bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene regulatory dynamics during the development of a paleopteran insect, the mayflyCloeon dipterum
Authors: Pallarès-Albanell Joan , Ortega-Flores Laia , Senar-Serra Tòt , Ruiz Antoni , Abril Josep F. , Rossello Maria , Almudi Isabel 
Published: May 2024

AbstractThe evolution of insects has been marked by the appearance of key body plan innovations and novel organs that promoted the outstanding ability of this lineage to adapt to new habitats, boosting the most successful radiation in animals. To understand the origin and evolution of these new structures, it is essential to investigate which are the genes and gene regulatory networks participating during the embryonic development of insects. Great efforts have been made to fully understand, from a gene expression and gene regulation point of view, the development of holometabolous insects, in particularDrosophila melanogaster, with the generation of numerous functional genomics resources and databases. Conversely, how hemimetabolous insects develop, and which are the dynamics of gene expression and gene regulation that control their embryogenesis, are still poorly characterized. Therefore, to provide a new platform to study gene regulation in insects, we generated ATAC-seq (Assay for transposase-Accessible Chromatin using sequencing) for the first time during the development of the mayflyCloeon dipterum.This new available resource will allow to better understand the dynamics of gene regulation during hemimetabolan embryogenesis, sinceC. dipterumbelongs to the paleopteran order of Ephemeroptera, the sister group to all other winged insects. These new datasets include six different time points of its embryonic development and identify accessible chromatin regions corresponding to both general and stage-specific promoters and enhancers. With these comprehensive datasets, we characterised pronounced changes in accessible chromatin between stages 8 and 10 of embryonic development, which correspond to the transition from the last stages of segmentation to organogenesis and appendage differentiation. The application of ATAC-seq in mayflies has contributed to identify the epigenetic mechanisms responsible for embryonic development in hemimetabolous insects and it will provide a fundamental resource to understand the evolution of gene regulation in winged insects.
Glycolytic metabolism modulation on spinal neuroinflammation and vital functions following cervical spinal cord injury
Authors: Michel-Flutot Pauline , Mansart Arnaud , Vinit Stéphane 
Published: May 2024

AbstractHigh spinal cord injuries (SCIs) often result in persistent diaphragm paralysis and respiratory dysfunction. Chronic neuroinflammation within the damaged spinal cord after injury plays a prominent role in limiting functional recovery by impeding neuroplasticity. In this study, we aimed to reduce glucose metabolism that supports neuroinflammatory processes in an acute preclinical model of C2 spinal cord lateral hemisection in rats. We administered 2-deoxy-D-glucose (2-DG; 200 mg/kg/day s.c., for 7 days) and evaluated the effect on respiratory function and chondroitin sulfate proteoglycans (CSPGs) production around spinal phrenic motoneurons. Contrary to our initial hypothesis, our 2-DG treatment did not have any effect on diaphragm activity and CSPGs production in injured rats, although slight increases in tidal volume were observed. Unexpectedly, it led to deleterious effects in uninjured (sham) animals, characterized by increased ventilation and CSPGs production. Ultimately, our results seem to indicate that this 2-DG treatment paradigm may create a neuroinflammatory state in healthy animals, without affecting the already established spinal inflammation in injured rats. Given the beneficial effects of 2-DG observed in other studies on neuronal activity and inflammation, adjusting 2-DG doses and/or increasing treatment duration should be explored to reduce deleterious inflammatory processes occurring after SCI.
Ebola virus infection of Flt3-dependent, conventional dendritic cells and antigen cross-presentation leads to high levels of T-cell activation
Authors: Niemetz Linda , Bodmer Bianca S. , Olal Catherine , Escudero-Pérez Beatriz , Hoehn Katharina , Bencsik András , Vickers Molly A. , Rodríguez Estefanía , Oestereich Lisa , Hoenen Thomas , Muñoz-Fontela César 
Published: May 2024

ABSTRACTSevere Ebola virus disease (EVD) is characterized by excess, dysregulated T-cell activation and high levels of inflammation. Previous studies have described that in vitro EBOV infection of monocyte-derived DCs (moDCs) inhibits DC maturation resulting in suppression of T-cell activation. However, it is unknown how other DC subsets distinct from moDCs respond to EBOV infection.To better understand how DCs initiate T cell activation during EBOV infection, we assessed the response of FMS-like tyrosine kinase 3 (Flt3)-dependent, conventional mouse DCs (cDCs) to EBOV infection, and developed a DC-T-cell co-culture system utilizing a recombinant EBOV expressing the model antigen ovalbumin.Our findings suggested that, in contrast to moDCs, cDC2 and cDC1 were poorly infected with EBOV, although both infected and bystander cDCs displayed high levels of activation. DCs were able to activate CD8 T cells via cross-presentation of EBOV antigens obtained from cell debris of EBOV-infected cells. Of note, rather than interfering with cross-presentation, EBOV infection enhanced the cross-presentation capacity of DCs.Our findings indicate that EBOV infection of Flt3-dependent cDCs, results in activation rather than inhibition leading to high levels of CD8 T-cell activation. With that we propose a mechanistic explanation for the excess T-cell activation observed in severe human EVD.
Design and development of a field-deployable water bath for loop-mediated isothermal amplification assay
Authors: Rafiq Nafisa , Verma Mohit S. 
Published: May 2024

AbstractNucleic acid testing has become a prominent method for rapid microbial detection. Unlike polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP) is a simple method of nucleic acid amplification where the reaction can be performed at a constant temperature and the output provided in a colorimetric format. A transparent water bath is a desirable instrument to perform the heating and observe the visual results. However, existing methods of heating water are not convenient for loading and unloading the test samples. Here, we developed a field-deployable water bath—an isothermal heater called IsoHeat for short–which is solely dedicated to performing LAMP reactions and can heat the water up to 85°C. Using 3D-printing and laser-cutting technology, we fabricated different parts and mechanically assembled the parts to develop the entire device. Users can commence the heating by pressing the start button on the screen after entering the target temperature. Subsequently, the device heats up the water bath and maintains the target temperature through a PID algorithm-based control system. We demonstrate that IsoHeat can operate in environmental temperatures ranging from 5-33 °C and it can conduct LAMP reactions in liquid format as well as in paper-based devices. IsoHeat is more efficient and user-friendly compared to a commercially available immersion-heating device, which is often used to perform LAMP reactions. This newly developed device would be helpful to detect pathogens conveniently in the field (e.g., at point-of-care for human applications, on farms for plant and animal applications, and in production facilities for food safety applications).
The Precision and Power of Population Branch Statistics in Identifying the Genomic Signatures of Local Adaptation
Authors: Shpak Max , Lawrence Kadee N. , Pool John E. 
Published: May 2024

AbstractPopulation branch statistics, which estimate the branch lengths of focal populations with respect to two outgroups, have been used as an alternative to FST-based genome-wide scans for identifying loci associated with local selective sweeps. In addition to the original population branch statistic (PBS), there are subsequently proposed branch rescalings: normalized population branch statistic (PBSn1), which adjusts focal branch length with respect to outgroup branch lengths at the same locus, and population branch excess (PBE), which also incorporates median branch lengths at other loci. PBSn1 and PBE have been proposed to be less sensitive to allele frequency divergence generated by background selection or geographically ubiquitous positive selection rather than local selective sweeps. However, the accuracy and statistical power of branch statistics have not been systematically assessed. To do so, we simulate genomes in representative large and small populations with varying proportions of sites evolving under genetic drift or background selection (approximated using variableNe), local selective sweeps, and geographically parallel selective sweeps. We then assess the probability that local selective sweep loci are correctly identified as outliers by FSTand by each of the branch statistics. We find that branch statistics consistently outperform FSTat identifying local sweeps. When background selection and/or parallel sweeps are introduced, PBSn1 and especially PBE correctly identify local sweeps among their top outliers at a higher frequency than PBS. These results validate the greater specificity of rescaled branch statistics such as PBE to detect population-specific positive selection, supporting their use in genomic studies focused on local adaptation.Significance StatementPopulation branch statistics are widely used in genome-wide scans to identify loci associated with local adaptation. This study finds that branch statistics are more accurate thanFSTat identifying local selective sweeps under a wide range of demographic parameters and models of evolution. It also demonstrates that certain branch statistics have improved ability to distinguish local adaptation from other models of natural selection.
Single-cell RNA-Sequencing Co-Expression Analysis with CFTR in Lung Tissue
Authors: Wang Cheng , Kanagarajah Kayshani , Wong Amy , Ratjen Felix , Strug Lisa J 
Published: May 2024

1AbstractBackgroundWhile cystic fibrosis is caused by loss-of-function variants in theCystic Fibrosis Transmembrane Conductance Regulator (CFTR), other modifier genes have been shown to associate with disease severity. Co-expression of modifiers with CFTR in normal tissue indicates a cooperative relationship and suggests the potential for compensation in the presence of CFTR dysfunction. We examined the co-expression relationships with CFTR in the lung using single cell RNA sequencing to pinpoint cell types and their modifiers involved in the forced expiratory volume in 1 second (FEV1)-based cystic fibrosis lung phenotype and support target cell-type prioritization for therapy1.MethodsSmartSeq2 single cell RNA sequencing data from non-cystic fibrosis lung tissue was used for evaluation of co-expression with CFTR and modifier genes. Zero-inflated negative binomial model was used to formally test the co-expression association. 10X Chromium based single cell RNA sequencing data from both cystic fibrosis and non-cystic fibrosis studies were assessed graphically to confirm conclusions from the SmartSeq2 primary analysis.ResultsDifferentiating basal, club and alveolar epithelial type 2 cells were found to have high proportions of cells expressing CFTR as well as the greatest number of significant co-expression relationships with the modifiers. In particular, among alveolar epithelial type 2 cells, we observed a strong co-expression trio relationship between CFTR, SLC6A14 and SLC26A9 (p < 0.05).ConclusionsCFTR-modifier gene co-expression suggests basal, club and alveolar epithelial type 2 cells show coordinated expression. Alveolar epithelial type 2 cells showed strong co-expression evidence with two of the most established cystic fibrosis modifier genes.
CRISPR Double Knockout Library Reveals Synthetic Lethal Gene Pairs in Triple-Negative Breast Cancer
Authors: Shao Shuai , Li Shangjia , Tang Shan , Fan Kunjie , Li Lang 
Published: May 2024

AbstractSynthetic lethality, a genetic interaction involving two or more genes whose combined loss results in cell death, has emerged as a promising strategy for targeted cancer therapy. By exploiting synthetic lethal interactions, cancer cells can be selectively targeted and eradicated while preserving healthy cells, minimizing off-target effects, and reducing toxicity. The development of PARP inhibitors for ovarian and breast cancer patients with BRCA mutations exemplifies the potential of synthetic lethality-based therapy. Various experimental approaches, including CRISPR/Cas9 screens, have been employed to identify synthetic lethal gene pairs. Our lab has developed a CRISPR double knockout library, leveraging the XDeathDB database for candidate gene selection. This comprehensive platform offers insights into 12 cell death modes and 149 cell death hallmark genes. We aim to construct a cell-death double knock-out library using these genes and perform double knock-out screening on MDA-MB-231, a representative cell line for TNBC chemo poor responders. The identified synergistic lethal gene pairs may serve as potential drug targets for treating TNBC.
Correlative multiscale 3D imaging of mouse primary and metastatic tumors by sequential light sheet and confocal fluorescence microscopy
Authors: Zheng Jingtian , Wu Yi-Chien , Cai Xiaoying , Phan Philana , Er Ekrem Emrah , Zhao Zongmin , Lee Steve Seung-Young 
Published: May 2024

AbstractThree-dimensional (3D) optical microscopy, combined with advanced tissue clearing, permitsin situinterrogation of the tumor microenvironment (TME) in large volumetric tumors for preclinical cancer research. Light sheet (also known as ultramicroscopy) and confocal fluorescence microscopy are often used to achieve macroscopic and microscopic 3D images of optically cleared tumor tissues, respectively. Although each technique offers distinct fields of view (FOVs) and spatial resolution, the combination of these two optical microscopy techniques to obtain correlative multiscale 3D images from the same tumor tissues has not yet been explored. To establish correlative multiscale 3D optical microscopy, we developed a method for optically marking defined regions of interest (ROIs) within a cleared mouse tumor by employing a UV light-activated visible dye and Z-axis position-selective UV irradiation in a light sheet microscope system. By integrating this method with subsequent tissue processing, including physical ROI marking, reversal of tissue clearing, tissue macrosectioning, and multiplex immunofluorescence, we established a workflow that enables the tracking and 3D imaging of ROIs within tumor tissues through sequential light sheet and confocal fluorescence microscopy. This approach allowed for quantitative 3D spatial analysis of the immune response in the TME of a mouse mammary tumor following cancer immunotherapy at multiple spatial scales. The workflow also facilitated the direct localization of a metastatic lesion within a whole mouse brain. These results demonstrate that our ROI tracking method and its associated workflow offer a novel approach for correlative multiscale 3D optical microscopy, with the potential to provide new insights into tumor heterogeneity, metastasis, and response to therapy at various spatial levels.
Determination of permissive and restraining cancer-associated fibroblast (DeCAF) subtypes
Authors: Peng Xianlu Laura , Kharitonova Elena V. , Xu Yi , Kearney Joseph F. , Luan Changfei , Chan Priscilla S. , Hariharan Arthi , McCabe Ian C. , Leary John R. , Morrison Ashley B. , Trembath Hannah E. , LaBella Michelle E. , Herera Loeza Silvia G. , Cliff Ashley , Kim Hong Jin , Belt Brian A. , Panni Roheena Z. , Linehan David C. , Damrauer Jeffrey S , Iuga Alina C. , Kim William Y. , Rashid Naim U. , Yeh Jen Jen 
Published: May 2024

AbstractCancer-associated fibroblast (CAF) subpopulations in pancreatic ductal adenocarcinoma (PDAC) have been identified using single-cell RNA sequencing (scRNAseq) with divergent characteristics, but their clinical relevance remains unclear. We translate scRNAseq-derived CAF cell-subpopulation-specific marker genes to bulk RNAseq data, and develop a single- sample classifier, DeCAF, for the classification of clinicallyrestraining andpermissive CAF subtypes. We validate DeCAF in 19 independent bulk transcriptomic datasets across four tumor types (PDAC, mesothelioma, bladder and renal cell carcinoma). DeCAF subtypes have distinct histology features, immune landscapes, and are prognostic and predict response to therapy across cancer types. We demonstrate that DeCAF is clinically replicable and robust for the classification of CAF subtypes in patients for multiple tumor types, providing a better framework for the future development and translation of therapies against permissive CAF subtypes and preservation of restraining CAF subtypes.SignificanceWe introduce a replicable and robust classifier, DeCAF, that delineates the significance of the role of permissive and restraining CAF subtypes in cancer patients. DeCAF is clinically tractable, prognostic and predictive of treatment response in multiple cancer types and lays the translational groundwork for the preclinical and clinical development of CAF subtype specific therapies.
In defense of the original Type I functional response: The frequency and population-dynamic effects of feeding on multiple prey at a time
Authors: Novak Mark , Coblentz Kyle E. , DeLong John P. 
Published: May 2024

AbstractEcologists differ in the degree to which they consider the linear Type I functional response to be an unrealistic versus sufficient representation of predator feeding rates. Empiricists tend to consider it unsuitably non-mechanistic and theoreticians tend to consider it necessarily simple. Holling’s original rectilinear Type I response is dismissed by satisfying neither desire, with most compromising on the smoothly saturating Type II response for which searching and handling are assumed to be mutually exclusive activities. We derive a “multiple-prey-at-a-time” response and a generalization that includes the Type III to reflect predators that can continue to search when handling an arbitrary number of already-captured prey. The multi-prey model clarifies the empirical relevance of the linear and rectilinear models and the conditions under which linearity can be a mechanistically-reasoned description of predator feeding rates, even when handling times are long. We find support for linearity in 35% of 2,591 compiled empirical datasets and support for the hypothesis that larger predator-prey body-mass ratios permit predators to search while handling greater numbers of prey. Incorporating the multi-prey response into the Rosenzweig-MacArthur population-dynamics model reveals that a non-exclusivity of searching and handling can lead to coexistence states and dynamics that are not anticipated by theory built on the Type I, II, or III response models. In particular, it can lead to bistable fixed-point and limit-cycle dynamics with long-term crawl-by transients between them under conditions where abundance ratios reflect top-heavy food webs and the functional response is linear. We conclude that functional response linearity should not be considered empirically unrealistic but also that more cautious inferences should be drawn in theory presuming the linear Type I to be appropriate.
XRCC1 mediates PARP1- and PAR-dependent recruitment of PARP2 to DNA damage sites
Authors: Lin Xiaohui , Leung Kay Sze Karina , Wolfe Kaitlynn F. , Lee Brian J. , Zha Shan 
Published: May 2024

ABSTRACTPoly-ADP-ribose polymerases 1 and 2 (PARP1 and PARP2) are crucial sensors of DNA-strand breaks and emerging cancer therapy targets. Once activated by DNA breaks, PARP1 and PARP2 generate poly-ADP-ribose (PAR) chains on themselves and other substrates to promote DNA single-strand break repair (SSBR). PARP1 can be activated by diverse DNA lesions, whereas PARP2 specifically recognizes 5’ phosphorylated nicks. They can be activated independently and provide mutual backup in the absence of the other. However, whether PARP1 and PARP2 have synergistic functions in DNA damage response remains elusive. Here, we show that PARP1 and the PAR chains generated by PARP1 recruit PARP2 to the vicinity of DNA damage sites through the scaffold protein XRCC1. Using quantitative live-cell imaging, we found that loss of XRCC1 markedly reduces irradiation-induced PARP2 foci in PARP1-proficient cells. The central BRCT domain (BRCT1) of XRCC1 binds to the PAR chain, while the C-terminal BRCT domain (BRCT2) of XRCC1 interacts with the catalytic domain of PARP2, facilitating its localization near the breaks. Together, these findings unveil a new function of XRCC1 in augmenting PARP2 recruitment in response to PARP1 activation and explain why PARP1, but not PARP2, is aggregated and hyperactivated in XRCC1-deficient cells.
N-Terminal proteomics reveals distinct protein degradation patterns in different types of human atherosclerotic plaques
Authors: Lorentzen Lasse G. , Yeung Karin , Eldrup Nikolaj , Eiberg Jonas P. , Davies Michael J. 
Published: May 2024

AbstractBACKGROUNDDestabilization and rupture of atherosclerotic plaques is a major cause of acute atherosclerotic cardiovascular events, including heart attack, ischemic stroke and peripheral arterial disease. Plaque destabilization is associated with extracellular matrix (ECM) modification and remodelling involving protease activity. Enzymatic cleavage generates protein fragments with new ‘ends’ (N-termini). We hypothesized that plaques susceptible to rupture would contain elevated levels of fragmented proteins with new N-termini. Identification of active proteases and their target proteins might allow categorization of plaque stability.METHODSPlaques from 21 patients who underwent carotid surgery due to symptomatic carotid artery stenosis were examined in an observational/cross-sectional study. The plaques were solubilized, digested, enriched for N-terminal fragments and analyzed by liquid chromatography-mass spectrometry.RESULTSThe above methodology detected 35349 peptides, with 19543 being N-terminal species; 6561 were subsequently identified and quantified. Multidimensional scaling analysis and hierarchical clustering indicate the presence of three distinct clusters, which correlate with gross macroscopic plaque morphology (soft, mixed, and hard), ultrasound classification (echolucent/echogenic) and presence of hemorrhage/ulceration. Major differences were identified in the complement of peptide fragments, consistent with alternative turnover and degradation pathways dependent on plaque type. Identified peptides include signal and pro-peptides from ECM synthesis/turnover, and many from protein fragmentation. Sequence analysis indicates the targeted proteins (including ECM species) and the proteases (including meprins, cathepsins, matrix metalloproteinases, elastase, kallikreins) involved in fragment generation.CONCLUSIONSThis study provides a large dataset of peptide fragments and proteases involved in plaque stability, mechanistic insights into remodelling, and possible biomarkers for improved atherosclerosis risk profiling.GRAPHICAL ABSTRACT