Complete genome sequence of Pseudomonas Phage Motto

We describe the complete genome sequence of bacteriophage Motto, which infects clinical strains of Pseudomonas aeruginosa . Motto is a T1-like siphovirus related to members of the family Drexlerviridae and has a capsid width of ~57 nm and a tail length of ~255 nm. The 49.9-kb genome contains 84 protein-coding genes

In vitro and in vivo evaluation of the biofilm-degrading Pseudomonas phage Motto, as a candidate for phage therapy

Infections caused by Pseudomonas aeruginosa are becoming increasingly difficult to treat due to the emergence of strains that have acquired multidrug resistance. Therefore, phage therapy has gained attention as an alternative to the treatment of pseudomonal infections. Phages are not only bactericidal but occasionally show activity against biofilm as well. In this study, we describe the Pseudomonas phage Motto, a T1-like phage that can clear P. aeruginosa infections in an animal model and also exhibits biofilm-degrading properties. The phage has a substantial anti-biofilm activity against strong biofilm-producing isolates (n = 10), with at least a twofold reduction within 24 h. To demonstrate the safety of using phage Motto, cytotoxicity studies were conducted with human cell lines (HEK 293 and RAW 264.7 macrophages). Using a previously established in vivo model, we demonstrated the efficacy of Motto in Caenorhabditis elegans, with a 90% survival rate when treated with the phage at a multiplicity of infection of 10

Complete genome sequence of the virulent Klebsiella pneumoniae Phage Geezett infecting multidrug-resistant clinical strains

Geezett was isolated from hospital sewage in Hangzhou, China, and exhibits lytic activity against clinical isolates of the nosocomial pathogen Klebsiella pneumoniae. The bacteriophage is a myovirus and has a double-stranded DNA (dsDNA) genome 50,707 bp long, containing 79 open reading frames (ORFs)

Co‐evolutionary adaptations of Acinetobacter baumannii and a clinical carbapenemase‐encoding plasmid during carbapenem exposure

Abstract: OXA‐23 is the predominant carbapenemase in carbapenem‐resistant Acinetobacter baumannii. The co‐evolutionary dynamics of A. baumannii and OXA‐23‐encoding plasmids are poorly understood. Here, we transformed A. baumannii ATCC 17978 with pAZJ221, a blaOXA−23‐containing plasmid from clinical A. baumannii isolate A221, and subjected the transformant to experimental evolution in the presence of a sub‐inhibitory concentration of imipenem for nearly 400 generations. We used population sequencing to track genetic changes at six time points and evaluated phenotypic changes. Increased fitness of evolving populations, temporary duplication of blaOXA−23 in pAZJ221, interfering allele dynamics, and chromosomal locus‐level parallelism were observed. To characterize genotype‐to‐phenotype associations, we focused on six mutations in parallel targets predicted to affect small RNAs and a cyclic dimeric (3′ → 5′) GMP‐metabolizing protein. Six isogenic mutants with or without pAZJ221 were engineered to test for the effects of these mutations on fitness costs and plasmid kinetics, and the evolved plasmid containing two copies of blaOXA−23 was transferred to ancestral ATCC 17978. Five of the six mutations contributed to improved fitness in the presence of pAZJ221 under imipenem pressure, and all but one of them impaired plasmid conjugation ability. The duplication of blaOXA−23 increased host fitness under carbapenem pressure but imposed a burden on the host in antibiotic‐free media relative to the ancestral pAZJ221. Overall, our study provides a framework for the co‐evolution of A. baumannii and a clinical blaOXA−23‐containing plasmid in the presence of imipenem, involving early blaOXA−23 duplication followed by chromosomal adaptations that improved the fitness of plasmid‐carrying cells

Mango anthracnose disease: the current situation and direction for future research

Mango anthracnose disease (MAD) is a destructive disease of mangoes, with estimated yield losses of up to 100% in unmanaged plantations. Several strains that constitute Colletotrichum complexes are implicated in MAD worldwide. All mangoes grown for commercial purposes are susceptible, and a resistant cultivar for all strains is not presently available on the market. The infection can widely spread before being detected since the disease is invincible until after a protracted latent period. The detection of multiple strains of the pathogen in Mexico, Brazil, and China has prompted a significant increase in research on the disease. Synthetic pesticide application is the primary management technique used to manage the disease. However, newly observed declines in anthracnose susceptibility to many fungicides highlight the need for more environmentally friendly approaches. Recent progress in understanding the host range, molecular and phenotypic characterization, and susceptibility of the disease in several mango cultivars is discussed in this review. It provides updates on the mode of transmission, infection biology and contemporary management strategies. We suggest an integrated and ecologically sound approach to managing MAD

New Insights into the Role of MHC Diversity in Devil Facial Tumour Disease

Devil facial tumour disease (DFTD) is a fatal contagious cancer that has decimated Tasmanian devil populations. The tumour has spread without invoking immune responses, possibly due to low levels of Major Histocompatibility Complex (MHC) diversity in Tasmanian devils. Animals from a region in north-western Tasmania have lower infection rates than those in the east of the state. This area is a genetic transition zone between sub-populations, with individuals from north-western Tasmania displaying greater diversity than eastern devils at MHC genes, primarily through MHC class I gene copy number variation. Here we test the hypothesis that animals that remain healthy and tumour free show predictable differences at MHC loci compared to animals that develop the disease

The IPBES Conceptual Framework - connecting nature and people

The first public product of the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES) is its Conceptual Framework. This conceptual and analytical tool, presented here in detail, will underpin all IPBES functions and provide structure and comparability to the syntheses that IPBES will produce at different spatial scales, on different themes, and in different regions. Salient innovative aspects of the IPBES Conceptual Framework are its transparent and participatory construction process and its explicit consideration of diverse scientific disciplines, stakeholders, and knowledge systems, including indigenous and local knowledge. Because the focus on co-construction of integrative knowledge is shared by an increasing number of initiatives worldwide, this framework should be useful beyond IPBES, for the wider research and knowledge-policy communities working on the links between nature and people, such as natural, social and engineering scientists, policy-makers at different levels, and decision-makers in different sectors of society

The CCR4-NOT deadenylation complex functions in the Nonsense Mediated mRNA decay pathway

Quality control mechanisms have evolved to guard the cell against defects in gene expression. The nonsense mediated mRNA decay (NMD) pathway is one of the most well studied surveillance mechanisms. It detects and triggers degradation of aberrant mRNAs that contain pre-mature termination codons (PTCs), preventing the accumulation of truncated polypeptides that are potentially deleterious to the cell. PTC recognition in eukaryotes results in the assembly of a surveillance complex on the mRNA, which triggers the degradation of the PTC-containing mRNA. The surveillance complex consists of the Up-frameshift (UPF) proteins (1 to 3) and in metazoa, the Suppressor with morphological effects on genitalia (SMG) proteins (1, 5 to 9). UPF1 undergoes a phosphorylation/dephosphorylation cycle that is a key event driving NMD. Upon PTC recognition, UPF1 is phosphorylated by the SMG1 kinase, initiating mRNA decay through the recruitment of the 14-3-3 domain-containing proteins SMG5, SMG6 and SMG7. SMG6 was shown to possess endonuclease activity that cleaves the target mRNA in the vicinity of the PTC. On the other hand, SMG5 and SMG7 form a heterodimer and recruit general cellular decay enzymes. SMG5 was shown to recruit the decapping enzyme DCP2 and its co-factors through PNRC2. SMG7 was shown to decay mRNA efficiently through its Proline-rich C-terminus (PC) region, which is necessary and sufficient for this activity. However, which decay factors are recruited to the target mRNA has remained unknown. The major part of my doctoral work focused on elucidating the significance of the SMG5:SMG7 heterodimer formation in NMD and understanding how SMG7 elicits decay of a NMD-targeted mRNA. Here, I could show that SMG5:SMG7 heterodimer formation is necessary for functional NMD and that SMG5 and SMG7 use distinct mechanisms to degrade NMD-targeted mRNA. SMG5 promotes decapping independently of deadenylation while SMG7 promotes deadenylation-dependent decapping through a direct interaction with POP2, a catalytic subunit of the CCR4-NOT deadenylase complex. This interaction is specific, as SMG7 did not bind to CAF1, a paralog of POP2. I could further demonstrate that POP2 contributes to NMD target degradation in human cells and that the SMG7-POP2 interaction was critical for NMD in cells depleted of SMG6. This indicated that SMG6 and SMG7 act redundantly to degrade NMD targets. Taken together, my work demonstrated how NMD employs diverse and partially redundant decay mechanisms to ensure that aberrant mRNAs are efficiently degraded. The CCR4-NOT deadenylase complex is the major component involved in the first step of cellular mRNA degradation. This complex catalyzes the removal of the poly(A) tail from the 3’-end of the mRNA, hence causing translational repression and committing the mRNA to degradation. The core components of the CCR4-NOT complex consist minimally of two modules, i.e. the NOT module that includes NOT1, NOT2 and NOT3, and the catalytic module that involves two deadenlyases, CCR4 and POP2/CAF1 bound to NOT1. In human cells, additional components have been identified, namely, CAF40/CNOT9, CNOT10 and CNOT11. These components are conserved in Drosophila cells, however the role of these proteins and how they are integrated into the complex remained unknown. Thus, the next part of my studies addressed the molecular characterization of the CCR4-NOT complex in Drosophila cells. In this part of my work, I could show that NOT10 binds directly to NOT11 and forms a novel module of the CCR4-NOT complex. This module docks directly on the N-terminus of NOT1 that was hence named the NOT10/11 Binding Domain (NOT10/11 BD). This direct interaction to NOT1 was mediated by NOT11 and is conserved in human cells