bluuebunny/crossref_metadata_2025_split huggingface dataset:
Native ultrastructure of fresh human brain vitrified directly from autopsy revealed by cryo-electron tomography with cryo-plasma focused ion beam milling
Authors: Creekmore Benjamin C. , Kixmoeller Kathryn , Black Ben E. , Lee Edward B. , Chang Yi-Wei 
Published: September 2023

AbstractUltrastructure of human brain tissue has traditionally been examined using electron microscopy (EM) following chemical fixation, staining, and mechanical sectioning, which limit attainable resolution and introduce artifacts. Alternatively, cryo-electron tomography (cryo-ET) offers the potential to image unfixed cellular samples at higher resolution while preserving their native structures, but it requires samples to be frozen free from crystalline ice and thin enough to image via transmission EM. Due to these requirements, cryo-ET has yet to be employed to investigate the native ultrastructure of unfixed, never previously frozen human brain tissue. Here we present a method for generating lamellae in human brain tissue obtained at time of autopsy that can be imaged via cryo-ET. We vitrify the tissue directly on cryo-EM grids via plunge-freezing, as opposed to high pressure freezing which is generally used for thick samples. Following vitrification, we use xenon plasma focused ion beam (FIB) milling to generate lamellae directly on-grid. In comparison to gallium FIB, which is commonly used for biological samples, xenon plasma FIB is powerful enough to efficiently mill large volume samples, such as human brain tissue. Additionally, our approach allows for lamellae to be generated at variable depth inside the tissue as opposed to being limited to starting at the surface of the tissue. Lamellae generated in Alzheimer’s disease brain tissue and imaged by cryo-ET reveal intact subcellular structures including components of autophagy and potential tau fibrils. Furthermore, we visualize myelin revealing intact compact myelin and functional cytoplasmic expansions such as cytoplasmic channels and the inner tongue. From these images we also measure the dimensions of myelin membranes, providing insight into how myelin basic protein forces out oligodendrocyte cytoplasm to form compact myelin and tightly links intracellular polar head groups of the oligodendrocyte plasma membrane. This approach provides a first view of unfixed, never previously frozen human brain tissue prepared by cryo-plasma FIB milling and imaged at high resolution by cryo-ET.
Multi-omic characterization of antibody-producing CHO cell lines elucidates metabolic reprogramming and nutrient uptake bottlenecks
Authors: Gopalakrishnan Saratram , Johnson William , Valderrama-Gomez Miguel A. , Icten Elcin , Tat Jasmine , Lay Fides , Diep Jonathan , Gomez Natalia , Stevens Jennitte , Schlegel Fabrice , Rolandi Pablo , Kontoravdi Cleo , Lewis Nathan 
Published: September 2023

AbstractCharacterizing the phenotypic diversity and metabolic capabilities of industrially relevant manufacturing cell lines is critical to bioprocess optimization and cell line development. Metabolic capabilities of the production hosts limit nutrient and resource channeling into desired cellular processes and can have a profound impact on productivity but cannot be directly inferred from measured data such as spent media concentrations or transcriptomics. Here, we present an integrated multi-omic characterization approach combining exo-metabolomics, transcriptomics, and genome-scale metabolic network analysis and apply it to three antibody-producing Chinese Hamster Ovary cell lines to reprogramming features associated with high-producer clones and metabolic bottlenecks limiting product production in an industrial bioprocess. Analysis of individual datatypes revealed a decreased nitrogenous byproduct secretion in high-producing clones and the topological changes in peripheral metabolic pathway expression associated with phase shifts. An integrated omics analysis in the context of the genome-scale metabolic model elucidated the differences in central metabolism and identified amino acid utilization bottlenecks limiting cell growth and antibody production that were not evident from exo-metabolomics or transcriptomics alone. Thus, we demonstrate the utility of a multi-omics characterization in providing an in-depth understanding of cellular metabolism, which is critical to efforts in cell engineering and bioprocess optimization.
Auranofin induces lethality driven by reactive oxygen species in high-grade serous ovarian cancer cells
Authors: Abdalbari Farah H. , Martinez-Jaramillo Elvis , Forgie Benjamin N. , Tran Estelle , Zorytcha Edith , Goyeneche Alicia A. , Telleria Carlos M. 
Published: September 2023

AbstractHigh-grade serous ovarian cancer (HGSOC) accounts for 70% of ovarian cancer cases in the clinical setting; the survival rate for this disease remains remarkably low due to the lack of long-term consolidation therapies following the standard platinum-based chemotherapy, which is not long lasting as the disease recurs as platinum resistant. The purpose of this study was to explore a novel treatment against HGSOC using the gold complex auranofin (AF). AF primarily functions as a pro-oxidant agent through the inhibition of thioredoxin reductase (TrxR), an antioxidant enzyme that is overexpressed in ovarian cancer. We investigated the effect of AF on TrxR activity and various mechanisms of cytotoxicity using HGSOC cells that are clinically sensitive or resistant to platinum. In addition, we studied the interaction between AF and another pro-oxidant agent, L-buthionine sulfoximine (L-BSO), an anti-glutathione (GSH) compound. We demonstrate that AF potently inhibits TrxR activity and reduces the vitality and viability of HGSOC cells regardless of their sensitivities to platinum. We show that AF induces accumulation of reactive oxygen species (ROS), triggers the depolarization of the mitochondrial membrane, and kills HGSOC cells by inducing apoptosis. Yet, AF-induced cell death is abrogated by the ROS-scavenger N-acetyl cysteine (NAC). In addition, the lethality of AF is associated with the activation of caspases-3/7 and the generation of DNA damage, effects that are also prevented by the presence of NAC. Finally, when AF and L-BSO are combined, we observed a synergistic lethality against HGSOC cells, which is mediated by a further increase in ROS together with a decrease in the levels of the antioxidant GSH. In summary, our results support the concept that AF can be used alone or in combination with L-BSO to kill HGSOC cells regardless of their platinum sensitivities suggesting that depletion of antioxidants is an efficient route for treating this disease.
Circadian regulation ofMGMTexpression and promoter methylation underlies daily rhythms in TMZ sensitivity in glioblastoma
Authors: Gonzalez-Aponte Maria F. , Damato Anna R. , Trebucq Laura Lucía , Simon Tatiana , Cárdenas-García Sandra P. , Cho Kevin , Patti Gary J. , Golombek Diego A. , Chiesa Juan José , Herzog Erik D. 
Published: September 2023

AbstractBackgroundGlioblastoma (GBM) is the most common primary brain tumor in adults. Despite extensive research and clinical trials, median survival post-treatment remains at 15 months. Thus, all opportunities to optimize current treatments and improve patient outcomes should be considered. A recent retrospective clinical study found that taking TMZ in the morning compared to the evening was associated with a 6-month increase in median survival in patients withMGMT-methylated GBM. Here, we hypothesized that TMZ efficacy depends on time-of-day and O6-Methylguanine-DNA Methyltransferase (MGMT) activity in murine and human models of GBM.Methods and ResultsIn vitrorecordings using real-time bioluminescence reporters revealed that GBM cells have intrinsic circadian rhythms in the expression of the core circadian clock genesBmal1andPer2, as well as in the DNA repair enzyme,MGMT. Independent measures ofMGMTtranscript levels and promoter methylation also showed daily rhythms intrinsic to GBM cells. These cells were more susceptible to TMZ when delivered at the daily peak ofBmal1transcription. We found thatin vivomorning administration of TMZ also decreased tumor size and increased body weight compared to evening drug delivery in mice bearing GBM xenografts. Finally, inhibition of MGMT activity with O6-Benzylguanine abrogated the daily rhythm in sensitivity to TMZin vitroby increasing sensitivity at both the peak and trough ofBmal1expression.ConclusionWe conclude that chemotherapy with TMZ can be dramatically enhanced by delivering at the daily maximum of tumorBmal1expression and minimum ofMGMTactivity.Graphical Abstract
COSMIC-dFBA: A novel multi-scale hybrid framework for bioprocess modeling
Authors: Gopalakrishnan Saratram , Johnson William , Valderrama-Gomez Miguel A. , Icten Elcin , Tat Jasmine , Ingram Michael , Shek Coral Fung , Chan Pik K. , Schlegel Fabrice , Rolandi Pablo , Kontoravdi Cleo , Lewis Nathan 
Published: September 2023

AbstractMetabolism governs cell performance in biomanufacturing, as it fuels growth and productivity. However, even in well-controlled culture systems, metabolism is dynamic, with shifting objectives and resources, thus limiting the predictive capability of mechanistic models for process design and optimization. Here, we present Cellular Objectives and State Modulation In bioreaCtors (COSMIC)-dFBA, a hybrid multi-scale modeling paradigm that accurately predicts cell density, antibody titer, and bioreactor metabolite concentration profiles. Using machine-learning, COSMIC-dFBA decomposes the instantaneous metabolite uptake and secretion rates in a bioreactor into weighted contributions from each cell state (growth or antibody-producing state) and integrates these with a genome-scale metabolic model. A major strength of COSMIC-dFBA is that it can be parameterized with only metabolite concentrations from spent media, although constraining the metabolic model with other omics data can further improve its capabilities. Using COSMIC-dFBA, we can predict the final cell density and antibody titer to within 10% of the measured data, and compared to a standard dFBA model, we found the framework showed a 90% and 72% improvement in cell density and antibody titer prediction, respectively. Thus, we demonstrate our hybrid modeling framework effectively captures cellular metabolism and expands the applicability of dFBA to model the dynamic conditions in a bioreactor.
Boosting biodiversity monitoring using smartphone-driven, rapidly accumulating community-sourced data
Authors: Atsumi Keisuke , Nishida Yuusuke , Ushio Masayuki , Nishi Hirotaka , Genroku Takanori , Fujiki Shogoro 
Published: September 2023

AbstractComprehensive biodiversity data is crucial for ecosystem protection. The ‘Biome’ mobile app, launched in Japan, efficiently gathers species observations from the public using species identification algorithms and gamification elements. The app has amassed >6M observations since 2019. Nonetheless, community-sourced data may exhibit spatial and taxonomic biases. Species distribution models (SDMs) estimate species distribution while accommodating such bias. Here, we investigated the quality ofBiomedata and its impact on SDM performance. Species identification accuracy exceeds 95% for birds, reptiles, mammals, and amphibians, but seed plants, mollusks, and fishes scored below 90%. Our SDMs for 132 terrestrial plants and animals across Japan revealed that incorporatingBiomedata into traditional survey data improved accuracy. For endangered species, traditional survey data required >2,000 records for accurate models (Boyce index ≥ 0.9), while blending the two data sources reduced this to around 300. The uniform coverage of urban-natural gradients byBiomedata, compared to traditional data biased towards natural areas, may explain this improvement. Combining multiple data sources better estimates species distributions, aiding in protected area designation and ecosystem service assessment. Establishing a platform for accumulating community-sourced distribution data will contribute to conserving and monitoring natural ecosystems.
Direct and indirect effects of the increase in atmospheric CO2and temperature on groundwater organisms
Authors: Schmidt Susanne I. , Svátková Miroslava , Kodeš Vít , Shabarova Tanja 
Published: September 2023

AbstractAtmospherically rising temperature and CO2impact all freshwater systems, including groundwater. Increasing CO2leads to more intense weathering of silicate rocks. Here, we tested whether the increased levels, the weathering, or rather the increasing temperature, impacted on fauna and prokaryotes in the groundwater ecosystem. We conducted the analyses separately for deep, i.e. secluded, and shallow, quaternary aquifers which exchange with the surface more intensely. Organism abundances and relative composition did not correlate with temperature or CO2levels. While many organisms rely on silica, in contrast, we found negative correlations between silica and fauna. The increases in silica over time, i.e. temporal trends, also partly correlated negatively with organisms. We hypothesize that the unexpected negative correlations are not direct effects, but indirectly indicate that groundwater communities do not adapt rapidly enough to changes. This jeopardizes future drinking water production which relies on the self-cleaning ecosystem services in groundwater.
Description ofPhylloneura rupestrissp. nov. (Odonata, Platycnemididae) from the Western Ghats, India with notes on its reproductive behavior
Authors: Chandran Ayikkara Vivek , Chandran Reji , Suraj S R , Jose Subin K. , Koparde Pankaj 
Published: September 2023

ABSTRACTPhylloneuraFraser, 1922 is a genus of damselflies which was till date regarded monotypic. It is represented by the nominate species,Phylloneura westermanni(Hagen in Selys, 1860) which is endemic to the Western Ghats in India. In our study, we came across a population ofPhylloneuranear Ponmudi hills, Thiruvananthapuram, which displayed morphological and behavioral differences fromP. westermanni. We describe it as a species new to science with detailed photographs and illustrations. We also provide notes on its reproductive behavior.
DEVIL peptides control cell growth and differentiation in different developmental processes
Authors: Alarcia Ana , Primo-Capella Amparo , Perpiñán Elena , Rossetto Priscilla , Ferrándiz Cristina 
Published: September 2023

AbstractThe DEVIL/ROTUNDIFOLIA-LIKE (DVL/RTFL) family of plant peptides is present in all land plants, but their biological role and mode of action remains largely unknown, in part due to the lack of reported phenotypes associated to DVL/RTFL loss of function. In this work we have generated high order mutants and characterized their phenotypes in reproductive development. Our results indicate thatdvlmutants are affected in cell elongation processes, mainly related to pollen tube growth, and they appear to provide robustness to these processes. We also show that DVL peptides may act in different domains to those where the corresponding genes are transcribed, suggesting a putative role in the coordination of organ growth by participating in cell-to-cell communication.
Nuclear speckles regulate HIF-2α programs and correlate with patient survival in kidney cancer
Authors: Alexander Katherine A. , Yu Ruofan , Skuli Nicolas , Coffey Nathan J. , Nguyen Son , Faunce Christine , Huang Hua , Dardani Ian P. , Good Austin L. , Lim Joan , Li Catherine , Biddle Nicholas , Joyce Eric F. , Raj Arjun , Lee Daniel , Keith Brian , Simon M. Celeste , Berger Shelley L. 
Published: September 2023

SUMMARYNuclear speckles are membrane-less bodies within the cell nucleus enriched in RNA biogenesis, processing, and export factors. In this study we investigated speckle phenotype variation in human cancer, finding a reproducible speckle signature, based on RNA expression of speckle-resident proteins, across >20 cancer types. Of these, clear cell renal cell carcinoma (ccRCC) exhibited a clear correlation between the presence of this speckle expression signature, imaging-based speckle phenotype, and clinical outcomes. ccRCC is typified by hyperactivation of the HIF-2α transcription factor, and we demonstrate here that HIF-2α drives physical association of a select subset of its target genes with nuclear speckles. Disruption of HIF-2α-driven speckle association via deletion of itsspeckle targetingmotifs (STMs)—defined in this study—led to defective induction of speckle-associating HIF-2α target genes without impacting non-speckle-associating HIF-2α target genes. We further identify the RNA export complex, TREX, as being specifically altered in speckle signature, and knockdown of key TREX component, ALYREF, also compromises speckle-associated gene expression. By integrating tissue culture functional studies with tumor genomic and imaging analysis, we show that HIF-2α gene regulatory programs are impacted by specific manipulation of speckle phenotype and by abrogation of speckle targeting abilities of HIF-2α. These findings suggest that, in ccRCC, a key biological function of nuclear speckles is to modulate expression of a specific subset of HIF-2α-regulated target genes that, in turn, influence patient outcomes. We also identify STMs in other transcription factors, suggesting that DNA-speckle targeting may be a general mechanism of gene regulation.HIGHLIGHTS– Nuclear speckles shown to reproducibly vary in cancer, predicting patient survival in ccRCC– HIF-2α drives DNA/gene-speckle contacts dependent on identified speckle targeting motifs within HIF-2α– Putative speckle targeting motifs are highly enriched among regulators of gene expression– Partitioning of transcription factor functional programs may be a major biological function of nuclear speckles
γδ T cells impair airway macrophage differentiation in lung adenocarcinoma
Authors: Raffo-Iraolagoitia Ximena L. , McFarlane Amanda J. , Kruspig Bjorn , Fercoq Frédéric , Secklehner Judith , De Donatis Marco , Mackey John B. G. , Wiesheu Robert , Laing Sarah , Hsieh Ya-Ching , Shaw Robin , Corbyn Ryan , Nixon Colin , Miller Crispin , Kirschner Kristina , Bain Calum C. , Murphy Daniel J. , Coffelt Seth B. , Carlin Leo M. 
Published: September 2023

AbstractProtecting mucosal barriers, γδ T cells hold promise for the development of new cancer immunotherapies. In mice, γδ T cells can largely be segregated into CD27+and CD27−cells, and their functions are modulated by interactions with surrounding cells. However, which cells communicate directly with γδ T cells in lung adenocarcinoma remains unknown. To address this, we combined flow cytometry, confocal microscopy, and scRNA-seq, using an autochthonous genetically engineered mouse model and different γδ T cell-deficient settings. We found that γδ T cells were increased in tumour-bearing lungs, with an altered phenotype. CD27−and CD27+γδ T cells differed in their localisation and interactions including their tropism for macrophages. Overall, we propose a model where CD27+γδ T cells undermine the differentiation of tumour-associated macrophages into airway macrophages, fostering a negative outcome in lung adenocarcinoma. Determining its translatability to human health may offer new avenues for immunotherapeutic strategies.SummaryGuardians of pulmonary homeostasis, γδ T cells remain enigmatic regarding their role in lung adenocarcinoma. Raffo-Iraolagoitia et al. report that a subset of γδ T cells impairs the differentiation of tumour-associated macrophages into airway macrophages, relevant for the outcome of lung adenocarcinoma.Graphical Abstract
Cell competition promotes metastatic intestinal cancer through a multistage process
Authors: García Ana Krotenberg , Ledesma-Terrón Mario , Vriend Joyce , van Luyk Merel E , Suijkerbuijk Saskia JE 
Published: September 2023

SummaryCell competition plays an instrumental role in quality control during tissue development and homeostasis. Nevertheless, cancer cells can exploit this process for their own proliferative advantage. In our study, we generated mixed murine organoids and microtissues to explore the impact of cell competition on liver metastasis. Unlike competition at the primary site, the initial effect on liver progenitor cells does not involve the induction of apoptosis. Instead, metastatic competition manifests as a multistage process. Initially, liver progenitors undergo compaction, which is followed by cell cycle arrest, ultimately forcing differentiation. Subsequently, the newly differentiated liver cells exhibit reduced cellular fitness, rendering them more susceptible to outcompetion by intestinal cancer cells. Notably, cancer cells leverage different interactions with different epithelial populations in the liver, using them as scaffolds to facilitate their growth. Consequently, tissue-specific mechanisms of cell competition are fundamental in driving metastatic intestinal cancer.
An Alternatively Spliced Gain-of-Function NT5C2 Isoform Contributes to Chemoresistance in Acute Lymphoblastic Leukemia
Authors: Torres-Diz Manuel , Reglero Clara , Falkenstein Catherine D , Castro Annette , Hayer Katharina E. , Radens Caleb M. , Quesnel-Vallières Mathieu , Ang Zhiwei , Sehgal Priyanka , Li Marilyn M. , Barash Yoseph , Tasian Sarah K. , Ferrando Adolfo , Thomas-Tikhonenko Andrei 
Published: September 2023

AbstractRelapsed or refractory B-cell acute lymphoblastic leukemia (B-ALL) is a major cause of pediatric cancer-related deaths. Relapse-specific mutations do not account for all chemotherapy failures in B- ALL patients, suggesting additional mechanisms of resistance. By mining RNA-seq datasets of paired diagnostic/relapse pediatric B-ALL samples, we discovered pervasive alternative splicing (AS) patterns linked to relapse and affecting drivers of resistance to glucocorticoids, anti-folates, and thiopurines. Most splicing variations represented cassette exon skipping, “poison” exon inclusion, and intron retention, phenocopying well-documented loss-of-function mutations. In contrast, relapse-associated AS of NT5C2 mRNA yielded an isoform with the functionally uncharacterized in-frame exon 6a. Incorporation of the 8-amino acid sequence SQVAVQKR into this enzyme created a putative phosphorylation site and resulted in elevated nucleosidase activity, which is a known consequence of gain-of-function mutations in NT5C2 and a common determinant of 6-mercaptopurine (6-MP) resistance. Consistent with this finding, NT5C2ex6a and the R238W hotspot variant conferred comparable levels of resistance to 6-MP in B-ALL cells both in vitro and in vivo. Furthermore, both the NT5C2ex6a and R238W variants induced collateral sensitivity to the inosine monophosphate dehydrogenase (IMPDH) inhibitor mizoribine. These results ascribe an important role for splicing perturbations in chemotherapy resistance in relapsed B-ALL and suggest that IMPDH inhibitors, including the commonly used immunosuppressive agent mycophenolate mofetil, could be a valuable therapeutic option for treating thiopurine-resistant leukemias.