RNA granules in flux: dynamics to balance physiology and pathology.

The life cycle of an mRNA is a complex process that is tightly regulated by interactions between the mRNA and RNA-binding proteins, forming molecular machines known as RNA granules. Various types of these membrane-less organelles form inside cells, including neurons, and contribute critically to various physiological processes. RNA granules are constantly in flux, change dynamically and adapt to their local environment, depending on their intracellular localization. The discovery that RNA condensates can form by liquid-liquid phase separation expanded our understanding of how compartments may be generated in the cell. Since then, a plethora of new functions have been proposed for distinct condensates in cells that await their validation in vivo. The finding that dysregulation of RNA granules (for example, stress granules) is likely to affect neurodevelopmental and neurodegenerative diseases further boosted interest in this topic. RNA granules have various physiological functions in neurons and in the brain that we would like to focus on. We outline examples of state-of-the-art experiments including timelapse microscopy in neurons to unravel the precise functions of various types of RNA granule. Finally, we distinguish physiologically occurring RNA condensation from aberrant aggregation, induced by artificial RNA overexpression, and present visual examples to discriminate both forms in neurons.

HEATR5B associates with dynein-dynactin and promotes motility of AP1-bound endosomal membranes.

The microtubule motor dynein mediates polarised trafficking of a wide variety of organelles, vesicles and macromolecules. These functions are dependent on the dynactin complex, which helps recruit cargoes to dynein's tail and activates motor movement. How the dynein-dynactin complex orchestrates trafficking of diverse cargoes is unclear. Here, we identify HEATR5B, an interactor of the adaptor protein-1 (AP1) clathrin adaptor complex, as a novel player in dynein-dynactin function. HEATR5B was recovered in a biochemical screen for proteins whose association with the dynein tail is augmented by dynactin. We show that HEATR5B binds directly to the dynein tail and dynactin and stimulates motility of AP1-associated endosomal membranes in human cells. We also demonstrate that the Drosophila HEATR5B homologue is an essential gene that selectively promotes dynein-based transport of AP1-bound membranes to the Golgi apparatus. As HEATR5B lacks the coiled-coil architecture typical of dynein adaptors, our data point to a non-canonical process orchestrating motor function on a specific cargo. We additionally show that HEATR5B promotes association of AP1 with endosomal membranes independently of dynein. Thus, HEATR5B co-ordinates multiple events in AP1-based trafficking.

The dsRBP Staufen2 governs RNP assembly of neuronal Argonaute proteins.

Mature microRNAs are bound by a member of the Argonaute (Ago1-4) protein family, forming the core of the RNA-induced silencing complex (RISC). Association of RISC with target mRNAs results in ribonucleoprotein (RNP) assembly involved in translational silencing or RNA degradation. Yet, the dynamics of RNP assembly and its underlying functional implications are unknown. Here, we have characterized the role of the RNA-binding protein Staufen2, a candidate Ago interactor, in RNP assembly. Staufen2 depletion resulted in the upregulation of Ago1/2 and the RISC effector proteins Ddx6 and Dcp1a. This upregulation was accompanied by the displacement of Ago1/2 from processing bodies, large RNPs implicated in RNA storage, and subsequent association of Ago2 with polysomes. In parallel, Staufen2 deficiency decreased global translation and increased dendritic branching. As the observed phenotypes can be rescued by Ago1/2 knockdown, we propose a working model in which both Staufen2 and Ago proteins depend on each other and contribute to neuronal homeostasis.

The meV XUV-RIXS facility at UE112-PGM1 of BESSY II.

Resonant inelastic X-ray scattering in the XUV-regime has been implemented at BESSY II, pushing for a few-meV bandwidth in inelastic X-ray scattering at transition metal M-edges, rare earth N-edges and the K-edges of light elements up to carbon with full polarization control. The new dedicated low-energy beamline UE112-PGM1 has been designed to provide 1 µm vertical and 20 µm horizontal beam dimensions that serve together with sub-micrometre solid-state sample positioning as the source point for a high-resolution plane grating spectrometer and a high-transmission Rowland spectrometer for rapid overview spectra. The design and commissioning results of the beamline and high-resolution spectrometer are presented. Helium autoionization spectra demonstrate a resolving power of the beamline better than 10 000 at 64 eV with a 300 lines mm-1 grating while the measured resolving power of the spectrometer in the relevant energy range is 3000 to 6000.

RGS4 RNA Secondary Structure Mediates Staufen2 RNP Assembly in Neurons.

RNA-binding proteins (RBPs) act as posttranscriptional regulators controlling the fate of target mRNAs. Unraveling how RNAs are recognized by RBPs and in turn are assembled into neuronal RNA granules is therefore key to understanding the underlying mechanism. While RNA sequence elements have been extensively characterized, the functional impact of RNA secondary structures is only recently being explored. Here, we show that Staufen2 binds complex, long-ranged RNA hairpins in the 3'-untranslated region (UTR) of its targets. These structures are involved in the assembly of Staufen2 into RNA granules. Furthermore, we provide direct evidence that a defined Rgs4 RNA duplex regulates Staufen2-dependent RNA localization to distal dendrites. Importantly, disrupting the RNA hairpin impairs the observed effects. Finally, we show that these secondary structures differently affect protein expression in neurons. In conclusion, our data reveal the importance of RNA secondary structure in regulating RNA granule assembly, localization and eventually translation. It is therefore tempting to speculate that secondary structures represent an important code for cells to control the intracellular fate of their mRNAs.

High frequency of benzimidazole resistance alleles in trichostrongyloids from Austrian sheep flocks in an alpine transhumance management system.

BACKGROUND: Infections of small ruminants with trichostrongyloid nematodes often result in reduced productivity and may be detrimental to the host. Anthelmintic resistance (AR) against most anthelmintic drug classes is now widespread amongst the trichostrongyloids. Baseline establishment, followed by regular monitoring of the level of AR, is necessary for farmers and veterinarians to make informed decisions about parasite management. The detection of single nucleotide polymorphisms (SNPs) is a sensitive method to detect AR against benzimidazoles (BZs), one of the most widely used anthelmintic classes. Alpine transhumance constitutes a special type of pasturing of sheep from many different farms, the aim of this study was to investigate the prevalence of benzimidazole resistance alleles in this particular management system. RESULTS: Sixteen sheep flocks in Styria and Salzburg in Austria were examined by pyrosequencing for SNPs at codons 167, 198 and 200 of the isotype-1 ß-tubulin gene. The frequency of the resistance-associated exchange F200Y was 87-100% for H. contortus, 77-100% for T. colubriformis and <  5-66% for T. circumcincta. Additionally, the F167Y polymorphism was detected in T. colubriformis from two farms at a frequency of 19 and 23% respectively. CONCLUSIONS: The high resistance allele frequency in H. contortus and T. colubriformis in the examined sheep population urgently calls for the development of new treatment strategies to sustainably control trichostrongyloid infections for this kind of pasturing, since the frequent mixing of flocks during the alpine summer grazing must be considered an important risk factor for the spread of resistant nematodes to a large number of farms.

Visualizing RNA granule transport and translation in living neurons.

In polarized cells, such as neurons, the synthesis of an mRNA does not ensure its proper cellular expression. Most mature transcripts require the association with RNA-binding proteins, resulting in the formation of RNA granules, which are then transported within the cytoplasm along the cytoskeleton and delivered to their proper subcellular locations, where they can be locally translated. Here we review current microscopy methods that have been developed to visualize RNA granule formation, transport and translation at the single cell level with a special emphasis on the MS2 and SunTag systems. They include the labeling of mRNAs and RNA-binding proteins in living cells or even the detection of newly synthesized proteins in situ.

Towards production of novel catalyst powders from supported size-selected clusters by multilayer deposition and dicing.

A multilayer deposition method has been developed with the potential to capture and process atomic clusters generated by a high flux cluster beam source. In this deposition mode a series of sandwich structures each consisting of three layers-a carbon support layer, cluster layer and polymer release layer-is sequentially deposited to form a stack of isolated cluster layers, as confirmed by through-focal aberration-corrected HAADF STEM analysis. The stack can then be diced into small pieces by a mechanical saw. The diced pieces are immersed in solvent to dissolve the polymer release layer and form small platelets of supported clusters.

A proximal retarding field analyzer for scanning probe energy loss spectroscopy.

A compact proximal retarding field analyzer for scanning probe energy loss spectroscopy measurements is described. Using the scanning tunneling microscope (STM) tip as a field emission (FE) electron source in conjunction with this analyzer, which is placed at a glancing angle to the surface plane, FE sample current and electron reflectivity imaging may be performed simultaneously. This is demonstrated in measurements of Ag nanostructures prepared on graphite by electron-beam lithography, where a material contrast of 13% is observed, with a lateral resolution of 25 nm, between the silver and graphite in electron reflectivity images. Topological contrast mechanisms such as edge enhancement and shadowing are also observed, giving rise to additional features in the electron reflectivity images. The same instrument configuration has been used to measure electron energy loss spectra on bare graphite, where the zero loss peak, π band plasmon loss peak and secondary electron peaks are observed. Using this simple and compact analyzer an STM, with sufficient open access to the tip-sample junction, may easily be augmented to provide simultaneous elemental and topographic mapping, supplementing STM image measurements with FE sample current and electron reflectivity images, as well as electron energy loss spectroscopy measurements, in the same instrument.

Associations between fasciolosis and milk production, and the impact of anthelmintic treatment in dairy herds.

Liver fluke is a ubiquitous parasite that causes extensive production losses in cattle and is a zoonosis. The aims of this study were to determine the prevalence of fasciolosis in 178 dairy cattle herds in Styria (federal state of Austria) and its influence on production, to detect the risk factors for infection, and to explore effective strategies in management and control. A questionnaire on farm management, prophylaxis, and therapy was developed and applied. Furthermore, production parameters (milk yield, milk protein content, butter fat content, non-return rate 90, calving to conception interval, service period) were recorded for 2014 and 2015, and a commercial ELISA for detection of Fasciola hepatica antibodies was applied in bulk tank milk in March 2014 and March 2015. Analysis of bulk tank milk samples showed a prevalence of 61.3% in 2014 and 45.5% in 2015. No associations could be found between F. hepatica exposure and farm structure or pasture management. Farms with highly positive (optical density ratio (ODR) ≥ 0.6 and lying above the upper interquartile range) antibody levels had a significantly lower annual milk yield of 438 kg per cow per year (p = 0.045), butterfat content of 0.091% (p = 0.004), and milk protein content of 0.046% (p = 0.024). However, fertility parameters were not significantly associated with liver fluke exposure. Anthelmintic treatment led to significantly lower antibody levels in the subsequent year (p = 0.042) and had a significant influence on protein content in milk (p = 0.003). This study highlighted the importance of fasciolosis in Austria and its influence on milk production and the need for veterinary advice regarding prophylactic measures to reduce economic losses.

Synaptically-targeted long non-coding RNA SLAMR promotes structural plasticity by increasing translation and CaMKII activity.

Long noncoding RNAs (lncRNAs) play crucial roles in maintaining cell homeostasis and function. However, it remains largely unknown whether and how neuronal activity impacts the transcriptional regulation of lncRNAs, or if this leads to synapse-related changes and contributes to the formation of long-term memories. Here, we report the identification of a lncRNA, SLAMR, which becomes enriched in CA1-hippocampal neurons upon contextual fear conditioning but not in CA3 neurons. SLAMR is transported along dendrites via the molecular motor KIF5C and is recruited to the synapse upon stimulation. Loss of function of SLAMR reduces dendritic complexity and impairs activity-dependent changes in spine structural plasticity and translation. Gain of function of SLAMR, in contrast, enhances dendritic complexity, spine density, and translation. Analyses of the SLAMR interactome reveal its association with CaMKIIα protein through a 220-nucleotide element also involved in SLAMR transport. A CaMKII reporter reveals a basal reduction in CaMKII activity with SLAMR loss-of-function. Furthermore, the selective loss of SLAMR function in CA1 disrupts the consolidation of fear memory in male mice, without affecting their acquisition, recall, or extinction, or spatial memory. Together, these results provide new molecular and functional insight into activity-dependent changes at the synapse and consolidation of contextual fear.

RNA granules in neuronal plasticity and disease.

RNA granules are dynamic entities controlling the spatiotemporal distribution and translation of RNA molecules. In neurons, a variety of RNA granules exist both in the soma and in cellular processes. They contain transcripts encoding signaling and synaptic proteins as well as RNA-binding proteins causally linked to several neurological disorders. In this review, we highlight that neuronal RNA granules exhibit properties of biomolecular condensates that are regulated upon maturation and physiological aging and how they are reversibly remodeled in response to neuronal activity to control local protein synthesis and ultimately synaptic plasticity. Moreover, we propose a framework of how neuronal RNA granules mature over time in healthy conditions and how they transition into pathological inclusions in the context of late-onset neurodegenerative diseases.

SLAMR, a synaptically targeted lncRNA, facilitates the consolidation of contextual fear memory.

LncRNAs are involved in critical processes for cell homeostasis and function. However, it remains largely unknown whether and how the transcriptional regulation of long noncoding RNAs results in activity-dependent changes at the synapse and facilitate formation of long-term memories. Here, we report the identification of a novel lncRNA, SLAMR, that becomes enriched in CA1- but not in CA3-hippocampal neurons upon contextual fear conditioning. SLAMR is transported to dendrites via the molecular motor KIF5C and recruited to the synapse in response to stimulation. Loss of function of SLAMR reduced dendritic complexity and impaired activity dependent changes in spine structural plasticity. Interestingly, gain of function of SLAMR enhanced dendritic complexity, and spine density through enhanced translation. Analyses of the SLAMR interactome revealed its association with CaMKIIα protein through a 220-nucleotide element and its modulation of CaMKIIα activity. Furthermore, loss-of-function of SLAMR in CA1 selectively impairs consolidation but neither acquisition, recall, nor extinction of fear memory and spatial memory. Together, these results establish a new mechanism for activity dependent changes at the synapse and consolidation of contextual fear.

RNA supply drives physiological granule assembly in neurons.

Membraneless cytoplasmic condensates of mRNAs and proteins, known as RNA granules, play pivotal roles in the regulation of mRNA fate. Their maintenance fine-tunes time and location of protein expression, affecting many cellular processes, which require complex protein distribution. Here, we report that RNA granules-monitored by DEAD-Box helicase 6 (DDX6)-disassemble during neuronal maturation both in cell culture and in vivo. This process requires neuronal function, as synaptic inhibition results in reversible granule assembly. Importantly, granule assembly is dependent on the RNA-binding protein Staufen2, known for its role in RNA localization. Altering the levels of free cytoplasmic mRNA reveals that RNA availability facilitates DDX6 granule formation. Specifically depleting RNA from DDX6 granules confirms RNA as an important driver of granule formation. Moreover, RNA is required for DDX6 granule assembly upon synaptic inhibition. Together, this data demonstrates how RNA supply favors RNA granule assembly, which not only impacts subcellular RNA localization but also translation-dependent synaptic plasticity, learning, and memory.

Thresholding of the Elliott-Yafet spin-flip scattering in multi-sublattice magnets by the respective exchange energies.

How different microscopic mechanisms of ultrafast spin dynamics coexist and interplay is not only relevant for the development of spintronics but also for the thorough description of physical systems out-of-equilibrium. In pure crystalline ferromagnets, one of the main microscopic mechanism of spin relaxation is the electron-phonon (el-ph) driven spin-flip, or Elliott-Yafet, scattering. Unexpectedly, recent experiments with ferro- and ferrimagnetic alloys have shown different dynamics for the different sublattices. These distinct sublattice dynamics are contradictory to the Elliott-Yafet scenario. In order to rationalize this discrepancy, it has been proposed that the intra- and intersublattice exchange interaction energies must be considered in the microscopic demagnetization mechanism, too. Here, using a temperature-dependent x-ray emission spectroscopy (XES) method, we address experimentally the element specific el-ph angular momentum transfer rates, responsible for the spin-flips in the respective (sub)lattices of Fe[Formula: see text]Ni[Formula: see text], Fe[Formula: see text]Ni[Formula: see text] and pure nickel single crystals. We establish how the deduced rate evolution with the temperature is linked to the exchange coupling constants reported for different alloy stoichiometries and how sublattice exchange energies threshold the related el-ph spin-flip channels. Thus, these results evidence that the Elliott-Yafet spin-flip scattering, thresholded by sublattice exchange energies, is the relevant microscopic process to describe sublattice dynamics in alloys and elemental magnetic systems.

Pumilio2 and Staufen2 selectively balance the synaptic proteome.

Neurons have the capacity to adapt to environmental stimuli, a phenomenon termed cellular plasticity. The underlying processes are controlled by a network of RNA-binding proteins (RBPs). Their precise impact, however, is largely unknown. To address this important question, we chose Pumilio2 (Pum2) and Staufen2 (Stau2), which both regulate synaptic transmission. Surprisingly, even though both RBPs dynamically interact with each other in neurons, their respective impact on the transcriptome and proteome is highly selective. Although Pum2 deficiency leads to reduced translation and protein expression, Stau2 depletion preferentially impacts RNA levels and increases protein abundance. Furthermore, we show that Pum2 activates expression of key GABAergic synaptic components, e.g., the GABAA receptor scaffold protein Gephyrin. Consequently, Pum2 depletion selectively reduced the amplitude of miniature inhibitory postsynaptic currents. Together, our data argue for an important role of RBPs to maintain proteostasis in order to control distinct aspects of synaptic transmission.

Abnormal thyroid hormone metabolism in mice lacking the monocarboxylate transporter 8.

In humans, inactivating mutations in the gene of the thyroid hormone transporter monocarboxylate transporter 8 (MCT8; SLC16A2) lead to severe forms of psychomotor retardation combined with imbalanced thyroid hormone serum levels. The MCT8-null mice described here, however, developed without overt deficits but also exhibited distorted 3,5,3'-triiodothyronine (T3) and thyroxine (T4) serum levels, resulting in increased hepatic activity of type 1 deiodinase (D1). In the mutants' brains, entry of T4 was not affected, but uptake of T3 was diminished. Moreover, the T4 and T3 content in the brain of MCT8-null mice was decreased, the activity of D2 was increased, and D3 activity was decreased, indicating the hypothyroid state of this tissue. In the CNS, analysis of T3 target genes revealed that in the mutants, the neuronal T3 uptake was impaired in an area-specific manner, with strongly elevated thyrotropin-releasing hormone transcript levels in the hypothalamic paraventricular nucleus and slightly decreased RC3 mRNA expression in striatal neurons; however, cerebellar Purkinje cells appeared unaffected, since they did not exhibit dendritic outgrowth defects and responded normally to T3 treatment in vitro. In conclusion, the circulating thyroid hormone levels of MCT8-null mice closely resemble those of humans with MCT8 mutations, yet in the mice, CNS development is only partially affected.

Degradation studies of new substitutes for perfluorinated surfactants.

Perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) are manmade, stable perfluorosurfactants. The properties of perfluoroalkylated compounds that cause them to persist in the environment are also the properties that made them attractive compounds for industrial usage for over 50 years. Due to the unique properties of the carbon-fluorine bond and the polarity of perfluoroalkyl groups, potential substitutes to replace perfluorinated surfactants in most cases continue to be perfluoroalkyl based. Thus, issues of persistence in the environment remain. There is a need to test emerging new substitute surfactants for biodegradability. This study involved degradability measurements of emerging perfluorinated surfactant substitutes. The stability of the substitutes of perfluorinated surfactants was tested by employing advanced oxidation processes, which were based on degradation by ultraviolet lamp, hydrogen peroxide, or both, followed by conventional tests, among them an automated method based on the manometric respirometry test (OECD 301 F; OxiTop), closed-bottle test (OECD 301 D), and standardized fixed-bed bioreactor on perfluorobutane sulfonate, fluorosurfactant Zonyl, two fluoraliphatic esters (NOVEC FC-4430 and NOVEC FC-4432), and 10-(trifluoromethoxy) decane 1 sulfonate. Most of these new surfactants are well established in the marketplace and have been used in several applications as alternatives to PFOS- and PFOA-based surfactants. Ready biodegradation tests for fluoroaliphatic esters, the fluorosurfactant Zonyl, perfluorobutane sulfonate, and 10-(trifluoromethoxy) decane-1-sulfonate using the manometric respirometry test (OxiTop) did not meet the ready biodegradability test criteria. However, 10-(trifluoromethoxy) decane-1-sulfonate was observed to be degradable when a standardized fixed-bed bioreactor test was applied.

Humanized radioiodinated minibody for imaging of prostate stem cell antigen-expressing tumors.

PURPOSE: Prostate stem cell antigen (PSCA) is a cell surface glycoprotein that is overexpressed in prostate cancer, including hormone refractory disease. Previous preclinical studies showed the intact anti-PSCA antibodies, 1G8 and hu1G8, localized specifically to PSCA-expressing xenografts. Optimal micro positron emission tomography (microPET) imaging using hu1G8, however, required a delay of 168 hours postinjection. In this study, the 2B3 minibody (an 80-kDa engineered antibody fragment) has been produced for rapid targeting and imaging. EXPERIMENTAL DESIGN: A gene encoding a PSCA-specific minibody, V(L)-linker-V(H)-hinge-huIgG1 C(H)3, was assembled. The minibody was expressed by secretion from mammalian cells and purified by cation exchange chromatography. Relative affinity and specificity were determined by competition ELISA and flow cytometry. Serial microPET imaging using a 124I-labeled minibody was conducted at 4 and 21 hours in mice bearing LAPC-9 AD, LAPC-9 AI, PC-3, and LNCaP-PSCA human prostate cancer xenografts. Tumor and tissue biodistribution was determined, and region of interest analysis of the images was conducted. RESULTS: Yields of 20 mg/L purified 2B3 minibody were obtained that showed specific binding to LNCaP-PSCA cells. Purified 2B3 minibody showed specific binding to LNCaP-PSCA cells with an apparent affinity of 46 nmol/L. Radioiodinated 2B3 minibody showed rapid nontarget tissue and blood clearance kinetics (t1/2beta = 11.2 hours). MicroPET scanning using the 124I-2B3 minibody showed both androgen-dependent and -independent tumors as early as 4 hours and excellent high contrast images at 21 hours postinjection. CONCLUSIONS: Imaging PSCA-positive prostate cancer is feasible using an intermediate size antibody fragment at 21 hours.

Video-assisted thoracic surgery (VATS) for resection of metastatic adenocarcinoma as an acceptable alternative.

BACKGROUND: Adenocarcinomas commonly metastasize to the lungs and can be resected using open thoracotomy or video-assisted thoracic surgery (VATS). This study reviews metastatic resections in primary adenocarcinoma patients, using both thoracotomy and VATS. We aim to compare long-term prognoses to test the efficacy and viability of VATS. METHODS: A retrospective review of primary adenocarcinoma patients who underwent resection of pulmonary metastases from 1990 to 2006 was carried out. Information was obtained by chart review. Endpoints analyzed were disease-free interval (DFI), survival time, and recurrence-free survival (RFS). RESULTS: In a total of 42 (16 male, 26 female; median age 58.5 years) primary adenocarcinoma patients, 21 patients underwent first pulmonary metastatic resection using VATS (7 male, 14 female; median age 57 years) and 21 using thoracotomy (9 male, 12 female; median age 59 years). Primary adenocarcinomas were mainly 27 colorectal (64%) and 11 breast (26%). Two VATS (10%) and three open patients (14%) had local recurrences of the original cancer. Median postoperative follow was 13.3 months [interquartile range (IQR) 4.5-32.8 months] for VATS and 36.9 months (IQR 19.3-48.6 months) after thoracotomy. Median DFI-1 was 22.3 months (IQR 13.5-40.6 months) for VATS patients and 35.6 months (IQR 26.7-61.3 months) for open patients. Second thoracic occurrences were noted in six VATS patients (median DFI-2 9.2 months), and in seven open patients (median DFI-2 21.5 months). Third thoracic occurrences were noted in one VATS patient (DFI-3 18.7 months) and in one thoracotomy patient (DFI-3 21.8 months). Odds ratio of recurrence showed 12.5% less chance of developing recurrence in VATS patients. Five-year RFS was 53% in VATS and 57% in thoracotomy patients. CONCLUSIONS: VATS has become a viable alternative to open thoracotomy for resection of pulmonary metastases. In cases of primary adenocarcinoma, VATS showed no increase in number of thoracic recurrences, and comparable RFS. Short-term follow-up is encouraging; long-term follow-up will be needed to confirm these results.