bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tailoring evidence into action: using a codesign approach for biodiversity information in the Tropical Andes
Authors: Valdez Jose W. , Pereira Henrique M. , Morejón Gustavo Francisco , Acosta-Muñoz Cristina , Bonet Garcia Francisco Javier , Castro Vergara Lucía , Xavier Claros R. , Gill Michael J. , Josse Carmen , Lafuente-Cartagena Indyra , Langstroth Robert , Sheppard Sidney Novoa , Orihuela Gabriela , Prieto-Albuja Francisco J. , Quillahuaman Natividad , Terán Marcos F. , Zambrana-Torrelio Carlos M. , Navarro Laetitia M. , Fernandez Miguel 
Published: May 2023

AbstractBiodiversity conservation is a complex and transdisciplinary problem that requires engagement and cooperation among scientific, societal, economic, and political institutions. However, historical approaches have often failed to bring together and address the needs of relevant stakeholders in decision-making processes. The Tropical Andes, a biodiversity hotspot where conservation efforts often conflict with socioeconomic issues and policies that prioritize economic development, provides an ideal model to develop and implement more effective approaches. In this study, we present a codesign approach that mainstreams and improves the flow of biodiversity information in the Tropical Andes, while creating tailored outputs that meet the needs of economic and societal stakeholders. We employed a consultative process that brought together biodiversity information users and producers at the local, national, and regional levels through a combination of surveys and workshops. This approach identified priority needs and limitations of the flow of biodiversity information in the region, which led to the co-design of user-relevant biodiversity indicators. By leveraging the existing capacities of biodiversity information users and producers, we were able to co-design multiple biodiversity indicators and prioritize two for full implementation ensuring that the data was findable, accessible, interoperable, and reusable based on the FAIR principles. This approach helped address limitations that were identified in the stakeholder engagement process, including gaps in data availability and the need for more accessible biodiversity information. Additionally, capacity-building workshops were incorporated for all stakeholders involved, which aimed to not only improve the current flow of biodiversity information in the region but also facilitate its future sustainability. Our approach can serve as a valuable blueprint for mainstreaming biodiversity information and making it more inclusive in the future, especially considering the diverse worldviews, values, and knowledge systems between science, policy, and practice.
Protein-Protein interaction and quantitative phosphoproteomic studies reveal potential mitochondrial substrates of protein phosphatase 2A-B’ζ holoenzyme
Authors: Elshobaky Ahmed , Lillo Cathrine , Hodén Kristian Persson , Kataya Amr R.A. 
Published: May 2023

AbstractProtein phosphatase 2A (PP2A) is a heterotrimeric conserved serine/threonine phosphatase complex including a catalytic, scaffolding, and regulatory subunit. Three A Subunits, 17 B subunits, and five C subunits are encoded by theArabidopsisgenome, allowing 255 possible PP2A holoenzyme combinations. The regulatory subunits are crucial for substrate specificity and PP2A complex localization and are classified into B, B’, and B’’ non-related families in land plants. InArabidopsis, the close homologs B’η, B’θ, B’γ, and B’ζ are further classified into a subfamily of B’ called B’η. Previous studies suggest a role of mitochondrial targeted PP2A subunit (B’ζ) in energy metabolism and plant innate immunity. Potentially, the PP2A-B’ζ holoenzyme is involved in the regulation of the mitochondrial succinate/fumarate translocator or affects enzymes involved in energy metabolism. To investigate this hypothesis, the interaction between PP2A-B’ζ and enzymes involved in the mitochondrial energy flow was investigated using bimolecular fluorescence complementation in tobacco and onion cells. Interaction of B’ζ subunit was confirmed with the Krebs cycle proteins Succinate/fumarate translocator (mSFC1), Malate dehydrogenase (mMDH2), and Aconitase (ACO3). Additional putative interacting candidates were deduced from comparing the enriched phosphoproteomes of wild type and B’ζ mutants: the mitochondrial regulatorArabidopsispentatricopeptide repeat 6 (PPR6) and the two metabolic enzymes Phosphoenolpyruvate carboxylase (PPC3) and Phosphoenolpyruvate carboxykinase (PCK1). Overall, this study identifies potential PP2A substrates and highlights the role of PP2A in regulating energy metabolism in mitochondria.
Noradrenergiclocus coeruleusactivity functionally partitions NREM sleep to gatekeep the NREM-REM sleep cycle
Authors: Osorio-Forero Alejandro , Foustoukos Georgios , Cardis Romain , Cherrad Najma , Devenoges Christiane , Fernandez Laura M.J. , Lüthi Anita 
Published: May 2023

AbstractThe noradrenergiclocus coeruleus(LC) is vital for brain states underlying wakefulness, whereas its roles for sleep remain uncertain. Combining mouse sleep-wake monitoring, behavioral manipulations, LC fiber photometry and closed-loop optogenetics, we found that LC neuronal activity partitioned non-rapid-eye-movement sleep (NREMS) into alternating brain and autonomic states that rule the NREMS-REMS cycle. High LC activity levels generated an autonomic-subcortical arousal state that facilitated cortical microarousals, while low levels were obligatory for REMS entries. Timed optogenetic LC inhibition revealed that this functional alternation set the duration of the NREMS-REMS cycle by ruling REMS entries during undisturbed sleep and when pressure for REMS was high. A stimulus-enriched, stress-promoting wakefulness increased high LC activity levels at the expense of low ones in subsequent NREMS, fragmenting NREMS through microarousals and delaying REMS onset. We conclude that LC activity fluctuations gatekeep the NREM-REMS cycle over recurrent infraslow intervals, but they also convey vulnerability to adverse wake experiences.
Binding of cortical functional modules by synchronous high frequency oscillations
Authors: Garrett Jacob C. , Verzhbinsky Ilya A. , Kaestner Erik , Carlson Chad , Doyle Werner K. , Devinsky Orrin , Thesen Thomas , Halgren Eric 
Published: May 2023

AbstractWhether high-frequency phase-locked oscillations facilitate integration (‘binding’) of information across widespread cortical areas is controversial. Here we show with intracranial EEG that cortico-cortical co-ripples (∼100ms long ∼90Hz oscillations) increase during reading and semantic decisions, at the times and co-locations when and where binding should occur. Fusiform wordform areas co-ripple with virtually all language areas, maximally from 200-400ms post-word-onset. Semantically-specified target words evoke strong co-rippling between wordform, semantic, executive and response areas from 400-800ms, with increased co-rippling between semantic, executive and response areas prior to correct responses. Co-ripples were phase-locked at zero-lag over long distances (>12cm), especially when many areas were co-rippling. General co-activation, indexed by non-oscillatory high gamma, was mainly confined to early latencies in fusiform and earlier visual areas, preceding co-ripples. These findings suggest that widespread synchronous co-ripples may assist the integration of multiple cortical areas for sustained periods during cognition.One Sentence SummaryWidespread visual, wordform, semantic, executive and response areas phase-lock at 90Hz during integrative semantic processing.
Components of Isolated Skeletal Muscle Differentiated Through Antibody Validation
Authors: Stephens Dominique C. , Mungai Margaret , Crabtree Amber , Beasley Heather K. , Garza-Lopez Edgar , Vang Larry , Neikirk Kit , Vue Zer , Vue Neng , Marshall Andrea G. , Turner Kyrin , Shao Jian-qiang , Sarker Bishnu , Murray Sandra , Gaddy Jennifer A. , Davis Jamaine , Damo Steven M. , Hinton Antentor O. 
Published: May 2023

SummaryIsolation of skeletal muscles allows for the exploration of many complex diseases. Fibroblasts and myoblast play important roles in skeletal muscle morphology and function. However, skeletal muscles are complex and made up of many cellular populations and validation of these populations is highly important. Therefore, in this article, we discuss a comprehensive method to isolate mice skeletal muscle, create satellite cells for tissue culture, and use immunofluorescence to validate our approach.Graphical Abstract
Creating Optimal Conditions for OPA1 Isoforms by Western Blot in Skeletal Muscle Cells and Tissue
Authors: Stephens Dominique C. , Mungai Margaret , Crabtree Amber , Beasley Heather K. , Garza-Lopez Edgar , Neikirk Kit , Bacevac Serif , Vang Larry , Vue Zer , Vue Neng , Marshall Andrea G. , Turner Kyrin , Shao Jianqiang , Murray Sandra , Gaddy Jennifer A. , Wanjalla Celestine , Davis Jamaine , Damo Steven , Hinton Antentor O. 
Published: May 2023

SummaryOPA1 is a dynamin-related GTPase that modulates various mitochondrial functions and is involved in mitochondrial morphology. There are eight different isoforms of OPA1 in humans and five different isoforms in mice that are expressed as short or long-form isoforms. These isoforms contribute to OPA1’s ability to control mitochondrial functions. However, isolating OPA1 all long and short isoforms through western blot has been a difficult task. To address this issue, we outline an optimized western blot protocol to isolate 5 different isoforms of OPA1 on the basis of different antibodies. This protocol can be used to study changes in mitochondrial structure and function.Tweetable AbstractWestern blot protocol optimization to visualize OPA1 isoforms.HighlightsProtocol for isolating OPA1 isoforms in primary skeletal muscle myoblast and myotubesSteps for running isolated skeletal muscle cells from muscle tissue on a gelHow to collect samples in preparation for western blottingDetection of OPA1 isoformsGraphical AbstractMethod SummarySamples for western blot analysis are isolated from lysed cells, loaded onto a gel, and ran using optimized conditions to better isolate OPA1 isoforms. Samples are transferred to a membrane for incubation and protein detection using OPA1 antibodies.
Ablation ofSam50is associated with fragmentation and alterations in metabolism in murine and human myotubes
Authors: Shao Bryanna , Killion Mason , Oliver Ashton , Vang Chia , Zeleke Faben , Neikirk Kit , Vue Zer , Garza-Lopez Edgar , Shao Jian-qiang , Mungai Margaret , Lam Jacob , Williams Qiana , Altamura Christopher T. , Whiteside Aaron , Kabugi Kinuthia , McKenzie Jessica , Koh Alice , Scudese Estevão , Vang Larry , Marshall Andrea G. , Crabtree Amber , Tanghal Janelle I. , Stephens Dominique , Koh Ho-Jin , Jenkins Brenita C. , Murray Sandra A. , Cooper Anthonya T. , Williams Clintoria , Damo Steven M. , McReynolds Melanie R. , Gaddy Jennifer A. , Wanjalla Celestine N. , Beasley Heather K. , Hinton Antentor 
Published: May 2023

AbstractThe Sorting and Assembly Machinery (SAM) Complex is responsible for assembling β-barrel proteins in the mitochondrial membrane. Comprising three subunits, Sam35, Sam37, and Sam50, the SAM complex connects the inner and outer mitochondrial membranes by interacting with the mitochondrial contact site and cristae organizing system (MICOS) complex. Sam50, in particular, stabilizes the mitochondrial intermembrane space bridging (MIB) complex, which is crucial for protein transport, respiratory chain complex assembly, and regulation of cristae integrity. While the role of Sam50 in mitochondrial structure and metabolism in skeletal muscle remains unclear, this study aims to investigate its impact. Serial block-face-scanning electron microscopy (SBF-SEM) and computer-assisted 3D renderings were employed to compare mitochondrial structure and networking inSam50-deficient myotubes from mice and humans with wild-type (WT) myotubes. Furthermore, autophagosome 3D structure was assessed in human myotubes. Mitochondrial metabolic phenotypes were assessed using Gas Chromatography-Mass Spectrometry-based metabolomics to explore differential changes in WT andSam50-deficient myotubes. The results revealed increased mitochondrial fragmentation and autophagosome formation inSam50-deficient myotubes compared to controls. Metabolomic analysis indicated elevated metabolism of propanoate and several amino acids, including ß-Alanine, phenylalanine, and tyrosine, along with increased amino acid and fatty acid metabolism inSam50-deficient myotubes. Furthermore, impairment of oxidative capacity was observed uponSam50ablation in both murine and human myotubes, as measured with the XF24 Seahorse Analyzer. Collectively, these findings support the critical role of Sam50 in establishing and maintaining mitochondrial integrity, cristae structure, and mitochondrial metabolism. By elucidating the impact ofSam50-deficiency, this study enhances our understanding of mitochondrial function in skeletal muscle.
A method for extracting an approximated connectome from libraries of single anatomically co-registered cell reconstructions
Authors: Manjunatha K.K.H. , Bruzzone M. , Nicoletti G. , Suweis S. , dal Maschio M. 
Published: May 2023

AbstractMapping functional brain information onto a circuit wiring diagram supporting possible brain circuit working mechanisms remains challenging. When available, the analysis of electron microscopy based high-resolution connectomes, leveraging synapse annotation, allows for unraveling portions of the nervous system’s wiring diagram or specific circuit motifs. However, obtaining a complete brain reconstruction with annotation of the synapses and extracting the general organization principles of the neuronal networks across the brain remains a demanding effort. To extend the available methods, we present here an approach to obtain an approximate brain connectome starting from libraries of single cell reconstructions co-registered in a reference anatomical space. Our approach relies on both the Strahler numbering of the nodes characterizing the cell morphological reconstructions and a proximity range criterion, to infer the general connectivity structures between the different cells, in the absence of synapse annotation. First, we confronted this approach on a ground truth derived from a fully annotated EM dataset ofDrosophila melanogaster. The connectivity modules identified with our approach show generally a similar organization compared to those resulting from the EM annotated dataset, in terms of Normalized Mutual Information and Adjusted Rand Index, always with high significance with respect to random null models. Building on this, we then applied this approach to extract an approximate connectome of the zebrafish larvae brain starting from a light microscopy-based dataset of about 3000 co-registered neuronal skeletonizations. Modularity analysis of the retrieved directed and undirected connectomes revealed a hierarchical organization of the resulting graph. The identified architecture encompasses a series of high-order brain-wide neuronal modules composed of a number of lower-order submodules. Importantly, we show that this approximated representation is sufficient for capturing precise and topographically organized connection patterns as well as known functional circuit architectures. In conclusion, we present a scalable, from-circuit-to-brain range, approach to reveal neuronal architectures supporting brain mechanisms, potentially suitable for hypothesis drawing and as for guiding the exploration of and integration with EM connectomes.
SNAP25 disease mutations change the energy landscape for synaptic exocytosis due to aberrant SNARE interactions
Authors: Kádková Anna , Murach Jacqueline , Østergaard Maiken , Malsam Andrea , Malsam Jörg , Lolicato Fabio , Nickel Walter , Söllner Thomas H. , Sørensen Jakob B. 
Published: May 2023

AbstractSNAP25 is one of three neuronal SNAREs driving synaptic vesicle exocytosis. We studied three mutations in SNAP25 that cause epileptic encephalopathy: V48F, and D166Y in the Synaptotagmin-1 (Syt1) binding interface, and I67N, which destabilizes the SNARE-complex. All three mutations reduced Syt1-dependent vesicle docking to SNARE-carrying liposomes and Ca2+-stimulated membrane fusionin vitroand in neurons. The V48F and D166Y mutants (with potency D166Y > V48F) led to reduced Readily Releasable Pool (RRP) size, due to increased spontaneous (mEPSC) release and decreased priming rates. These mutations lowered the energy barrier for fusion and increased the release probability, which are gain-of-function features not found inSyt1knockout (KO) neurons; normalized mEPSC release rates were higher (potency D166Y>V48F) than in theSyt1KO. These mutations (potency D166Y > V48F) increased spontaneous association to partner SNAREs, resulting in unregulated membrane fusion. In contrast, the I67N mutant decreased mEPSC frequency and evoked EPSC amplitudes due to an increase in the apparent height of the energy barrier for fusion, whereas the RRP size was unaffected. This could be partly compensated by positive charges lowering the energy barrier. Overall, pathogenic mutations in SNAP25 cause complex changes in the energy landscape for priming and fusion.
Age- and caste-independent piRNAs in the germline and miRNA profiles linked to caste and fecundity in the antTemnothorax rugatulus
Authors: Seistrup Ann-Sophie , Choppin Marina , Govind Shamitha , Feldmeyer Barbara , Kever Marion , Karaulanov Emil , Séguret Alice , Karunanithi Sivarajan , Almeida Miguel V. , Ketting René F. , Foitzik Susanne 
Published: May 2023

AbstractSocial insects are models for phenotypic plasticity: the generation of different phenotypes from the same genotype. Ant queens and workers differ not only in their morphology and behaviour, but also in their fecundity and lifespan, which is often several times higher in queens. However, the gene regulatory mechanisms underlying these differences are not yet well understood. Since ant queens can live and reproduce for more than two decades, they need to protect their germline from the activity of transposable elements (TEs). This protection may be redundant in short-lived, often sterile workers. We have analysed the expression of two protective classes of smallRNAs, microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), in different tissues, castes, and age classes of the ant speciesTemnothorax rugatulus. We show that piRNAs are particularly active in the ovaries of queens. TEs are clear targets of the piRNAs in this ant species, and piRNA-specific sequence signatures in the ovaries of all queens regardless of age indicate that young and old queens have similarly active piRNA pathways. Interestingly, the reduced ovaries of the workers also showed the same level of piRNA activity. This was not only the case in young, fertile workers from queenless nests, but also in the presumably older foragers, which have almost completely regressed ovaries. These findings suggest that the germline in these ants is invariably protected by piRNA activity, irrespective of ovarian development. The brain and thorax of queens also contained piRNAs, but at lower levels, and the piRNA-specific ping-pong signatures were strongly reduced in these tissues. We also annotated and analysed miRNAs in different tissues. We confidently detected the expression of 304 miRNAs. Of these, 10 were enriched in the brain and three to the thorax, whereas 83 were specific to the ovaries. 105 miRNAs were found to be expressed in all three tissues. We also identified miRNAs whose expression potentially is related to ant caste, fecundity, and age, suggesting that caste-specific gene activity may be regulated in part by miRNAs. In contrast, our studies of piRNA activity indicate similar profiles across caste, fecundity and age groups, but strong tissue specificity with the highest piRNA mediated TE protection in the germline.
Time-gated Fluorescence Lifetime Imaging in the Near Infrared Regime; A Comprehensive Study Toward In Vivo Imaging
Authors: Harel Meital , Arbiv Uri , Ankri Rinat 
Published: May 2023

AbstractFluorescence lifetime imaging has an enormous impact on our understanding of biological systems, both in vitro and in vivo. It is a powerful tool for the non-invasive in vitro and in vivo biomolecular and cellular investigations. In particular, it has the potential to target and multiplex different species with high sensitivity and specificity, providing a fast and noninvasive readout at low cost. In this work, we present a time-saving Monte Carlo (MC) simulation of fluorescent photons scattering within a turbid medium, followed by phasor analyzes which enabled the simple multiplexing of different targets in one frame. We then demonstrate a simple and fast method for wide-field FLI in the near-infrared (NIR) region, where tissue scattering and autofluorescence are significantly lower, to enable imaging of deep tissue, using the state-of-the-art timed single-photon avalanche diode array camera (SPAD), SPAD512S. In particular, we show how phasor scattering increases with depth. However, using appropriate background correction, a simple “cut-off” method, and averaging, we can multiplex two targets in one image to a depth of 1 cm in tissue. Our results show that it is possible to perform in vivo FLI under challenging conditions, using standard NIR fluorophores with short lifetimes.
Genomic, effector protein and culture-based analysis ofCyclaneusma minusin New Zealand provides evidence for multiple morphotypes
Authors: Tarallo M. , Dobbie K. , Leite L. Nunes , Waters T. , Gillard K. , Sen D. , McDougal R.L. , Mesarich C.H. , Bradshaw R.E. 
Published: May 2023

AbstractCyclaneusma needle cast, caused byCyclaneusma minus, affectsPinusspecies around the world. Previous studies suggested the presence of two distinct morphotypes in New Zealand, ‘verum’ and ‘simile’. Traditional mycological analyses revealed a third morphotype with clear differences in colony morphology and cardinal growth rates at varying temperatures. Genome sequencing of eightC. minusisolates provided further evidence of the existence of a third morphotype, named ‘novus’ in this study. To further analyse these morphotypes, we predicted candidate effector proteins for all eight isolates, and also characterized a cell-death eliciting effector family, Ecp32, which is present in other pine phytopathogens. In concordance with their distinct classification into three different morphotypes, the number of Ecp32 family members differed, with patterns of pseudogenization and some family members being found exclusively in some morphotypes. We also showed that proteins belonging to the Ecp32 family trigger cell death responses in non-hostNicotianaspecies, and, as previously demonstrated for other plant pathogens, theC. minusproteins belonging to the Ecp32 family adopt a β-trefoil fold. Understanding the geographical range and variations in virulence and pathogenicity of these morphotypes will provide a better understanding of pine needle diseases as well as enable the development of more durable methods to control this disease.