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Search Results: 1 - 10 of 555797 matches for " Arthur A. B. Bergen "
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A New Strategy to Identify and Annotate Human RPE-Specific Gene Expression
Judith C. Booij,Jacoline B. ten Brink,Sigrid M. A. Swagemakers,Annemieke J. M. H. Verkerk,Anke H. W. Essing,Peter J. van der Spek,Arthur A. B. Bergen
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0009341
Abstract: To identify and functionally annotate cell type-specific gene expression in the human retinal pigment epithelium (RPE), a key tissue involved in age-related macular degeneration and retinitis pigmentosa.
Gene Expression and Functional Annotation of the Human Ciliary Body Epithelia
Sarah F. Janssen, Theo G. M. F. Gorgels, Koen Bossers, Jacoline B. ten Brink, Anke H. W. Essing, Martijn Nagtegaal, Peter J. van der Spek, Nomdo M. Jansonius, Arthur A. B. Bergen
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0044973
Abstract: Purpose The ciliary body (CB) of the human eye consists of the non-pigmented (NPE) and pigmented (PE) neuro-epithelia. We investigated the gene expression of NPE and PE, to shed light on the molecular mechanisms underlying the most important functions of the CB. We also developed molecular signatures for the NPE and PE and studied possible new clues for glaucoma. Methods We isolated NPE and PE cells from seven healthy human donor eyes using laser dissection microscopy. Next, we performed RNA isolation, amplification, labeling and hybridization against 44×k Agilent microarrays. For microarray conformations, we used a literature study, RT-PCRs, and immunohistochemical stainings. We analyzed the gene expression data with R and with the knowledge database Ingenuity. Results The gene expression profiles and functional annotations of the NPE and PE were highly similar. We found that the most important functionalities of the NPE and PE were related to developmental processes, neural nature of the tissue, endocrine and metabolic signaling, and immunological functions. In total 1576 genes differed statistically significantly between NPE and PE. From these genes, at least 3 were cell-specific for the NPE and 143 for the PE. Finally, we observed high expression in the (N)PE of 35 genes previously implicated in molecular mechanisms related to glaucoma. Conclusion Our gene expression analysis suggested that the NPE and PE of the CB were quite similar. Nonetheless, cell-type specific differences were found. The molecular machineries of the human NPE and PE are involved in a range of neuro-endocrinological, developmental and immunological functions, and perhaps glaucoma.
Gene Expression and Functional Annotation of the Human and Mouse Choroid Plexus Epithelium
Sarah F. Janssen, Sophie J. F. van der Spek, Jacoline B. ten Brink, Anke H. W. Essing, Theo G. M. F. Gorgels, Peter J. van der Spek, Nomdo M. Jansonius, Arthur A. B. Bergen
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0083345
Abstract: Background The choroid plexus epithelium (CPE) is a lobed neuro-epithelial structure that forms the outer blood-brain barrier. The CPE protrudes into the brain ventricles and produces the cerebrospinal fluid (CSF), which is crucial for brain homeostasis. Malfunction of the CPE is possibly implicated in disorders like Alzheimer disease, hydrocephalus or glaucoma. To study human genetic diseases and potential new therapies, mouse models are widely used. This requires a detailed knowledge of similarities and differences in gene expression and functional annotation between the species. The aim of this study is to analyze and compare gene expression and functional annotation of healthy human and mouse CPE. Methods We performed 44k Agilent microarray hybridizations with RNA derived from laser dissected healthy human and mouse CPE cells. We functionally annotated and compared the gene expression data of human and mouse CPE using the knowledge database Ingenuity. We searched for common and species specific gene expression patterns and function between human and mouse CPE. We also made a comparison with previously published CPE human and mouse gene expression data. Results Overall, the human and mouse CPE transcriptomes are very similar. Their major functionalities included epithelial junctions, transport, energy production, neuro-endocrine signaling, as well as immunological, neurological and hematological functions and disorders. The mouse CPE presented two additional functions not found in the human CPE: carbohydrate metabolism and a more extensive list of (neural) developmental functions. We found three genes specifically expressed in the mouse CPE compared to human CPE, being ACE, PON1 and TRIM3 and no human specifically expressed CPE genes compared to mouse CPE. Conclusion Human and mouse CPE transcriptomes are very similar, and display many common functionalities. Nonetheless, we also identified a few genes and pathways which suggest that the CPE between mouse and man differ with respect to transport and metabolic functions.
Pseudoxanthoma Elasticum: Cardiac Findings in Patients and Abcc6-Deficient Mouse Model
Fabrice Prunier, Gwenola Terrien, Yannick Le Corre, Ailea L. Y. Apana, Lo?c Bière, Gilles Kauffenstein, Alain Furber, Arthur A. B. Bergen, Theo G. M. F. Gorgels, Olivier Le Saux, Georges Leftheriotis, Ludovic Martin
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0068700
Abstract: Background Pseudoxanthoma elasticum (PXE), caused by mutations in the ABCC6 gene, is a rare multiorgan disease characterized by the mineralization and fragmentation of elastic fibers in connective tissue. Cardiac complications reportedly associated with PXE are mainly based on case reports. Methods A cohort of 67 PXE patients was prospectively assessed. Patients underwent physical examination, electrocardiogram, transthoracic echocardiography, cardiac magnetic resonance imaging (CMR), treadmill testing, and perfusion myocardial scintigraphy (SPECT). Additionally, the hearts of a PXE mouse models (Abcc6?/?) and wild-type controls (WT) were analyzed. Results Three patients had a history of proven coronary artery disease. In total, 40 patients underwent exercise treadmill tests, and 28 SPECT. The treadmill tests were all negative. SPECT showed mild perfusion abnormalities in two patients. Mean left ventricular (LV) dimension and function values were within the normal range. LV hypertrophy was found in 7 (10.4%) patients, though the hypertrophy etiology was unknown for 3 of those patients. Echocardiography revealed frequent but insignificant mitral and tricuspid valvulopathies. Mitral valve prolapse was present in 3 patients (4.5%). Two patients exhibited significant aortic stenosis (3.0%). While none of the functional and histological parameters diverged significantly between the Abcc6?/? and WT mice groups at age of 6 and 12 months, the 24-month-old Abcc6?/? mice developed cardiac hypertrophy without contractile dysfunction. Conclusions Despite sporadic cases, PXE does not appear to be associated with frequent cardiac complications. However, the development of cardiac hypertrophy in the 24-month-old Abcc6?/? mice suggests that old PXE patients might be prone to developing late cardiopathy.
The ERCC6 Gene and Age-Related Macular Degeneration
Dominique C. Baas,Dominiek D. Despriet,Theo G. M. F. Gorgels,Julie Bergeron-Sawitzke,André G. Uitterlinden,Albert Hofman,Cornelia M. van Duijn,Joanna E. Merriam,R. Theodore Smith,Gaetano R. Barile,Jacoline B. ten Brink,Johannes R. Vingerling,Caroline C. W. Klaver,Rando Allikmets,Michael Dean,Arthur A. B. Bergen
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0013786
Abstract: Age-related macular degeneration (AMD) is the leading cause of irreversible visual loss in the developed countries and is caused by both environmental and genetic factors. A recent study (Tuo et al., PNAS) reported an association between AMD and a single nucleotide polymorphism (SNP) (rs3793784) in the ERCC6 (NM_000124) gene. The risk allele also increased ERCC6 expression. ERCC6 is involved in DNA repair and mutations in ERCC6 cause Cockayne syndrome (CS). Amongst others, photosensitivity and pigmentary retinopathy are hallmarks of CS.
A Genome-Wide Association Study of Optic Disc Parameters
Wishal D. Ramdas equal contributor,Leonieke M. E. van Koolwijk equal contributor,M. Kamran Ikram equal contributor,Nomdo M. Jansonius,Paulus T. V. M. de Jong,Arthur A. B. Bergen,Aaron Isaacs,Najaf Amin,Yurii S. Aulchenko,Roger C. W. Wolfs,Albert Hofman,Fernando Rivadeneira,Ben A. Oostra,Andre G. Uitterlinden,Pirro Hysi,Christopher J. Hammond,Hans G. Lemij,Johannes R. Vingerling ,Caroline C. W. Klaver equal contributor,Cornelia M. van Duijn equal contributor
PLOS Genetics , 2010, DOI: 10.1371/journal.pgen.1000978
Abstract: The optic nerve head is involved in many ophthalmic disorders, including common diseases such as myopia and open-angle glaucoma. Two of the most important parameters are the size of the optic disc area and the vertical cup-disc ratio (VCDR). Both are highly heritable but genetically largely undetermined. We performed a meta-analysis of genome-wide association (GWA) data to identify genetic variants associated with optic disc area and VCDR. The gene discovery included 7,360 unrelated individuals from the population-based Rotterdam Study I and Rotterdam Study II cohorts. These cohorts revealed two genome-wide significant loci for optic disc area, rs1192415 on chromosome 1p22 (p = 6.72×10?19) within 117 kb of the CDC7 gene and rs1900004 on chromosome 10q21.3-q22.1 (p = 2.67×10?33) within 10 kb of the ATOH7 gene. They revealed two genome-wide significant loci for VCDR, rs1063192 on chromosome 9p21 (p = 6.15×10?11) in the CDKN2B gene and rs10483727 on chromosome 14q22.3-q23 (p = 2.93×10?10) within 40 kbp of the SIX1 gene. Findings were replicated in two independent Dutch cohorts (Rotterdam Study III and Erasmus Rucphen Family study; N = 3,612), and the TwinsUK cohort (N = 843). Meta-analysis with the replication cohorts confirmed the four loci and revealed a third locus at 16q12.1 associated with optic disc area, and four other loci at 11q13, 13q13, 17q23 (borderline significant), and 22q12.1 for VCDR. ATOH7 was also associated with VCDR independent of optic disc area. Three of the loci were marginally associated with open-angle glaucoma. The protein pathways in which the loci of optic disc area are involved overlap with those identified for VCDR, suggesting a common genetic origin.
Common Genetic Determinants of Intraocular Pressure and Primary Open-Angle Glaucoma
Leonieke M. E. van Koolwijk equal contributor,Wishal D. Ramdas equal contributor,M. Kamran Ikram,Nomdo M. Jansonius,Francesca Pasutto,Pirro G. Hysi,Stuart Macgregor,Sarah F. Janssen,Alex W. Hewitt,Ananth C. Viswanathan,Jacoline B. ten Brink,S. Mohsen Hosseini,Najaf Amin,Dominiek D. G. Despriet,Jacqueline J. M. Willemse-Assink,Rogier Kramer,Fernando Rivadeneira,Maksim Struchalin,Yurii S. Aulchenko,Nicole Weisschuh,Matthias Zenkel,Christian Y. Mardin,Eugen Gramer,Ulrich Welge-Lüssen,Grant W. Montgomery,Francis Carbonaro,Terri L. Young,The DCCT/EDIC Research Group,Céline Bellenguez,Peter McGuffin,Paul J. Foster,Fotis Topouzis,Paul Mitchell,Jie Jin Wang,Tien Y. Wong,Monika A. Czudowska,Albert Hofman,Andre G. Uitterlinden,Roger C. W. Wolfs,Paulus T. V. M. de Jong,Ben A. Oostra,Andrew D. Paterson,Wellcome Trust Case Control Consortium 2,David A. Mackey,Arthur A. B. Bergen,André Reis,Christopher J. Hammond,Johannes R. Vingerling,Hans G. Lemij,Caroline C. W. Klaver,Cornelia M. van Duijn
PLOS Genetics , 2012, DOI: 10.1371/journal.pgen.1002611
Abstract: Intraocular pressure (IOP) is a highly heritable risk factor for primary open-angle glaucoma and is the only target for current glaucoma therapy. The genetic factors which determine IOP are largely unknown. We performed a genome-wide association study for IOP in 11,972 participants from 4 independent population-based studies in The Netherlands. We replicated our findings in 7,482 participants from 4 additional cohorts from the UK, Australia, Canada, and the Wellcome Trust Case-Control Consortium 2/Blue Mountains Eye Study. IOP was significantly associated with rs11656696, located in GAS7 at 17p13.1 (p = 1.4×10?8), and with rs7555523, located in TMCO1 at 1q24.1 (p = 1.6×10?8). In a meta-analysis of 4 case-control studies (total N = 1,432 glaucoma cases), both variants also showed evidence for association with glaucoma (p = 2.4×10?2 for rs11656696 and p = 9.1×10?4 for rs7555523). GAS7 and TMCO1 are highly expressed in the ciliary body and trabecular meshwork as well as in the lamina cribrosa, optic nerve, and retina. Both genes functionally interact with known glaucoma disease genes. These data suggest that we have identified two clinically relevant genes involved in IOP regulation.
Performance of high-throughput DNA quantification methods
Kashif A Haque, Ruth M Pfeiffer, Michael B Beerman, Jeff P Struewing, Stephen J Chanock, Andrew W Bergen
BMC Biotechnology , 2003, DOI: 10.1186/1472-6750-3-20
Abstract: The OD method was the DNA quantification method most concordant with the reference sample among the three methods evaluated. A large fraction of the total variance for all three methods (36.0–95.7%) was explained by sample-to-sample variation, whereas the amount of variance attributable to sample handling was small (0.8–17.5%). Residual error (3.2–59.4%), corresponding to un-modelled factors, contributed a greater extent to the total variation than the sample handling procedures.The application of a specific DNA quantification method to a particular molecular genetic laboratory protocol must take into account the accuracy and precision of the specific method, as well as the requirements of the experimental workflow with respect to sample volumes and throughput. While OD was the most concordant and precise DNA quantification method in this study, the information provided by the quantitative PCR assay regarding the suitability of DNA samples for PCR may be an essential factor for some protocols, despite the decreased concordance and precision of this method.Molecular genetic studies hold the promise of identifying genetic factors that influence human disease susceptibility and outcome [1]. However, large sample sizes are required to find small to moderate sized genetic effects in association studies [2]. Technical advances in genotype and sequence analysis, together with essentially unlimited availability of sequence and sequence variation information, have substantially increased the scope of human genetic studies. It is now possible to examine many polymorphisms or sequences in high-throughput settings, using significantly less DNA per assay (~1–5 ng) than in the past decade. Nevertheless, conservation of precious DNA samples represents a critical goal for the efficient utilization of research resources. One area of technological development essential for success in high-throughput genotyping is the quantification of DNA. Accurate and precise DNA quantification is n
Interlocu es e saberes docentes em intera es on-line: um estudo de caso com professores de matemática Teachers' interlocution and knowledge in online interactions: a case study with mathematics teachers
Marcelo A. Bairral,Arthur B. Powell
Pro-Posi??es , 2013,
Abstract: Integrando matemática, educa o, comunica o, TIC e ciência cognitiva, este artigo é resultado de um projeto de pesquisa em Educa o Matemática que, através de estudos empíricos, tem como objetivo analisar situa es cognitivas e condi es pedagógicas que favore am a aprendizagem em ambientes virtuais. O enquadramento teórico da investiga o é baseado em estudos sobre aprendizagem matemática que combinam a comunica o e o pensamento, bem como as intera es e as interlocu es. Aqui analisamos reflex es on-line entre os professores de Matemática dentro de um ambiente chamado Virtual Math Teams (VMT), colaborando para resolver um problema de geometria do táxi. Ilustramos diferentes tipos de interlocu o (informativa, negociativa, avaliativa e interpretativa), bem como domínios de conhecimentos (epistemologia, didática e media o) identificados com o conhecimento profissional dos professores. Nossos resultados indicam que interlocu es interpretativas e negociativas têm maior potencial para aprimorar o pensamento matemático dos interlocutores. O estudo também destaca que, por meio da identifica o e da análise de propriedades de interlocu o, os pesquisadores podem obter insights sobre o conhecimento profissional dos professores. Integrating mathematics, education, communication, ICT, and cognitive science, this study is the result of a research program in mathematics education that aims to analyze cognitive situations and pedagogic conditions, through empirical studies, that favor learning in virtual environments. The theoretical framework of the investigation is based on studies of mathematics learning that combine communication and thought as well as interactions and interlocutions. In this article, we analyze interactions among mathematics teachers who interact online within an environment, called Virtual Math Teams (VMT), collaborating to solve a problem in taxicab geometry. We illustrate different types of interlocution (evaluative, informative, interpretative, negotiatory) as well as knowledge domains (epistemology, didactics, and mediation) identified by the teachers' professional knowledge. Our results indicate that interpretative and negotiatory interlocutions have greater potential to enhance interlocutors' mathematical thinking. Our study also highlights that by identifying and analyzing interlocution properties, researchers can obtain insights into the teachers' professional knowledge.
A Needs Analysis of Undergraduate Students of Communicative Skills: The Case of Tertiary Institutions in Ghana  [PDF]
Philip Arthur Gborsong, Joseph B. A. Afful, Wincharles Coker, Osei Yaw Akoto, Rita Twumasi, Araba Baiden
Open Journal of Modern Linguistics (OJML) , 2015, DOI: 10.4236/ojml.2015.55037
Abstract: For over three decades now, research on undergraduate student pedagogy has shifted focus from an error analysis tradition to an emphasis on learner needs. As part of this shift, we examined the needs of students who offered Communicative Skills in an English-medium university in Ghana, and whether their needs were discipline-specific. Data were collected from two hundred and forty students and twenty lecturers, using a two-pronged sampling method. Major results showed a great need for grammar and writing skills among students, though they held that note taking and note making skills, outlining and skimming be expunged from the programme. The study also indicated that although teachers of Communicative Skills preferred a variationist approach, the reverse was the case among their students. Surprisingly, while students desired to be exposed to modern skills such as CV and Proposal writing, their instructors, on the other hand, were of the view that paragraph and essay development were not so useful. The study, thus, resonates with proclivities for further interventionist methods, specialist instructor (re)training and future research in undergraduate student writing.
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