JoVE Visualize What is visualize?
Stop Reading. Start Watching.
Advanced Search
Stop Reading. Start Watching.
Regular Search
Find video protocols related to scientific articles indexed in Pubmed.
Gene-centric meta-analysis in 87,736 individuals of European ancestry identifies multiple blood-pressure-related loci.
Vinicius Tragante, Michael R Barnes, Santhi K Ganesh, Matthew B Lanktree, Wei Guo, Nora Franceschini, Erin N Smith, Toby Johnson, Michael V Holmes, Sandosh Padmanabhan, Konrad J Karczewski, Berta Almoguera, John Barnard, Jens Baumert, Yen-Pei Christy Chang, Clara C Elbers, Martin Farrall, Mary E Fischer, Tom R Gaunt, Johannes M I H Gho, Christian Gieger, Anuj Goel, Yan Gong, Aaron Isaacs, Marcus E Kleber, Irene Mateo Leach, Caitrin W McDonough, Matthijs F L Meijs, Olle Melander, Christopher P Nelson, Ilja M Nolte, Nathan Pankratz, Tom S Price, Jonathan Shaffer, Sonia Shah, Maciej Tomaszewski, Peter J van der Most, Erik P A van Iperen, Judith M Vonk, Kate Witkowska, Caroline O L Wong, Li Zhang, Amber L Beitelshees, Gerald S Berenson, Deepak L Bhatt, Morris Brown, Amber Burt, Rhonda M Cooper-DeHoff, John M Connell, Karen J Cruickshanks, Sean P Curtis, George Davey-Smith, Christian Delles, Ron T Gansevoort, Xiuqing Guo, Shen Haiqing, Claire E Hastie, Marten H Hofker, G Kees Hovingh, Daniel S Kim, Susan A Kirkland, Barbara E Klein, Ronald Klein, Yun R Li, Steffi Maiwald, Christopher Newton-Cheh, Eoin T O'Brien, N Charlotte Onland-Moret, Walter Palmas, Afshin Parsa, Brenda W Penninx, Mary Pettinger, Ramachandran S Vasan, Jane E Ranchalis, Paul M Ridker, Lynda M Rose, Peter Sever, Daichi Shimbo, Laura Steele, Ronald P Stolk, Barbara Thorand, Mieke D Trip, Cornelia M van Duijn, W Monique Verschuren, Cisca Wijmenga, Sharon Wyatt, J Hunter Young, Aeilko H Zwinderman, Connie R Bezzina, Eric Boerwinkle, Juan P Casas, Mark J Caulfield, Aravinda Chakravarti, Daniel I Chasman, Karina W Davidson, Pieter A Doevendans, Anna F Dominiczak, Garret A FitzGerald, John G Gums, Myriam Fornage, Hakon Hakonarson, Indrani Halder, Hans L Hillege, Thomas Illig, Gail P Jarvik, Julie A Johnson, John J P Kastelein, Wolfgang Koenig, Meena Kumari, Winfried März, Sarah S Murray, Jeffery R O'Connell, Albertine J Oldehinkel, James S Pankow, Daniel J Rader, Susan Redline, Muredach P Reilly, Eric E Schadt, Kandice Kottke-Marchant, Harold Snieder, Michael Snyder, Alice V Stanton, Martin D Tobin, André G Uitterlinden, Pim van der Harst, Yvonne T van der Schouw, Nilesh J Samani, Hugh Watkins, Andrew D Johnson, Alex P Reiner, Xiaofeng Zhu, Paul I W de Bakker, Daniel Levy, Folkert W Asselbergs, Patricia B Munroe, Brendan J Keating.
Am. J. Hum. Genet.
PUBLISHED: 02-20-2014
Show Abstract
Hide Abstract
Blood pressure (BP) is a heritable risk factor for cardiovascular disease. To investigate genetic associations with systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP), and pulse pressure (PP), we genotyped ~50,000 SNPs in up to 87,736 individuals of European ancestry and combined these in a meta-analysis. We replicated findings in an independent set of 68,368 individuals of European ancestry. Our analyses identified 11 previously undescribed associations in independent loci containing 31 genes including PDE1A, HLA-DQB1, CDK6, PRKAG2, VCL, H19, NUCB2, RELA, HOXC@ complex, FBN1, and NFAT5 at the Bonferroni-corrected array-wide significance threshold (p < 6 × 10(-7)) and confirmed 27 previously reported associations. Bioinformatic analysis of the 11 loci provided support for a putative role in hypertension of several genes, such as CDK6 and NUCB2. Analysis of potential pharmacological targets in databases of small molecules showed that ten of the genes are predicted to be a target for small molecules. In summary, we identified previously unknown loci associated with BP. Our findings extend our understanding of genes involved in BP regulation, which may provide new targets for therapeutic intervention or drug response stratification.
Related JoVE Video
Multi-parameter assessment of platelet inhibition and its stability during aspirin and clopidogrel therapy.
Thromb. Res.
PUBLISHED: 01-21-2014
Show Abstract
Hide Abstract
Poor response to antiplatelet drugs is associated with adverse outcomes. We assessed platelet inhibition and its stability and tested correlation and agreement between platelet function assays.
Related JoVE Video
Atrial Fibrillation associated chromosome 4q25 variants are not associated with PITX2c expression in human adult left atrial appendages.
PLoS ONE
PUBLISHED: 01-01-2014
Show Abstract
Hide Abstract
Atrial Fibrillation (AF), the most common sustained arrhythmia, has a strong genetic component, but the mechanism by which common genetic variants lead to increased AF susceptibility is unknown. Genome-wide association studies (GWAS) have identified that the single nucleotide polymorphisms (SNPs) most strongly associated with AF are located on chromosome 4q25 in an intergenic region distal to the PITX2 gene. Our objective was to determine whether the AF-associated SNPs on chromosome 4q25 were associated with PITX2c expression in adult human left atrial appendages. Analysis of a lone AF GWAS identified four independent AF risk SNPs at chromosome 4q25. Human adult left atrial appendage tissue was obtained from 239 subjects of European Ancestry and used for SNP analysis of genomic DNA and determination of PITX2c RNA expression levels by quantitative PCR. Subjects were divided into three groups based on their history of AF and pre-operative rhythm. AF rhythm subjects had higher PITX2c expression than those with history of AF but in sinus rhythm. PITX2c expression was not associated with the AF risk SNPs in human adult left atrial appendages in all subjects combined or in each of the three subgroups. However, we identified seven SNPs modestly associated with PITX2c expression located in the introns of the ENPEP gene, ?54 kb proximal to PITX2. PITX2c expression in human adult left atrial appendages is not associated with the chromosome 4q25 AF risk SNPs; thus, the mechanism by which these SNPs are associated with AF remains enigmatic.
Related JoVE Video
Weighted gene coexpression network analysis of human left atrial tissue identifies gene modules associated with atrial fibrillation.
Circ Cardiovasc Genet
PUBLISHED: 07-17-2013
Show Abstract
Hide Abstract
Genetic mechanisms of atrial fibrillation (AF) remain incompletely understood. Previous differential expression studies in AF were limited by small sample size and provided limited understanding of global gene networks, prompting the need for larger-scale, network-based analyses.
Related JoVE Video
Pattern recognition for identification of lysozyme droplet solution chemistry.
Colloids Surf B Biointerfaces
PUBLISHED: 06-25-2013
Show Abstract
Hide Abstract
Pattern formation during evaporation of a colloidal sessile droplet is a phenomenon relevant to a wide variety of scientific disciplines. The patterns remaining on the substrate are indicative of the transport mechanisms and phase transitions occurring during evaporation and may reflect the solution chemistry of the fluid [1-18]. Pattern formation during evaporation of droplets of biofluids has also been examined and these complex patterns may reflect the health of the patient [23-31]. Automatic detection of variations in the fluid composition based on these deposit patterns could lead to rapid screening for diagnostic or quality control purposes. In this study, a pattern recognition algorithm is presented to differentiate between deposits containing various solution compositions. The deposits studied are from droplets of simplified, model biological fluids of aqueous lysozyme and NaCl solutions. For the solution concentrations examined here, the deposit patterns are dependent upon the initial solution composition. Deposit images are represented by extracting features using the Gabor wavelet, similar to the method used for iris recognition. Two popular pattern recognition algorithms are used to classify the deposits. The k-means clustering algorithm is used to test if incremental changes in solution concentration result in reproducible and statistically interpretable variations in the deposit patterns. The k-nearest neighbor algorithm is also used to classify the deposit images by solution concentration based on a set of training images for each class. Here, we demonstrate that the deposit patterns may act as a "fingerprint" for identification of solution chemistry. The results of this study are very promising, with classification accuracies of 90-97.5%.
Related JoVE Video
GWAS of 126,559 individuals identifies genetic variants associated with educational attainment.
Cornelius A Rietveld, Sarah E Medland, Jaime Derringer, Jian Yang, Tonu Esko, Nicolas W Martin, Harm-Jan Westra, Konstantin Shakhbazov, Abdel Abdellaoui, Arpana Agrawal, Eva Albrecht, Behrooz Z Alizadeh, Najaf Amin, John Barnard, Sebastian E Baumeister, Kelly S Benke, Lawrence F Bielak, Jeffrey A Boatman, Patricia A Boyle, Gail Davies, Christiaan de Leeuw, Niina Eklund, Daniel S Evans, Rudolf Ferhmann, Krista Fischer, Christian Gieger, Håkon K Gjessing, Sara Hägg, Jennifer R Harris, Caroline Hayward, Christina Holzapfel, Carla A Ibrahim-Verbaas, Erik Ingelsson, Bo Jacobsson, Peter K Joshi, Astanand Jugessur, Marika Kaakinen, Stavroula Kanoni, Juha Karjalainen, Ivana Kolčić, Kati Kristiansson, Zoltan Kutalik, Jari Lahti, Sang H Lee, Peng Lin, Penelope A Lind, Yongmei Liu, Kurt Lohman, Marisa Loitfelder, George McMahon, Pedro Marques Vidal, Osorio Meirelles, Lili Milani, Ronny Myhre, Marja-Liisa Nuotio, Christopher J Oldmeadow, Katja E Petrovic, Wouter J Peyrot, Ozren Polašek, Lydia Quaye, Eva Reinmaa, John P Rice, Thais S Rizzi, Helena Schmidt, Reinhold Schmidt, Albert V Smith, Jennifer A Smith, Toshiko Tanaka, Antonio Terracciano, Matthijs J H M van der Loos, Veronique Vitart, Henry Völzke, Jürgen Wellmann, Lei Yu, Wei Zhao, Jüri Allik, John R Attia, Stefania Bandinelli, François Bastardot, Jonathan Beauchamp, David A Bennett, Klaus Berger, Laura J Bierut, Dorret I Boomsma, Ute Bültmann, Harry Campbell, Christopher F Chabris, Lynn Cherkas, Mina K Chung, Francesco Cucca, Mariza de Andrade, Philip L De Jager, Jan-Emmanuel De Neve, Ian J Deary, George V Dedoussis, Panos Deloukas, Maria Dimitriou, Guðný Eiríksdóttir, Martin F Elderson, Johan G Eriksson, David M Evans, Jessica D Faul, Luigi Ferrucci, Melissa E Garcia, Henrik Grönberg, Vilmundur Guðnason, Per Hall, Juliette M Harris, Tamara B Harris, Nicholas D Hastie, Andrew C Heath, Dena G Hernandez, Wolfgang Hoffmann, Adriaan Hofman, Rolf Holle, Elizabeth G Holliday, Jouke-Jan Hottenga, William G Iacono, Thomas Illig, Marjo-Riitta Järvelin, Mika Kähönen, Jaakko Kaprio, Robert M Kirkpatrick, Matthew Kowgier, Antti Latvala, Lenore J Launer, Debbie A Lawlor, Terho Lehtimäki, Jingmei Li, Paul Lichtenstein, Peter Lichtner, David C Liewald, Pamela A Madden, Patrik K E Magnusson, Tomi E Mäkinen, Marco Masala, Matt McGue, Andres Metspalu, Andreas Mielck, Michael B Miller, Grant W Montgomery, Sutapa Mukherjee, Dale R Nyholt, Ben A Oostra, Lyle J Palmer, Aarno Palotie, Brenda W J H Penninx, Markus Perola, Patricia A Peyser, Martin Preisig, Katri Räikkönen, Olli T Raitakari, Anu Realo, Susan M Ring, Samuli Ripatti, Fernando Rivadeneira, Igor Rudan, Aldo Rustichini, Veikko Salomaa, Antti-Pekka Sarin, David Schlessinger, Rodney J Scott, Harold Snieder, Beate St Pourcain, John M Starr, Jae Hoon Sul, Ida Surakka, Rauli Svento, Alexander Teumer, , Henning Tiemeier, Frank J A van Rooij, David R Van Wagoner, Erkki Vartiainen, Jorma Viikari, Peter Vollenweider, Judith M Vonk, Gérard Waeber, David R Weir, H-Erich Wichmann, Elisabeth Widén, Gonneke Willemsen, James F Wilson, Alan F Wright, Dalton Conley, George Davey-Smith, Lude Franke, Patrick J F Groenen, Albert Hofman, Magnus Johannesson, Sharon L R Kardia, Robert F Krueger, David Laibson, Nicholas G Martin, Michelle N Meyer, Danielle Posthuma, A Roy Thurik, Nicholas J Timpson, André G Uitterlinden, Cornelia M van Duijn, Peter M Visscher, Daniel J Benjamin, David Cesarini, Philipp D Koellinger.
Science
PUBLISHED: 05-30-2013
Show Abstract
Hide Abstract
A genome-wide association study (GWAS) of educational attainment was conducted in a discovery sample of 101,069 individuals and a replication sample of 25,490. Three independent single-nucleotide polymorphisms (SNPs) are genome-wide significant (rs9320913, rs11584700, rs4851266), and all three replicate. Estimated effects sizes are small (coefficient of determination R(2) ? 0.02%), approximately 1 month of schooling per allele. A linear polygenic score from all measured SNPs accounts for ?2% of the variance in both educational attainment and cognitive function. Genes in the region of the loci have previously been associated with health, cognitive, and central nervous system phenotypes, and bioinformatics analyses suggest the involvement of the anterior caudate nucleus. These findings provide promising candidate SNPs for follow-up work, and our effect size estimates can anchor power analyses in social-science genetics.
Related JoVE Video
Loci influencing blood pressure identified using a cardiovascular gene-centric array.
Santhi K Ganesh, Vinicius Tragante, Wei Guo, Yiran Guo, Matthew B Lanktree, Erin N Smith, Toby Johnson, Berta Almoguera Castillo, John Barnard, Jens Baumert, Yen-Pei Christy Chang, Clara C Elbers, Martin Farrall, Mary E Fischer, Nora Franceschini, Tom R Gaunt, Johannes M I H Gho, Christian Gieger, Yan Gong, Aaron Isaacs, Marcus E Kleber, Irene Mateo Leach, Caitrin W McDonough, Matthijs F L Meijs, Olle Mellander, Cliona M Molony, Ilja M Nolte, Sandosh Padmanabhan, Tom S Price, Ramakrishnan Rajagopalan, Jonathan Shaffer, Sonia Shah, Haiqing Shen, Nicole Soranzo, Peter J van der Most, Erik P A van Iperen, Jessica van Setten, Jessic A Van Setten, Judith M Vonk, Li Zhang, Amber L Beitelshees, Gerald S Berenson, Deepak L Bhatt, Jolanda M A Boer, Eric Boerwinkle, Ben Burkley, Amber Burt, Aravinda Chakravarti, Wei Chen, Rhonda M Cooper-DeHoff, Sean P Curtis, Albert Dreisbach, David Duggan, Georg B Ehret, Richard R Fabsitz, Myriam Fornage, Ervin Fox, Clement E Furlong, Ron T Gansevoort, Marten H Hofker, G Kees Hovingh, Susan A Kirkland, Kandice Kottke-Marchant, Abdullah Kutlar, Andrea Z LaCroix, Taimour Y Langaee, Yun R Li, Honghuang Lin, Kiang Liu, Steffi Maiwald, Rainer Malik, , Gurunathan Murugesan, Christopher Newton-Cheh, Jeffery R O'Connell, N Charlotte Onland-Moret, Willem H Ouwehand, Walter Palmas, Brenda W Penninx, Carl J Pepine, Mary Pettinger, Joseph F Polak, Vasan S Ramachandran, Jane Ranchalis, Susan Redline, Paul M Ridker, Lynda M Rose, Hubert Scharnag, Nicholas J Schork, Daichi Shimbo, Alan R Shuldiner, Sathanur R Srinivasan, Ronald P Stolk, Herman A Taylor, Barbara Thorand, Mieke D Trip, Cornelia M van Duijn, W Monique Verschuren, Cisca Wijmenga, Bernhard R Winkelmann, Sharon Wyatt, J Hunter Young, Bernhard O Boehm, Mark J Caulfield, Daniel I Chasman, Karina W Davidson, Pieter A Doevendans, Garret A FitzGerald, John G Gums, Hakon Hakonarson, Hans L Hillege, Thomas Illig, Gail P Jarvik, Julie A Johnson, John J P Kastelein, Wolfgang Koenig, Winfried März, Braxton D Mitchell, Sarah S Murray, Albertine J Oldehinkel, Daniel J Rader, Muredach P Reilly, Alex P Reiner, Eric E Schadt, Roy L Silverstein, Harold Snieder, Alice V Stanton, André G Uitterlinden, Pim van der Harst, Yvonne T van der Schouw, Nilesh J Samani, Andrew D Johnson, Patricia B Munroe, Paul I W de Bakker, Xiaofeng Zhu, Daniel Levy, Brendan J Keating, Folkert W Asselbergs.
Hum. Mol. Genet.
PUBLISHED: 01-08-2013
Show Abstract
Hide Abstract
Blood pressure (BP) is a heritable determinant of risk for cardiovascular disease (CVD). To investigate genetic associations with systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP) and pulse pressure (PP), we genotyped ?50 000 single-nucleotide polymorphisms (SNPs) that capture variation in ?2100 candidate genes for cardiovascular phenotypes in 61 619 individuals of European ancestry from cohort studies in the USA and Europe. We identified novel associations between rs347591 and SBP (chromosome 3p25.3, in an intron of HRH1) and between rs2169137 and DBP (chromosome1q32.1 in an intron of MDM4) and between rs2014408 and SBP (chromosome 11p15 in an intron of SOX6), previously reported to be associated with MAP. We also confirmed 10 previously known loci associated with SBP, DBP, MAP or PP (ADRB1, ATP2B1, SH2B3/ATXN2, CSK, CYP17A1, FURIN, HFE, LSP1, MTHFR, SOX6) at array-wide significance (P < 2.4 × 10(-6)). We then replicated these associations in an independent set of 65 886 individuals of European ancestry. The findings from expression QTL (eQTL) analysis showed associations of SNPs in the MDM4 region with MDM4 expression. We did not find any evidence of association of the two novel SNPs in MDM4 and HRH1 with sequelae of high BP including coronary artery disease (CAD), left ventricular hypertrophy (LVH) or stroke. In summary, we identified two novel loci associated with BP and confirmed multiple previously reported associations. Our findings extend our understanding of genes involved in BP regulation, some of which may eventually provide new targets for therapeutic intervention.
Related JoVE Video
Recent advances in pediatric gastroenterology, hepatology and nutrition.
F1000Prime Rep
PUBLISHED: 01-01-2013
Show Abstract
Hide Abstract
Pediatric gastroenterology, hepatology and nutrition are rapidly evolving, exciting and diverse disciplines. Because the field is so expansive, this commentary highlights important trends, rather than narrowly focusing on specific advances. Examples of advances in the highest impact and rapidly moving areas of pediatric gastroenterology are reviewed, including the intestinal microbiome, biomedical genomics, the biology of unique gastrointestinal cell types, and microRNAs (miRNAs).
Related JoVE Video
Safety of pediatric percutaneous liver biopsy performed by interventional radiologists.
J. Pediatr. Gastroenterol. Nutr.
PUBLISHED: 07-27-2011
Show Abstract
Hide Abstract
National data suggest that pediatric percutaneous liver biopsy is increasingly being performed by interventional radiologists rather than pediatric gastroenterologists. The objective of the present report is to describe the safety and effectiveness of percutaneous liver biopsy performed by interventional radiologists in a large cohort of children and to compare the results with the existing literature on biopsies performed by pediatric gastroenterologists.
Related JoVE Video
Renal inflammation and elevated blood pressure in a mouse model of reduced {beta}-ENaC.
Am. J. Physiol. Renal Physiol.
PUBLISHED: 05-04-2011
Show Abstract
Hide Abstract
Previous studies suggest ?-epithelial Na(+) channel protein (?-ENaC) may mediate myogenic constriction, a mechanism of blood flow autoregulation. A recent study demonstrated that mice with reduced levels of ?-ENaC (?-ENaC m/m) have delayed correction of whole kidney blood flow responses, suggesting defective myogenic autoregulatory capacity. Reduced renal autoregulatory capacity is linked to renal inflammation, injury, and hypertension. However, it is unknown whether ?-ENaC m/m mice have any complications associated with reductions in autoregulatory capacity such as renal inflammation, injury, or hypertension. To determine whether the previously observed altered autoregulatory control was associated with indicators of renal injury, we evaluated ?-ENaC m/m mice for signs of renal inflammation and tissue remodeling using marker expression. We found that inflammatory and remodeling markers, such as IL-1?, IL-6, TNF-?, collagen III and transforming growth factor-?, were significantly upregulated in ?-ENaC m/m mice. To determine whether renal changes were associated with changes in long-term control of blood pressure, we used radiotelemetry and found that 5-day mean arterial blood pressure (MAP) was significantly elevated in ?-ENaC m/m (120 ± 3 vs. 105 ± 2 mmHg, P = 0.016). Our findings suggest loss of ?-ENaC is associated with early signs of renal injury and increased MAP.
Related JoVE Video
Platelet CD36 surface expression levels affect functional responses to oxidized LDL and are associated with inheritance of specific genetic polymorphisms.
Blood
PUBLISHED: 04-08-2011
Show Abstract
Hide Abstract
CD36 modulates platelet function via binding to oxidized LDL (oxLDL), cell-derived microparticles, and thrombospondin-1. We hypothesized that the level of platelet CD36 expression may be associated with inheritance of specific genetic polymorphisms and that this would determine platelet reactivity to oxLDL. Analysis of more than 500 subjects revealed that CD36 expression levels were consistent in individual donors over time but varied widely among donors (200-14,000 molecules per platelet). Platelet aggregometry and flow cytometry in a subset of subjects with various CD36 expression levels revealed a high level of correlation (r² = 0.87) between platelet activation responses to oxLDL and level of CD36 expression. A genome-wide association study of 374 white subjects from the Cleveland Clinic ASCLOGEN study showed strong associations of single nucleotide polymorphisms in CD36 with platelet surface CD36 expression. Most of these findings were replicated in a smaller subset of 25 black subjects. An innovative gene-based genome-wide scan provided further evidence that single nucleotide polymorphisms in CD36 were strongly associated with CD36 expression. These studies show that CD36 expression on platelets varies widely, correlates with functional responses to oxLDL, and is associated with inheritance of specific CD36 genetic polymorphisms, and suggest that inheritance of specific CD36 polymorphisms could affect thrombotic risk.
Related JoVE Video
Dietary ?3 fatty acids modulate the substrate for post-operative atrial fibrillation in a canine cardiac surgery model.
Cardiovasc. Res.
PUBLISHED: 11-30-2010
Show Abstract
Hide Abstract
Pre-treatment with dietary ?3 polyunsaturated fatty acids (?3-PUFA) has been reported to reduce the incidence of new-onset atrial fibrillation (AF) following cardiac surgery. In a canine cardiac surgery model, we evaluated the impact of dietary ?3-PUFA on atrial electrophysiological properties, inflammatory markers, the atrial endothelin-1 (ET-1) system, and the expression and distribution of connexin 43.
Related JoVE Video
A common connexin-40 gene promoter variant affects connexin-40 expression in human atria and is associated with atrial fibrillation.
Circ Arrhythm Electrophysiol
PUBLISHED: 11-13-2010
Show Abstract
Hide Abstract
A common single-nucleotide polymorphism (SNP) in the promoter of the Connexin-40 (Cx40) gene GJA5 was suggested to affect Cx40 promoter activity and the risk of atrial fibrillation (AF), but the role of other common Cx40 polymorphisms is unknown.
Related JoVE Video
Pathway-based analysis for genome-wide association studies using supervised principal components.
Genet. Epidemiol.
PUBLISHED: 09-16-2010
Show Abstract
Hide Abstract
Many complex diseases are influenced by genetic variations in multiple genes, each with only a small marginal effect on disease susceptibility. Pathway analysis, which identifies biological pathways associated with disease outcome, has become increasingly popular for genome-wide association studies (GWAS). In addition to combining weak signals from a number of SNPs in the same pathway, results from pathway analysis also shed light on the biological processes underlying disease. We propose a new pathway-based analysis method for GWAS, the supervised principal component analysis (SPCA) model. In the proposed SPCA model, a selected subset of SNPs most associated with disease outcome is used to estimate the latent variable for a pathway. The estimated latent variable for each pathway is an optimal linear combination of a selected subset of SNPs; therefore, the proposed SPCA model provides the ability to borrow strength across the SNPs in a pathway. In addition to identifying pathways associated with disease outcome, SPCA also carries out additional within-category selection to identify the most important SNPs within each gene set. The proposed model operates in a well-established statistical framework and can handle design information such as covariate adjustment and matching information in GWAS. We compare the proposed method with currently available methods using data with realistic linkage disequilibrium structures, and we illustrate the SPCA method using the Wellcome Trust Case-Control Consortium Crohn Disease (CD) data set.
Related JoVE Video
Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height.
Matthew B Lanktree, Yiran Guo, Muhammed Murtaza, Joseph T Glessner, Swneke D Bailey, N Charlotte Onland-Moret, Guillaume Lettre, Halit Ongen, Ramakrishnan Rajagopalan, Toby Johnson, Haiqing Shen, Christopher P Nelson, Norman Klopp, Jens Baumert, Sandosh Padmanabhan, Nathan Pankratz, James S Pankow, Sonia Shah, Kira Taylor, John Barnard, Bas J Peters, Cliona M Maloney, Maximilian T Lobmeyer, Alice Stanton, M Hadi Zafarmand, Simon P R Romaine, Amar Mehta, Erik P A van Iperen, Yan Gong, Tom S Price, Erin N Smith, Cecilia E Kim, Yun R Li, Folkert W Asselbergs, Larry D Atwood, Kristian M Bailey, Deepak Bhatt, Florianne Bauer, Elijah R Behr, Tushar Bhangale, Jolanda M A Boer, Bernhard O Boehm, Jonathan P Bradfield, Morris Brown, Peter S Braund, Paul R Burton, Cara Carty, Hareesh R Chandrupatla, Wei Chen, John Connell, Chrysoula Dalgeorgou, Anthonius de Boer, Fotios Drenos, Clara C Elbers, James C Fang, Caroline S Fox, Edward C Frackelton, Barry Fuchs, Clement E Furlong, Quince Gibson, Christian Gieger, Anuj Goel, Diederik E Grobbee, Claire Hastie, Philip J Howard, Guan-Hua Huang, W Craig Johnson, Qing Li, Marcus E Kleber, Barbara E K Klein, Ronald Klein, Charles Kooperberg, Bonnie Ky, Andrea LaCroix, Paul Lanken, Mark Lathrop, Mingyao Li, Vanessa Marshall, Olle Melander, Frank D Mentch, Nuala J Meyer, Keri L Monda, Alexandre Montpetit, Gurunathan Murugesan, Karen Nakayama, Dave Nondahl, Abiodun Onipinla, Suzanne Rafelt, Stephen J Newhouse, F George Otieno, Sanjey R Patel, Mary E Putt, Santiago Rodriguez, Radwan N Safa, Douglas B Sawyer, Pamela J Schreiner, Claire Simpson, Suthesh Sivapalaratnam, Sathanur R Srinivasan, Christine Suver, Gary Swergold, Nancy K Sweitzer, Kelly A Thomas, Barbara Thorand, Nicholas J Timpson, Sam Tischfield, Martin Tobin, Maciej Tomaszewski, Maciej Tomaszweski, W M Monique Verschuren, Chris Wallace, Bernhard Winkelmann, Haitao Zhang, Dongling Zheng, Li Zhang, Joseph M Zmuda, Robert Clarke, Anthony J Balmforth, John Danesh, Ian N Day, Nicholas J Schork, Paul I W de Bakker, Christian Delles, David Duggan, Aroon D Hingorani, Joel N Hirschhorn, Marten H Hofker, Steve E Humphries, Mika Kivimäki, Debbie A Lawlor, Kandice Kottke-Marchant, Jessica L Mega, Braxton D Mitchell, David A Morrow, Jutta Palmen, Susan Redline, Denis C Shields, Alan R Shuldiner, Patrick M Sleiman, George Davey Smith, Martin Farrall, Yalda Jamshidi, David C Christiani, Juan P Casas, Alistair S Hall, Pieter A Doevendans, Jason D Christie, Gerald S Berenson, Sarah S Murray, Thomas Illig, Gerald W Dorn, Thomas P Cappola, Eric Boerwinkle, Peter Sever, Daniel J Rader, Muredach P Reilly, Mark Caulfield, Philippa J Talmud, Eric Topol, James C Engert, Kai Wang, Anna Dominiczak, Anders Hamsten, Sean P Curtis, Roy L Silverstein, Leslie A Lange, Marc S Sabatine, Mieke Trip, Danish Saleheen, John F Peden, Karen J Cruickshanks, Winfried März, Jeffrey R O'Connell, Olaf H Klungel, Cisca Wijmenga, Anke Hilse Maitland-van der Zee, Eric E Schadt, Julie A Johnson, Gail P Jarvik, George J Papanicolaou, , Struan F A Grant, Patricia B Munroe, Kari E North, Nilesh J Samani, Wolfgang Koenig, Tom R Gaunt, Sonia S Anand, Yvonne T van der Schouw, Nicole Soranzo, Garret A FitzGerald, Alex Reiner, Robert A Hegele, Hakon Hakonarson, Brendan J Keating.
Am. J. Hum. Genet.
PUBLISHED: 09-14-2010
Show Abstract
Hide Abstract
Height is a classic complex trait with common variants in a growing list of genes known to contribute to the phenotype. Using a genecentric genotyping array targeted toward cardiovascular-related loci, comprising 49,320 SNPs across approximately 2000 loci, we evaluated the association of common and uncommon SNPs with adult height in 114,223 individuals from 47 studies and six ethnicities. A total of 64 loci contained a SNP associated with height at array-wide significance (p < 2.4 × 10(-6)), with 42 loci surpassing the conventional genome-wide significance threshold (p < 5 × 10(-8)). Common variants with minor allele frequencies greater than 5% were observed to be associated with height in 37 previously reported loci. In individuals of European ancestry, uncommon SNPs in IL11 and SMAD3, which would not be genotyped with the use of standard genome-wide genotyping arrays, were strongly associated with height (p < 3 × 10(-11)). Conditional analysis within associated regions revealed five additional variants associated with height independent of lead SNPs within the locus, suggesting allelic heterogeneity. Although underpowered to replicate findings from individuals of European ancestry, the direction of effect of associated variants was largely consistent in African American, South Asian, and Hispanic populations. Overall, we show that dense coverage of genes for uncommon SNPs, coupled with large-scale meta-analysis, can successfully identify additional variants associated with a common complex trait.
Related JoVE Video
Association of left atrial endothelin-1 with atrial rhythm, size, and fibrosis in patients with structural heart disease.
Circ Arrhythm Electrophysiol
PUBLISHED: 05-21-2010
Show Abstract
Hide Abstract
Atrial fibrillation (AF) promotes atrial remodeling and can develop secondary to heart failure or mitral valve disease. Cardiac endothelin-1 (ET-1) expression responds to wall stress and can promote myocyte hypertrophy and interstitial fibrosis. We tested the hypothesis that atrial ET-1 is elevated in AF and is associated with AF persistence.
Related JoVE Video
ZAS3 accentuates transforming growth factor ? signaling in epithelial cells.
Cell. Signal.
PUBLISHED: 05-10-2010
Show Abstract
Hide Abstract
In mammals, the ZAS family of transcription factors activates or represses transcription depending on the cellular context. In the current study, we explored the interaction between ZAS3 and TGF?1 signaling in epithelial cells using HEK293 cells and the intestinal epithelial cell line, RIE-1. Endogenous ZAS3 expression was detected in each cell line and the small intestine of mice. Additionally, endogenous ZAS3 expression was increased in both whole cell and nuclear lysates by TGF?1 and in vivo in TGF?-overexpressing mice, indicating a potential interaction between ZAS3 and TGF?. ZAS3 transfection enhanced TGF?1 activation of a luciferase reporter in both HEK293 and RIE-1 cells. Analysis of truncated ZAS3 constructs revealed a 155 amino acid, N-terminal sequence between amino acids 106 and 261 that was required for enhancement of TGF?1-mediated transcription. Co-immunoprecipitation experiments with nuclear extracts from TGF?1-stimulated HEK293 cells revealed an association between ZAS3 and the Smad complex. Additionally, transfected ZAS3 decreased the association between the Smad complex and the TGF? transcriptional repressors Ski and SnoN, indicating a possible mechanism for the enhancement of transcription by exogenous ZAS3. These observations were confirmed by site-directed mutagenesis of ZAS domains homologous with Smad-interacting domains in Ski and SnoN. Finally, ZAS3 transfection enhanced the TGF?1-mediated induction of ?-smooth muscle actin in HEK293 cells, indicating that ZAS3 plays a functional role in TGF? signaling. In conclusion, we have identified an interaction between ZAS3 and Smad proteins that enhances TGF? signaling. Since TGF? signaling is primarily known as a negatively regulated pathway, the enhancement of signaling by ZAS3 has novel implications for understanding TGF? biology.
Related JoVE Video
Vectorial TGFbeta signaling in polarized intestinal epithelial cells.
J. Cell. Physiol.
PUBLISHED: 05-01-2010
Show Abstract
Hide Abstract
Polarized gastrointestinal epithelial cells form tight junctions that spatially separate apical and basolateral cell membrane domains. These domains harbor functionally distinct proteins that contribute to cellular homeostasis and morphogenesis. Transforming growth factor beta (TGFbeta) is a critical regulator of gastrointestinal epithelial cell growth and differentiation. Functional assays of vectorial TGFbeta signaling and immunofluorescence techniques were used to determine the localization of TGFbeta receptors and ligand secretion in polarizing Caco-2 cells, a colon cancer cell line. Results were compared to the nontransformed MDCK cell line. In both Caco-2 and MDCK cells, addition of TGFbeta1 to the basolateral medium resulted in phosphorylation of Smad2. No phosphorylation was observed when TGFbeta1 was added to the apical chamber, indicating that receptor signaling is localized at the basolateral membrane. In support of this, immunofluorescence and biotinylation assays show receptor localization along the basolateral membrane. Secretion of TGFbeta1 from MDCK and Caco-2 cells into the apical or basolateral medium was measured by ELISA. Interestingly, secretion was exclusively apical in the nontransformed MDCK line and basolateral in transformed Caco-2 cells. Collectively, these results show basolateral domain specificity in localization of the TGFbeta receptor signaling apparatus. These observations have important implications for understanding the biology of TGFbeta in polarized epithelia, including elements of communication between epithelial and mesenchymal layers, and will prove useful in the design of therapeutics that target TGFbeta function.
Related JoVE Video
Extracellular acidosis activates ASIC-like channels in freshly isolated cerebral artery smooth muscle cells.
Am. J. Physiol., Cell Physiol.
PUBLISHED: 02-24-2010
Show Abstract
Hide Abstract
Recent studies suggest that certain acid-sensing ion channels (ASIC) are expressed in vascular smooth muscle cells (VSMCs) and are required for VSMC functions. However, electrophysiological evidence of ASIC channels in VSMCs is lacking. The purpose of this study was to test the hypothesis that isolated cerebral artery VSMCs express ASIC-like channels. To address this hypothesis, we used RT-PCR, Western blotting, immunolabeling, and conventional whole cell patch-clamp technique. We found extracellular H(+)-induced inward currents in 46% of cells tested (n = 58 of 126 VSMCs, pH 6.5-5.0). The percentage of responsive cells and the current amplitude increased as the external H(+) concentration increased (pH(6.0), n = 28/65 VSMCs responsive, mean current density = 8.1 +/- 1.2 pA/pF). Extracellular acidosis (pH(6.0)) shifted the whole cell reversal potential toward the Nernst potential of Na(+) (n = 6) and substitution of extracellular Na(+) by N-methyl-d-glucamine abolished the inward current (n = 6), indicating that Na(+) is a major charge carrier. The broad-spectrum ASIC blocker amiloride (20 microM) inhibited proton-induced currents to 16.5 +/- 8.7% of control (n = 6, pH(6.0)). Psalmotoxin 1 (PcTx1), an ASIC1a inhibitor and ASIC1b activator, had mixed effects: PcTx1 either 1) abolished H(+)-induced currents (11% of VSMCs, 5/45), 2) enhanced or promoted activation of H(+)-induced currents (76%, 34/45), or 3) failed to promote H(+) activation in nonresponsive VSMCs (13%, 6/45). These findings suggest that freshly dissociated cerebral artery VSMCs express ASIC-like channels, which are predominantly formed by ASIC1b.
Related JoVE Video
Common variants in KCNN3 are associated with lone atrial fibrillation.
Nat. Genet.
PUBLISHED: 01-22-2010
Show Abstract
Hide Abstract
Atrial fibrillation (AF) is the most common sustained arrhythmia. Previous studies have identified several genetic loci associated with typical AF. We sought to identify common genetic variants underlying lone AF. This condition affects a subset of individuals without overt heart disease and with an increased heritability of AF. We report a meta-analysis of genome-wide association studies conducted using 1,335 individuals with lone AF (cases) and 12,844 unaffected individuals (referents). Cases were obtained from the German AF Network, Heart and Vascular Health Study, the Atherosclerosis Risk in Communities Study, the Cleveland Clinic and Massachusetts General Hospital. We identified an association on chromosome 1q21 to lone AF (rs13376333, adjusted odds ratio = 1.56; P = 6.3 x 10(-12)), and we replicated this association in two independent cohorts with lone AF (overall combined odds ratio = 1.52, 95% CI 1.40-1.64; P = 1.83 x 10(-21)). rs13376333 is intronic to KCNN3, which encodes a potassium channel protein involved in atrial repolarization.
Related JoVE Video
Genome-wide association study of PR interval.
Nat. Genet.
PUBLISHED: 01-10-2010
Show Abstract
Hide Abstract
The electrocardiographic PR interval (or PQ interval) reflects atrial and atrioventricular nodal conduction, disturbances of which increase risk of atrial fibrillation. We report a meta-analysis of genome-wide association studies for PR interval from seven population-based European studies in the CHARGE Consortium: AGES, ARIC, CHS, FHS, KORA, Rotterdam Study, and SardiNIA (N = 28,517). We identified nine loci associated with PR interval at P < 5 x 10(-8). At the 3p22.2 locus, we observed two independent associations in voltage-gated sodium channel genes, SCN10A and SCN5A. Six of the loci were near cardiac developmental genes, including CAV1-CAV2, NKX2-5 (CSX1), SOX5, WNT11, MEIS1, and TBX5-TBX3, providing pathophysiologically interesting candidate genes. Five of the loci, SCN5A, SCN10A, NKX2-5, CAV1-CAV2, and SOX5, were also associated with atrial fibrillation (N = 5,741 cases, P < 0.0056). This suggests a role for common variation in ion channel and developmental genes in atrial and atrioventricular conduction as well as in susceptibility to atrial fibrillation.
Related JoVE Video
Practical use of the raw electroencephalogram waveform during general anesthesia: the art and science.
Anesth. Analg.
PUBLISHED: 07-18-2009
Show Abstract
Hide Abstract
Quantitative electroencephalogram (qEEG) monitors are often used to estimate depth of anesthesia and intraoperative recall during general anesthesia. As with any monitor, the processed numerical output is often misleading and has to be interpreted within a clinical context. For the safe clinical use of these monitors, a clear mental picture of the expected raw electroencephalogram (EEG) patterns, as well as a knowledge of the common EEG artifacts, is absolutely necessary. This has provided the motivation to write this tutorial. We describe, and give examples of, the typical EEG features of adequate general anesthesia, effects of noxious stimulation, and adjunctive drugs. Artifacts are commonly encountered and may be classified as arising from outside the head, from the head but outside the brain (commonly frontal electromyogram), or from within the brain (atypical or pathologic). We include real examples of clinical problem-solving processes. In particular, it is important to realize that an artifactually high qEEG index is relatively common and may result in dangerous anesthetic drug overdose. The anesthesiologist must be certain that the qEEG number is consistent with the apparent state of the patient, the doses of various anesthetic drugs, and the degree of surgical stimulation, and that the qEEG number is consistent with the appearance of the raw EEG signal. Any discrepancy must be a stimulus for the immediate critical examination of the patients state using all the available information rather than reactive therapy to "treat" a number.
Related JoVE Video
Screening and surveillance recommendations for pediatric gastrointestinal polyposis syndromes.
J. Pediatr. Gastroenterol. Nutr.
PUBLISHED: 03-21-2009
Show Abstract
Hide Abstract
Inherited polyposis syndromes are relatively rare disorders in pediatric gastroenterology practice, even in busy academic settings. It is important, however, for pediatric gastroenterologists to be aware of the serious health risks for children and their families affected by these disorders. The diagnosis of a polyp syndrome is often made in the first or second decade of life, long before the risk of gastrointestinal neoplasia. Pediatric gastroenterologists must be prepared then to offer families predictive genetic screening as well as endoscopic surveillance when appropriately indicated. The current overview is designed to provide general guidelines and, whenever possible, evidence-based recommendations for genetic testing, endoscopic surveillance and other screening approaches for children with inherited gastrointestinal polyposis syndromes. In this presentation, the focus is on screening for neoplastic change and complications in the gastrointestinal tract. It is important to understand that extraintestinal cancers are frequent in some of these disorders and the reader is referred to other authoritative sources for additional information about comprehensive health screening outside the gastrointestinal system.
Related JoVE Video
hnRNP I inhibits Notch signaling and regulates intestinal epithelial homeostasis in the zebrafish.
PLoS Genet.
PUBLISHED: 02-06-2009
Show Abstract
Hide Abstract
Regulated intestinal stem cell proliferation and differentiation are required for normal intestinal homeostasis and repair after injury. The Notch signaling pathway plays fundamental roles in the intestinal epithelium. Despite the fact that Notch signaling maintains intestinal stem cells in a proliferative state and promotes absorptive cell differentiation in most species, it remains largely unclear how Notch signaling itself is precisely controlled during intestinal homeostasis. We characterized the intestinal phenotypes of brom bones, a zebrafish mutant carrying a nonsense mutation in hnRNP I. We found that the brom bones mutant displays a number of intestinal defects, including compromised secretory goblet cell differentiation, hyperproliferation, and enhanced apoptosis. These phenotypes are accompanied by a markedly elevated Notch signaling activity in the intestinal epithelium. When overexpressed, hnRNP I destabilizes the Notch intracellular domain (NICD) and inhibits Notch signaling. This activity of hnRNP I is conserved from zebrafish to human. In addition, our biochemistry experiments demonstrate that the effect of hnRNP I on NICD turnover requires the C-terminal portion of the RAM domain of NICD. Our results demonstrate that hnRNP I is an evolutionarily conserved Notch inhibitor and plays an essential role in intestinal homeostasis.
Related JoVE Video
Salt-induced pattern formation in evaporating droplets of lysozyme solutions.
Colloids Surf B Biointerfaces
Show Abstract
Hide Abstract
Solute self-organization during evaporation of colloidal sessile droplets has attracted the attention of researchers over the past few decades due to a variety of technological applications. Recently, pattern formation during evaporation of various biofluids has been studied due to potential applications in screening and diagnosis. The complex morphological patterns in the deposit are unique to various disorders and are influenced by various physical mechanisms occurring during evaporation. These complex patterns can be better understood by studying evaporation of model solutions of biological relevance. Here, we examine the general features of pattern formation during sessile droplet evaporation of aqueous lysozyme solutions with varying concentrations of NaCl. Lysozyme is a globular protein found in biological fluids such as tears and saliva. The morphological evolution of the droplet is studied by time-lapse video during evaporation via reflection optical microscopy. The final deposits exhibit an amorphous peripheral ring and interior regions containing crystallites and dendritic forms, dependent on NaCl concentration. Scanning electron microscopy (SEM) images demonstrate the multi-scale hierarchical nature of these structures.
Related JoVE Video
Low prevalence of connexin-40 gene variants in atrial tissues and blood from atrial fibrillation subjects.
BMC Med. Genet.
Show Abstract
Hide Abstract
The atrial gap junction protein connexin-40 (Cx40) has been implicated to play an important role in atrial conduction and development of atrial fibrillation (AF). However, the frequency of Cx40 mutations in AF populations and their impact on Cx40 expression remains unclear. In this study, we sought to identify polymorphisms in the Cx40 gene GJA5, investigate the potential functional role of these polymorphisms, and determine their allelic frequencies. The prevalence of nonsynonymous Cx40 mutations in blood and atrial tissue was also compared to mutation frequencies reported in prior studies.
Related JoVE Video
Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci.
Folkert W Asselbergs, Yiran Guo, Erik P A van Iperen, Suthesh Sivapalaratnam, Vinicius Tragante, Matthew B Lanktree, Leslie A Lange, Berta Almoguera, Yolande E Appelman, John Barnard, Jens Baumert, Amber L Beitelshees, Tushar R Bhangale, Yii-Der Ida Chen, Tom R Gaunt, Yan Gong, Jemma C Hopewell, Toby Johnson, Marcus E Kleber, Taimour Y Langaee, Mingyao Li, Yun R Li, Kiang Liu, Caitrin W McDonough, Matthijs F L Meijs, Rita P S Middelberg, Kiran Musunuru, Christopher P Nelson, Jeffery R O'Connell, Sandosh Padmanabhan, James S Pankow, Nathan Pankratz, Suzanne Rafelt, Ramakrishnan Rajagopalan, Simon P R Romaine, Nicholas J Schork, Jonathan Shaffer, Haiqing Shen, Erin N Smith, Sam E Tischfield, Peter J van der Most, Jana V van Vliet-Ostaptchouk, Niek Verweij, Kelly A Volcik, Li Zhang, Kent R Bailey, Kristian M Bailey, Florianne Bauer, Jolanda M A Boer, Peter S Braund, Amber Burt, Paul R Burton, Sarah G Buxbaum, Wei Chen, Rhonda M Cooper-DeHoff, L Adrienne Cupples, Jonas S deJong, Christian Delles, David Duggan, Myriam Fornage, Clement E Furlong, Nicole Glazer, John G Gums, Claire Hastie, Michael V Holmes, Thomas Illig, Susan A Kirkland, Mika Kivimäki, Ronald Klein, Barbara E Klein, Charles Kooperberg, Kandice Kottke-Marchant, Meena Kumari, Andrea Z LaCroix, Laya Mallela, Gurunathan Murugesan, Jose Ordovas, Willem H Ouwehand, Wendy S Post, Richa Saxena, Hubert Scharnagl, Pamela J Schreiner, Tina Shah, Denis C Shields, Daichi Shimbo, Sathanur R Srinivasan, Ronald P Stolk, Daniel I Swerdlow, Herman A Taylor, Eric J Topol, Elina Toskala, Joost L van Pelt, Jessica van Setten, Salim Yusuf, John C Whittaker, A H Zwinderman, , Sonia S Anand, Anthony J Balmforth, Gerald S Berenson, Connie R Bezzina, Bernhard O Boehm, Eric Boerwinkle, Juan P Casas, Mark J Caulfield, Robert Clarke, John M Connell, Karen J Cruickshanks, Karina W Davidson, Ian N M Day, Paul I W de Bakker, Pieter A Doevendans, Anna F Dominiczak, Alistair S Hall, Catharina A Hartman, Christian Hengstenberg, Hans L Hillege, Marten H Hofker, Steve E Humphries, Gail P Jarvik, Julie A Johnson, Bernhard M Kaess, Sekar Kathiresan, Wolfgang Koenig, Debbie A Lawlor, Winfried März, Olle Melander, Braxton D Mitchell, Grant W Montgomery, Patricia B Munroe, Sarah S Murray, Stephen J Newhouse, N Charlotte Onland-Moret, Neil Poulter, Bruce Psaty, Susan Redline, Stephen S Rich, Jerome I Rotter, Heribert Schunkert, Peter Sever, Alan R Shuldiner, Roy L Silverstein, Alice Stanton, Barbara Thorand, Mieke D Trip, Michael Y Tsai, Pim van der Harst, Ellen van der Schoot, Yvonne T van der Schouw, W M Monique Verschuren, Hugh Watkins, Arthur A M Wilde, Bruce H R Wolffenbuttel, John B Whitfield, G Kees Hovingh, Christie M Ballantyne, Cisca Wijmenga, Muredach P Reilly, Nicholas G Martin, James G Wilson, Daniel J Rader, Nilesh J Samani, Alex P Reiner, Robert A Hegele, John J P Kastelein, Aroon D Hingorani, Philippa J Talmud, Hakon Hakonarson, Clara C Elbers, Brendan J Keating, Fotios Drenos.
Am. J. Hum. Genet.
Show Abstract
Hide Abstract
Genome-wide association studies (GWASs) have identified many SNPs underlying variations in plasma-lipid levels. We explore whether additional loci associated with plasma-lipid phenotypes, such as high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), total cholesterol (TC), and triglycerides (TGs), can be identified by a dense gene-centric approach. Our meta-analysis of 32 studies in 66,240 individuals of European ancestry was based on the custom ?50,000 SNP genotyping array (the ITMAT-Broad-CARe array) covering ?2,000 candidate genes. SNP-lipid associations were replicated either in a cohort comprising an additional 24,736 samples or within the Global Lipid Genetic Consortium. We identified four, six, ten, and four unreported SNPs in established lipid genes for HDL-C, LDL-C, TC, and TGs, respectively. We also identified several lipid-related SNPs in previously unreported genes: DGAT2, HCAR2, GPIHBP1, PPARG, and FTO for HDL-C; SOCS3, APOH, SPTY2D1, BRCA2, and VLDLR for LDL-C; SOCS3, UGT1A1, BRCA2, UBE3B, FCGR2A, CHUK, and INSIG2 for TC; and SERPINF2, C4B, GCK, GATA4, INSR, and LPAL2 for TGs. The proportion of explained phenotypic variance in the subset of studies providing individual-level data was 9.9% for HDL-C, 9.5% for LDL-C, 10.3% for TC, and 8.0% for TGs. This large meta-analysis of lipid phenotypes with the use of a dense gene-centric approach identified multiple SNPs not previously described in established lipid genes and several previously unknown loci. The explained phenotypic variance from this approach was comparable to that from a meta-analysis of GWAS data, suggesting that a focused genotyping approach can further increase the understanding of heritability of plasma lipids.
Related JoVE Video
Characteristic size for onset of coffee-ring effect in evaporating lysozyme-water solution droplets.
J Phys Chem B
Show Abstract
Hide Abstract
Liquid droplets containing suspended particles deposited on a solid surface often form a ring-like structure due to the redistribution of solute during evaporation, a phenomenon known as the "coffee ring effect". The complex patterns left on the substrate after evaporation are characteristic of the nature of the solute and the particle transport mechanisms. In this study, the morphological evolution and conditions for coffee ring formation for simplified model biological solutions of DI water and lysozyme are examined by AFM and optical microscopy. Lysozyme is a globular protein found in high concentration, for example, in human tears and saliva. The drop diameters studied are very small, ranging from 1 to 50 ?m. In this size range, protein motion and the resulting dried residue morphology are highly influenced by the decreased evaporation time of the drop. In this work, we consider the effect of droplet size and concentration on the morphology of the deposited drop as well as the minimal conditions for coffee ring formation in this system. Two distinct deposit types are observed: a simple cap-shaped deposit for drops with small diameters and a ring-like deposit at larger diameters. Ring formation occurs at a critical diameter, which depends systematically on initial lysozyme concentration.
Related JoVE Video
SF3B1 haploinsufficiency leads to formation of ring sideroblasts in myelodysplastic syndromes.
Blood
Show Abstract
Hide Abstract
Whole exome/genome sequencing has been fundamental in the identification of somatic mutations in the spliceosome machinery in myelodysplastic syndromes (MDSs) and other hematologic disorders. SF3B1, splicing factor 3b subunit 1 is mutated in 60%-80% of refractory anemia with ring sideroblasts (RARS) and RARS associated with thrombocytosis (RARS-T), 2 distinct subtypes of MDS and MDS/myeloproliferative neoplasms (MDSs/MPNs). An idiosyncratic feature of RARS/RARS-T is the presence of abnormal sideroblasts characterized by iron overload in the mitochondria, called RS. Based on the high frequency of mutations of SF3B1 in RARS/RARS-T, we investigated the consequences of SF3B1 alterations. Ultrastructurally, SF3B1 mutants showed altered iron distribution characterized by coarse iron deposits compared with wild-type RARS patients by transmission electron microscopy. SF3B1 knockdown experiments in K562 cells resulted in down-regulation of U2-type intron-splicing by RT-PCR. RNA-sequencing analysis of SF3B1 mutants showed differentially used genes relevant in MDS pathogenesis, such as ASXL1, CBL, EZH, and RUNX families. A SF3B pharmacologic inhibitor, meayamycin, induced the formation of RS in healthy BM cells. Further, BM aspirates of Sf3b1 heterozygous knockout mice showed RS by Prussian blue. In conclusion, we report the first experimental evidence of the association between SF3B1 and RS phenotype. Our data suggest that SF3B1 haploinsufficiency leads to RS formation.
Related JoVE Video
Meta-analysis identifies six new susceptibility loci for atrial fibrillation.
Nat. Genet.
Show Abstract
Hide Abstract
Atrial fibrillation is a highly prevalent arrhythmia and a major risk factor for stroke, heart failure and death. We conducted a genome-wide association study (GWAS) in individuals of European ancestry, including 6,707 with and 52,426 without atrial fibrillation. Six new atrial fibrillation susceptibility loci were identified and replicated in an additional sample of individuals of European ancestry, including 5,381 subjects with and 10,030 subjects without atrial fibrillation (P < 5 × 10(-8)). Four of the loci identified in Europeans were further replicated in silico in a GWAS of Japanese individuals, including 843 individuals with and 3,350 individuals without atrial fibrillation. The identified loci implicate candidate genes that encode transcription factors related to cardiopulmonary development, cardiac-expressed ion channels and cell signaling molecules.
Related JoVE Video
Whole genome expression differences in human left and right atria ascertained by RNA sequencing.
Circ Cardiovasc Genet
Show Abstract
Hide Abstract
The left and right atria have different susceptibilities toward developing arrhythmias, with left atrial arrhythmias more commonly observed. To understand the molecular basis for such differences, we catalogued micro (mi)RNA and mRNA expression differences by next generation sequencing.
Related JoVE Video
Knockout of Mkp-1 exacerbates colitis in Il-10-deficient mice.
Am. J. Physiol. Gastrointest. Liver Physiol.
Show Abstract
Hide Abstract
Il-10-deficient mice develop colitis associated with exaggerated Th1/Th17 responses and are a valuable model of inflammatory bowel disease. Mkp-1 is a major negative regulator of MAPKs, and its expression is enhanced by IL-10. To understand the role of Mkp-1 in the regulation of intestinal mucosal immune responses, we studied the effect of Mkp-1 deletion on the pathogenesis of colitis in Il-10(-/-) mice. We found that knockout of Mkp-1 on an Il-10(-/-) background accelerated the development of colitis. Compared with Il-10(-/-) mice, colitis not only appeared earlier but also was more severe in Il-10(-/-)/Mkp-1(-/-) mice. Il-10(-/-) mice exhibited a mild intestinal inflammation in the specific pathogen-free environment, and rectal prolapse rarely appeared before 6 mo of age. In contrast, the majority of Il-10(-/-)/Mkp-1(-/-) mice developed severe colitis rapidly and presented with rectal prolapse after only 2-3 mo. The colon of Il-10(-/-)/Mkp-1(-/-) mice showed diffuse transmural chronic inflammation and mucosal hyperplasia, with significantly more proliferating crypt epithelial cells than those of Il-10(-/-) mice. In addition to the severe colitis, Il-10(-/-)/Mkp-1(-/-) mice also developed conjunctivitis and blepharitis. The colon of Il-10(-/-)/Mkp-1(-/-) mice contained significantly higher levels of proinflammatory cytokines and exhibited greater MAPK activities than did the colon of Il-10(-/-) mice. Splenocytes and lymphocytes from Il-10(-/-)/Mkp-1(-/-) mice produced higher levels of Th1 cytokines ex vivo upon activation than did cells from Il-10(-/-) mice. Our studies support a pivotal role of Mkp-1 as a negative regulator of mucosal immune responses and highlight its protective function against inflammatory bowel disease.
Related JoVE Video
Characteristics of evoked potential multiple EEG recordings in patients with chronic pain by means of parallel factor analysis.
Comput Math Methods Med
Show Abstract
Hide Abstract
This paper presents an alternative method, called as parallel factor analysis (PARAFAC) with a continuous wavelet transform, to analyze of brain activity in patients with chronic pain in the time-frequency-channel domain and quantifies differences between chronic pain patients and controls in these domains. The event related multiple EEG recordings of the chronic pain patients and non-pain controls with somatosensory stimuli (pain, random pain, touch, random touch) are analyzed. Multiple linear regression (MLR) is applied to describe the effects of aging on the frequency response differences between patients and controls. The results show that the somatosensory cortical responses occurred around 250?ms in both groups. In the frequency domain, the neural response frequency in the pain group (around 4?Hz) was less than that in the control group (around 5.5?Hz) under the somatosensory stimuli. In the channel domain, cortical activation was predominant in the frontal region for the chronic pain group and in the central region for controls. The indices of active ratios were statistical significant between the two groups in the frontal and central regions. These findings demonstrate that the PARAFAC is an interesting method to understanding the pathophysiological characteristics of chronic pain.
Related JoVE Video
Lysozyme pattern formation in evaporating drops.
Langmuir
Show Abstract
Hide Abstract
Liquid droplets containing suspended particles deposited on a solid, flat surface generally form ringlike structures due to the redistribution of solute during evaporation (the "coffee ring effect"). The forms of the deposited patterns depend on interactions between solute(s), solvent, and substrate. In this study, deposition patterns from droplets of a simplified model biological fluid (DI water + lysozyme) are examined by scanning probe and optical microscopy. The overall lysozyme residue morphology is complex (with both a perimeter "rim" and undulating interior) but varies little with concentration. However, the final packing of lysozyme molecules is strongly dependent on initial concentration.
Related JoVE Video
Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci.
Richa Saxena, Clara C Elbers, Yiran Guo, Inga Peter, Tom R Gaunt, Jessica L Mega, Matthew B Lanktree, Archana Tare, Berta Almoguera Castillo, Yun R Li, Toby Johnson, Marcel Bruinenberg, Diane Gilbert-Diamond, Ramakrishnan Rajagopalan, Benjamin F Voight, Ashok Balasubramanyam, John Barnard, Florianne Bauer, Jens Baumert, Tushar Bhangale, Bernhard O Böhm, Peter S Braund, Paul R Burton, Hareesh R Chandrupatla, Robert Clarke, Rhonda M Cooper-DeHoff, Errol D Crook, George Davey-Smith, Ian N Day, Anthonius de Boer, Mark C H de Groot, Fotios Drenos, Jane Ferguson, Caroline S Fox, Clement E Furlong, Quince Gibson, Christian Gieger, Lisa A Gilhuijs-Pederson, Joseph T Glessner, Anuj Goel, Yan Gong, Struan F A Grant, Diederick E Grobbee, Claire Hastie, Steve E Humphries, Cecilia E Kim, Mika Kivimäki, Marcus Kleber, Christa Meisinger, Meena Kumari, Taimour Y Langaee, Debbie A Lawlor, Mingyao Li, Maximilian T Lobmeyer, Anke-Hilse Maitland-van der Zee, Matthijs F L Meijs, Cliona M Molony, David A Morrow, Gurunathan Murugesan, Solomon K Musani, Christopher P Nelson, Stephen J Newhouse, Jeffery R O'Connell, Sandosh Padmanabhan, Jutta Palmen, Sanjey R Patel, Carl J Pepine, Mary Pettinger, Thomas S Price, Suzanne Rafelt, Jane Ranchalis, Asif Rasheed, Elisabeth Rosenthal, Ingo Ruczinski, Sonia Shah, Haiqing Shen, Günther Silbernagel, Erin N Smith, Annemieke W M Spijkerman, Alice Stanton, Michael W Steffes, Barbara Thorand, Mieke Trip, Pim van der Harst, Daphne L van der A, Erik P A van Iperen, Jessica van Setten, Jana V van Vliet-Ostaptchouk, Niek Verweij, Bruce H R Wolffenbuttel, Taylor Young, M Hadi Zafarmand, Joseph M Zmuda, , Michael Boehnke, David Altshuler, Mark McCarthy, W H Linda Kao, James S Pankow, Thomas P Cappola, Peter Sever, Neil Poulter, Mark Caulfield, Anna Dominiczak, Denis C Shields, Deepak L Bhatt, Deepak Bhatt, Li Zhang, Sean P Curtis, John Danesh, Juan P Casas, Yvonne T van der Schouw, N Charlotte Onland-Moret, Pieter A Doevendans, Gerald W Dorn, Martin Farrall, Garret A FitzGerald, Anders Hamsten, Robert Hegele, Aroon D Hingorani, Marten H Hofker, Gordon S Huggins, Thomas Illig, Gail P Jarvik, Julie A Johnson, Olaf H Klungel, William C Knowler, Wolfgang Koenig, Winfried März, James B Meigs, Olle Melander, Patricia B Munroe, Braxton D Mitchell, Susan J Bielinski, Daniel J Rader, Muredach P Reilly, Stephen S Rich, Jerome I Rotter, Danish Saleheen, Nilesh J Samani, Eric E Schadt, Alan R Shuldiner, Roy Silverstein, Kandice Kottke-Marchant, Philippa J Talmud, Hugh Watkins, Folkert W Asselbergs, Folkert Asselbergs, Paul I W de Bakker, Jeanne McCaffery, Cisca Wijmenga, Marc S Sabatine, James G Wilson, Alex Reiner, Donald W Bowden, Hakon Hakonarson, David S Siscovick, Brendan J Keating.
Am. J. Hum. Genet.
Show Abstract
Hide Abstract
To identify genetic factors contributing to type 2 diabetes (T2D), we performed large-scale meta-analyses by using a custom ?50,000 SNP genotyping array (the ITMAT-Broad-CARe array) with ?2000 candidate genes in 39 multiethnic population-based studies, case-control studies, and clinical trials totaling 17,418 cases and 70,298 controls. First, meta-analysis of 25 studies comprising 14,073 cases and 57,489 controls of European descent confirmed eight established T2D loci at genome-wide significance. In silico follow-up analysis of putative association signals found in independent genome-wide association studies (including 8,130 cases and 38,987 controls) performed by the DIAGRAM consortium identified a T2D locus at genome-wide significance (GATAD2A/CILP2/PBX4; p = 5.7 × 10(-9)) and two loci exceeding study-wide significance (SREBF1, and TH/INS; p < 2.4 × 10(-6)). Second, meta-analyses of 1,986 cases and 7,695 controls from eight African-American studies identified study-wide-significant (p = 2.4 × 10(-7)) variants in HMGA2 and replicated variants in TCF7L2 (p = 5.1 × 10(-15)). Third, conditional analysis revealed multiple known and novel independent signals within five T2D-associated genes in samples of European ancestry and within HMGA2 in African-American samples. Fourth, a multiethnic meta-analysis of all 39 studies identified T2D-associated variants in BCL2 (p = 2.1 × 10(-8)). Finally, a composite genetic score of SNPs from new and established T2D signals was significantly associated with increased risk of diabetes in African-American, Hispanic, and Asian populations. In summary, large-scale meta-analysis involving a dense gene-centric approach has uncovered additional loci and variants that contribute to T2D risk and suggests substantial overlap of T2D association signals across multiple ethnic groups.
Related JoVE Video

What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.