An optimized targeted Next-Generation Sequencing approach for sensitive detection of single nucleotide variants

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NGS based detection of low-level SNVs is feasible with sensitivities up to 10⁻⁴.

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PCR-induced bias could be significantly reduced by the choice of adequate enzymes.

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The prevalent transition vs. transversion bias affects site-specific detection limits.

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Results from clinical data validated the feasibility of NGS-based MRD detection.

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Results help to select suitable biomarkers for MRD quantification.

Monitoring of minimal residual disease (MRD) has become an important clinical aspect for early relapse detection during follow-up care after cancer treatment. Still, the sensitive detection of single base pair point mutations via Next-Generation Sequencing (NGS) is hampered mainly due to high substitution error rates. We evaluated the use of NGS for the detection of low-level variants on an Ion Torrent PGM system. As a model case we used the c.1849G > T (p.Val617Phe) mutation of the JAK2-gene. Several reaction parameters (e.g. choice of DNA-polymerase) were evaluated and a comprehensive analysis of substitution errors was performed. Using optimized conditions, we reliably detected JAK2 c.1849G > T VAFs in the range of 0.01–0.0015% which, in combination with results obtained from clinical data, validated the feasibility of NGS-based MRD detection. Particularly, PCR-induced transitions (mainly G > A and C > T) were the major source of error, which could be significantly reduced by the application of proofreading enzymes. The integration of NGS results for several common point mutations in various oncogenes (i.e. IDH1 and 2, c-KIT, DNMT3A, NRAS, KRAS, BRAF) revealed that the prevalent transition vs. transversion bias (3.57:1) has an impact on site-specific detection limits of low-level mutations. These results may help to select suitable markers for MRD detection and to identify individual cut-offs for detection and quantification.

Composite vector formulation for multiple siRNA delivery as a host targeting antiviral in a cell culture model of hepatitis C virus (HCV) infection

Hepatitis C virus (HCV) infection is a major cause of chronic liver disease and cancer worldwide. RNA interference (RNAi)-based gene therapies have emerged recently as a promising tool to treat chronic viral infections. Indeed, small interfering RNAs (siRNAs) provide an opportunity to target host factors required for the viral life cycle. In this study, we evaluated a novel nanovector-based approach for siRNA delivery in a model of chronically infected hepatic cells. We designed original composite nanoparticles by coating the calcium phosphate core with siRNAs targeting HCV host-factors and pyridylthiourea-grafted polyethyleneimine (πPEI). Using combinations of different siRNAs, we observed an efficient and prolonged decrease of HCV replication. Moreover, we showed that the layer-by-layer technique of coating applied to our nanoparticles triggers a sequential release of siRNAs acting on different steps of the HCV life cycle. Together, our results demonstrate the efficacy of these nanoparticles for siRNA delivery and open new perspectives for antiviral therapies.

Diagnostic approach in lymphoplasmacytic plaque

BACKGROUND

Lymphoplasmacytic plaque (LPP) is a recently described rare skin disease characterized by a dense dermal lymphohistiocytic infiltrate with polyclonal plasma cells. The clinical picture is distinct with reddish to brownish plaque with a predilection for the lower leg. LPP typically affects children.

OBJECTIVE

To define clinical and histologic criteria of LPP and to develop a diagnostic flow chart.

METHODS

We investigated six of our own LPP cases. Immunoglobulin light chains, IgG, IgG4, CD31, CD163 as a histiocytic marker were examined by immunohistochemistry. PCR-based molecular studies were conducted for borrelia sp., mycobacterial and leishmania sp. Moreover, 10 cases, which have been reported in the literature, were checked for the same features.

RESULTS

We could differentiate three main histological patterns (superficial band-like only, [deep] dermal only and mixed). Acanthosis and interface dermatitis are key features in cases with a superficial band-like or mixed infiltrate. Granulomas and giant cells could be only found in about 30% of the cases. The number of plasma cells was variable accounting for 5-40% of the infiltrate. The number of blood vessels was increased in the majority of the cases. 'Free-floating' collagen bundles surrounded by histiocytes (pseudorosettes) were identified as a new histological feature. An infectious agent could be excluded in all cases.

CONCLUSIONS

LPP is a long-standing skin disease, which may also occur in adults and in other body regions than the lower leg. Reproducible clinical and histological criteria allow delineating a diagnostic work-up for LPP.

Shifting and extension of phenological periods with increasing temperature along elevational transects in southern Bavaria

The impact of global warming on phenology has been widely studied, and almost consistently advancing spring events have been reported. Especially in alpine regions, an extraordinary rapid warming has been observed in the last decades. However, little is known about phenological phases over the whole vegetation period at high elevations. We observed 12 phenological phases of seven tree species and measured air temperature at 42 sites along four transects of about 1000 m elevational range in the years 2010 and 2011 near Garmisch-Partenkirchen, Germany. Site- and species-specific onset dates for the phenological phases were determined and related to elevation, temperature lapse rates and site-specific temperature sums. Increasing temperatures induced advanced spring and delayed autumn phases, in which both yielded similar magnitudes. Delayed leaf senescence could therefore have been underestimated until now in extending the vegetation period. Not only the vegetation period, but also phenological periods extended with increasing temperature. Moreover, sensitivity to elevation and temperature strongly depends on the specific phenological phase. Differences between species and groups of species (deciduous, evergreen, high elevation) were found in onset dates, phenological response rates and also in the effect of chilling and forcing temperatures. Increased chilling days highly reduced forcing temperature requirements for deciduous trees, but less for evergreen trees. The problem of shifted species associations and phenological mismatches due to species-specific responses to increasing temperature is a recent topic in ecological research. Therefore, we consider our findings from this novel, dense observation network in an alpine area of particular importance to deepen knowledge on phenological responses to climate change.

Evaluation of exercise capacity after severe stroke using robotics-assisted treadmill exercise: a proof-of-concept study

BACKGROUND

Robotics-assisted treadmill exercise (RATE) with focus on motor recovery has become popular in early post-stroke rehabilitation but low endurance for exercise is highly prevalent in these individuals. This study aimed to develop an exercise testing method using robotics-assisted treadmill exercise to evaluate aerobic capacity after severe stroke.

METHODS

Constant load testing (CLT) based on body weight support (BWS) control, and incremental exercise testing (IET) based on guidance force (GF) control were implemented during RATE. Analyses focussed on step change, step response kinetics, and peak performance parameters of oxygen uptake.

RESULTS

Three subjects with severe motor impairment 16-23 days post-stroke were included. CLT yielded reasonable step change values in oxygen uptake, whereas response kinetics of oxygen uptake showed low goodness of fit. Peak performance parameters were not obtained during IET.

CONCLUSION

Exercise testing in post-stroke individuals with severe motor impairments using a BWS control strategy for CLT is deemed feasible and safe. Our approach yielded reasonable results regarding cardiovascular performance parameters. IET based on GF control does not provoke peak cardiovascular performance due to uncoordinated walking patterns. GF control needs further development to optimally demand active participation during RATE. The findings warrant further research regarding the evaluation of exercise capacity after severe stroke.

About the change in boiling behaviour of water with coolant additives in PWR

The present study investigates the effect of boric acid and lithium hydroxide on flow boiling phenomena in pressurized water reactors. The experiments were conducted in a boiling loop with up to 40 bar and 250 °C. The bubble size distribution was determined with a wire-mesh sensor. The results showed no indication that reactor-typical concentrations of boric acid or lithium hydroxide have a safety-relevant influence on the boiling behavior in pressurized water reactors.

Tendencias poblacionales recientes de la avutarda hubara en las Islas Canarias: análisis metodológico y estado de conservación

Recent population trends of the houbara bustard in the Canary Islands. Methods and conservation status Determining conservation status requires rigorous and reliable data about population sizes and trends, especially if they have to be applied to islands where the species have small populations. The Canary bustard houbara (Chlamydotis undulata fuertaventurae) is catalogued as ‘in danger’ by the Red Book of the Birds of Spain. This work analyzes the value of previously published information on the species using the method of adjacent linear transects separated by 200 m, as a baseline for establishing robust population trends in 30 important areas (ranging from 1.3 to 12.8 km2) for the houbara in the islands of Lanzarote and Fuerteventura (Canary Islands). Censuses were repeated on the same dates (from November to December) and localities as those carried out in 1994, 2004 and 2006. The detection probability of the houbara was estimated by means of distance sampling, being 0.42 up to 250 m from the observer, and 0.82 in the main census belt of 100 m on either side of the line transect. The method of adjacent linear transects —counting the maximum number of hubaras detected— provides accurate figures of population densities (detection of 95.2% of the birds). The previous estimations of houbara densities can therefore be considered highly trustworthy, with a probable average underestimation of only 5 %. Nevertheless, the confidence intervals of density estimations using only one census were very large. Therefore, with only one census per sampling area and year it is not possible to obtain precise estimates of houbara densities with small variation around the average value. This raises concern when trying to obtain solid evidence about the increases–decreases of houbara populations comparing different dates or study areas. The density of the Canary Island hubara bustard decreased significantly from 2004/2006 to 2011 in eight areas of Fuerteventura (Vega Vieja, Los Alares–Pocetas, Matas Blancas, Lorenzo– Diviso, Corralejo, Lajares and Fimapaire) and in two areas of Lanzarote (Argana and La Santa). Conversely, the density of the houbara significantly increased in three areas of Lanzarote (Zonzamas, Guatiza and Llano de las Maretas). As a whole, average population density did not differ significantly between 2004/2006 and 2011 in Fuerteventura (slight decrease of 29% in 2011), but there was a significant increase in Lanzarote (increase of 60% from 2004/2006 to 2011). The change in density from 2004/2006 to 2011 tended to be an increase in areas further from paved roads, and a decrease in locations predominantly covered by loose sandy soils.

The risk of infections in HIV-HCV coinfected patients during antiviral therapy with pegIFN+RBV

OBJECTIVES

Antiviral treatment with pegIFN/RBV decreases ANC and CD4+ cell count. An association between neutropenia, a low CD4+ cell count and infections has not been demonstrated so far in HIV-HCV coinfected patients.

METHODS

The incidence, type, and severity of infections were recorded in 85 HIV-HCV coinfected and 164 monoinfected patients receiving pegIFN/RBV for 48 weeks. ANC and CD4+ cell count were assessed every 4 weeks during therapy.

RESULTS

The incidence of infections was significantly higher in HIV-HCV than HCV-Mono (38% vs. 15%; p = 0.001). Types of infections: pneumonia (n = 16/n = 24), bacteraemia/sepsis (n = 5/n = 2), skin infections (n = 15/n = 12), urinary tract infections (n = 4/n = 1), OIs (n = 10/n = 1). The incidence of neutropenia grade 1, 2 3 or 4 was similar in HIV-HCV and HCV-Mono, respectively. The incidence of infections was not associated with neutropenia (HCV-Mono: p = 0.584; HIV-HCV: p = 0.23) or with CD4+ cell counts <200/μL (HIV-HCV: p = 0.29). OIs occurred more often in HIV-HCV patients with CD4+ cell count <200/μL (p = 0.024).

CONCLUSIONS

Up to 38% and 15% of HIV-HCV coinfected and HCV-monoinfected patients develop infections during pegIFN+RBV therapy but without any correlation to neutropenia. Antibacterial prophylaxis/treatment should be considered early in HIV-HCV coinfected patients developing CD4+ cell counts <200/μL during antiviral therapy as these patients have an increased risk of OIs.

Biomimetic collagen scaffolds with anisotropic pore architecture

Sponge-like matrices with a specific three-dimensional structural design resembling the actual extracellular matrix of a particular tissue show significant potential for the regeneration and repair of a broad range of damaged anisotropic tissues. The manipulation of the structure of collagen scaffolds using a freeze-drying technique was explored in this work as an intrinsically biocompatible way of tailoring the inner architecture of the scaffold. The research focused on the influence of temperature gradients, imposed during the phase of crystallisation of collagen suspensions, upon the degree of anisotropy in the microstructures of the scaffolds produced. Moulding technology was employed to achieve differences in heat transfer rates during the freezing processes. For this purpose various moulds with different configurations were developed with a view to producing uniaxial and multi-directional temperature gradients across the sample during this process. Scanning electron microscopy analysis of different cross-sections (longitudinal and horizontal) of scaffolds revealed that highly aligned matrices with axially directed pore architectures were obtained where single unidirectional temperature gradients were induced. Altering the freezing conditions by the introduction of multiple temperature gradients allowed collagen scaffolds to be produced with complex pore orientations, and anisotropy in pore size and alignment.