Recombination Events in Putative Tail Fibre Gene in Litunavirus Phages Infecting Pseudomonas aeruginosa and Their Phylogenetic Consequences.

Recombination is the main driver of bacteriophage evolution. It may serve as a tool for extending the phage host spectrum, which is significant not only for phages' ecology but also for their utilisation as therapeutic agents of bacterial infections. The aim of this study was to detect the recombination events in the genomes of Litunavirus phages infecting Pseudomonas aeruginosa, and present their impact on phylogenetic relations within this phage group. The phylogenetic analyses involved: the whole-genome, core-genome (Schitoviridae conserved genes), variable genome region, and the whole-genome minus variable region. Interestingly, the recombination events taking place in the putative host recognition region (tail fibre protein gene and the adjacent downstream gene) significantly influenced tree topology, suggesting a strong phylogenetic signal. Our results indicate the recombination between phages from two genera Litunavirus and Luzeptimavirus and demonstrate its influence on phage phylogeny.

Drivers' Subjective Assessment of the Ease of Finding a Vacant Parking Space in an Area Equipped with Vehicle Detection Devices.

The growing traffic on city streets leads to traffic disruptions, lowering the level of road safety, as well as the problem of finding a vacant parking space. Drivers looking for a vacant parking space on the street generate so-called search traffic. Paid parking zones are introduced to increase the availability of parking spaces for more drivers in many cities around the world. The development in the technology and information sector has contributed to the development of systems guiding drivers to vacant parking spaces. This article aims to analyze drivers' subjective assessment of the ease of finding a vacant parking space in an area equipped with vehicle detection devices. Data from the Municipal Roads Authority in Gliwice (Poland) were obtained for the study, covering the use of parking spaces in the paid parking zone covered by dynamic parking information. Moreover, a survey was conducted among users of the paid parking zone in Gliwice. The answers of the respondents were used to build a logit model that allows determining the probability of a driver's positive subjective assessment of the ease of finding a vacant parking space in an area equipped with vehicle detection devices. The results from the model allow the characterization of drivers who positively assess the ease of finding a vacant parking space in the area equipped with vehicle detection devices. In addition, it is possible to reach a group of drivers who negatively assessed the ease of finding a vacant parking space to learn about the factors that may cause them to change their assessment to a positive one. The research results allow city authorities to better manage parking spaces equipped with vehicle detection devices in the paid parking zone. This may change the negative assessment of the ease of finding a vacant parking space into a positive one.

Going to extremes - a metagenomic journey into the dark matter of life.

The Virus-X-Viral Metagenomics for Innovation Value-project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. Specifically, the project was set to analyse and exploit viral metagenomes with the ultimate goal of developing new gene products with high innovation value for applications in biotechnology, pharmaceutical, medical, and the life science sectors. Viral gene pool analysis is also essential to obtain fundamental insight into ecosystem dynamics and to investigate how viruses influence the evolution of microbes and multicellular organisms. The Virus-X Consortium, established in 2016, included experts from eight European countries. The unique approach based on high throughput bioinformatics technologies combined with structural and functional studies resulted in the development of a biodiscovery pipeline of significant capacity and scale. The activities within the Virus-X consortium cover the entire range from bioprospecting and methods development in bioinformatics to protein production and characterisation, with the final goal of translating our results into new products for the bioeconomy. The significant impact the consortium made in all of these areas was possible due to the successful cooperation between expert teams that worked together to solve a complex scientific problem using state-of-the-art technologies as well as developing novel tools to explore the virosphere, widely considered as the last great frontier of life.

Bacteriophages vB_Sen-TO17 and vB_Sen-E22, Newly Isolated Viruses from Chicken Feces, Specific for Several Salmonella enterica Strains.

Two newly discovered bacteriophages, isolated from chicken feces and infecting Salmonella enterica strains, are described in this report. These phages have been named vB_Sen-TO17 and vB_Sen-E22, and we present their molecular and functional characterization. Both studied viruses are able to infect several S. enterica strains and develop lytically, but their specific host ranges differ significantly. Electron microscopic analyses of virions have been performed, and full genome sequences were determined and characterized, along with molecular phylogenetic studies. Genomes of vB_Sen-TO17 (ds DNA of 41,658 bp) and vB_Sen-E22 (dsDNA of 108,987 bp) are devoid of homologs of any known or putative gene coding for toxins or any other proteins potentially deleterious for eukaryotic cells. Both phages adsorbed efficiently (>95% adsorbed virions) within 10 min at 42 °C (resembling chicken body temperature) on cells of most tested host strains. Kinetics of lytic development of vB_Sen-TO17 and vB_Sen-E22, determined in one-step growth experiments, indicated that development is complete within 30-40 min at 42 °C, whereas burst sizes vary from 9 to 79 progeny phages per cell for vB_Sen-TO17 and from 18 to 64 for vB_Sen-E22, depending on the host strain. Virions of both phages were relatively stable (from several percent to almost 100% survivability) under various conditions, including acidic and alkaline pH values (from 3 to 12), temperatures from -80 °C to 60 °C, 70% ethanol, chloroform, and 10% DMSO. These characteristics of vB_Sen-TO17 and vB_Sen-E22 indicate that these phages might be considered in further studies on phage therapy, particularly in attempts to eliminate S. enterica from chicken intestine.

Characterization of the Bacteriophage vB_EfaS-271 Infecting Enterococcus faecalis.

A newly isolated bacteriophage infecting Enterococcus faecalis strains has been characterized, including determination of its molecular features. This phage, named vB_EfaS-271, has been classified as a Siphoviridae member, according to electron microscopy characterization of the virions, composed of a 50 nm-diameter head and a long, flexible, noncontractable tail (219 × 12.5 nm). Analysis of the whole dsDNA genome of this phage showed that it consists of 40,197 bp and functional modules containing genes coding for proteins that are involved in DNA replication (including DNA polymerase/primase), morphogenesis, packaging and cell lysis. Mass spectrometry analysis allowed us to identify several phage-encoded proteins. vB_EfaS-271 reveals a relatively narrow host range, as it is able to infect only a few E. faecalis strains. On the other hand, it is a virulent phage (unable to lysogenize host cells), effectively and quickly destroying cultures of sensitive host bacteria, with a latent period as short as 8 min and burst size of approximately 70 phages per cell at 37 °C. This phage was also able to destroy biofilms formed by E. faecalis. These results contribute to our understanding of the biodiversity of bacteriophages, confirming the high variability among these viruses and indicating specific genetic and functional features of vB_EfaS-271.

Characteristics of a Series of Three Bacteriophages Infecting Salmonella enterica Strains.

Molecular and functional characterization of a series of three bacteriophages, vB_SenM-1, vB_SenM-2, and vB_SenS-3, infecting various Salmonella enterica serovars and strains is presented. All these phages were able to develop lytically while not forming prophages. Moreover, they were able to survive at pH 3. The phages revealed different host ranges within serovars and strains of S. enterica, different adsorption rates on host cells, and different lytic growth kinetics at various temperatures (in the range of 25 to 42 °C). They efficiently reduced the number of cells in the bacterial biofilm and decreased the biofilm mass. Whole genome sequences of these phages have been determined and analyzed, including their phylogenetic relationships. In conclusion, we have demonstrated detailed characterization of a series of three bacteriophages, vB_SenM-1, vB_SenM-2, and vB_SenS-3, which reveal favorable features in light of their potential use in phage therapy of humans and animals, as well as for food protection purposes.

Characterization of a bacteriophage, vB_Eco4M-7, that effectively infects many Escherichia coli O157 strains.

The characterization of a recently isolated bacteriophage, vB_Eco4M-7, which effectively infects many, though not all, Escherichia coli O157 strains, is presented. The genome of this phage comprises double-stranded DNA, 68,084 bp in length, with a GC content of 46.2%. It contains 96 putative open reading frames (ORFs). Among them, the putative functions of only 35 ORFs were predicted (36.5%), whereas 61 ORFs (63.5%) were classified as hypothetical proteins. The genome of phage vB_Eco4M-7 does not contain genes coding for integrase, recombinase, repressors or excisionase, which are the main markers of temperate viruses. Therefore, we conclude that phage vB_Eco4M-7 should be considered a lytic virus. This was confirmed by monitoring phage lytic development by a one-step growth experiment. Moreover, the phage forms relatively small uniform plaques (1 mm diameter) with no properties of lysogenization. Electron microscopic analyses indicated that vB_Eco4M-7 belongs to the Myoviridae family. Based on mass spectrometric analyses, including the fragmentation pattern of unique peptides, 33 phage vB_Eco4M-7 proteins were assigned to annotated open reading frames. Importantly, genome analysis suggested that this E. coli phage is free of toxins and other virulence factors. In addition, a similar, previously reported but uncharacterized bacteriophage, ECML-117, was also investigated, and this phage exhibited properties similar to vB_Eco4M-7. Our results indicate that both studied phages are potential candidates for phage therapy and/or food protection against Shiga toxin-producing E. coli, as the majority of these strains belong to the O157 serotype.

Revision of Gyrodactylus salaris phylogeny inspired by new evidence for Eemian crossing between lineages living on grayling in Baltic and White sea basins.

In this research, grayling-specific Gyrodactylus salaris Malmberg, 1957 isolates from Baltic Sea basin were collected in Sweden for the first time. Samples were obtained in three drainage systems: Kalixälven (River Kaitum), Ljungan (River Sölvbacka strömmar), and Umeälven (River Juktån). Three molecular markers were analysed: nuclear ITS rDNA (Internal Transcribed Spacer) and ADNAM1 (Anonymous DNA Marker 1), and mitochondrial cox1 gene. As a result, four new mitochondrial haplotypes were identified (III-C1tt, III-C1ttht, IX-A1tt and X-A1tt). The ADNAM1 analyses resulted in revealing two new alleles (WS4 and BS9) and two new genotypes (T6 and T7). T7 seems to be an indicator of ancient crossing between Baltic and White Sea lineages of the parasite which happened during a first 3000-year period of Eemian interglacial about 130,000 years ago in the connection between Baltic and White Sea. Molecular clock estimates were adjusted, revealing the mean substitution rate and the divergence rate among branches of 3.6% (95% HPD: 2.2%-5.2%) and 7.2% per million years, respectively. As a result, cox1 phylogeny rooted with the introgressed haplotypes has been revised and altered in accordance to new data, revealing fourteen equidistant lineages five of which have been excluded from the study. Based on the new phylogenetic approach, including the molecular clock, this work suggests an overall revision of G. salaris phylogeny and attempts at precisely drawing the division of lineages within this polytypic species as well as proposes unification in nomenclature for its strains.

Characterization of Bacteriophage vB-EcoS-95, Isolated From Urban Sewage and Revealing Extremely Rapid Lytic Development.

Morphological, biological, and genetic characteristics of a virulent Siphoviridae phage, named vB-EcoS-95, is reported. This phage was isolated from urban sewage. It was found to infect some Escherichia coli strains giving clear plaques. The genome of this phage is composed of 50,910 bp and contains 89 ORFs. Importantly, none of the predicted ORFs shows any similarity with known pathogenic factors that would prevent its use in medicine. Genome sequence analysis of vB-EcoS-95 revealed 74% similarity to genomic sequence of Shigella phage pSf-1. Compared to pSf-1, phage vb-EcoS-95 does not infect Shigella strains and has an efficient bacteriolytic activity against some E. coli strains. One-step growth analysis revealed that this phage has a very short latent period (4 min), and average burst size of 115 plaque forming units per cell, which points to its high infectivity of host cells and strong lytic activity. The bacteriolytic effect of vB-EcoS-95 was tested also on biofilm-producing strains. These results indicate that vB-EcoS-95 is a newly discovered E. coli phage that may be potentially used to control the formation of biofilms.

Biodiversity of bacteriophages: morphological and biological properties of a large group of phages isolated from urban sewage.

A large scale analysis presented in this article focuses on biological and physiological variety of bacteriophages. A collection of 83 bacteriophages, isolated from urban sewage and able to propagate in cells of different bacterial hosts, has been obtained (60 infecting Escherichia coli, 10 infecting Pseudomonas aeruginosa, 4 infecting Salmonella enterica, 3 infecting Staphylococcus sciuri, and 6 infecting Enterococcus faecalis). High biological diversity of the collection is indicated by its characteristics, both morphological (electron microscopic analyses) and biological (host range, plaque size and morphology, growth at various temperatures, thermal inactivation, sensitivity to low and high pH, sensitivity to osmotic stress, survivability upon treatment with organic solvents and detergents), and further supported by hierarchical cluster analysis. By the end of the research no larger collection of phages from a single environmental source investigated by these means had been found. The finding was confirmed by whole genome analysis of 7 selected bacteriophages. Moreover, particular bacteriophages revealed unusual biological features, like the ability to form plaques at low temperature (4 °C), resist high temperature (62 °C or 95 °C) or survive in the presence of an organic solvents (ethanol, acetone, DMSO, chloroform) or detergent (SDS, CTAB, sarkosyl) making them potentially interesting in the context of biotechnological applications.

IL-19 is a component of the pathogenetic IL-23/IL-17 cascade in psoriasis.

Psoriasis is a common chronic inflammatory disease with characteristic skin alterations and functions as a model of immune-mediated disorders. Cytokines have a key role in psoriasis pathogenesis. Here, we demonstrated that out of 30 individually quantified cytokines, IL-19 showed the strongest differential expression between psoriatic lesions and healthy skin. Cutaneous IL-19 overproduction was reflected by elevated IL-19 blood levels that correlated with psoriasis severity. Accordingly, anti-psoriatic therapies substantially reduced both cutaneous and systemic IL-19 levels. IL-19 production was induced in keratinocytes by IL-17A and was further amplified by tumor necrosis factor-α and IL-22. Among skin cells, keratinocytes were found to be important targets of IL-19. IL-19 alone, however, regulated only a few keratinocyte functions. While increasing the production of S100A7/8/9 and, to a moderate extent, also IL-1ß, IL-20, chemokine C-X-C motif ligand 8, and matrix metalloproteinase 1, IL-19 had no clear influence on the differentiation, proliferation, or migration of these cells. Importantly, IL-19 amplified many IL-17A effects on keratinocytes, including the induction of ß-defensins, IL-19, IL-23p19, and T helper type 17-cell- and neutrophil-attracting chemokines. In summary, IL-19 as a component of the IL-23/IL-17 axis strengthens the IL-17A action and might be a biomarker for the activity of this axis in chronic inflammatory disorders.

Depression is a frequent co-morbidity in patients with acne inversa.

BACKGROUND: Acne inversa (AI) is a common chronic inflammatory disease that has a profound impact on the patientsí quality of life. We hypothesized a higher level of depression in AI patients compared to controls. OBJECTIVES: We studied depression in patients with AI and control subjects. Additionally, we evaluated whether the severity of the disease, anxiety, sexual distress and acute inflammation may have an influence on depression. PATIENTS AND METHODS: The Hospital Anxiety and Depression Scale (HADS) was given to 90 voluntary study participants to assess depression in AI patients and in age-, gender-, and BMI-matched controls. Moreover, the correlation between depression and conjectural influencing factors was evaluated. RESULTS: This study demonstrated that AI patients have a higher depression score than matched controls. Importantly, 38.6% of AI patients are affected by depression compared to 2.4% of the control subjects. In contrast to the duration of the disease and the AI patientsí age, anxiety and sexual distress showed a strong correlation with the degree of depression. CONCLUSIONS: Patients with AI have a higher risk of developing depression. Physicians should be alert to the possible development of depression when treating patients with this disorder.

Diversity of tailed phages in Baltic Sea sediment: large number of siphoviruses with extremely long tails.

We present the first attempt at quantitative analysis of morphological diversity of tailed viruses obtained from marine sediments without ultracentrifugation or enrichment on specific host strains. Sandy mud samples were collected in the Gulf of Gdansk in the spring, autumn and winter. VLPs were analyzed by transmission electron microscopy. The distribution of three groups of tailed phages was similar in all seasons (Siphoviridae: 52% on average; Myoviridae: 42%; Podoviridae: 6%). 19% of siphoviruses had prolate heads. Interestingly, 11% of siphoviral particles had tails longer than 300 nm, and 6% longer than 600 nm.

Increased prevalence of metabolic syndrome in patients with acne inversa.

BACKGROUND: Acne inversa (AI; also designated as Hidradenitis suppurativa) is a common chronic inflammatory skin disease, localized in the axillary, inguinal and perianal skin areas that causes painful, fistulating sinuses with malodorous purulence and scars. Several chronic inflammatory diseases are associated with the metabolic syndrome and its consequences including arteriosclerosis, coronary heart disease, myocardial infraction, and stroke. So far, the association of AI with systemic metabolic alterations is largely unexplored. METHODS AND FINDINGS: A hospital-based case-control study in 80 AI patients and 100 age- and sex-matched control participants was carried out. The prevalence of central obesity (odds ratio 5.88), hypertriglyceridemia (odds ratio 2.24), hypo-HDL-cholesterolemia (odds ratio 4.56), and hyperglycemia (odds ratio 4.09) in AI patients was significantly higher than in controls. Furthermore, the metabolic syndrome, previously defined as the presence of at least three of the five alterations listed above, was more common in those patients compared to controls (40.0% versus 13.0%; odds ratio 4.46, 95% confidence interval 2.02 to 9.96; P<0.001). AI patients with metabolic syndrome also had more pronounced metabolic alterations than controls with metabolic syndrome. Interestingly, there was no correlation between the severity or duration of the disease and the levels of respective parameters or the number of criteria defining the metabolic syndrome. Rather, the metabolic syndrome was observed in a disproportionately high percentage of young AI patients. CONCLUSIONS: This study shows for the first time that AI patients have a high prevalence of the metabolic syndrome and all of its criteria. It further suggests that the inflammation present in AI patients does not have a major impact on the development of metabolic alterations. Instead, evidence is given for a role of metabolic alterations in the development of AI. We recommend monitoring of AI patients in order to correct their modifiable cardiovascular risk factors.

Profound disturbances of sexual health in patients with acne inversa.

BACKGROUND: Acne inversa (AI) leads chronically to painful eruptions and extensive scarring in predominantly intimate areas. We hypothesized an impairment of sexual life caused by the disease. OBJECTIVES: By means of validated questionnaires, sexual health and quality of life were assessed in patients with AI and in healthy control subjects. METHODS: A self-administered questionnaire was given to 85 voluntary study participants. In all, 45 women (24 patients vs 21 control subjects) and 40 men (20 patients vs 20 control subjects) were enrolled in the study. The Female Sexual Function Index, the International Index of Erectile Function, and the Frankfurt Self-Concept Scale for Sexuality were used to assess sexual health. Quality of life was measured with the Dermatology Life Quality Index. RESULTS: This study demonstrated, for the first time to our knowledge, that patients with AI have sexual dysfunctions and sexual distress in comparison with matched control subjects. Sexual distress was particularly higher in female than in male patients with AI. Surprisingly, severity of cutaneous alterations correlated neither with sexual dysfunctions nor with sexual distress. However, the sexual dysfunction and sexual distress negatively correlated with the quality of life in female patients with AI who had a lower quality of life compared with gender-matched control subjects and male patients. LIMITATIONS: Small sample size is the main limitation of this study. CONCLUSIONS: Sexual health is diminished in patients with AI. We underscore the need for physicians to implement attention on the impact of AI on sexual health and quality of life when treating patients for this disease.