Bacteriophage ϕMAM1, a viunalikevirus, is a broad-host-range, high-efficiency generalized transducer that infects environmental and clinical isolates of the enterobacterial genera Serratia and Kluyvera.

Members of the enterobacterial genus Serratia are ecologically widespread, and some strains are opportunistic human pathogens. Bacteriophage ϕMAM1 was isolated on Serratia plymuthica A153, a biocontrol rhizosphere strain that produces the potently bioactive antifungal and anticancer haterumalide oocydin A. The ϕMAM1 phage is a generalized transducing phage that infects multiple environmental and clinical isolates of Serratia spp. and a rhizosphere strain of Kluyvera cryocrescens. Electron microscopy allowed classification of ϕMAM1 in the family Myoviridae. Bacteriophage ϕMAM1 is virulent, uses capsular polysaccharides as a receptor, and can transduce chromosomal markers at frequencies of up to 7 × 10(-6) transductants per PFU. We also demonstrated transduction of the complete 77-kb oocydin A gene cluster and heterogeneric transduction of a plasmid carrying a type III toxin-antitoxin system. These results support the notion of the potential ecological importance of transducing phages in the acquisition of genes by horizontal gene transfer. Phylogenetic analyses grouped ϕMAM1 within the ViI-like bacteriophages, and genomic analyses revealed that the major differences between ϕMAM1 and other ViI-like phages arise in a region encoding the host recognition determinants. Our results predict that the wider genus of ViI-like phages could be efficient transducing phages, and this possibility has obvious implications for the ecology of horizontal gene transfer, bacterial functional genomics, and synthetic biology.This research was supported by the EU Marie-Curie Intra-European Fellowship for Career Development (FP7-PEOPLE-2011-IEF) grant number 298003. The Salmond lab is supported by funding through the Biotechnology and Biological Sciences Research Council (BBSRC, UK). We thank Hazel Aucken and Kornelia Smalla for kindly supplying the environmental and clinical isolates. We would also like to thank Jeremy N. Skepper (Department of Anatomy, University of Cambridge) for assistance in transmission electron microscopy and Alison Rawlinson for technical support.This is the accepted manuscript. The final version is available from the American Society for Microbiology at http://aem.asm.org/content/80/20/6446.lon

Toward Robust Sensing for Autonomous Vehicles: An Adversarial Perspective

Autonomous Vehicles rely on accurate and robust sensor observations for safety critical decision-making in a variety of conditions. Fundamental building blocks of such systems are sensors and classifiers that process ultrasound, RADAR, GPS, LiDAR and camera signals~\cite{Khan2018}. It is of primary importance that the resulting decisions are robust to perturbations, which can take the form of different types of nuisances and data transformations, and can even be adversarial perturbations (APs). Adversarial perturbations are purposefully crafted alterations of the environment or of the sensory measurements, with the objective of attacking and defeating the autonomous systems. A careful evaluation of the vulnerabilities of their sensing system(s) is necessary in order to build and deploy safer systems in the fast-evolving domain of AVs. To this end, we survey the emerging field of sensing in adversarial settings: after reviewing adversarial attacks on sensing modalities for autonomous systems, we discuss countermeasures and present future research directions

Biosynthesis of the antifungal haterumalide, oocydin A, in Serratia, and its regulation by quorum sensing, RpoS and Hfq.

Polyketides represent an important class of bioactive natural products with a broad range of biological activities. We identified recently a large trans-acyltransferase (AT) polyketide synthase gene cluster responsible for the biosynthesis of the antifungal, anti-oomycete and antitumor haterumalide, oocydin A (ooc). Using genome sequencing and comparative genomics, we show that the ooc gene cluster is widespread within biocontrol and phytopathogenic strains of the enterobacteria, Serratia and Dickeya. The analysis of in frame deletion mutants confirmed the role of a hydroxymethylglutaryl-coenzyme A synthase cassette, three flavin-dependent tailoring enzymes, a free-standing acyl carrier protein and two hypothetical proteins in oocydin A biosynthesis. The requirement of the three trans-acting AT domains for the biosynthesis of the macrolide was also demonstrated. Expression of the ooc gene cluster was shown to be positively regulated by an N-acyl-L-homoserine lactone-based quorum sensing system, but operating in a strain-dependent manner. At a post-transcriptional level, the RNA chaperone, Hfq, plays a key role in oocydin A biosynthesis. The Hfq-dependent regulation is partially mediated by the stationary phase sigma factor, RpoS, which was also shown to positively regulate the synthesis of the macrolide. Our results reveal differential regulation of the divergently transcribed ooc transcriptional units, highlighting the complexity of oocydin A production.This research was supported by the EU Marie-Curie Intra-European Fellowship for Career Development (FP7-PEOPLE-2011-IEF) Grant No. 298003. The Salmond laboratory is supported by funding through the Biotechnology and Biological Sciences Research Council, BBSRC (UK). Work with plant pathogens was carried out under DEFRA Licence No. 50864/197900/1.This is the final version of the article. It first appeared from Wiley via http://dx.doi.org/10.1111/1462-2920.1283

The broad-spectrum antibiotic, zeamine, kills the nematode worm Caenorhabditis elegans.

Soil bacteria can be prolific producers of secondary metabolites and other biologically active compounds of economic and clinical importance. These natural products are often synthesized by large multi-enzyme complexes such as polyketide synthases (PKSs) or non-ribosomal peptide synthases (NRPSs). The plant-associated Gram-negative bacterium, Serratia plymuthica A153, produces several secondary metabolites and is capable of killing the nematode worm Caenorhabditis elegans; a commonly used model for the study of bacterial virulence. In this study, we show that disruption of the hybrid PKS/NRPS zeamine (zmn) gene cluster results in the attenuation of "fast-killing" of C. elegans, indicating that zeamine has nematicidal activity. C. elegans also exhibits age-dependent susceptibility to zeamine, with younger worms being most sensitive to the bioactive molecule. The zmn gene cluster is widely distributed within Serratia and phytopathogenic Dickeya species and investigation of strains harboring the zmn gene cluster showed that several of them are highly virulent in C. elegans. Zeamine was described previously as a phytotoxin and broad-spectrum antibacterial compound. In addition to its nematicidal properties, we show here that zeamine can also kill Saccharomyces cerevisiae and Schizosaccharomyces pombe. The expression of the zmn gene cluster and regulation of zeamine production were also investigated. Transcription of the cluster was growth phase-dependent, and was modulated by the post-transcriptional RNA chaperone, Hfq. The results of this study show that zeamine is a highly toxic molecule with little, or no, apparent host specificity in very diverse biological systems. In its current form, zeamine(s) may be useful as a lead compound suitable for chemical modification and structure-activity assays. However, because of widespread non-selective toxicity in multiple bioassays, unmodified zeamine(s) is unlikely to be suitable as a therapeutic antibiotic.MAMV was supported by the EU Marie-Curie Intra-European Fellowship for Career Development (FP7-PEOPLE-2011-IEF), grant number 298003. The Salmond laboratory is supported by funding through the Biotechnology and Biological Sciences Research Council (BBSRC; UK). Work with plant pathogens was carried out under DEFRA licence No. 50864/197900/1.This is the final version of the article. It first appeared at http://dx.doi.org/10.3389/fmicb.2015.0013

Multi-host lifestyle in plant-beneficial bacteria: an evolutionary advantage for survival and dispersal?

Plants harbour a wide diversity of microorganisms that efficiently colonize different internal and external plant organs and compartments, including the phyllosphere (above-ground plant surface), spermosphere (seeds and area surrounding seeds), endosphere (internal tissues) and rhizosphere (roots and soil in the vicinity of plant roots), establishing complex and dynamic interactions with the host plants (Trivedi et al., 2020). The plant microbiome plays major roles in the nutrition, growth and resistance against biotic and abiotic threats (Trivedi et al., 2020; Bakker and Berendsen, 2022; Yuan et al., 2022) and there is complex communication between microorganisms and their plant hosts (Berlanga- Clavero et al., 2020; Rico-Jiménez et al., 2022). Indeed, the secretion of a great variety of plant compounds directs the assembly of plant-associated microbial communities and it has been proposed that plants produce a range of chemical signals to selectively recruit specific microorganisms in order to assemble protective microbiomes that enable them to cope with the imposed biotic and abiotic stresses (Rizaludin et al., 2021; Rolli et al., 2021; Trivedi et al., 2022). As a consequence of this selective pressure exerted by the plants, the microbial composition of the rhizosphere and the non-rooted bulk soil differ – with the rhizosphere having a larger microbial abundance but lower diversity (Berlanga- Clavero et al., 2020; Sokol et al., 2022).Spanish Ministry for Science and Innovation/Agencia Estatal de Investigacion PID2019-103972GA-I00 RYC2019-026481-

Obtaining and Structural Characterization of M-type Hexaferrites Doped with Two Cations in the Fe3+ Sites

A study of the microstructural and structural properties of M-type barium hexaferrites (BaM) samples doped with two dopants in the Fe3+ sites: (Co3+, Al3+), (Co2+, Ti4+) and (Co2+, Sn4+) is reported. The samples were obtained using the conventional ceramic method. The structure was investigated by using of X-ray diffraction (XRD) to determine the dopant distribution in the Fe3+ sites

Exploiting vulnerabilities of deep neural networks for privacy protection

Adversarial perturbations can be added to images to protect their content from unwanted inferences. These perturbations may, however, be ineffective against classifiers that were not seen during the generation of the perturbation, or against defenses based on re-quantization, median filtering or JPEG compression. To address these limitations, we present an adversarial attack that is specifically designed to protect visual content against unseen classifiers and known defenses. We craft perturbations using an iterative process that is based on the Fast Gradient Signed Method and that randomly selects a classifier and a defense, in each iteration. This randomization prevents an undesirable overfitting to a specific classifier or defense. We validate the proposed attack in both targeted and untargeted settings on the private classes of the Places365-Standard dataset. Using ResNet18, ResNet50, AlexNet and DenseNet161 as classifiers, the performance of the proposed attack exceeds that of eleven state-of-the-art attacks

A note on the SG(m) test

López et al. (Reg Sci Urban Econ 40(2–3):106–115, 2010) introduce a nonparametric test of spatial dependence, called SG(m). The test is claimed to be consistent and asymptotically Chi-square distributed. Elsinger (Reg Sci Urban Econ 43(5):838–840, 2013) raises doubts about the two properties. Using a particular counterexample, he shows that the asymptotic distribution of the SG(m) test may be far from the Chi-square family; the property of consistency is also questioned. In this note, the authors want to clarify the properties of the SG(m) test. We argue that the cause of the conflict is in the specification of the symbolization map. The discrepancies can be solved by adjusting some of the definitions made in the original paper. Moreover, we introduce a permutational bootstrapped version of the SG(m) test, which is powerful and robust to the underlying statistical assumptions. This bootstrapped version may be very useful in an applied context

Biosynthesis of the acetyl-CoA carboxylase-inhibiting antibiotic, andrimid in Serratia is regulated by Hfq and the LysR-type transcriptional regulator, AdmX.

Infections due to multidrug-resistant bacteria represent a major global health challenge. To combat this problem, new antibiotics are urgently needed and some plant-associated bacteria are a promising source. The rhizobacterium Serratia plymuthica A153 produces several bioactive secondary metabolites, including the anti-oomycete and antifungal haterumalide, oocydin A and the broad spectrum polyamine antibiotic, zeamine. In this study, we show that A153 produces a second broad spectrum antibiotic, andrimid. Using genome sequencing, comparative genomics and mutagenesis, we defined new genes involved in andrimid (adm) biosynthesis. Both the expression of the adm gene cluster and regulation of andrimid synthesis were investigated. The biosynthetic cluster is operonic and its expression is modulated by various environmental cues, including temperature and carbon source. Analysis of the genome context of the adm operon revealed a gene encoding a predicted LysR-type regulator, AdmX, apparently unique to Serratia strains. Mutagenesis and gene expression assays demonstrated that AdmX is a transcriptional activator of the adm gene cluster. At the post-transcriptional level, the expression of the adm cluster is positively regulated by the RNA chaperone, Hfq, in an RpoS-independent manner. Our results highlight the complexity of andrimid biosynthesis - an antibiotic with potential clinical and agricultural utility.We thank Kornelia Smalla and Ian Toth for the generous donation of bacterial strains. Work in the Salmond laboratory is supported by funding through the Biotechnology and Biological Sciences Research Council (UK). M.A.M. was supported by the EU Marie-Curie Intra-European Fellowship for Career Development (FP7-PEOPLE-2011-IEF) Grant No. 298003 and the Spanish Ministry of Economy and Competitiveness Postdoctoral Research Program, Juan de la Cierva (BVA-2009-0200). The Krell laboratory is supported by FEDER funds and Fondo Social Europeo through grants from the Junta de Andalucía (grant CVI-7335) and the Spanish Ministry for Economy 1and Competitiveness (grants BIO2013-42297 and RTC-2014-1777-3)