Limited Resolution Power Research Articles

From continental Asia into the world: Global historical biogeography of the saltbush genus Atriplex (Chenopodieae, Chenopodioideae, Amaranthaceae)

Atriplex is the most species-rich genus of Amaranthaceae and one of the largest C4 clades in eudicots. Distributed predominantly in the arid subtropical and temperate regions worldwide, many Atriplex species dominate the plant communities of harsh and inhospitable inland and coastal habitats. Current threats of aridification and salinisation increase the ecological and economic value of this highly stress tolerant xerophytic genus. We compiled sequence data of approximately 80 % (208 spp.) of all currently recognised species and carried out a phylogenetic reconstruction using nuclear-encoded internal and external transcribed spacers. In addition, time divergence estimation analysis and ancestral area reconstruction were carried out to reconstruct the worldwide spread of Atriplex. Our results show that Atriplex originated in continental Asia during the Oligocene and dispersed from there across the world, often via long-distance dispersal from the Aralo-Caspian and the Pontic regions, or the floristic province of Turkestan. The highest alpha diversity was retrieved from arid habitats of Australia and the New World resulting from extensive radiation events of the Late Miocene and Pliocene. Most dispersal events took place into the Mediterranean region. Atriplex invaded most continents several times independently from different regions throughout the continuous cooling trend of the Neogene and the Quaternary. Despite limited resolution power of the used molecular markers, this study allows for a more comprehensive understanding of the evolutionary history of Atriplex and lays the foundation for future evolutionary studies of saltbushes.

Identification of Photorhabdus symbionts by MALDI-TOF MS

Species of the bacterial genus Photorhabus live in a symbiotic relationship with Heterorhabditis entomopathogenic nematodes. Besides their use as biological control agents against agricultural pests, some Photorhabdus species are also a source of natural products and are of medical interest due to their ability to cause tissue infections and subcutaneous lesions in humans. Given the diversity of Photorhabdus species, rapid and reliable methods to resolve this genus to the species level are needed. In this study, we evaluated the potential of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of Photorhabdus species. To this end, we established a collection of 54 isolates consisting of type strains and multiple field strains that belong to each of the validly described species and subspecies of this genus. Reference spectra for the strains were generated and used to complement a currently available database. The extended reference database was then used for identification based on the direct transfer sample preparation method and the protein fingerprint of single colonies. High-level discrimination of distantly related species was observed. However, lower discrimination was observed with some of the most closely related species and subspecies. Our results therefore suggest that MALDI-TOF MS can be used to correctly identify Photorhabdus strains at the genus and species level, but has limited resolution power for closely related species and subspecies. Our study demonstrates the suitability and limitations of MALDI-TOF-based identification methods for assessment of the taxonomic position and identification of Photorhabdus isolates.

Crustal structure beneath the Qilian Orogen Zone from multiscale seismic tomography

The Qilian Orogen Zone (QOZ), located in the north margin of the Tibetan Plateau, is the key area for understanding the deformation and dynamics process of Tibet. Numerous geological and geophysical studies have been carried out on the mechanics of the Tibetan Plateau deformation and uplift; however, the detailed structure and deformation style of the Qilian Orogen Zone have remained uncertain due to poor geophysical data coverage and limited resolution power of inversion algorithms. In this study, we analyze the P-wave velocity structure beneath the Qilian Orogen Zone, obtained by applying multi-scale seismic tomography technique to P-wave arrival time data recorded by regional seismic networks. The seismic tomography algorithm used in this study employs sparsity constraints on the wavelet representation of the velocity model via L1-norm regularization. This algorithm can deal efficiently with uneven-sampled volumes, and can obtain multi-scale images of the velocity model. Our results can be summarized as follows: (1) The crustal velocity structure is strongly inhomogeneous and consistent with the surface geological setting. Significant low-velocity anomalies exist in the crust of northeastern Tibet, and slight high-velocity anomalies exist beneath the Qaidam Basin and Alxa terrane. (2) The Qilian Orogen Zone can be divided into two main parts by the Laji Shan Faults: the northwestern part with a low-velocity feature, and the southeastern part with a high-velocity feature at the upper and middle crust. (3) Our tomographic images suggest that northwestern and southeastern Qilian Orogen Zones have undergone different tectonic processes. In the northwest Qilian Orogen Zone, the deformation and growth of the Northern Tibetan Plateau has extended to the Heli Shan and Beida Shan region by northward over-thrusting at the upper crust and thickening in the lower crust. We speculate that in the southeast Qilian Orogen Zone the deformation and growth of the Northern Tibet Plateau were of strike-slip style at the upper crust; in the lower crust, the evidence suggests ductile shear extrusion style and active frontage extension to the Alxa terrane. (4) The multi-scale seismic tomography technique provides multi-scale analysis and sparse constraints, which has allowed to us obtain stable, high-resolution results.

Digital PCR to assess hematopoietic chimerism after allogeneic stem cell transplantation

Analysis of hematopoietic chimerism after allogeneic stem cell transplantation represents a crucial method to evaluate donor-cell engraftment. Whereas sensitivity of classical approaches for chimerism monitoring is limited to ≥1%, quantitative polymerase chain reaction (qPCR)-based techniques readily detect one patient cell in >1,000 donor cells, thus facilitating application of chimerism assessment as a surrogate for minimal residual disease. However, due to methodologic specificities, qPCR combines its high sensitivity with limited resolution power in the state of mixed chimerism (e.g., >10% patient cells). Our aim was to overcome this limitation by employing a further development of qPCR, namely digital PCR (dPCR), for chimerism analysis. For proof-of-principle, we established more than 10 dPCR assays detecting Indel polymorphisms or Y-chromosome sequences and tested them on artificial cell mixtures and patient samples. Employing artificial cell mixtures, we found that dPCR allows exact quantification of chimerism over several orders of magnitude. Digital PCR results proved to be highly reproducible (deviation<5%), particularly in the "difficult" range of mixed chimerism. Excellent performance of the new assays was confirmed by analysis of multiple retrospective blood samples from patients after allogeneic stem cell transplantation, in comparison with established qPCR (14 patients) and short-tandem repeat PCR (4 patients) techniques. Finally, dPCR is easy to perform, needs only small amounts of DNA for chimerism assessment (65ng corresponds to a sensitivity of approximately 0.03%), and does not require the use of standard curves and replicate analysis. In conclusion, dPCR represents a very promising method for routine chimerism monitoring.

Record linkage of hospital discharge register with population register: Experiences at Statistics Netherlands

This paper describes the first-time linking by Statistics Netherlands of the hospital discharge register (HDR), held by Prismant, with the population register (PR). This linkage is the first step in building an integrated population-based health statistics dataset at individual level, using existing register data as much as possible. The linkage of the HDR with the PR has proved to be successful: 87.6% of the HDR records could be uniquely linked to a person record in the PR, 8.7% were multiply linked, and 3.6% of the records could not be linked. The multiple linkages are a natural result of the limited resolution power of the linkage key (date of birth, sex, postal code). The 3.6% non-linkages are also plausible, given a rate of approximately 2% administrative errors in both registers. The quality of the linkage was further studied by estimating the level of mismatches (false positive linkages): this rate was estimated to be in the order of magnitude of approximately 1%, and in any case less than 3%. It was concluded that the linkage of the Dutch HDR with the PR is of good quality and that it forms an adequate basis for statistical analyses.

Possibilities and limits of photon correlation spectroscopy in determining polymer molecular weight distributions

The effect of concentration and polydispersity on the collective diffusion coefficient D c , evaluated using Photon Correlation Spectroscopy (PCS), has been investigated on poly(methyl methacrylate) (PMMA) in acetone solutions. The concentration dependence of the collective diffusion coefficient follows a linear regression law, the slope being fairly independent of polydispersity, molecular weight and temperature. The diffusion coefficient at infinite dilution D 0 obeys the scaling law D 0 = AM w -v in the range from M w = 10000 to M w = 800000; the value of the scaling exponent, v = 0.57, proves the good solvent quality of acetone. The inversion of the scattered intensity autocorrelation data by the regularization method CONTIN allowed the evaluation of the molecular weight distribution function of the polymeric samples. Although this algorithm gives valuable information on average quantities or on the width of the distribution, it has limited resolution power; therefore a comparison with the results obtained by Size Exclusion Chromatography (SEC) was carried out for a set of samples having monomodal and bimodal distribution functions.

Bacterial phylogeny based on comparative sequence analysis.

Comparative sequence analysis of small subunit rRNA is currently one of the most important methods for the elucidation of bacterial phylogeny as well as bacterial identification. Phylogenetic investigations targeting alternative phylogenetic markers such as large subunit rRNA, elongation factors, and ATPases have shown that 16S rRNA-based trees reflect the history of the corresponding organisms globally. However, in comparison with three to four billion years of evolution the phylogenetic information content of these markers is limited. Consequently, the limited resolution power of the marker molecules allows only a spot check of the evolutionary history of microorganisms. This is often indicated by locally different topologies of trees based on different markers, data sets or the application of different treeing approaches. Sequence peculiarities as well as methods and parameters for data analysis were studied with respect to their effects on the results of phylogenetic investigations. It is shown that only careful data analysis starting with a proper alignment, followed by the analysis of positional variability, rates and character of change, testing various data selections, applying alternative treeing methods and, finally, performing confidence tests, allows reasonable utilization of the limited phylogenetic information.

The flat zone approach: A general low-level region merging segmentation method

This paper presents a segmentation method, the flat zone approach, that avoids some limitations of the watershed-plus-markers method. The watershed-plus-markers approach, which is the traditional segmentation technique in mathematical morphology, has two inherent problems: (1) the possible separation of a piecewise-constant region of the input image into several regions in the output partition, and (2) the problem of obtaining markers (connected components of pixels signaling significant regions) for features that are one or two pixels wide. These problems are related to the limited resolution power (for feature extraction) of gradient operators. The flat zone approach extends the region marker concept (to contain the entire (and not part of) regions) and requires neither the computation of a gradient function nor the modification of the support of the input image in order to increase the size of the features. Our approach works on the graph formed by the image flat zones (or piecewise-constant regions). This fact ensures that the input image regions are not broken and can consider all input flat zones regardless their size. An inclusion relationship between the flat zones of the input image and the regions of the output partition is imposed. That is, a flat zone segmentation method is a region (flat zone) merging method and behaves like a connected operator. Our method is robust (in the sense that it is invariant under certain intensity value transformations) and uses a hierarchical waiting queue algorithm that makes it extremely efficient.

Applications in renal immunopathology of reflection contrast microscopy, a novel superior light microscopical technique

In renal immunopathology subdivision of glomerulopathies is based upon immunofluorescence patterns on deposition sites of electrondense deposits along the glomerular capillary wall and the mesangium. However, immunofluorescence has a relatively limited resolution power, while the laborious and expensive technique of electronmicroscopy (EM) allows for inspection of only highly magnified, small areas of tissue. This difference in both resolution power and sample size calls for a bridging technique, that allows direct comparison of immunohistochemistry at the light microscopical (LM) level to immuno-EM techniques. For these purposes we have applied a novel high-resolution LM technique, named reflection contrast microsocopy (RCM), on a series of experimental models of glomerulopathies. This microscope, originally designed by Ploem [1], requires a light microscope equipped with an epi-illuminator and specific optics [2, 3], and facilities for plastic embedding and ultrathin sectioning similar to those used for EM purposes. In this paper the possibilities for application of RCM in renal immunopathology will be outlined and its perspectives will be discussed.

Effect of prolonged normobaric hyperoxia on regional cerebral metabolic rate for glucose in conscious rats

The CNS tolerance to prolonged normobaric hyperoxia (NH) was investigated using alternations in regional cerebral metabolic rate for glucose (rCMRgl) as a sensitive measure of brain oxygen poisoning. Conscious rats were continously exposed either to air or to oxygen for 24 h at atmospheric pressure inside a closed and ventilated environmental chamber. The rCMRgl was measured during ongoing air or oxygen exposures by [ 14C]2-deoxyglucose (2-DG) autoradiographic technique. No significant difference in the rCMRgl of 29 neuroanatomical structures investigated was found between two groups of air- and oxygen-exposed rats. At the same time however, a significant reduction in the respiratory frequency (f) was observed only in the oxygen-exposed rats. It is suggested that brain energy metabolism is not affected at least up to 24 h NH in conscious rats. The NH-induced reduction in f on the other hand, may be due to alterations in afferent inputs from peripheral and central chemoreceptors or lung stretch receptors. Furthermore, since slight changes in rCMRgl of small neuroanatomical structures are not detectable by limited resolution power of [ 14C]2-DG autoradiographic technique, a subtle NH-induced damage to central respiratory control mechanisms cannot yet be ruled out.

Central nervous system glucose utilization rate during oxygen-induced respiratory changes at 2 atmospheres oxygen in the rat

Hyperbaric oxygenation (HBO) at pressures higher than 3 atmospheres absolute (ATA) primarily affects the CNS, while at lower pressures, the respiratory functions are predominantly changed. Due to the outstanding respiratory manifestations of HBO at pressures lower than 3 ATA O 2, the possible overlapping neurological effects of oxygen toxicity may not be easily identified. However, rats exposed for 1 and 4 h to 2 ATA O 2 have shown increases in the regional cerebral metabolic rate for glucose (rCMRgl) when neither visible signs of respiratory nor nervous distress were observed. The purpose of the present study was to differentiate between the CNS and the respiratory effects of HBO at 2 ATA during development of the early signs of the respiratory distress. Changes in the rCMRgl measured by [ 14C]-2-deoxyglucose (2-DG) autoradiographic technique and respiratory frequency (Rf) were used as criteria for determination of CNS and respiratory effects of HBO, respectively. The results demonstrate no differences in the rCMRgl (28 major structures examined) among 3 groups of conscious rats exposed to 2 ATA O 2 and normoxia at 1 and 2 ATA. At the same time a significant reduction was found in the Rf of the oxygen-exposed rats. In conclusion the respiratory system at 2 ATA O 2 is apparently affected earlier than, and independent from the CNS. However, due to limited resolution power of the [ 14C]2-DG technique, the effect of HBO on certain undetected central respiratory control centers cannot yet be ruled out.