2025 Hyper Recent •CC0 1.0 Universal

This work is dedicated to the public domain. No rights reserved.

Access Preprint From Server
April 2nd, 2025
Version: 1
University of Maryland Eastern Shore
genomics
biorxiv

Protocol for Extracting Circulating Cell-Free DNA from Murine Saliva: Insights into Oral and Systemic Disease Research

Elamin, I.Open in Google Scholar•Rao, M. S.Open in Google Scholar•Figliozzi, R. W.Open in Google Scholar•Maahs, J. C.Open in Google Scholar•Balish, M.Open in Google Scholar•Hsia, S. V.Open in Google Scholar•Fugolin, A. P. P.Open in Google Scholar•Fan, J.Open in Google Scholar

Circulating cell-free DNA (cfDNA) consists of small fragments of extracellular DNA from mammalian and bacterial cells found in bodily fluids such as blood and saliva, and it has been strongly recognized as a critical biomarker for various disease diagnoses, prognoses, and therapeutic monitoring. In this study, we present a reproducible protocol for efficiently isolating cfDNA from murine saliva using an innovative swabbing method in conjunction with the QIAamp MinElute ccfDNA Mini Kit. The quantification of isolated cfDNA is detected by a Qubit Fluorometer. Moreover, qualification assessment is conducted through BioAnalyzer analysis. This protocol facilitates research on saliva-derived cfDNA in the context of oral and systemic diseases in murine models.

Similar Papers

biorxiv
Thu Apr 03 2025
Trypanosoma cruzi Has 32 Chromosomes: A Telomere-to-Telomere Assembly Defines Its Karyotype.
Trypanosoma cruzi, the causative agent of Chagas disease, exhibits remarkable genomic plasticity and possesses an expanded genome rich in multigene families. However, its precise chromosomal composition has remained elusive due to challenges in resolving repetitive regions. Using PacBio HiFi long-read sequencing, we assembled the complete nuclear genome of the Dm28c strain into 32 telomere-to-telo...
Greif, G.
•
Diaz-Viraque, F.
•
Chiribao, M. L.
•
Sanz-Rodriguez, C.
•
Robello, C.
biorxiv
Thu Apr 03 2025
Neisseria gonorrhoeae LIN codes: a Robust, Multi-Resolution Lineage Nomenclature
Investigation of the bacterial pathogen Neisseria gonorrhoeae is complicated by extensive horizontal gene transfer: a process which disrupts phylogenetic signals and impedes our understanding of population structure. The ability to identify N. gonorrhoeae lineages in a consistent manner is essential for surveillance of this increasingly antimicrobial resistant organism, and to facilitate efficient...
Unitt, A.
•
Krisna, M. A.
•
Parfitt, K. M.
•
Jolley, K. A.
...•
Harrison, O. B.
biorxiv
Thu Apr 03 2025
Expression spectrum of TE-derived transcripts in human adult tissues
Abstract Transposable elements (TEs) are vital components of eukaryotic genomes and have played a critical role in genome evolution. Although most TEs are silenced in the mammalian genome, increasing evidence suggests that certain TEs are actively involved in gene regulation during early developmental stages. However, the extent to which human TEs drive gene transcription in adult tissues remains ...
Miao, B.
•
Zhang, B.
•
WU, T. P.
•
Luo, X.
...•
Yang, Y.
biorxiv
Thu Apr 03 2025
CREsted: modeling genomic and synthetic cell type-specific enhancers across tissues and species
Sequence-based deep learning models have become the state of the art for the analysis of the genomic regulatory code. Particularly for transcriptional enhancers, deep learning models excel at deciphering sequence features and grammar that underlie their spatiotemporal activity. To enable end-to-end enhancer modeling and design, we developed a software and modeling package, called CREsted. It combi...
Kempynck, N.
•
De Winter, S.
•
Blaauw, C. H.
•
Konstantakos, V.
...•
Aerts, S.
biorxiv
Thu Apr 03 2025
Entry and exit of Fragilariopsis cylindrus diatoms from the polar night: evidence for chromatin-mediated genome control
Regulation of the epigenome landscape plays a crucial role in adaptation to environmental changes. However, the molecular mechanisms by which epigenome landscapes are established and tuned to adjust the cellular status to environmental cues remain poorly understood, especially in unicellular photosynthetic eukaryotes. Polar microalgae must adapt to extreme variations in light and temperature for s...
Joli, N.
•
Bourbousse, C.
•
Leduque, B.
•
Tirichine Delacour, L.
...•
Bowler, C.
biorxiv
Thu Apr 03 2025
Improving interpretability of transcription factor binding models with DNA shape features
Deep learning models in genomics that predict molecular phenotypes from DNA sequence traditionally focus on one-hot encoded representations. Here, we develop a novel model that extends this approach by incorporating DNA structural attributes indicative of local shape alongside canonical sequence inputs. This augmentation provides an additional axis for model interpretability and aids in identifyin...
Keivanfar, R. L.
•
Yang, F.
•
Pollard, K. S.
•
Ioannidis, N. M.
biorxiv
Thu Apr 03 2025
Development of a core genome multilocus sequence typing (cgMLST) scheme and life identification number (LIN) code classification system for Staphylococcus aureus
Staphylococcus aureus infects both humans and animals, and antimicrobial resistance, including multidrug resistance, complicates treatment of S. aureus infections. Understanding S. aureus population structure and the distribution of genetic lineages is central to understanding the biology, epidemiology, and pathogenesis of this organism. This study exploited a large, publicly available dataset of ...
Hadjirin, N. F.
•
Yassine, I.
•
Bray, J. E.
•
Maiden, M. C. J.
...•
Brueggemann, A. B.
biorxiv
Wed Apr 02 2025
UniversalEPI: a generalized attention-based deep ensemble model to accurately predict enhancer-promoter interactions across diverse cell types and conditions
Interactions between enhancers and gene promoters provide insights into gene regulation. Experimental techniques, including Hi-C, that map these enhancer-promoter interactions (EPIs), have high costs and labor requirements, which limits their use. Therefore, in silico methods have been developed to predict EPIs computationally, but there are challenges with the generalizability and accuracy of exi...
Grover, A.
•
Zhang, L.
•
Muser, T.
•
Häfliger, S.
...•
Boeva, V.
biorxiv
Wed Apr 02 2025
Response to Tabin et al-Concerns about ancient DNA sequences reported from a Late Pleistocene individual from Southeast Asia
Tabin et al suspect a high error rate and abnormal error content in the MZR genome data from our published study, from which they raised concerns about the reliability and useability of our published sequences. Given the poor environmental conditions (such as warm climate and acidic soil in the low latitude area of Southwest China), as well as the non-ideal fossil material (cranium) for DNA extrac...
Zhang, X.
•
He, Y.
•
Ji, X.
•
Su, B.
biorxiv
Wed Apr 02 2025
Machine learning-predicted chromatin organization landscape across pediatric tumors
Structural variants (SVs) are increasingly recognized as important contributors to oncogenesis through their effects on 3D genome folding. Recent advances in whole-genome sequencing have enabled large-scale profiling of SVs across diverse tumors, yet experimental characterization of their individual impact on genome folding remains infeasible. Here, we leveraged a convolutional neural network, Aki...
Gjoni, K.
•
Zhang, S.
•
Yan, R. E.
•
Zhang, B.
...•
Pollard, K. S.