Phenocopy – A Strategy to Qualify Chemical Compounds during Hit-to-Lead and/or Lead Optimization

A phenocopy is defined as an environmentally induced phenotype of one individual which is identical to the genotype-determined phenotype of another individual. The phenocopy phenomenon has been translated to the drug discovery process as phenotypes produced by the treatment of biological systems with new chemical entities (NCE) may resemble environmentally induced phenotypic modifications. Various new chemical entities exerting inhibition of the kinase activity of Transforming Growth Factor β Receptor I (TGF-βR1) were qualified by high-throughput RNA expression profiling. This chemical genomics approach resulted in a precise time-dependent insight to the TGF-β biology and allowed furthermore a comprehensive analysis of each NCE's off-target effects. The evaluation of off-target effects by the phenocopy approach allows a more accurate and integrated view on optimized compounds, supplementing classical biological evaluation parameters such as potency and selectivity. It has therefore the potential to become a novel method for ranking compounds during various drug discovery phases

AeroCom phase III multi-model evaluation of the aerosol life cycle and optical properties using ground- and space-based remote sensing as well as surface in situ observations

Within the framework of the AeroCom (Aerosol Comparisons between Observations and Models) initiative, the state-of-the-art modelling of aerosol optical properties is assessed from 14 global models participating in the phase III control experiment (AP3). The models are similar to CMIP6/AerChemMIP Earth System Models (ESMs) and provide a robust multi-model ensemble. Inter-model spread of aerosol species lifetimes and emissions appears to be similar to that of mass extinction coefficients (MECs), suggesting that aerosol optical depth (AOD) uncertainties are associated with a broad spectrum of parameterised aerosol processes. Total AOD is approximately the same as in AeroCom phase I (AP1) simulations. However, we find a 50% decrease in the optical depth (OD) of black carbon (BC), attributable to a combination of decreased emissions and lifetimes. Relative contributions from sea salt (SS) and dust (DU) have shifted from being approximately equal in AP1 to SS contributing about 2/3 of the natural AOD in AP3. This shift is linked with a decrease in DU mass burden, a lower DU MEC, and a slight decrease in DU lifetime, suggesting coarser DU particle sizes in AP3 compared to AP1. Relative to observations, the AP3 ensemble median and most of the participating models underestimate all aerosol optical properties investigated, that is, total AOD as well as fine and coarse AOD (AOD(f), AOD(c)), Angstrom exponent (AE), dry surface scattering (SCdry), and absorption (AC(dry)) coefficients. Compared to AERONET, the models underestimate total AOD by ca. 21% +/- 20% (as inferred from the ensemble median and interquartile range). Against satellite data, the ensemble AOD biases range from -37% (MODIS-Terra) to -16% (MERGED-FMI, a multi-satellite AOD product), which we explain by differences between individual satellites and AERONET measurements themselves. Correlation coefficients (R) between model and observation AOD records are generally high (R > 0.75), suggesting that the models are capable of capturing spatiotemporal variations in AOD. We find a much larger underestimate in coarse AOD(c) (similar to-45% +/- 25 %) than in fine AOD(f) (similar to-15% +/- 25 %) with slightly increased inter-model spread compared to total AOD. These results indicate problems in the modelling of DU and SS. The AOD(c) bias is likely due to missing DU over continental land masses (particularly over the United States, SE Asia, and S. America), while marine AERONET sites and the AATSR SU satellite data suggest more moderate oceanic biases in AOD(c). Column AEs are underestimated by about 10% +/- 16 %. For situations in which measurements show AE > 2, models underestimate AERONET AE by ca. 35 %. In contrast, all models (but one) exhibit large overestimates in AE when coarse aerosol dominates (bias ca. +140% if observed AE < 0.5). Simulated AE does not span the observed AE variability. These results indicate that models overestimate particle size (or underestimate the fine-mode fraction) for fine-dominated aerosol and underestimate size (or overestimate the fine-mode fraction) for coarse-dominated aerosol. This must have implications for lifetime, water uptake, scattering enhancement, and the aerosol radiative effect, which we can not quantify at this moment. Comparison against Global Atmosphere Watch (GAW) in situ data results in mean bias and inter-model variations of -35% +/- 25% and -20% +/- 18% for SCdry and AC(dry), respectively. The larger underestimate of SCdry than AC(dry) suggests the models will simulate an aerosol single scattering albedo that is too low. The larger underestimate of SCdry than ambient air AOD is consistent with recent findings that models overestimate scattering enhancement due to hygroscopic growth. The broadly consistent negative bias in AOD and surface scattering suggests an underestimate of aerosol radiative effects in current global aerosol models. Considerable inter-model diversity in the simulated optical properties is often found in regions that are, unfortunately, not or only sparsely covered by ground-based observations. This includes, for instance, the Sahara, Amazonia, central Australia, and the South Pacific. This highlights the need for a better site coverage in the observations, which would enable us to better assess the models, but also the performance of satellite products in these regions. Using fine-mode AOD as a proxy for present-day aerosol forcing estimates, our results suggest that models underestimate aerosol forcing by ca. -15 %, however, with a considerably large interquartile range, suggesting a spread between -35% and +10 %.Peer reviewe

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Standard Operating Procedures (SOPs) for Palliative Care in German Comprehensive Cancer Centers - an evaluation of the implementation status

Background The working group for palliative medicine within the Comprehensive Cancer Center (CCC) network funded by the German Cancer Aid in Germany has developed and published 14 Standard Operating Procedures (SOPs) for palliative care in CCCs. This study analyzed to what extent these SOPs have been implemented in the clinical routine in the CCC network one year after their publication. Methods An online-based survey on the implementation status, limitations in daily practice and further themes was conducted between April and July 2018. In total, 125 health professionals in specialized palliative care from all 16 CCC locations were invited to participate. The data were analyzed descriptively using SPSS. Results The response rate was 52.8%. More than half of the respondents (57.6%) knew about the free availability of SOPs on the CCC network website. The extent to which each SOP was being used actively in practice by the survey respondents ranged from a low of 22.7% (for the “Fatigue” SOP) to a highest of 48.5% (for the “Palliative Sedation” and “Respiratory Distress” SOPs). The respondents became aware of the SOP through recommendations from colleagues, team meetings or from the head of the department. The SOPs “Respiratory distress of an adult palliative patient” and “Palliative sedation” were perceived as the most practically oriented and understandable. Barriers to use SOPs were mainly limited time resources and lack of knowledge of existence and availability. Conclusions In practice, better knowledge about the SOPs and at the same time increased use can be achieved through systematic training or discussion of SOPs in regular team meetings. There is a need to take measures to optimize the implementation in clinical practice

Novel Approach for Genotyping Varicella-Zoster Virus Strains from Germany▿

In this study, we present a novel genotyping scheme to classify German wild-type varicella-zoster virus (VZV) strains and to differentiate them from the Oka vaccine strain (genotype B). This approach is based on analysis of four loci in open reading frames (ORFs) 51 to 58, encompassing a total length of 1,990 bp. The new genotyping scheme produced identical clusters in phylogenetic analyses compared to full-genome sequences from well-characterized VZV strains. Based on genotype A, D, B, and C reference strains, a dichotomous identification key (DIK) was developed and applied for VZV strains obtained from vesicle fluid and liquor samples originating from 42 patients suffering from varicella or zoster between 2003 and 2006. Sequencing of regions in ORFs 51, 52, 53, 56, 57, and 58 identified 18 single-nucleotide polymorphisms (SNPs), including two novel ones, SNP 89727 and SNP 92792 in ORF51 and ORF52, respectively. The DIK as well as phylogenetic analysis by Bayesian inference showed that 14 VZV strains belonged to genotype A, and 28 VZV strains were classified as genotype D. Neither Japanese (vaccine)-like B strains nor recombinant-like C strains were found within the samples from Germany. The novel genotyping scheme and the DIK were demonstrated to be practical and simple and allow the highly efficient replication of phylogenetic patterns in VZV initially derived from full-genome DNA sequence analyses. Therefore, this approach may allow us to draw a more comprehensive picture of wild-type VZV strains circulating in Germany and Central Europe by high-throughput procedures in the future

Molecular Analysis of Varicella-Zoster Virus Strains Circulating in Tanzania Demonstrating the Presence of Genotype M1 ▿

Based on analysis of 16,392 bp encompassing the complete open reading frames (ORFs) 1, 5, 31, 36, 37, 47, 60, 62, 67, and 68 of the genome of genotype M1 varicella-zoster virus (VZV) was found in swab samples originating from eight Tanzanian zoster patients. Moreover, sequence analysis suggests recombination events between different VZV genotypes within ORFs 1, 31, 60, and 67

Host-Associated Absence of Human Puumala Virus Infections in Northern and Eastern Germany

Human hantavirus disease cases, caused by Puumala virus (PUUV), are mainly recorded in western and southern areas of Germany. This bank vole reservoir survey confirmed PUUV presence in these regions but its absence in northern and eastern regions. PUUV occurrence is associated with the presence of the Western bank vole phylogroup

Neurodegeneration by α-synuclein-specific T cells in AAV-A53T-α-synuclein Parkinson’s disease mice

Background Antigen-specific neuroinflammation and neurodegeneration are characteristic for neuroimmunological diseases. In Parkinson’s disease (PD) pathogenesis, α-synuclein is a known culprit. Evidence for α-synuclein-specific T cell responses was recently obtained in PD. Still, a causative link between these α-synuclein responses and dopaminergic neurodegeneration had been lacking. We thus addressed the functional relevance of α-synuclein-specific immune responses in PD in a mouse model. Methods We utilized a mouse model of PD in which an Adeno-associated Vector 1/2 serotype (AAV1/2) expressing human mutated A53T-α-Synuclein was stereotactically injected into the substantia nigra (SN) of either wildtype C57BL/6 or Recombination-activating gene 1 (RAG1)$^{-/-}$ mice. Brain, spleen, and lymph node tissues from different time points following injection were then analyzed via FACS, cytokine bead assay, immunohistochemistry and RNA-sequencing to determine the role of T cells and inflammation in this model. Bone marrow transfer from either CD4$^{+}$/CD8$^{-}$, CD4$^{-}$/CD8$^{+}$, or CD4$^{+}$/CD8$^{+}$ (JHD$^{-/-}$) mice into the RAG-1$^{-/-}$ mice was also employed. In addition to the in vivo studies, a newly developed A53T-α-synuclein-expressing neuronal cell culture/immune cell assay was utilized. Results AAV-based overexpression of pathogenic human A53T-α-synuclein in dopaminergic neurons of the SN stimulated T cell infiltration. RNA-sequencing of immune cells from PD mouse brains confirmed a pro-inflammatory gene profile. T cell responses were directed against A53T-α-synuclein-peptides in the vicinity of position 53 (68–78) and surrounding the pathogenically relevant S129 (120–134). T cells were required for α-synuclein-induced neurodegeneration in vivo and in vitro, while B cell deficiency did not protect from dopaminergic neurodegeneration. Conclusions Using T cell and/or B cell deficient mice and a newly developed A53T-α-synuclein-expressing neuronal cell culture/immune cell assay, we confirmed in vivo and in vitro that pathogenic α-synuclein peptide-specific T cell responses can cause dopaminergic neurodegeneration and thereby contribute to PD-like pathology

The effect of spironolactone on diastolic function in haemodialysis patients

Heart failure with preserved ejection fraction (HFpEF) is highly prevalent in patients on maintenance haemodialysis (HD) and lacks effective treatment. We investigated the effect of spironolactone on cardiac structure and function with a specific focus on diastolic function parameters. The MiREnDa trial examined the effect of 50 mg spironolactone once daily versus placebo on left ventricular mass index (LVMi) among 97 HD patients during 40 weeks of treatment. In this echocardiographic substudy, diastolic function was assessed using predefined structural and functional parameters including E/e'. Changes in the frequency of HFpEF were analysed using the comprehensive 'HFA-PEFF score'. Complete echocardiographic assessment was available in 65 individuals (59.5 ± 13.0 years, 21.5% female) with preserved left ventricular ejection fraction (LVEF &amp;gt; 50%). At baseline, mean E/e' was 15.2 ± 7.8 and 37 (56.9%) patients fulfilled the criteria of HFpEF according to the HFA-PEFF score. There was no significant difference in mean change of E/e' between the spironolactone group and the placebo group (+ 0.93 ± 5.39 vs. + 1.52 ± 5.94, p = 0.68) or in mean change of left atrial volume index (LAVi) (1.9 ± 12.3 ml/