Search

The Gerda collaboration is performing a sensitive search for neutrinoless double beta decay of 76Ge at the INFN Laboratori Nazionali del Gran Sasso, Italy. The upgrade of the Gerda experiment from Phase I to Phase II has been concluded in December 2015. The first Phase II data release shows that the goal to suppress the background by one order of magnitude compared to Phase I has been achieved. Gerda is thus the first experiment that will remain “background-free” up to its design exposure (100 kgyear). It will reach thereby a half-life sensitivity of more than 10 26 year within 3 years of data collection. This paper describes in detail the modifications and improvements of the experimental setup for Phase II and discusses the performance of individual detector components.

Internal contaminations of 238U, 235U and 232Th in the bulk of high purity germanium detectors are potential backgrounds for experiments searching for neutrinoless double beta decay of 76Ge. The data from GERDA Phase I have been analyzed for alpha events from the decay chain of these contaminations by looking for full decay chains and for time correlations between successive decays in the same detector. No candidate events for a full chain have been found. Upper limits on the activities in the range of a few nBq/kg for 226Ra, 227Ac and 228Th, the long-lived daughter nuclides of 238U, 235U and 232Th, respectively, have been derived. With these upper limits a background index in the energy region of interest from 226Ra and 228Th contamination is estimated which satisfies the prerequisites of a future ton scale germanium double beta decay experiment.

Neutrinoless double electron capture is a process that, if detected, would give evidence of lepton number violation and the Majorana nature of neutrinos. A search for neutrinoless double electron capture of 36Ar has been performed with germanium detectors installed in liquid argon using data from Phase I of the GERmanium Detector Array (Gerda) experiment at the Gran Sasso Laboratory of INFN, Italy. No signal was observed and an experimental lower limit on the half-life of the radiative neutrinoless double electron capture of 36Ar was established: T1 / 2> 3.6 × 1021 years at 90% CI.

The GERmanium Detector Array (Gerda) experiment, located at the Gran Sasso underground laboratory in Italy, is built for the search of 0vββ decay in 76Ge. Gerda operates bare high purity germanium detectors submersed in liquid Argon (LAr). Phase I of the experiment was completed reaching an exposure of about 21 kg.yr with a background level of 10-2 cts/(keV.kg.yr). Gerda Phase I set a limit on the 0vββ decay of 76Ge of T1/20v > 2.1.1025 yr. In Phase II 35 kg of germanium detectors enriched in 76Ge are operated to reach an exposure of 100 kg.yr. The design goal is to reduce the background by one order of magnitude to reach the sensitivity for T1/20v = (1026) yr. The Phase II setup comprises thirty newly produced Broad Energy Germanium (BEGe) detectors. They contribute to the background reduction with better energy resolution and enhanced pulse shape discrimination. To achieve the necessary background reduction, the setup was complemented with LAr veto. The hardware upgrade for Phase II was finished and all detectors were deployed in December 2015. We present the first results of Phase II with 10.8 kg.yr exposure reached in June 2016.

The GErmanium Detector Array (Gerda) experiment, located at the Laboratori Nazionali del Gran Sass15, searches for the 0νββ decay of 76Ge. Gerda Phase II was started in December 2015, aiming to reach a sensitivity on the 0νββ decay half-life larger than 1026 yr in three yr of data taking with about 100 kg·yr exposure with background index of about 10-3 cts/(keV·kg·yr). The major upgrade of Phase II is the deployment of thirty newly produced Broad Energy Germanium detectors. They contribute to the background reduction with better energy resolution and enhanced pulse shape discrimination. To achieve the necessary background reduction, the setup was complemented with LAr veto. After 6 months of operation a first data release with 10.8 kg·yr exposure was performed, showing that the background goal has been achieved. A new lower limit on the 0νββ decay half life of 76Ge of 5.3·1025 yr (90% C.L.) has been set.

A search for neutrinoless ββ decay processes accompanied with Majoron emission has been performed using data collected during Phase I of the GERmanium Detector Array (GERDA) experiment at the Laboratori Nazionali del Gran Sasso of INFN (Italy). Processes with spectral indices n = 1, 2, 3, 7 were searched for. No signals were found and lower limits of the order of 1023 yr on their half-lives were derived, yielding substantially improved results compared to previous experiments with 76Ge. A new result for the half-life of the neutrino-accompanied ββ decay of 76Ge with significantly reduced uncertainties is also given, resulting in (Formula presented.) yr.

An optimized digital shaping filter has been developed for the Gerda experiment which searches for neutrinoless double beta decay in $$^{76}$$76Ge. The Gerda Phase I energy calibration data have been reprocessed and an average improvement of 0.3 keV in energy resolution (FWHM) corresponding to 10 % at the $$Q$$Q value for $$0\nu \beta \beta $$0νββ decay in $$^{76}$$76Ge is obtained. This is possible thanks to the enhanced low-frequency noise rejection of this Zero Area Cusp (ZAC) signal shaping filter.

The GERmanium Detector Array (Gerda) at the Gran Sasso Underground Laboratory (LNGS) searches for the neutrinoless double beta decay (0νββ) of 76Ge. Germanium detectors made of material with an enriched 76Ge fraction act simultaneously as sources and detectors for this decay. During Phase I of theexperiment mainly refurbished semi-coaxial Ge detectors from former experiments were used. For the upcoming Phase II, 30 new 76Ge enriched detectors of broad energy germanium (BEGe)-type were produced. A subgroup of these detectors has already been deployed in Gerda during Phase I. The present paper reviews the complete production chain of these BEGe detectors including isotopic enrichment, purification, crystal growth and diode production. The efforts in optimizing the mass yield and in minimizing the exposure of the 76Ge enriched germanium to cosmic radiation during processing are described. Furthermore, characterization measurements in vacuum cryostats of the first subgroup of seven BEGe detectors and their long-term behavior in liquid argon are discussed. The detector performance fulfills the requirements needed for the physics goals of Gerda Phase II.

Background: Macrophage migration inhibitory factor (MIF) is a pleiotropic cytokine and mediator of acute and chronic inflammatory diseases. MIF is overexpressed in various tumours and has been suggested as a molecular link between chronic inflammation and cancer. MIF overexpression is observed in breast cancer but its causal role in the development of this tumour entity is unclear.Methods: MIF levels in breast cancer cell lines were determined by ELISA and Western blot. CD74 was measured by Western blot, fluorescence microscopy and flow cytometry. Cell proliferation was studied by BrdU incorporation, cell adhesion by Matrigel adhesion assay, and cell invasion by migration assay through Matrigel-coated filters using the Transwell system. MIF expression in primary human breast cancers was measured by tissue microarray and a semi-quantitative immunoreactivity score (IRS) and comparison with histopathological parameters and patient outcome data.Results: MIF was abundantly expressed in the non-invasive breast cancer cell lines MDA-MB-468 and ZR-75-1, but not in invasive MDA-MB-231 cells, which in turn expressed higher levels of the MIF-receptor CD74. Stimulation with exogenous MIF led to a dramatic upregulation of MIF secretion (50-fold) in MDA-MB-231 cells. Autocrine MIF promoted tumour cell proliferation, as indicated by blockade of MIF or CD74 in MDA-MB-231 and MDA-MB-468, and MDA-MB-231 invasiveness was enhanced by exogenous MIF. We correlated the expression of MIF with histopathological parameters and patient outcome data, using a tissue microarray of 175 primary invasive breast cancers and 35 normal control tissues. MIF was upregulated in breast cancer versus normal tissue (median IRS = 8 versus 6). MIF expression showed positive correlations with progesterone (p = 0.006) and estrogen (p = 0.028) receptor expression, markers of a favourable prognosis and a negative correlation to tumour size (p = 0.007). In line with these data, disease-specific overall (OS) as well as recurrence-free (RFS) survival was significantly improved in breast cancer patients with abundant cytosolic MIF expression compared to MIF low expressers (5-year OS = 67% versus 50%, p = 0.0019; 5-year RFS = 52% versus 36%, p = 0.0327).Conclusion: We conclude that intracellular expression of MIF in breast cancer cells is beneficial, whereas extracellular MIF may play a pro-oncogenic role in promoting breast cancer cell-stroma interactions. [ABSTRACT FROM AUTHOR]

Camera traps are becoming widely used for wildlife monitoring and management. However, manual analysis of the resulting image sets is labor-intensive, time-consuming and costly. This study shows that automated computer vision techniques can be extremely helpful in this regard, as they can rapidly and automatically extract valuable information from the images. Specific training with a set of 1600 images obtained from a study where wild animals approaching wild boar carcasses were monitored enabled the model to detect five different classes of animals automatically in their natural environment with a mean average precision of 98.11%, namely 'wild boar', 'fox', 'raccoon dog', 'deer' and 'bird'. In addition, sequences of images were automatically analyzed and the number of wild boar visits and respective group sizes were determined. This study may help to improve and speed up the monitoring of the potential spread of African swine fever virus in areas where wild boar are affected.

NMR (nuclear magnetic resonance) spectroscopy allows for important atomistic insights into the structure and dynamics of biological macromolecules; however, reliable assignments of experimental spectra are often difficult. Herein, quantum mechanical/molecular mechanical (QM/MM) calculations can provide crucial support. A major problem for the simulations is that experimental NMR signals are time-averaged over much longer time scales, and since computed chemical shifts are highly sensitive to local changes in the electronic and structural environment, sufficiently large averages over representative structural ensembles are essential. This entails high computational demands for reliable simulations. For NMR measurements in biological systems, a nucleus of major interest is 31 P since it is both highly present (e.g., in nucleic acids) and easily observable. The focus of our present study is to develop a robust and computationally cost-efficient framework for simulating 31 P NMR chemical shifts of nucleotides. We apply this scheme to study the different stages of the ATP hydrolysis reaction catalyzed by p97. Our methodology is based on MM molecular dynamics (MM-MD) sampling, followed by QM/MM structure optimizations and NMR calculations. Overall, our study is one of the most comprehensive QM-based 31 P studies in a protein environment and the first to provide computed NMR chemical shifts for multiple nucleotide states in a protein environment. This study sheds light on a process that is challenging to probe experimentally and aims to bridge the gap between measured and calculated NMR spectroscopic properties.

The human enzyme p97 regulates various cellular pathways by unfolding hundreds of protein substrates in an ATP-dependent manner, making it an essential component of protein homeostasis and an impactful pharmacological target. The hexameric complex undergoes substantial conformational changes throughout its catalytic cycle. Here we elucidate the molecular motions that occur at the active site in the temporal window immediately before and after ATP hydrolysis by merging cryo-EM, NMR spectroscopy and molecular dynamics simulations. p97 populates a metastable reaction intermediate, the ADP·P i state, which is poised between hydrolysis and product release. Detailed snapshots reveal that the active site is finely tuned to trap and eventually discharge the cleaved phosphate. Signalling pathways originating at the active site coordinate the action of the hexamer subunits and couple hydrolysis with allosteric conformational changes. Our multidisciplinary approach enables a glimpse into the sophisticated spatial and temporal orchestration of ATP handling by a prototype AAA+ protein., (© 2024. The Author(s).)

A search for full energy depositions from bosonic keV-scale dark matter candidates of masses between 65 and 1021 keV has been performed with data collected during Phase II of the GERmanium Detector Array (Gerda) experiment. Our analysis includes direct dark matter absorption as well as dark Compton scattering. With a total exposure of 105.5 kg years, no evidence for a signal above the background has been observed. The resulting exclusion limits deduced with either Bayesian or Frequentist statistics are the most stringent direct constraints in the major part of the 140-1021 keV mass range. As an example, at a mass of 150 keV the dimensionless coupling of dark photons and axion-like particles to electrons has been constrained to α ' / α < 8.7 × 10 - 24 and g ae < 3.3 × 10 - 12 at 90% credible interval (CI), respectively. Additionally, a search for peak-like signals from beyond the Standard Model decays of nucleons and electrons is performed. We find for the inclusive decay of a single neutron in 76 Ge a lower lifetime limit of τ n > 1.5 × 10 24 years and for a proton τ p > 1.3 × 10 24 years at 90% CI. For the electron decay e - → ν e γ a lower limit of τ e > 5.4 × 10 25 years at 90% CI has been determined., Supplementary Information: The online version contains supplementary material available at 10.1140/epjc/s10052-024-13020-0., (© The Author(s) 2024.)

Background & Aims: Particulate hepatitis B core antigen (HBcoreAg) is a potent immunogen used as a vaccine carrier platform. HBcoreAg produced in E. coli encapsidates random bacterial RNA ( b RNA). Using the heterologous protein-prime, viral-vector-boost therapeutic hepatitis B vaccine TherVacB , we compared the properties of different HBcoreAg forms. We explored how the content of HBcoreAg modulates antigen stability, immunogenicity, and antiviral efficacy., Methods: b RNA was removed from HBcoreAg by capsid disassembly, followed by reassembly in the absence or presence of specific nucleic acid-based adjuvants poly I:C or CpG. The morphology and structure of empty, b RNA-containing and adjuvant-loaded HBcoreAg were monitored by electron microscopy and nuclear magnetic resonance spectroscopy. Empty, b RNA-containing or adjuvant-loaded HBcoreAg were applied together with HBsAg and with or without nucleic acid-based external adjuvants within the TherVacB regimen in both wild-type and HBV-carrier mice., Results: While HBcoreAg retained its structure upon b RNA removal, its stability and immunogenicity decreased significantly. Loading HBcoreAg with nucleic acid-based adjuvants re-established stability of the capsid-like antigen. Immunization with poly I:C- or CpG-loaded HBcoreAg induced high antibody titers against co-administered HBsAg. When applied within the TherVacB regimen, they activated vigorous HBcoreAg- and HBsAg-specific T-cell responses in wild-type and HBV-carrier mice, requiring a significantly lower dose of adjuvant compared to externally added adjuvant. Finally, immunization with adjuvant-loaded HBcoreAg mixed with HBsAg led to long-term control of persistent HBV replication in the HBV-carrier mice., Conclusion: Adjuvant-loaded HBcoreAg retained capsid integrity and stability, was as immunogenic in vivo as externally adjuvanted HBcoreAg, requiring lower adjuvant levels, and supported immunity against co-administered, non-adjuvanted HBsAg. Thus, adjuvant-loaded HBcoreAg represents a promising novel platform for vaccine development., Impact and Implications: Hepatitis B core antigen (HBcoreAg) recapitulates the capsid of the HBV that hosts the viral genome. Produced recombinantly, it is not infectious but emerges as a potent immunogen in vaccine development. In this preclinical study, we show that loading HBcoreAg with defined nucleic-acid-based adjuvants on the one hand stabilizes the HBcoreAg with standardized capsid content and, on the other hand, efficiently promotes the immunity of HBcoreAg and a co-administered antigen, allowing for reduced adjuvant doses. Therefore, adjuvant-loaded HBcoreAg not only serves as an encouraging option for therapeutic hepatitis B vaccines, but could also act as an efficient adjuvant delivery system for other types of vaccine., Competing Interests: UP is a co-founder, shareholder, and board member of SCG Cell Therapy. UP serves as ad hoc advisor for Abbott, Aligos, Arbutus, Gilead, GSK, Merck, Sanofi, Roche, and VirBiotech. UP and ADK are named as inventors on a patent application describing the therapeutic vaccination scheme TherVacB (PCT/EP2017/050553). The remaining authors declare no competing interests. Please refer to the accompanying ICMJE disclosure forms for further details., (© 2023 The Author(s).)

We present the measurement of the two-neutrino double-β decay rate of ^{76}Ge performed with the GERDA Phase II experiment. With a subset of the entire GERDA exposure, 11.8 kg yr, the half-life of the process has been determined: T&#95;{1/2}^{2ν}=(2.022±0.018&#95;{stat}±0.038&#95;{syst})×10^{21}  yr. This is the most precise determination of the ^{76}Ge two-neutrino double-β decay half-life and one of the most precise measurements of a double-β decay process. The relevant nuclear matrix element can be extracted: M&#95;{eff}^{2ν}=(0.101±0.001).

The ability to detect liquid argon scintillation light from within a densely packed high-purity germanium detector array allowed the Gerda experiment to reach an exceptionally low background rate in the search for neutrinoless double beta decay of 76 Ge. Proper modeling of the light propagation throughout the experimental setup, from any origin in the liquid argon volume to its eventual detection by the novel light read-out system, provides insight into the rejection capability and is a necessary ingredient to obtain robust background predictions. In this paper, we present a model of the Gerda liquid argon veto, as obtained by Monte Carlo simulations and constrained by calibration data, and highlight its application for background decomposition., (© The Author(s) 2023.)

We search for tri-nucleon decays of 76 Ge in the dataset from the GERmanium Detector Array (GERDA) experiment. Decays that populate excited levels of the daughter nucleus above the threshold for particle emission lead to disintegration and are not considered. The ppp-, ppn-, and pnn-decays lead to 73 Cu, 73 Zn, and 73 Ga nuclei, respectively. These nuclei are unstable and eventually proceed by the beta decay of 73 Ga to 73 Ge (stable). We search for the 73 Ga decay exploiting the fact that it dominantly populates the 66.7 keV 73 m Ga state with half-life of 0.5 s. The nnn-decays of 76 Ge that proceed via 73 m Ge are also included in our analysis. We find no signal candidate and place a limit on the sum of the decay widths of the inclusive tri-nucleon decays that corresponds to a lower lifetime limit of 1.2 × 10 26  yr  (90% credible interval). This result improves previous limits for tri-nucleon decays by one to three orders of magnitude., (© The Author(s) 2023.)

Antimicrobial resistance (AMR) is a serious global health threat with extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales as the most critical ones. Studies on AMR in wild birds imply a possible dissemination function and indicate their potential role as sentinel animals. This study aimed to gain a deeper insight into the AMR burden of wild waterfowl by sampling semi-wild mallard ducks used as sentinels and to identify if AMR bacteria could be recommended to be added to the pathogens of public health risks to be screened for. In total, 376 cloacal and pooled fecal samples were collected from the sentinel plant over a period of two years. Samples were screened for ESBL-carrying E. coli and isolates found further analyzed using antimicrobial susceptibility testing and whole-genome sequencing. Over the sampling period, 4.26% (16/376) of the samples were positive for ESBL-producing E. coli . Bla CTX-M-1 and bla CTX-M-32 were the most abundant CTX-M types. Although none of the top global sequence types (ST) could be detected, poultry-derived ST115 and non-poultry-related STs were found and could be followed over time. The current study revealed low cases of ESBL-producing E. coli in semi-wild mallard ducks, which proves the suitability of sentinel surveillance for AMR detection in water-associated wildlife.

The aim of the study was to determine the prevalence of ESBL/AmpC-producing Escherichia ( E .) coli and to investigate their on-farm distribution on an exemplary dairy farm. For this purpose, sample sizes were calculated, and fecal samples were collected from cattle of all ages and analyzed for the presence of ESBL/AmpC- E. coli using selective media supplemented with cefotaxime. These antibiotic-resistant bacteria were detected in 22.5% of the samples tested. The prevalence was highest in the calf age group, in which 100% of the collected fecal samples were positive. With increasing age, the prevalence decreased in the other sample groups. While ESBL/AmpC E. coli could still be detected in young stock (15%) and breeding heifers (5%), no resistant pathogens could be detected in adult animals. Whole-genome sequencing of the ESBL/AmpC- E. coli isolates revealed, first, that all isolates were ESBL producers (CTX-M-1 and CTX-M-15) and, second, that ST362, which is known as a biofilm producer, was dominant in the calves (85%, n = 17). Based on these results and the evaluation of a questionnaire, possible causes for the occurrence of ESBL/AmpC- E. coli were discussed and recommendations for the reduction in transmission were formulated. Unlike most German dairy farms, no waste milk feeding was apparent; therefore, factors reducing ESBL/AmpC- E. coli are primarily related to an improvement in hygiene management to prevent biofilms, e.g., in nipple buckets, but also to question the use of antibiotics, e.g., in the treatment of diarrheic calves.

The hepatitis B virus (HBV) is the leading cause of persistent liver infections. Its DNA-based genome is synthesized through reverse transcription of an RNA template inside the assembled capsid shell. In addition to the structured assembly domain, the capsid protein harbors a C-terminal extension that mediates both the enclosure of RNA during capsid assembly and the nuclear entry of the capsid during infection. The arginine-rich motifs within this extension, though common to many viruses, have largely escaped atomic-scale investigation. Here, we leverage solution and solid-state nuclear magnetic resonance spectroscopy at ambient and cryogenic temperatures, under dynamic nuclear polarization signal enhancement, to investigate the organization of the genome within the capsid. Transient interactions with phosphate groups of the RNA backbone confine the arginine-rich motifs to the interior capsid space. While no secondary structure is induced in the C-terminal extension, interactions with RNA counteract the formation of a disulfide bond, which covalently tethers this peptide arm onto the inner capsid surface. Electrostatic and covalent contributions thus compete in the spatial regulation of capsid architecture. This disulfide switch represents a coupling mechanism between the structured assembly domain of the capsid and the enclosed nucleic acids. In particular, it enables the redox-dependent regulation of the exposure of the C-terminal extension on the capsid surface, which is required for nuclear uptake of the capsid. Phylogenetic analysis of capsid proteins from hepadnaviruses points toward a function of this switch in the persistence of HBV infections.

The behavior of animals is related to their health and welfare status. The latter plays a particular role in animal experiments, where continuous monitoring is essential for animal welfare. In this study, we focus on red foxes in an experimental setting and study their behavior. Although animal behavior is a complex concept, it can be described as a combination of body posture and activity. To measure body posture and activity, video monitoring can be used as a non-invasive and cost-efficient tool. While it is possible to analyze the video data resulting from the experiment manually, this method is time consuming and costly. We therefore use computer vision to detect and track the animals over several days. The detector is based on a neural network architecture. It is trained to detect red foxes and their body postures, i.e., 'lying', 'sitting', and 'standing'. The trained algorithm has a mean average precision of 99.91%. The combination of activity and posture results in nearly continuous monitoring of animal behavior. Furthermore, the detector is suitable for real-time evaluation. In conclusion, evaluating the behavior of foxes in an experimental setting using computer vision is a powerful tool for cost-efficient real-time monitoring.

Antimicrobial resistance (AMR) is a serious global health threat and extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales are a major contributor. This study aimed to gain a deeper insight into the AMR burden of wild animals. In total, 1595 fecal samples were collected by two systematic searches in Mecklenburg-Western Pomerania, north-east Germany. Samples were screened for ESBL-carrying Escherichia (E.) coli and isolates found were further analyzed using antimicrobial susceptibility testing and whole-genome sequencing. We found an estimated prevalence of 1.2% ESBL-producing E. coli in wild boar and 1.1% in wild ruminants. CTX-M-1 was the most abundant CTX-M type. We also examined fecal samples from wild boar and wild ruminants using shotgun metagenomics to gain insight into the resistome in wild animals. The latter revealed significantly lower normalized counts for AMR genes in wildlife samples compared to farm animals. The AMR gene levels were lower in wild ruminants than in wild boar. In conclusion, our study revealed a low prevalence of ESBL-producing E. coli and a low overall AMR gene burden in wild boar and wild ruminants, probably due to the secluded location of the search area.

The GERmanium Detector Array (Gerda) collaboration searched for neutrinoless double- β decay in 76 Ge using isotopically enriched high purity germanium detectors at the Laboratori Nazionali del Gran Sasso of INFN. After Phase I (2011-2013), the experiment benefited from several upgrades, including an additional active veto based on LAr instrumentation and a significant increase of mass by point-contact germanium detectors that improved the half-life sensitivity of Phase II (2015-2019) by an order of magnitude. At the core of the background mitigation strategy, the analysis of the time profile of individual pulses provides a powerful topological discrimination of signal-like and background-like events. Data from regular 228 Th calibrations and physics data were both considered in the evaluation of the pulse shape discrimination performance. In this work, we describe the various methods applied to the data collected in Gerda Phase II corresponding to an exposure of 103.7 kg year. These methods suppress the background by a factor of about 5 in the region of interest around Q β β = 2039  keV, while preserving ( 81 ± 3 ) % of the signal. In addition, an exhaustive list of parameters is provided which were used in the final data analysis., (© The Author(s) 2022.)

Mammalian cells release different types of vesicles, collectively termed extracellular vesicles (EVs). EVs contain cellular microRNAs (miRNAs) with an apparent potential to deliver their miRNA cargo to recipient cells to affect the stability of individual mRNAs and the cells' transcriptome. The extent to which miRNAs are exported via the EV route and whether they contribute to cell-cell communication are controversial. To address these issues, we defined multiple properties of EVs and analyzed their capacity to deliver packaged miRNAs into target cells to exert biological functions. We applied well-defined approaches to produce and characterize purified EVs with or without specific viral miRNAs. We found that only a small fraction of EVs carried miRNAs. EVs readily bound to different target cell types, but EVs did not fuse detectably with cellular membranes to deliver their cargo. We engineered EVs to be fusogenic and document their capacity to deliver functional messenger RNAs. Engineered fusogenic EVs, however, did not detectably alter the functionality of cells exposed to miRNA-carrying EVs. These results suggest that EV-borne miRNAs do not act as effectors of cell-to-cell communication., Competing Interests: The authors have declared that no competing interests exist.

Animal activity is an indicator for its welfare and manual observation is time and cost intensive. To this end, automatic detection and monitoring of live captive animals is of major importance for assessing animal activity, and, thereby, allowing for early recognition of changes indicative for diseases and animal welfare issues. We demonstrate that machine learning methods can provide a gap-less monitoring of red foxes in an experimental lab-setting, including a classification into activity patterns. Therefore, bounding boxes are used to measure fox movements, and, thus, the activity level of the animals. We use computer vision, being a non-invasive method for the automatic monitoring of foxes. More specifically, we train the existing algorithm 'you only look once' version 4 (YOLOv4) to detect foxes, and the trained classifier is applied to video data of an experiment involving foxes. As we show, computer evaluation outperforms other evaluation methods. Application of automatic detection of foxes can be used for detecting different movement patterns. These, in turn, can be used for animal behavioral analysis and, thus, animal welfare monitoring. Once established for a specific animal species, such systems could be used for animal monitoring in real-time under experimental conditions, or other areas of animal husbandry.

Enzyme catalysis is omnipresent in the cell. The mechanisms by which highly evolved protein folds enable rapid and specific chemical transformation of substrates belong to the marvels of structural biology. Targeting of enzymes with inhibitors has immediate application in drug discovery, from chemotherapeutics over antibiotics to antivirals. NMR spectroscopy combines multiple assets for the investigation of enzyme function. The non-invasive technique can probe enzyme structure and dynamics and map interactions with substrates, cofactors and inhibitors at the atomic level. With experiments performed at close to native conditions, catalytic transformations can be monitored in real time, giving access to kinetic parameters. The power of NMR in the solid state, in contrast with solution, lies in the absence of fundamental size limitations, which is crucial for enzymes that are either membrane-embedded or assemble into large soluble complexes exceeding hundreds of kilodaltons in molecular weight. Here we review recent progress in solid-state NMR methodology, which has taken big leaps in the past years due to steady improvements in hardware design, notably magic angle spinning, and connect it to parallel biochemical advances that enable isotope labelling of increasingly complex enzymes. We first discuss general concepts and requirements of the method and then highlight the state-of-the-art in sample preparation, structure determination, dynamics and interaction studies. We focus on examples where solid-state NMR has been instrumental in elucidating enzyme mechanism, alone or in integrative studies., (© 2020 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.)

The GERmanium Detector Array (Gerda) collaboration searched for neutrinoless double- β decay in 76 Ge with an array of about 40 high-purity isotopically-enriched germanium detectors. The experimental signature of the decay is a monoenergetic signal at Q β β = 2039.061 ( 7 )  keV in the measured summed energy spectrum of the two emitted electrons. Both the energy reconstruction and resolution of the germanium detectors are crucial to separate a potential signal from various backgrounds, such as neutrino-accompanied double- β decays allowed by the Standard Model. The energy resolution and stability were determined and monitored as a function of time using data from regular 228 Th calibrations. In this work, we describe the calibration process and associated data analysis of the full Gerda dataset, tailored to preserve the excellent resolution of the individual germanium detectors when combining data over several years., (© The Author(s) 2021.)

Neutrinoless double- β decay of 76 Ge is searched for with germanium detectors where source and detector of the decay are identical. For the success of future experiments it is important to increase the mass of the detectors. We report here on the characterization and testing of five prototype detectors manufactured in inverted coaxial (IC) geometry from material enriched to 88% in 76 Ge. IC detectors combine the large mass of the traditional semi-coaxial Ge detectors with the superior resolution and pulse shape discrimination power of point contact detectors which exhibited so far much lower mass. Their performance has been found to be satisfactory both when operated in vacuum cryostat and bare in liquid argon within the Gerda setup. The measured resolutions at the Q -value for double- β decay of 76 Ge ( Q β β  = 2039 keV) are about 2.1 keV full width at half maximum in vacuum cryostat. After 18 months of operation within the ultra-low background environment of the GERmanium Detector Array (Gerda) experiment and an accumulated exposure of 8.5 kg · year, the background index after analysis cuts is measured to be 4 . 9 - 3.4 + 7.3 × 10 - 4 counts / ( keV · kg · year ) around Q β β . This work confirms the feasibility of IC detectors for the next-generation experiment Legend., (© The Author(s) 2021.)

The GERmanium Detector Array (GERDA) experiment searched for the lepton-number-violating neutrinoless double-β (0νββ) decay of ^{76}Ge, whose discovery would have far-reaching implications in cosmology and particle physics. By operating bare germanium diodes, enriched in ^{76}Ge, in an active liquid argon shield, GERDA achieved an unprecedently low background index of 5.2×10^{-4} counts/(keV kg yr) in the signal region and met the design goal to collect an exposure of 100 kg yr in a background-free regime. When combined with the result of Phase I, no signal is observed after 127.2 kg yr of total exposure. A limit on the half-life of 0νββ decay in ^{76}Ge is set at T&#95;{1/2}>1.8×10^{26}  yr at 90% C.L., which coincides with the sensitivity assuming no signal.

Extracellular vesicles (EVs) are emerging fundamental players in viral infections by shuttling viral components, mediating immune responses and likely the spread of the virus. However, the obstacles involved in purifying EVs and removing contaminating viral particles in a reliable and effective manner bottlenecks the full potential for the development of clinical and diagnostic treatment options targeting EV. Because of the similarities in size, density, membrane composition and mode of biogenesis of EVs and virions there are no standardized approaches for virus-removal from EV preparations yet. Functional EV studies also require EV samples that are devoid of antibody contaminants. Consequently, the study of EVs in virology needs reliable and effective protocols to purify EVs and remove contaminating antibodies and viral particles. Here, we established a protocol for EV purification from hepatitis B virus (HBV)-containing plasma by a combination of size-exclusion chromatography and affinity-based purification. After purification, EV samples were free of virus-sized particles, HBV surface antigen, HBV core antigen, antibodies or infectious material. Viral genomic contamination was also decreased following purification. By using appropriate antibodies and size parameters, this protocol could potentially be applied to purification of EVs from other viral samples. In summary, we established a fast, reproducible and robust approach for the removal of HBV from EV preparations. Looking forward to the point of purifying EVs from clinical samples, this method should enable studies shedding light on the underlying mechanisms of EVs in viral infections and their diagnostic and prognostic potential., Competing Interests: The position of Daniela Stadler was in part financed by a research grant from ALIOS BioPharma., (© 2020 The Authors. Journal of Extracellular Vesicles published by Wiley Periodicals LLC on behalf of International Society for Extracellular Vesicles.)

New hepatitis B virions released from infected hepatocytes are the result of an intricate maturation process that starts with the formation of the nucleocapsid providing a confined space where the viral DNA genome is synthesized via reverse transcription. Virion assembly is finalized by the enclosure of the icosahedral nucleocapsid within a heterogeneous envelope. The latter contains integral membrane proteins of three sizes, collectively known as hepatitis B surface antigen, and adopts multiple conformations in the course of the viral life cycle. The nucleocapsid conformation depends on the reverse transcription status of the genome, which in turn controls nucleocapsid interaction with the envelope proteins for virus exit. In addition, after secretion the virions undergo a distinct maturation step during which a topological switch of the large envelope protein confers infectivity. Here we review molecular determinants for envelopment and models that postulate molecular signals encoded in the capsid scaffold conducive or adverse to the recruitment of envelope proteins.

The human ATPase p97, also known as valosin containing protein or Cdc48, is a highly abundant AAA+ engine that fuels diverse energy-consuming processes in the human cell. p97 represents a potential target for cancer therapy and its malfunction causes a degenerative disease. Here, we monitor the enzymatic activity of p97 in real time via an NMR-based approach that allows us to follow the steps that couple ATP turnover to mechanical work. Our data identify a transient reaction intermediate, the elusive ADP.P i nucleotide state, which has been postulated for many ATPases but has so far escaped direct detection. In p97, this species is crucial for the regulation of adenosine triphosphate turnover in the first nucleotide-binding domain. We further demonstrate how the enzymatic cycle is detuned by disease-associated gain-of-function mutations. The high-resolution insight obtained into conformational transitions in both protein and nucleotide bridges the gap between static enzyme structures and the dynamics of substrate conversion. Our approach relies on the close integration of solution- and solid-state NMR methods and is generally applicable to shed light on the mechanochemical operating modes of large molecular engines.

Sup35p is a protein from Saccharomyces cerevisiae . It can propagate using a prion-like mechanism, which means that it can recruit non-prion soluble Sup35p into insoluble fibrils. Sup35p is a large protein showing three distinct domains, N, M and an extended globular domain. We have previously studied the conformations of the full-length and truncated NM versions carrying poly-histidine tags on the N-terminus. Comparison with structural data from C-terminally poly-histidine tagged NM from the literature surprisingly revealed discrepancies. Here we investigated fibrils from the untagged, as well as a C-terminally poly-histidine tagged NM construct, using solid-state NMR. We find that the conformation of untagged NM is very close to the N-terminally tagged NM and confirms our previous findings. The C-terminal poly-histidine tag, in contrast, drastically changes the NM fibril structure, and yields data consistent with results obtained previously on this construct. We conclude that the C-terminally located Sup35p globular domain influences the structure of the fibrillar core at the N domain, as previously shown. We further conclude, based on the present data, that small tags on NM C-terminus have a substantial, despite different, impact. Modifications at this remote localization thus shows an unexpected influence on the fibril structure, and importantly also its propensity to induce [PSI+] ., (Copyright © 2020 Bousset, Luckgei, Kabani, Gardiennet, Schütz, Melki, Meier and Böckmann.)

We present the first search for bosonic superweakly interacting massive particles (super-WIMPs) as keV-scale dark matter candidates performed with the GERDA experiment. GERDA is a neutrinoless double-β decay experiment which operates high-purity germanium detectors enriched in ^{76}Ge in an ultralow background environment at the Laboratori Nazionali del Gran Sasso (LNGS) of INFN in Italy. Searches were performed for pseudoscalar and vector particles in the mass region from 60  keV/c^{2} to 1  MeV/c^{2}. No evidence for a dark matter signal was observed, and the most stringent constraints on the couplings of super-WIMPs with masses above 120  keV/c^{2} have been set. As an example, at a mass of 150  keV/c^{2} the most stringent direct limits on the dimensionless couplings of axionlike particles and dark photons to electrons of g&#95;{ae}<3×10^{-12} and α^{'}/α<6.5×10^{-24} at 90% credible interval, respectively, were obtained.

A discovery that neutrinos are Majorana fermions would have profound implications for particle physics and cosmology. The Majorana character of neutrinos would make possible the neutrinoless double-β (0νββ) decay, a matter-creating process without the balancing emission of antimatter. The GERDA Collaboration searches for the 0νββ decay of 76 Ge by operating bare germanium detectors in an active liquid argon shield. With a total exposure of 82.4 kg⋅year, we observe no signal and derive a lower half-life limit of T 1/2 > 0.9 × 10 26 years (90% C.L.). Our T 1/2 sensitivity, assuming no signal, is 1.1 × 10 26 years. Combining the latter with those from other 0νββ decay searches yields a sensitivity to the effective Majorana neutrino mass of 0.07 to 0.16 electron volts., (Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

The GERmanium Detector Array (Gerda) is a low background experiment located at the Laboratori Nazionali del Gran Sasso in Italy, which searches for neutrinoless double-beta decay of 76 Ge into 76 Se+2e - . Gerda has been conceived in two phases. Phase II, which started in December 2015, features several novelties including 30 new 76 Ge enriched detectors. These were manufactured according to the Broad Energy Germanium (BEGe) detector design that has a better background discrimination capability and energy resolution compared to formerly widely-used types. Prior to their installation, the new BEGe detectors were mounted in vacuum cryostats and characterized in detail in the Hades underground laboratory in Belgium. This paper describes the properties and the overall performance of these detectors during operation in vacuum. The characterization campaign provided not only direct input for Gerda Phase II data collection and analyses, but also allowed to study detector phenomena, detector correlations as well as to test the accuracy of pulse shape simulation codes., (© The Author(s) 2019.)

The GERDA experiment searches for the lepton-number-violating neutrinoless double-β decay of ^{76}Ge (^{76}Ge→^{76}Se+2e^{-}) operating bare Ge diodes with an enriched ^{76}Ge fraction in liquid argon. The exposure for broad-energy germanium type (BEGe) detectors is increased threefold with respect to our previous data release. The BEGe detectors feature an excellent background suppression from the analysis of the time profile of the detector signals. In the analysis window a background level of 1.0&#95;{-0.4}^{+0.6}×10^{-3}  counts/(keV kg yr) has been achieved; if normalized to the energy resolution this is the lowest ever achieved in any 0νββ experiment. No signal is observed and a new 90% C.L. lower limit for the half-life of 8.0×10^{25}  yr is placed when combining with our previous data. The expected median sensitivity assuming no signal is 5.8×10^{25}  yr.

Luminescent conjugated polythiophenes bind to amyloid proteins with high affinity. Their fluorescence properties, which are modulated by the detailed conformation in the bound state, are highly sensitive to structural features of the amyloid. Polythiophenes therefore represent diagnostic markers for the detection and differentiation of pathological amyloid aggregates. We clarify the binding site and mode of two different polythiophenes to fibrils of the prion domain of the HET-s protein by solid-state NMR and correlate these findings with their fluorescence properties. We demonstrate how amyloid dyes recognize distinct binding sites with specific topological features. Regularly spaced surface charge patterns and well-accessible grooves on the fibril surface define the pharmacophore of the amyloid, which in turn determines the binding mode and fluorescence wavelength of the polythiophene.

We have previously shown that Congo red (CR) binds site specifically to amyloid fibrils formed by HET-s(218-289) with the long axis of the CR molecule almost parallel to the fibril axis. HADDOCK docking studies indicated that CR adopts a roughly planar conformation with the torsion angle ϕ characterizing the relative orientation of the two phenyl rings being a few degrees. In this study, we experimentally determine the torsion angle ϕ at the center of the CR molecule when bound to HET-s(218-289) amyloid fibrils using solid-state NMR tensor-correlation experiments. The method described here relies on the site-specific 13 C labeling of CR and on the analysis of the two-dimensional magic-angle spinning tensor-correlation spectrum of 13 C 2 -CR. We determined the torsion angle ϕ to be 19°.

p97/VCP, a member of the AAA+ (ATPases associated with diverse cellular activities) family of proteins, is implicated in the etiology of a group of degenerative diseases affecting bone and muscle tissue as well as the central nervous system. Methyl-TROSY-based NMR studies have previously revealed how disease-causing mutations deregulate a subtle dynamic conformational equilibrium involving the N-terminal domain (NTD) with implications for the binding of certain adaptors, providing insight into how disease mutations lead to abnormal function. Herein the conformational plasticity of the p97 system is explored in an attempt to identify hotspots that can serve as targets for restoring function in disease mutants by shifting the position of the NTD back to its wild-type location. Although p97 is overall robust with respect to extensive mutagenesis throughout the protein involving conservative substitutions of hydrophobic residues, key positions have been identified that alter the NTD equilibrium; these lie in specific regions that localize to the interface between the NTD and the D1 nucleotide-binding domain of the complex. Notably, for a severe disease mutant involving an R155C substitution the NTD equilibrium can be shifted back to its wild-type position by mutation at a secondary site with restoration of wild-type two-pronged binding of the UBXD1 adaptor protein that is impaired in disease; this underlies the potential for recovering function by targeting p97 disease mutants with drug molecules., Competing Interests: The authors declare no conflict of interest.

The COP9 signalosome (CSN) is a multi-protein complex that is highly conserved in eukaryotes. Due to its regulatory impact on processes such as cell cycle, DNA damage response and apoptosis, the CSN is essential for mammalian cells. One of the best-studied functions of the CSN is the deNEDDylation of cullin-RING ligases (CRLs) via its catalytically active subunit CSN5/JAB1, thereby triggering the degradation of various target proteins. CSN5 was found to be overexpressed in many human cancer entities, including colon adenocarcinoma. Overactivation of WNT signaling is known as a key step in colon cancer development. Recently, we found that depletion of CSN5 in colorectal cancer (CRC) cells affects WNT signaling by downregulation of β-catenin. To investigate changes in gene expression associated with the CSN5 knockdown, we performed a microarray using cDNA from the CRC cell line SW480. We found the WNT ligand WNT6 and the WNT inhibitors DKK1 and DKK4 differentially regulated in CSN5 knockdown cells. DKK1 expression and DKK1 protein levels depended on CSN5 in different CRC cell lines. In addition, DKK1 secretion was increased following CSN5 knockdown, affecting WNT signaling in SW480 cells. Consequently, blocking of secreted DKK1 in cell-conditioned media abolished β-catenin downregulation in SW480 cells, while treatment with recombinant DKK1 mimicked the CSN5 knockdown effect. Furthermore, knockdown of DKK1 was able to rescue the proliferative deficiency of CSN5 knockdown cells. We conclude that downregulation of WNT signaling in colorectal cancer cells resulting from CSN5 knockdown is mediated, at least in part, by elevated DKK1 secretion. Moreover, experiments with the NEDDylation inhibitor MLN-4924 indicated that DKK1 expression is regulated by a so far unidentified repressor, the stability of which could be controlled by a CSN-regulated CRL., (Copyright © 2017. Published by Elsevier Inc.)

Prions cause transmissible spongiform encephalopathies for which no treatment exists. Prions consist of PrP(Sc), a misfolded and aggregated form of the cellular prion protein (PrP(C)). We explore the antiprion properties of luminescent conjugated polythiophenes (LCPs) that bind and stabilize ordered protein aggregates. By administering a library of structurally diverse LCPs to the brains of prion-infected mice via osmotic minipumps, we found that antiprion activity required a minimum of five thiophene rings bearing regularly spaced carboxyl side groups. Solid-state nuclear magnetic resonance analyses and molecular dynamics simulations revealed that anionic side chains interacted with complementary, regularly spaced cationic amyloid residues of model prions. These findings allowed us to extract structural rules governing the interaction between LCPs and protein aggregates, which we then used to design a new set of LCPs with optimized binding. The new set of LCPs showed robust prophylactic and therapeutic potency in prion-infected mice, with the lead compound extending survival by >80% and showing activity against both mouse and hamster prions as well as efficacy upon intraperitoneal administration into mice. These results demonstrate the feasibility of targeted chemical design of compounds that may be useful for treating diseases of aberrant protein aggregation such as prion disease., (Copyright © 2015, American Association for the Advancement of Science.)

Alzheimer's disease (AD) is the most common form of dementia. Aggregation of amyloid β (Aβ), a peptide of 39-43 residues length, into insoluble fibrils is considered to initiate the disease. Determination of the molecular structure of Aβ fibrils is technically challenging and is a significant goal in AD research that may lead to design of effective therapeutical inhibitors of Aβ aggregation. Here, we present chemical-shift assignments for fibrils formed by highly pure recombinant Aβ1-40 with the Osaka E22Δ mutation that is found in familial AD. We show that that all regions of the peptide are rigid, including the N-terminal part often believed to be flexible in Aβ wt.

Despite its central importance for understanding the molecular basis of Alzheimer's disease (AD), high-resolution structural information on amyloid β-peptide (Aβ) fibrils, which are intimately linked with AD, is scarce. We report an atomic-resolution fibril structure of the Aβ1-40 peptide with the Osaka mutation (E22Δ), associated with early-onset AD. The structure, which differs substantially from all previously proposed models, is based on a large number of unambiguous intra- and intermolecular solid-state NMR distance restraints., (© 2014 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution Non-Commercial NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.)

Aim: To investigate the role of acyl-CoA synthetase 5 (ACSL5) activity in Wnt signaling in intestinal surface epithelia., Methods: Several cell lines were used to investigate the ACSL5-dependent expression and synthesis of Wnt2B, a mitochondrially expressed protein of the Wnt signaling family. Wnt activity was functionally assessed with a luciferase reporter assay. ACSL5-related biochemical Wnt2B modifications were investigated with a modified acyl-exchange assay. The findings from the cell culture models were verified using an Apc(min/+) mouse model as well as normal and neoplastic diseased human intestinal tissues., Results: In the presence of ACSL5, Wnt2B was unable to translocate into the nucleus and was enriched in mitochondria, which was paralleled by a significant decrease in Wnt activity. ACSL5-dependent S-palmitoylation of Wnt2B was identified as a molecular reason for mitochondrial Wnt2B accumulation. In cell culture systems, a strong relation of ACSL5 expression, Wnt2B palmitoylation, and degree of malignancy were found. Using normal mucosa, the association of ACSL5 and Wnt2B was seen, but in intestinal neoplasias the mechanism was only rudimentarily observed., Conclusion: ACSL5 mediates antiproliferative activities via Wnt2B palmitoylation with diminished Wnt activity. The molecular pathway is probably relevant for intestinal homeostasis, overwhelmed by other pathways in carcinogenesis.

Sup35p is a yeast prion and is responsible for the [PSI(+)] trait in Saccharomyces cerevisiae. With 685 amino acids, full-length soluble and fibrillar Sup35p are challenging targets for structural biology as they cannot be investigated by X-ray crystallography or NMR in solution. We present solid-state NMR studies of fibrils formed by the full-length Sup35 protein. We detect an ordered and rigid core of the protein that gives rise to narrow and strong peaks, while large parts of the protein show either static disorder or dynamics on time scales which interfere with dipolar polarization transfer or shorten the coherence lifetime. Thus, only a small subset of resonances is observed in 3D spectra. Here we describe in detail the sequential assignments of the 22 residues for which resonances are observed in 3D spectra: their chemical shifts mostly corresponding to β-sheet secondary structure. We suspect that these residues form the amyloid core of the fibril.

Sup35pNM represents the N-terminal and middle (M) domains of the yeast Saccharomyces cerevisiae prion Sup35p. This fragment is commonly used for structural and functional studies of Sup35p. We here present a solid-state NMR study of fibrils formed by this fragment and show that sequential assignments can be obtained for the rigid and well-ordered parts of the protein using 3D spectroscopy. We describe in detail the sequential assignment of the 22 residues yielding strong, narrow signals with chemical shifts that correspond mostly to β-sheet secondary-structured amino acids that form the fibril core.