database of Modification
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Proteins are the most abundant component of the cell nucleus, where they perform a plethora of functions, including the assembly of long DNA molecules into condensed chromatin, DNA replication and repair, regulation of gene expression, synthesis of RNA molecules and their modification. Proteins are important components of nuclear bodies and are involved in the maintenance of the nuclear architecture, transport across the nuclear envelope and cell division. Given their importance, the current poor knowledge of plant nuclear proteins and their dynamics during the cell's life and division is striking. Several factors hamper the analysis of the plant nuclear proteome, but the most critical seems to be the contamination of nuclei by cytosolic material during their isolation. With the availability of an efficient protocol for the purification of plant nuclei, based on flow cytometric sorting, contamination by cytoplasmic remnants can be minimized. Moreover, flow cytometry allows the separation of nuclei in different stages of the cell cycle (G1, S, and G2). This strategy has led to the identification of large number of nuclear proteins from barley (Hordeum vulgare), thus triggering the creation of a dedicated database called UNcleProt, http://barley.gambrinus.ueb.cas.cz/ .
- Klíčová slova
- barley, cell cycle, database, flow-cytometry, localization, mass spectrometry, nuclear proteome, nucleus,
- MeSH
- buněčný cyklus * MeSH
- data mining MeSH
- databáze proteinů * MeSH
- jaderné proteiny klasifikace metabolismus MeSH
- ječmen (rod) cytologie MeSH
- rostlinné proteiny klasifikace metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- jaderné proteiny MeSH
- rostlinné proteiny MeSH
This contribution lays the foundation for the European database of explanted UHMWPE liners from total joint replacements. Three EU countries (Czech Republic, Italy and Spain) have joined their datasets containing anonymized patient data (such as age and BMI), manufacturer data (such as information on UHMWPE crosslinking, thermal treatment and sterilization), orthopedic evaluation (such as total duration of the implant in vivo and reasons for its revision) and material characterization (such as oxidative degradation and micromechanical properties). The joined database contains more than 500 entries, exhibiting gradual growth, and it is beginning to show interesting trends, which are discussed in our contribution, including (i) strong correlations between UHMWPE oxidative degradation, degree of crystallinity and microhardness; (ii) statistically significant differences between UHMWPE liners with different types of sterilization; (iii) realistic correlations between the extent of oxidative degradation and the observed reasons for total joint replacement failures. Our final objective and task for the future is to continuously expand the database, involving researchers from other European countries, in order to create a robust tool that will contribute to the better understanding of structure-properties-performance relationships in the field of arthroplasty implants.
- Klíčová slova
- European database, UHMWPE, micromechanical properties, oxidative degradation, retrieval study, total joint replacements, ultrahigh molecular weight polyethylene,
- Publikační typ
- časopisecké články MeSH
UNLABELLED: Insecticide resistance is an increasingly global problem that hampers pest control. We sought the mechanism responsible for survival following pyrethroid treatment and the factors connected to paralysis/death of the pollen beetle Meligethes aeneus through a proteome-level analysis using nanoLC coupled with Orbitrap Fusion™ Tribrid™ mass spectrometry. A tolerant field population of beetles was treated with deltamethrin, and the ensuing proteome changes were observed in the survivors (resistant), dead (paralyzed) and control-treated beetles. The protein database consisted of the translated transcriptome, and the resulting changes were manually annotated via BLASTP. We identified a number of high-abundance changes in which there were several dominant proteins, e.g., the electron carrier cytochrome b5, ribosomal proteins 60S RPL28, 40S RPS23 and RPS26, eIF4E-transporter, anoxia up-regulated protein, 2 isoforms of vitellogenin and pathogenesis-related protein 5. Deltamethrin detoxification was influenced by different cytochromes P450, which were likely boosted by increased cytochrome b5, but glutathione-S-transferase ε and UDP-glucuronosyltransferases also contributed. Moreover, we observed changes in proteins related to RNA interference, RNA binding and epigenetic modifications. The high changes in ribosomal proteins and associated factors suggest specific control of translation. Overall, we showed modulation of expression processes by epigenetic markers, alternative splicing and translation. Future functional studies will benefit. BIOLOGICAL SIGNIFICANCE: Insects develop pesticide resistance, which has become one of the key issues in plant protection. This growing resistance increases the demand for pesticide applications and the development of new substances. Knowledge in the field regarding the resistance mechanism and its responses to pesticide treatment provides us the opportunity to propose a solution for this issue. Although the pollen beetle Meligethes aeneus was effectively controlled with pyrethroids for many years, there have been reports of increasing resistance. We show protein changes including production of isoforms in response to deltamethrin at the protein level. These results illustrate the insect's survival state as a resistant beetle and in its paralyzed state (evaluated as dead) relative to resistant individuals.
- Klíčová slova
- Anoxia up-regulated protein, Cytochrome b5, Epigenetics, Pathogenesis-related protein 5, Pesticide resistance, Ribosomal proteins,
- MeSH
- brouci účinky léků genetika metabolismus MeSH
- databáze genetické * MeSH
- hmyzí proteiny genetika metabolismus MeSH
- insekticidy toxicita MeSH
- nitrily toxicita MeSH
- proteomika metody MeSH
- pyl metabolismus MeSH
- pyrethriny toxicita MeSH
- rezistence k insekticidům genetika MeSH
- transkriptom * MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- decamethrin MeSH Prohlížeč
- hmyzí proteiny MeSH
- insekticidy MeSH
- nitrily MeSH
- pyrethriny MeSH
The similarity search in theoretical mass spectra generated from protein sequence databases is a widely accepted approach for identification of peptides from query mass spectra produced by shotgun proteomics. Growing protein sequence databases and noisy query spectra demand database indexing techniques and better similarity measures for the comparison of theoretical spectra against query spectra. We employ a modification of previously proposed parameterized Hausdorff distance for comparisons of mass spectra. The new distance outperforms the original distance, the angle distance and state-of-the-art peptide identification tools OMSSA and X!Tandem in the number of identified peptides even though the q-value is only 0.001. When a precursor mass filter is used as a database indexing technique, our method outperforms OMSSA in the speed of search. When variable modifications are not searched, the search time is similar to X!Tandem. We show that the precursor mass filter is an efficient database indexing technique for high-accuracy data even though many variable modifications are being searched. We demonstrate that the number of identified peptides is bigger when variable modifications are searched separately by more search runs of a peptide identification engine. Otherwise, the false discovery rates are affected by mixing unmodified and modified spectra together resulting in a lower number of identified peptides. Our method is implemented in the freely available application SimTandem which can be used in the framework TOPP based on OpenMS.
The genetic alphabet consists of the four letters: C, A, G, and T in DNA and C,A,G, and U in RNA. Triplets of these four letters jointly encode 20 different amino acids out of which proteins of all organisms are built. This system is universal and is found in all kingdoms of life. However, bases in DNA and RNA can be chemically modified. In DNA, around 10 different modifications are known, and those have been studied intensively over the past 20 years. Scientific studies on DNA modifications and proteins that recognize them gave rise to the large field of epigenetic and epigenomic research. The outcome of this intense research field is the discovery that development, ageing, and stem-cell dependent regeneration but also several diseases including cancer are largely controlled by the epigenetic state of cells. Consequently, this research has already led to the first FDA approved drugs that exploit the gained knowledge to combat disease. In recent years, the ~150 modifications found in RNA have come to the focus of intense research. Here we provide a perspective on necessary and expected developments in the fast expanding area of RNA modifications, termed epitranscriptomics.
- Klíčová slova
- European funding, database of Modification, detection of RNA modification, epitranscriptomics, model systems,
- MeSH
- DNA nádorová * genetika metabolismus MeSH
- epigeneze genetická * MeSH
- epigenomika normy MeSH
- lidé MeSH
- nádory * genetika metabolismus MeSH
- regulace genové exprese u nádorů * MeSH
- RNA nádorová * genetika metabolismus MeSH
- stanovení celkové genové exprese metody normy MeSH
- transkriptom * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Evropa MeSH
- Názvy látek
- DNA nádorová * MeSH
- RNA nádorová * MeSH
The purpose of this quick guide is to help new modelers who have little or no background in comparative modeling yet are keen to produce high-resolution protein 3D structures for their study by following systematic good modeling practices, using affordable personal computers or online computational resources. Through the available experimental 3D-structure repositories, the modeler should be able to access and use the atomic coordinates for building homology models. We also aim to provide the modeler with a rationale behind making a simple list of atomic coordinates suitable for computational analysis abiding to principles of physics (e.g., molecular mechanics). Keeping that objective in mind, these quick tips cover the process of homology modeling and some postmodeling computations such as molecular docking and molecular dynamics (MD). A brief section was left for modeling nonprotein molecules, and a short case study of homology modeling is discussed.
- MeSH
- algoritmy MeSH
- aminokyseliny chemie MeSH
- biologické modely MeSH
- databáze proteinů MeSH
- internet MeSH
- ionty MeSH
- koncentrace vodíkových iontů MeSH
- ligandy MeSH
- počítačová simulace MeSH
- posttranslační úpravy proteinů MeSH
- proteiny chemie MeSH
- rozpouštědla MeSH
- sbalování proteinů MeSH
- simulace molekulární dynamiky MeSH
- simulace molekulového dockingu MeSH
- software MeSH
- strojové učení MeSH
- strukturní homologie proteinů MeSH
- voda MeSH
- výpočetní biologie metody MeSH
- zobrazování trojrozměrné metody MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- aminokyseliny MeSH
- ionty MeSH
- ligandy MeSH
- proteiny MeSH
- rozpouštědla MeSH
- voda MeSH
This article presents a steganographic method StegoNN based on neural networks. The method is able to identify a photomontage from presented signed images. Unlike other academic approaches using neural networks primarily as classifiers, the StegoNN method uses the characteristics of neural networks to create suitable attributes which are then necessary for subsequent detection of modified photographs. This also results in a fact that if an image is signed by this technique, the detection of modifications does not need any external data (database of non-modified originals) and the quality of the signature in various parts of the image also serves to identify modified (corrupted) parts of the image. The experimental study was performed on photographs from CoMoFoD Database and its results were compared with other approaches using this database based on standard metrics. The performed study showed the ability of the StegoNN method to detect corrupted parts of an image and to mark places which have been most probably image-manipulated. The usage of this method is suitable for reportage photography, but in general, for all cases where verification (provability) of authenticity and veracity of the presented image are required.
- Klíčová slova
- CoMoFoD database, Neural network, Photomontage, Steganography, StegoNN,
- MeSH
- databáze faktografické normy MeSH
- fotografování metody normy MeSH
- lidé MeSH
- neuronové sítě * MeSH
- reprodukovatelnost výsledků MeSH
- rozpoznávání automatizované metody normy MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Mass spectrometry (MS) based proteomics have achieved a near-complete proteome coverage in humans and in several other organisms, producing a wealth of information stored in databases and bioinformatics resources. Recent implementation of selected/multiple reaction monitoring (SRM/MRM) technology in targeted proteomics introduced the possibility of quantitatively follow-up specific protein targets in a hypothesis-driven experiment. In contrast to immunoaffinity-based workflows typically used in biological and clinical research for protein quantification, SRM/MRM is characterized by high selectivity, large capacity for multiplexing (approx. 200 proteins per analysis) and rapid, cost-effective transition from assay development to deployment. The concept of SRM/MRM utilizes triple quadrupole (QqQ) mass analyzer to provide inherent reproducibility, unparalleled sensitivity and selectivity to efficiently differentiate isoforms, post-translational modifications and mutated forms of proteins. SRM-like targeted acquisitions such as parallel reaction monitoring (PRM) are pioneered on high resolution/accurate mass (HR/AM) platforms based on the quadrupole-orbitrap (Q-orbitrap) mass spectrometer. The expansion of HR/AM also caused development in data independent acquisition (DIA). This review presents a step-by-step tutorial on development of SRM/MRM protein assay intended for researchers without prior experience in proteomics. We discus practical aspects of SRM-based quantitative proteomics workflow, summarize milestones in basic biological and medical research as well as recent trends and emerging techniques.
- Klíčová slova
- Data independent acquisition (DIA), Parallel reaction monitoring (PRM), Selected/multiple reaction monitoring (SRM/MRM), Sequential windowed acquisition of all theoretical fragmentation spectra (SWATH), Tandem mass spectrometry (MS/MS), Targeted quantitative proteomics tutorial,
- MeSH
- hmotnostní spektrometrie * MeSH
- lidé MeSH
- posttranslační úpravy proteinů MeSH
- proteom MeSH
- proteomika metody MeSH
- reprodukovatelnost výsledků MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- Názvy látek
- proteom MeSH
The complete amino acid sequences of the hemagglutinin (HA) glycoprotein of three equine-2 influenza viruses from tropical Africa are presented in comparison with that of a well characterized European equine-2 virus (Suffolk/89) and a consensus sequence from the database. The sequences of the tropical African viruses were deduced from the complete nucleotide sequences of their HA genes reported earlier. Mutational changes in the nucleotide sequences resulted in amino acid changes in the HA which led to the introduction of a new asparagine-linked (N-linked) glycosylation site in two viruses. This new glycosylation site enhanced the infectivity of these viruses as investigated by plaque assay, virus titration in embryonated chicken eggs and tunicamycin treatment. The role of N-linked glycosylation of influenza virus HA glycoprotein in virus infectivity, antigenicity and immunogenicity is discussed in the light of the results of our previous and present investigations.
- MeSH
- asparagin chemie MeSH
- cytopatogenní efekt virový MeSH
- glykosylace účinky léků MeSH
- hemaglutininové glykoproteiny viru chřipky chemie genetika fyziologie MeSH
- konsenzuální sekvence MeSH
- kultivované buňky MeSH
- kuřecí embryo MeSH
- molekulární sekvence - údaje MeSH
- posttranslační úpravy proteinů * účinky léků MeSH
- sekvence aminokyselin MeSH
- sekvenční homologie aminokyselin MeSH
- sekvenční seřazení MeSH
- tunikamycin farmakologie MeSH
- virulence genetika MeSH
- virus chřipky A genetika patogenita MeSH
- zvířata MeSH
- Check Tag
- kuřecí embryo MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- srovnávací studie MeSH
- Geografické názvy
- Nigérie MeSH
- Názvy látek
- asparagin MeSH
- hemaglutininové glykoproteiny viru chřipky MeSH
- tunikamycin MeSH
Food adulteration is one of the most serious problems regarding food safety and quality worldwide. Besides misleading consumers, it poses a considerable health risk associated with the potential non-labeled allergen content. Fish and fish products are one of the most expensive and widely traded commodities, which predisposes them to being adulterated. Among all fraud types, replacing high-quality or rare fish with a less valuable species predominates. Because fish differ in their allergen content, specifically the main one, parvalbumin, their replacement can endanger consumers. This underlines the need for reliable, robust control systems for fish species identification. Various methods may be used for the aforementioned purpose. DNA-based methods are favored due to the characteristics of the target molecule, DNA, which is heat resistant, and the fact that through its sequencing, several other traits, including the recognition of genetic modifications, can be determined. Thus, they are considered to be powerful tools for identifying cases of food fraud. In this review, the major DNA-based methods applicable for fish meat and product authentication and their commercial applications are discussed, the possibilities of detecting genetic modifications in fish are evaluated, and future trends are highlighted, emphasizing the need for comprehensive and regularly updated online database resources.
- Klíčová slova
- DNA-based methods, fish, food fraud, food quality, genetically modified organism (GMO), polymerase chain reaction (PCR), species identification,
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
