bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early human lung immune cell development and its role in epithelial cell fate
Authors: Barnes Josephine L. , He Peng , Yoshida Masahiro , Worlock Kaylee B. , Lindeboom Rik G.H. , Suo Chenqu , Pett J. Patrick , Wilbrey-Clark Anna , Dann Emma , Mamanova Lira , Richardson Laura , Oliver Amanda J. , Pennycuick Adam , Allen-Hyttinen Jessica , Herczeg Iván T. , Hynds Robert E. , Teixeira Vitor H. , Haniffa Muzlifah , Lim Kyungtae , Sun Dawei , Rawlins Emma L. , Polanski Krzysztof , Lyons Paul A. , Marioni John C. , Tuong Zewen Kelvin , Clatworthy Menna R. , Reading James L. , Janes Sam M. , Teichmann Sarah A. , Meyer Kerstin B. , Nikolić Marko Z. 
Published: December 2022

AbstractDuring human development, lungs develop their roles of gas exchange and barrier function. Recent single cell studies have focused on epithelial and mesenchymal cell types, but much less is known about the developing lung immune cells, although the airways are a major site of mucosal immunity after birth. An open question is whether tissue-resident immune cells play a role in shaping the tissue as it developsin utero. In order to address this, we profiled lung immune cells using scRNAseq, smFISH and immunohistochemistry. At the embryonic stage, we observed an early wave of innate immune cells, including ILCs, NK, myeloid cells and lineage progenitors. By the canalicular stage, we detected naive T lymphocytes high in cytotoxicity genes, and mature B lymphocytes, including B1 cells. Our analysis suggests that fetal lungs provide a niche for full B cell maturation. Given the abundance of immune cells, we investigated their possible effect on epithelial maturation and found that IL-1β drives epithelial progenitor exit from self-renewal and differentiation to basal cellsin vitro.In vivo, IL-1β-producing myeloid cells were found adjacent to epithelial tips, suggesting that immune cells may direct the developing lung epithelium.
Strategies and experimental tips for optimized quantitative single-molecule studies of membrane and membrane-associated proteins
Authors: Magrassi Raffaella , Picollo Alessandra , Diaspro Alberto , Zanacchi Francesca Cella 
Published: December 2022

AbstractThe study of stoichiometry and supra-molecular organization of membrane (and membrane-associated) proteins plays a key role in understanding membrane structure and function. Single-molecule localization techniques (SML), besides providing imaging at unprecedented resolution, also offer quantitative tools such as stepwise photobleaching (SP) experiments and quantitative single-molecule localization (qSMLM). SML is becoming widely present in imaging core facilities but addressing biological problems by molecular counting experiments still remains not straightforward since experimental approaches for sample preparation require particular attention.We will focus on the experimental aspects that may prevent successful quantitative SML experiments of membrane-associated proteins.Depending on the specific experiment, to avoid artifacts and to miscount, fine-tuning of the expression levels and proper staining procedures are required, as well as optimized protocols and controls for counting.The work aims to highlight the crucial aspects that must be faced when quantitative single-molecule experiments are performed, helping to match the gap between sample preparation and the application of quantitative fluorescence microscopy techniques.
Systematic engineering of plant cytochrome P450 system identifies a comprehensive strategy for expression of highly functional P450 enzymes inEscherichia coli
Authors: Poborsky Michal , Crocoll Christoph , Motawie Mohammed Saddik , Halkier Barbara Ann 
Published: December 2022

AbstractCytochrome P450s catalyse diverse and unique chemical reactions, which makes them invaluable enzymes in nature and industry. Metabolic engineers leverage these unique catalytic properties when refactoring plant biosynthetic pathways into microbial cell factories. However, due to their hydrophobic anchor, microbial expression of membrane-bound cytochrome P450s is challenging. An arsenal of protein engineering strategies was developed to improve their expression inEscherichia coli, but extensive screening is often necessary to tailor the engineering approach to an individual enzyme. Here, we propose a universal strategy that allows the expression of highly active cytochrome P450s inE. coliby systematically evaluating six common N-terminal modifications and their effect onin vivoactivity of enzymes from the CYP79 and CYP83 families. We identified transmembrane domain truncation as the only strategy that had a significantly positive effect on all seven tested enzymes, increasing product titres between 2- to 170-fold. When comparing the changes in protein titre and product generation, we show that higher expression does not always translate to higherin vivoactivity, thus making protein titre an unreliable screening target. Our results demonstrate that transmembrane domain truncation improvesin vivoactivity across a broad range of cytochrome P450s with diverse N-terminal sequences and could be applied as the modification-of-choice to avoid the time-consuming screening process and accelerate the future design ofE. colicell factories.
Evaluation of a scalable approach to generate cell-type specific transcriptomic profiles of mesenchymal lineage cells
Authors: Dillard Luke J , Rosenow Will T , Calabrese Gina M , Mesner Larry D , Al-Barghouthi Basel M , Abood Abdullah , Farber Emily A , Onengut-Gumuscu Suna , Tommasini Steven M , Horowitz Mark A , Rosen Clifford J , Yao Lutian , Qin Ling , Farber Charles R 
Published: December 2022

AbstractGenome-wide association studies (GWASs) have revolutionized our understanding of the genetics of complex diseases, such as osteoporosis; however, the challenge has been converting associations to causal genes. Studies have demonstrated the utility of transcriptomics data in linking disease-associated variants to genes; though for osteoporosis, few population transcriptomics datasets have been generated on bone or bone cells, and an even smaller number have profiled individual cell-types. To begin to evaluate approaches to address this challenge, we profiled the transcriptomes of bone marrow-derived stromal cells (BMSCs) cultured under osteogenic conditions, a popular model of osteoblast differentiation and activity, from five Diversity Outbred (DO) mice using single-cell RNA-seq (scRNA-seq). The goal of the study was to determine if BMSCs could serve as a model for the generation of cell-type specific transcriptomic profiles of mesenchymal lineage cells derived from large populations of mice to inform genetic studies. We demonstrate that dissociation of BMSCs from a heavily mineralized matrix had little effect on viability or their transcriptomic signatures. Furthermore, we show that BMSCs cultured under osteogenic conditions are diverse and consist of cells with characteristics of mesenchymal progenitors, marrow adipogenic lineage precursors (MALPs), osteoblasts, osteocyte-like cells, and immune cells. Importantly, all cells were nearly identical from a transcriptomic perspective to cells isolated directly from bone. We also demonstrated the ability to multiplex single cells and subsequently assign cells to their “mouse-of-origin” using demultiplexing approaches based on genotypes inferred from coding SNPs. We employed scRNA-seq analytical tools to confirm the biological identity of profiled cell-types. SCENIC was used to reconstruct gene regulatory networks (GRNs) and we showed that identified cell-types show GRNs expected of osteogenic and pre-adipogenic lineage cells. Further, CELLECT analysis showed that osteoblasts, osteocyte-like cells, and MALPs captured a significant component of BMD heritability. Together, these data suggest that BMSCs cultured under osteogenic conditions coupled with scRNA-seq can be used as a scalable and biologically informative model to generate cell-type specific transcriptomic profiles of mesenchymal lineage cells in large mouse, and potentially human, populations.
Armed to the teeth: the underestimated diversity in tooth shape in snakes and its relationship to feeding constraints
Authors: Segall Marion , Houssin Céline , Delapré Arnaud , Cornette Raphaël , Milgram Joshua , Shahar Ron , Herrel Anthony , Dumont Maïtena 
Published: December 2022

AbstractTeeth are one of the most studied hard tissues in vertebrates. Their structure, composition and shape are related to dietary specialization in many species. At first glance, snake teeth all look similar; conical, sharp, curved. Yet, snakes, like other vertebrates, have very diverse diets that may have affected their shape. We compared the morphology of the teeth of 63 species that cover both the phylogenetic and dietary diversity of snakes. We predicted that prey properties play a role in shaping snakes teeth along with their feeding behavior. Limblessness combined to the peculiar feeding behavior of snakes impose strong functional constraints on their teeth, especially during arboreal or aquatic feeding. Our results show that prey hardness, foraging substrate and the main feeding constraint are drivers of tooth shape, size, and curvature. We highlight two main morphotypes: long, slender, curved with a thin layer of hard tissue for snakes that need a good grip on their prey and short, stout, less curved teeth in snakes that eat hard or long prey. Our study demonstrates the diversity of tooth morphology in snakes and the need to investigate the underlying functional implications to better understand the evolution of teeth in vertebrates.
Turtle body size evolution is determined by lineage-specific specializations rather than global trends
Authors: Farina Bruna M. , Godoy Pedro L. , Benson Roger B.J. , Langer Max C. , Ferreira Gabriel S. 
Published: December 2022

ABSTRACTOrganisms display considerable variety of body sizes and shapes, and macroevolutionary investigations help to understand the evolutionary dynamics behind to such variations. Turtles (Testudinata) show great body size disparity, especially when their rich fossil record is accounted for. We explored body size evolution in turtles, testing which factors might influence the observed patterns and evaluating the existence of long-term directional trends. We constructed the most comprehensive body size dataset for the group to date, tested for correlation with paleotemperature, estimated ancestral body sizes, and performed macroevolutionary model-fitting analyses. We found no evidence for directional body size evolution, even when using very flexible models, thereby rejecting the occurrence of Cope’s rule. We also found no significant effect of paleotemperature on overall through-time body size patterns. In contrast, we found a significant influence of habitat preference on turtle body size. Freshwater turtles display a rather homogenous body size distribution through time. In contrast, terrestrial and marine turtles show more pronounced variation, with terrestrial forms being restricted to larger body sizes, up to the origin of testudinids in the Cenozoic, and marine turtles undergoing a reduction in body size disparity after the extinctions of many groups in the mid-Cenozoic. Our results therefore suggest that long-term, generalized patterns are probably explained by factors specific to certain groups and related at least partly to habitat use.
Preclinical development of non-viral gene therapy for patients with advanced pancreatic cancer
Authors: Barbey Odile , Lulka Hubert , Hanoun Naima , Belhadj-Tahar Hafid , Vernejoul Fabienne , Cambois Gilles , Tiraby Michèle , Buscail Louis , Gross Fabian , Cordelier Pierre 
Published: December 2022

ABSTRACTPancreatic ductal adenocarcinoma remains one of the greatest challenges in oncology for which therapeutic intervention is urgently needed. We demonstrated that the intratumoral gene transfer of somatostatin receptor 2, to combat tumor aggressiveness, or of deoxycytidine kinase and uridylate monophosphate kinase, to sensitize to gemcitabine chemotherapy, has antitumoral potential. Here, we describe the development of CYL-02 non-viral gene-therapy product, that comprises a DNA-plasmid encoding for the three aforementioned genes complexed with PolyEthylEnimine (22 kDa). In this work, we performed preclinical toxicology, biodistribution and therapeutic activity studies of CYL-02 in experimental models of pancreatic cancer. We demonstrated the safety of CYL-02 and defined the maximal tolerated dose in two animal species. CYL-02 co-administrated with gemcitabine did not increase gemcitabine toxicity. Biodistribution studies revealed that CYL-02 is rapidly cleared from blood following intravenous administration, and sequestered in tumors following intratumoral injection. CYL-02 drives the expression of therapeutic genes in cancer cells and strongly sensitizes tumor cells to gemcitabine, with significant inhibition of tumor cells dissemination. This study was instrumental for the later use of CYL-02 in patients with advanced pancreatic cancer, demonstrating that rigorous and thorough preclinical investigations are informative for the clinical transfer of gene therapy against pancreatic cancer.GRAPHICAL ABSTRACT
Comparingin silicoandin vitromethods for classification of BCS II and CYP3A4 and MDR-1 substrate specificity
Authors: Fagerholm Urban 
Published: December 2022

ABSTRACTBackgroundPrevious work has shown considerable laboratory variability of Biopharmaceutics Classification System (BCS) classification, efflux ratio in intestinal cell lines and cytochrome P450 (CYP450)-metabolism pathways. Such variability and inconsistency create uncertainty in predictions of human clinical pharmacokinetics and the pharmacokinetic optimization process and is a problem when developing correspondingin silicomethods.Objectives and MethodologyOne objective of the study was to quantify the degree of laboratory inconsistency for BCS II-classing, MDR-1 and CYP3A4 substrate specificity (substrate/non-substrate). Another objective was to predict BCS II-classing, MDR-1 and CYP3A4 substrate specificity usingin silicomethodology and compare results to laboratory data/classifications.Results and Discussion27 BCS II-classified drugs (with non-contradictory BCS-classing in various sources) were found. 17 (63 %) had anin vivofraction absorbed (fa) of ≥90 % and belong toin vivoBCS I. Within silicomethodology, 74 % correct BCS-classing was reached for the same set of compounds. The mean prediction error for fawas 1.2-fold. MDR-1 and CYP3A4 substrate specificities were collected for 346 and 808 compounds, respectively. For MDR-1, 143 of the compounds had reported data in at least two studies, and out of these, 49 (34 %) and 18 (13 %) had contradictory (reported as both substate and non-substrate) and uncertain substrate specificities, respectively. For CYP3A4, 42 (9.8 %) out of 427 compounds showed inconsistency between laboratories. Within silicomethodology, MDR-1 and CYP3A4 classification predictions were incorrect for 13 and 15 % of compounds.ConclusionThe results show considerable variability/inconsistency for BCS II-classing (63 % inconsistency between BCS II-classing andin vivofa) and MDR-1 (34 % inconsistency between sources) and CYP3A4 (10 % inconsistency between sources) substrate specificities. Corresponding estimates obtained within silicomethodology are 22, 13 and 15 %, respectively, demonstrating the power and applicability of such technology.
Steroid hormone imbalance drives macrophage infiltration andSpp1/osteopontin+foam cell differentiation in the prostate
Authors: Popovics Petra , Skalitzky Kegan O. , Schroeder Elise , Jain Asha , Silver Samara V. , Van Fritz Francesca , Uchtmann Kristen S. , Vezina Chad M. , Ricke William A. 
Published: December 2022

AbstractBenign Prostatic Hyperplasia (BPH) occurs progressively with aging in men and drives deteriorating symptoms collectively known as Lower Urinary Tract Symptoms (LUTS). Age associated changes in circulating steroid hormones, and prostate inflammation have been postulated in the etiology of BPH/LUTS. The link between hormones and inflammation in the development of BPH/LUTS is conflicting because they may occur independently or as sequential steps in disease pathogenesis. This study aimed to decipher the prostatic immune landscape in a mouse model of lower urinary tract dysfunction (LUTD). Steroid hormone imbalance was generated by the surgical implantation of testosterone (T) and estradiol (E2) pellets to male C57BL/6J mice and gene expression analysis was performed on ventral prostates (VP). These experiments identified an increase in the expression of macrophage markers andSpp1/osteopontin (OPN). Localization studies of OPN pinpointed that OPN+ macrophages travel to the prostate lumen and transition into lipid accumulating foam cells. We also observed a significantly increased number of tissue macrophages in the VP which was prevented in OPN knockout (OPN-KO) mice. In contrast, mast cells, but not macrophages, were significantly elevated in the dorsal prostate of T+E2 treated mice which was diminished in OPN-KO mice. Steroid hormone implantation progressively increased urinary frequency, which was ameliorated in OPN-KO mice. Our study underscores the role of age associated steroid hormone imbalances as a mechanism of expanding the prostatic macrophage population, their luminal translocation and foam cell differentiation.
Predicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networks
Authors: Luo Xiao , Kang Xiongbin , Schönhuth Alexander 
Published: December 2022

AbstractDiseases that have a complex genetic architecture tend to suffer from considerable amounts of genetic variants that, although playing a role in the disease, have not yet been revealed as such. Two major causes for this phenomenon are genetic variants that do not stack up effects, but interact in complex ways; in addition, as recently suggested, the omnigenic model postulates that variants interact in a holistic manner to establish disease phenotypes.We present DiseaseCapsule, as a capsule network based approach that explicitly addresses to capture the hierarchical structure of the underlying genome data, and has the potential to fully capture the non-linear relationships between variants and disease. DiseaseCapsule is the first such approach to operate in a whole-genome manner when predicting disease occurrence from individual genotype profiles.In experiments, we evaluated DiseaseCapsule on amyotrophic lateral sclerosis (ALS) and Parkinson’s disease (PD), with a particular emphasis on ALS because known known to have a complex genetic architecture, so being affected by considerable missing heritability (40%). On ALS, Disease-Capsule achieves 86.9% accuracy on held out test data in predicting disease occurrence, thereby outperforming all other approaches by large margins. Also, DiseaseCapsule required sufficiently less training data for reaching optimal performance. Last but not leaset, the systematic exploitation of the network architecture yielded 922 genes of particular interest, and 644 ”non-additive” genes that are crucial factors in DiseaseCapsule, but have no effect within linear schemes.
ohun: an R package for diagnosing and optimizing automatic sound event detection
Authors: Araya-Salas Marcelo , Smith-Vidaurre Grace , Chaverri Gloriana , Brenes Juan C. , Chirino Fabiola , Elizondo-Calvo Jorge , Rico-Guevara Alejandro 
Published: December 2022

AbstractAnimal acoustic signals are widely used in diverse research areas due to the relative ease with which sounds can be registered across a wide range of taxonomic groups and research settings. However, bioacoustics research can quickly generate large data sets, which might prove challenging to analyze promptly. Although many tools are available for the automated detection of sounds, choosing the right approach can be difficult only a few tools provide a framework for evaluating detection performance. Here we presentohun, an R package intended to facilitate automated sound detection.ohunprovides functions to diagnose and optimize detection routines and compare performance among different detection approaches. The package uses reference annotations containing the time position of target sounds in a training data set to evaluate detection routines performance using common signal detection theory indices. This can be done both with routine outputs imported from other software and detections run within the package. The package also provides functions to organize acoustic data sets in a format amenable to detection analyses. ohun also includes energy-based and template-based detection methods, two commonly used automatic approaches in bioacoustic research. We show how ohun automatically can be used to detect vocal signals with case studies of adult male zebra finch (Taenopygia gutata) songs and Spix’s disc-winged bat (Thyroptera tricolor) ultrasonic social calls. We also include examples of how to evaluate the detection performance of ohun and external software. Finally, we provide some general suggestions to improve detection performance.
Absolute scattering length density profile of liposome bilayers obtained by SAXS combined with GIXOS - a tool to determine model biomembrane structure
Authors: Shen Chen , Woelk Christian , Kikhney Alexey G. , Torres Jaume , Surya Wahyu , Harvey Richard D. , Bello Gianluca 
Published: December 2022

AbstractLipid membranes play an essential role in biology, acting as host matrices for biomolecules like proteins and facilitating their functions. Their structures, and structural responses to physiologically relevant interactions, i.e. with membrane proteins, provide key information for understanding biophysical mechanisms. Hence, there is a crucial need of methods to understand the effects of membrane host molecules on the lipid bilayer structure. Here, we present a purely experimental method for obtaining the absolute scattering length density (SLD) profile and the area per lipid of liposomal bilayers, by aiding the analysis of small angle X-ray scattering (SAXS) data with the volume of bare headgroups obtained from fast (20-120s) grazing incidence off-specular scattering (GIXOS) data from monolayers of the same model membrane lipid composition. The GIXOS data experimentally demonstrate that the variation of the bare headgroup volume upon lipid packing density change is small enough to allow its usage as a reference value without knowing the lipid packing stage in a bilayer. This approach also bares the advantage that the reference volume is obtained at the same aqueous environment as used for the model membrane bilayers. We demonstrate the validity of this method using several typical membrane compositions, as well as one example of a phospholipid membrane with an incorporated transmembrane peptide. This methodology allows to obtain absolute scale values rather than relative scale by using solely X-ray-based instrumentation, retaining a similar resolution of SAXS experiments. The presented method has high potential to understand structural effects of membrane proteins on the biomembrane structure.