bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extinction probabilities of small structured populations: adequate short-term model predictions inFolsomia candida
Authors: Van Dooren Tom J. M. , Haccou Patsy , Hermus Gerard , Tully Thomas 
Published: August 2024

SummaryPopulation management requires predictions of extinction risk based on a general understanding of these risks and on system-specific modelling. Life tables, available for numerous populations and species, permit calculating population growth and the construction of multi-type branching process models which predict population survivorship and ultimate extinction probabilities. We exemplify this approach and tailor it to an experimental model to predict extinction probabilities per unit of time.In age-structured populations, founders from different age classes lead to different predicted extinction probabilities. Age effects interact with environmental effects such as culling levels, which influence population growth rates. We assess the accuracy of predictions based on an age-structured matrix model, in an extinction experiment over an eight-week period on the springtailFolsomia candida, with crossed founder age and culling level treatments.Using parameter estimates from an accessory experiment, the fit of model predictions to observed extinction probabilities was generally good. A modified branching process model which allowed culling events between and at observations reduced prediction error. However, additionally maximizing the likelihood of observed extinction probabilities based on survival and fecundity parameters, or on a parameter which concentrated fecundity within a subinterval, did not significantly reduce prediction error according to the AICc.Our study shows that satisfactory predictions of establishment probabilities and of the initial persistence of small populations can be made using multi-type branching processes and available parameter estimates. Predictions can be improved by integrating knowledge of when events occur within intervals. This can be done without additional parameter estimation.
Predictive Dynamic Control Accurately Maps the Design Space for 2,3-Butanediol Production
Authors: Gotsmy Mathias , Erian Anna , Marx Hans , Pflügl Stefan , Zanghellini Jürgen 
Published: August 2024

Abstract2,3-Butanediol is a valuable raw material for many industries. Compared to its classical production from petroleum, novel fermentation-based manufacturing is an ecologically superior alternative. To be also economically feasible, the production bioprocesses need to be well optimized.Here, we adapted and applied a novel process optimization algorithm, dynamic control flux-balance analysis (dcFBA), for 2,3-butanediol production inE. coli. First, we performed two-stage fed-batch process simulations with varying process lengths. There, we found that the solution space can be separated into a proportionality and a trade-off region.With the information of the simulations we were able to design close-to-optimal production processes for maximizing titer and productivity, respectively. Experimental validations resulted in a titer of 43.6±9.9 g L−1and a productivity of 1.93 ± 0.08 g L−1h−1. Subsequently, we optimized a continuous two-reactor process setup for 2,3-butanediol productivity. We found that in this mode, it is possible to increase the productivity more than threefold with minor impact on the titer and yield.Biotechnological process optimization is cumbersome, therefore, many processes are run in suboptimal conditions. We are confident that the methods presented here, will help to make many biotechnological productions economically feasible in the future.HighlightsPrecise simulations are used to sample the process solution space.Our simulations uncover big productivity potential in the 2,3-butanediol production.Experiments validate the predictions and show a 2,3-butanediol productivity improvement of 104 %.
Analysis Of Respiratory Syncytial Virus Reveals Conserved Rna Secondary Structural Motifs And Impact Viral Lifecycle
Authors: Thornhill Elena M , Andrews Ryan J. , Lozier Zachary , Carino Elizabeth , Rameix-Welti Marie-Anne , Eléouët Jean-François , Moss Walter N. , Verhoeven David 
Published: August 2024

AbstractAn analysis that combined bioinformatics, comparative sequence/structural analysis, and experimental assays has been completed on respiratory syncytial virus (RSV). Both the genomic RNA and its reverse complement were studied using the novel bioinformatics pipeline ScanFold, which predicted 49 regions on RSV RNAs that appear to encode functional secondary structures (based on their unusually stable sequence order). Multiple motifs appear to be conserved between RSV and related virus strains, including one region within the F gene, which had a highly favorable overall prediction metric of a paired secondary structure. This motif was subjected to additional experimental analyses using SHAPE analysis to confirm ScanFold predicted secondary structure. In subsequent analysis, RSV F mRNA transcripts were made by in vitro transcription using T7 polymerase and transcripts which relaxed the predicted secondary structure yielded slightly higher mRNA transcripts and protein expression levels as wildtype F. However, using reverse genetics for comparison of viruses containing wildtype or relaxed F suggested that the predicted secondary structures may be critical for RSV replication in cells. To our knowledge, this is the first study to examine conserved RNA structures across multiple RSV strains and may help identify potential therapeutic targets to inhibit.
Opposing actomyosin pools generate cortical flows that establish epithelial polarity
Authors: Shi Yu , Ohler Lauren S. , de Jesus Bailey N. , Dickinson Daniel J. 
Published: August 2024

AbstractEpithelial cell polarity, defined by distinct apical and basolateral domains, is fundamental for animal embryonic development and organ function. During organogenesis, epithelia often develop from unpolarized precursor cells. How mammalian epithelial cells establish polarityde novofrom an initially unpolarized state has remained unclear, in part due to an inability to observe this process in real time in non-transformed cellular systems. Here, we leverage recent advances in 3D spheroid culture of mouse embryonic stem cells, fluorescent protein knock-in and live imaging techniques to study the process of epithelial polarity establishment. We show that apical myosin activity, regulated by Myosin Light Chain Kinase (MLCK), is crucial for the establishment and maintenance of epithelial polarity. Actomyosin cortical flows transport ZO-1, a tight junction component that interacts with apical polarity proteins, to establish the apical membrane. A second pool of myosin, regulated by Rho kinase, localizes basally and balances apically directed flow. Our result imply that epithelial polarity emerges as a consequence of actomyosin-driven cytoskeletal rearrangements.
Acute Activation of Genes Through Transcriptional Condensates Impact Non-target Genes in a Chromatin Domain
Authors: Bohra Darshika , Islam Zubairul , Nidharshan Sundarraj , Mazumder Aprotim , Notani Dimple 
Published: August 2024

AbstractTranscription activation of genes by estrogen is driven by enhancers, which are often located within the same Topologically Associating Domain (TAD) as non-targeted promoters. We investigated how acute enhancer-driven activation affects neighbouring non-target genes within the same TAD. Using single-molecule RNA FISH (smFISH), we tracked the transcription ofTFF1(enhancer-targeted) andTFF3(non-targeted) during estrogen stimulation. We observed mutually exclusive expression patterns:TFF1expression peaked at 1 hour, whileTFF3reached its peak at 3 hours, afterTFF1’s activation had diminished. Chromatin looping data indicated that the enhancer loops withTFF1but notTFF3, suggesting thatTFF3upregulation is not due to direct enhancer-promoter interactions. CRISPR deletion of theTFF1enhancer and 1,6-hexanediol (HD) exposure revealed that theTFF1enhancer:promoter undergo Liquid-Liquid Phase Separation (LLPS), which sequesters the transcriptional machinery and inhibitsTFF3expression. As estrogen signalling wanes or LLPS is disrupted,TFF1expression declines whileTFF3expression increases. Our findings reveal that enhancer-driven activation can indirectly influence neighbouring genes, highlighting a dynamic shift in gene expression as signalling progresses.
H3K4me2 distinguishes a distinct class of enhancers during the maternal-to-zygotic transition
Authors: Hurton Matthew D. , Miller Jennifer M. , Lee Miler T. 
Published: August 2024

AbstractAfter egg fertilization, an initially silent embryonic genome is transcriptionally activated during the maternal-to-zygotic transition. In zebrafish, maternal vertebrate pluripotency factors Nanog, Pou5f3 (OCT4 homolog), and Sox19b (SOX2 homolog) (NPS) play essential roles in orchestrating embryonic genome activation, acting as “pioneers” that open condensed chromatin and mediate acquisition of activating histone modifications. However, some embryonic gene transcription still occurs in the absence of these factors, suggesting the existence of other mechanisms regulating genome activation. To identify chromatin signatures of these unknown pathways, we profiled the histone modification landscape of zebrafish embryos using CUT&RUN. Our regulatory map revealed two subclasses of enhancers distinguished by presence or absence of H3K4me2. Enhancers lacking H3K4me2 tend to require NPS factors for de novo activation, while enhancers bearing H3K4me2 are epigenetically bookmarked by DNA hypomethylation to recapitulate gamete activity in the embryo, independent of NPS pioneering. Thus, parallel enhancer activation pathways combine to induce transcriptional reprogramming to pluripotency in the early embryo.
EML4-ALK variant-specific genetic interactions shape lung tumorigenesis
Authors: Diaz-Jimenez Alberto , Shuldiner Emily G. , Somogyi Kalman , Gonzalez Oscar , Akkas Filiz , Murray Christopher W. , Andrejka Laura , Tsai Min K. , Brors Benedikt , Sivakumar Smruthy , Sisoudiya Saumya D. , Sokol Ethan S. , Petrov Dmitri A. , Winslow Monte M. , Sotillo Rocio 
Published: August 2024

ABSTRACTOncogenic fusions of EML4 and ALK occur in ∼5% of lung adenocarcinomas. More than 15 EML4-ALK variants with distinct breakpoints withinEML4have been identified, but the functional differences between these variants remain poorly understood. Here we use CRISPR/Cas9 somatic genome editing to generate autochthonous mouse models of the two most common EML4-ALK variants, V1 and V3, and show that V3 is more oncogenic than V1. By integrating these models with multiplexed genome editing, we quantify the effects of 29 putative tumor suppressor genes on V1- and V3-driven lung cancer growthin vivoand show that many tumor suppressor genes have dramatically variant-specific effects on tumorigenesis. Analysis of a novel dataset representing the largest human EML4-ALK lung cancer cohort to date identified alterations in the genomic landscape depending on the EML4-ALK variant. These findings demonstrate functional heterogeneity among EML4-ALK variants, suggesting that EML4-ALK variants behave more like distinct oncogenes than a uniform entity. More broadly, these findings highlight the dramatic impact of oncogenic fusions partner proteins on tumor biology.
A novel iPSC model of Bryant-Li-Bhoj neurodevelopmental syndrome demonstrates the role of histone H3.3 in neuronal differentiation and maturation
Authors: Sangree Annabel K. , Angireddy Rajesh , Bryant Laura M. , Layo-Carris Dana E. , Lubin Emily E. , Wang Xiao Min , Clark Kelly J. , Durham Emily E. , Bhoj Elizabeth J. 
Published: August 2024

ABSTRACTBackgroundBryant-Li-Bhoj neurodevelopmental syndrome (BLBS) is neurogenetic disorder caused by variants inH3-3AandH3-3B,the two genes that encode the histone H3.3 protein. Ninety-nine percent of individuals with BLBS show developmental delay/intellectual disability, but the mechanism by which variants in H3.3 result in these phenotypes is not yet understood. As a result, only palliative interventions are available to individuals living with BLBS.MethodsHere, we investigate how one BLBS-causative variant,H3-3Bp.Leu48Arg (L48R), affects neurodevelopment using an induced pluripotent stem cell (iPSC) model differentiated to 2D neural progenitor cells (NPCs), 2D forebrain neurons (FBNs), and 3D dorsal forebrain organoids (DFBOs). We employ a multi-omic approach in the 2D models to quantify the resulting changes in gene expression and chromatin accessibility. We used immunofluorescence (IF) staining to define the identities of cells in the 3D DFBOs.ResultsIn the 2D systems, we found dysregulation of both gene expression and chromatin accessibility of genes important for neuronal fate, maturation, and function in H3.3 L48R compared to control. Our work in 3D organoids corroborates these findings, demonstrating altered proportions of radial glia and mature neuronal cells.ConclusionsThese data provide the first mechanistic insights into the pathogenesis of BLBS from a human-derived model of neurodevelopment, which suggest that the L48R increasesH3-3Bexpression, resulting in the hyper-deposition of H3.3 into the nucleosome which underlies changes in gene expression and chromatin accessibility. Functionally, this causes dysregulation of cell adhesion, neurotransmission, and the balance between excitatory and inhibitory signaling. These results are a crucial step towards preclinical development and testing of targeted therapies for this and related disorders.
Super-Resolution Simplified: Sub-10nm Imaging Over Large Areas and Deep Penetration via SDC-OPR and DNA-PAINT
Authors: Zaza Cecilia , Joseph Megan D. , Dalby Olivia P. L. , Walther Rhian F. , Kołątaj Karol , Chiarelli Germán , Pichaud Franck , Acuna Guillermo P. , Simoncelli Sabrina 
Published: August 2024

ABSTRACTSingle molecule localization microscopy (SMLM) is constrained by selective illumination configurations to achieve high signal-to-background ratio (SBR), forcing trade-offs between penetration depth, field-of-view (FOV), and spatial resolution. We demonstrate that a Spinning Disc confocal microscope with Optical Photon Reassignment (SDC-OPR) in combination with DNA-PAINT effectively balances these limitations. This system enables high-resolution imaging through multiple cellular layers, enhancing spatial resolution while remaining practical and accessible for diverse biological applications.
A consortium-based approach to adaptive laboratory evolution ofAcinetobacter baylyiADP1 for lignin valorization
Authors: Maiti Suchismita , Singh Prashant , Vishnu Prasad J , Muthukrishnan Anantha Barathi , Blank Lars M. , Jayaraman Guhan 
Published: August 2024

ABSTRACTThe utility ofAcinetobacter baylyiADP1 (ADP1) for lignin valorization has yet to be sufficiently investigated compared to other organisms such asPseudomonas,Rhodococcus,etc. In this study, a two-step Adaptive Laboratory Evolution (ALE) process was used to evolve a unique ADP1 strain (A. baylyiSAG_185). Initially, several ADP1 strains were evolved for substrate tolerance to specific lignin-related aromatics (LRAs). Subsequently, a consortium of these strains was adaptively evolved in a mixture of LRAs, which resulted in the evolution of SAG_185. This strain was capable of simultaneous utilization of multiple LRAs at higher concentrations as well as grow on a depolymerized lignin-rich residue obtained from enzymatic hydrolysis of pre-treated corncob. This is the first report on such an evolutionary strategy.Whole-genome sequence analysis of all the evolved strains revealed large-scale mutations involving insertion sequences (IS). In particular, SAG_185 revealed a critical mutation in the vanR repressor gene, resulting in the up-regulation of vanAB genes required to convert vanillate to the key intermediate, protocatechuate (PCA). Additionally, there were two large deletions of 9kb and 38kb DNA segments, including genes for putative transcriptional regulators of LysR, MarR and AraC family. The evolved strains also showed mutations in the hcaE gene, responsible for the uptake of LRAs. The vast number of mutations in hypothetical proteins, transporter and regulatory sequences indicate the underlying effects of these regions on the uptake of multiple LRAs. Overall, our findings provide potential targets for reverse engineering of A. baylyi ADP1 for lignin valorization.IMPORTANCEThis study shows a novel strategy for adaptive laboratory evolution, which can be generically adopted to evolve bacterial strains for taking up multiple substrates which are toxic at higher concentrations. We developed a two-step evolutionary strategy to evolve a unique strain, A. baylyi SAG_185, which could take up multiple lignin-related aromatic monomers at higher concentrations as well as grow on depolymerized lignin. Initially, individual strains were adapted to utilize single aromatic monomers at higher concentrations. After many unsuccessful attempts to adapt these strains for utilizing multiple monomers, a consortium of the five evolved strains were grown on a mixture of aromatics and adapted to utilize all the monomers at high concentrations. The adapted consortia resulted in the evolution of SAG_185. Whole-genome sequence analysis of all these strains gave rise to many interesting insights on potential genetic targets for reverse engineering of A. baylyi ADP1 for lignin valorization.
Distinct pathogenic influence of anti-HMGCR+ and anti-SRP+ immune-mediated necrotizing myopathy autoantibodies on engineered muscle function
Authors: Lad Heta , Esteban Ernest Myguel , Tiper Yekaterina , Mahoudeau Alexandrine , Xie Zhuoye , Tendrel Berenice , Allenbach Yves , Benveniste Olivier , Gilbert Penney M. 
Published: August 2024

AbstractImmune-mediated necrotizing myopathy (IMNM) is a subgroup of idiopathic inflammatory myopathies associated with anti-signal recognition particle (SRP) or anti-3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) autoantibodies. However, the demonstration of a direct pathogenic effect of IMNM patient autoantibodies on skeletal muscle contractile force, independent of the downstream activation of the complement pathway, has yet to be reported. Thus, the goal of this study was to leverage a custom 3D-human skeletal muscle microtissue (hMMT) culture platform, that enables muscle cell contractile apparatus maturation and the analysis of contractile function, to evaluate the direct effect of total immunoglobulins (IgGs) isolated from IMNM patients with amplification of anti-SRP+or anti-HMGCR+autoantibodies. hMMTs capable of force generation were treated with total IgGs, isolated from 3 SRP+ and 3 HMGCR+ patients plasma, and delivered in complement inactivated media for 4 days. hMMT health was then evaluated by quantifying the peak force and contraction kinetics in response to electrical field stimulation and by performing histological analysis of sarcomere and myotube structures. Treating hMMTs with total IgGs from anti-HMGCR+patients resulted in a decline in tetanus contractile force, though sarcomere Z-line architecture analysis revealed no significant influences on sarcomere organization. hMMT treatment with total IgGs from anti-SRP+patients induced muscle atrophy, observed via significantly smaller myotube diameter, but this did not translate to a decline in contractile function. This study demonstrates that anti-SRP and anti-HMGCR autoantibodies exert direct, but distinct influences on IMNM-associated skeletal muscle pathogenesis, which may inform IMNM therapy development.
Imputation of cancer proteomics data with a deep model that learns from many datasets
Authors: Harris Lincoln , Noble William S. 
Published: August 2024

AbstractMissing values are a major challenge in the analysis of mass spectrometry proteomics data. Missing values hinder reproducibility, decrease statistical power for identifying differentially expressed (DE) proteins and make it challenging to analyze low-abundance proteins. We present Lupine, a deep learning-based method for imputing, or estimating, missing values in tandem mass tag (TMT) proteomics data. Lupine is, to our knowledge, the first imputation method that is designed to learn jointly from many datasets, and we provide evidence that this approach leads to more accurate predictions. We validated Lupine by applying it to TMT data from>1,000 cancer patient samples spanning ten cancer types from the Clinical Proteomics Tumor Atlas Consortium (CPTAC). Lupine outperforms the state of the art for TMT imputation, identifies more DE proteins than other methods, corrects for TMT batch effects, and learns a meaningful representation of proteins and patient samples. Lupine is implemented as an open source Python package.
Synchronous L1 retrotransposition events promote chromosomal crossover early in human tumorigenesis
Authors: Zumalave Sonia , Santamarina Martin , Espasandín Nuria P. , Garcia-Souto Daniel , Temes Javier , Baker Toby M. , Pequeño-Valtierra Ana , Otero Iago , Rodríguez-Castro Jorge , Oitabén Ana , Álvarez Eva G. , Otero Paula , Díaz-Arias Iria , Martínez-Fernández Mónica , Van Loo Peter , Cristofari Gael , Rodriguez-Martin Bernardo , Tubio Jose M. C. 
Published: August 2024

AbstractL1 retrotransposition is a significant source of genomic variation in human epithelial tumours, which can contribute to tumorigenesis. However, fundamental questions about the causes and consequences of L1 activity in cancer genomes remain unresolved, primarily due to the limitations of short-read sequencing technologies. Here, we employ multiplatform sequencing, with an emphasis on long reads, to analyse a fine selection of 10 tumours exhibiting high rates of somatic retrotransposition, encompassing over 6000 events. The analysis of L1 locus-specific single-nucleotide variants reveals a novel panorama of L1 loci activity. Furthermore, examination of the internal structure of somatic L1s uncovers the mechanisms behind their inactivation. A hidden landscape of chromosomal aberrations emerges in the light of long reads, where reciprocal translocations mediated by L1 insertion represent frequent events. Resolution of L1 bridges’ configuration elucidates the mechanisms of their formation, where typically two independent, but synchronous, somatic L1 insertions drive the reciprocal exchange between non-homologous chromosomes. Timing analyses indicate that L1 retrotransposition is an early driver of chromosomal instability, active before the first whole-genome doubling event. Overall, these findings highlight L1 activity as a more significant contributor to tumour genome plasticity than previously recognized, extending its impact beyond simple insertional mutagenesis.