Screening structure and predicting toxicity of pesticide adjuvants using molecular dynamics simulation and machine learning for minimizing environmental impacts.

Surfactants as synergistic agents are necessary to improve the stability and utilization of pesticides, while their use is often accompanied by unexpected release into the environment. However, there are no efficient strategies available for screening low-toxicity surfactants, and traditional toxicity studies rely on extensive experimentation which are not predictive. Herein, a commonly used agricultural adjuvant Triton X (TX) series was selected to study the function of amphipathic structure to their toxicity in zebrafish. Molecular dynamics (MD) simulations, transcriptomics, metabolomics and machine learning (ML) were used to study the toxic effects and predict the toxicity of various TX. The results showed that TX with a relatively short hydrophilic chain was highly toxic to zebrafish with LC50 of 1.526 mg/L. However, TX with a longer hydrophilic chain was more likely to damage the heart, liver and gonads of zebrafish through the arachidonic acid metabolic network, suggesting that the effect of surfactants on membrane permeability is the key to determine toxic results. Moreover, biomarkers were screened through machine learning, and other hydrophilic chain lengths were predicted to affect zebrafish heart health potentially. Our study provides an advanced adjuvants screening method to improve the bioavailability of pesticides while reducing environmental impacts.

Development and Application of a High-Precision Portable Digital Compass System for Improving Combined Navigation Performance.

There are not many high-precision, portable digital compass solutions available right now that can enhance combined navigation systems' overall functionality. Additionally, there is a dearth of writing about these products. This is why a tunnel magnetoresistance (TMR) sensor-based high-precision portable digital compass system is designed. First, the least-squares method is used to compensate for compass inaccuracy once the ellipsoid fitting method has corrected manufacturing and installation errors in the digital compass system. Second, the digital compass's direction angle data is utilized to offset the combined navigation system's mistake. The final objective is to create a high-performing portable TMR digital compass system that will enhance the accuracy and stability of the combined navigation system (abbreviated as CNS). According to the experimental results, the digital compass's azimuth accuracy was 4.1824° before error compensation and 0.4580° after it was applied. The combined navigation system's path is now more accurate overall and is closer to the reference route than it was before the digital compass was added. Furthermore, compared to the combined navigation route without the digital compass, the combined navigation route with the digital compass included is more stable while traveling through the tunnel. It is evident that the digital compass system's design can raise the integrated navigation system's accuracy and stability. The integrated navigation system's overall performance may be somewhat enhanced by this approach.

Salinity-Driven Interface Self-Assembly of a Biological Amphiphilic Emulsifier to Form Stable Janus Core-Shell Emulsion for Enhancing Agrichemical Delivery.

Agrichemical losses are a severe threat to the ecological environment. Additionally, some agrichemical compounds contain abundant salt, which increases the instability of formulations, leading to a lower agrichemical utilization and soil hardening. Fortunately, the biological amphiphilic emulsifier sodium deoxycholate alleviates these problems by forming stable Janus core-shell emulsions through salinity-driven interfacial self-assembly. According to the interfacial behavior, dilational rheology, and molecular dynamics simulations, Janus-emulsion molecules are more closely arranged than traditional-emulsion molecules and generate an oil-water interfacial film that transforms into a gel film. In addition, at the same spray volume, the deposition area of the Janus emulsion increased by 37.70% compared with that of the traditional emulsion. Owing to the topology effect and deformation, the Janus emulsion adheres to rice micropapillae, achieving better flush resistance. Meanwhile, based on response of the Janus emulsion to stimulation by carbon dioxide (CO2), the emulsion lost to the soil can form a rigid shell for inhibiting the release of pesticides and metal ions from harming the soil. The pyraclostrobin release rate decreased by 50.89% at 4 h after the Janus emulsion was exposed to CO2. The Chao1 index of the Janus emulsion was increased by 12.49% as compared to coconut oil delivery in soil microbial community. The Janus emulsion ingested by harmful organisms can be effectively absorbed in the intestine to achieve better control effects. This study provides a simple and effective strategy, which turns waste into treasure, by combining metal ions in agrichemicals with natural amphiphilic molecules to prepare stable emulsions for enhancing agrichemical rainfastness and weakening environmental risk.

Abnormal phase separation of biomacromolecules in human diseases.

Membrane-less organelles (MLOs) formed through liquid-liquid phase separation (LLPS) are associated with numerous important biological functions, but the abnormal phase separation will also dysregulate the physiological processes. Emerging evidence points to the importance of LLPS in human health and diseases. Nevertheless, despite recent advancements, our knowledge of the molecular relationship between LLPS and diseases is frequently incomplete. In this review, we outline our current understanding about how aberrant LLPS affects developmental disorders, tandem repeat disorders, cancers and viral infection. We also examine disease mechanisms driven by aberrant condensates, and highlight potential treatment approaches. This study seeks to expand our understanding of LLPS by providing a valuable new paradigm for understanding phase separation and human disorders, as well as to further translate our current knowledge regarding LLPS into therapeutic discoveries.

Analysis of visual quality after multifocal intraocular lens implantation in post-LASIK cataract patients.

With the development of refractive corneal surgery, excimer laser in situ keratomileusis (LASIK) has become a common refractive surgery procedure. However, post-LASIK patients are at increased risk of developing cataracts as they age and often require IOL implantation. The choice of IOLs is particularly important for these patients, who have smaller residual refractive error and have higher requirements for post-cataract vision recovery and visual quality than the general population. Multifocal IOLs are widely used in clinical practice for patients with high visual acuity needs, such as cataract patients after refractive keratomileusis, due to their advantages of providing excellent near and distance visual acuity; however, compared to monofocal IOLs, multifocal IOLs can lead to postoperative problems related to visual quality such as increased higher order aberrations and decreased contrast sensitivity. Therefore, whether multifocal IOLs have advantages for post-LASIK cataract patients, such as improving the visual quality of such patients, has attracted attention. In this paper, we analyze the current status of research on the implantation of multifocal IOLs in post-LASIK cataract patients by domestic and foreign experts, review and summarize the relevant literature, and propose further discussion in the context of the actual situation of postoperative visual quality and vision recovery.

The combined use of a plant growth promoting Bacillus sp. strain and GABA promotes the growth of rice under salt stress by regulating antioxidant enzyme system, enhancing photosynthesis and improving soil enzyme activities.

Salt stress poses a global challenge for agriculture, crop growth, and food production. In this study, a strain of rhizobacteria with both plant growth-promoting (PGP) traits and salt tolerance was isolated. The strain was identified as Bacillus pumilus via 16 S rDNA sequencing and was named B. pumilus JIZ13. This strain had the potential to solubilize phosphates and produce 1-aminocyclopropane-1-carboxylic acid deaminase, siderophores, and indole-3-acetic acid. After 35 days of salt stress exposure, the root length, plant height, dry weight, fresh weight, and relative water content of rice plants inoculated with strain JIZ13 were significantly higher than those without inoculation. Interestingly, the PGP properties of strain JIZ13 were significantly improved by the exogenous addition of gamma-aminobutyric acid (GABA). Moreover, GABA also enhanced the growth and development of rice plants under salt stress by providing substrates for the tricarboxylic acid cycle. Furthermore, the synergistic roles of GABA and strain JIZ13 in mitigating the damage caused by salt stress in rice plants was investigated. The results showed that the co-application of GABA and JIZ13 significantly increased photosynthetic efficiency, chlorophyll accumulation, antioxidant levels, levels of osmotic adjustment substances, and biomass of rice under salinity stress. In addition, the activities of urease, protease, invertase, and catalase enzymes in soil significantly improved under the combination of strain JIZ13 and GABA and increased by 39.65%, 36.88%, 70.21%, and 65.23%, respectively, compared to those without rhizobacterial and GABA additions. The enhancement of these four soil enzyme activities might thus improve soil quality and increase root elongation and biomass in rice plants. The results of this study provide the first evidence that PGP-rhizobacterial strain JIZ13 along with GABA can attenuate the negative effects of salt stress in rice plants.

The simple strategy to improve pesticide bioavailability and minimize environmental risk by effective and ecofriendly surfactants.

Low pesticide efficiency has caused serious environmental pollution and economic loss, which are closely related to each link in the targeted delivery of pesticides. However, the existing strategies for improving pesticide utilization rate are not comprehensive, and the regulation of foliar absorption and biological activity has been neglected. As surfactants are the most important agricultural synergists, the impact, wetting, adhesion, and leaf retention behaviors of pyraclostrobin (PYR) droplets containing the surfactant Triton X (TX) series on hydrophobic scallion leaf surfaces were studied. The results showed that TX-102 can sufficiently reduce the splash and roll of droplets when they impact inclined leaves, owing to its low dynamic surface tension. Moderate wetting ability and high adhesion also maximizes leaf retention of the TX-102-added PYR solution sprayed on scallion leaves. Furthermore, TX-102 improved the permeation and absorption of PYR in scallion leaves through the synergistic effects of opening the stomata and dissolving the waxy layer. The synergistic bioactivity of TX-102 against pathogenic fungi Alternaria porri and its safety to non-target organism zebrafish have also been demonstrated. Our study provides a more comprehensive theoretical rationale for screening adjuvants to improve the effectiveness and bioavailability of pesticides and reduce the risk of pesticides entering the environment.

Combined application of H2S and a plant growth promoting strain JIL321 regulates photosynthetic efficacy, soil enzyme activity and growth-promotion in rice under salt stress.

Salinity stress is one of the most harmful abiotic stresses that inhibit crop growth and grain yield. In this study, a salt-tolerant bacterium was isolated from the soil of the rice rhizosphere and named Myroides sp. JIL321, based on the results of the phylogenetic tree analysis. The strain JIL321 tolerated up to 1, 283.37 mM of NaCl and exhibited positive plant growth-promoting traits, such as the production of indole acetic acid (IAA) and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. Therefore, the effects of JIL321 on rice (Oryza sativa L.) under salinity stress were determined. The inoculation of strain JIL321 significantly increased the chlorophyll content and the accumulation of osmotic adjustment substances, such as proline and soluble sugars, in rice expose to salt stress. Additionally, strain JIL321 inoculation significantly enhanced the activities of some enzymes commonly found in soil, such as urease, invertase and catalase. Moreover, the production of hydrogen sulfide (H2S), a pivotal signaling molecule, was also induced in rice by salt stress. Treatment with sodium hydrogen sulfide (NaHS, H2S donor) improved salt stress tolerance of the rice, while treatment with hypotaurine (HT, H2S scavenger) significantly suppressed it. Interestingly, NaHS treatment also improved the production of IAA and ACC deaminase in strain JIL321 under 0 mM and 150 mM salt concentrations. The combined treatment of JIL321 and NaHS could further improve the growth of salt-stressed rice seedlings, most likely due to the interaction effect between H2S and strain JIL321. To our knowledge, this study is the first to demonstrate that the combined use of H2S and plant growth-promoting bacteria could alleviate the adverse effects of salt stress on rice plants, and further verifies the novel role of H2S as a signaling molecule that enhance the tolerance of plant to abiotic stresses.

Effects of three cooking methods on content changes and absorption efficiencies of carotenoids in maize.

Maize is a staple source of certain carotenoids for the human diet, but food processing is an important factor affecting the carotenoid content and absorption. In this study, we investigated the content changes of carotenoids in maize under three cooking methods (boiling kernels, preparing porridge and preparing tortilla). Also, using the in vitro digestion model, we assessed the effects of the cooking methods on carotenoid absorption efficiencies (digestion stability, micellization efficiency and bioaccessibility). The results indicated that the carotenoid content obviously increased in the boiled kernels, but its carotenoid bioaccessibility was the lowest compared to that of porridge and tortilla. Tortilla presented the highest digestion stability of ß-carotene (309 ± 63%) and bioaccessibility of xanthophylls (22.4 ± 0.5% for lutein and 18.5 ± 1.0% for zeaxanthin) among the three cooked products during in vitro digestion. The contents of carotenoids in the porridge were all the lowest among the three cooked products; however, the low concentration level of xanthophylls reduced the competitive effect on ß-carotene micellization, which increased the bioaccessibility of ß-carotene to 52.1 ± 5.0%. Additionally, the content of xanthophylls (lutein + zeaxanthin) in digesta significantly and positively correlated with the ß-carotene content in digesta, whereas it negatively correlated with the micellization of ß-carotene. This correlation between the xanthophylls and ß-carotene was not affected by the cooking methods. These results together suggest that tortilla and porridge are better dietary choices for the intake of xanthophylls and ß-carotene, respectively, among maize-based foods. Furthermore, the absorption of ß-carotene was influenced by the content of xanthophylls whatever the cooking method.

Draft genome of the Northern snakehead, Channa argus.

The Northern snakehead (Channa argus), a member of the Channidae family of the Perciformes, is an economically important freshwater fish native to East Asia. In North America, it has become notorious as an intentionally released invasive species. Its ability to breathe air with gills and migrate short distances over land makes it a good model for bimodal breath research. Therefore, recent research has focused on the identification of relevant candidate genes. Here, we performed whole genome sequencing of C. argus to construct its draft genome, aiming to offer useful information for further functional studies and identification of target genes related to its unusual facultative air breathing. Findings: We assembled the C. argus genome with a total of 140.3 Gb of raw reads, which were sequenced using the Illumina HiSeq2000 platform. The final draft genome assembly was approximately 615.3 Mb, with a contig N50 of 81.4 kb and scaffold N50 of 4.5 Mb. The identified repeat sequences account for 18.9% of the whole genome. The 19 877 protein-coding genes were predicted from the genome assembly, with an average of 10.5 exons per gene. Conclusion: We generated a high-quality draft genome of C. argus, which will provide a valuable genetic resource for further biomedical investigations of this economically important teleost fish.

Transcriptome signatures in common carp spleen in response to Aeromonas hydrophila infection.

The common carp is an important aquaculture species that is worldwide distributed. Nowadays, intensive rearing in aquaculture increases the susceptibility of fish to various pathogens such as Aeromonas hydrophila, which has caused severe damage to carp production. However, systematic analysis on the host response of common carp against A. hydrophila is less studied. In order to better understand the common carp immune response process against bacteria at the global gene expression level, we examined transcriptional profiles of the common carp spleen at three timepoints following experimental infection with A. hydrophila. A total of 545 million 125-bp paired end reads were generated, and all trimmed clean reads were mapped onto the common carp whole genome sequence. Comparison of the transcriptomes between the treatment and control group fish revealed 2900 unigenes with significantly differential expression, including 732, 936, 928 genes up-regulated, and 248, 475, 700 genes down-regulated at 4 h, 12 h, 24 h post infection respectively. The captured significantly differentially expressed genes are mainly involved in the pathways including junction/adhesion, pathogen recognition, cell surface receptor signaling, and immune system process/defense response. Our study will provide fundamental information on molecular mechanism underlying the immune response of teleost against bacterial infection and might suggest strategies for selection of resistant strains of common carp in aquaculture.

Comparative transcriptome analysis between aquatic and aerial breathing organs of Channa argus to reveal the genetic basis underlying bimodal respiration.

Aerial breathing in fish was an important adaption for successful survival in hypoxic water. All aerial breathing fish are bimodal breathers. It is intriguing that they can obtain oxygen from both air and water. However, the genetic basis underlying bimodal breathing has not been extensively studied. In this study, we performed next-generation sequencing on a bimodal breathing fish, the Northern snakehead, Channa argus, and generated a transcriptome profiling of C. argus. A total of 53,591 microsatellites and 26,378 SNPs were identified and classified. A Ka/Ks analysis of the unigenes indicated that 63 genes were under strong positive selection. Furthermore, the transcriptomes from the aquatic breathing organ (gill) and the aerial breathing organ (suprabranchial chamber) were sequenced and compared, and the results showed 1,966 genes up-regulated in the gill and 2,727 genes up-regulated in the suprabranchial chamber. A gene pathway analysis concluded that four functional categories were significant, of which angiogenesis and elastic fibre formation were up-regulated in the suprabranchial chamber, indicating that the aerial breathing organ may be more efficient for gas exchange due to its highly vascularized and elastic structure. In contrast, ion uptake and transport and acid-base balance were up-regulated in the gill, indicating that the aquatic breathing organ functions in ion homeostasis and acid-base balance, in addition to breathing. Understanding the genetic mechanism underlying bimodal breathing will shed light on the initiation and importance of aerial breathing in the evolution of vertebrates.

Genome wide identification of scavenger receptors class A in common carp (Cyprinus carpio) and their expression following Aeromonas hydrophila infection.

Scavenger receptors class A (SCARAs) is a subgroup of diverse families of pattern recognition receptors that bind a range of ligands, and play important roles in innate immune processes through pathogens detection, adhesion, endocytosis, and phagocytosis. However, most studies of SCARAs have focused on mammals, and much less is known of SCARAs in fish species. In this study, we identified 7 SCARAs across the common carp genome, which were classified into four subclasses according to comparative genomic analysis including sequence similarities analysis, gene structure and functional domain prediction. Further phylogenetic and syntenic analysis supported their annotation and orthologies. Through examining gene copy number of SCARA genes across several vertebrates, SCARA2, SCARA3 and SCARA4 were found have undergone gene duplication. The expression patterns of SCARAs in common carp were examined during early developmental stages, in healthy tissues, and after Aeromonas hydrophila infection. Most SCARA genes were ubiquitously expressed during common carp early developmental stages, and presented diverse patterns in various healthy tissues, with relatively high expression levels in spleen, liver, intestine, gill and brain, indicating their critical roles likely in maintaining homeostasis and host immune response activities. After A. hydrophila infection, most SCARA genes were up-regulated at 4 h post infection in mucosal tissue intestine, while generally up-regulated at 12 h post infection in spleen, suggesting a tissue-specific pattern of regulation. Taken together, all these results suggested that SCARA genes played important roles in host immune response to A. hydrophila infection in common carp, and provided important genomic resources for future studies on fish disease management.

Genome-wide identification, phylogeny, and expression of fibroblast growth genes in common carp.

Fibroblast growth factors (FGFs) are a large family of polypeptide growth factors, which are found in organisms ranging from nematodes to humans. In vertebrates, a number of FGFs have been shown to play important roles in developing embryos and adult organisms. Among the vertebrate species, FGFs are highly conserved in both gene structure and amino-acid sequence. However, studies on teleost FGFs are mainly limited to model species, hence we investigated FGFs in the common carp genome. We identified 35 FGFs in the common carp genome. Phylogenetic analysis revealed that most of the FGFs are highly conserved, though recent gene duplication and gene losses do exist. By examining the copy number of FGFs in several vertebrate genomes, we found that eight FGFs in common carp have undergone gene duplications, including FGF6a, FGF6b, FGF7, FGF8b, FGF10a, FGF11b, FGF13a, and FGF18b. The expression patterns of all FGFs were examined in various tissues, including the blood, brain, gill, heart, intestine, muscle, skin, spleen and kidney, showing that most of the FGFs were ubiquitously expressed, indicating their critical role in common carp. To some extent, examination of gene families with detailed phylogenetic or orthology analysis verified the authenticity and accuracy of assembly and annotation of the recently published common carp whole genome sequences. Gene families are also considered as a unique source for evolutionary studies. Moreover, the whole set of common carp FGF gene family provides an important genomic resource for future biochemical, physiological, and phylogenetic studies on FGFs in teleosts.

The complete mitochondrial genome of Rasbora borapetensis (Cypriniformes: Cyprinidae: Rasbora).

The traditional polymerase chain reaction method was employed to obtain the complete mitochondrial genome of Rasbora borapetensis. The mitogenome was determined to be a 16,510 bp long circular molecule. It contained the typical complement of 13 protein-coding genes, 2 rRNAs and 22 tRNAs. This is first report on the complete mitogenome sequence of R. borapetensis.

The complete mitochondrial genome of Microdevario kubotai (Cypriniformes:Cyprinidae:Danioninae:Microdevario).

The traditional polymerase chain reaction method was employed to obtain the complete mitochondrial genome of Microdevario kubotai. The mitogenome was determined to be a 16,566 bp long circular molecule. It contained the typical complement of 13 protein-coding genes, 2 rRNAs and 22 tRNAs. This is first report on the complete mitogenome sequence of M. kubotai.

The complete mitochondrial genome of Channa marulius (Perciformes: Channidae: Channa).

The traditional polymerase chain reaction method was employed to obtain the complete mitochondrial genome of Channa marulius from Pakistan. The mitogenome was determined to be 16,569 bp in length. It contains 13 protein-coding genes, 2 rRNAs and 22 tRNAs. This is the first report on the complete mitogenome sequence of C. marulius.

The complete mitochondrial genome of Paracheirodon axelrodi (Characiformes:Characidae:Paracheirodon).

The complete mitochondrial genome of Paracheirodon axelrodi was obtained by the traditional polymerase chain reaction method. The mitogenome was determined to be a 17,100 bp long circular molecule. It contains the typical complement of 13 protein-coding genes, 2 rRNAs and 22 tRNAs. This is first report on the complete mitogenome sequence of P. axelrodi.

Complete mitochondrial genomes of two ornamental fishes.

The complete mitochondrial genomes of two ornamental fishes, black molly (Poecilia sphenops) and blue gourami (Trichogaster trichopterus), were obtained by the traditional polymerase chain reaction (PCR)-based sequencing approach. The mitogenomes of P. sphenops and T. trichopterus are determined as 16,533 bp and 16,456 bp in length, respectively. Both the genomes include 22 transfer RNA genes, 13 protein-coding genes and 2 ribosomal RNA genes. Phylogenetic tree was constructed based on the complete mitogenomes of these two species and closely related 20 teleost species to assess their phylogenic relationship and evolution.

Transcriptional Profiling Reveals Differential Gene Expression of Amur Ide (Leuciscus waleckii) during Spawning Migration.

Amur ide (Leuciscus waleckii), an important aquaculture species, inhabits neutral freshwater but can tolerate high salinity or alkalinity. As an extreme example, the population in Dali Nor lake inhabits alkalized soda water permanently, and migrates from alkaline water to neutral freshwater to spawn. In this study, we performed comparative transcriptome profiling study on the livers of Amur ide to interrogate the expression differences between the population that permanently inhabit freshwater in Ganggeng Nor lake (FW) and the spawning population that recently migrated from alkaline water into freshwater (SM). A total of 637,234,880 reads were generated, resulting in 53,440 assembled contigs that were used as reference sequences. Comparisons of these transcriptome files revealed 444 unigenes with significant differential expression (p-value ≤ 0.01, fold-change ≥ 2), including 246 genes that were up-regulated in SM and 198 genes that were up-regulated in FW. The gene ontology (GO) enrichment analysis and KEGG pathway analysis indicated that the mTOR signaling pathway, Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling pathway, and oxidative phosphorylation were highly likely to affect physiological changes during spawning migration. Overall, this study demonstrates that transcriptome changes played a role in Amur ide spawning migration. These results provide a foundation for further analyses on the physiological and molecular mechanisms underlying Amur ide spawning migration.