The apple transcription factor MdZF-HD11 regulates fruit softening by promoting Mdß-GAL18 expression.

Fruit ripening and the associated softening are major determinants of fruit quality and post-harvest shelf life. Although the mechanisms underlying fruit softening have been intensively studied, there are limited reports on the regulation of fruit softening in apples (Malus domestica). Here, we identified a zinc finger homeodomain transcription factor MdZF-HD11that trans-activates the promoter of Mdß-GAL18, which encodes a pectin-degradation enzyme associated with cell wall metabolism. Both MdZF-HD11 and Mdß-GAL18 genes were up-regulated by exogenous ethylene treatment and repressed by 1-methylcyclopropene treatment. Further experiments revealed that MdZF-HD11 binds directly to the Mdß-GAL18 promoter and up-regulates its transcription. Moreover, using transgenic apple fruit calli, we found that overexpression of Mdß-GAL18 or MdZF-HD11 significantly enhanced ß-galactosidase activity, and overexpression of MdZF-HD11 induced the expression of Mdß-GAL18. We also discovered that transient overexpression of Mdß-GAL18 or MdZF-HD11 in 'Golden Delicious' apple significantly increased the release of ethylene, reduced fruit firmness, promoted the transformation of skin color from green to yellow, and accelerated ripening and softening of the fruit. Finally, the overexpression of MdZF-HD11 in tomato also promoted fruit softening. Collectively, these results indicate that ethylene-induced MdZF-HD11 interacts with Mdß-GAL18 to promote the post-harvest softening of apple.

Ultrasound treatment alleviates external pericarp browning and improves fruit quality of pomegranate during storage.

BACKGROUND: Ultrasound treatment has a beneficial role in horticultural production from harvest to consumption. The quality traits and microbiological load in pomegranate fruit were explored during 30 days' storage at 20 °C after 10 min and 30 min ultrasound treatments. RESULTS: Ultrasound treatment significantly reduced the microbiological load during storage, providing a relatively clean and suitable storage environment. This was especially true for the 30 min treatment, which also maintained relatively lower weight loss and kept the browning rate below 5% during storage. Meanwhile, the fruit treated with ultrasound had higher ascorbic acid and anthocyanin content, which provided better antibacterial properties and higher nutraceutical properties until the end of storage. The 30 min ultrasound treatment significantly delayed the decrease in catalase (CAT) enzyme activity and the increase in peroxidase (POD) enzyme activity. Combined with weighted gene co-expression network analysis (WGCNA), and correlation analysis, color indicators and antioxidant activity induced by ultrasound treatment were responsible for the relatively higher fruit quality of pomegranate. CONCLUSION: Ultrasound treatment can improve the sensory quality and nutritional characteristics of pomegranate fruits during storage, and reduce the microbiological load. Ultrasound for 30 min was better than 10 min for prolonging the storage life of pomegranate. Our results will provide valuable information for ultrasound application in other horticultural products. © 2023 Society of Chemical Industry.

Measurement Method of Physical Parameters of Two-Phase Flow Based on Dual-Frequency Demodulation.

Oil-water two-phase flow commonly occurs in the process of crude oil electric dehydration. Here, through dynamic changes in the water content and conductivity of oil-water two-phase flow in the process of electric dehydration, the influence of water content and conductivity on the efficiency and stability of electric dehydration is analyzed. Using real-time in-line measurements of water content and conductivity, the electric dehydration system is kept in an optimal state, which provides a basis for realizing efficient oil-water separation. Measurements of the physical parameters of oil-water two-phase flow is affected by many factors, such as the temperature of the two-phase flow, composition of the two-phase flow medium, structure of the measurement sensor, coupling of the conventional resistance-capacitance excitation signal, and processing of the measurement data. This complexity causes, some shortcomings to the control system, such as a large measurement error, limited measurement range, inability to measure the medium water phase as a conductive water phase, etc., and not meeting the requirements of the electric dehydration process. To solve that the conductivity and water content of high-conductivity crude oil emulsions cannot be measured synchronously, the RC relationship of oil-water emulsions is measured synchronously using dual-frequency digital demodulation technology, which verifies the feasibility of our test method for the synchronous measurement of physical parameters of homogeneous oil-water two-phase flow. Experimental results show that the novel measuring method (which is within the target measuring range) can be used to measure water content 0~40% and conductivity 1 ms/m~100 ms/m. The measuring error of the water content is less than 2%, and the measuring error of the conductivity is less than 5%.

Nrf2 attenuates methamphetamine-induced myocardial injury by regulating oxidative stress and apoptosis in mice.

OBJECTIVES: Methamphetamine (MA) abuse is a serious social problem worldwide. Cardiovascular complications were the second leading cause of death among MA abusers. We aimed to clarify the effects of MA on myocardial injury, oxidative stress, and apoptosis in myocardial cells and to explore the potential mechanism of nuclear factor-erythroid factor 2-related factor 2 (Nrf2) in MA-induced oxidative stress and apoptosis. METHODS: An acute cardiac toxicity model of MA was established by intraperitoneal injection of MA (2 mg/kg) for 5 days. Nrf2 activation (by sulforaphane (SFN) 1 h before MA injection) and Nrf2 gene knockout were performed to explore the regulatory effects of Nrf2 on cardiac toxicity. RESULTS: The protein expressions of Nrf2 (p < .001) and heme oxygenase-1 (HO-1) were increased (p < .01), suggesting that MA activated the Nrf2/HO-1 pathway. In the MA group, cardiac injury score (p < .001) and cardiac troponin I (cTnI) protein expression increased (p < .01). Malondialdehyde (MDA) content increased (p < .001), superoxide dismutase (SOD) activity decreased (p < .05). Protein expressions of Caspase-3 (p < .001) and Bax (p < .001) increased, and Bcl-2 decreased (p < .001) as well. These changes were reversed by activation of Nrf2 but became more pronounced after Nrf2 knockout, suggested that the activation and knockout of Nrf2 attenuated and aggravated MA-induced myocardial injury, oxidative stress and apoptosis in myocardial cells, respectively. CONCLUSIONS: MA administration induced myocardial injury, oxidative stress, and apoptosis in mice. Nrf2 attenuated MA-induced myocardial injury by regulating oxidative stress and apoptosis, thus playing a protective role.

Qualitative and Quantitative Analysis of Five Indoles or Indazole Amide Synthetic Cannabinoids in Suspected E-Cigarette Oil by GC-MS.

OBJECTIVES: To establish the GC-MS qualitative and quantitative analysis methods for the synthetic cannabinoids, its main matrix and additives in suspicious electronic cigarette (e-cigarette) oil samples. METHODS: The e-cigarette oil samples were analyzed by GC-MS after diluted with methanol. Synthetic cannabinoids, its main matrix and additives in e-cigarette oil samples were qualitatively analyzed by the characteristic fragment ions and retention time. The synthetic cannabinoids were quantitatively analyzed by using the selective ion monitoring mode. RESULTS: The linear range of each compound in GC-MS quantitative method was 0.025-1 mg/mL, the matrix recovery rate was 94%-103%, the intra-day precision relative standard deviations (RSD) was less than 2.5%, and inter-day precision RSD was less than 4.0%. Five indoles or indazole amide synthetic cannabinoids were detected in 25 e-cigarette samples. The main matrixes of e-cigarette samples were propylene glycol and glycerol. Additives such as N,2,3-trimethyl-2-isopropyl butanamide (WS-23), glycerol triacetate and nicotine were detected in some samples. The content range of synthetic cannabinoids in 25 e-cigarette samples was 0.05%-2.74%. CONCLUSIONS: The GC-MS method for synthesizing cannabinoid, matrix and additive in e-cigarette oil samples has good selectivity, high resolution, low detection limit, and can be used for simultaneous qualitative and quantitative analysis of multiple components; The explored fragment ion fragmentation mechanism of the electron bombardment ion source of indole or indoxamide compounds helps to identify such substances or other compounds with similar structures in cases.

Rutaecarpine ameliorates cardiomyocyte injury induced by high glucose by promoting TRPV1-mediated autophagy.

AIM: Diabetic cardiomyopathy (DCM) is a dominant factor contributing to diabetic death. Rutaecarpine has many cardiovascular biological effects and anti-high-glucose activity. Therefore, this paper aimed to investigate the impact of rutaecarpine on high glucose (HG)-elicited cardiomyocyte injury. METHOD: Cell counting kit 8 (CCK-8) and 5-ethynyl-2'-deoxyuridine (EdU), TdT-mediated dUTP Nick-End Labeling (TUNEL) assays judged H9c2 cell activity and apoptosis, and oxidative stress was assessed by corresponding assay kits. The expression of apoptosis, oxidative stress, autophagy-associated factors and TRPV1 were examined with western blot. IF assay tested GFP-LC3 expression. RESULTS: As a result, rutaecarpine had no obvious effect on the viability of H9c2 cells while elevated HG-exposed H9c2 cell viability. Rutaecarpine inhibited the apoptosis and oxidative stress of H9c2 cells induced by HG. In addition, rutaecarpine activated TRPV1 to induce autophagy. However, inhibition of TRPV1 inactivated the autophagy, which drove HG-evoked H9c2 apoptosis and oxidative stress. CONCLUSIONS: In conclusion, rutaecarpine suppressed HG-stimulated H9c2 cell viability injury, apoptosis as well as oxidative stress via promoting TRPV1-mediated autophagy (Fig. 10, Ref. 40).

Nrf2 protects against methamphetamine-induced nephrotoxicity by mitigating oxidative stress and autophagy in mice.

Methamphetamine (MA) is a widely abused drug that can cause kidney damage. However, the molecular mechanism remains unclear. Nuclear factor erythroid 2-related factor 2 (Nrf2) is a key transcription factor that regulates resistance to oxidative and proteotoxic stress. In this study, we investigated the role of Nrf2 in MA-induced renal injury in mice. Nrf2 was pharmacologically activated and genetically knocked-out in mice. The animal model of MA-induced nephrotoxicity was established by injecting MA (2 mg/kg) intraperitoneally twice a day for 5 days. Histopathological alterations were shown in the MA-exposed kidneys. MA significantly increased renal function biomarkers and kidney injury molecule-1 (KIM-1) levels. MA decreased superoxide dismutase activity and increased malondialdehyde levels. Autophagy-related factors (LC3 and Beclin 1) were elevated in MA-treated mice. Furthermore, Nrf2 increased in the MA-exposed kidneys. Activation of Nrf2 may attenuate histopathological changes in the kidneys of MA-treated mice. Pre-administration of Nrf2 agonist significantly decreased KIM-1 expression, oxidative stress, and autophagy in the kidneys after MA toxicity. In contrast, Nrf2 knockout mice treated with MA lost renal tubular morphology. Nrf2 deficiency increased KIM-1 expression, oxidative stress, and autophagy in the MA-exposed kidneys. Our results demonstrate that Nrf2 may protect against MA-induced nephrotoxicity by mitigating oxidative stress and autophagy.

Comparative Physiological and Transcriptome Analysis Reveals Potential Pathways and Specific Genes Involved in Waterlogging Tolerance in Apple Rootstocks.

Apple (Malus × domestica Borkh.) is one of the most cultivated fruit crops in China. Apple trees frequently encounter waterlogging stress, mainly due to excess rainfall, soil compaction, or poor soil drainage, results in yellowing leaves and declined fruit quality and yield in some regions. However, the mechanism underlying the response to waterlogging has not been well elucidated. Therefore, we performed a physiological and transcriptomic analysis to examine the differential responses of two apple rootstocks (waterlogging-tolerant M. hupehensis and waterlogging-sensitive M. toringoides) to waterlogging stress. The results showed that M. toringoides displayed more severe leaf chlorosis during the waterlogging treatment than M. hupehensis. Compared with M. hupehensis, the more severe leaf chlorosis induced by waterlogging stress in M. toringoides was highly correlated with increased electrolyte leakage and superoxide radicals, hydrogen peroxide accumulation, and increased stomata closure. Interestingly, M. toringoides also conveyed a higher ethylene production under waterlogging stress. Furthermore, RNA-seq revealed that a total of 13,913 common differentially expressed genes (DEGs) were differentially regulated between M. hupehensis and M. toringoides under waterlogging stress, especially those DEGs involved in the biosynthesis of flavonoids and hormone signaling. This suggests a possible link of flavonoids and hormone signaling to waterlogging tolerance. Taken together, our data provide the targeted genes for further investigation of the functions, as well as for future molecular breeding of waterlogging-tolerant apple rootstocks.

The engineered CRISPR-Mb2Cas12a variant enables sensitive and fast nucleic acid-based pathogens diagnostics in the field.

Existing CRISPR/Cas12a-based diagnostic platforms offer accurate and vigorous monitoring of nucleic acid targets, but have the potential to be further optimized for more efficient detection. Here, we profiled 16 Cas12a orthologs, focusing on their trans-cleavage activity and their potential as diagnostic enzymes. We observed the Mb2Cas12a has more robust trans-cleavage activity than other orthologs, especially at lower temperatures. An engineered Mb2Cas12a-RRVRR variant presented robust trans-cleavage activity and looser PAM constraints. Moreover, we found the existing one-pot assay, which simultaneously performed Recombinase Polymerase Amplification (RPA) and Cas12a reaction in one system, resulted in the loss of single-base discrimination during diagnosis. Therefore, we designed a reaction vessel that physically separated the RPA and Cas12a steps while maintaining a closed system. This isolated but closed system made diagnostics more sensitive and specific and effectively prevented contamination. This shelved Mb2Cas12a-RRVRR variant-mediated assay detected various targets in less than 15 min and exhibited equal or greater sensitivity than qPCR when detecting bacterial pathogens, plant RNA viruses and genetically modified crops. Overall, our findings further improved the efficiency of the current CRISPR-based diagnostic system and undoubtedly have great potential for highly sensitive and specific detection of multiple sample types.

HSP27 Interacts with Nonstructural Proteins of Porcine Reproductive and Respiratory Syndrome Virus and Promotes Viral Replication.

Heat shock protein 27 (HSP27) is a multifunctional protein and belongs to the small HSP family. It has been shown that HSP27 is involved in viral replication as a cellular chaperone, but the function of HSP27 during porcine reproductive and respiratory syndrome virus (PRRSV) infections remains unexplored. Here, we found that PRRSV replication can induce HSP27 expression and phosphorylation in vitro. HSP27 overexpression promoted PRRSV replication, whereas its knockdown reduced PRRSV proliferation. Additionally, suppressing HSP27 phosphorylation reduced PRRSV replication and the level of viral double-stranded RNA (dsRNA), a marker of the viral replication and transcription complexes (RTCs). Furthermore, HSP27 can interact with multiple viral nonstructural proteins (nsps), including nsp1α, nsp1ß, nsp5, nsp9, nsp11 and nsp12. Suppressing the phosphorylation of HSP27 almost completely disrupted its interaction with nsp1ß and nsp12. Altogether, our study revealed that HSP27 plays an important role in PRRSV replication.

New trends of new psychoactive substances (NPS)-infused chocolate: Identification and quantification of trace level of NPS in complex matrix by GC-MS and NMR.

For the first time, the identification and quantification of trace level of new psychoactive substances (NPS) in a complex chocolate matrix have been reported. Since the beginning of 2022, suspected NPS-infused chocolate samples confiscated in inbound packages have been continuously sent to our laboratory for analysis. The qualitative gas chromatography-mass spectrometry (GC-MS) results were verified by 1H nuclear magnetic resonance (1H NMR) and 19F NMR to distinguish between potential aromatic isomers. A total of 11 NPS including deoxymethoxetamine, 3-OH-PCP, 6-APB, 4-APB, 4-OH-MiPT, 3-FEA, 2-FEA, 3-MMC, bromazolam, 2-FDCK, and ADB-BUTINACA were detected in 65 seized chocolate samples. A general 1H quantitative NMR (1H qNMR) method for quantification of 297 types of NPS in complex chocolate matrixes was devised for the first time after rigorous analysis of various critical features of merit, including suitable deuterated solvent, internal standard, quantitative peaks, and instrument acquisition parameters. Validation of the method using six different types of NPS afforded limits of detection of 0.05-0.1 mg/mL, limits of quantification of 0.01-0.03 mg/mL, repeatability and reproducibility lower than 0.5% and 3.6%, recoveries of 91.7%∼104.4%, and absence of matrix effect. The quantitative analysis of 65 seized chocolate samples by 1H qNMR and 19F qNMR showed that the content of NPS was in the range of 0.5 mg/g∼44.1 mg/g. Generally, the developed qNMR method was simple, fast, precise, and can be performed without reference materials of NPS. Since the type and content of NPS are relatively random, chocolate consumers will face huge health risks. Therefore, this new trend of NPS-infused chocolate deserves and requires more attention from national NPS monitoring departments as well as forensic laboratories.

Identification and analytical characterization of N-propyl norbutylone, N-butyl norbutylone, N-benzyl norheptedrone, and N-pyrrolidinyl-3,4-DMA.

In this study, the analytical characterization of three cathinones and one N-pyrrolidinyl-substituted amphetamine derivative is described: 1-([3,4-methylenedioxyphenyl])-2-(propylamino)butan-1-one (N-propyl norbutylone 1), 1-([3,4-methylenedioxyphenyl])-2-(butylamino)butan-1-one (N-butyl norbutylone 2), 2-(benzylamino)-1-phenylheptan-1-one (N-benzyl norheptedrone 3), and 1-(1-[3,4-dimethoxyphenyl]propan-2-yl)pyrrolidine (N-pyrrolidinyl-3,4-DMA 4). The identification was based on ultra-high-performance liquid chromatography-quadrupole time-of-flight-mass spectrometry (UHPLC-QTOF-MS), gas chromatography-orbitrap MS (GC-Orbitrap-MS), nuclear magnetic resonance spectroscopy (NMR), and Fourier transform infrared (FT-IR). GC-Orbitrap-MS, with higher mass accuracy, benefit more on the accurate structure elucidation of product ions compared with the low-resolution GC-MS. The collision-induced dissociation (CID) and electron ionization (EI) pathways of these compounds were examined to assist forensic laboratories in elucidating the structure of new psychoactive substances (NPS) with similar structure in their case work. In addition, electron activated dissociation (EAD) was applied to analyze N-benzyl norheptedrone, which showed only one product ion in the CID mode. The result showed that for compound with limited product ions in the CID mode, the EAD mode can give more complementary information for structure elucidation. In addition, quantitative NMR (qNMR) was applied for the quantification of four powdered/crystal and two herbal blend seized samples. To our knowledge, no analytical data about the compounds 3 and 4 have appeared until now, making this the first report on these compounds.

A new biologic paleoaltimetry indicating Late Miocene rapid uplift of northern Tibet Plateau.

The uplift of the Tibet Plateau (TP) during the Miocene is crucial to understanding the evolution of Asian monsoon regimes and alpine biodiversity. However, the northern Tibet Plateau (NTP) remains poorly investigated. We use pollen records of montane conifers (Tsuga, Podocarpus, Abies, and Picea) as a new paleoaltimetry to construct two parallel midrange paleoelevation sequences in the NTP at 1332 ± 189 m and 433 ± 189 m, respectively, during the Middle Miocene [~15 million years ago (Ma)]. Both midranges increased rapidly to 3685 ± 87 m in the Late Miocene (~11 Ma) in the east, and to 3589 ± 62 m at ~7 Ma in the west. Our estimated rises in the east and west parts of the NTP during 15 to 7 Ma, together with data from other TP regions, indicate that during the Late Miocene the entire plateau may have reached a high elevation close to that of today, with consequent impacts on atmospheric precipitation and alpine biodiversity.

In Situ Fluorescence Probing of the Formation of Calcium Phosphate Prenucleation Clusters.

Initial-stage prenucleation clusters (PNCs) are critical in calcium phosphate (CaP) biomineralization and thus the formation mechanisms of human bones and teeth. However, several features of PNCs require further examination, e.g., structure, ionic stoichiometry, kinetics, thermodynamics, and nucleation mechanism. In this study, we used poly(acrylic acid) (PAA)-Ca(Eu) complexes with partial Eu3+ substitution as pre-PNCs and established a fluorescence method to study PNC formation in situ based on Eu-O charge-transfer transitions. The kinetics and thermodynamics of PNC formation were explored by probing the fluorescence changes of Eu-O charge-transfer transitions during bonding between the pre-PNCs and PO43-. PNC formation was consistent with the pseudo-second-order kinetic and Langmuir isothermal adsorption models. The flexible structures of PNCs aided in regulating the subsequent nucleation and crystallization. This study provides an in situ fluorescence probing method with critical guiding significance in addressing the features of PNC formation, in addition to biomineralization.

The application of 19F NMR spectroscopy for the analysis of fluorinated new psychoactive substances (NPS).

In this study, fluorine-19 nuclear magnetic resonance spectroscopy (19F NMR) served as a highly specific tool for identification of fluorinated new psychoactive substances (NPS) as well as a suitable analytical method for the accurate quantification of fluorinated NPS in different seized samples. In the first part of the study, 19F NMR spectroscopy of a number of different fluorinated NPS, including 51 synthetic cannabinoids, 8 synthetic cathinones, 7 phenethylamines, 8 fentanyl analogues, and 9 other types of compounds was conducted. The chemical shifts and multiplet of the primary fluorides (RCH2F), fluorobenzenes (ortho-ArF, meta-ArF, and para-ArF), and trifluoromethylbenzenes (ArCF3) were discussed in detail to illustrate the role of 19F signals as special fingerprints in assisting the structure identification of fluorine-containing NPS. To the best of our knowledge, this study is the largest evaluation of fluorinated NPS compounds by 19F NMR. The second part of this study dealt with the problems encountered in the 19F quantification procedure and the criteria to be considered for successful quantification by 19F NMR. General high field (HF)- and low field (LF)- 19F qNMR methods for the quantification of fluorinated NPS were established after the thorough discussion of NMR spectrum acquisition and processing parameters such as: transmitter frequency offset (O1P), spin-lattice relaxation time (T1), and different baseline correction methods. The limit of quantifications (LOQs) for HF-19F qNMR varied between 0.1 mg/mL and 0.2 mg/mL, and for LF-19F qNMR varied between 1.0 mg/mL and 2.0 mg/mL. The limit of detections (LODs) for HF-19F qNMR varied between 0.03 mg/mL and 0.06 mg/mL, and for LF-19F qNMR varied between 0.3 mg/mL and 0.6 mg/mL. Finally, the developed methods were applied for the quantification of fluorinated-NPS in seventeen herbal blends, e-liquid, tablet, and powder NPS seizures.

Cannabidiol prevents methamphetamine-induced neurotoxicity by modulating dopamine receptor D1-mediated calcium-dependent phosphorylation of methyl-CpG-binding protein 2.

In the past decade, methamphetamine (METH) abuse has sharply increased in the United States, East Asia, and Southeast Asia. METH abuse not only leads to serious drug dependence, but also produces irreversible neurotoxicity. Currently, there are no approved pharmacotherapies for the treatment of METH use disorders. Cannabidiol (CBD), a major non-psychoactive (and non-addictive) cannabinoid from the cannabis plant, shows neuroprotective, antioxidative, and anti-inflammatory properties under METH exposure. At present, however, the mechanisms underlying these properties remain unclear, which continues to hinder research on its therapeutic potential. In the current study, computational simulations showed that CBD and METH may directly bind to the dopamine receptor D1 (DRD1) via two overlapping binding sites. Moreover, CBD may compete with METH for the PHE-313 binding site. We also found that METH robustly induced apoptosis with activation of the caspase-8/caspase-3 cascade in-vitro and in-vivo, while CBD pretreatment prevented these changes. Furthermore, METH increased the expression of DRD1, phosphorylation of Methyl-CpG-binding protein 2 (MeCP2) at serine 421 (Ser421), and level of intracellular Ca2+ in-vitro and in-vivo, but these effects were blocked by CBD pretreatment. The DRD1 antagonist SCH23390 significantly prevented METH-induced apoptosis, MeCP2 phosphorylation, and Ca2+ overload in-vitro. In contrast, the DRD1 agonist SKF81297 markedly increased apoptosis, MeCP2 phosphorylation, and Ca2+ overload, which were blocked by CBD pretreatment in-vitro. These results indicate that CBD prevents METH-induced neurotoxicity by modulating DRD1-mediated phosphorylation of MeCP2 and Ca2+ signaling. This study suggests that CBD pretreatment may resist the effects of METH on DRD1 by competitive binding.

Deconvolution of tumor composition using partially available DNA methylation data.

BACKGROUND: Deciphering proportions of constitutional cell types in tumor tissues is a crucial step for the analysis of tumor heterogeneity and the prediction of response to immunotherapy. In the process of measuring cell population proportions, traditional experimental methods have been greatly hampered by the cost and extensive dropout events. At present, the public availability of large amounts of DNA methylation data makes it possible to use computational methods to predict proportions. RESULTS: In this paper, we proposed PRMeth, a method to deconvolve tumor mixtures using partially available DNA methylation data. By adopting an iteratively optimized non-negative matrix factorization framework, PRMeth took DNA methylation profiles of a portion of the cell types in the tissue mixtures (including blood and solid tumors) as input to estimate the proportions of all cell types as well as the methylation profiles of unknown cell types simultaneously. We compared PRMeth with five different methods through three benchmark datasets and the results show that PRMeth could infer the proportions of all cell types and recover the methylation profiles of unknown cell types effectively. Then, applying PRMeth to four types of tumors from The Cancer Genome Atlas (TCGA) database, we found that the immune cell proportions estimated by PRMeth were largely consistent with previous studies and met biological significance. CONCLUSIONS: Our method can circumvent the difficulty of obtaining complete DNA methylation reference data and obtain satisfactory deconvolution accuracy, which will be conducive to exploring the new directions of cancer immunotherapy. PRMeth is implemented in R and is freely available from GitHub ( https://github.com/hedingqin/PRMeth ).

Polyacrylic Acid-Ca(Eu) Nanoclusters as a Luminescence Sensor of Phosphate Ion.

In this study, we synthesized polyacrylic acid (PAA)-Ca (Eu) nanoclusters as a luminescence sensor of phosphate ion by a complex method, and we aimed to achieve the quantitative detection of PO43− based on the sensitivity of the charge transfer band of Eu3+ to anionic ligand. The resulting PAA-Ca(Eu) nanoclusters showed a well-dispersed and a dot-like morphology, with an ultra-small diameter (the average size of 2.17 nm) under high resolution transmission electron microscopy(HRTEM) observation. A dynamic light scattering particle size analyzer (DLS) showed a hydrodynamic size of 2.39 nm. The (PAA)-Ca (Eu) nanoclusters as a luminescence sensor showed a significantly higher sensitivity for PO43− than other anions (CO32−, SiO32−, SO42−, SO32−, Br−, Cl−, F−). The luminescence intensity displayed a linear increase (y = 19.32x + 74.75, R2 > 0.999) in a PO43 concentration range (0−10 mM) with the concentration of PO43− increase, and the limit of detection was 0.023 mM. The results showed good recovery rates and low relative standard deviations. These (PAA)-Ca (Eu) nanoclusters are hopeful to become a luminescence sensor for quantitatively detecting PO43−.

A sensitive visual method for onsite detection of quarantine pathogenic bacteria from horticultural crops using an LbCas12a variant system.

Pre-planting testing of seeds and plantlets for the existence of quarantine pathogens is an important phytosanitary measure. The CRISPR-mediated molecular diagnostic methodologies are being developed for pathogens detection, but many challenges remain. Here, we profiled an engineered Crispr/LbCas12a variant (LbCas12a-5M) that has more robust trans-cleavage activity and a wider PAM sequences (TNTN) preference than wild type. We developed a procedure for screening specific sequences of bacterial plant pathogens, and the designed species-specific crRNA displayed no cross-reactions with other bacterial species. Combined with a simple extraction of bacterial DNA, an LbCas12a-5M-based visual detection technique was established and optimized for detecting quarantine pathogens Erwinia amylovora and Acidovorax citrulli with detection limits up to 40 CFU/reaction and a sensitivity consistent with qPCR assay. This protocol was faster and simpler than qPCR, requiring 40 min or less from sample preparation. We further validated the potential application of the method by showing that it can be used for rapid and accurate diagnosis of A. citrulli on seeds of watermelon, with 100% agreement with the results of qPCR assay. The developed method simplifies the detection of pathogens and provides cost-effective countermeasures to quarantine interventions.

Phenylalanine 4-Hydroxylase Contributes to Endophytic Bacterium Pseudomonas fluorescens' Melatonin Biosynthesis.

Melatonin acts both as an antioxidant and as a growth regulatory substance in plants. Pseudomonas fluorescens endophytic bacterium has been shown to produce melatonin and increase plant resistance to abiotic stressors through increasing endogenous melatonin. However, in bacteria, genes are still not known to be melatonin-related. Here, we reported that the bacterial phenylalanine 4-hydroxylase (PAH) may be involved in the 5-hydroxytryptophan (5-HTP) biosynthesis and further influenced the subsequent production of melatonin in P. fluorescens. The purified PAH protein of P. fluorescens not only hydroxylated phenylalanine but also exhibited l-tryptophan (l-Trp) hydroxylase activity by converting l-Trp to 5-HTP in vitro. However, bacterial PAH displayed lower activity and affinity for l-Trp than l-phenylalanine. Notably, the PAH deletion of P. fluorescens blocked melatonin production by causing a significant decline in 5-HTP levels and thus decreased the resistance to abiotic stress. Overall, this study revealed a possible role for bacterial PAH in controlling 5-HTP and melatonin biosynthesis in bacteria, and expanded the current knowledge of melatonin production in microorganisms.