analysis; (4) used the ultrasonic and pathological, transmission electron microscopy (TEM) test as well as a Western blot to evaluate cardiac function, myocardial-injury areas, and autophagy in vivo; (5) transfected primary cardiomyocytes treated them with lncRNA H19 and SJTY 3-MA to establish SJTYD subgroups in which the H19 protected against DCM and the 3-MA inhibited autophagy; and (6) carried out immunofluorescence staining and Western blot to test the phosphorylated levels of phosphoinositide 3-kinase (PI3K)/ protein kinase B (AKT)/ mammalian target of rapamycin (mTOR) as well as autophagy levels in vitro. Results: The bioinformatics analysis indicated that SJTYD significantly modulated lncRNA H19 as well as the mTOR pathway. The vevo2100's results indicated the SJTYD reversed the cardiac-dysfunction parameters in DCM. The Masson' staining, TEM, and Western blot demonstrated that the SJTYD could suppress the myocardial-injury areas as well as the numbers of autophagosomes and the expression proteins of autophagy in vivo. The SJTYD promoted the phosphorylated-levels of PI3K, AKT, and mTOR and decreased the levels of autophagy proteins. LC3A-II and Beclin-1; lncRNA H19 amplified the SJTYD's role; and 3-MA reversed those effects, as tested using immunofluorescence and Western blot in primary cardiomyocytes. Conclusions: The SJTYD can protect against diabetic myocardial injury by inhibiting cardiomyocyte autophagy through the activation of lncRNA H19, reactive oxygen species (ROS), and the PI3K/Akt/mTOR signaling pathway. SJTYD may be an effective strategy to ameliorate diabetic myocardial injuries.

Expression of the gonad-specific small heat shock protein, CfHSP20.2, in the spruce budworm, Choristoneura fumiferana (Clem.).

Small heat shock proteins (sHSPs) play important roles in insect development and stress resistance. However, the in vivo functions and mechanisms of action remain largely unknown or unclear for most members of the sHSPs in insects. This study investigated the expression of CfHSP20.2 in the spruce budworm, Choristoneura fumiferana (Clem.) under normal and heat-stress conditions. Under normal conditions, CfHSP20.2 transcript and protein were highly and constantly expressed in the testes of male larvae, pupae and young adults and in the ovaries of female late-stage pupae and adults. After adult eclosion, CfHSP20.2 remained highly and almost constantly expressed in the ovaries, but in contrast, was downregulated in the testes. Upon heat stress, CfHSP20.2 was upregulated in the gonads and non-gonadal tissues in both sexes. These results indicate that CfHSP20.2 expression is gonad-specific and heat-inducible. This provides evidence that the CfHSP20.2 protein plays important roles during reproductive development under normal environmental conditions, while under heat-stress conditions, it may also enhance the thermal tolerance of the gonads and non-gonadal tissues.

ERF5 enhances protocorm-like body regeneration via enhancement of STM expression in Dendrobium orchid.

Orchid plants develop protocorms upon germination and produce protocorm-like structures called protocorm-like bodies (PLBs) from protocorms and somatic cells via tissue culture. Protocorm-like bodies have broad technical application potential in the orchid industry and their regeneration is a distinct developmental process in the plant kingdom. However, little is known about this unparalleled developmental program. In this study, we identified a PLB-abundant gene, ethylene response factor (ERF), and a transcription factor named DoERF5, and determined its important role in PLB regeneration in Dendrobium orchid. Overexpression of DoERF5 in Dendrobium greatly enhanced the PLB regeneration from PLB and stem explants, and upregulated the expression of WOUND-INDUCED DEDIFFERENTIATION (DoWIND) homologs and SHOOT MERISTEMLESS (DoSTM), as well as the genes involved in cytokinin biosynthesis (DoIPT) and the cytokinin response factors (DoARRs). However, silencing DoERF5 reduced the regeneration rate of PLBs, and downregulated the expression of DoWIND homologs, DoSTM and DoARRs. We demonstrated that DoERF5 is directly bound to the DoSTM promoter and regulates its expression. In addition, overexpression of DoSTM in Dendrobium orchid resulted in favorable regeneration of PLBs. Our results clarify that DoERF5 regulates the regeneration of PLB by enhancing DoSTM expression. Our findings provide new insights into how DoERF5 mediates PLB regeneration and offers technical potential in improving clonal propagation, preservation, and the bioengineering of orchids.

Key emergency response technologies for abrupt air pollution accidents in China.

Abrupt air pollution accidents can endanger people's health and destroy the local ecological environment. The appropriate emergency response can minimize the harmful effects of accidents and protect people's lives and property. This paper provides an overview of the key emergency response technologies for abrupt air pollution accidents around the globe with emphasis on the major achievements that China has obtained in recent years. With decades of effort, China has made significant progress in emergency monitoring technologies and equipment, source estimation technologies, pollutant dispersion simulation technologies and others. Many effective domestic emergency monitoring instruments (e.g., portable DOAS/FT-IR systems, portable FID/PID systems, portable GC-MS systems, scanning imaging remote sensing systems, and emergency monitoring vehicles) had been developed which can meet the demands for routine emergency response activities. A monitoring layout technique combining air dispersion simulation, fuzzy comprehensive evaluation, and a post-optimality analysis was proposed to identify the optimal monitoring layout scheme under the constraints of limited monitoring resources. Multiple source estimation technologies, including the forward method and the inversion method, have been established and evaluated under various scenarios. Multi-scale dynamic pollution dispersion simulation systems with high temporal and spatial resolution were further developed. A comprehensive emergency response platform integrating database support, source estimation, monitoring schemes, fast monitoring of pollutants, pollution predictions and risk assessment was developed based on the technical idea of "source identification - model simulation - environmental monitoring" dynamic interactive feedback. It is expected that the emergency response capability for abrupt air pollution accidents will gradually improve in China.

Atmospheric environment monitoring technology and equipment in China: A review and outlook.

Accurate monitoring of the atmospheric environment and its evolution are important for understanding the sources, chemical mechanisms, and transport processes of air pollution and carbon emissions in China, and for regulatory and control purposes. This study gives an overview of atmospheric environment monitoring technology and equipment in China and summarizes the major achievements obtained in recent years. China has made great progress in the development of atmospheric environment monitoring technology and equipment with decades of effort. The manufacturing level of atmospheric environment monitoring equipment and the quality of products have steadily improved, and a technical & production system that can meet the requirements of routine monitoring activities has been initiated. It is expected that domestic atmospheric environment monitoring technology and equipment will be able to meet future demands for routine monitoring activities in China and provide scientific assistance for addressing air pollution problems.

ProbeTools: designing hybridization probes for targeted genomic sequencing of diverse and hypervariable viral taxa.

BACKGROUND: Sequencing viruses in many specimens is hindered by excessive background material from hosts, microbiota, and environmental organisms. Consequently, enrichment of target genomic material is necessary for practical high-throughput viral genome sequencing. Hybridization probes are widely used for enrichment in many fields, but their application to viral sequencing faces a major obstacle: it is difficult to design panels of probe oligo sequences that broadly target many viral taxa due to their rapid evolution, extensive diversity, and genetic hypervariability. To address this challenge, we created ProbeTools, a package of bioinformatic tools for generating effective viral capture panels, and for assessing coverage of target sequences by probe panel designs in silico. In this study, we validated ProbeTools by designing a panel of 3600 probes for subtyping the hypervariable haemagglutinin (HA) and neuraminidase (NA) genome segments of avian-origin influenza A viruses (AIVs). Using in silico assessment of AIV reference sequences and in vitro capture on egg-cultured viral isolates, we demonstrated effective performance by our custom AIV panel and ProbeTools' suitability for challenging viral probe design applications. RESULTS: Based on ProbeTool's in silico analysis, our panel provided broadly inclusive coverage of 14,772 HA and 11,967 NA reference sequences. For each reference sequence, we calculated the percentage of nucleotide positions covered by our panel in silico; 90% of HA and NA references sequences had at least 90.8 and 95.1% of their nucleotide positions covered respectively. We also observed effective in vitro capture on a representative collection of 23 egg-cultured AIVs that included isolates from wild birds, poultry, and humans and representatives from all HA and NA subtypes. Forty-two of forty-six HA and NA segments had over 98.3% of their nucleotide positions significantly enriched by our custom panel. These in vitro results were further used to validate ProbeTools' in silico coverage assessment algorithm; 89.2% of in silico predictions were concordant with in vitro results. CONCLUSIONS: ProbeTools generated an effective panel for subtyping AIVs that can be deployed for genomic surveillance, outbreak prevention, and pandemic preparedness. Effective probe design against hypervariable AIV targets also validated ProbeTools' design and coverage assessment algorithms, demonstrating their suitability for other challenging viral capture applications.