bluuebunny/crossref_metadata_2025_split huggingface dataset:
Erythropoietin production in embryonic neural cells is controlled by hypoxia-inducible factors and histone deacetylases in an undifferentiated state
Authors: Iwamura Yuma , Nakai Taku , Kato Koichiro , Ishioka Hirotaka , Yamamoto Masayuki , Hirano Ikuo , Suzuki Norio 
Published: March 2024

AbstractDuring mammalian development, production sites of the erythroid growth factor erythropoietin (EPO) shift from the neural tissues to the liver in embryos and to the adult kidneys. Embryonic neural EPO-producing (NEP) cells, a subpopulation of neuroepithelial and neural crest cells, express theEpogene between embryonic day (E) 8.5 and E11.5 to promote primitive erythropoiesis in mice. WhileEpogene expression in the liver and kidney is induced under hypoxic conditions through hypoxia-inducible transcription factor (HIF) 2α, theEpogene regulatory mechanisms in NEP cells remain to be elucidated. This study confirms the presence of cells coexpressing the genes encoding EPO and HIF2α in E9.5 neural tubes, where the hypoxic microenvironment activates HIF1α. In human neural progenitors and mouse embryonic neural tissues, a HIF-activating compound upregulatedEPOexpression, and this induction was blocked by inhibiting HIFs. Additionally, a cell line of NEP cell derivatives that no longer expressed theEpogene demonstrated that histone deacetylase inhibitors (HDACIs) reactivate EPO production while rejuvenating the cells. HDACIs also inducedEPOgene expression in SK-N-BE(2)c human neuroblastoma cells and mouse primary neural crest cells. Thus, EPO production is controlled by epigenetic mechanisms and hypoxia signaling in an immature state of hypoxic NEP cells.
Under the radar: differential responses of bed bugs to an entomopathogen, environmental bacteria, and a human pathogen
Authors: Walt Hunter K. , Bronzato-Badial Aline , Maedo Sophie E. , Hinton Joseph A. , King Jonas G. , Pietri Jose E. , Hoffmann Federico G. 
Published: March 2024

AbstractBackgroundBed bugs (Hemiptera: Cimicidae) are a widely distributed, obligately blood-feeding insect, but they have never been linked to pathogen transmission in humans. Most other hematophagous insects that frequently bite humans transmit pathogens, and it is unclear why bed bugs do not. One hypothesis is that bed bugs have evolved a highly robust immune system because their mating system, traumatic insemination, exposes females to consistent wounding and bacterial infections. Although this has been proposed, very little is known about the bed bug immune system and how bed bugs respond to microbial challenges. Understanding the bed bug immune system could give insight to why bed bugs are not known to transmit disease and under what circumstances they could, while also facilitating biological control efforts involving microbes.MethodsTo investigate the immune response of bed bugs to bacterial challenges, we exposed female bed bugs to three bacterial challenges. 1.)Pseudomonas fluorescens, an entomopathogen known to have harmful effects to bed bugs, 2.) bacteria cultured from a bed bug enclosure likely encountered during traumatic insemination, and 3.)Borrelia duttoni, a human vector-borne pathogen that causes relapsing fever. We compared the transcriptomes of infected bed bugs with uninfected bed bugs, focusing on immune-related genes. We also conducted phylogenetic analyses to understand patterns of gene duplication and function of potentially immune-related genes.ResultsWe found many known immune effector genes upregulated in response toP. fluorescensand traumatic insemination-associated bacteria, but interestingly, not in response toB. duttoni. Furthermore, we found significant overlap in the genes differentially expressed in response toP. fluorescensand the traumatic insemination associated bacteria, and betweenP. fluorescensandB. duttoni, but no significant overlap between traumatic insemination bacteria andB. duttoni. We also show that bed bug diptericin-like antimicrobial peptides underwent a lineage-specific gene duplication, and that they may have further functional specialization. Finally, we identify previously overlooked candidates for future study of immune function in bed bugs, including some putative cuticle-associated genes, a laccase-like gene, and a mucin-like gene.ConclusionsBy taking comprehensive transcriptomic approach, our study is an important step in understanding how bed bugs respond to diverse immune challenges.
Rewinding the developmental tape shows how bears break a developmental rule
Authors: Stenberg Otto E. , Moustakas-Verho Jacqueline E. , Jernvall Jukka 
Published: March 2024

AbstractMammals have evolved a broad variety of dental morphologies. Nevertheless, the development of the mammalian dentition is considered highly conserved. Molar size proportions exemplify this as a system where small changes in shared developmental mechanisms yield a defined range of morphological outcomes. The Inhibitory Cascade (IC) model states that as molars develop in a sequence, the first developing anterior molars inhibit the development of subsequent posterior ones. The IC model thus predicts a trend of linear tooth size change along the molar row, as has been observed in a wide range of mammalian taxa with otherwise differing dental morphology. Perhaps the starkest exceptions to the IC rule are bears, in which the second molar is the largest and the third molar is disproportionally small. Here we sought to illuminate when and how during development the bear dentition falls of the IC prediction. We examined molar proportions in seven bear species. The results indicate that development of bear molars deviates from IC expectation already during patterning. Yet, during the earlier cap stage, size proportions of bear molars still seem to adhere to the IC model predictions. Overall, these analyses are suggestive that irrespective of the final outcome, the process of initial splitting of the molar-forming region into individual teeth is conserved and follows the IC rule.
Direct pharmacological AMPK activation inhibits mucosal SARS-CoV-2 infection by reducing lipid metabolism, restoring autophagy flux and the type I IFN response
Authors: Cottignies-Calamarte Andrea , Marteau Flora , He Feifan , Belouzard Sandrine , Dubuisson Jean , Tudor Daniela , Viollet Benoit , Bomsel Morgane 
Published: March 2024

AbstractAMP-activated protein kinase (AMPK) plays a central role in regulating cell energy balance. When activated, AMPK supresses energy-consuming pathways such as lipid and protein synthesis while increasing nutrient availability through the activation of autophagy. These pathways downstream AMPK activation contribute to SARS-CoV-2 infection, which hijacks autophagy and accumulates lipid droplets in viral factories to support viral replication. Here, we assessed the antiviral activity of the direct pan-AMPK allosteric activator MK-8722in vitro.MK-8722 efficiently inhibited infection of Alpha and Omicron SARS-CoV-2 variants in Vero76 and human bronchial epithelial Calu-3 cells at micromolar concentration. This inhibition relied on restoring the autophagic flux, which redirected newly synthesized viral proteins for degradation, and on a reduction in lipid metabolism, which affected the viral factories. Furthermore, MK-8722 treatment increased the type I interferon (IFN-I) response. Post-infection treatment with MK-8722 was enough to inhibit efficiently viral replication and restore the IFN-I response. Finally, MK-8722 treatment did not alter the SARS-CoV-2-specific CD8+T cell response mounted upon Spike vaccination. Overall, by activating AMPK, MK-8722 acts as an effective antiviral against SARS-CoV-2 infection, even when applied post-exposure, paving the way for preclinical tests aimed at inhibiting viral replication and improving patients’ symptoms.Graphical abstractHighlightsMK-8722 exerts post-exposure antiviral activityMK-8722 induces a decrease in cellular lipid contentMK-8722 promotes an increase in the autophagic flux of viral componentsMK-8722 promotes the restoration of the IFN-I activityMK-8722 antiviral activity is compatible with virus-specific T cell responses
Siderophore piracy enables the nasal commensalStaphylococcus lugdunensisto antagonize the pathogenStaphylococcus aureus
Authors: Rosenstein Ralf , Salazar Benjamin O. Torres , Sauer Claudia , Heilbronner Simon , Krismer Bernhard , Peschel Andreas 
Published: March 2024

AbstractBacterial pathogens such asStaphylococcus aureuscolonize body surfaces of part of the human population, which represents a critical risk factor for skin disorders and invasive infections. However, such pathogens do not belong to the human core microbiomes – beneficial ‘commensal’ bacteria can often prevent the persistence of certain pathogens – using molecular strategies that are only superficially understood. We recently reported that the commensal bacteriumStaphylococcus lugdunensisproduces the novel antibiotic lugdunin, which eradicatesS. aureusfrom nasal microbiomes of hospitalized patients. However, it has remained unclear ifS. lugdunensismay affectS. aureuscarriage in the general population and howS. lugdunensiscarriage could be promoted to enhance itsS. aureus-eliminating capacity. We could cultivateS. lugdunensisfrom the noses of 6.3% of healthy human volunteers. In addition,S. lugdunensisDNA could be identified in metagenomes of many culture-negative nasal samples indicating that cultivation success depends on a specific bacterial threshold density. HealthyS. lugdunensiscarriers had a 5.2-fold lower propensity to be colonized byS. aureusindicating that lugdunin can eliminateS. aureusalso in healthy humans.S. lugdunensis-positive microbiomes were dominated by eitherStaphylococcus epidermidis,Corynebacteriumspecies, orDolosigranulum pigrum. These and further bacterial commensals, whose abundance was positively associated withS. lugdunensis, promotedS. lugdunensisgrowth in co-culture. Such mutualistic interactions depended on the production of iron-scavenging siderophores by supporting commensals, and on the capacity ofS. lugdunensisto import siderophores. These findings underscore the importance of microbiome homeostasis for eliminating pathogen colonization. Elucidating mechanisms that drive microbiome interactions will become crucial for microbiome-precision editing approaches.
Differential gene expression and chromatin accessibility in the medial prefrontal cortex associated with individual differences in rat behavioral models of opioid use disorder
Authors: Liu Shirelle X. , Muelken Peter , Maxim Zia L. , Ramakrishnan Aarthi , Estill Molly S. , LeSage Mark G. , Smethells John R. , Shen Li , Tran Phu V. , Harris Andrew C. , Gewirtz Jonathan C. 
Published: March 2024

AbstractOpioid use disorder (OUD) is a neuropsychological disease that has a devastating impact on public health. Substantial individual differences in vulnerability exist, the neurobiological substrates of which remain unclear. To address this question, we investigated genome-wide gene transcription (RNA-seq) and chromatin accessibility (ATAC-seq) in the medial prefrontal cortex (mPFC) of male and female rats exhibiting differential vulnerability in behavioral paradigms modeling different phases of OUD: Withdrawal-Induced Anhedonia (WIA), Demand, and Reinstatement. Ingenuity Pathway Analysis (IPA) of RNA-seq revealed greater changes in canonical pathways in Resilient (vs. Saline) rats in comparison to Vulnerable (vs. Saline) rats across 3 paradigms, suggesting brain adaptations that might contribute to resilience to OUD across its trajectory. Analyses of gene networks and upstream regulators implicated processes involved in oligodendrocyte maturation and myelination in WIA, neuroinflammation in Demand, and metabolism in Reinstatement. Motif analysis of ATAC-seq showed changes in chromatin accessibility to a small set of transcription factor (TF) binding sites as a function either of opioid exposure (i.e., morphine versus saline) generally or of individual vulnerability specifically. Some of these were shared across the 3 paradigms and others were unique to each. In conclusion, we have identified changes in biological pathways, TFs, and their binding motifs that vary with paradigm and OUD vulnerability. These findings point to the involvement of distinct transcriptional and epigenetic mechanisms in response to opioid exposure, vulnerability to OUD, and different stages of the disorder.
Gluk4-containing kainate receptors regulate synaptic communication in the motor cortex and reduce axon degeneration in adult mice
Authors: Ricci Raphael , Fletcher Jessica L , Makowiecki Kalina , Pepper Renee E , Fortune Alastair , Cullen Carlie L , Connelly William M , Charlesworth Jac , Blackburn Nicholas B , Pitman Kimberley A , Young Kaylene M 
Published: March 2024

AbstractGlutamate-gated kainate receptors comprising the Gluk4 subunit (encoded byGrik4) are highly expressed by neurons in the central nervous system. We report thatGrik4mRNA is widely expressed by neurons in the adult mouse motor cortex, where GluK4-containing kainate receptors account for ∼60% of the kainate evoked current in layer V pyramidal neurons. To elucidate their role in motor circuit regulation, we analysed the behaviour of mice that lacked the pore forming domain of the GluK4 subunit (Grik4-/-mice).Grik4-/-mice were hyperactive, had an abnormal gait, and impaired motor coordination. At postnatal day (P)60, layer V pyramidal neurons received fewer miniature excitatory post synaptic currents, had a reduced density of thin spines on their basal dendrites, and a reduced density of VGlut1 puncta at the soma, consistent with neurons receiving fewer excitatory synaptic connections.Grik4-/-mice also lost ∼44% of their callosal axons between P60 and P180 and the amplitude of the callosal compound action potential was reduced by ∼25-30%. RNA sequencing data support the capacity forGrik4to modulate synaptic and neuroprotective signalling pathways.
Label-free imaging of intracellular structures in living mammalian cells via external apodization phase-contrast microscopy
Authors: Ohno Hiroshi , Nishimura Takenori , Kainoh Kenta , Ohashi Yoshitaka , Onodera Naoko , Kano Mayuko , Sari Lay Nurhana , Masuda Masato , Tamura Yoshiaki , Hayashi Yusuke , Yamamoto Yusuke , Takahashi Shin-Ichiro , Mishima Yuta , Yoneyama Yosuke , Takeuchi Yoshinori , Sekiya Motohiro , Matsuzaka Takashi , Miyamoto Takafumi , Shimano Hitoshi 
Published: March 2024

AbstractDeveloping techniques to visualize intracellular structures, which influence the spatiotemporal functionality of biomolecules, is essential for elucidating mechanisms governing cellular behavior. In this study, we demonstrate that label-free external apodization phase-contrast (ExAPC) microscopy serves as a valuable tool for the simultaneous observation of various intracellular structures with high spatiotemporal resolution, while successfully mitigating halo artifacts. Additionally, through quantitative analysis of images obtained by combining ExAPC microscopy with fluorescence microscopy, we identified distinct heterogeneities in biomolecular condensates, lipid droplets, and mitochondria. Our findings highlight the potential of ExAPC microscopy to provide detailed insights into alterations in intracellular structures associated with diverse cellular processes, corroborating the existing knowledge and potentially contributing to the discovery of novel cellular mechanisms.
Methionine cycle in a pair of serotonergic neurons regulates diet-dependent behavior and longevity through a neuron-gut signaling
Authors: Rahman Sabnam Sahin , Bhattacharjee Shreya , Prakash Govind , Motwani Simran , Nair Tripti , Keerthana Rachamadugu Sai , Mukhopadhyay Arnab 
Published: March 2024

AbstractThe folate-methionine cycle (Met-C) is a central metabolic pathway that is regulated by vitamin B12 (B12), a micronutrient obtained exclusively from diet and microbiota. This metabolic hub supports amino acid, nucleotide and lipid biosynthesis apart from its central role of providing one carbon (-CH3) moiety for methylation reactions. While deficiency of B12 as well as polymorphism in enzymes of the Met-C has been clinically attributed to neurological and metabolic disorders, how this pathway cell non-autonomously regulates systemic physiological processes is less understood. Using a B12-sensitive mutant ofCaenorhabditis elegans, we show that the neuronal Met-C responds to differential B12 content in diet to regulate p38-MAPK activation in intestinal cells, thereby modulating cytoprotective gene expression, stress tolerance and longevity. Mechanistically, B12-driven changes in the metabolic flux through the Met-C in the serotonergic ADF neurons of the mutant lead to the release of serotonin (5-hydroxytryptamine, 5-HT). 5-HT activates its receptor, MOD-1, in the post-synaptic interneurons that then secretes the neuropeptide FLR-2. FLR-2 binds to FSHR-1, its cognate receptor in the intestine, and induces the phase transition of the SARM domain protein TIR-1, thereby activating the p38-MAPK pathway. Importantly, this cascade influences the foraging behaviour of the mutant worms such that they prefer a B12-rich diet. Together, our study reveals a dynamic neuron-gut signaling axis that helps an organism modulate behaviour and life history traits based on the neuronal Met-C metabolic flux determined by B12 availability in its diet. Understandably, disruption of the optimum functioning of this axis may have debilitating effects on the health of an organism and the survival of the species.
Sticking together: Independent evolution of biofilm formation in different species of staphylococci has occurred multiple times via different pathways
Authors: Crossman Lisa , Sims Leanne , Dean Rachael , Felgate Heather , Calvo Teresa Diaz , Hill Claire , McNamara Iain , Webber Mark A , Wain John 
Published: March 2024

AbstractVarious species of staphylococci cause a wide range of infections, including implant-associated infections which are often difficult to treat due to the presence of biofilms. Whilst some proteins involved in biofilm formation are known, the differences in biofilm production between staphylococcal species remains understudied. Currently biofilm formation byStaphylococcus aureusis better understood than for other members of the genus as more research effort has focused on this species.We assembled a panel of 385 non-aureus Staphylococcusisolates of 19 species from prosthetic joint infection as well as other clinical sources and reference strains. We assessed the biofilm forming ability of all strains using a high-throughput crystal violet assay. This identified distinct biofilm formation categories and we then compared the prevalence of Pfam domains and identified those which distinguished the categories as well as using machine learning to identify amino acid 20-mers linked to biofilm formation.This identified some domains within proteins already positively linked to biofilm formation but we also identified important domains not previously linked to biofilm formation. RT-qPCR confirmed the expression of selected genes predicted to encode important domains within biofilms inStaphylococcus epidermidis.The prevalence and distribution of biofilm associated domains showed a link to phylogeny, suggesting differentStaphylococcusspecies have independently evolved different mechanisms of biofilm production.This work has identified different routes to biofilm formation in diverse species ofStaphylococcusas well as suggesting independent evolution of biofilm has occurred multiple times across the genus. Understanding the mechanisms of biofilm formation in any given species is likely to require detailed study of relevant strains and the ability to generalise across the genus may be limited.
A quantitative pipeline to assess secretion of human leptin coding variants reveals mechanisms underlying leptin deficiencies
Authors: Baird Harry J. M. , Shun-Shion Amber S. , de Oliveira Edson Mendes , Stalder Danièle , Eden Jessica , Chambers Joseph E. , Farooqi I. Sadaf , Gershlick David C. , Fazakerley Daniel J. 
Published: March 2024

AbstractThe hormone leptin, primarily secreted by adipocytes, plays a crucial role in regulating whole-body energy homeostasis. Homozygous loss-of-function mutations in the leptin gene(LEP)cause hyperphagia and severe obesity, primarily through alterations in leptin’s affinity for its receptor or changes in serum leptin concentrations. Although serum concentrations are influenced by various factors (e.g., gene expression, protein synthesis, stability in the serum), proper delivery of leptin from its site of synthesis in the endoplasmic reticulum via the secretory pathway to the extracellular serum is a critical step. However, the regulatory mechanisms and specific machinery involved in this trafficking route, particularly in the context of humanLEPmutations, remain largely unexplored.We have employed the Retention Using Selective Hooks (RUSH) system to elucidate the secretory pathway of leptin. We have refined this system into a medium-throughput assay for examining the pathophysiology of a range of obesity-associatedLEPvariants. Our results reveal that leptin follows the default secretory pathway, with no additional regulatory steps identified prior to secretion.Through screening of leptin variants, we identified three mutations that lead to proteasomal degradation of leptin and one mutant that significantly decreased leptin secretion, likely through aberrant disulfide bond formation. These observations have identified novel pathogenic effects of leptin variants, which can be informative for therapeutics and diagnostics. Finally, our novel quantitative screening platform can be adapted for other secreted proteins.
CRISPR-Cas9 editing efficiency in fission yeast is not limited by homology search and is improved by combining gap-repair with fluoride selection
Authors: Fernandez Ronan , Berro Julien 
Published: March 2024

AbstractProtocols for CRISPR-Cas9 editing have been implemented in most model organisms, including fission yeast, for which some improvements have also been later described. Here, we report an improvement to the CRISPR-Cas9 protocol in fission yeast, as we combine a cloning free gap-repair method with our previously described fluoride selection marker, which speeds up genome editing. We also report a wide variability of editing efficiencies at different loci along the genome, and we demonstrate that this variability cannot be explained by the location of the edited sequences in the genome. Lastly, our attempt at improving editing efficiency by targeting the donor DNA to the cut site using a HaloTag strategy to link the donor DNA to two proteins of the homologous recombination repair machinery (Rad51 or Rad52) fell short, which shows that editing efficiency in fission yeast is likely not limited by homology search.
Targeting Iron - Respiratory Reciprocity Promotes Bacterial Death
Authors: Sharifian Gh. Mohammad , Norouzi Fatemeh , Sorci Mirco , Zaid Tanweer S , Pier Gerald B. , Achimovich Alecia , Ongwae George M. , Liang Binyong , Ryan Margaret , Lemke Michael , Belfort Georges , Gadjeva Mihaela , Gahlmann Andreas , Pires Marcos M. , Venter Henrietta , Harris Thurl E. , Laurie Gordon W. 
Published: March 2024

ABSTRACTDiscovering new bacterial signaling pathways offers unique antibiotic strategies. Here, through an unbiased resistance screen of 3,884 gene knockout strains, we uncovered a previously unknown non-lytic bactericidal mechanism that sequentially couples three transporters and downstream transcription to lethally suppress respiration of the highly virulentP. aeruginosastrain PA14 - one of three species on the WHO’s ‘Priority 1: Critical’ list. By targeting outer membrane YaiW, cationic lacritin peptide ‘N-104’ translocates into the periplasm where it ligates outer loops 4 and 2 of the inner membrane transporters FeoB and PotH, respectively, to suppress both ferrous iron and polyamine uptake. This broadly shuts down transcription of many biofilm-associated genes, including ferrous iron-dependent TauD and ExbB1. The mechanism is innate to the surface of the eye and is enhanced by synergistic coupling with thrombin peptide GKY20. This is the first example of an inhibitor of multiple bacterial transporters.