The Complex Evolutionary History of Aminoacyl-tRNA Synthetases

Aminoacyl-tRNA synthetases (AARSs) are a superfamily of enzymes responsible for the faithful translation of the genetic code and have lately become a prominent target for synthetic biologists. Our large-scale analysis of \u3e2500 prokaryotic genomes reveals the complex evolutionary history of these enzymes and their paralogs, in which horizontal gene transfer played an important role. These results show that a widespread belief in the evolutionary stability of this superfamily is misconceived. Although AlaRS, GlyRS, LeuRS, IleRS, ValRS are the most stable members of the family, GluRS, LysRS and CysRS often have paralogs, whereas AsnRS, GlnRS, PylRS and SepRS are often absent from many genomes. In the course of this analysis, highly conserved protein motifs and domains within each of the AARS loci were identified and used to build a web-based computational tool for the genome-wide detection of AARS coding sequences. This is based on hidden Markov models (HMMs) and is available together with a cognate database that may be used for specific analyses. The bioinformatics tools that we have developed may also help to identify new antibiotic agents and targets using these essential enzymes. These tools also may help to identify organisms with alternative pathways that are involved in maintaining the fidelity of the genetic code

Motivation and job satisfaction among medical and nursing staff in a Cyprus public general hospital

<p>Abstract</p> <p>Background</p> <p>The objective of this study was to investigate how medical and nursing staff of the Nicosia General Hospital is affected by specific motivation factors, and the association between <it>job satisfaction </it>and <it>motivation</it>. Furthermore, to determine the motivational drive of socio-demographic and job related factors in terms of improving work performance.</p> <p>Methods</p> <p>A previously developed and validated instrument addressing four work-related motivators (<it>job attributes, remuneration, co-workers and achievements</it>) was used. Two categories of health care professionals, medical doctors and dentists (N = 67) and nurses (N = 219) participated and motivation and job satisfaction was compared across socio-demographic and occupational variables.</p> <p>Results</p> <p>The survey revealed that <it>achievements </it>was ranked first among the four main motivators, followed by <it>remuneration</it>, <it>co-workers </it>and <it>job attributes</it>. The factor <it>remuneration </it>revealed statistically significant differences according to gender, and hospital sector, with female doctors and nurses and accident and emergency (A+E) outpatient doctors reporting greater mean scores (p < 0.005). The medical staff showed statistically significantly lower job satisfaction compared to the nursing staff. Surgical sector nurses and those >55 years of age reported higher job satisfaction when compared to the other groups.</p> <p>Conclusions</p> <p>The results are in agreement with the literature which focuses attention to management approaches employing both monetary and non-monetary incentives to motivate health care professionals. Health care professionals tend to be motivated more by intrinsic factors, implying that this should be a target for effective employee motivation. Strategies based on the survey's results to enhance employee motivation are suggested.</p

HPV16-Genotyper: A Computational Tool for Risk-Assessment, Lineage Genotyping and Recombination Detection in HPV16 Sequences, Based on a Large-Scale Evolutionary Analysis

Previous analyses have identified certain but limited evidence of recombination among HPV16 genomes, in accordance with a general perception that DNA viruses do not frequently recombine. In this evolutionary/bioinformatics study we have analyzed more than 3600 publicly available complete and partial HPV16 genomes. By studying the phylogenetic incongruence, similarity plots and the distribution patterns of lineage-specific SNPs, we identify several potential recombination events between the two major HPV16 evolutionary clades. These two clades comprise the (widely considered) phenotypically more benign (lower risk) lineage A and the (widely considered) phenotypically more aggressive (higher risk) non-European lineages B, C and D. We observe a frequency of potential recombinant sequences ranging between 0.3 and 1.2% which is low, but nevertheless considerable. Our findings have clinical implications and highlight that HPV16 genotyping and risk assessment based only on certain genomic regions and not the entire genome may provide a false genotype and, therefore, its associated risk estimate. Finally, based on this analysis, we have developed a bioinformatics tool that automates the entire process of HPV16 lineage genotyping, recombination detection and further identifies, within the submitted sequences, SNPs that have been reported in the literature to increase the risk of cancer

A Comparative Analysis of the Core Proteomes within and among the Bacillus subtilis and Bacillus cereus Evolutionary Groups Reveals the Patterns of Lineage- and Species-Specific Adaptations.

By integrating phylogenomic and comparative analyses of 1104 high-quality genome sequences, we identify the core proteins and the lineage-specific fingerprint proteins of the various evolutionary clusters (clades/groups/species) of the Bacillus genus. As fingerprints, we denote those core proteins of a certain lineage that are present only in that particular lineage and absent in any other Bacillus lineage. Thus, these lineage-specific fingerprints are expected to be involved in particular adaptations of that lineage. Intriguingly, with a few notable exceptions, the majority of the Bacillus species demonstrate a rather low number of species-specific fingerprints, with the majority of them being of unknown function. Therefore, species-specific adaptations are mostly attributed to highly unstable (in evolutionary terms) accessory proteomes and possibly to changes at the gene regulation level. A series of comparative analyses consistently demonstrated that the progenitor of the Cereus Clade underwent an extensive genomic expansion of chromosomal protein-coding genes. In addition, the majority (76-82%) of the B. subtilis proteins that are essential or play a significant role in sporulation have close homologs in most species of both the Subtilis and the Cereus Clades. Finally, the identification of lineage-specific fingerprints by this study may allow for the future development of highly specific vaccines, therapeutic molecules, or rapid and low-cost molecular tests for species identification

Analysis of the Pseudomonas aeruginosa oprD gene from clinical and environmental isolates

Genomes are constantly evolving. Our report highlights the wide mutational diversity of clinical as well as environmental isolates, compared with the laboratory strain(s), through the systematic genetic analysis of a chromosomal porin gene (oprD) in relation to a specific antibiotic resistance. Mutational inactivation of the oprD gene is associated with carbapenem resistance in Pseudomonas aeruginosa. The sequence of the oprD gene of 55 Pseudomonas aeruginosa natural isolates obtained from across the world - from sources as diverse as patients and rhizospheres - was analysed. A microscale mosaic structure for this gene - resulting from multiple intra- and possibly interspecies recombinational events - is reported. An array of independent and seemingly fast-occurring defective oprD mutations were found, none of which had been described before. A burn wound isolate demonstrated unusually high overall sequence variability typical of mutator strains. We also present evidence for the existence of OprD homologues in other fluorescent pseudomonads.SCOPUS: ar.jFLWINinfo:eu-repo/semantics/publishe

Evolution and taxonomic distribution of nonribosomal peptide and polyketide synthases

The majority of nonribosomal peptide synthases and type I polyketide synthases are multimodular megasynthases of oligopeptide and polyketide secondary metabolites, respectively. Owing to their multimodular architecture, they synthesize their metabolites in assembly line logic. The ongoing genomic revolution together with the application of computational tools has provided the opportunity to mine the various genomes for these enzymes and identify those organisms that produce many oligopeptide and polyketide metabolites. In addition, scientists have started to comprehend the molecular mechanisms of megasynthase evolution, by duplication, recombination, point mutation and module skipping. This knowledge and computational analyses have been implemented towards predicting the specificity of these megasynthases and the structure of their end products. It is an exciting field, both for gaining deeper insight into their basic molecular mechanisms and exploiting them biotechnologically

Investigation of Serotype Prevalence of <em>Escherichia coli</em> Strains Isolated from Layer Poultry in Greece and Interactions with Other Infectious Agents

Colibacillosis is the most common bacterial disease in poultry and it is caused by avian pathogenic Escherichia coli (APEC), which is assigned to various O-serogroups. Previous studies have shown that APEC strains are more often related to certain O-serogroups such asO78, O2 and O1. E. coli has been reported to act either as a primary or secondary agent in complicating other infections. The aim of this study was to investigate the occurrence of and characterize the O-serogroups of E. coli strains isolated from commercial layer and layer breeder flocks showing macroscopic lesions of colibacillosis and increased or normal mortality in Greece. Furthermore, we attempted to assess the interaction between infectious agents such as Mycoplasma gallisepticum (MG), Mycoplasma synoviae (MS), infectious bronchitis (IBV) and infectious laryngotracheitis (ILT) with E. coli infections in layer flocks with increased mortality. Our study revealed that in addition to the common serogroups (O78, O2), many other, and less common serogroups were identified, including O111. The O78, O111 and O2 serogroups were frequently detected in flocks with lesions of colibacillosis and increased mortality whereas O2, O88 and O8 were reported more commonly in birds with colibacillosis lesions but normal mortality rates. These data provide important information for colibacillosis monitoring and define preventative measures, especially by using effective vaccination programs because E. coli vaccines are reported to mainly offer homologous protection. Finally, concerning the association of the four tested infectious agents with E. coli mortality, our study did not reveal a statistically significant effect of the above infectious agents tested with E. coli infection mortality

Impact of Mt. Olympus Honeys on Virulence Factors Implicated in Pathogenesis Exerted by <i>Pseudomonas aeruginosa</i>

The aim of this study was to examine the impact of twenty honey samples, harvested in Mt. Olympus (Greece), on the virulence factors implicated in P. aeruginosa pathogenesis. Six key virulence factors (protease and elastase activity, pyocyanin and pyoverdine concentration, biofilm formation, and swimming motility) were selected in order to assess the effect of the tested honeys compared with Manuka honey. All tested honeys demonstrated a significant inhibition of protease and elastase activity compared with the control. Six and thirteen honeys exerted superior protease (no inhibition zone) and elastase (values lower than 55%) activity, respectively, compared with Manuka honey. Seventeen tested honeys exhibited reduced pyoverdine production compared with the control; all tested honeys, except for one, showed an inhibitory effect on pyocyanin production compared with the control. Regarding swimming motility, nine tested honeys demonstrated significantly higher inhibition compared with Manuka honey. Honey concentrations (6% v/v and 8% v/v) had the most profound impact, as they reduced biofilm formation to less than 20% compared with the control. Overall, our data demonstrate a significant inhibition of the virulence factors in the tested Mt. Olympus honeys, highlighting the strong antimicrobial activity against P. aeruginosa, an antibiotic-resistant pathogen of growing concern, which is implicated in severe nosocomial infections globally

Synergistic Antimicrobial Activity of Supplemented Medical-Grade Honey against Pseudomonas aeruginosa Biofilm Formation and Eradication

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