bioRxiv : the preprint server for biology最新文献_第10页

Guided Differentiation of Pluripotent Stem Cells into Heterogeneously Differentiating Cultures of Cardiac Cells. 用于心脏细胞多样性的多能干细胞的引导分化。

bioRxiv : the preprint server for biology Pub Date : 2025-02-19 DOI: 10.1101/2023.07.21.550072

Erik McIntire, Kenneth A Barr, Natalia M Gonzales, Olivia L Allen, Yoav Gilad

{"title":"Guided Differentiation of Pluripotent Stem Cells into Heterogeneously Differentiating Cultures of Cardiac Cells.","authors":"Erik McIntire, Kenneth A Barr, Natalia M Gonzales, Olivia L Allen, Yoav Gilad","doi":"10.1101/2023.07.21.550072","DOIUrl":"10.1101/2023.07.21.550072","url":null,"abstract":"In principle, induced pluripotent stem cells (iPSCs) can differentiate into any cell type in the body. The challenge is to find a way to rapidly expand the dimensionality of cell types and cell states we can characterize. To address this, we developed a guided differentiation protocol to produce heterogeneous differentiating cultures of cardiac cell types (cardiac HDCs) in 16 days. Cardiac HDCs are three-dimensional, rhythmically contracting cell aggregates that harbor a temporally and functionally diverse range of cardiac-relevant cell types. We characterize cardiac HDCs from 47 iPSC lines using single-cell RNA-sequencing to identify cardiomyocytes, epicardial cells, cardiac fibroblasts, endothelial cells, and hematopoietic cells, along with both ectodermal and endodermal derivatives. This guided differentiation approach prioritizes simplicity by minimizing the reagents and steps required, thereby enabling rapid and cost-effective experimental throughput. We expect cardiac HDCs to provide a scalable cardiac model for population-level studies of gene regulatory variation and gene-by-environment interactions.","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/99/31/nihpp-2023.07.21.550072v1.PMC10370173.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9927211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Septin organization is regulated by the Gpa1 Ubiquitination Domain and Endocytic Machinery during the yeast pheromone response. G-α-Gpa1通过其泛素化结构域和内分泌机制在酿酒酵母的交配投射中指导septin定位。

bioRxiv : the preprint server for biology Pub Date : 2025-02-19 DOI: 10.1101/2023.06.16.545321

Cory P Johnson, Sudati Shrestha, Andrew Hart, Katherine F Jarvis, Loren E Genrich, Sarah G Latario, Nicholas Leclerc, Tetiana Systuk, Matthew Scandura, Remi P Geohegan, André Khalil, Joshua B Kelley

{"title":"Septin organization is regulated by the Gpa1 Ubiquitination Domain and Endocytic Machinery during the yeast pheromone response.","authors":"Cory P Johnson, Sudati Shrestha, Andrew Hart, Katherine F Jarvis, Loren E Genrich, Sarah G Latario, Nicholas Leclerc, Tetiana Systuk, Matthew Scandura, Remi P Geohegan, André Khalil, Joshua B Kelley","doi":"10.1101/2023.06.16.545321","DOIUrl":"10.1101/2023.06.16.545321","url":null,"abstract":"The septin cytoskeleton plays a key role in the morphogenesis of the yeast mating projection, forming structures at the base of the projection. The yeast mating response uses the G-protein coupled receptor (GPCR), Ste2, to detect mating pheromone and initiate mating projection morphogenesis. Desensitization of the Gα, Gpa1, by the Regulator of G-protein Signaling (RGS), Sst2, is required for proper septin organization and morphogenesis. We hypothesized that Gpa1 would utilize known septin regulators to control septin organization. We found that single deletions of the septin chaperone Gic1, the Cdc42 GAP Bem3, and the endocytic adaptor proteins Ent1 and Ent2 rescued the polar cap accumulation of septins in the hyperactive Gα. We hypothesized that hyperactive Gα might increase the rate of endocytosis of a pheromone-responsive cargo, thereby altering where septins are localized. Mathematical modeling predicted that changes in endocytosis could explain the septin organizations we find in WT and mutant cells. Our results show that Gpa1-induced disorganization of septins requires clathrin-mediated endocytosis. Both the GPCR and the Gα are known to be internalized by clathrin-mediated endocytosis during the pheromone response. Deletion of the GPCR C-terminus to block internalization partially rescued septin organization. However, deleting the Gpa1 ubiquitination domain required for its endocytosis completely abrogated septin accumulation at the polarity site. Our data support a model where the location of endocytosis serves as a spatial mark for septin structure assembly and that desensitization of the Gα delays its endocytosis sufficiently that septins are placed peripheral to the site of Cdc42 polarity.","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d7/58/nihpp-2023.06.16.545321v1.PMC10312744.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9751602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multimodal identification of the mouse brain using simultaneous Ca ²⁺ imaging and fMRI. 利用同步 Ca 2+ 成像和 fMRI 对小鼠大脑进行多模式识别。

bioRxiv : the preprint server for biology Pub Date : 2025-02-18 DOI: 10.1101/2024.05.24.594620

Francesca Mandino, Corey Horien, Xilin Shen, Gabriel Desrosiers-Grégoire, Wendy Luo, Marija Markicevic, R Todd Constable, Xenophon Papademetris, Mallar M Chakravarty, Richard F Betzel, Evelyn M R Lake

{"title":"Multimodal identification of the mouse brain using simultaneous Ca 2+ imaging and fMRI.","authors":"Francesca Mandino, Corey Horien, Xilin Shen, Gabriel Desrosiers-Grégoire, Wendy Luo, Marija Markicevic, R Todd Constable, Xenophon Papademetris, Mallar M Chakravarty, Richard F Betzel, Evelyn M R Lake","doi":"10.1101/2024.05.24.594620","DOIUrl":"10.1101/2024.05.24.594620","url":null,"abstract":"Individual differences in neuroimaging are of interest to clinical and cognitive neuroscientists based on their potential for guiding the personalized treatment of various heterogeneous neurological conditions and diseases. Despite many advantages, the workhorse in this arena, BOLD (blood-oxygen-level-dependent) functional magnetic resonance imaging (fMRI) suffers from low spatiotemporal resolution and specificity as well as a propensity for noise and spurious signal corruption. To better understand individual differences in BOLD-fMRI data, we can use animal models where fMRI, alongside complementary but more invasive contrasts, can be accessed. Here, we apply simultaneous wide-field fluorescence calcium imaging and BOLD-fMRI in mice to interrogate individual differences using a connectome-based identification framework adopted from the human fMRI literature. This approach yields high spatiotemporal resolution cell-type specific signals (here, from glia, excitatory, as well as inhibitory interneurons) from the whole cortex. We found mouse multimodal connectome-based identification to be successful and explored various features of these data.","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11142213/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141201477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Multimodal delineation of a layer of effector function among exhausted CD8 T cells in tumors. 实体瘤中罕见的强效效应CD8 T细胞的多模式鉴定。

bioRxiv : the preprint server for biology Pub Date : 2025-02-16 DOI: 10.1101/2023.09.26.559470

Arja Ray, Molly Bassette, Kenneth H Hu, Lomax F Pass, Tristan Courau, Bushra Samad, Alexis Combes, Vrinda Johri, Brittany Davidson, Katherine Wai, Patrick Ha, Grace Hernandez, Itzia Zaleta-Linares, Matthew F Krummel

{"title":"Multimodal delineation of a layer of effector function among exhausted CD8 T cells in tumors.","authors":"Arja Ray, Molly Bassette, Kenneth H Hu, Lomax F Pass, Tristan Courau, Bushra Samad, Alexis Combes, Vrinda Johri, Brittany Davidson, Katherine Wai, Patrick Ha, Grace Hernandez, Itzia Zaleta-Linares, Matthew F Krummel","doi":"10.1101/2023.09.26.559470","DOIUrl":"10.1101/2023.09.26.559470","url":null,"abstract":"The anti-tumor function of CD8 T cells is limited through well-established pathways of T cell exhaustion (TEX). Strategies to capture emergent functional states amongst this dominant trajectory of dysfunction are necessary to find pathways to durable anti-tumor immunity. By leveraging transcriptional reporting (by the fluorescent protein TFP) of the T cell activation marker Cd69, related to upstream AP-1 transcription factors, we define a classifier for potent versus suboptimal CD69+ activation states arising from T cell stimulation. In tumors, this delineation acts an additional functional readout along the TEX differentiation trajectory, within and across TEX subsets, marked by enhanced effector cytokine and granzyme B production. The more potent state remains differentially prominent in a T cell-mediated tumor clearance model, where they also show increased engagement in the microenvironment and are superior in tumor cell killing. Employing multimodal CITE-Seq in human head and neck tumors enables a similar strategy to identify Cd69RNAhiCD69+ cells that also have enhanced functional features in comparison to Cd69RNAloCD69+ cells, again within and across intratumoral CD8 T cell subsets. Refining the contours of the T cell functional landscape in tumors in this way paves the way for the identification of rare exceptional effectors, with imminent relevance to cancer treatment.","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/04/1a/nihpp-2023.09.26.559470v1.PMC10557647.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41157185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CellSAM: A Foundation Model for Cell Segmentation. 细胞分割的基础模型。

bioRxiv : the preprint server for biology Pub Date : 2025-02-16 DOI: 10.1101/2023.11.17.567630

Uriah Israel, Markus Marks, Rohit Dilip, Qilin Li, Changhua Yu, Emily Laubscher, Ahamed Iqbal, Elora Pradhan, Ada Ates, Martin Abt, Caitlin Brown, Edward Pao, Shenyi Li, Alexander Pearson-Goulart, Pietro Perona, Georgia Gkioxari, Ross Barnowski, Yisong Yue, David Van Valen

{"title":"CellSAM: A Foundation Model for Cell Segmentation.","authors":"Uriah Israel, Markus Marks, Rohit Dilip, Qilin Li, Changhua Yu, Emily Laubscher, Ahamed Iqbal, Elora Pradhan, Ada Ates, Martin Abt, Caitlin Brown, Edward Pao, Shenyi Li, Alexander Pearson-Goulart, Pietro Perona, Georgia Gkioxari, Ross Barnowski, Yisong Yue, David Van Valen","doi":"10.1101/2023.11.17.567630","DOIUrl":"10.1101/2023.11.17.567630","url":null,"abstract":"Cells are a fundamental unit of biological organization, and identifying them in imaging data - cell segmentation - is a critical task for various cellular imaging experiments. While deep learning methods have led to substantial progress on this problem, most models are specialist models that work well for specific domains but cannot be applied across domains or scale well with large amounts of data. In this work, we present CellSAM, a universal model for cell segmentation that generalizes across diverse cellular imaging data. CellSAM builds on top of the Segment Anything Model (SAM) by developing a prompt engineering approach for mask generation. We train an object detector, CellFinder, to automatically detect cells and prompt SAM to generate segmentations. We show that this approach allows a single model to achieve human-level performance for segmenting images of mammalian cells, yeast, and bacteria collected across various imaging modalities. We show that CellSAM has strong zero-shot performance and can be improved with a few examples via few-shot learning. Additionally, we demonstrate how CellSAM can be applied across diverse bioimage analysis workflows. A deployed version of CellSAM is available at https://cellsam.deepcell.org/.","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10690226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138479505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Changes of cell-type diversity in the polyp-to-medusa metagenesis of the scyphozoan jellyfish Aurelia coerulea (formerly sp.1). 水母（原sp.1）从水螅到水母发育过程中细胞类型多样性的变化。

bioRxiv : the preprint server for biology Pub Date : 2025-02-15 DOI: 10.1101/2023.08.24.554571

Oliver Link, Stefan M Jahnel, Kristin Janicek, Johanna Kraus, Juan Daniel Montenegro, Bob Zimmerman, Brittney Wick, Alison G Cole, Ulrich Technau

{"title":"Changes of cell-type diversity in the polyp-to-medusa metagenesis of the scyphozoan jellyfish Aurelia coerulea (formerly sp.1).","authors":"Oliver Link, Stefan M Jahnel, Kristin Janicek, Johanna Kraus, Juan Daniel Montenegro, Bob Zimmerman, Brittney Wick, Alison G Cole, Ulrich Technau","doi":"10.1101/2023.08.24.554571","DOIUrl":"10.1101/2023.08.24.554571","url":null,"abstract":"The life cycle of most medusozoan cnidarians is marked by the metagenesis from the asexually reproducing sessile polyp and the sexually reproducing motile medusa. At present it is unknown to what extent this drastic morphological transformation is accompanied by changes in the cell type composition. Here, we provide a single cell transcriptome atlas of the cosmopolitan scyphozoan Aurelia coerulea focussing on changes in cell-type composition during the transition from polyp to medusa. Notably, this transition marked by an increase in cell type diversity, including an expansion of neural subtypes. We find that two families of neuronal lineages are specified by homologous transcription factors in the sea anemone Nematostella vectensis and Aurelia coerulea, suggesting an origin in the common ancestor of medusozoans and anthozoans about 500 Myr ago. Our analysis suggests that gene duplications might be drivers for the increase of cellular complexity during the evolution of cnidarian neuroglandular lineages. One key medusozoan-specific cell type is the striated muscle in the subumbrella. Analysis of muscle fiber anatomy and gene expression raises the possibility that the striated muscles arise from a population of smooth muscle cells during strobilation. Although smooth and striated muscles are phenotypically distinct, both have a similar contractile complex, in contrast to bilaterian smooth and striated muscles. This suggests that in Aurelia, smooth and striated muscle cells may derive from the same progenitor cells.","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11844373/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84405827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The information bottleneck as a principle underlying multi-area cortical representations during decision-making. 决策过程中的皮层信息瓶颈。

bioRxiv : the preprint server for biology Pub Date : 2025-02-15 DOI: 10.1101/2023.07.12.548742

Michael Kleinman, Tian Wang, Derek Xiao, Ebrahim Feghhi, Kenji Lee, Nicole Carr, Yuke Li, Nima Hadidi, Chandramouli Chandrasekaran, Jonathan C Kao

{"title":"The information bottleneck as a principle underlying multi-area cortical representations during decision-making.","authors":"Michael Kleinman, Tian Wang, Derek Xiao, Ebrahim Feghhi, Kenji Lee, Nicole Carr, Yuke Li, Nima Hadidi, Chandramouli Chandrasekaran, Jonathan C Kao","doi":"10.1101/2023.07.12.548742","DOIUrl":"10.1101/2023.07.12.548742","url":null,"abstract":"Decision-making emerges from distributed computations across multiple brain areas, but it is unclear why the brain distributes the computation. In deep learning, artificial neural networks use multiple areas (or layers) and form optimal representations of task inputs. These optimal representations are sufficient to perform the task well, but minimal so they are invariant to other irrelevant variables. We recorded single neurons and multiunits in dorsolateral prefrontal cortex (DLPFC) and dorsal premotor cortex (PMd) in monkeys during a perceptual decision-making task. We found that while DLPFC represents task-related inputs required to compute the choice, the downstream PMd contains a minimal sufficient, or optimal, representation of the choice. To identify a mechanism for how cortex may form these optimal representations, we trained a multi-area recurrent neural network (RNN) to perform the task. Remarkably, DLPFC and PMd resembling representations emerged in the early and late areas of the multi-area RNN, respectively. The DLPFC-resembling area partially orthogonalized choice information and task inputs and this choice information was preferentially propagated to downstream areas through selective alignment with inter-area connections, while remaining task information was not. Our results suggest that cortex uses multi-area computation to form minimal sufficient representations by preferential propagation of relevant information between areas.","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10369960/pdf/nihpp-2023.07.12.548742v1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9884104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Disruption of Synaptic Endoplasmic Reticulum Luminal Protein Containment in Drosophila Atlastin Mutants. Atlastin突变体突触前ER网络的高分辨率成像。

bioRxiv : the preprint server for biology Pub Date : 2025-02-15 DOI: 10.1101/2023.09.01.555994

Mónica C Quiñones-Frías, Dina M Ocken, Avital Rodal

{"title":"Disruption of Synaptic Endoplasmic Reticulum Luminal Protein Containment in Drosophila Atlastin Mutants.","authors":"Mónica C Quiñones-Frías, Dina M Ocken, Avital Rodal","doi":"10.1101/2023.09.01.555994","DOIUrl":"10.1101/2023.09.01.555994","url":null,"abstract":"The endoplasmic reticulum (ER) extends throughout neurons and regulates many neuronal functions, including neurite outgrowth, neurotransmission, and synaptic plasticity. Mutations in proteins that control ER shape are linked to the neurodegenerative disorder Hereditary Spastic Paraplegia (HSP), yet the ultrastructure and dynamics of neuronal ER remain largely unexplored, especially at presynaptic terminals. Using super-resolution and live imaging in D. melanogaster larval motor neurons, we investigated ER structure at presynaptic terminals of wild-type animals and null mutants of the ER shaping protein and HSP-linked gene, Atlastin. Previous studies using an ER luminal marker reported diffuse localization at Atlastin mutant presynaptic terminals, which was attributed to ER fragmentation. However, using an ER membrane marker, we discovered that Atlastin mutant ER forms robust networks with only mild defects in structural dynamics, indicating the primary defect is functional rather than architectural. We demonstrate that Atlastin mutants progressively displace overexpressed luminal ER proteins to the cytosol during larval development, specifically at synapses, while these proteins remain correctly localized in cell bodies, axons, and muscles. This synaptic-specific displacement phenotype, previously unreported in non-neuronal cells, emphasizes the importance of studying neurons to understand HSP pathogenesis.","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/c6/5c/nihpp-2023.09.01.555994v1.PMC10491308.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10263491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Barcode-free multiplex plasmid sequencing using Bayesian analysis and nanopore sequencing. 使用贝叶斯分析和纳米孔测序的无条形码多重质粒测序。

bioRxiv : the preprint server for biology Pub Date : 2025-02-13 DOI: 10.1101/2023.04.12.536413

Masaaki Uematsu, Jeremy M Baskin

{"title":"Barcode-free multiplex plasmid sequencing using Bayesian analysis and nanopore sequencing.","authors":"Masaaki Uematsu, Jeremy M Baskin","doi":"10.1101/2023.04.12.536413","DOIUrl":"10.1101/2023.04.12.536413","url":null,"abstract":"Plasmid construction is central to life science research, and sequence verification is arguably its costliest step. Long-read sequencing has emerged as a competitor to Sanger sequencing, with the principal benefit that whole plasmids can be sequenced in a single run. Nevertheless, the current cost of nanopore sequencing is still prohibitive for routine sequencing during plasmid construction. We develop a computational approach termed Simple Algorithm for Very Efficient Multiplexing of Oxford Nanopore Experiments for You (SAVEMONEY) that guides researchers to mix multiple plasmids and subsequently computationally de-mixes the resultant sequences. SAVEMONEY defines optimal mixtures in a pre-survey step, and following sequencing, executes a post-analysis workflow involving sequence classification, alignment, and consensus determination. By using Bayesian analysis with prior probability of expected plasmid construction error rate, high-confidence sequences can be obtained for each plasmid in the mixture. Plasmids differing by as little as two bases can be mixed for submission as a single sample for nanopore sequencing, and routine multiplexing of even six plasmids per 180 reads can still maintain high accuracy of consensus sequencing. SAVEMONEY should further democratize whole-plasmid sequencing by nanopore and related technologies, driving down the effective cost of whole-plasmid sequencing to lower than that of a single Sanger sequencing run.","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/14/e4/nihpp-2023.04.12.536413v2.PMC10120676.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9391431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Normative evidence weighing and accumulation in correlated environments. 相关环境中的规范证据加权和积累。

bioRxiv : the preprint server for biology Pub Date : 2025-02-08 DOI: 10.1101/2024.05.29.596489

Nathan Tardiff, Jiwon Kang, Joshua I Gold

引用次数: 0