Genome Sequence of SN1, a Bacteriophage That Infects \u3ci\u3eSphaerotilus natans\u3c/i\u3e and \u3ci\u3ePseudomonas aeruginosa\u3c/i\u3e

Phage SN1 infects Sphaerotilus natans and Pseudomonas aeruginosa strains. Its genome consists of 61,858 bp (64.3% GC) and 89 genes, including 32 with predicted functions. SN1 genome is very similar to Pseudomonas phage M6, which contains hypermodified thymidines. Genome analyses revealed similar base-modifying genes as those found in M6. Phage SN1 was isolated in 1979 from activated sludge samples obtained from a wastewater treatment plant (Lincoln, Nebraska, USA) using S. natans ATCC 13338 as the host (1, 2). An early study showed that the siphophage SN1 has unusual bases in its genome as confirmed by cellulose thin-layer chromatography (1). Its genomic DNA also showed resistance to type II restriction endonucleases (2). Host range studies indicate that phage SN1 can also infect Pseudomonas aeruginosa strains PAO33 and OT684 (2). Here, phage SN1 was amplified with its host S. natans ATCC 13338 in nutrient broth (3 g/L beef extract, 5 g/L peptone) and agitated at 30°C (2). Cell debris were removed by filtration (0.45 mm) and filtrates were stored at 4°C until use. Phage SN1 also infected P. aeruginosa PAO1 (HER1153) in TSB/TSA medium at 30°C using both plaque assays and lysis of liquid cultures. Species identification of the above two host strains was confirmed by 16S sequencing

Genome Sequence of SN1, a Bacteriophage That Infects \u3ci\u3eSphaerotilus natans\u3c/i\u3e and \u3ci\u3ePseudomonas aeruginosa\u3c/i\u3e

Phage SN1 infects Sphaerotilus natans and Pseudomonas aeruginosa strains. Its genome consists of 61,858 bp (64.3% GC) and 89 genes, including 32 with predicted functions. SN1 genome is very similar to Pseudomonas phage M6, which contains hypermodified thymidines. Genome analyses revealed similar base-modifying genes as those found in M6

Lactobacillli expressing llama VHH fragments neutralise Lactococcus phages

<p>Abstract</p> <p>Background</p> <p>Bacteriophages infecting lactic acid bacteria (LAB) are widely acknowledged as the main cause of milk fermentation failures. In this study, we describe the surface-expression as well as the secretion of two functional llama heavy-chain antibody fragments, one binding to the major capsid protein (MCP) and the other to the receptor-binding proteins (RBP) of the lactococcal bacteriophage p2, by lactobacilli in order to neutralise lactococcal phages.</p> <p>Results</p> <p>The antibody fragment VHH5 that is directed against the RBP, was fused to a c-<it>myc </it>tag and expressed in a secreted form by a <it>Lactobacillus </it>strain. The fragment VHH2 that is binding to the MCP, was fused to an E-tag and anchored on the surface of the lactobacilli. Surface expression of VHH2 was confirmed by flow cytometry using an anti-E-tag antibody. Efficient binding of both the VHH2 and the secreted VHH5 fragment to the phage antigens was shown in ELISA. Scanning electron microscopy showed that lactobacilli expressing VHH2 anchored at their surface were able to bind lactococcal phages. A neutralisation assay also confirmed that the secreted VHH5 and the anchored VHH2 fragments prevented the adsorption of lactococcal phages to their host cells.</p> <p>Conclusion</p> <p>Lactobacilli were able to express functional VHH fragments in both a secreted and a cell surface form and reduced phage infection of lactococcal cells. Lactobacilli expressing llama heavy-chain antibody fragments represent a novel way to limit phage infection.</p

Characterization of two polyvalent phages infecting Enterobacteriaceae

Bacteriophages display remarkable genetic diversity and host specificity. In this study, we explore phages infecting bacterial strains of the Enterobacteriaceae family because of their ability to infect related but distinct hosts. We isolated and characterized two novel virulent phages, SH6 and SH7, using a strain of Shigella flexneri as host bacterium. Morphological and genomic analyses revealed that phage SH6 belongs to the T1virus genus of the Siphoviridae family. Conversely, phage SH7 was classified in the T4virus genus of the Myoviridae family. Phage SH6 had a short latent period of 16 min and a burst size of 103 ± 16 PFU/infected cell while the phage SH7 latent period was 23 min with a much lower burst size of 26 ± 5 PFU/infected cell. Moreover, phage SH6 was sensitive to acidic conditions (pH < 5) while phage SH7 was stable from pH 3 to 11 for 1 hour. Of the 35 bacterial strains tested, SH6 infected its S. flexneri host strain and 8 strains of E. coli. Phage SH7 lysed additionally strains of E. coli O157:H7, Salmonella Paratyphi, and Shigella dysenteriae. The broader host ranges of these two phages as well as their microbiological properties suggest that they may be useful for controlling bacterial populations

Characterization of CRISPR-Cas systems in the Ralstonia solanacearum species complex

Clustered regularly interspaced short palindromic repeats (CRISPRs) are composed of an array of short DNA repeat sequences separated by unique spacer sequences that are flanked by associated (Cas) genes. CRISPR‐Cas systems are found in the genomes of several microbes and can act as an adaptive immune mechanism against invading foreign nucleic acids, such as phage genomes. Here, we studied the CRISPR‐Cas systems in plant‐pathogenic bacteria of the Ralstonia solanacearum species complex (RSSC). A CRISPR‐Cas system was found in 31% of RSSC genomes present in public databases. Specifically, CRISPR‐Cas types I‐E and II‐C were found, with I‐E being the most common. The presence of the same CRISPR‐Cas types in distinct Ralstonia phylotypes and species suggests the acquisition of the system by a common ancestor before Ralstonia species segregation. In addition, a Cas1 phylogeny (I‐E type) showed a perfect geographical segregation of phylotypes, supporting an ancient acquisition. Ralstoniasolanacearum strains CFBP2957 and K60T were challenged with a virulent phage, and the CRISPR arrays of bacteriophage‐insensitive mutants (BIMs) were analysed. No new spacer acquisition was detected in the analysed BIMs. The functionality of the CRISPR‐Cas interference step was also tested in R. solanacearum CFBP2957 using a spacer‐protospacer adjacent motif (PAM) delivery system, and no resistance was observed against phage phiAP1. Our results show that the CRISPR‐Cas system in R. solanacearum CFBP2957 is not its primary antiviral strategy

Complete genome sequence of Escherichia coli Siphophage BRET

The lytic Escherichia coli siphophage BRET was isolated from a chicken obtained at a local market in Abidjan, Côte d’Ivoire. Its linear genome sequence consists of 59,550 bp (43.4% GC content) and contains 88 predicted genes, including 4 involved in archaeosine biosynthesis. Phage BRET is related (95% nucleotide identity) to Enterobacteria phage JenK

Physiological characterization of Typhlatya cave shrimps: linking habitat with aerobic metabolism

The anchialine environment is characterized by a vertical stratification of water masses with different salinities. Cave shrimps of the genus Typhlatya are widespread inhabitants of the aquifer in fresh, brackish, and marine groundwater. Here we describe physiological aspects of three of the most abundant and widespread Typhlatya species that thrive in the fresh and marine groundwater habitats of the anchialine ecosystem of the Yucatan Peninsula. The aerobic scope (AS) of Typhlatya mitchelli, Typhlatya pearsei and Typhlatya dzilamensis was estimated through induced physical activity, whilst monitoring protein carbonylation and lipid peroxidation (as indicators of cellular damage), lactate accumulation (as an indicator of anaerobic metabolism) and the antioxidant system response. The critical thermal limits (CTL) of all three species as an additional measure of physiological plasticity were also determined. Our results showed that metabolic rates, AS and CTL were similar amongst the two species that inhabit fresh groundwater habitats, and differed markedly from T. dzilamensis, a species typically found in marine groundwater. The antioxidant system response in all three Typhlatya species accompanied the levels of aerobic metabolism following physical activity. However, the large amount of GSH observed in T. dzilamensis may be indicative of an adaptive trait to a more heterogeneous environment. The differences observed among Typhlatya species reflect different physiological adaptations that correspond to the environmental heterogeneity of their natural habitats. Our results suggest that the marine groundwater species, T. dzilamensis, could be better prepared to respond to a naturally more heterogeneous environment, in contrast to Typhlatya mitchelli and Typhlatya pearsei which rarely face environmental clines in the fresh groundwater habitat. Our findings contribute to a better understanding of the consequences of environmental change on ecologically important species that are restricted to live in the aquifer

Generation of Immortal Cell Lines from the Adult Pituitary: Role of cAMP on Differentiation of SOX2-Expressing Progenitor Cells to Mature Gonadotropes

The pituitary is a complex endocrine tissue composed of a number of unique cell types distinguished by the expression and secretion of specific hormones, which in turn control critical components of overall physiology. The basic function of these cells is understood; however, the molecular events involved in their hormonal regulation are not yet fully defined. While previously established cell lines have provided much insight into these regulatory mechanisms, the availability of representative cell lines from each cell lineage is limited, and currently none are derived from adult pituitary. We have therefore used retroviral transfer of SV40 T-antigen to mass immortalize primary pituitary cell culture from an adult mouse. We have generated 19 mixed cell cultures that contain cells from pituitary cell lineages, as determined by RT-PCR analysis and immunocytochemistry for specific hormones. Some lines expressed markers associated with multipotent adult progenitor cells or transit-amplifying cells, including SOX2, nestin, S100, and SOX9. The progenitor lines were exposed to an adenylate cyclase activator, forskolin, over 7 days and were induced to differentiate to a more mature gonadotrope cell, expressing significant levels of α-subunit, LHβ, and FSHβ mRNAs. Additionally, clonal populations of differentiated gonadotropes were exposed to 30 nM gonadotropin-releasing hormone and responded appropriately with a significant increase in α-subunit and LHβ transcription. Further, exposure of the lines to a pulse paradigm of GnRH, in combination with 17β-estradiol and dexamethasone, significantly increased GnRH receptor mRNA levels. This array of adult-derived pituitary cell models will be valuable for both studies of progenitor cell characteristics and modulation, and the molecular analysis of individual pituitary cell lineages

Cross-sectional examination of 24-hour movement behaviours among 3-and 4-year-old children in urban and rural settings in low-income, middle-income and high-income countries : the SUNRISE study protocol

Introduction 24-hour movement behaviours (physical activity, sedentary behaviour and sleep) during the early years are associated with health and developmental outcomes, prompting the WHO to develop Global guidelines for physical activity, sedentary behaviour and sleep for children under 5 years of age. Prevalence data on 24-hour movement behaviours is lacking, particularly in low-income and middle-income countries (LMICs). This paper describes the development of the SUNRISE International Study of Movement Behaviours in the Early Years protocol, designed to address this gap. Methods and analysis SUNRISE is the first international cross-sectional study that aims to determine the proportion of 3- and 4-year-old children who meet the WHO Global guidelines. The study will assess if proportions differ by gender, urban/rural location and/or socioeconomic status. Executive function, motor skills and adiposity will be assessed and potential correlates of 24-hour movement behaviours examined. Pilot research from 24 countries (14 LMICs) informed the study design and protocol. Data are collected locally by research staff from partnering institutions who are trained throughout the research process. Piloting of all measures to determine protocol acceptability and feasibility was interrupted by COVID-19 but is nearing completion. At the time of publication 41 countries are participating in the SUNRISE study. Ethics and dissemination The SUNRISE protocol has received ethics approved from the University of Wollongong, Australia, and in each country by the applicable ethics committees. Approval is also sought from any relevant government departments or organisations. The results will inform global efforts to prevent childhood obesity and ensure young children reach their health and developmental potential. Findings on the correlates of movement behaviours can guide future interventions to improve the movement behaviours in culturally specific ways. Study findings will be disseminated via publications, conference presentations and may contribute to the development of local guidelines and public health interventions.Peer reviewe

A proposed new bacteriophage subfamily: “Jerseyvirinae”

© 2015, Springer-Verlag Wien. Based on morphology and comparative nucleotide and protein sequence analysis, a new subfamily of the family Siphoviridae is proposed, named “Jerseyvirinae” and consisting of three genera, “Jerseylikevirus”, “Sp3unalikevirus” and “K1glikevirus”. To date, this subfamily consists of 18 phages for which the genomes have been sequenced. Salmonella phages Jersey, vB_SenS_AG11, vB_SenS-Ent1, vB_SenS-Ent2, vB_SenS-Ent3, FSL SP-101, SETP3, SETP7, SETP13, SE2, SS3e and wksl3 form the proposed genus “Jerseylikevirus”. The proposed genus “K1glikevirus” consists of Escherichia phages K1G, K1H, K1ind1, K1ind2 and K1ind3. The proposed genus “Sp3unalikevirus” contains one member so far. Jersey-like phages appear to be widely distributed, as the above phages were isolated in the UK, Canada, the USA and South Korea between 1970 and the present day. The distinguishing features of this subfamily include a distinct siphovirus morphotype, genomes of 40.7-43.6kb (49.6-51.4mol% G+C), a syntenic genome organisation, and a high degree of nucleotide sequence identity and shared proteins. All known members of the proposed subfamily are strictly lytic