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

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 most cost-effective method novel AMP discovery consequently many computational tools prediction recently developed. In this article, we...

Abstract Protein aggregation is behind the genesis of incurable diseases and imposes constraints on drug discovery industrial production formulation proteins. Over years, we have been advancing Aggresscan3D (A3D) method, aiming to deepen our comprehension protein assist engineering solubility. Since its inception, A3D has become one most popular structure-based predictors because performance, modular functionalities, RESTful service for extensive screenings, intuitive user interface....

NanoString nCounter is a medium-throughput technology used in mRNA and miRNA differential expression studies. It offers several advantages, including the absence of an amplification step ability to analyze low-grade samples. Despite its considerable strengths, popularity platform experimental research stabilized 2022 2023, this trend may continue upcoming years. Such stagnation could potentially be attributed standardized analytical pipeline or indication optimal processing methods for data...

ABSTRACT Bacterial biofilm formation is a widespread phenomenon and complex process requiring set of genes facilitating the initial adhesion, maturation, production extracellular polymeric matrix subsequent dispersal bacteria. Most studies on Escherichia coli have investigated nonpathogenic E. K-12 strains. Due to extensive focus laboratory strains in most studies, there poor information regarding by pathogenic isolates. In this study, we genotypically phenotypically characterized 187 human...

Amyloids are proteins associated with several clinical disorders, including Alzheimer's, and Creutzfeldt-Jakob's. Despite their diversity, all amyloid can undergo aggregation initiated by short segments called hot spots. To find the patterns defining spots, we trained predictors of amyloidogenicity, using n-grams random forest classifiers. Since amyloidogenicity may not depend on exact sequence amino acids but more general properties, tested 524,284 reduced acid alphabets different lengths...

The ratio between living and dead cells is an important parameter in microalgae culture environmental monitoring. Fast, robust automated analytical methods for monitoring growth biotechnological pharmaceutical applications optimizing production strains are needed. We developed a pipeline the automatic binary classification of microalgae. compared multispectral fluorescence microscopy flow cytometry as readout platforms. Images Chlorella vulgaris suspension cultures were captured features...

Accurate post-mortem interval (PMI) estimation is essential in forensic investigations. Although various methods for PMI determination have been developed, only an approximate still achievable, and accurate indication challenging. Therefore, this study, we employed gas chromatography-mass spectrometry (GC-MS)-based metabolomics to assess changes porcine blood samples collected with without the addition of anticoagulant (EDTA). Our study aimed identify metabolites dependent on EDTA time...

Hydrogen–deuterium exchange monitored by mass spectrometry (HDX–MS) is a well-established and powerful technique used to study protein dynamics stability capturing local global unfolding events in structures. However, this technique, obtaining region-specific information requires proteolytic digestion that breaks the into peptide fragments, causing HDX data reflect averages over these fragments rather than individual amino acids. We propose new computational method provides deuterium uptake...

The rapid and simultaneous detection of DNA protein biomarkers is necessary to detect the outbreak a disease or monitor disease. For example, cardiovascular diseases are major cause adult mortality worldwide. We have developed rapidly adaptable platform assess using microfluidic technology. Our model mimics autoantibodies against three proteins, C-reactive (CRP), brain natriuretic peptide (BNP), low-density lipoprotein (LDL). Cell-free mitochondrial (cfmDNA) controls detected via...

Abstract Protein aggregation has been associated with aging and different pathologies represents a bottleneck in the industrial production of biotherapeutics. Numerous past studies performed Escherichia coli other model organisms have allowed to dissect biophysical principles underlying this process. This knowledge fuelled development computational tools, such as Aggrescan 3D (A3D) forecast re-design protein aggregation. Here, we present A3D Model Organism Database (A3D-MODB)...

Missing values are commonly observed in metabolomics data from mass spectrometry. Imputing them is crucial because it assures completeness, increases the statistical power of analyses, prevents inaccurate results, and improves quality exploratory analysis, modeling, machine learning. Numerous Value Imputation Algorithms (MVIAs) employ heuristics or models to replace missing information with estimates. In context data, we identified 52 MVIAs implemented across 70 R functions. Nevertheless,...

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

Information about the impact of interactions between amyloid proteins on their fibrillization propensity is scattered among many experimental articles and presented in unstructured form. We manually curated information located almost 200 publications (selected out 562 initially considered), obtaining details 883 experimentally studied 46 or peptides. also proposed a novel standardized terminology for description amyloid-amyloid interactions, which included our database, covering all...

Quantification cycle (Cq) and amplification efficiency (AE) are parameters mathematically extracted from raw data to characterize quantitative PCR (qPCR) reactions quantify the copy number in a sample. Little attention has been paid effects of preprocessing use smoothing or filtering approaches compensate for noisy data. Existing algorithms largely taken granted, it is unclear which various methods most informative. We investigated effect on curve data.We obtained published high-replicate...

Abstract Motivation: Both the quantitative real-time polymerase chain reaction (qPCR) and isothermal amplification (qIA) are standard methods for nucleic acid quantification. Numerous read-out technologies have been developed. Despite continuous interest in amplification-based techniques, there only few tools pre-processing of data. However, a transparent tool precise control raw data is indispensable several scenarios, example, during development new instruments. Results: chipPCR an R...

Summary The vast biodiversity of the microbial world and how little is known about it, has already been revealed by extensive metagenomics analyses. Our rudimentary knowledge microbes stems from difficulties concerning their isolation culture in laboratory conditions, which necessary for describing phenotype, among other things, biotechnological purposes. An important component understudied ecosystems methanogens, archaea producing a potent greenhouse‐effect gas methane. Therefore, we...

We evaluated prevalence and distribution of antibiotic resistant E. coli in three categories: animals (goats, pigs, poultry, cattle, sheep), humans (butchers, meat sellers, animal farm workers, buyers) food products (milk, cheese, beef, chicken, yoghurt) from selected farms South-West Nigeria. The biofilm formation, phylogrouping detection biofilm-associated genes were further analyzed. Out a total number 280 samples that collected, 216 strains isolated. isolating (96%) was higher than (89%)...

Bacterial host tropism is a primary determinant of the range organisms they can infect. Salmonella serotypes are differentiated into host-restricted and host-adapted specialists, host-unrestricted generalists. In order to elucidate underlying molecular mechanisms specificity in infection, we investigated role intestinal cell receptor zymogen granule membrane glycoprotein 2 (GP2), which recognized by FimH adhesin type 1 fimbriae found Enterobacteriaceae. We compared four human two porcine GP2...

Abstract Real-time quantitative polymerase chain reaction (qPCR) data are found to display periodic patterns in the fluorescence intensity as a function of sample number for fixed cycle number. This behavior is seen technical replicate datasets recorded on several different commercial instruments; it occurs baseline region and typically increases with increasing growth plateau regions. Autocorrelation analysis reveals periodicities 12 96-well systems 24 384-well system, indicating...