Adenosine triphosphatases of thermophilic archaeal double-stranded DNA viruses

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Black Mesoporous Silicon as a Contrast Agent for LED-Based 3D Photoacoustic Tomography

Mesoporous silicon (PSi) nanoparticles have been widely studied in different biomedical imaging modalities due to their several beneficial material properties. However, they have not been found to be suitable for photoacoustic imaging due to their poor photothermal conversion performance. In the present study, biodegradable black mesoporous silicon (BPSi) nanoparticles with strong light absorbance were developed as superior image contrast agents for photoacoustic tomography (PAT), which was realized with a light-emitting diode (LED) instead of the commonly used laser. LED-based PAT offers the advantages of low cost, compactness, good mobility, and easy operation as compared to the traditional laser-based PAT modality. Nevertheless, the poor imaging sensitivity of the LED-PAT systems has been the main barrier to prevent their wide biomedical application because the LED light has low optical energy. The present study demonstrated that the imaging sensitivity of the LED-PAT system was significantly enhanced with the PEGylated BPSi (PEG–BPSi) nanoparticles. The PEG–BPSi nanoparticles were clearly detectable with a low concentration of 0.05 mg/mL in vitro and with an LED radiation energy of 5.2 μJ. The required concentration of the PEG–BPSi nanoparticles was 10 times lesser than that of the reference gold nanoparticles to reach the corresponding level of the imaging contrast. The ex vivo studies demonstrated that the submillimeter BPSi nanoparticle-based absorbers were distinguishable in chicken breast tissues. The strong contrast provided by the BPSi particles indicated that these particles can be utilized as novel contrast agents in PAT, especially in LED-based systems with low light intensity

BtuB-Dependent Infection of the T5-like Yersinia Phage phi R2-01

Yersinia enterocolitica is a food-borne Gram-negative pathogen responsible for several gastrointestinal disorders. Host-specific lytic bacteriophages have been increasingly used recently as an alternative or complementary treatment to combat bacterial infections, especially when antibiotics fail. Here, we describe the proteogenomic characterization and host receptor identification of the siphovirus vB_YenS_phi R2-01 (in short, phi R2-01) that infects strains of several Yersinia enterocolitica serotypes. The phi R2-01 genome contains 154 predicted genes, 117 of which encode products that are homologous to those of Escherichia bacteriophage T5. The phi R2-01 and T5 genomes are largely syntenic, with the major differences residing in areas encoding hypothetical phi R2-01 proteins. Label-free mass-spectrometry-based proteomics confirmed the expression of 90 of the phi R2-01 genes, with 88 of these being either phage particle structural or phage-particle-associated proteins. In vitro transposon-based host mutagenesis and phi R2-01 adsorption experiments identified the outer membrane vitamin B12 receptor BtuB as the host receptor. This study provides a proteogenomic characterization of a T5-type bacteriophage and identifies specific Y. enterocolitica strains sensitive to infection with possible future applications of phi R2-01 as a food biocontrol or phage therapy agent.Peer reviewe

BtuB-Dependent Infection of the T5-like Yersinia Phage ϕR2-01

Yersinia enterocolitica is a food-borne Gram-negative pathogen responsible for several gastrointestinal disorders. Host-specific lytic bacteriophages have been increasingly used recently as an alternative or complementary treatment to combat bacterial infections, especially when antibiotics fail. Here, we describe the proteogenomic characterization and host receptor identification of the siphovirus vB_YenS_ϕR2-01 (in short, ϕR2-01) that infects strains of several Yersinia enterocolitica serotypes. The ϕR2-01 genome contains 154 predicted genes, 117 of which encode products that are homologous to those of Escherichia bacteriophage T5. The ϕR2-01 and T5 genomes are largely syntenic, with the major differences residing in areas encoding hypothetical ϕR2-01 proteins. Label-free mass-spectrometry-based proteomics confirmed the expression of 90 of the ϕR2-01 genes, with 88 of these being either phage particle structural or phage-particle-associated proteins. In vitro transposon-based host mutagenesis and ϕR2-01 adsorption experiments identified the outer membrane vitamin B12 receptor BtuB as the host receptor. This study provides a proteogenomic characterization of a T5-type bacteriophage and identifies specific Y. enterocolitica strains sensitive to infection with possible future applications of ϕR2-01 as a food biocontrol or phage therapy agent

Bacteriophages fEV-1 and fD1 Infect Yersinia pestis

Bacteriophages vB_YpeM_fEV-1 (fEV-1) and vB_YpeM_fD1 (fD1) were isolated from incoming sewage water samples in Turku, Finland, using Yersinia pestis strains EV76 and KIM D27 as enrichment hosts, respectively. Genomic analysis and transmission electron microscopy established that fEV-1 is a novel type of dwarf myovirus, while fD1 is a T4-like myovirus. The genome sizes are 38 and 167 kb, respectively. To date, the morphology and genome sequences of some dwarf myoviruses have been described; however, a proteome characterization such as the one presented here, has currently been lacking for this group of viruses. Notably, fEV-1 is the first dwarf myovirus described for Y. pestis. The host range of fEV-1 was restricted strictly to Y. pestis strains, while that of fD1 also included other members of Enterobacterales such as Escherichia coli and Yersinia pseudotuberculosis. In this study, we present the life cycles, genomes, and proteomes of two Yersinia myoviruses, fEV-1 and fD1

Bacteriophages fEV-1 and fD1 Infect Yersinia pestis

Bacteriophages vB_YpeM_fEV-1 (fEV-1) and vB_YpeM_fD1 (fD1) were isolated from incoming sewage water samples in Turku, Finland, using Yersinia pestis strains EV76 and KIM D27 as enrichment hosts, respectively. Genomic analysis and transmission electron microscopy established that fEV-1 is a novel type of dwarf myovirus, while fD1 is a T4-like myovirus. The genome sizes are 38 and 167 kb, respectively. To date, the morphology and genome sequences of some dwarf myoviruses have been described; however, a proteome characterization such as the one presented here, has currently been lacking for this group of viruses. Notably, fEV-1 is the first dwarf myovirus described for Y. pestis. The host range of fEV-1 was restricted strictly to Y. pestis strains, while that of fD1 also included other members of Enterobacterales such as Escherichia coli and Yersinia pseudotuberculosis. In this study, we present the life cycles, genomes, and proteomes of two Yersinia myoviruses, fEV-1 and fD1

Universal platform for quantitative analysis of DNA transposition

<p>Abstract</p> <p>Background</p> <p>Completed genome projects have revealed an astonishing diversity of transposable genetic elements, implying the existence of novel element families yet to be discovered from diverse life forms. Concurrently, several better understood transposon systems have been exploited as efficient tools in molecular biology and genomics applications. Characterization of new mobile elements and improvement of the existing transposition technology platforms warrant easy-to-use assays for the quantitative analysis of DNA transposition.</p> <p>Results</p> <p>Here we developed a universal <it>in vivo </it>platform for the analysis of transposition frequency with class II mobile elements, i.e., DNA transposons. For each particular transposon system, cloning of the transposon ends and the cognate transposase gene, in three consecutive steps, generates a multifunctional plasmid, which drives inducible expression of the transposase gene and includes a mobilisable <it>lacZ</it>-containing reporter transposon. The assay scores transposition events as blue microcolonies, papillae, growing within otherwise whitish <it>Escherichia coli </it>colonies on indicator plates. We developed the assay using phage Mu transposition as a test model and validated the platform using various MuA transposase mutants. For further validation and to illustrate universality, we introduced IS<it>903 </it>transposition system components into the assay. The developed assay is adjustable to a desired level of initial transposition via the control of a plasmid-borne <it>E. coli </it>arabinose promoter. In practice, the transposition frequency is modulated by varying the concentration of arabinose or glucose in the growth medium. We show that variable levels of transpositional activity can be analysed, thus enabling straightforward screens for hyper- or hypoactive transposase mutants, regardless of the original wild-type activity level.</p> <p>Conclusions</p> <p>The established universal papillation assay platform should be widely applicable to a variety of mobile elements. It can be used for mechanistic studies to dissect transposition and provides a means to screen or scrutinise transposase mutants and genes encoding host factors. In succession, improved versions of transposition systems should yield better tools for molecular biology and offer versatile genome modification vehicles for many types of studies, including gene therapy and stem cell research.</p

The C-Type Lectin of the Aggrecan G3 Domain Activates Complement

Excessive complement activation contributes to joint diseases such as rheumatoid arthritis and osteoarthritis during which cartilage proteins are fragmented and released into the synovial fluid. Some of these proteins and fragments activate complement, which may sustain inflammation. The G3 domain of large cartilage proteoglycan aggrecan interacts with other extracellular matrix proteins, fibulins and tenascins, via its C-type lectin domain (CLD) and has important functions in matrix organization. Fragments containing G3 domain are released during normal aggrecan turnover, but increasingly so in disease. We now show that the aggrecan CLD part of the G3 domain activates the classical and to a lesser extent the alternative pathway of complement, via binding of C1q and C3, respectively. The complement control protein (CCP) domain adjacent to the CLD showed no effect on complement initiation. The binding of C1q to G3 depended on ionic interactions and was decreased in D2267N mutant G3. However, the observed complement activation was attenuated due to binding of complement inhibitor factor H to CLD and CCP domains. This was most apparent at the level of deposition of terminal complement components. Taken together our observations indicate aggrecan CLD as one factor involved in the sustained inflammation of the joint

Craniofacial and oral alterations in patients with Neurofibromatosis 1

Neurofibromatosis type 1 (NF1) is one of the most common inherited syndromes. The literature on craniofacial alterations associated with NF1 has been limited and partially contradictory. This review is based on literature search and the results of the clinical study "Craniofacial and Oral Alterations and Speech in patients with Neurofibromatosis 1", carried out at the University of Turku and Turku University Hospital, Finland in 2006-2012. By the end of 2012, a total of 110 NF1 patients, 54 female and 56 male patients, were examined. A part of our results confirms pre-existing understanding, a part is contradictory to previous considerations based mainly on case reports, and some are entirely novel. Specifically, our results confirmed that enlargement the mandibular canal is the most common abnormality of the mandible in patients with NF1. It should be noted, however, that this finding does not require treatment. Caries was not a major problem. In fact, it was less frequent in NF1 patients compared to reference population. These findings abrogate some previous perceptions. Novel findings of our project include periapical cemental dysplasia in females; short jaws, a finding which usually does not affect bite; and immunohistological analysis of oral mucosal abnormalities. Pioneering study on speech showed that various deviations were very common: As many as 94% of the participants showed some alterations. To conclude, the awareness of craniofacial alterations common in NF1would help avoiding unnecessary and even harmful involvement, e.g. of periapical cemental dysplasia or enlarged mandibular canal which do not require treatment

Learning how to understand complexity and deal with sustainability challenges : A framework for a comprehensive approach and its application in university education

Sustainability challenges such as climate change, biodiversity loss, poverty and rapid urbanization are complex and strongly interrelated. In order to successfully deal with these challenges, we need comprehensive approaches that integrate knowledge from multiple disciplines and perspectives and emphasize interconnections. In short, they aid in observing matters in a wider perspective without losing an understanding of the details. In order to teach and learn a comprehensive approach, we need to better understand what comprehensive thinking actually is. In this paper, we present a conceptual framework for a comprehensive approach, termed the GHH framework. The framework comprises three dimensions: generalism, holism, and holarchism. It contributes to the academic community's understanding of comprehensive thinking and it can be used for integrating comprehensive thinking into education. Also, practical examples of the application of the framework in university teaching are presented. We argue that an ideal approach to sustainability challenges and complexity in general is a balanced, dialectical combination of comprehensive and differentiative approaches. The current dominance of specialization, or the differentiative approach, in university education calls for a stronger emphasis on comprehensive thinking skills. Comprehensiveness should not be considered as a flawed approach, but should instead be considered as important an aspect in education as specialized and differentiative skills. (C) 2017 Elsevier B.V. All rights reserved.Peer reviewe