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Search Results: 1 - 10 of 11185 matches for " Mario Fasold "
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Estimating RNA-quality using GeneChip microarrays
Mario Fasold, Hans Binder
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-186
Abstract: Microarray intensity data contains information to estimate the RNA quality of the sample. We here study the interplay of the characteristics of RNA surface hybridization with the effects of partly truncated transcripts on probe intensity. The 3′/5′ intensity gradient, the basis of microarray RNA quality measures, is shown to depend on the degree of competitive binding of specific and of non-specific targets to a particular probe, on the degree of saturation of the probes with bound transcripts and on the distance of the probe from the 3′-end of the transcript. Increasing degrees of non-specific hybridization or of saturation reduce the 3′/5′ intensity gradient and if not taken into account, this leads to biased results in common quality measures for GeneChip arrays such as affyslope or the control probe intensity ratio. We also found that short probe sets near the 3′-end of the transcripts are prone to non-specific hybridization presumable because of inaccurate positional assignment and the existence of transcript isoforms with variable 3′ UTRs. Poor RNA quality is associated with a decreased amount of RNA material hybridized on the array paralleled by a decreased total signal level. Additionally, it causes a gene-specific loss of signal due to the positional bias of transcript abundance which requires an individual, gene-specific correction. We propose a new RNA quality measure that considers the hybridization mode. Graphical characteristics are introduced allowing assessment of RNA quality of each single array (‘tongs plot’ and ‘degradation hook’). Furthermore, we suggest a method to correct for effects of RNA degradation on microarray intensities.The presented RNA degradation measure has best correlation with the independent RNA integrity measure RIN, and therefore presents itself as a valuable tool for quality control and even for the study of RNA degradation. When RNA degradation effects are detected in microarray experiments, a correction of the induced bias i
Mismatch and G-Stack Modulated Probe Signals on SNP Microarrays
Hans Binder,Mario Fasold,Torsten Glomb
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0007862
Abstract: Single nucleotide polymorphism (SNP) arrays are important tools widely used for genotyping and copy number estimation. This technology utilizes the specific affinity of fragmented DNA for binding to surface-attached oligonucleotide DNA probes. We analyze the variability of the probe signals of Affymetrix GeneChip SNP arrays as a function of the probe sequence to identify relevant sequence motifs which potentially cause systematic biases of genotyping and copy number estimates.
G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration
Mario Fasold, Peter F Stadler, Hans Binder
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-207
Abstract: Longer runs of three or more consecutive G along the probe sequence and in particular triple degenerated G at its solution end ((GGG)1-effect) are associated with exceptionally large probe intensities on GeneChip expression arrays. This intensity bias is related to non-specific hybridization and affects both perfect match and mismatch probes. The (GGG)1-effect tends to increase gradually for microarrays of later GeneChip generations. It was found for DNA/RNA as well as for DNA/DNA probe/target-hybridization chemistries. Amplification of sample RNA using T7-primers is associated with strong positive amplitudes of the G-bias whereas alternative amplification protocols using random primers give rise to much smaller and partly even negative amplitudes.We applied positional dependent sensitivity models to analyze the specifics of probe intensities in the context of all possible short sequence motifs of one to four adjacent nucleotides along the 25meric probe sequence. Most of the longer motifs are adequately described using a nearest-neighbor (NN) model. In contrast, runs of degenerated guanines require explicit consideration of next nearest neighbors (GGG terms). Preprocessing methods such as vsn, RMA, dChip, MAS5 and gcRMA only insufficiently remove the G-bias from data.Positional and motif dependent sensitivity models accounts for sequence effects of oligonucleotide probe intensities. We propose a positional dependent NN+GGG hybrid model to correct the intensity bias associated with probes containing poly-G motifs. It is implemented as a single-chip based calibration algorithm for GeneChips which can be applied in a pre-correction step prior to standard preprocessing.Fig. 1a shows the surface image of a hybridized Affymetrix GeneChip expression array. Its area of about 1.6 cm2 divides into a grid of nearly one million probe spots of size (11 × 11) μm2. Each of them is covered by a 'turf' of 25meric oligonucleotides attached to the chip surface. Their sequence is chose
Conservation and losses of avian non-coding RNA loci
Paul P. Gardner,Mario Fasold,Sarah W. Burge,Maria Ninova,Jana Hertel,Stephanie Kehr,Tammy E. Steeves,Sam Griffiths-Jones,Peter F. Stadler
Quantitative Biology , 2014,
Abstract: Here we present the results of a large-scale bioinformatic annotation of non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models of hand-curated families from the Rfam database to infer conserved RNA families within each avian genome. We supplement these annotations with predictions from the tRNA annotation tool, tRNAscan-SE and microRNAs from miRBase. We show that a number of lncRNA-associated loci are conserved between birds and mammals, including several intriguing cases where the reported mammalian lncRNA function is not conserved in birds. We also demonstrate extensive conservation of classical ncRNAs (e.g., tRNAs) and more recently discovered ncRNAs (e.g., snoRNAs and miRNAs) in birds. Furthermore, we describe numerous "losses" of several RNA families, and attribute these to genuine loss, divergence or missing data. In particular, we show that many of these losses are due to the challenges associated with assembling Avian microchromosomes. These combined results illustrate the utility of applying homology-based methods for annotating novel vertebrate genomes.
Critical Discussion of "Synchronized Flow", Simulation of Pedestrian Evacuation, and Optimization of Production Processes
D. Helbing,I. Farkas,D. Fasold,M. Treiber,T. Vicsek
Physics , 2002,
Abstract: We critically discuss the concept of ``synchronized flow'' from a historical, empirical, and theoretical perspective. Problems related to the measurement of vehicle data are highlighted, and questionable interpretations are identified. Moreover, we propose a quantitative and consistent theory of the empirical findings based on a phase diagram of congested traffic states, which is universal for all conventional traffic models having the same instability diagram and a fundamental diagram. New empirical and simulation data supporting this approach are presented as well. We also give a short overview of the various phenomena observed in panicking pedestrian crowds relevant from the point of evacuation of buildings, ships, and stadia. Some of these can be applied to the optimization of production processes, e.g. the ``slower-is-faster effect''.
Assessing Technical Performance in Differential Gene Expression Experiments with External Spike-in RNA Control Ratio Mixtures
Sarah A. Munro,Steve P. Lund,P. Scott Pine,Hans Binder,Djork-Arné Clevert,Ana Conesa,Joaquin Dopazo,Mario Fasold,Sepp Hochreiter,Huixiao Hong,Nederah Jafari,David P. Kreil,Pawe? P. ?abaj,Sheng Li,Yang Liao,Simon Lin,Joseph Meehan,Christopher E. Mason,Javier Santoyo,Robert A. Setterquist,Leming Shi,Wei Shi,Gordon K. Smyth,Nancy Stralis-Pavese,Zhenqiang Su,Weida Tong,Charles Wang,Jian Wang,Joshua Xu,Zhan Ye,Yong Yang,Ying Yu,Marc Salit
Quantitative Biology , 2014, DOI: 10.1038/ncomms6125
Abstract: There is a critical need for standard approaches to assess, report, and compare the technical performance of genome-scale differential gene expression experiments. We assess technical performance with a proposed "standard" dashboard of metrics derived from analysis of external spike-in RNA control ratio mixtures. These control ratio mixtures with defined abundance ratios enable assessment of diagnostic performance of differentially expressed transcript lists, limit of detection of ratio (LODR) estimates, and expression ratio variability and measurement bias. The performance metrics suite is applicable to analysis of a typical experiment, and here we also apply these metrics to evaluate technical performance among laboratories. An interlaboratory study using identical samples shared amongst 12 laboratories with three different measurement processes demonstrated generally consistent diagnostic power across 11 laboratories. Ratio measurement variability and bias were also comparable amongst laboratories for the same measurement process. Different biases were observed for measurement processes using different mRNA enrichment protocols.
Different architectures of collagen fibrils enforce different fibrillogenesis mechanisms  [PDF]
Mario Raspanti
Journal of Biomedical Science and Engineering (JBiSE) , 2010, DOI: 10.4236/jbise.2010.312152
Abstract: According to current knowledge on collagen fibril-logenesis, collagen fibrils are formed by a cooperative process involving lateral fusion of small protofibrils. Almost all the experimental research, however, was carried out on tendon collagen, whose fibrils are characterized by approximately straight subfibrils. By contrast, in most tissues the collagen fibril sub-units follow a helical course in which geometrical constraints prevent lateral fusions, thereby implying a different mechanism where collagen fibrils grow by addition of individual microfibrils rather than by lateral fusion of pre-assembled subfibrils. The proc-ess at the origin of these fibrils may provide a simple, automatic explanation for the remarkable uniformity in fibrils size observed in most tissues without re-quiring the intervention of unknown mechanisms of diameter control. Other mechanisms of growth con-trol remain indispensable to terminate the fibril-logenesis process in tendons and ligaments.
Methods to Be Developed for Some First Applications of Mitochondrial Filamentation  [PDF]
Mario Gosalvez
Open Journal of Biophysics (OJBIPHY) , 2013, DOI: 10.4236/ojbiphy.2013.31A006
Abstract:

The new field of mitochondrial filamentation and its first potential applications are just getting underway (1-7), following a series of pilot experiments in our laboratory over the past few decades (8-14). I should like to give a brief overview of the role that some new methods are playing in this emerging area of physiological bioenergetics, supported by a few references to our contributions as I scarcely have the faculties now to understand other specific contributions. This new field is brimming with promises for medicine, science and society, in general. I cannot and must not be concrete or comprehensive, because I honestly feel that it is now that matters are really beginning to take off, assisted by the most appropriate international capabilities.

Metabolic control of respiration and glycolysis of tumoral cells  [PDF]
Mario Gosalvez
Advances in Biological Chemistry (ABC) , 2013, DOI: 10.4236/abc.2013.31011
Abstract:

The contribution of the author’s groups on the control of energy metabolism of cancer cells has been concisely reviewed. It is proposed that Otto Warburg’s “respiratory defect” of tumoral cells resides in an alteration of the recurrent filamentation cycle of mitochondria. These give those organelles an affinity lower for ADP than the affinity of the tumor cell isoenzyme of pyruvate kinase. These two findings may explain the essentials of the intimate mechanism of the aerobic glycolysis of cancer cells.

An experimental proposal for low order laboratory animals’ extension of metabolic life  [PDF]
Mario Gosalvez
Advances in Biological Chemistry (ABC) , 2013, DOI: 10.4236/abc.2013.36060
Abstract:

Essential bibliography, with therein references included, is presented owing to the contribution of the author groups to Mitochondrial Filamentation, which is a new emerging field of physiological energy metabolism. These studies provide the first seed concept for trials to extend the metabolic life, for a few days, in low order laboratory mammals killed by electrocution, as a first type of accidental death. It is proposed, essentially, to cool out the corpses very soon after death at 12oC-14oC and take advantage of the effect super magnetism to counteract the force of gravity to install a net recurrent cycle of oxygen consumption and oxygen production by filamented mitochondria in all the organism tissues. Once the cause of death had been corrected adequately, it is possible to try the reanimation to experience the full life of the corpse with highly sophisticated methodology.

 

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