Genome analysis and classification of Xanthomonas bacteriophage AhaSv, a new member of the genus Salvovirus.

Xanthomonas phage AhaSv was isolated from lake water. Genome sequencing showed that its genome is a linear dsDNA molecule with a length of 55,576 bp and a G+C content of 63.23%. Seventy-one open reading frames (ORFs) were predicted, and no tRNAs were found in the genome. Phylogenetic analysis showed that AhaSv is closely related to members of the genus Salvovirus of the family Casjensviridae. Intergenomic similarity values between phage AhaSv and homologous phages were up to 90.6%, suggesting that phage AhaSv should be considered a member of a new species in the genus Salvovirus.

Characteristics and whole-genome analysis of a novel Pseudomonas syringae pv. tomato bacteriophage D6 isolated from a karst cave.

Pseudomonas syringae is a gram-negative plant pathogen that infects plants such as tomato and poses a threat to global crop production. In this study, a novel lytic phage infecting P. syringae pv. tomato DC3000, named phage D6, was isolated and characterized from sediments in a karst cave. The latent period of phage D6 was found to be 60 min, with a burst size of 16 plaque-forming units per cell. Phage D6 was stable at temperatures between 4 and 40 °C but lost infectivity when heated to 70 °C. Its infectivity was unaffected at pH 6-10 but became inactivated at pH ≤ 5 or ≥ 12. The genome of phage D6 is a linear double-stranded DNA of 307,402 bp with a G + C content of 48.43%. There is a codon preference between phage D6 and its host, and the translation of phage D6 gene may not be entirely dependent on the tRNA library provided by the host. A total of 410 open reading frames (ORFs) and 14 tRNAs were predicted in its genome, with 92 ORFs encoding proteins with predicted functions. Phage D6 showed low genomic similarity to known phage genomes in the GenBank and Viral sequence databases. Genomic and phylogenetic analyses revealed that phage D6 is a novel phage. The tomato plants were first injected with phage D6, and subsequently with Pst DC3000, using the foliar spraying and root drenching inoculum approach. Results obtained after 14 days indicated that phage D6 inoculation decreased P. syringae-induced symptoms in tomato leaves and inhibited the pathogen's growth in the leaves. The amount of Pst DC3000 was reduced by 150- and 263-fold, respectively. In conclusion, the lytic phage D6 identified in this study belongs to a novel phage within the Caudoviricetes class and has potential for use in biological control of plant diseases.

Root endophytic bacterial community composition of Aconitum carmichaelii debx. from three main producing areas in China.

Aconitum carmichaelii Debx. is famous for the bioactive aconitum alkaloids as traditional Chinese medicine. Endophytic bacteria play vital roles in plant growth, health, and the production of secondary metabolites such as alkaloids. In this study, we employed 16 S rRNA amplicon high-throughput sequencing to determine the root endophytic bacterial community of A. carmichaelii Debx. collected from three main producing areas including the geo-authentic area in China, high performance liquid chromatography to measure the contents of six bioactive alkaloids and correlation analysis to explore the relationship among environmental factors, alkaloids contents, and endophytic bacterial community. The results indicated that the root core microbiota of A. carmichaelii Debx. was dominated by Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Root endophytic bacterial community in the geo-authentic area was distinct from the other two regions. Soil nitrogen contents, organic matter, and temperature were the main factors contributing to the endophytic bacterial community structure. Significant correlation was found between alkaloids contents and some bacterial genera. Particularly, the abundance of Lactobacillus was positively correlated with the contents of benzoyl-mesaconitine and benzoyl-aconine. This study provided the first insight into the root endophytic bacterial community composition of A. carmichaelii Debx., and can direct further isolation of functional bacterial strains.

Organohydrogels with High-Speed Lubrication by Confining Polymer Chain Mobility by an Interpenetrated Heteronetwork.

Hydrogels with pure hydrophilic network have received much attention due to their excellent low frictional behavior. However, the lubrication performance of hydrogels is not satisfied under high-speed condition due to the energy dissipation caused by adsorbed polymer chains as well as the failure of lubricating mechanisms accompanied by the transition of lubrication regime. In this work, interpenetrating double-network organohydrogels were constructed by combining hydrophilic and oleophilic polymer networks to modify the physiochemical properties of surface polymer chains, especially the chain mobility. The oleophilic polymer network spatially restricting the mobility of the swollen hydrophilic network in water, resulted in a low coefficient of friction (ca. 0.01) compared with conventional hydrogels at high speed (0.1 m s-1 ). Meanwhile, the organohydrogels had superior wear resistance, with almost no wear observed on the sliding track after 5 k cycles of rubbing at high speed. The design concept of organohydrogels can be extended to a variety of low-wear, highly-lubricating materials.

Arthrobacter cavernae sp. nov., a novel actinobacterium isolated from sediment of karst cave.

A novel, Gram-stain-positive, aerobic, non-endospore-forming, non-motile and rod-shaped bacterium designated PO-11T was isolated from sediment of karst cave collected in Libo county, Guizhou Province, PR China. The isolate grew optimally on R2A agar at 25 °C, pH 8.0 and with 0.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that PO-11T belonged to the genus Arthrobacter and was most closely related to Arthrobacter methylotrophus TGAT (98.3 % sequence similarity), Arthrobacter alkaliphilus LC6T (97.7 %) and Arthrobacter ramosus CCM1646T (97.1 %). Genome sequencing revealed a genome size of 4 073 119 bp and the genomic DNA G+C content was 66.16 mol%. Its DNA-DNA relatedness values with A. methylotrophus TGAT, A. alkaliphilus LC6T and A. ramosus CCM1646T were 23.0, 22.9 and 23.2 %, respectively. The main fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The major respiratory quinone was MK-9(H2). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, glycolipid, phosphatidylethanolamine, phosphatidylinositol and unidentified lipids. Thus, based on phylogenetic and phenotypic and chemotaxonomic data, strain PO-11T represents a novel species of the genus Arthrobacter, for which the name Arthrobacter cavernae sp. nov. is proposed. The type strain is strain PO-11T (=CCTCC AB 2021070T=LMG 32459T).

Co-occurrence pattern and function prediction of bacterial community in Karst cave.

BACKGROUND: Karst caves are considered as extreme environments with nutrition deficiency, darkness, and oxygen deprivation, and they are also the sources of biodiversity and metabolic pathways. Microorganisms are usually involved in the formation and maintenance of the cave system through various metabolic activities, and are indicators of changes environment influenced by human. Zhijin cave is a typical Karst cave and attracts tourists in China. However, the bacterial diversity and composition of the Karst cave are still unclear. The present study aims to reveal the bacterial diversity and composition in the cave and the potential impact of tourism activities, and better understand the roles and co-occurrence pattern of the bacterial community in the extreme cave habitats. RESULTS: The bacterial community consisted of the major Proteobacteria, Actinobacteria, and Firmicutes, with Proteobacteria being the predominant phylum in the rock, soil, and stalactite samples. Compositions and specialized bacterial phyla of the bacterial communities were different among different sample types. The highest diversity index was found in the rock samples with a Shannon index of 4.71. Overall, Zhijin cave has relatively lower diversity than that in natural caves. The prediction of function showed that various enzymes, including ribulose-bisphosphate carboxylase, 4-hydroxybutyryl-CoA dehydratase, nitrogenase NifH, and Nitrite reductase, involved in carbon and nitrogen cycles were detected in Zhijin cave. Additionally, the modularity indices of all co-occurrence network were greater than 0.40 and the species interactions were complex across different sample types. Co-occurring positive interactions in the bacteria groups in different phyla were also observed. CONCLUSION: These results uncovered that the oligotrophic Zhijin cave maintains the bacterial communities with the diverse metabolic pathways, interdependent and cooperative co-existence patterns. Moreover, as a hotspot for tourism, the composition and diversity of bacterial community are influenced by tourism activities. These afford new insights for further exploring the adaptation of bacteria to extreme environments and the conservation of cave ecosystem.

A degressive quantum convolutional neural network for quantum state classification and code recognition.

With the rapid development of quantum computing, a variety of quantum convolutional neural networks (QCNNs) are proposed. However, only 1/2n2 features of an n-qubits input are transferred to the next layer in a quantum pooling layer, which results in the accuracy reduction. To solve this problem, a QCNN with a degressive circuit is proposed. In order to enhance the ability of extracting global features, we remove the parameters sharing strategy in the quantum convolutional layer and design a quantum convolutional kernel with global eyesight. In addition, to prevent a sharp feature reduction, a degressive parameterized quantum circuit is adopted to construct the pooling layer. Then the Z-basis measurement is only performed on the first qubit to control the operations on other qubits. Compared with the state-of-the-art QCNN, i.e., hybrid quantum-classical convolutional neural network, the accuracy of our model increased by 0.9%, 1%, and 3%, respectively, in three tasks: quantum state classification, binary code recognition, and quaternary code recognition.

Gene redundancy and gene compensation of insulin-like peptides in the oocyte development of bean beetle.

Bean beetle (Callosobruchus maculatus) exhibits clear phenotypic plasticity depending on population density; However, the underlying molecular mechanism remains unknown. Compared to low-density individuals, high-density individuals showed a faster terminal oocyte maturity rate. Four insulin-like peptide (ILP) genes were identified in the bean beetle, which had higher expression levels in the head than in the thorax and abdomen. The population density could regulate the expression levels of CmILP1-3, CmILP2-3, and CmILP1 as well as CmILP3 in the head, thorax, and abdomen, respectively. RNA interference results showed that each CmILP could regulate terminal oocyte maturity rate, indicating that there was functional redundancy among CmILPs. Silencing each CmILP could lead to down-regulation of some other CmILPs, however, CmILP3 was up-regulated in the abdomen after silencing CmILP1 or CmILP2. Compared to single gene silencing, silencing CmILP3 with CmILP1 or CmILP2 at the same time led to more serious retardation in oocyte development, suggesting CmILP3 could be up-regulated to functionally compensate for the down-regulation of CmILP1 and CmILP2. In conclusion, population density-dependent plasticity in terminal oocyte maturity rate of bean beetle was regulated by CmILPs, which exhibited gene redundancy and gene compensation.

Characterization and genomic analysis of a lytic Stenotrophomonas maltophilia short-tailed phage A1432 revealed a new genus of the family Mesyanzhinovviridae.

Stenotrophomonas maltophilia (S. maltophilia) is an emerging opportunistic pathogen that exhibits resistant to a majority of commonly used antibiotics. Phages have the potential to serve as an alternative treatment for S. maltophilia infections. In this study, a lytic phage, A1432, infecting S. maltophilia YCR3A-1, was isolated and characterized from a karst cave. Transmission electron microscopy revealed that phage A1432 possesses an icosahedral head and a shorter tail. Phage A1432 demonstrated a narrow host range, with an optimal multiplicity of infection of 0.1. The one-step growth curve indicated a latent time of 10 min, a lysis period of 90 min, a burst size of 43.2 plaque-forming units per cell. In vitro bacteriolytic activity test showed that phage A1432 was capable to inhibit the growth of S. maltophilia YCR3A-1 in an MOI-dependent manner after 2 h of co-culture. BLASTn analysis showed that phage A1432 genome shares the highest similarity (81.46%) with Xanthomonas phage Xoo-sp2 in the NCBI database, while the query coverage was only 37%. The phage contains double-stranded DNA with a genome length of 61,660 bp and a GC content of 61.92%. It is predicted to have 79 open reading frames and one tRNA, with no virulence or antibiotic resistance genes. Phylogenetic analysis using terminase large subunit and DNA polymerase indicated that phage A1432 clustered with members of the Bradleyvirinae subfamily but diverged into a distinct branch. Further phylogenetic comparison analysis using Average Nucleotide Identity, proteomic phylogenetic analysis, genomic network analysis confirmed that phage A1432 belongs to a novel genus within the Bradleyvirinae subfamily, Mesyanzhinovviridae family. Additionally, phylogenetic analysis of the so far isolated S. maltophilia phages revealed significant genetic diversity among these phages. The results of this research will contribute valuable information for further studies on their morphological and genetic diversity, will aid in elucidating the evolutionary mechanisms that give rise to them.

Partial Alleviation of Homologous Superinfection Exclusion of SeMNPV Latently Infected Cells by G1 Phase Infection and G2/M Phase Arrest.

Viral infection can regulate the cell cycle, thereby promoting viral replication. Hijacking and altering the cell cycle are important for the virus to establish and maintain a latent infection. Previously, Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV)-latently infected P8-Se301-C1 cells, which grew more slowly than Se301 cells and interfered with homologous SeMNNPV superinfection, were established. However, the effects of latent and superinfection with baculoviruses on cell cycle progression remain unknown. In this study, the cell cycle profiles of P8-Se301-C1 cells and SeMNPV or Autographa californica multiple nucleopolyhedrovirus (AcMNPV)-infected P8-Se301-C1 cells were characterized by flow cytometry. The results showed that replication-related genes MCM4, PCNA, and BAF were down-regulated (p < 0.05) in P8-Se301-C1 cells, and the S phase of P8-Se301-C1 cells was longer than that of Se301 cells. P8-Se301-C1 cells infected with SeMNPV did not arrest in the G2/M phase or affect the expression of Cyclin B and cyclin-dependent kinase 1 (CDK1). Furthermore, when P8-Se301-C1 cells were infected with SeMNPV after synchronized treatment with hydroxyurea and nocodazole, light microscopy and qRT-PCR analysis showed that, compared with unsynchronized cells and S and G2/M phase cells, SeMNPV-infected P8-Se301-C1 cells in G1 phase induced G2/M phase arrest, and the amount of virus adsorption and intracellular viral DNA replication were significantly increased (p < 0.05). In addition, budded virus (BV) production and occlusion body (OB)-containing cells were both increased at 120 h post-infection (p < 0.05). The expression of Cyclin B and CDK1 was significantly down-regulated at 48 h post-infection (p < 0.05). Finally, the arrest of SeMNPV-infected G1 phase cells in the G2/M phase increased BV production (p < 0.05) and the number of OB-containing cells. In conclusion, G1 phase infection and G2/M arrest are favorable to SeMNPV proliferation in P8-Se301-C1 cells, thereby alleviating the homologous superinfection exclusion. The results contribute to a better understanding of the relationship between baculoviruses and insect cell cycle progression and regulation.

Bio-Inspired Active Self-Cleaning Surfaces via Filament-Like Sweepers Array.

Hydrodynamic forces from moving fluids can be utilized to remove contaminants which is an ideal fouling-release strategy for underwater surfaces. However, the hydrodynamic forces in the viscous sublayer are greatly reduced owing to the no-slip condition, which restricts their practical applications. Here, inspired by sweeper tentacles of corals, an active self-cleaning surface with flexible filament-like sweepers are reported. The sweepers can penetrate the viscous sublayer by utilizing energy from outer turbulent flows and remove contaminants with adhesion strength of >30 kPa. Under an oscillating flow, the removal rate of the single sweeper can reach up to 99.5% due to dynamic buckling movements. In addition, the sweepers array can completely clean its coverage area within 10 s through coordinated movements as symplectic waves. The active self-cleaning surface depends on the fluid-structure coupling between sweepers and flows, which breaks the concept of conventional self-cleaning.

Prediction and characterization of prophages of Stenotrophomonas maltophilia reveals a remarkable phylogenetic diversity of prophages.

Prophages, which enables bacterial hosts to acquire novel traits, and increase genetic variation and evolutionary innovation, are considered to be one of the greatest drivers of bacterial diversity and evolution. Stenotrophomonas maltophilia is widely distributed and one of the most important multidrug resistant bacteria in hospitals. However, the distribution and genetic diversity of S. maltophilia prophages have not been elucidated. In this study, putative prophages were predicted in S. maltophilia genomes by using virus prediction tools, and the genetic diversity and phylogeny of S. maltophilia and the prophages they harbor were further analyzed. A total of 356 prophage regions were predicted from 88 S. maltophilia genomes. Among them, 144 were intact prophages, but 77.09% of the intact prophages did not match any known phage sequences in the public database. The number of prophage carried by S. maltophilia is related to its host habitat and is an important factor affecting the size of the host genome, but it is not related to the genetic diversity of the prophage. The prediction of auxiliary genes encoded by prophage showed that antibiotic resistance genes was not predicted for any of the prophages except for one questionable prophage, while 53 virulence genes and 169 carbohydrate active enzymes were predicted from 11.24 and 44.1% prophages, respectively. Most of the prophages (72.29%) mediated horizontal gene transfer of S. maltophilia genome, but only involved in 6.25% of the horizontal gene transfer events. In addition, CRISPR prediction indicated 97.75% S. maltophilia strains contained the CRISPR-Cas system containing 818 spacer sequences. However, these spacer sequences did not match any known S. maltophilia phages, and only a few S. maltophilia prophages. Comparative genomic analysis revealed a highly conserved and syntenic organization with genomic rearrangement between the prophages and the known related S. maltophilia phages. Our results indicate a high prevalence and genetic diversity of prophages in the genome of S. maltophilia, as well as the presence of a large number of uncharacterized phages. It provides an important complement to understanding the diversity and biological characteristics of phages, as well as the interactions and evolution between bacteria and phages.

Role of Anti-Beta-1-Adrenergic Receptor Antibodies in Cardiac Dysfunction in Patients with Cirrhotic Cardiomyopathy.

Cirrhotic cardiomyopathy (CCM) is a recognized complication of cirrhosis and is associated with poor outcomes, especially under challenges such as surgery/liver transplantation. However, the mechanism is not clear, and the treatment is not specific. The present study aimed to evaluate the role of anti-ß1-adrenergic receptor antibodies (anti-ß1-AR) in CCM. We enrolled 3 groups: healthy controls, cirrhotic patients without CCM, and patients with CCM. We found that the anti-ß1-AR levels in the CCM group were significantly higher than that in the non-CCM group; anti-ß1-AR was positively correlated to NT-proBNP, negatively correlated to left ventricular ejection fraction, fractional shortening ((r = - 0.466, P < 0.05), and the ratio of peak early (E wave) and atrial (A wave) flow velocities (E/A (r = - 0.475, P < 0.05) in CCM patients. Anti-ß1-AR is a useful predictive biomarker for the presence of CCM and eventually may also have therapeutic implications. Clinical Trials Registration: Chinese Clinical Trials No. ChiCTR 2,000,037,730.

Gut bacteria reflect the adaptation of Diestrammena japanica (Orthoptera: Rhaphidophoridae) to the cave.

The gut microbiota is essential for the nutrition, growth, and adaptation of the host. Diestrammena japanica, a scavenger that provides energy to the cave ecosystem, is a keystone species in the karst cave in China. It inhabits every region of the cave, regardless of the amount of light. However, its morphology is dependent on the intensity of light. Whether the gut bacteria reflect its adaptation to the cave environment remains unknown. In this research, D. japanica was collected from the light region, weak light region, and dark region of three karst caves. The gut bacterial features of these individuals, including composition, diversity, potential metabolism function, and the co-occurrence network of their gut microbiota, were investigated based on 16S rRNA gene deep sequencing assay. The residues of amino acids in the ingluvies were also evaluated. In addition, we explored the contribution of gut bacteria to the cave adaptation of D. japanica from three various light zones. Findings showed that gut bacteria were made up of 245 operational taxonomic units (OTUs) from nine phyla, with Firmicutes being the most common phylum. Although the composition and diversity of the gut bacterial community of D. japanica were not significantly different among the three light regions, bacterial groups may serve different functions for D. japanica in differing light strengths. D. japanica has a lower rate of metabolism in cave habitats than in light regions. We infer that the majority of gut bacteria are likely engaged in nutrition and supplied D. japanica with essential amino acids. In addition, gut bacteria may play a role in adapting D. japanica's body size. Unveiling the features of the gut bacterial community of D. japanica would shed light on exploring the roles of gut bacteria in adapting hosts to karst cave environments.

Biocontrol and plant growth promotion potential of endophytic Bacillus subtilis JY-7-2L on Aconitum carmichaelii Debx.

Aconitum carmichaelii Debx. is a famous medicinal plant rich in alkaloids and widely used to treat various human diseases in Asian countries. However, southern blight caused by Sclerotium rolfsii severely hampered the yield of A. carmichaelii. Beneficial microbe-based biological control is becoming a promising alternative and an environmentally friendly approach for the management of plant diseases. In this study, we evaluated the biocontrol potential of an endophytic bacterial strain JY-7-2L, which was isolated from the leaves of A. carmichaelii, against southern blight in vitro and by a series of field experiments. JY-7-2L was identified as Bacillus subtilis based on multi-locus sequence analysis. JY-7-2L showed strong antagonistic activity against S. rolfsii in vitro and on A. carmichaelii root slices by dual-culture assay. Cell-free culture filtrate of JY-7-2L significantly inhibited the hyphal growth, sclerotia formation, and germination of S. rolfsii. In addition, volatile compounds produced by JY-7-2L completely and directly inhibited the growth of S. rolfsii. Furthermore, JY-7-2L was proved to produce hydrolytic enzymes including glucanase, cellulase, protease, indole acetic acid, and siderophore. The presence of bacA, fenA, fenB, fenD, srfAA, and baeA genes by PCR amplification indicated that JY-7-2L was able to produce antifungal lipopeptides and polyketides. Field trials indicated that application of the JY-7-2L fermentation culture significantly reduced southern blight disease severity by up to 30% with a long-acting duration of up to 62 days. Meanwhile, JY-7-2L significantly promoted the fresh and dry weights of the stem, main root, and lateral roots of A. carmichaelii compared to non-inoculation and/or commercial B. subtilis product treatments. Taken together, JY-7-2L can be used as a promising biocontrol agent for the control of southern blight in A. carmichaelii.

Preparation of Magnesium Hydroxide Flame Retardant from Hydromagnesite and Enhance the Flame Retardant Performance of EVA.

In this study, hydromagnesite, a rare natural hydrated alkaline magnesium carbonate, was used to synthesize magnesium hydroxide (MH) as a flame retardant for ethylene-vinyl acetate (EVA) to enhance its fire resistance and smoke suppression. Various concentrations of sodium hydroxide (NaOH) were used to alter the morphology and the flame-retardant efficiency of synthesized MH. EVA/MH composites were prepared through melt blending, and the influence of NaOH on the flame retardancy and mechanical properties was investigated by means of the limiting oxygen index (LOI), cone calorimeter test (CCT) and tensile test. The flame retardancy results demonstrated that composites exhibited remarkably improved flame retardant properties after introducing MH, reflected by an increase in the LOI value from 20% for neat EVA to roughly 38%. Additionally, the peak of heat release rate (pHRR), the total heat release (THR) and the peak of the smoke production rate for EVA3 were decreased by 37.6%, 20.7% and 44.4% compared with neat EVA, respectively. In the meantime, increasing char residues were also observed. The incorporation of different MH concentrations had a limited effect on the mechanical properties of the EVA/MH composites.

A phosphodiesterase type-5 inhibitor, sildenafil, induces sperm capacitation and penetration into porcine oocytes in a chemically defined medium.

The present study was undertaken to determine the effect of a phosphodiesterase (PDE) type-5 (cyclic guanosine monophosphate-specific) inhibitor, sildenafil, on capacitation and penetration of boar spermatozoa in a basic chemically defined medium (adenosine- and theophylline-free PGM-tac4). When ejaculated spermatozoa were cultured for 90 minutes in the absence or presence of sildenafil at 2.5 mM, the inhibitor significantly increased the percentage of capacitated/acrosome-reacted spermatozoa, as a result of the chlortetracycline assay. When fresh spermatozoa were co-cultured with oocytes in the presence of sildenafil at a different concentration (0, 2.5, 25, or 250 µM), higher sildenafil concentrations (25 and 250 µM) significantly resulted in higher sperm penetration rates. When oocytes matured in vitro were co-cultured with spermatozoa in the presence of 25 µM sildenafil or 25 mM caffeine benzoate for 8 hours, the incidence of penetrated oocytes did not differ between two groups, whereas the incidence of monospermic oocytes in penetrated one was significantly higher in the presence of sildenafil. Immunocytochemical analysis reported the presence of PDE type-5 on the acrosome region of boar spermatozoa. These results report that regulation of cyclic guanosine monophosphate-specific PDE type-5 by sildenafil somehow can increase the penetrability of boar spermatozoa in vitro.