bluuebunny/crossref_metadata_2025_split huggingface dataset:
Competitive interaction between ATP and GTP regulates mitochondrial ATP-sensitive potassium channels
Authors: Palácio Plinio Bezerra , de Freitas Soares Geovanna Carvalho , Bezerra Lima Gabriella Moreira , Oliveira Cunha Pedro Lourenzo , Nunes Varela Anna Lidia , Facundo Heberty Tarso 
Published: January 2023

AbstractMitochondrial ATP-sensitive K+channels (mitoKATP) have been recently characterized structurally, and possess a protein through which K+enters mitochondria (MitoKIR), and a regulatory subunit (mitoSUR). The mitoSUR regulatory subunit is an ATP-binding cassette (ABC) protein isoform 8 (ABCB8). Opening of these channels is known to be cardioprotective, but the molecular and physiological mechanisms that activate them are not fully known. Here, to better understand the molecular and physiological mechanisms of activators (GTP) and inhibitors (ATP) on the activity of mitoKATP, we exposed isolated mitochondria to both nucleotides. We also used molecular docking directed to the nucleotide-binding domain of human ABCB8/mitoSUR to test a comparative model of ATP and GTP effects. As expected, we find that ATP dose-dependently inhibits mitoKATP activity (IC50= 21.24 ± 1.4 mM). However, simultaneous exposure of mitochondria to GTP dose-dependently (EC50= 13.19 ± 1.33 mM) reversed ATP inhibition. Pharmacological and computational studies suggest that GTP reverses ATP activity competitively. Docking directed to the site of crystallized ADP reveals that both nucleotides bind to mitoSUR with high affinity, with their phosphates directed to the Mg2+ion and the walker A motif of the protein (SGGGKTT). These effects, when combined, result in GTP binding, ATP displacement, mitochondrial ATP-sensitive K+transport, and lower formation of reactive oxygen species. Overall, our findings demonstrate the basis for ATP and GTP binding in mitoSUR using a combination of biochemical, pharmacological, and computational experiments. Future studies may reveal the extent to which the balance between ATP and GTP actions contribute toward cardioprotection against ischemic events.
Θ-Net: Achieving Enhanced Phase-Modulated Optical Nanoscopyin silicothrough a computational‘string of beads’architecture
Authors: Kaderuppan Shiraz S/O , Wong Eugene Wai Leong , Sharma Anurag , Woo Wai Lok 
Published: January 2023

AbstractWe present herein atripletstring of concatenated O-Net (‘bead’) architectures (formulated as discussed in our previous study) which we term ‘Θ-Net’ as a means of improving the viability of generated super-resolved (SR) imagesin silico. In the present study, we assess the quality of the afore-mentioned SR images with that obtained via other popular frameworks (such as ANNA-PALM, BSRGAN and 3D RCAN). Models developed from our proposed framework result in images which more closely approach the gold standard of the SEM-verified test sample as a means of resolution enhancement for optical microscopical imaging, unlike previous DNNs. In addition,cross-domain (transfer) learningwas also utilized to enhance the capabilities of models trained on DIC datasets, where phasic variations are not as prominently manifested as amplitude/intensity differences in the individual pixels [unlike phase contrast microscopy (PCM)]. The present study thus demonstrates the viability of our current multi-paradigm architecture in attaining ultra-resolved images under poor signal-to-noise ratios, while eliminating the need fora prioriPSF & OTF information. Due to the wide-scale use of optical microscopy for inspection & quality analysis in various industry sectors, the findings of this study would be anticipated to exhibit a far-ranging impact on several engineering fronts.
Lung-mimicking 3-Dimensional hydrogel culture system recapitulates key tuberculosis phenotypes and demonstrates pyrazinamide efficacy
Authors: Gupta Vishal K. , Abhirami P.S. , Vijaya Vaishnavi V. , Jyothsna K.M. , Jeyasankar Sharumathi , Raghunathan Varun , Agarwal Rachit 
Published: January 2023

AbstractFaithful mimics of tuberculosis (TB) infection are needed to provide mechanistic insights into the complex host-pathogen interactions and accelerate drug discovery. Currentin vitromodels only allow short investigation durations, present divergent transcriptional signatures to human infections, and are unreliable drug discovery platforms. We developed a 3D collagen culture system mimicking the lung microenvironment (collagen fibres, pore size and stiffness), where we incorporatedMycobacterium tuberculosis(Mtb) infected human THP-1 or primary monocytes. Dual RNA-sequencing revealed high mammalian gene expression similarity with patient samples compared to 2D macrophage infections. Similarly, gene expression of bacteria was much more representative toin vivogene expression compared to bacteria in 2D cultures (114 genes in 3D vs 21 genes in 2D). Key phenotypes observed in humans, such as foamy macrophages and mycobacterial cords (never seen in any otherin vitroculture system), were reproduced in our model. Our system overcomes many challenges associated with the traditional platforms, including showing remarkable efficacy with clinically relevant concentrations of first-line anti-TB drug pyrazinamide, not seen in any otherin vitromodel, making it reliable, readily adoptable for tuberculosis studies and drug screening.Significance statementMtb is a slow-growing pathogen which modulates host response over time. The currentin vitroplatforms offer a very short study duration to study, are unreliable as drug discovery platforms, and the phenotypic and genotypic traits of the host and pathogen differ. The collagen-I hydrogel culture system developed in this study addresses these challenges by successfully recapitulating several key phenotypes observed in human infections. Dual RNA sequence also showed excellent gene expression similarities for both the host and the bacteria. Furthermore, remarkable efficacy with the antibiotic Pyrazinamide was demonstrated, a first forin vitrocultures despite over 50 years of clinical use of the drug. We expect our platform to be exploited widely for drug discovery and understanding host-pathogen interactions.
Dominant gingers – discovery and inheritance of a new shell polymorphism in the great pond snailLymnaea stagnalis
Authors: Ledder Matthijs , Nakadera Yumi , Staikou Alexandra , Koene Joris M. 
Published: January 2023

AbstractColor polymorphism is a classic study system for evolutionary genetics. One of the most color-polymorphic animal taxa is mollusks, but the investigation for the genetic basis of color determination is often hindered by their life history and limited availability of genetic resources. Here we report on the discovery of shell color polymorphism in a much-used model species, the great pond snailLymnaea stagnalis. While their shell is usually beige, some individuals from a Greek population show a distinct red shell color, which we nicknamed Ginger. Moreover, we found that the inheritance fits simple, single-locus Mendelian inheritance with dominance of the Ginger allele. We also compared crucial life history traits between Ginger and wild type individuals, and found no differences between morphs. We conclude that the relative simplicity of this polymorphism will provide new opportunities for a deeper understanding of the genetic basis of shell color polymorphism and its evolutionary origin.
Guide to the construction and use of an adaptive optics two-photon microscope with direct wavefront sensing
Authors: Yao Pantong , Liu Rui , Broginni Thomas , Thunemann Martin , Kleinfeld David 
Published: January 2023

ABSTRACTTwo-photon microscopy, combined with appropriate optical labeling, has enabled the study of structure and function throughout nervous systems. This methodology enables, for example, the measurement and tracking of sub-micrometer structures within brain cells, the spatio-temporal mapping of spikes in individual neurons, and the spatio-temporal mapping of transmitter release in individual synapses. Yet the spatial resolution of two-photon microscopy rapidly degrades as imaging is attempted at depths more than a few scattering lengths into tissue, i.e., below the superficial layers that constitute the top 300 to 400 µm of neocortex. To obviate this limitation, we measure the wavefront at the focus of the excitation beam and utilize adaptive optics that alters the incident wavefront to achieve an improved focal volume. We describe the constructions, calibration, and operation of a two-photon microscopy that incorporates adaptive optics to restore diffraction-limited resolution throughout the nearly 900 µm depth of mouse cortex. Our realization utilizes a guide star formed by excitation of red-shifted dye within the blood serum to directly measure the wavefront. We incorporate predominantly commercial optical, optomechanical, mechanical, and electronic components; computer aided design models of the exceptional custom components are supplied. The design is modular and allows for expanded imaging and optical excitation capabilities. We demonstrate our methodology in mouse neocortex by imaging the morphology of somatostatin-expressing neurons at 700 µm beneath the pia, calcium dynamics of layer 5b projection neurons, and glutamate transmission to L4 neurons.
Three-dimensional morphological analysis revealed the cell patterning bases for the sexual dimorphism development in the liverwortMarchantia polymorpha
Authors: Cui Yihui , Hisanaga Tetsuya , Kajiwara Tomoaki , Yamaoka Shohei , Kohchi Takayuki , Goh Tatsuaki , Nakajima Keiji 
Published: January 2023

AbstractIn land plants, sexual dimorphism can develop in both diploid sporophytes and haploid gametophytes. While developmental processes of sexual dimorphism have been extensively studied in the sporophytic reproductive organs of model flowering plants such as stamens and carpels ofArabidopsis thaliana, those occurring in gametophyte generation are less well characterized due to the lack of amenable model systems. We here performed three-dimensional morphological analyses of gametophytic sexual branch differentiation in the liverwortMarchantia polymorpha, using high-depth confocal imaging and a computational cell segmentation technique. Our analysis revealed that specification of germline precursors initiates in a very early stage of sexual branch development where incipient branch primordia are barely recognizable in the apical notch region. Moreover, spatial distribution patterns of germline precursors differ between males and females from the initial stage of primordium development in a manner dependent on the master sexual differentiation regulator MpFGMYB. In later stages, distribution patterns of germline precursors predict the sex-specific gametangia arrangement and receptacle morphologies seen in mature sexual branches. Taken together, our data suggests a tightly coupled progression of germline segregation and sexual dimorphism development inM. polymorpha.
Integrative ensemble modelling of cetuximab sensitivity in colorectal cancer PDXs
Authors: Perron Umberto , Grassi Elena , Chatzipli Aikaterini , Viviani Marco , Karakoc Emre , Trastulla Lucia , Isella Claudio , Zanella Eugenia R , Klett Hagen , Molineris Ivan , Schueler Julia , Esteller Manel , Medico Enzo , Conte Nathalie , McDermott Ultan , Trusolino Livio , Bertotti Andrea , Iorio Francesco 
Published: January 2023

AbstractPatient-derived xenografts (PDXs) are tumour fragments engrafted into mice for preclinical studies. PDXs offer clear advantages over simplerin vitrocancer models - such as cancer cell lines (CCLs) and organoids - in terms of structural complexity, heterogeneity, and stromal interactions. We characterised 231 colorectal cancer PDXs at the genomic, transcriptomic, and epigenetic level and measured their response to cetuximab, an EGFR inhibitor in clinical use for metastatic colorectal cancer. After assessing PDXs’ quality, stability, and molecular concordance with publicly available patient cohorts, we trained, interpreted, and validated an integrated ensemble classifier (CeSta) which takes in input the PDXs’multi-omiccharacterisation and predicts their sensitivity to cetuximab treatment (AUROC > 0.9). Our study shows that large PDX collections can be used to train accurate, interpretable models of drug sensitivity, which 1) better recapitulate patient-derived therapeutic biomarkers than other models trained on CCL data, 2) can be robustly validated across independent PDX cohorts, and 3) can be used for the development of novel therapeutic biomarkers.
Homeostatic activation of Aryl Hydrocarbon Receptor by dietary ligands dampens cutaneous allergic responses by controlling Langerhans cells migration
Authors: Cros Adeline , de Juan Alba , Leclere Renaud , Sampaio Julio L , Maurin Mathieu , Heurtebise-Chrétien Sandrine , Segura Elodie 
Published: January 2023

AbstractDietary compounds can affect the development of inflammatory responses at distant sites. However, mechanisms involved remain incompletely understood. Here we addressed the influence on allergic responses of dietary agonists of Aryl Hydrocarbon Receptor (AhR). In cutaneous papain-induced allergy, we found that lack of dietary AhR ligands exacerbates allergic responses. This phenomenon was tissue-specific, as airway allergy was unaffected by the diet. In addition, lack of dietary AhR ligands worsened asthma-like allergy in a model of ‘atopic march’. Mice deprived of dietary AhR ligands displayed impaired Langerhans cell migration, leading to exaggerated T cell responses. Mechanistically, dietary AhR ligands regulated the inflammatory profile of epidermal cells, without affecting barrier function. In particular, we evidenced TGF-β hyperproduction in the skin of mice deprived of dietary AhR ligands, explaining Langerhans cell retention. Our work identifies an essential role for homeostatic activation of AhR by dietary ligands in the dampening of cutaneous allergic responses and uncovers the importance of the gutskin axis in the development of allergic diseases.
Designed Ankyrin Repeat Proteins for detecting prostate-specific antigen expressionin vivo
Authors: Gut Melanie , Dreier Birgit , Furler Sven , Sobek Jens , Plückthun Andreas , Holland Jason P. 
Published: January 2023

AbstractLate-stage prostate cancer often acquires resistance to conventional chemotherapies and transforms into a hormone-refractory, drug-resistant, and non-curative disease. Developing non-invasive tools to detect the biochemical changes that correlate with drug efficacy and reveal the onset of drug resistance would have important ramifications in managing the treatment regimen for individual patients. Here, we report the selection of new Designed Ankyrin Repeat Proteins (DARPins) that show high affinity toward prostate-specific antigen (PSA), a biomarker used in clinical monitoring of prostate cancer. Ribosome display andin vitroscreening tools were used to select PSA-binding DARPins based on their binding affinity, selectivity, and chemical constitution. Surface plasmon resonance measurements demonstrated that the four lead candidates bind to PSA with nanomolar affinity. DARPins were site-specifically functionalised at a uniqueC-terminal cysteine with the hexadentateaza-nonamacrocyclic chelate (NODAGA) for subsequent radiolabelling with the positron-emitting radionuclide68Ga. [68Ga]GaNODAGA-DARPins showed high stability toward transchelation and were stable in human serum for >2 h. Radioactive binding assays using streptavidin-loaded magnetic beads confirmed that the functionalisation and radiolabelling did not compromise the specificity of [68Ga]GaNODAGA-DARPins toward PSA. Biodistribution experiments in athymic nude mice bearing subcutaneous prostate cancer xenografts derived from the LNCaP cell line revealed that three of the four [68Ga]GaNODAGA-DARPins displayed specific tumour-bindingin vivo. For DARPin-6, tumour-uptake in the normal group reached 4.16 ± 0.58 %ID g-1(n= 3; 2 h post-administration) and was reduced by ∼50% in the blocking group (2.47 ± 0.42 %ID g-1;n= 3;P-value = 0.018). Collectively, the experimental results support the future development of new PSA-specific imaging agents for potential use in monitoring the efficacy of androgen receptor (AR)-targeted therapies.
Life-history traits, pace of life and dispersal among and within five species ofTrichogrammawasps: a comparative analysis
Authors: Guicharnaud Chloé , Groussier Géraldine , Beranger Erwan , Lamy Laurent , Vercken Elodie , Dahirel Maxime 
Published: January 2023

AbstractMajor traits defining the life history of organisms are often not independent from each other, with most of their variation aligning along key axes such as the pace-of-life axis. We can define a pace-of-life axis structuring reproduction and development time as a continuum from less-fecund, longer-developing ‘slow’ types to more-fecund, shorter-developing ‘fast’ types. Such axes, along with their potential associations or syndromes with other traits such as dispersal, are however not universal; in particular, support for their presence may be taxon and taxonomic scale-dependent. Knowing about such life-history strategies may be especially important for understanding eco-evolutionary dynamics, as these trait syndromes may constrain trait variation or be correlated with other traits. To understand how life-history traits and effective dispersal covary, we measured these traits in controlled conditions for 28 lines from five species ofTrichogramma, which are small endoparasitoid wasps frequently used as a biological model in experimental evolution but also in biocontrol against Lepidoptera pests. We found partial evidence of a pace-of-life axis at the interspecific level: species with higher fecundity also had faster development time. However, faster-developing species also were more likely to delay egg-laying, a trait that is usually interpreted as “slow”. There was no support for similar covariation patterns at the within-species line level. There was limited variation in effective dispersal between species and lines, and accordingly, we did not detect any correlation between effective dispersal probability and life-history traits. We discuss how expanding our experimental design by accounting for the density-dependence of both the pace of life and dispersal might improve our understanding of those traits and how they interact with each other. Overall, our results highlight the importance of exploring covariation at the “right” taxonomic scale, or multiple taxonomic scales, to understand the (co)evolution of life-history traits. They also suggest that optimizing both reproductive and development traits to maximize the efficiency of biocontrol may be difficult in programs using only one species.
Brain age as an estimator of neurodevelopmental outcome: A deep learning approach for neonatal cot-side monitoring
Authors: Ansari Amir , Pillay Kirubin , Baxter Luke , Arasteh Emad , Dereymaeker Anneleen , Mellado Gabriela Schmidt , Jansen Katrien , Naulaers Gunnar , Bhatt Aomesh , Van Huffel Sabine , Hartley Caroline , De Vos Maarten , Slater Rebeccah 
Published: January 2023

AbstractThe preterm neonate can experience stressors that affect the rate of brain maturation and lead to long-term neurodevelopmental deficits. However, some neonates who are born early follow normal developmental trajectories. Extraction of data from electroencephalography (EEG) signals can be used to calculate the neonate’s brain age which can be compared to their true age. Discrepancies between true age and brain age (the brain age delta) can then be used to quantify maturational deviation, which has been shown to correlate with long-term abnormal neurodevelopmental outcomes. Nevertheless, current brain age models that are based on traditional analytical techniques are less suited to clinical cot-side monitoring due to their dependency on long-duration EEG recordings, the need to record activity across multiple EEG channels, and the manual calculation of predefined EEG features which is time-consuming and may not fully capture the wealth of information in the EEG signal. In this study, we propose an alternative deep-learning approach to determine brain age, which operates directly on the EEG, using a Convolutional Neural Network (CNN) block based on the Inception architecture (called Sinc). Using this deep-learning approach on a dataset of preterm infants with normal neurodevelopmental outcomes (where we assume brain age = postmenstrual age), we can calculate infant brain age with a Mean Absolute Error (MAE) of 0.78 weeks (equivalent to a brain age estimation error for the infant within +/− 5.5 days of their true age). Importantly, this level of accuracy can be achieved by recording only 20 minutes of EEG activity from a single channel. This compares favourably to the degree of accuracy that can be achieved using traditional methods that require long duration recordings (typically >2 hours of EEG activity) recorded from a higher density 8-electrode montage (MAE = 0.73 weeks). Importantly, the deep learning model’s brain age deltas also distinguish between neonates with normal and severely abnormal outcomes (Normal MAE = 0.71 weeks, severely abnormal MAE = 1.27 weeks, p=0.02, one-way ANOVA), making it highly suited for potential clinical applications. Lastly, in an independent dataset collected at an independent site, we demonstrate the model’s generalisability in age prediction, as accurate age predictions were also observed (MAE of 0.97 weeks).HighlightsPreterm stress exposure leads to long-term neurodevelopmental deficitsDeficits are quantifiable using EEG-based brain age prediction errorsOur deep-learning solution for brain age prediction outperforms previous approachesPredictions are achieved with only 20 mins EEG and a single bipolar channelPrediction errors correlate with long-term Bayley scale neurodevelopmental outcomes
Sensitive clustering of protein sequences at tree-of-life scale using DIAMOND DeepClust
Authors: Buchfink Benjamin , Ashkenazy Haim , Reuter Klaus , Kennedy John A. , Drost Hajk-Georg 
Published: January 2023

AbstractThe biosphere genomics era is transforming life science research, but existing methods struggle to efficiently reduce the vast dimensionality of the protein universe. We present DIAMOND DeepClust, an ultra-fast cascaded clustering method optimized to cluster the 19 billion protein sequences currently defining the protein biosphere. As a result, we detect 1.7 billion clusters of which 32% hold more than one sequence. This means that 544 million clusters represent 94% of all known proteins, illustrating that clustering across the tree of life can significantly accelerate comparative studies in the Earth BioGenome era.
Mast cell-derived BH4 is a critical mediator of postoperative pain
Authors: Starkl Philipp , Jonsson Gustav , Artner Tyler , Turnes Bruna Lenfers , Serhan Nadine , Oliveira Tiago , Gail Laura-Marie , Stejskal Karel , Channon Keith M. , Köcher Thomas , Stary Georg , Klang Victoria , Gaudenzio Nicolas , Knapp Sylvia , Woolf Clifford J. , Penninger Josef M. , Cronin Shane J.F. 
Published: January 2023

AbstractPostoperative pain affects most patients after major surgery and can transition to chronic pain. Here, we discovered that postoperative pain hypersensitivity correlated with markedly increased local levels of the metabolite BH4. Gene transcription and reporter mouse analyses after skin injury identified neutrophils, macrophages and mast cells as primary postoperative sources of GTP cyclohydrolase-1 (Gch1) expression, the rate-limiting enzyme in BH4 production. While specificGch1deficiency in neutrophils or macrophages had no effect, mice deficient in mast cells or mast cell-specificGch1showed drastically decreased postoperative pain after surgery. Skin injury induced the nociceptive neuropeptide substance P, which directly triggers the release of BH4-dependent serotonin in mouse and human mast cells. Substance P receptor blockade substantially ameliorated postoperative pain. Our findings underline the unique position of mast cells at the neuro-immune interface and highlight substance P-driven mast cell BH4 production as promising therapeutic targets for the treatment of postoperative pain.