En Route to Targeted Ribosome Editing to Replenish Skin Anchor Protein LAMB3 in Junctional Epidermolysis Bullosa.

Severe junctional epidermolysis bullosa is a rare genetic, postpartum lethal skin disease, predominantly caused by nonsense/premature termination codon (PTC) sequence variants in LAMB3 gene. LAMB3 encodes LAMB3, the ß subunit of epidermal-dermal skin anchor laminin 332. Most translational reads of a PTC mRNA deliver truncated, nonfunctional proteins, whereas an endogenous PTC readthrough mechanism produces full-length protein at minimal and insufficient levels. Conventional translational readthrough-inducing drugs amplify endogenous PTC readthrough; however, translational readthrough-inducing drugs are either proteotoxic or nonselective. Ribosome editing is a more selective and less toxic strategy. This technique identified ribosomal protein L35/uL29 (ie, RpL35) and RpL35-ligands repurposable drugs artesunate and atazanavir as molecular tools to increase production levels of full-length LAMB3. To evaluate ligand activity in living cells, we monitored artesunate and atazanavir treatment by dual luciferase reporter assays. Production levels of full-length LAMB3 increased up to 200% upon artesunate treatment, up to 150% upon atazanavir treatment, and up to 170% upon combinatorial treatment of RpL35 ligands at reduced drug dosage, with an unrelated PTC reporter being nonresponsive. Proof of bioactivity of RpL35 ligands in selective increase of full-length LAMB3 provides the basis for an alternative, targeted therapeutic route to replenish LAMB3 in severe junctional epidermolysis bullosa.

Emerging Personalized Opportunities for Enhancing Translational Readthrough in Rare Genetic Diseases and Beyond.

Nonsense mutations trigger premature translation termination and often give rise to prevalent and rare genetic diseases. Consequently, the pharmacological suppression of an unscheduled stop codon represents an attractive treatment option and is of high clinical relevance. At the molecular level, the ability of the ribosome to continue translation past a stop codon is designated stop codon readthrough (SCR). SCR of disease-causing premature termination codons (PTCs) is minimal but small molecule interventions, such as treatment with aminoglycoside antibiotics, can enhance its frequency. In this review, we summarize the current understanding of translation termination (both at PTCs and at cognate stop codons) and highlight recently discovered pathways that influence its fidelity. We describe the mechanisms involved in the recognition and readthrough of PTCs and report on SCR-inducing compounds currently explored in preclinical research and clinical trials. We conclude by reviewing the ongoing attempts of personalized nonsense suppression therapy in different disease contexts, including the genetic skin condition epidermolysis bullosa.

Electrolysis in reduced gravitational environments: current research perspectives and future applications.

Electrochemical energy conversion technologies play a crucial role in space missions, for example, in the Environmental Control and Life Support System (ECLSS) on the International Space Station (ISS). They are also vitally important for future long-term space travel for oxygen, fuel and chemical production, where a re-supply of resources from Earth is not possible. Here, we provide an overview of currently existing electrolytic energy conversion technologies for space applications such as proton exchange membrane (PEM) and alkaline electrolyzer systems. We discuss the governing interfacial processes in these devices influenced by reduced gravitation and provide an outlook on future applications of electrolysis systems in, e.g., in-situ resource utilization (ISRU) technologies. A perspective of computational modelling to predict the impact of the reduced gravitational environment on governing electrochemical processes is also discussed and experimental suggestions to better understand efficiency-impacting processes such as gas bubble formation and detachment in reduced gravitational environments are outlined.

A data management infrastructure for the integration of imaging and omics data in life sciences.

BACKGROUND: As technical developments in omics and biomedical imaging increase the throughput of data generation in life sciences, the need for information systems capable of managing heterogeneous digital assets is increasing. In particular, systems supporting the findability, accessibility, interoperability, and reusability (FAIR) principles of scientific data management. RESULTS: We propose a Service Oriented Architecture approach for integrated management and analysis of multi-omics and biomedical imaging data. Our architecture introduces an image management system into a FAIR-supporting, web-based platform for omics data management. Interoperable metadata models and middleware components implement the required data management operations. The resulting architecture allows for FAIR management of omics and imaging data, facilitating metadata queries from software applications. The applicability of the proposed architecture is demonstrated using two technical proofs of concept and a use case, aimed at molecular plant biology and clinical liver cancer research, which integrate various imaging and omics modalities. CONCLUSIONS: We describe a data management architecture for integrated, FAIR-supporting management of omics and biomedical imaging data, and exemplify its applicability for basic biology research and clinical studies. We anticipate that FAIR data management systems for multi-modal data repositories will play a pivotal role in data-driven research, including studies which leverage advanced machine learning methods, as the joint analysis of omics and imaging data, in conjunction with phenotypic metadata, becomes not only desirable but necessary to derive novel insights into biological processes.

Drug Development for Target Ribosomal Protein rpL35/uL29 for Repair of LAMB3R635X in Rare Skin Disease Epidermolysis Bullosa.

INTRODUCTION: Epidermolysis bullosa (EB) describes a family of rare genetic blistering skin disorders. Various subtypes are clinically and genetically heterogeneous, and a lethal postpartum form of EB is the generalized severe junctional EB (gs-JEB). gs-JEB is mainly caused by premature termination codon (PTC) mutations in the skin anchor protein LAMB3 (laminin subunit beta-3) gene. The ribosome in majority of translational reads of LAMB3PTC mRNA aborts protein synthesis at the PTC signal, with production of a truncated, nonfunctional protein. This leaves an endogenous readthrough mechanism needed for production of functional full-length Lamb3 protein albeit at insufficient levels. Here, we report on the development of drugs targeting ribosomal protein L35 (rpL35), a ribosomal modifier for customized increase in production of full-length Lamb3 protein from a LAMB3PTC mRNA. METHODS: Molecular docking studies were employed to identify small molecules binding to human rpL35. Molecular determinants of small molecule binding to rpL35 were further characterized by titration of the protein with these ligands as monitored by nuclear magnetic resonance (NMR) spectroscopy in solution. Changes in NMR chemical shifts were used to map the docking sites for small molecules onto the 3D structure of the rpL35. RESULTS: Molecular docking studies identified 2 FDA-approved drugs, atazanavir and artesunate, as candidate small-molecule binders of rpL35. Molecular interaction studies predicted several binding clusters for both compounds scattered throughout the rpL35 structure. NMR titration studies identified the amino acids participating in the ligand interaction. Combining docking predictions for atazanavir and artesunate with rpL35 and NMR analysis of rpL35 ligand interaction, one binding cluster located near the N-terminus of rpL35 was identified. In this region, the nonidentical binding sites for atazanavir and artesunate overlap and are accessible when rpL35 is integrated in its natural ribosomal environment. CONCLUSION: Atazanavir and artesunate were identified as candidate compounds binding to ribosomal protein rpL35 and may now be tested for their potential to trigger a rpL35 ribosomal switch to increase production of full-length Lamb3 protein from a LAMB3PTC mRNA for targeted systemic therapy in treating gs-JEB.

Design-Considerations regarding Silicon/Graphite and Tin/Graphite Composite Electrodes for Lithium-Ion Batteries.

An analytical model is proposed to investigate properties of composite electrodes that utilize more than one active material. We demonstrate how the equations can be applied to aid in the design of electrodes by comparing silicon-graphite and tin-graphite composite negative electrodes as examples with practical relevance. Based on simple assumptions, the results show how volume expansion tolerance and initial porosity are important factors for the achievable gravimetric and volumetric capacities as well as volumetric energy density. A Si-alloy/graphite composite electrode is used as an experimental system to corroborate the formulated analysis. Kinetic limitations are also addressed based on a novel heuristic approach.

qPortal: A platform for data-driven biomedical research.

Modern biomedical research aims at drawing biological conclusions from large, highly complex biological datasets. It has become common practice to make extensive use of high-throughput technologies that produce big amounts of heterogeneous data. In addition to the ever-improving accuracy, methods are getting faster and cheaper, resulting in a steadily increasing need for scalable data management and easily accessible means of analysis. We present qPortal, a platform providing users with an intuitive way to manage and analyze quantitative biological data. The backend leverages a variety of concepts and technologies, such as relational databases, data stores, data models and means of data transfer, as well as front-end solutions to give users access to data management and easy-to-use analysis options. Users are empowered to conduct their experiments from the experimental design to the visualization of their results through the platform. Here, we illustrate the feature-rich portal by simulating a biomedical study based on publically available data. We demonstrate the software's strength in supporting the entire project life cycle. The software supports the project design and registration, empowers users to do all-digital project management and finally provides means to perform analysis. We compare our approach to Galaxy, one of the most widely used scientific workflow and analysis platforms in computational biology. Application of both systems to a small case study shows the differences between a data-driven approach (qPortal) and a workflow-driven approach (Galaxy). qPortal, a one-stop-shop solution for biomedical projects offers up-to-date analysis pipelines, quality control workflows, and visualization tools. Through intensive user interactions, appropriate data models have been developed. These models build the foundation of our biological data management system and provide possibilities to annotate data, query metadata for statistics and future re-analysis on high-performance computing systems via coupling of workflow management systems. Integration of project and data management as well as workflow resources in one place present clear advantages over existing solutions.

A Novel Mutation in RPL10 (Ribosomal Protein L10) Causes X-Linked Intellectual Disability, Cerebellar Hypoplasia, and Spondylo-Epiphyseal Dysplasia.

RPL10 encodes ribosomal protein L10 (uL16), a highly conserved multifunctional component of the large ribosomal subunit, involved in ribosome biogenesis and function. Using X-exome resequencing, we identified a novel missense mutation (c.191C>T; p.(A64V)) in the N-terminal domain of the protein, in a family with two affected cousins presenting with X-linked intellectual disability, cerebellar hypoplasia, and spondylo-epiphyseal dysplasia (SED). We assessed the impact of the mutation on the translational capacity of the cell using yeast as model system. The mutation generates a functional ribosomal protein, able to complement the translational defects of a conditional lethal mutation of yeast rpl10. However, unlike previously reported mutations, this novel RPL10 missense mutation results in an increase in the actively translating ribosome population. Our results expand the mutational and clinical spectrum of RPL10 identifying a new genetic cause of SED and highlight the emerging role of ribosomal proteins in the pathogenesis of neurodevelopmental disorders.

Intuitive web-based experimental design for high-throughput biomedical data.

Big data bioinformatics aims at drawing biological conclusions from huge and complex biological datasets. Added value from the analysis of big data, however, is only possible if the data is accompanied by accurate metadata annotation. Particularly in high-throughput experiments intelligent approaches are needed to keep track of the experimental design, including the conditions that are studied as well as information that might be interesting for failure analysis or further experiments in the future. In addition to the management of this information, means for an integrated design and interfaces for structured data annotation are urgently needed by researchers. Here, we propose a factor-based experimental design approach that enables scientists to easily create large-scale experiments with the help of a web-based system. We present a novel implementation of a web-based interface allowing the collection of arbitrary metadata. To exchange and edit information we provide a spreadsheet-based, humanly readable format. Subsequently, sample sheets with identifiers and metainformation for data generation facilities can be created. Data files created after measurement of the samples can be uploaded to a datastore, where they are automatically linked to the previously created experimental design model.

Infrared studies of the potential controlled adsorption of sodium dodecyl sulfate at the Au(111) electrode surface.

Quantitative subtractively normalized interfacial Fourier transform infrared reflection spectroscopy (SNIFTIRS) was used to determine the conformation and orientation of sodium dodecyl sulfate (SDS) molecules adsorbed at the single crystal Au(111) surface. The SDS molecules form a hemimicellar/hemicylindrical (phase I) structure for the range of potentials between -200 ≤ E < 450 mV and condensed (phase II) film for electrode potentials ≥500 mV vs Ag/AgCl. The SNIFTIRS measurements indicate that the alkyl chains within the two adsorbed states of SDS film are in the liquid-crystalline state rather than the gel state. However, the sulfate headgroup is in an oriented state in phase I and is disordered in phase II. The newly acquired SNIFTIR spectroscopy measurements were coupled with previous electrochemical, atomic force microscopy, and neutron reflectivity data to improve the current existing models of the SDS film adsorbed on the Au(111) surface. The IR data support the existence of a hemicylindrical film for SDS molecules adsorbed at the Au(111) surface in phase I and suggest that the structure of the condensed film in phase II can be more accurately modeled by a disordered bilayer.

Body mass estimations for Plateosaurus engelhardti using laser scanning and 3D reconstruction methods.

Both body mass and surface area are factors determining the essence of any living organism. This should also hold true for an extinct organism such as a dinosaur. The present report discusses the use of a new 3D laser scanner method to establish body masses and surface areas of an Asian elephant (Zoological Museum of Copenhagen, Denmark) and of Plateosaurus engelhardti, a prosauropod from the Upper Triassic, exhibited at the Paleontological Museum in Tübingen (Germany). This method was used to study the effect that slight changes in body shape had on body mass for P. engelhardti. It was established that body volumes varied between 0.79 m(3) (slim version) and 1.14 m(3) (robust version), resulting in a presumable body mass of 630 and 912 kg, respectively. The total body surface areas ranged between 8.8 and 10.2 m(2), of which, in both reconstructions of P. engelhardti, approximately 33% account for the thorax area alone. The main difference between the two models is in the tail and hind limb reconstruction. The tail of the slim version has a surface area of 1.98 m(2), whereas that of the robust version has a surface area of 2.73 m(2). The body volumes calculated for the slim version were as follows: head 0.006 m(3), neck 0.016 m(3), fore limbs 0.020 m(3), hind limbs 0.08 m(3), thoracic cavity 0.533 m(3), and tail 0.136 m(3). For the robust model, the following volumes were established: 0.01 m(3) head, neck 0.026 m(3), fore limbs 0.025 m(3), hind limbs 0.18 m(3), thoracic cavity 0.616 m(3), and finally, tail 0.28 m(3). Based on these body volumes, scaling equations were used to assess the size that the organs of this extinct dinosaur have.

Postoperative chemotherapy may not be necessary for patients with ypN0-category after neoadjuvant chemoradiotherapy of rectal cancer.

PURPOSE: After neoadjuvant radiochemotherapy and surgery, there is no general agreement about whether postoperative chemotherapy is necessary. With the help of clinical and pathohistologic data, prognostic factors were determined as a basis for the decision to spare a patient additional chemotherapy or to urgently recommend it. RESULTS: Ninety-five patients treated with neoadjuvant 5-fluorouracil-based radiochemotherapy (November 4, 1997 and June 15, 2004) without distant metastases and an R0 (microscopically complete) resection were evaluated. Adjuvant chemotherapy (5-fluorouracil or 5-fluorouracil/folinic acid) was given to 65 of 95 patients (68.4 percent). The disease-free survival rate after 36 months was chosen as the target parameter (median follow-up, 36 months). METHODS: The five-year survival rate for all patients was 80.3 +/- 5.6 percent; the five-year disease-free survival was 78.1 +/- 5.1 percent; the five-year local control rate was 94.2 +/- 5.1 percent. In the univariate and multivariate analysis of the disease-free survival, the pathohistologic lymph node status after radiochemotherapy (ypN) was the only significant prognostic parameter. Disease-free survival (36 months) for patients without lymph node metastases (ypN0) was excellent, independent of whether they had received postoperative chemotherapy (n = 43; 87.5 +/- 6.0 percent) or not (n = 29; 87.7 +/- 6.7 percent). Patients with ypN2 status have, despite chemotherapy, a poor disease-free survival at 30 +/- 17.6 percent after 36 months. CONCLUSIONS: These retrospective data suggest that, for some patients, postoperative chemotherapy can be spared. For patients with ypN2 status, an intensification of the postoperative chemotherapy should be considered. Further evaluation in prospective studies is urgently recommended.

Step edge sputtering yield at grazing incidence ion bombardment.

The surface morphology of Pt(111) was investigated by scanning tunneling microscopy after 5 keV Ar+ ion bombardment at grazing incidence in dependence of the ion fluence and in the temperature range between 625 and 720 K. The average erosion rate was found to be strongly dependent on the ion fluence and the substrate temperature during bombardment. This dependence is traced back to the variation of step concentration with temperature and fluence. We develop a simple model allowing us to determine separately the constant sputtering yields for terraces and for impact area stripes in front of ascending steps. The experimentally determined yield of these stripes--the step-edge sputtering yield--is in excellent agreement with our molecular dynamics simulations performed for the experimental situation.

Synthesis and reactivity of calix[4]arene-supported group 4 imido complexes.

New mononuclear titanium and zirconium imido complexes [M(NR)(R'(2)calix)] [M=Ti, R'=Me, R=tBu (1), R=2,6-C(6)H(3)Me(2) (2), R=2,6-C(6)H(3)iPr(2) (3), R=2,4,6-C(6)H(2)Me(3) (4); M=Ti, R'=Bz, R=tBu (5), R=2,6-C(6)H(3)Me(2) (6), R=2,6-C(6)H(3)iPr(2) (7); M=Zr, R'=Me, R=2,6-C(6)H(3)iPr(2) (8)] supported by 1,3-diorganyl ether p-tert-butylcalix[4]arenes (R'(2)calix) were prepared in good yield from the readily available complexes [MCl(2)(Me(2)calix)], [Ti(NR)Cl(2)(py)(3)], and [Ti(NR)Cl(2)(NHMe(2))(2)]. The crystallographically characterised complex [Ti(NtBu)(Me(2)calix)] (1) reacts readily with CO(2), CS(2), and p-tolyl-isocyanate to give the isolated complexes [Ti[N(tBu)C(O)O](Me(2)calix)] (10), [[Ti(mu-O)(Me(2)calix)](2)] (11), [[Ti(mu-S)(Me(2)calix)](2)] (12), and [Ti[N(tBu)C(O)N(-4-C(6)H(4)Me)](Me(2)calix)] (13). In the case of CO(2) and CS(2), the addition of the heterocumulene to the Ti-N multiple bond is followed by a cycloreversion reaction to give the dinuclear complexes 11 and 12. The X-ray structure of 13.4(C(7)H(8)) clearly establishes the N,N'-coordination mode of the ureate ligand in this compound. Complex 1 undergoes tert-butyl/arylamine exchange reactions to form 2, 3, [Ti(N-4-C(6)H(4)Me)(Me(2)calix)] (14), [Ti(N-4-C(6)H(4)Fc)(Me(2)calix)] (15) [Fc=Fe(eta(5)-C(5)H(5))(eta(5)-C(5)H(4))], and [[Ti(Me(2)calix)](2)[mu-(N-4-C(6)H(4))(2)CH(2)]] (16). Reaction of 1 with H(2)O, H(2)S and HCl afforded the compounds [[Ti(mu-O)(Me(2)calix)](2)] (11), [[Ti(mu-S)(Me(2)calix)](2)] (12), and [TiCl(2)(Me(2)calix)] in excellent yields. Furthermore, treatment of 1 with two equivalents of phenols results in the formation of [Ti(O-4-C(6)H(4)R)(2)(Me(2)calix)] (R=Me 17 or tBu 18), [Ti(O-2,6-C(6)H(3)Me(2))(2)(Me(2)calix)] (19) and [Ti(mbmp)(Me(2)calix)] (20; H(2)mbmp=2,2'-methylene-bis(4-methyl-6-tert-butylphenol) or CH(2)([CH(3)][C(4)H(9)]C(6)H(2)-OH)(2)). The bis(phenolate) compounds 17 and 18 with para-substituted phenolate ligands undergo elimination and/or rearrangement reactions in the nonpolar solvents pentane or hexane. The metal-containing products of the elimination reactions are dinuclear complexes [[Ti(O-4-C(6)H(4)R)(Mecalix)](2)] [R=Me (23) or tBu (24)] where Mecalix=monomethyl ether of p-tert-butylcalix[4]arene. The products of the rearrangement reaction are [Ti(O-4-C(6)H(4)Me)(2) (paco-Me(2)calix)] (25) and [Ti(O-4-C(6)H(4)tBu)(2)(paco-Me(2)calix)] (26), in which the metallated calix[4]arene ligand is coordinated in a form reminiscent of the partial cone (paco) conformation of calix[4]arene. In these compounds, one of the methoxy groups is located inside the cavity of the calix[4]arene ligand. The complexes 24, 25 and 26 have been crystallographically characterised. Complexes with sterically more demanding phenolate ligands, namely 19 and 20 and the analogous zirconium complexes [Zr(O-4-C(6)H(4)Me)(2)(Me(2)calix)] (21) and [Zr(O-2,6-C(6)H(3)Me(2))(2)(Me(2)calix)] (22) do not rearrange. Density functional calculations for the model complexes [M(OC(6)H(5))(2)(Me(2)calix)] with the calixarene possessing either cone or partial cone conformations are briefly presented.