Stick-slip unfolding favors self-association of expanded HTT mRNA.

In Huntington's Disease (HD) and related disorders, expansion of CAG trinucleotide repeats produces a toxic gain of function in affected neurons. Expanded huntingtin (expHTT) mRNA forms aggregates that sequester essential RNA binding proteins, dysregulating mRNA processing and translation. The physical basis of RNA aggregation has been difficult to disentangle owing to the heterogeneous structure of the CAG repeats. Here, we probe the folding and unfolding pathways of expHTT mRNA using single-molecule force spectroscopy. Whereas normal HTT mRNAs unfold reversibly and cooperatively, expHTT mRNAs with 20 or 40 CAG repeats slip and unravel non-cooperatively at low tension. Slippage of CAG base pairs is punctuated by concerted rearrangement of adjacent CCG trinucleotides, trapping partially folded structures that readily base pair with another RNA strand. We suggest that the conformational entropy of the CAG repeats, combined with stable CCG base pairs, creates a stick-slip behavior that explains the aggregation propensity of expHTT mRNA.

Navigating the complexities of multi-domain protein folding.

Proteome complexity has expanded tremendously over evolutionary time, enabling biological diversification. Much of this complexity is achieved by combining a limited set of structural units into long polypeptides. This widely used evolutionary strategy poses challenges for folding of the resulting multi-domain proteins. As a consequence, their folding differs from that of small single-domain proteins, which generally fold quickly and reversibly. Co-translational processes and chaperone interactions are important aspects of multi-domain protein folding. In this review, we discuss some of the recent experimental progress toward understanding these processes.

Time-resolving state-specific molecular dissociation with XUV broadband absorption spectroscopy.

The electronic and nuclear dynamics inside molecules are essential for chemical reactions, where different pathways typically unfold on ultrafast timescales. Extreme ultraviolet (XUV) light pulses generated by free-electron lasers (FELs) allow atomic-site and electronic-state selectivity, triggering specific molecular dynamics while providing femtosecond resolution. Yet, time-resolved experiments are either blind to neutral fragments or limited by the spectral bandwidth of FEL pulses. Here, we combine a broadband XUV probe pulse from high-order harmonic generation with an FEL pump pulse to observe dissociation pathways leading to fragments in different quantum states. We temporally resolve the dissociation of a specific O2+ state into two competing channels by measuring the resonances of ionic and neutral fragments. This scheme can be applied to investigate convoluted dynamics in larger molecules relevant to diverse science fields.

Discovery of a selective and biologically active low-molecular weight antagonist of human interleukin-1ß.

Human interleukin-1ß (hIL-1ß) is a pro-inflammatory cytokine involved in many diseases. While hIL-1ß directed antibodies have shown clinical benefit, an orally available low-molecular weight antagonist is still elusive, limiting the applications of hIL-1ß-directed therapies. Here we describe the discovery of a low-molecular weight hIL-1ß antagonist that blocks the interaction with the IL-1R1 receptor. Starting from a low affinity fragment-based screening hit 1, structure-based optimization resulted in a compound (S)-2 that binds and antagonizes hIL-1ß with single-digit micromolar activity in biophysical, biochemical, and cellular assays. X-ray analysis reveals an allosteric mode of action that involves a hitherto unknown binding site in hIL-1ß encompassing two loops involved in hIL-1R1/hIL-1ß interactions. We show that residues of this binding site are part of a conformationally excited state of the mature cytokine. The compound antagonizes hIL-1ß function in cells, including primary human fibroblasts, demonstrating the relevance of this discovery for future development of hIL-1ß directed therapeutics.

Monitoring Distracted Driving Behaviours with Smartphones: An Extended Systematic Literature Review.

Driver behaviour monitoring is a broad area of research, with a variety of methods and approaches. Distraction from the use of electronic devices, such as smartphones for texting or talking on the phone, is one of the leading causes of vehicle accidents. With the increasing number of sensors available in vehicles, there is an abundance of data available to monitor driver behaviour, but it has only been available to vehicle manufacturers and, to a limited extent, through proprietary solutions. Recently, research and practice have shifted the paradigm to the use of smartphones for driver monitoring and have fuelled efforts to support driving safety. This systematic review paper extends a preliminary, previously carried out author-centric literature review on smartphone-based driver monitoring approaches using snowballing search methods to illustrate the opportunities in using smartphones for driver distraction detection. Specifically, the paper reviews smartphone-based approaches to distracted driving behaviour detection, the smartphone sensors and detection methods applied, and the results obtained.

AP profiling resolves co-translational folding pathway and chaperone interactions in vivo.

Natural proteins have evolved to fold robustly along specific pathways. Folding begins during synthesis, guided by interactions of the nascent protein with the ribosome and molecular chaperones. However, the timing and progression of co-translational folding remain largely elusive, in part because the process is difficult to measure in the natural environment of the cytosol. We developed a high-throughput method to quantify co-translational folding in live cells that we term Arrest Peptide profiling (AP profiling). We employed AP profiling to delineate co-translational folding for a set of GTPase domains with very similar structures, defining how topology shapes folding pathways. Genetic ablation of major nascent chain-binding chaperones resulted in localized folding changes that suggest how functional redundancies among chaperones are achieved by distinct interactions with the nascent protein. Collectively, our studies provide a window into cellular folding pathways of complex proteins and pave the way for systematic studies on nascent protein folding at unprecedented resolution and throughput.

3D-2D Distance Maps Conversion Enhances Classification of Craniosynostosis.

OBJECTIVE: Diagnosis of craniosynostosis using photogrammetric 3D surface scans is a promising radiation-free alternative to traditional computed tomography. We propose a 3D surface scan to 2D distance map conversion enabling the usage of the first convolutional neural networks (CNNs)-based classification of craniosynostosis. Benefits of using 2D images include preserving patient anonymity, enabling data augmentation during training, and a strong under-sampling of the 3D surface with good classification performance. METHODS: The proposed distance maps sample 2D images from 3D surface scans using a coordinate transformation, ray casting, and distance extraction. We introduce a CNN-based classification pipeline and compare our classifier to alternative approaches on a dataset of 496 patients. We investigate into low-resolution sampling, data augmentation, and attribution mapping. RESULTS: Resnet18 outperformed alternative classifiers on our dataset with an F1-score of 0.964 and an accuracy of 98.4%. Data augmentation on 2D distance maps increased performance for all classifiers. Under-sampling allowed 256-fold computation reduction during ray casting while retaining an F1-score of 0.92. Attribution maps showed high amplitudes on the frontal head. CONCLUSION: We demonstrated a versatile mapping approach to extract a 2D distance map from the 3D head geometry increasing classification performance, enabling data augmentation during training on 2D distance maps, and the usage of CNNs. We found that low-resolution images were sufficient for a good classification performance. SIGNIFICANCE: Photogrammetric surface scans are a suitable craniosynostosis diagnosis tool for clinical practice. Domain transfer to computed tomography seems likely and can further contribute to reducing ionizing radiation exposure for infants.

Studying root-environment interactions in structured microdevices.

When interacting with the environment, plant roots integrate sensory information over space and time in order to respond appropriately under non-uniform conditions. The complexity and dynamic properties of soil across spatial and temporal scales pose a significant technical challenge for research into the mechanisms that drive metabolism, growth, and development in roots, as well as on inter-organismal networks in the rhizosphere. Synthetic environments, combining microscopic access and manipulation capabilities with soil-like heterogeneity, are needed to elucidate the intriguing antagonism that characterizes subsurface ecosystems. Microdevices have provided opportunities for innovative approaches to observe, analyse, and manipulate plant roots and advanced our understanding of their development, physiology, and interactions with the environment. Initially conceived as perfusion platforms for root cultivation under hydroponic conditions, microdevice design has, in recent years, increasingly shifted to better reflect the complex growth conditions in soil. Heterogeneous micro-environments have been created through co-cultivation with microbes, laminar flow-based local stimulation, and physical obstacles and constraints. As such, structured microdevices provide an experimental entry point into the complex network behaviour of soil communities.

Efficacy of Oral Rabies Vaccine Baits Containing SPBN GASGAS in Domestic Dogs According to International Standards.

(1) Background: The oral vaccination of free-roaming dogs against rabies has been developed as a promising complementary tool for mass dog vaccination. However, no oral rabies vaccine has provided efficacy data in dogs according to international standards. (2) Methods: To test the immunogenicity and efficacy of the third-generation oral rabies virus vaccine strain, SPBN GASGAS, in domestic dogs, dogs were offered an egg-flavoured bait containing 3.0 mL of the vaccine (107.5 FFU/mL) or a placebo egg-flavoured bait. Subsequently, these 25 vaccinated and 10 control animals were challenged approximately 6 months later with a dog rabies virus isolate. Blood samples were collected at different time points postvaccination and examined by ELISA and RFFIT. (3) Results: All but 1 of the 25 vaccinated dogs survived the challenge infection; meanwhile, all 10 control dogs succumbed to rabies. The serology results showed that all 25 vaccinated dogs seroconverted in ELISA (>40% PB); meanwhile, only 13 of the 25 vaccinated dogs tested seropositive ≥ 0.5 IU/mL) in RFFIT. (4) Conclusions: The SPBN GASGAS rabies virus vaccine meets the efficacy requirements for live oral rabies vaccines as laid down by the European Pharmacopoeia and the WOAH Terrestrial Manual. SPBN GASGAS already fulfilled the safety requirements for oral rabies vaccines targeted at dogs. Hence, the egg-flavoured bait containing SPBN GASGAS is the first oral vaccine bait that complies with WOAH recommendations for the intended use of oral vaccination of free-roaming dogs against rabies.

[A naturalistic study on the effects of antidepressants (e. g. SSRI) and acetyl salicylic acid (ASA) on the self-rated perception of the psychotherapeutic process of inpatient psychosomatic treatment and its results: Could ASA be beneficial?] / Eine naturalistische Untersuchung zur Auswirkung häufiger antidepressiver Medikationen (wie SSRI) und der Acetylsalicylsäure (ASS) auf die Selbstbeurteilungen der Wahrnehmung und des Ergebnisses stationärer Psychotherapie: Könnte ASS förderlich sein?

Objectives: Psychic perceptions are at the core of psychotherapeutic processes and modifiable by certain psychopharmacologic agents including antidepressants and cyclooxygenase (COX) inhibitors like acetylsalicylic acid (ASA). Methods: We analyzed the medical records of 208 participants, and used the weekly mean dosages and the number of weeks in therapy to predict ward experience (Stationserfahrungsbogen) and symptom burden (symptom-check list 90-R) by means of linear regression analyses and four repeated measures. Results: Time predicted symptom relief. ASA signified a more favorable ward experience and a trend towards less suffering. Antidepressants did not predict symptom burden or ward experience, except for amitriptyline's inverse relationship with process perception. Discussion: Regarding process perception and therapy outcome, amitriptyline might have unfavorable effects at dose reductions, whereas COX-inhibition could be beneficial at higher dosages. Similar findings have already been described with regard to COX-inhibition in depression and schizophrenia.

Oral Rabies Vaccine Strain SPBN GASGAS: Genetic Stability after Serial In Vitro and In Vivo Passaging.

Oral vaccination of wildlife has shown to be a very effective management tool in rabies control. Evaluation of the genetic stability of vaccine viruses before distributing vaccine baits in the environment is essential because all available oral rabies vaccines, including the genetically engineered rabies virus vaccine strain SPBN GASGAS (Rabitec), are based on replication-competent viruses. To evaluate the genetic stability of this vaccine strain, five serial passages of the Master Seed Virus (MSV) in the production cell line BHK21 Cl13 were performed. Furthermore, to test possible reversion to virulence, a back-passage study in suckling mouse brain (SMB) was performed. Subsequently, the pooled 5th SMB passage was inoculated intracerebrally (i.c.) in adult and suckling mice. The full genome sequences of the isolated 5th passage, in vivo and in vitro, were compared at both the consensus and the quasispecies level with the MSV. Additionally, the full genome sequence of the 6th SMB passage from the individual animals was determined and compared. Full-length integration of the double glycoprotein and modified base substitutions at amino acid position 194 and 333 of the glycoprotein could be verified in all 5th and 6th passage samples. Overall, 11 single nucleotide polymorphisms (SNPs) were detected in the 5th pooled SMB passage, 4 with frequency between 10 and 20%, and 7 with between 2.5 and 10%. SNPs that resulted in amino acid exchange were found in genes: N (one SNP), G (four SNPs), and L (three SNPs). However, none of these SNPs were associated with reversion to virulence since all adult mice inoculated i.c. with this material survived. In the individual samples of the 6th SMB passage 24 additional SNPs (>2.5%) were found, of which only 1 SNP (L-gene, position 6969) had a prevalence of >50% in 3 of 17 samples. The obtained results confirmed the stable expression of genetic modifications and the genetic stability of the consensus strain after serial in vivo and in vitro passaging.

Evidence for the recruitment of florivorous plant bugs as pollinators.

Angiosperm flowers and their animal visitors have co-evolved for at least 140 Ma, and early flowers were likely used mainly as mating and feeding sites by several groups of insects, including beetles, flies, true bugs, and thrips. Earlier studies suggested that shifts from such neutral or antagonistic relationships toward mutualistic pollination interactions between flowers and insects occurred repeatedly during angiosperm evolution. However, the evolutionary mechanisms and adaptations, which accompanied shifts toward effective pollination, are barely understood, and evidence for such scenarios has been lacking. Here, we show that Syngonium hastiferum (Araceae), a Neotropical representative of an otherwise beetle-pollinated clade, is pollinated by plant bugs (Miridae; Heteroptera), which are florivores of Syngonium schottianum and other Araceae species. We found that S. hastiferum differs in several floral traits from its beetle-pollinated relatives. Scent emission and thermogenesis occur in the morning instead of the evening hours, and its pollen surface is spiny instead of smooth. Furthermore, the floral scent of S. hastiferum includes a previously unknown natural product, (Z)-3-isopropylpent-3-en-1-ol, which we show to have a function in specifically attracting the plant bug pollinators. This is the first known case of a specialized plant bug pollination system and provides clear evidence for the hypothesis that the adoption of antagonistic florivores as pollinators can drive flower diversification. VIDEO ABSTRACT.

CNN-Based Classification of Craniosynostosis Using 2D Distance Maps.

Craniosynostosis is a condition associated with the premature fusion of skull sutures affecting infants. 3D photogrammetric scans are a promising alternative to computed tomography scans in cases of single suture or nonsyndromic synostosis for diagnostic imaging, but oftentimes diagnosis is not automated and relies on additional cephalometric measure-ments and the experience of the surgeon. We propose an alternative representation of the infant's head shape created from 3D photogrammetric surface scans as 2D distance maps. Those 2D distance maps rely on ray casting to extract distances from a center point to the head surface, arranging them into a 2D image grid. We use the distance map for an original convolutional neural network (CNN)-based classification approach, which is evaluated on a publicly available synthetic dataset for benchmarking and also tested on clinical data. Qualitative differences of different head shapes can be ob-served in the distance maps. The CNN-based classifier achieves accuracies of 100 % on the publicly available synthetic dataset and 98.86 % on the clinical test set. Our distance map approach demonstrates the diagnostic value of 3D photogrammetry and the possibility of automatic, CNN-based diagnosis. Future steps include the improvement of the mapping method and testing the CNN on more pathologies.

Tethering Complex Proteins and Protein Complexes for Optical Tweezers Experiments.

Tethering proteins to force probes, typically micrometer-sized beads, is a prerequisite for dissecting their properties with optical tweezers. DNA handles serve as spacers between the tethered protein of interest and the bead surface. Attachment sites of the DNA handles to both the surface of beads and to the protein of interest must be mechanically stable for optical tweezers experiments. The most prominent method for attaching DNA handles to proteins utilizes thiol chemistry, linking modified DNA to engineered cysteines in the target protein. This method, although experimentally straightforward, is impractical for the large number of proteins that endogenously contain multiple or essential cysteines at undesired positions. Here, we describe two alternative approaches that take advantage of genetically encoded tag sequences in the target protein. The first method uses the enzymes Sfp and BirA, and the second uses the more recently described SpyTag-SpyCatcher system. We outline the process of generating the DNA handles themselves, as well as how to make the DNA-protein chimeras for carrying out optical tweezers experiments. These methods have robustly worked for several diverse and complex proteins, including ones that are difficult to produce or purify, and for protein-containing complexes such as the ribosome. They will be useful in cases where chemistry-based approaches are impractical or not feasible.

Co-Translational Folding of Multi-Domain Proteins.

The majority of proteins in nature are composed of multiple domains connected in a single polypeptide. How these long sequences fold into functional structures without forming toxic misfolds or aggregates is poorly understood. Their folding is inextricably linked to protein synthesis and interactions with cellular machinery, making mechanistic studies challenging. Recent progress has revealed critical features of multi-domain protein folding in isolation and in the context of translation by the ribosome. In this review, we discuss challenges and progress in understanding multi-domain protein folding, and highlight how molecular interactions shape folding and misfolding pathways. With the development of new approaches and model systems, the stage is now set for mechanistically exploring the folding of large multi-domain proteins.

Next generation single-molecule techniques: Imaging, labeling, and manipulation in vitro and in cellulo.

Owing to their unique abilities to manipulate, label, and image individual molecules in vitro and in cellulo, single-molecule techniques provide previously unattainable access to elementary biological processes. In imaging, single-molecule fluorescence resonance energy transfer (smFRET) and protein-induced fluorescence enhancement in vitro can report on conformational changes and molecular interactions, single-molecule pull-down (SiMPull) can capture and analyze the composition and function of native protein complexes, and single-molecule tracking (SMT) in live cells reveals cellular structures and dynamics. In labeling, the abilities to specifically label genomic loci, mRNA, and nascent polypeptides in cells have uncovered chromosome organization and dynamics, transcription and translation dynamics, and gene expression regulation. In manipulation, optical tweezers, integration of single-molecule fluorescence with force measurements, and single-molecule force probes in live cells have transformed our mechanistic understanding of diverse biological processes, ranging from protein folding, nucleic acids-protein interactions to cell surface receptor function.

Synchronized Real-time Measurement of Sec-mediated Protein Translocation.

The Sec translocon, consisting of a heterotrimeric transmembrane channel (SecYEG) and an associated ATPase (SecA), catalyzes the export of unfolded proteins from the cytosol in bacteria. Kinetically resolving protein translocation at high resolution yields mechanistic insight into the process. Translocation is typically followed by measuring the protection of proteins transported into lipid vesicles, which only allows visualization of translocation after it has already been completed and limits time resolution. Here, we describe the implementation of an assay for measuring translocation in real-time. By priming the reconstituted translocon with suitably engineered substrate proteins, the kinetics of the actual translocation process can be resolved at high resolution. To analyze translocation kinetics, we developed a detailed kinetic model of the process that includes on-pathway and off-pathway processes. Together, this experimental protocol and model permit detailed mechanistic analyses of Sec-dependent protein translocation. Graphic abstract: Synchronized real-time measurements, combined with a detailed kinetic model, enable a mechanistic analysis of protein transport.

Smart Scar Care-Industry 4.0 in Individualized Compression Garments: A Randomized Controlled Crossover Feasibility Study.

BACKGROUND: We tested the workflow and comparability of compression garments (CG) automatically knitted from 3D-body-scan data (3DBSD) versus manually measured data for scar treatment. Industry 4.0 has found its way into surgery, enhancing the trend toward personalized medicine, which plays an increasingly important role in CG scar therapy. Therefore, we conducted a study to evaluate the workflow from 3DBSD to fast and precisely knitted CG and compared it with standard of care. METHODS: A randomized controlled crossover feasibility study was conducted as part of the individual medical technology research project "Smart Scar Care." Objective and patient-reported outcome measures were documented for 10 patients with hypertrophic burn scars at baseline and after wearing CG automatically knitted from 3DBSD versus CG from manually measured data for one month. RESULTS: The "scan-to-knit" workflow and the study design were feasible in 10 of 10 patients. No adverse effects were found. 3DBSD showed a bias of half a centimeter compared with manually measured data and wider limits of agreement. With respect to fit, comfort, suitability, Vancouver Scar Scale, Patient and Observer Scar Assessment Scale, stiffness and microcirculation, this was a promising pilot study. Stiffness and blood flow were increased in scars compared with normal skin. The highest rank correlations were found between pain and itch, stiffness and Patient and Observer Scar Assessment Scale, Vancouver Scar Scale, and pain. CONCLUSIONS: These results indicate that automatically knitted CG using 3DBSD could become an alternative to the standard of care, especially with regard to economical and faster patient care. The produced scan data opens the door for objective scar science.

Facile tethering of stable and unstable proteins for optical tweezers experiments.

Single-molecule force spectroscopy with optical tweezers has emerged as a powerful tool for dissecting protein folding. The requirement to stably attach "molecular handles" to specific points in the protein of interest by preparative biochemical techniques is a limiting factor in applying this methodology, especially for large or unstable proteins that are difficult to produce and isolate. Here, we present a streamlined approach for creating stable and specific attachments using autocatalytic covalent tethering. The high specificity of coupling allowed us to tether ribosome-nascent chain complexes, demonstrating its suitability for investigating complex macromolecular assemblies. We combined this approach with cell-free protein synthesis, providing a facile means of preparing samples for single-molecule force spectroscopy. The workflow eliminates the need for biochemical protein purification during sample preparation for single-molecule measurements, making structurally unstable proteins amenable to investigation by this powerful single-molecule technique. We demonstrate the capabilities of this approach by carrying out pulling experiments with an unstructured domain of elongation factor G that had previously been refractory to analysis. Our approach expands the pool of proteins amenable to folding studies, which should help to reduce existing biases in the currently available set of protein folding models.

Co-translational folding of nascent polypeptides: Multi-layered mechanisms for the efficient biogenesis of functional proteins.

The coupling of protein synthesis and folding is a crucial yet poorly understood aspect of cellular protein folding. Over the past few years, it has become possible to experimentally follow and define protein folding on the ribosome, revealing principles that shape co-translational folding and distinguish it from refolding in solution. Here, we highlight some of these recent findings from biochemical and biophysical studies and their potential significance for cellular protein biogenesis. In particular, we focus on nascent chain interactions with the ribosome, interactions within the nascent protein, modulation of translation elongation rates, and the role of mechanical force that accompanies nascent protein folding. The ability to obtain mechanistic insight in molecular detail has set the stage for exploring the intricate process of nascent protein folding. We believe that the aspects discussed here will be generally important for understanding how protein synthesis and folding are coupled and regulated.