bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methylglyoxal-derived hydroimidazolone, MG-H1, increases food intake by altering tyramine signaling via the GATA transcription factor ELT-3 in Caenorhabditis elegans
Authors: Shanmugam Muniesh Muthaiyan , Chaudhuri Jyotiska , Sellegounder Durai , Sahu Amit Kumar , Guha Sanjib , Chamoli Manish , Hodge Brian , Roberts Charis , Lithgow Gordon , Sarpong Richmond , Kapahi Pankaj 
Published: August 2022

ABSTRACTThe Maillard reaction, a chemical reaction between amino acids and sugars, is exploited to produce flavorful food almost everywhere, from the baking industry to our everyday life. However, the Maillard reaction also takes place in all cells, from prokaryotes to eukaryotes, leading to the formation of Advanced Glycation End-products (AGEs). AGEs are a heterogeneous group of compounds resulting from the irreversible reaction between biomolecules and α-dicarbonyls (α-DCs), including methylglyoxal (MGO), an unavoidable byproduct of anaerobic glycolysis and lipid peroxidation. We previously demonstrated that Caenorhabditis elegans mutants lacking the glod-4 glyoxalase enzyme displayed enhanced accumulation of α-DCs, reduced lifespan, increased neuronal damage, and touch hypersensitivity. Here, we demonstrate that glod-4 mutation increased food intake and identify that MGO-derived hydroimidazolone, MG-H1, is a mediator of the observed increase in food intake. RNA-seq analysis in glod-4 knockdown worms identified upregulation of several neurotransmitters and feeding genes. Suppressor screening of the overfeeding phenotype identified the tdc-1-tyramine-tyra-2/ser-2 signaling as an essential pathway mediating AGEs (MG-H1) induced feeding in glod-4 mutants. We also identified the elt-3 GATA transcription factor as an essential upstream factor for increased feeding upon accumulation of AGEs by partially regulating the expression of tdc-1 and tyra-2 genes. Further, the lack of either tdc-1 or tyra-2/ser-2 receptors suppresses the reduced lifespan and rescues neuronal damage observed in glod-4 mutants. Thus, in C. elegans, we identified an elt-3 regulated tyramine-dependent pathway mediating the toxic effects of MGO and associated AGEs. Understanding this signaling pathway is essential to modulate hedonistic overfeeding behavior observed in modern AGEs rich diets.
Investigating the relationship between CRISPR-Cas content and growth rate in bacteria
Authors: Liu Zhi-Ling , Hu En-Ze , Niu Deng-Ke 
Published: August 2022

AbstractCRISPR-Cas systems provide adaptive immunity for prokaryotic cells by recognizing and eliminating the recurrent genetic invaders whose sequences had been captured in a prior infection and stored in the CRISPR arrays as spacers. However, the biological/environmental factors determining the efficiency of this immune system have yet to be fully characterized. Recent studies in cultured bacteria showed that slowing the growth rate of bacterial cells could promote their acquisition of novel spacers. This study examined the relationship between the CRISPR-Cas content and the minimal doubling time across the bacteria and the archaea domains. Every completely sequenced genome could be used to predict a minimal doubling time. With a large dataset of 4142 bacterial samples, we found that the predicted minimal doubling times are positively correlated with spacer number and other parameters of the CRISPR-Cas systems, like array number,Casgene cluster number, andCasgene number. Different datasets gave different results. Weak results were obtained in analyzing bacterial empirical minimal doubling times and the archaea domain. Still, the conclusion of more spacers in slowly-grown prokaryotes was supported. In addition, we found that the minimal doubling times are negatively correlated with the occurrence of prophages, and the spacer numbers per array are negatively associated with the number of prophages. These observations support the existence of an evolutionary trade-off between bacterial growth and adaptive defense against virulent phages.
Phage-antibiotic combinations to control Pseudomonas aeruginosa-Candida two-species biofilms
Authors: Manohar Prasanth , Loh Belinda , Nachimuthu Ramesh , Leptihn Sebastian 
Published: August 2022

AbstractPhage-antibiotic combinations to treat bacterial infections are gaining increased attention due to the synergistic effects often observed when applying both components together. This synergy has also been observed for bacteria embedded in biofilms as many phages are capable of degrading the heterogeneous material, often preventing antibiotic compounds from reaching the embedded bacteria. Most studies however focus on a single pathogen, although in many clinical cases multiple species are present at the site of infection. The aim of this study was to investigate the anti-biofilm activity of phage-antibiotic/antifungal combinations on single- and dual-species biofilms formed by the bacterium P. aeruginosa and the fungal pathogen Candida albicans, two microorganisms commonly found together in cystic fibrosis patients. The Pseudomonas phage Motto in combination with ciprofloxacin had significant anti-biofilm activity in disintegrating 24-hour-old pseudomonal biofilms. Also, other antibiotic combinations, such as cefotaxime, gentamicin, meropenem and tetracycline showed substantial effects on biofilms. We then compared biofilms formed by P. aeruginosa alone with the dual-species biofilms formed by bacteria and C. albicans. Here, we found that the phage together with the antifungal fluconazole was active against 6-hour-old dual-species biofilms but showed only negligible activity against 24-hour-old biofilms. Similarly, the combination of antibacterial compounds together with the phage showed no synergistic effects on biofilms formed by P. aeruginosa and C. albicans. This study lays the first foundation for potential therapeutic approaches to treat infections caused by bacteria and fungi using phage-antibiotic combinations.
Golgi localized Arl15 regulates cargo transport, cell adhesion and motility
Authors: Sharma Prerna , Venkatesh Pooja Hoovina , Paddillaya Neha , Shah Nikita , Rajeshwari BR , Dakua Archishman , Penmatsa Aravind , Balasubramanian Nagaraj , Gundiah Namrata , Setty Subba Rao Gangi 
Published: August 2022

AbstractArf-like GTPases (Arls) regulate membrane trafficking and cytoskeletal organization. Genetic studies predicted a role for Arl15 in type-2 diabetes, insulin resistance, adiposity, and rheumatoid arthritis. Recent studies indicate a possible role for Arl15 in multiple physiological processes, including magnesium homeostasis. However, the molecular function of Arl15 is poorly defined. We evaluated the role of Arl15 in vesicular transport using techniques to quantify cargo trafficking, to mechanobiology. Fluorescence microscopy of stably expressing Arl15-GFP HeLa cells showed its localization to the Golgi and cell surface, including filopodia, and a cohort to recycling endosomes. The dissociation of Golgi, using small molecular inhibitors or the expression of Arf1 dominant-negative mutant, completely mislocalized Arl15 to the cytosol. Interestingly, site-directed mutagenesis analysis identified a novel V80A mutation in the GTP-binding domain that turns Arl15 into a dominant-negative form with reduced number of filopodia. Depletion of Arl15 in HeLa cells caused mislocalization of cargo, such as caveolin-2 and STX6, from the Golgi. Arl15 knockdown cells displayed reduced filopodial number, altered focal adhesion kinase organization, and enhanced soluble and receptor-mediated cargo uptake without affecting the TfR recycling. Arl15 knockdown decreased cell migration and enhanced cell spreading and adhesion strength. Traction force microscopy experiments revealed that Arl15 depleted cells exert higher tractions and generate multiple focal adhesion points during the initial phase of cell adhesion as compared to control cells. Collectively, these studies demonstrated a functional role for Arl15 in the Golgi, which includes regulating cargo transport to organize membrane domains at the cell surface.Key pointsArl15 primarily localizes to Golgi and plasma membrane, including filopodiaMembrane localization of Arl15 is dependent on Golgi integrity or Arf1 activationArl15 knockdown mislocalizes STX6-dependent Golgi localized cargo required for cell surface organization and reduces the filopodial numberArl15 is involved in cell spreading, adhesion, and migration
A Web-based Software Resource for Interactive Analysis of Multiplex Tissue Imaging Datasets
Authors: Creason Allison L. , Watson Cameron , Gu Qiang , Persson Daniel , Sargent Luke , Chen Yu-An , Lin Jia-Ren , Sivagnanam Shamilene , Wünnemann Florian , Nirmal Ajit J. , Chin Koei , Feiler Heidi S. , Coussens Lisa M. , Schapiro Denis , Grüning Björn , Sorger Peter K. , Sokolov Artem , Goecks Jeremy 
Published: August 2022

AbstractHighly multiplexed tissue imaging (MTI) are powerful spatial proteomics technologies that enablein situsingle-cell characterization of tissues. However, analysis and visualization of MTI datasets remains challenging, and we developed the Galaxy-ME software hub to address this challenge.Galaxy-ME is a web-based, interactive software hub that enables end-to-end analysis and visualization of MTI datasets and is accessible to everyone. To demonstrate its utility, Galaxy-ME was used to analyze datasets obtained from multiple MTI assays and evaluate assay concordance in both normal and cancerous tissues. Galaxy-ME is a publicly available web resource.
Disentangling the effects of eutrophication and natural variability on macrobenthic communities across French coastal lagoons
Authors: Jones Auriane G. , Schaal Gauthier , Boyé Aurélien , Creemers Marie , Derolez Valérie , Desroy Nicolas , Fiandrino Annie , Mouton Théophile L. , Simier Monique , Smith Niamh , Ouisse Vincent 
Published: August 2022

AbstractCoastal lagoons are transitional ecosystems that host a unique diversity of species and support many ecosystem services. Owing to their position at the interface between land and sea, they are also subject to increasing human impacts, which alter their ecological functioning. Because coastal lagoons are naturally highly variable in their environmental conditions, disentangling the effects of anthropogenic disturbances like eutrophication from those of natural variability is a challenging, yet necessary issue to address. Here, we analyze a dataset composed of macrobenthic invertebrate abundances and environmental variables (hydro-morphology, water, sediment and macrophytes) gathered across 29 Mediterranean coastal lagoons located in France, to characterize the main drivers of community composition and structure. Using correlograms, linear models and variance partitioning, we found that lagoon hydro-morphology (connection to the sea and lagoon surface), which affects the level of environmental variability (salinity and temperature), as well as lagoon-scale benthic habitat diversity (using macrophyte morphotypes) seemed to regulate macrofauna distribution, while eutrophication and associated stressors like low dissolved oxygen, acted upon the existing communities, mainly by reducing species richness and diversity. Furthermore, M-AMBI, a multivariate index composed of species richness, Shannon diversity and AMBI (AZTI’s Marine Biotic Index) and currently used to evaluate the ecological state of French coastal lagoons, was more sensitive to eutrophication (18%) than to natural variability (9%), with nonetheless 49% of its variability explained jointly by both. To improve the robustness of benthic indicators like M-AMBI and increase the effectiveness of lagoon benthic habitat management, we call for a revision of the ecological groups at the base of the AMBI index and of the current lagoon typology which could be inspired by the lagoon-sea connection levels used in this study.
First Record of Aedes (Stegomyia) albopictus (Diptera: Culicidae) in the state of Acre, Brazil
Authors: da Costa Rocha Ricardo , da Silva Cardoso Acigelda , de Souza Janis Lunier , da Silva Pereira Eliana , de Amorim Marcio Fernandes , de Souza Maria Socorro Martins , de Lima Medeiros Cleomar , Monteiro Maria Francisca Mendes , de Oliveira Meneguetti Dionatas Ulises , de Paula Marcia Bicudo , Brilhante Andreia Fernandes , Lima-Camara Tamara Nunes 
Published: August 2022

AbstractIntroductionAedes (Stegomyia) albopictus (Skuse, 1854) was reported in Brazil for the first time in 1986, and has displayed successful expansion throughout the Brazilian territory.MethodsDuring a routine activity to control dengue conducted by the Division of Entomology of the Municipal Health Department in Rio Branco, adults and immatures of Culicidae were collected in a peri-urban area.ResultsThe Culicidae forms identified indicated that they belonged to the species Ae. albopictus.ConclusionsThis is the first official record of the presence of Ae. albopictus in the state of Acre, confirming its current presence in all Brazilian states.
Diversity and function of methyl-coenzyme M reductase-encoding archaea in Yellowstone hot springs revealed by metagenomics and mesocosm experiments
Authors: Lynes Mackenzie M. , Krukenberg Viola , Jay Zackary J. , Kohtz Anthony J. , Gobrogge Christine A. , Spietz Rachel L. , Hatzenpichler Roland 
Published: August 2022

AbstractMetagenomic studies on geothermal environments have been central in recent discoveries on the diversity of archaeal methane and alkane metabolism. Here, we investigated the methanogenic populations inhabiting terrestrial geothermal features in Yellowstone National Park (YNP) by combining amplicon sequencing with metagenomics and mesocosm experiments. Detection of gene amplicons of methyl-coenzyme M reductase subunit A (mcrA) indicated a wide diversity of Mcr-encoding archaea across geothermal features with differing physicochemical regimes. From three selected hot springs we recovered twelve Mcr-encoding metagenome assembled genomes (MAGs) affiliated with lineages of cultured methanogens as well as Candidatus (Ca.) Methanomethylicia, Ca. Hadesarchaeia, and Archaeoglobi. These MAGs encoded the potential for hydrogenotrophic, aceticlastic, or hydrogen-dependent methylotrophic methanogenesis, or anaerobic short-chain alkane oxidation. While Mcr-encoding archaea represented a minor fraction of the microbial community of hot springs, mesocosm experiments with methanogenic precursors resulted in stimulation of methanogenic activity and the enrichment of lineages affiliated with Methanosaeta and Methanothermobacter as well as with uncultured Mcr-encoding archaea including Ca. Korarchaeia, Ca. Nezhaarchaeia, and Archaeoglobi. Altogether, we revealed that diverse Mcr-encoding populations with the metabolic potential to produce methane from different precursors persist in the geothermal environments of YNP. This study highlights the importance of combining environmental metagenomics with laboratory-based experiments to expand our understanding of uncultured Mcr-encoding archaea and their potential impact on microbial carbon transformations in geothermal environments and beyond.
In airway epithelium, basal stem cells and their stress fibers remodel during the unjamming transition
Authors: Phung Thien-Khoi N. , Mitchel Jennifer A. , O’Sullivan Michael J. , Park Jin-Ah 
Published: August 2022

AbstractUnder homeostatic conditions, epithelial cells remain non-migratory. However, during embryonic developmental and pathological processes, they become migratory. The mechanism underlying the transition between non-migratory and migratory epithelial cells is a fundamental question of cellular biology. In well-differentiated primary human bronchial epithelial cell layers, non-migratory epithelial cells become migratory through an unjamming transition (UJT). We have previously identified the hallmarks of UJT: apical cell elongation and collective cellular migration. These indicate that UJT is driven by intercellular force modulation, but the nature of these forces in pseudostratified epithelia is unknown. Here, we identify structural characteristics of basal stem cells that are indicative of force generation. During the UJT, basal stem cells elongate and enlarge, and their stress fibers lengthen and align. These morphological changes in basal stem cells correspond to the previously defined hallmarks of the UJT. Moreover, basal cell elongation and stress fiber lengthening precedes apical cell elongation. Together, these structural changes in basal stem cells suggest that in pseudostratified airway epithelium, basal stem cells may be the origin of the traction forces through stress fiber modeling during the UJT.Summary StatementOur image analysis of pseudostratified airway epithelium reveals basal stem cells as the likely source of traction forces driving collective cellular migration during an unjamming transition.
Egocentric value maps of the near-body environment
Authors: Bufacchi Rory John , Somervail Richard , Fitzpatrick Aoife Maria , Caminiti Roberto , Iannetti Gian Domenico 
Published: August 2022

AbstractBody-part centric response fields are pervasive: they are observed in single neurons, fMRI, EEG, and multiple behavioural measures. This prevalence across scales and measures makes them excellent candidates for studying systems-level neuroscience. Nonetheless, they remain poorly understood because we lack a unifying formal explanation of their origins and role in wider brain function. Here, we provide such explanation.We use reinforcement learning to analytically explain the existence of body-part centric receptive fields, also known as peripersonal field. We then simulate multiple experimental findings considered foundational in the peripersonal space literature. Our results demonstrate that peripersonal fields naturally arise from two simple and plausible assumptions about living agents: 1) they experience reward when they contact objects in the environment, and 2) they act to maximise reward. These simple assumptions are enough to explain empirical findings on stimulus kinematics, tool use, valence, and network-architecture.Our explanation provides further insight. First, it offers multiple empirically testable predictions. Second, it offers a formal description of the notion that the world-agent state is encoded in parieto-premotor cortices, using motor primitives: peripersonal fields provide building blocks that together create a short-term model of the world near the agent in terms of its future states; a successor representation. This short-term, close-range egocentric peripersonal map is analogous to the long-term, long-range allocentric spatial map of place and grid cells, which underlie locomotion and navigation to reach distant objects. Together, these allocentric and egocentric maps allow efficient interactions with a changing environment across multiple spatial and temporal scales.Abstract Figure
SiGra: Single-cell spatial elucidation through image-augmented graph transformer
Authors: Tang Ziyang , Zhang Tonglin , Yang Baijian , Su Jing , Song Qianqian 
Published: August 2022

ABSTRACTThe recent advances in high-throughput molecular imaging push the spatial transcriptomics technologies to the subcellular resolution, which breaks the limitations of both single-cell RNA-seq and array-based spatial profiling. The latest released single-cell spatial transcriptomics data from NanoString CosMx and MERSCOPE platforms contains multi-channel immunohistochemistry images with rich information of cell types, functions, and morphologies of cellular compartments. In this work, we developed a novel method, Single-cell spatial elucidation through image-augmented Graph transformer (SiGra), to reveal spatial domains and enhance the substantially sparse and noisy transcriptomics data. SiGra applies hybrid graph transformers over a spatial graph that comprises high-content images and gene expressions of individual cells. SiGra outperformed state-of-the-art methods on both single-cell spatial profiles and spot-level spatial transcriptomics data from complex tissues. The inclusion of immunohistochemistry images improved the model performance by 37% (95%CI: 27% – 50%). SiGra improves the characterization of intratumor heterogeneity and intercellular communications in human lung cancer samples, meanwhile recovers the known microscopic anatomy in both human brain and mouse liver tissues. Overall, SiGra effectively integrates different spatial modality data to gain deep insights into the spatial cellular ecosystems.
Autophagy is associated with survival and resiliency of fibroblasts in long-term decaying post-mortem parenchymal tissue
Authors: McAndrews Kathleen M. , McGrail Daniel J. , Gansmo Liv B. , Che Sara P.Y. , Chakravarti Deepavali , LeBleu Valerie S. , Kalluri Raghu 
Published: August 2022

AbstractFibroblasts are spindle-shaped mesenchymal cells and an abundantly studied cell type that are easy to culture. Their adaptive response in culture conditions allows for use in many different cell biological experiments, including their utility in generating induced pluripotent stem cells. Despite extensive use of fibroblasts in cell and molecular biology and genetics experiments, fundamental evaluation of their resiliency and survival programs, in comparison with other cell types, is undetermined. Here, we demonstrate that fibroblasts exhibit remarkable survival capacity in post-mortem tissue decaying at room temperature and can be cultured from ear, tail, kidney, lung, fetal, and mammary tumor tissue after 12-hours of post-mortem tissue decay. Fibroblasts can be cultured from ear and lung tissue after 24-hours, and from ear after up to 120-hours of post-mortem tissue decay. Gene expression profiling of post-mortem lung tissue fibroblasts compared to fresh tissue cultured fibroblasts suggested a transition to a more quiescent phenotype with activation of nutrient scavenging pathways as evidenced by downregulation of genes associated with DNA replication, ribosomes, cell cycle, and spliceosomes as well as upregulation of genes associated metabolism, autophagy, and lysosomes. Measurement of light chain 3B (LC3B)-I/LC3B-II ratio and lysosomal-associated membrane protein (LAMP)-1 indicate that autophagy is increased in post-mortem fibroblasts, with evidence for potential increase in autolysosomes and senescence program. Our study provides evidence for the ability of normal fibroblasts to overcome extreme stress conditions and offers new insights into cell survival mechanisms and aging, with potential utility in tissue regeneration and repair.