Genomic characterization of two nickie-like bacteriophages that infect the kiwifruit canker phytopathogen Pseudomonas syringae pv. actinidiae.

Here, we report the genomic characterization of two siphophages, named hairong and ZY21, that infect the kiwifruit canker phytopathogen Pseudomonas syringae pv. actinidiae. The genome sequences of hairong (112,842 bp) and ZY21 (112,006 bp) were determined. Global sequence comparison showed that hairong, ZY21, and two phages of the genus Nickievirus (nickie and psageB1) are similar but are not closely related to any other known phage, and they comprise a unique phylogenetic cluster. Moreover, hairong represents a new genus related to Nickievirus. Comparative genomic analysis revealed some common features shared by the four nickie-like phages.

Isolation of axenic cyanobacterium and the promoting effect of associated bacterium on axenic cyanobacterium.

BACKGROUND: Harmful cyanobacterial blooms have attracted wide attention all over the world as they cause water quality deterioration and ecosystem health issues. Microcystis aeruginosa associated with a large number of bacteria is one of the most common and widespread bloom-forming cyanobacteria that secret toxins. These associated bacteria are considered to benefit from organic substrates released by the cyanobacterium. In order to avoid the influence of associated heterotrophic bacteria on the target cyanobacteria for physiological and molecular studies, it is urgent to obtain an axenic M. aeruginosa culture and further investigate the specific interaction between the heterotroph and the cyanobacterium. RESULTS: A traditional and reliable method based on solid-liquid alternate cultivation was carried out to purify the xenic cyanobacterium M. aeruginosa FACHB-905. On the basis of 16S rDNA gene sequences, two associated bacteria named strain B905-1 and strain B905-2, were identified as Pannonibacter sp. and Chryseobacterium sp. with a 99 and 97% similarity value, respectively. The axenic M. aeruginosa FACHB-905A (Microcystis 905A) was not able to form colonies on BG11 agar medium without the addition of strain B905-1, while it grew well in BG11 liquid medium. Although the presence of B905-1 was not indispensable for the growth of Microcystis 905A, B905-1 had a positive effect on promoting the growth of Microcystis 905A. CONCLUSIONS: The associated bacteria were eliminated by solid-liquid alternate cultivation method and the axenic Microcystis 905A was successfully purified. The associated bacterium B905-1 has the potentiality to promote the growth of Microcystis 905A. Moreover, the purification technique for cyanobacteria described in this study is potentially applicable to a wider range of unicellular cyanobacteria.

DNA Packaging and Genomics of the Salmonella 9NA-Like Phages.

We present the genome sequences of Salmonella enterica tailed phages Sasha, Sergei, and Solent. These phages, along with Salmonella phages 9NA, FSL_SP-062, and FSL_SP-069 and the more distantly related Proteus phage PmiS-Isfahan, have similarly sized genomes of between 52 and 57 kbp in length that are largely syntenic. Their genomes also show substantial genome mosaicism relative to one another, which is common within tailed phage clusters. Their gene content ranges from 80 to 99 predicted genes, of which 40 are common to all seven and form the core genome, which includes all identifiable virion assembly and DNA replication genes. The total number of gene types (pangenome) in the seven phages is 176, and 59 of these are unique to individual phages. Their core genomes are much more closely related to one another than to the genome of any other known phage, and they comprise a well-defined cluster within the family Siphoviridae To begin to characterize this group of phages in more experimental detail, we identified the genes that encode the major virion proteins and examined the DNA packaging of the prototypic member, phage 9NA. We show that it uses a pac site-directed headful packaging mechanism that results in virion chromosomes that are circularly permuted and about 13% terminally redundant. We also show that its packaging series initiates with double-stranded DNA cleavages that are scattered across a 170-bp region and that its headful measuring device has a precision of ±1.8%.IMPORTANCE The 9NA-like phages are clearly highly related to each other but are not closely related to any other known phage type. This work describes the genomes of three new 9NA-like phages and the results of experimental analysis of the proteome of the 9NA virion and DNA packaging into the 9NA phage head. There is increasing interest in the biology of phages because of their potential for use as antibacterial agents and for their ecological roles in bacterial communities. 9NA-like phages that infect two bacterial genera have been identified to date, and related phages infecting additional Gram-negative bacterial hosts are likely to be found in the future. This work provides a foundation for the study of these phages, which will facilitate their study and potential use.

Structure of Staphylococcal Enterotoxin N: Implications for Binding Properties to Its Cellular Proteins.

Staphylococcus aureus strains produce a unique family of immunostimulatory exotoxins termed as bacterial superantigens (SAgs), which cross-link major histocompatibility complex class II (MHC II) molecule and T-cell receptor (TCR) to stimulate large numbers of T cells at extremely low concentrations. SAgs are associated with food poisoning and toxic shock syndrome. To date, 26 genetically distinct staphylococcal SAgs have been reported. This study reports the first X-ray structure of newly characterized staphylococcal enterotoxin N (SEN). SEN possesses the classical two domain architecture that includes an N-terminal oligonucleotide-binding fold and a C-terminal ß-grasp domain. Amino acid and structure alignments revealed that several critical amino acids that are proposed to be responsible for MHC II and TCR molecule engagements are variable in SEN, suggesting that SEN may adopt a different binding mode to its cellular receptors. This work helps better understand the mechanisms of action of SAgs.

Complete genome of a novel mycobacteriophage WXIN isolated in Wuhan, China.

OBJECTIVES: The rising of antibiotic resistance has sparked a renewed interest in mycobacteriophage as alternative therapeutic strategies against mycobacterial infections. So far, the vast majority of mycobacteriophages have been isolated using the model species Mycobacterium smegmatis, implying an overwhelming majority of mycobacteriophages in the environment remain uncultured, unclassified, and their specific hosts and infection strategies are still unknown. This study was undertaken to isolate and characterize novel mycobacteriophages targeting Mycobacterium septicum. DATA DESCRIPTION: Here a novel mycobacteriophage WXIN against M. septicum was isolated from soil samples in Wuhan, China. Whole genome analysis indicates that the phage genome consists of 115,158 bp with a GC content of 61.9%. Of the 260 putative open reading frames, 46 may be associated with phage packaging, structure, lysis, lysogeny, genome modification/replication, and other functional roles. The limited genome-wide similarity, along with phylogenetic trees constructed based on viral proteome and orthologous genes show that phage WXIN represents a novel cluster distantly related to cluster J mycobacteriophages (genus Omegavirus). Overall, these results provide novel insights into the genomic properties of mycobacteriophages, highlighting the great genetic diversity of mycobacteriophages in relation to their hosts.

Dosimetry and efficiency comparison of knowledge-based and manual planning using volumetric modulated arc therapy for craniospinal irradiation.

BACKGROUND: Craniospinal irradiation (CSI) poses a challenge to treatment planning due to the large target, field junction, and multiple organs at risk (OARs) involved. The aim of this study was to evaluate the performance of knowledge-based planning (KBP) in CSI by comparing original manual plans (MP), KBP RapidPlan initial plans (RPI), and KBP RapidPlan final plans (RPF), which received further re-optimization to meet the dose constraints. PATIENTS AND METHODS: Dose distributions in the target were evaluated in terms of coverage, mean dose, conformity index (CI), and homogeneity index (HI). The dosimetric results of OARs, planning time, and monitor unit (MU) were evaluated. RESULTS: All MP and RPF plans met the plan goals, and 89.36% of RPI plans met the plan goals. The Wilcoxon tests showed comparable target coverage, CI, and HI for the MP and RPF groups; however, worst plan quality was demonstrated in the RPI plans than in MP and RPF. For the OARs, RPF and RPI groups had better dosimetric results than the MP group (P < 0.05 for optic nerves, eyes, parotid glands, and heart). The planning time was significantly reduced by the KBP from an average of 677.80 min in MP to 227.66 min (P < 0.05) and 307.76 min (P < 0.05) in RPI, and RPF, respectively. MU was not significantly different between these three groups. CONCLUSIONS: The KBP can significantly reduce planning time in CSI. Manual re-optimization after the initial KBP is recommended to enhance the plan quality.

Immune pathway activation in neurons triggers neural damage after stroke.

Ischemic brain injury is a severe medical condition with high incidences in elderly people without effective treatment for the resulting neural damages. Using a unilateral mouse stroke model, we analyze single-cell transcriptomes of ipsilateral and contralateral cortical penumbra regions to objectively reveal molecular events with single-cell resolution at 4 h and 1, 3, and 7 days post-injury. Here, we report that neurons are among the first cells that sense the lack of blood supplies by elevated expression of CCAAT/enhancer-binding protein ß (C/EBPß). To our surprise, the canonical inflammatory cytokine gene targets for C/EBPß, including interleukin-1ß (IL-1ß) and tumor necrosis factor α (TNF-α), are subsequently induced also in neuronal cells. Neuronal-specific silencing of C/EBPß or IL-1ß and TNF-α substantially alleviates downstream inflammatory injury responses and is profoundly neural protective. Taken together, our findings reveal a neuronal inflammatory mechanism underlying early pathological triggers of ischemic brain injury.

Virus-Like Particles Based on the Novel Goose Parvovirus (NGPV) VP2 Protein Protect Ducks against NGPV Challenge.

Novel goose parvovirus (NGPV), a genetic variant of goose parvovirus, has been spreading throughout China since 2015 and mainly infects ducklings with the symptoms of growth retardation, beak atrophy, and protruding tongue, leading to huge economic losses every year. A safe and effective vaccine is urgently needed to control NGPV infection. In this study, virus-like particles (VLPs) of NPGV were assembled and evaluated for their immunogenicity. The VP2 protein of NGPV was expressed in Spodoptera frugiperda insect cells using baculovirus as vector. The VP2 protein was efficiently expressed in the nucleus of insect cells, and the particles with a circular or hexagonal shape and a diameter of approximately 30 nm, similar to the NGPV virion, were observed using transmission electron microscopy (TEM). The purified particles were confirmed to be composed of VP2 using western blot and TEM, indicating that the VLPs of NGPV were successfully assembled. Furthermore, the immunogenicity of the VLPs of NGPV was evaluated in Cherry Valley ducks. The level of NGPV serum antibodies increased significantly at 1-4 weeks post-immunization. No clinical symptoms or deaths of ducks occurred in all groups after being challenged with NGPV at 4 weeks post-immunization. There was no viral shedding in the immunized group. However, viral shedding was detected at 3-7 days post-challenge in the non-immunized group. Moreover, VLPs can protect ducks from histopathological lesions caused by NGPV and significantly reduce viral load in tissue at 5 days post-challenge. Based on these findings, NGPV VLPs are promising candidates for vaccines against NGPV.

Center-surround interaction with adaptive inhibition: a computational model for contour detection.

The broad region outside the classical receptive field (CRF) of a neuron in the primary visual cortex (V1), namely non-CRF (nCRF), exerts robust modulatory effects on the responses to visual stimuli presented within the CRF. This modulating effect is mostly suppressive, which plays important roles in visual information processing. One possible role is to extract object contours from disorderly background textures. In this study, a two-scale based contour extraction model, inspired by the inhibitory interactions between CRF and nCRF of V1 neurons, is presented. The kernel idea is that the side and end subregions of nCRF work in different manners, i.e., while the strength of side inhibition is consistently calculated just based on the local features in the side regions at a fine spatial scale, the strength of end inhibition adaptively varies in accordance with the local features in both end and side regions at both fine and coarse scales. Computationally, the end regions exert weaker inhibition on CRF at the locations where a meaningful contour more likely exists in the local texture and stronger inhibition at the locations where the texture elements are mainly stochastic. Our results demonstrate that by introducing such an adaptive mechanism into the model, the non-meaningful texture elements are removed dramatically, and at the same time, the object contours are extracted effectively. Besides the superior performance in contour detection over other inhibition-based models, our model provides a better understanding of the roles of nCRF and has potential applications in computer vision and pattern recognition.

Modest sexual size dimorphism and allometric growth: a study based on growth and gonad development in the wolf spider Pardosa pseudoannulata (Araneae: Lycosidae).

Sexual size dimorphism (SSD) is a notable phenomenon in terrestrial animals, and it is correlated with unusual morphological traits. To date, the underlying sex-specific growth strategies throughout the ontogenetic stage of spiders are poorly understood. Here, we comprehensively investigated how the growth trajectories and gonad development shaped SSD in the wolf spider Pardosa pseudoannulata (Araneae: Lycosidae). We also hypothesized the potential growth allometry among the carapace, abdomen, and gonads of spiders in both sexes. By measuring the size of the carapace and abdomen, investigating developmental duration and growth rate, describing the gonadal sections, and calculating the area of gonads at all instars from hatching to maturity, we demonstrated that SSD results from sex-specific growth strategies. Our results indicated that the growth and developmental differences between both sexes appeared at early life stages, and there was allometric growth in the carapace, abdomen, and gonads between males and females.

Microcalorimetric, spectroscopic and microscopic investigation on the toxic effects of CdTe quantum dots on Halobacterium halobium R1.

The biological effect of CdTe quantum dots (QDs) on Halobacterium halobium R1 (H. halobium R1) growth was analyzed by a microcalorimetric technique. By using a TAM air eight channels microcalorimeter, the thermogenic curves of H. halobium R1 growth were obtained at 37 °C. To analyze the results, the maximum heat power (P(m)) and the growth rate constants (k) were determined, which showed that they were correlated to the concentration of QDs. The addition of quantum dots caused a gradual increase of P(m) and k at low concentrations of QDs, and a conspicuous decrease at high concentrations. For confirmation, the turbidity (OD(600)) and respiratory rate at different concentrations of QDs were studied. The morphology of H. halobium R1 cells both in the absence and presence of QDs was examined by transmission electron microscopy (TEM). The results of these studies were corroborated with ones derived from microcalorimetry. In this work, the mechanism of cytotoxicity of QDs was explored through fluorescence spectroscopy, inductively coupled plasma mass spectrometry (ICP-MS) and microcalorimetry. It was clear that metabolic mechanism of H. halobium R1 growth was changed by the addition of QDs. To the best of our knowledge, the thermokinetics and toxicology of CdTe QDs against H. halobium R1 were obtained for the first time by microcalorimetry.

Methylome and transcriptome analyses reveal insights into the epigenetic basis for the good survival of hypomethylated ER-positive breast cancer subtype.

BACKGROUND: Breast cancer (BRCA) is a heterogeneous disease, characterized by different histopathological and clinical features and responses to various therapeutic measures. Despite the research progress of DNA methylation in classification and diagnosis of BRCA and the close relationship between DNA methylation and hormone receptor status, especially estrogen receptor (ER), the epigenetic mechanisms in various BRCA subtypes and the biomarkers associated with diagnostic characteristics of patients under specific hormone receptor status remain elusive. RESULTS: In this study, we collected and analyzed methylation data from 785 invasive BRCA and 98 normal breast tissue samples from The Cancer Genome Atlas (TCGA) database. Consensus classification analysis revealed that ER-positive BRCA samples were constitutive of two distinct methylation subgroups; with the hypomethylated subgroup showing good survival probability. This finding was further supported by another cohort of ER-positive BRCA containing 30 subjects. Additionally, we identified 977 hypomethylated CpG loci showing significant associations with good survival probability in ER-positive BRCA. Genes with these loci were enriched in cancer-related pathways (e.g., Wnt signaling pathway). Among them, the upregulated 47 genes were also in line with good survival probability of ER-positive BRCA, while they showed significantly negative correlations between their expression and methylation level of certain hypomethylated loci. Functional assay in numerous literatures provided further evidences supporting that some of the loci have close links with the modulation of tumor-suppressive mechanisms via regulation gene transcription (e.g., SFRP1 and WIF1). CONCLUSIONS: Our study identified a hypomethylated ER-positive BRCA subtype. Notably, this subgroup presented the best survival probability compared with the hypermethylated ER-positive and hypomethylated ER-negative BRCA subtypes. Specifically, we found that certain upregulated genes (e.g., SFRP1 and WIF1) have great potential to suppress the progression of ER-positive BRCA, concurrently exist negative correlations between their expression and methylation of corresponding hypomethylated CpG loci. Therefore, our study indicates that different epigenetic mechanisms likely exist in ER-positive BRCA and provides novel clinical biomarkers specific to ER-positive BRCA diagnosis and therapy.

[Effect of low-intensity pulsed ultrasound stimulation on maturation of regenerate bone].

OBJECTIVE: To explore the effect of low intensity pulsed ultrasound stimulation (LIPUS) on the maturation of regenerate bone in a rabbit limb lengthening model. METHODS: Sixty skeletal mature female New Zealand white rabbits were randomly divided into an LIPUS treatment group and a control group. All rabbits were underwent mid-diaphyseal tibial osteotomy and immobilized in an Orthofix M103 Mini lengther. Gradual distraction at 0.5 mm every 12 h for 10 d was performed at day 7 postoperatively. A 4-week course of LIPUS treatment group was applied over the distraction site for 20 min daily starting immediately after the completion of the distraction only for the treatment group. Rabbits were euthanized and the mid-diaphyseal tibia was harvested for evaluation at 4, 8, and 12 wk after the completion of the bone lengthening protocol. Radiographic analysis was performed to study the formation of bone callus using the ImageJ software at 12 wk after the completion of the bone lengthening protocol. Bone mineral density (BMD) of regenerate bone was measured by Dual energy X-ray absorptiometry (DEXA). Torsional testing to failure was performed on the tibia specimens at 8 and 12 wk after the completion of the bone lengthening protocol. RESULTS: Radiographic measurement showed higher relative gray scale of bone callus in the LIPUS group than that in the control group at 12 wk (P<0.05). BMD in the LIPUS group was significantly higher than that in control group at 8 and 12 wk (P<0.05). Biomechanical testing showed that the ultimate torque, ultimate torsional stiffness, and energy absorption at failure of regenerated bone at 8 and 12 wk in the LIPUS treatment group were better than those in the control group (P<0.05). CONCLUSION: LIPUS as a biophysical stimulation may accelerate the formation and maturation of regenerate bone in rabbit tibia lengthening model.

Complete Genome Sequence of Salmonella enterica Serovar Enteritidis Myophage Mooltan.

Salmonella enterica serovar Enteritidis is a Gram-negative bacterium and one of the most common foodborne pathogens. Biocontrol using bacteriophage in food products or animals is one possible means by which pathogenic salmonellosis infection could be inhibited. Here, we report the complete genome sequence of the T4-like Salmonella Enteritidis myophage Mooltan.

Complete Genome Sequence of Salmonella enterica Serovar Heidelberg Siphophage Sepoy.

Phage Sepoy infects Salmonella enterica serovar Heidelberg, a Gram-negative bacterium that causes severe foodborne illnesses. Bacteriophages infecting this pathogen may be used as biocontrol agents for preventing Salmonella foodborne diseases. Here, we present the complete genome sequence of Sepoy, a T5-like siphophage.

Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Siphophage Seabear.

Salmonella enterica serovar Typhimurium is a foodborne pathogen that causes gastroenteritis. Due to increases in antibiotic resistance, bacteriophage therapy may be an alternative method for preventing Salmonella foodborne infections. We report here the complete genome sequence of a T5-like phage, Seabear, which was isolated against S. Typhimurium.

Complete Genome Sequence of Salmonella enterica Serovar Enteritidis Siphophage Seafire.

Bacteriophages infecting Salmonella enterica subsp. enterica serovar Enteritidis may be used as biocontrol agents in food products or animals for preventing foodborne diseases caused by this pathogen. The complete genome sequence of phage Seafire, a T5-like siphophage infecting S. Enteritidis, is described in this report.

Effect of rhamnolipids on degradation of anthracene by two newly isolated strains, Sphingomonas sp. 12A and Pseudomonas sp. 12B.

Anthracene is a PAH that is not readily degraded, plus its degradation mechanism is still not clear. Thus, two strains of bacteria-degrading bacteria were isolated from longterm petroleum-polluted soil and identified as Sphingomonas sp. 12A and Pseudomonas sp. 12B by a 16S rRNA sequence analysis. To further enhance the anthracene-degrading ability of the two strains, the biosurfactants produced by Pseudomonas aeruginosa W3 were used, which were characterized as rhamnolipids. It was found that these rhamnolipids dramatically increased the solubility of anthracene, and a reverse-phase HPLC assay showed that the anthracene degradation percentage after 18 days with Pseudomonas sp. 12B was significantly enhanced from 34% to 52%. Interestingly, their effect on the degradation by Sphingomonas sp. 12A was much less, from 35% to 39%. Further study revealed that Sphingomonas sp. 12A also degraded the rhamnolipids, which may have hampered the effect of the rhamnolipids on the anthracene degradation.

Tea saponin reduces the damage of Ectropis obliqua to tea crops, and exerts reduced effects on the spiders Ebrechtella tricuspidata and Evarcha albaria compared to chemical insecticides.

BACKGROUND: Tea is one of the most economically important crops in China. However, the tea geometrid (Ectropis obliqua), a serious leaf-feeding pest, causes significant damage to tea crops and reduces tea yield and quality. Spiders are the most dominant predatory enemies in the tea plantation ecosystem, which makes them potentially useful biological control agents of E. obliqua. These highlight the need for alternative pest control measures. Our previous studies have shown that tea saponin (TS) exerts insecticidal activity against lepidopteran pests. Here, we investigate whether TS represents a potentially new alternative insecticide with no harm to spiders. METHODS: We investigated laboratory bioactivities and the field control properties of TS solution against E. obliqua. (i) A leaf-dip bioassay was used to evaluate the toxicity of TS to 3rd-instar E. obliqua larvae and effects of TS on the activities of enzymes glutathione-S-transferase (GST), acetylcholinesterase (AChE), carboxylesterase (CES) and peroxidase (POD) of 3rd-instar E. obliqua larvae in the laboratory. (ii) Topical application was used to measure the toxicity of 30% TS (w/v) and two chemical insecticides (10% bifenthrin EC and 50% diafenthiuron SC) to two species of spider, Ebrechtella tricuspidata and Evarcha albaria. (iii) Field trials were used to investigate the controlling efficacy of 30% TS against E. obliqua larvae and to classify the effect of TS to spiders in the tea plantation. RESULTS: The toxicity of TS to 3rd-instar E. obliqua larvae occurred in a dose-dependent manner and the LC50 was 164.32 mg/mL. Activities of the detoxifying-related enzymes, GST and POD, increased in 3rd-instar E. obliqua larvae, whereas AChE and CES were inhibited with time by treatment with TS. Mortalities of E. tricuspidata and E. albaria after 48 h with 30% TS treatment (16.67% and 20%, respectively) were significantly lower than those with 10% bifenthrin EC (80% and 73.33%, respectively) and 50% diafenthiuron EC (43.33% and 36.67%, respectively). The highest controlling efficacy of 30% TS was 77.02% at 5 d after treatment, which showed no difference to 10% bifenthrin EC or 50% diafenthiuron SC. 30% TS was placed in the class N (harmless or slightly harmful) of IOBC (International Organization of Biological Control) categories for natural enemies, namely spiders. CONCLUSIONS: Our results indicate that TS is a botanical insecticide that has a good controlling efficacy in E. obliqua larvae, which suggests it has promise as application in the integrated pest management (IPM) envisaged for tea crops.

Cloning and characterization of a haloarchaeal heat shock protein 70 functionally expressed in Escherichia coli.

The Hsp70 molecular chaperone machine is constituted by the 70-kDa heat shock protein Hsp70 (DnaK), cochaperone protein Hsp40 (DnaJ) and a nucleotide-exchange factor GrpE. Although it is one of the best-characterized molecular chaperone machines, little is known about it in archaea. A 5.2-kb region containing the hsp70 (dnaK) gene was cloned from Natrinema sp. J7 strain and sequenced. It contained the Hsp70 chaperone machine gene locus arranged unidirectionally in the order of grpE, hsp70 and hsp40 (dnaJ). The hsp70 gene from Natrinema sp. J7 was overexpressed in Escherichia coli BL21 (DE3). The recombinant Hsp70 protein was in a soluble and active form, and its ATPase activity was optimally active in 2.0 M KCl, whereas NaCl had less effect. In vivo, the haloarchaeal hsp70 gene allowed an E. coli dnak-null mutant to propagate lambda phages and grow at 42 degrees C. The results suggested that haloarchaeal Hsp70 should be beneficial for extreme halophiles survival in low-salt environments.