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Molecular dynamics simulations are carried out to study the transport properties of water molecules across 1.34 nm long single-walled carbon nanotubes (SWCNTs) under hydrostatic pressure with different directions. It is found that when the deflection angle φ between the hydrostatic pressure and the tube-axis direction changes from 0 ° to 90 ° , the net flux shows significant differences. It is interesting to note that the maximum flux is counter-intuitively obtained at φ = 45 ° , which is about three times that of at φ = 0 °. This enhancement is mainly attributed to the excellent intermolecular structure, the orientation distribution, and the filling rate of in-tube water at φ = 45 °. Yet, it is worth noting that with the increase of the length of the SWCNT, the anomalous effect will gradually weaken until it almost disappears. Our work is of great significance for the practical application of high-efficiency nanofiltration membranes under pressure gradients. [ABSTRACT FROM AUTHOR]

Aquatic insects are well adapted to freshwater environments, but the molecular basis of these adaptations remains largely unknown. Most firefly species (Coleoptera: Lampyridae) are terrestrial, but the larvae of several species are aquatic. Here, larval and adult transcriptomes from Aquatica leii (freshwater) and Lychnuris praetexta (terrestrial) were generated to test whether the genes associated with metabolic efficiency and morphology have undergone adaptive evolution to fresh water. The aquatic fireflies had a significantly lower ratio of nonsynonymous to synonymous substitutions than the terrestrial insects, indicating a genomewide evolutionary constraint in the aquatic fireflies. We identified 341 fast‐evolving genes and 116 positively selected genes in the aquatic fireflies. Of these, 76 genes exhibiting both fast evolution and positive selection were primarily involved in ATP production, energy metabolism and the hypoxia response. We identified 7,271 differentially expressed genes (DEGs) in A. leii (adults versus larvae) and 8,309 DEGs in L. praetexta (adults versus larvae). DEGs specific to the aquatic firefly (n = 1,445) were screened via interspecific comparisons (A. leii versus L. praetexta) and were significantly enriched for genes involved in metabolic efficiency (e.g., ATP production, hypoxia, and immune responses) and certain aspects of morphology (e.g., cuticle chitin, tracheal and compound eye morphology). These results indicate that sequence and expression‐level changes in genes associated with both metabolic efficiency and morphological attributes related to the freshwater lifestyle contributed to freshwater adaptation in fireflies. This study provides new insights into the molecular mechanisms of aquatic adaptation in insects. [ABSTRACT FROM AUTHOR]

Abstract Many studies have reported that behavior and bioluminescence of fireflies could be affected by changes in environment conditions. However, little is known about how the deterioration of the aquatic environment affects aquatic fireflies, particularly with respect to molecular responses following exposure to water pollutants, such as benzo(a)pyrene (BaP), which is a key indicator in environmental risk assessment because of the hazards it poses. Here, whole transcriptome sequencing and gene expression analysis were performed on freshwater fireflies (Luciola leii) exposed to BaP (concentration of 0.01 mg/L). Four transcriptomic libraries were constructed for the control and treatment groups, including two biological replicates. From the mixed pools (each pool contains 60 individuals from three time points), a total of 54,282 unigenes were assembled. Furthermore, 329,337 of Single-nucleotide Polymorphisms (SNPs) and 1324 of Simple Sequence Repeats (SSRs) were predicted using bioinformatics, which is useful for the future development of molecular markers. Subsequently, 2414 differently expressed genes (DEGs) were identified in response to BaP stress in comparison to the control, including 1350 up-regulated and 1064 down-regulated DEGs. Functional enrichment showed that these DEGs are primarily related to innate immunity; xenobiotic biodegradation and response, biomacromolecule metabolism, biosynthesis, and absorption. Eight key BaP-responsive DEGs were screened to survey the dynamic changes of expression in response to BaP stress at different time points, and to validate the RNA sequencing data using quantitative real-time PCR. The results indicate that the expression of genes encoding UGT, CYP3A, CYP9, CYP6AS5 and ADHP were induced, while those encoding UGT2B10L, PTGDS, and ALDH were reduced, to participate in response to the BaP exposure and potentially help counteract the adverse effects of BaP. This investigation provides insight into the toxicological response of fireflies to the occurrence of water deterioration. Graphical abstract Unlabelled Image Highlights • 29,297 of 54,282 genes obtained in Luciola leii transcriptome were annotated. • Most DEGs were involved in xenobiotic biodegradation, biomacromolecule metabolism. • This study discovered a set of useful SSR and SNP molecular markers. • Eight DEGs were identified as key BaP-responsive genes. • This study firstly explored transcriptional response to BaP in aquatic insects. [ABSTRACT FROM AUTHOR]

Abstract The gills of fish are large mucosal surfaces that are very important portals for pathogen entry. Investigations have shown that microRNAs (miRNAs) are key regulators of immune response to bacterial infections in the gills of fish; however, how miRNA expression changes in response to infection by Gram-positive bacteria remains largely unknown. To further investigate the immunological role of miRNAs in fish gills under pathogen stress induced by Gram-positive bacterial infection, this study investigated Staphylococcus aureus (SA)-induced changes in the miRNAs levels in gills of adult zebrafish (Danio rerio). miRNA microarrays were used to analyze expression profiles of known miRNA in the gills of zebrafish in response to SA infection and compared these to uninfected control fish. A total of 30 differentially expressed miRNAs (DEMs) were identified. Target genes likely regulated by DEMs were predicted, and functional enrichment analyses were performed. The results indicated that DEM targets were primarily involved in innate immune processes, apoptosis, defense responses, and antibacterial responses. Pathways involving bacterial infection, innate immunity, metabolic process, disease, and apoptosis were mediated by DEMs. Furthermore, real-time quantitative PCR experiments for nine key SA -responsive DEMs that regulated the " SA infection" pathway validated the accuracy of microarray results. Dynamic variations in gene expression were surveyed in detail for these key SA -responsive DEMs for PBS control and at 6, 12, 24, and 48 h after SA challenge in detail. This study provides novel insight into the mechanisms underlying the miRNA regulation during the SA -induced immune response in zebrafish gills, and provides basic knowledge on the innate immune response against Gram-positive bacterial infection in bony fish. Highlights • DEM profiling was analyzed in zebrafish gills between control and SA -treated groups. • 30 differentially expressed miRNAs (DEMs) were identified after SA challenge. • The experiment of qRT-PCR validated the accuracy of miRNA microarrays. • This is the first time to investigate antibacterial response of mass miRNA expression in zebrafish gills. [ABSTRACT FROM AUTHOR]

Abstract Amphioxus is a key model for studying comparative immunity of vertebrates. Circular RNA (circRNA), as RNAs with a circular structure, has received little attention until recently, where several studies have reported that circRNA expression changes are involved in the immune response in animals. However, circRNA and its immune role in amphioxus have not been previously studied. Here, circRNAs in Chinese amphioxus (Branchiostoma belcheri) were sequenced, and 1859 circRNAs were identified using two algorithms (find_circ and CIRI). The analysis of miRNA target sites on circRNAs showed that 332 circRNAs may function as miRNA sponges. Furthermore, we identified circRNAs that were conserved between B. belcheri and vertebrates, tracing the origin of these circRNAs within chordates. Additionally, in combination with several key antiviral immune (poly(I:C), pIC) pathways identified in our previous B. belcheri studies, nine circRNAs potentially involved in these pathways were identified using bioinformatic predictions. Among these nine circRNAs, eight were selected to examine their expression response in B. belcheri challenged by pIC in comparison to control using real-time quantitative PCR. The results showed that four circRNAs were induced as part of the antiviral response against pIC, while expression of two circRNAs was decreased, and the expression levels of the remaining two were not significantly altered after pIC challenge. This work is the first to identify circRNAs and reveal their antiviral role in amphioxus. Therefore, it opens a new window to explore the comparative immunology of circRNAs in chordates and the regulatory roles of circRNAs in antiviral immunity in amphioxus. Highlights • 1859 circRNAs were identified in adult Branchiostoma belcheri. • 332 circRNAs are identified potentially as miRNA sponges. • Six circRNAs showed a gene expression alteration in response to pIC challenge. • This is the first time to identify circRNAs and investigate their immune response in amphioxus. [ABSTRACT FROM AUTHOR]

Abstract Amphioxus has been widely used as a model for the comparative immunology of vertebrates. Studies have reported that gene expression changes in the amphioxus gill in response to biotic stress, such as microbial and their mimic challenge, but little is known about how gene expression is affected by abiotic stress in the marine environment, such as nitrite. A lack of information regarding gene expression response to abiotic stress hinders a comprehensive understanding of gill defense response in amphioxus. Here, RNA sequencing was used to carry out gene expression profiling analyses of Branchiostoma belcheri gills under nitrite stress. Six libraries were created for the control and treatment groups, including three biological replicates. In total, 2416 differently expressed genes (DEGs) were detected in response to nitrite stress, of which 1522 DEGs were up-regulated in the treatment group in comparison to the control, while the remaining 894 DEGs were down-regulated genes. Functional enrichment revealed that these DEGs are primarily involved in disease, innate immunity, xenobiotic biodegradation and metabolism, and biomolecular processes and apoptosis. We screened 11 key nitrite-responsive DEGs to detect their expression responses to nitrite stress at different time points, and validate the sequencing data using real time quantitative PCR. The results indicated that the expression of gene encoding CYP3A, POD, CASPR1, GST, MAO, DDH, and XDH/XO were induced, while those encoding MRC, GT, DNASE1L, and RIPK5 were reduced, to participate in the anti-nitrite response. This study provides a useful resource for research of molecular toxicology in amphioxus under environmental stress. Highlights • Gene expression profiling was analyzed in Branchiostoma belcheri gills between control and nitrite-treated groups. • 2,416 genes presented expression response to nitrite stress. • The analysis of qRT-PCR confirmed the accuracy of expression profiling results. • We screened 11 key nitrite-responsive DEGs. [ABSTRACT FROM AUTHOR]

Abstract Amphioxus, a cephalochordate found in sand habitats in shallow in-shore seawaters, has been widely used as a model in comparative immunology of chordates. However, the role of microRNAs (miRNAs) in amphioxus under abiotic stress, particularly xenobiotics with strong toxicity, remains largely unknown. Here, a widespread marine contaminant, benzo(a)pyrene (BaP) is used to evaluate its toxic effects on miRNA expression of amphioxus. Six small RNA libraries were sequenced from Branchiostoma belcheri. A total of 144 known and 157 novel miRNAs were identified using deep sequencing and bioinformatics approaches. A total of 58 differentially expressed miRNAs (DEMs) were screened, including 25 up- and 33 down-regulated DEMs under BaP stress. Target genes possibly regulated by DEMs were predicted, and their functional enrichment analyses were performed. Targets of DEMs are primarily involved in xenobiotic and cellular homeostasis, catabolic and transport process. They could be largely linked to nine immune- and toxin detoxification-related pathways, including metabolism of xenobiotics by cytochrome P450, drug metabolism-other enzymes, and drug metabolism-cytochrome P450, etc. Furthermore, quantitative real-time PCR (qRT-PCR) analysis for 12 key BaP-responsive DEMs validates the accuracy of deep sequencing. Experiments were then conducted to investigate their expression responses to BaP stress at different time intervals in detail to further determine their expression dynamic in responses of B. belcheri towards BaP exposure. This study, to the best of our knowledge, investigates the regulatory roles of miRNAs in the toxicological response of amphioxus for the first time, providing valuable information for the protection of lone existing cephalochordate amphioxus. Highlights • We identified 58 differently expressed miRNAs in B. belcheri treated by BaP. • BaP affected xenobiotic and cellular homeostasis, catabolic and transport process. • Immune- and toxin detoxification-related pathways affected by BaP were identified. • Expression response of amphioxus miRNAs to toxic stress was investigated firstly. [ABSTRACT FROM AUTHOR]

Given mitochondrion is the 'energy and oxygen usage factories', adaptive signatures of mitochondrial genes have been extensively investigated in vertebrates from different altitudes, but few studies focus on insects. Here, we sequenced the complete mitochondrial genome (mitogenome) of Dolycoris. baccarum living in the Tibetan Plateau (DBHC, ∼3200 m above sea level (asl)) and conducted a detailed comparative analysis with another D. baccarum mitogenome (DBQY) from relatively low altitude (∼1300 m asl). All the 37 mitochondrial genes were highly conserved and under purifying selection, except for two mitochondrial protein-coding genes (MPCGs) (atp6 and nad5) that showed positively selected signatures. We therefore further examined non-synonymous substitutions in atp6 and nad5, by sequencing more individuals from three populations with different altitudes. We found that these non-synonymous substitutions were polymorphic in these populations, likely due to relaxed selection constraints in different altitudes. Purifying selection in all mitochondrial genes may be due to their functional importance for the precision of ATP production usually. Length difference in mitochondrial control regions between DBHC and DBQY was also conversed at the population level, indicating that sequence size adjustments in control region may be associated with adaptation to divergent altitudes. Quantitatively real-time PCR analysis for 12 MPCGs showed that gene expression patterns had a significant change between the two populations, suggesting that expression levels of MPCGs could be modulated by divergent environmental pressures (e.g. oxygen content and ambient temperature). These results provided an important guide for further uncovering genetic mechanisms of ecological adaptation in insects. [ABSTRACT FROM AUTHOR]

Grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora ) are the most important pests in alpine meadows of the Tibetan Plateau (TP) and have well adapted to high-altitude environments. To further understand the evolutionary history and their adaptation to the TP, we newly determined seven complete TP Gynaephora mitogenomes. Compared to single genes, whole mitogenomes provided the best phylogenetic signals and obtained robust results, supporting the monophyly of the TP Gynaephora species and a phylogeny of Arctiinae + (Aganainae + Lymantriinae). Incongruent phylogenetic signals were found among single mitochondrial genes, none of which recovered the same phylogeny as the whole mitogenome. We identified six best-performing single genes using Shimodaira-Hasegawa tests and found that the combinations of rrnS and either cox1 or cox3 generated the same phylogeny as the whole mitogenome, indicating the phylogenetic potential of these three genes for future evolutionary studies of Gynaephora . The TP Gynaephora species were estimated to radiate on the TP during the Pliocene and Quaternary, supporting an association of the diversification and speciation of the TP Gynaephora species with the TP uplifts and associated climate changes during this time. Selection analyses revealed accelerated evolutionary rates of the mitochondrial protein-coding genes in the TP Gynaephora species, suggesting that they accumulated more nonsynonymous substitutions that may benefit their adaptation to high altitudes. Furthermore, signals of positive selection were detected in nad5 of two Gynaephora species with the highest altitude-distributions, indicating that this gene may contribute to Gynaephora ’s adaptation to divergent altitudes. This study adds to the understanding of the TP Gynaephora evolutionary relationships and suggests a link between mitogenome evolution and ecological adaptation to high-altitude environments in grassland caterpillars. [ABSTRACT FROM AUTHOR]

Amphioxus, a basal chordate, is widely considered to be an existing proxy of the invertebrate ancestor of vertebrates, and it exhibits susceptibility to various pathogen infections and pathogenic mimic challenges. Here, in order to understand more clearly its antibacterial mechanisms, we analyzed the ribosomal RNA (rRNA)-depleted transcriptome of Chinese amphioxus ( Branchiostoma belcheri ) infected with Vibrio parahaemolyticus ( V. p. ) via next-generation deep sequencing technology (RNA-seq). We identified a total of 3214 differentially expressed genes (DEGs) by comparing V. p. -infected and control transcriptome libraries, including 2219 significantly up-regulated and 995 significantly down-regulated DEGs in V. p. -infected amphioxus. The DEGs with the top 10 most dramatic expression fold changes after V. p. infection, as well as 53 immune-related DEGs (IRDs) belonging to four primary categories of innate immunity were analyzed further. Through gene ontology (GO) and pathway enrichment analysis, DEGs were found to be primarily related to immune processes, apoptosis, catabolic and metabolic processes, binding and enzyme activity, while pathways involving bacterial infection, immune signaling, immune response, cancer, and apoptosis were overrepresented. We validated the RNA-seq results by detecting the expression levels of 10 IRDs using qRT-PCR, and we surveyed the dynamic variation in gene expression for these IRDs at 0, 6, 12, 24, and 48 h after V. p. treatment. Subsequently, according to the RNA-seq results, the presence of a primitive Toll-like receptor (TLR)-mediated antibacterial immune signaling pathway was predicted in B. belcheri . This study provides valuable information regarding antibacterial immunity for further research into the evolution of immunity in vertebrates and broadens our understanding of the innate immune response against bacterial invasion in amphioxus. [ABSTRACT FROM AUTHOR]

The dipole distributions of water molecules across the channel of single-walled carbon nanotubes (SWCNTs) under high pressure gradient P are studied using molecular dynamics (MD) simulations. It is found that the profiles of the dipole distributions are highly symmetrical with two peak values around 30° and 150° at zero or low pressure gradient ( P ≤ 6MPa), and remarkably asymmetric with the main peak around 30° under high pressure gradient ( P ≥ 12MPa). The reason is mainly that molecules can enter into the SWCNTs from two ends under low pressure water, whereas the water molecules can only enter into the tube from one end under high pressure. Further, it also implies that water molecules prefer to retain the hydrogens forward when entering into and passing through the nanotube. Our observations may be instructive for future applications in nanometer scale fluid devices and biological channels. [ABSTRACT FROM AUTHOR]

Amphioxus, a cephalochordate, is a key model animal for studying the evolution of vertebrate immunity. Recently, studies have revealed that microRNA (miRNA) expression profiles change significantly in the amphioxus gill after immune stimulation, but it remains largely unknown how gene expression responds to immune stress. Elucidating gene expression changes in the amphioxus gill will provide a deeper understanding of the evolution of gill immunity in vertebrates. Here, we used high-throughput RNA sequencing technology (RNA-seq) to conduct tag-based digital gene expression profiling (DGE) analyses of the gills of control Branchiostoma belcheri and of those exposed to the viral mimic, poly(I:C) (pIC). Six libraries were created for the control and treatment groups including three biological replicates per group. A total of 1999 differently expressed genes (DEGs) were obtained, with 571 and 1428 DEGs showing up- or down-regulation, respectively, in the treatment group. Enrichment analysis of gene ontology (GO) terms and pathways revealed that the DEGs were primarily related to immune and defense response, apoptosis, human disease, cancer, protein metabolism, enzyme activity, and regulatory processes. In addition, eight DEGs were randomly selected to validate the RNA-seq data using real-time quantitative PCR (qRT-PCR), and the results confirmed the accuracy of the RNA-seq approach. Next, we screened eight key responding genes to examine the dynamic changes in expression levels at different time points in more detail. The results indicated that expressions of TRADD, MARCH, RNF31, NF-κb, CYP450, TNFRSF6B, IFI and LECT1 were induced to participate in the antiviral response against pIC. This study provides a valuable resource for understanding the role of the amphioxus gill in antiviral immunity and the evolution of gill immunity in vertebrates. [ABSTRACT FROM AUTHOR]

Changes in gene expression patterns can reflect the adaptation of organisms to divergent environments. Quantitative real-time PCR ( qRT- PCR) is an important tool for ecological adaptation studies at the gene expression level. The quality of the results of qRT- PCR analysis largely depends on the availability of reliable reference genes ( RGs). To date, reliable RGs have not been determined for adaptive evolution studies in insects using a standard approach. Here, we evaluated the reliability of 17 candidate RGs for five Gynaephora populations inhabiting various altitudes of the Tibetan Plateau ( TP) using four independent (geNorm, NormFinder, BestKeeper, and the deltaCt method) and one comprehensive (RefFinder) algorithms. Our results showed that EF1-α, RPS15, and RPS13 were the top three most suitable RGs, and a combination of these three RGs was the most optimal for normalization. Conversely, RPS2, ACT, and RPL27 were the most unstable RGs. The expression profiles of two target genes ( HSP70 and HSP90) were used to confirm the reliability of the chosen RGs. Additionally, the expression patterns of four other genes ( GPI, HIF1A, HSP20, and USP) associated with adaptation to extreme environments were assessed to explore the adaptive mechanisms of TP Gynaephora species to divergent environments. Each of these six target genes showed discrepant expression patterns among the five populations, suggesting that the observed expression differences may be associated with the local adaptation of Gynaephora to divergent altitudinal environments. This study is a useful resource for studying the adaptive evolution of TP Gynaephora to divergent environments using qRT- PCR, and it also acts as a guide for selecting suitable RGs for ecological and evolutionary studies in insects. [ABSTRACT FROM AUTHOR]

The adaptive evolution of animals to high-elevation environments has been extensively studied in vertebrates, while few studies have focused on insects. Gynaephora species (Lepidoptera: Lymantriinae) are endemic to the Qinghai-Tibetan Plateau (QTP) and represent an important insect pest of alpine meadows. Here, we present a detailed comparative analysis of the mitochondrial genomes (mitogenomes) of two Gynaephora species inhabiting different high-elevation environments: G. alpherakii and G. menyuanensis . The results indicated that the general mitogenomic features (genome size, nucleotide composition, codon usage and secondary structures of tRNAs) were well conserved between the two species. All of mitochondrial protein-coding genes were evolving under purifying selection, suggesting that selection constraints may play a role in ensuring adequate energy production. However, a number of substitutions and indels were identified that altered the protein conformations of ATP8 and NAD1, which may be the result of adaptive evolution of the two Gynaephora species to different high-elevation environments. Levels of gene expression for nine mitochondrial genes in nine different developmental stages were significantly suppressed in G. alpherakii , which lives at the higher elevation (~ 4800 m above sea level), suggesting that gene expression patterns could be modulated by atmospheric oxygen content and environmental temperature. These results enhance our understanding of the genetic bases for the adaptive evolution of insects endemic to the QTP. [ABSTRACT FROM AUTHOR]

The Coleoptera (beetles) exhibits tremendous morphological, ecological, and behavioral diversity. To better understand the phylogenetics and evolution of beetles, we sequenced three complete mitogenomes from two families (Cleridae and Meloidae), which share conserved mitogenomic features with other completely sequenced beetles. We assessed the influence of six datasets and three inference methods on topology and nodal support within the Coleoptera. We found that both Bayesian inference and maximum likelihood with homogeneous-site models were greatly affected by nucleotide compositional heterogeneity, while the heterogeneous-site mixture model in PhyloBayes could provide better phylogenetic signals for the Coleoptera. The amino acid dataset generated more reliable tree topology at the higher taxonomic levels (i.e. suborders and series), where the inclusion of rRNA genes and the third positions of protein-coding genes improved phylogenetic inference at the superfamily level, especially under a heterogeneous-site model. We recovered the suborder relationships as (Archostemata + Adephaga) + (Myxophaga + Polyphaga). The series relationships within Polyphaga were recovered as (Scirtiformia + (Elateriformia + ((Bostrichiformia + Scarabaeiformia + Staphyliniformia) + Cucujiformia))). All superfamilies within Cucujiformia were recovered as monophyletic. We obtained a cucujiform phylogeny of (Cleroidea + (Coccinelloidea + ((Lymexyloidea + Tenebrionoidea) + (Cucujoidea + (Chrysomeloidea + Curculionoidea))))). This study showed that although tree topologies were sensitive to data types and inference methods, mitogenomic data could provide useful information for resolving the Coleoptera phylogeny at various taxonomic levels by using suitable datasets and heterogeneous-site models. [ABSTRACT FROM AUTHOR]

Energy absorption on a nanometer scale is vital for biochemical and climate systems. This paper reports that a two times amplification in absorption efficiency of mid-infrared (MIR) radiations can be achieved by water molecules confined in carbon nanotubes with a small radius compared to the bulk water absorption. This absorption enhancement is closely associated with the configurational change of water molecules into a unidirectional alignment under the nanotube confinement, which greatly augments the transition probability concerning the MIR absorption. In addition, the effect of confinement due to a (6,6) carbon nanotube is found to be very robust, equivalent to that of a 5 V/nm static electric field. These findings can be used to design energy-efficient nanodevices to modulate the microclimate variables by converting the redundant ambient MIR irradiation into the prompt heat conduction and are instructive for understanding the specific functioning of relevant biological channels. [ABSTRACT FROM AUTHOR]

Water permeation across a single-walled carbon nanotube has been studied in the presence of static electric fields (SEFs) with different directions under hydrostatic pressures. With the angle between the SEF direction and tube axis increasing from 0 ∘ to 90 ∘ , the water flux decreases gradually until almost vanishes, and the maximum value at 0 ∘ is approximately four times the case without SEFs. The phenomenon is attributed to the alignment of the polar water molecules along the SEF direction. We also show that water permeation properties are dependent on the field strength due mainly to thermal fluctuations of water molecules. [ABSTRACT FROM AUTHOR]

Gynaephora (Lepidoptera Erebidae: Lymantriinae) is a small genus, consisting of 15 nominated species, of which eight species are endemic to the Qinghai-Tibetan Plateau (QTP). In this study, we employed both mitochondrial and nuclear loci to infer a molecular phylogeny for the eight QTP Gynaephora spp. We used the phylogeny to estimate divergence dates in a molecular dating analysis and to delimit species. This information allowed us to investigate associations between the diversification history of the eight QTP species and geological and climatic events. Phylogenetic analyses indicated that the eight QTP species formed a monophyletic group with strong supports in both Bayesian and maximum likelihood analyses. The low K2P genetic distances between the eight QTP species suggested that diversification occurred relatively quickly and recently. Out of the eight species, five species were highly supported as monophyletic, which were also recovered by species delimitation analyses. Samples of the remaining three species (G. aureata, G. rouergensis, and G. minora) mixed together, suggesting that further studies using extensive population sampling and comprehensive morphological approaches are necessary to clarify their species status. Divergence time estimation results demonstrated that the diversification and speciation of Gynaephora on the QTP began during the late Miocene/early Pliocene and was potentially affected by the QTP uplift and associated climate changes during this time. [ABSTRACT FROM AUTHOR]

Insect mitochondrial genome (mitogenome) are the most extensively used genetic information for molecular evolution, phylogenetics and population genetics. Pentatomomorpha (>14,000 species) is the second largest infraorder of Heteroptera and of great economic importance. To better understand the diversity and phylogeny within Pentatomomorpha, we sequenced and annotated the complete mitogenome of Corizus tetraspilus (Hemiptera: Rhopalidae), an important pest of alfalfa in China. We analyzed the main features of the C. tetraspilus mitogenome, and provided a comparative analysis with four other Coreoidea species. Our results reveal that gene content, gene arrangement, nucleotide composition, codon usage, rRNA structures and sequences of mitochondrial transcription termination factor are conserved in Coreoidea. Comparative analysis shows that different protein-coding genes have been subject to different evolutionary rates correlated with the G+C content. All the transfer RNA genes found in Coreoidea have the typical clover leaf secondary structure, except for trnS1 (AGN) which lacks the dihydrouridine (DHU) arm and possesses a unusual anticodon stem (9 bp vs. the normal 5 bp). The control regions (CRs) among Coreoidea are highly variable in size, of which the CR of C. tetraspilus is the smallest (440 bp), making the C. tetraspilus mitogenome the smallest (14,989 bp) within all completely sequenced Coreoidea mitogenomes. No conserved motifs are found in the CRs of Coreoidea. In addition, the A+T content (60.68%) of the CR of C. tetraspilus is much lower than that of the entire mitogenome (74.88%), and is lowest among Coreoidea. Phylogenetic analyses based on mitogenomic data support the monophyly of each superfamily within Pentatomomorpha, and recognize a phylogenetic relationship of (Aradoidea + (Pentatomoidea + (Lygaeoidea + (Pyrrhocoroidea + Coreoidea)))). [ABSTRACT FROM AUTHOR]

Higher plasma urate level is reported to be associated with a reduced risk and slower progression of Parkinson's disease ( PD). In this study, we explored the effects of urate on dopaminergic neurons in nigrostriatal pathway in the 6-hydroxydopamine (6- OHDA) unilaterally lesioned rats. Uric acid ( UA), when given twice daily at 200 mg/kg intraperitoneally for 10 consecutive days, elevated urate (the anionic form of UA) in plasma and striatum by 55% and 36.8%, respectively, as compared with vehicle group. This regimen of UA was found to ameliorate the behavioral deficits, dopaminergic neuron loss as well as dopamine depletion in the nigrostriatal system. Moreover, UA administration was capable of increasing glutathione level and superoxide dismutase activity while decreasing malondialdehyde accumulation in striatum. In addition, the phosphorylation of both protein kinase B (Akt) and glycogen synthase kinase 3 beta ( GSK3β) in the lesioned striata of 6- OHDA-lesioned rats was dramatically reduced as compared with sham-operated rats. This reduction was attenuated in the Parkinsonian rats receiving UA treatment. Similarly, in vitro findings showed that UA alleviated the decrease in Akt activation and the increase in GSK3β activity caused by 6- OHDA. Furthermore, neuroprotection by urate and its regulation on GSK3β phosphorylation at Ser9 was found to be abolished in the presence of PI3K inhibitor. Therefore, our findings demonstrated that urate was able to protect dopaminergic neurons in rat nigrostriatal pathway against the neurotoxicity of 6- OHDA, and showed that its beneficial effects may be related to its regulation on Akt/ GSK3β signaling. [ABSTRACT FROM AUTHOR]

Abstract: The effect of lightning channel tortuosity on the associated electromagnetic (EM) fields in the time domain is investigated quantitatively from a new point of view. Due to the vanishing of geometric symmetry when taking into account the tortuosity of lightning channels, it is necessary to calculate the associated EM fields in the Cartesian coordinate system. An efficient technique is adopted to produce tortuous lightning channels and then the fractal dimension of the channel is calculated automatically by a program. The results show that at close distances, the dependence of EM fields on azimuth is significant, the ratio of MF peaks at two coaxial points with the channel base may reach about 4 and that of the EF may be larger than 2. With increased distance, the dependence of waveform on azimuth weakens. At distances of 10 km and 100 km, the current peaks derived from the EF peaks show good consistency with the current peak adopted, with an uncertainty less than 25%. [Copyright &y& Elsevier]

In this paper the principle for developing 3D mesh of flat triangles on arbitrary surfaces to its closest flattened 2D mesh is proposed. Such principle is proved equivalent to the condition that the finite element method (FEM) residual forces of the 2D-mesh member structure are equal to zero. The incremental FEM method and iterative procedures are derived for eliminating such residual forces. For developable 3D mesh of flat triangles, the method of this paper will give the accurate flattened 2D mesh, and for non-developable 3D mesh, this paper can lead to the closest flattened 2D mesh. The obtained 2D mesh can also be taken as the flattened form of the curved surface, which is described by the 3D mesh of flat triangles. Numerical examples show that the method of this paper has stable convergence and high efficiency. [Copyright &y& Elsevier]

The complete mitochondrial genome (mitogenome) of Dolycoris baccarum (Hemiptera: Pentatomidae) has been sequenced and annotated in this study. This mitogenome is 16,549 bp in length with an A+T content of 73.4%, and contains the typical 37 genes that are arranged in the same order as that of the putative ancestor of hexapods. All protein-coding genes (PCGs) start with ATN codons except for cox1 that uses TTG as the initial codon. Eleven PCGs stop with termination codon TAA, and cox1 and cox2 have single T as the incomplete stop codon. All the transfer RNA genes have the typical clover leaf secondary structure, except for trnS1 (AGN) that lacks the dihydrouridine arm as known in many other metazoa. The control region is located between rrnS and trnI, and is composed of 479 bp of non-repeat region and 1401 bp of repeat region. This is the third completely sequenced mitogenome from the family Pentatomidae of Hemiptera. [ABSTRACT FROM AUTHOR]

We sequenced and annotated the complete mitochondrial genome (mitogenome) of Gynaephora menyuanensis (Lepidoptera: Lymantriidae), which is a major pest in alpine meadows and endemic to the Qinghai-Tibetan Plateau. This mitogenome is 15,770 bp in length with an A+T content of 81.48%, and contains 37 typical animal mitochondrial genes that are arranged in the same order as that of other lepidopteran species. All protein-coding genes (PCGs) start with a typical ATN codon, with the exception of cox1, which begins with CGA. Eleven PCGs stop with termination codon TAA, whereas cox2 and nad4 have single T as the incomplete stop codon. All of the 22 transfer RNA genes present the typical clover leaf secondary structure. The A+T-rich region is located between rrnS and trnM with a length of 449 bp, and contains a 19 bp poly-T stretch as found in other lepidopteran mitogenomes. This is the second completely sequenced mitogenome from the family Lymantriidae of Lepidoptera, providing important molecular information to phylogenetic and population genetic researches. [ABSTRACT FROM AUTHOR]

• BaP triggers distinct microRNA transcriptional profiles in aquatic firefly. • BaP significantly affected xenobiotic degradation and energy production, etc. • Six immune- and detoxification-related pathways are significantly affected by BaP. • Eleven DEMs were identified as key BaP-responsive miRNAs. • Firstly explore miRNA expression changes to water pollutants in aquatic insects. Larval aquatic fireflies in fresh water are adversely affected by water pollutants such as benzo(a)pyrene (BaP). However, their response to BaP stress at the microRNA (miRNA)-regulatory level remains unknown. Here, transcriptomes containing 31,872 genes and six miRNA transcriptional profiles were obtained for Aquatica wuhana larvae, and comparative analysis was performed between larvae exposed to BaP (0.01 mg/L) and unexposed controls. Fifteen of 114 miRNAs identified via bioinformatics were detected as differentially expressed (DEMs) upon BaP exposure. Analysis results of predicted target genes of DEM suggests that BaP exposure primarily triggered transcriptional changes of miRNA associated with five major regulatory categories: 1) osmotic balance, 2) energy metabolic efficiency, 3) development, 4) xenobiotic metabolism (oxidative stress), and 5) innate immune response. Based on six innate immune- and xenobiotic metabolism-related pathways enriched by the predicted DEM targets, 11 key BaP-responsive DEMs were further screened to investigate dynamic changes of expression in response to BaP stress at five time points, and also to validate the miRNA sequencing data using quantitative real-time PCR. This study provides valuable information for the protection of firefly resources and supplements the understanding of miRNA regulatory mechanisms in response to water deterioration. [ABSTRACT FROM AUTHOR]

The transport properties of water molecules through single-walled carbon nanotubes (SWCNT) under static electric fields (SEFs) with different directions were studied by molecular dynamics simulations. It is found that the net water flux in the SEF direction opposite to the hydrostatic pressure direction is much larger than that in the same direction under the electric field intensity 0. 01 < E 0 ≤ 0. 6 V/nm. The reason is mainly that the SEF tunes the polarization direction of the water chain in the SWCNT, leading to different barrier height to be overcome for water molecules channeling across the SWCNT. Further, it also implies that water molecule chains moving forward with the oxygen atom can pass through the nanotube faster than that with the hydrogen atom forward. These findings may be instructive to regulate the water transport properties using the SEF in nanofluid devices and biological nano-channels. • The water flux can be increased significantly by regulating the direction of electric fields. • Water-molecule chains with oxygen atoms moving forward move faster through narrow nanotubes. [ABSTRACT FROM AUTHOR]

• Exposure to 30 μg/L HgCl2 up-regulated 1,788 and down-regulated 469 genes. • Most DEGs were related to xenobiotic biodegradation, development, oxidative stress. • Two metabolic pathways were identified to be key for HgCl 2 metabolism. • 10 DEGs were identified as key HgCl 2 -responsive genes. • We firstly investigated transcriptional changes to HgCl 2 in zebrafish intestine. Mercury is a widely used heavy metal that causes pollution to aquatic environments and severely affects the health of fish. Little is known about how heavy metal pollutants affect fish, particularly for gene expression within important organs such as the intestine. Herein, whole transcriptome sequencing was performed on zebrafish (Danio rerio) intestine tissue after HgCl 2 (HGC, 30 μg/L) exposure. A total of 2,257 differentially expressed genes (DEGs) were identified, including 1,788 up- and 469 down-regulated genes. Functional enrichment analysis revealed that these DEGs were primarily related to xenobiotic biodegradation, biomacromolecule metabolism, development, oxidative defense, and immune response. Ten key HGC-responsive DEGs were screened to survey the dynamic changes of expression in response to HGC exposure at different time points, and were also used to validate RNA sequencing data using quantitative real-time PCR (qPCR). Results indicate that the expression of genes encoding UGT1AB, GSTT1B, GSTO1, GSTM2, UGT5G1, GSTT1A, GSTR, GSTM3, GSTA1, and GSTP2 were significantly upregulated in response to the HGC exposure, and potentially help to counteract the adverse effects of HGC. This study provides insight into fish molecular toxicological responses to heavy metals and method on environmental risk assessment. [ABSTRACT FROM AUTHOR]

We determined the complete mitogenome of Pyrrhocoris tibialis (Hemiptera: Heteroptera: Pyrrhocoridae) to better understand the diversity and phylogeny within Pentatomomorpha, which is the second largest infra-order of Heteroptera. Gene content, gene arrangement, nucleotide composition, codon usage, ribosomal RNA (rRNA) structures, and sequences of the mitochondrial transcription termination factor were well conserved in Pyrrhocoroidea. Different protein-coding genes have been subject to different evolutionary rates correlated with the G + C content. The size of control regions (CRs) was highly variable among mitogenomes of three sequenced Pyrrhocoroidea species, with the P. tibialis CR being the largest. All the transfer RNA genes found in Pyrrhocoroidea had the typical clover leaf secondary structure, except for trnS1 (AGN), which lacked the dihydrouridine arm and possessed an unusual anticodon stem (9 bp vs. the normal 5 bp). A total of three different phylogenetic relationships among the five super-families of Pentatomomorpha were obtained using three analytical methods (MrBayes and RAxML under site-homogeneous models and PhyloBayes under a site-heterogeneous CAT + GTR model) and two mitogenomic datasets (nucleotides and amino acids). The tree topology test using seven methods statistically supported a phylogeny of (Aradoidea + (Pentatomoidea + (Lygaeoidea + (Pyrrhocoroidea + Coreoidea)))) as the best topology, as recognized by both RAxML and MrBayes based on the two datasets. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome (mitogenome) ofGynaephora alpherakii(Lepidoptera: Lymantriidae) has been sequenced and annotated in this study. This mitogenome is 15,755 bp in length with an A + T content of 81.44%, and contains 37 typical animal mitochondrial genes that are arranged in the same order as that of other lepidopteran species. All protein-coding genes (PCGs) start with a typical ATN codon, with the exception ofcox1which uses CGA as the initial codon. All of the 22 transfer RNA genes present the typical clover leaf secondary structure. The A + T-rich region is located betweenrrnSandtrnMwith a length of 449 bp, and contains a 19 bp poly-T stretch as found in other lepidopteran mitogenomes. This is the third completely sequenced mitogenome from the family Lymantriidae of Lepidoptera. [ABSTRACT FROM PUBLISHER]

The complete mitochondrial genome (mitogenome) ofPoratrioza sinica(Hemiptera: Psyllidae) has been sequenced and annotated in this study. This mitogenome is 14,863 bp in length with an A + T content of 72.0%, and contains 37 typical animal mitochondrial genes that are arranged in the same order as that of the putative ancestral insect mitogenome. All protein-coding genes start with ATN codons except fornad5, which uses TTG as the initial codon. All the transfer RNA genes have the typical cloverleaf structure, except fortrnS1(AGN) which lacks the dihydrouridine (DHU) arm. The control region is 700 bp in length with 82.4% A + T content. This is the second completely sequenced mitogenome from the family Psyllidae of Hemiptera. [ABSTRACT FROM AUTHOR]

Dietary shifts can alter the relative availability of different nutrients and are therefore associated with metabolic adaptation in animals. The Coccinellidae (ladybirds) exhibits three major types of feeding habits and provides a useful model to study the effects of dietary changes on the evolution of mitogenomes, which encode proteins directly involved in energy metabolism. Here, mitogenomes of three coccinellid species were newly sequenced. These data were combined with other ten previously sequenced coccinellid mitogenomes to explore the relationship between mitogenome evolution and diets. Our results indicate that mitogenomic data can be effectively used to resolve phylogenetic relationships of Coccinellidae. Strong codon usage bias in coccinellid mitogenomes was predominantly determined by nucleotide composition. The 13 mitochondrial protein‐coding genes (PCGs) globally evolved under negative constraints, with some PCGs showing a stronger purifying selection. Six PCGs (nad3, nad4L, and nad5 from Complex I; cox1 and cox3 from Complex IV; and atp6 from Complex V) displayed signs of positive selection. Of these, adaptive changes in cox3 were potentially associated with metabolic differences resulting from dietary shifts in Coccinellidae. Our results provide insights into the adaptive evolution of coccinellid mitogenomes in response to both dietary shifts and other life history traits. [ABSTRACT FROM AUTHOR]

Amphioxus is a closest living proxy to the ancestor of cephalochordates with vertebrates, and key animal for novel understanding in the evolutionary origin of vertebrate body plan, genome, tissues and immune system. Reliable analyses using quantitative real-time PCR (qRT-PCR) for answering these scientific questions is heavily dependent on reliable reference genes (RGs). In this study, we evaluated stability of thirteen candidate RGs in qRT-PCR for different developmental stages and tissues of amphioxus by four independent (geNorm, NormFinder, BestKeeper and deltaCt) and one comparative algorithms (RefFinder). The results showed that the top two stable RGs were the following: (1) S20 and 18 S in thirteen developmental stages, (2) EF1A and ACT in seven normal tissues, (3) S20 and L13 in both intestine and hepatic caecum challenged with lipopolysaccharide (LPS), and (4) S20 and EF1A in gill challenged with LPS. The expression profiles of two target genes (EYA and HHEX) in thirteen developmental stages were used to confirm the reliability of chosen RGs. This study identified optimal RGs that can be used to accurately measure gene expression under these conditions, which will benefit evolutionary and functional genomics studies in amphioxus. [ABSTRACT FROM AUTHOR]

[Display omitted] • We newly sequenced 21 transcriptomes representing six cucujiform superfamilies. • We inferred the phylogeny and evolution of cucujiform beetles using large-scale genomic data. • The monophyly of each of the six superfamilies were recovered. • We recovered a new and robust superfamily-level phylogeny within Cucujiformia. • Our results revealed a Permian origin of Cucujiformia and supported the hypothesis of a CTR. Cucujiformia, the largest taxon in the order Coleoptera, exhibits extraordinary morphological, ecological, and behavioral diversity. This infraorder is currently divided into seven superfamilies, but considerably incongruent relationships among superfamilies have been reported by recent phylogenomic studies. Here, we combined the 21 newly sequenced transcriptomes representing six superfamilies with nine previously published cucujiform genomes/transcriptomes to elucidate the phylogeny and evolution of Cucujiformia. The monophyly of each of five superfamilies were consistently supported by all phylogenetic analyses based on the twelve datasets (matrix occupancy, amino acid and nucleotide data) and the two analytical methods (maximum likelihood method and Bayesian inference). Both the amino acid datasets and the RY recoded nucleotide datasets recovered the monophyly of Cucujoidea. Topology test results statistically supported the following robust superfamily-level phylogeny in Cucujiformia: (Coccinelloidea, (Cleroidea, (Tenebrionoidea, (Cucujoidea, (Chrysomeloidea, Curculionoidea))))). Our divergence time analyses recovered a Permian origin of Cucujiformia and a Jurassic–Cretaceous origin of most superfamilies. The diversification of phytophagous beetles that occurred in the Cretaceous can be attributed to its co-evolution with angiosperms, supporting the hypothesis of a Cretaceous Terrestrial Revolution. [ABSTRACT FROM AUTHOR]

Simple Summary: To date, it is rare to study the effects of environmental toxicants (e.g., abamectin, a widely used pesticide) on mitochondrial energy metabolism in vitro from a subcellular level in insects, especially from an omics perspective (e.g., metabolomics) due to insufficient samples of mitochondria. The fat body of the German cockroach (Blattella germanica) plays an important role for detoxification, with responses of critical subcellular components (e.g., mitochondria) to abamectin. When B. germanica were fed abamectin, their in vitro mitochondrial morphology was affected, with changes in activity of key enzymes involved in energy metabolism. Furthermore, metabonomic analysis of in vitro mitochondria of B. germanica uncovered a set of metabolites and their pathways related to mitochondrial energy metabolism in response to abamectin feeding/stress. These molecules and pathways were primarily involved in ATP production and energy consumption including oxidative phosphorylation, TCA cycle, and pentose phosphate pathway. The current work is a good example of investigations on subcellular toxicology from multiple perspectives (morphology, physiology, and metabolomics). Mitochondria are the leading organelle for energy metabolism. The toxic effects of environmental toxicants on mitochondrial morphology, energy metabolism, and their determination of cell fate have already been broadly studied. However, minimal research exists on effects of environmental toxicants such as pesticides on mitochondrial energy metabolism at in vitro subcellular level, particularly from an omics perspectives (e.g., metabolomics). Here, German cockroach (Blattella germanica) was fed diets with (0.01 and 0.001 mg/mL) and without abamectin, and highly purified fat body mitochondria were isolated. Swelling measurement confirmed abnormal mitochondrial swelling caused by abamectin stress. The activity of two key mitochondrial energy metabolism-related enzymes, namely succinic dehydrogenase and isocitrate dehydrogenase, was significantly affected. The metabolomic responses of the isolated mitochondria to abamectin were analyzed via untargeted liquid chromatography/mass spectrometry metabolomics technology. Fifty-two differential metabolites (DMs) were identified in the mitochondria between the 0.001 mg/mL abamectin-fed and the control groups. Many of these DMs were significantly enriched in pathways involved in ATP production and energy consumption (e.g., oxidative phosphorylation, TCA cycle, and pentose phosphate pathway). Nineteen of the DMs were typically related to energy metabolism. This study is valuable for further understanding mitochondrial toxicology under environmental toxicants, particularly its subcellular level. [ABSTRACT FROM AUTHOR]

Phenyllactic acid (PLA) has been demonstrated to possess antibacterial activity and capacity to prolong food shelf life. However, studies on the performance of PLA in inhibiting Staphylococcus aureus and its effectiveness when applied to dairy products are largely lacking. Here, antibacterial activity (planktonic and biofilm states) of PLA against S. aureus CICC10145 (S. aureus _45) were investigated. The results showed that PLA inhibited growth of S. aureus _45 and formation of S. aureus _45 biofilm. Next, the antibacterial action target of PLA was uncovered from both physiological and phenotypic perspectives. The results showed that PLA decreased cell metabolic activity and cell viability, damaged cell membrane integrity, triggered leakage of intracellular contents (DNA, proteins, and ATP), and caused oxidative stress damage and morphological deformation of S. aureus _45. In practical application, the antibacterial activity of PLA against S. aureus _45 cells was further confirmed in skim milk and cheese as dairy food models, and the antibacterial effects can be adequately maintained during storage for 21 d, at least at 4°C. These findings suggested that PLA could be a potential candidate for controlling S. aureus outgrowth in dairy foods. [ABSTRACT FROM AUTHOR]

Phenyllactic acid (PLA) has been demonstrated to possess antibacterial activity and capacity to prolong food shelf life. However, studies on the performance of PLA in inhibiting Staphylococcus aureus and its effectiveness when applied to dairy products are largely lacking. Here, antibacterial activity (planktonic and biofilm states) of PLA against S. aureus CICC10145 (S. aureus _45) were investigated. The results showed that PLA inhibited growth of S. aureus _45 and formation of S. aureus _45 biofilm. Next, the antibacterial action target of PLA was uncovered from both physiological and phenotypic perspectives. The results showed that PLA decreased cell metabolic activity and cell viability, damaged cell membrane integrity, triggered leakage of intracellular contents (DNA, proteins, and ATP), and caused oxidative stress damage and morphological deformation of S. aureus _45. In practical application, the antibacterial activity of PLA against S. aureus _45 cells was further confirmed in skim milk and cheese as dairy food models, and the antibacterial effects can be adequately maintained during storage for 21 d, at least at 4°C. These findings suggested that PLA could be a potential candidate for controlling S. aureus outgrowth in dairy foods. [ABSTRACT FROM AUTHOR]

Western honey bee (Apis mellifera) is widely used in investigations involved in gut flora, and the gut flora of their workers have been demonstrated to be completely colonized within 7 days of emergence. However, colonization rules of the gut flora remain largely unknown. Here, metagenomic 16S rRNA gene data were generated to study colonization rules of the gut flora in workers by detecting dynamics in diversity and the relative abundance of gut bacteria across 14 time points post-emergence from pupal case, including 0 pupation-hours/control, 12, 24, 36, 48, 60, 72, 84, 96, 108, 120, 132, 144, and 156 post-emergence-hours (peh). Via comparison analysis of bacterial operational taxonomic units across these time points, diversity values of the gut flora presented the maximum at 0 peh. Among these points, 0–24 peh maintained the relatively higher diversity than the other time points. Furthermore, dynamic changes in several core gut bacteria (e.g., Lactobacillus, Bifidobacterium, Frischella, Snodgrassella, and Gilliamella) were analyzed in detail, and their biological function was linked to several host biological characteristics such as ecological adaptation, aging, gut health, dietary alterations and diversity, digestion and absorption, and metabolisms during colonization. This study is valuable for the understanding of colonization rules and the contribution of the gut flora to workers. [ABSTRACT FROM AUTHOR]

Bacteriocins inhibit various foodborne bacteria in planktonic and biofilm forms. However, bacteriocins with antibacterial and antibiofilm activity against Staphylococcus argenteus, a pathogen that can cause food poisoning, are still poorly known. Here, the novel bacteriocin LSB1 derived from Lactobacillus plantarum CGMCC 1.12934 was purified and characterized extensively. LSB1 had a molecular weight of 1425.78 Da and an amino acid sequence of YIFVTGGVVSSLGK. Moreover, LSB1 exhibited excellent stability under heat and acid–base stress and presented sensitivity to pepsin and proteinase K. LSB1 exhibited an extensive antimicrobial spectrum against both Gram‐positive and Gram‐negative bacteria. Minimum inhibitory concentration of LSB1 against S. argenteus_70917 was 10.36 µg/ml, which was lower than that of most of the previously found bacteriocins against Staphylococcus strains. Furthermore, LSB1 significantly inhibited S. argenteus_70917 planktonic cells (p < 0.01) and decreased their viability. Scanning electron microscopy analysis revealed that cell membrane permeability of S. argenteus_70917 upon exposure to LSB1 showed leakage of cytoplasmic contents and rupture, leading to cell death. In addition, biofilm formation ability of S. argenteus_70917 was significantly (p < 0.01) impaired by LSB1, with the percent inhibition of 35% at 10 µg/ml and 80% at 20 µg/ml. Overall, this study indicates that LSB1 can be considered a potential antibacterial agent in the control of S. argenteus in both planktonic and biofilm states. Practical Application: Foodborne pathogenic bacteria, such as Staphylococcus argenteus, and their biofilms represent potential risks for food safety. In recent years, customers' demand for "natural" products has increased food control. This study describes the novel bacteriocin LSB1 produced by the lactic acid bacterium species Lactobacillus plantarum. LSB1 showed strong antibacterial and antibiofilm activity against S. argenteus as well as thermal and acid–alkaline stability. Furthermore, the mechanisms of action of LSB1 on S. argenteus were preliminarily explored. These results indicate that LSB1 might be potentially used as an effective and natural food preservative. [ABSTRACT FROM AUTHOR]

Staphylococcus aureus and its biofilm have emerged as a significant threat to the safety of dairy products. In recent years, lactic acid bacteria (LAB) bacteriocins have been widely acknowledged as the potential natural antibacterial substance in food biopreservation due to their excellent antibacterial effects. However, few LAB bacteriocins with antibacterial and antibiofilm activity against S. aureus have been reported in dairy products. In the present study, a novel bacteriocin LSX01 of Lactobacillus paracasei LS-6 isolated from a traditional fermented yogurt produced in Yunnan, China, was purified and characterized extensively. The LSX01 possessed a molecular weight of 967.49 Da and an AA sequence of LDQAGISYT. The minimum inhibitory concentration of LSX01 against S. aureus_ 45 was 16.90 μg/mL, which was close to or lower than the previously reported bacteriocins. The LSX01 exhibited an extensive antimicrobial spectrum against both gram-positive and gram-negative bacteria. Moreover, LSX01 exhibited excellent tolerance to heat and acid-base treatments, and sensitivity to the proteolytic enzymes, such as pepsin and proteinase K. Furthermore, the treatment of S. aureus_ 45 planktonic cells with LSX01 significantly reduced their metabolic activity and disrupted the cell membrane integrity. Scan electron microscopy results demonstrated that LSX01 induced cytoplasmic content leakage and cell deformation. Additionally, biofilm formation of S. aureus_ 45 was also significantly inhibited by LSX01. Overall, the results suggested that the novel LAB bacteriocin LSX01 possessed antibacterial activity and antibiofilm activity against S. aureus and, hence, could have potential for improving safety of dairy products. [ABSTRACT FROM AUTHOR]

Foot dystonia occurs in patients with Parkinson's disease (PD) and leads to pain, malformation, and difficulty with walking. Botulinum toxin injections may be effective for foot dystonia, but the extent of improvement and effects on motor function are unclear. In this study, we performed botulinum toxin injections for foot dystonia in 25 patients with PD. At 3 weeks and 3 months post-infection, we assessed changes in plantar pressure distribution utilizing the Pressure Plate system; dystonia using the Modified Ashworth Spasm score; pain using the visual analog scale (VAS) score; and lower extremity function using the Calf-raise Senior (CRS) test, Timed Up and Go (TUG) test, and gait parameters (eg, stride length, step length). We found improved Modified Ashworth Spasm score (p < 0.01) and VAS score (p < 0.01) post-injection. CRS test score (3 weeks, p = 0.006; 3 months, p = 0.068), stride length (3 weeks, p = 0.012; 3 months, p = 0.715), and step length (3 weeks, p = 0.011; 3 months, p = 0.803) also improved. Plantar pressure distribution improved after botulinum toxin injection (metatarsal 1, 3 weeks, p = 0.031; 3 months, p = 0.144; metatarsal 2, 3 weeks, p = 0.049; 3 months, p = 0.065; metatarsal 3, 3 weeks, p = 0.002; 3 months, p = 0.017; metatarsal 4, 3 weeks, p = 0.017; 3 months, p = 0.144; medial heel, 3 weeks, p = 0.01; 3 months, p = 0.395; lateral heel, 3 weeks, p = 0.035; 3 months, p = 0.109). Botulinum toxin injection for foot dystonia in patients with PD can reduce spasms and pain and normalize plantar pressure distribution, which improves balance and lower extremity function. [Display omitted] • Foot dystonia occurs in 1.2% patients with Parkinson's disease and it leads to pain, malformation, and difficulty with walking. • Botulinum toxin injection for foot dystonia can relieve lower extremity pain and spasm in patients with Parkinson's disease. • Gait analysis revealed that botulinum toxin can also improve lower extremity function. [ABSTRACT FROM AUTHOR]

Multidrug-resistant (MDR) Staphylococcus aureus biofilms have emerged as a serious threat to human health. Recently, the development of antibiotic replacement therapy has gained much attention due to the potential application of bacteriocin. The present study sought to evaluate the antibacterial effect of bacteriocin XJS01 against MDR S. aureus , a previously reported bacteriocin against S. aureus strain 2612:1606BL1486 (S. aureus _26, an MDR strain demonstrated here), and its potential application as an antibiofilm agent. The minimum bactericide concentration of XJS01 against MDR S. aureus _26 was 33.18 μg/mL. XJS01 exhibited excellent storage stability and resistance against acid and reduced the density of established MDR S. aureus _26 biofilm. The hemolytic and HEK293T cytotoxicity activities of XJS01 and the histological analyses in mice confirmed its safety. Moreover, XJS01 effectively disrupted the MDR S. aureus _26 biofilm established on the skin wound surface and reduced the biofilm-isolated bacteria, thereby decreasing the release of pro-inflammatory cytokines and the proliferation of alternatively activated macrophages. Compared to mupirocin, XJS01 exhibited an excellent therapeutic effect on mice skin wounds, confirming it to be a potential alternative to antibiotics. • This study, for the first time, used purified bacteriocin to treat skin MDR bacteria biofilm. • This is the first reported purified bacteriocin against biofilm-isolated bacteria in skin wound. • In vitro and in vivo experiments demonstrated biosafety of the bacteriocin. • Bacteriocin decrease pro-inflammatory cytokines and promote AAMs. • Bacteriocin exhibits great potential as an alternative to antibiotics. [ABSTRACT FROM AUTHOR]

Distinct expression of the miRNAs has rarely been explored in basal cell carcinoma (BCC) of skin, and the regulatory role of miRNAs in BCC development remains quite opaque. Here, we collected control tissues from adjacent noncancerous skin (n = 15; control group) and tissues at tumor centers from patients with cheek BCC (n = 15; BCC group) using punch biopsies. After six small RNA sequencing- (sRNA-seq-) based miRNA expression profiles were generated for both BCC and controls, including three biological replicates, we conducted comparative analysis on the sRNA-seq dataset, discovering 181 differentially expressed miRNAs (DEMs) out of the 1,873 miRNAs in BCCs. In order to validate the sRNA-seq data, expression of 15 randomly selected DEMs was measured using the TaqMan probe-based quantitative real-time PCR. Functional analysis of predicted target genes of DEMs in BCCs shows that these miRNAs are primarily involved in various types of cancers, immune response, epithelial growth, and morphogenesis, as well as energy production and metabolism, indicating that BCC development is caused, at least in part, by changes in miRNA regulation for biological and disease processes. In particular, the "basal cell carcinoma pathways" were found to be enriched by predicted DEM targets, and regulatory relationships between DEMs and their targeted genes in this pathway were further uncovered. These results revealed the association between BCCs and abundant miRNA molecules that regulate target genes, functional modules, and signaling pathways in carcinogenesis. [ABSTRACT FROM AUTHOR]

Antibacterial mechanism of bacteriocins against foodborne S. aureus is still to be explored, particularly in proteomics, and a deep and comprehensive study on application of bacteriocins for preservation of raw pork is required. Here, proteomic mechanism of Lactobacillus salivarius bacteriocin XJS01 against foodborne S. aureus 2612:1606BL1486 (S. aureus _26) and its preservation effect on raw pork loins stored at 4 °C for 12 days was investigated. The results showed that 301 differentially abundant proteins (DAPs) were identified between XJS01-treated and -free groups (control group) using Tandem mass tag (TMT) quantitative proteomics technology, which were primarily involved in amino acids and carbohydrate metabolism, cytolysis, defense response, cell apoptosis, cell killing, adhesion, and oxygen utilization of S. aureus _26. Bacterial secretion system (SRP) and cationic antimicrobial peptide resistance may be key pathways to maintain protein secretion and counteract the deleterious effects on S. aureus _26 caused by XJS01. In addition, XJS01 could significantly improve the preservation of raw pork loins by the evaluation results of sensory and antibacterial activity on the meat surface. Overall, this study showed that XJS01 induced a complex organism response in S. aureus , and it could be potential pork preservative. • Bacteriocin XJS01 elicit proteomic response involved in metabolism, cytolysis, and defense response in S. aureus. • SRP and CAMP resistance pathways are key targets of action of XJS01. • XJS01 significantly improved the preservation of raw pork loins. • XJS01 could be a potential biocontrol agent on pork. [ABSTRACT FROM AUTHOR]

The mechanisms underlying the toxicity of environmental stress are unclear for marine macrobenthos. Copper/Cu has posed the most serious threats to amphioxus, an ancient and model benthic cephalochordate. Herein, a dynamic change in the physiological parameters (GR, SOD, ATP, and MDA) was detected with ROS accumulation in Branchiostoma belcheri exposed to 0.3 mg·L−1 Cu. Transcriptomes and microRNAomes of B. belcheri were generated to investigate the molecular mechanisms by which this amphioxus copes with Cu exposure. Time-specific genes identified at different time points after exposure were involved in the stimulus and immune response, detoxification and ionic homeostasis, aging and the nervous system, sequentially, with prolongation of exposure time, forming a dynamic process of molecular response to Cu stress. In total, 57 differentially expressed miRNAs were identified under Cu stress. Transcriptomics–miRNAomics analyses indicate that these miRNAs targeted genes associated with many key biological processes such as xenobiotics degradation, oxidative stress, and energy metabolism. The constructed miRNA – mRNA - pathway network uncovered a broad post-transcriptional regulatory mechanism in B. belcheri to cope with Cu stress. Overall, this integrated analyses show that enhanced defense response, accelerated ROS elimination, and repressed ATP production constitute a comprehensive strategy to cope with Cu toxicity in the ancient macrobenthos. [Display omitted] • Cu exposure caused oxidant stress mainly resulted from increased ROS in amphioxus. • A dynamic process of molecular response to Cu stress was uncovered. • Cu exposure elicited a broad post-transcriptional regulatory mechanism in amphioxus to cope with the toxicity. • We uncovered the miRNA - mRNA - pathway regulatory network in amphioxus to cope with the Cu toxicity. [ABSTRACT FROM AUTHOR]

Milk poses a high-risk for microbial contamination (e.g., Salmonella Enteritidis) and spoilage. In recent years, lactic acid bacteria (LAB) bacteriocins have been widely acknowledged as the potential natural antibacterial substance in food biopreservation due to their excellent antibacterial effects. However, studies on the benefits of LAB bacteriocins for maintenance of milk quality were lacking. In the present study, a novel bacteriocin RSQ01 of Lactococcus lactis was purified and characterized extensively. The RSQ01 possessed a molecular weight of 1.90 kDa and an amino acid sequence of GTPSGGADGIGFAFHPEEVG, which exhibited an extensive antimicrobial spectrum against both gram-positive and gram-negative bacteria. Moreover, RSQ01 exhibited excellent tolerance to heat and acid-base treatments, and sensitivity to the proteolytic enzymes, such as trypsin, proteinase K, and pepsin, with a MIC value of 11.63 μg/mL against S. Enteritidis_35. Furthermore, RSQ01 maintained the nutritional composition, antioxidant parameters, and sensory properties of milk. Additionally, 238 differentially abundant metabolites (DAMs) were identified between the RSQ01 -treated and -free milk by global metabolomics, which were assigned to eight categories/superclasses (e.g., organic acids and derivatives, lipids and lipid-like molecules, and organoheterocyclic compound). Finally, fourteen metabolic pathways enriched by DAMs were primarily involved in amino acid, lipids, and organic acid metabolism (e.g. , phenylalanine/pyrimidine/tryptophan metabolism, glycerophospholipid metabolism, and C5-branched dibasic acid metabolism). The results provide evidence suggesting that abundance changes in metabolomes caused by RSQ01 contributed to the milk quality. Overall, this study indicated potential of RSQ01 in milk preservation. • A new bacteriocin RSQ01 showed good antibacterial properties. • RSQ01 has a satisfactory fresh-keeping effect on a pasteurized milk. • Metabolomics changes caused by RSQ01 benefited to milk quality. [ABSTRACT FROM AUTHOR]

Serum urate levels are reported to be significantly lowered in patients with Parkinson's disease (PD) and inversely correlated to the risk and progression of PD. However, the mechanism by which urate affects PD is poorly understood. Here we showed that treatment with uric acid (UA) resulted in an autophagy activity enhancement in PC12 cells in dose- and time-dependent manners, as indicated by LC3-II increase and P62 decrease. Moreover, UA was still able to increase the LC3-II level and the number of LC3 puncta in the presence of Bafilomycin A1, a lysosomal inhibitor. These changes of autophagic markers were preceded by mTOR inhibition and ULK1 activation. Co-treatment with 3-benzyl-5-((2-nitrophenoxy) methyl)-dihydrofuran-2(3H)-one (3BDO), an mTOR activator, abolished the UA-induced LC3-II increase. More importantly, UA reduced SNCA/α-synuclein accumulation in PC12 cells that overexpress wildtype or A53T mutant SNCA, and this was blocked by Bafilomycin A1 co-treatment. The in vivo study showed that UA administration was able to modulate the levels of autophagy markers, increase the autophagosome/autolysosome formation, and reduce SNCA accumulation in the midbrain of SNCA A53T transgenic mice. Taken together, our findings suggest that UA could induce autophagy activation via an mTOR-dependent signaling and ameliorate SNCA accumulation. This implicates that urate-elevating agent may become a potential strategy for PD therapy. [ABSTRACT FROM AUTHOR]

Antibacterial activity and mechanism of action of bacteriocins against bacteria that cause pork contamination remain unclear. Here, antibacterial activity of bacteriocin LFX01 against two important indicator strains (i.e. , Staphylococcus aureus and Escherichia coli) and its mechanism of action were investigated. The results showed antibacterial activity of LFX01 against growth and biofilm formation of S. aureus _26 (strain 2612:1606BL1486) and E. coli _02 (strain CMCC(B)44102). Additionally, the results demonstrated that LFX01 could decrease cell metabolic activity, disrupt cell membrane permeability and integrity, and trigger leakage of intracellular contents (e.g. , K+, ATP, and lactic dehydrogenase). Furthermore, gel retardation showed that LFX01 could bind to the genomic DNA of indicator strains, disrupting DNA structure. These results uncovered mechanism of action of LFX01 against indicator strains from physiological and phenotypic levels. When applied to the surface of fresh pork models, the antibacterial activity of LFX01 against indicator strains was further confirmed. These findings suggested that LFX01 could be a potential pork preservative for controlling foodborne pathogens. • LFX01 has antibacterial activity against S. aureus and E. coli. • LFX01 triggered leakage of intracellular contents, and disrupted cell metabolic activity and DNA structure. • LFX01 significantly inhibited S. aureus and E. coli on raw pork. • LFX01 could be a potential pork preservative. [ABSTRACT FROM AUTHOR]