Detection of peptides lies at the core of bottom-up proteomics analyses. We examined a Bayesian approach to peptide detection, integrating match-based models (fragments, retention time, isotopic distribution, and precursor mass) and peptide prior probability models under a unified probabilistic framework. To assess the relevance of these models and their various combinations, we employed a complete- and a tail-complete search of a low-precursor-mass synthetic peptide library based on oncogenic KRAS peptides. The fragment match was by far the most informative match-based model, while the retention time match was the only remaining such model with an appreciable impact--increasing correct detections by around 8 %. A peptide prior probability model built from a reference proteome greatly improved the detection over a uniform prior, essentially transforming de novo sequencing into a reference-guided search. The knowledge of a correct sequence tag in advance to peptide-spectrum matching had only a moderate impact on peptide detection unless the tag was long and of high certainty. The approach also derived more precise error rates on the analyzed combinatorial peptide library than those estimated using PeptideProphet and Percolator, showing its potential applicability for the detection of homologous peptides. Although the approach requires further computational developments for routine data analysis, it illustrates the value of peptide prior probabilities and presents a Bayesian approach for their incorporation into peptide detection.

• Klíčová slova
• Bayes’ theorem, Tandem mass spectrometry, combinatorial peptide library, peptide detection, prior probability,
• MeSH
• algoritmy MeSH
• Bayesova věta MeSH
• databáze proteinů MeSH
• peptidová knihovna * MeSH
• peptidy * analýza   MeSH
• proteom analýza   MeSH
• proteomika MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• peptidová knihovna * MeSH
• peptidy * MeSH
• proteom MeSH

Large insert genomic DNA libraries are useful resources for genomic studies. Although the genome of Xenopus tropicalis stands as the amphibian reference genome because it benefitted from large-scale sequencing studies, physical mapping resources such as BAC libraries are lagging behind. Here we present the construction and characterization of a BAC library that covers the whole X. tropicalis genome. We prepared this BAC library from the genomic DNA of X. tropicalis females of the Adiopodoume strain. We characterized BAC clones by screening for specific loci, by chromosomal localization using FISH and by systematic BAC end sequencing. The median insert size is about 110kbp and the library coverage is around six genome equivalents. We obtained a total of 163,787 BAC end sequences with mate pairs for 77,711 BAC clones. We mapped all BAC end sequences to the reference X. tropicalis genome assembly to enable the identification of BAC clones covering specific loci. Overall, this BAC library resource complements the knowledge of the X. tropicalis genome and should further promote its use as a reference genome for developmental biology studies and amphibian comparative genomics.

• Klíčová slova
• Amphibian, BAC library, Genomics, Xenopus tropicalis,
• MeSH
• genomika metody   MeSH
• genová knihovna * MeSH
• hybridizace in situ fluorescenční MeSH
• játra chemie   MeSH
• mapování chromozomů MeSH
• proteiny Xenopus genetika   MeSH
• sekvenční analýza DNA MeSH
• umělé bakteriální chromozomy genetika   MeSH
• Xenopus genetika   MeSH
• zvířata MeSH
• Check Tag
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• proteiny Xenopus MeSH

SUMMARY: AEON.py is a Python library for the analysis of the long-term behaviour in very large asynchronous Boolean networks. It provides significant computational improvements over the state-of-the-art methods for attractor detection. Furthermore, it admits the analysis of partially specified Boolean networks with uncertain update functions. It also includes techniques for identifying viable source-target control strategies and the assessment of their robustness with respect to parameter perturbations. AVAILABILITY AND IMPLEMENTATION: All relevant results are available in Supplementary Materials. The tool is accessible through https://github.com/sybila/biodivine-aeon-py. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

• MeSH
• genová knihovna MeSH
• software * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

• Klíčová slova
• LIBRARIES, HOSPITAL *,
• MeSH
• knihovny * MeSH
• lidé MeSH
• nemocniční knihovny * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

MOTIVATION: Current techniques of protein engineering focus mostly on re-designing small targeted regions or defined structural scaffolds rather than constructing combinatorial libraries of versatile compositions and lengths. This is a missed opportunity because combinatorial libraries are emerging as a vital source of novel functional proteins and are of interest in diverse research areas. RESULTS: Here, we present a computational tool for Combinatorial Library Design (CoLiDe) offering precise control over protein sequence composition, length and diversity. The algorithm uses evolutionary approach to provide solutions to combinatorial libraries of degenerate DNA templates. We demonstrate its performance and precision using four different input alphabet distribution on different sequence lengths. In addition, a model design and experimental pipeline for protein library expression and purification is presented, providing a proof-of-concept that our protocol can be used to prepare purified protein library samples of up to 1011-1012 unique sequences. CoLiDe presents a composition-centric approach to protein design towards different functional phenomena. AVAILABILITYAND IMPLEMENTATION: CoLiDe is implemented in Python and freely available at https://github.com/voracva1/CoLiDe. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

• MeSH
• algoritmy * MeSH
• genová knihovna MeSH
• proteinové inženýrství MeSH
• proteiny * genetika   MeSH
• sekvence aminokyselin MeSH
• software MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• proteiny * MeSH

Single-chain antibodies (scFv) exhibiting specific binding to Lawsonia intracellularis were isolated from a phagemid library expressing scFvs molecules on the surface of filamentous bacteriophages. For scFv selection whole bacterial cells were used and individual clones were tested in ELISA test. The total of seven unique clones with different fingerprint profiles was isolated. All clones were able to bind specifically in immunofluorescence assay. This is the first report of species specific recombinant antibodies against L. intracellularis.

• MeSH
• Lawsonia (bakterie) imunologie   MeSH
• lidé MeSH
• peptidová knihovna * MeSH
• protilátky bakteriální genetika   imunologie   izolace a purifikace   MeSH
• specificita protilátek * MeSH
• variabilní oblast imunoglobulinu genetika   imunologie   izolace a purifikace   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• peptidová knihovna * MeSH
• protilátky bakteriální MeSH
• variabilní oblast imunoglobulinu MeSH

The authors give a short history of the association, beginning with its establishment (1986) and a survey of its activities up to the summer of 1994, and its organization. They write about conditions and terms of membership, about aims and objectives of the association: to improve co-operation among European medical libraries, to raise standards of library and information services as well as professionality of librarians and information officers and their continuous education, especially in regard to new technologies. The authors also emphasize the European character and principles of tolerance that enable a connection of medical nursing, veterinary and pharmaceutical libraries/librarians in these specializations in various countries. It is necessary for information users to learn modern library methods, including information skills for the learning process (libraries of medical faculties). No less important is the role of libraries for research and evaluation of research. A survey of Czechoslovak and Czech participation in EAHIL is also given here. The course of the Fourth European Conference of Medical and Health Libraries on Oslo (from 28th June to 2nd July, 1994) is shortly described. Further library conference activities are also mentioned: 7th International Congress of Medical Librarianship in Washington, DC, May 10-12, 1995; Fourth Nordic Conference for Medical Libraries, Copenhagen (Denmark), August 21-24, 1995; EAHIL Symposium on Cooperation of Medical Libraries, Prague (Czech Republic), September 21-22, 1995; Fifth European Conference of Medical and Health Libraries, Coimbra (Portugal), September 18-21, 1996.

• MeSH
• knihovnické spolky * MeSH
• lékařské knihovny * MeSH
• Publikační typ
• anglický abstrakt MeSH
• časopisecké články MeSH
• Geografické názvy
• Česká republika MeSH
• Evropa MeSH

Mass spectral libraries have proven to be essential for mass spectrum annotation, both for library matching and training new machine learning algorithms. A key step in training machine learning models is the availability of high-quality training data. Public libraries of mass spectrometry data that are open to user submission often suffer from limited metadata curation and harmonization. The resulting variability in data quality makes training of machine learning models challenging. Here we present a library cleaning pipeline designed for cleaning tandem mass spectrometry library data. The pipeline is designed with ease of use, flexibility, and reproducibility as leading principles.Scientific contributionThis pipeline will result in cleaner public mass spectral libraries that will improve library searching and the quality of machine-learning training datasets in mass spectrometry. This pipeline builds on previous work by adding new functionality for curating and correcting annotated libraries, by validating structure annotations. Due to the high quality of our software, the reproducibility, and improved logging, we think our new pipeline has the potential to become the standard in the field for cleaning tandem mass spectrometry libraries.

• Klíčová slova
• Library cleaning, Mass spectrometry, Metabolomics, Metadata, Python Package,
• Publikační typ
• časopisecké články MeSH

Clostridium difficile infections cause gastrointestinal disorders and can lead to life-threatening conditions. The symptoms can vary from severe diarrhea to the formation of pseudomembranous colitis and therefore trigger a need for new therapies. The initial step of disease is the binding of the bacterial enterotoxins toxin A and B to the cell surface of epithelial intestinal cells. Scavenging of the toxins is crucial to inhibit their fatal effect in the human body and circumvent the administration of antibiotics. Cell surface glycans are common as ligands for TcdA. Although crucial for carbohydrate-protein interactions, a multivalent presentation of glycans for binding has been hardly considered. Here, we establish a neo-glycoprotein-based glycan library to identify an effective multivalent glycan ligand for TcdA. It comprises 40 different glycan epitopes based on N-acetyllactosamine precursors. Nine structures exhibit strong binding of the receptor domain. Among them, the Lewisy-Lewisx-epitope shows the best performance for binding both the receptor domain and the holotoxin. Therefore, the glycan was synthesized de novo and coupled to BSA as a scaffold for multivalent presentation. The corresponding neo-glycoprotein facilitates the proper scavenging of TcdA in vitro and effectively protects HT29 cells from TcdA-induced cell damage.

• MeSH
• bakteriální toxiny metabolismus   MeSH
• buňky HT-29 MeSH
• enterotoxiny metabolismus   MeSH
• genová knihovna MeSH
• glykoproteiny metabolismus   MeSH
• lidé MeSH
• polysacharidy metabolismus   MeSH
• vazba proteinů MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• bakteriální toxiny MeSH
• enterotoxiny MeSH
• glykoproteiny MeSH
• polysacharidy MeSH
• tcdA protein, Clostridium difficile MeSH Prohlížeč

The development of canine immunotolerant monoclonal antibodies can accelerate the invention of new medicines for both canine and human diseases. We develop a methodology to clone the naive, somatically mutated variable domain repertoire from canine B cell mRNA using 5'RACE PCR. A set of degenerate primers were then designed and used to clone variable domain genes into archival "holding" plasmid libraries. These archived variable domain genes were then combinatorially ligated to produce a scFv M13 phage library. Next-generation long-read and short-read DNA sequencing methodologies were developed to annotate features of the cloned library including CDR diversity and IGHV/IGKV/IGLV subfamily distribution. A synthetic immunoglobulin G was developed from this scFv library to the canine immune checkpoint receptor PD-1. This synthetic platform can be used to clone and annotate archived antibody variable domain genes for use in perpetuity in order to develop improved preclinical models for the treatment of complex human diseases.

• Klíčová slova
• CP: cancer biology, CP: immunology, canine physiology, next-generation sequencing, scfv phage libraries, translational research, veterinary medicine,
• MeSH
• antigeny CD279 imunologie   MeSH
• jednořetězcové protilátky * imunologie   genetika   MeSH
• lidé MeSH
• monoklonální protilátky imunologie   genetika   MeSH
• nádory imunologie   terapie   MeSH
• peptidová knihovna MeSH
• psi MeSH
• rekombinantní proteiny imunologie   genetika   MeSH
• translační biomedicínský výzkum MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• psi MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• antigeny CD279 MeSH
• jednořetězcové protilátky * MeSH
• monoklonální protilátky MeSH
• peptidová knihovna MeSH
• rekombinantní proteiny MeSH