bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elevated levels of iodide promote peroxidase-mediated protein iodination and inhibit protein chlorination
Authors: Jokumsen Kathrine V. , Huhle Valerie H. , Hägglund Per M. , Davies Michael J. , Gamon Luke F. 
Published: February 2024

AbstractAt inflammatory sites, immune cells generate oxidants including H₂O₂. Myeloperoxidase (MPO), released by activated leukocytes employs H₂O₂ and halide/pseudohalides to form hypohalous acids that mediate pathogen killing. Hypochlorous acid (HOCl) is a major species formed. Excessive or misplaced HOCl formation damages host tissues with this linked to multiple inflammatory diseases. Previously (Redox Biology, 2020, 28, 101331) we reported that iodide (I⁻) modulates MPO-mediated protein damage by decreasing HOCl generation with concomitant hypoiodous acid (HOI) formation. HOI may however impact on protein structure, so in this study we examined whether and how HOI, from peroxidase/H₂O₂/I⁻ systems+Cl⁻, modifies proteins. Experiments employed MPO and lactoperoxidase (LPO) and multiple proteins (serum albumins, anastellin), with both chemical (intact protein and peptide mass mapping, LC-MS) and structural (SDS-PAGE) changes assessed. LC-MS analyses revealed dose-dependent iodination of anastellin and albumins by LPO/H2O2with increasing I⁻. Incubation of BSA with MPO/H2O2/Cl⁻ revealed modest chlorination (Tyr286, Tyr475, ∼4%) and Met modification. Lower levels of these species, and extensive iodination at specific Tyr and His residues (>20% modification with>10 µM I⁻) were detected with increasing I⁻. Anastellin dimerization was inhibited by increasing I⁻, but less marked changes were observed with albumins. These data confirm that I⁻ competes with Cl⁻ for MPO and is an efficient HOCl scavenger. These processes decrease protein chlorination and oxidation, but result in extensive iodination. This is consistent with published data on the presence of iodinated Tyr on neutrophil proteins. The biological implications of protein iodination relative to chlorination require further clarification.
Automated plankton monitoring suggests a key role of microzooplankton and temperature for predicting dynamics of phytoplankton size classes
Authors: Merkli Stefanie , Merz Ewa , Reyes Marta , Ntetsika Pinelopi , Dennis Stuart R. , Isles Peter D.F. , Kyathanahally Sreenath , Baity-Jesi Marco , To Sze-Wing , Merico Agostino , Pomati Francesco 
Published: February 2024

AbstractThe interplay between abiotic (resource supply, temperature) and biotic (grazing) factors determines growth and loss processes in phytoplankton through resource competition and trophic interactions, which are mediated by morphological traits like size. Here, we study the relative importance of grazers, water physics and chemistry on the daily net accumulation rates (AR) of individual phytoplankton from natural communities, grouped into six size classes from circa 10 to 500 μm. Using a Random Forest modelling approach and four years of daily data from a lake, we find that water temperature is generally a pivotal control of all phytoplankton AR. At the same time, nutrients and light are important for the smallest and the largest classes. Mesozooplankton abundance is a key predictor of the AR for small phytoplankton, with microzooplankton being important for the middle-size range. In our data, large and small phytoplankton have different (seasonal) blooming patterns: small forms are favoured by low temperature and grazing, and high phosphorus levels. Larger forms show positive ARs at high temperatures and low phosphorus (being relatively insensitive to zooplankton grazing). These results help us understand the opportunities and limitations of using size to explain and model phytoplankton responses to biotic and abiotic environmental change.
Odor-induced persistent neural activity in associative encoding in humans
Authors: Tarrida Joan , Moreno Manuel , Vidal Jordi , Panyella David , Marco-Pallarés Josep , Fuentemilla Lluís 
Published: February 2024

AbstractThis study explored the impact of brief exposure to odor cues on sustained neural activity during a 6-second delay period before memory encoding of a picture image. Combining univariate and multivariate ERP analytical approaches, our results align with nonhuman data, indicating that odor cues induced sustained neural activity in humans, persisting beyond the odor exposure throughout the nearly 6-second delay period. We observed higher amplitude of sustained ERPs for unpleasant compared to pleasant odor cues. Additionally, participants exhibited more confident memory recall for pictures preceded by unpleasant rather than pleasant odor cues during encoding, underscoring the influence of brief odor cues on memory formation for temporally distant events. In conclusion, this study revealed that brief exposure to odor cues induced sustained neural activity in humans, with distinct effects on memory formation along the pleasantness dimension, emphasizing the lasting impact of olfactory stimuli on cognitive processes.
The ciliary protein C2cd3 is required for mandibular musculoskeletal tissue patterning
Authors: Brooks Evan C. , Han Simon J.Y. , Bonatto Paese Christian Louis , Lewis Amya A. , Aarnio-Peterson Megan , Brugmann Samantha A. 
Published: February 2024

AbstractThe mandible is composed of several musculoskeletal tissues including bone, cartilage, and tendon that require precise patterning to ensure structural and functional integrity. Interestingly, most of these tissues are derived from one multipotent cell population called cranial neural crest cells (CNCCs). How CNCCs are properly instructed to differentiate into various tissue types remains nebulous. To better understand the mechanisms necessary for the patterning of mandibular musculoskeletal tissues we utilized the avian mutanttalpid2(ta2) which presents with several malformations of the facial skeleton including dysplastic tendons, mispatterned musculature, and bilateral ectopic cartilaginous processes extending off Meckel’s cartilage. We found an ectopic epithelial BMP signaling domain in theta2mandibular prominence (MNP) that correlated with the subsequent expansion ofSOX9+ cartilage precursors. These findings were validated with conditional murine models suggesting an evolutionarily conserved mechanism for CNCC-derived musculoskeletal patterning. Collectively, these data support a model in which cilia are required to define epithelial signal centers essential for proper musculoskeletal patterning of CNCC-derived mesenchyme.
BTK and MMP9 regulate NLRP3 inflammasome-dependent cytokine and NET responses in primary neutrophils
Authors: Leal Vinicius N. C. , Bork Francesca , von Guilleaume Juli-Christin , Greve Carsten L. , Bugl Stefanie , Danker Bettina , Bittner Zsofía A. , Grimbacher Bodo , Pontillo Alessandra , Weber Alexander N. R. 
Published: February 2024

AbstractBackgroundInflammation is a double-edged state of immune activation that is required to resolve threats harmful to the host but can also cause severe collateral damage. Polymorphonuclear neutrophils (PMN,) the primary leukocyte population in humans, mediate inflammation through the release of cytokines and neutrophil extracellular traps (NETs). Whilst the pathophysiological importance of NETs is unequivocal, the multiple molecular pathways driving NET release are not fully defined. Recently, NET release was linked to the NLRP3 inflammasome which is regulated by Bruton’s tyrosine kinase (BTK) in macrophages.ObjectiveAs NLRP3 inflammasome regulation by BTK has not been studied in neutrophils, we here explored a potential regulatory role of BTK in primary murine and human neutrophils and matched monocytes or macrophages from Btk-deficient vs WT mice or healthy donors (HD) vsBTKdeficient X-linked agammaglobulinemia (XLA) patients, respectively.MethodsCytokine, MPO and MMP-9 release were quantified by ELISA, NET release and inflammasome formation by immunofluorescence.ResultsSurprisingly, in both mouse and human primary neutrophils, we observed a significant increase in NLRP3 inflammasome-dependent IL-1β and NETs when BTK was absent or inhibited, whereas IL-1β release was decreased in corresponding primary mouse macrophages or human PBMC, respectively. This suggests a negative regulatory role of BTK in neutrophil NLRP3 activation. Both IL-1β and NET release in mouse and human primary neutrophils were strictly dependent on NLRP3, caspase-1 and, surprisingly, MMP-9.ConclusionThis highlights BTK and MMP-9 as novel and versatile inflammasome regulators and may have implications for the clinical use of BTK inhibitors.Key messagesNeutrophils contribute to inflammation by release of interleukin-1β and Neutrophil Extracellular Traps (NETs) via the NLRP3 inflammasomeBruton’s tyrosine kinase (BTK) is a negative regulator of NLRP3-mediated primary human neutrophil functions, whereas it positively regulates NLRP3 in monocytesMMP-9 is both effector and regulator of the neutrophil NLRP3 inflammasomeCapsule summaryHere we report that interleukin-1β and Neutrophil Extracellular Traps (NETs) release via the NLRP3 inflammasome is negatively regulated by Bruton’s tyrosine kinase (BTK) in primary neutrophils. Thus, targeting BTK using FDA-approved inhibitors might increase neutrophil functions.
Agrobacterium-mediatedCuscuta campestristransformation as a tool for understanding plant-plant interactions
Authors: Adhikari Supral , Mudalige Asha , Phillips Lydia , Lee Hyeyoung , Bernal-Galeano Vivian , Gruszewski Hope , Westwood James H. , Park So-Yon 
Published: February 2024

SummaryCuscuta campestris, a stem parasitic plant, has served as a valuable model plant for the exploration of plant-plant interactions and molecular trafficking. However, a major barrier toC. campestrisresearch is that a method to generate stable transgenic plants has not yet been developed. Here, we describe the development of aCuscutatransformation protocol using various reporter genes (GFP, GUS, or RUBY) and morphogenic genes (CcWUS2andCcGRF/GIF), ultimately leading to a robust protocol forAgrobacterium-mediatedC. campestristransformation. The stably transformed and regenerated RUBYC. campestrisplants produced haustoria, the signature organ of parasitic plants, and these were functional in forming host attachments. The locations of T-DNA integration in the parasite genome were confirmed through TAIL-PCR. TransformedC. campestrisalso produced flowers and transgenic seeds exhibiting betalain pigment, providing proof of germline transmission of the RUBY transgene. Furthermore, the RUBY reporter is not only a useful selectable marker for theAgrobacterium-mediated transformation, but also provides insight into the movement of molecules fromC. campestristo the host during parasitism. Thus, the protocol for transformation ofC. campestrisreported here overcomes a major obstacle toCuscutaresearch and opens new possibilities for studying parasitic plants and their interactions with hosts.
Contractility of cardiac and skeletal muscle tissue increases with environmental stiffness
Authors: Kah Delf , Lell Julia , Wach Tina , Spörrer Marina , Dessalles Claire A. , Wiedenmann Sandra , Gerum Richard C. , Vergarajauregui Silvia L. , Esser Tilman U. , Böhringer David , Engel Felix B. , Thievessen Ingo , Fabry Ben 
Published: February 2024

AbstractThe mechanical interplay between contractility and mechanosensing in striated muscles is of fundamental importance for tissue morphogenesis, load adaptation, and disease progression, but remains poorly understood. In this study, we investigate the dependence of contractile force generation of cardiac and skeletal muscle on environmental stiffness. Usingin vitroengineered muscle micro-tissues that are attached to flexible elastic pillars, we vary the stiffness of the microenvironment over three orders of magnitude and study its effect on contractility. We find that the active contractile force upon electrical stimulation of both cardiac and skeletal micro-tissues increases with environmental stiffness according to a strong power-law relationship. To explore the role of adhesion-mediated mechanotransduction processes, we deplete the focal adhesion protein β-parvin in skeletal micro-tissues. This reduces the absolute contractile force but leaves the mechanoresponsiveness unaffected. Our findings highlight the influence of external stiffness on the adaptive behavior of muscle tissue and shed light on the complex mechanoadaptation processes in striated muscle.
Comparative pollinator conservation potential of coffee agroforestry relative to coffee monoculture and tropical rainforest in the DR Congo
Authors: Jonas Depecker , Filip Vandelook , Kurt Jordaens , Achik Dorchin , Benjamin Ntumba Katshela , Ieben Broeckhoven , Benoit Dhed’a , Arne Devriese , Lien Deckers , Piet Stoffelen , Olivier Honnay 
Published: February 2024

AbstractAnimal-pollination is crucial in the reproduction of many crops grown in the tropics, including the self-incompatible Robusta coffee.Coffea canephoraPierre ex A. Froehner. is indigenous to the Congo basin where it is growing in the rainforest understorey yet providing very low yields. Cultivation therefore mainly occurs in either unshaded monocultures or in agroforestry systems. Here we surveyed the Diptera (true flies) and Hymenoptera (bees) communities that are putative coffee pollinating organisms in the Yangambi region in DR Congo, and we assessed the comparative benefits of coffee agroforestry and monocultures to the coffee pollinator community. To assess a base line value of pollinator conservation value of the agroforestry system, we also compared it with natural rainforest. Using white pan traps, we identified 9,597 specimens. Natural rainforest harboured a higher number of individuals, as well as a higher number of species than both agroforestry and coffee monoculture systems, with no differences between the latter two land-uses. The Simpson diversity and Pielou’s evenness on the other hand did not differ among land-uses. Furthermore, we observed different responses in species richness and diversity to land-use between Diptera and Hymenoptera. Our analyses of pollinator community composition showed a high dissimilarity between natural rainforest and the two cultivation systems, without significant differences between the latter land-uses. Specifically, the community composition of the agroforestry and coffee monoculture systems were totally different, rather than a subset of the community composition of the natural rainforest. Our study indicates that rehabilitation of agricultural land through intercropping fruit trees may not always enhance the pollinator community and that the studied agroforestry system falls short of matching the pollinator conservation potential found in natural rainforests. A more optimal selection of tree species intercropped with coffee may both enhance the conservation value of the agroforestry system and the provisioning of pollination services.
Mechanistic Analysis of Riboswitch Ligand Interactions Provides Insights into Pharmacological Control over Gene Expression
Authors: Parmar Shaifaly , Bume Desta Doro , Conelly Colleen , Boer Robert , Prestwood Peri R. , Wang Zhen , Labuhn Henning , Sinnadurai Krishshanthi , Feri Adeline , Ouellet Jimmy , Homan Philip , Numata Tomoyuki , Schneekloth John S. 
Published: February 2024

ABSTRACTRiboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Understanding the mechanisms by which small molecules impact riboswitch activity is key to developing potent, selective ligands for these and other RNA targets. We report the structure-informed design of chemically diverse synthetic ligands for PreQ1riboswitches. Multiple X-ray co-crystal structures of synthetic ligands with theThermoanaerobacter tengcongensis(Tte)-PreQ1riboswitch confirm a common binding site with the cognate ligand, despite considerable chemical differences among the ligands. Structure probing assays demonstrate that one ligand causes conformational changes similar to PreQ1in six structurally and mechanistically diverse PreQ1riboswitch aptamers. Single-molecule force spectroscopy is used to demonstrate differential modes of riboswitch stabilization by the ligands. Binding of the natural ligand brings about the formation of a persistent, folded pseudoknot structure, whereas a synthetic ligand decreases the rate of unfolding through a kinetic mechanism. Single round transcription termination assays show the biochemical activity of the ligands, while a GFP reporter system reveals compound activity in regulating gene expression in live cells without toxicity. Taken together, this study reveals that diverse small molecules can impact gene expression in live cells by altering conformational changes in RNA structures through distinct mechanisms.
Design and construction towards a pan-microbial toolkit
Authors: Gilbert Charlie , Crits-Christoph Alexander , Ledieu-Dherbécourt Elise , Kang Shinyoung Clair , Brumwell Stephanie L. , Lee Henry H. , Ostrov Nili 
Published: February 2024

AbstractEstablishing genetic tractability in non-model microbes requires identifying genetic parts that function in a target host. However, the paucity and purported narrow host range of available parts means that successful identification is governed by serendipity. Instead, a more comprehensive and scalable process would be desirable. Here, we describe the design principles for a pan-microbial genetic toolkit in which phylogenetically-diverse parts can be assembled and tested for function in microbes using high-throughput readouts. The architecture is based on Golden Gate Assembly, which simplifies the addition of parts and the construction of combinatorial libraries. We used this framework to develop two modules: first, thePOSSUM(PlasmidOrigins andSelection MarkerSforUndomesticatedMicrobes) module for identification of replicating plasmids in non-model microbes which includes 29 plasmid origin of replication sequences, 23 selection markers, and 30 unique DNA sequences for tracking by sequencing; second, theMACKEREL(Modular, NGS-trACKableExpRessionELement) module, for identification of functional gene expression cassettes which includes 426 bacterial promoter-RBS sequences driving fluorescent reporter expression, trackable by flow cytometry. We demonstrate the use of these libraries to screen for functional promoter-RBS variants in 6 non-model microbes. Continued efforts to expand this pan-microbial toolbox will accelerate efforts to improve genetic tractability and guide research across the tree of life.
Microtubules and actin filaments direct nuclear movement during the polarisation ofMarchantiaspore cells
Authors: Attrill Sarah , Dolan Liam 
Published: February 2024

ABSTRACTMulticellular organisms typically develop from single cells, the polarity of which establishes the first body axis of the organism. The multicellular haploid stage of land plants develops from a single haploid cell produced by meiosis – the spore. Starting from a non-polar state, these spores develop polarity and divide asymmetrically to establish the first apical-basal axis of the plant body. In the spore of the liverwort,Marchantia polymorpha, we show that the nucleus migrates from the cell centroid to the side of the cell to define the future basal pole. A microtubule organising centre leads this migration by initiating a dense microtubules array towards the cortex at the basal pole. Simultaneously, cortical microtubules disappear from the apical hemisphere but persist near the basal pole. A dense network of fine actin filaments also accumulates between the nucleus and the basal cell cortex. These data demonstrate that microtubules and actin filaments reorganise during the polarisation of theM. polymorphaspore. We speculate that signals orient microtubules and actin filaments during spore polarisation, resulting in the formation of a fine actin filament network between the nucleus and cell cortex that moves the nucleus to the future basal pole.SUMMARY STATEMENTMicrotubules and actin filament dynamics are required for the basal movement of the nucleus which establishes cell asymmetry before cell division in theMarchantiaspore.
Characterisation of mesenchymal stromal cells in the skin of Atlantic salmon
Authors: Ruiz Daniels R. , Salisbury S.J. , Sveen L. , Taylor R.S , Vaadal M. , Tengs T. , Monaghan S.J. , Villamayor P.R. , Ballantyne M. , Penaloza C. , Fast M.D. , Bron J.E. , Houston R. , Robinson N. , Robledo D. 
Published: February 2024

ABSTRACTBackgroundThe skin serves as the first line of defence for an organism against the external environment. Despite the global significance of salmon in aquaculture, a critical component of this first line of defence, mesenchymal stromal cells, remains unexplored. These pluripotent cells can differentiate into various tissues, including bone, cartilage, tendon, ligament, adipocytes, dermis, muscle and connective tissue within the skin. These cells are pivotal for preserving the integrity of skin tissue throughout an organism’s lifespan and actively participate in wound healing processes.ResultsIn this study, we characterise mesenchymal stromal cells in detail for the first time in healthy Atlantic salmon tissue and during the wound healing process. Single-nucleus sequencing and spatial transcriptomics revealed the transcriptional dynamics of these cells, elucidating the differentiation pathways leading to osteogenic and fibroblast lineages in the skin of Atlantic salmon. We charted their activity during an in vivo wound healing time course, showing clear evidence of their active role during this process, as they become transcriptionally more active during the remodelling stage of wound healing.ConclusionsFor the first time, we chart the activity of sub-clusters of differentiating stromal cells during the process of wound healing, revealing different spatial niches of the various MSC subclusters, and setting the stage for investigations into the manipulation of MSCs to improve fish health.
Arp2/3 complex-dependent actin regulation protects the survival of tissue-resident mast cells
Authors: Kaltenbach Lukas , Mihlan Michael , Ulferts Svenja , Müsken Mathias , Glaser Katharina M. , Mittler Gerhard , Babina Magda , Innocenti Metello , Grosse Robert , Stradal Theresia E.B. , Lämmermann Tim 
Published: February 2024

AbstractActin network dynamics are pivotal in governing the motility and effector functions of immune cells. The Arp2/3 complex is a key regulator of actin filament branching, with mutations in its subunits being linked with human immunodeficiencies. While known for its role in phagocytosis and cell migration, our study uncovers a critical role of the Arp2/3 complex in safeguarding the tissue residency of mast cells (MCs), essential immune cells in allergies, venom detoxification and antigen-specific avoidance. Mechanistically, we show that MCs require Arp2/3-regulated actin filament assembly to resist their integrin-mediated mechano-coupling with their tissue niche. Arp2/3 complex depletion directs MCs into cell cycle arrest and death, which can be rescued by inhibiting their mechanical interactions with extracellular matrix. Our findings underscore the Arp2/3 complex as a mechano-protective element for maintaining MC survival and longevity in tissues, highlighting the importance of actin regulation in preserving the homeostasis of a tissue-resident immune cell population.One Sentence SummaryArp2/3 complex protects the tissue homeostasis of resident mast cell networks