bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fitting agent-based models to tumor images using representation learning
Authors: Cess Colin G. , Finley Stacey D. 
Published: January 2023

AbstractAgent-based models (ABMs) have enabled great advances in the study of tumor development and therapeutic response, allowing researchers to explore the spatiotemporal evolution of the tumor and its microenvironment. However, these models face serious drawbacks in the realm of parameterization – ABM parameters are typically set individually based on various data and literature sources, rather than through a rigorous parameter estimation approach. While ABMs can be fit to time-course data, that type of data loses the spatial information that is a defining feature of ABMs. Tumor images provide spatial information; however, such images only represent individual timepoints, limiting their utility in calibrating the tumor dynamics predicted by ABMs. Furthermore, it is exceedingly difficult to compare tumor images to ABM simulations beyond a qualitative visual comparison. Without a quantitative method of comparing the similarity of tumor images to ABM simulations, a rigorous parameter fitting is not possible. Here, we present a novel approach that applies neural networks to represent both tumor images and ABM simulations as low dimensional points, with the distance between points acting as a quantitative measure of difference between the two. This enables a quantitative comparison of tumor images and ABM simulations, where the distance between simulated and experimental images can be minimized using standard parameter-fitting algorithms. Here, we describe this method and present two examples to demonstrate the application of the approach to estimate parameters for two distinct ABMs. Overall, we provide a novel method to robustly estimate ABM parameters.
Pervasive GxE interactions shape adaptive trajectories and the exploration of the phenotypic space in artificial selection experiments
Authors: Desbiez-Piat Arnaud , Ressayre Adrienne , Marchadier Elodie , Noly Alicia , Remoué Carine , Vitte Clémentine , Belcram Harry , Bourgais Aurélie , Galic Nathalie , Le Guilloux Martine , Tenaillon Maud I. , Dillmann Christine 
Published: January 2023

AbstractQuantitative genetics models have shown that long-term selection responses depend on initial variance and mutational influx. Understanding limits of selection requires quantifying the role of mutational variance. However, correlative responses to selection on non-focal traits can perturb the selection response on the focal trait; and generations are often confounded with selection environments so that genotype by environment (GxE) interactions are ignored. The Saclay Divergent Selection Experiments (DSE) on maize flowering time were used to track the fate of individual mutations combining genotyping data and phenotyping data from yearly measurements (DSEYM) and common garden experiments (DSECG) with four objectives (1) to quantify the relative contribution of standing and mutational variance to the selection response, (2) to estimate genotypic mutation effects, (3) to study the impact of GxE interactions in the selection response, (4) to analyze how trait correlations modulate the exploration of the phenotypic space. We validated experimentally the expected enrichment of fixed beneficial mutations with an average effect of +0.278 and +0.299 days to flowering, depending on the genetic background. Fixation of unfavorable mutations reached up to 25% of incoming mutations, a genetic load possibly due to antagonistic pleiotropy, whereby mutations fixed in the selection environment (DSEYM) turned to be unfavorable in the evaluation environment (DSECG). Global patterns of trait correlations were conserved across genetic backgrounds but exhibited temporal patterns. Traits weakly or uncorrelated with flowering time triggered stochastic exploration of the phenotypic space, owing to microenvironment-specific fixation of standing variants and pleiotropic mutational input.
Cost-effective DNA methylation profiling by FML-seq
Authors: Foley Joseph W. , Zhu Shirley X. , West Robert B. 
Published: January 2023

AbstractCurrent methods for profiling DNA methylation require costly reagents, sequencing, or labor time. We introduce FML-seq, a sequencing library protocol that greatly reduces all these costs. Relative to other techniques tested on the same human cell lines, FML-seq produces similar measurements of absolute and differential cytosine methylation at a fraction of the price. FML-seq enables inexpensive, high-throughput experimental designs for large-scale epigenetics research projects.
Tobramycin adaptation alters the antibiotic susceptibility ofPseudomonas aeruginosaquorum sensing-null mutants
Authors: Abisado-Duque Rhea G. , Townsend Kade A. , Mckee Brielle M. , Woods Kathryn , Koirala Pratik , Holder Alexandra J. , Craddock Vaughn D. , Cabeen Matthew , Chandler Josephine R. 
Published: January 2023

ABSTRACTThe opportunistic bacteriumPseudomonas aeruginosauses the LasR-I quorum sensing system to increase resistance to the aminoglycoside antibiotic tobramycin. Paradoxically,lasR-null mutants are commonly isolated from chronic human infections treated with tobramycin, suggesting there may be a mechanism allowing thelasR-null mutants to persist under tobramycin selection. We hypothesized that the effects of inactivatinglasRon tobramycin resistance might be dependent on the presence or absence of other gene mutations in that strain, a phenomenon known as epistasis. To test this hypothesis, we inactivatedlasRin several highly tobramycin-resistant isolates from long-term evolution experiments. We show that the effects of ΔlasRon tobramycin resistance are strain dependent, which is due to a single mutation in thefusA1gene encoding the translation elongation factor EF-G1A (G61A nucleotide substitution). ThefusA1G61A mutation confers a strong selective advantage to ΔlasRmutants under tobramycin treatment. The effects offusA1G61A on ΔlasR-dependent tobramycin resistance are dependent on the MexXY efflux pump and the MexXY regulator ArmZ. ThefusA1mutation also modulates ΔlasRmutant resistance to two other antibiotics, ciprofloxacin and ceftazidime. Our results provide a possible explanation for the emergence oflasR-null mutants in clinical isolates and illustrate the importance of epistatic gene interactions in the evolution of quorum sensing.
E4F1 and ZNF148 are transcriptional activators of the A57C and wildtypeTERTpromoter
Authors: Chua Boon Haow , Ferry Laure , Domrane Cecilia , Anuar Nurkaiyisah Zaal , Wittek Anna , Jha Sudhakar , Butter Falk , Tenen Daniel G. , Defossez Pierre-Antoine , Kappei Dennis 
Published: January 2023

ABSTRACTPoint mutations within theTERTpromoter are the most recurrent somatic non-coding mutations identified across different cancer types, including glioblastoma, melanoma, hepatocellular carcinoma, and bladder cancer. They are most abundant at C146T and C124T and rarer at A57C, with the latter originally described as a familial case but subsequently shown also to occur somatically. All three mutations createde novoETS (E-twenty-six specific) binding sites and result in the reactivation of theTERTgene, allowing cancer cells to achieve replicative immortality. Here, we employed a systematic proteomics screen to identify transcription factors preferentially binding to the C146T, C124T and A57C mutations. While we confirmed binding of multiple ETS factors to the mutant C146T and C124T sequences, we identified E4F1 as an A57C-specific binder and ZNF148 as aTERTWT binder that is excluded from theTERTpromoter by the C124T allele. Both proteins are activating transcription factors that bind specifically to the A57C and wildtype (at position 124)TERTpromoter sequence in corresponding cell lines and upregulateTERTtranscription and telomerase activity. Our work describes new regulators of TERT gene expression with possible roles in cancer.
Genome-wide association studies reveal novel loci associated with pyrethroid and organophosphate resistance inAnopheles gambiaes.l.
Authors: Lucas Eric R. , Nagi Sanjay C. , Egyir-Yawson Alexander , Essandoh John , Dadzie Sam , Chabi Joseph , Djogbénou Luc S. , Medjigbodo Adandé A. , Edi Constant V. , Ketoh Guillaume K. , Koudou Benjamin G. , Van’t Hof Arjen E. , Rippon Emily J. , Pipini Dimitra , Harding Nicholas J. , Dyer Naomi A. , Cerdeira Louise T. , Clarkson Chris S. , Kwiatkowski Dominic P. , Miles Alistair , Donnelly Martin J. , Weetman David 
Published: January 2023

AbstractResistance to insecticides inAnophelesmosquitoes threatens the effectiveness of the most widespread tools currently used to control malaria. The genetic underpinnings of resistance are still only partially understood, with much of the variance in resistance phenotype left unexplained. We performed a multi-country large scale genome-wide association study of resistance to two insecticides widely used in malaria control: deltamethrin and pirimiphos-methyl. Using a bioassay methodology designed to maximise the phenotypic difference between resistant and susceptible samples, we sequenced 969 phenotyped femaleAn. gambiaeandAn. coluzziifrom ten locations across four countries in West Africa (Benin, Côte d’Ivoire, Ghana and Togo), identifying single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) segregating in the populations. The patterns of resistance association were highly multiallelic and variable between populations, with different genomic regions contributing to resistance, as well as different mutations within a given region. While the strongest and most consistent association with deltamethrin resistance came from the region aroundCyp6aa1, this resistance was based on a combination of several independent CNVs inAn. coluzzii, and on a non-CNV bearing haplotype inAn. gambiae. Further signals involved a range of cytochrome P450, mitochondrial, and immunity genes. Similarly, for pirimiphos-methyl, while the strongest signal came from the region ofAce1, more widespread signals included cytochrome P450s, glutathione S-transferases, and a subunit of thenAChRtarget site of neonicotinoid insecticides. The regions aroundCyp9k1and theTepfamily of immune genes were associated with resistance to both insecticide classes, suggesting possible cross-resistance mechanisms. These locally-varying, multigenic and multiallelic patterns highlight the challenges involved in genomic monitoring and surveillance of resistance, and form the basis for improvement of methods used to detect and predict resistance. Based on simulations of resistance variants, we recommend that yet larger scale studies, exceeding 500 phenotyped samples per population, are required to better identify associated genomic regions.
Exploring the Interdependence of TKS4 and CD2AP: Implications for EMT Process and Early Detection in Colon Cancer
Authors: Kurilla Anita , László Loretta , Takács Tamás , Tilajka Álmos , Lukács Laura , Novák Julianna , Pancsa Rita , Buday László , Vas Virag 
Published: January 2023

AbstractBackgroundColon cancer is a leading cause of death worldwide. Although several biomarkers have been developed, more sensitive and specific methods are needed for its early detection. TKS4 and CD2AP scaffold proteins have been already linked to dynamic actin assembly-related processes, such as colon cancer cell migration, although their co-instructive role during tumour-formation remains unknown. Therefore, this study was designed to validate TKS4-CD2AP interaction and study the interdependent effect of TKS4/CD2AP on oncogenic events.MethodsCD2AP was identified as a novel TKS4 interacting partner in six cell lines via co-immunoprecipitation-mass spectrometry. The interaction was validated via western blot, immunocytochemistry, DuoLink assay and peptide microarray. Gene silencing and overexpressing experiments were performed to uncover the cooperative effects of TKS4 and CD2AP in cell movement and in epithelial-mesenchymal transition (EMT). The expression levels of TKS4 and CD2AP mRNAs were quantified using a human colon cancer array, and the results were subjected to bioinformatic database analysis.ResultsThe molecular biology analysis revealed that one of the SH3-domain of CD2AP interacts with a proline-rich short linear motif in TKS4. Functional studies showed that TKS4 and CD2AP form a scaffold complex that regulates migration- and EMT-related pathways of colon cancer cells. The relative TKS4 and CD2AP expression level measurements pointed out that CD2AP/TKS4 ratio is a sensitive biomarker for the identification of tumorous colon tissue.ConclusionsThis is the first study demonstrating the TKS4-CD2AP protein-protein interaction in vitro and in vivo and their interdependent regulative effect on mesenchymal transition-like process in colon cancer. Furthermore, the results highlight that the relative expression levels of CD2AP and TKS4 might serve as a biomarker for the diagnosis of early-stage colon cancer.
In vitroandin vivoevidences propound therapeutic potential of Lipocalin 2 in cervical carcinoma
Authors: Dwivedi Nehanjali , Mazumder Tahmina , Veeraraghavan Gayathri , Siva Ramanujam , Smitha P K , Ranade Rohit , Das Manjula , Dhar Sujan K 
Published: January 2023

AbstractCervical cancer (CC), the second most common in developing countries and the third most common in developed nations, is the fourth most common type of cancer in women overall. The HPV16 high-risk genotype of the virus, which is responsible for about 61% of cervical cancer incidences, was found to have higher LCN2 levels in advanced clinical CC stages. In this study, we assessed the impact of suppressing LCN2 activity after treatment with an anti-LCN2 monoclonal antibody (MAb) in bothin vitroandin vivosettings. Anti-LCN2 antibody was found to reduce proliferation and invasion of HeLa cells, the first immortal cells from a HPV positive aggressive adenocarcinoma of the cervix. LCN2 and its ligand MMP9 was found to be highly expressed in the cells and abrogated on treatment with anti-LCN2. The five receptors of LCN2 - SLC22A17, MC1R, MC2R, MC4R and LRP2 were barely detected with or without treatment. Anti-LCN2 Mab caused tumors to regress and softenin vivo, in a xenograft mouse model. Analysis of histology images of the treated and untreated tumor established the necrotic capability of the therapeutic molecule explaining the regression and softening of the tumor. Differential gene expression analysis between untreated and treated tumor proved that LCN2 inhibition abolished the migratory, invasive, and hypoxic pathways while significantly increasing the necrosis and cell death pathways in tumor after treatment with the monoclonal antibody. LCN2 inhibition was shown molecularly to lead to tumor regression via a negative feedback loop of LCN2 through the TNFα-IL17 axis exponentially increasing the effect of the anti-LCN2 monoclonal antibody. In conclusion, LCN2 appears to be a viable therapeutic target, and the monoclonal antibody used in this study can be further developed for clinical usage in cervical cancer.
scDual-Seq ofToxoplasma gondii-infected mouse bone marrow-derived dendritic cells reveals host cell heterogeneity and differential infection dynamics
Authors: Hildebrandt Franziska , Mohammed Mubasher , Dziedziech Alexis , Bhandage Amol , Divne Anna-Maria , Barrenäs Fredrik , Barragan Antonio , Henriksson Johan , Ankarklev Johan 
Published: January 2023

SUMMARYHost-parasite interactions include complex interplays between an invading and a defending organism, each continuously adapting to gain the upper hand. The protozoan parasite,Toxoplasma gondii, can invade every nucleated cell type in a vertebrate host, including immune cells while the host mounts a protective response.Here, we utilize Dual-scSeq to parse out heterogeneous transcription of bone marrow-derived dendritic cells (BMDCs) infected withT. gondiitype I, RH (LDM) or type II, ME49 (PTG) parasites, over multiple time points post infection.We find that the two parasite lineages distinctly manipulate two subpopulations of infected BMDCs. Co-expression networks establish host and parasite genes, with implications for modulation of host immunity and host-pathogen interactions. Integration of published data validates immune pathways and suggests novel candidate genes involved in host-pathogen interactions. This study aims to provide a comprehensive resource for future characterization of host-pathogen interplay among other protozoan parasites within their host niches, as well as that of bacterial and viral pathogens.
An intravenous DNA-binding priming agent protects cell-free DNA and improves the sensitivity of liquid biopsies
Authors: Tabrizi Shervin , Martin-Alonso Carmen , Xiong Kan , Blewett Timothy , Sridhar Sainetra , An Zhenyi , Patel Sahil , Rodriguez-Aponte Sergio , Naranjo Christopher A. , Wang Shih-Ting , Shea Douglas , Golub Todd R. , Bhatia Sangeeta N. , Adalsteinsson Viktor , Love J. Christopher 
Published: January 2023

AbstractBlood-based, or “liquid,” biopsies enable minimally invasive diagnostics but have limits on sensitivity due to scarce cell-free DNA (cfDNA). Improvements to sensitivity have primarily relied on enhancing sequencing technologyex vivo. Here, we sought to augment the level of circulating tumor DNA (ctDNA) detected in a blood draw by attenuating the clearance of cfDNAin vivo. We report a first-in-class intravenous DNA-binding priming agent given 2 hours prior to a blood draw to recover more cfDNA. The DNA-binding antibody minimizes nuclease digestion and organ uptake of cfDNA, decreasing its clearance at 1 hour by over 150-fold. To improve plasma persistence and limit potential immune interactions, we abrogated its Fc-effector function. We found that it protects GC-rich sequences and DNase-hypersensitive sites, which are ordinarily underrepresented in cfDNA. In tumor-bearing mice, priming improved tumor DNA recovery by 19-fold and sensitivity for detecting cancer from 6% to 84%. These results suggest a novel method to enhance the sensitivity of existing DNA-based cancer testing using blood biopsies.
Screening megasynthetase mutants at high throughput using droplet microfluidics
Authors: Pourmasoumi Farzaneh , Hengoju Sundar , Beck Katharina , Stephan Philipp , Klopfleisch Lukas , Hoernke Maria , Rosenbaum Miriam A. , Kries Hajo 
Published: January 2023

AbstractNonribosomal peptide synthetases (NRPSs) are giant enzymatic assembly lines that deliver many pharmaceutically valuable natural products, including antibiotics. As the search for new antibiotics motivates attempts to redesign nonribosomal metabolic pathways, more robust and rapid sorting and screening platforms are needed. Here, we establish a microfluidic platform that reliably detects production of the model nonribosomal peptide gramicidin S. The detection is based on calcein-filled sensor liposomes yielding increased fluorescence upon permeabilization. From a library of NRPS mutants, the sorting platform enriches the gramicidin S producer 14.5-fold, decreases the number of stop codons 250-fold, and generates enrichment factors correlating with enzyme activity. Screening for NRPS activity with a reliable non-binary sensor will enable more sophisticated structure-activity studies and new engineering applications in the future.
Comprehensive detection of structural variation and transposable element differences between wild type laboratory lineages ofC. elegans
Authors: Bush Zachary D. , Naftaly Alice F. S. , Dinwiddie Devin , Albers Cora , Hillers Kenneth J. , Libuda Diana E. 
Published: January 2023

AbstractGenomic structural variations (SVs) and transposable elements (TEs) can be significant contributors to genome evolution, altered gene expression, and risk of genetic diseases. Recent advancements in long-read sequencing have greatly improved the quality ofde novogenome assemblies and enhanced the detection of sequence variants at the scale of hundreds or thousands of bases. Comparisons between two diverged wild isolates ofCaenorhabditis elegans, the Bristol and Hawaiian strains, have been widely utilized in the analysis of small genetic variations. Genetic drift, including SVs and rearrangements of repeated sequences such as TEs, can occur over time from long-term maintenance of wild type isolates within the laboratory. To comprehensively detect both large and small structural variations as well as TEs due to genetic drift, we generatedde novogenome assemblies and annotations for each strain from our lab collection using both long- and short-read sequencing and compared our assemblies and annotations with that of other lab wild type strains. Within our lab assemblies, we annotate over 3.1Mb of sequence divergence between the Bristol and Hawaiian isolates: 337,584 SNPs, 94,503 small insertion-deletions (<50bp), and 4,334 structural variations (>50bp). Further, we define the location and movement of specific DNA TEs between N2 Bristol and CB4856 Hawaiian wild type isolates. Specifically, we find the N2 Bristol genome has 20.6% more TEs from theTc1/marinerfamily than the CB4856 Hawaiian genome. Moreover, we identified Zator elements as the most abundant and mobile TE family in the genome. Using specific TE sequences with unique SNPs, we also identify 38 TEs that moved intrachromosomally and 9 TEs that moved interchromosomally between the N2 Bristol and CB4856 Hawaiian genomes. By comparing thede novogenome assembly of our lab collection Bristol isolate to the VC2010 Bristol assembly, we also reveal that lab lineages display over 2 Mb of total variation: 1,162 SNPs, 1,528 indels, and 897 SVs with 95% of the variation due to SVs. Overall, our work demonstrates the unique contribution of SVs and TEs to variation and genetic drift between wild type laboratory strains assumed to be isogenic despite growing evidence of genetic drift and phenotypic variation.Author SummaryFor multiple model organisms, propagation of wild type strains in independent labs can lead to multiple phenotypic differences over time. To assess recombination, map mutations, and understand genomic changes during speciation,Caenorhabditis elegansresearchers primarily use the wild type isolates Bristol and Hawaiian. Here, we map structural variations, transposable elements, and sequence divergence between the Bristol and Hawaiian natural isolates and between genomes of different lab lineages of these same strains.
Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts
Authors: Hansen Zoe A. , Vasco Karla A. , Rudrik James T. , Scribner Kim T. , Zhang Lixin , Manning Shannon D. 
Published: January 2023

AbstractEnteric pathogens cause widespread foodborne illness and are increasingly found to harbor antimicrobial resistance. The ecological impact of these pathogens on the human gut microbiome and resistome, however, has yet to be fully elucidated. This study applied shotgun metagenome sequencing to stools from 60 patients (cases) with enteric bacterial infections for comparison to stools collected from the same patients’ post-recovery (follow-ups). Overall, the case samples harbored more antimicrobial resistance genes (ARGs) and had greater resistome diversity than the follow-up samples (p<0.001), while follow-ups had much more diverse microbiomes (p<0.001). Although cases were primarily defined by generaEscherichia, Salmonella, andShigellaalong with ARGs for multi-compound and multidrug resistance, follow-ups had a greater abundance of Bacteroidetes and Firmicutes phyla and genes for tetracycline, macrolides, lincosamides, and streptogramins (MLS), and aminoglycoside resistance. A host-tracking analysis revealed thatEscherichiawas the primary carrier of ARGs in both cases and follow-ups, with a greater abundance occurring during infection. Eleven distinct extended spectrum beta-lactamases (ESBLs) were identified during infection, some of which appear to be lost or transferred to different microbial hosts upon recovery. The increasing incidence of disease caused by foodborne pathogens, coupled with their evolving role in harboring and transferring antimicrobial resistance determinants within communities, justifies further examination of the repercussions of enteric infection on human gut ecology.