RNA m6A modification facilitates DNA methylation during maize kernel development.

N6-methyladenosine (m6A) in mRNA and 5-methylcytosine (5mC) in DNA have critical functions for regulating gene expression and modulating plant growth and development. However, the interplay between m6A and 5mC is an elusive territory and remains unclear mechanistically in plants. We reported an occurrence of crosstalk between m6A and 5mC in maize (Zea mays) via the interaction between mRNA adenosine methylase (ZmMTA), the core component of the m6A methyltransferase complex, and decrease in DNA methylation 1 (ZmDDM1), a key chromatin-remodeling factor that regulates DNA methylation. Genes with m6A modification were coordinated with a much higher level of DNA methylation than genes without m6A modification. Dysfunction of ZmMTA caused severe arrest during maize embryogenesis and endosperm development, leading to a significant decrease in CHH methylation in the 5' region of m6A-modified genes. Instead, loss of function of ZmDDM1 had no noteworthy effects on ZmMTA-related activity. This study establishes a direct link between m6A and 5mC during maize kernel development and provides insights into the interplay between RNA modification and DNA methylation.

Pyridine-containing substrate analogs are restricted from accessing the human cytochrome P450 8B1 active site by tryptophan 281.

The human oxysterol 12α-hydroxylase cytochrome P450 8B1 (CYP8B1) is a validated drug target for both type 2 diabetes and nonalcoholic fatty liver disease, but effective selective inhibitors are not yet available. Herein, steroidal substrate-mimicking compounds with a pyridine ring appended to the C12 site of metabolism were designed as inhibitors, synthesized, and evaluated in terms of their functional and structural interactions with CYP8B1. While the pyridine nitrogen was intended to coordinate the CYP8B1 active site heme iron, none of these compounds elicited shifts in the CYP8B1 Soret absorbance consistent with this type of interaction. However, when CYP8B1 was cocrystallized with the pyridine-containing compound with the 3-keto-Δ4 steroid backbone most similar to the endogenous substrate, it was apparent that this ligand was bound in a channel leading to the active site, instead of near the heme iron. Inspection of this structure suggested that tryptophan 281 directly above the heme might restrict active site binding of potential inhibitors with this design. This hypothesis was supported when a CYP8B1 W281F mutation did allow all three compounds to coordinate the heme iron as designed. These results indicated that the design of next-generation CYP8B1 inhibitors should be compatible with the low-ceiling tryptophan immediately above the heme iron.

Human cytochrome P450 3A7 binding four copies of its native substrate dehydroepiandrosterone 3-sulfate.

Human fetal cytochrome P450 3A7 (CYP3A7) is involved in both xenobiotic metabolism and the estriol biosynthetic pathway. Although much is understood about cytochrome P450 3A4 and its role in adult drug metabolism, CYP3A7 is poorly characterized in terms of its interactions with both categories of substrates. Herein, a crystallizable mutated form of CYP3A7 was saturated with its primary endogenous substrate dehydroepiandrosterone 3-sulfate (DHEA-S) to yield a 2.6 Å X-ray structure revealing the unexpected capacity to simultaneously bind four copies of DHEA-S. Two DHEA-S molecules are located in the active site proper, one in a ligand access channel, and one on the hydrophobic F'-G' surface normally embedded in the membrane. While neither DHEA-S binding nor metabolism exhibit cooperative kinetics, the current structure is consistent with cooperativity common to CYP3A enzymes. Overall, this information suggests that mechanism(s) of CYP3A7 interactions with steroidal substrates are complex.

Maize decrease in DNA methylation 1 targets RNA-directed DNA methylation on active chromatin.

DNA methylation plays vital roles in repressing transposable element activity and regulating gene expression. The chromatin-remodeling factor Decrease in DNA methylation 1 (DDM1) is crucial for maintaining DNA methylation across diverse plant species, and is required for RNA-directed DNA methylation (RdDM) to maintain mCHH islands in maize (Zea mays). However, the mechanisms by which DDM1 is involved in RdDM are not well understood. In this work, we used chromatin immunoprecipitation coupled with high-throughput sequencing to ascertain the genome-wide occupancy of ZmDDM1 in the maize genome. The results revealed that ZmDDM1 recognized an 8-bp-long GC-rich degenerate DNA sequence motif, which is enriched in transcription start sites and other euchromatic regions. Meanwhile, 24-nucleotide siRNAs and CHH methylation were delineated at the edge of ZmDDM1-occupied sites. ZmDDM1 co-purified with Argonaute 4 (ZmAGO4) proteins, providing further evidence that ZmDDM1 is a component of RdDM complexes in planta. Consistent with this, the vast majority of ZmDDM1-targeted regions co-localized with ZmAGO4-bound genomic sites. Overall, our results suggest a model that ZmDDM1 may be recruited to euchromatic regions via recognition of a GC-rich motif, thereby remodeling chromatin to provide access for RdDM activities in maize.

Nanoscale insights into hematology: super-resolved imaging on blood cell structure, function, and pathology.

Fluorescence nanoscopy, also known as super-resolution microscopy, has transcended the conventional resolution barriers and enabled visualization of biological samples at nanometric resolutions. A series of super-resolution techniques have been developed and applied to investigate the molecular distribution, organization, and interactions in blood cells, as well as the underlying mechanisms of blood-cell-associated diseases. In this review, we provide an overview of various fluorescence nanoscopy technologies, outlining their current development stage and the challenges they are facing in terms of functionality and practicality. We specifically explore how these innovations have propelled forward the analysis of thrombocytes (platelets), erythrocytes (red blood cells) and leukocytes (white blood cells), shedding light on the nanoscale arrangement of subcellular components and molecular interactions. We spotlight novel biomarkers uncovered by fluorescence nanoscopy for disease diagnosis, such as thrombocytopathies, malignancies, and infectious diseases. Furthermore, we discuss the technological hurdles and chart out prospective avenues for future research directions. This review aims to underscore the significant contributions of fluorescence nanoscopy to the field of blood cell analysis and disease diagnosis, poised to revolutionize our approach to exploring, understanding, and managing disease at the molecular level.

The structure and characterization of human cytochrome P450 8B1 supports future drug design for nonalcoholic fatty liver disease and diabetes.

Human cytochrome P450 8B1 (CYP8B1) is involved in conversion of cholesterol to bile acids. It hydroxylates the steroid ring at C12 to ultimately produce the bile acid cholic acid. Studies implicated this enzyme as a good drug target for nonalcoholic fatty liver disease and type 2 diabetes, but there are no selective inhibitors known for this enzyme and no structures to guide inhibitor development. Herein, the human CYP8B1 protein was generated and used to identify and characterize interactions with a series of azole inhibitors, which tend to be poorly selective P450 inhibitors. Structurally related miconazole, econazole, and tioconazole bound with submicromolar dissociation constants and were effective inhibitors of the native reaction. CYP8B was cocrystallized with S-tioconazole to yield the first X-ray structure. This inhibitor bound in the active site with its azole nitrogen coordinating the heme iron, consistent with inhibitor binding and inhibition assay data. Additionally, the CYP8B1 active site was compared with similar P450 enzymes to identify features that may facilitate the design of more selective inhibitors. Selective inhibitors should promote a better understanding of the role of CYP8B1 inhibition in normal physiology and disease states and provide a possible treatment for nonalcoholic fatty liver disease and type 2 diabetes.

Advances on removal of organophosphorus pesticides with electrochemical technology.

Widespread use of organophosphorus pesticides (OPs), especially superfluous and unreasonable use, had brought huge harm to the environment and food chain. It is because only a small part of the pesticides sprayed reached the target, and the rest slid across the soil, causing pollution of groundwater and surface water resources. These pesticides accumulate in the environment, causing environmental pollution. Therefore, in recent years, the control and degradation of OPs have become a public spotlight and research hotspot. Due to its unique advantages such as versatility, environmental compatibility, controllability, and cost-effectiveness compatibility, electrochemical technology has become one of the most promising methods for degradation of OPs. The fundamental knowledge about electrochemical degradation on OPs was introduced in this review. Then, a comprehensive overview of four main types of practical electrochemical technologies to degrade pesticides were presented and evaluated. The knowledge contained herein should conduce to better understand the degradation of pesticides by electrochemical technology, and better exploit the degradation of pesticides in the environment and food. Overall, the objective of this review is to provide comprehensive guidance for rational design and application of electrochemical technology in the degradation of OPs for the safety of the environment and food chain in the future.

Routine analysis of pesticides in foodstuffs: Emerging ambient ionization mass spectrometry as an alternative strategy to be on your radar.

Pesticides residues in foodstuffs are longstanding of great concern to consumers and governments, thus reliable evaluation techniques for these residues are necessary to ensure food safety. Emerging ambient ionization mass spectrometry (AIMS), a transformative technology in the field of analytical chemistry, is becoming a promising and solid evaluation technology due to its advantages of direct, real-time and in-situ ionization on samples without complex pretreatments. To provide useful guidance on the evaluation techniques in the field of food safety, we offered a comprehensive review on the AIMS technology and introduced their novel applications for the analysis of residual pesticides in foodstuffs under different testing scenarios (i.e., quantitative, screening, imaging, high-throughput detection and rapid on-site analysis). Meanwhile, the creative combination of AIMS with high-resolution mass analyzer (e.g., orbitrap and time-of-flight) was fundamentally mentioned based on recent studies about the detection and evaluation of multi-residual pesticides between 2015 and 2021. Finally, the technical challenges and prospects associated with AIMS operation in food industry were discussed.

Ratiometric electrochemical aptasensor for the sensitive detection of carcinoembryonic antigen based on a hairpin DNA probe and exonuclease I-assisted target recycling.

A novel ratiometric electrochemical aptasensor was constructed for the detection of carcinoembryonic antigen (CEA) based on a hairpin DNA (hpDNA) probe and exonuclease Ⅰ (Exo Ⅰ)-assisted target recycling amplification strategy. A thiolated methylene blue (MB)-labeled hpDNA as the internal control element was fixed on the surface of the gold nanoparticles (AuNPs)-modified gold electrode (AuE) through Au-S bonds. A ferrocene (Fc)-modified aptamer DNA (Fc-Apt) was partially hybridized with hpDNA to form a Fc-Apt/hpDNA duplex. Due to the specific recognition of Fc-Apt to CEA, the presence of CEA caused dissociation of Fc-Apt from the duplex, and further triggered the degradation process of Exo Ⅰ and recycling of CEA. Hence, the Fc tags were released from the electrode surface and the oxidation peak current of Fc (IFc) decreased while that of MB (IMB) remained stable owing to the distance between MB tags and the electrode unchanged. A linear relationship was observed between IFc/IMB and the logarithm of CEA concentration from 10 pg mL-1 to 100 ng mL-1 with a detection limit of 1.9 pg mL-1. Moreover, the developed aptasensor had been applied to detect CEA in diluted human serum with satisfactory results, indicating its great potential in practical applications.

Progress on aptamer-based SERS sensors for food safety and quality assessment: methodology, current applications and future trends.

It is well known that food safety has aroused extensive attentions from governments to researchers and to food industries. As a versatile technology based on molecular interactions, aptamer sensors which could specifically identify a wide range of food contaminants have been extensively studied in recent years. Surface-enhanced Raman spectroscopy integrated aptamer combines the advantages of both technologies, not only in the ability to specifically identify a wide range of food contaminants, but also in the ultra-high sensitivity, simplicity, portable and speed. To provide beneficial insights into the evaluation techniques in the field of food safety, we offer a comprehensive review on the design strategies for aptamer-SERS sensors in different scenarios, including non-nucleic acid amplification methods ("on/off" mode, sandwich mode, competition model and catalytic model) and nucleic acid amplification methods (hybridization chain reaction, rolling circle amplification, catalytic hairpin assembly). Meanwhile, a special attention is paid to the application of aptamer-SERS sensors in biological (foodborne pathogenic, bacteria and mycotoxins) and chemical contamination (drug residues, metal ions, and food additives) of food matrix. Finally, the challenges and prospects of developing reliable aptamer-SERS sensors for food safety were discussed, which are expected to offer a strong guidance for further development and extended applications.

Current Progress on Antibiotic Sensing Based on Ratiometric Fluorescent Sensors.

Antibiotics, which can be used as veterinary drugs, are widely used in the prevention and treatment of infectious diseases for animals. However, overuse of antibiotics had caused serious problems on food contamination and human harm. For control such public issues, several of techniques have been in recent years. Ratiometric fluorescent (RF) technique, as one of the most promising strategies for quantitatively evaluated analytes, had been extensively developed for the readily measurements on the two different fluorescent emission intensities. In this review, the construction strategies for recent RF sensors will be mainly focused on. Meanwhile, the recent advances and new tendencies for detection of antibiotics based on RF technique shall be introduced. Finally, outlooks on the opportunities and challenges for quantitative fluorescence sensing on antibiotics will be summarized.

Sensitive Techniques for POCT Sensing on the Residues of Pesticides and Veterinary Drugs in Food.

For the immense requirement on agriculture and animal husbandry, application of pesticides and veterinary drugs had become a normal state in the farming and ranching areas. However, to intently pursue the yields, large quantities of residues of pesticides and veterinary drugs have caused serious harm to both the environment and the food industry. To control and solve such an issue, a variety of novel techniques were developed in recent years. In this review, the development and features about point-of-care-testing (POCT) detection on the residues of pesticides and veterinary drugs, such as, electrochemistry (EC), enzyme-linked immunosorbent assay (ELISA) and nano-techniques, were systematically introduced. For each topic, we first interpreted the strategies and detailed account of such technical contributions on detection and assessment of the residues. Finally, the advantages and perspectives about mentioned techniques for ultrasensitive assessment and sensing on pesticides and veterinary drugs were summarized.

Carbon quantum dot-based fluorometric nitrite assay by exploiting the oxidation of iron(II) to iron(III).

The authors describe a simple and economical fluorescence method for the determination of nitrite by utilizing the fact that nitrite possesses strong oxidation in acidic solution and is capable to transform iron(II) into iron(III) ions. The latter quenches the fluorescence of carbon quantum dots (CQDs) based on the fluorescence static and dynamic quenching effect. The optimum reaction conditions and other analytical parameters are investigated to enhance the sensitivity of the method. At the excitation wavelength of 360 nm, this probe has a linear response in the 10 to 400 µM nitrite concentration range, with a correlation coefficient of R2 = 0.9958 (n = 3) and a detection limit of 0.48 µM. This method was successfully applied to the determination of nitrite in three different sausage samples and gave recoveries in the range between 101.8 to 103.0%, demonstrating the accuracy, reliability and potential application of this assay for monitoring nitrite. Graphical Abstract The carbon quantum dot/iron(II) ions system was used for the fluorometric detection of nitrite in food and environmental water. This probe exploits the oxidizing property of nitrite in acidic solution. Iron(II) is oxidized to iron(III) which exerts a strong fluorescence quenching effect.

Guanfu base A, an antiarrhythmic alkaloid of Aconitum coreanum, Is a CYP2D6 inhibitor of human, monkey, and dog isoforms.

Guanfu base A (GFA) is a novel heterocyclic antiarrhythmic drug isolated from Aconitum coreanum (Lèvl.) rapaics and is currently in a phase IV clinical trial in China. However, no study has investigated the influence of GFA on cytochrome P450 (P450) drug metabolism. We characterized the potency and specificity of GFA CYP2D inhibition based on dextromethorphan O-demethylation, a CYP2D6 probe substrate of activity in human, mouse, rat, dog, and monkey liver microsomes. In addition, (+)-bufuralol 1'-hydroxylation was used as a CYP2D6 probe for the recombinant form (rCYP2D6), 2D1 (rCYP2D1), and 2D2 (rCYP2D2) activities. Results show that GFA is a potent noncompetitive inhibitor of CYP2D6, with inhibition constant Ki = 1.20 ± 0.33 µM in human liver microsomes (HLMs) and Ki = 0.37 ± 0.16 µM for the human recombinant form (rCYP2D6). GFA is also a potent competitive inhibitor of CYP2D in monkey (Ki = 0.38 ± 0.12 µM) and dog (Ki = 2.4 ± 1.3 µM) microsomes. However, GFA has no inhibitory activity on mouse or rat CYP2Ds. GFA did not exhibit any inhibition activity on human recombinant CYP1A2, 2A6, 2C8, 2C19, 3A4, or 3A5, but showed slight inhibition of 2B6 and 2E1. Preincubation of HLMs and rCYP2D6 resulted in the inactivation of the enzyme, which was attenuated by GFA or quinidine. Beagle dogs treated intravenously with dextromethorphan (2 mg/ml) after pretreatment with GFA injection showed reduced CYP2D metabolic activity, with the Cmax of dextrorphan being one-third that of the saline-treated group and area under the plasma concentration-time curve half that of the saline-treated group. This study suggests that GFA is a specific CYP2D6 inhibitor that might play a role in CYP2D6 medicated drug-drug interaction.

Removal of the large inverted repeat from the plastid genome reveals gene dosage effects and leads to increased genome copy number.

The chloroplast genomes of most plants and algae contain a large inverted repeat (IR) region that separates two single-copy regions and harbours the ribosomal RNA operon. We have addressed the functional importance of the IR region by removing an entire copy of the 25.3-kb IR from the tobacco plastid genome. Using plastid transformation and subsequent selectable marker gene elimination, we precisely excised the IR, thus generating plants with a substantially reduced plastid genome size. We show that the lack of the IR results in a mildly reduced plastid ribosome number, suggesting a gene dosage benefit from the duplicated presence of the ribosomal RNA operon. Moreover, the IR deletion plants contain an increased number of plastid genomes, suggesting that genome copy number is regulated by measuring total plastid DNA content rather than by counting genomes. Together, our findings (1) demonstrate that the IR can enhance the translation capacity of the plastid, (2) reveal the relationship between genome size and genome copy number, and (3) provide a simplified plastid genome structure that will facilitate future synthetic biology applications.

The influence of biological rhythms on the initial onset of status epilepticus in critically ill inpatients and the study of its predictive Model.

This study aims to explore the relationship between the circadian rhythms of critically ill patients and the incidence of Status Epilepticus (SE), and to develop a predictive model based on circadian rhythm indicators and clinical factors. We conducted a diurnal rhythm analysis of vital sign data from 4413 patients, discovering significant differences in the circadian rhythms of body temperature, blood oxygen saturation, and heart rate between the SE and non-SE groups, which were correlated with the incidence of SE. We also employed various machine learning algorithms to identify the ten most significant variables and developed a predictive model with strong performance and clinical applicability. Our research provides a new perspective and methodology for the study of biological rhythms in critically ill patients, offering new evidence and tools for the prevention and treatment of SE. Our findings are consistent or similar to some in the literature, while differing from or supplementing others. We observed significant differences in the vital signs of epileptic patients at different times of the day across various diagnostic time groups, reflecting the regulatory effects of circadian rhythms. We suggest heightened monitoring and intervention of vital signs in critically ill patients, especially during late night to early morning hours, to reduce the risk of SE and provide more personalized treatment plans.

Experience of Disease Acceptance in Chinese Patients with Newly Diagnosed Crohn's Disease: A Descriptive Qualitative Study.

Background: High levels of disease acceptance are important predictors of improved psychological well-being, treatment outcomes, and enhanced quality of life. Relatively few studies have focused on the process of disease acceptance in patients with Crohn's disease (CD), particularly those who are newly diagnosed. Purpose: To explore the disease acceptance process in newly diagnosed CD patients. Patients and Methods: A descriptive qualitative approach was employed. Sixteen CD patients from 2 tertiary hospitals in Hangzhou, Zhejiang were recruited through purposive sampling using a maximum variation strategy. Semi-structured interviews were conducted. The interviews were transcribed verbatim and analysed using conventional content analysis. Results: Five phases of the psychosocial process of the "acceptance journey" of newly diagnosed CD patients emerged from the data analysis: (1) praying for the illness to not be CD; (2) not being able to accept CD; (3) having to accept CD; (4) knowing that CD should be acceptable; and (5) starting to accept CD. Patients at the stage of "starting to accept CD" are more proactive and motivated to face the disease, and their overall acceptance of the disease is higher than that of the previous stages. However, by the end of the interview, 2 patients remained at the stage of "having to accept CD", and 3 patients remained at the stage of "knowing that CD should be acceptable". Two patients entered the stage of "starting to accept CD" and then reverted back to one of the previous stages. Conclusion: The "acceptance journey" of newly diagnosed CD patients is dynamic, individual and reversible. Traditional Chinese cultural values such as respect for authority, the philosophy of wu-wei and family responsibility contribute to the acceptance of CD in Chinese patients. Hence, there is a need to provide early and culturally tailored psychological support or interventions according to the stages of acceptance.

Comparative effects of Guanfu base A and Guanfu base G on HERG K+ channel.

BACKGROUND: Guanfu base A (GFA) and Guanfu base G (GFG) are chemicals isolated from Aconitum coreanum. The potassium channel encoded by the human ether-a-go-go related gene (HERG) plays an important role in repolarization of the cardiac action potential. The purpose of the present study was to investigate the effects of GFA and GFG on the HERG channel and its structure-function relationship. METHODS: The effects of GFA and GFG were investigated in human embryonic kidney 293 (HEK293) cells transiently transfected with HERG complementary DNA using a whole-cell patch clamp technique. RESULTS: GFA and GFG inhibited HERG channel current in concentration-, voltage-, and time-dependent manners. The IC50 for GFA and GFG was 1.64 mM and 17.9 µM, respectively. Both GFA and GFG shifted the activation curve in a negative direction and accelerated channel inactivation but showed no effect on the inactivation curve. Moreover, GFG also accelerated channel recovery from inactivation. CONCLUSIONS: Both GFA and GFG blocked HERG channel current. This effect was stronger after GFG treatment rather than GFA treatment. This blockade was dependent on open and inactivated channel states. These results indicate that GFA could be a rather promising antiarrhythmic drug without severe side effects, whereas GFG could cause QT prolongation and requires further research.

Efficient synthesis of Guanfu base G via highly regioselective lipase-catalyzed acylation in non-aqueous phase.

Lipase-catalyzed acylation of Guanfu alcohol-amine (GFAA) with vinyl acetate (VA) was performed in non-aqueous system for the preparation of Guanfu base G (GFG), a plant-originated alkaloid with significant antiarrhythmic activity. Among the eight lipases from different origins, Novozym 435 was found to be the best biocatalyst. The most suitable molecular sieve amount, substrate concentration, molar ratio of VA to GFAA, enzyme amount and reaction temperature were proved to be 40 mg/mL, 6 µmol/mL, 10:1, 2mg/mL and 50 °C, respectively. A maximum GFG yield of 37.4% was achieved under the selected conditions with methanol served as the optimal reaction medium. The structure of the acetylated product was elucidated by (1)H NMR and (13)C NMR analysis.