A pair of 4D NMR experiments for the backbone assignment of disordered proteins is presented. The experiments exploit (13)C direct detection and non-uniform sampling of the indirectly detected dimensions, and provide correlations of the aliphatic proton (H(α), and H(β)) and carbon (C(α), C(β)) resonance frequencies to the protein backbone. Thus, all the chemical shifts regularly used to map the transient secondary structure motifs in the intrinsically disordered proteins (H(α), C(α), C(β), C', and N) can be extracted from each spectrum. Compared to the commonly used assignment strategy based on matching the C(α) and C(β) chemical shifts, inclusion of the H(α) and H(β) provides up to three extra resonance frequencies that decrease the chance of ambiguous assignment. The experiments were successfully applied to the original assignment of a 12.8 kDa intrinsically disordered protein having a high content of proline residues (26 %) in the sequence.
- MeSH
- Carbon Isotopes chemistry MeSH
- Molecular Sequence Data MeSH
- Nuclear Magnetic Resonance, Biomolecular methods MeSH
- Proline chemistry MeSH
- Proteins chemistry MeSH
- Protein Structure, Secondary MeSH
- Amino Acid Sequence MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Two novel 5D NMR experiments (CACONCACO, NCOCANCO) for backbone assignment of disordered proteins are presented. The pulse sequences exploit relaxation properties of the unstructured proteins and combine the advantages of (13)C-direct detection, non-uniform sampling, and longitudinal relaxation optimization to maximize the achievable resolution and minimize the experimental time. The pulse sequences were successfully tested on the sample of partially disordered delta subunit from RNA polymerase from Bacillus subtilis. The unstructured part of this 20 kDa protein consists of 81 amino acids with frequent sequential repeats. A collection of 0.0003% of the data needed for a conventional experiment with linear sampling was sufficient to perform an unambiguous assignment of the disordered part of the protein from a single 5D spectrum.
- MeSH
- Bacillus subtilis enzymology MeSH
- Bacterial Proteins chemistry MeSH
- DNA-Directed RNA Polymerases chemistry MeSH
- Carbon Isotopes MeSH
- Protein Conformation MeSH
- Nuclear Magnetic Resonance, Biomolecular methods MeSH
- Proteins chemistry MeSH
- Amino Acid Sequence MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
... Exercises 45 -- 4 Theoretical distributions 48 -- 4.1 Introduction 48 -- 4.2 Probability 49 -- 4.3 Samples ... ... distribution 63 -- 4.8 The Poisson distribution 66 -- 4.9 Mathematical calculations 68 -- 4.10 The Uniform ... ... 149 -- Exercises 149 -- 8 Principles of statistical analysis 152 -- 8.1 Introduction 152 -- 8.2 Sampling ... ... distributions 153 -- 8.3 A demonstration of the distribution of sample means 155 -- 8.4 Estimation 160 ... ... -- 8.5 Hypothesis testing 165 -- 8.6 Non-parametric methods 171 -- 8.7 Statistical modelling 173 -- ...
First edition xii, 611 stran : ilustrace ; 25 cm
- MeSH
- Data Interpretation, Statistical MeSH
- Medicine MeSH
- Computers MeSH
- Data Collection MeSH
- Statistics as Topic MeSH
- Research MeSH
- Publication type
- Monograph MeSH
A strategy for complete backbone and side-chain resonance assignment of disordered proteins with highly repetitive sequence is presented. The protocol is based on three resolution-enhanced NMR experiments: 5D HN(CA)CONH provides sequential connectivity, 5D HabCabCONH is utilized to identify amino acid types, and 5D HC(CC-TOCSY)CONH is used to assign the side-chain resonances. The improved resolution was achieved by a combination of high dimensionality and long evolution times, allowed by non-uniform sampling in the indirect dimensions. Random distribution of the data points and Sparse Multidimensional Fourier Transform processing were used. Successful application of the assignment procedure to a particularly difficult protein, δ subunit of RNA polymerase from Bacillus subtilis, is shown to prove the efficiency of the strategy. The studied protein contains a disordered C-terminal region of 81 amino acids with a highly repetitive sequence. While the conventional assignment methods completely failed due to a very small differences in chemical shifts, the presented strategy provided a complete backbone and side-chain assignment.
- MeSH
- Algorithms MeSH
- Deuterium MeSH
- Fourier Analysis MeSH
- Nitrogen Isotopes MeSH
- Carbon Isotopes MeSH
- Molecular Sequence Data MeSH
- Nuclear Magnetic Resonance, Biomolecular methods MeSH
- Proteins chemistry MeSH
- Repetitive Sequences, Nucleic Acid MeSH
- Protein Structure, Secondary MeSH
- Amino Acid Sequence MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
The human diet is recognised as one possible major exposure route to the overall perfluorinated alkylated substances (PFAS) burden of the human population, resulting directly from contamination of dietary food items, as well as migration of PFAS from food packaging or cookware. Most European countries carry out national monitoring programs (food basket studies) to monitor contamination with pollutants. Usually, for PFASs, non-coordinated approaches are used in Europe, since food basket studies are mainly carried out by national authorities following national requirements and questions, making comparisons between different countries difficult. A harmonised sampling campaign collecting similar food items in a uniform procedure enabling direct comparison between different regions in Europe was designed. We selected four countries (Belgium, Czech Republic, Italy and Norway), representing the four regions of Europe: West, East, South and North. In spring 2010 and 2011, 20 different types of vegetables were sampled in Belgium, Czech Republic, Italy and Norway. Perfluorinated carboxylic acids (PFCAs) were the main group of detected PFASs, with perfluorinated octanoic acid (PFOA) as the most abundant PFCA (with exception of samples from Czech Republic), followed by perfluorinated hexanoic acid and perfluorinated nonanoic acid. Dietary intake estimates for PFOA show only low human exposure due to vegetable consumption for adults and children, mostly governed by high intake of potatoes.
- MeSH
- Diet statistics & numerical data MeSH
- Child MeSH
- Adult MeSH
- Fluorocarbons analysis MeSH
- Soil Pollutants analysis MeSH
- Humans MeSH
- Hazardous Substances analysis MeSH
- Environmental Exposure analysis statistics & numerical data MeSH
- Vegetables chemistry MeSH
- Environmental Pollution statistics & numerical data MeSH
- Check Tag
- Child MeSH
- Adult MeSH
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Belgium MeSH
- Czech Republic MeSH
- Italy MeSH
- Norway MeSH
Camera trapping with capture-recapture analyses has provided estimates of the abundances of elusive species over the last two decades. Closed capture-recapture models (CR) based on the recognition of individuals and incorporating natural heterogeneity in capture probabilities are considered robust tools; however, closure assumption is often questionable and the use of an Mh jackknife estimator may fail in estimations of real abundance when the heterogeneity is high and data is sparse. A novel, spatially explicit capture-recapture (SECR) approach based on the location-specific capture histories of individuals overcomes the limitations of closed models. We applied both methods on a closed population of 16 critically endangered Western Derby elands in the fenced 1,060-ha Fathala reserve, Senegal. We analyzed the data from 30 cameras operating during a 66-day sampling period deployed in two densities in grid and line arrays. We captured and identified all 16 individuals in 962 trap-days. Abundances were estimated in the programs CAPTURE (models M0, Mh and Mh Chao) and R, package secr (basic Null and Finite mixture models), and compared with the true population size. We specified 66 days as a threshold in which SECR provides an accurate estimate in all trapping designs within the 7-times divergent density from 0.004 to 0.028 camera trap/ha. Both SECR models showed uniform tendency to overestimate abundance when sampling lasted shorter with no major differences between their outputs. Unlike the closed models, SECR performed well in the line patterns, which indicates promising potential for linear sampling of properly defined habitats of non-territorial and identifiable herbivores in dense wooded savanna conditions. The CR models provided reliable estimates in the grid and we confirmed the advantage of Mh Chao estimator over Mh jackknife when data appeared sparse. We also demonstrated the pooling of trapping occasions with an increase in the capture probabilities, avoiding violation of results.
- MeSH
- Population Density * MeSH
- Ruminants * MeSH
- Models, Theoretical * MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Senegal MeSH
We aimed to determine the impact of Ca(2+)-related disorders induced in intact animal hearts on ultrastructure of the cardiomyocytes prior to occurrence of severe arrhythmias. Three types of acute experiments were performed that are known to be accompanied by disturbances in Ca(2+) handling. Langedorff-perfused rat or guinea pig hearts subjected to K(+)-deficient perfusion to induce ventricular fibrillation (VF), burst atrial pacing to induce atrial fibrillation (AF) and open chest pig heart exposed to intramyocardial noradrenaline infusion to induce ventricular tachycardia (VT). Tissue samples for electron microscopic examination were taken during basal condition, prior and during occurrence of malignant arrhythmias. Cardiomyocyte alterations preceding occurrence of arrhythmias consisted of non-uniform sarcomere shortening, disruption of myofilaments and injury of mitochondria that most likely reflected cytosolic Ca(2+) disturbances and Ca(2+) overload. These disorders were linked with non-uniform pattern of neighboring cardiomyocytes and dissociation of adhesive junctions suggesting defects in cardiac cell-to-cell coupling. Our findings identified heterogeneously distributed high [Ca(2+)](i)-induced subcellular injury of the cardiomyocytes and their junctions as a common feature prior occurrence of VT, VF or AF. In conclusion, there is a link between Ca(2+)-related disorders in contractility and coupling of the cardiomyocytes pointing out a novel paradigm implicated in development of severe arrhythmias.
- MeSH
- Potassium MeSH
- Homeostasis MeSH
- Myocytes, Cardiac metabolism ultrastructure MeSH
- Rats MeSH
- Guinea Pigs MeSH
- Norepinephrine MeSH
- Calcium Metabolism Disorders complications pathology MeSH
- Swine MeSH
- Arrhythmias, Cardiac etiology metabolism MeSH
- Animals MeSH
- Check Tag
- Rats MeSH
- Guinea Pigs MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
It has been observed that the prevalence of dental caries among children has declined in the last decade in Germany. However, despite of these improvements there is still a proportion of children suffering from dental decay. AIMS: The aims of this study were to evaluate if a social gradient in the prevalence of dental caries exists and, based on those findings, to develop a strategy to target those children with heightened risk to develop dental caries in order to assist oral health care professionals to refocus the current uniform school-based dental health programme to a caries preventive strategy based on a directed population approach. DESIGN: A representative, random sample of 12-year olds in Freiburg (Germany) was examined and dental caries was recorded using WHO criteria. Educational attainment of the child's parents was used as an indicator of socio-economic status and classified by use of the CASMIN Educational Classification. RESULTS: A total of 322 children participated. An examination of dental caries score revealed that its distribution was positively skewed. For this reason this study provides summary analyses based on medians and a non-parametric rank-sum test. The Kruskal-Wallis H-test showed a significant difference between median scores across the different educational levels (p-value = 0.015) which was due to lower dental caries levels in children with non-deprived social background. CONCLUSIONS: In order to reduce current social inequalities in child oral health the current uniform school-based dental health programme at secondary school level should be developed to a targeted school-based screening and prevention programme.
Ciele. Prítomnosť odlišného fungovania položiek (DIF) v psychodiagnostickom nástroji môže indikovať prítomnosť skreslenia medzi skúmanými skupinami. Štúdia je zameraná na analýzu DIF medzi mužmi a ženami v slovenskej verzii NEO päťfaktorového osobnostného inventára (NEO-FFI). Výskumný súbor. Výskumný súbor tvorí 1016 respondentov (40,6% mužov) zo Slovenska, s priemerným vekom 25,97 rokov (SD= 13,42). Štatistická analýza. Pre analýzu DIF bolo využitý Mantelov test v programe DIFAS 5.0, ordinálna logistická regresia a metóda Poly-SIBTEST. Výsledky. Finálne bolo identifikovaných 18 položiek so stredným alebo veľkým DIF, 6 z nich bolo identifikovaných všetkými tromi použitými metódami. Jedna položka vykazovala neuniformné DIF. Odstránenie identifikovaných DIF položiek spôsobilo významnejšiu zmenu v miere rodových rozdielov v škále Otvorenosť voči skúsenosti. Možné faktory spôsobujúce DIF sú diskutované. Prítomnosť identifikovaných DIF položiek nenaznačuje, že NEO-FFI je závažne skresľujúce voči mužom alebo ženám. Obmedzenia štúdie. Limitáciou tejto štúdie je najmä použitie všeobecného výskumného súboru. Ďalšie štúdie by mohli overiť tieto zistenia na vekovo špecifických súboroch.
Objectives. Presence of differential item functioning (DIF) in psychological measurement tools can indicate the presence of bias between groups. The present study is focused on analysing DIF between males and females in the Slovak version of NEO Five Factor Inventory (NEO-FFI). Sample and settings. The sample consists of 1016 respondents (40,6% males) from Slovakia, with mean age of 25.97 years (SD=13.42). Statistical analysis. For DIF analysis Mantel’s test in DIFAS 5.0 software, ordinal logistic regression and Poly-SIBTEST were used. Results. The final results show 18 items with medium and large uniform DIF, 6 of them identified by all the methods used. One item showing purely non-uniform DIF was identified. Deletion of identified DIF items caused notable change in scale score differences between males and females in Openness to experience scale. Possible factors causing DIF are discussed. Presence of the identified DIF items does not suggest that NEO-FFI is severely biased against males or females. Limitation. Limitation of the present study lies mainly in the general sample. Future studies should verify these findings on age specific samples.
- Keywords
- Big Five,
- MeSH
- Adult MeSH
- Extraversion, Psychological MeSH
- Gender Identity * MeSH
- Data Interpretation, Statistical MeSH
- Introversion, Psychological MeSH
- Middle Aged MeSH
- Humans MeSH
- Adolescent MeSH
- Young Adult MeSH
- Neuroticism MeSH
- Personality Inventory * MeSH
- Aged, 80 and over MeSH
- Aged MeSH
- Self Report MeSH
- Check Tag
- Adult MeSH
- Middle Aged MeSH
- Humans MeSH
- Adolescent MeSH
- Young Adult MeSH
- Aged, 80 and over MeSH
- Aged MeSH
Description of protein dynamics is known to be essential in understanding their function. Studies based on a well established [Formula: see text] NMR relaxation methodology have been applied to a large number of systems. However, the low dispersion of [Formula: see text] chemical shifts very often observed within intrinsically disordered proteins complicates utilization of standard 2D HN correlated spectra because a limited number of amino acids can be characterized. Here we present a suite of triple resonance HNCO-type NMR experiments for measurements of five [Formula: see text] relaxation parameters ([Formula: see text], [Formula: see text], NOE, cross-correlated relaxation rates [Formula: see text] and [Formula: see text]) in doubly [Formula: see text],[Formula: see text]-labeled proteins. We show that the third spectral dimension combined with non-uniform sampling provides relaxation rates for almost all residues of a protein with extremely poor chemical shift dispersion, the C terminal domain of [Formula: see text]-subunit of RNA polymerase from Bacillus subtilis. Comparison with data obtained using a sample labeled by [Formula: see text] only showed that the presence of [Formula: see text] has a negligible effect on [Formula: see text], [Formula: see text], and on the cross-relaxation rate (calculated from NOE and [Formula: see text]), and that these relaxation rates can be used to calculate accurate spectral density values. Partially [Formula: see text]-labeled sample was used to test if the observed increase of [Formula: see text] [Formula: see text] in the presence of [Formula: see text] corresponds to the [Formula: see text] dipole-dipole interactions in the [Formula: see text],[Formula: see text]-labeled sample.
