bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of RyR2 distribution in HEK293 cells and mouse cardiac myocytes using 3D MINFLUX microscopy
Authors: Clowsley Alexander H , Meletiou Anna , Lučinskaitė Evelina , Jansen Isabelle , Jones Peter P. , Louch William E. , Soeller Christian 
Published: July 2023

AbstractThe cardiac type 2 ryanodine receptor (RyR2) is a large homotetramer of a ∼560 kD subunit and is the molecular pathway through which the majority of Ca2+enters the cytosol during cardiac activation. It constitutes the molecular basis of the process of calcium induced calcium release where activation of RyR2s can be locally regenerative giving rise to local release events termed Ca2+sparks. Accordingly, the molecular distribution of RyR2 in cardiac myocytes has been of great interest. Here we present the first purely optical data of RyR2 distribution with sub-molecular resolution by applying 3D MINFLUX fluorescence super-resolution microscopy. We demonstrate that by using single-domain antibodies (sdABs) against fluorescent protein domains in engineered RyR2 fluorescent protein fusions we can determine the location of individual RyR2 subunits with high precision (∼3 nm) in all directions. This allows determining not only the location but also the 3D orientation of individual RyR2 channels in intact cells. In practice, this capability is currently limited by a relatively modest effective labeling efficiency (∼10 % subunit detection efficiency translating into ∼35% RyR2 labeling efficiency) which we measurein-situusing a novel procedure enabled by the true molecular resolution of MINFLUX microscopy. The new data suggests a resolution to apparent discrepancies between previous data from electron microscopy and super-resolution data that may be at least partially explained by effects of labeling efficiency. The methodology developed here will be critical to reveal the full complexity of RyR2 and related Ca2+handling proteins in 3D as well as their relationship to contractile function. Our new approaches may be applicable to other multi-subunit complexes in cardiac muscle and other cell types.
Functional hierarchies in brain dynamics characterized by signal reversibility in ferret cortex
Authors: Idesis Sebastian , Geli Sebastian , Faskowitz Joshua , Vohryzek Jakub , Perl Yonatan Sanz , Pieper Florian , Galindo-Leon Edgar , Engel Andreas K. , Deco Gustavo 
Published: July 2023

AbstractBrain signal irreversibility has been shown to be a promising approach to study neural dynamics. Nevertheless, the relation with cortical hierarchy and the influence of different electrophysiological features is not completely understood. In this study, we recorded local field potentials (LFPs) during spontaneous behavior, including awake and sleep periods, using custom micro-electrocorticographic (μECoG) arrays implanted in ferrets. In contrast to humans, ferrets remain less time in each state across the sleep-wake cycle. We deployed a diverse set of metrics in order to measure the levels of complexity of the different behavioral states. In particular, brain irreversibility, which allows us to quantify the level of non-equilibrium captured by the arrow of time of the signal, revealed the hierarchical organization of the ferret’s cortex. We found different signatures of irreversibility and functional hierarchy of large-scale dynamics in three different brain states (active awake, quiet awake, and deep sleep), showing a lower level of irreversibility in the deep sleep stage, compared to the other. Irreversibility also allowed us to disentangle the influence of different brain regions and frequency bands in this process, showing a predominance of the parietal area and the theta band. Furthermore, when inspecting the embedded dynamic through a Hidden Markov Model, the deep sleep stage was revealed to have a lower switching rate and lower entropy production. These results suggest functional hierarchies in organization that can be revealed through thermodynamic features and information theory metrics.
Investigating the neural basis of schematic false memories by examining schematic and lure pattern similarity
Authors: Carpenter Catherine M. , Dennis Nancy A. 
Published: July 2023

AbstractSchemas allow us to make assumptions about the world based upon previous experiences and aid in memory organization and retrieval. However, a reliance on schemas may also result in increased false memories to schematically related lures. Prior neuroimaging work has linked schematic processing in memory tasks to activity in prefrontal, visual, and temporal regions. Yet, it is unclear what type of processing in these regions underlies memory errors. The current study examined where schematic lures exhibit greater neural similarity to schematic targets, leading to this memory error, as compared to neural overlap with non-schematic lures, which, like schematic lures, are novel items at retrieval. Results showed that patterns of neural activity in ventromedial prefrontal cortex, medial frontal gyrus, middle temporal gyrus, hippocampus, and occipital cortices exhibited greater neural pattern similarity for schematic targets and schematic lures than between schematic lures and non-schematic lures. As such, results suggest that schematic membership, and not object history, may be more critical to the neural processes underlying memory retrieval in the context of a strong schema.
e-Health Multimodal Interventions for Older Adults with Chronic Non-Cancer Pain: A Scoping Review Protocol
Authors: De Lucia Annalisa , Chiarotto Alessandro , Pasini Ilenia , Pachera Sara , Del Piccolo Lidia , Perlini Cinzia , Donisi Valeria 
Published: July 2023

AbstractBackgroundChronic non-cancer pain (CNCP) is one of the most prevalent health conditions among the elderly, with a considerable impact on the person’s physical, mental and social functioning. The use of a bio-psycho-social multidisciplinary approach has become widely recommended for more likely effective management of chronic pain. In recent years, the growing development and application of e-Health (or digital health) within pain medicine has been showing encouraging results. However, the application of such technologies in the field of pain management among elderly is yet understudied, particularly in regard to the potential impacts of multimodal therapies (i.e., interventions which integrate a physical and a psychological component) provided via digital devices.ObjectiveThe overall aim of this scoping review is to systematically map the existing literature about the e-Health multimodal interventions designed for older adults with CNCP.MethodsMultiple electronic databases (PubMed, Cochrane CENTRAL, Web of Science, PsycINFO) will be searched for relevant articles to August 2023. The review will adhere to the Joanna Briggs Institute (JBI) methodology and will utilize the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for scoping reviews (PRISMA-ScR) reporting guideline and checklist. All eligible studies will be evaluated against the 16-item Quality Assessment Tool (QATSDD). The extracted information will be presented in tabular form along with a narrative summary that is in line with the scoping review’s objective.
Microtubule association of TRIM3 revealed by differential extraction proteomics
Authors: Glover Hannah L. , Mendes Marta , Gomes-Neto Joana , Rusilowicz-Jones Emma V. , Rigden Daniel J. , Dittmar Gunnar , Urbé Sylvie , Clague Michael J. 
Published: July 2023

AbstractThe microtubule network is formed from polymerised Tubulin subunits and associating proteins, which govern microtubule dynamics and a diverse array of functions. To identify novel microtubule binding proteins, we have developed an unbiased biochemical assay, which relies on the selective extraction of cytosolic proteins from cells, whilst leaving behind the microtubule network. Candidate proteins are linked to microtubules by their sensitivities to the depolymerising drug Nocodazole or the microtubule stabilising drug, Taxol, which is quantitated by mass spectrometry. Our approach is benchmarked by co-segregation of Tubulin and previously established microtubule-binding proteins. We then identify several novel candidate microtubule binding proteins, from which we have selected the ubiquitin E3 ligase TRIM3 (Tripartite motif-containing protein 3) for further characterisation. We map TRIM3 microtubule binding to its C-terminal NHL-repeat region. We show that TRIM3 is required for the accumulation of acetylated Tubulin, following treatment with Taxol. Furthermore, loss of TRIM3, partially recapitulates the reduction in Nocodazole-resistant microtubules characteristic of Alpha-Tubulin Acetyltransferase 1 (ATAT1) depletion. These results can be explained by a decrease in ATAT1 following depletion of TRIM3 that is independent of transcription.
Somatic DIS3 mutations in Multiple Myeloma arise early in clonal evolution, but are later counterselected due to toxicity
Authors: Kuliński Tomasz M. , Gewartowska Olga , Mroczek Seweryn , Szpila Marcin , Sałas Katarzyna , Liudkovska Vladyslava , Dziembowski Andrzej 
Published: July 2023

AbstractDIS3 encodes an essential ribonucleic subunit of the nuclear exosome complex, responsible for degrading RNA in the nucleus. Somatic DIS3 mutations drive translocations in B cells, leading to multiple myeloma (MM). Clinical data analysis reveals that 42% of DIS3 mutations occur at three recurrent residues (D479, D488, and R780). These mutations, deactivating DIS3 exonucleolytic activity, are never homozygous, often appearing as minor subclones in advanced MM. Surprisingly, mutant DIS3 alleles undergo loss-of-heterozygosity, correlating with frequent del(13q) encompassing DIS3. Overexpression of wild-type DIS3 enhances growth and viability of DIS3-mutated MM cells, while CRISPR-mediated knock-out of the mutant variant, followed by longitudinal co-culture, replicates its elimination through counterselection, observed in the natural course of the disease. In mice, the heterozygous DIS3D479mutation is embryolethal, confirming its dominant toxic effects. Transcriptome analysis of patients and cell lines reveals specific transcriptional signatures of DIS3 mutations with accumulation of non-coding unstable RNA species and including secondary indications of decreased proliferation. All these signatures are reversible upon mutant DIS3 loss-of-heterozygosity. DIS3 is an intriguing hit-and-run oncogene that drives MM, but is subsequently eliminated during clonal evolution.
Multiple Myeloma associated DIS3 mutations drive AID-dependent IGH Translocations
Authors: Kuliński Tomasz M. , Gewartowska Olga , Mahé Mélanie , Kasztelan Karolina , Durys Janina , Stroynowska-Czerwińska Anna , Jedynak-Slyvka Marta , Owczarek Ewelina P. , Chaudhury Debadeep , Nowotny Marcin , Pękowska Aleksandra , Séraphin Bertrand , Dziembowski Andrzej 
Published: July 2023

SummaryRole of dominant DIS3 mutations in multiple myeloma (MM) remains elusive. These mutations decrease the exoribonucleolytic activity of DIS3, a key nuclear RNA-degrading enzyme. Utilizing knock-in mice with clinical Dis3 G766R variant, we demonstrate an increased frequency of aberrant chromosomal translocations in B-cells, leading to plasmacytoma, an early-stage MM model. DIS3-dependent translocations display characteristics of aberrant activation-induced deaminase (AID) activity. In clinical MM samples with DIS3 mutations, driver genes also show AID-dependent lesions. Mechanistically, mutated DIS3 accumulates on chromatin-associated RNA substrates, including aberrant AID action sites, fostering oncogenic chromosomal rearrangements. Translocations occur during immunoglobulin class switch recombination, a process otherwise unaffected in MM patients or mice with mutated DIS3. Dis3 G766R mutation does not alter chromatin architecture in activated B-cells but hijacks it to bring together enhancers with proto-oncogenes permanently. In conclusion, gain-of-function DIS3 mutations increase nuclear exosome and AID affinity to chromatin, facilitating IGH translocations and driving MM transformation.
Deep estimation of the intensity and timing of selection from ancient genomes
Authors: Laval Guillaume , Patin Etienne , Quintana-Murci Lluis , Kerner Gaspard 
Published: July 2023

SUMMARYLeveraging past allele frequencies has proven to be key to identify the impact of natural selection across time. However, this approach often suffers from imprecise estimations of the intensity (s) and timing (T) of selection particularly when ancient samples are scarce in specific epochs. Here, we aimed at bypassing the computation of past allele frequencies by implementing new convolutional neural networks (CNNs) algorithms that directly use ancient genotypes sampled across time to refine the estimations of selection parameters. Using computer simulations, we first show that genotype-based CNNs consistently outperform an approximate Bayesian computation (ABC) approach based on past allele frequency trajectories, regardless of the selection model assumed and of the amount of ancient genotypes available. When applying this method to empirical data from modern and ancient Europeans, we confirmed the reported excess of selection events in post-Neolithic Europe, independently of the continental subregion studied. Furthermore, we substantially refined the ABC-based estimations ofsandTfor a set of positively-and negatively-selected variants recently identified, including iconic cases of positive selection and experimentally validated disease-risk variants. Thanks to our CNN predictions we provide support to the history of recent and strong selection in northern Europe associated to the Black Death pandemic and confirm the heavy burden recently imposed by tuberculosis in Europe. These findings collectively support that detecting the imprints of natural selection on ancient genomes are crucial for unraveling the past history of severe human diseases.
A conserved fertilization complex of Izumo1, Spaca6, and Tmem81 mediates sperm-egg interaction in vertebrates
Authors: Deneke Victoria E. , Blaha Andreas , Lu Yonggang , Draper Jonne M. , Phan Clara S. , Panser Karin , Schleiffer Alexander , Jacob Laurine , Humer Theresa , Stejskal Karel , Krssakova Gabriela , Handler Dominik , Kamoshita Maki , Vance Tyler D.R. , Roitinger Elisabeth , Lee Jeffrey E. , Ikawa Masahito , Pauli Andrea 
Published: July 2023

ABSTRACTFertilization, the fusion of sperm and egg, is essential for sexual reproduction. While several proteins have been demonstrated to be essential for the binding and fusion of gametes in vertebrates, the molecular mechanisms driving this key process are poorly understood. Here, we performed a protein interaction screen using AlphaFold-Multimer to uncover protein-protein interactions in fertilization. This screen resulted in the prediction of a trimeric complex composed of the essential fertilization factors Izumo1 and Spaca6, and Tmem81, a protein previously not implicated in fertilization. We show that Tmem81 is a conserved, testis-expressed transmembrane protein that is evolutionarily related to Izumo1 and Spaca6 and is essential for male fertility in fish and mice. Consistent with trimer formationin vivo, zebrafishizumo1-/-,spaca6-/-, andtmem81-/-mutants exhibit the same sperm-egg binding defect and show co-depletion of all three proteins in sperm. Moreover, we provide experimental evidence that Izumo1, Spaca6, and Tmem81 interact in zebrafish sperm. Strikingly, the Izumo1-Spaca6 interaction is predicted to form a cleft that serves as a binding site for Bouncer, the only identified egg protein essential for fertilization in zebrafish. Together, these results provide compelling evidence for a conserved sperm factor complex in vertebrates that forms a specific interface for the sperm-egg interaction required for successful fertilization.
Analysis of behavioral flow resolves latent phenotypes
Authors: von Ziegler Lukas M. , Roessler Fabienne K. , Sturman Oliver , Waag Rebecca , Privitera Mattia , Duss Sian N , O’Connor Eoin C. , Bohacek Johannes 
Published: July 2023

AbstractThe nuanced detection of rodent behavior in preclinical biomedical research is essential for understanding disease conditions, genetic phenotypes, and internal states. Recent advances in machine vision and artificial intelligence have popularized data-driven methods that segment complex animal behavior into clusters of behavioral motifs. However, despite the rapid progress, several challenges remain: Statistical power typically decreases due to multiple testing correction, poor transferability of clustering approaches across experiments limits practical applications, and individual differences in behavior are not considered. Here, we introduce “behavioral flow analysis” (BFA), which creates a single metric for all observed transitions between behavioral motifs. Then, we establish a “classifier-in-the-middle” approach to stabilize clusters and enable transferability of our analyses across datasets. Finally, we combine these approaches with dimensionality reduction techniques, enabling “behavioral flow fingerprinting” (BFF) for individual animal assessment. We validate our approaches across large behavioral datasets with a total of 443 open field recordings that we make publicly available, comparing various stress protocols with pharmacologic and brain-circuit interventions. Our analysis pipeline is compatible with a range of established clustering approaches, it increases statistical power compared to conventional techniques, and has strong reproducibility across experiments within and across laboratories. The efficient individual phenotyping allows us to classify stress-responsiveness and predict future behavior. This approach aligns with animal welfare regulations by reducing animal numbers, and enhancing information extracted from experimental animals
Blood pressure pulsations modulate olfactory bulb neuronal activity via mechanosensitive ion channels
Authors: Salameh Luna Jammal , Bitzenhofer Sebastian H. , Hanganu-Opatz Ileana L. , Dutschmann Mathias , Egger Veronica 
Published: July 2023

AbstractThe transmission of heartbeat through the cerebral vascular system is known to cause intracranial pressure pulsations. Here we describe that arterial pressure pulsations within the brain can directly modulate central neuronal activity. In a semi-intact rat brain preparation, pressure pulsations elicit correlated local field oscillations in the olfactory bulb (OB) that are sensitive to hypoxia and block of mechanosensitive channels. We find that mitral cell spiking activity is in part synchronized to these oscillations. Indeed, in awake animals the firing of a subset of OB neurons is entrained to heartbeat within ∼ 20 ms. Several lines of evidence indicate the expression of a mechanosensitive ion channel within the mitral cell membranes, most likely Piezo2, implementing a pressure pulsation transduction pathway and thus baroreception within the OB. We propose that this intrinsic interoceptive mechanism modulates OB neuronal activity e.g. during arousal and also could influence brain activity on a wider scale.
Beyond 40 fluorescent probes for deep phenotyping of blood mononuclear cells, using spectral technology
Authors: Schmutz Sandrine , Commere Pierre-Henri , Montcuquet Nicolas , Cumano Ana , Ait-Mansour Cédric , Novault Sophie , Hasan Milena 
Published: July 2023

ABSTRACTThe analytical capability of flow cytometry is crucial for differentiating the growing number of cell subsets found in human blood. This is important for accurate immunophenotyping of patients with few cells and a large number of parameters to monitor.Here, we present a 43-parameter panel to analyze peripheral blood mononuclear cells from healthy individuals using 41 fluorescence-labelled monoclonal antibodies, an autofluorescent channel, and a viability dye. We demonstrate minimal population distortions that lead to optimized population identification and reproducible results. We have applied an advanced approach in panel design, in selection of sample acquisition parameters and in data analysis. Appropriate autofluorescence identification and integration in the unmixing matrix, allowed for resolution of unspecific signals and increased dimensionality. Addition of one laser without assigned fluorochrome resulted in decreased fluorescence spill over and improved discrimination of cell subsets. It also increased staining index when autofluorescence was integrated in the matrix. We conclude that spectral flow cytometry is highly valuable tool for high-end immunophenotyping, and that fine-tuning of major experimental steps is key for taking advantage of its full capacity.
Phenotypic screen-based discovery of a small molecule that can increase adult neurogenesis and improve memory
Authors: Davies Julie , Hoerder-Suabedissen Anna , Musaelyan Ksenia , Torroba Blanca , Daubney Jesse , Untermoser Nicole , Carter Tom , Bauer Ulrich , Walker Roderick , Harris Kate S. , Bromhead Liam , Suresh Megalakshi , Fouka Penelope , Li Yichen , Davies Steve , Webber Caleb , Bannerman David , Terstappen Georg , Russell Angela , Szele Francis G. 
Published: July 2023

AbstractStem cells and neurogenesis persist in the postnatal and adult brain. Adult brain stem cells can be neuroprotective in disease and augment hippocampal-dependent cognitive function and thus are an important therapeutic target. Although many molecules have been discovered that regulate neurogenesis, few studies have attempted to amplify the process pharmacologically as a therapeutic goal. To address this gap, we used murine neurosphere cultures from the two major stem cell niches: the subventricular zone (SVZ) and the subgranular zone (SGZ). We screened compounds sharing pharmacophores with known inducers of neurogenesis and found several dozen proneurogenic compounds in anin vitrophenotypic screen. One, OXS-N1 was stable, and had acceptable absorption, distribution, metabolism, and excretion profiles in animal studies. OXS-N1 could increase neurogenesis in the SVZ and SGZ in WT mice after both intraperitoneal and oral administration. The number of newborn neurons (BrdU+/NeuN+) was increased; however, the number of activated stem cells (BrdU+/GFAP+) was not, suggesting an effect on neurogenesis independent of stem cell activation. This was supported by OXS-N1 increasing neurosphere differentiation but not proliferation. OXS-N1 also increased neurogenesis and improved performance in a Y maze cognitive task in PDGF-APPSw,Ind mice, a model of Alzheimer’s disease. RNAseq of SVZ and SGZ neurospheres in turn showed that genes associated with synaptic function were significantly increased by OXS-N1. Our study demonstrates the utility of phenotypic screening for the identification of molecules that increase neurogenesis and might be of therapeutic relevance.