bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal Dynamics of Apoptosis-Induced Proliferation in Pupal Wing Development: Implications for Regenerative Ability
Authors: Ahmed-de-Prado Sara , Estella Carlos , Baonza Antonio 
Published: July 2023

AbstractThe ability of animals to regenerate damaged tissue is a complex process that involves various cellular mechanisms. As animals age, they lose their regenerative abilities, making it essential to understand the underlying mechanisms that limit regenerative ability during aging.Drosophila melanogasterwing imaginal discs are epithelial structures that can regenerate after tissue injury. While significant research has focused on investigating regenerative responses during larval stages, particularly regarding the regulation and function of the JNK pathway, our comprehension of the regenerative potential of pupal wings and the underlying mechanisms contributing to the decline of regenerative responses remains limited. This study explores the temporal dynamics during pupal development of the proliferative response triggered by the induction of cell death, a typical regenerative response. Our results indicate that the apoptosis-induced proliferation response can be initiated as late as 30 hours after pupa formation (APF), when in normal circumstances cell proliferation ceases at around 20 hours APF. Furthermore, our data revealed that after 35 hours APF, cell death alone fails to induce further proliferation. Interestingly, the failure of reinitiating the cell cycle beyond this time point is not attributed to an incapacity to activate the JNK pathway. Instead, one of the constraining factors in the apoptotic-induced proliferation process during pupal development seems to be the activity level of ecdysone-responsive genes.Author SummaryAnimals have the remarkable ability to regenerate damaged tissues, but this regenerative potential diminishes with age. Understanding the mechanisms underlying age-related decline in regenerative abilities is crucial. Drosophila melanogaster wing imaginal discs provide a valuable model for studying tissue regeneration. While significant research has focused on regenerative responses during larval stages, our understanding of the regenerative potential and mechanisms in pupal wings remains limited.In this study, we investigate the temporal dynamics of the proliferative response triggered by cell death during late during the development, in pupal development. Our findings reveal that the apoptosis-induced proliferation response can occur during pupal development, even after normal cell proliferation has ceased. However, at late stages of pupal development this response does not occur. We have found that, the inability to reinitiate the cell cycle beyond this time point is influenced by the activity of the hormone ecdysone and its-responsive genes.These findings shed light on the dynamic processes involved in tissue regeneration during pupal development. This study expands our understanding of the complex interplay between cell death, proliferation, and gene activity during tissue regeneration, providing valuable insights for future research in regenerative biology.
Emergence of novel non-aggregative variants under negative frequency-dependent selection inKlebsiella variicola
Authors: Nucci Amandine , Janaszkiewicz Juliette , Rocha Eduardo P.C. , Rendueles Olaya 
Published: July 2023

ABSTRACTKlebsiella variicolais an emergent human pathogen causing diverse infections, including in the urinary tract. However, little is known about the evolution and maintenance of genetic diversity in this species, the molecular mechanisms and their population dynamics. Here, we characterized the emergence of a novel rdar-like morphotype which is contingent both on the genetic background and the environment. We show that mutations in either the nitrogen assimilation control gene(nac)or the type III fimbriae regulator,mrkH,suffice to generate rdar-like colonies. These morphotypes are primarily selected for the reduced inter-cellular aggregation as a result of loss-of-function yielding reduced fimbriae expression. Additionally, these clones also display increased growth rate and reduced biofilm formation. Direct competitions between rdar and wild type clone show that mutations inmrkHprovide large fitness advantages. In artificial urine, the morphotype is under strong negative frequency-dependent selection and is able to socially exploit wild type strains. An exhaustive search formrkHmutants in public databases revealed thatca8% of natural isolates analysed had truncated MrkH proteins many of which were due to insertions of IS elements, including a reported clinical isolate with rdar morphology. These strains were all isolated from human, mostly from urine. The decreased aggregation of these mutants could have important clinical implications as such clones could better disperse within the host allowing colonisation of other body sites and leading to systemic infections.One-sentence SummaryReport of the emergence of a novel non-aggregative colony morphology inK. variicolaand the first example of social exploitation in theKlebsiellagenus.
Estimating temporally variable selection intensity from ancient DNA data II
Authors: Lyu Wenyang , Dai Xiaoyang , Beaumont Mark , Yu Feng , He Zhangyi 
Published: July 2023

AbstractRecent technological innovations, such as next generation sequencing and DNA hybridisation enrichment, have made it possible to recover DNA information from historical and archaeological biological materials, which has motivated the development of various statistical approaches for inferring selection from allele frequency time series data. Recently, He et al. (2023a,b) introduced methods that can utilise ancient DNA (aDNA) data in the form of genotype likelihoods, therefore enabling the modelling of sample uncertainty arising from DNA molecule damage and fragmentation. However, their performance suffers from the underlying dependency on the allele age. Here we introduce a novel particle marginal Metropolis-Hastings within Gibbs framework for Bayesian inference of time-varying selection from aDNA data in the form of genotype like-lihoods. To circumvent the performance issue encountered in He et al. (2023a,b), we devise a novel numerical scheme for backward-in-time simulation of the Wright-Fisher diffusion and mix forward- and backward-in-time simulations in the particle filter for likelihood computation. Our framework also enables us to reconstruct the underlying population allele frequency trajectories, integrate temporal information in genotype likelihood calculations and test hypotheses on the drivers of past selection events. We conduct extensive evaluations through simulations and show its utility with an application to aDNA data from pigmentation loci in ancient horses.
High-throughput 3D imaging flow cytometry of adherent 3D cell cultures
Authors: Yamashita Minato , Tamamitsu Miu , Kirisako Hiromi , Goda Yuki , Chen Xiaoyao , Hattori Kazuki , Ota Sadao 
Published: July 2023

AbstractThree-dimensional (3D) cell cultures are indispensable in recapitulatingin vivoenvironments. Among many 3D culture methods, the strategy to culture adherent cells on hydrogel beads to form spheroid-like structures is powerful for maintaining high cell viability and functions through an efficient supply of nutrients and oxygen. However, high-throughput, scalable technologies for 3D imaging of individual cells cultured on the hydrogel scaffolds are lacking. This study reports the development of a high-throughput, scalable 3D imaging flow cytometry (3D-iFCM) platform for analyzing spheroid models on hydrogel beads. This platform is realized by integrating a single objective lens-based fluorescence light-sheet microscopy with a microfluidic device employing a combination of hydrodynamic and acoustofluidic focusing techniques. This integration enabled an unprecedentedly high-throughput, robust optofluidic 3D imaging, processing 513 cells s-1and a total of more than 104cells within a minute. The large dataset obtained allows us to quantify and compare the nuclear morphology of adhering and suspended cells, revealing adhering cells have smaller nuclei with non-round surfaces. This platform’s high throughput, robustness, and precision for analyzing the morphology of subcellular compartments in 3D culture models holds promising potential for various biomedical analyses, including image-based phenotypic screening of drugs with spheroids or organoids.
Mapping the dynamics of epigenetic adaptation during heterochromatin misregulation
Authors: Larkin Ajay , Kunze Colin , Seman Melissa , Levashkevich Alexander , Curran Justin , Morris-Evans Dionysus , Lemieux Sophia , Khalil Ahmad S. , Ragunathan Kaushik 
Published: July 2023

SUMMARYA classical and well-established mechanism that enables cells to adapt to new and adverse conditions is the acquisition of beneficial genetic mutations. Much less is known about epigenetic mechanisms that allow cells to develop novel and adaptive phenotypes without altering their genetic blueprint. It has been recently proposed that histone modifications, such as heterochromatin-defining H3K9 methylation (H3K9me), normally reserved to maintain genome integrity, can be redistributed across the genome to establish new and potentially adaptive phenotypes. To uncover the dynamics of this process, we developed a precision engineered genetic approach to trigger H3K9me redistribution on-demand in fission yeast. This enabled us to trace genome-scale RNA and chromatin changes over time prior to and during adaptation in long-term continuous cultures. Establishing adaptive H3K9me occurs over remarkably slow time-scales relative to the initiating stress. During this time, we captured dynamic H3K9me redistribution events ultimately leading to cells converging on an optimal adaptive solution. Upon removal of stress, cells relax to new transcriptional and chromatin states rather than revert to their initial (ground) state, establishing a tunable memory for a future adaptive epigenetic response. Collectively, our tools uncover the slow kinetics of epigenetic adaptation that allow cells to search for and heritably encode adaptive solutions, with implications for drug resistance and response to infection.
Patient-specific computational models predict prognosis in B cell lymphoma by quantifying pro-proliferative and anti-apoptotic signatures from genetic sequencing data
Authors: Norris Richard , Jones John , Mancini Erika , Chevassut Timothy , Pepper Chris , Pepper Andrea , Mitchell Simon 
Published: July 2023

AbstractGenetic heterogeneity and co-occurring driver mutations impact clinical outcomes in blood cancers. Grouping tumours into clusters based on genetic alterations is prognostically informative. However, predicting the emergent effect of co-occurring mutations that impact multiple complex and interacting signalling networks remains challenging. Here, we used mathematical models to predict the impact of co-occurring mutations on cellular signalling and cell fates in diffuse large B cell lymphoma (DLBCL) and multiple myeloma (MM). Simulations predicted adverse impact on clinical prognosis when combinations of mutations induced both pro-proliferative and anti-apoptotic signalling. So, we established a pipeline to integrate patient-specific mutational profiles into personalised lymphoma models. Using this approach, we identified a subgroup (19%) of patients characterised by simultaneous upregulation of anti-apoptotic and pro-proliferative (AAPP) signalling. AAPP patients have dismal prognosis and can be identified within all current genomic and cell-of-origin classifications. Combining personalised molecular simulations with mutational clustering enabled stratification of patients into clinically informative prognostic categories: good (80% progression-free survival at 120 months), intermediate (median progression-free survival of 93 months), and poor (AAPP, median progression-free survival of 26 months). This study shows that personalised computational models enable identification of novel high-risk patient subgroups, providing a valuable tool for future risk-stratified clinical trials.
Genome-wide screen identifies new set of genes for improved heterologous laccase expression inSaccharomyces cerevisiae
Authors: Strawn Garrett , Wong Ryan , Young Barry , Davey Michael , Nislow Corey , Conibear Elizabeth , Loewen Christopher , Mayor Thibault 
Published: July 2023

AbstractThe yeastSaccharomyces cerevisiaeis widely used as a host cell for recombinant protein production due to its fast growth, cost-effective culturing, and ability to secrete large and complex proteins. However, one major drawback is the relatively low yield of produced proteins compared to other host systems. To address this issue, we developed an overlay assay to screen the yeast knockout collection and identify mutants that enhance recombinant protein production, specifically focusing on the secretion of theTrametes trogiifungal laccase enzyme. Gene ontology analysis of these mutants revealed an enrichment of processes including vacuolar targeting, vesicle trafficking, proteolysis, and glycolipid metabolism. We confirmed that a significant portion of these mutants also showed increased activity of the secreted laccase when grown in liquid culture. Notably, we found that the combination of deletions ofOCA6, a tyrosine phosphatase, along withPMT1 orPMT2, two ER membrane protein-O-mannosyltransferases involved in ER quality control, andSKI3, a component of the SKI complex responsible for mRNA degradation, further increased secreted laccase activity. Conversely, we also identified over 200 gene deletions that resulted in decreased secreted laccase activity, including many genes that encode for mitochondrial proteins and components of the ER-associated degradation pathway. Intriguingly, the deletion of the ER DNAJ co-chaperoneSCJ1led to almost no secreted laccase activity. When we expressedSCJ1from a low-copy plasmid, laccase secretion was restored. However, overexpression of Scj1p had a detrimental effect, indicating that precise dosing of key chaperone proteins is crucial for optimal recombinant protein expression.ImportanceOur study showcases a newly developed high throughput screening technique to identify yeast mutant strains that exhibit an enhanced capacity for recombinant protein production. Using a genome-wide approach, we show that vesicle trafficking plays a crucial role in protein production, as the genes associated with this process are notably enriched in our screen. Furthermore, we demonstrate that a specific set of gene deletions, which were not previously recognized for their impact on recombinant laccase production, can be effectively manipulated in combination to increase the production of heterologous proteins. This study offers potential strategies for enhancing the overall yield of recombinant proteins and provides new avenues for further research in optimizing protein production systems.
Mmp17-deficient mice exhibit heightened goblet cell effector expression in the colon and increased resistance to chronicTrichuris murisinfection
Authors: Vornewald Pia M. , Forman Ruth , Yao Rouan , Pamar Naveen , Lindholm Håvard T. , Martín-Alonso Mara , Else Kathryn J. , Oudhoff Menno J. 
Published: July 2023

ABSTRACTIntestinal epithelial homeostasis is maintained by intrinsic and extrinsic signals. The extrinsic signals include those provided by mesenchymal cell populations that surround intestinal crypts and is further facilitated by the extracellular matrix (ECM), which is modulated by proteases such as matrix metalloproteinases (MMPs). Extrinsic signals ensure an appropriate balance between intestinal epithelial proliferation and differentiation. This study explores the role of MMP17, which is expressed by mesenchymal cells, in intestinal homeostasis and during immunity to infection. Mice lacking MMP17 expressed high levels of goblet-cell associated genes, such as CLCA1 and RELM-β, which are normally associated with immune responses to infection. Nevertheless,Mmp17KO mice did not have altered resistance during a bacterialCitrobacter rodentiuminfection. However, when challenged with a low dose of the helminthTrichuris muris,Mmp17KO mice had increased resistance, without a clear role for an altered immune response during infection. Mechanistically, we did not find changes in traditional modulators of goblet cell effectors such as the NOTCH pathway or specific cytokines. Instead, we found elevated BMP signaling inMmp17KO mouse large intestinal crypts that we propose to alter the goblet cell maturation state. Together, our data suggests that MMP17 extrinsically alters the goblet cell maturation stateviaa BMP signaling axis, which is sufficient to alter clearance in a helminth infection model.
Mapping Single-molecule Protein Complexes in 3D with DNA Nanoswitch Calipers
Authors: Shrestha Prakash , Yang Darren , Shih William M. , Wong Wesley P. 
Published: July 2023

AbstractThe ability to accurately map the 3D geometry of single-molecule complexes in trace samples would lead to new insights into molecular mechanics and provide an approach for single-molecule structural proteomics. To enable this, we have developed a high-resolution force-spectroscopy method capable of measuring multiple distances between labeled sites in natively folded protein complexes. Our approach combines reconfigurable nanoscale devices we call DNA Nanoswitch Calipers, which we have previously introduced, with a force-based barcoding system to distinguish each measurement location. We demonstrate our approach by reconstructing the tetrahedral geometry of biotin-binding sites in natively folded streptavidin, with 1.5-2.5Åagreement to previously reported structures.
3D bioprinting directly affects proteomic signature and myogenic maturation in muscle pericytes-derived human myo-substitute
Authors: Reggio Alessio , Fuoco Claudia , Paolis Francesca De , Testa Stefano , Celikkin Nehar , Bernardini Sergio , Baldi Jacopo , Biagini Roberto , Seliktar Dror , Cirillo Carmine , Grumati Paolo , Cannata Stefano , Costantini Marco , Gargioli Cesare 
Published: July 2023

AbstractSkeletal muscle tissue engineering (SMTE) has recently emerged to address major clinical challenges such as volumetric muscle loss. Here, we report a rotary wet-spinning (RoWS) biofabrication technique for producing human myo-substitutes with biomimetic architectures and functions. We show how the proposed technique may be used to establish a well-tailored, anisotropic microenvironment that promotes exceptional myogenic differentiation of human skeletal muscle-derived pericytes (hPeri). Using high-resolution mass spectrometry-based proteomics with the integration of literature-derived signaling networks, we uncovered that i) 3D biomimetic matrix environment (PEG-Fibrinogen) confers a lower mitogenicity microenvironment compared to standard 2D cultures, favoring the formation of contractile-competent bundles of pericytes-derived myotubes in an anchoring-independent 3D state, and ii) the bioprinting method promotes an upregulation of muscle matrix structural protein besides increasing contractile machinery proteins with respect to 3D bulk cultures. Finally,in vivoinvestigations demonstrate that the 3D bioprinted myo-substitute is fully compatible with the host ablated muscular tissue, exhibiting myo-substitute engraftment and muscle regeneration in a mouse VML model. Overall, the results show that 3D bioprinting has a superior capability for controlling the myogenic differentiation process on a macroscale and, with future refining, may have the potential to be translated into clinical practice.
A method to correct for local alterations in DNA copy number that bias functional genomics assays applied to antibiotic-treated bacteria
Authors: Sullivan Geraldine J. , Barquist Lars , Cain Amy K. 
Published: July 2023

AbstractFunctional genomics techniques, such as transposon insertion sequencing and RNA sequencing, are key to studying relative differences in mutant fitness or gene expression under selective conditions. However, certain stress conditions, mutations, or antibiotics can directly interfere with DNA synthesis, resulting in systematic changes in local DNA copy number along the chromosome. This can lead to artefacts in sequencing-based functional genomics data when comparing antibiotic treatment to an unstressed control, with relative differences in gene-wise read counts being the result of alterations in chromosomal replication dynamics rather than selection or direct gene regulation. We term this artefact ‘chromosomal location bias’ and implement a principled statistical approach to correct for it by calculating local normalization factors along the chromosome. These normalization factors are then directly incorporated in statistical analyses using standard RNA-sequencing analysis methods without modifying the read counts themselves, preserving important information about the mean-variance relationship in the data. We illustrate the utility of this approach by generating and analysing a ciprofloxacin-treated transposon insertion sequencing dataset inEscherichia colias a case study. We show that ciprofloxacin treatment generates chromosomal location bias in the resulting data, and we further demonstrate that failing to correct for this bias leads to false predictions of mutant drug sensitivity as measured by minimum inhibitory concentrations. We have developed an R package and user-friendly graphical Shiny application, ChromoCorrect, that detects and corrects for chromosomal bias in read count data, enabling the application of functional genomics technologies to the study of antibiotic stress.IMPORTANCEAltered gene dosage due to changes in DNA replication has been observed under a variety of stresses with a variety of experimental techniques. However, the implications of changes in gene dosage for sequencing-based functional genomics assays are rarely considered. We present a statistically principled approach to correcting for the effect of changes in gene dosage, enabling testing for differences in the fitness effects or regulation of individual genes in the presence of confounding differences in DNA copy number. We show that failing to correct for these effects can lead to incorrect predictions of resistance phenotype when applying functional genomics assays to investigate antibiotic stress, and we provide a user-friendly application to detect and correct for changes in DNA copy number.
Unreviewed science in the news: The evolution of preprint media coverage from 2014-2021
Authors: Fleerackers Alice , Shores Kenneth , Chtena Natascha , Alperin Juan Pablo 
Published: July 2023

AbstractIt has been argued that preprint coverage during the COVID-19 pandemic constituted a paradigm shift in journalism norms and practices. This study examines whether, in what ways, and to what extent this is the case using a sample of 11,538 preprints posted on four preprint servers—bioRxiv, medRxiv, arXiv, and SSRN—that received coverage in 94 English-language media outlets between 2014–2021. We compared mentions of these preprints with mentions of a comparison sample of 397,446 peer reviewed research articles indexed in the Web of Science to identify changes in the share of media coverage that mentioned preprints before and during the pandemic. We found that preprint media coverage increased at a slow but steady rate pre-pandemic, then spiked dramatically. This increase applied only to COVID-19-related preprints, with minimal or no change in coverage of preprints on other topics. In addition, the rise in preprint coverage was most pronounced among health and medicine-focused media outlets, which barely covered preprints before the pandemic but mentioned more COVID-19 preprints than outlets focused on any other topic. These results suggest that the growth in coverage of preprints seen during the pandemic period may imply a shift in journalistic norms, including a changing outlook on reporting preliminary, unvetted research.