An efficient procedure for genotyping single nucleotide polymorphisms

Analysis of single nucleotide polymorphisms (SNPs) has been and will be increasingly utilized in various genetic disciplines, particularly in studying genetic determinants of complex diseases. Such studies will be facilitated by rapid, simple, low cost and high throughput methodologies for SNP genotyping. One such method is reported here, named tetra-primer ARMS-PCR, which employs two primer pairs to amplify, respectively, the two different alleles of a SNP in a single PCR reaction. A computer program for designing primers was developed. Tetra-primer ARMS-PCR was combined with microplate array diagonal gel electrophoresis, gaining the advantage of high throughput for gel-based resolution of tetra-primer ARMS-PCR products. The technique was applied to analyse a number of SNPs and the results were completely consistent with those from an independent method, restriction fragment length polymorphism analysis.

Functional polymorphism in the regulatory region of gelatinase B gene in relation to severity of coronary atherosclerosis

BACKGROUND

Gelatinase B, a matrix metalloproteinase that has proteolytic activity against connective tissue proteins, has been suggested to be important in the connective tissue remodeling processes associated with atherogenesis and plaque rupture. This study tested the hypothesis that sequence variation in the promoter region of the gelatinase B gene influences its expression, predisposing individuals carrying certain genetic variants to more severe atherosclerosis.

METHODS AND RESULTS

Single-strand conformation polymorphism analysis was carried out to search the promoter region of the gene encoding gelatinase B for naturally occurring genetic variation. As a result, an unreported common polymorphism was detected, which arose from a cytosine (C) to thymidine (T) transition at position -1562 relative to the start of transcription. Transient transfection experiments and DNA-protein interaction assays indicated that the T allele had a higher promoter activity than the C allele, which appeared to be due to preferential binding of a putative transcription repressor protein to the C allelic promoter. A sample of 584 male patients with myocardial infarction and 645 age-matched male healthy control subjects were genotyped. The allele frequencies were not significantly different between the cases and control subjects. However, in 374 patients with available angiographic data, 26% of those carrying 1 or 2 copies of the T allele had >50% stenosis in 3 coronary arteries, whereas only 15% of C/C homozygotes had triple-vessel disease.

CONCLUSIONS

These data suggest that this functional genetic variation influences gelatinase B gene promoter activity in an allele-specific manner and has an effect on atherosclerotic phenotype.

Structural requirements for glycolipid antigen recognition by CD1b-restricted T cells

The human CD1b protein presents lipid antigens to T cells, but the molecular mechanism is unknown. Identification of mycobacterial glucose monomycolate (GMM) as a CD1b-presented glycolipid allowed determination of the structural requirements for its recognition by T cells. Presentation of GMM to CD1b-restricted T cells was not affected by substantial variations in its lipid tails, but was extremely sensitive to chemical alterations in its carbohydrate or other polar substituents. These findings support the view that the recently demonstrated hydrophobic CD1 groove binds the acyl chains of lipid antigens relatively nonspecifically, thereby positioning the hydrophilic components for highly specific interactions with T cell antigen receptors.

Progression of coronary atherosclerosis is associated with a common genetic variant of the human stromelysin-1 promoter which results in reduced gene expression

There is a common polymorphism in the promoter sequence of the human stromelysin-1 gene, with one allele having a run of six adenosines (6A) and the other five adenosines (5A). We have previously reported, in a 3-year follow-up study of patients with coronary atherosclerosis, that those patients who are homozygous for the 6A allele show a more rapid progression of the disease. In this study, we have investigated whether the 5A/6A promoter polymorphism plays a role in the regulation of stromelysin-1 gene expression. In transient transfection experiments, a stromelysin-1 promoter construct with 6A at the polymorphic site was found to express less of the chloramphenicol acetyltransferase reporter gene than a construct containing 5A. Electrophoretic mobility shift assay and DNase I footprinting revealed the interaction of one or more nuclear protein(s) with the DNA sequence at the 5A/6A polymorphic site. The binding of one of the nucleoprotein factors was more readily detectable with an oligonucleotide probe corresponding to the 6A allele as compared with a probe corresponding to the 5A allele. Replacing the core binding sequence with a random DNA sequence abolished the interaction between the nuclear protein(s) and the probe and also increased reporter gene expression in transiently transfected cells. Thus, the common 5A/6A polymorphism of the human stromelysin-1 promoter appears to play an important role in regulating stromelysin-1 gene expression and may be involved in the progression of coronary heart disease.

Polymorphism in matrix metalloproteinase gene promoters: implication in regulation of gene expression and susceptibility of various diseases

The matrix metalloproteinases (MMPs) can degrade a range of extracellular matrix proteins and have been implicated in connective tissue destruction and remodelling associated with cancer invasion and metastasis, cartilage destruction in arthritis, atherosclerotic plaque rupture, and the development of aneurysms. Recently, naturally occurring sequence variation has been detected in the promoter of a number of MMP genes. These genetic polymorphisms have been shown to have allele-specific effects on the transcriptional activities of MMP gene promoters, and to be associated with susceptibility to coronary heart disease, aneurysms and cancers. These findings indicate that variation in the MMP genes may contribute to inter-individual differences in susceptibility to these common, complex diseases, likely through effects on the balance between the synthesis and degradation of extracellular matrix proteins.

Analysis of gene expression profiles in human systemic lupus erythematosus using oligonucleotide microarray

Epidemiologic studies suggest a strong genetic component for susceptibility to systemic lupus erythematosus (SLE). To investigate the genetic mechanism of pathogenesis of SLE, we studied the difference in gene expression of peripheral blood cells between 10 SLE patients and 18 healthy controls using oligonucleotide microarray. When gene expression for patients was compared to the mean of normal controls, among the 3002 target genes, 61 genes were identified with greater than a two-fold change difference in expression level. Of these genes, 24 were upregulated and 37 downregulated in at least half of the patients. By the Welch's ANOVA/Welch's t-test, all these 61 genes were significantly different (P<0.05) between SLE patients and normal controls. Among these genes with differential expression, IFN-omega and Ly6E (TSA-1/Sca-2) may play an important role in the mechanism of SLE pathogenesis. TSA-1 antigens may represent an important alternative pathway for T-cell activation that may be involved in IFN-mediated immunomodulation. Hierarchical clustering showed that patient samples were clearly separated from controls based on their gene expression profile. These results demonstrate that high-density oligonucleotide microarray has the potential to explore the mechanism of pathogenesis of systemic lupus erythematosus.

Preliminary report: genetic variation in the human stromelysin promoter is associated with progression of coronary atherosclerosis

Stromelysin is a member of the family of metalloproteinases that degrade extracellular matrix. In situ hybridisation and histopathological studies suggest that stromelysin activity may be important in the connective tissue remodelling processes associated with atherogenesis and plaque rupture. Single strand conformation polymorphism analysis identified a common polymorphism in the stromelysin gene promoter located 1171 bp upstream from the start of transcription in which one allele has a run of six adenosines (6A) and another has five adenosines (5A). 72 men with coronary heart disease, were genotyped. They were participants in the St Thomas' Atherosclerosis Regression Study who were randomised to receive usual care (UC), dietary intervention (D), or diet plus cholestyramine (DC), with angiography at baseline and at 39 months. In these patients the frequency of the 5A allele was 0.49 (95% CI from 0.41 to 0.57) and was not significantly different from that in a sample of 354 healthy UK men. In the UC group, patients who were homozygous for the 6A allele showed greater progression of angiographic disease than those with other genotypes: the minimum absolute width of coronary segments decreased by 0.04 (SEM 0.10) mm for 5A5A, 0.20 (0.07) mm for 5A6A, and 0.67 (0.19) mm for 6A6A (P < 0.01). The findings were similar but slightly less significant for the change in mean absolute width of coronary segments (P < 0.05). No significant associations were seen in patients in the D or DC groups. In data pooled from the three treatment groups, the 6A6A genotype was significantly associated with greater progression of coronary atherosclerosis than other genotypes in patients with baseline percentage diameter stenosis less than 20% (P < 0.05), but not in those with baseline percentage diameter stenosis greater than or equal to 20%. These results provide the first evidence of a link between genetic variation in stromelysin and progression of coronary atherosclerosis and support the hypothesis that connective tissue remodeling mediated by metalloproteinases contribute to the pathogenesis of atherosclerosis.

Renal afferent impulses, the posterior hypothalamus, and hypertension in rats with chronic renal failure

Hypertension in 5/6 nephrectomized (CRF) rats is partly related to increased activity of the sympathetic nervous system. We have previously shown a greater norepinephrine turnover rate in the posterior hypothalamic nuclei and locus coeruleus of CRF than control rats. Dorsal rhizotomy prevented the rise in blood pressure and the increase in NE turnover rate in the posterior hypothalamus and the locus coeruleus. The studies suggest that afferent impulses from the kidney to central integrative structures in the brain may be responsible for hypertension in CRF rats. To further evaluate the role of renal afferent nerves in the regulation of blood pressure, and whether renal afferent pathways integrate with the posterior hypothalamus, we studied the effects of an intrarenal injection of 50 microliters of 10% phenol on blood pressure and NE secretion from the posterior hypothalamus of Sprague-Dawley rats. Mean arterial pressure increased from 89 +/- 4.0 to 114 +/- 4.3 mm Hg in rats which received intrarenal injection of phenol, but it did not change in rats that received vehicle (95 +/- 4.3 and 89 +/- 3.6 mm Hg, respectively). Renal denervation totally prevented the increase in blood pressure caused by intrarenal injection of phenol. The secretion of NE from the posterior hypothalamus increased from 139 +/- 4.8 to 250 +/- 9.9 pg/ml (P < 0.01) in rats that received intrarenal phenol, but it did not change in rats which received vehicle or in those with renal denervation. In CRF rats NE secretion from the posterior hypothalamus was greater than in control and CRF rats subjected to dorsal rhizotomy. These studies show that afferent impulses from an injured kidney increase NE secretion from the posterior hypothalamus and raise blood pressure. NE secretion is higher in the posterior hypothalamus of CRF than control rats. The posterior hypothalamus appears to be an important integrative structure of the sympathetic regulation of blood pressure.

Allele-specific regulation of matrix metalloproteinase-12 gene activity is associated with coronary artery luminal dimensions in diabetic patients with manifest coronary artery disease

Both the processes of atherosclerosis and plaque rupture are indicated to be influenced by matrix metalloproteinase (MMP) activity. We therefore searched for common functional variation in the matrix metalloelastase (MMP-12) gene locus that may be implicated in coronary artery disease. Single-strand conformation polymorphism analysis of DNA from healthy individuals detected a common polymorphism within the MMP-12 gene promoter (an A-to-G substitution at position -82). The frequency of the G allele was 0. 19. The polymorphism influences the binding of the transcription factor activator protein-1 (AP-1) in electromobility shift assay. A higher binding affinity of AP-1 to the A allele was associated with higher MMP-12 promoter activity in vitro in transient transfection studies in U937 and murine lung macrophage (MALU) cells. Phorbol 12-myristate 13-acetate (PMA) and insulin, 2 known activators of AP-1, increased the binding of AP-1 to the MMP-12 promoter, with higher affinity for the A allele. In transfection experiments, both the A and the G alleles responded to insulin and PMA, the A allele showing higher promoter activity than the G allele. Furthermore, Western blot analysis demonstrated that insulin increased MMP-12 protein production. To analyze whether the -82 A/G polymorphism is associated with coronary artery disease, 367 consecutive patients who underwent percutaneous transluminal coronary angiography with stent implantation were genotyped. In patients (n=71) with diabetes, the A allele was associated with a smaller luminal diameter. In conclusion, a common functional polymorphism within the MMP-12 promoter influences coronary artery luminal dimensions in diabetic patients with manifest coronary artery disease.

The 4G/5G Genetic Polymorphism in the Promoter of the Plasminogen Activator Inhibitor-1 (PAI-1) Gene Is Associated with Differences in Plasma PAI-1 Activity but not with Risk of Myocardial Infarction in the ECTIM Study

We have investigated the interrelationships of plasma PAI-1 activity, the PAI-1 4G/5G polymorphism and risk of myocardial infarction (MI) in the ECTIM study, a case-control study of MI based in Belfast, Lille, Strasbourg and Toulouse. Mean PAI-1 levels in cases were similar across all centres but in controls, levels in the French centres were significantly higher. Only in Belfast were PAI-1 levels higher in cases (11.7AU/ml) than controls (10.5AU/ml). The PAI-1 4G allele frequency was similar in cases and controls (0.55 and 0.54). In all groups, 4G homozygotes had the highest mean plasma PAI-1 level (4G4G vs 5G5G; cases overall: 14.2 vs 12.1 AU/ml; controls overall: 15.0 vs 12.6AU/ml), with the heterozygotes generally intermediate. The data from Belfast are consistent with the literature implicating PAI-1 level as an MI risk factor. In ECTIM, the PAI-1 4G/5G polymorphism is not a genetic risk factor for MI but is associated with PAI-1 activity. Thus homozygosity for the 4G allele may predispose to elevated PAI-1 and impaired fibrinolysis, perhaps requiring interaction with other genetic or environmental factors to influence MI risk.

The structure of a Michaelis serpin-protease complex

Serine protease inhibitors (serpins) regulate the activities of circulating proteases. Serpins inhibit proteases by acylating the serine hydroxyl at their active sites. Before deacylation and complete proteolysis of the serpin can occur, massive conformational changes are triggered in the serpin while maintaining the covalent linkage between the protease and serpin. Here we report the structure of a serpin-trypsin Michaelis complex, which we visualized by using the S195A trypsin mutant to prevent covalent complex formation. This encounter complex reveals a more extensive interaction surface than that present in small inhibitor-protease complexes and is a template for modeling other serpin-protease pairs. Mutations of several serpin residues at the interface reduced the inhibitory activity of the serpin. The serine residue C-terminal to the scissile peptide bond is found in a closer than usual interaction with His 57 at the active site of trypsin.

Structural basis for interaction of FGF-1, FGF-2, and FGF-7 with different heparan sulfate motifs

Stromal cell-derived FGF-7 binds and activates only the resident FGFR2IIIb in epithelial cells while FGF-1 and FGF-2 exhibit a broader interaction with multiple isoforms of FGFR. Here we report the structure of FGF-7 that has been solved to 3.1 A resolution by molecular replacement with the structure of a dual function chimera of FGF-7 and FGF-1 (FGF-7/1) which was resolved to 2.3 A. Comparison of the FGF-7 structure to that of FGF-1 and FGF-2 revealed the strongly conserved Calpha backbone among the three FGF polypeptides and the surface hydrophobic patch that forms the primary receptor-binding domain. In contrast, a decrease and dispersion of the positive surface charge density characterized the heparin-binding domain of FGF-7 defined by homology to that of FGF-1 and FGF-2 in complexes with heparin. A simple heparin hexasaccharide that cocrystallized with FGF-1 and FGF-2 and protected both against protease in solution failed to exhibit the same properties with FGF-7. In contrast to FGF-1 and FGF-2, protection of FGF-7 was enhanced by heparin oligosaccharides of increased length with those exhibiting a 3-O-sulfate being the most effective. Protection of FGF-7 required interaction with specifically the fraction of crude heparin retained on antithrombin affinity columns. Conversely, heparin enriched by affinity for immobilized FGF-7 exhibited anti-factor Xa activity similar to that purified on an antithrombin affinity matrix. In contrast, an FGF-1 affinity matrix enriched the fraction of crude heparin with low anti-factor Xa activity. The results provide a structural basis to suggest that the unique FGF-7 heparin-binding (HB) domain underlies a specific restriction in respect to composition and length of the heparan sulfate motif that may impact specificity of localization, stability, and trafficking of FGF-7 in the microenvironment, and formation and activation of the FGFR2IIIb kinase signaling complex in epithelial cells.

Panagiotopoulou E, Panagoulias I, Pandini CE, Panduro Vazquez JG, Pani P, Panitkin S, Pantea D, Paolozzi L, Papadopoulou TD, Papageorgiou K, Paramonov A, Paredes Hernandez D, Parker AJ, Parker MA, Parker KA, Parodi F, Parsons JA, Parzefall U, Pascuzzi VR, Pasqualucci E, Passaggio S, Pastore F, Pásztor G, Pataraia S, Pater JR, Pauly T, Pearce J, Pearson B, Pedersen LE, Pedersen M, Pedraza Lopez S, Pedro R, Peleganchuk SV, Penc O, Peng C, Peng H, Penwell J, Peralva BS, Perego MM, Perepelitsa DV, Perez Codina E, Perini L, Pernegger H, Perrella S, Peschke R, Peshekhonov VD, Peters K, Peters RFY, Petersen BA, Petersen TC, Petit E, Petridis A, Petridou C, Petroff P, Petrolo E, Petrov M, Petrucci F, Pettersson NE, Peyaud A, Pezoa R, Phillips PW, Piacquadio G, Pianori E, Picazio A, Piccaro E, Piccinini M, Pickering MA, Piegaia R, Pilcher JE, Pilkington AD, Pin AWJ, Pinamonti M, Pinfold JL, Pingel A, Pires S, Pirumov H, Pitt M, Plazak L, Pleier MA, Pleskot V, Plotnikova E, Pluth D, Poettgen R, Poggioli L, Pohl D, Polesello G, Poley A, Policicchio A, Polifka R, Polini A, Pollard CS, Polychronakos V, Pommès K, Pontecorvo L, Pope BG, Popeneciu GA, Poppleton A, Pospisil S, Potamianos K, Potrap IN, Potter CJ, Potter CT, Poulard G, Poveda J, Pozdnyakov V, Pozo Astigarraga ME, Pralavorio P, Pranko A, Prell S, Price D, Price LE, Primavera M, Prince S, Prokofiev K, Prokoshin F, Protopopescu S, Proudfoot J, Przybycien M, Puddu D, Purohit M, Puzo P, Qian J, Qin G, Qin Y, Quadt A, Quayle WB, Queitsch-Maitland M, Quilty D, Raddum S, Radeka V, Radescu V, Radhakrishnan SK, Radloff P, Rados P, Ragusa F, Rahal G, Raine JA, Rajagopalan S, Rammensee M, Rangel-Smith C, Ratti MG, Rauch DM, Rauscher F, Rave S, Ravenscroft T, Ravinovich I, Raymond M, Read AL, Readioff NP, Reale M, Rebuzzi DM, Redelbach A, Redlinger G, Reece R, Reed RG, Reeves K, Rehnisch L, Reichert J, Reiss A, Rembser C, Ren H, Rescigno M, Resconi S, Rezanova OL, Reznicek P, Rezvani R, Richter R, Richter S, Richter-Was E, Ricken O, Ridel M, Rieck P, Riegel CJ, Rieger J, Rifki O, Rijssenbeek M, Rimoldi A, Rimoldi M, Rinaldi L, Ristić B, Ritsch E, Riu I, Rizatdinova F, Rizvi E, Rizzi C, Robertson SH, Robichaud-Veronneau A, Robinson D, Robinson JEM, Robson A, Roda C, Rodina Y, Rodriguez Perez A, Rodriguez Rodriguez D, Roe S, Rogan CS, Røhne O, Roloff J, Romaniouk A, Romano M, Romano Saez SM, Romero Adam E, Rompotis N, Ronzani M, Roos L, Ros E, Rosati S, Rosbach K, Rose P, Rosien NA, Rossetti V, Rossi E, Rossi LP, Rosten JHN, Rosten R, Rotaru M, Roth I, Rothberg J, Rousseau D, Rozanov A, Rozen Y, Ruan X, Rubbo F, Rudolph MS, Rühr F, Ruiz-Martinez A, Rurikova Z, Rusakovich NA, Ruschke A, Russell HL, Rutherfoord JP, Ruthmann N, Ryabov YF, Rybar M, Rybkin G, Ryu S, Ryzhov A, Rzehorz GF, Saavedra AF, Sabato G, Sacerdoti S, Sadrozinski HFW, Sadykov R, Safai Tehrani F, Saha P, Sahinsoy M, Saimpert M, Saito T, Sakamoto H, Sakurai Y, Salamanna G, Salamon A, Salazar Loyola JE, Salek D, Sales De Bruin PH, Salihagic D, Salnikov A, Salt J, Salvatore D, Salvatore F, Salvucci A, Salzburger A, Sammel D, Sampsonidis D, Sánchez J, Sanchez Martinez V, Sanchez Pineda A, Sandaker H, Sandbach RL, Sandhoff M, Sandoval C, Sankey DPC, Sannino M, Sansoni A, Santoni C, Santonico R, Santos H, Santoyo Castillo I, Sapp K, Sapronov A, Saraiva JG, Sarrazin B, Sasaki O, Sato K, Sauvan E, Savage G, Savard P, Savic N, Sawyer C, Sawyer L, Saxon J, Sbarra C, Sbrizzi A, Scanlon T, Scannicchio DA, Scarcella M, Scarfone V, Schaarschmidt J, Schacht P, Schachtner BM, Schaefer D, Schaefer L, Schaefer R, Schaeffer J, Schaepe S, Schaetzel S, Schäfer U, Schaffer AC, Schaile D, Schamberger RD, Scharf V, Schegelsky VA, Scheirich D, Schernau M, Schiavi C, Schier S, Schillo C, Schioppa M, Schlenker S, Schmidt-Sommerfeld KR, Schmieden K, Schmitt C, Schmitt S, Schmitz S, Schneider B, Schnoor U, Schoeffel L, Schoening A, Schoenrock BD, Schopf E, Schott M, Schouwenberg JFP, Schovancova J, Schramm S, Schreyer M, Schuh N, Schulte A, Schultens MJ, Schultz-Coulon HC, Schulz H, Schumacher M, Schumm BA, Schune P, Schwartzman A, Schwarz TA, Schweiger H, Schwemling P, Schwienhorst R, Schwindling J, Schwindt T, Sciolla G, Scuri F, Scutti F, Searcy J, Seema P, Seidel SC, Seiden A, Seifert F, Seixas JM, Sekhniaidze G, Sekhon K, Sekula SJ, Seliverstov DM, Semprini-Cesari N, Serfon C, Serin L, Serkin L, Sessa M, Seuster R, Severini H, Sfiligoj T, Sforza F, Sfyrla A, Shabalina E, Shaikh NW, Shan LY, Shang R, Shank JT, Shapiro M, Shatalov PB, Shaw K, Shaw SM, Shcherbakova A, Shehu CY, Sherwood P, Shi L, Shimizu S, Shimmin CO, Shimojima M, Shirabe S, Shiyakova M, Shmeleva A, Shoaleh Saadi D, Shochet MJ, Shojaii S, Shope DR, Shrestha S, Shulga E, Shupe MA, Sicho P, Sickles AM, Sidebo PE, Sideras Haddad E, Sidiropoulou O, Sidorov D, Sidoti A, Siegert F, Sijacki D, Silva J, Silverstein SB, Simak V, Simic L, Simion S, Simioni E, Simmons B, Simon D, Simon M, Sinervo P, Sinev NB, Sioli M, Siragusa G, Sivoklokov SY, Sjölin J, Skinner MB, Skottowe HP, Skubic P, Slater M, Slavicek T, Slawinska M, Sliwa K, Slovak R, Smakhtin V, Smart BH, Smestad L, Smiesko J, Smirnov SY, Smirnov Y, Smirnova LN, Smirnova O, Smith JW, Smith MNK, Smith RW, Smizanska M, Smolek K, Snesarev AA, Snyder IM, Snyder S, Sobie R, Socher F, Soffer A, Soh DA, Sokhrannyi G, Solans Sanchez CA, Solar M, Soldatov EY, Soldevila U, Solodkov AA, Soloshenko A, Solovyanov OV, Solovyev V, Sommer P, Son H, Song HY, Sood A, Sopczak A, Sopko V, Sorin V, Sosa D, Sotiropoulou CL, Soualah R, Soukharev AM, South D, Sowden BC, Spagnolo S, Spalla M, Spangenberg M, Spanò F, Sperlich D, Spettel F, Spieker TM, Spighi R, Spigo G, Spiller LA, Spousta M, St. Denis RD, Stabile A, Stamen R, Stamm S, Stanecka E, Stanek RW, Stanescu C, Stanescu-Bellu M, Stanitzki MM, Stapnes S, Starchenko EA, Stark GH, Stark J, Staroba P, Starovoitov P, Stärz S, Staszewski R, Steinberg P, Stelzer B, Stelzer HJ, Stelzer-Chilton O, Stenzel H, Stewart GA, Stillings JA, Stockton MC, Stoebe M, Stoicea G, Stolte P, Stonjek S, Stradling AR, Straessner A, Stramaglia ME, Strandberg J, Strandberg S, Strandlie A, Strauss M, Strizenec P, Ströhmer R, Strom DM, Stroynowski R, Strubig A, Stucci SA, Stugu B, Styles NA, Su D, Su J, Suchek S, Sugaya Y, Suk M, Sulin VV, Sultansoy S, Sumida T, Sun S, Sun X, Sundermann JE, Suruliz K, Suster CJE, Sutton MR, Suzuki S, Svatos M, Swiatlowski M, Swift SP, Sykora I, Sykora T, Ta D, Taccini C, Tackmann K, Taenzer J, Taffard A, Tafirout R, Taiblum N, Takai H, Takashima R, Takeshita T, Takubo Y, Talby M, Talyshev AA, Tan KG, Tanaka J, Tanaka M, Tanaka R, Tanaka S, Tanioka R, Tannenwald BB, Tapia Araya S, Tapprogge S, Tarem S, Tartarelli GF, Tas P, Tasevsky M, Tashiro T, Tassi E, Tavares Delgado A, Tayalati Y, Taylor AC, Taylor GN, Taylor PTE, Taylor W, Teischinger FA, Teixeira-Dias P, Temming KK, Temple D, Ten Kate H, Teng PK, Teoh JJ, Tepel F, Terada S, Terashi K, Terron J, Terzo S, Testa M, Teuscher RJ, Theveneaux-Pelzer T, Thomas JP, Thomas-Wilsker J, Thompson PD, Thompson AS, Thomsen LA, Thomson E, Tibbetts MJ, Ticse Torres RE, Tikhomirov VO, Tikhonov YA, Timoshenko S, Tipton P, Tisserant S, Todome K, Todorov T, Todorova-Nova S, Tojo J, Tokár S, Tokushuku K, Tolley E, Tomlinson L, Tomoto M, Tompkins L, Toms K, Tong B, Tornambe P, Torrence E, Torres H, Torró Pastor E, Toth J, Touchard F, Tovey DR, Trefzger T, Tricoli A, Trigger IM, Trincaz-Duvoid S, Tripiana MF, Trischuk W, Trocmé B, Trofymov A, Troncon C, Trottier-McDonald M, Trovatelli M, Truong L, Trzebinski M, Trzupek A, Tseng JCL, Tsiareshka PV, Tsipolitis G, Tsirintanis N, Tsiskaridze S, Tsiskaridze V, Tskhadadze EG, Tsui KM, Tsukerman II, Tsulaia V, Tsuno S, Tsybychev D, Tu Y, Tudorache A, Tudorache V, Tulbure TT, Tuna AN, Tupputi SA, Turchikhin S, Turgeman D, Turk Cakir I, Turra R, Tuts PM, Ucchielli G, Ueda I, Ughetto M, Ukegawa F, Unal G, Undrus A, Unel G, Ungaro FC, Unno Y, Unverdorben C, Urban J, Urquijo P, Urrejola P, Usai G, Usui J, Vacavant L, Vacek V, Vachon B, Valderanis C, Valdes Santurio E, Valencic N, Valentinetti S, Valero A, Valery L, Valkar S, Valls Ferrer JA, Van Den Wollenberg W, Van Der Deijl PC, van der Graaf H, van Eldik N, van Gemmeren P, Van Nieuwkoop J, van Vulpen I, van Woerden MC, Vanadia M, Vandelli W, Vanguri R, Vaniachine A, Vankov P, Vardanyan G, Vari R, Varnes EW, Varol T, Varouchas D, Vartapetian A, Varvell KE, Vasquez JG, Vasquez GA, Vazeille F, Vazquez Schroeder T, Veatch J, Veeraraghavan V, Veloce LM, Veloso F, Veneziano S, Ventura A, Venturi M, Venturi N, Venturini A, Vercesi V, Verducci M, Verkerke W, Vermeulen JC, Vest A, Vetterli MC, Viazlo O, Vichou I, Vickey T, Vickey Boeriu OE, Viehhauser GHA, Viel S, Vigani L, Villa M, Villaplana Perez M, Vilucchi E, Vincter MG, Vinogradov VB, Vittori C, Vivarelli I, Vlachos S, Vlasak M, Vogel M, Vokac P, Volpi G, Volpi M, von der Schmitt H, von Toerne E, Vorobel V, Vorobev K, Vos M, Voss R, Vossebeld JH, Vranjes N, Vranjes Milosavljevic M, Vrba V, Vreeswijk M, Vuillermet R, Vukotic I, Wagner P, Wagner W, Wahlberg H, Wahrmund S, Wakabayashi J, Walder J, Walker R, Walkowiak W, Wallangen V, Wang C, Wang C, Wang F, Wang H, Wang H, Wang J, Wang J, Wang K, Wang R, Wang SM, Wang T, Wang W, Wanotayaroj C, Warburton A, Ward CP, Wardrope DR, Washbrook A, Watkins PM, Watson AT, Watson MF, Watts G, Watts S, Waugh BM, Webb S, Weber MS, Weber SW, Weber SA, Webster JS, Weidberg AR, Weinert B, Weingarten J, Weiser C, Weits H, Wells PS, Wenaus T, Wengler T, Wenig S, Wermes N, Werner MD, Werner P, Wessels M, Wetter J, Whalen K, Whallon NL, Wharton AM, White A, White MJ, White R, Whiteson D, Wickens FJ, Wiedenmann W, Wielers M, Wiglesworth C, Wiik-Fuchs LAM, Wildauer A, Wilk F, Wilkens HG, Williams HH, Williams S, Willis C, Willocq S, Wilson JA, Wingerter-Seez I, Winklmeier F, Winston OJ, Winter BT, Wittgen M, Wolf TMH, Wolff R, Wolter MW, Wolters H, Worm SD, Wosiek BK, Wotschack J, Woudstra MJ, Wozniak KW, Wu M, Wu M, Wu SL, Wu X, Wu Y, Wyatt TR, Wynne BM, Xella S, Xi Z, Xu D, Xu L, Yabsley B, Yacoob S, Yamaguchi D, Yamaguchi Y, Yamamoto A, Yamamoto S, Yamanaka T, Yamauchi K, Yamazaki Y, Yan Z, Yang H, Yang H, Yang Y, Yang Z, Yao WM, Yap YC, Yasu Y, Yatsenko E, Yau Wong KH, Ye J, Ye S, Yeletskikh I, Yildirim E, Yorita K, Yoshida R, Yoshihara K, Young C, Young CJS, Youssef S, Yu DR, Yu J, Yu JM, Yu J, Yuan L, Yuen SPY, Yusuff I, Zabinski B, Zacharis G, Zaidan R, Zaitsev AM, Zakharchuk N, Zalieckas J, Zaman A, Zambito S, Zanello L, Zanzi D, Zeitnitz C, Zeman M, Zemla A, Zeng JC, Zeng Q, Zenin O, Ženiš T, Zerwas D, Zhang D, Zhang F, Zhang G, Zhang H, Zhang J, Zhang L, Zhang L, Zhang M, Zhang R, Zhang R, Zhang X, Zhang Z, Zhao X, Zhao Y, Zhao Z, Zhemchugov A, Zhong J, Zhou B, Zhou C, Zhou L, Zhou L, Zhou M, Zhou N, Zhu CG, Zhu H, Zhu J, Zhu Y, Zhuang X, Zhukov K, Zibell A, Zieminska D, Zimine NI, Zimmermann C, Zimmermann S, Zinonos Z, Zinser M, Ziolkowski M, Živković L, Zobernig G, Zoccoli A, zur Nedden M, Zwalinski L. Performance of the ATLAS trigger system in 2015

During 2015 the ATLAS experiment recorded [Formula: see text] of proton-proton collision data at a centre-of-mass energy of [Formula: see text]. The ATLAS trigger system is a crucial component of the experiment, responsible for selecting events of interest at a recording rate of approximately 1 kHz from up to 40 MHz of collisions. This paper presents a short overview of the changes to the trigger and data acquisition systems during the first long shutdown of the LHC and shows the performance of the trigger system and its components based on the 2015 proton-proton collision data.

Genetic variation at the matrix metalloproteinase-9 locus on chromosome 20q12.2-13.1

Allelic association methods are better suited than linkage analysis for mapping of susceptibility genes that confer modest increases in risk in complex diseases. In both family- and population-based association studies, it is very useful to have prior knowledge of all sequence variants and the degree of linkage disequilibrium in a candidate gene region. In this study, we scanned sequence variants in a 2.2-kb promoter sequence and all 13 exons (totalling 3.3 kb) of the matrix metalloproteinase-9 gene, which is associated with coronary heart disease and a candidate for other diseases involving connective tissue remodelling, such as cancer metastasis. The sequences had a total of ten variable sites, four in the promoter, five in the coding region (three of which alter the amino acid encoded) and one in the 3' untranslated sequence. Sequence inspection suggests that some of the variants will have a functional impact on either level of expression or enzymatic activity. Tight linkage disequilibrium was detected between variants across the entire length of the gene (approximately 9 kb), and frequencies of different haplotypes were determined. The data provide an essential tool for studies of the possible contribution of genetic variation at the matrix metalloproteinase-9 locus to genetically determined susceptibility to a number of important diseases. The results also provide experimental data on the extent of linkage disequilibrium in the general population, which is yet to be resolved.

Nicotine induced changes in gene expression by human coronary artery endothelial cells

The primary role of cigarette smoking in the development of coronary heart disease is to cause damage to the vascular endothelium, leading to endothelial cell dysfunction and initiating the pathogenesis of coronary atherosclerosis. We studied the response of human coronary artery endothelial cells to nicotine exposure by examining the expression of a panel of genes encoding molecules that have been shown to be involved in atherogenesis. Treatment of primary human coronary artery endothelial cells with nicotine for 24 h at concentrations (10(-5) and 10(-7) M) similar to those in the blood of smokers resulted in increased mRNA levels of endothelial nitric oxide synthase, angiotensin-I converting enzyme, tissue-type plasminogen activator, plasminogen activator inhibitor-1, von Willebrand factor, and vascular cell adhesion molecule-1. No change was detected in the expression levels of the genes encoding basic fibroblast growth factor, endothelin-1, endothelial leukocyte adhesion molecule-1 and matrix metalloproteinase-2 under these conditions. These data indicate that nicotine alters the expression of a number of endothelial genes whose products play major roles in regulating the vascular tone and thrombogenicity, making a contribution to the understanding of the effects of cigarette smoking on the development of coronary atherosclerosis.

Interleukin (IL)-10 inhibits IL-6 production in microglia by preventing activation of NF-kappaB

The purpose of this study was to determine if interleukin (IL)-10 inhibits lipopolysaccharide (LPS)-induced IL-6 production in microglia by inhibiting activation of nuclear factor-kappaB (NF-kappaB). N13 microglia (a murine microglial cell line) and primary microglia from neonatal mice were cultured in the presence or absence of LPS and increasing amounts of murine IL-10 for 24 h. As predicted, LPS treatment increased supernatant IL-6 concentration in both N13 and primary microglia cultures. Pretreatment with IL-10, however, decreased LPS-induced IL-6 secretion in a dose-dependent manner in both culture systems. Likewise, ribonuclease protection assays showed that LPS increased steady-state IL-6 mRNA levels, but that pretreatment with IL-10 blocked the LPS-induced increase in IL-6 mRNA. Because NF-kappaB is the predominant transcription factor responsible for IL-6 transcription in response to inflammatory stimuli, it was hypothesized that IL-10 inhibited IL-6 production by preventing nuclear translocation of NF-kappaB. Consistent with this idea, LPS increased nuclear translocation of NF-kappaB as assessed by gel mobility shift assay. Supershift assays and immunocytochemical staining showed that both the p50 and p65 subunits of NF-kappaB translocated from the cytoplasm to the nucleus upon LPS stimulation. Pretreatment with IL-10, however, inhibited LPS-induced activation of NF-kappaB. Furthermore, inhibition of NF-kappaB activity with tosyl-Phe-chloromethlyketone (a serine protease inhibitor that prevents degradation of the NF-kappaB-IkappaB complex), completely blocked LPS-induced IL-6 production. These data suggest that IL-10 inhibited IL-6 production in microglia by decreasing the activity of NF-kappaB and, therefore, extend what little is known of the intricate relationship between anti-inflammatory and inflammatory cytokines in the central nervous system.

VEGF polymorphisms and severity of atherosclerosis

INTRODUCTION

Vascular endothelial growth factor (VEGF) is a potent angiogenic factor, and neovascularisation has been shown to be important in atherosclerotic plaque development. There is some disagreement as to whether VEGF acts as a pro-atherosclerotic or anti-atherosclerotic factor. In the present study we have sought to clarify this by determining genotypes and haplotypes for three reportedly functional VEGF SNPs in a large series of well documented coronary atherosclerosis patients.

METHODS

VEGF -2578, -1154, and -634 single nucleotide polymorphisms were genotyped in 984 subjects from the Southampton Atherosclerosis Study, using the 5' nuclease assay for allelic discrimination (TaqMan).

RESULTS

VEGF -2578 genotypes showed a significantly different distribution in patients without myocardial infarction when stratified according to number of diseased arteries. VEGF -2578 was also associated with mean number of stenotic segments in the same patient group. The AA genotype was a risk factor and CC was protective. These associations were significant before and after adjustment for classic risk factors, and were reflected in associations between VEGF haplotypes and the number of diseased arteries and stenotic segments. As VEGF -2578 CC has been provisionally shown to be associated with higher VEGF expression than the AA genotype, these results are consistent with a protective effect for VEGF in atherosclerosis development. Some changes in VEGF -1154 genotype frequencies were also detected, but no significant associations were detected for any one particular genotype.

CONCLUSIONS

This study provides preliminary evidence that VEGF polymorphism is associated with development of atherosclerosis, possibly via regulation of VEGF expression, supporting a protective effect for VEGF in atherosclerosis. These results require replication in an independent study group, combined with study of additional candidate polymorphisms in the VEGF gene.