bluuebunny/crossref_metadata_2025_split huggingface dataset:
The consequences of mismatched buffers in spectral cell sorting
Authors: Dapaah Rita A. S. , Ferrer-Font Laura , Shi Xiaoshan , Hall Christopher , Thompson Sam , Costa Larissa Catharina , Mage Peter L. , Tyznik Aaron J. , Lundsten Kelly , Walker Rachael V 
Published: August 2024

ABSTRACTAlthough spectral flow cytometry has become a ubiquitous tool for cell analysis, the use of spectral cytometry on cell sorters requires additional considerations arising from the unique requirements of sorting workflows. Here, we show that care should be taken when ascertaining the purity of a sort on a spectral cell sorter, as the mismatch of buffers used for initial sample suspension and the buffers used for sort collection can affect the unmixing of the data, potentially giving rise to erroneous purity check results.
Cell size and selection for stress-induced cell fusion in unicellular eukaryotes
Authors: Liu Xiaoyuan , Pitchford Jonathan W. , Constable George W. A. 
Published: August 2024

AbstractIn unicellular organisms, sexual reproduction typically begins with the fusion of two cells (plasmogamy) followed by the fusion of their two haploid nuclei (karyogamy) and finally meiosis. Most work on the evolution of sexual reproduction focuses on the benefits of the genetic recombination that takes place during meiosis. However, the selection pressures that may have driven the early evolution of binary cell fusion, which sets the stage for the evolution of karyogamy by bringing nuclei together in the same cell, have seen less attention. In this paper we develop a model for the coevolution of cell size and binary cell fusion rate. The model assumes that larger cells experience a survival advantage from their larger cytoplasmic volume. We find that under favourable environmental conditions, populations can evolve to produce larger cells that undergo obligate binary cell fission. However, under challenging environmental conditions, populations can evolve to subsequently produce smaller cells under binary cell fission that nevertheless retain a survival advantage by fusing with other cells. The model thus parsimoniously recaptures the empirical observation that sexual reproduction is typically triggered by adverse environmental conditions in many unicellular eukaryotes and draws conceptual links to the literature on the evolution of multicellularity.Author summarySexual reproduction is commonly observed, both in eukaryotic microorganisms and in higher multicellular organisms. Sex has evolved despite numerous apparent costs, including investment in finding a partner and the energetic requirements of sexual reproduction. Binary cell fusion is a process that sets the stage for sexual reproduction by bringing nuclei from different cells into contact. Here, we provide a mathematical explanation of the advantage conferred by binary cell fusion due to increased cell mass. We show that when unicellular organisms have the option to invest in either cell fusion or cell mass, they can evolve to fuse together as rapidly as possible in the face of adverse environments, instead of increasing their mass. These results are consistent with the empirical observation that sexual reproduction is often triggered by environmental stress in unicellular eukaryotes. Our results imply an advantage to cell fusion, which helps to shed light on the early evolution of sexual reproduction itself.
SegFinder: an automated tool for identifying RNA virus genome segments through co-occurrence in multiple sequenced samples
Authors: Liu Xue , Kong Jianbin , Shan Yongtao , Yang Ziyue , Miao Jiafan , Pan Yuanfei , Luo Tianyang , Shi Zhiyuan , Wang Yingmei , Gou Qinyu , Yang Chunhui , Li Chunmei , Li Shaochuan , Zhang Xu , Sun Yanni , Holmes Edward C. , Guo Deyin , Shi Mang 
Published: August 2024

AbstractMetagenomic sequencing has expanded the RNA virosphere, but many identified viral genomes remain incomplete, especially for segmented viruses. Traditional methods relying on sequence homology struggle to identify highly divergent segments and group them confidently within a single virus species. To address this, we developed a new bioinformatic tool – SegFinder – that identifies virus genome segments based on their common co-occurrence at similar abundance within segmented viruses. SegFinder successfully re-discovered all segments from a test data set of individual mosquito transcriptomes, which was also used to establish parameter thresholds for reliable segment identification. Using these optimal parameters, we applied SegFinder to 858 libraries from eight metagenomic sequencing projects, including vertebrates, invertebrates, plants, and environmental samples. Furthermore, we identified 108 (excluding RdRP) unique viral genome segments, of which 55 were novel and 32 showed no recognizable sequence homology to known sequences but which were verified by the presence of conserved sequences at the genome termini. SegFinder is also able to identify segmented genome structures in viruses previously considered to be predominantly unsegmented, and in doing so expanded the number of known families and orders of segmented RNA viruses, making it a valuable tool in an era of large-scale parallel sequencing.
Blockade of rheumatoid arthritis synovial fluid-induced sensory neuron activation by JAK inhibitors
Authors: Li Yuening , Gray Elizabeth H. , Ross Rosie , Zebochin Irene , Lock Amy , Fedele Laura , Kamajaya Louisa Janice , Marrow Rebecca J. , Ryan Sarah , Röderer Pascal , Brüstle Oliver , John Susan , Denk Franziska , Taams Leonie S. 
Published: August 2024

AbstractObjectiveClinical studies suggest that compared to anti-TNF treatment, JAK inhibitors (JAKi) are superior in reducing pain in rheumatoid arthritis (RA). The underlying mechanisms for this observation are still unknown. Sensory neurons transmit noxious signals from inflamed joints to the central nervous system, where a pain percept is generated. We investigated whether JAKi exert direct effects on sensory neurons.MethodsIn-house and public RNA sequencing datasets of sensory neurons were analysed for relevant JAK/STAT and cytokine-receptor gene expression. Human induced pluripotent stem cell (IPSC)-derived sensory neurons were stimulated with serum and synovial fluid (SF) from individuals with RA, or with selected cytokines that were found in RA SF by Luminex. Phosphorylation of STAT3 (pSTAT3) was assessed by Western blot. Sensory neuron activation was examined by recording neuronal firing using multi-electrode array and measuring expression levels of pain-relevant genes with STAT3-binding sites.ResultsCell-free RA synovial fluid induced pSTAT3 in IPSC-derived sensory neurons, an effect which was completely blocked by the JAKi tofacitinib. Compared to paired serum, RA SF was enriched for the JAK/STAT cytokines IL-6, IL-11, LIF, IFN-alpha and IFN-beta, with their requisite receptors present on sensory neurons. Stimulation of IPSC- derived sensory neurons with these recombinant cytokines recapitulated pSTAT3 induction in these cells. Furthermore, IL-6+sIL-6R or LIF upregulated expression of pain-relevant genes which was blocked by tofacitinib. Finally, we provided evidence that LIF can induce neuronal sensitisation.ConclusionOur data indicate that JAKi can act directly on sensory neurons, providing a potential mechanistic explanation for their suggested superior analgesic properties.
Comparative effects of proton and photon irradiation on the molecular and cellular profiles of triple-negative breast cancer: the crucial impact of VEGFC on tumor microenvironment remodeling
Authors: Sarlak Saharnaz , Marotte Delphine , Morfoisse Florent , Pierantoni Alessandra , Sirera Jessy , Tsai Meng-Chen , Vidal Marie , Hérault Joël , Garmy-Susini Barbara , Doyen Jérôme , Luciano Frédéric , Pagès Gilles 
Published: August 2024

AbstractMetastatic triple-negative breast cancers (TNBC) are among the most aggressive types of breast cancer and are often treated with adjuvant radiotherapy and chemotherapy. Despite initial efficacy, relapses are common, leading to poor prognosis. Understanding the response of tumor microenvironment to radiotherapy is crucial, particularly comparing photon (X) and proton (P) radiotherapy due to proton radiation’s reduced side effects.MethodsWe investigated the effects of single and multiple X and P irradiations on various cell types within the tumor microenvironment, including vascular and lymphatic endothelial cells, fibroblasts, and TNBC tumor cells. VEGFC, a key factor in lymphatic vessel formation and metastasis, was a primary focus. We used protein arrays to evaluate the effects of irradiation and examined the impact of VEGFC inactivation on the sensitivity to X and P radiation. Additionally, we tested tumor-forming capabilities of irradiated cells and assessed the impact of genetic or therapeutic VEGFC inhibition on TNBC growth. Transcriptomic and proteomic analyses further characterized the differences between X and P tumors, providing deeper insights into their distinct molecular profiles.ResultsBoth X and P irradiations caused a transient increase in VEGFC levels, along with other pro-angiogenic, pro-lymphangiogenic, and pro-fibrotic factors, such as angiopoietin 2, artemin, endostatin, IGFBP2, serpinE1, PDGFA, and DPPIV. Endothelial cells exposed to multiple rounds of radiation showed enhanced proliferation but lost the ability to form pseudo vessels, indicating an endothelial-mesenchymal transition. Tumor cells lacking VEGFC were more sensitive to radiation, and anti-VEGFC antibodies significantly suppressed TNBC cells’ proliferation, both naïve and multi-irradiated. Tumor xenografts formed by multi-irradiated cells grew larger in nude mice, particularly following proton irradiation, while X-irradiated tumors exhibited a more pro-lymphangiogenic phenotype compared to P-irradiated tumors.ConclusionsOur findings show that while P multi-irradiated TNBC cells form larger tumors, X multi-irradiated tumors are more aggressive, with elevated expression of genes linked to angiogenesis, lymphangiogenesis, and endothelial-mesenchymal transition. Targeting VEGFC during photon or proton radiotherapy could reduce metastasis and improve TNBC prognosis.
Human PC4 supports telomere stability and viability in cells utilizing the alternative lengthening of telomeres mechanism
Authors: Salgado Sara , Abreu Patricia L. , Moleirinho Beatriz , Larcombe Lee , Azzalin Claus M. 
Published: August 2024

AbstractCancer cells with an activated Alternative Lengthening of Telomeres (ALT) mechanism elongate telomeres via homology-directed repair. Sustained telomeric replication stress is an essential trigger of ALT activity; however, it can lead to cell death if not properly restricted. By analyzing publicly available data from genome-wide CRISPR KO screenings, we have identified the multifunctional protein PC4 as a novel factor essential for ALT cell viability. Depletion of PC4 using siRNAs results in rapid ALT cell death, while telomerase-positive cells show minimal effects. PC4 depletion induces replication stress and telomere fragility primarily in ALT cells, and increases ALT activity. PC4 binds to telomeric DNA in cells, and its binding is enhanced by telomeric replication stress. Finally, a mutant PC4 with partly impaired single stranded DNA binding activity is capable to localize to telomeres and suppress ALT activity and telomeric replication stress. We propose that PC4 supports ALT cell viability, at least partly, by averting telomere dysfunction. Targeted inhibition of PC4 holds promise for innovative therapies to eradicate ALT cancers.
GPRC6A is a Potential Therapeutic Target for Metformin Regulation of Glucose Homeostasis in Mice
Authors: Pi Min , Agarwal Rupesh , Smith Micholas Dean , Smith Jeremy C. , Quarles L. Darryl 
Published: August 2024

AbstractUnderstanding the mechanism of metformin actions in treating type 2 diabetes is limited by an incomplete knowledge of the specific protein targets mediating its metabolic effects. Metformin has structural similarities to L-Arginine (2-amino-5-guanidinopentanoic acid), which is a ligand for GPRC6A, a Family C G-protein coupled receptor that regulates energy metabolism. Ligand activation of GPRC6A results in lowering of blood glucose and other metabolic changes resembling the therapeutic effect of metformin. In the current study, we tested if metformin activates GPRC6A. We used Alphafold2 to develop a structural model for L-Arginine (L-Arg) binding to the extracellu-lar bilobed venus flytrap domain (VFT) of GPRC6A. We found that metformin docked to the site in the VFT that overlaps the binding site for L-Arg. Metformin resulted in a dose-dependent stimulation of GPRC6A activity in HEK-293 cells transfected with full-length wild-type GPRC6A but not in untransfected control cells. In addition, metformin failed to activate an alternatively spliced GPRC6A isoform lacking the putative binding site in the VFT. More specifically, mutation of the predicted metformin key binding residues Glu170 and Asp303 in the GPRC6A VFT resulted in loss of metformin receptor activation in vitro. The in vivo role of GPRC6A in mediating the effects of metformin was tested in Gprc6a-/- mice. Administration of therapeutic doses of metformin lowered blood glucose levels following a glucose tolerance test in wild-type but not Gprc6a-/- mice. Finally, we EN300, created by adding a carboxymethyl group from L-Arg to the biguanide backbone of metformin. EN300 showed dose-dependent stimulation of GPRC6A activity in vitro with greater potency than L-Arginine, but less than met-formin. Thus, we suggest that GPRC6A is a potential molecular target for metformin which may be used to understand the therapeutic actions of metformin and develop novel small molecules to treat T2D.
Vaccines combining slow delivery and follicle targeting of antigens increase germinal center B cell clonal diversity and clonal expansion
Authors: Rodrigues Kristen A. , Zhang Yiming J. , Aung Aereas , Morgan Duncan M. , Maiorino Laura , Yousefpour Parisa , Gibson Grace , Ozorowski Gabriel , Gregory Justin R. , Amlashi Parastoo , Buckley Maureen , Ward Andrew B. , Schief William R. , Love J. Christopher , Irvine Darrell J. 
Published: August 2024

AbstractVaccines incorporating slow delivery, multivalent antigen display, or immunomodulation through adjuvants have an important role to play in shaping the humoral immune response. Here we analyzed mechanisms of action of a clinically relevant combination adjuvant strategy, where phosphoserine (pSer)-tagged immunogens bound to aluminum hydroxide (alum) adjuvant (promoting prolonged antigen delivery to draining lymph nodes) are combined with a potent saponin nanoparticle adjuvant termed SMNP (which alters lymph flow and antigen entry into lymph nodes). When employed with a stabilized HIV Env trimer antigen in mice, this combined adjuvant approach promoted substantial enhancements in germinal center (GC) and antibody responses relative to either adjuvant alone. Using scRNA-seq and scBCR-seq, we found that the alum-pSer/SMNP combination both increased the diversity of GC B cell clones and increased GC B cell clonal expansion, coincident with increases in the expression ofMycand the proportion of S-phase GC B cells. To gain insight into the source of these changes in the GC response, we analyzed antigen biodistribution and structural integrity in draining lymph nodes and found that the combination adjuvant approach, but not alum-pSer delivery or SMNP alone, promoted accumulation of highly intact antigen on follicular dendritic cells, reflecting an integration of the slow antigen delivery and altered lymph node uptake effects of these two adjuvants. These results demonstrate how adjuvants with complementary mechanisms of action impacting vaccine biodistribution and kinetics can synergize to enhance humoral immunity.
Nup107 is a crucial regulator of torso-mediated metamorphic transition inDrosophila melanogaster
Authors: Kawadkar Jyotsna , Joshi Pradyumna Ajit , Mishra Ram Kumar 
Published: August 2024

AbstractNuclear pore complexes (NPCs), composed of nucleoporins (Nups), affect nucleocytoplasmic transport, thus influencing cell division and gene regulation. Nup107 subcomplex members have been studied in housekeeping functions, diseases, and developmental disorders.We report a unique regulatory function for Nup107 in metamorphic transition duringDrosophiladevelopment. RNAi-mediatedNup107depleted larvae were arrested in the third-instar larval stage and completely ceased to pupariate. The pupariation defect is primarily due to inhibited nuclear translocation and transcriptional activation by EcR. We unequivocally demonstrate the involvement of Nup107 in the transcription of theHalloweengenes, modulating ecdysone biosynthesis and the EcR pathway activation. The regulation of EcR-mediated metamorphosis by the receptor tyrosine kinase,torso, is well documented. Accordingly, overexpression of thetorsoand MAP-kinase pathway activator,rasV12, in theNup107depletion background rescues the phenotypes, implying that Nup107 is an epistatic regulator of Torso-mediated activation of EcR signaling during metamorphosis.
Local nesting resources rather than floral food alter ground-nesting bee communities in grazed habitats
Authors: Collins Shannon M. , Taylor Laura A. , Wright Karen W. , Lichtenberg Elinor M. 
Published: August 2024

AbstractUnderstanding how the availability of both trophic and non-trophic resources impacts key ecosystem service providers is crucial for informing conservation efforts. Non-trophic resources such as shelter can play critical roles in ecosystem function and resilience by affecting predation and pathogen rates, reproductive success, and interspecific interactions. However, non-trophic resources are often overlooked. This holds true for insect pollinators; impacts of shelter on community dynamics and pollination remain poorly understood.Because most bee species spend most of their lives underground, we explored whether nesting habitat characteristics are key drivers of ground-nesting bee abundance, diversity, and community composition. We additionally compared impacts of aboveground versus belowground nesting habitat characteristics, as the latter have received significantly less attention. Nesting habitat characteristics we considered included bare ground cover; and soil texture, compaction, and depth. We also included floral abundance and richness. We focused on rangelands, natural or semi-natural grasslands that are managed for livestock grazing, where management can dramatically alter trophic and non-trophic resources. Thus, we also investigated impacts of grazing management on bee habitat.We found that belowground, but not aboveground, nesting habitat characteristics were important for ground-nesting bee assemblages. Ground-nesting bee abundance and richness were highest at sites with sandier soils. More compacted soils also supported higher bee abundance.Our results suggest that livestock grazing management may indirectly impact ground-nesting bee abundance through impacts on floral abundance. Sites with longer grazing rest periods had higher floral abundance, and sites with higher floral abundance supported more ground-nesting bees (but not more bee species).Policy implications:Our study highlights the importance of considering non-trophic resources in conservation and restoration management. Managers should be cautious in using an aboveground measure such as bare ground as an indicator of bee habitat quality. Rather, we recommend that belowground habitat characteristics such as soil texture and compaction be included in habitat quality assessments. Evidence-based rangeland conservation and restoration planning may need to manage for ground-nesting bees’ preferred levels of soil compaction. Additionally, management-insensitive habitat characteristics such as soil texture may be important considerations for site prioritization in pollinator habitat conservation and restoration efforts.
Pseudomonas aeruginosapopulation dynamics in a vancomycin-induced murine model of gastrointestinal carriage
Authors: Lebrun-Corbin Marine , Cheung Bettina H. , Hullahalli Karthik , Dailey Katherine , Bailey Keith , Waldor Matthew K. , Wunderink Richard G. , Bachta Kelly E. R. , Hauser Alan R. 
Published: August 2024

ABSTRACTPseudomonas aeruginosais a common nosocomial pathogen and a major cause of morbidity and mortality in hospitalized patients. Multiple reports highlight thatP. aeruginosagastrointestinal colonization may precede systemic infections by this pathogen. Gaining a deeper insight into the dynamics ofP. aeruginosagastrointestinal carriage is an essential step in managing gastrointestinal colonization and could contribute to preventing bacterial transmission and progression to systemic infection. Here, we present a clinically relevant mouse model relying on parenteral vancomycin pretreatment and a single orogastric gavage of a controlled dose ofP. aeruginosa.Robust carriage was observed with multiple clinical isolates, and carriage persisted for up to 60 days. Histological and microbiological examination of mice indicated that this model indeed represented carriage and not infection. We then used a barcodedP. aeruginosalibrary along with the sequence tag-based analysis of microbial populations (STAMPR) analytic pipeline to quantify bacterial population dynamics and bottlenecks during the establishment of the gastrointestinal carriage. Analysis indicated that most of theP. aeruginosapopulation was rapidly eliminated in the stomach, but the few bacteria that moved to the small intestine and the caecum expanded significantly. Hence, the stomach constitutes a significant barrier against gastrointestinal carriage ofP. aeruginosa,which may have clinical implications for hospitalized patients.IMPORTANCEWhileP. aeruginosais rarely part of the normal human microbiome, carriage of the bacterium is quite frequent in hospitalized patients and residents of long-term care facilities.P. aeruginosacarriage is a precursor to infection. Options for treating infections caused by difficult-to-treatP. aeruginosastrains are dwindling, underscoring the urgency to better understand and impede pre-infection stages, such as colonization. Here, we use vancomycin-treated mice to model antibiotic-treated patients who become colonized withP. aeruginosain their gastrointestinal tracts. We identify the stomach as a major barrier to the establishment of gastrointestinal carriage. These findings suggest that efforts to prevent gastrointestinal colonization should focus not only on judicious use of antibiotics but also on investigation into how the stomach eliminates orally ingestedP. aeruginosa.
Intermittent Theta Burst Stimulation Drives Bi-Directional Changes in Excitability in Prefrontal Cortex
Authors: Salimi Morteza , Nazari Milad , Mishler Jonathan , Mishra Jyoti , Ramanathan Dhakshin S 
Published: August 2024

AbstractTheta burst stimulation (TBS), an FDA-cleared treatment for depression, is hypothesized to modulate excitability in the prefrontal cortex, though this has not definitively been shown in vivo. We performed calcium imaging on glutamatergic neurons in awake rodents to understand the effects of theta burst stimulation at a cellular level. Our findings provide the first direct evidence that TBS bidirectionally modulates glutamatergic activity when delivered in vivo and directly links calcium activity changes during stimulation with post-stimulation plasticity.