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Abstract Extracellularly released molecular inflammasome assemblies -ASC specks- cross-seed Aβ amyloid in Alzheimer’s disease. Here we show that ASC governs the extent of inflammation-induced amyloid A (AA) amyloidosis, a systemic disease caused by the aggregation and peripheral deposition of the acute-phase reactant serum amyloid A (SAA) in chronic inflammatory conditions. Using super-resolution microscopy, we found that ASC colocalized tightly with SAA in human AA amyloidosis. Recombinant ASC specks accelerated SAA fibril formation and mass spectrometry after limited proteolysis showed that ASC interacts with SAA via its pyrin domain (PYD). In a murine model of inflammatory AA amyloidosis, splenic amyloid load was conspicuously decreased in Pycard −/− mice which lack ASC. Treatment with anti-ASCPYD antibodies decreased amyloid loads in wild-type mice suffering from AA amyloidosis. The prevalence of natural anti-ASC IgG (−logEC50 ≥ 2) in 19,334 hospital patients was

Downstream pebble variability in river systems is assessed through various methods, with recent emphasis on efficient, time-saving semi-automatic processes involving photography and digital analysis. The Inaouène Valley, however, lacked a comprehensive survey of its main channel using either manual or image-based methods. This study bridges this gap by combining both approaches to analyze the downstream evolution of surface pebbles' morphometric parameters along approximately 60 km of the Inaouène's middle reach. Our research focuses on two key aspects: grain size and particle shape. Results reveal a general downstream trend of size fining, increasing circularity and decreasing elongation, primarily attributed to abrasion and travel distance. Notably, this pattern is interrupted by localized variations associated with tributary inputs and sediment recycling processes. This study significantly contributes to the understanding of fluvial sediment dynamics in the Inaouène Valley. Its findings have broad implications, supporting ecological assessment and restoration efforts, while also informing decision-making in river engineering and management. By providing a comprehensive analysis of pebble characteristics and their downstream evolution, this research establishes a foundation for future geomorphological studies and practical applications in river system management.

Abstract The physical interactome of a protein can be altered upon perturbation, modulating cell physiology and contributing to disease. Identifying interactome differences of normal and disease states of proteins could help understand disease mechanisms, but current methods do not pinpoint structure-specific PPIs and interaction interfaces proteome-wide. We used limited proteolysis–mass spectrometry (LiP–MS) to screen for structure-specific PPIs by probing for protease susceptibility changes of proteins in cellular extracts upon treatment with specific structural states of a protein. We first demonstrated that LiP–MS detects well-characterized PPIs, including antibody–target protein interactions and interactions with membrane proteins, and that it pinpoints interfaces, including epitopes. We then applied the approach to study conformation-specific interactors of the Parkinson’s disease hallmark protein alpha-synuclein (aSyn). We identified known interactors of aSyn monomer and amyloid fibrils and provide a resource of novel putative conformation-specific aSyn interactors for validation in further studies. We also used our approach on GDP- and GTP-bound forms of two Rab GTPases, showing detection of differential candidate interactors of conformationally similar proteins. This approach is applicable to screen for structure-specific interactomes of any protein, including posttranslationally modified and unmodified, or metabolite-bound and unbound protein states.

The aggregation of the protein α-synuclein is closely associated with several neurodegenerative disorders and as such the structures of the amyloid fibril aggregates have high scientific and medical significance. However, there are dozens of unique atomic-resolution structures of these aggregates, and such a highly polymorphic nature of the α-synuclein fibrils hampers efforts in disease-relevant in vitro studies on α-synuclein amyloid aggregation. In order to better understand the factors that affect polymorph selection, we studied the structures of α-synuclein fibrils in vitro as a function of pH and buffer using cryo-EM helical reconstruction. We find that in the physiological range of pH 5.8–7.4, a pH-dependent selection between Type 1, 2, and 3 polymorphs occurs. Our results indicate that even in the presence of seeds, the polymorph selection during aggregation is highly dependent on the buffer conditions, attributed to the non-polymorph-specific nature of secondary nucleation. We also uncovered two new polymorphs that occur at pH 7.0 in phosphate-buffered saline. The first is a monofilament Type 1 fibril that highly resembles the structure of the juvenile-onset synucleinopathy polymorph found in patient-derived material. The second is a new Type 5 polymorph that resembles a polymorph that has been recently reported in a study that used diseased tissues to seed aggregation. Taken together, our results highlight the shallow amyloid energy hypersurface that can be altered by subtle changes in the environment, including the pH which is shown to play a major role in polymorph selection and in many cases appears to be the determining factor in seeded aggregation. The results also suggest the possibility of producing disease-relevant structure in vitro.

Abstract For years, proteasomal degradation was predominantly attributed to the ubiquitin-26S proteasome pathway. However, it is now evident that the core 20S proteasome can independently target proteins for degradation. With approximately half of the cellular proteasomes comprising free 20S complexes, this degradation mechanism is not rare. Identifying 20S-specific substrates is challenging due to the dual-targeting of some proteins to either 20S or 26S proteasomes and the non-specificity of proteasome inhibitors. Consequently, knowledge of 20S proteasome substrates relies on limited hypothesis-driven studies. To comprehensively explore 20S proteasome substrates, we employed advanced mass spectrometry, along with biochemical and cellular analyses. This systematic approach revealed hundreds of 20S proteasome substrates, including proteins undergoing specific N- or C-terminal cleavage, possibly for regulation. Notably, these substrates were enriched in RNA- and DNA-binding proteins with intrinsically disordered regions, often found in the nucleus and stress granules. Under cellular stress, we observed reduced proteolytic activity in oxidized proteasomes, with oxidized protein substrates exhibiting higher structural disorder compared to unmodified proteins. Overall, our study illuminates the nature of 20S substrates, offering crucial insights into 20S proteasome biology.

We estimate the seismic attenuation of P and S waves in the polar firn and underlying ice by spectral analysis of diving, refracted, and reflected waves from active-source three-component seismic signals obtained in 2010 on the Whillans Ice Stream (WIS), a fast-flowing ice stream in West Antarctica. The resulting quality factors are then successfully modeled using a rock-physics theory of wave propagation that combines White's mesoscopic attenuation theory of interlayer flow with that of Biot/squirt flow. The first theory describes an equivalent viscoelastic medium consisting of a stack of two alternating thin porous layers, both of which have thicknesses that are much greater than the pore size but smaller than the wavelength. On the other hand, in the so-called Biot/squirt-flow model, there are two loss mechanisms, namely the global Biot flow and the local flow from fluid-filled microcracks (or grain contacts) to the pore space and back, where the former is dominant over the latter. The fluid saturating the pores is assumed to be fluidized snow, defined as a mixture of snow particles and air, such as powder, with a rigidity modulus of zero.

Summary: The selection of renewable energy technologies is widely based on the economic index levelized cost of electricity (LCOE). However, the LCOE ignores the potential temporal mismatch between electricity generation and actual grid demand: this aspect is accounted for in the new index named actual cost of electricity (ACOE), here proposed. This index provides a more accurate economic assessment of renewable energy, minimizing the number of assumptions to be made and outlining the benefits of including a storage. The proposed index is tested across ten cases encompassing three renewable technologies: wind, photovoltaic, and concentrated solar power. The outcomes show that the actual renewable electricity generation of a plant can be reduced by 40%–50% when accounting for the actual electricity demand, resulting in an ACOE exceeding the LCOE by up to 100/150 $/MWh. In addition, the ACOE enables the identification of breakthrough conditions that make storage adoption economically feasible.

Abstract Background Muscle pain and stiffness are strictly interconnected. Injuries frequently occur during sport activities, causing muscle pain, with or without stiffness, and require effective as well as fast-acting treatments. Topical products can be ideal for the treatment of such physical alterations as they are convenient and simple to use. In this study, it was investigated the application of a novel topical formulation, EGYFIL™, for the treatment of pain and stiffness due to muscle contracture, trauma, and/or overtraining. The lotion is composed of hyaluronic acid, a well-known ingredient for the pain alleviation, mixed with skin conditioning SH-Polypeptide-6 and SH-Oligopeptide-1, embedded in it. Methods Twenty-six patients with pain and/or stiffness were enrolled. After a screening visit (Time 0, t0), patients were treated for the first time with the IP. The treatment consisted of topical application of the pain lotion. Level of pain and stiffness were measured with Numerical Rating Scale (NRS). Patients’ pain and/or stiffness were evaluated at t0 (prior to using the product), after three hours (t1), and after three days (t2) of treatment. Participants were free to apply and re-apply the product ad libitum over the course of the study period (3 days). Potential adverse events (AE) and tolerance were evaluated during each visit. Results There was a 22% decrease in pain in the first three hours (p

Chronic kidney disease (CKD) is affecting more and more individuals over time. The importance of the increased prevalence is enhanced by the close association with the increased risk of poor individual outcomes such as death, fatal and non-fatal cardiovascular (CV) events and progression to end stage kidney disease (ESKD). ESKD requires replacement treatment such as hemodialysis (HD), a particular and complex context that unfortunately has been rarely considered in observational studies in the last few decades. The current perspective of HD as a bridge to kidney transplant requires greater attention from observational and experimental research both in the prevention and treatment of CV events in ESKD patients. We present a narrative review by performing a literature review to extrapolate the most significant articles exploring the CV risk, in particular coronary artery disease (CAD), in ESKD and evaluating possible innovative diagnostic and therapeutic tools in these patients. The risk of CAD increases linearly when the estimated glomerular filtration rate (eGFR) declines and reached the most significant level in ESKD patients. Several diagnostic techniques have been evaluated to predict CAD in ESKD such as laboratory tests (Troponin-T, N-terminal pro b-type natriuretic peptide, alkaline phosphatase), echocardiography and imaging techniques for vascular calcifications evaluation. Similarly, treatment is based on lifestyle changes, medical therapy and invasive techniques such as coronary artery bypass grafting (CABG) and percutaneous coronary intervention (PCI). Unfortunately in the literature there are no clear indications of the usefulness and validity of biomarkers and possible treatments in ESKD patients. Considering the ESKD weight in terms of prevalence and costs it is necessary to implement clinical research in order to develop prognostic reliable biomarkers for CV and CAD risk prediction, in patients with ESKD. It should be highlighted that HD is a peculiar setting that offers the opportunity to implement research and facilitates patient monitoring by favoring the design of clinical trials.

Background: A relationship between the geometry and symmetry of Willis’ circle and intracranial aneurysms was reported for anterior communicating and posterior communicating (PCom) aneurysms. A similar association with the middle cerebral artery (MCA) aneurysms instead appeared weaker. Methods: We reviewed 432 patients from six Italian centers with unilateral MCA aneurysms, analyzing the relationship between the caliber and symmetry of Willis’ circle and the presence of ruptured and unruptured presentation. CT-angiograms were evaluated to assess Willis’ circle geometrical characteristics and the MCA aneurysm side, dimension and rupture status. Results: The hypoplasia of the first segment of the anterior cerebral artery (A1) was in approximately one-quarter of patients and PCom hypoplasia was in almost 40%. About 9% had a fetal PCom ipsilaterally to the aneurysm. By comparing the aneurysmal and healthy sides, only the PCom hypoplasia appeared significantly higher in the affected side. Finally, the caliber of the internal carotid artery (ICA) and the first segment of MCA (M1) caliber were significantly greater in patients with unruptured aneurysms, and PCom hypoplasia appeared related to the incidence of an ipsilateral MCA aneurysm and its risk of rupture. Conclusions: Although according to these findings asymmetries of Willis’ circle are shown to be a risk factor for MCA aneurysm formation and rupture, the indifferent association with ipsilateral or contralateral hypoplasia remains a datum of difficult hemodynamic interpretation, thereby raising the concern that this association may be more casual than causal.

Abstract This study corresponds to the first large-scale genetic analysis of inherited eye diseases (IED) in Argentina and describes the comprehensive genetic profile of a large cohort of patients. Medical records of 22 ophthalmology and genetics services throughout 13 Argentinian provinces were analyzed retrospectively. Patients with a clinical diagnosis of an ophthalmic genetic disease and a history of genetic testing were included. Medical, ophthalmological and family history was collected. A total of 773 patients from 637 families were included, with 98% having inherited retinal disease. The most common phenotype was retinitis pigmentosa (RP, 62%). Causative variants were detected in 379 (59%) patients. USH2A, RPGR, and ABCA4 were the most common disease-associated genes. USH2A was the most frequent gene associated with RP, RDH12 early-onset severe retinal dystrophy, ABCA4 Stargardt disease, PROM1 cone-rod dystrophy, and BEST1 macular dystrophy. The most frequent variants were RPGR c.1345 C > T, p.(Arg449*) and USH2A c.15089 C > A, p.(Ser5030*). The study revealed 156/448 (35%) previously unreported pathogenic/likely pathogenic variants and 8 possible founder mutations. We present the genetic landscape of IED in Argentina and the largest cohort in South America. This data will serve as a reference for future genetic studies, aid diagnosis, inform counseling, and assist in addressing the largely unmet need for clinical trials to be conducted in the region.

Abstract Background Since its inception, proteomics has essentially operated in a discovery mode with the goal of identifying and quantifying the maximal number of proteins in a sample. Increasingly, proteomic measurements are also supporting hypothesis-driven studies, in which a predetermined set of proteins is consistently detected and quantified in multiple samples. Selected reaction monitoring (SRM) is a targeted mass spectrometric technique that supports the detection and quantification of specific proteins in complex samples at high sensitivity and reproducibility. Here, we describe ATAQS, an integrated software platform that supports all stages of targeted, SRM-based proteomics experiments including target selection, transition optimization and post acquisition data analysis. This software will significantly facilitate the use of targeted proteomic techniques and contribute to the generation of highly sensitive, reproducible and complete datasets that are particularly critical for the discovery and validation of targets in hypothesis-driven studies in systems biology. Result We introduce a new open source software pipeline, ATAQS (Automated and Targeted Analysis with Quantitative SRM), which consists of a number of modules that collectively support the SRM assay development workflow for targeted proteomic experiments (project management and generation of protein, peptide and transitions and the validation of peptide detection by SRM). ATAQS provides a flexible pipeline for end-users by allowing the workflow to start or end at any point of the pipeline, and for computational biologists, by enabling the easy extension of java algorithm classes for their own algorithm plug-in or connection via an external web site. This integrated system supports all steps in a SRM-based experiment and provides a user-friendly GUI that can be run by any operating system that allows the installation of the Mozilla Firefox web browser. Conclusions Targeted proteomics via SRM is a powerful new technique that enables the reproducible and accurate identification and quantification of sets of proteins of interest. ATAQS is the first open-source software that supports all steps of the targeted proteomics workflow. ATAQS also provides software API (Application Program Interface) documentation that enables the addition of new algorithms to each of the workflow steps. The software, installation guide and sample dataset can be found in http://tools.proteomecenter.org/ATAQS/ATAQS.html

Abstract Several theories have tried to elucidate the mechanisms behind the pathophysiology of chronic subdural hematoma (CSDH). However, this process is complex and remains mostly unknown. In this study we performed a retrospective randomised analysis comparing the cortical atrophy of 190 patients with unilateral CSDH, with 190 healthy controls. To evaluate the extent of cortical atrophy, CT scan images were utilised to develop an index that is the ratio of the maximum diameter sum of 3 cisterns divided by the maximum diameter of the skull at the temporal lobe level. Also, we reported, for the first time, the ultrastructural analyses of the CSDH using a combination of immunohistochemistry methods and transmission electron microscopy techniques. Internal validation was performed to confirm the assessment of the different degrees of cortical atrophy. Relative Cortical Atrophy Index (RCA index) refers to the sum of the maximum diameter of three cisterns (insular cistern, longitudinal cerebral fissure and cerebral sulci greatest) with the temporal bones' greatest internal distance. This index, strongly related to age in healthy controls, is positively correlated to the preoperative and post-operative maximum diameter of hematoma and the midline shift in CSDH patients. On the contrary, it negatively correlates to the Karnofsky Performance Status (KPS). The Area Under the Receiver Operating Characteristics (AUROC) showed that RCA index effectively differentiated cases from controls. Immunohistochemistry analysis showed that the newly formed CD-31 positive microvessels are higher in number than the CD34-positive microvessels in the CSDH inner membrane than in the outer membrane. Ultrastructural observations highlight the presence of a chronic inflammatory state mainly in the CSDH inner membrane. Integrating these results, we have obtained an etiopathogenetic model of CSDH. Cortical atrophy appears to be the triggering factor activating the cascade of transendothelial cellular filtration, inflammation, membrane formation and neovascularisation leading to the CSDH formation.

Abstract The complexity of many cellular and organismal traits results from the integration of genetic and environmental factors via molecular networks. Network structure and effect propagation are best understood at the level of functional modules, but so far, no concept has been established to include the global network state. Here, we show when and how genetic perturbations lead to molecular changes that are confined to small parts of a network versus when they lead to modulation of network states. Integrating multi‐omics profiling of genetically heterogeneous budding and fission yeast strains with an array of cellular traits identified a central state transition of the yeast molecular network that is related to PKA and TOR (PT) signaling. Genetic variants affecting this PT state globally shifted the molecular network along a single‐dimensional axis, thereby modulating processes including energy and amino acid metabolism, transcription, translation, cell cycle control, and cellular stress response. We propose that genetic effects can propagate through large parts of molecular networks because of the functional requirement to centrally coordinate the activity of fundamental cellular processes.

Gap junction channels (GJCs) mediate intercellular communication by connecting two neighbouring cells and enabling direct exchange of ions and small molecules. Cell coupling via connexin-43 (Cx43) GJCs is important in a wide range of cellular processes in health and disease (Churko and Laird, 2013; Liang et al., 2020; Poelzing and Rosenbaum, 2004), yet the structural basis of Cx43 function and regulation has not been determined until now. Here, we describe the structure of a human Cx43 GJC solved by cryo-EM and single particle analysis at 2.26 Å resolution. The pore region of Cx43 GJC features several lipid-like densities per Cx43 monomer, located close to a putative lateral access site at the monomer boundary. We found a previously undescribed conformation on the cytosolic side of the pore, formed by the N-terminal domain and the transmembrane helix 2 of Cx43 and stabilized by a small molecule. Structures of the Cx43 GJC and hemichannels (HCs) in nanodiscs reveal a similar gate arrangement. The features of the Cx43 GJC and HC cryo-EM maps and the channel properties revealed by molecular dynamics simulations suggest that the captured states of Cx43 are consistent with a closed state.

To mark the 15th anniversary of Nature Methods, we asked scientists from across diverse fields of basic biology research for their views on the most exciting and essential methodological challenges that their communities are poised to tackle in the near future.

This paper summarizes a project seminar in analytical chemistry that includes a method comparison approach and collaborative learning. In this project seminar, 12 students worked in four groups, each of which focused on one method for quantitative element analysis, including flame atomic absorption spectroscopy, inductively coupled plasma mass spectrometry, inductively coupled plasma optical emission spectroscopy, and X-ray fluorescence spectroscopy. The seminar was structured into two phases. In the first phase, students became familiar with their method and instrumentation through characterizing the method's capabilities for the analysis of a steel reference sample and then sharing and comparing results between groups. In the second phase, all groups used insights gained during the first phase to design and perform experiments with their methods to solve an analytical challenge. Specifically, the aim of each group was to quantify major, minor, and trace element concentrations from periglacial sediment layers from the hills southeast of Zürich, Switzerland. At the end of phase two, the student-groups presented and compared their results in a joint public poster presentation. Assessment was based on material produced by the participants: posters, teaching materials, method profiles, and written reports. The course evaluation indicates a high satisfaction with the course. The student-centered approach enabled students to get extensive hands-on experience in order to acquire subject-specific skills as well as soft skills. It is well-suited for upper-level undergraduate and graduate students for specialization in analytical chemistry. Further insights, observations, potential for improvement, and limitations are discussed.

Alluvial fan and terrace formation is traditionally interpreted as a fluvial system response to Quaternary climate oscillations under the backdrop of slow and steady tectonic activity. However, several recent studies challenge this conventional wisdom, showing that such landforms can evolve rapidly as a geomorphic system responds to catastrophic and stochastic events, like large-magnitude mass wasting. Here, we contribute to this topic through a detailed field, geochronological, and numerical modelling investigation of thick (>50 m) alluvial sequences in the Klados catchment in southwestern Crete, Greece. The Klados River catchment lies in a Mediterranean climate, is largely floored by carbonate bedrock, and is characterised by well-preserved alluvial terraces and inset fans at the river mouth that exceed the volumes of alluvial deposits in neighbouring catchments of similar size. Previous studies interpreted the genesis and evolution of these deposits to result from a combination of Pleistocene sea-level variation and the region's long-term tectonic activity. We show that the >20 m thick lower fan unit, previously thought to be late Pleistocene in age, unconformably buries a paleoshoreline uplifted in the first centuries CE, placing the depositional age of this unit firmly in the late Holocene. The depositional timing is supported by seven new radiocarbon dates that indicate middle to late Holocene ages for the entire fan and terrace sequence. Furthermore, we report new evidence of a previously unidentified valley-filling landslide deposit that is locally 100 m above the modern stream elevation, and based on cross-cutting relationships, it predates the alluvial sequence. Observations indicate the highly erodible landslide deposit as the source of the alluvial fill sediment. We identify the likely landslide detachment area as a large rockfall scar at the steepened head of the catchment. A landslide volume of 9.08×107 m3 is estimated based on volume reconstructions of the mapped landslide deposit and the inferred scar location. We utilise landslide runout modelling to validate the hypothesis that a high-magnitude rockfall would pulverise and send material downstream, filling the valley up to ∼100 m. This partial liquefaction is required for the rockfall to form a landslide body of the extent observed in the valley and is consistent with the sedimentological characteristics of the landslide deposit. Based on the new age control and the identification of the landslide deposit, we hypothesise that the rapid post-landslide aggradation and incision cycles of the alluvial deposits are not linked to long-term tectonic uplift or climate variations but rather stochastic events such as mobilisation of sediment in large earthquakes, storm events, or ephemeral blockage in the valley's narrow reaches. The Klados case study represents a model environment for how stochastically driven events can mimic climate-induced sedimentary archives and lead to deposition of thick alluvial sequences within hundreds to thousands of years, and it illustrates the ultrasensitivity of mountainous catchments to external perturbations after catastrophic events.

Permafrost in the NE European Russian Arctic is suffering from some of the highest degradation rates in the world. The rising mean annual air temperature causes warming permafrost, the increase in the active layer thickness (ALT), and the reduction of the permafrost extent. These phenomena represent a serious risk for infrastructures and human activities. ALT characterization is important to estimate the degree of permafrost degradation. We used a multidisciplinary approach to investigate the ALT distribution in the Khanovey railway station area (close to Vorkuta, Arctic Russia), where thaw subsidence leads to railroad vertical deformations up to 2.5 cm/year. Geocryological surveys, including vegetation analysis and underground temperature measurements, together with the faster and less invasive electrical resistivity tomography (ERT) geophysical method, were used to investigate the frozen/unfrozen ground settings between the railroad and the Vorkuta River. Borehole stratigraphy and landscape microzonation indicated a massive prevalence of clay and silty clay sediments at shallow depths in this area. The complex refractive index method (CRIM) was used to integrate and quantitatively validate the results. The data analysis showed landscape heterogeneity and maximum ALT and permafrost thickness values of about 7 and 50 m, respectively. The active layer was characterized by resistivity values ranging from about 30 to 100 Ωm, whereas the underlying permafrost resistivity exceeded 200 Ωm, up to a maximum of about 10 kΩm. In the active layer, there was a coexistence of frozen and unfrozen unconsolidated sediments, where the ice content estimated using the CRIM ranged from about 0.3 – 0.4 to 0.9. Moreover, the transition zone between the active layer base and the permafrost table, whose resistivity values ranged from 100 to 200 Ωm for this kind of sediments, showed ice contents ranging from 0.9 to 1.0. Taliks were present in some depressions of the study area, characterized by minimum resistivity values lower than 10 Ωm. This thermokarst activity was more active close to the railroad because of the absence of insulating vegetation. This study contributes to better understanding of the spatial variability of cryological conditions, and the result is helpful in addressing engineering solutions for the stability of the railway.