Comparison of liposome entrapment parameters by optical and atomic absorption spectrophotometry

Methods for the complete characterization of liposomes prepared by ether-injection are described in detail. The validity of atomic absorption spectrophotometry Ior measuring markers of trapped volume was checked by comparative determinations of markers with established optical spectrophotometrical methods. The favorable results usingl atomic absorption spectrophotometry to quantitate the marker Mn²⁺ are of particular relevance as manganese ion is also the paramagnetic probe in n.m.r, measurements of water permeability of lipo-somes; our results indicate that in such measurements no other marker need be incorporated.     

Water exchange through erythrocyte membranes: p-choloromercuribenzene sulfonate inhibition of water diffusion in ghosts studied by a nuclear magnetic resonance technique

A comparison of water diffusion in human erythrocytes and ghosts revealed a longer relaxation time in ghosts, A comparison of water diffusion in human erythrocytes and ghosts revealed a longer relaxation time in ghosts, corresponding to a decreased exchange rate. However, the diffusional permeability of ghosts was not significantly different from that of erythrocytes . The changes in water diffusion following exposure to p-chloromercuribenzene sulfonate (PCMBS) have been studied on ghosts suspended in isotonic solutions. It was found that a significant inhibitory effect of PCMBS on water diffusion occurred only after several minutes of incubation at 37°C. No inhibition was noticed after short incubation at 0°C as previously used in some labelling experiments. This indicates the location in the membrane interior of the SH groups involved in water diffusion across human erythrocyte membranes. The nuclear magnetic resonance ( n . m . r . ) method appears as a useful tool for studying changes in water diffusiofl in erythrocyte ghosts with the aim of locating the water channel.     

Outlier detection in BLAST hits

Background

An important task in a metagenomic analysis is the assignment of taxonomic labels to sequences in a sample. Most widely used methods for taxonomy assignment compare a sequence in the sample to a database of known sequences. Many approaches use the best BLAST hit(s) to assign the taxonomic label. However, it is known that the best BLAST hit may not always correspond to the best taxonomic match. An alternative approach involves phylogenetic methods, which take into account alignments and a model of evolution in order to more accurately define the taxonomic origin of sequences. Similarity-search based methods typically run faster than phylogenetic methods and work well when the organisms in the sample are well represented in the database. In contrast, phylogenetic methods have the capability to identify new organisms in a sample but are computationally quite expensive.

Results

We propose a two-step approach for metagenomic taxon identification; i.e., use a rapid method that accurately classifies sequences using a reference database (this is a filtering step) and then use a more complex phylogenetic method for the sequences that were unclassified in the previous step. In this work, we explore whether and when using top BLAST hit(s) yields a correct taxonomic label. We develop a method to detect outliers among BLAST hits in order to separate the phylogenetically most closely related matches from matches to sequences from more distantly related organisms. We used modified BILD (Bayesian Integral Log-Odds) scores, a multiple-alignment scoring function, to define the outliers within a subset of top BLAST hits and assign taxonomic labels. We compared the accuracy of our method to the RDP classifier and show that our method yields fewer misclassifications while properly classifying organisms that are not present in the database. Finally, we evaluated the use of our method as a pre-processing step before more expensive phylogenetic analyses (in our case TIPP) in the context of real 16S rRNA datasets.

Conclusion

Our experiments make a good case for using a two-step approach for accurate taxonomic assignment. We show that our method can be used as a filtering step before using phylogenetic methods and provides a way to interpret BLAST results using more information than provided by E-values and bit-scores alone.

     

Water exchange through erythrocyte membranes: Nuclear magnetic resonance studies on resealed ghosts compared to human erythrocytes

Summary The water diffusion across human erythrocyte membrane has been studied on intact cells and resealed ghosts by a doping NMR technique. Although the water exchange time of ghosts was longer than that of erythrocytes, no significant differences in their diffusional permeability were noticed for temperatures in the range 2–43°C. Contrary to what was previously noticed in erythrocytes, no significant increase in the water exchange time of ghosts in the acid range of pH occurred.     

Water exchange through erythrocyte membranes: Nuclear magnetic resonance studies on the effects of inhibitors and of chemical modification of human membranes

The changes in water diffusion across human erythrocyte membranes following exposure to various inhibitors and proteolytic enzymes have been studied on isolated erythrocytes suspended in isotonic buffered solutions. An important issue was to investigate whether the sulfhydryl reacting reagents that have been applied in osmotic experiments showed similar effects on diffusional permeability. It was found that mercurials, including mersalyl, were the only sulfhydryl reacting reagents that were efficient inhibitors. Under optimal conditions a similar degree of inhibition (around 45%) was found with all mercury-containing sulfhydryl reagents. Other reagents, including the sulfhydryl reagent DTNB, phloretin, or H2DIDS, the specific inhibitor of the anion transport system in erythrocyte membrane, did not appear to inhibit significantly the diffusional permeability. No changes in water diffusion were noticed after exposure to erythrocytes to trypsin and chymotrypsin. A new kind of experiments was that in which the effects of exposure of erythrocytes to two or more agents were studied. It was found that none of the chemical manipulations of membranes that did not affect water diffusion hampered the inhibitory action of mercurials. These findings show that the SH groups involved in water diffusion across erythrocyte membrane do not react with any of the other SH reagents aside from mercurials and that the molecular mechanism of water transport is not affected by chymotryptic cleavage of band 3 protein into the 60 and 35 kD fragments. The NMR method appears as a useful tool for studying changes in water diffusion in erythrocyte membranes following various chemical manipulations of the membranes with the aim of locating the water channel.     

Catheter-based impedance measurements in the right atrium for continuously monitoring hematocrit and estimating blood viscosity changes; an in vivo feasibility study in swine

Hematocrit is the most important determinant of whole blood viscosity and it affects thrombosis. As hematocrit can be measured accurately in vitro by using an electrical impedance technique, aim of the present study is to investigate the diagnostic potential of using this technique in vivo to continuously monitor hematocrit.

Characteristics of a special catheter for in vivo measurement of electrical resistivity in blood in the right atrium are described. In five anesthetized swine hematocrit is monitored continuously with this catheter while different levels of hemoconcentration are induced. In addition, blood viscosity is increased by inducing ‘acute phase’ reaction the day before surgery, resulting in variable degree of elevated fibrinogen levels in the five swine. Good reproducibility of the resistivity measurements (S.D.<0.01) and excellent correlation between resistivity data in vivo and hematocrit levels in each swine are found (r²=0.95–0.99). Furthermore, stepwise regression analysis of data from all swine shows a highly significant contribution also of other important parameters of blood viscosity, such as fibrinogen, total protein and temperature (cumulative r²=0.97).

Determining hematocrit continuously in vivo by electrical resistivity measurements with a catheter in the right atrium is feasible and these measurements correlate significantly also with other important parameters of blood viscosity.     

Integrating sign surveys and telemetry data for estimating brown bear (Ursus arctos) density in the Romanian Carpathians

Accurate population size estimates are important information for sustainable wildlife management. The Romanian Carpathians harbor the largest brown bear (Ursus arctos) population in Europe, yet current management relies on estimates of density that lack statistical oversight and ignore uncertainty deriving from track surveys. In this study, we investigate an alternative approach to estimate brown bear density using sign surveys along transects within a novel integration of occupancy models and home range methods. We performed repeated surveys along 2‐km segments of forest roads during three distinct seasons: spring 2011, fall‐winter 2011, and spring 2012, within three game management units and a Natura 2000 site. We estimated bears abundances along transects using the number of unique tracks observed per survey occasion via N‐mixture hierarchical models, which account for imperfect detection. To obtain brown bear densities, we combined these abundances with the effective sampling area of the transects, that is, estimated as a function of the median (± bootstrapped SE) of the core home range (5.58 ± 1.08 km²) based on telemetry data from 17 bears tracked for 1‐month periods overlapping our surveys windows. Our analyses yielded average brown bear densities (and 95% confidence intervals) for the three seasons of: 11.5 (7.8–15.3), 11.3 (7.4–15.2), and 12.4 (8.6–16.3) individuals/100 km². Across game management units, mean densities ranged between 7.5 and 14.8 individuals/100 km². Our method incorporates multiple sources of uncertainty (e.g., effective sampling area, imperfect detection) to estimate brown bear density, but the inference fundamentally relies on unmarked individuals only. While useful as a temporary approach to monitor brown bears, we urge implementing DNA capture–recapture methods regionally to inform brown bear management and recommend increasing resources for GPS collars to improve estimates of effective sampling area.     

Effect of feedback on test ordering behaviour of general practitioners.

OBJECTIVE--To assess the effect of feedback on the test ordering behaviour of general practitioners. DESIGN--Comparison of requests at two diagnostic centres, and internal comparison between tests which were discussed in feedback and tests which were not. SETTING--A diagnostic centre in Maastricht giving feedback and another elsewhere in the Netherlands (laboratory A) not giving feedback. SUBJECTS--All 85 general practitioners in the region of Maastricht, and all general practitioners in the region of laboratory A. MAIN OUTCOME MEASURES--Numbers of tests requested by general practitioners. RESULTS--Requests at the Maastricht diagnostic centre decreased soon after the onset of feedback whereas there was a persistent increase in requests at laboratory A. Tests that were discussed showed the strongest decrease (maximum 40%), though tests that were not discussed decreased as well (maximum 27%). CONCLUSIONS--Feedback on diagnostic requests may exert a strong influence on request behaviour. Four years after the onset of feedback the effects were still noticeable.     

Negative autoregulation by FAS mediates robust fetal erythropoiesis

Tissue development is regulated by signaling networks that control developmental rate and determine ultimate tissue mass. Here we present a novel computational algorithm used to identify regulatory feedback and feedforward interactions between progenitors in developing erythroid tissue. The algorithm makes use of dynamic measurements of red cell progenitors between embryonic days 12 and 15 in the mouse. It selects for intercellular interactions that reproduce the erythroid developmental process and endow it with robustness to external perturbations. This analysis predicts that negative autoregulatory interactions arise between early erythroblasts of similar maturation stage. By studying embryos mutant for the death receptor FAS, or for its ligand, FASL, and by measuring the rate of FAS-mediated apoptosis in vivo, we show that FAS and FASL are pivotal negative regulators of fetal erythropoiesis, in the manner predicted by the computational model. We suggest that apoptosis in erythroid development mediates robust homeostasis regulating the number of red blood cells reaching maturity.