Search Results (4)

Archaeal cell factories are becoming of great interest given their ability to produce a broad range of value-added compounds. Moreover, the Archaea domain often includes extremophilic microorganisms, facilitating their cultivation at the industrial level under nonsterile conditions. Halophilic archaea are studied for their ability to grow in environments with high NaCl concentrations. In this study, nine strains of Halobacterium salinarum were isolated from three different types of salted food, sausage casings, salted codfish, and bacon, and their genomes were sequenced along with the genome of the collection strain CECT 395. A comparative genomic analysis was performed on these newly sequenced genomes and the publicly available ones for a total of 19 H. salinarum strains. We elucidated the presence of unique gene clusters of the species in relation to the different ecological niches of isolation (salted foods, animal hides, and solar saltern sediments). Moreover, genome mining at the single-strain level highlighted the metabolic potential of H. salinarum UC4242, which revealed the presence of different protechnological genes (vitamins and myo-inositol biosynthetic pathways, aroma- and texture-related features, and antimicrobial compounds). Despite the presence of genes of potential concern (e.g., those involved in biogenic amine production), all the food isolates presented archaeocin-related genes (halocin-C8 and sactipeptides). Full article

The human gut contains an expanse of largely unstudied bacteriophages. Among the most common are crAss-like phages, which were predicted to infect Bacteriodetes hosts. CrAssphage, the first crAss-like phage to be discovered, contains a protein encoding a Bacteroides-associated carbohydrate-binding often N-terminal (BACON) domain tandem repeat. Because protein domain tandem repeats are often hotspots of evolution, BACON domains may provide insight into the evolution of crAss-like phages. Here, we studied the biodiversity and evolution of BACON domains in bacteriophages by analysing over 2 million viral contigs. We found a high biodiversity of BACON in seven gut phage lineages, including five known crAss-like phage lineages and two novel gut phage lineages that are distantly related to crAss-like phages. In three BACON-containing phage lineages, we found that BACON domain tandem repeats were associated with phage tail proteins, suggestive of a possible role of these repeats in host binding. In contrast, individual BACON domains that did not occur in tandem were not found in the proximity of tail proteins. In two lineages, tail-associated BACON domain tandem repeats evolved largely through horizontal transfer of separate domains. In the third lineage that includes the prototypical crAssphage, the tandem repeats arose from several sequential domain duplications, resulting in a characteristic tandem array that is distinct from bacterial BACON domains. We conclude that phage tail-associated BACON domain tandem repeats have evolved in at least two independent cases in gut bacteriophages, including in the widespread gut phage crAssphage. Full article

Hyperspectral remote sensing imagery contains much more information in the spectral domain than does multispectral imagery. The consecutive and abundant spectral signals provide a great potential for classification and anomaly detection. In this study, two real hyperspectral data sets were used for anomaly detection. One data set was an Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) data covering the post-attack World Trade Center (WTC) and anomalies are fire spots. The other data set called SpecTIR contained fabric panels as anomalies compared to their background. Existing anomaly detection algorithms including the Reed–Xiaoli detector (RXD), the blocked adaptive computation efficient outlier nominator (BACON), the random selection based anomaly detector (RSAD), the weighted-RXD (W-RXD), and the probabilistic anomaly detector (PAD) are reviewed here. The RXD generally sets strict assumptions to the background, which cannot be met in many scenarios, while BACON, RSAD, and W-RXD employ strategies to optimize the estimation of background information. The PAD firstly estimates both background information and anomaly information and then uses the information to conduct anomaly detection. Here, the BACON, RSAD, W-RXD, and PAD outperformed the RXD in terms of detection accuracy, and W-RXD and PAD required less time than BACON and RSAD. Full article

A few literary scholars have long claimed that Shakespeare did not write some of his best plays (history plays and tragedies) and proposed at one time or another various suspect authorship candidates. Most modern-day scholars of Shakespeare have rejected this claim, arguing that strong evidence that Shakespeare wrote the plays and poems being his name appears on them as the author. This has caused and led to an ongoing scholarly academic debate for quite some long time. Stylometry is a fast-growing field often used to attribute authorship to anonymous or disputed texts. Stylometric attempts to resolve this literary puzzle have raised interesting questions over the past few years. The following paper contributes to “the Shakespeare authorship question” by using a mathematically-based methodology to examine the hypothesis that Shakespeare wrote all the disputed plays traditionally attributed to him. More specifically, the mathematically based methodology used here is based on Mean Proximity, as a linear hierarchical clustering method, and on Principal Components Analysis, as a non-hierarchical linear clustering method. It is also based, for the first time in the domain, on Self-Organizing Map U-Matrix and Voronoi Map, as non-linear clustering methods to cover the possibility that our data contains significant non-linearities. Vector Space Model (VSM) is used to convert texts into vectors in a high dimensional space. The aim of which is to compare the degrees of similarity within and between limited samples of text (the disputed plays). The various works and plays assumed to have been written by Shakespeare and possible authors notably, Sir Francis Bacon, Christopher Marlowe, John Fletcher, and Thomas Kyd, where “similarity” is defined in terms of correlation/distance coefficient measure based on the frequency of usage profiles of function words, word bi-grams, and character triple-grams. The claim that Shakespeare authored all the disputed plays traditionally attributed to him is falsified in favor of the alternative authors according to the stylistic criteria and analytic methodology used. The result of this validated analysis is empirically-based, objective, and involves replicable evidence which can be used in conjunction with existing arguments to resolve the question of whether or not Shakespeare of Stratford-upon-Avon wrote all the disputed plays traditionally attributed to him. Full article