MyoV: a deep learning-based tool for the automated quantification of muscle fibers.

Accurate approaches for quantifying muscle fibers are essential in biomedical research and meat production. In this study, we address the limitations of existing approaches for hematoxylin and eosin-stained muscle fibers by manually and semiautomatically labeling over 660 000 muscle fibers to create a large dataset. Subsequently, an automated image segmentation and quantification tool named MyoV is designed using mask regions with convolutional neural networks and a residual network and feature pyramid network as the backbone network. This design enables the tool to allow muscle fiber processing with different sizes and ages. MyoV, which achieves impressive detection rates of 0.93-0.96 and precision levels of 0.91-0.97, exhibits a superior performance in quantification, surpassing both manual methods and commonly employed algorithms and software, particularly for whole slide images (WSIs). Moreover, MyoV is proven as a powerful and suitable tool for various species with different muscle development, including mice, which are a crucial model for muscle disease diagnosis, and agricultural animals, which are a significant meat source for humans. Finally, we integrate this tool into visualization software with functions, such as segmentation, area determination and automatic labeling, allowing seamless processing for over 400 000 muscle fibers within a WSI, eliminating the model adjustment and providing researchers with an easy-to-use visual interface to browse functional options and realize muscle fiber quantification from WSIs.

Enzyme-cargo encapsulation peptides bind between tessellating tiles of the bacterial microcompartment shell.

Bacterial microcompartments are prokaryotic organelles comprising encapsulated enzymes within a thin protein shell. They facilitate metabolic processing including propanediol, choline, glycerol, and ethanolamine utilization, and they accelerate carbon fixation in cyanobacteria. Enzymes targeted to the inside of the microcompartment frequently possess a cargo-encapsulation peptide, but the site to which the peptide binds is unclear. We provide evidence that the encapsulation peptides bind to the hydrophobic groove formed between tessellating subunits of the shell proteins. In silico docking studies provide a compelling model of peptide binding to this prominent hydrophobic groove. This result is consistent with the now widely accepted view that the convex side of the shell oligomers faces the lumen of the microcompartment. The binding of the encapsulation peptide to the groove between tessellating shell protein tiles explains why it has been difficult to define the peptide binding site using other methods, provides a mechanism by which encapsulation-peptide bearing enzymes can promote shell assembly, and explains how the presence of cargo affects the size and shape of the bacterial microcompartment. This knowledge may be exploited in engineering microcompartments or disease prevention by hampering cargo encapsulation.

Natural variation in OsSEC13 HOMOLOG 1 modulates redox homeostasis to confer cold tolerance in rice.

Rice (Oryza sativa L.) is a cold-sensitive species that often faces cold stress, which adversely affects yield productivity and quality. However, the genetic basis for low-temperature adaptation in rice remains unclear. Here, we demonstrate that 2 functional polymorphisms in O. sativa SEC13 Homolog 1 (OsSEH1), encoding a WD40-repeat nucleoporin, between the 2 subspecies O. sativa japonica and O. sativa indica rice, may have facilitated cold adaptation in japonica rice. We show that OsSEH1 of the japonica variety expressed in OsSEH1MSD plants (transgenic line overexpressing the OsSEH1 allele from Mangshuidao [MSD], cold-tolerant landrace) has a higher affinity for O. sativa metallothionein 2b (OsMT2b) than that of OsSEH1 of indica. This high affinity of OsSEH1MSD for OsMT2b results in inhibition of OsMT2b degradation, with decreased accumulation of reactive oxygen species and increased cold tolerance. Transcriptome analysis indicates that OsSEH1 positively regulates the expression of the genes encoding dehydration-responsive element-binding transcription factors, i.e. OsDREB1 genes, and induces the expression of multiple cold-regulated genes to enhance cold tolerance. Our findings highlight a breeding resource for improving cold tolerance in rice.

Palladium-Catalyzed [3 + 2] Cycloaddition of 4-Vinyl-4-Butyrolactones with Alkenes: Synthesis of Spirocyclopentane Compounds.

A palladium-catalyzed [3 + 2] cycloaddition of 4-vinyl-4-butyrolactones (VBLs) with alkenes has been developed to afford various spirocyclopentane products in high yields with excellent diastereoselectivities. The scale-up reaction and further derivations of the product worked well, demonstrating the potential application of the current reaction in organic synthesis.

Non-peptidic inhibitors targeting SARS-CoV-2 main protease: A review.

The COVID-19 pandemic continues to pose a threat to global health, and sounds the alarm for research & development of effective anti-coronavirus drugs, which are crucial for the patients and urgently needed for the current epidemic and future crisis. The main protease (Mpro) stands as an essential enzyme in the maturation process of SARS-CoV-2, playing an irreplaceable role in regulating viral RNA replication and transcription. It has emerged as an ideal target for developing antiviral agents against SARS-CoV-2 due to its high conservation and the absence of homologous proteases in the human body. Among the SARS-CoV-2 Mpro inhibitors, non-peptidic compounds hold promising prospects owing to their excellent antiviral activity and improved metabolic stability. In this review, we offer an overview of research progress concerning non-peptidic SARS-CoV-2 Mpro inhibitors since 2020. The efforts delved into molecular structures, structure-activity relationships (SARs), biological activity, and binding modes of these inhibitors with Mpro. This review aims to provide valuable clues and insights for the development of anti-SARS-CoV-2 agents as well as broad-spectrum coronavirus Mpro inhibitors.

Temperature-induced embryonic diapause in chickens is mediated by PKC-NF-κB-IRF1 signaling.

BACKGROUND: Embryonic diapause (dormancy) is a state of temporary arrest of embryonic development that is triggered by unfavorable conditions and serves as an evolutionary strategy to ensure reproductive survival. Unlike maternally-controlled embryonic diapause in mammals, chicken embryonic diapause is critically dependent on the environmental temperature. However, the molecular control of diapause in avian species remains largely uncharacterized. In this study, we evaluated the dynamic transcriptomic and phosphoproteomic profiles of chicken embryos in pre-diapause, diapause, and reactivated states. RESULTS: Our data demonstrated a characteristic gene expression pattern in effects on cell survival-associated and stress response signaling pathways. Unlike mammalian diapause, mTOR signaling is not responsible for chicken diapause. However, cold stress responsive genes, such as IRF1, were identified as key regulators of diapause. Further in vitro investigation showed that cold stress-induced transcription of IRF1 was dependent on the PKC-NF-κB signaling pathway, providing a mechanism for proliferation arrest during diapause. Consistently, in vivo overexpression of IRF1 in diapause embryos blocked reactivation after restoration of developmental temperatures. CONCLUSIONS: We concluded that embryonic diapause in chicken is characterized by proliferation arrest, which is the same with other spices. However, chicken embryonic diapause is strictly correlated with the cold stress signal and mediated by PKC-NF-κB-IRF1 signaling, which distinguish chicken diapause from the mTOR based diapause in mammals.

Effect of Various Fruit Extracts on Angiotensin I-Converting Enzyme (ACE) and Kallikrein (KLK) Activities.

Hypertension is one of the main risk factors for cardiovascular disease and causes widespread morbidity and mortality worldwide. The aim of this work was to screen the fruit with high angiotensin I-converting enzyme (ACE) inhibitory activity and kallikrein (KLK) promotion activity by three different extraction methods from 22 kinds of fruits. Results showed that the aqueous extracts of fresh kiwifruit significantly inhibited ACE activity (47.71%), whereas the KLK activity was also inhibited (4.56%). This indicated that the substances inhibiting ACE activity existed in kiwifruit might be small molecular substances such as polyphenols. The nonpolar substance existed in the ethanol extracts of grape inhibited ACE activity significantly. The enzymatic hydrolysates of red grape significantly promoted KLK activity, whereas its ethanol extracts significantly inhibited KLK activity. This results suggested that the components that lower blood pressure and raise blood pressure are generally presented in the same fruit, the former are mostly water-soluble substances, while the latter are generally alcohol-soluble substances. If certain or individual components can be isolated from edible fruits, they may significantly affect blood pressure in humans.

High-Performance Ammonia Electrosynthesis from Nitrate in a NaOH-KOH-H2O Ternary Electrolyte.

A glut of dinitrogen-derived ammonia (NH3) over the past century has resulted in a heavily imbalanced nitrogen cycle and consequently, the large-scale accumulation of reactive nitrogen such as nitrates in our ecosystems has led to detrimental environmental issues. Electrocatalytic upcycling of waste nitrogen back into NH3 holds promise in mitigating these environmental impacts and reducing reliance on the energy-intensive Haber-Bosch process. Herein, we report a high-performance electrolyzer using an ultrahigh alkalinity electrolyte, NaOH-KOH-H2O, for low-cost NH3 electrosynthesis. At 3,000 mA/cm2, the device with a Fe-Cu-Ni ternary catalyst achieves an unprecedented faradaic efficiency (FE) of 92.5±1.5 % under a low cell voltage of 3.83 V; whereas at 1,000 mA/cm2, an FE of 96.5±4.8 % under a cell voltage of only 2.40 V was achieved. Techno-economic analysis revealed that our device cuts the levelized cost of ammonia electrosynthesis by ~40 % ($30.68 for Fe-Cu-Ni vs. $48.53 for Ni foam per kmol-NH3). The NaOH-KOH-H2O electrolyte together with the Fe-Cu-Ni ternary catalyst can enable the high-throughput nitrate-to-ammonia applications for affordable and scalable real-world wastewater treatments.

Quinolines and isoquinolines as HIV-1 inhibitors: Chemical structures, action targets, and biological activities.

Human immunodeficiency virus type 1 (HIV-1), a lentivirus that causes acquired immunodeficiency syndrome (AIDS), poses a serious threat to global public health. Since the advent of the first drug zidovudine, a number of anti-HIV agents acting on different targets have been approved to combat HIV/AIDS. Among the abundant heterocyclic families, quinoline and isoquinoline moieties are recognized as promising scaffolds for HIV inhibition. This review intends to highlight the advances in diverse chemical structures and abundant biological activity of quinolines and isoquinolines as anti-HIV agents acting on different targets, which aims to provide useful references and inspirations to design and develop novel HIV inhibitors for medicinal chemists.

Cloning and functional analysis of the novel rice blast resistance gene Pi65 in japonica rice.

KEY MESSAGE: Pi65, a leucine-rich repeat receptor-like kinase (LRR-RLK) domain cloned from Oryza sativa japonica, is a novel rice blast disease resistance gene. Rice blast seriously threatens rice production worldwide. Utilizing the rice blast resistance gene to breed rice blast-resistant varieties is one of the best ways to control rice blast disease. Using a map-based cloning strategy, we cloned a novel rice blast resistance gene, Pi65, from the resistant variety GangYu129 (abbreviated GY129, Oryza sativa japonica). Overexpression of Pi65 in the susceptible variety LiaoXing1 (abbreviated LX1, Oryza sativa japonica) enhanced rice blast resistance, while knockout of Pi65 in GY129 resulted in susceptibility to rice blast disease. Pi65 encodes two transmembrane domains, with 15 LRR domains and one serine/threonine protein kinase catalytic domain, conferring resistance to isolates of Magnaporthe oryzae (abbreviated M. oryzae) collected from Northeast China. There were sixteen amino acid differences between the Pi65 resistance and susceptible alleles. Compared with the Pi65-resistant allele, the susceptible allele exhibited one LRR domain deletion. Pi65 was constitutively expressed in whole plants, and it could be induced in the early stage of M. oryzae infection. Transcriptome analysis revealed that numerous genes associated with disease resistance were specifically upregulated in GY129 24 h post inoculation (HPI); in contrast, photosynthesis and carbohydrate metabolism-related genes were particularly downregulated at 24 HPI, demonstrating that disease resistance-associated genes were activated in GY129 (carrying Pi65) after rice blast fungal infection and that cellular basal metabolism and energy metabolism were inhibited simultaneously. Our study provides genetic resources for improving rice blast resistance and enriches the study of rice blast resistance mechanisms.

Temporal Expression of Myogenic Regulatory Genes in Different Chicken Breeds during Embryonic Development.

The basic units of skeletal muscle in all vertebrates are multinucleate myofibers, which are formed from the fusion of mononuclear myoblasts during the embryonic period. In order to understand the regulation of embryonic muscle development, we selected four chicken breeds, namely, Cornish (CN), White Plymouth Rock (WPR), White Leghorn (WL), and Beijing-You Chicken (BYC), for evaluation of their temporal expression patterns of known key regulatory genes (Myomaker, MYOD, and MSTN) during pectoral muscle (PM) and thigh muscle (TM) development. The highest expression level of Myomaker occurred from embryonic days E13 to E15 for all breeds, indicating that it was the crucial stage of myoblast fusion. Interestingly, the fast-growing CN showed the highest gene expression level of Myomaker during the crucial stage. The MYOD gene expression at D1 was much higher, implying that MYOD might have an important role after hatching. Histomorphology of PM and TM suggested that the myofibers was largely complete at E17, which was speculated to have occurred because of the expression increase in MSTN and the expression decrease in Myomaker. Our research contributes to lay a foundation for the study of myofiber development during the embryonic period in different chicken breeds.

Untargeted rapid differentiation and targeted growth tracking of fungal contamination in rice grains based on headspace-gas chromatography-ion mobility spectrometry.

BACKGROUND: Milled rice are prone to be contaminated with spoilage or toxigenic fungi during storage, which may pose a real threat to human health. Most traditional methods require long periods of time for enumeration and quantification. However, headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS) technology could characterize the complex volatile organic compounds (VOCs) released from samples in a non-destructive and environmentally friendly manner. Thus, this study described an innovative HS-GC-IMS strategy for analyzing VOC profiles to detect fungal contamination in milled rice. RESULTS: A total of 24 typical target compounds were identified. Analysis of variance-partial least squares regression (APLSR) showed significant correlations between the target compounds and colony counts of fungi. While the changes of selected volatile components (acetic acid, 3-hydroxy-2-butanone and oct-en-3-ol) in fungi-inoculated rice had sufficiently high positive correlations with the colony counts, the logistic model could effectively be used to monitor the growth of individual fungus (R2  = 0.902-0.980). PLSR could effectively be used to predict fungal colony counts in rice samples (R2  = 0.831-0.953), and the different fungi-inoculated rice samples at 24 h could be successfully distinguished by support vector machine (SVM) (94.6%). The ability of HS-GC-IMS to monitor fungal infection would help to prevent contaminated rice grains from entering the food chain. CONCLUSIONS: This result indicated that HS-GC-IMS three-dimensional fingerprints may be appropriate for the early detection of fungal infection in rice grains. © 2021 Society of Chemical Industry.

Serum proteomic analysis of novel predictive serum proteins for neurological prognosis following cardiac arrest.

Early prognostication of neurological outcome in comatose patients after cardiac arrest (CA) is vital for clinicians when assessing the survival time of sufferers and formulating appropriate treatment strategies to avoid the withdrawal of life-sustaining treatment (WLST) from patients. However, there is still a lack of sensitive and specific serum biomarkers for early and accurate identification of these patients. Using an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic approach, we discovered 55 differentially expressed proteins, with 39 up-regulated secreted serum proteins and 16 down-regulated secreted serum proteins between three comatose CA survivors with good versus poor neurological recovery. Then, four proteins were selected and were validated via an enzyme-linked immunosorbent assay (ELISA) approach in a larger-scale sample containing 32 good neurological outcome patients and 46 poor neurological outcome patients, and it was confirmed that serum angiotensinogen (AGT) and alpha-1-antitrypsin (SERPINA1) were associated with neurological function and prognosis in CA survivors. A prognostic risk score was developed and calculated using a linear and logistic regression model based on a combination of AGT, SERPINA1 and neuron-specific enolase (NSE) with an area under the curve of 0.865 (P < .001), and the prognostic risk score was positively correlated with the CPC value (R = 0.708, P < .001). We propose that the results of the risk score assessment not only reveal changes in biomarkers during neurological recovery but also assist in enhancing current therapeutic strategies for comatose CA survivors.

Indole derivatives as tubulin polymerization inhibitors for the development of promising anticancer agents.

The α- and ß-tubulins are the major polypeptide components of microtubules (MTs), which are attractive targets for anticancer drug development. Indole derivatives display a variety of biological activities including antitumor activity. In recent years, a great number of indole derivatives as tubulin polymerization inhibitors have sprung up, which encourages medicinal chemists to pursue promising inhibitors with improved antitumor activities, excellent physicochemical, pharmacokinetic and pharmacodynamic properties. In this review, the recent progress from 2010 to present in the development of indole derivatives as tubulin polymerization inhibitors was summarized and reviewed, which would provide useful clues and inspirations for further design of outstanding tubulin polymerization inhibitors.

Characterization and inhibition of four fungi producing citrinin in various culture media.

PURPOSE: This study aimed to investigate the effects of different fermentation conditions (culture medium, temperature, incubation time, pH value and additive) on citrinin production by four fungi. RESULTS: Among the culture media, potato dextrose medium had lowest citrinin production, followed by yeast sucrose medium and monosodium glutamate medium. The lowest citrinin contents were produced by Monascus anka (M. anka) in potato dextrose medium and yeast sucrose medium, Aspergillus oryzae AS3.042 (A. oryzae) produced the lowest citrinin production in monosodium glutamate medium. The optimum fermentation temperatures for citrinin production by Aspergillus niger (A. niger) and Penicillium citrinum (P. citrinum) were at 30 °C, whereas those by M. anka and A. oryzae were at 35 °C. Citrinin synthesis by four fungi were completely inhibited with a pH value of less than 5.4. By adding ethylene diamine tetraacetic acid (EDTA) or triammonium citrate into monosodium glutamate medium, citrinin production by A. oryzae and A. niger were totally inhibited. Ammonium sulfate completely inhibited citrinin production by A. oryzae, M. anka and P. citrinum, and ammonium nitrate completely inhibited citrinin production by A. oryzae. CONCLUSIONS: These results indicated that the suitable fermentation conditions could make considerable contributions to the reduction of citrinin production. This study provided an effective way for decreasing the citrinin production.

Early identification of Aspergillus spp. contamination in milled rice by E-nose combined with chemometrics.

BACKGROUND: Rice grains can be contaminated easily by certain fungi during storage and in the market chain, thus generating a risk for humans. Most classical methods for identifying and rectifying this problem are complex and time-consuming for manufacturers and consumers. However, E-nose technology provides analytical information in a non-destructive and environmentally friendly manner. Two-feature fusion data combined with chemometrics were employed for the determination of Aspergillus spp. contamination in milled rice. RESULTS: Linear discriminant analysis (LDA) indicated that the efficiency of fusion signals ('80th s values' and 'area values') outperformed that of independent E-nose signals. Linear discriminant analysis showed clear discrimination of fungal species in stored milled rice for four groups on day 2, and the discrimination accuracy reached 92.86% by using an extreme learning machine (ELM). Gas chromatography-mass spectrometry (GC-MS) analysis showed that the volatile compounds had close relationships with fungal species in rice. The quantification results of colony counts in milled rice showed that the monitoring models based on ELM and the genetic algorithm optimized support vector machine (GA-SVM) (R2  = 0.924-0.983) achieved better performances than those based on partial least squares regression (PLSR) (R2  = 0.877-0.913). The ability of the E-nose to monitor fungal infection at an early stage would help to prevent contaminated rice grains from entering the food chains. CONCLUSIONS: The results indicated that an E-nose coupled with ELM or GA-SVM algorithm could be a useful tool for the rapid detection of fungal infection in milled rice, to prevent contaminated rice from entering the food chain. © 2021 Society of Chemical Industry.

Crystalline Red Phosphorus Nanoribbons: Large-Scale Synthesis and Electrochemical Nitrogen Fixation.

Two dimensional (2D) nanoribbons constitute an emerging nanoarchitecture for advanced microelectronics and energy conversion due to the stronger size confinement effects compared to traditional nanosheets. Triclinic crystalline red phosphorus (cRP) composed by a layered structure is a promising 2D phosphorus allotrope and the tube-like substructure is beneficial to the construction of nanoribbons. In this work, few-layer cRP nanoribbons are synthesized and the effectiveness in the electrochemical nitrogen reduction reaction (NRR) is investigated. An iodine-assisted chemical vapor transport (CVT) method is developed to synthesize circa 10 g of bulk cRP lumps with a yield of over 99 %. With the aid of probe ultrasonic treatment, high-quality cRP microcrystals are exfoliated into few-layer nanoribbons (cRP NRs) with large aspect ratios. As non-metallic materials, cRP NRs are suitable for the electrochemical nitrogen reduction reaction. The ammonia yield is 15.4 µg h-1 mgcat. -1 at -0.4 V vs. reversible hydrogen electrode in a neutral electrolyte under ambient conditions and the Faradaic efficiency is 9.4 % at -0.2 V. Not only is cRP a promising catalyst, but also the novel strategy expands the application of phosphorus-based 2D structures beyond that of traditional nanosheets.

Free Amino Acid Recognition: A Bisbinaphthyl-Based Fluorescent Probe with High Enantioselectivity.

A novel fluorescent probe based on a bisbinaphthyl structure has been designed and synthesized. This compound in combination with Zn(II) has exhibited highly enantioselective fluorescence enhancement with 13 common free amino acids. For example, its enantiomeric fluorescent enhancement ratios ( ef or Δ IL/Δ ID) in the presence of the following amino acids are extremely high: 177 for valine, 199 for methionine, 186 for phenylalanine, 118 for leucine, and 89 for alanine. The observed high enantioselectivity and the extent of the substrate scope are unprecedented in the fluorescent recognition of free amino acids. This fluorescent probe can be applied to determine the enantiomeric composition of the structurally diverse chiral amino acids. NMR and mass spectroscopic investigations have provided clues to elucidate the observed high enantioselectivity.

Biphasic Enantioselective Fluorescent Recognition of Amino Acids by a Fluorophilic Probe.

A fluorophilic fluorescent probe based on a perfluoroalkyl-substituted bis(binaphthyl) compound was designed and synthesized. It displayed a highly enantioselective fluorescence response toward structurally diverse amino acids in a biphasic fluorous/aqueous system with enantiomeric fluorescent enhancement ratio (ef; ΔID /ΔIL ) values up to 45.2 (histidine). It can be used to determine the enantiomeric compositions of amino acids and also allows the amino acid enantiomers to be visually discriminated. NMR and mass-spectroscopic investigations provided insights into the observed high enantioselectivity. This biphasic fluorescent recognition was used to determine the enantiomeric composition of the crude phenylalanine products generated by an enzyme-catalyzed asymmetric hydrolysis under various reaction conditions. The fluorous-phase-based fluorescence measurement under the biphasic conditions was able to minimize the interference of other reaction components and thus has potential in asymmetric reaction screening.

Isolation and identification of nucleosides/nucleotides raising testosterone and NO levels of mice serum from Chinese chive (Allium tuberosum) leaves.

Our previous study found that Chinese chive could significantly (p < 0.01) raise testosterone and nitric oxide (NO) levels in mice serum. However, the specific functional components of this traditional remedy are still unknown. In order to isolate and identify the active constituents from Chinese chive for enhancing testosterone and NO levels, the Chinese chive leaves were extracted by petroleum ether, ethyl acetate, n-butanol and water respectively. Results indicated that the n-butanol extract had a significant effect on NO and testosterone blood levels. Subsequently, n-butanol extract was further isolated by D101 macroporous adsorption and eluted with 50% ethanol and then isolated by Sephadex LH-20 and preparative high-performance liquid chromatography to obtain nucleosides. The fraction eluted with 70% ethanol was further isolated by RP-18 and pre-HPLC to obtain nucleotides. Four novel compounds were identified, and their effects on testosterone and NO levels of male mice were evaluated. Results showed that nucleotides, especially the adenosine in Chinese chive leaves, increased serum testosterone and NO levels in male mice, which had not been reported before. This finding might bring into perspective the treatment strategy for those doctors who treat hormone deficiencies, and might be suitable for using in functional food.