Thermal imaging: The digital eye facilitates high-throughput phenotyping traits of plant growth and stress responses.

Plant phenotyping is important for plants to cope with environmental changes and ensure plant health. Imaging techniques are perceived as the most critical and reliable tools for studying plant phenotypes. Thermal imaging has opened up new opportunities for nondestructive imaging of plant phenotyping. However, a comprehensive summary of thermal imaging in plant phenotyping is still lacking. Here we discuss the progress and future prospects of thermal imaging for assessing plant growth and stress responses. First, we classify thermal imaging into ground-based and aerial platforms based on their adaptability to different experimental environments (including laboratory, greenhouse, and field). It is convenient to collect phenotypic information of different dimensions. Second, in order to enhance the efficiency of thermal image processing, automatic algorithms based on deep learning are employed instead of traditional manual methods, greatly reducing the time cost of experiments. Considering its ease of implementation, handling and instant response, thermal imaging has been widely used in research on environmental stress, crop yield, and seed vigor. We have found that thermal imaging can detect thermal energy dissipation caused by living organisms (e.g., pests, viruses, bacteria, fungi, and oomycetes), enabling early disease diagnosis. It also recognizes changes leaf surface temperatures resulting from reduced transpiration rates caused by nutrient deficiency, drought, salinity, or freezing. Furthermore, thermal imaging predicts crop yield under different water states and forecasts the viability of dormant seeds after water absorption by monitoring temperature changes in the seeds. This work will assist biologists and agronomists in studying plant phenotypes and serve a guide for breeders to develop high-yielding, stress-tolerant, and superior crops.

Bioinformatics toolbox for exploring target mutation-induced drug resistance.

Drug resistance is increasingly among the main issues affecting human health and threatening agriculture and food security. In particular, developing approaches to overcome target mutation-induced drug resistance has long been an essential part of biological research. During the past decade, many bioinformatics tools have been developed to explore this type of drug resistance, and they have become popular for elucidating drug resistance mechanisms in a low cost, fast and effective way. However, these resources are scattered and underutilized, and their strengths and limitations have not been systematically analyzed and compared. Here, we systematically surveyed 59 freely available bioinformatics tools for exploring target mutation-induced drug resistance. We analyzed and summarized these resources based on their functionality, data volume, data source, operating principle, performance, etc. And we concisely discussed the strengths, limitations and application examples of these tools. Specifically, we tested some predictive tools and offered some thoughts from the clinician's perspective. Hopefully, this work will provide a useful toolbox for researchers working in the biomedical, pesticide, bioinformatics and pharmaceutical engineering fields, and a good platform for non-specialists to quickly understand drug resistance prediction.

Web tools support predicting protein-nucleic acid complexes stability with affinity changes.

Numerous biological processes, such as transcription, replication, and translation, rely on protein-nucleic acid interactions (PNIs). Demonstrating the binding stability of protein-nucleic acid complexes is vital to deciphering the code for PNIs. Numerous web-based tools have been developed to attach importance to protein-nucleic acid stability, facilitating the prediction of PNIs characteristics rapidly. However, the data and tools are dispersed and lack comprehensive integration to understand the stability of PNIs better. In this review, we first summarize existing databases for evaluating the stability of protein-nucleic acid binding. Then, we compare and evaluate the pros and cons of web tools for forecasting the interaction energies of protein-nucleic acid complexes. Finally, we discuss the application of combining models and capabilities of PNIs. We may hope these web-based tools will facilitate the discovery of recognition mechanisms for protein-nucleic acid binding stability. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.

Web support for the more efficient discovery of kinase inhibitors.

Kinases have a crucial role in cell signaling and are important drug targets, given that aberrant kinase activity has been linked to most disease areas. Therefore, kinase inhibitors (KIs) have significant potential as new therapeutics. In recent years, an increasing amount of computational resources have been developed to design ideal scaffold and selective KIs more efficiently. Thus, in this review, we systematically examine the computational tools used in KI research, and discuss and compare the characteristics and limitations of these resources. Such a discussion will facilitate the design of new KIs and provide a learning platform for nonspecialists.

In Silico Resources of Drug-Likeness as a Mirror: What Are We Lacking in Pesticide-Likeness?

Unfavorable bioavailability is an important aspect underlying the failure of drug candidates. Computational approaches for evaluating drug-likeness can minimize these risks. Over the past decades, computational approaches for evaluating drug-likeness have sped up the process of drug development and were also quickly derived to pesticide-likeness. As a result of many critical differences between drugs and pesticides, many kinds of methods for drug-likeness cannot be used for pesticide-likeness. Therefore, it is crucial to comprehensively compare and analyze the differences between drug-likeness and pesticide-likeness, which may provide a basis for solving the problems encountered during the evaluation of pesticide-likeness. Here, we systematically collected the recent advances of drug-likeness and pesticide-likeness and compared their characteristics. We also evaluated the current lack of studies on pesticide-likeness, the molecular descriptors and parameters adopted, the pesticide-likeness model on pesticide target organisms, and comprehensive analysis tools. This work may guide researchers to use appropriate methods for developing pesticide-likeness models. It may also aid non-specialists to understand some important concepts in drug-likeness and pesticide-likeness.

Web repositories of natural agents promote pests and pathogenic microbes management.

The grand challenge to meet the increasing demands for food by a rapidly growing global population requires protecting crops from pests. Natural active substances play a significant role in the sustainable pests and pathogenic microbes management. In recent years, natural products- (NPs), antimicrobial peptides- (AMPs), medicinal plant- and plant essential oils (EOs)-related online resources have greatly facilitated the development of pests and pathogenic microbes control agents in an efficient and economical manner. However, a comprehensive comparison, analysis and summary of these existing web resources are still lacking. Here, we surveyed these databases of NPs, AMPs, medicinal plants and plant EOs with insecticidal, antibacterial, antiviral and antifungal activity, and we compared their functionality, data volume, data sources and applicability. We comprehensively discussed the limitation of these web resources. This study provides a toolbox for bench scientists working in the pesticide, botany, biomedical and pharmaceutical engineering fields. The aim of the review is to hope that these web resources will facilitate the discovery and development of potential active ingredients of pests and pathogenic microbes control agents.

Bioinformatic tools support decision-making in plant disease management.

Food loss due to pathogens is a major concern in agriculture, requiring the need for advanced disease detection and prevention measures to minimize pathogen damage to plants. Novel bioinformatic tools have opened doors for the low-cost rapid identification of pathogens and prevention of disease. The number of these tools is growing fast and a comprehensive and comparative summary of these resources is currently lacking. Here, we review all current bioinformatic tools used to identify the mechanisms of pathogen pathogenicity, plant resistance protein identification, and the detection and treatment of plant disease. We compare functionality, data volume, data sources, performance, and applicability of all tools to provide a comprehensive toolbox for researchers in plant disease management.

Automated synthesis: current platforms and further needs.

Organic synthesis is a vital process that is a mainstay of drug discovery. However, traditional manual-based approaches to organic synthesis might not be economical, especially in a research environment where budgets are increasingly restricted and the effective use of manpower and materials is crucial. Hence, there is a strong interest in automating the synthesis process, resulting in a growth in synthesis automation, especially of systems and configuration. Here, we systematically summarize recently developed automated systems for organic synthesis. This review will be useful for computational scientists aiming to develop novel tools and also for non-specialists and students to understand the frontier of automated synthesis.

NaOH-Promoted Chemoselective Cascade Cyclization of Cyclopropyl Esters with Unsaturated Imines: Access to Bioactive Cyclopenta[c]pyridine Derivatives.

A chemoselective cascade cycloaddition reaction is developed for green and efficient access to cyclopenta[c]pyridine derivatives. Simple and inexpensive NaOH is used as the sole catalyst for this process. The δ-carbon of cyclopropyl ester is activated as a nucleophilic carbon to initiate highly chemoselective cascade reactions. Cyclopenta[c]pyridines bearing various substituents are afforded in excellent yields. Preliminary studies on the bioactivities of the afforded products show promising antibacterial activities for potential applications in plant protections.

Rational Optimization and Action Mechanism of Novel Imidazole (or Imidazolium)-Labeled 1,3,4-Oxadiazole Thioethers as Promising Antibacterial Agents against Plant Bacterial Diseases.

The emergence and widespread occurrence of plant bacterial diseases that cause global production constraints have become major challenges to agriculture worldwide. To promote the discovery and development of new bactericides, imidazole-labeled 1,3,4-oxadiazole thioethers were first fabricated by integrating the crucially bioactive scaffolds of the imidazole motif and 1,3,4-oxadiazole skeleton in a single molecular architecture. Subsequently, a superior antibacterial compound A6 was gradually discovered possessing excellent competence against plant pathogens Xanthomonas oryzae pv oryzae and Xanthomonas axonopodis pv citri with EC50 values of 0.734 and 1.79 µg/mL, respectively. These values were better than those of commercial agents bismerthiazol (92.6 µg/mL) and thiodiazole copper (77.0 µg/mL). Further modifying the imidazole moiety into the imidazolium scaffold led to the discovery of an array of potent antibacterial compounds providing the corresponding minimum EC50 values of 0.295 and 0.607 µg/mL against the two strains. Moreover, a plausible action mechanism for attacking pathogens was proposed based on the concentration dependence of scanning electron microscopy, transmission electron microscopy, and fluorescence microscopy images. Given the simple molecular structures, easy synthetic procedure, and highly efficient bioactivity, imidazole (or imidazolium)-labeled 1,3,4-oxadiazole thioethers can be further explored and developed as promising indicators for the development of commercial drugs.

Synthesis and biological evaluation of pyridinium-functionalized carbazole derivatives as promising antibacterial agents.

Various pyridinium-functionalized carbazole derivatives were constructed by coupling the key fragments of carbazole skeleton and pyridinium nucleus in a single molecular architecture. Antibacterial bioassays revealed that some of the title compounds displayed impressive bioactivities against plant pathogens such as Xanthomonas oryzae pv. oryzae, Ralstonia solanacearum, and Xanthomonas axonopodis pv. citri with minimal EC50 values of up to 0.4, 0.3, and 0.3mg/L, respectively. These bioactivities were achieved by systematically tuning and optimizing bridging linker, alkyl length of the tailor, and substituents on the carbazole scaffold. Compared with the bioactivity of the lead compound (AP-10), antibacterial efficacy dramatically increased by approximately 13-, 104- and 21-fold. This finding suggested that these compounds can serve as new lead compounds in research on antibacterial chemotherapy.

A reaction mode of carbene-catalysed aryl aldehyde activation and induced phenol OH functionalization.

The research in the field of asymmetric carbene organic catalysis has primarily focused on the activation of carbon atoms in non-aromatic scaffolds. Here we report a reaction mode of carbene catalysis that allows for aromatic aldehyde activation and remote oxygen atom functionalization. The addition of a carbene catalyst to the aldehyde moiety of 2-hydroxyl aryl aldehyde eventually enables dearomatization and remote OH activation. The catalytic process generates a type of carbene-derived intermediate with an oxygen atom as the reactive centre. Inexpensive achiral urea co-catalyst works cooperatively with the carbene catalyst, leading to consistent enhancement of the reaction enantioselectivity. Given the wide presence of aromatic moieties and heteroatoms in natural products and synthetic functional molecules, we expect our reaction mode to significantly expand the power of carbene catalysis in asymmetric chemical synthesis.

Construction of Fused Pyrrolidines and ß-Lactones by Carbene-Catalyzed C-N, C-C, and C-O Bond Formations.

A carbene-catalyzed intermolecular C-N bond formation, which initiates a highly selective cascade reaction for the synthesis of pyrrolidine fused ß-lactones, is disclosed. The nitrogen-containing bicyclic ß-lactone products are obtained with good yields and excellent stereoselectivities. Synthetic transformations of the reaction products into useful functional molecules, such as amino catalysts, can be efficiently realized under mild reaction conditions. Mechanistically, this study provides insights into modulating the reactivities of heteroatoms, such as nitrogen atoms, in challenging carbene-catalyzed asymmetric carbon-heteroatom bond-forming reactions.

Polyhalides as Efficient and Mild Oxidants for Oxidative Carbene Organocatalysis by Radical Processes.

Simple and inexpensive polyhalides (CCl4 and C2 Cl6 ) have been found to be effective and versatile oxidants in removing electrons from Breslow intermediates under N-heterocyclic carbene (NHC) catalysis. This oxidative reaction involves multiple single-electron-transfer (SET) processes and several radical intermediates. The α, ß, and γ-carbon atoms of aldehydes and enals could be readily functionalized. Given the low cost of the oxidants and the broad applicability of the reactions, this study is expected to greatly enhance the feasibility of oxidative NHC catalysis for large-scale applications. Also this new SET radical process with polyhalides as single-electron oxidants will open a new avenue in the development of NHC-catalyzed radical reactions.

Enantioselective Nucleophilic ß-Carbon-Atom Amination of Enals: Carbene-Catalyzed Formal [3+2] Reactions.

An enantioselective ß-carbon amination for enals is disclosed. The nitrogen atom from a protected hydrazine with suitable electronic properties readily behaves as a nucleophile. Addition of the nitrogen nucleophile to a catalytically generated N-heterocyclic-carbene-bound α,ß-unsaturated acyl azolium intermediate constructs a new carbon-nitrogen bond asymmetrically. The pyrazolidinone products from our catalytic reactions are common scaffolds in bioactive molecules, and can be easily transformed into useful compounds such as ß(3) -amino-acid derivatives.

Access to P-Stereogenic Phosphinates via N-Heterocyclic Carbene-Catalyzed Desymmetrization of Bisphenols.

A carbene-catalyzed desymmetrization of prochiral bisphenol compounds bearing remote P-stereogenic centers is disclosed. The catalytic reactions can be performed on gram scales with 1 mol % N-heterocyclic carbene (NHC) catalyst, providing efficient access to enantiomerically enriched P-stereogenic phosphinates. The chiral phosphinates prepared with our method can find widespread applications as asymmetric organic catalysts and ligands.

Carbene-Catalyzed Dynamic Kinetic Resolution of Carboxylic Esters.

Carbene-catalyzed reaction of carboxylic esters has the potential to offer effective synthetic solutions that cannot be readily achieved by using the more conventional aldehyde-type substrates. Here we report the first carbene-catalyzed dynamic kinetic resolution of α,α-disubstituted carboxylic esters with up to 99:1 er and 99% yield. The present study clearly illustrates the unique power of carbene-catalyzed reactions of readily available and easy to handle carboxylic esters.

Novel hydrazone derivatives containing pyridine amide moiety: Design, synthesis, and insecticidal activity.

A series of novel hydrazone derivatives containing pyridine amide moiety were designed, synthesized, and evaluated for their insecticidal activity. Bioassays indicated that some of the target compounds exhibited good insecticidal activities against Nilaparvata lugens (N. lugens), Plutella xylostella (P. xylostella), Mythimna separata (M. separata), Helicoverpa armigera (H. armigera), Pyrausta nubilalis (P. nubilalis), and Culex pipiens pallens (C. pipiens pallens). In particular, compound 5j revealed excellent insecticidal activity against C. pipiens pallens, with the 50% lethal concentration (LC50) and the 95% lethal concentration (LC95) values of 2.44 and 5.76 mg/L, respectively, which were similar to those of chlorpyrifos (3.26 and 6.98 mg/L, respectively), tebufenozide (1.22 and 2.49 mg/L, respectively), and RH-5849 (2.61 and 6.37 mg/L, respectively). These results indicated that hydrazone derivatives containing pyridine amide moiety could be developed as novel and promising insecticides.