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Map Analysis (map + analysis)
Selected AbstractsSDS-PAGE and two-dimensional maps in a radial gel formatELECTROPHORESIS, Issue 3 2010Renato Millioni Abstract A novel method for performing 2-D map analysis is here reported, consisting in a modification of the second dimension run, which is performed not in a conventional square- or rectangular-size gel, but in a radial surface. This has the advantage of permitting resolution of closely adjacent bands, representing strings of isoforms of similar or identical mass but of closely spaced isoelectric points. When used in a mono-dimensional, SDS-PAGE format, this system allows the simultaneous running of 62 sample tracks. Examples are given of separation of plasma and urinary proteins. [source] Using sex-averaged genetic maps in multipoint linkage analysis when identity-by-descent status is incompletely knownGENETIC EPIDEMIOLOGY, Issue 5 2006Tasha E. Fingerlin Abstract The ratio of male and female genetic map distances varies dramatically across the human genome. Despite these sex differences in genetic map distances, most multipoint linkage analyses use sex-averaged genetic maps. We investigated the impact of using a sex-averaged genetic map instead of sex-specific maps for multipoint linkage analysis of affected sibling pairs when identity-by-descent states are incompletely known due to missing parental genotypes and incomplete marker heterozygosity. If either all or no parental genotypes were available, for intermarker distances of 10, 5, and 1,cM, we found no important differences in the expected maximum lod score (EMLOD) or location estimates of the disease locus between analyses that used the sex-averaged map and those that used the true sex-specific maps for female:male genetic map distance ratios 1:10 and 10:1. However, when genotypes for only one parent were available and the recombination rate was higher in females, the EMLOD using the sex-averaged map was inflated compared to the sex-specific map analysis if only mothers were genotyped and deflated if only fathers were genotyped. The inflation of the lod score when only mothers were genotyped led to markedly increased false-positive rates in some cases. The opposite was true when the recombination rate was higher in males; the EMLOD was inflated if only fathers were genotyped, and deflated if only mothers were genotyped. While the effects of missing parental genotypes were mitigated for less extreme cases of missingness, our results suggest that when possible, sex-specific maps should be used in linkage analyses. Genet. Epidemiol. 2006. © 2006 Wiley-Liss, Inc. [source] PROTEOLYTIC ACTIVITY OF LACTOBACILLUS SAKEI, LACTOBACILLUS FARCIMINIS AND LACTOBACILLUS PLANTARUM ON SARCOPLASMIC PROTEINS OF PORK LEANJOURNAL OF FOOD BIOCHEMISTRY, Issue 3 2004ANNA LISA BASSO The aim of this study was to assess the proteolytic activity of Lactobacillus sakei (DSM 6333), L. plantarum (B21), and to a lesser extent, L. farciminis (DSM 20184) on meat sarcoplasmic proteins. The protein composition was assayed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and capillary electrophoresis after incubation of meat extract inoculated with bacteria. All strains showed proteolytic activity: a band about 94 kDa disappeared in samples inoculated with L. farciminis and L. plantarum and strongly decreased in those inoculated with L. sakei. The intensity of the bands with a molecular weight between 94 and 38 kDa decreased in all samples. Capillary electrophoresis analysis ascertained the disappearance of the fractions corresponding to 8.64 and 8.66 min retention time in all samples. The bands corresponding to 94 kDa and 38 kDa were, respectively, identified as glycogen phosphorylase muscle isoform and glyceraldehyde 3-phosphate dehydrogenase, by in situ digestion of protein gel bands and peptide map analysis using Matrix Assisted Laser Desorption/Ionization - Time of Flight Mass Spectrometry (MALDI-TOF MS). [source] The resonant structure of Jupiter's Trojan asteroids , I. Long-term stability and diffusionMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 4 2006P. Robutel ABSTRACT We study the global dynamics of the jovian Trojan asteroids by means of the frequency map analysis. We find and classify the main resonant structures that serve as skeleton of the phase space near the Lagrangian points. These resonances organize and control the long-term dynamics of the Trojans. Besides the secondary and secular resonances, that have already been found in other asteroid sets in mean motion resonance (e.g. main belt, Kuiper belt), we identify a new type of resonance that involves secular frequencies and the frequency of the great inequality, but not the libration frequency. Moreover, this new family of resonances plays an important role in the slow transport mechanism that drives Trojans from the inner stable region to eventual ejections. Finally, we relate this global view of the dynamics with the observed Trojans, identify the asteroids that are close to these resonances and study their long-term behaviour. [source] Optical properties of InN grown on templates with controlled surface polaritiesPHYSICA STATUS SOLIDI (A) APPLICATIONS AND MATERIALS SCIENCE, Issue 10 2010Ronny Kirste Abstract The structural and optical properties of InN layers grown on GaN/sapphire templates with controlled Ga-/N-polar surfaces are investigated. Raman spectroscopy and XRD reciprocal space map analysis suggest that the InN layers were grown strain free with a high crystal quality. A line shape analysis of the A1(LO) Raman mode yields to a decreasing carrier concentration for the sample grown on Ga-polar substrate. Low temperature photoluminescence measurements exhibit a shift to lower energies of the luminescence maximum for the sample grown on Ga-polar GaN probably due to a reduced carrier concentration and thus, a decreased Burstein,Moss shift. Following this, we demonstrate that the use of polarity controlled GaN/sapphire substrates leads to unstrained layers with good structural and optical properties. [source] Re-refinement from deposited X-ray data can deliver improved models for most PDB entriesACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2009Robbie P. Joosten The deposition of X-ray data along with the customary structural models defining PDB entries makes it possible to apply large-scale re-refinement protocols to these entries, thus giving users the benefit of improvements in X-ray methods that have occurred since the structure was deposited. Automated gradient refinement is an effective method to achieve this goal, but real-space intervention is most often required in order to adequately address problems detected by structure-validation software. In order to improve the existing protocol, automated re-refinement was combined with structure validation and difference-density peak analysis to produce a catalogue of problems in PDB entries that are amenable to automatic correction. It is shown that re-refinement can be effective in producing improvements, which are often associated with the systematic use of the TLS parameterization of B factors, even for relatively new and high-resolution PDB entries, while the accompanying manual or semi-manual map analysis and fitting steps show good prospects for eventual automation. It is proposed that the potential for simultaneous improvements in methods and in re-refinement results be further encouraged by broadening the scope of depositions to include refinement metadata and ultimately primary rather than reduced X-ray data. [source] Cladistic coding of genomic mapsCLADISTICS, Issue 5 2002Cyril Gallut A new method of genomic maps analysis is described. The purpose of the method is to reconstruct phylogenetic relationships from the genomic organization of taxa. Our approach is based on gene order coding. This coding allows the description of genome topology without a prior hypothesis about evolutionary events and phylogenetic relationships. Different characters are used for each gene: (1) presence/absence, (2) orientation, and (3) relative position. The relative position of a particular gene inside the genome is the pair of genes surrounding it. The relative position character represents all the positions of a gene in the sampled genomes. It is coded as a multistate character. Our coding method has a priori variable cost implications on operators such as inversion, transposition, and gene loss/gain, which we discuss. The overall approach best fits the "duplication, random loss" evolutionary model. The coding method allows the reconstitution of a possible hypothetical common ancestor genome at each node of the tree. This reconstitution is based on the character states' optimization; it comes down to choosing, among all possible optimizations, the optimization compatible with a complete genome topology at each internal node. The multistate coding of gene relative position, which is an undeniable advantage of this method, permits this reconstitution. [source] | ||||||||||||||||