What's the Problem? Cultural Capability and Learning from Historical Performance

Contains the cis-eQTLs with P value < 5 % for T-cells obtained from early undifferentiated arthritis patients. (TXT 1162 kb

Cell attachment of human dermal fibroblasts to fibrillin-1 and fibrillin-2 protein fragments.

<p>(A) Cell attachment of human dermal fibroblasts (HDF) to PF17-1, PF17-2 and PF17-1 WMS. HDF were added to cell culture plate wells pre-incubated with increasing concentrations of protein fragments (0–10 nM), for 1 hour. After removal of non-adhered cells, adhered cells were stained with crystal violet and the optical densities (OD) at 570 nm were measured as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048634#s2" target="_blank">Materials and Methods</a>. Values were normalized to the percentage of cell attachment of PF17-1 at 10 nM. Also shown are the statistical significances of the difference to PF17-1 where P value <0.05, *; <0.01, **.</p

Calculated radii of gyration and hydrodynamic radii of PF17-1 and PF17-1 WMS.

<p>Table showing the calculated values for hydrodynamic radius, radius of gyration, and frictional ratios for protein fragments PF17-1 and PF17-1 WMS. Values from experimental results (exp) were calculated from SAXS data (using Guinier approximation) and analytical ultracentrifugation data (AUC) (using Sednterp). Theoretical (theo) values for the hydrodynamic radius and radius of gyration were calculated from rigid-body models generated from SAXS data using SASREF, using the programs CRYSOL, HYDROPRO and SOMO. Theoretical frictional ratio values were also calculated from rigid –body models using HYDROPRO.</p

Schematic of recombinant fibrillin-1 and fibrillin-2 domain swap fragments and their heparin binding properties.

<p>(A) Domain structures of fibrillin-1 and fibrillin-2 are shown, with a key of the different domains, N-glycosylation sites, and the C-terminal furin cleavage site. Fibrillin-1 contains a proline-rich region and fibrillin-2 contains a glycine-rich region. A protein fragment containing the cell adhesion RGD site (indicated) of TB4 (white fill) and heparin binding site of TB5 (black fill) was produced for fibrillin-1 (PF17-1) and fibrillin-2 (PF17-2). (B) All protein fragments used in this study are shown indicating which domains have been swapped. Fibrillin-1 domains are shown in light grey and Fibrillin-2 domains shown in dark grey, along with the number indicating the position on SDS-PAGE. (C) SDS-PAGE of all PF17-1 and PF17-2 fragments run under non-reducing (NR) and reducing conditions (R). All proteins run between the 75 and 100 Kda protein markers. (D) Heparin binding of PF17-1, PF17-2 and PF17-1/2 domain swaps. Binding was analyzed using Surface Plasmon Resonance, and the response difference (Resp. Diff.) normalized to PF17-1 response level at 800 nM for each experiment and was plotted against concentration. Resp. Diff. is the heparin-immobilized flow cell minus the control flow cell. The value shown is average normalized response difference and SEM of three separate experiments. Representative sensorgrams are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048634#pone.0048634.s001" target="_blank">Figure S1</a>. (<b>E</b>) Graph plotting the average normalized response difference to PF17-1 and SEM at 800 nM of at least three separate experiments. Also shown are the statistical significance of the difference to PF17-1 where P value = >0.05 ns; <0.001 ***.</p

Heparin binding of the GD/AD mutants of fibrillin-1 protein fragment PF17-1.

<p>(A) Sequence of human FBN 1 TB5, indicating the fibrillin-1 residue positions of the GD/AD point mutations along with their corresponding phenotype. (B) Heparin binding of PF17-1, and the GD/AD point mutations. Binding was analyzed using surface plasmon resonance, and the average response difference (Resp. Diff.) for three separate experiments normalized to PF17-1 response level at 400 nM for each experiment and SEM is shown. Resp. Diff is the heparin-immobilized flow cell minus the control flow cell. Also shown are the statistical significances of the difference to PF17-1 where P value >0.05, ns; <0.001, ***. (C) Structural model of fibrillin-1 TB5 (orange) and anterior/posterior cbEGF domains (cyan), showing the position of the GD/AD point mutations (i). Also shown (ii) is the same structural model indicating the region of the WMS deletion (magenta) and the Arg residues implicated in heparin binding (shown as spheres). The structural model was created using SwissModel as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048634#s2" target="_blank">Material and Methods</a>.</p

Rigid-body models of PF17-1 and PF17-1 WMS generated from SAXS analysis. (

<p>A) Rigid Body models were generated from experimental scattering data for PF17-1 and PF17-1 WMS using SASREF. Over 20 rigid-body models were generated for each experiment and the resulting models were aligned, and a volume frequency map was generated using DAMAVER. The most probable shape from the frequency map was generated using DAMFILT, which is shown in magenta for PF17-1 and green for PF17-1 WMS, along with the rigid body model for each protein fragment that had the lowest chi squared value determined by SASREF. The overlaid/merge of the PF17-1 and PF17-1 WMS DAMFILT structures, showing their similarity are shown in the center. (B) Rigid-body model of PF17-1, showing the cbEGF domains in cyan and dark teal and TB domains in orange. The position of the RGD motif of TB4 is shown in red and the position of the 8 amino acid deletion in PF17-1 WMS is shown in magenta. (C) Model of EGF28-TB5-EGF29 of PF17-1, showing the four Arg residues involved in heparin binding as ball and sticks and the loop of 8 amino acids deleted in PF17-1WMS in magenta. The structural model was created using SwissModel, as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048634#s2" target="_blank">Materials and Methods</a>.</p

Heparin binding of the point mutations of fibrillin-2 protein fragment PF17-2.

<p>(A) Sequence alignment of human fibrillin-1 and fibrillin-2 TB5, indicating the fibrillin-1 residue positions of the two heparin binding sites (indicated), and the corresponding residue numbers of fibrillin-2. Boxed section represents the 8 amino acid WMS deletion. (B) Heparin binding of PF17-1, PF17-2 and PF17-2 point mutations, including a fragment with all four point mutations designated PF17-2 Quad. Binding was analyzed using Surface Plasmon Resonance, and the average response difference (Resp. Diff.) for three separate experiments normalized to PF17-1 response level at 800 nM for each experiment and SEM is shown. Resp. Diff is the heparin-immobilized flow cell minus the control flow cell. Also shown are the statistical significances of the difference to PF17-1 where P value >0.05, ns; <0.05, *; <0.01, **; <0.001, ***. A representative sensorgram for all concentrations and affinity plots is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048634#pone.0048634.s002" target="_blank">Figure S2</a>. (C) Structural model of fibrillin-2 TB5 (beige) and anterior/posterior EGF domains (red), showing the position of the point mutations, which fall on either side of the TB domain, indicating the two heparin binding sites. A structural model was created using SwissModel, as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048634#s2" target="_blank">Material and Methods</a>.</p

Heparin binding of the WMS mutant of fibrillin-1 protein fragment PF17-1. (

<p>A) Sequence trace from mammalian expression vector pCEP-pu/AC7 containing fibrillin-1 PF17-1 WMS mutant. The sequence trace generated by Finch TV V1.4 with the two codons either side of the 24 bp deletion (boxed) is shown. Below is a section of the resulting Blast search showing the alignment with human fibrillin-1, indicating the same two codons. Also shown is the corresponding amino acid sequence aligned with the last base pair of each codon. (B) Chromatographic trace of size exclusion chromatography of PF17-1 WMS fragment using Superdex S200 10/300 GL column (GE Healthcare), showing peaks and retention volume of monomer and dimer of PF17-1 WMS. (C) SDS-PAGE of all PF17-1 WMS monomer and dimer fragments run under non-reducing (NR) and reducing conditions (Red). (D) Heparin binding of PF17-1, PF17-1 WMS monomer and dimer protein fragments. Binding was analyzed using Surface Plasmon Resonance, and the response difference (Resp. Diff.) normalized to PF17-1 response level at 800 nM for each experiment was plotted against concentration. Resp. Diff. is the heparin-immobilized flow cell minus the control flow cell. The value shown is average normalized Resp. Diff. and SEM of three separate experiments. Representative sensorgrams are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048634#pone.0048634.s003" target="_blank">Figure S3C</a>.</p

Type II diabetes mellitus and cardiovascular markers in humans: a prospective study in hellenic homogeneous population

Approximately 200 million people, worldwide, are currently having Type 2 diabetes mellitus (T2DM), a prevalence that has been predicted to increase to 366 million by 2030. Atherosclerotic coronary heart disease (CHD) and other forms of cardiovascular disease (CYD) are the major cause of mortality in T2DM as well as a major contributor to morbidity and lifetime costs. A number of unfavorable conditions predisposing to CVD coexist with diabetic status including hyperglycaemia, dyslipidaemia, inflammation and coagulation, many of which may be closely associated with insulin resistance. In addition, mutations and polymorphisms in a number of genes have also been linked with monogenic and polygenic forms of T2DM. In this respect, the possible relationship between these disorders and a number of biochemical factors in a selection of different age groups of diabetic patients was studied. The purpose of the present work was the identification of biochemical parameters in plasma, which may serve as predisposition factors to CVD in T2DM patients of different age. The variability of hyperglycaemia, dyslipidaemia, and inflammation with age progression were studied. Four different diabetic groups allocated based on the subjects age (Group A:15-25 years old; Group 13:26-40 years old; Group C:40-60 years old; Group D:60-80 years old) and consisting of ten patients each, in parallel with ten matched for age, sex and ethnic origin healthy controls, were screened for glucose, insulin, lipid profile (total cholesterol, triglycerides, LDL and HDL) and inflammatory mediators (Homocysteine, CRP, IL-6, TNF-a). Significant differences were observed between the expression of biochemical markers among different age groups. Hyperglycaemia showed no variability with age whereas dyslipidaemia correlated positively with age progression, as well as obesity, low physical activity and family history of heart disease or diabetes. Marked inflammation was prominent only in Groups C and D. The present study indicates that different biochemical parameters may be used for assessment of CVD risk in T2DM patients of variable age

Overview of MS 6q23 interactions.

<p>Tracks are labelled as follows: A–LD regions targeted in ‘region’ Capture Hi-C; B–Gene regions targeted in ‘promoter’ Capture Hi-C; C–RefSeq genes (packed for clarity); D–MS index SNPs; E–MS LD regions; F–Interactions observed in the GM12878 B-cell line and G–Interactions observed in the Jurkat T-cell line. Promoter and region Capture Hi-C experiments have been merged for clarity. The genomic region chr6:136,650,000–137,280,000 has been omitted for clarity. All co-ordinates are based on GRCh37. Generated using the WashU EpiGenome Browser (<a href="http://epigenomegateway.wustl.edu/browser/" target="_blank">http://epigenomegateway.wustl.edu/browser/</a>).</p