Analysis of Slow-Cycling Variants of the Light-Inducible Nuclear Protein Export System LEXY in Mammalian Cells.

The optogenetic tool LEXY consists of the second light oxygen voltage (LOV) domain of Avena sativa phototropin 1 mutated to contain a nuclear export signal. It allows exporting from the nucleus with blue light proteins of interest (POIs) genetically fused to it. Mutations slowing the dark recovery rate of the LOV domain within LEXY were recently shown to allow for better depletion of some POIs from the nucleus in Drosophila embryos and for the usage of low light illumination regimes. We investigated these variants in mammalian cells and found they increase the cytoplasmic localization of the proteins we tested after illumination, but also during the dark phases, which corresponds to higher leakiness of the system. These data suggest that, when aiming to sequester into the nucleus a protein with a cytoplasmic function, the original LEXY is preferable. The iLEXY variants are, instead, advantageous when wanting to deplete the nucleus of the POI as much as possible.

finDr: A web server for in silico D-peptide ligand identification.

In the rapidly expanding field of peptide therapeutics, the short in vivo half-life of peptides represents a considerable limitation for drug action. D-peptides, consisting entirely of the dextrorotatory enantiomers of naturally occurring levorotatory amino acids (AAs), do not suffer from these shortcomings as they are intrinsically resistant to proteolytic degradation, resulting in a favourable pharmacokinetic profile. To experimentally identify D-peptide binders to interesting therapeutic targets, so-called mirror-image phage display is typically performed, whereby the target is synthesized in D-form and L-peptide binders are screened as in conventional phage display. This technique is extremely powerful, but it requires the synthesis of the target in D-form, which is challenging for large proteins. Here we present finDr, a novel web server for the computational identification and optimization of D-peptide ligands to any protein structure (https://findr.biologie.uni-freiburg.de/). finDr performs molecular docking to virtually screen a library of helical 12-mer peptides extracted from the RCSB Protein Data Bank (PDB) for their ability to bind to the target. In a separate, heuristic approach to search the chemical space of 12-mer peptides, finDr executes a customizable evolutionary algorithm (EA) for the de novo identification or optimization of D-peptide ligands. As a proof of principle, we demonstrate the validity of our approach to predict optimal binders to the pharmacologically relevant target phenol soluble modulin alpha 3 (PSMα3), a toxin of methicillin-resistant Staphylococcus aureus (MRSA). We validate the predictions using in vitro binding assays, supporting the success of this approach. Compared to conventional methods, finDr provides a low cost and easy-to-use alternative for the identification of D-peptide ligands against protein targets of choice without size limitation. We believe finDr will facilitate D-peptide discovery with implications in biotechnology and biomedicine.

Ion Mobility in Thick and Thin Poly-3,4 Ethylenedioxythiophene Films-From EQCM to Actuation.

Conductive polymer actuators and sensors rely on controlled ion transport coupled to a potential/charge change. In order to understand and control such devices, it is of paramount importance to understand the factors that determine ion flux at various conditions, including the synthesis potential. In this work, the ion transport in thinner poly-3,4-ethylenedioxythiophene (PEDOT) films during charge/discharge driven by cyclic voltammetry is studied by consideration of the electrochemical quartz crystal microbalance (EQCM) and the results are compared to the actuation responses of thicker films that have been synthesized with the same conditions in the bending and linear expansion modes. The effects of polymerization potentials of 1.0 V, 1.2 V, and 1.5 V are studied to elucidate how polymerization potential contributes to actuation, as well the involvement of the EQCM. In this work, it is revealed that there is a shift from anion-dominated to mixed to cation-dominated activity with increased synthesis potential. Scanning electron microscopy shows a decrease in porosity for the PEDOT structure with increasing synthesis potential. EQCM analysis of processes taking place at various potentials allows the determination of appropriate potential windows for increased control over devices.

Optogenetic Control of Nucleocytoplasmic Protein Transport.

The transport of proteins between the nucleus and the cytosol is a vital process regulating cellular activity. The ability to spatiotemporally control the nucleocytoplasmic transport of a protein of interest allows for elucidating its function taking into account the dynamic and heterogeneous nature of biological processes contrary to conventional knockin, knockout, and chemically induced overexpression strategies. We recently developed two optogenetic tools, called LINuS and LEXY, for reversibly controlling with blue light the nuclear import and export of proteins of interest, respectively. Here we describe how to use them to control the localization of a protein of interest in cultured mammalian cells using a fluorescence microscope.

Mechanism and site of action of big dynorphin on ASIC1a.

Acid-sensing ion channels (ASICs) are proton-gated cation channels that contribute to neurotransmission, as well as initiation of pain and neuronal death following ischemic stroke. As such, there is a great interest in understanding the in vivo regulation of ASICs, especially by endogenous neuropeptides that potently modulate ASICs. The most potent endogenous ASIC modulator known to date is the opioid neuropeptide big dynorphin (BigDyn). BigDyn is up-regulated in chronic pain and increases ASIC-mediated neuronal death during acidosis. Understanding the mechanism and site of action of BigDyn on ASICs could thus enable the rational design of compounds potentially useful in the treatment of pain and ischemic stroke. To this end, we employ a combination of electrophysiology, voltage-clamp fluorometry, synthetic BigDyn analogs, and noncanonical amino acid-mediated photocrosslinking. We demonstrate that BigDyn binding results in an ASIC1a closed resting conformation that is distinct from open and desensitized states induced by protons. Using alanine-substituted BigDyn analogs, we find that the BigDyn modulation of ASIC1a is primarily mediated through electrostatic interactions of basic amino acids in the BigDyn N terminus. Furthermore, neutralizing acidic amino acids in the ASIC1a extracellular domain reduces BigDyn effects, suggesting a binding site at the acidic pocket. This is confirmed by photocrosslinking using the noncanonical amino acid azidophenylalanine. Overall, our data define the mechanism of how BigDyn modulates ASIC1a, identify the acidic pocket as the binding site for BigDyn, and thus highlight this cavity as an important site for the development of ASIC-targeting therapeutics.

Magnesium but not nicotinamide prevents vascular calcification in experimental uraemia.

BACKGROUND: Optimal phosphate control is an unmet need in chronic kidney disease (CKD). High serum phosphate increases calcification burden and is associated with mortality and cardiovascular disease in CKD. Nicotinamide (NA) alone or in combination with calcium-free phosphate binders might be a strategy to reduce phosphate levels and calcification and thus impact cardiovascular disease in CKD. METHODS: We studied the effect of NA alone and in combination with magnesium carbonate (MgCO3) as a potential novel treatment strategy. CKD was induced in dilute brown non-agouti/2 mice by subtotal nephrectomy followed by a high-phosphate diet (HP) and 7 weeks of treatment with NA, MgCO3 or their combination. Control mice underwent subtotal nephrectomy and received an HP or underwent sham surgery and received standard chow plus NA. RESULTS: CKD mice showed increased serum fibroblast growth factor 23 and calcium-phosphate product that was normalized by all treatment regimes. NA alone increased soft tissue and vascular calcification, whereas any treatment with MgCO3 significantly reduced calcification severity in CKD. While MgCO3 supplementation alone resulted in decreased calcification severity, it resulted in increased intestinal expression of the phosphate transporters type II sodium-dependent phosphate transporter 1 (Pit-1). Combined therapy of MgCO3 and NA reduced tissue calcification and normalized expression levels of intestinal phosphate transporter proteins. CONCLUSIONS: In conclusion, the data indicate that NA increases while MgCO3 reduces ectopic calcification severity. Augmented expression of intestinal phosphate transporters by MgCO3 treatment was abolished by the addition of NA. However, the clinical relevance of the latter remains to be explored. Importantly, the data suggest no benefit of NA regarding treatment of calcification in addition to MgCO3.

Sclerostin deficiency modifies the development of CKD-MBD in mice.

Sclerostin is a soluble antagonist of canonical Wnt signaling and a strong inhibitor of bone formation. We present experimental data on the role of sclerostin in chronic kidney disease - bone mineral disorder (CKD-MBD). METHODS: We performed 5/6 nephrectomies in 36-week-old sclerostin-deficient (SOST-/-) B6-mice and in C57BL/6J wildtype (WT) mice. Animals received a high phosphate diet for 11weeks. The bones were analyzed by high-resolution micro-computed tomography (µCT) and quantitative bone histomorphometry. Aortic tissue was analyzed regarding the extent of vascular calcification. RESULTS: All nephrectomized mice had severe renal failure, and parathyroid hormone was highly increased compared to corresponding sham animals. All SOST-/- animals revealed the expected high bone mass phenotype. Overall, the bone compartment in WT and SOST-/- mice responded similarly to nephrectomy. In uremic WT animals, µCT data at both the distal femur and lumbar spine revealed significantly increased trabecular volume compared to non-uremic WTs. In SOST-/- mice, the differences between trabecular bone volume were less pronounced when comparing uremic with sham animals. Cortical thickness and cortical bone density at the distal femur decreased significantly and comparably in both genotypes after 5/6 nephrectomy compared to sham animals (cortical bone density -18% and cortical thickness -32%). Overall, 5/6 nephrectomy and concomitant hyperparathyroidism led to a genotype-independent loss of cortical bone volume and density. Overt vascular calcification was not detectable in either of the genotypes. CONCLUSION: Renal osteodystrophy changes were more pronounced in WT mice than in SOST-/- mice. The high bone mass phenotype of sclerostin deficiency was detectable also in the setting of chronic renal failure with severe secondary hyperparathyroidism.

Aggregation, Validation, and Generalization of Qualitative Data - Methodological and Practical Research Strategies Illustrated by the Research Process of an empirically Based Typology.

The article deals with the question of how aggregated data which allow for generalizable insights can be generated from single-case based qualitative investigations. Thereby, two central challenges of qualitative social research are outlined: First, researchers must ensure that the single-case data can be aggregated and condensed so that new collective structures can be detected. Second, they must apply methods and practices to allow for the generalization of the results beyond the specific study. In the following, we demonstrate how and under what conditions these challenges can be addressed in research practice. To this end, the research process of the construction of an empirically based typology is described. A qualitative study, conducted within the framework of the Luxembourg Youth Report, is used to illustrate this process. Specifically, strategies are presented which increase the likelihood of generalizability or transferability of the results, while also highlighting their limitations.

Prevalence and epidemiology of pathological gambling at Naval Medical Center Portsmouth psychiatry clinic.

OBJECTIVE: Gambling has exploded in popularity, but pathological gambling (PG) is infrequently diagnosed. The objectives of this study were to calculate the prevalence of PG in a psychiatry clinic, to determine whether PG is underdiagnosed, and to analyze risk factors for PG. METHODS: A survey was completed by 584 outpatients presenting to the Naval Medical Center Portsmouth psychiatry clinic over 6 months. Epidemiological data, smoking status, and alcohol use were assessed, and the South Oaks Gambling Screen was administered. RESULTS: The prevalence of PG determined with the South Oaks Gambling Screen was 1.4%. The electronically documented prevalence of PG was 0.04%. Male subjects, smokers, and subjects with an alcohol problem were more likely to have a gambling problem. Active duty members did not have statistically significantly higher rates of PG. CONCLUSIONS: PG is markedly underdiagnosed. Military members are not at elevated risk for PG, relative to their dependents. Further research and greater awareness of PG are needed.