PDBFlex: exploring flexibility in protein structures.

The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software

Computational analysis of the active sites in binary and ternary complexes of the vitamin D receptor

Abstract We have developed a program CCOMP that compares overlapping fragments of two protein complexes and identifies differently oriented amino acids. CCOMP initially performs a sequence alignment of the analyzed receptors, then superimposes the corresponding aligned residues, and finally calculates the root mean square deviation (RMSD) of individual atoms, every amino acid and the entire complex. Thus, amino acids important for functional differences between both complexes can be detected. Application of CCOMP to 1␣,25-(OH) 2 D 3 -hVDR (1DB1) [Proc. Natl. Acad. Sci. U.S.A. 9

Droplet-Microscopy of the Protozoa

The world of the protozoa is one that is still not wholly understood, and certainly not by the average person. Of course one thing that can be immediately appreciated is the many interesting nuances amongst their number (something that is not lost on the creator of this site, one Piotr Rotkiewicz, who holds a PhD in chemistry). The site itself contains 184 pictures (drawn from 84 genera) of various protozoa, ranging from the well-known paramecium to the marine spiroloculina. All of the images have been taken by a number of different microscopes, and visitors to the site are also provided with some detailed information about these devices. The site has a nice collage that brings together images of protozoa from 45 different genera that gives users some sense of the relative size of each organism. The site is rounded out by an extensive set of outside links to other relevant websites, and a list of suggested readings

Comparison of tomographic coronary artery calcification index (calcium score) and ultrasonographic measurement of intima-media complex thickness in diabetic subjects

Background: At present, there is a number of diagnostic imaging procedures allowing for the evaluation of atherosclerosis. The earliest, subclinical stage of atherosclerosis can be visualized with the development of computed tomography (CT) and ultrasound (US) techniques. Therefore, the purpose of this study was to assess the degree of coronary artery calcification and carotid intima-media thickness in diabetic subjects divided into different age groups. Material/Methods: Fifty-six men, aged from 18 to 72 were included in the study. Participants were divided into 4 groups according to age (18-30, 31-45, 46-60 and more than 60 years). Two tests were performed: coronary calcium score (CS) determination and intima-media thickness (IMT) in ultrasound. CS was performed using a multi-slice scanner. Images were analyzed using the Agatson method. Ultrasound examinations were performed using a 9-12-MHz linear transducer. Results: The correlation coefficient between calcium score index (CSI) and age of patients was 0.52 (p<0.001). The correlation between duration of diabetes and CSI was significantly lower (r=0.3; p<0.05). The increase of IMT is associated with age to a much greater extent and the correlation coefficient was 0.63 (p<0.001). IMT depended on the duration of diabetes, but the correlation was also weak (r=0.35; p<0.01). Conclusions: Comparison of the findings obtained in the presented study and in the group of healthy subjects proves that influence of diabetes on vascular deterioration may be observed, even among young individuals. Obtained results allow to make the following conclusions: 1. Calcium score index remains low in the group of male patients with diabetes before the age of 45. 2. Intima-media thickness correlates well with age (r=0.6; p<0.05) and weaker with the duration of diabetes (r=0.35; p<0.05). 3. IMT assessment may be a useful tool to identify the increased predisposition to atherosclerosis, also before the age of 30

PDBFlex: exploring flexibility in protein structures.

The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software

Echokardiograficzna ilościowa analiza spoczynkowej funkcji mięśnia sercowego w celu oceny żywotności po zawale serca &#8212; porównanie z rezonansem magnetycznym

Background and aim: The study was set out to assess feasibility and diagnostic value of the echocardiographic quantitative analysis of the resting regional systolic function (i.e. strain and strain rate) with use of the speckle tracking (2D strain) for myocardial viability assessment in patients with acute myocardial infarction (MI) treated with primary angioplasty. The reference method was the late enhancement magnetic resonance imaging (LE MRI). Methods: The study group consisted of 40 patients (29 men, mean age 61 &#177; 9 years) in whom resting echocardiographic examination was performed 7&#8211;10 days after MI with peak systolic longitudinal strain (STS) and systolic longitudinal strain rate (SLSR) measurement by 2D strain technique on external workstation (EchoPac 6.1.0., GE Vingmed Ultrasound). Within 72 h LE MRI was performed in all patients, with visual assessment of late enhancement in all segments of the left ventricle. Viability of a segment was assessed based on two distinct, frequently adopted criteria: LE extent &#8804; 50% or &#8804; 75% of the wall thickness. Results: Due to suboptimal image quality 70 (10.9%) of the segments were excluded from 2D strain analysis. In the analysis of akinetic and dyskinetic segments, SLS and SLSR measurements with 2D strain technique had good discrimination value for viability defined as LE extent of &#8804; 75% by MRI (area under the ROC curve 0.715 and 0.705, respectively; diagnostic accuracy of the criterion SLS &#8804; &#8211;7.61% was 72.8%; diagnostic accuracy of the criterion SLSR &#8804; &#8211;0.79/s was 64.9%). However, when the &#8804; 50% viability criterion by LE MRI was used, only SLS measurement could be used for viability assessment, with sufficient diagnostic value (area under the ROC curve 0.620; diagnostic accuracy of the criterion SLS &#8804; &#8211;9.77% was 57%). In the analysis of all segments, including hypokinetic and normokinetic segments, SLS and SLSR measurements did not provide additional information, beyond that of the visual viability analysis. Conclusions: Resting quantitative echocardiographic analysis of myocardial function seems to be a promising tool for myocardial viability assessment. There is a trend towards greater diagnostic value of SLS than SLSR measurements. Kardiol Pol 2011; 69, 9: 915&#8211;922Wstęp i cel: Celem pracy była ocena możliwości zastosowania i wartości diagnostycznej echokardiograficznej ilościowej analizy spoczynkowej regionalnej funkcji skurczowej (odkształcenia i tempa odkształcenia) techniką śledzenia markerów akustycznych (2D strain) w celu oceny żywotności mięśnia sercowego u pacjentów po ostrym zawale leczonym metodą pierwotnej angioplastyki. Metodą referencyjną była technika późnego wzmocnienia w rezonansie magnetycznym (LE MRI). Metody: Do badania włączono 40 pacjentów (29 mężczyzn, śr. wiek 61 &#177; 9 lat), u których w 7.&#8211;10. dniu po zawale wykonano spoczynkowe badanie echokardiograficzne z pomiarami maksymalnego skurczowego podłużnego odkształcenia (SLS) oraz maksymalnego skurczowego tempa podłużnego odkształcenia (SLSR) techniką 2D strain na zewnętrznej stacji roboczej (EchoPac 6.1.0., GE Vingmed Ultrasound). W ciągu 72 godzin przeprowadzono u wszystkich pacjentów badanie techniką LE MRI z wizualną oceną wielkości obszaru późnego wzmocnienia w segmentach mięśnia lewej komory. Żywotność segmentów określano na podstawie dwóch różnych, powszechnie stosowanych kryteriów: LE obejmujące &#8804 50% lub &#8804 75% grubości mięśnia. Wyniki: Z powodu suboptymalnej jakości obrazu 70 (10,9%) segmentów wyłączono z analizy techniką 2D strain. W analizie segmentów akinetycznych i dyskinetycznych pomiary SLS i SLSR techniką 2D strain charakteryzowały się dobrą zdolnością do wykrywania żywotności definiowanej jako LE w MRI obejmujące 0&#8211;75% grubości mięśnia sercowego &#8212; pole pod krzywą ROC odpowiednio 0,715 i 0,705; dokładność diagnostyczna kryterium SLS &#8804; &#8211;7,61% = 72,8%; dokładność diagnostyczna kryterium SLSR &#8804 &#8211;0,79/s = 64,9%. Jednak przy zastosowaniu jako kryterium żywotności &#8804 50% grubości mięśnia objętego przez LE w MRI można w celu jej wykrywania zastosować tylko pomiar SLS, choć i on ma jedynie dostateczną wartość diagnostyczną (pole powierzchni pod krzywą ROC 0,620; dokładność diagnostyczna kryterium SLS &#8804 &#8211;9,77% = 57%). W ocenie żywotności wszystkich segmentów lewej komory (w tym ocenianych wizualnie jako normokinetyczne i hipokinetyczne) pomiary SLS i SLSR nie wnosiły dodatkowych, istotnych informacji w stosunku do wizualnej oceny kurczliwości. Wnioski: Spoczynkowa ilościowa echokardiograficzna analiza funkcji mięśnia sercowego wydaje się obiecującym narzędziem w ocenie jego żywotności. Zauważalna jest tendencja do większej wartości diagnostycznej pomiarów SLS niż SLSR. Kardiol Pol 2011; 69, 9: 915&#8211;92