Informacja

Drogi użytkowniku, aplikacja do prawidłowego działania wymaga obsługi JavaScript. Proszę włącz obsługę JavaScript w Twojej przeglądarce.

Wyszukujesz frazę "proteomics" wg kryterium: Wszystkie pola


Wyświetlanie 1-37 z 37
Tytuł:
Proteomics in studies of Staphylococcus aureus virulence
Autorzy:
Bonar, Emilia
Wójcik, Iwona
Wladyka, Benedykt
Powiązania:
https://bibliotekanauki.pl/articles/1038964.pdf
Data publikacji:
2015
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
Staphylococcus aureus
proteomics
virulence factors
secretome
surfacome
Opis:
Staphylococcus aureus is a widespread, opportunistic pathogen that causes community and hospital acquired infections. Its high pathogenicity is driven by multifactorial and complex mechanisms determined by the ability of the bacterium to express a wide variety of virulence factors. The proteome secreted into extracellular milieu is a rich reservoir of such factors which include mainly nonenzymatic toxins and enzymes. Simultaneously, membrane proteins, membrane-cell wall interface proteins and cell wall-associated proteins also strongly influence staphylococcal virulence. Proteomics shows a great potential in exploring the role of the extracellular proteome in cell physiology, including the pathogenic potential of particular strains of staphylococci. In turn, understanding the bacterial physiology including the interconnections of particular factors within the extracellular proteomes is a key to the development of the ever needed, novel antibacterial strategies. Here, we briefly overview the latest applications of gel-based and gel-free proteomic techniques in the identification of the virulence factors within S. aureus secretome and surfacome. Such studies are of utmost importance in understanding the host-pathogen interactions, analysis of the role of staphylococcal regulatory systems and also the detection of posttranslational modifications emerging as important modifiers of the infection process.
Źródło:
Acta Biochimica Polonica; 2015, 62, 3; 367-381
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Proteomics of E.coli Nissle 1917 in response to Cocos nucifera sap and wine
Autorzy:
Chandrasekhar, K
Pramoda Kumari, J.
Powiązania:
https://bibliotekanauki.pl/articles/11862.pdf
Data publikacji:
2015
Wydawca:
Przedsiębiorstwo Wydawnictw Naukowych Darwin / Scientific Publishing House DARWIN
Tematy:
proteomics
Escherichia coli
plant response
coconut palm
Cocos nucifera
sap
wine
protein
probiotic
identification
scanning
Opis:
In the present study, we described the protein profile experimentally by 2D-PAGE and MALDI analysis to understand the stress mechanisms of cocoti sap and wine on E.coli Nissle 1917. We isolated one newly expressed protein from cocoti wine treated gel which is not present in both control and cocoti sap treated sample i.e. P21 prophage-derived head-stabilizing proteinVG03_ECOL6 (3n1) also called as Head protein gp3. This protein mainly activities related to the viral life cycle. It helps to attach the viral gene into host. The growth rate was delayed in cocoti wine treated E.coli Nissle 1917 when compared to control and cocoti sap treated samples. Stress mechanism induce many proteins they are involved in metabolic process, hydrolase activity, lyase activity, quinone binding, phosphotransferase system, carbohydrate metabolism, DNA binding, DNA repair, transferase activity, oxidoreductase, purine metabolism, transcription antitermination, transcription regulation and other related activities. We proved that the predicted protein structure quality, resolution, density and error plot values by QMEAN analysis. Based on these results, only two differentially expressed proteins under sap stress showed that the significant results, which were N-acetylgalactosamine-specific phosphotransferase enzyme IIB component 1, PTPB1_ECOLI and DinI-like protein Z3305/ECs2939 in prophage CP-933VDINI1_ECO57. In case of wine stress, the differentially expressed proteins were Transcription anti-termination protein RFAH- ECO57 NusA and PUR7- eco24- phosphoribosylamidazole-succinocarboxamide synthase showed significant results. ProtParam analysis indicating that the multiple physico-chemical characters of differentially expressed proteins were differed and compared. The phylogenetic tree represents the relationship in-between the differentially expressed proteins, were showed siblings (related) as well as monophytic clade.
Źródło:
International Letters of Natural Sciences; 2015, 41
2300-9675
Pojawia się w:
International Letters of Natural Sciences
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A short review on proteomics and its applications
Autorzy:
Chandrasekhar, K.
Dileep, A.
Lebonah, D.E.
Pramoda Kumari, J.
Powiązania:
https://bibliotekanauki.pl/articles/11309.pdf
Data publikacji:
2014
Wydawca:
Przedsiębiorstwo Wydawnictw Naukowych Darwin / Scientific Publishing House DARWIN
Tematy:
proteomics
application
protein function
protein structure
stress condition
metabolism
2-D electrophoresis
disease treatment
novel protein
Opis:
Proteomics is the large scale of study of proteins, particularly their function and structure. Proteomics is an excellent approach for studying changes in metabolism in response to different stress conditions. In the present review focused on different types of techniques for the analysis of expressed proteins. The techniques includes 2-D gel electrophoresis, MALDI-TOF/MS etc., play a vital role for the analysis of novel proteins and their role in disease maintenance and treatment. The review also concentrated on applicative perspective of proteomics in the fields of biomedical, agriculture and food.
Źródło:
International Letters of Natural Sciences; 2014, 12, 1
2300-9675
Pojawia się w:
International Letters of Natural Sciences
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Proteomics profiles reveal the potential roles of proteins involved in chicken macrophages stimulated by Lipopolysaccharide
Autorzy:
Li, S.
Chen, Y.
Xue, W.
Wang, Q.
Huai, Z.
An, C.
Wang, Y.
Powiązania:
https://bibliotekanauki.pl/articles/16647586.pdf
Data publikacji:
2023
Wydawca:
Polska Akademia Nauk. Czasopisma i Monografie PAN
Tematy:
chicken macrophage (HD11)
immune response
lipopolysaccharide (LPS)
proteomics
Opis:
Lipopolysaccharide (LPS), a core part of gram-negative bacteria, is crucial for inducing an inflammatory response in living things. In the current study, we used LPS from Salmonella to stimulate chicken macrophages (HD11). Proteomics was used to investigate immune-related proteins and their roles further. Proteomics investigation revealed 31 differential expression proteins (DEPs) after 4 hours of LPS infection. 24 DEPs expressions were up-regulated, while seven were down-regulated. In this investigation, ten DEPs were mainly enriched in S. aureus infection, complement, and coagulation cascades, which were all implicated in the inflammatory response and clearance of foreign pathogens. Notably, complement C3 was shown to be up-regulated in all immune-related pathways, indicating that it is a potential protein in this study. This work contributes to a better understanding and clarification of the processes of Salmonella infection in chickens. It might bring up new possibilities for treating and breeding Salmonella-infected chickens.
Źródło:
Polish Journal of Veterinary Sciences; 2023, 26, 2; 265-274
1505-1773
Pojawia się w:
Polish Journal of Veterinary Sciences
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Redox-mediated regulation of wheat seed dormancy revealed through modification-specific proteomics
Autorzy:
Bykova, N.
Hoehn, B.
Rampitsch, C.
Hu, J.
Fan, T.
Powiązania:
https://bibliotekanauki.pl/articles/80787.pdf
Data publikacji:
2013
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
conference
seed dormancy
wheat
Triticum aestivum
reactive oxygen species
hormonal balance
cysteine
proteomics
abiotic stress
biotic stress
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 2
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Modular structurality and emergent functionality within knowledge representation systems
Autorzy:
Fedyniuk, Adam
Powiązania:
https://bibliotekanauki.pl/articles/429209.pdf
Data publikacji:
2016
Wydawca:
Uniwersytet Papieski Jana Pawła II w Krakowie
Tematy:
metamodelling
ontology
proteomics
connectomics
centrality
philosophy of information
Opis:
There are various approaches to ontology metamodelling, and the notion of biologically inspired modular knowledge representation systems can provide insight in the workings of such phenomena as emergent properties of network structures. What is more relevant from knowledge engineering standpoint, such approach could provide innovation and enhancement of the level of expression as well as overall functionality of modular ontologies. To do so, one needs to find biological structures that would be the basis for modularity on different levels of hierarchy within the artificial system. Network analysis tools as well as systems biology and biocomputing provide a framework for research in this field.
Źródło:
Semina Scientiarum; 2016, 15
1644-3365
Pojawia się w:
Semina Scientiarum
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Cell wall proteome of pathogenic fungi
Autorzy:
Karkowska-Kuleta, Justyna
Kozik, Andrzej
Powiązania:
https://bibliotekanauki.pl/articles/1038959.pdf
Data publikacji:
2015
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
proteomics
fungal pathogens
cell wall
Candida
Aspergillus
Cryptococcus
Opis:
A fast development of a wide variety of proteomic techniques supported by mass spectrometry coupled with high performance liquid chromatography has been observed in recent years. It significantly contributes to the progress in research on the cell wall, very important part of the cells of pathogenic fungi. This complicated structure composed of different polysaccharides, proteins, lipids and melanin, plays a key role in interactions with the host during infection. Changes in the set of the surface-exposed proteins under different environmental conditions provide an effective way for pathogens to respond, adapt and survive in the new niches of infection. This work summarizes the current state of knowledge on proteins, studied both qualitatively and quantitatively, and found within the cell wall of fungal pathogens for humans, including Candida albicans, Candida glabrata, Aspergillus fumigatus, Cryptococcus neoformans and other medically important fungi. The described proteomic studies involved the isolation and fractionation of particular sets of proteins of interest with various techniques, often based on differences in their linkages to the polysaccharide scaffold. Furthermore, the proteinaceous contents of extracellular vesicles ("virulence bags") of C. albicans, C. neoformans, Histoplasma capsulatum and Paracoccidioides brasiliensis are compared, because their production can partially explain the problem of non-classical protein secretion by fungi. The role assigned to surface-exposed proteins in pathogenesis of fungal infections is enormously high, thus justifying the need for further investigation of cell wall proteomes.
Źródło:
Acta Biochimica Polonica; 2015, 62, 3; 339-351
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
DIAGNOSTIC POTENTIAL OF SELECTED SALIVARY PROTEOMICS FOR AUTONOMIC NERVOUS SYSTEM ACTIVITY ASSESSMENT
Autorzy:
Dobrek, Lukasz
Powiązania:
https://bibliotekanauki.pl/articles/2137800.pdf
Data publikacji:
2020-05-14
Wydawca:
Fundacja Edukacji Medycznej, Promocji Zdrowia, Sztuki i Kultury Ars Medica
Tematy:
saliva
vasoactive intestinal peptide
neuropeptide Y
chromogranin A
α-amylase
Opis:
The clinical assessment of autonomic nervous system (ANS) functioning, enabling the diagnosis of autonomic neuropathy present in the course of many diseases, is currently based on performing simple cardiovascular reflexes (Ewing tests), analyzing heart rate variability (HRV) or heart rate turbulence (HRT), examining skin sweating or recording neurophysiological tests (e.g. microneurography). Laboratory assessment of ANS function is very scarce and practically only includes the plasma assessment of noradrenaline as a surrogate for the biochemical indicator of sympathetic activity. Recently, the possibility of evaluation of selected compounds present in saliva as laboratory markers of not only oral diseases but also systemic diseases has been raised. This work focuses on a brief description of the anatomy and physiology of the salivary glands and describes the formation of saliva, its composition and the use of this bodily fluid in laboratory diagnostics. In addition, the paper specifically discusses the possibility of determining selected compounds that are considered to reflect autonomic activity. A review of the literature indicates primarily four proteomics: two neuropeptides (vasoactive intestinal peptide (VIP) and neuropeptide Y (NPY) that are co-transmitters in autonomic fibers, chromogranin A, a synaptic vesicle protein and α-amylase, a hydrolytic enzyme pre-digesting carbohydrates in the oral cavity. These are currently the most widely investigated agents for their usefulness as laboratory markers of ANS activity.
Źródło:
Acta Neuropsychologica; 2020, 18(2); 285-303
1730-7503
2084-4298
Pojawia się w:
Acta Neuropsychologica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
New proteases of the chloroplast envelope – what do they do there?
Autorzy:
Adam, Z.
Powiązania:
https://bibliotekanauki.pl/articles/80681.pdf
Data publikacji:
2013
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
conference
protease
chloroplast
thylakoid
proteomics
allene oxide synthase
jasmonic acid
serine protease
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 3
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Is stallion epididymal fluid phosphoproteome affected by the equine reproductive season?
Autorzy:
Dyrda, K.
Orzołek, A.
Ner-Kluza, J.
Wysocki, P.
Powiązania:
https://bibliotekanauki.pl/articles/2087138.pdf
Data publikacji:
2021
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
stallion
proteomics
epididymal fluid
phosphoproteins
Źródło:
Polish Journal of Veterinary Sciences; 2021, 24, 4; 487-495
1505-1773
Pojawia się w:
Polish Journal of Veterinary Sciences
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Progress and challenges in the proteomics of domestic pig in research on the female reproductive system
Autorzy:
Kolakowska, J.
Franczak, A.
Saini, Ravi Kanth Rao
Souchelnytskyi, Serhiy
Powiązania:
https://bibliotekanauki.pl/articles/961364.pdf
Data publikacji:
2016
Wydawca:
Uniwersytet Warmińsko-Mazurski w Olsztynie / Polskie Towarzystwo Magnezologiczne im. Prof. Juliana Aleksandrowicza
Opis:
The proteomics of pigs is developing dynamically, attracting much attention among representatives of medical and health sciences, veterinary medicine, agricultural and natural sciences. The pig has been widely studied in genetics and genomics. However, proteomic applications are still awaiting more extensive implementation, both in the use of pigs as animal models in biomedicine sciences, and in the exploration of physiological tracts important for pig production. Underdeveloped databases for identification and analysis of porcine proteins as well as the scarcity of detailed information on similarities and differences between humans and pigs at the molecular level are hampering the pig proteomics. However, the use of pigs in proteomic studies in both physiological and biomedical sciences is prevalent comparing to other farm animals. The focus of the reported pig model proteomics studies is on exploring physiology and diseases, and on improving pig breading and productivity. This species has been used as a model in proteomics studies involved in ocular, brain, nutritional and reproduction research, etc. In the present paper we discuss technologies and bioinformatic tools used in studies of a proteome to verify the peptide- and protein-based content and we summarize the current status of proteomic studies of pigs. We focus on studies of the female reproductive system because the examination and understanding of the biology of oocytes, the oviduct and the uterus could facilitate the identification of mechanisms involved in the prenatal development, and it may help to develop new treatment for infertility of farm animals.
Źródło:
Journal of Elementology; 2016, 21, 4
1644-2296
Pojawia się w:
Journal of Elementology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Renal function during metabolic acidosis
Autorzy:
Kurpinska, A.K.
Skrzypczak, W.F.
Powiązania:
https://bibliotekanauki.pl/articles/3008.pdf
Data publikacji:
2010
Wydawca:
Instytut Medycyny Wsi
Tematy:
renal function
metabolic acidosis
acid-case imbalance
acid-base homeostasis
renal tubule
excretion
reabsorption
proteomics
Źródło:
Journal of Pre-Clinical and Clinical Research; 2010, 04, 1
1898-2395
Pojawia się w:
Journal of Pre-Clinical and Clinical Research
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A distributed algorithm for protein identification from tandem mass spectrometry data
Autorzy:
Orzechowska, Katarzyna
Rubel, Tymon
Kurjata, Robert
Zaremba, Krzysztof
Powiązania:
https://bibliotekanauki.pl/articles/2097435.pdf
Data publikacji:
2022
Wydawca:
Polskie Towarzystwo Promocji Wiedzy
Tematy:
proteomics
mass spectrometry
distributed computing
Apache Spark
Opis:
Tandem mass spectrometry is an analytical technique widely used in proteomics for the high-throughput characterization of proteins in biological samples. Modern in-depth proteomic studies require the collection of even millions of mass spectra representing short protein fragments (peptides). In order to identify the peptides, the measured spectra are most often scored against a database of amino acid sequences of known proteins. Due to the volume of input data and the sizes of proteomic databases, this is a resource-intensive task, which requires an efficient and scalable computational strategy. Here, we present SparkMS, an algorithm for peptide and protein identification from mass spectrometry data explicitly designed to work in a distributed computational environment. To achieve the required performance and scalability, we use Apache Spark, a modern framework that is becoming increasingly popular not only in the field of “big data” analysis but also in bioinformatics. This paper describes the algorithm in detail and demonstrates its performance on a large proteomic dataset. Experimental results indicate that SparkMS scales with the number of worker nodes and the increas-ing complexity of the search task. Furthermore, it exhibits a protein identification efficiency comparable to X!Tandem, a widely-used proteomic search engine.
Źródło:
Applied Computer Science; 2022, 18, 2; 16--27
1895-3735
Pojawia się w:
Applied Computer Science
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Mass spectrometry approaches in proteomic and metabolomic studies
Autorzy:
Rodziewicz, P.
Swarcewicz, B.
Chmielewska, K.
Powiązania:
https://bibliotekanauki.pl/articles/80650.pdf
Data publikacji:
2014
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
proteomics
metabolomics
genomic DNA
nuclear magnetic resonance
mass spectrometry
Fourier transform infrared spectroscopy
Raman spectroscopy
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2014, 95, 3
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Oxidative signalling in seed germination and dormancy
Autorzy:
Bailly, C.
Powiązania:
https://bibliotekanauki.pl/articles/81220.pdf
Data publikacji:
2013
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
conference
seed dormancy
germination
genetic background
environment condition
abscisic acid
gibberellin
reactive oxygen species
Arabidopsis
proteomics
transcriptomics
transduction
hormone signalling
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 2
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Immunogenic proteins in the somatic proteome of the adult cestode Hymenolepis diminuta - a proteomic approach
Autorzy:
Mlocicki, D.
Bien, J.
Salamatin, R.
Sulima, A.
Powiązania:
https://bibliotekanauki.pl/articles/6559.pdf
Data publikacji:
2016
Wydawca:
Polskie Towarzystwo Parazytologiczne
Tematy:
immunogenic protein
cestode
Hymenolepis diminuta
parasite
proteomics
Źródło:
Annals of Parasitology; 2016, 62, Suppl.
0043-5163
Pojawia się w:
Annals of Parasitology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Corpora amylacea from multiple sclerosis brain tissue consists of aggregated neuronal cells
Autorzy:
Selmaj, Krzysztof
Pawłowska, Zofia
Walczak, Agata
Koziołkiewicz, Wiktor
Raine, Cedric
Cierniewski, Czesław
Powiązania:
https://bibliotekanauki.pl/articles/1040812.pdf
Data publikacji:
2008
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
proteomics
neuronal aggregates
corpora amylacea
multiple sclerosis
Opis:
In this report, we describe proteomic analysis of corpora amylacea collected by postmortem laser microdissection from multiple sclerosis (MS) brain lesions. Using low level protein loads (about 30 µg), a combination of two-dimensional electrophoresis with matrix-assisted laser desorption/ionization-time of flight mass spectrometry and database interrogations we identified 24 proteins of suspected neuronal origin. In addition to major cytoskeletal proteins like actin, tubulin, and vimentin, we identified a variety of proteins implicated specifically in cellular motility and plasticity (F-actin capping protein), regulation of apoptosis and senescence (tumor rejection antigen-1, heat shock proteins, valosin-containing protein, and ubiquitin-activating enzyme E1), and enzymatic pathways (glyceraldehyde-3-dehydrogenase, protein disulfide isomerase, protein disulfide isomerase related protein 5, lactate dehydrogenase). Samples taken from regions in the vicinity of corpora amylacea showed only traces of cellular proteins suggesting that these bodies may represent remnants of neuronal aggregates with highly polymerized cytoskeletal material. Our data provide evidence supporting the concept that biogenesis of corpora amylacea involves degeneration and aggregation of cells of neuronal origin.
Źródło:
Acta Biochimica Polonica; 2008, 55, 1; 43-50
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Forest tree research in post genomic era. Introduction to systems biology of broadleaves
Autorzy:
Staszak, A.M.
Pawlowski, T.A.
Powiązania:
https://bibliotekanauki.pl/articles/41059.pdf
Data publikacji:
2012
Wydawca:
Polska Akademia Nauk. Instytut Dendrologii PAN
Tematy:
forest tree
tree
genomics
proteomics
woody plant
biology
broadleaf
plant reproduction
plant physiology
Opis:
Trees are long living organisms, rarely used in molecular experiments because of large size of the genome and long time of reproduction cycle. Sequencing data from Populus trichocarpa genome allowed for the development of research on the processes associated with tree biology such as secondary wood formation, long-term perennial growth, seasonal changes, biotic interactions, evolution etc. Reference data enable the investigation of non-model trees such as Quercus or Fagus, having ecological and economic significance. During projects scientists use genomic, transcriptomic, proteomic and metabolomic approaches which contribute to better understanding of the physiological processes regulating tree biology. Data collected from these multiple studies need to be integrated. The integration of data is the subject of the newly established field of science called systems biology. This review presents progress in tree research after finishing the sequencing project of Populus. It concentrates on modern trends in 'omics' and systems biology study of temperate broadleave trees during the last 10 years of studies.
Źródło:
Dendrobiology; 2012, 68
1641-1307
Pojawia się w:
Dendrobiology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
High throughput protein production
Autorzy:
Tworak, A.
Podkowinski, J.
Figlerowicz, M.
Powiązania:
https://bibliotekanauki.pl/articles/80317.pdf
Data publikacji:
2011
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
activity
cloning
DNA sequencing
expression
high throughput
human genome
Human Genome Project
large scale proteomics
new technology
protein folding
protein production
purification
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2011, 92, 2
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Mass spectrometry as a useful tool for identifying new therapeutic targets on the cell surface of pathogenic fungi from the genus Candida
Autorzy:
Karkowska-Kuleta, J.
Bocheńska, O.
Powiązania:
https://bibliotekanauki.pl/articles/115505.pdf
Data publikacji:
2014
Wydawca:
Fundacja na Rzecz Młodych Naukowców
Tematy:
proteomics
pathogenic fungi
candidiasis
mass spectrometry
Opis:
Mass spectrometry (MS) is a universal technique with a wide range of applications, including proteomic studies of different organisms, particularly the characterization and sequencing of proteins isolated from specific cellular compartments. It is used for the identification of elements exposed on the cell surface of microbial pathogens, which are involved in the initial contact with the human host, and then in the further development of infection. Given the increasing frequency of invasive fungal infections caused by pathogenic yeast from the genus Candida, especially among patients with severe immunological impairments, it appears advisable to study the diversity of cell wall proteins that arise during subsequent stages of infection and that are responsible for several important phenomena correlated with pathogenesis. This study employed a liquid chromatograph-coupled mass spectrometer equipped with an electrospray ionization source (ESI), and an ion trap analyser. For tandem mass spectrometry, two approaches for fragmentation of ions - collision-induced dissociation (CID) and electron transfer dissociation (ETD) - were used to analyse the mixtures of peptides generated after tryptic digestion of fungal cell wall proteins (i.e. the “bottom-up” approach). Several surface proteins from Candida spp. were identified which could be potential drug targets and candidates for vaccine development.
Źródło:
Challenges of Modern Technology; 2014, 5, 1; 7-14
2082-2863
2353-4419
Pojawia się w:
Challenges of Modern Technology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A proteomics approach to identify the differential protein level in cardiac muscle of diabetic rat
Autorzy:
Karthik, Dhanaraj
Vijayakumar, Ravichandran
Pazhanichamy, Kalailingam
Ravikumar, Sivanesan
Powiązania:
https://bibliotekanauki.pl/articles/1039290.pdf
Data publikacji:
2014
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
diabetes mellitus
cardiac muscle proteome
2D electrophoresis
MALDI-TOF-MS
phylogenetic analysis
Opis:
Background: Cardiovascular proteomics investigation reveals the characterization and elucidation of the novel therapeutic targets and strategies to prevent the development of heart failure associated diabetic complication by using 2DE and MS. Methods: The experimental animals were made diabetic with a single intraperitoneal injection of alloxan (150 mg/kg of bw). Albino rats were randomly divided into four individual groups: Group-I control (n=6), group-II alloxan-induced diabetic rats, untreated (n=6), group-III (n=6) and group-IV (n=6) alloxan-induced diabetic rats were treated with aqueous and ethanolic extracts of Cynodon dactylon for 15 days, respectively. Animals were euthanized to collect the heart tissues and blood samples. 2DE sample preparation, gel running and staining (n=6: each groups) were performed at the same time to avoid variation. The result of six gel images from each group were analyzed and evaluated as one match set with 2D software (P<0.05). Results: The above experiment revealed two up-regulated proteins in group-II i.e. NTF4 and ETFB. Conclusions: NTF4 is a neuro-protective agent for neuro-degenerative diseases. It will prevent diabetic secondary complications, such as diabetic polyneuropathy and cardiomyopathy. ETFB is active in the mitochondria, the energy-producing centres in cells. It is clear from the experiment that because of up-regulation of ETFB more energy is availabile and the electron transfer for heart during diabetes is possible, what leads to reduce the oxidative stress and free-radical formation. The up-regulated proteins reduced CVD that occurred just before overt hyperglycaemia due to administration of C. dactylon. This approach established the preliminary reference map for decoding cellular mechanisms linked between pathogenesis CVD and diabetes.
Źródło:
Acta Biochimica Polonica; 2014, 61, 2; 285-293
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Electronegativity and intrinsic disorder of preeclampsia-related proteins
Autorzy:
Polanco, Carlos
Castañón-González, Jorge
Uversky, Vladimir
Buhse, Thomas
Samaniego Mendoza, José
Calva, Juan
Powiązania:
https://bibliotekanauki.pl/articles/1038693.pdf
Data publikacji:
2017
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
preeclampsia
intrinsically disordered proteins
structural proteomics
bioinformatics
antimicrobial peptides
polarity index method
lipoproteins
angiogenesis proteins
Opis:
Preeclampsia, hemorrhage, and infection are the leading causes of maternal death in underdeveloped countries. Since several proteins associated with preeclampsia are known, we conducted a computational study which evaluated the commonness and potential functionality of intrinsic disorder of these proteins and also made an attempt to characterize their origin. The origin of the preeclampsia-related proteins was assessed with a supervised technique, a Polarity Index Method (PIM), which evaluates the electronegativity of proteins based solely on their sequence. The commonness of intrinsic disorder was evaluated using several disorder predictors from the PONDR family, the charge-hydropathy plot (CH-plot) and cumulative distribution function (CDF) analyses, and using the MobiDB web-based tool, whereas potential functionality of intrinsic disorder was studied with the D2P2 resource and ANCHOR predictor of disorder-based binding sites, and the STRING tool was used to build the interactivity networks of the preeclampsia-related proteins. Peculiarities of the PIM-derived polar profile of the group of preeclampsia-related proteins were then compared with profiles of a group of lipoproteins, antimicrobial peptides, angiogenesis-related proteins, and the intrinsically disordered proteins. Our results showed a high graphical correlation between preeclampsia proteins, lipoproteins, and the angiogenesis proteins. We also showed that many preeclampsia-related proteins contain numerous functional disordered regions. Therefore, these bioinformatics results led us to assume that the preeclampsia proteins are highly associated with the lipoproteins group, and that some preeclampsia-related proteins contain significant amounts of functional disorders.
Źródło:
Acta Biochimica Polonica; 2017, 64, 1; 99-111
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Identification of mare colostrum proteins
Identyfikacja bialek siary klaczy – badania wstępne
Autorzy:
Medeńska, W.
Dratwa-Chałupnik, A.
Ożgo, M.
Cichy, A.
Pikuła, R.
Bobik, J.
Powiązania:
https://bibliotekanauki.pl/articles/3131472.pdf
Data publikacji:
2020
Wydawca:
Zachodniopomorski Uniwersytet Technologiczny w Szczecinie. Wydawnictwo Uczelniane ZUT w Szczecinie
Tematy:
colostrum
mare
proteomics
animal feeding
functional protein
foal growth
development
two-dimensional electrophoresis
Źródło:
Acta Scientiarum Polonorum. Zootechnica; 2020, 19, 4; 25-31
1644-0714
Pojawia się w:
Acta Scientiarum Polonorum. Zootechnica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A novel approach for identifying DNA repair pathways proteins using an evolutionary approach: Plasmodium falciparum case study
Autorzy:
Milanowska, K.
Wojtczak, J.
Powiązania:
https://bibliotekanauki.pl/articles/80413.pdf
Data publikacji:
2016
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
DNA repair
pathway
ortholog
pipeline
Plasmodium falciparum
proteomics
protein
profile analysis
Hidden Markov model
multiple sequence alignment
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2016, 97, 4
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Method for mass spectrometry spectrum deisotoping based on fuzzy inference systems
Autorzy:
Glodek, Anna
Polańska, Joanna
Powiązania:
https://bibliotekanauki.pl/articles/747419.pdf
Data publikacji:
2018
Wydawca:
Polskie Towarzystwo Matematyczne
Tematy:
fuzzy logic, fuzzy inference systems, deisotoping, mass spectrometry, algorithms, proteomics, applied mathematics
fuzzy logic, fuzzy inference systems, deisotoping, mass spectrometry, algorithms, MALDI ToF
Opis:
Celem niniejszego artykułu jest omówienie zaproponowanego algorytmu do identyfikacji obwiedni izotopowych, opartego na teorii systemów rozmytych. Obecnie proteomika jest ściśle powiązana z chorobami nowotworowymi. Dlatego też bardzo ważne jest precyzyjne zidentyfikowanie białek znajdujących się w obszarze raka; stosowana jest w tym celu spektrometria masowa. Jedną z technik spektrometrii masowej jest MALDI. Otrzymane dane będące widmem masowym składają się ze stosunku masy do ładunku jonów oraz intensywnosci pików. W celu przetworzenia danych, usunięcia szumu, linii bazowej etc. stosuje się przetwarzanie wstępne. Identyfikacja obwiedni izotopowych jest częścią procesu przetwarzania wstępnego w proteomice. Polega ona na identyfikacji izotopów wchodzących w skład obwiedni izotopowej, a także pozwala na zredukowanie wymiaru danych. Istnieje wiele algorytmów do identyfikacji obwiedni izotopowej, jednak każdy z nich dedykowany jest dla innego rodzaju techniki spektrometrii masowej (MALDI, LC-MS, ESI, etc.) bądź dla konkretnego rodzaju cząsteczek. Dlatego też zaproponowany algorytm został oparty na teorii systemów rozmytych, a reguły wnioskowania zostały oparte na wieloletnich doświadczeniach eksperta w dziedzinie spektrometrii masowej. Przetestowany był on na danych uzyskanych z Instytutu Onkologii im. Marii Skłodowskiej-Curie w Gliwicach, pochodzących z badań nad rakiem głowy i szyi dla losowo wybranej grupy peptydów i lipidów. Wyniki autorskiego algorytmu do identyfikacji obwiedni izotopowych porównano z jedną z istniejących metod do identyfikacji obwiedni izotopowych.
Nowadays, mass spectrometry is widely used in proteomics for confident and precise identification of the protein. One of the most important steps in the signal analysis is deisotoping because some peaks in the spectrum are not the unique compound, but there are members of an isotopic envelope. Although the mass spectrometry is present in proteomics for a long time already, the problem of isotope peaks identification is not solved yet. The existing algorithms, usually designed for the particular type of spectrometer, are semi-supervised and do not give satisfactory results. We propose a new algorithm based on fuzzy inference systems that can accurately identify the isotopic envelopes in the spectrum of the complex structure.
Źródło:
Mathematica Applicanda; 2018, 46, 1
1730-2668
2299-4009
Pojawia się w:
Mathematica Applicanda
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Desorption/ionization on silicon for small molecules: a promising alternative to MALDI TOF.
Autorzy:
Kraj, Agnieszka
Dylag, Tomasz
Gorecka-Drzazga, Anna
Bargiel, Sylwester
Dziuban, Jan
Silberring, Jerzy
Powiązania:
https://bibliotekanauki.pl/articles/1043452.pdf
Data publikacji:
2003
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
proteomics
porous silicon
catecholamines
peptides
DIOS
mass spectrometry
desorption/ionization
MALDI TOF
Opis:
A method has been developed for laser desorption/ionization of catecholamines from porous silicon. This methodology is particularly attractive for analysis of small molecules. MALDI TOF mass spectrometry, although a very sensitive technique, utilizes matrices that need to be mixed with the sample prior to their analysis. Each matrix produces its own background, particularly in the low-molecular mass region. Therefore, detection and identification of molecules below 400 Da can be difficult. Desorption/ionization of samples deposited on porous silicon does not require addition of a matrix, thus, spectra in the low-molecular mass region can be clearly readable. Here, we describe a method for the analysis of catecholamines. While MALDI TOF is superior for proteomics/peptidomics, desorption/ionization from porous silicon can extend the operating range of a mass spectrometer for studies on metabolomics (small organic molecules and their metabolites, such as chemical neurotransmitters, prostaglandins, steroids, etc.).
Źródło:
Acta Biochimica Polonica; 2003, 50, 3; 783-787
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Urinary proteomic strategies in biomarkers discovery of renal diseases
Autorzy:
Ciechanowicz, A.K.
Ozgo, M .
Herosimczyk, A.
Kurpinska, A.
Klonowska, A.
Lepczynski, A.
Stanski, L.R.
Powiązania:
https://bibliotekanauki.pl/articles/3155.pdf
Data publikacji:
2011
Wydawca:
Instytut Medycyny Wsi
Tematy:
proteomics
biomarker discovery
human disease
renal disease
chromatography
electrophoresis
mass spectrometry
kidney
urine
Źródło:
Journal of Pre-Clinical and Clinical Research; 2011, 05, 1
1898-2395
Pojawia się w:
Journal of Pre-Clinical and Clinical Research
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Isolation and identification of zinc ions and heparin binding proteins in yellow fraction of the red deer Cervus Elaphus L. semen
Autorzy:
Orzołek, A.
Dyrda, K.
Rafalska, K.
Wysocki, P.
Kordan, W.
Giżejewski, W.
Powiązania:
https://bibliotekanauki.pl/articles/2087223.pdf
Data publikacji:
2021
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
red deer
yellow fraction
ZnBPs
HBPs
proteomics
Źródło:
Polish Journal of Veterinary Sciences; 2021, 24, 1; 69-78
1505-1773
Pojawia się w:
Polish Journal of Veterinary Sciences
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Transcriptome and proteome changes accompanying increased vigor of osmoprimed rape (Brassica napus L.) seeds
Autorzy:
Kubala, S.
Lechowska, K.
Wojtyla, L.
Kosmala, A.
Quinet, M.
Lutts, S.
Garnczarska, M.
Powiązania:
https://bibliotekanauki.pl/articles/81285.pdf
Data publikacji:
2013
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
conference
osmopriming
seed germination
stress tolerance
Brassica napus
rapeseed
transcriptome
proteomics
gene encoding
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 3
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Surfaceome of pathogenic yeasts, Candida parapsilosis and Candida tropicalis, revealed with the use of cell surface shaving method and shotgun proteomic approach
Autorzy:
Karkowska-Kuleta, Justyna
Zajac, Dorota
Bochenska, Oliwia
Kozik, Andrzej
Powiązania:
https://bibliotekanauki.pl/articles/1038923.pdf
Data publikacji:
2015
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
cell surface shaving
proteomics
fungal pathogens
cell wall
Candida
Opis:
In the course of infections caused by pathogenic yeasts from the genus Candida, the fungal cell surface is the first line of contact with the human host. As the surface-exposed proteins are the key players in these interactions, their identification can significantly contribute to discovering the mechanisms of pathogenesis of two emerging pathogens from this genus, C. parapsilosis and C. tropicalis. Therefore, the aim of the present study was to identify the cell wall-attached proteins of these two species with the use of cell surface shaving and a shotgun proteomic approach. Different morphological forms of C. parapsilosis and C. tropicalis cells obtained after growth under various conditions were subjected to this treatment. This allowed to indicate the most abundant cell surface proteins on the basis of the normalized spectral abundance factors. In case of yeast-like forms these were, among others, proteins similar to a chitinase, glyceraldehyde-3-phosphate dehydrogenase and an inducible acid phosphatase for C. parapsilosis, and a constitutive acid phosphatase, pyruvate decarboxylase and glyceraldehyde-3-phosphate dehydrogenase for C. tropicalis. In case of pseudohyphal forms, proteins similar to a cell surface mannoprotein Mp65, chitinase and glycosylphosphatidylinositol-anchored transglycosylase Crh11 were identified at the cell surface of C. parapsilosis. The Rbt1 cell wall protein, a hyphally regulated cell wall protein and proteins from agglutinin-like sequence protein family were found as the most abundant on C. tropicalis pseudohyphae. Apart from the abovementioned proteins, several additional covalently bound and atypical cell wall proteins were also identified. These results extend the current knowledge regarding the molecular basis of virulence of these two non-albicans Candida species.
Źródło:
Acta Biochimica Polonica; 2015, 62, 4; 807-819
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
iTRAQ-based quantitative proteomics analysis reveals inhibitory mechanismsof the antimicrobial peptide MDAP-2 against Salmonella gallinarum
Autorzy:
Zhang, Y.
Yu, S.
Ying, X.
Jia, B.
Liu, L.
Liu, J.
Kong, L.
Pei, Z.
Ma, H.
Powiązania:
https://bibliotekanauki.pl/articles/2087299.pdf
Data publikacji:
2020
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
Salmonella gallinarum
AMP
iTRAQ
inhibitory mechanism
Źródło:
Polish Journal of Veterinary Sciences; 2020, 23, 3; 405-414
1505-1773
Pojawia się w:
Polish Journal of Veterinary Sciences
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Carbonylation-targeted proteomics of NaCl-stressed plants revealing early oxidative events in various cellular compartments
Autorzy:
Mano, J.
Nagata, M.
Okamura, S.
Shiraya, T.
Mitsui, T.
Powiązania:
https://bibliotekanauki.pl/articles/80594.pdf
Data publikacji:
2013
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
conference
lipid peroxide
reactive carbonyl species
reactive oxygen species
plant environment
stress response
Arabidopsis thaliana
4-hydroxynonenal
immunoblotting
sodium chloride stress
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 2
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Sperm mitochondrial dysfunction and oxidative stress as possible reasons for isolated asthenozoospermia
Autorzy:
Nowicka-Bauer, K.
Lepczynski, A.
Ozgo, M.
Kamieniczna, M.
Fraczek, M.
Stanski, L.
Olszewska, M.
Malcher, A.
Skrzypczak, W.
Kurpisz, M.K.
Powiązania:
https://bibliotekanauki.pl/articles/70952.pdf
Data publikacji:
2018
Wydawca:
Polskie Towarzystwo Fizjologiczne
Tematy:
sperm motility
mitochondrial dysfunction
asthenozoospermia
oxidative stress
reactive oxygen species
proteomics
patient
Źródło:
Journal of Physiology and Pharmacology; 2018, 69, 3
0867-5910
Pojawia się w:
Journal of Physiology and Pharmacology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Identyfikacja białek z wykorzystaniem techniki Peptide Mass Fingerprinting (PMF). Część II - algorytmy scoringu
The identification of proteins by Peptide Mass Fingerprinting (PMF). Part II - the scoring algorithms
Autorzy:
Kamińska, H.
Podbielska, H.
Powiązania:
https://bibliotekanauki.pl/articles/261443.pdf
Data publikacji:
2011
Wydawca:
Politechnika Wrocławska. Wydział Podstawowych Problemów Techniki. Katedra Inżynierii Biomedycznej
Tematy:
proteomika
identyfikacja protein
spektrometria masowa
peptide mass fingerprinting
schematy scoringu
proteomics
identification of proteins
mass spectrometry
scoring schemes
Opis:
Postęp w dziedzinie komputerów oraz rozwój Internetu zrewolucjonizował, proces identyfikacji białek oraz przyczynił się do szybkiego wzrostu proteomicznych baz danych. Krótko po wprowadzeniu pierwszej technologii identyfikacji białek z widm spektrometrów masowych PMF (Peptide Mass Fingerprinting) okazało się, że algorytmy wykorzystywane do wyszukiwania w bazie danych protein odpowiadających wynikom eksperymentu mają kluczowe znaczenie dla wysokiej poprawności identyfikacji. Rozwój metody PMF był zatem uwarunkowany nie tylko przez usprawnienia techniczne schematu, ale przede wszystkim przez zastosowanie rozmaitych metod matematycznych i statystycznych (tzw. algorytmów scoringu) przy wyszukiwaniu poprawnych rozwiązań. Kolejnym krokiem w informatycznym usprawnieniu identyfikacji było opracowanie metod walidacji jej rezultatów na podstawie istniejących baz danych lub też symulacji. Walidacja rezultatów pozwoliła na wyeliminowanie większości błędów pierwszego rodzaju w identyfikacji metodą PMF. Przez wzgląd na powszechność stosowania metody, a także jej ulepszenia autorzy postanowili podsumować obecny stan wiedzy w tym zakresie. Praca została podzielona na dwie części: w pierwszej przedstawiono opis historii powstania metody PMF wraz z charakterystyką jej części eksperymentalnej i opisem najpopularniejszych baz danych stosowanych przy identyfikacji, natomiast druga część jest poświęcona zagadnieniom algorytmicznym związanym z wyszukiwaniem w bazie danych protein najlepiej odzwierciedlających białko analizowane w próbce. Bioinformatyczne ujęcie identyfikacji białek w drugiej części nawiązuje do specyfikacji eksperymentu, omówionej w części pierwszej publikacji. Druga część pracy w szczegółowy sposób opisuje główne aspekty porównywania mas teoretycznych i eksperymentalnych, tj. trawienie in silico, rozpoznawanie modyfikacji białek, dopasowywanie mas oraz kalibrację poprawnych dopasowań. Opisane zostały także sposoby budowania funkcji scoringowych oraz algorytmy walidacji ich wartości. Dodatkowo, w pracy przedstawiono najbardziej znane funkcje scoringowe oraz pełny przegląd oprogramowania do identyfikacji białek metodą PMF.
The internet and computer science progress have revolutionized the process of protein identification and contributed to the growth of proteomics databases. Just after discovering the first technology for protein identification from the mass spectra PMF (peptide mass fingerprinting), it appeared that the algorithms searching databases for proteins corresponding to experiment results have crucial meaning for the sensitivity and specificity of the identification procedure. Therefore, the development of PMF method was conditioned by both the technological improvements in the PMF scheme and the application of various mathematical and statistical methods (so called: scoring algorithms) to the searching of correct identifications. The next step in the development of an identification procedure was to work out the methods for identification results validation, according to the proteomics databases content or simulations. The results validation allowed to eliminate the most of unwanted false positives in the PMF identification. Regarding the method common use, as well as its improvements which are still present, the authors decide to summarize the current level of knowledge related to this topic. The publication is divided into two parts. The first one is devoted to the origins of PMF scheme, the characteristics of its experimental part and a description of the most popular databases used in the identification procedure. The second part relates to the algorithmic issues of searching the database protein, which reflects the sample content best. From the bioinformatics point of view the protein identification in the second part of publication refers to the experiment specification described in the first part. The second part of the publication describes in details the aspects of theoretical and experimental masses comparison, i.e. in silico digestion, the discrimination of protein modifications, the pairing of masses and the calibration of matches. Moreover, the scoring functions building manners and the algorithms for scoring functions values validation were also taken into the consideration. Additionally, we present the most known scoring schemes with the comprehensive review of the PMF protein identification software.
Źródło:
Acta Bio-Optica et Informatica Medica. Inżynieria Biomedyczna; 2011, 17, 3; 239-247
1234-5563
Pojawia się w:
Acta Bio-Optica et Informatica Medica. Inżynieria Biomedyczna
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Transdziedzinowe aspekty struktur modularnych. O aplikacji modularyzacji w ramach inżynierii wiedzy i kognitywistyki.
Trans-Domain Aspects of Modular Structures. Applying Modularization in Knowledge Engineering and Cognitive Science.
Autorzy:
Fedyniuk, Adam
Powiązania:
https://bibliotekanauki.pl/articles/521718.pdf
Data publikacji:
2017
Wydawca:
Uniwersytet Warmińsko-Mazurski w Olsztynie
Tematy:
metamodelowanie
modularność
inżynieria wiedzy
konektomika
proteomika
centralność
teoria sieci,
ontologie
interdyscyplinarność
metamodeling
modularity
knowledge engineering connectomics, proteomics
centrality
network theory
ontologies
interdisciplinarity
Opis:
Zastosowanie struktury modularnej w ramach różnych rozwiązań: tak inżynieryjnych, jak i teoretycznych niesie ze sobą pewne ograniczenia. Problemy te są bardzo widoczne w obrębie dyskursu na temat projektowania modularnych ontologii oraz wdrażania technologii Semantic Web. Pomimo szerokiego zakresu problemów związanych z aplikacją modularności w inżynierii wiedzy, istnieje wciąż niewyczerpane źródło innowacji oraz nowoczesnych inspiracji dla przezwyciężania problemów z metamodelowaniem, projektowaniem oraz hybrydyzacją systemów reprezentacji wiedzy. Inspirowanie się naturalnymi przejawami struktur modularnych może stanowić źródło wielu innowacji oraz podłoże do opracowania nowych podejść tak w dziedzinie inżynierii wiedzy, jak kognitywistyki. Z uwagi na nawiązanie do obliczeniowego charakteru struktur modularnych obecnych w rozmaitych dziedzinach o charakterze interdyscyplinarnym, można dotrzeć do konkluzji, że pewne obserwowalne prawidłowości związane z organizacją sieci (np. stopniami i rodzajami centralności) są w istocie transdziedzinowe (tzn. wykraczają poza dziedzinę, w której zostały pierwotnie zastosowane, mając potencjał do wykorzystania w innej dziedzinie badającej struktury relacyjne różnego rodzaju) bądź przynajmniej mają charakter projekcyjny w odniesieniu do metamodelowania ontologii.
The application of modular structure in the context of various solutions, both engineering and theoretical, possesses certain limitations. The problems that arise are very salient amidst the discourse concerning the design of modular ontologies and implementation of Semantic Web technologies. Despite a wide array of obstacles related to aptly used modularity in knowledge engineering, there is still a never-ending source of inspiration for the solutions concerning metamodeling, designing and hybridizing knowledge representation systems. Being inspired by natural occurrences of modular structures can be a potent source of innovation and a foundation for developing new approaches both in the domain of knowledge engineering and cognitive science. Due to reference to the computational character of the modular structures present in various domains that are deemed interdisciplinary, one can arrive at the conclusion that certain observed regularities connected with network organisation (i.e., centrality types and measures) are in fact trans-domain (they go beyond their respective domain and have application in a different domain that concerns itself with studying relational structures of various forms) or they possess at least the projectional character in regard to ontology metamodeling.
Źródło:
Humanistyka i Przyrodoznawstwo; 2017, 23; 25-41
1234-4087
Pojawia się w:
Humanistyka i Przyrodoznawstwo
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Identyfikacja białek z wykorzystaniem techniki Peptide Mass. Część I - charakterystyka eksperymentu identyfikacji
The identification of proteins by Peptide Mass Fingerprinting (PMF). Part I - properties of the identification experiment
Autorzy:
Kamińska, H.
Podbielska, H.
Powiązania:
https://bibliotekanauki.pl/articles/261316.pdf
Data publikacji:
2011
Wydawca:
Politechnika Wrocławska. Wydział Podstawowych Problemów Techniki. Katedra Inżynierii Biomedycznej
Tematy:
proteomika
identyfikacja protein
spektrometria masowa
schematy scoringu
proteomics
identification of proteins
mass spectrometry
peptide mass fingerprinting
scoring schemes
Opis:
Wprowadzenie w spektrometrach jonizacji typu MALDI zrewolucjonizowało proces identyfikacji białek. Automatyzacja procesu identyfikacji oraz bezpośrednie połączenie analizy spektrometrem masowym z separacją białek dwuwymiarową elektroforezą żelową (2D-GE) pociągnęły za sobą znaczny rozwój proteomiki. Późniejszy rozrost proteomicznych baz danych pozwolił na zwiększenie dokładności identyfikacji, z wykorzystaniem pierwszej w historii techniki wydajnej identyfikacji białek – peptide mass fingerprinting, w skrócie: PMF. Metoda peptide mass fingerprinting pozwala identyfikować białka z widm masowych uzyskanych w wyniku analizy próbki spektrometrem masowym. Przez wzgląd na powszechność stosowania metody, jak i ciągle obserwowane jej ulepszenia, autorzy postanowili podsumować obecny stan wiedzy w tym zakresie. Praca została podzielona na dwie części: w pierwszej znajduje się opis historii powstania metody PMF wraz z charakterystyką części eksperymentalnej i opisem najpopularniejszych baz danych stosowanych przy identyfikacji, natomiast druga część pracy jest poświęcona zagadnieniom algorytmicznym, związanym z wyszukiwaniem w bazie danych protein najlepiej odzwierciedlających białko analizowane w próbce. Specyfikacja eksperymentu w pierwszej części pracy uwzględnia zarówno opis metody separacji, trawienia białek w próbce, jak i późniejszej ich analizy z wykorzystaniem spektrometru masowego. Eksperymentalne fazy metody PMF są opisane z uwzględnieniem ich cech biochemicznych, mających wpływ na dalsze etapy schematu identyfikacji.
The development of MALDI ionization method in mass spectrometers, had revolutionized the protein identification procedure. The automation of an identification procedure and the mass spectrometry direct connection to the protein separation with the two-dimensional gel electrophoresis (2D-GE) implicated the significant proteomics development. The later growth of the proteomics databases contributed to the enhancement of the identification accuracy, by using the first method of effective protein identification in the history: the peptide mass fingerprinting (PMF). The peptide mass fingerprinting enabled the protein identification from the mass spectra acquired by the mass spectrometry sample analysis. Due to the common use of method and its continuous improvements, the authors decided to summarize the current state of the knowledge in this field of science. The publication is divided into two parts. The first one is devoted to the origins of PMF scheme, the characteristics of its experimental part and a description of the most popular databases used in the identification procedure. The second part relates to the algorithmic issues of searching the database protein, which reflects the sample content in the best way. The experiment specification in the first part takes into the consideration the description of separation and sample digestion methods, as well as the later protein sample analysis by the mass spectrometer. The experimental steps of the PMF method are described according to their biochemical properties, having an impact for the later stages of the identification procedure.
Źródło:
Acta Bio-Optica et Informatica Medica. Inżynieria Biomedyczna; 2011, 17, 2; 153-160
1234-5563
Pojawia się w:
Acta Bio-Optica et Informatica Medica. Inżynieria Biomedyczna
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Identification of serum proteome components associated with progression of non-small cell lung cancer
Autorzy:
Pietrowska, Monika
Jelonek, Karol
Michalak, Malwina
Roś, Małgorzata
Rodziewicz, Paweł
Chmielewska, Klaudia
Polański, Krzysztof
Polańska, Joanna
Gdowicz-Kłosok, Agnieszka
Giglok, Monika
Suwiński, Rafał
Tarnawski, Rafał
Dziadziuszko, Rafał
Rzyman, Witold
Widłak, Piotr
Powiązania:
https://bibliotekanauki.pl/articles/1039297.pdf
Data publikacji:
2014
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
cancer staging
early detection
lung cancer
proteomics
serum biomarkers
Opis:
The aim of the present study was to perform comparative analysis of serum from patients with different stages of non-small cell lung cancer (NSCLC) using the three complementary proteomic approaches to identify proteome components associated with the progression of cancer. Serum samples were collected before any treatment from 200 patients with NSCLC, including 103 early stage, 64 locally advanced and 33 metastatic cancer samples, and from 200 donors without malignancy. The low-molecular-weight fraction of serum proteome was MALDI-profiled in all samples. Serum proteins were characterized using 2D-PAGE and LC-MS/MS approaches in a representative group of 30 donors. Several significant differences were detected between serum samples collected from patients with early stage cancer and patients with locally advanced cancer, as well as between patients with metastatic cancer and patients with local disease. Of note, serum components discriminating samples from early stage cancer and healthy persons were also detected. In general, about 70 differentiating serum proteins were identified, including inflammatory and acute phase proteins already reported to be associated with the progression of lung cancer (serum amyloid A or haptoglobin). Several differentiating proteins, including apolipoprotein H or apolipoprotein A1, were not previously associated with NSCLC. No significant differences in patterns of serum proteome components were detected between patients with adenocarcinoma and squamous cell carcinoma. In conclusion, we identified the biomarker candidates with potential importance for molecular proteomic staging of NSCLC. Additionally, several serum proteome components revealed their potential applicability in early detection of the lung cancer.
Źródło:
Acta Biochimica Polonica; 2014, 61, 2; 325-331
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
    Wyświetlanie 1-37 z 37

    Ta witryna wykorzystuje pliki cookies do przechowywania informacji na Twoim komputerze. Pliki cookies stosujemy w celu świadczenia usług na najwyższym poziomie, w tym w sposób dostosowany do indywidualnych potrzeb. Korzystanie z witryny bez zmiany ustawień dotyczących cookies oznacza, że będą one zamieszczane w Twoim komputerze. W każdym momencie możesz dokonać zmiany ustawień dotyczących cookies