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![]() ![]() Left: the enzyme-centric approach pioneered by Marahiel and co-workers. Both of these approaches relied on BLAST searches for colocalized B and C enzymes, followed by a manual search for short open reading frames (ORFs) adjacent to the enzymes ( Figure 2).Īpproaches to lasso peptide genome mining. The first isolation of a new lasso peptide from genome mining approaches followed shortly from the group of Mohamed Marahiel, who published the gene cluster and structure of the antimicrobial lasso peptide capistruin in 2008. The group of Konstantin Severinov, who carried out seminal work in characterizing the antimicrobial function of MccJ25, suggested that gene clusters resembling that of MccJ25 were present in the genomes of several different bacteria, primarily clustered in proteobacteria and actinobacteria. ![]() The first indications of genome mining for lasso peptides appear in the literature in 2007. The colocalization of these genes within a cluster on prokaryotic chromosomes or plasmids is the foundation for lasso peptide genome mining. Finally, the lasso is formed via the action of an asparagine synthetase homolog, the C protein, that presumably both activates the Glu or Asp residue with ATP and templates the lasso structure ( Figure 1). This precursor is processed by a peptidase, the B protein, with a cysteine catalytic triad into leader and core peptides. Like other RiPPs (ribosomally synthesized and post-translationally modified peptides), lasso peptides are born from a precursor peptide, or A protein. This early work laid out the blueprints for lasso peptide biosynthesis. This relatively early example of gene cluster sequencing was facilitated by the fact that the gene cluster for MccJ25 is found on a plasmid. The first lasso peptide gene cluster sequenced was for MccJ25, and appeared in 1999. Like genome mining for other microbial natural products, lasso peptide genome mining depends on the existence of gene clusters encoding the biosynthesis of lasso peptides. We last reviewed this topic in 2014, so this review will focus primarily on new lasso peptide genome mining tools and experimental validation from 2015 onward.Įarly efforts at lasso peptide genome mining ![]() Here instead we focus on genomics-guided approaches for lasso peptide discovery. Lasso peptides that have been discovered by activity-guided approaches have been reviewed elsewhere extensively. Another compelling example of an antimicrobial lasso peptide discovered by activity-guided approaches is lariatin, which has activity against mycobacteria including M. Shortly thereafter, microcin J25 (MccJ25), the most well-studied lasso peptide, was discovered in a search for new antimicrobial compounds in infant fecal bacteria. The first report of a lasso peptide was in 1991 with the discovery of anantin via an activity-based approach. The second macrocycle is generated via a mechanical bond established by threading the C-terminal tail of the peptide through the isopeptide-bonded macrocycle ( Figure 1). The first is formed via a covalent isopeptide bond between the N-terminus of the peptide and either a glutamate or aspartate sidechain. The lasso structure can be thought of as two macrocycles. This slipknotted structure is close in size to many chemically-synthesized rotaxanes and often endows these peptides with proteolytic resistance and thermal resistance. Lasso peptides are a class of ribosomally-derived natural products categorized by their 1-rotaxane structure. ![]() ![]() ![]() ![]() Experimental results, undertaken on C-band NASA/JPL AIRSAR airborne data show that the coherent information exploited by the proposed detector allows distinguishing ships from the background sea better than detectors based on incoherent information, i.e., the total backscattered power and the cross-polarised backscattering intensity. In, a ship detection algorithm that combines the polarisation cross-entropy feature derived from the eigen-decomposition of the polSAR coherency matrix and a CFAR method was proposed. The results demonstrate the importance of statistical modelling of sea clutter in developing CFAR methods and that the proposed detector outperforms the conventional two-parameter CFAR especially when a low target-to-clutter ratio (TCR) applies. In, a constant false alarm rate (CFAR) method was proposed to detect ships-according to the polarimetric whitening filter detector-in simulated and actual C-band NASA (National Aeronautics and Space Administration)/JPL (Jet Propulsion Laboratory) AIRSAR (Airborne SAR) airborne polSAR imagery. Hence, for the purpose of this study, a brief overview of polSAR methods to monitor marine vessels is due. This effect, together with the availability of more advanced Earth observation satellite missions equipped with polarimetric SAR (polSAR) imaging sensors, triggered the development of scattering-based marine vessel observation approaches. However, the difference in sea–ship backscattering is severely affected by SAR imaging parameters, e.g., incident wavelength and incidence angle, meteo-marine conditions and by the properties of the marine vessel, e.g., the material it consists of, the heading, and the geometric structure. Generally speaking, SAR observation of ships relies on the fact that the metallic structures of marine vessels are characterised by a backscattered signal stronger than the one from the surrounding sea. ![]() When dealing with the latter, several methods, which are either based on single- or multi-polarisation measurements, have been proposed. SAR monitoring of marine vessels is an important application that triggered the development of many approaches that can be roughly classified in image processing- and scattering-based methods. The synthetic aperture radar (SAR) is a microwave remote sensing tool that, due to its all-day and almost all-weather imaging capabilities together with its fine spatial resolution and wide area coverage, is a key instrument for open ocean and coastal area surveillance, including the observation of metallic targets at sea. Experimental results show that: (1) the polarised scattering component is more sensitive to the incidence angle with respect to the unpolarised one (2) the co-polarised channel under horizontal polarisation dominated the polarimetric backscattering from the fishing trawler at lower angles of incidence, while both co-polarised channels contribute to the polarimetric backscattering at higher incidence angles (3) the HV polarisation provides the largest target-to-clutter ratio at lower incidence angles, while the HH polarisation should be preferred at higher angles of incidence. Experimental results highlight the key role played by the incidence angle on both coherent, i.e., co-polarisation signature and pedestal height, and incoherent, i.e., multi-polarisation and total backscattering power, polarimetric scattering descriptors. This unique opportunity is provided by a premium L-band UAVSAR airborne dataset that consists of five full-polarimetric synthetic aperture radar scenes collected in the Gulf of Mexico. Hence, in this study, for the first time, the polarimetric scattering of the same ship, i.e., a small fishing trawler, which is imaged multiple times under the same sea state conditions but in a wide range of incidence angles, is analysed. ![]() Nonetheless, how changes in the incidence angle affect the scattering of ships still needs to be further investigated since only a sparse analysis, i.e., on different kinds of ships of different sizes observed at multiple incidence angles, has been performed. Nonetheless, the capability of polarimetric synthetic aperture radar to observe marine vessels is significantly affected by several imaging and environmental parameters, including the incidence angle. When advanced synthetic aperture radar imaging systems are considered, the full scattering information is available that was demonstrated to be beneficial in developing improved ship detection and classification algorithms. The synthetic aperture radar is shown to be a key sensor to provide effective and continuous observation of ships due to its unique imaging capabilities. The monitoring of ships is of paramount importance for ocean and coastal area surveillance. ![]() |
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