The human ABC transporter pseudogene family: Evidence for transcription and gene-pseudogene interference

<p>Abstract</p> <p>Background</p> <p>Pseudogenes are an integral component of the human genome. Little attention, however, has so far been paid to the phenomenon that some pseudogenes are transcriptionally active. Recently, we demonstrated that the human ortholog of the rodent testis-specific ATP-binding cassette (ABC) transporter Abca17 is a ubiquitously transcribed pseudogene (<it>ABCA17P</it>). The aim of the present study was to establish a complete inventory of all ABC transporter pseudogenes in the human genome and to identify transcriptionally active ABC transporter pseudogenes. Moreover, we tested the hypothesis that a regulatory interdependency exists between ABC transporter pseudogenes and their parental protein coding equivalents.</p> <p>Results</p> <p>Systematic bioinformatic analysis revealed the existence of 22 ABC transporter pseudogenes within the human genome. We identified two clusters on chromosomes 15 and 16, respectively, which harbor almost half of all pseudogenes (n = 10). Available information from EST and mRNA databases and RT-PCR expression profiling indicate that a large portion of the ABC transporter pseudogenes (45%, n = 10) are transcriptionally active and some of them are expressed as alternative splice variants. We demonstrate that both pseudogenes of the pseudoxanthoma elasticum gene <it>ABCC6</it>, <it>ABCC6P1 </it>and <it>ABCC6P2</it>, are transcribed. <it>ABCC6P1 </it>and <it>ABCC6 </it>possess near-identical promoter sequences and their tissue-specific expression profiles are strikingly similar raising the possibility that they form a gene-pseudogene dual transcription unit. Intriguingly, targeted knockdown of the transcribed pseudogene <it>ABCC6P1 </it>resulted in a significant reduction of <it>ABCC6 </it>mRNA expression levels.</p> <p>Conclusion</p> <p>The human genome contains a surprisingly small number of ABC transporter pseudogenes relative to other known gene families. They are unevenly distributed across the chromosomes. Importantly, a significant portion of the ABC transporter pseudogenes is transcriptionally active. The downregulation of <it>ABCC6 </it>mRNA levels by targeted suppression of the expression of its pseudogene <it>ABCC6P1 </it>provides evidence, for the first time, for a regulatory interdependence of a transcribed pseudogene and its protein coding counterpart in the human genome.</p

Isolated focal lesion in the splenium of the corpus callosum in a patient with acute viral hepatitis A

Mitochondrial dysfunction - Nm vs ctr - FDR5. (XLS 46 kb

The Effect of Processing Technique and Reference Frame Definition on Noise in CGPS Position Time Series

In this presentation we investigate the effects of GPS processing techniques and strategies, and the related reference frame realization, on the stochastic properties of continuous GPS (CGPS) position time series. It was of particular interest to establish whether and how different GPS processing techniques and strategies, e.g. double differencing (DD) and precise point positioning (PPP), and the use of different orbit and clock products, and/or the definition of the reference frame (partly dependent on the applied strategy) affect the colored noise content of time series. We used CGPS position time series from 15 different solutions obtained from seven different analysis centers as part of the European Sea Level Service - Research Infrastructure project (ESEAS-RI) using the GIPSY OASIS II, GAMIT and Bernese GPS softwares. All time series analyzed have at least three years of data for the period between 2000 and 2005. Furthermore, a selected set of position time series was also analyzed using Empirical Orthogonal Function (EOF) analysis. The noise content of the first 15 modes, representing the solution-specific common mode time series for each of the selected solutions were then also investigated for colored noise. Using Maximum Likelihood Estimation (MLE) a white, a white plus flicker, a white plus power- law and a white plus first-order Gauss-Markov (FOGM) noise model were fitted to the position and EOF time series data. For both the position and EOF time series the parameter model included a constant, a rate and harmonic terms with annual, semi-annual, 4- monthly, 3-monthly, 2.4-monthly and 13.66 day periods. Position jumps were modeled at logged epochs or at visible discontinuities in the time series. The MLE showed that in most cases the best fitting noise model is a combination of white plus power-law noise with average spectral indices in the range between -0.5 and -1.4. This model is closely followed by the combination of white plus flicker and white plus FOGM noise. The noise properties of the EOF time series follow predominantly a white plus power-law character, with the first few modes indicating a white plus flicker noise behavior. In general, DD solutions contain less noise than PPP solutions and that regional reference frame definitions further reduce the amount of noise in the time series

Warfarin dose and INR related to genotypes of CYP2C9 and VKORC1 in patients with myocardial infarction

<p>Abstract</p> <p>Background</p> <p>Warfarin treatment has a narrow therapeutic range, requiring meticulous monitoring and dosage titration. Individual dosage requirement has recently partly been explained by genetic variation of the warfarin metabolizing enzyme CYP2C9 and the Vitamin K-activating enzyme VKORC1. In the WARIS-II study, comparing three different antithrombotic regimens after myocardial infarction, warfarin treatment reduced thrombotic events, but was associated with more frequent bleeding than use of acetylsalisylic acid (ASA) alone.</p> <p>Aims</p> <p>The primary aim of the present study was to investigate the relation between genotypes of CYP2C9 and VKORC1 and warfarin maintenance dose in myocardial infarction. The secondary aim was to relate the genotypes to international normalized ratio (INR).</p> <p>Methods</p> <p>Genotyping was performed in 212 myocardial infarction patients from the WARIS-II study by robotic isolation of DNA from EDTA whole blood (MagNa Pure LC) before PCR amplification (LightCycler) and melting point analysis.</p> <p>Results</p> <p>The 420 C>T substitution of CYP2C9*2, the 1075 A>C substitution of CYP2C9*3 and the 1173 C>T substitution of VKORC1 had minor allele frequencies of, 11.3%, 5.7% and 36.6% respectively. Warfarin weekly dose varied between 17 mg and 74 mg among the patients. INR did not vary between genotypes. Warfarin dosage requirement was significantly associated with CYP2C9 and VKORC1 genotypes, treatment group and age. The VKORC1 genotype contributed 24.5% to the interindividual variation in warfarin dosage, whereas the combined CYP2C9 genotypes were only responsible for 7.2% of the dose variation.</p> <p>Conclusion</p> <p>CYP2C9 and VKORC1 genotype frequencies in myocardial infarction patients appear similar to other patient groups and have similar impact on warfarin maintenance dose.</p

Biological properties of extracellular vesicles and their physiological functions

In the past decade, extracellular vesicles (EVs) have been recognized as potent vehicles of intercellular communication, both in prokaryotes and eukaryotes. This is due to their capacity to transfer proteins, lipids and nucleic acids, thereby influencing various physiological and pathological functions of both recipient and parent cells. While intensive investigation has targeted the role of EVs in different pathological processes, for example, in cancer and autoimmune diseases, the EV-mediated maintenance of homeostasis and the regulation of physiological functions have remained less explored. Here, we provide a comprehensive overview of the current understanding of the physiological roles of EVs, which has been written by crowd-sourcing, drawing on the unique EV expertise of academia-based scientists, clinicians and industry based in 27 European countries, the United States and Australia. This review is intended to be of relevance to both researchers already working on EV biology and to newcomers who will encounter this universal cell biological system. Therefore, here we address the molecular contents and functions of EVs in various tissues and body fluids from cell systems to organs. We also review the physiological mechanisms of EVs in bacteria, lower eukaryotes and plants to highlight the functional uniformity of this emerging communication system

Minimal information for studies of extracellular vesicles 2018 (MISEV2018):a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines for the field in 2014. We now update these “MISEV2014” guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points

Biological properties of extracellular vesicles and their physiological functions

María Yáñez-Mó#, Pia R.-M. Siljander#, Zoraida Andreu, Apolonija Bedina Zavec, Francesc E. Borràs, Edit I. Buzas, Krisztina Buzas, Enriqueta Casal, Francesco Cappello, Joana Carvalho, Eva Colás, Anabela Cordeiro-da Silva, Stefano Fais, Juan M. Falcon-Perez, Irene M. Ghobrial, Bernd Giebel, Mario Gimona, Michael Graner, Ihsan Gursel, Mayda Gursel, Niels H. H. Heegaard, An Hendrix30, Peter Kierulf, Katsutoshi Kokubun, Maja Kosanovic, Veronika Kralj-Iglic, Eva-Maria Krämer-Albers, Saara Laitinen, Cecilia Lässer, Thomas Lener, Erzsébet Ligeti, Aija Linē, Georg Lipps, Alicia Llorente, Jan Lötvall, Mateja Manček-Keber, Antonio Marcilla, Maria Mittelbrunn, Irina Nazarenko, Esther N.M. Nolte-‘t Hoen, Tuula A. Nyman, Lorraine O'Driscoll, Mireia Olivan, Carla Oliveira, Éva Pállinger, Hernando A. del Portillo, Jaume Reventós, Marina Rigau, Eva Rohde, Marei Sammar, Francisco Sánchez-Madrid, N. Santarém1, Katharina Schallmoser, Marie Stampe Ostenfeld, Willem Stoorvogel, Roman Stukelj, Susanne G. Van der Grein, M. Helena Vasconcelos, Marca H. M. Wauben and Olivier De WeverIn the past decade, extracellular vesicles (EVs) have been recognized as potent vehicles of intercellular communication, both in prokaryotes and eukaryotes. This is due to their capacity to transfer proteins, lipids and nucleic acids, thereby influencing various physiological and pathological functions of both recipient and parent cells.While intensive investigation has targeted the role of EVs in different pathological processes, for example, in cancer and autoimmune diseases, the EV-mediated maintenance of homeostasis and the regulation of physiological functions have remained less explored. Here, we provide a comprehensive overview of the current understanding of the physiological roles of EVs, which has been written by crowd-sourcing, drawing on the unique EV expertise of academia-based scientists, clinicians and industry based in 27 European countries, the United States and Australia. This review is intended to be of relevance to both researchers already working on EV biology and to newcomers who will encounter this universal cell biological system. Therefore, here we address the molecular contents and functions of EVs in various tissues and body fluids from cell systems to organs. We also review the physiological mechanisms of EVs in bacteria, lower eukaryotes and plants to highlight the functional uniformity of this emerging communication system.Peer reviewe

Authorship: attitudes and practice among Norwegian researchers

Background Attitudes to, and practices of, scientific authorship vary. We have studied this variation among researchers in a university hospital and medical school in Norway. Methods We invited all faculty, researchers and PhD students at Oslo University Hospital and the Faculty of Medicine, University of Oslo (approximately 2700) by e-mail to answer a web-based questionnaire in January 2013. We asked the researchers to report their authorship experiences and to score their agreement with, and ability to practice according to, 13 statements on authorship qualifications and criteria on a five-point Likert scale (1 = completely agree, 5 = completely disagree). The statements were taken from the International Committee of Medical Journal Editors (ICMJE) and other recommendations on authorship. Results 654 questionnaires were returned (response rate 24%); 25% of the respondents had published less than five scientific articles, 43% five to 49, and 32% more than 50 articles. 97% reported knowledge of defined authorship criteria, and 68% regarded breaches of these as scientific misconduct. 36% had experienced pressure to include undeserved authors in their papers, more in basic science (46%) than in community medicine (25%). 29% reported that they had been denied authorship they believed they deserved. Researchers with less than six years of research experience found authorship decisions more difficult than more experienced researchers (48% vs 30%). The respondents’ agreement with the statements on authorship was higher than their self-reported ability to follow them for all statements. Average scores for agreement and practice for all statements combined were 1.4 vs 2.3. The discrepancy between attitude and practice declined with publishing experience. For the core ICMJE authorship requirements the average difference between attitude and practice was 1.2 among those who had published less than 5 articles and 0.7 among those who had published 50 articles or more (p < 0.05). Conclusions Almost all the responding researchers had knowledge of formal authorship requirements. Most of them agreed with the criteria, but found it harder to put them into practice. More experienced researchers found decisions on authorship and about the order of authors easier than less experienced researchers