adhesiomeR: a tool for Escherichia coli adhesin classification and analysis.

Adhesins are crucial factors in the virulence of bacterial pathogens such as Escherichia coli. However, to date no resources have been dedicated to the detailed analysis of E. coli adhesins.

Characterization of clumpy adhesion of to human cells and associated factors influencing antibiotic sensitivity.

Unlabelled: intestinal infection pathotypes are characterized by distinct adhesion patterns, including the recently described clumpy adhesion phenotype. Here, we identify and characterize the genetic factors contributing to the clumpy adhesion of strain 4972. In this strain, the transcriptome and proteome of adhered bacteria were found to be distinct from planktonic bacteria in the supernatant.

Characterization of signal and transit peptides based on motif composition and taxon-specific patterns.

Targeting peptides or presequences are N-terminal extensions of proteins that encode information about their cellular localization. They include signal peptides (SP), which target proteins to the endoplasmic reticulum, and transit peptides (TP) directing proteins to the organelles of endosymbiotic origin: chloroplasts and mitochondria. TPs were hypothesized to have evolved from antimicrobial peptides (AMPs), which are responsible for the host defence against microorganisms, including bacteria, fungi and viruses.

Prediction of protein subplastid localization and origin with PlastoGram.

Due to their complex history, plastids possess proteins encoded in the nuclear and plastid genome. Moreover, these proteins localize to various subplastid compartments. Since protein localization is associated with its function, prediction of subplastid localization is one of the most important steps in plastid protein annotation, providing insight into their potential function.

Genomic characterization of enterohaemolysin-encoding haemolytic of animal and human origin.

Enterohaemolysin (Ehx) and alpha-haemolysin are virulence-associated factors (VAFs) causing the haemolytic phenotype in . It has been shown that chromosomally and plasmid-encoded alpha-haemolysin are characteristic of specific pathotypes, virulence-associated factors and hosts. However, the prevalence of alpha- and enterohaemolysin does not overlap in the majority of pathotypes.

The dynamic landscape of peptide activity prediction.

Peptides are known to possess a plethora of beneficial properties and activities: antimicrobial, anticancer, anti-inflammatory or the ability to cross the blood-brain barrier are only a few examples of their functional diversity. For this reason, bioinformaticians are constantly developing and upgrading models to predict their activity , generating a steadily increasing number of available tools. Although these efforts have provided fruitful outcomes in the field, the vast and diverse amount of resources for peptide prediction can turn a simple prediction into an overwhelming searching process to find the optimal tool.

Benchmarks in antimicrobial peptide prediction are biased due to the selection of negative data.

Antimicrobial peptides (AMPs) are a heterogeneous group of short polypeptides that target not only microorganisms but also viruses and cancer cells. Due to their lower selection for resistance compared with traditional antibiotics, AMPs have been attracting the ever-growing attention from researchers, including bioinformaticians. Machine learning represents the most cost-effective method for novel AMP discovery and consequently many computational tools for AMP prediction have been recently developed.

Genome placement of alpha-haemolysin cluster is associated with alpha-haemolysin sequence variation, adhesin and iron acquisition factor profile of .

Since the discovery of haemolysis many studies focused on a deeper understanding of this phenotype in and its association with other virulence genes, diseases and pathogenic attributes/functions in the host. Our virulence-associated factor profiling and genome-wide association analysis of genomes of haemolytic and nonhaemolytic unveiled high prevalence of adhesins, iron acquisition genes and toxins in haemolytic bacteria. In the case of fimbriae with high prevalence, we analysed sequence variation of FimH, EcpD and CsgA, and showed that different adhesin variants were present in the analysed groups, indicating altered adhesive capabilities of haemolytic and nonhaemolytic .

Whatever makes them stick - Adhesins of avian pathogenic Escherichia coli.

Avian pathogenic Escherichia coli (APEC) is associated with extraintestinal infections and the development of colibacillosis, causing high mortality in farm birds and extensive losses in the poultry industry worldwide. The virulence of APEC is a complex phenomenon associated with numerous mechanisms involving a variety of extracellular and intracellular structures to overcome host barriers. Initial bacterial attachment or adhesion to host cells is vital to bacterial pathogenesis and is determined by various adhesins.

The Photosynthetic Adventure of Paulinella Spp.

Paulinella photosynthetic species are unicellular, silica shell-forming amoebas classified into the supergroup Rhizaria. They crawl at the bottom of freshwater and brackish environments with the help of filose pseudopodia. These protists have drawn the attention of the scientific community because of two photosynthetic bodies, called chromatophores, that fill up their cells permitting fully photoautotrophic existence.

CancerGram: An Effective Classifier for Differentiating Anticancer from Antimicrobial Peptides.

Antimicrobial peptides (AMPs) constitute a diverse group of bioactive molecules that provide multicellular organisms with protection against microorganisms, and microorganisms with weaponry for competition. Some AMPs can target cancer cells; thus, they are called anticancer peptides (ACPs). Due to their small size, positive charge, hydrophobicity and amphipathicity, AMPs and ACPs interact with negatively charged components of biological membranes.

Proteomic Screening for Prediction and Design of Antimicrobial Peptides with AmpGram.

Antimicrobial peptides (AMPs) are molecules widespread in all branches of the tree of life that participate in host defense and/or microbial competition. Due to their positive charge, hydrophobicity and amphipathicity, they preferentially disrupt negatively charged bacterial membranes. AMPs are considered an important alternative to traditional antibiotics, especially at the time when multidrug-resistant bacteria being on the rise.