Molecular Design of Novel Herbicide and Insecticide Seed Compounds with Machine Learning.

Pesticides are widely used to improve crop productivity by eliminating weeds and pests. Conventional pesticide development involves synthesizing compounds, testing their activities, and studying their effects on the ecosystem. However, as pesticide discovery has an extremely low success rate, many compounds must be synthesized and tested. To overcome the high human, financial, and time costs of this process, machine learning is attracting increasing attention. In this study, we used machine learning for the molecular design of novel seed compounds for herbicides and insecticides. Classification models were constructed by using compounds that had been tested as herbicides and insecticides, and an inverse analysis of the constructed models was conducted. In the molecular design of herbicides, we proposed 186 new samples as herbicides using ensemble learning and a method for expressing explanatory variables that consider the relationships among eight weed species. For the molecular design of insecticides, we used undersampling and ensemble learning for the analysis of unbalanced data. Based on approximately 340,000 compounds, 12 potential insecticides were proposed, of which 2 exhibited actual activity when tested. These results demonstrate the potential of the developed machine-learning method for rapidly identifying novel herbicides and insecticides.

Recombinant cyclin B-Cdk1-Suc1 capable of multi-site mitotic phosphorylation in vitro.

Cyclin-dependent kinase 1 (Cdk1) complexed with cyclin B phosphorylates multiple sites on hundreds of proteins during mitosis. However, it is not fully understood how multi-site mitotic phosphorylation by cyclin B-Cdk1 controls the structures and functions of individual substrates. Here we develop an easy-to-use protocol to express recombinant vertebrate cyclin B and Cdk1 in insect cells from a single baculovirus vector and to purify their complexes with excellent homogeneity. A series of in-vitro assays demonstrate that the recombinant cyclin B-Cdk1 can efficiently and specifically phosphorylate the SP and TP motifs in substrates. The addition of Suc1 (a Cks1 homolog in fission yeast) accelerates multi-site phosphorylation of an artificial substrate containing TP motifs. Importantly, we show that mitosis-specific multi-subunit and multi-site phosphorylation of the condensin I complex can be recapitulated in vitro using recombinant cyclin B-Cdk1-Suc1. The materials and protocols described here will pave the way for dissecting the biochemical basis of critical mitotic processes that accompany Cdk1-mediated large-scale phosphorylation.

Variations in the cystic duct: frequency and the relationship among insertion sides and heights on the bile duct.

BACKGROUND: Evaluation of the cystic duct anatomy prior to bile duct or gallbladder surgery is important, to decrease the risk of bile duct injury. This study aimed to clarify the frequency of cystic duct variations and the relationship between them. METHODS: Data of 205 patients who underwent cholecystectomy after imaging at Sada Hospital, Japan, were analyzed. The Chi-square test was used to analyze the relationships among variations. RESULTS: The lateral and posterior sides of the bile duct were the two most common insertion points (92 patients, 44.9%), and the middle height was the most common insertion height (135 patients, 65.9%). Clinically important variations (spiral courses, parallel courses, low insertions, and right hepatic duct draining) relating to the risk of bile duct injury were observed in 24 patients (11.7%). Regarding the relationship between the insertion sides and heights, we noticed that the posterior insertion frequently existed in low insertions (75.0%, P < 0.001) and did not exist in high insertions. In contrast, the anterior insertion coexisted with high and never low insertions. Spiral courses have two courses: anterior and posterior, and anterior ones were only found in high insertion cases. CONCLUSIONS: The insertion point of the cystic duct and the spiral courses tended to be anterior or lateral superiorly and posterior inferiorly. Clinically significant variations in cystic duct insertions are common and surgeons should be cautious about these variations to avoid complications.

Conserved infections and reproductive phenotypes of Wolbachia symbionts in Asian tortrix moths.

Wolbachia is a ubiquitous endosymbiotic bacterium that manipulates insect reproduction. A notable feature of Wolbachia is male killing (MK), whereby sons of infected females are killed during development; however, the evolutionary processes by which Wolbachia acquired the MK ability remain unclear. The tea tortrix moth Homona magnanima (Tortricidae) harbours three non-MK Wolbachia strains (wHm-a, wHm-b and wHm-c) and an MK strain wHm-t. Although wHm-t and wHm-c are closely related, only wHm-t has an MK-associated prophage region. To understand the evolutionary processes underlying the emergence of MK wHm-t, we examined Wolbachia infections and phenotypes in 62 tortricid species collected from 39 localities across Japan, Taiwan, Vietnam and Indonesia. PCR assays detected wHm-c relatives in 51 species and triple infection of wHm-a, wHm-b and wHm-c in 31 species. Apart from Taiwanese H. magnanima, no species exhibited the MK phenotype and were positive for the wHm-t-specific prophage. While wHm-t infection was dominant in Taiwanese H. magnanima, wHm-a, wHm-b and wHm-c were dominant in Japanese H. magnanima populations. These results suggest that wHm-a, wHm-b and wHm-c strains descended from a common ancestor with repeated infection loss and that wHm-t evolved from the wHm-c acquiring MK ability in allopatric populations of H. magnanima.

Regulation of condensin II by self-suppression and release mechanisms.

In vertebrates, two distinct condensin complexes, condensin I and condensin II, cooperate to drive mitotic chromosome assembly. It remains largely unknown how the two complexes differentially contribute to this process at a mechanistic level. We have previously dissected the role of individual subunits of condensin II by introducing recombinant complexes into Xenopus egg extracts. Here we extend these efforts by introducing a modified functional assay using extracts depleted of topoisomerase IIα (topo IIα), which allows us to further elucidate the functional similarities and differences between condensin I and condensin II. The intrinsically disordered C-terminal region of the CAP-D3 subunit (the D3 C-tail) is a major target of Cdk1 phosphorylation, and phosphorylation-deficient mutations in this region impair condensin II functions. We also identify a unique helical structure in CAP-D3 (the D3 HEAT docker) that is predicted to directly interact with CAP-G2. Deletion of the D3 HEAT docker, along with the D3 C-tail, enhances the ability of condensin II to assemble mitotic chromosomes. Taken together, we propose a self-suppression mechanism unique to condensin II that is released by mitotic phosphorylation. Evolutionary implications of our findings are also discussed.

Spectrally narrow band-edge photoluminescence from AgInS2-based core/shell quantum dots for electroluminescence applications.

This study presents a facile synthesis of cadmium-free ternary and quaternary quantum dots (QDs) and their application to light-emitting diode (LED) devices. AgInS2 ternary QDs, developed as a substitute for cadmium chalcogenide QDs, exhibited spectrally broad photoluminescence due to intrinsic defect levels. Our group has successfully achieved narrow band-edge PL by a coating with gallium sulfide shell. Subsequently, an intrinsic difficulty in the synthesis of multinary compound QDs, which often results in unnecessary byproducts, was surmounted by a new approach involving the nucleation of silver sulfide followed by material conversion to the intended composition (silver indium gallium sulfide). By fine-tuning this reaction and bringing the starting material closer to stoichiometric compositional ratios, atom economy was further improved. These QDs have been tested in LED applications, but the standard device encountered a significant defective emission that would have been eliminated by the gallium sulfide shells. This problem is addressed by introducing gallium oxide as a new electron transport layer.

Remimazolam for Pediatric Procedural Sedation: Results of an Institutional Pilot Program.

Remimazolam, an ultra-short-acting benzodiazepine sedative, was first approved in 2020 in Japan as a general anesthetic for adults. However, its utilization in pediatric settings remains unexplored and, to date, is confined to isolated case reports due to a lack of specific pediatric labeling. The primary objective of our study was to evaluate the safety profile of remimazolam when used for procedural sedation in children following dosages established in adult protocols. Additional parameters, including dosage per kg of body weight, duration of the procedure, efficacy (measured as successful completion of the procedure), the necessity for supplemental medications, and changes in physiological parameters, such as the heart rate (HR) and mean arterial blood pressure (MAP), were assessed. Our study encompassed 48 children with an average age of 7.0 years. The objective Tracking and Reporting Outcomes of Procedural Sedation tool indicated no adverse events. In our cohort, propofol and ketamine were used as adjunctive treatments in 8 and 39 patients, respectively, with successful completion of all procedures. Notable hemodynamic variability was observed, with 88.4% of patients experiencing a ≥20% change (increase or decrease) and 62.8% experiencing a ≥30% change in MAP. Additionally, a ≥20% change in HR was observed in 54.3% of patients, and a ≥30% change was observed in 34.8% of patients. Nevertheless, none of the patients required pharmacological intervention to manage these hemodynamic fluctuations. Our findings suggest that remimazolam, when supplemented with propofol or ketamine, could offer a safe and effective pathway for administering procedural sedation in pediatric populations.

Elasticity control of entangled chromosomes: Crosstalk between condensin complexes and nucleosomes.

Condensin-mediated loop extrusion is now considered as the main driving force of mitotic chromosome assembly. Recent experiments have shown, however, that a class of mutant condensin complexes deficient in loop extrusion can assemble chromosome-like structures in Xenopus egg extracts, although these structures are somewhat different from those assembled by wild-type condensin complexes. In the absence of topoisomerase II (topo II), the mutant condensin complexes produce an unusual round-shaped structure termed a bean, which consists of a DNA-dense central core surrounded by a DNA-sparse halo. The mutant condensin complexes accumulate in the core, whereas histones are more concentrated in the halo than in the core. We consider that this peculiar structure serves as a model system to study how DNA entanglements, nucleosomes, and condensin functionally crosstalk with each other. To gain insight into how the bean structure is formed, here we construct a theoretical model. Our theory predicts that the core is formed by attractive interactions between mutant condensin complexes, whereas the halo is stabilized by the energy reduction through the selective accumulation of nucleosomes. The formation of the halo increases the elastic free energy due to the DNA entanglement in the core, but the latter free energy is compensated by condensin complexes that suppress the assembly of nucleosomes.

Remimazolam as an Adjunct to General Anesthesia in Children: Adverse Events and Outcomes in a Large Cohort of 418 Cases.

Remimazolam was first approved in 2020 as a general anesthetic for adults and still does not have pediatric labeling. Our study will be the first pilot program that administers remimazolam as an adjunct to a general endotracheal anesthetic in children. Between August 2020 and December 2022, electronic medical records were collected for all children who received remimazolam during anesthesia. The remimazolam dosing regimen was extrapolated from the adult package insert, with intravenous induction doses of 12 mg/kg/h administered until the desired effect was achieved. Subsequent infusions were given at a rate of 1-2 mg/kg/h, accompanied by intermittent boluses of 0.2 mg/kg, with all dosing adjustments made according to the anesthesiologist's clinical discretion. A total of 418 children (mean 4.6 yrs, 68.7% ASA 1 and 2) underwent surgeries which averaged 81.2 min. A total of 75.2% of patients had greater than a 20% change (increase or decrease) in MAP (lowest or highest) from baseline, and 203 (49.3%) patients had greater than a 30% change (increase or decrease) in MAP (lowest or highest) from baseline. A total of 5% received ephedrine to treat unanticipated hemodynamic variability. Discharge criteria were met within an average of 13.8 min after arrival at the post-anesthesia care unit. Remimazolam may offer the benefits of rapid recovery following general endotracheal anesthesia. The risk of hemodynamic variability which necessitates and responds to ephedrine should be anticipated.

The relationship between ß-amylase and the degradation of starch temporarily stored in rice leaf blades.

Starch is stored temporarily in the leaves during the day but degraded during the night. In this study, we investigated the relationship between diurnal changes in starch content in rice leaf blades and the mRNA levels of ß-amylase genes. In addition to the known plastid-type ß-amylases OsBAM2 and OsBAM3, OsBAM4, and OsBAM5 were also identified as plastid targeted proteins. In the leaf blades, starch contents, which reached its maximum at the end of day, showed two periods of marked decrease: from 18:00 to 21:00 and from 24:00 to 6:00. The expression of OsBAM2, OsBAM3, OsBAM4, and OsBAM5 was maintained at a low level from 18:00 to 21:00 but increased strongly after midnight. Furthermore, ß-amylase activity gradually increased after 21:00, reaching a maximum during the early morning. These results suggest that in rice leaf blades, ß-amylase plays an important role in starch degradation by being highly active from midnight to dawn.

Synthesis and herbicidal activity of optically active cinmethylin, its enantiomer, and C3-substituted cinmethylin analogs.

We investigated the synthesis and herbicidal activity of optically active cinmethylin, its enantiomer, and C3-substituted cinmethylin analogs. Optically active cinmethylin could be obtained in seven steps with the Sharpless asymmetric dihydroxylation of α-terpinene. The synthesized cinmethylin and its enantiomer showed similar herbicidal activity, which was independent of the stereochemistry. Next, we synthesized cinmethylin analogs with various substituents at the C3 position. We found that analogs with methylene, oxime, ketone, or methyl groups at the C3 position show excellent herbicidal activity.

Monitoring the compaction of single DNA molecules in Xenopus egg extract in real time.

DNA compaction is required for the condensation and resolution of chromosomes during mitosis, but the relative contribution of individual chromatin factors to this process is poorly understood. We developed a physiological, cell-free system using high-speed Xenopus egg extracts and optical tweezers to investigate real-time mitotic chromatin fiber formation and force-induced disassembly on single DNA molecules. Compared to interphase extract, which compacted DNA by ~60%, metaphase extract reduced DNA length by over 90%, reflecting differences in whole-chromosome morphology under these two conditions. Depletion of the core histone chaperone ASF1, which inhibits nucleosome assembly, decreased the final degree of metaphase fiber compaction by 29%, while depletion of linker histone H1 had a greater effect, reducing total compaction by 40%. Compared to controls, both depletions reduced the rate of compaction, led to more short periods of decompaction, and increased the speed of force-induced fiber disassembly. In contrast, depletion of condensin from metaphase extract strongly inhibited fiber assembly, resulting in transient compaction events that were rapidly reversed under high force. Altogether, these findings support a speculative model in which condensin plays the predominant role in mitotic DNA compaction, while core and linker histones act to reduce slippage during loop extrusion and modulate the degree of DNA compaction.

Cell cycle-specific loading of condensin I is regulated by the N-terminal tail of its kleisin subunit.

Condensin I is a pentameric protein complex that plays an essential role in mitotic chromosome assembly in eukaryotic cells. Although it has been shown that condensin I loading is mitosis specific, it remains poorly understood how the robust cell cycle regulation of condensin I is achieved. Here, we set up a panel of in vitro assays to demonstrate that cell cycle-specific loading of condensin I is regulated by the N-terminal tail (N-tail) of its kleisin subunit CAP-H. Deletion of the N-tail accelerates condensin I loading and chromosome assembly in Xenopus egg mitotic extracts. Phosphorylation-deficient and phosphorylation-mimetic mutations in the CAP-H N-tail decelerate and accelerate condensin I loading, respectively. Remarkably, deletion of the N-tail enables condensin I to assemble mitotic chromosome-like structures even in interphase extracts. Together with other extract-free functional assays in vitro, our results uncover one of the multilayered mechanisms that ensure cell cycle-specific loading of condensin I onto chromosomes.

Biological soil disinfestation compatible with renewable energy production for sustainable agriculture.

Biological soil disinfestation (BSD) is biotechnology to control soil-borne plant pathogens based on the anaerobic-reducing environment in soil and the functions of indigenous microbes. A new sustainable agricultural technology, the GET system, which produces and recovers methane as renewable energy from paddy fields, has a structure and principles similar to those of BSD technology. To confirm the potential of the GET system as BSD technology, the microbial community structures in the GET system were analyzed using next-generation sequencing. Thirty-four phyla were detected: 31 bacterial and 3 archaeal. Firmicutes dominated during the experimental period, which plays an important role in BSD functions such as organic decomposition, nitrate removal, and soil-borne pathogen elimination. The ability of the GET system to control soil-borne pathogens as well as produce renewable energy was demonstrated.

Molecular dissection of condensin II-mediated chromosome assembly using in vitro assays.

In vertebrates, condensin I and condensin II cooperate to assemble rod-shaped chromosomes during mitosis. Although the mechanism of action and regulation of condensin I have been studied extensively, our corresponding knowledge of condensin II remains very limited. By introducing recombinant condensin II complexes into Xenopus egg extracts, we dissect the roles of its individual subunits in chromosome assembly. We find that one of two HEAT subunits, CAP-D3, plays a crucial role in condensin II-mediated assembly of chromosome axes, whereas the other HEAT subunit, CAP-G2, has a very strong negative impact on this process. The structural maintenance of chromosomes ATPase and the basic amino acid clusters of the kleisin subunit CAP-H2 are essential for this process. Deletion of the C-terminal tail of CAP-D3 increases the ability of condensin II to assemble chromosomes and further exposes a hidden function of CAP-G2 in the lateral compaction of chromosomes. Taken together, our results uncover a multilayered regulatory mechanism unique to condensin II, and provide profound implications for the evolution of condensin II.

Cell cycle-specific phase separation regulated by protein charge blockiness.

Dynamic morphological changes of intracellular organelles are often regulated by protein phosphorylation or dephosphorylation1-6. Phosphorylation modulates stereospecific interactions among structured proteins, but how it controls molecular interactions among unstructured proteins and regulates their macroscopic behaviours remains unknown. Here we determined the cell cycle-specific behaviour of Ki-67, which localizes to the nucleoli during interphase and relocates to the chromosome periphery during mitosis. Mitotic hyperphosphorylation of disordered repeat domains of Ki-67 generates alternating charge blocks in these domains and increases their propensity for liquid-liquid phase separation (LLPS). A phosphomimetic sequence and the sequences with enhanced charge blockiness underwent strong LLPS in vitro and induced chromosome periphery formation in vivo. Conversely, mitotic hyperphosphorylation of NPM1 diminished a charge block and suppressed LLPS, resulting in nucleolar dissolution. Cell cycle-specific phase separation can be modulated via phosphorylation by enhancing or reducing the charge blockiness of disordered regions, rather than by attaching phosphate groups to specific sites.

A loop extrusion-independent mechanism contributes to condensin I-mediated chromosome shaping.

Condensin I is a five-subunit protein complex that is central to mitotic chromosome assembly in eukaryotic cells. Despite recent progress, its molecular mechanisms of action remain to be fully elucidated. By using Xenopus egg extracts as a functional assay, we find that condensin I complexes harboring mutations in its kleisin subunit CAP-H produce chromosomes with confined axes in the presence of topoisomerase IIα (topo IIα) and highly compact structures (termed "beans") with condensin-positive central cores in its absence. The bean phenotype depends on the SMC ATPase cycle and can be reversed by subsequent addition of topo IIα. The HEAT repeat subunit CAP-D2, but not CAP-G, is essential for the bean formation. Notably, loop extrusion activities of the mutant complexes cannot explain the chromosomal defects they exhibit in Xenopus egg extracts, implying that a loop extrusion-independent mechanism contributes to condensin I-mediated chromosome assembly and shaping. We provide evidence that condensin-condensin interactions underlie these processes.

Synthesis and herbicidal activity of 3-substituted toxoflavin analogs.

We investigated the synthesis and herbicidal activity of 23 toxoflavin analogs, 1a-w, in which aromatic rings (R) were introduced into the C-3 position. In paddy field conditions, 1k (R=2-CF3-C6H4) and 1w (R=2-thienyl) showed excellent herbicidal activity. Under upland field conditions, we found that toxoflavin analogs 1a (R=C6H5), 1n (R=2-CH3O-C6H4), and 1p (R=4-CH3O-C6H4) exhibited wide herbicidal spectrum against Echinochloa crus-galli (L) var. crus-galli (ECHCG), Chenopodium album, and Amaranthus viridis (AMAVI). The analog with the 2-fluoro group on benzene ring 1b also showed high herbicidal activity against both ECHCG and AMAVI.

Usefulness of several factors and clinical scoring models in preoperative diagnosis of complicated appendicitis.

BACKGROUND: The preoperative distinction between uncomplicated and complicated appendicitis is important to determine the appropriate treatments, such as antibiotics, surgery, or interval appendectomy. Computed tomography (CT) plays an important role; however, combining clinical and imaging factors may make preoperative evaluation more reliable. This study evaluated and analyzed cases and the usefulness of several preoperative factors and clinical scoring models to detect complicated appendicitis. METHODS: A total of 203 patients preoperatively diagnosed with acute appendicitis at our facility were included. Complicated appendicitis was defined as appendicitis with gangrene, perforated appendix, and/or abscess formation. Preoperative factors were collected from published clinical scoring models; patient information, symptoms, signs, results of laboratory tests, and findings of CT. Factors were analyzed using a chi-squared test and the Mann-Whitney U test. RESULTS: The preoperative factors were compared between 151 uncomplicated and 52 complicated appendicitis patients. The significant factors were age ≥40, duration of symptoms >24 hours, body temperature ≥37.3°C, high levels of CRP, findings in CT scan (appendix diameter ≥10 mm, stranding of the adjacent fat, presence of fluid collection, and suspicion of abscess or perforation). We also evaluated the usefulness of clinical scoring models for the detection of complicated appendicitis and found the Appendicitis Inflammatory Response score and two prediction models (Atema score and Imaoka score) showed significance (p < 0.05). High serum CRP level was significantly associated with complicated appendicitis (p < 0.001), and the predicted existence rates of complicated appendicitis were 52.7% for serum CRP level ≥50mg/L, 74.4% for ≥100mg/L, and 82.6% for ≥150mg/L. CONCLUSION: The results demonstrated several preoperative factors and clinical scoring models to increase suspicion of complicated appendicitis. Specifically, high serum levels of CRP may be a useful factor in predicting complicated appendicitis prior to surgery when supported by clinical findings and imaging; however, further research is needed.

Efficacy of Intranodal Neoantigen Peptide-pulsed Dendritic Cell Vaccine Monotherapy in Patients With Advanced Solid Tumors: A Retrospective Analysis.

BACKGROUND/AIM: Neoantigens are tumor-specific antigens that emerge due to gene mutations in tumor cells, and are highly antigenic epitopes that escape central immune tolerance in the thymus, making cancer vaccine therapy a desirable option. PATIENTS AND METHODS: Tumor neoantigens were predicted in 17 patients with advanced cancer. They were resistant to the standard treatment regime, and their synthetic peptides were pulsed to the patient's monocyte-derived dendritic cells (DCs), and administered to the patient's lymph nodes via ultrasound. RESULTS: Some patients showed sustained tumor shrinkage after this treatment, while some did not respond, showing no ELISpot reaction. Although the number of mutations and the predicted neoantigen epitopes differed between patients, the clinical effect depended more on the presence or absence of an immune response after vaccination rather than the number of neoantigens. CONCLUSION: Intranodal neoantigen peptide-pulsed DC vaccine administration therapy has clinical and immunological efficacy and safety.